--- /dev/null
+* Clustal Omega:
+Fabian Sievers UCD Dublin, Ireland
+Andreas Wilm UCD Dublin, Ireland
+David Dineen UCD Dublin, Ireland
+Johannes Söding Gene Center Munich, Germany
+Michael Remmert Gene Center Munich, Germany
+
+* Clustal 2
+Mark Larkin UCD Dublin, Ireland
+
+* Clustal 1.X
+Toby Gibson EMBL Heidelberg, Germany
+Des Higgins UCC Cork, Ireland
+Julie Thompson IGBMC Strasbourg, France
+
+* Contributors:
+Chenna Ramu EMBL Heidelberg, Germany
+Nigel Brown EMBL Heidelberg, Germany
+
+
--- /dev/null
+ GNU GENERAL PUBLIC LICENSE
+ Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
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+
+ Preamble
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+ GNU GENERAL PUBLIC LICENSE
+ TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+ 0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
+under the terms of this General Public License. The "Program", below,
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+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
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+
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+under Section 2) in object code or executable form under the terms of
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+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
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+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
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+
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+
+ Gnomovision version 69, Copyright (C) year name of author
+ Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
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+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may
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+
+You should also get your employer (if you work as a programmer) or your
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+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ <signature of Ty Coon>, 1 April 1989
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.
--- /dev/null
+2010-06-17 Release 0.0.1 (Dubliniensis)
+
+ First "release" as program has been able for a while to perform
+ all basic tasks without problems.
+
+ Non-standard features already built-in include:
+ HMM-iteration (using HMMER for building an HMM) and guide-tree
+ iteration. On top of that HMM input works fine and
+ background-frequencies are added to the HHalign process.
+
+ Known issues: RNA/DNA alignment is considered buggy. Aligned
+ sequences have to be dealigned for HHalign to work properly.
+
+ The HMMER version message can be ignored if no HMM-iteration
+ was used.
--- /dev/null
+# Doxyfile 1.5.8
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project
+#
+# All text after a hash (#) is considered a comment and will be ignored
+# The format is:
+# TAG = value [value, ...]
+# For lists items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (" ")
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# This tag specifies the encoding used for all characters in the config file
+# that follow. The default is UTF-8 which is also the encoding used for all
+# text before the first occurrence of this tag. Doxygen uses libiconv (or the
+# iconv built into libc) for the transcoding. See
+# http://www.gnu.org/software/libiconv for the list of possible encodings.
+
+DOXYFILE_ENCODING = UTF-8
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
+# by quotes) that should identify the project.
+
+PROJECT_NAME = "Clustal Omega"
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number.
+# This could be handy for archiving the generated documentation or
+# if some version control system is used.
+
+PROJECT_NUMBER = 1.0.2
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
+# base path where the generated documentation will be put.
+# If a relative path is entered, it will be relative to the location
+# where doxygen was started. If left blank the current directory will be used.
+
+OUTPUT_DIRECTORY = ./doc/doxygen/
+
+# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
+# 4096 sub-directories (in 2 levels) under the output directory of each output
+# format and will distribute the generated files over these directories.
+# Enabling this option can be useful when feeding doxygen a huge amount of
+# source files, where putting all generated files in the same directory would
+# otherwise cause performance problems for the file system.
+
+CREATE_SUBDIRS = NO
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all constant output in the proper language.
+# The default language is English, other supported languages are:
+# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
+# Croatian, Czech, Danish, Dutch, Farsi, Finnish, French, German, Greek,
+# Hungarian, Italian, Japanese, Japanese-en (Japanese with English messages),
+# Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, Polish,
+# Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak, Slovene,
+# Spanish, Swedish, and Ukrainian.
+
+OUTPUT_LANGUAGE = English
+
+# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
+# include brief member descriptions after the members that are listed in
+# the file and class documentation (similar to JavaDoc).
+# Set to NO to disable this.
+
+BRIEF_MEMBER_DESC = YES
+
+# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
+# the brief description of a member or function before the detailed description.
+# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+# brief descriptions will be completely suppressed.
+
+REPEAT_BRIEF = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator
+# that is used to form the text in various listings. Each string
+# in this list, if found as the leading text of the brief description, will be
+# stripped from the text and the result after processing the whole list, is
+# used as the annotated text. Otherwise, the brief description is used as-is.
+# If left blank, the following values are used ("$name" is automatically
+# replaced with the name of the entity): "The $name class" "The $name widget"
+# "The $name file" "is" "provides" "specifies" "contains"
+# "represents" "a" "an" "the"
+
+ABBREVIATE_BRIEF =
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
+# Doxygen will generate a detailed section even if there is only a brief
+# description.
+
+ALWAYS_DETAILED_SEC = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
+# inherited members of a class in the documentation of that class as if those
+# members were ordinary class members. Constructors, destructors and assignment
+# operators of the base classes will not be shown.
+
+INLINE_INHERITED_MEMB = NO
+
+# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
+# path before files name in the file list and in the header files. If set
+# to NO the shortest path that makes the file name unique will be used.
+
+FULL_PATH_NAMES = YES
+
+# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
+# can be used to strip a user-defined part of the path. Stripping is
+# only done if one of the specified strings matches the left-hand part of
+# the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the
+# path to strip.
+
+STRIP_FROM_PATH =
+
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
+# the path mentioned in the documentation of a class, which tells
+# the reader which header file to include in order to use a class.
+# If left blank only the name of the header file containing the class
+# definition is used. Otherwise one should specify the include paths that
+# are normally passed to the compiler using the -I flag.
+
+STRIP_FROM_INC_PATH =
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
+# (but less readable) file names. This can be useful is your file systems
+# doesn't support long names like on DOS, Mac, or CD-ROM.
+
+SHORT_NAMES = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
+# will interpret the first line (until the first dot) of a JavaDoc-style
+# comment as the brief description. If set to NO, the JavaDoc
+# comments will behave just like regular Qt-style comments
+# (thus requiring an explicit @brief command for a brief description.)
+
+JAVADOC_AUTOBRIEF = NO
+
+# If the QT_AUTOBRIEF tag is set to YES then Doxygen will
+# interpret the first line (until the first dot) of a Qt-style
+# comment as the brief description. If set to NO, the comments
+# will behave just like regular Qt-style comments (thus requiring
+# an explicit \brief command for a brief description.)
+
+QT_AUTOBRIEF = NO
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
+# treat a multi-line C++ special comment block (i.e. a block of //! or ///
+# comments) as a brief description. This used to be the default behaviour.
+# The new default is to treat a multi-line C++ comment block as a detailed
+# description. Set this tag to YES if you prefer the old behaviour instead.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
+# member inherits the documentation from any documented member that it
+# re-implements.
+
+INHERIT_DOCS = YES
+
+# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
+# a new page for each member. If set to NO, the documentation of a member will
+# be part of the file/class/namespace that contains it.
+
+SEPARATE_MEMBER_PAGES = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab.
+# Doxygen uses this value to replace tabs by spaces in code fragments.
+
+TAB_SIZE = 4
+
+# This tag can be used to specify a number of aliases that acts
+# as commands in the documentation. An alias has the form "name=value".
+# For example adding "sideeffect=\par Side Effects:\n" will allow you to
+# put the command \sideeffect (or @sideeffect) in the documentation, which
+# will result in a user-defined paragraph with heading "Side Effects:".
+# You can put \n's in the value part of an alias to insert newlines.
+
+ALIASES =
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
+# sources only. Doxygen will then generate output that is more tailored for C.
+# For instance, some of the names that are used will be different. The list
+# of all members will be omitted, etc.
+
+OPTIMIZE_OUTPUT_FOR_C = YES
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
+# sources only. Doxygen will then generate output that is more tailored for
+# Java. For instance, namespaces will be presented as packages, qualified
+# scopes will look different, etc.
+
+OPTIMIZE_OUTPUT_JAVA = NO
+
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources only. Doxygen will then generate output that is more tailored for
+# Fortran.
+
+OPTIMIZE_FOR_FORTRAN = NO
+
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+# sources. Doxygen will then generate output that is tailored for
+# VHDL.
+
+OPTIMIZE_OUTPUT_VHDL = NO
+
+# Doxygen selects the parser to use depending on the extension of the files it parses.
+# With this tag you can assign which parser to use for a given extension.
+# Doxygen has a built-in mapping, but you can override or extend it using this tag.
+# The format is ext=language, where ext is a file extension, and language is one of
+# the parsers supported by doxygen: IDL, Java, Javascript, C#, C, C++, D, PHP,
+# Objective-C, Python, Fortran, VHDL, C, C++. For instance to make doxygen treat
+# .inc files as Fortran files (default is PHP), and .f files as C (default is Fortran),
+# use: inc=Fortran f=C
+
+EXTENSION_MAPPING =
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should
+# set this tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
+# func(std::string) {}). This also make the inheritance and collaboration
+# diagrams that involve STL classes more complete and accurate.
+
+BUILTIN_STL_SUPPORT = NO
+
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
+# enable parsing support.
+
+CPP_CLI_SUPPORT = NO
+
+# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
+# Doxygen will parse them like normal C++ but will assume all classes use public
+# instead of private inheritance when no explicit protection keyword is present.
+
+SIP_SUPPORT = NO
+
+# For Microsoft's IDL there are propget and propput attributes to indicate getter
+# and setter methods for a property. Setting this option to YES (the default)
+# will make doxygen to replace the get and set methods by a property in the
+# documentation. This will only work if the methods are indeed getting or
+# setting a simple type. If this is not the case, or you want to show the
+# methods anyway, you should set this option to NO.
+
+IDL_PROPERTY_SUPPORT = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES, then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
+# all members of a group must be documented explicitly.
+
+DISTRIBUTE_GROUP_DOC = NO
+
+# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
+# the same type (for instance a group of public functions) to be put as a
+# subgroup of that type (e.g. under the Public Functions section). Set it to
+# NO to prevent subgrouping. Alternatively, this can be done per class using
+# the \nosubgrouping command.
+
+SUBGROUPING = YES
+
+# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
+# is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically
+# be useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+
+TYPEDEF_HIDES_STRUCT = NO
+
+# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
+# determine which symbols to keep in memory and which to flush to disk.
+# When the cache is full, less often used symbols will be written to disk.
+# For small to medium size projects (<1000 input files) the default value is
+# probably good enough. For larger projects a too small cache size can cause
+# doxygen to be busy swapping symbols to and from disk most of the time
+# causing a significant performance penality.
+# If the system has enough physical memory increasing the cache will improve the
+# performance by keeping more symbols in memory. Note that the value works on
+# a logarithmic scale so increasing the size by one will rougly double the
+# memory usage. The cache size is given by this formula:
+# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
+# corresponding to a cache size of 2^16 = 65536 symbols
+
+SYMBOL_CACHE_SIZE = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
+# documentation are documented, even if no documentation was available.
+# Private class members and static file members will be hidden unless
+# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+
+EXTRACT_ALL = YES
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
+# will be included in the documentation.
+
+EXTRACT_PRIVATE = NO
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file
+# will be included in the documentation.
+
+EXTRACT_STATIC = NO
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
+# defined locally in source files will be included in the documentation.
+# If set to NO only classes defined in header files are included.
+
+EXTRACT_LOCAL_CLASSES = YES
+
+# This flag is only useful for Objective-C code. When set to YES local
+# methods, which are defined in the implementation section but not in
+# the interface are included in the documentation.
+# If set to NO (the default) only methods in the interface are included.
+
+EXTRACT_LOCAL_METHODS = NO
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base
+# name of the file that contains the anonymous namespace. By default
+# anonymous namespace are hidden.
+
+EXTRACT_ANON_NSPACES = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
+# undocumented members of documented classes, files or namespaces.
+# If set to NO (the default) these members will be included in the
+# various overviews, but no documentation section is generated.
+# This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_MEMBERS = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy.
+# If set to NO (the default) these classes will be included in the various
+# overviews. This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_CLASSES = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
+# friend (class|struct|union) declarations.
+# If set to NO (the default) these declarations will be included in the
+# documentation.
+
+HIDE_FRIEND_COMPOUNDS = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
+# documentation blocks found inside the body of a function.
+# If set to NO (the default) these blocks will be appended to the
+# function's detailed documentation block.
+
+HIDE_IN_BODY_DOCS = NO
+
+# The INTERNAL_DOCS tag determines if documentation
+# that is typed after a \internal command is included. If the tag is set
+# to NO (the default) then the documentation will be excluded.
+# Set it to YES to include the internal documentation.
+
+INTERNAL_DOCS = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
+# file names in lower-case letters. If set to YES upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+
+CASE_SENSE_NAMES = YES
+
+# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
+# will show members with their full class and namespace scopes in the
+# documentation. If set to YES the scope will be hidden.
+
+HIDE_SCOPE_NAMES = NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
+# will put a list of the files that are included by a file in the documentation
+# of that file.
+
+SHOW_INCLUDE_FILES = YES
+
+# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
+# is inserted in the documentation for inline members.
+
+INLINE_INFO = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
+# will sort the (detailed) documentation of file and class members
+# alphabetically by member name. If set to NO the members will appear in
+# declaration order.
+
+SORT_MEMBER_DOCS = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
+# brief documentation of file, namespace and class members alphabetically
+# by member name. If set to NO (the default) the members will appear in
+# declaration order.
+
+SORT_BRIEF_DOCS = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
+# hierarchy of group names into alphabetical order. If set to NO (the default)
+# the group names will appear in their defined order.
+
+SORT_GROUP_NAMES = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
+# sorted by fully-qualified names, including namespaces. If set to
+# NO (the default), the class list will be sorted only by class name,
+# not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the
+# alphabetical list.
+
+SORT_BY_SCOPE_NAME = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or
+# disable (NO) the todo list. This list is created by putting \todo
+# commands in the documentation.
+
+GENERATE_TODOLIST = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or
+# disable (NO) the test list. This list is created by putting \test
+# commands in the documentation.
+
+GENERATE_TESTLIST = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or
+# disable (NO) the bug list. This list is created by putting \bug
+# commands in the documentation.
+
+GENERATE_BUGLIST = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
+# disable (NO) the deprecated list. This list is created by putting
+# \deprecated commands in the documentation.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional
+# documentation sections, marked by \if sectionname ... \endif.
+
+ENABLED_SECTIONS =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
+# the initial value of a variable or define consists of for it to appear in
+# the documentation. If the initializer consists of more lines than specified
+# here it will be hidden. Use a value of 0 to hide initializers completely.
+# The appearance of the initializer of individual variables and defines in the
+# documentation can be controlled using \showinitializer or \hideinitializer
+# command in the documentation regardless of this setting.
+
+MAX_INITIALIZER_LINES = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
+# at the bottom of the documentation of classes and structs. If set to YES the
+# list will mention the files that were used to generate the documentation.
+
+SHOW_USED_FILES = YES
+
+# If the sources in your project are distributed over multiple directories
+# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
+# in the documentation. The default is NO.
+
+SHOW_DIRECTORIES = NO
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
+# This will remove the Files entry from the Quick Index and from the
+# Folder Tree View (if specified). The default is YES.
+
+SHOW_FILES = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
+# Namespaces page.
+# This will remove the Namespaces entry from the Quick Index
+# and from the Folder Tree View (if specified). The default is YES.
+
+SHOW_NAMESPACES = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command <command> <input-file>, where <command> is the value of
+# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
+# provided by doxygen. Whatever the program writes to standard output
+# is used as the file version. See the manual for examples.
+
+FILE_VERSION_FILTER =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed by
+# doxygen. The layout file controls the global structure of the generated output files
+# in an output format independent way. The create the layout file that represents
+# doxygen's defaults, run doxygen with the -l option. You can optionally specify a
+# file name after the option, if omitted DoxygenLayout.xml will be used as the name
+# of the layout file.
+
+LAYOUT_FILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated
+# by doxygen. Possible values are YES and NO. If left blank NO is used.
+
+QUIET = YES
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated by doxygen. Possible values are YES and NO. If left blank
+# NO is used.
+
+WARNINGS = YES
+
+# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
+# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
+# automatically be disabled.
+
+WARN_IF_UNDOCUMENTED = YES
+
+# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some
+# parameters in a documented function, or documenting parameters that
+# don't exist or using markup commands wrongly.
+
+WARN_IF_DOC_ERROR = YES
+
+# This WARN_NO_PARAMDOC option can be abled to get warnings for
+# functions that are documented, but have no documentation for their parameters
+# or return value. If set to NO (the default) doxygen will only warn about
+# wrong or incomplete parameter documentation, but not about the absence of
+# documentation.
+
+WARN_NO_PARAMDOC = YES
+
+# The WARN_FORMAT tag determines the format of the warning messages that
+# doxygen can produce. The string should contain the $file, $line, and $text
+# tags, which will be replaced by the file and line number from which the
+# warning originated and the warning text. Optionally the format may contain
+# $version, which will be replaced by the version of the file (if it could
+# be obtained via FILE_VERSION_FILTER)
+
+WARN_FORMAT = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning
+# and error messages should be written. If left blank the output is written
+# to stderr.
+
+WARN_LOGFILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag can be used to specify the files and/or directories that contain
+# documented source files. You may enter file names like "myfile.cpp" or
+# directories like "/usr/src/myproject". Separate the files or directories
+# with spaces.
+
+INPUT = ./src/clustal ./src/clustal-omega.h ./src/clustal-omega.c
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
+# also the default input encoding. Doxygen uses libiconv (or the iconv built
+# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
+# the list of possible encodings.
+
+INPUT_ENCODING = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank the following patterns are tested:
+# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
+# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
+
+FILE_PATTERNS = *.h *.c
+
+# The RECURSIVE tag can be used to turn specify whether or not subdirectories
+# should be searched for input files as well. Possible values are YES and NO.
+# If left blank NO is used.
+
+RECURSIVE = NO
+
+# The EXCLUDE tag can be used to specify files and/or directories that should
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+
+EXCLUDE = ./src/config.h
+
+# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
+# directories that are symbolic links (a Unix filesystem feature) are excluded
+# from the input.
+
+EXCLUDE_SYMLINKS = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories. Note that the wildcards are matched
+# against the file with absolute path, so to exclude all test directories
+# for example use the pattern */test/*
+
+EXCLUDE_PATTERNS =
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+
+EXCLUDE_SYMBOLS =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or
+# directories that contain example code fragments that are included (see
+# the \include command).
+
+EXAMPLE_PATH = ./src/
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank all files are included.
+
+EXAMPLE_PATTERNS =
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude
+# commands irrespective of the value of the RECURSIVE tag.
+# Possible values are YES and NO. If left blank NO is used.
+
+EXAMPLE_RECURSIVE = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or
+# directories that contain image that are included in the documentation (see
+# the \image command).
+
+IMAGE_PATH =
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command <filter> <input-file>, where <filter>
+# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
+# input file. Doxygen will then use the output that the filter program writes
+# to standard output.
+# If FILTER_PATTERNS is specified, this tag will be
+# ignored.
+
+INPUT_FILTER =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis.
+# Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match.
+# The filters are a list of the form:
+# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
+# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER
+# is applied to all files.
+
+FILTER_PATTERNS =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will be used to filter the input files when producing source
+# files to browse (i.e. when SOURCE_BROWSER is set to YES).
+
+FILTER_SOURCE_FILES = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will
+# be generated. Documented entities will be cross-referenced with these sources.
+# Note: To get rid of all source code in the generated output, make sure also
+# VERBATIM_HEADERS is set to NO.
+
+SOURCE_BROWSER = NO
+
+# Setting the INLINE_SOURCES tag to YES will include the body
+# of functions and classes directly in the documentation.
+
+INLINE_SOURCES = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
+# doxygen to hide any special comment blocks from generated source code
+# fragments. Normal C and C++ comments will always remain visible.
+
+STRIP_CODE_COMMENTS = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES
+# then for each documented function all documented
+# functions referencing it will be listed.
+
+REFERENCED_BY_RELATION = NO
+
+# If the REFERENCES_RELATION tag is set to YES
+# then for each documented function all documented entities
+# called/used by that function will be listed.
+
+REFERENCES_RELATION = NO
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
+# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
+# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
+# link to the source code.
+# Otherwise they will link to the documentation.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code
+# will point to the HTML generated by the htags(1) tool instead of doxygen
+# built-in source browser. The htags tool is part of GNU's global source
+# tagging system (see http://www.gnu.org/software/global/global.html). You
+# will need version 4.8.6 or higher.
+
+USE_HTAGS = NO
+
+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
+# will generate a verbatim copy of the header file for each class for
+# which an include is specified. Set to NO to disable this.
+
+VERBATIM_HEADERS = YES
+
+#---------------------------------------------------------------------------
+# configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
+# of all compounds will be generated. Enable this if the project
+# contains a lot of classes, structs, unions or interfaces.
+
+ALPHABETICAL_INDEX = NO
+
+# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
+# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
+# in which this list will be split (can be a number in the range [1..20])
+
+COLS_IN_ALPHA_INDEX = 5
+
+# In case all classes in a project start with a common prefix, all
+# classes will be put under the same header in the alphabetical index.
+# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
+# should be ignored while generating the index headers.
+
+IGNORE_PREFIX =
+
+#---------------------------------------------------------------------------
+# configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
+# generate HTML output.
+
+GENERATE_HTML = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `html' will be used as the default path.
+
+HTML_OUTPUT = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
+# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
+# doxygen will generate files with .html extension.
+
+HTML_FILE_EXTENSION = .html
+
+# The HTML_HEADER tag can be used to specify a personal HTML header for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard header.
+
+HTML_HEADER =
+
+# The HTML_FOOTER tag can be used to specify a personal HTML footer for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard footer.
+
+HTML_FOOTER =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
+# style sheet that is used by each HTML page. It can be used to
+# fine-tune the look of the HTML output. If the tag is left blank doxygen
+# will generate a default style sheet. Note that doxygen will try to copy
+# the style sheet file to the HTML output directory, so don't put your own
+# stylesheet in the HTML output directory as well, or it will be erased!
+
+HTML_STYLESHEET =
+
+# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
+# files or namespaces will be aligned in HTML using tables. If set to
+# NO a bullet list will be used.
+
+HTML_ALIGN_MEMBERS = YES
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded. For this to work a browser that supports
+# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
+# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
+
+HTML_DYNAMIC_SECTIONS = NO
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files
+# will be generated that can be used as input for Apple's Xcode 3
+# integrated development environment, introduced with OSX 10.5 (Leopard).
+# To create a documentation set, doxygen will generate a Makefile in the
+# HTML output directory. Running make will produce the docset in that
+# directory and running "make install" will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
+# it at startup.
+# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html for more information.
+
+GENERATE_DOCSET = NO
+
+# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
+# feed. A documentation feed provides an umbrella under which multiple
+# documentation sets from a single provider (such as a company or product suite)
+# can be grouped.
+
+DOCSET_FEEDNAME = "Doxygen generated docs"
+
+# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
+# should uniquely identify the documentation set bundle. This should be a
+# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
+# will append .docset to the name.
+
+DOCSET_BUNDLE_ID = org.doxygen.Project
+
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files
+# will be generated that can be used as input for tools like the
+# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
+# of the generated HTML documentation.
+
+GENERATE_HTMLHELP = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
+# be used to specify the file name of the resulting .chm file. You
+# can add a path in front of the file if the result should not be
+# written to the html output directory.
+
+CHM_FILE =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
+# be used to specify the location (absolute path including file name) of
+# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
+# the HTML help compiler on the generated index.hhp.
+
+HHC_LOCATION =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
+# controls if a separate .chi index file is generated (YES) or that
+# it should be included in the master .chm file (NO).
+
+GENERATE_CHI = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
+# is used to encode HtmlHelp index (hhk), content (hhc) and project file
+# content.
+
+CHM_INDEX_ENCODING =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
+# controls whether a binary table of contents is generated (YES) or a
+# normal table of contents (NO) in the .chm file.
+
+BINARY_TOC = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members
+# to the contents of the HTML help documentation and to the tree view.
+
+TOC_EXPAND = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and QHP_VIRTUAL_FOLDER
+# are set, an additional index file will be generated that can be used as input for
+# Qt's qhelpgenerator to generate a Qt Compressed Help (.qch) of the generated
+# HTML documentation.
+
+GENERATE_QHP = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
+# be used to specify the file name of the resulting .qch file.
+# The path specified is relative to the HTML output folder.
+
+QCH_FILE =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#namespace
+
+QHP_NAMESPACE =
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#virtual-folders
+
+QHP_VIRTUAL_FOLDER = doc
+
+# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to add.
+# For more information please see
+# http://doc.trolltech.com/qthelpproject.html#custom-filters
+
+QHP_CUST_FILTER_NAME =
+
+# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the custom filter to add.For more information please see
+# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">Qt Help Project / Custom Filters</a>.
+
+QHP_CUST_FILTER_ATTRS =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this project's
+# filter section matches.
+# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">Qt Help Project / Filter Attributes</a>.
+
+QHP_SECT_FILTER_ATTRS =
+
+# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
+# be used to specify the location of Qt's qhelpgenerator.
+# If non-empty doxygen will try to run qhelpgenerator on the generated
+# .qhp file.
+
+QHG_LOCATION =
+
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
+# top of each HTML page. The value NO (the default) enables the index and
+# the value YES disables it.
+
+DISABLE_INDEX = NO
+
+# This tag can be used to set the number of enum values (range [1..20])
+# that doxygen will group on one line in the generated HTML documentation.
+
+ENUM_VALUES_PER_LINE = 4
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information.
+# If the tag value is set to FRAME, a side panel will be generated
+# containing a tree-like index structure (just like the one that
+# is generated for HTML Help). For this to work a browser that supports
+# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+,
+# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are
+# probably better off using the HTML help feature. Other possible values
+# for this tag are: HIERARCHIES, which will generate the Groups, Directories,
+# and Class Hierarchy pages using a tree view instead of an ordered list;
+# ALL, which combines the behavior of FRAME and HIERARCHIES; and NONE, which
+# disables this behavior completely. For backwards compatibility with previous
+# releases of Doxygen, the values YES and NO are equivalent to FRAME and NONE
+# respectively.
+
+GENERATE_TREEVIEW = NONE
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
+# used to set the initial width (in pixels) of the frame in which the tree
+# is shown.
+
+TREEVIEW_WIDTH = 250
+
+# Use this tag to change the font size of Latex formulas included
+# as images in the HTML documentation. The default is 10. Note that
+# when you change the font size after a successful doxygen run you need
+# to manually remove any form_*.png images from the HTML output directory
+# to force them to be regenerated.
+
+FORMULA_FONTSIZE = 10
+
+#---------------------------------------------------------------------------
+# configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
+# generate Latex output.
+
+GENERATE_LATEX = YES
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `latex' will be used as the default path.
+
+LATEX_OUTPUT = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked. If left blank `latex' will be used as the default command name.
+
+LATEX_CMD_NAME = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
+# generate index for LaTeX. If left blank `makeindex' will be used as the
+# default command name.
+
+MAKEINDEX_CMD_NAME = makeindex
+
+# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
+# LaTeX documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_LATEX = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used
+# by the printer. Possible values are: a4, a4wide, letter, legal and
+# executive. If left blank a4wide will be used.
+
+PAPER_TYPE = a4wide
+
+# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
+# packages that should be included in the LaTeX output.
+
+EXTRA_PACKAGES =
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
+# the generated latex document. The header should contain everything until
+# the first chapter. If it is left blank doxygen will generate a
+# standard header. Notice: only use this tag if you know what you are doing!
+
+LATEX_HEADER =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
+# is prepared for conversion to pdf (using ps2pdf). The pdf file will
+# contain links (just like the HTML output) instead of page references
+# This makes the output suitable for online browsing using a pdf viewer.
+
+PDF_HYPERLINKS = YES
+
+# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
+# plain latex in the generated Makefile. Set this option to YES to get a
+# higher quality PDF documentation.
+
+USE_PDFLATEX = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
+# command to the generated LaTeX files. This will instruct LaTeX to keep
+# running if errors occur, instead of asking the user for help.
+# This option is also used when generating formulas in HTML.
+
+LATEX_BATCHMODE = NO
+
+# If LATEX_HIDE_INDICES is set to YES then doxygen will not
+# include the index chapters (such as File Index, Compound Index, etc.)
+# in the output.
+
+LATEX_HIDE_INDICES = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
+# The RTF output is optimized for Word 97 and may not look very pretty with
+# other RTF readers or editors.
+
+GENERATE_RTF = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `rtf' will be used as the default path.
+
+RTF_OUTPUT = rtf
+
+# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
+# RTF documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_RTF = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
+# will contain hyperlink fields. The RTF file will
+# contain links (just like the HTML output) instead of page references.
+# This makes the output suitable for online browsing using WORD or other
+# programs which support those fields.
+# Note: wordpad (write) and others do not support links.
+
+RTF_HYPERLINKS = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's
+# config file, i.e. a series of assignments. You only have to provide
+# replacements, missing definitions are set to their default value.
+
+RTF_STYLESHEET_FILE =
+
+# Set optional variables used in the generation of an rtf document.
+# Syntax is similar to doxygen's config file.
+
+RTF_EXTENSIONS_FILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
+# generate man pages
+
+GENERATE_MAN = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `man' will be used as the default path.
+
+MAN_OUTPUT = man
+
+# The MAN_EXTENSION tag determines the extension that is added to
+# the generated man pages (default is the subroutine's section .3)
+
+MAN_EXTENSION = .3
+
+# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
+# then it will generate one additional man file for each entity
+# documented in the real man page(s). These additional files
+# only source the real man page, but without them the man command
+# would be unable to find the correct page. The default is NO.
+
+MAN_LINKS = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES Doxygen will
+# generate an XML file that captures the structure of
+# the code including all documentation.
+
+GENERATE_XML = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `xml' will be used as the default path.
+
+XML_OUTPUT = xml
+
+# The XML_SCHEMA tag can be used to specify an XML schema,
+# which can be used by a validating XML parser to check the
+# syntax of the XML files.
+
+XML_SCHEMA =
+
+# The XML_DTD tag can be used to specify an XML DTD,
+# which can be used by a validating XML parser to check the
+# syntax of the XML files.
+
+XML_DTD =
+
+# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
+# dump the program listings (including syntax highlighting
+# and cross-referencing information) to the XML output. Note that
+# enabling this will significantly increase the size of the XML output.
+
+XML_PROGRAMLISTING = YES
+
+#---------------------------------------------------------------------------
+# configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
+# generate an AutoGen Definitions (see autogen.sf.net) file
+# that captures the structure of the code including all
+# documentation. Note that this feature is still experimental
+# and incomplete at the moment.
+
+GENERATE_AUTOGEN_DEF = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES Doxygen will
+# generate a Perl module file that captures the structure of
+# the code including all documentation. Note that this
+# feature is still experimental and incomplete at the
+# moment.
+
+GENERATE_PERLMOD = NO
+
+# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
+# the necessary Makefile rules, Perl scripts and LaTeX code to be able
+# to generate PDF and DVI output from the Perl module output.
+
+PERLMOD_LATEX = NO
+
+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
+# nicely formatted so it can be parsed by a human reader.
+# This is useful
+# if you want to understand what is going on.
+# On the other hand, if this
+# tag is set to NO the size of the Perl module output will be much smaller
+# and Perl will parse it just the same.
+
+PERLMOD_PRETTY = YES
+
+# The names of the make variables in the generated doxyrules.make file
+# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
+# This is useful so different doxyrules.make files included by the same
+# Makefile don't overwrite each other's variables.
+
+PERLMOD_MAKEVAR_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
+# evaluate all C-preprocessor directives found in the sources and include
+# files.
+
+ENABLE_PREPROCESSING = YES
+
+# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
+# names in the source code. If set to NO (the default) only conditional
+# compilation will be performed. Macro expansion can be done in a controlled
+# way by setting EXPAND_ONLY_PREDEF to YES.
+
+MACRO_EXPANSION = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
+# then the macro expansion is limited to the macros specified with the
+# PREDEFINED and EXPAND_AS_DEFINED tags.
+
+EXPAND_ONLY_PREDEF = NO
+
+# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
+# in the INCLUDE_PATH (see below) will be search if a #include is found.
+
+SEARCH_INCLUDES = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by
+# the preprocessor.
+
+INCLUDE_PATH =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will
+# be used.
+
+INCLUDE_FILE_PATTERNS =
+
+# The PREDEFINED tag can be used to specify one or more macro names that
+# are defined before the preprocessor is started (similar to the -D option of
+# gcc). The argument of the tag is a list of macros of the form: name
+# or name=definition (no spaces). If the definition and the = are
+# omitted =1 is assumed. To prevent a macro definition from being
+# undefined via #undef or recursively expanded use the := operator
+# instead of the = operator.
+
+PREDEFINED =
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
+# this tag can be used to specify a list of macro names that should be expanded.
+# The macro definition that is found in the sources will be used.
+# Use the PREDEFINED tag if you want to use a different macro definition.
+
+EXPAND_AS_DEFINED =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
+# doxygen's preprocessor will remove all function-like macros that are alone
+# on a line, have an all uppercase name, and do not end with a semicolon. Such
+# function macros are typically used for boiler-plate code, and will confuse
+# the parser if not removed.
+
+SKIP_FUNCTION_MACROS = YES
+
+#---------------------------------------------------------------------------
+# Configuration::additions related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES option can be used to specify one or more tagfiles.
+# Optionally an initial location of the external documentation
+# can be added for each tagfile. The format of a tag file without
+# this location is as follows:
+#
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+#
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where "loc1" and "loc2" can be relative or absolute paths or
+# URLs. If a location is present for each tag, the installdox tool
+# does not have to be run to correct the links.
+# Note that each tag file must have a unique name
+# (where the name does NOT include the path)
+# If a tag file is not located in the directory in which doxygen
+# is run, you must also specify the path to the tagfile here.
+
+TAGFILES =
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create
+# a tag file that is based on the input files it reads.
+
+GENERATE_TAGFILE =
+
+# If the ALLEXTERNALS tag is set to YES all external classes will be listed
+# in the class index. If set to NO only the inherited external classes
+# will be listed.
+
+ALLEXTERNALS = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
+# in the modules index. If set to NO, only the current project's groups will
+# be listed.
+
+EXTERNAL_GROUPS = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of `which perl').
+
+PERL_PATH = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
+# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
+# or super classes. Setting the tag to NO turns the diagrams off. Note that
+# this option is superseded by the HAVE_DOT option below. This is only a
+# fallback. It is recommended to install and use dot, since it yields more
+# powerful graphs.
+
+CLASS_DIAGRAMS = YES
+
+# You can define message sequence charts within doxygen comments using the \msc
+# command. Doxygen will then run the mscgen tool (see
+# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+# the mscgen tool resides. If left empty the tool is assumed to be found in the
+# default search path.
+
+MSCGEN_PATH =
+
+# If set to YES, the inheritance and collaboration graphs will hide
+# inheritance and usage relations if the target is undocumented
+# or is not a class.
+
+HIDE_UNDOC_RELATIONS = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz, a graph visualization
+# toolkit from AT&T and Lucent Bell Labs. The other options in this section
+# have no effect if this option is set to NO (the default)
+
+HAVE_DOT = YES
+
+# By default doxygen will write a font called FreeSans.ttf to the output
+# directory and reference it in all dot files that doxygen generates. This
+# font does not include all possible unicode characters however, so when you need
+# these (or just want a differently looking font) you can specify the font name
+# using DOT_FONTNAME. You need need to make sure dot is able to find the font,
+# which can be done by putting it in a standard location or by setting the
+# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory
+# containing the font.
+
+DOT_FONTNAME = FreeSans
+
+# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
+# The default size is 10pt.
+
+DOT_FONTSIZE = 10
+
+# By default doxygen will tell dot to use the output directory to look for the
+# FreeSans.ttf font (which doxygen will put there itself). If you specify a
+# different font using DOT_FONTNAME you can set the path where dot
+# can find it using this tag.
+
+DOT_FONTPATH =
+
+# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect inheritance relations. Setting this tag to YES will force the
+# the CLASS_DIAGRAMS tag to NO.
+
+CLASS_GRAPH = YES
+
+# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect implementation dependencies (inheritance, containment, and
+# class references variables) of the class with other documented classes.
+
+COLLABORATION_GRAPH = YES
+
+# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for groups, showing the direct groups dependencies
+
+GROUP_GRAPHS = YES
+
+# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
+# collaboration diagrams in a style similar to the OMG's Unified Modeling
+# Language.
+
+UML_LOOK = NO
+
+# If set to YES, the inheritance and collaboration graphs will show the
+# relations between templates and their instances.
+
+TEMPLATE_RELATIONS = NO
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
+# tags are set to YES then doxygen will generate a graph for each documented
+# file showing the direct and indirect include dependencies of the file with
+# other documented files.
+
+INCLUDE_GRAPH = YES
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
+# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
+# documented header file showing the documented files that directly or
+# indirectly include this file.
+
+INCLUDED_BY_GRAPH = YES
+
+# If the CALL_GRAPH and HAVE_DOT options are set to YES then
+# doxygen will generate a call dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable call graphs
+# for selected functions only using the \callgraph command.
+
+CALL_GRAPH = NO
+
+# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
+# doxygen will generate a caller dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable caller
+# graphs for selected functions only using the \callergraph command.
+
+CALLER_GRAPH = NO
+
+# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
+# will graphical hierarchy of all classes instead of a textual one.
+
+GRAPHICAL_HIERARCHY = YES
+
+# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# then doxygen will show the dependencies a directory has on other directories
+# in a graphical way. The dependency relations are determined by the #include
+# relations between the files in the directories.
+
+DIRECTORY_GRAPH = YES
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+# generated by dot. Possible values are png, jpg, or gif
+# If left blank png will be used.
+
+DOT_IMAGE_FORMAT = png
+
+# The tag DOT_PATH can be used to specify the path where the dot tool can be
+# found. If left blank, it is assumed the dot tool can be found in the path.
+
+DOT_PATH =
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that
+# contain dot files that are included in the documentation (see the
+# \dotfile command).
+
+DOTFILE_DIRS =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
+# nodes that will be shown in the graph. If the number of nodes in a graph
+# becomes larger than this value, doxygen will truncate the graph, which is
+# visualized by representing a node as a red box. Note that doxygen if the
+# number of direct children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
+# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+
+DOT_GRAPH_MAX_NODES = 50
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
+# graphs generated by dot. A depth value of 3 means that only nodes reachable
+# from the root by following a path via at most 3 edges will be shown. Nodes
+# that lay further from the root node will be omitted. Note that setting this
+# option to 1 or 2 may greatly reduce the computation time needed for large
+# code bases. Also note that the size of a graph can be further restricted by
+# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+
+MAX_DOT_GRAPH_DEPTH = 0
+
+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
+# background. This is disabled by default, because dot on Windows does not
+# seem to support this out of the box. Warning: Depending on the platform used,
+# enabling this option may lead to badly anti-aliased labels on the edges of
+# a graph (i.e. they become hard to read).
+
+DOT_TRANSPARENT = NO
+
+# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
+# files in one run (i.e. multiple -o and -T options on the command line). This
+# makes dot run faster, but since only newer versions of dot (>1.8.10)
+# support this, this feature is disabled by default.
+
+DOT_MULTI_TARGETS = NO
+
+# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
+# generate a legend page explaining the meaning of the various boxes and
+# arrows in the dot generated graphs.
+
+GENERATE_LEGEND = YES
+
+# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
+# remove the intermediate dot files that are used to generate
+# the various graphs.
+
+DOT_CLEANUP = YES
+
+#---------------------------------------------------------------------------
+# Options related to the search engine
+#---------------------------------------------------------------------------
+
+# The SEARCHENGINE tag specifies whether or not a search engine should be
+# used. If set to NO the values of all tags below this one will be ignored.
+
+SEARCHENGINE = NO
--- /dev/null
+# Doxyfile 1.5.8
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project
+#
+# All text after a hash (#) is considered a comment and will be ignored
+# The format is:
+# TAG = value [value, ...]
+# For lists items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (" ")
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# This tag specifies the encoding used for all characters in the config file
+# that follow. The default is UTF-8 which is also the encoding used for all
+# text before the first occurrence of this tag. Doxygen uses libiconv (or the
+# iconv built into libc) for the transcoding. See
+# http://www.gnu.org/software/libiconv for the list of possible encodings.
+
+DOXYFILE_ENCODING = UTF-8
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
+# by quotes) that should identify the project.
+
+PROJECT_NAME = "@PACKAGE_NAME@"
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number.
+# This could be handy for archiving the generated documentation or
+# if some version control system is used.
+
+PROJECT_NUMBER = @PACKAGE_VERSION@
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
+# base path where the generated documentation will be put.
+# If a relative path is entered, it will be relative to the location
+# where doxygen was started. If left blank the current directory will be used.
+
+OUTPUT_DIRECTORY = ./doc/doxygen/
+
+# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
+# 4096 sub-directories (in 2 levels) under the output directory of each output
+# format and will distribute the generated files over these directories.
+# Enabling this option can be useful when feeding doxygen a huge amount of
+# source files, where putting all generated files in the same directory would
+# otherwise cause performance problems for the file system.
+
+CREATE_SUBDIRS = NO
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all constant output in the proper language.
+# The default language is English, other supported languages are:
+# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
+# Croatian, Czech, Danish, Dutch, Farsi, Finnish, French, German, Greek,
+# Hungarian, Italian, Japanese, Japanese-en (Japanese with English messages),
+# Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, Polish,
+# Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak, Slovene,
+# Spanish, Swedish, and Ukrainian.
+
+OUTPUT_LANGUAGE = English
+
+# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
+# include brief member descriptions after the members that are listed in
+# the file and class documentation (similar to JavaDoc).
+# Set to NO to disable this.
+
+BRIEF_MEMBER_DESC = YES
+
+# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
+# the brief description of a member or function before the detailed description.
+# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+# brief descriptions will be completely suppressed.
+
+REPEAT_BRIEF = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator
+# that is used to form the text in various listings. Each string
+# in this list, if found as the leading text of the brief description, will be
+# stripped from the text and the result after processing the whole list, is
+# used as the annotated text. Otherwise, the brief description is used as-is.
+# If left blank, the following values are used ("$name" is automatically
+# replaced with the name of the entity): "The $name class" "The $name widget"
+# "The $name file" "is" "provides" "specifies" "contains"
+# "represents" "a" "an" "the"
+
+ABBREVIATE_BRIEF =
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
+# Doxygen will generate a detailed section even if there is only a brief
+# description.
+
+ALWAYS_DETAILED_SEC = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
+# inherited members of a class in the documentation of that class as if those
+# members were ordinary class members. Constructors, destructors and assignment
+# operators of the base classes will not be shown.
+
+INLINE_INHERITED_MEMB = NO
+
+# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
+# path before files name in the file list and in the header files. If set
+# to NO the shortest path that makes the file name unique will be used.
+
+FULL_PATH_NAMES = YES
+
+# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
+# can be used to strip a user-defined part of the path. Stripping is
+# only done if one of the specified strings matches the left-hand part of
+# the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the
+# path to strip.
+
+STRIP_FROM_PATH =
+
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
+# the path mentioned in the documentation of a class, which tells
+# the reader which header file to include in order to use a class.
+# If left blank only the name of the header file containing the class
+# definition is used. Otherwise one should specify the include paths that
+# are normally passed to the compiler using the -I flag.
+
+STRIP_FROM_INC_PATH =
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
+# (but less readable) file names. This can be useful is your file systems
+# doesn't support long names like on DOS, Mac, or CD-ROM.
+
+SHORT_NAMES = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
+# will interpret the first line (until the first dot) of a JavaDoc-style
+# comment as the brief description. If set to NO, the JavaDoc
+# comments will behave just like regular Qt-style comments
+# (thus requiring an explicit @brief command for a brief description.)
+
+JAVADOC_AUTOBRIEF = NO
+
+# If the QT_AUTOBRIEF tag is set to YES then Doxygen will
+# interpret the first line (until the first dot) of a Qt-style
+# comment as the brief description. If set to NO, the comments
+# will behave just like regular Qt-style comments (thus requiring
+# an explicit \brief command for a brief description.)
+
+QT_AUTOBRIEF = NO
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
+# treat a multi-line C++ special comment block (i.e. a block of //! or ///
+# comments) as a brief description. This used to be the default behaviour.
+# The new default is to treat a multi-line C++ comment block as a detailed
+# description. Set this tag to YES if you prefer the old behaviour instead.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
+# member inherits the documentation from any documented member that it
+# re-implements.
+
+INHERIT_DOCS = YES
+
+# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
+# a new page for each member. If set to NO, the documentation of a member will
+# be part of the file/class/namespace that contains it.
+
+SEPARATE_MEMBER_PAGES = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab.
+# Doxygen uses this value to replace tabs by spaces in code fragments.
+
+TAB_SIZE = 4
+
+# This tag can be used to specify a number of aliases that acts
+# as commands in the documentation. An alias has the form "name=value".
+# For example adding "sideeffect=\par Side Effects:\n" will allow you to
+# put the command \sideeffect (or @sideeffect) in the documentation, which
+# will result in a user-defined paragraph with heading "Side Effects:".
+# You can put \n's in the value part of an alias to insert newlines.
+
+ALIASES =
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
+# sources only. Doxygen will then generate output that is more tailored for C.
+# For instance, some of the names that are used will be different. The list
+# of all members will be omitted, etc.
+
+OPTIMIZE_OUTPUT_FOR_C = YES
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
+# sources only. Doxygen will then generate output that is more tailored for
+# Java. For instance, namespaces will be presented as packages, qualified
+# scopes will look different, etc.
+
+OPTIMIZE_OUTPUT_JAVA = NO
+
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources only. Doxygen will then generate output that is more tailored for
+# Fortran.
+
+OPTIMIZE_FOR_FORTRAN = NO
+
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+# sources. Doxygen will then generate output that is tailored for
+# VHDL.
+
+OPTIMIZE_OUTPUT_VHDL = NO
+
+# Doxygen selects the parser to use depending on the extension of the files it parses.
+# With this tag you can assign which parser to use for a given extension.
+# Doxygen has a built-in mapping, but you can override or extend it using this tag.
+# The format is ext=language, where ext is a file extension, and language is one of
+# the parsers supported by doxygen: IDL, Java, Javascript, C#, C, C++, D, PHP,
+# Objective-C, Python, Fortran, VHDL, C, C++. For instance to make doxygen treat
+# .inc files as Fortran files (default is PHP), and .f files as C (default is Fortran),
+# use: inc=Fortran f=C
+
+EXTENSION_MAPPING =
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should
+# set this tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
+# func(std::string) {}). This also make the inheritance and collaboration
+# diagrams that involve STL classes more complete and accurate.
+
+BUILTIN_STL_SUPPORT = NO
+
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
+# enable parsing support.
+
+CPP_CLI_SUPPORT = NO
+
+# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
+# Doxygen will parse them like normal C++ but will assume all classes use public
+# instead of private inheritance when no explicit protection keyword is present.
+
+SIP_SUPPORT = NO
+
+# For Microsoft's IDL there are propget and propput attributes to indicate getter
+# and setter methods for a property. Setting this option to YES (the default)
+# will make doxygen to replace the get and set methods by a property in the
+# documentation. This will only work if the methods are indeed getting or
+# setting a simple type. If this is not the case, or you want to show the
+# methods anyway, you should set this option to NO.
+
+IDL_PROPERTY_SUPPORT = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES, then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
+# all members of a group must be documented explicitly.
+
+DISTRIBUTE_GROUP_DOC = NO
+
+# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
+# the same type (for instance a group of public functions) to be put as a
+# subgroup of that type (e.g. under the Public Functions section). Set it to
+# NO to prevent subgrouping. Alternatively, this can be done per class using
+# the \nosubgrouping command.
+
+SUBGROUPING = YES
+
+# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
+# is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically
+# be useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+
+TYPEDEF_HIDES_STRUCT = NO
+
+# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
+# determine which symbols to keep in memory and which to flush to disk.
+# When the cache is full, less often used symbols will be written to disk.
+# For small to medium size projects (<1000 input files) the default value is
+# probably good enough. For larger projects a too small cache size can cause
+# doxygen to be busy swapping symbols to and from disk most of the time
+# causing a significant performance penality.
+# If the system has enough physical memory increasing the cache will improve the
+# performance by keeping more symbols in memory. Note that the value works on
+# a logarithmic scale so increasing the size by one will rougly double the
+# memory usage. The cache size is given by this formula:
+# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
+# corresponding to a cache size of 2^16 = 65536 symbols
+
+SYMBOL_CACHE_SIZE = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
+# documentation are documented, even if no documentation was available.
+# Private class members and static file members will be hidden unless
+# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+
+EXTRACT_ALL = YES
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
+# will be included in the documentation.
+
+EXTRACT_PRIVATE = NO
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file
+# will be included in the documentation.
+
+EXTRACT_STATIC = NO
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
+# defined locally in source files will be included in the documentation.
+# If set to NO only classes defined in header files are included.
+
+EXTRACT_LOCAL_CLASSES = YES
+
+# This flag is only useful for Objective-C code. When set to YES local
+# methods, which are defined in the implementation section but not in
+# the interface are included in the documentation.
+# If set to NO (the default) only methods in the interface are included.
+
+EXTRACT_LOCAL_METHODS = NO
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base
+# name of the file that contains the anonymous namespace. By default
+# anonymous namespace are hidden.
+
+EXTRACT_ANON_NSPACES = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
+# undocumented members of documented classes, files or namespaces.
+# If set to NO (the default) these members will be included in the
+# various overviews, but no documentation section is generated.
+# This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_MEMBERS = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy.
+# If set to NO (the default) these classes will be included in the various
+# overviews. This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_CLASSES = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
+# friend (class|struct|union) declarations.
+# If set to NO (the default) these declarations will be included in the
+# documentation.
+
+HIDE_FRIEND_COMPOUNDS = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
+# documentation blocks found inside the body of a function.
+# If set to NO (the default) these blocks will be appended to the
+# function's detailed documentation block.
+
+HIDE_IN_BODY_DOCS = NO
+
+# The INTERNAL_DOCS tag determines if documentation
+# that is typed after a \internal command is included. If the tag is set
+# to NO (the default) then the documentation will be excluded.
+# Set it to YES to include the internal documentation.
+
+INTERNAL_DOCS = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
+# file names in lower-case letters. If set to YES upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+
+CASE_SENSE_NAMES = YES
+
+# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
+# will show members with their full class and namespace scopes in the
+# documentation. If set to YES the scope will be hidden.
+
+HIDE_SCOPE_NAMES = NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
+# will put a list of the files that are included by a file in the documentation
+# of that file.
+
+SHOW_INCLUDE_FILES = YES
+
+# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
+# is inserted in the documentation for inline members.
+
+INLINE_INFO = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
+# will sort the (detailed) documentation of file and class members
+# alphabetically by member name. If set to NO the members will appear in
+# declaration order.
+
+SORT_MEMBER_DOCS = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
+# brief documentation of file, namespace and class members alphabetically
+# by member name. If set to NO (the default) the members will appear in
+# declaration order.
+
+SORT_BRIEF_DOCS = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
+# hierarchy of group names into alphabetical order. If set to NO (the default)
+# the group names will appear in their defined order.
+
+SORT_GROUP_NAMES = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
+# sorted by fully-qualified names, including namespaces. If set to
+# NO (the default), the class list will be sorted only by class name,
+# not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the
+# alphabetical list.
+
+SORT_BY_SCOPE_NAME = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or
+# disable (NO) the todo list. This list is created by putting \todo
+# commands in the documentation.
+
+GENERATE_TODOLIST = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or
+# disable (NO) the test list. This list is created by putting \test
+# commands in the documentation.
+
+GENERATE_TESTLIST = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or
+# disable (NO) the bug list. This list is created by putting \bug
+# commands in the documentation.
+
+GENERATE_BUGLIST = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
+# disable (NO) the deprecated list. This list is created by putting
+# \deprecated commands in the documentation.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional
+# documentation sections, marked by \if sectionname ... \endif.
+
+ENABLED_SECTIONS =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
+# the initial value of a variable or define consists of for it to appear in
+# the documentation. If the initializer consists of more lines than specified
+# here it will be hidden. Use a value of 0 to hide initializers completely.
+# The appearance of the initializer of individual variables and defines in the
+# documentation can be controlled using \showinitializer or \hideinitializer
+# command in the documentation regardless of this setting.
+
+MAX_INITIALIZER_LINES = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
+# at the bottom of the documentation of classes and structs. If set to YES the
+# list will mention the files that were used to generate the documentation.
+
+SHOW_USED_FILES = YES
+
+# If the sources in your project are distributed over multiple directories
+# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
+# in the documentation. The default is NO.
+
+SHOW_DIRECTORIES = NO
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
+# This will remove the Files entry from the Quick Index and from the
+# Folder Tree View (if specified). The default is YES.
+
+SHOW_FILES = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
+# Namespaces page.
+# This will remove the Namespaces entry from the Quick Index
+# and from the Folder Tree View (if specified). The default is YES.
+
+SHOW_NAMESPACES = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command <command> <input-file>, where <command> is the value of
+# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
+# provided by doxygen. Whatever the program writes to standard output
+# is used as the file version. See the manual for examples.
+
+FILE_VERSION_FILTER =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed by
+# doxygen. The layout file controls the global structure of the generated output files
+# in an output format independent way. The create the layout file that represents
+# doxygen's defaults, run doxygen with the -l option. You can optionally specify a
+# file name after the option, if omitted DoxygenLayout.xml will be used as the name
+# of the layout file.
+
+LAYOUT_FILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated
+# by doxygen. Possible values are YES and NO. If left blank NO is used.
+
+QUIET = YES
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated by doxygen. Possible values are YES and NO. If left blank
+# NO is used.
+
+WARNINGS = YES
+
+# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
+# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
+# automatically be disabled.
+
+WARN_IF_UNDOCUMENTED = YES
+
+# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some
+# parameters in a documented function, or documenting parameters that
+# don't exist or using markup commands wrongly.
+
+WARN_IF_DOC_ERROR = YES
+
+# This WARN_NO_PARAMDOC option can be abled to get warnings for
+# functions that are documented, but have no documentation for their parameters
+# or return value. If set to NO (the default) doxygen will only warn about
+# wrong or incomplete parameter documentation, but not about the absence of
+# documentation.
+
+WARN_NO_PARAMDOC = YES
+
+# The WARN_FORMAT tag determines the format of the warning messages that
+# doxygen can produce. The string should contain the $file, $line, and $text
+# tags, which will be replaced by the file and line number from which the
+# warning originated and the warning text. Optionally the format may contain
+# $version, which will be replaced by the version of the file (if it could
+# be obtained via FILE_VERSION_FILTER)
+
+WARN_FORMAT = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning
+# and error messages should be written. If left blank the output is written
+# to stderr.
+
+WARN_LOGFILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag can be used to specify the files and/or directories that contain
+# documented source files. You may enter file names like "myfile.cpp" or
+# directories like "/usr/src/myproject". Separate the files or directories
+# with spaces.
+
+INPUT = ./src/clustal ./src/clustal-omega.h ./src/clustal-omega.c
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
+# also the default input encoding. Doxygen uses libiconv (or the iconv built
+# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
+# the list of possible encodings.
+
+INPUT_ENCODING = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank the following patterns are tested:
+# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
+# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
+
+FILE_PATTERNS = *.h *.c
+
+# The RECURSIVE tag can be used to turn specify whether or not subdirectories
+# should be searched for input files as well. Possible values are YES and NO.
+# If left blank NO is used.
+
+RECURSIVE = NO
+
+# The EXCLUDE tag can be used to specify files and/or directories that should
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+
+EXCLUDE = ./src/config.h
+
+# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
+# directories that are symbolic links (a Unix filesystem feature) are excluded
+# from the input.
+
+EXCLUDE_SYMLINKS = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories. Note that the wildcards are matched
+# against the file with absolute path, so to exclude all test directories
+# for example use the pattern */test/*
+
+EXCLUDE_PATTERNS =
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+
+EXCLUDE_SYMBOLS =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or
+# directories that contain example code fragments that are included (see
+# the \include command).
+
+EXAMPLE_PATH = ./src/
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank all files are included.
+
+EXAMPLE_PATTERNS =
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude
+# commands irrespective of the value of the RECURSIVE tag.
+# Possible values are YES and NO. If left blank NO is used.
+
+EXAMPLE_RECURSIVE = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or
+# directories that contain image that are included in the documentation (see
+# the \image command).
+
+IMAGE_PATH =
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command <filter> <input-file>, where <filter>
+# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
+# input file. Doxygen will then use the output that the filter program writes
+# to standard output.
+# If FILTER_PATTERNS is specified, this tag will be
+# ignored.
+
+INPUT_FILTER =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis.
+# Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match.
+# The filters are a list of the form:
+# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
+# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER
+# is applied to all files.
+
+FILTER_PATTERNS =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will be used to filter the input files when producing source
+# files to browse (i.e. when SOURCE_BROWSER is set to YES).
+
+FILTER_SOURCE_FILES = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will
+# be generated. Documented entities will be cross-referenced with these sources.
+# Note: To get rid of all source code in the generated output, make sure also
+# VERBATIM_HEADERS is set to NO.
+
+SOURCE_BROWSER = NO
+
+# Setting the INLINE_SOURCES tag to YES will include the body
+# of functions and classes directly in the documentation.
+
+INLINE_SOURCES = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
+# doxygen to hide any special comment blocks from generated source code
+# fragments. Normal C and C++ comments will always remain visible.
+
+STRIP_CODE_COMMENTS = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES
+# then for each documented function all documented
+# functions referencing it will be listed.
+
+REFERENCED_BY_RELATION = NO
+
+# If the REFERENCES_RELATION tag is set to YES
+# then for each documented function all documented entities
+# called/used by that function will be listed.
+
+REFERENCES_RELATION = NO
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
+# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
+# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
+# link to the source code.
+# Otherwise they will link to the documentation.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code
+# will point to the HTML generated by the htags(1) tool instead of doxygen
+# built-in source browser. The htags tool is part of GNU's global source
+# tagging system (see http://www.gnu.org/software/global/global.html). You
+# will need version 4.8.6 or higher.
+
+USE_HTAGS = NO
+
+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
+# will generate a verbatim copy of the header file for each class for
+# which an include is specified. Set to NO to disable this.
+
+VERBATIM_HEADERS = YES
+
+#---------------------------------------------------------------------------
+# configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
+# of all compounds will be generated. Enable this if the project
+# contains a lot of classes, structs, unions or interfaces.
+
+ALPHABETICAL_INDEX = NO
+
+# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
+# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
+# in which this list will be split (can be a number in the range [1..20])
+
+COLS_IN_ALPHA_INDEX = 5
+
+# In case all classes in a project start with a common prefix, all
+# classes will be put under the same header in the alphabetical index.
+# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
+# should be ignored while generating the index headers.
+
+IGNORE_PREFIX =
+
+#---------------------------------------------------------------------------
+# configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
+# generate HTML output.
+
+GENERATE_HTML = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `html' will be used as the default path.
+
+HTML_OUTPUT = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
+# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
+# doxygen will generate files with .html extension.
+
+HTML_FILE_EXTENSION = .html
+
+# The HTML_HEADER tag can be used to specify a personal HTML header for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard header.
+
+HTML_HEADER =
+
+# The HTML_FOOTER tag can be used to specify a personal HTML footer for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard footer.
+
+HTML_FOOTER =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
+# style sheet that is used by each HTML page. It can be used to
+# fine-tune the look of the HTML output. If the tag is left blank doxygen
+# will generate a default style sheet. Note that doxygen will try to copy
+# the style sheet file to the HTML output directory, so don't put your own
+# stylesheet in the HTML output directory as well, or it will be erased!
+
+HTML_STYLESHEET =
+
+# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
+# files or namespaces will be aligned in HTML using tables. If set to
+# NO a bullet list will be used.
+
+HTML_ALIGN_MEMBERS = YES
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded. For this to work a browser that supports
+# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
+# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
+
+HTML_DYNAMIC_SECTIONS = NO
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files
+# will be generated that can be used as input for Apple's Xcode 3
+# integrated development environment, introduced with OSX 10.5 (Leopard).
+# To create a documentation set, doxygen will generate a Makefile in the
+# HTML output directory. Running make will produce the docset in that
+# directory and running "make install" will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
+# it at startup.
+# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html for more information.
+
+GENERATE_DOCSET = NO
+
+# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
+# feed. A documentation feed provides an umbrella under which multiple
+# documentation sets from a single provider (such as a company or product suite)
+# can be grouped.
+
+DOCSET_FEEDNAME = "Doxygen generated docs"
+
+# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
+# should uniquely identify the documentation set bundle. This should be a
+# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
+# will append .docset to the name.
+
+DOCSET_BUNDLE_ID = org.doxygen.Project
+
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files
+# will be generated that can be used as input for tools like the
+# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
+# of the generated HTML documentation.
+
+GENERATE_HTMLHELP = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
+# be used to specify the file name of the resulting .chm file. You
+# can add a path in front of the file if the result should not be
+# written to the html output directory.
+
+CHM_FILE =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
+# be used to specify the location (absolute path including file name) of
+# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
+# the HTML help compiler on the generated index.hhp.
+
+HHC_LOCATION =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
+# controls if a separate .chi index file is generated (YES) or that
+# it should be included in the master .chm file (NO).
+
+GENERATE_CHI = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
+# is used to encode HtmlHelp index (hhk), content (hhc) and project file
+# content.
+
+CHM_INDEX_ENCODING =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
+# controls whether a binary table of contents is generated (YES) or a
+# normal table of contents (NO) in the .chm file.
+
+BINARY_TOC = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members
+# to the contents of the HTML help documentation and to the tree view.
+
+TOC_EXPAND = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and QHP_VIRTUAL_FOLDER
+# are set, an additional index file will be generated that can be used as input for
+# Qt's qhelpgenerator to generate a Qt Compressed Help (.qch) of the generated
+# HTML documentation.
+
+GENERATE_QHP = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
+# be used to specify the file name of the resulting .qch file.
+# The path specified is relative to the HTML output folder.
+
+QCH_FILE =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#namespace
+
+QHP_NAMESPACE =
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#virtual-folders
+
+QHP_VIRTUAL_FOLDER = doc
+
+# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to add.
+# For more information please see
+# http://doc.trolltech.com/qthelpproject.html#custom-filters
+
+QHP_CUST_FILTER_NAME =
+
+# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the custom filter to add.For more information please see
+# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">Qt Help Project / Custom Filters</a>.
+
+QHP_CUST_FILTER_ATTRS =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this project's
+# filter section matches.
+# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">Qt Help Project / Filter Attributes</a>.
+
+QHP_SECT_FILTER_ATTRS =
+
+# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
+# be used to specify the location of Qt's qhelpgenerator.
+# If non-empty doxygen will try to run qhelpgenerator on the generated
+# .qhp file.
+
+QHG_LOCATION =
+
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
+# top of each HTML page. The value NO (the default) enables the index and
+# the value YES disables it.
+
+DISABLE_INDEX = NO
+
+# This tag can be used to set the number of enum values (range [1..20])
+# that doxygen will group on one line in the generated HTML documentation.
+
+ENUM_VALUES_PER_LINE = 4
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information.
+# If the tag value is set to FRAME, a side panel will be generated
+# containing a tree-like index structure (just like the one that
+# is generated for HTML Help). For this to work a browser that supports
+# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+,
+# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are
+# probably better off using the HTML help feature. Other possible values
+# for this tag are: HIERARCHIES, which will generate the Groups, Directories,
+# and Class Hierarchy pages using a tree view instead of an ordered list;
+# ALL, which combines the behavior of FRAME and HIERARCHIES; and NONE, which
+# disables this behavior completely. For backwards compatibility with previous
+# releases of Doxygen, the values YES and NO are equivalent to FRAME and NONE
+# respectively.
+
+GENERATE_TREEVIEW = NONE
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
+# used to set the initial width (in pixels) of the frame in which the tree
+# is shown.
+
+TREEVIEW_WIDTH = 250
+
+# Use this tag to change the font size of Latex formulas included
+# as images in the HTML documentation. The default is 10. Note that
+# when you change the font size after a successful doxygen run you need
+# to manually remove any form_*.png images from the HTML output directory
+# to force them to be regenerated.
+
+FORMULA_FONTSIZE = 10
+
+#---------------------------------------------------------------------------
+# configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
+# generate Latex output.
+
+GENERATE_LATEX = YES
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `latex' will be used as the default path.
+
+LATEX_OUTPUT = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked. If left blank `latex' will be used as the default command name.
+
+LATEX_CMD_NAME = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
+# generate index for LaTeX. If left blank `makeindex' will be used as the
+# default command name.
+
+MAKEINDEX_CMD_NAME = makeindex
+
+# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
+# LaTeX documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_LATEX = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used
+# by the printer. Possible values are: a4, a4wide, letter, legal and
+# executive. If left blank a4wide will be used.
+
+PAPER_TYPE = a4wide
+
+# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
+# packages that should be included in the LaTeX output.
+
+EXTRA_PACKAGES =
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
+# the generated latex document. The header should contain everything until
+# the first chapter. If it is left blank doxygen will generate a
+# standard header. Notice: only use this tag if you know what you are doing!
+
+LATEX_HEADER =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
+# is prepared for conversion to pdf (using ps2pdf). The pdf file will
+# contain links (just like the HTML output) instead of page references
+# This makes the output suitable for online browsing using a pdf viewer.
+
+PDF_HYPERLINKS = YES
+
+# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
+# plain latex in the generated Makefile. Set this option to YES to get a
+# higher quality PDF documentation.
+
+USE_PDFLATEX = YES
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
+# command to the generated LaTeX files. This will instruct LaTeX to keep
+# running if errors occur, instead of asking the user for help.
+# This option is also used when generating formulas in HTML.
+
+LATEX_BATCHMODE = NO
+
+# If LATEX_HIDE_INDICES is set to YES then doxygen will not
+# include the index chapters (such as File Index, Compound Index, etc.)
+# in the output.
+
+LATEX_HIDE_INDICES = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
+# The RTF output is optimized for Word 97 and may not look very pretty with
+# other RTF readers or editors.
+
+GENERATE_RTF = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `rtf' will be used as the default path.
+
+RTF_OUTPUT = rtf
+
+# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
+# RTF documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_RTF = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
+# will contain hyperlink fields. The RTF file will
+# contain links (just like the HTML output) instead of page references.
+# This makes the output suitable for online browsing using WORD or other
+# programs which support those fields.
+# Note: wordpad (write) and others do not support links.
+
+RTF_HYPERLINKS = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's
+# config file, i.e. a series of assignments. You only have to provide
+# replacements, missing definitions are set to their default value.
+
+RTF_STYLESHEET_FILE =
+
+# Set optional variables used in the generation of an rtf document.
+# Syntax is similar to doxygen's config file.
+
+RTF_EXTENSIONS_FILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
+# generate man pages
+
+GENERATE_MAN = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `man' will be used as the default path.
+
+MAN_OUTPUT = man
+
+# The MAN_EXTENSION tag determines the extension that is added to
+# the generated man pages (default is the subroutine's section .3)
+
+MAN_EXTENSION = .3
+
+# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
+# then it will generate one additional man file for each entity
+# documented in the real man page(s). These additional files
+# only source the real man page, but without them the man command
+# would be unable to find the correct page. The default is NO.
+
+MAN_LINKS = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES Doxygen will
+# generate an XML file that captures the structure of
+# the code including all documentation.
+
+GENERATE_XML = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `xml' will be used as the default path.
+
+XML_OUTPUT = xml
+
+# The XML_SCHEMA tag can be used to specify an XML schema,
+# which can be used by a validating XML parser to check the
+# syntax of the XML files.
+
+XML_SCHEMA =
+
+# The XML_DTD tag can be used to specify an XML DTD,
+# which can be used by a validating XML parser to check the
+# syntax of the XML files.
+
+XML_DTD =
+
+# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
+# dump the program listings (including syntax highlighting
+# and cross-referencing information) to the XML output. Note that
+# enabling this will significantly increase the size of the XML output.
+
+XML_PROGRAMLISTING = YES
+
+#---------------------------------------------------------------------------
+# configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
+# generate an AutoGen Definitions (see autogen.sf.net) file
+# that captures the structure of the code including all
+# documentation. Note that this feature is still experimental
+# and incomplete at the moment.
+
+GENERATE_AUTOGEN_DEF = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES Doxygen will
+# generate a Perl module file that captures the structure of
+# the code including all documentation. Note that this
+# feature is still experimental and incomplete at the
+# moment.
+
+GENERATE_PERLMOD = NO
+
+# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
+# the necessary Makefile rules, Perl scripts and LaTeX code to be able
+# to generate PDF and DVI output from the Perl module output.
+
+PERLMOD_LATEX = NO
+
+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
+# nicely formatted so it can be parsed by a human reader.
+# This is useful
+# if you want to understand what is going on.
+# On the other hand, if this
+# tag is set to NO the size of the Perl module output will be much smaller
+# and Perl will parse it just the same.
+
+PERLMOD_PRETTY = YES
+
+# The names of the make variables in the generated doxyrules.make file
+# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
+# This is useful so different doxyrules.make files included by the same
+# Makefile don't overwrite each other's variables.
+
+PERLMOD_MAKEVAR_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
+# evaluate all C-preprocessor directives found in the sources and include
+# files.
+
+ENABLE_PREPROCESSING = YES
+
+# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
+# names in the source code. If set to NO (the default) only conditional
+# compilation will be performed. Macro expansion can be done in a controlled
+# way by setting EXPAND_ONLY_PREDEF to YES.
+
+MACRO_EXPANSION = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
+# then the macro expansion is limited to the macros specified with the
+# PREDEFINED and EXPAND_AS_DEFINED tags.
+
+EXPAND_ONLY_PREDEF = NO
+
+# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
+# in the INCLUDE_PATH (see below) will be search if a #include is found.
+
+SEARCH_INCLUDES = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by
+# the preprocessor.
+
+INCLUDE_PATH =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will
+# be used.
+
+INCLUDE_FILE_PATTERNS =
+
+# The PREDEFINED tag can be used to specify one or more macro names that
+# are defined before the preprocessor is started (similar to the -D option of
+# gcc). The argument of the tag is a list of macros of the form: name
+# or name=definition (no spaces). If the definition and the = are
+# omitted =1 is assumed. To prevent a macro definition from being
+# undefined via #undef or recursively expanded use the := operator
+# instead of the = operator.
+
+PREDEFINED =
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
+# this tag can be used to specify a list of macro names that should be expanded.
+# The macro definition that is found in the sources will be used.
+# Use the PREDEFINED tag if you want to use a different macro definition.
+
+EXPAND_AS_DEFINED =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
+# doxygen's preprocessor will remove all function-like macros that are alone
+# on a line, have an all uppercase name, and do not end with a semicolon. Such
+# function macros are typically used for boiler-plate code, and will confuse
+# the parser if not removed.
+
+SKIP_FUNCTION_MACROS = YES
+
+#---------------------------------------------------------------------------
+# Configuration::additions related to external references
+#---------------------------------------------------------------------------
+
+# The TAGFILES option can be used to specify one or more tagfiles.
+# Optionally an initial location of the external documentation
+# can be added for each tagfile. The format of a tag file without
+# this location is as follows:
+#
+# TAGFILES = file1 file2 ...
+# Adding location for the tag files is done as follows:
+#
+# TAGFILES = file1=loc1 "file2 = loc2" ...
+# where "loc1" and "loc2" can be relative or absolute paths or
+# URLs. If a location is present for each tag, the installdox tool
+# does not have to be run to correct the links.
+# Note that each tag file must have a unique name
+# (where the name does NOT include the path)
+# If a tag file is not located in the directory in which doxygen
+# is run, you must also specify the path to the tagfile here.
+
+TAGFILES =
+
+# When a file name is specified after GENERATE_TAGFILE, doxygen will create
+# a tag file that is based on the input files it reads.
+
+GENERATE_TAGFILE =
+
+# If the ALLEXTERNALS tag is set to YES all external classes will be listed
+# in the class index. If set to NO only the inherited external classes
+# will be listed.
+
+ALLEXTERNALS = NO
+
+# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
+# in the modules index. If set to NO, only the current project's groups will
+# be listed.
+
+EXTERNAL_GROUPS = YES
+
+# The PERL_PATH should be the absolute path and name of the perl script
+# interpreter (i.e. the result of `which perl').
+
+PERL_PATH = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
+# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
+# or super classes. Setting the tag to NO turns the diagrams off. Note that
+# this option is superseded by the HAVE_DOT option below. This is only a
+# fallback. It is recommended to install and use dot, since it yields more
+# powerful graphs.
+
+CLASS_DIAGRAMS = YES
+
+# You can define message sequence charts within doxygen comments using the \msc
+# command. Doxygen will then run the mscgen tool (see
+# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
+# documentation. The MSCGEN_PATH tag allows you to specify the directory where
+# the mscgen tool resides. If left empty the tool is assumed to be found in the
+# default search path.
+
+MSCGEN_PATH =
+
+# If set to YES, the inheritance and collaboration graphs will hide
+# inheritance and usage relations if the target is undocumented
+# or is not a class.
+
+HIDE_UNDOC_RELATIONS = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz, a graph visualization
+# toolkit from AT&T and Lucent Bell Labs. The other options in this section
+# have no effect if this option is set to NO (the default)
+
+HAVE_DOT = YES
+
+# By default doxygen will write a font called FreeSans.ttf to the output
+# directory and reference it in all dot files that doxygen generates. This
+# font does not include all possible unicode characters however, so when you need
+# these (or just want a differently looking font) you can specify the font name
+# using DOT_FONTNAME. You need need to make sure dot is able to find the font,
+# which can be done by putting it in a standard location or by setting the
+# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory
+# containing the font.
+
+DOT_FONTNAME = FreeSans
+
+# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
+# The default size is 10pt.
+
+DOT_FONTSIZE = 10
+
+# By default doxygen will tell dot to use the output directory to look for the
+# FreeSans.ttf font (which doxygen will put there itself). If you specify a
+# different font using DOT_FONTNAME you can set the path where dot
+# can find it using this tag.
+
+DOT_FONTPATH =
+
+# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect inheritance relations. Setting this tag to YES will force the
+# the CLASS_DIAGRAMS tag to NO.
+
+CLASS_GRAPH = YES
+
+# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect implementation dependencies (inheritance, containment, and
+# class references variables) of the class with other documented classes.
+
+COLLABORATION_GRAPH = YES
+
+# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for groups, showing the direct groups dependencies
+
+GROUP_GRAPHS = YES
+
+# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
+# collaboration diagrams in a style similar to the OMG's Unified Modeling
+# Language.
+
+UML_LOOK = NO
+
+# If set to YES, the inheritance and collaboration graphs will show the
+# relations between templates and their instances.
+
+TEMPLATE_RELATIONS = NO
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
+# tags are set to YES then doxygen will generate a graph for each documented
+# file showing the direct and indirect include dependencies of the file with
+# other documented files.
+
+INCLUDE_GRAPH = YES
+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
+# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
+# documented header file showing the documented files that directly or
+# indirectly include this file.
+
+INCLUDED_BY_GRAPH = YES
+
+# If the CALL_GRAPH and HAVE_DOT options are set to YES then
+# doxygen will generate a call dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable call graphs
+# for selected functions only using the \callgraph command.
+
+CALL_GRAPH = NO
+
+# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
+# doxygen will generate a caller dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable caller
+# graphs for selected functions only using the \callergraph command.
+
+CALLER_GRAPH = NO
+
+# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
+# will graphical hierarchy of all classes instead of a textual one.
+
+GRAPHICAL_HIERARCHY = YES
+
+# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# then doxygen will show the dependencies a directory has on other directories
+# in a graphical way. The dependency relations are determined by the #include
+# relations between the files in the directories.
+
+DIRECTORY_GRAPH = YES
+
+# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
+# generated by dot. Possible values are png, jpg, or gif
+# If left blank png will be used.
+
+DOT_IMAGE_FORMAT = png
+
+# The tag DOT_PATH can be used to specify the path where the dot tool can be
+# found. If left blank, it is assumed the dot tool can be found in the path.
+
+DOT_PATH =
+
+# The DOTFILE_DIRS tag can be used to specify one or more directories that
+# contain dot files that are included in the documentation (see the
+# \dotfile command).
+
+DOTFILE_DIRS =
+
+# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
+# nodes that will be shown in the graph. If the number of nodes in a graph
+# becomes larger than this value, doxygen will truncate the graph, which is
+# visualized by representing a node as a red box. Note that doxygen if the
+# number of direct children of the root node in a graph is already larger than
+# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
+# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
+
+DOT_GRAPH_MAX_NODES = 50
+
+# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
+# graphs generated by dot. A depth value of 3 means that only nodes reachable
+# from the root by following a path via at most 3 edges will be shown. Nodes
+# that lay further from the root node will be omitted. Note that setting this
+# option to 1 or 2 may greatly reduce the computation time needed for large
+# code bases. Also note that the size of a graph can be further restricted by
+# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
+
+MAX_DOT_GRAPH_DEPTH = 0
+
+# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
+# background. This is disabled by default, because dot on Windows does not
+# seem to support this out of the box. Warning: Depending on the platform used,
+# enabling this option may lead to badly anti-aliased labels on the edges of
+# a graph (i.e. they become hard to read).
+
+DOT_TRANSPARENT = NO
+
+# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
+# files in one run (i.e. multiple -o and -T options on the command line). This
+# makes dot run faster, but since only newer versions of dot (>1.8.10)
+# support this, this feature is disabled by default.
+
+DOT_MULTI_TARGETS = NO
+
+# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
+# generate a legend page explaining the meaning of the various boxes and
+# arrows in the dot generated graphs.
+
+GENERATE_LEGEND = YES
+
+# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
+# remove the intermediate dot files that are used to generate
+# the various graphs.
+
+DOT_CLEANUP = YES
+
+#---------------------------------------------------------------------------
+# Options related to the search engine
+#---------------------------------------------------------------------------
+
+# The SEARCHENGINE tag specifies whether or not a search engine should be
+# used. If set to NO the values of all tags below this one will be ignored.
+
+SEARCHENGINE = NO
--- /dev/null
+The impatient can try:
+
+$ ./configure
+$ make
+$ make install
+
+
+Clustal-Omega needs argtable2 (http://argtable.sourceforge.net/). If
+argtable2 is installed in a non-standard directory you might have to
+point configure to its installation directory. For example, if you are
+on a Mac and have argtable installed via MacPorts then you should use
+the following command line:
+
+$ ./configure CFLAGS='-I/opt/local/include' LDFLAGS='-L/opt/local/lib'
+
+ClustalO will automatically support multi-threading if your compiler
+supports OpenMP. For some reason automake's OpenMP detection for
+Apple's gcc is broken. You can force OpenMP detection by calling configure
+like so:
+
+$ ./configure OPENMP_CFLAGS='-fopenmp' CFLAGS='-DHAVE_OPENMP'
+
+You could use a non-Apple gcc installed via MacPorts, adding
+
+CC=/opt/local/bin/gcc-mp-4.5
+
+to the configure call (you will have to change the exact string to match
+your gcc version).
+
+See below for generic installation instructions:
+
+----------------------------------------------------------------------
+
+
+
+Installation Instructions
+*************************
+
+Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005,
+2006, 2007, 2008, 2009 Free Software Foundation, Inc.
+
+ Copying and distribution of this file, with or without modification,
+are permitted in any medium without royalty provided the copyright
+notice and this notice are preserved. This file is offered as-is,
+without warranty of any kind.
+
+Basic Installation
+==================
+
+ Briefly, the shell commands `./configure; make; make install' should
+configure, build, and install this package. The following
+more-detailed instructions are generic; see the `README' file for
+instructions specific to this package. Some packages provide this
+`INSTALL' file but do not implement all of the features documented
+below. The lack of an optional feature in a given package is not
+necessarily a bug. More recommendations for GNU packages can be found
+in *note Makefile Conventions: (standards)Makefile Conventions.
+
+ The `configure' shell script attempts to guess correct values for
+various system-dependent variables used during compilation. It uses
+those values to create a `Makefile' in each directory of the package.
+It may also create one or more `.h' files containing system-dependent
+definitions. Finally, it creates a shell script `config.status' that
+you can run in the future to recreate the current configuration, and a
+file `config.log' containing compiler output (useful mainly for
+debugging `configure').
+
+ It can also use an optional file (typically called `config.cache'
+and enabled with `--cache-file=config.cache' or simply `-C') that saves
+the results of its tests to speed up reconfiguring. Caching is
+disabled by default to prevent problems with accidental use of stale
+cache files.
+
+ If you need to do unusual things to compile the package, please try
+to figure out how `configure' could check whether to do them, and mail
+diffs or instructions to the address given in the `README' so they can
+be considered for the next release. If you are using the cache, and at
+some point `config.cache' contains results you don't want to keep, you
+may remove or edit it.
+
+ The file `configure.ac' (or `configure.in') is used to create
+`configure' by a program called `autoconf'. You need `configure.ac' if
+you want to change it or regenerate `configure' using a newer version
+of `autoconf'.
+
+ The simplest way to compile this package is:
+
+ 1. `cd' to the directory containing the package's source code and type
+ `./configure' to configure the package for your system.
+
+ Running `configure' might take a while. While running, it prints
+ some messages telling which features it is checking for.
+
+ 2. Type `make' to compile the package.
+
+ 3. Optionally, type `make check' to run any self-tests that come with
+ the package, generally using the just-built uninstalled binaries.
+
+ 4. Type `make install' to install the programs and any data files and
+ documentation. When installing into a prefix owned by root, it is
+ recommended that the package be configured and built as a regular
+ user, and only the `make install' phase executed with root
+ privileges.
+
+ 5. Optionally, type `make installcheck' to repeat any self-tests, but
+ this time using the binaries in their final installed location.
+ This target does not install anything. Running this target as a
+ regular user, particularly if the prior `make install' required
+ root privileges, verifies that the installation completed
+ correctly.
+
+ 6. You can remove the program binaries and object files from the
+ source code directory by typing `make clean'. To also remove the
+ files that `configure' created (so you can compile the package for
+ a different kind of computer), type `make distclean'. There is
+ also a `make maintainer-clean' target, but that is intended mainly
+ for the package's developers. If you use it, you may have to get
+ all sorts of other programs in order to regenerate files that came
+ with the distribution.
+
+ 7. Often, you can also type `make uninstall' to remove the installed
+ files again. In practice, not all packages have tested that
+ uninstallation works correctly, even though it is required by the
+ GNU Coding Standards.
+
+ 8. Some packages, particularly those that use Automake, provide `make
+ distcheck', which can by used by developers to test that all other
+ targets like `make install' and `make uninstall' work correctly.
+ This target is generally not run by end users.
+
+Compilers and Options
+=====================
+
+ Some systems require unusual options for compilation or linking that
+the `configure' script does not know about. Run `./configure --help'
+for details on some of the pertinent environment variables.
+
+ You can give `configure' initial values for configuration parameters
+by setting variables in the command line or in the environment. Here
+is an example:
+
+ ./configure CC=c99 CFLAGS=-g LIBS=-lposix
+
+ *Note Defining Variables::, for more details.
+
+Compiling For Multiple Architectures
+====================================
+
+ You can compile the package for more than one kind of computer at the
+same time, by placing the object files for each architecture in their
+own directory. To do this, you can use GNU `make'. `cd' to the
+directory where you want the object files and executables to go and run
+the `configure' script. `configure' automatically checks for the
+source code in the directory that `configure' is in and in `..'. This
+is known as a "VPATH" build.
+
+ With a non-GNU `make', it is safer to compile the package for one
+architecture at a time in the source code directory. After you have
+installed the package for one architecture, use `make distclean' before
+reconfiguring for another architecture.
+
+ On MacOS X 10.5 and later systems, you can create libraries and
+executables that work on multiple system types--known as "fat" or
+"universal" binaries--by specifying multiple `-arch' options to the
+compiler but only a single `-arch' option to the preprocessor. Like
+this:
+
+ ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+ CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
+ CPP="gcc -E" CXXCPP="g++ -E"
+
+ This is not guaranteed to produce working output in all cases, you
+may have to build one architecture at a time and combine the results
+using the `lipo' tool if you have problems.
+
+Installation Names
+==================
+
+ By default, `make install' installs the package's commands under
+`/usr/local/bin', include files under `/usr/local/include', etc. You
+can specify an installation prefix other than `/usr/local' by giving
+`configure' the option `--prefix=PREFIX', where PREFIX must be an
+absolute file name.
+
+ You can specify separate installation prefixes for
+architecture-specific files and architecture-independent files. If you
+pass the option `--exec-prefix=PREFIX' to `configure', the package uses
+PREFIX as the prefix for installing programs and libraries.
+Documentation and other data files still use the regular prefix.
+
+ In addition, if you use an unusual directory layout you can give
+options like `--bindir=DIR' to specify different values for particular
+kinds of files. Run `configure --help' for a list of the directories
+you can set and what kinds of files go in them. In general, the
+default for these options is expressed in terms of `${prefix}', so that
+specifying just `--prefix' will affect all of the other directory
+specifications that were not explicitly provided.
+
+ The most portable way to affect installation locations is to pass the
+correct locations to `configure'; however, many packages provide one or
+both of the following shortcuts of passing variable assignments to the
+`make install' command line to change installation locations without
+having to reconfigure or recompile.
+
+ The first method involves providing an override variable for each
+affected directory. For example, `make install
+prefix=/alternate/directory' will choose an alternate location for all
+directory configuration variables that were expressed in terms of
+`${prefix}'. Any directories that were specified during `configure',
+but not in terms of `${prefix}', must each be overridden at install
+time for the entire installation to be relocated. The approach of
+makefile variable overrides for each directory variable is required by
+the GNU Coding Standards, and ideally causes no recompilation.
+However, some platforms have known limitations with the semantics of
+shared libraries that end up requiring recompilation when using this
+method, particularly noticeable in packages that use GNU Libtool.
+
+ The second method involves providing the `DESTDIR' variable. For
+example, `make install DESTDIR=/alternate/directory' will prepend
+`/alternate/directory' before all installation names. The approach of
+`DESTDIR' overrides is not required by the GNU Coding Standards, and
+does not work on platforms that have drive letters. On the other hand,
+it does better at avoiding recompilation issues, and works well even
+when some directory options were not specified in terms of `${prefix}'
+at `configure' time.
+
+Optional Features
+=================
+
+ If the package supports it, you can cause programs to be installed
+with an extra prefix or suffix on their names by giving `configure' the
+option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
+
+ Some packages pay attention to `--enable-FEATURE' options to
+`configure', where FEATURE indicates an optional part of the package.
+They may also pay attention to `--with-PACKAGE' options, where PACKAGE
+is something like `gnu-as' or `x' (for the X Window System). The
+`README' should mention any `--enable-' and `--with-' options that the
+package recognizes.
+
+ For packages that use the X Window System, `configure' can usually
+find the X include and library files automatically, but if it doesn't,
+you can use the `configure' options `--x-includes=DIR' and
+`--x-libraries=DIR' to specify their locations.
+
+ Some packages offer the ability to configure how verbose the
+execution of `make' will be. For these packages, running `./configure
+--enable-silent-rules' sets the default to minimal output, which can be
+overridden with `make V=1'; while running `./configure
+--disable-silent-rules' sets the default to verbose, which can be
+overridden with `make V=0'.
+
+Particular systems
+==================
+
+ On HP-UX, the default C compiler is not ANSI C compatible. If GNU
+CC is not installed, it is recommended to use the following options in
+order to use an ANSI C compiler:
+
+ ./configure CC="cc -Ae -D_XOPEN_SOURCE=500"
+
+and if that doesn't work, install pre-built binaries of GCC for HP-UX.
+
+ On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot
+parse its `<wchar.h>' header file. The option `-nodtk' can be used as
+a workaround. If GNU CC is not installed, it is therefore recommended
+to try
+
+ ./configure CC="cc"
+
+and if that doesn't work, try
+
+ ./configure CC="cc -nodtk"
+
+ On Solaris, don't put `/usr/ucb' early in your `PATH'. This
+directory contains several dysfunctional programs; working variants of
+these programs are available in `/usr/bin'. So, if you need `/usr/ucb'
+in your `PATH', put it _after_ `/usr/bin'.
+
+ On Haiku, software installed for all users goes in `/boot/common',
+not `/usr/local'. It is recommended to use the following options:
+
+ ./configure --prefix=/boot/common
+
+Specifying the System Type
+==========================
+
+ There may be some features `configure' cannot figure out
+automatically, but needs to determine by the type of machine the package
+will run on. Usually, assuming the package is built to be run on the
+_same_ architectures, `configure' can figure that out, but if it prints
+a message saying it cannot guess the machine type, give it the
+`--build=TYPE' option. TYPE can either be a short name for the system
+type, such as `sun4', or a canonical name which has the form:
+
+ CPU-COMPANY-SYSTEM
+
+where SYSTEM can have one of these forms:
+
+ OS
+ KERNEL-OS
+
+ See the file `config.sub' for the possible values of each field. If
+`config.sub' isn't included in this package, then this package doesn't
+need to know the machine type.
+
+ If you are _building_ compiler tools for cross-compiling, you should
+use the option `--target=TYPE' to select the type of system they will
+produce code for.
+
+ If you want to _use_ a cross compiler, that generates code for a
+platform different from the build platform, you should specify the
+"host" platform (i.e., that on which the generated programs will
+eventually be run) with `--host=TYPE'.
+
+Sharing Defaults
+================
+
+ If you want to set default values for `configure' scripts to share,
+you can create a site shell script called `config.site' that gives
+default values for variables like `CC', `cache_file', and `prefix'.
+`configure' looks for `PREFIX/share/config.site' if it exists, then
+`PREFIX/etc/config.site' if it exists. Or, you can set the
+`CONFIG_SITE' environment variable to the location of the site script.
+A warning: not all `configure' scripts look for a site script.
+
+Defining Variables
+==================
+
+ Variables not defined in a site shell script can be set in the
+environment passed to `configure'. However, some packages may run
+configure again during the build, and the customized values of these
+variables may be lost. In order to avoid this problem, you should set
+them in the `configure' command line, using `VAR=value'. For example:
+
+ ./configure CC=/usr/local2/bin/gcc
+
+causes the specified `gcc' to be used as the C compiler (unless it is
+overridden in the site shell script).
+
+Unfortunately, this technique does not work for `CONFIG_SHELL' due to
+an Autoconf bug. Until the bug is fixed you can use this workaround:
+
+ CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash
+
+`configure' Invocation
+======================
+
+ `configure' recognizes the following options to control how it
+operates.
+
+`--help'
+`-h'
+ Print a summary of all of the options to `configure', and exit.
+
+`--help=short'
+`--help=recursive'
+ Print a summary of the options unique to this package's
+ `configure', and exit. The `short' variant lists options used
+ only in the top level, while the `recursive' variant lists options
+ also present in any nested packages.
+
+`--version'
+`-V'
+ Print the version of Autoconf used to generate the `configure'
+ script, and exit.
+
+`--cache-file=FILE'
+ Enable the cache: use and save the results of the tests in FILE,
+ traditionally `config.cache'. FILE defaults to `/dev/null' to
+ disable caching.
+
+`--config-cache'
+`-C'
+ Alias for `--cache-file=config.cache'.
+
+`--quiet'
+`--silent'
+`-q'
+ Do not print messages saying which checks are being made. To
+ suppress all normal output, redirect it to `/dev/null' (any error
+ messages will still be shown).
+
+`--srcdir=DIR'
+ Look for the package's source code in directory DIR. Usually
+ `configure' can determine that directory automatically.
+
+`--prefix=DIR'
+ Use DIR as the installation prefix. *note Installation Names::
+ for more details, including other options available for fine-tuning
+ the installation locations.
+
+`--no-create'
+`-n'
+ Run the configure checks, but stop before creating any output
+ files.
+
+`configure' also accepts some other, not widely useful, options. Run
+`configure --help' for more details.
+
--- /dev/null
+# Some useful automake documentation:
+# http://www.openismus.com/documents/linux/automake/automake.shtml
+# http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html
+
+# we do not use GNU-style files: NEWS README AUTHORS ChangeLog
+#AUTOMAKE_OPTIONS = foreign
+
+ACLOCAL_AMFLAGS=-I m4
+SUBDIRS = src
+# SUBDIRS = src tests
+
+dist_doc_DATA = README
+
+EXTRA_DIST = Doxyfile
+
+pkgconfigdir = $(libdir)/pkgconfig
+pkgconfig_DATA = clustalo.pc
+
+
+bug-tests: all
+ cd bug-tests && $(SHELL) bug-tests.sh;
+
+#dist-hook:
+# svnversion . > $(distdir)/src/svnversion.h 2>/dev/null
+
--- /dev/null
+# Makefile.in generated by automake 1.10.2 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+@SET_MAKE@
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+ @cd $(distuninstallcheck_dir) \
+ && test `$(distuninstallcheck_listfiles) | wc -l` -le 1 \
+ || { echo "ERROR: files left after uninstall:" ; \
+ if test -n "$(DESTDIR)"; then \
+ echo " (check DESTDIR support)"; \
+ fi ; \
+ $(distuninstallcheck_listfiles) ; \
+ exit 1; } >&2
+distcleancheck: distclean
+ @if test '$(srcdir)' = . ; then \
+ echo "ERROR: distcleancheck can only run from a VPATH build" ; \
+ exit 1 ; \
+ fi
+ @test `$(distcleancheck_listfiles) | wc -l` -eq 0 \
+ || { echo "ERROR: files left in build directory after distclean:" ; \
+ $(distcleancheck_listfiles) ; \
+ exit 1; } >&2
+check-am: all-am
+check: check-recursive
+all-am: Makefile $(DATA)
+installdirs: installdirs-recursive
+installdirs-am:
+ for dir in "$(DESTDIR)$(docdir)" "$(DESTDIR)$(pkgconfigdir)"; do \
+ test -z "$$dir" || $(MKDIR_P) "$$dir"; \
+ done
+install: install-recursive
+install-exec: install-exec-recursive
+install-data: install-data-recursive
+uninstall: uninstall-recursive
+
+install-am: all-am
+ @$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
+
+installcheck: installcheck-recursive
+install-strip:
+ $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
+ install_sh_PROGRAM="$(INSTALL_STRIP_PROGRAM)" INSTALL_STRIP_FLAG=-s \
+ `test -z '$(STRIP)' || \
+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
+
+maintainer-clean-generic:
+ @echo "This command is intended for maintainers to use"
+ @echo "it deletes files that may require special tools to rebuild."
+clean: clean-recursive
+
+clean-am: clean-generic clean-libtool mostlyclean-am
+
+distclean: distclean-recursive
+ -rm -f $(am__CONFIG_DISTCLEAN_FILES)
+ -rm -f Makefile
+distclean-am: clean-am distclean-generic distclean-libtool \
+ distclean-tags
+
+dvi: dvi-recursive
+
+dvi-am:
+
+html: html-recursive
+
+info: info-recursive
+
+info-am:
+
+install-data-am: install-dist_docDATA install-pkgconfigDATA
+
+install-dvi: install-dvi-recursive
+
+install-exec-am:
+
+install-html: install-html-recursive
+
+install-info: install-info-recursive
+
+install-man:
+
+install-pdf: install-pdf-recursive
+
+install-ps: install-ps-recursive
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-recursive
+ -rm -f $(am__CONFIG_DISTCLEAN_FILES)
+ -rm -rf $(top_srcdir)/autom4te.cache
+ -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-recursive
+
+mostlyclean-am: mostlyclean-generic mostlyclean-libtool
+
+pdf: pdf-recursive
+
+pdf-am:
+
+ps: ps-recursive
+
+ps-am:
+
+uninstall-am: uninstall-dist_docDATA uninstall-pkgconfigDATA
+
+.MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) install-am \
+ install-strip
+
+.PHONY: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) CTAGS GTAGS \
+ all all-am am--refresh check check-am clean clean-generic \
+ clean-libtool ctags ctags-recursive dist dist-all dist-bzip2 \
+ dist-gzip dist-lzma dist-shar dist-tarZ dist-zip distcheck \
+ distclean distclean-generic distclean-libtool distclean-tags \
+ distcleancheck distdir distuninstallcheck dvi dvi-am html \
+ html-am info info-am install install-am install-data \
+ install-data-am install-dist_docDATA install-dvi \
+ install-dvi-am install-exec install-exec-am install-html \
+ install-html-am install-info install-info-am install-man \
+ install-pdf install-pdf-am install-pkgconfigDATA install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs installdirs-am maintainer-clean \
+ maintainer-clean-generic mostlyclean mostlyclean-generic \
+ mostlyclean-libtool pdf pdf-am ps ps-am tags tags-recursive \
+ uninstall uninstall-am uninstall-dist_docDATA \
+ uninstall-pkgconfigDATA
+
+
+bug-tests: all
+ cd bug-tests && $(SHELL) bug-tests.sh;
+
+#dist-hook:
+# svnversion . > $(distdir)/src/svnversion.h 2>/dev/null
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
--- /dev/null
+\r
+\r
+CLUSTAL-OMEGA is a general purpose multiple sequence alignment program\r
+for proteins.\r
+\r
+\r
+\r
+INTRODUCTION\r
+\r
+Clustal-Omega is a general purpose multiple sequence alignment (MSA)\r
+program for proteins. It produces high quality MSAs and is capable of\r
+handling data-sets of hundreds of thousands of sequences in reasonable\r
+time.\r
+\r
+In default mode, users give a file of sequences to be aligned and\r
+these are clustered to produce a guide tree and this is used to guide\r
+a "progressive alignment" of the sequences. There are also facilities\r
+for aligning existing alignments to each other, aligning a sequence to\r
+an alignment and for using a hidden Markov model (HMM) to help guide\r
+an alignment of new sequences that are homologous to the sequences\r
+used to make the HMM. This latter procedure is referred to as\r
+"external profile alignment" or EPA.\r
+\r
+Clustal-Omega uses HMMs for the alignment engine, based on the HHalign\r
+package from Johannes Soeding [1]. Guide trees are made using an\r
+enhanced version of mBed [2] which can cluster very large numbers of\r
+sequences in O(N*log(N)) time. Multiple alignment then proceeds by\r
+aligning larger and larger alignments using HHalign, following the\r
+clustering given by the guide tree.\r
+\r
+In its current form Clustal-Omega can only align protein sequences but\r
+not DNA/RNA sequences. It is envisioned that DNA/RNA will become\r
+available in a future version.\r
+\r
+\r
+\r
+SEQUENCE INPUT:\r
+\r
+-i, --in, --infile={<file>,-}\r
+ Multiple sequence input file (- for stdin)\r
+\r
+--hmm-in=<file>\r
+ HMM input files\r
+\r
+--dealign\r
+ Dealign input sequences\r
+\r
+--profile1, --p1=<file>\r
+ Pre-aligned multiple sequence file (aligned columns will be kept fixed)\r
+\r
+--profile2, --p2=<file>\r
+ Pre-aligned multiple sequence file (aligned columns will be kept fixed)\r
+\r
+\r
+For sequence and profile input Clustal-Omega uses the Squid library\r
+from Sean Eddy [3].\r
+\r
+\r
+Clustal-Omega accepts 3 types of sequence input: (i) a sequence file\r
+with un-aligned or aligned sequences, (ii) profiles (a multiple\r
+alignment in a file) of aligned sequences, (iii) a HMM. Valid\r
+combinations of the above are:\r
+\r
+(a) one file with un-aligned or aligned sequences (i); the sequences\r
+ will be aligned, and the alignment will be written out. For this\r
+ mode use the -i flag. If the sequences are aligned (all sequences\r
+ have the same length and at least one sequence has at least one\r
+ gap), then the alignment is turned into a HMM, the sequences are\r
+ de-aligned and the now un-aligned sequences are aligned using the\r
+ HMM as an External Profile for External Profile Alignment (EPA).\r
+ If no EPA is desired use the --dealign flag.\r
+\r
+ Use the above option to make a multiple alignment from a set of\r
+ sequences. A sequence file must contain more than one sequence (at\r
+ least two sequences).\r
+\r
+(b) two profiles (ii)+(ii); the columns in each profile will be kept\r
+ fixed and the alignment of the two profiles will be written\r
+ out. Use the --p1 and --p2 flags for this mode.\r
+\r
+ Use this option to align two alignments (profiles) together.\r
+\r
+(c) one file with un/aligned sequences (i) and one profile (ii); the\r
+ profile is converted into a HMM and the un-aligned sequences will\r
+ be multiply aligned (using the HMM background information) to form\r
+ a profile; this constructed profile is aligned with the input\r
+ profile; the columns in each profile (the original one and the one\r
+ created from the un-aligned sequences) will be kept fixed and the\r
+ alignment of the two profiles will be written out. Use the -i flag\r
+ in conjunction with the --p1 flag for this mode.\r
+ The un/aligned sequences file (i) must contain at least two\r
+ sequences. If a single sequence has to be aligned with a profile\r
+ the profile-profile option (b) has to be used.\r
+\r
+ Use the above option to add new sequences to an existing\r
+ alignment.\r
+\r
+(d) one file with un-aligned sequences (i) and one HMM (iii); the\r
+ un-aligned sequences will be aligned to form a profile, using the\r
+ HMM as an External Profile. So far only one HMM can be input and\r
+ only HMMer2 and HMMer3 formats are allowed. The alignment will be\r
+ written out; the HMM information is discarded. As, at the moment,\r
+ only one HMM can be used, no HMM is produced if the sequences are\r
+ already aligned. Use the -i flag in conjunction with the --hmm-in\r
+ flag for this mode. Multiple HMMs can be inputted, however, in the\r
+ current version all but the first HMM will be ignored.\r
+\r
+ Use this option to make a new multiple alignment of sequences from\r
+ the input file and use the HMM as a guide (EPA).\r
+\r
+\r
+Invalid combinations of the above are:\r
+\r
+(v) an un/aligned sequence file containing just one sequence (i)\r
+\r
+(w) an un/aligned sequence file containing just one sequence and a profile\r
+ (i)+(ii)\r
+\r
+(x) an un/aligned sequence file containing just one sequence and a HMM\r
+ (i)+(iii)\r
+\r
+(y) two or more HMMs (iii)+(iii)+... cannot be aligned to one another.\r
+\r
+(z) one profile (ii) cannot be aligned with a HMM (iii)\r
+\r
+\r
+The following MSA file formats are allowed:\r
+\r
+ a2m=fasta, (vienna)\r
+ clustal,\r
+ msf,\r
+ phylip,\r
+ selex,\r
+ stockholm\r
+\r
+\r
+Prior to MSA, Clustal-Omega de-aligns all sequence input (i). However,\r
+alignment information is automatically converted into a HMM and used\r
+during MSA, unless the --dealign flag is specifically set. Profiles\r
+(ii) are not de-aligned.\r
+\r
+The Clustal-Omega alignment engine can at the moment not process\r
+DNA/RNA. If a sequence input file (i) or a profile (ii) is interpreted\r
+as DNA/RNA the program will terminate during the file input stage.\r
+\r
+\r
+\r
+CLUSTERING:\r
+\r
+ --distmat-in=<file>\r
+ Pairwise distance matrix input file (skips distance computation)\r
+\r
+ --distmat-out=<file>\r
+ Pairwise distance matrix output file\r
+\r
+ --guidetree-in=<file>\r
+ Guide tree input file\r
+ (skips distance computation and guide tree clustering step)\r
+\r
+ --guidetree-out=<file>\r
+ Guide tree output file\r
+\r
+ --full\r
+ Use full distance matrix for guide-tree calculation (slow; mBed is default)\r
+\r
+ --full-iter\r
+ Use full distance matrix for guide-tree calculation during iteration (mBed is default)\r
+\r
+\r
+In order to produce a multiple alignment Clustal-Omega requires a\r
+guide tree which defines the order in which sequences/profiles are\r
+aligned. A guide tree in turn is constructed, based on a distance\r
+matrix. Conventionally, this distance matrix is comprised of all the\r
+pair-wise distances of the sequences. The distance measure\r
+Clustal-Omega uses for pair-wise distances of un-aligned sequences is\r
+the k-tuple measure [4], which was also implemented in Clustal 1.83\r
+and ClustalW2 [5,6]. If the sequences inputted via -i are aligned\r
+Clustal-Omega uses the Kimura-corrected pairwise aligned identities\r
+[7]. The computational effort (time/memory) to calculate and store a\r
+full distance matrix grows quadratically with the number of sequences.\r
+Clustal-Omega can improve this scalability to N*log(N) by employing a\r
+fast clustering algorithm called mBed [2]; this option is\r
+automatically invoked (default). If a full distance matrix evaluation\r
+is desired, then the --full flag has to be set. The mBed mode\r
+calculates a reduced set of pair-wise distances. These distances are\r
+used in a k-means algorithm, that clusters at most 100 sequences. For\r
+each cluster a full distance matrix is calculated. No full distance\r
+matrix (of all input sequences) is calculated in mBed mode. If there\r
+are less than 100 sequences in the input, then in effect a full\r
+distance matrix is calculated in mBed mode, however, no distance\r
+matrix can be outputted (see below).\r
+\r
+\r
+Clustal-Omega uses Muscle's [8] fast UPGMA implementation to construct\r
+its guide trees from the distance matrix. By default, the distance\r
+matrix is used internally to construct the guide tree and is then\r
+discarded. By specifying --distmat-out the internal distance matrix\r
+can be written to file. This is only possible in --full mode. The\r
+guide trees by default are used internally to guide the multiple\r
+alignment and are then discarded. By specifying the --guidetree-out\r
+option these internal guide trees can be written out to\r
+file. Conversely, the distance calculation and/or guide tree building\r
+stage can be skipped, by reading in a pre-calculated distance matrix\r
+and/or pre-calculated guide tree. These options are invoked by\r
+specifying the --distmat-in and/or --guidetree-in flags,\r
+respectively. However, distance matrix reading is disabled in the\r
+current version. By default, distance matrix and guide tree files are\r
+not over-written, if a file with the specified name already exists. In\r
+this case Clustal-Omega aborts during the command-line processing\r
+stage. To force over-writing of already existing files use the --force\r
+flag (see MISCELLANEOUS). In mBed mode a full distance matrix cannot\r
+be outputted, distance matrix output is only possible in --full mode.\r
+mBed or --full distance mode do not affect the ability to write out\r
+guide-trees.\r
+\r
+Guide trees can be iterated to refine the alignment (see section\r
+ITERATION). Clustal-Omega takes the alignment, that was produced\r
+initially and constructs a new distance matrix from this alignment.\r
+The distance measure used at this stage is the Kimura distance [7]. By\r
+default, Clustal-Omega constructs a reduced distance matrix at this\r
+stage using the mBed algorithm, which will then be used to create an\r
+improved (iterated) new guide tree. To turn off mBed-like clustering\r
+at this stage the --full-iter flag has to be set. While Kimura\r
+distances in general are much faster to calculate than k-tuple\r
+distances, time and memory requirements still scale quadratically with\r
+the number of sequences and --full-iter clustering should only be\r
+considered for smaller cases (<< 10,000 sequences).\r
+\r
+\r
+\r
+ALIGNMENT OUTPUT:\r
+\r
+ -o, --out, --outfile={file,-} Multiple sequence alignment output file (default: stdout)\r
+\r
+ --outfmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]} MSA output file format (default: fasta)\r
+\r
+\r
+By default Clustal-Omega writes its results (alignments) to stdout. An\r
+output file can be specified with the -o flag. Output to stdout is not\r
+possible in verbose mode (-v, see MISCELLANEOUS) as verbose/debugging\r
+messages would interfere with the alignment output. By default,\r
+alignment files are not over-written, if a file with the specified\r
+name already exists. In this case Clustal-Omega aborts during the\r
+command-line processing stage. To force over-writing of already\r
+existing files use the --force flag (see MISCELLANEOUS).\r
+\r
+Clustal-Omega can output alignments in various formats by setting the\r
+--outfmt flag:\r
+\r
+ * for Fasta format set: --outfmt=a2m or --outfmt=fa or --outfmt=fasta\r
+\r
+ * for Clustal format set: --outfmt=clu or --outfmt=clustal\r
+\r
+ * for Msf format: set --outfmt= msf\r
+\r
+ * for Phylip format set: --outfmt=phy or --outfmt=phylip\r
+\r
+ * for Selex format set: --outfmt=selex\r
+\r
+ * for Stockholm format set: --outfmt=st or --outfmt=stockholm\r
+\r
+ * for Vienna format set: --outfmt=vie or --outfmt=vienna\r
+\r
+\r
+ITERATION:\r
+\r
+ --iterations, --iter=<n> Number of (combined guide tree/HMM) iterations\r
+\r
+ --max-guidetree-iterations=<n> Maximum guide tree iterations\r
+\r
+ --max-hmm-iterations=<n> Maximum number of HMM iterations\r
+\r
+\r
+By default, Clustal-Omega calculates (or reads in) a guide tree and\r
+performs a multiple alignment in the order specified by this guide\r
+tree. This alignment is then outputted. Clustal-Omega can 'iterate'\r
+its guide tree. The hope is that the (Kimura) distances, that can be\r
+derived from the initial alignment, will give rise to a better guide\r
+tree, and by extension, to a better alignment.\r
+\r
+A similar rationale applies to HMM-iteration. MSAs in general are very\r
+'vulnerable' at their early stages. Sequences that are aligned at an\r
+early stage remain fixed for the rest of the MSA. Another way of\r
+putting this is: 'once a gap, always a gap'. This behaviour can be\r
+mitigated by HMM iteration. An initial alignment is created and turned\r
+into a HMM. This HMM can help in a new round of MSA to 'anticipate'\r
+where residues should align. This is using the HMM as an External\r
+Profile and carrying out iterative EPA. In practice, individual\r
+sequences and profiles are aligned to the External HMM, derived after\r
+the initial alignment. Pseudo-count information is then transferred to\r
+the (internal) HMM, corresponding to the individual\r
+sequence/profile. The now somewhat 'softened' sequences/profiles are\r
+then in turn aligned in the order specified by the guide\r
+tree. Pseudo-count transfer is reduced with the size of the\r
+profile. Individual sequences attain the greatest pseudo-count\r
+transfer, larger profiles less so. Pseudo-count transfer to profiles\r
+larger than, say, 10 is negligible. The effect of HMM iteration is\r
+more pronounced in larger test sets (that is, with more sequences).\r
+\r
+Both, HMM- and guide tree-iteration come at a cost of increasing the\r
+run-time. One round of guide tree iteration adds on (roughly) the time\r
+it took to construct the initial alignment. If, for example, the\r
+initial alignment took 1min, then it will take (roughly) 2min to\r
+iterate the guide tree once, 3min to iterate the guide tree twice, and\r
+so on. HMM-iteration is more costly, as each round of iteration adds\r
+three times the time required for the alignment stage. For example, if\r
+the initial alignment took 1min, then each additional round of HMM\r
+iteration will add on 3min; so 4 iterations will take 13min\r
+(=1min+4*3min). The factor of 3 stems from the fact that at every\r
+stage both intermediate profiles have to be aligned with the\r
+background HMM, and finally the (softened) HMMs have to be aligned as\r
+well. All times are quoted for single processors.\r
+\r
+By default, guide tree iteration and HMM-iteration are coupled. This\r
+means, at each iteration step both, guide tree and HMM, are\r
+re-calculated. This is invoked by setting the --iter flag. For\r
+example, if --iter=1, then first an initial alignment is produced\r
+(without external HMM background information and using k-tuple\r
+distances to calculate the guide tree). This initial alignment is then\r
+used to re-calculate a new guide tree (using Kimura distances) and to\r
+create a HMM. The new guide tree and the HMM are then used to produce\r
+a new MSA.\r
+\r
+Iteration of guide tree and HMM can be de-coupled. This means that the\r
+number of guide tree iterations and HMM iterations can be\r
+different. This can be done by combining the --iter flag with the\r
+--max-guidetree-iterations and/or the --max-hmm-iterations flag. The\r
+number of guide tree iterations is the minimum of --iter and\r
+--max-guidetree-iterations, while the number of HMM iterations is the\r
+minimum of --iter and --max-hmm-iterations. If, for example, HMM\r
+iteration should be performed 5 times but guide tree iteration should\r
+be performed only 3 times, then one should set --iter=5 and\r
+--max-guidetree-iterations=3. All three flags can be specified at the\r
+same time (however, this makes no sense). It is not sufficient just to\r
+specify --max-guidetree-iterations and --max-hmm-iterations but not\r
+--iter. If any iteration is desired --iter has to be set.\r
+\r
+\r
+LIMITS (will exit early, if exceeded):\r
+\r
+ --maxnumseq=<n> Maximum allowed number of sequences\r
+\r
+ --maxseqlen=<l> Maximum allowed sequence length\r
+\r
+Limits can be imposed on the number of sequences in the input file\r
+and/or the lengths of the sequences. This cap can be set with the\r
+--maxnumseq and --maxseqlen flags, respectively. Clustal-Omega will\r
+exit early, if these limits are exceeded.\r
+\r
+\r
+MISCELLANEOUS:\r
+\r
+ --auto Set options automatically (might overwrite some of your options)\r
+\r
+ --threads=<n> Number of processors to use\r
+\r
+ -l, --log=<file> Log all non-essential output to this file\r
+\r
+ -h, --help Print help and exit\r
+\r
+ -v, --verbose Verbose output (increases if given multiple times)\r
+\r
+ --version Print version information and exit\r
+\r
+ --long-version Print long version information and exit\r
+\r
+ --force Force file overwriting\r
+\r
+\r
+Users may feel unsure which options are appropriate in certain\r
+situations even though using ClustalO without any special options\r
+should give you the desired results. The --auto flag tries to\r
+alleviate this problem and selects accuracy/speed flags according to\r
+the number of sequences. For all cases will use mBed and thereby\r
+possibly overwrite the --full option. For more than 1,000 sequences\r
+the iteration is turned off as the effect of iteration is more\r
+noticeable for 'larger' problems. Otherwise iterations are set to 1 if\r
+not already set to a higher value by the user. Expert users may want\r
+to avoid this flag and exercise more fine tuned control by selecting\r
+the appropriate options manually.\r
+\r
+Certain parts of the MSA calculation have been parallelised. Most\r
+noticeably, the distance matrix calculation, and certain aspects of\r
+the HMM building stage. Clustal-Omega uses OpenMP. By default,\r
+Clustal-Omega will attempt to use as many threads as possible. For\r
+example, on a 4-core machine Clustal-Omega will attempt to use 4\r
+threads. The number of threads can be limited by setting the --threads\r
+flag. This may be desirable, for example, in the case of\r
+benchmarking/timing.\r
+\r
+Usually, non-essential (verbose) output is written to screen. This\r
+output can be written to file by specifying the --log flag.\r
+\r
+Help is available by specifying the -h flag.\r
+\r
+By default Clustal-Omega does not print any information to stdout\r
+(other than the final alignment, if no output file is\r
+specified). Information concerning the progress of the alignment can\r
+be obtained by specifying one verbosity flag (-v). This may be\r
+desirable, to verify what Clustal-Omega is actually doing at the\r
+moment. If two verbosity flags (-v -v) are specified, command-line\r
+flags (explicitly and implicitly set) are printed in addition to the\r
+progress report. Triple verbose level (-v -v -v) is the most verbose\r
+level. In addition to single- and double-verbose information much more\r
+information is displayed: input sequences and names, details of the\r
+tree construction and intermediate alignments. Tree construction\r
+information includes pairwise distances. The number of pairwise\r
+distances scales with the square of the number of sequences, and\r
+double verbose mode is probably only useful for a small number of\r
+sequences.\r
+\r
+The current version number of Clustal-Omega can be displayed by\r
+setting the --version flag.\r
+\r
+The current version number of Clustal-Omega as well as the code-name\r
+and the build date can be displayed by setting the --long-version\r
+flag.\r
+\r
+By default, Clustal-Omega does not over-write files. These can be (i)\r
+alignment output, (ii) distance matrix and (iii) guide\r
+tree. Overwriting can be forced by setting the --force flag.\r
+\r
+\r
+EXAMPLES:\r
+\r
+./clustalo -i globin.fa\r
+\r
+Clustal-Omega reads the sequence file globin.fa, aligns the sequences\r
+and prints the result to screen in fasta/a2m format.\r
+\r
+\r
+./clustalo -i globin.fa -o globin.sto --outfmt=st\r
+\r
+If the file globin.sto does not exist, then Clustal-Omega reads the\r
+sequence file globin.fa, aligns the sequences and prints the result to\r
+globin.sto in Stockholm format. If the file globin.sto does exist\r
+already, then Clustal-Omega terminates the alignment process before\r
+reading globin.fa.\r
+\r
+\r
+./clustalo -i globin.fa -o globin.aln --outfmt=clu --force\r
+\r
+Clustal-Omega reads the sequence file globin.fa, aligns the sequences\r
+and prints the result to globin.aln in Clustal format, overwriting the\r
+file globin.aln, if it already exists.\r
+\r
+\r
+./clustalo -i globin.fa --distmat-out=globin.mat --guidetree-out=globin.dnd --force\r
+\r
+Clustal-Omega reads the sequence file globin.fa, aligns the sequences,\r
+prints the result to screen in fasta/a2m format (default), the guide\r
+tree to globin.dnd and the distance matrix to globin.mat, overwriting\r
+those files if they already exist.\r
+\r
+\r
+./clustalo -i globin.fa --guidetree-in=globin.dnd\r
+\r
+Clustal-Omega reads the files globin.fa and globin.dnd, skipping\r
+distance calculation and guide tree creation, using instead the guide\r
+tree specified in globin.dnd.\r
+\r
+\r
+./clustalo -i globin.fa --hmm-in=PF00042.hmm\r
+\r
+Clustal-Omega reads the sequence file globin.fa and the HMM file\r
+PF00042.hmm (in HMMer2 or HMMer3 format). It then performs the\r
+alignment, transferring pseudo-count information contained in\r
+PF00042.hmm to the sequences/profiles during the MSA.\r
+\r
+\r
+./clustalo -i globin.sto\r
+\r
+Clustal-Omega reads the file globin.sto (of aligned sequences in\r
+Stockholm format). It converts the alignment into a HMM, de-aligns the\r
+sequences and re-aligns them, transferring pseudo-count information to\r
+the sequences/profiles during the MSA. The guide tree is constructed\r
+using a full distance matrix of Kimura distances.\r
+\r
+\r
+./clustalo -i globin.sto --dealign\r
+\r
+Clustal-Omega reads the file globin.sto (of aligned sequences in\r
+Stockholm format). It de-aligns the sequences and then re-aligns\r
+them. No HMM is produced in the process, no pseudo-count information\r
+is transferred. Consequently, the output must be the same as for\r
+unaligned output (like in the first example ./clustalo -i globin.fa)\r
+\r
+\r
+./clustalo -i globin.fa --iter=2\r
+\r
+Clustal-Omega reads the file globin.fa, creates a UPGMA guide tree\r
+built from k-tuple distances, and performs an initial alignment. This\r
+initial alignment is converted into a HMM and a new guide tree is\r
+built from the Kimura distances of the initial alignment. The\r
+un-aligned sequences are then aligned (for the second time but this\r
+time) using pseudo-count information from the HMM created after the\r
+initial alignment (and using the new guide tree). This second\r
+alignment is then again converted into a HMM and a new guide tree is\r
+constructed. The un-aligned sequences are then aligned (for a third\r
+time), again using pseudo-count information of the HMM from the\r
+previous step and the most recent guide tree. The final alignment is\r
+written to screen.\r
+\r
+\r
+./clustalo -i globin.fa --iter=5 --max-guidetree-iterations=1\r
+\r
+Clustal-Omega reads the file globin.fa, creates a UPGMA guide tree\r
+built from k-tuple distances, and performs an initial alignment. This\r
+initial alignment is converted into a HMM and a new guide tree is\r
+built from the Kimura distances of the initial alignment. The\r
+un-aligned sequences are then aligned (for the second time but this\r
+time) using pseudo-count information from the HMM created after the\r
+initial alignment (and using the new guide tree). For the last 4\r
+iterations the guide tree is left unchanged and only HMM iteration is\r
+performed. This means that intermediate alignments are converted to\r
+HMMs, and these intermediate HMMs are used to guide the MSA during\r
+subsequent iteration stages.\r
+\r
+\r
+./clustalo -i globin.fa -o globin.a2m -v\r
+\r
+In case the file globin.a2m does not exist, Clustal-Omega reads the\r
+file globin.fa, prints a progress report to screen and writes the\r
+alignment in (default) Fasta format to globin.a2m. The progress report\r
+consists of the number of threads used, the number of sequences read,\r
+the current progress in the k-tuple distance calculation, completion\r
+of the guide tree computation and current progress of the MSA stage.\r
+If the file globin.a2m already exists Clustal-Omega aborts before\r
+reading the file globin.fa. Note that in verbose mode an output file\r
+has to be specified, because progress/debugging information, which is\r
+printed to screen, would interfere with the alignment being printed to\r
+screen.\r
+\r
+\r
+./clustalo -i PF00042_full.fa --dealign --full --outfmt=vie -o PF00042_full.vie --force\r
+\r
+Clustal-Omega reads the file PF00042_full.fa. This file contains\r
+several thousand aligned sequences. --dealign tells Clustal-Omega to\r
+erase all alignment information and re-align the sequences from\r
+scratch. As there are several thousand sequences calculating a full\r
+distance matrix may be slow. Setting the --full flag specifically\r
+selects the full distance mode over the default mBed mode. The\r
+alignment is then written out in Vienna format (fasta format all on\r
+one line, no line breaks per sequence) to file PF00042_full.vie.\r
+\r
+\r
+./clustalo -i PF00042_full.fa --dealign --outfmt=vie -o PF00042_full.vie --force\r
+\r
+Clustal-Omega reads the file PF00042_full.fa. This file contains\r
+several thousand aligned sequences. --dealign tells Clustal-Omega to\r
+erase all alignment information and re-align the sequences from\r
+scratch. Calculating the distance matrix will be done by mBed\r
+(default). Clustal-Omega will calculate pairwise distances to a\r
+small number of reference sequences only. This will give a significant\r
+speed-up. The speed-up is greater for larger families (more\r
+sequences). The alignment is then written out in Vienna format (fasta\r
+format all on one line, no line breaks per sequence) to file\r
+PF00042_full.vie.\r
+\r
+\r
+./clustalo --p1=globin.sto --p2=PF00042_full.vie -o globin+pf00042.fa\r
+\r
+Clustal-Omega reads files globin.sto and PF00042_full.vie of aligned\r
+sequences (profiles). Both profiles are then aligned. The relative\r
+positions of residues in both profiles are not changed during this\r
+alignment, however, columns of gaps may be inserted into the profiles,\r
+respectively. The final alignment is written to file globin+pf00042.fa\r
+in fasta format.\r
+\r
+\r
+./clustalo -i globin.fa --p1=PF00042_full.vie -o pf00042+globin.fa\r
+\r
+Clustal-Omega reads file globin.fa of un-aligned sequences and the\r
+profile (of aligned sequences) in file PF00042_full.vie. A HMM is\r
+created from the profile. This HMM is used to guide the alignment of\r
+the un-aligned sequences in globin.fa. The profile that was generated\r
+during this alignment of un-aligned globin.fa sequences is then\r
+aligned to the input profile PF00042_full.vie. The relative positions\r
+of residues in profile PF00042_full.vie is not changed during this\r
+alignment, however, columns of gaps may be inserted into the\r
+profile. The final alignment is output to file pf00042+globin.fa in\r
+fasta format. The alignment in this example may be slightly different\r
+from the alignment in the previous example, because no HMM guidance\r
+was used generate the profile globin.sto. In this example HMM guidance\r
+was used to align the sequences in globin.fa; the hope being that this\r
+intermediate alignment will have profited from the bigger profile.\r
+\r
+\r
+\r
+LITERATURE:\r
+\r
+[1] Johannes Soding (2005) Protein homology detection by HMM-HMM\r
+ comparison. Bioinformatics 21 (7): 951–960.\r
+\r
+[2] Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG. Sequence\r
+ embedding for fast construction of guide trees for multiple\r
+ sequence alignment. Algorithms Mol Biol. 2010 May 14;5:21.\r
+\r
+[3] http://www.genetics.wustl.edu/eddy/software/#squid\r
+\r
+[4] Wilbur and Lipman, 1983; PMID 6572363\r
+\r
+[5] Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: improving\r
+ the sensitivity of progressive multiple sequence alignment through\r
+ sequence weighting, position-specific gap penalties and weight\r
+ matrix choice. Nucleic Acids Res., 22, 4673-4680.\r
+\r
+[6] Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA,\r
+ McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD,\r
+ Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version\r
+ 2.0. Bioinformatics, 23, 2947-2948.\r
+\r
+[7] Kimura M (1980). "A simple method for estimating evolutionary\r
+ rates of base substitutions through comparative studies of\r
+ nucleotide sequences". Journal of Molecular Evolution 16: 111–120.\r
+\r
+[8] Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high\r
+ accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.\r
+\r
--- /dev/null
+IMPORTANT
+---------
+
+- consensus output (sto,aln) and compatibilety with bioperl/biopython
+
+- Split Homfam refs in two. Use one part as background HMM, the other parts
+ for benchmarking
+
+- Implement meta flags:
+ accurate: --iterations 3
+ default: --mbed --iterations 1
+ fast: --mbed
+ and for more than 10k sequences: --mbed --mbed-iter
+
+- SSE instructions for hhalign (little use in ClustalO frontend; DD)
+ /
+ Patch new code which already contains SSE instructions
+
+ also fix automake/configure then
+
+- Multi-HMMs; also for Pfam+iteration (FS)
+
+- Show degradation of alignment quality when using x reference sequences
+ added to y random/false sequences
+ (Lio Pachter)
+
+- Seed pre-alignment with M-Coffee, MSAProbs, ...
+
+- GUI/API:
+ Will have to catch/override exits from source.
+ find . -name \*.c -or -name \*.cpp -or -name \*.h | xargs grep 'exit('
+ Also best to allow for user override of
+ void Fatal(char *msg, ...);
+ void Error(char *msg, ...);
+ void Warn(char *msg, ...);
+ void Info(int level, char *msg, ...);
+
+
+- Soeding: DNA/RNA alignment incl. reading of nucleotide HMMs
+
+- Automatic HMM-selection/search/download for input
+
+- Structure input: Psipred predictions are apparently part of their
+ hhms and should therefore be ready to use (part automatic
+ HMM-selection)
--- /dev/null
+# generated automatically by aclocal 1.10.2 -*- Autoconf -*-
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+# with or without modifications, as long as this notice is preserved.
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+ # Extract the definition of DEPDIR, am__include, and am__quote
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+}
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+
+# AM_OUTPUT_DEPENDENCY_COMMANDS
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+ [AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"])
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+
+
+# Copyright (C) 1996, 1998, 1999, 2000, 2001, 2002, 2003, 2005
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 3
+
+AC_DEFUN([AM_WITH_DMALLOC],
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+])
+
+AU_DEFUN([fp_WITH_DMALLOC], [AM_WITH_DMALLOC])
+
+# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005
+# Free Software Foundation, Inc.
+#
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+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 8
+
+# AM_CONFIG_HEADER is obsolete. It has been replaced by AC_CONFIG_HEADERS.
+AU_DEFUN([AM_CONFIG_HEADER], [AC_CONFIG_HEADERS($@)])
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+# Do all the work for Automake. -*- Autoconf -*-
+
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
+# 2005, 2006, 2008 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 13
+
+# This macro actually does too much. Some checks are only needed if
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+# The call with PACKAGE and VERSION arguments is the old style
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+# Copyright (C) 2001, 2003, 2005 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
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+# AM_PROG_INSTALL_SH
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+# Copyright (C) 2003, 2005 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
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+# serial 2
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+# Check whether the underlying file-system supports filenames
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+
+# Check to see how 'make' treats includes. -*- Autoconf -*-
+
+# Copyright (C) 2001, 2002, 2003, 2005 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 3
+
+# AM_MAKE_INCLUDE()
+# -----------------
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+AC_SUBST([am__include])
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+
+# Fake the existence of programs that GNU maintainers use. -*- Autoconf -*-
+
+# Copyright (C) 1997, 1999, 2000, 2001, 2003, 2004, 2005
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
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+# serial 5
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+# AM_MISSING_PROG(NAME, PROGRAM)
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+# Copyright (C) 2003, 2004, 2005, 2006 Free Software Foundation, Inc.
+#
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+# gives unlimited permission to copy and/or distribute it,
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+
+# Helper functions for option handling. -*- Autoconf -*-
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+# Copyright (C) 2001, 2002, 2003, 2005, 2008 Free Software Foundation, Inc.
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+# serial 4
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+# Check to make sure that the build environment is sane. -*- Autoconf -*-
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+# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005
+# Free Software Foundation, Inc.
+#
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+# serial 4
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+# AM_SANITY_CHECK
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+AC_MSG_RESULT(yes)])
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+# Copyright (C) 2001, 2003, 2005 Free Software Foundation, Inc.
+#
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+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
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+# AM_PROG_INSTALL_STRIP
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+
+# Copyright (C) 2006 Free Software Foundation, Inc.
+#
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+# _AM_SUBST_NOTMAKE(VARIABLE)
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+# Check how to create a tarball. -*- Autoconf -*-
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+# Copyright (C) 2004, 2005 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
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+# serial 2
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+# _AM_PROG_TAR(FORMAT)
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+ am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
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--- /dev/null
+prefix=@prefix@
+exec_prefix=@exec_prefix@
+libdir=@libdir@
+includedir=@includedir@
+
+Name: clustal-omega
+Description: @PACKAGE_NAME@ library.
+Version: @PACKAGE_VERSION@
+Requires:
+Libs: -L${libdir} -lclustalo
+Cflags: -I${includedir}/clustalo/
+
--- /dev/null
+#! /bin/sh
+# Attempt to guess a canonical system name.
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
+# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008
+# Free Software Foundation, Inc.
+
+timestamp='2008-01-23'
+
+# This file is free software; you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
+# 02110-1301, USA.
+#
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+
+# Originally written by Per Bothner <per@bothner.com>.
+# Please send patches to <config-patches@gnu.org>. Submit a context
+# diff and a properly formatted ChangeLog entry.
+#
+# This script attempts to guess a canonical system name similar to
+# config.sub. If it succeeds, it prints the system name on stdout, and
+# exits with 0. Otherwise, it exits with 1.
+#
+# The plan is that this can be called by configure scripts if you
+# don't specify an explicit build system type.
+
+me=`echo "$0" | sed -e 's,.*/,,'`
+
+usage="\
+Usage: $0 [OPTION]
+
+Output the configuration name of the system \`$me' is run on.
+
+Operation modes:
+ -h, --help print this help, then exit
+ -t, --time-stamp print date of last modification, then exit
+ -v, --version print version number, then exit
+
+Report bugs and patches to <config-patches@gnu.org>."
+
+version="\
+GNU config.guess ($timestamp)
+
+Originally written by Per Bothner.
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001,
+2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
+
+help="
+Try \`$me --help' for more information."
+
+# Parse command line
+while test $# -gt 0 ; do
+ case $1 in
+ --time-stamp | --time* | -t )
+ echo "$timestamp" ; exit ;;
+ --version | -v )
+ echo "$version" ; exit ;;
+ --help | --h* | -h )
+ echo "$usage"; exit ;;
+ -- ) # Stop option processing
+ shift; break ;;
+ - ) # Use stdin as input.
+ break ;;
+ -* )
+ echo "$me: invalid option $1$help" >&2
+ exit 1 ;;
+ * )
+ break ;;
+ esac
+done
+
+if test $# != 0; then
+ echo "$me: too many arguments$help" >&2
+ exit 1
+fi
+
+trap 'exit 1' 1 2 15
+
+# CC_FOR_BUILD -- compiler used by this script. Note that the use of a
+# compiler to aid in system detection is discouraged as it requires
+# temporary files to be created and, as you can see below, it is a
+# headache to deal with in a portable fashion.
+
+# Historically, `CC_FOR_BUILD' used to be named `HOST_CC'. We still
+# use `HOST_CC' if defined, but it is deprecated.
+
+# Portable tmp directory creation inspired by the Autoconf team.
+
+set_cc_for_build='
+trap "exitcode=\$?; (rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null) && exit \$exitcode" 0 ;
+trap "rm -f \$tmpfiles 2>/dev/null; rmdir \$tmp 2>/dev/null; exit 1" 1 2 13 15 ;
+: ${TMPDIR=/tmp} ;
+ { tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||
+ { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } ||
+ { tmp=$TMPDIR/cg-$$ && (umask 077 && mkdir $tmp) && echo "Warning: creating insecure temp directory" >&2 ; } ||
+ { echo "$me: cannot create a temporary directory in $TMPDIR" >&2 ; exit 1 ; } ;
+dummy=$tmp/dummy ;
+tmpfiles="$dummy.c $dummy.o $dummy.rel $dummy" ;
+case $CC_FOR_BUILD,$HOST_CC,$CC in
+ ,,) echo "int x;" > $dummy.c ;
+ for c in cc gcc c89 c99 ; do
+ if ($c -c -o $dummy.o $dummy.c) >/dev/null 2>&1 ; then
+ CC_FOR_BUILD="$c"; break ;
+ fi ;
+ done ;
+ if test x"$CC_FOR_BUILD" = x ; then
+ CC_FOR_BUILD=no_compiler_found ;
+ fi
+ ;;
+ ,,*) CC_FOR_BUILD=$CC ;;
+ ,*,*) CC_FOR_BUILD=$HOST_CC ;;
+esac ; set_cc_for_build= ;'
+
+# This is needed to find uname on a Pyramid OSx when run in the BSD universe.
+# (ghazi@noc.rutgers.edu 1994-08-24)
+if (test -f /.attbin/uname) >/dev/null 2>&1 ; then
+ PATH=$PATH:/.attbin ; export PATH
+fi
+
+UNAME_MACHINE=`(uname -m) 2>/dev/null` || UNAME_MACHINE=unknown
+UNAME_RELEASE=`(uname -r) 2>/dev/null` || UNAME_RELEASE=unknown
+UNAME_SYSTEM=`(uname -s) 2>/dev/null` || UNAME_SYSTEM=unknown
+UNAME_VERSION=`(uname -v) 2>/dev/null` || UNAME_VERSION=unknown
+
+# Note: order is significant - the case branches are not exclusive.
+
+case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in
+ *:NetBSD:*:*)
+ # NetBSD (nbsd) targets should (where applicable) match one or
+ # more of the tupples: *-*-netbsdelf*, *-*-netbsdaout*,
+ # *-*-netbsdecoff* and *-*-netbsd*. For targets that recently
+ # switched to ELF, *-*-netbsd* would select the old
+ # object file format. This provides both forward
+ # compatibility and a consistent mechanism for selecting the
+ # object file format.
+ #
+ # Note: NetBSD doesn't particularly care about the vendor
+ # portion of the name. We always set it to "unknown".
+ sysctl="sysctl -n hw.machine_arch"
+ UNAME_MACHINE_ARCH=`(/sbin/$sysctl 2>/dev/null || \
+ /usr/sbin/$sysctl 2>/dev/null || echo unknown)`
+ case "${UNAME_MACHINE_ARCH}" in
+ armeb) machine=armeb-unknown ;;
+ arm*) machine=arm-unknown ;;
+ sh3el) machine=shl-unknown ;;
+ sh3eb) machine=sh-unknown ;;
+ sh5el) machine=sh5le-unknown ;;
+ *) machine=${UNAME_MACHINE_ARCH}-unknown ;;
+ esac
+ # The Operating System including object format, if it has switched
+ # to ELF recently, or will in the future.
+ case "${UNAME_MACHINE_ARCH}" in
+ arm*|i386|m68k|ns32k|sh3*|sparc|vax)
+ eval $set_cc_for_build
+ if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \
+ | grep __ELF__ >/dev/null
+ then
+ # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout).
+ # Return netbsd for either. FIX?
+ os=netbsd
+ else
+ os=netbsdelf
+ fi
+ ;;
+ *)
+ os=netbsd
+ ;;
+ esac
+ # The OS release
+ # Debian GNU/NetBSD machines have a different userland, and
+ # thus, need a distinct triplet. However, they do not need
+ # kernel version information, so it can be replaced with a
+ # suitable tag, in the style of linux-gnu.
+ case "${UNAME_VERSION}" in
+ Debian*)
+ release='-gnu'
+ ;;
+ *)
+ release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'`
+ ;;
+ esac
+ # Since CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM:
+ # contains redundant information, the shorter form:
+ # CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM is used.
+ echo "${machine}-${os}${release}"
+ exit ;;
+ *:OpenBSD:*:*)
+ UNAME_MACHINE_ARCH=`arch | sed 's/OpenBSD.//'`
+ echo ${UNAME_MACHINE_ARCH}-unknown-openbsd${UNAME_RELEASE}
+ exit ;;
+ *:ekkoBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-ekkobsd${UNAME_RELEASE}
+ exit ;;
+ *:SolidBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-solidbsd${UNAME_RELEASE}
+ exit ;;
+ macppc:MirBSD:*:*)
+ echo powerpc-unknown-mirbsd${UNAME_RELEASE}
+ exit ;;
+ *:MirBSD:*:*)
+ echo ${UNAME_MACHINE}-unknown-mirbsd${UNAME_RELEASE}
+ exit ;;
+ alpha:OSF1:*:*)
+ case $UNAME_RELEASE in
+ *4.0)
+ UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
+ ;;
+ *5.*)
+ UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
+ ;;
+ esac
+ # According to Compaq, /usr/sbin/psrinfo has been available on
+ # OSF/1 and Tru64 systems produced since 1995. I hope that
+ # covers most systems running today. This code pipes the CPU
+ # types through head -n 1, so we only detect the type of CPU 0.
+ ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1`
+ case "$ALPHA_CPU_TYPE" in
+ "EV4 (21064)")
+ UNAME_MACHINE="alpha" ;;
+ "EV4.5 (21064)")
+ UNAME_MACHINE="alpha" ;;
+ "LCA4 (21066/21068)")
+ UNAME_MACHINE="alpha" ;;
+ "EV5 (21164)")
+ UNAME_MACHINE="alphaev5" ;;
+ "EV5.6 (21164A)")
+ UNAME_MACHINE="alphaev56" ;;
+ "EV5.6 (21164PC)")
+ UNAME_MACHINE="alphapca56" ;;
+ "EV5.7 (21164PC)")
+ UNAME_MACHINE="alphapca57" ;;
+ "EV6 (21264)")
+ UNAME_MACHINE="alphaev6" ;;
+ "EV6.7 (21264A)")
+ UNAME_MACHINE="alphaev67" ;;
+ "EV6.8CB (21264C)")
+ UNAME_MACHINE="alphaev68" ;;
+ "EV6.8AL (21264B)")
+ UNAME_MACHINE="alphaev68" ;;
+ "EV6.8CX (21264D)")
+ UNAME_MACHINE="alphaev68" ;;
+ "EV6.9A (21264/EV69A)")
+ UNAME_MACHINE="alphaev69" ;;
+ "EV7 (21364)")
+ UNAME_MACHINE="alphaev7" ;;
+ "EV7.9 (21364A)")
+ UNAME_MACHINE="alphaev79" ;;
+ esac
+ # A Pn.n version is a patched version.
+ # A Vn.n version is a released version.
+ # A Tn.n version is a released field test version.
+ # A Xn.n version is an unreleased experimental baselevel.
+ # 1.2 uses "1.2" for uname -r.
+ echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
+ exit ;;
+ Alpha\ *:Windows_NT*:*)
+ # How do we know it's Interix rather than the generic POSIX subsystem?
+ # Should we change UNAME_MACHINE based on the output of uname instead
+ # of the specific Alpha model?
+ echo alpha-pc-interix
+ exit ;;
+ 21064:Windows_NT:50:3)
+ echo alpha-dec-winnt3.5
+ exit ;;
+ Amiga*:UNIX_System_V:4.0:*)
+ echo m68k-unknown-sysv4
+ exit ;;
+ *:[Aa]miga[Oo][Ss]:*:*)
+ echo ${UNAME_MACHINE}-unknown-amigaos
+ exit ;;
+ *:[Mm]orph[Oo][Ss]:*:*)
+ echo ${UNAME_MACHINE}-unknown-morphos
+ exit ;;
+ *:OS/390:*:*)
+ echo i370-ibm-openedition
+ exit ;;
+ *:z/VM:*:*)
+ echo s390-ibm-zvmoe
+ exit ;;
+ *:OS400:*:*)
+ echo powerpc-ibm-os400
+ exit ;;
+ arm:RISC*:1.[012]*:*|arm:riscix:1.[012]*:*)
+ echo arm-acorn-riscix${UNAME_RELEASE}
+ exit ;;
+ arm:riscos:*:*|arm:RISCOS:*:*)
+ echo arm-unknown-riscos
+ exit ;;
+ SR2?01:HI-UX/MPP:*:* | SR8000:HI-UX/MPP:*:*)
+ echo hppa1.1-hitachi-hiuxmpp
+ exit ;;
+ Pyramid*:OSx*:*:* | MIS*:OSx*:*:* | MIS*:SMP_DC-OSx*:*:*)
+ # akee@wpdis03.wpafb.af.mil (Earle F. Ake) contributed MIS and NILE.
+ if test "`(/bin/universe) 2>/dev/null`" = att ; then
+ echo pyramid-pyramid-sysv3
+ else
+ echo pyramid-pyramid-bsd
+ fi
+ exit ;;
+ NILE*:*:*:dcosx)
+ echo pyramid-pyramid-svr4
+ exit ;;
+ DRS?6000:unix:4.0:6*)
+ echo sparc-icl-nx6
+ exit ;;
+ DRS?6000:UNIX_SV:4.2*:7* | DRS?6000:isis:4.2*:7*)
+ case `/usr/bin/uname -p` in
+ sparc) echo sparc-icl-nx7; exit ;;
+ esac ;;
+ sun4H:SunOS:5.*:*)
+ echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
+ echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*)
+ echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ sun4*:SunOS:6*:*)
+ # According to config.sub, this is the proper way to canonicalize
+ # SunOS6. Hard to guess exactly what SunOS6 will be like, but
+ # it's likely to be more like Solaris than SunOS4.
+ echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ sun4*:SunOS:*:*)
+ case "`/usr/bin/arch -k`" in
+ Series*|S4*)
+ UNAME_RELEASE=`uname -v`
+ ;;
+ esac
+ # Japanese Language versions have a version number like `4.1.3-JL'.
+ echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'`
+ exit ;;
+ sun3*:SunOS:*:*)
+ echo m68k-sun-sunos${UNAME_RELEASE}
+ exit ;;
+ sun*:*:4.2BSD:*)
+ UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
+ test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3
+ case "`/bin/arch`" in
+ sun3)
+ echo m68k-sun-sunos${UNAME_RELEASE}
+ ;;
+ sun4)
+ echo sparc-sun-sunos${UNAME_RELEASE}
+ ;;
+ esac
+ exit ;;
+ aushp:SunOS:*:*)
+ echo sparc-auspex-sunos${UNAME_RELEASE}
+ exit ;;
+ # The situation for MiNT is a little confusing. The machine name
+ # can be virtually everything (everything which is not
+ # "atarist" or "atariste" at least should have a processor
+ # > m68000). The system name ranges from "MiNT" over "FreeMiNT"
+ # to the lowercase version "mint" (or "freemint"). Finally
+ # the system name "TOS" denotes a system which is actually not
+ # MiNT. But MiNT is downward compatible to TOS, so this should
+ # be no problem.
+ atarist[e]:*MiNT:*:* | atarist[e]:*mint:*:* | atarist[e]:*TOS:*:*)
+ echo m68k-atari-mint${UNAME_RELEASE}
+ exit ;;
+ atari*:*MiNT:*:* | atari*:*mint:*:* | atarist[e]:*TOS:*:*)
+ echo m68k-atari-mint${UNAME_RELEASE}
+ exit ;;
+ *falcon*:*MiNT:*:* | *falcon*:*mint:*:* | *falcon*:*TOS:*:*)
+ echo m68k-atari-mint${UNAME_RELEASE}
+ exit ;;
+ milan*:*MiNT:*:* | milan*:*mint:*:* | *milan*:*TOS:*:*)
+ echo m68k-milan-mint${UNAME_RELEASE}
+ exit ;;
+ hades*:*MiNT:*:* | hades*:*mint:*:* | *hades*:*TOS:*:*)
+ echo m68k-hades-mint${UNAME_RELEASE}
+ exit ;;
+ *:*MiNT:*:* | *:*mint:*:* | *:*TOS:*:*)
+ echo m68k-unknown-mint${UNAME_RELEASE}
+ exit ;;
+ m68k:machten:*:*)
+ echo m68k-apple-machten${UNAME_RELEASE}
+ exit ;;
+ powerpc:machten:*:*)
+ echo powerpc-apple-machten${UNAME_RELEASE}
+ exit ;;
+ RISC*:Mach:*:*)
+ echo mips-dec-mach_bsd4.3
+ exit ;;
+ RISC*:ULTRIX:*:*)
+ echo mips-dec-ultrix${UNAME_RELEASE}
+ exit ;;
+ VAX*:ULTRIX*:*:*)
+ echo vax-dec-ultrix${UNAME_RELEASE}
+ exit ;;
+ 2020:CLIX:*:* | 2430:CLIX:*:*)
+ echo clipper-intergraph-clix${UNAME_RELEASE}
+ exit ;;
+ mips:*:*:UMIPS | mips:*:*:RISCos)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+#ifdef __cplusplus
+#include <stdio.h> /* for printf() prototype */
+ int main (int argc, char *argv[]) {
+#else
+ int main (argc, argv) int argc; char *argv[]; {
+#endif
+ #if defined (host_mips) && defined (MIPSEB)
+ #if defined (SYSTYPE_SYSV)
+ printf ("mips-mips-riscos%ssysv\n", argv[1]); exit (0);
+ #endif
+ #if defined (SYSTYPE_SVR4)
+ printf ("mips-mips-riscos%ssvr4\n", argv[1]); exit (0);
+ #endif
+ #if defined (SYSTYPE_BSD43) || defined(SYSTYPE_BSD)
+ printf ("mips-mips-riscos%sbsd\n", argv[1]); exit (0);
+ #endif
+ #endif
+ exit (-1);
+ }
+EOF
+ $CC_FOR_BUILD -o $dummy $dummy.c &&
+ dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` &&
+ SYSTEM_NAME=`$dummy $dummyarg` &&
+ { echo "$SYSTEM_NAME"; exit; }
+ echo mips-mips-riscos${UNAME_RELEASE}
+ exit ;;
+ Motorola:PowerMAX_OS:*:*)
+ echo powerpc-motorola-powermax
+ exit ;;
+ Motorola:*:4.3:PL8-*)
+ echo powerpc-harris-powermax
+ exit ;;
+ Night_Hawk:*:*:PowerMAX_OS | Synergy:PowerMAX_OS:*:*)
+ echo powerpc-harris-powermax
+ exit ;;
+ Night_Hawk:Power_UNIX:*:*)
+ echo powerpc-harris-powerunix
+ exit ;;
+ m88k:CX/UX:7*:*)
+ echo m88k-harris-cxux7
+ exit ;;
+ m88k:*:4*:R4*)
+ echo m88k-motorola-sysv4
+ exit ;;
+ m88k:*:3*:R3*)
+ echo m88k-motorola-sysv3
+ exit ;;
+ AViiON:dgux:*:*)
+ # DG/UX returns AViiON for all architectures
+ UNAME_PROCESSOR=`/usr/bin/uname -p`
+ if [ $UNAME_PROCESSOR = mc88100 ] || [ $UNAME_PROCESSOR = mc88110 ]
+ then
+ if [ ${TARGET_BINARY_INTERFACE}x = m88kdguxelfx ] || \
+ [ ${TARGET_BINARY_INTERFACE}x = x ]
+ then
+ echo m88k-dg-dgux${UNAME_RELEASE}
+ else
+ echo m88k-dg-dguxbcs${UNAME_RELEASE}
+ fi
+ else
+ echo i586-dg-dgux${UNAME_RELEASE}
+ fi
+ exit ;;
+ M88*:DolphinOS:*:*) # DolphinOS (SVR3)
+ echo m88k-dolphin-sysv3
+ exit ;;
+ M88*:*:R3*:*)
+ # Delta 88k system running SVR3
+ echo m88k-motorola-sysv3
+ exit ;;
+ XD88*:*:*:*) # Tektronix XD88 system running UTekV (SVR3)
+ echo m88k-tektronix-sysv3
+ exit ;;
+ Tek43[0-9][0-9]:UTek:*:*) # Tektronix 4300 system running UTek (BSD)
+ echo m68k-tektronix-bsd
+ exit ;;
+ *:IRIX*:*:*)
+ echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'`
+ exit ;;
+ ????????:AIX?:[12].1:2) # AIX 2.2.1 or AIX 2.1.1 is RT/PC AIX.
+ echo romp-ibm-aix # uname -m gives an 8 hex-code CPU id
+ exit ;; # Note that: echo "'`uname -s`'" gives 'AIX '
+ i*86:AIX:*:*)
+ echo i386-ibm-aix
+ exit ;;
+ ia64:AIX:*:*)
+ if [ -x /usr/bin/oslevel ] ; then
+ IBM_REV=`/usr/bin/oslevel`
+ else
+ IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
+ fi
+ echo ${UNAME_MACHINE}-ibm-aix${IBM_REV}
+ exit ;;
+ *:AIX:2:3)
+ if grep bos325 /usr/include/stdio.h >/dev/null 2>&1; then
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #include <sys/systemcfg.h>
+
+ main()
+ {
+ if (!__power_pc())
+ exit(1);
+ puts("powerpc-ibm-aix3.2.5");
+ exit(0);
+ }
+EOF
+ if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy`
+ then
+ echo "$SYSTEM_NAME"
+ else
+ echo rs6000-ibm-aix3.2.5
+ fi
+ elif grep bos324 /usr/include/stdio.h >/dev/null 2>&1; then
+ echo rs6000-ibm-aix3.2.4
+ else
+ echo rs6000-ibm-aix3.2
+ fi
+ exit ;;
+ *:AIX:*:[456])
+ IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
+ if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then
+ IBM_ARCH=rs6000
+ else
+ IBM_ARCH=powerpc
+ fi
+ if [ -x /usr/bin/oslevel ] ; then
+ IBM_REV=`/usr/bin/oslevel`
+ else
+ IBM_REV=${UNAME_VERSION}.${UNAME_RELEASE}
+ fi
+ echo ${IBM_ARCH}-ibm-aix${IBM_REV}
+ exit ;;
+ *:AIX:*:*)
+ echo rs6000-ibm-aix
+ exit ;;
+ ibmrt:4.4BSD:*|romp-ibm:BSD:*)
+ echo romp-ibm-bsd4.4
+ exit ;;
+ ibmrt:*BSD:*|romp-ibm:BSD:*) # covers RT/PC BSD and
+ echo romp-ibm-bsd${UNAME_RELEASE} # 4.3 with uname added to
+ exit ;; # report: romp-ibm BSD 4.3
+ *:BOSX:*:*)
+ echo rs6000-bull-bosx
+ exit ;;
+ DPX/2?00:B.O.S.:*:*)
+ echo m68k-bull-sysv3
+ exit ;;
+ 9000/[34]??:4.3bsd:1.*:*)
+ echo m68k-hp-bsd
+ exit ;;
+ hp300:4.4BSD:*:* | 9000/[34]??:4.3bsd:2.*:*)
+ echo m68k-hp-bsd4.4
+ exit ;;
+ 9000/[34678]??:HP-UX:*:*)
+ HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
+ case "${UNAME_MACHINE}" in
+ 9000/31? ) HP_ARCH=m68000 ;;
+ 9000/[34]?? ) HP_ARCH=m68k ;;
+ 9000/[678][0-9][0-9])
+ if [ -x /usr/bin/getconf ]; then
+ sc_cpu_version=`/usr/bin/getconf SC_CPU_VERSION 2>/dev/null`
+ sc_kernel_bits=`/usr/bin/getconf SC_KERNEL_BITS 2>/dev/null`
+ case "${sc_cpu_version}" in
+ 523) HP_ARCH="hppa1.0" ;; # CPU_PA_RISC1_0
+ 528) HP_ARCH="hppa1.1" ;; # CPU_PA_RISC1_1
+ 532) # CPU_PA_RISC2_0
+ case "${sc_kernel_bits}" in
+ 32) HP_ARCH="hppa2.0n" ;;
+ 64) HP_ARCH="hppa2.0w" ;;
+ '') HP_ARCH="hppa2.0" ;; # HP-UX 10.20
+ esac ;;
+ esac
+ fi
+ if [ "${HP_ARCH}" = "" ]; then
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+
+ #define _HPUX_SOURCE
+ #include <stdlib.h>
+ #include <unistd.h>
+
+ int main ()
+ {
+ #if defined(_SC_KERNEL_BITS)
+ long bits = sysconf(_SC_KERNEL_BITS);
+ #endif
+ long cpu = sysconf (_SC_CPU_VERSION);
+
+ switch (cpu)
+ {
+ case CPU_PA_RISC1_0: puts ("hppa1.0"); break;
+ case CPU_PA_RISC1_1: puts ("hppa1.1"); break;
+ case CPU_PA_RISC2_0:
+ #if defined(_SC_KERNEL_BITS)
+ switch (bits)
+ {
+ case 64: puts ("hppa2.0w"); break;
+ case 32: puts ("hppa2.0n"); break;
+ default: puts ("hppa2.0"); break;
+ } break;
+ #else /* !defined(_SC_KERNEL_BITS) */
+ puts ("hppa2.0"); break;
+ #endif
+ default: puts ("hppa1.0"); break;
+ }
+ exit (0);
+ }
+EOF
+ (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
+ test -z "$HP_ARCH" && HP_ARCH=hppa
+ fi ;;
+ esac
+ if [ ${HP_ARCH} = "hppa2.0w" ]
+ then
+ eval $set_cc_for_build
+
+ # hppa2.0w-hp-hpux* has a 64-bit kernel and a compiler generating
+ # 32-bit code. hppa64-hp-hpux* has the same kernel and a compiler
+ # generating 64-bit code. GNU and HP use different nomenclature:
+ #
+ # $ CC_FOR_BUILD=cc ./config.guess
+ # => hppa2.0w-hp-hpux11.23
+ # $ CC_FOR_BUILD="cc +DA2.0w" ./config.guess
+ # => hppa64-hp-hpux11.23
+
+ if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) |
+ grep __LP64__ >/dev/null
+ then
+ HP_ARCH="hppa2.0w"
+ else
+ HP_ARCH="hppa64"
+ fi
+ fi
+ echo ${HP_ARCH}-hp-hpux${HPUX_REV}
+ exit ;;
+ ia64:HP-UX:*:*)
+ HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
+ echo ia64-hp-hpux${HPUX_REV}
+ exit ;;
+ 3050*:HI-UX:*:*)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #include <unistd.h>
+ int
+ main ()
+ {
+ long cpu = sysconf (_SC_CPU_VERSION);
+ /* The order matters, because CPU_IS_HP_MC68K erroneously returns
+ true for CPU_PA_RISC1_0. CPU_IS_PA_RISC returns correct
+ results, however. */
+ if (CPU_IS_PA_RISC (cpu))
+ {
+ switch (cpu)
+ {
+ case CPU_PA_RISC1_0: puts ("hppa1.0-hitachi-hiuxwe2"); break;
+ case CPU_PA_RISC1_1: puts ("hppa1.1-hitachi-hiuxwe2"); break;
+ case CPU_PA_RISC2_0: puts ("hppa2.0-hitachi-hiuxwe2"); break;
+ default: puts ("hppa-hitachi-hiuxwe2"); break;
+ }
+ }
+ else if (CPU_IS_HP_MC68K (cpu))
+ puts ("m68k-hitachi-hiuxwe2");
+ else puts ("unknown-hitachi-hiuxwe2");
+ exit (0);
+ }
+EOF
+ $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` &&
+ { echo "$SYSTEM_NAME"; exit; }
+ echo unknown-hitachi-hiuxwe2
+ exit ;;
+ 9000/7??:4.3bsd:*:* | 9000/8?[79]:4.3bsd:*:* )
+ echo hppa1.1-hp-bsd
+ exit ;;
+ 9000/8??:4.3bsd:*:*)
+ echo hppa1.0-hp-bsd
+ exit ;;
+ *9??*:MPE/iX:*:* | *3000*:MPE/iX:*:*)
+ echo hppa1.0-hp-mpeix
+ exit ;;
+ hp7??:OSF1:*:* | hp8?[79]:OSF1:*:* )
+ echo hppa1.1-hp-osf
+ exit ;;
+ hp8??:OSF1:*:*)
+ echo hppa1.0-hp-osf
+ exit ;;
+ i*86:OSF1:*:*)
+ if [ -x /usr/sbin/sysversion ] ; then
+ echo ${UNAME_MACHINE}-unknown-osf1mk
+ else
+ echo ${UNAME_MACHINE}-unknown-osf1
+ fi
+ exit ;;
+ parisc*:Lites*:*:*)
+ echo hppa1.1-hp-lites
+ exit ;;
+ C1*:ConvexOS:*:* | convex:ConvexOS:C1*:*)
+ echo c1-convex-bsd
+ exit ;;
+ C2*:ConvexOS:*:* | convex:ConvexOS:C2*:*)
+ if getsysinfo -f scalar_acc
+ then echo c32-convex-bsd
+ else echo c2-convex-bsd
+ fi
+ exit ;;
+ C34*:ConvexOS:*:* | convex:ConvexOS:C34*:*)
+ echo c34-convex-bsd
+ exit ;;
+ C38*:ConvexOS:*:* | convex:ConvexOS:C38*:*)
+ echo c38-convex-bsd
+ exit ;;
+ C4*:ConvexOS:*:* | convex:ConvexOS:C4*:*)
+ echo c4-convex-bsd
+ exit ;;
+ CRAY*Y-MP:*:*:*)
+ echo ymp-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*[A-Z]90:*:*:*)
+ echo ${UNAME_MACHINE}-cray-unicos${UNAME_RELEASE} \
+ | sed -e 's/CRAY.*\([A-Z]90\)/\1/' \
+ -e y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/ \
+ -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*TS:*:*:*)
+ echo t90-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*T3E:*:*:*)
+ echo alphaev5-cray-unicosmk${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ CRAY*SV1:*:*:*)
+ echo sv1-cray-unicos${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ *:UNICOS/mp:*:*)
+ echo craynv-cray-unicosmp${UNAME_RELEASE} | sed -e 's/\.[^.]*$/.X/'
+ exit ;;
+ F30[01]:UNIX_System_V:*:* | F700:UNIX_System_V:*:*)
+ FUJITSU_PROC=`uname -m | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
+ FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+ FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
+ echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+ exit ;;
+ 5000:UNIX_System_V:4.*:*)
+ FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
+ FUJITSU_REL=`echo ${UNAME_RELEASE} | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/ /_/'`
+ echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
+ exit ;;
+ i*86:BSD/386:*:* | i*86:BSD/OS:*:* | *:Ascend\ Embedded/OS:*:*)
+ echo ${UNAME_MACHINE}-pc-bsdi${UNAME_RELEASE}
+ exit ;;
+ sparc*:BSD/OS:*:*)
+ echo sparc-unknown-bsdi${UNAME_RELEASE}
+ exit ;;
+ *:BSD/OS:*:*)
+ echo ${UNAME_MACHINE}-unknown-bsdi${UNAME_RELEASE}
+ exit ;;
+ *:FreeBSD:*:*)
+ case ${UNAME_MACHINE} in
+ pc98)
+ echo i386-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+ amd64)
+ echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+ *)
+ echo ${UNAME_MACHINE}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
+ esac
+ exit ;;
+ i*:CYGWIN*:*)
+ echo ${UNAME_MACHINE}-pc-cygwin
+ exit ;;
+ *:MINGW*:*)
+ echo ${UNAME_MACHINE}-pc-mingw32
+ exit ;;
+ i*:windows32*:*)
+ # uname -m includes "-pc" on this system.
+ echo ${UNAME_MACHINE}-mingw32
+ exit ;;
+ i*:PW*:*)
+ echo ${UNAME_MACHINE}-pc-pw32
+ exit ;;
+ *:Interix*:[3456]*)
+ case ${UNAME_MACHINE} in
+ x86)
+ echo i586-pc-interix${UNAME_RELEASE}
+ exit ;;
+ EM64T | authenticamd)
+ echo x86_64-unknown-interix${UNAME_RELEASE}
+ exit ;;
+ IA64)
+ echo ia64-unknown-interix${UNAME_RELEASE}
+ exit ;;
+ esac ;;
+ [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*)
+ echo i${UNAME_MACHINE}-pc-mks
+ exit ;;
+ i*:Windows_NT*:* | Pentium*:Windows_NT*:*)
+ # How do we know it's Interix rather than the generic POSIX subsystem?
+ # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we
+ # UNAME_MACHINE based on the output of uname instead of i386?
+ echo i586-pc-interix
+ exit ;;
+ i*:UWIN*:*)
+ echo ${UNAME_MACHINE}-pc-uwin
+ exit ;;
+ amd64:CYGWIN*:*:* | x86_64:CYGWIN*:*:*)
+ echo x86_64-unknown-cygwin
+ exit ;;
+ p*:CYGWIN*:*)
+ echo powerpcle-unknown-cygwin
+ exit ;;
+ prep*:SunOS:5.*:*)
+ echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
+ exit ;;
+ *:GNU:*:*)
+ # the GNU system
+ echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
+ exit ;;
+ *:GNU/*:*:*)
+ # other systems with GNU libc and userland
+ echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr '[A-Z]' '[a-z]'``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-gnu
+ exit ;;
+ i*86:Minix:*:*)
+ echo ${UNAME_MACHINE}-pc-minix
+ exit ;;
+ arm*:Linux:*:*)
+ eval $set_cc_for_build
+ if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \
+ | grep -q __ARM_EABI__
+ then
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ else
+ echo ${UNAME_MACHINE}-unknown-linux-gnueabi
+ fi
+ exit ;;
+ avr32*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ cris:Linux:*:*)
+ echo cris-axis-linux-gnu
+ exit ;;
+ crisv32:Linux:*:*)
+ echo crisv32-axis-linux-gnu
+ exit ;;
+ frv:Linux:*:*)
+ echo frv-unknown-linux-gnu
+ exit ;;
+ ia64:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ m32r*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ m68*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ mips:Linux:*:*)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #undef CPU
+ #undef mips
+ #undef mipsel
+ #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
+ CPU=mipsel
+ #else
+ #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
+ CPU=mips
+ #else
+ CPU=
+ #endif
+ #endif
+EOF
+ eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n '
+ /^CPU/{
+ s: ::g
+ p
+ }'`"
+ test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
+ ;;
+ mips64:Linux:*:*)
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #undef CPU
+ #undef mips64
+ #undef mips64el
+ #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL)
+ CPU=mips64el
+ #else
+ #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB)
+ CPU=mips64
+ #else
+ CPU=
+ #endif
+ #endif
+EOF
+ eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n '
+ /^CPU/{
+ s: ::g
+ p
+ }'`"
+ test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; }
+ ;;
+ or32:Linux:*:*)
+ echo or32-unknown-linux-gnu
+ exit ;;
+ ppc:Linux:*:*)
+ echo powerpc-unknown-linux-gnu
+ exit ;;
+ ppc64:Linux:*:*)
+ echo powerpc64-unknown-linux-gnu
+ exit ;;
+ alpha:Linux:*:*)
+ case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in
+ EV5) UNAME_MACHINE=alphaev5 ;;
+ EV56) UNAME_MACHINE=alphaev56 ;;
+ PCA56) UNAME_MACHINE=alphapca56 ;;
+ PCA57) UNAME_MACHINE=alphapca56 ;;
+ EV6) UNAME_MACHINE=alphaev6 ;;
+ EV67) UNAME_MACHINE=alphaev67 ;;
+ EV68*) UNAME_MACHINE=alphaev68 ;;
+ esac
+ objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null
+ if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi
+ echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC}
+ exit ;;
+ parisc:Linux:*:* | hppa:Linux:*:*)
+ # Look for CPU level
+ case `grep '^cpu[^a-z]*:' /proc/cpuinfo 2>/dev/null | cut -d' ' -f2` in
+ PA7*) echo hppa1.1-unknown-linux-gnu ;;
+ PA8*) echo hppa2.0-unknown-linux-gnu ;;
+ *) echo hppa-unknown-linux-gnu ;;
+ esac
+ exit ;;
+ parisc64:Linux:*:* | hppa64:Linux:*:*)
+ echo hppa64-unknown-linux-gnu
+ exit ;;
+ s390:Linux:*:* | s390x:Linux:*:*)
+ echo ${UNAME_MACHINE}-ibm-linux
+ exit ;;
+ sh64*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ sh*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ sparc:Linux:*:* | sparc64:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ vax:Linux:*:*)
+ echo ${UNAME_MACHINE}-dec-linux-gnu
+ exit ;;
+ x86_64:Linux:*:*)
+ echo x86_64-unknown-linux-gnu
+ exit ;;
+ xtensa*:Linux:*:*)
+ echo ${UNAME_MACHINE}-unknown-linux-gnu
+ exit ;;
+ i*86:Linux:*:*)
+ # The BFD linker knows what the default object file format is, so
+ # first see if it will tell us. cd to the root directory to prevent
+ # problems with other programs or directories called `ld' in the path.
+ # Set LC_ALL=C to ensure ld outputs messages in English.
+ ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \
+ | sed -ne '/supported targets:/!d
+ s/[ ][ ]*/ /g
+ s/.*supported targets: *//
+ s/ .*//
+ p'`
+ case "$ld_supported_targets" in
+ elf32-i386)
+ TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu"
+ ;;
+ a.out-i386-linux)
+ echo "${UNAME_MACHINE}-pc-linux-gnuaout"
+ exit ;;
+ coff-i386)
+ echo "${UNAME_MACHINE}-pc-linux-gnucoff"
+ exit ;;
+ "")
+ # Either a pre-BFD a.out linker (linux-gnuoldld) or
+ # one that does not give us useful --help.
+ echo "${UNAME_MACHINE}-pc-linux-gnuoldld"
+ exit ;;
+ esac
+ # Determine whether the default compiler is a.out or elf
+ eval $set_cc_for_build
+ sed 's/^ //' << EOF >$dummy.c
+ #include <features.h>
+ #ifdef __ELF__
+ # ifdef __GLIBC__
+ # if __GLIBC__ >= 2
+ LIBC=gnu
+ # else
+ LIBC=gnulibc1
+ # endif
+ # else
+ LIBC=gnulibc1
+ # endif
+ #else
+ #if defined(__INTEL_COMPILER) || defined(__PGI) || defined(__SUNPRO_C) || defined(__SUNPRO_CC)
+ LIBC=gnu
+ #else
+ LIBC=gnuaout
+ #endif
+ #endif
+ #ifdef __dietlibc__
+ LIBC=dietlibc
+ #endif
+EOF
+ eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n '
+ /^LIBC/{
+ s: ::g
+ p
+ }'`"
+ test x"${LIBC}" != x && {
+ echo "${UNAME_MACHINE}-pc-linux-${LIBC}"
+ exit
+ }
+ test x"${TENTATIVE}" != x && { echo "${TENTATIVE}"; exit; }
+ ;;
+ i*86:DYNIX/ptx:4*:*)
+ # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there.
+ # earlier versions are messed up and put the nodename in both
+ # sysname and nodename.
+ echo i386-sequent-sysv4
+ exit ;;
+ i*86:UNIX_SV:4.2MP:2.*)
+ # Unixware is an offshoot of SVR4, but it has its own version
+ # number series starting with 2...
+ # I am not positive that other SVR4 systems won't match this,
+ # I just have to hope. -- rms.
+ # Use sysv4.2uw... so that sysv4* matches it.
+ echo ${UNAME_MACHINE}-pc-sysv4.2uw${UNAME_VERSION}
+ exit ;;
+ i*86:OS/2:*:*)
+ # If we were able to find `uname', then EMX Unix compatibility
+ # is probably installed.
+ echo ${UNAME_MACHINE}-pc-os2-emx
+ exit ;;
+ i*86:XTS-300:*:STOP)
+ echo ${UNAME_MACHINE}-unknown-stop
+ exit ;;
+ i*86:atheos:*:*)
+ echo ${UNAME_MACHINE}-unknown-atheos
+ exit ;;
+ i*86:syllable:*:*)
+ echo ${UNAME_MACHINE}-pc-syllable
+ exit ;;
+ i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*)
+ echo i386-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ i*86:*DOS:*:*)
+ echo ${UNAME_MACHINE}-pc-msdosdjgpp
+ exit ;;
+ i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*)
+ UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'`
+ if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then
+ echo ${UNAME_MACHINE}-univel-sysv${UNAME_REL}
+ else
+ echo ${UNAME_MACHINE}-pc-sysv${UNAME_REL}
+ fi
+ exit ;;
+ i*86:*:5:[678]*)
+ # UnixWare 7.x, OpenUNIX and OpenServer 6.
+ case `/bin/uname -X | grep "^Machine"` in
+ *486*) UNAME_MACHINE=i486 ;;
+ *Pentium) UNAME_MACHINE=i586 ;;
+ *Pent*|*Celeron) UNAME_MACHINE=i686 ;;
+ esac
+ echo ${UNAME_MACHINE}-unknown-sysv${UNAME_RELEASE}${UNAME_SYSTEM}${UNAME_VERSION}
+ exit ;;
+ i*86:*:3.2:*)
+ if test -f /usr/options/cb.name; then
+ UNAME_REL=`sed -n 's/.*Version //p' </usr/options/cb.name`
+ echo ${UNAME_MACHINE}-pc-isc$UNAME_REL
+ elif /bin/uname -X 2>/dev/null >/dev/null ; then
+ UNAME_REL=`(/bin/uname -X|grep Release|sed -e 's/.*= //')`
+ (/bin/uname -X|grep i80486 >/dev/null) && UNAME_MACHINE=i486
+ (/bin/uname -X|grep '^Machine.*Pentium' >/dev/null) \
+ && UNAME_MACHINE=i586
+ (/bin/uname -X|grep '^Machine.*Pent *II' >/dev/null) \
+ && UNAME_MACHINE=i686
+ (/bin/uname -X|grep '^Machine.*Pentium Pro' >/dev/null) \
+ && UNAME_MACHINE=i686
+ echo ${UNAME_MACHINE}-pc-sco$UNAME_REL
+ else
+ echo ${UNAME_MACHINE}-pc-sysv32
+ fi
+ exit ;;
+ pc:*:*:*)
+ # Left here for compatibility:
+ # uname -m prints for DJGPP always 'pc', but it prints nothing about
+ # the processor, so we play safe by assuming i386.
+ echo i386-pc-msdosdjgpp
+ exit ;;
+ Intel:Mach:3*:*)
+ echo i386-pc-mach3
+ exit ;;
+ paragon:*:*:*)
+ echo i860-intel-osf1
+ exit ;;
+ i860:*:4.*:*) # i860-SVR4
+ if grep Stardent /usr/include/sys/uadmin.h >/dev/null 2>&1 ; then
+ echo i860-stardent-sysv${UNAME_RELEASE} # Stardent Vistra i860-SVR4
+ else # Add other i860-SVR4 vendors below as they are discovered.
+ echo i860-unknown-sysv${UNAME_RELEASE} # Unknown i860-SVR4
+ fi
+ exit ;;
+ mini*:CTIX:SYS*5:*)
+ # "miniframe"
+ echo m68010-convergent-sysv
+ exit ;;
+ mc68k:UNIX:SYSTEM5:3.51m)
+ echo m68k-convergent-sysv
+ exit ;;
+ M680?0:D-NIX:5.3:*)
+ echo m68k-diab-dnix
+ exit ;;
+ M68*:*:R3V[5678]*:*)
+ test -r /sysV68 && { echo 'm68k-motorola-sysv'; exit; } ;;
+ 3[345]??:*:4.0:3.0 | 3[34]??A:*:4.0:3.0 | 3[34]??,*:*:4.0:3.0 | 3[34]??/*:*:4.0:3.0 | 4400:*:4.0:3.0 | 4850:*:4.0:3.0 | SKA40:*:4.0:3.0 | SDS2:*:4.0:3.0 | SHG2:*:4.0:3.0 | S7501*:*:4.0:3.0)
+ OS_REL=''
+ test -r /etc/.relid \
+ && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid`
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4.3${OS_REL}; exit; }
+ /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \
+ && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;;
+ 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*)
+ /bin/uname -p 2>/dev/null | grep 86 >/dev/null \
+ && { echo i486-ncr-sysv4; exit; } ;;
+ m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*)
+ echo m68k-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ mc68030:UNIX_System_V:4.*:*)
+ echo m68k-atari-sysv4
+ exit ;;
+ TSUNAMI:LynxOS:2.*:*)
+ echo sparc-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ rs6000:LynxOS:2.*:*)
+ echo rs6000-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*)
+ echo powerpc-unknown-lynxos${UNAME_RELEASE}
+ exit ;;
+ SM[BE]S:UNIX_SV:*:*)
+ echo mips-dde-sysv${UNAME_RELEASE}
+ exit ;;
+ RM*:ReliantUNIX-*:*:*)
+ echo mips-sni-sysv4
+ exit ;;
+ RM*:SINIX-*:*:*)
+ echo mips-sni-sysv4
+ exit ;;
+ *:SINIX-*:*:*)
+ if uname -p 2>/dev/null >/dev/null ; then
+ UNAME_MACHINE=`(uname -p) 2>/dev/null`
+ echo ${UNAME_MACHINE}-sni-sysv4
+ else
+ echo ns32k-sni-sysv
+ fi
+ exit ;;
+ PENTIUM:*:4.0*:*) # Unisys `ClearPath HMP IX 4000' SVR4/MP effort
+ # says <Richard.M.Bartel@ccMail.Census.GOV>
+ echo i586-unisys-sysv4
+ exit ;;
+ *:UNIX_System_V:4*:FTX*)
+ # From Gerald Hewes <hewes@openmarket.com>.
+ # How about differentiating between stratus architectures? -djm
+ echo hppa1.1-stratus-sysv4
+ exit ;;
+ *:*:*:FTX*)
+ # From seanf@swdc.stratus.com.
+ echo i860-stratus-sysv4
+ exit ;;
+ i*86:VOS:*:*)
+ # From Paul.Green@stratus.com.
+ echo ${UNAME_MACHINE}-stratus-vos
+ exit ;;
+ *:VOS:*:*)
+ # From Paul.Green@stratus.com.
+ echo hppa1.1-stratus-vos
+ exit ;;
+ mc68*:A/UX:*:*)
+ echo m68k-apple-aux${UNAME_RELEASE}
+ exit ;;
+ news*:NEWS-OS:6*:*)
+ echo mips-sony-newsos6
+ exit ;;
+ R[34]000:*System_V*:*:* | R4000:UNIX_SYSV:*:* | R*000:UNIX_SV:*:*)
+ if [ -d /usr/nec ]; then
+ echo mips-nec-sysv${UNAME_RELEASE}
+ else
+ echo mips-unknown-sysv${UNAME_RELEASE}
+ fi
+ exit ;;
+ BeBox:BeOS:*:*) # BeOS running on hardware made by Be, PPC only.
+ echo powerpc-be-beos
+ exit ;;
+ BeMac:BeOS:*:*) # BeOS running on Mac or Mac clone, PPC only.
+ echo powerpc-apple-beos
+ exit ;;
+ BePC:BeOS:*:*) # BeOS running on Intel PC compatible.
+ echo i586-pc-beos
+ exit ;;
+ SX-4:SUPER-UX:*:*)
+ echo sx4-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-5:SUPER-UX:*:*)
+ echo sx5-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-6:SUPER-UX:*:*)
+ echo sx6-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-7:SUPER-UX:*:*)
+ echo sx7-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-8:SUPER-UX:*:*)
+ echo sx8-nec-superux${UNAME_RELEASE}
+ exit ;;
+ SX-8R:SUPER-UX:*:*)
+ echo sx8r-nec-superux${UNAME_RELEASE}
+ exit ;;
+ Power*:Rhapsody:*:*)
+ echo powerpc-apple-rhapsody${UNAME_RELEASE}
+ exit ;;
+ *:Rhapsody:*:*)
+ echo ${UNAME_MACHINE}-apple-rhapsody${UNAME_RELEASE}
+ exit ;;
+ *:Darwin:*:*)
+ UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown
+ case $UNAME_PROCESSOR in
+ unknown) UNAME_PROCESSOR=powerpc ;;
+ esac
+ echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE}
+ exit ;;
+ *:procnto*:*:* | *:QNX:[0123456789]*:*)
+ UNAME_PROCESSOR=`uname -p`
+ if test "$UNAME_PROCESSOR" = "x86"; then
+ UNAME_PROCESSOR=i386
+ UNAME_MACHINE=pc
+ fi
+ echo ${UNAME_PROCESSOR}-${UNAME_MACHINE}-nto-qnx${UNAME_RELEASE}
+ exit ;;
+ *:QNX:*:4*)
+ echo i386-pc-qnx
+ exit ;;
+ NSE-?:NONSTOP_KERNEL:*:*)
+ echo nse-tandem-nsk${UNAME_RELEASE}
+ exit ;;
+ NSR-?:NONSTOP_KERNEL:*:*)
+ echo nsr-tandem-nsk${UNAME_RELEASE}
+ exit ;;
+ *:NonStop-UX:*:*)
+ echo mips-compaq-nonstopux
+ exit ;;
+ BS2000:POSIX*:*:*)
+ echo bs2000-siemens-sysv
+ exit ;;
+ DS/*:UNIX_System_V:*:*)
+ echo ${UNAME_MACHINE}-${UNAME_SYSTEM}-${UNAME_RELEASE}
+ exit ;;
+ *:Plan9:*:*)
+ # "uname -m" is not consistent, so use $cputype instead. 386
+ # is converted to i386 for consistency with other x86
+ # operating systems.
+ if test "$cputype" = "386"; then
+ UNAME_MACHINE=i386
+ else
+ UNAME_MACHINE="$cputype"
+ fi
+ echo ${UNAME_MACHINE}-unknown-plan9
+ exit ;;
+ *:TOPS-10:*:*)
+ echo pdp10-unknown-tops10
+ exit ;;
+ *:TENEX:*:*)
+ echo pdp10-unknown-tenex
+ exit ;;
+ KS10:TOPS-20:*:* | KL10:TOPS-20:*:* | TYPE4:TOPS-20:*:*)
+ echo pdp10-dec-tops20
+ exit ;;
+ XKL-1:TOPS-20:*:* | TYPE5:TOPS-20:*:*)
+ echo pdp10-xkl-tops20
+ exit ;;
+ *:TOPS-20:*:*)
+ echo pdp10-unknown-tops20
+ exit ;;
+ *:ITS:*:*)
+ echo pdp10-unknown-its
+ exit ;;
+ SEI:*:*:SEIUX)
+ echo mips-sei-seiux${UNAME_RELEASE}
+ exit ;;
+ *:DragonFly:*:*)
+ echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
+ exit ;;
+ *:*VMS:*:*)
+ UNAME_MACHINE=`(uname -p) 2>/dev/null`
+ case "${UNAME_MACHINE}" in
+ A*) echo alpha-dec-vms ; exit ;;
+ I*) echo ia64-dec-vms ; exit ;;
+ V*) echo vax-dec-vms ; exit ;;
+ esac ;;
+ *:XENIX:*:SysV)
+ echo i386-pc-xenix
+ exit ;;
+ i*86:skyos:*:*)
+ echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE}` | sed -e 's/ .*$//'
+ exit ;;
+ i*86:rdos:*:*)
+ echo ${UNAME_MACHINE}-pc-rdos
+ exit ;;
+esac
+
+#echo '(No uname command or uname output not recognized.)' 1>&2
+#echo "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" 1>&2
+
+eval $set_cc_for_build
+cat >$dummy.c <<EOF
+#ifdef _SEQUENT_
+# include <sys/types.h>
+# include <sys/utsname.h>
+#endif
+main ()
+{
+#if defined (sony)
+#if defined (MIPSEB)
+ /* BFD wants "bsd" instead of "newsos". Perhaps BFD should be changed,
+ I don't know.... */
+ printf ("mips-sony-bsd\n"); exit (0);
+#else
+#include <sys/param.h>
+ printf ("m68k-sony-newsos%s\n",
+#ifdef NEWSOS4
+ "4"
+#else
+ ""
+#endif
+ ); exit (0);
+#endif
+#endif
+
+#if defined (__arm) && defined (__acorn) && defined (__unix)
+ printf ("arm-acorn-riscix\n"); exit (0);
+#endif
+
+#if defined (hp300) && !defined (hpux)
+ printf ("m68k-hp-bsd\n"); exit (0);
+#endif
+
+#if defined (NeXT)
+#if !defined (__ARCHITECTURE__)
+#define __ARCHITECTURE__ "m68k"
+#endif
+ int version;
+ version=`(hostinfo | sed -n 's/.*NeXT Mach \([0-9]*\).*/\1/p') 2>/dev/null`;
+ if (version < 4)
+ printf ("%s-next-nextstep%d\n", __ARCHITECTURE__, version);
+ else
+ printf ("%s-next-openstep%d\n", __ARCHITECTURE__, version);
+ exit (0);
+#endif
+
+#if defined (MULTIMAX) || defined (n16)
+#if defined (UMAXV)
+ printf ("ns32k-encore-sysv\n"); exit (0);
+#else
+#if defined (CMU)
+ printf ("ns32k-encore-mach\n"); exit (0);
+#else
+ printf ("ns32k-encore-bsd\n"); exit (0);
+#endif
+#endif
+#endif
+
+#if defined (__386BSD__)
+ printf ("i386-pc-bsd\n"); exit (0);
+#endif
+
+#if defined (sequent)
+#if defined (i386)
+ printf ("i386-sequent-dynix\n"); exit (0);
+#endif
+#if defined (ns32000)
+ printf ("ns32k-sequent-dynix\n"); exit (0);
+#endif
+#endif
+
+#if defined (_SEQUENT_)
+ struct utsname un;
+
+ uname(&un);
+
+ if (strncmp(un.version, "V2", 2) == 0) {
+ printf ("i386-sequent-ptx2\n"); exit (0);
+ }
+ if (strncmp(un.version, "V1", 2) == 0) { /* XXX is V1 correct? */
+ printf ("i386-sequent-ptx1\n"); exit (0);
+ }
+ printf ("i386-sequent-ptx\n"); exit (0);
+
+#endif
+
+#if defined (vax)
+# if !defined (ultrix)
+# include <sys/param.h>
+# if defined (BSD)
+# if BSD == 43
+ printf ("vax-dec-bsd4.3\n"); exit (0);
+# else
+# if BSD == 199006
+ printf ("vax-dec-bsd4.3reno\n"); exit (0);
+# else
+ printf ("vax-dec-bsd\n"); exit (0);
+# endif
+# endif
+# else
+ printf ("vax-dec-bsd\n"); exit (0);
+# endif
+# else
+ printf ("vax-dec-ultrix\n"); exit (0);
+# endif
+#endif
+
+#if defined (alliant) && defined (i860)
+ printf ("i860-alliant-bsd\n"); exit (0);
+#endif
+
+ exit (1);
+}
+EOF
+
+$CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null && SYSTEM_NAME=`$dummy` &&
+ { echo "$SYSTEM_NAME"; exit; }
+
+# Apollos put the system type in the environment.
+
+test -d /usr/apollo && { echo ${ISP}-apollo-${SYSTYPE}; exit; }
+
+# Convex versions that predate uname can use getsysinfo(1)
+
+if [ -x /usr/convex/getsysinfo ]
+then
+ case `getsysinfo -f cpu_type` in
+ c1*)
+ echo c1-convex-bsd
+ exit ;;
+ c2*)
+ if getsysinfo -f scalar_acc
+ then echo c32-convex-bsd
+ else echo c2-convex-bsd
+ fi
+ exit ;;
+ c34*)
+ echo c34-convex-bsd
+ exit ;;
+ c38*)
+ echo c38-convex-bsd
+ exit ;;
+ c4*)
+ echo c4-convex-bsd
+ exit ;;
+ esac
+fi
+
+cat >&2 <<EOF
+$0: unable to guess system type
+
+This script, last modified $timestamp, has failed to recognize
+the operating system you are using. It is advised that you
+download the most up to date version of the config scripts from
+
+ http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
+and
+ http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
+
+If the version you run ($0) is already up to date, please
+send the following data and any information you think might be
+pertinent to <config-patches@gnu.org> in order to provide the needed
+information to handle your system.
+
+config.guess timestamp = $timestamp
+
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
+
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null`
+/bin/uname -X = `(/bin/uname -X) 2>/dev/null`
+
+hostinfo = `(hostinfo) 2>/dev/null`
+/bin/universe = `(/bin/universe) 2>/dev/null`
+/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null`
+/bin/arch = `(/bin/arch) 2>/dev/null`
+/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null`
+/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null`
+
+UNAME_MACHINE = ${UNAME_MACHINE}
+UNAME_RELEASE = ${UNAME_RELEASE}
+UNAME_SYSTEM = ${UNAME_SYSTEM}
+UNAME_VERSION = ${UNAME_VERSION}
+EOF
+
+exit 1
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "timestamp='"
+# time-stamp-format: "%:y-%02m-%02d"
+# time-stamp-end: "'"
+# End:
--- /dev/null
+#! /bin/sh
+# Configuration validation subroutine script.
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
+# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008
+# Free Software Foundation, Inc.
+
+timestamp='2008-01-16'
+
+# This file is (in principle) common to ALL GNU software.
+# The presence of a machine in this file suggests that SOME GNU software
+# can handle that machine. It does not imply ALL GNU software can.
+#
+# This file is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street - Fifth Floor, Boston, MA
+# 02110-1301, USA.
+#
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+
+# Please send patches to <config-patches@gnu.org>. Submit a context
+# diff and a properly formatted ChangeLog entry.
+#
+# Configuration subroutine to validate and canonicalize a configuration type.
+# Supply the specified configuration type as an argument.
+# If it is invalid, we print an error message on stderr and exit with code 1.
+# Otherwise, we print the canonical config type on stdout and succeed.
+
+# This file is supposed to be the same for all GNU packages
+# and recognize all the CPU types, system types and aliases
+# that are meaningful with *any* GNU software.
+# Each package is responsible for reporting which valid configurations
+# it does not support. The user should be able to distinguish
+# a failure to support a valid configuration from a meaningless
+# configuration.
+
+# The goal of this file is to map all the various variations of a given
+# machine specification into a single specification in the form:
+# CPU_TYPE-MANUFACTURER-OPERATING_SYSTEM
+# or in some cases, the newer four-part form:
+# CPU_TYPE-MANUFACTURER-KERNEL-OPERATING_SYSTEM
+# It is wrong to echo any other type of specification.
+
+me=`echo "$0" | sed -e 's,.*/,,'`
+
+usage="\
+Usage: $0 [OPTION] CPU-MFR-OPSYS
+ $0 [OPTION] ALIAS
+
+Canonicalize a configuration name.
+
+Operation modes:
+ -h, --help print this help, then exit
+ -t, --time-stamp print date of last modification, then exit
+ -v, --version print version number, then exit
+
+Report bugs and patches to <config-patches@gnu.org>."
+
+version="\
+GNU config.sub ($timestamp)
+
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001,
+2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
+
+help="
+Try \`$me --help' for more information."
+
+# Parse command line
+while test $# -gt 0 ; do
+ case $1 in
+ --time-stamp | --time* | -t )
+ echo "$timestamp" ; exit ;;
+ --version | -v )
+ echo "$version" ; exit ;;
+ --help | --h* | -h )
+ echo "$usage"; exit ;;
+ -- ) # Stop option processing
+ shift; break ;;
+ - ) # Use stdin as input.
+ break ;;
+ -* )
+ echo "$me: invalid option $1$help"
+ exit 1 ;;
+
+ *local*)
+ # First pass through any local machine types.
+ echo $1
+ exit ;;
+
+ * )
+ break ;;
+ esac
+done
+
+case $# in
+ 0) echo "$me: missing argument$help" >&2
+ exit 1;;
+ 1) ;;
+ *) echo "$me: too many arguments$help" >&2
+ exit 1;;
+esac
+
+# Separate what the user gave into CPU-COMPANY and OS or KERNEL-OS (if any).
+# Here we must recognize all the valid KERNEL-OS combinations.
+maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
+case $maybe_os in
+ nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \
+ uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \
+ storm-chaos* | os2-emx* | rtmk-nova*)
+ os=-$maybe_os
+ basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
+ ;;
+ *)
+ basic_machine=`echo $1 | sed 's/-[^-]*$//'`
+ if [ $basic_machine != $1 ]
+ then os=`echo $1 | sed 's/.*-/-/'`
+ else os=; fi
+ ;;
+esac
+
+### Let's recognize common machines as not being operating systems so
+### that things like config.sub decstation-3100 work. We also
+### recognize some manufacturers as not being operating systems, so we
+### can provide default operating systems below.
+case $os in
+ -sun*os*)
+ # Prevent following clause from handling this invalid input.
+ ;;
+ -dec* | -mips* | -sequent* | -encore* | -pc532* | -sgi* | -sony* | \
+ -att* | -7300* | -3300* | -delta* | -motorola* | -sun[234]* | \
+ -unicom* | -ibm* | -next | -hp | -isi* | -apollo | -altos* | \
+ -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\
+ -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \
+ -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \
+ -apple | -axis | -knuth | -cray)
+ os=
+ basic_machine=$1
+ ;;
+ -sim | -cisco | -oki | -wec | -winbond)
+ os=
+ basic_machine=$1
+ ;;
+ -scout)
+ ;;
+ -wrs)
+ os=-vxworks
+ basic_machine=$1
+ ;;
+ -chorusos*)
+ os=-chorusos
+ basic_machine=$1
+ ;;
+ -chorusrdb)
+ os=-chorusrdb
+ basic_machine=$1
+ ;;
+ -hiux*)
+ os=-hiuxwe2
+ ;;
+ -sco6)
+ os=-sco5v6
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco5)
+ os=-sco3.2v5
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco4)
+ os=-sco3.2v4
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco3.2.[4-9]*)
+ os=`echo $os | sed -e 's/sco3.2./sco3.2v/'`
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco3.2v[4-9]*)
+ # Don't forget version if it is 3.2v4 or newer.
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco5v6*)
+ # Don't forget version if it is 3.2v4 or newer.
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -sco*)
+ os=-sco3.2v2
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -udk*)
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -isc)
+ os=-isc2.2
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -clix*)
+ basic_machine=clipper-intergraph
+ ;;
+ -isc*)
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
+ ;;
+ -lynx*)
+ os=-lynxos
+ ;;
+ -ptx*)
+ basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'`
+ ;;
+ -windowsnt*)
+ os=`echo $os | sed -e 's/windowsnt/winnt/'`
+ ;;
+ -psos*)
+ os=-psos
+ ;;
+ -mint | -mint[0-9]*)
+ basic_machine=m68k-atari
+ os=-mint
+ ;;
+esac
+
+# Decode aliases for certain CPU-COMPANY combinations.
+case $basic_machine in
+ # Recognize the basic CPU types without company name.
+ # Some are omitted here because they have special meanings below.
+ 1750a | 580 \
+ | a29k \
+ | alpha | alphaev[4-8] | alphaev56 | alphaev6[78] | alphapca5[67] \
+ | alpha64 | alpha64ev[4-8] | alpha64ev56 | alpha64ev6[78] | alpha64pca5[67] \
+ | am33_2.0 \
+ | arc | arm | arm[bl]e | arme[lb] | armv[2345] | armv[345][lb] | avr | avr32 \
+ | bfin \
+ | c4x | clipper \
+ | d10v | d30v | dlx | dsp16xx \
+ | fido | fr30 | frv \
+ | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \
+ | i370 | i860 | i960 | ia64 \
+ | ip2k | iq2000 \
+ | m32c | m32r | m32rle | m68000 | m68k | m88k \
+ | maxq | mb | microblaze | mcore | mep \
+ | mips | mipsbe | mipseb | mipsel | mipsle \
+ | mips16 \
+ | mips64 | mips64el \
+ | mips64vr | mips64vrel \
+ | mips64orion | mips64orionel \
+ | mips64vr4100 | mips64vr4100el \
+ | mips64vr4300 | mips64vr4300el \
+ | mips64vr5000 | mips64vr5000el \
+ | mips64vr5900 | mips64vr5900el \
+ | mipsisa32 | mipsisa32el \
+ | mipsisa32r2 | mipsisa32r2el \
+ | mipsisa64 | mipsisa64el \
+ | mipsisa64r2 | mipsisa64r2el \
+ | mipsisa64sb1 | mipsisa64sb1el \
+ | mipsisa64sr71k | mipsisa64sr71kel \
+ | mipstx39 | mipstx39el \
+ | mn10200 | mn10300 \
+ | mt \
+ | msp430 \
+ | nios | nios2 \
+ | ns16k | ns32k \
+ | or32 \
+ | pdp10 | pdp11 | pj | pjl \
+ | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \
+ | pyramid \
+ | score \
+ | sh | sh[1234] | sh[24]a | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \
+ | sh64 | sh64le \
+ | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \
+ | sparcv8 | sparcv9 | sparcv9b | sparcv9v \
+ | spu | strongarm \
+ | tahoe | thumb | tic4x | tic80 | tron \
+ | v850 | v850e \
+ | we32k \
+ | x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \
+ | z8k)
+ basic_machine=$basic_machine-unknown
+ ;;
+ m6811 | m68hc11 | m6812 | m68hc12)
+ # Motorola 68HC11/12.
+ basic_machine=$basic_machine-unknown
+ os=-none
+ ;;
+ m88110 | m680[12346]0 | m683?2 | m68360 | m5200 | v70 | w65 | z8k)
+ ;;
+ ms1)
+ basic_machine=mt-unknown
+ ;;
+
+ # We use `pc' rather than `unknown'
+ # because (1) that's what they normally are, and
+ # (2) the word "unknown" tends to confuse beginning users.
+ i*86 | x86_64)
+ basic_machine=$basic_machine-pc
+ ;;
+ # Object if more than one company name word.
+ *-*-*)
+ echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
+ exit 1
+ ;;
+ # Recognize the basic CPU types with company name.
+ 580-* \
+ | a29k-* \
+ | alpha-* | alphaev[4-8]-* | alphaev56-* | alphaev6[78]-* \
+ | alpha64-* | alpha64ev[4-8]-* | alpha64ev56-* | alpha64ev6[78]-* \
+ | alphapca5[67]-* | alpha64pca5[67]-* | arc-* \
+ | arm-* | armbe-* | armle-* | armeb-* | armv*-* \
+ | avr-* | avr32-* \
+ | bfin-* | bs2000-* \
+ | c[123]* | c30-* | [cjt]90-* | c4x-* | c54x-* | c55x-* | c6x-* \
+ | clipper-* | craynv-* | cydra-* \
+ | d10v-* | d30v-* | dlx-* \
+ | elxsi-* \
+ | f30[01]-* | f700-* | fido-* | fr30-* | frv-* | fx80-* \
+ | h8300-* | h8500-* \
+ | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \
+ | i*86-* | i860-* | i960-* | ia64-* \
+ | ip2k-* | iq2000-* \
+ | m32c-* | m32r-* | m32rle-* \
+ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \
+ | m88110-* | m88k-* | maxq-* | mcore-* \
+ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \
+ | mips16-* \
+ | mips64-* | mips64el-* \
+ | mips64vr-* | mips64vrel-* \
+ | mips64orion-* | mips64orionel-* \
+ | mips64vr4100-* | mips64vr4100el-* \
+ | mips64vr4300-* | mips64vr4300el-* \
+ | mips64vr5000-* | mips64vr5000el-* \
+ | mips64vr5900-* | mips64vr5900el-* \
+ | mipsisa32-* | mipsisa32el-* \
+ | mipsisa32r2-* | mipsisa32r2el-* \
+ | mipsisa64-* | mipsisa64el-* \
+ | mipsisa64r2-* | mipsisa64r2el-* \
+ | mipsisa64sb1-* | mipsisa64sb1el-* \
+ | mipsisa64sr71k-* | mipsisa64sr71kel-* \
+ | mipstx39-* | mipstx39el-* \
+ | mmix-* \
+ | mt-* \
+ | msp430-* \
+ | nios-* | nios2-* \
+ | none-* | np1-* | ns16k-* | ns32k-* \
+ | orion-* \
+ | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \
+ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \
+ | pyramid-* \
+ | romp-* | rs6000-* \
+ | sh-* | sh[1234]-* | sh[24]a-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \
+ | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \
+ | sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \
+ | sparclite-* \
+ | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \
+ | tahoe-* | thumb-* \
+ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \
+ | tron-* \
+ | v850-* | v850e-* | vax-* \
+ | we32k-* \
+ | x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \
+ | xstormy16-* | xtensa*-* \
+ | ymp-* \
+ | z8k-*)
+ ;;
+ # Recognize the basic CPU types without company name, with glob match.
+ xtensa*)
+ basic_machine=$basic_machine-unknown
+ ;;
+ # Recognize the various machine names and aliases which stand
+ # for a CPU type and a company and sometimes even an OS.
+ 386bsd)
+ basic_machine=i386-unknown
+ os=-bsd
+ ;;
+ 3b1 | 7300 | 7300-att | att-7300 | pc7300 | safari | unixpc)
+ basic_machine=m68000-att
+ ;;
+ 3b*)
+ basic_machine=we32k-att
+ ;;
+ a29khif)
+ basic_machine=a29k-amd
+ os=-udi
+ ;;
+ abacus)
+ basic_machine=abacus-unknown
+ ;;
+ adobe68k)
+ basic_machine=m68010-adobe
+ os=-scout
+ ;;
+ alliant | fx80)
+ basic_machine=fx80-alliant
+ ;;
+ altos | altos3068)
+ basic_machine=m68k-altos
+ ;;
+ am29k)
+ basic_machine=a29k-none
+ os=-bsd
+ ;;
+ amd64)
+ basic_machine=x86_64-pc
+ ;;
+ amd64-*)
+ basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ amdahl)
+ basic_machine=580-amdahl
+ os=-sysv
+ ;;
+ amiga | amiga-*)
+ basic_machine=m68k-unknown
+ ;;
+ amigaos | amigados)
+ basic_machine=m68k-unknown
+ os=-amigaos
+ ;;
+ amigaunix | amix)
+ basic_machine=m68k-unknown
+ os=-sysv4
+ ;;
+ apollo68)
+ basic_machine=m68k-apollo
+ os=-sysv
+ ;;
+ apollo68bsd)
+ basic_machine=m68k-apollo
+ os=-bsd
+ ;;
+ aux)
+ basic_machine=m68k-apple
+ os=-aux
+ ;;
+ balance)
+ basic_machine=ns32k-sequent
+ os=-dynix
+ ;;
+ blackfin)
+ basic_machine=bfin-unknown
+ os=-linux
+ ;;
+ blackfin-*)
+ basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'`
+ os=-linux
+ ;;
+ c90)
+ basic_machine=c90-cray
+ os=-unicos
+ ;;
+ convex-c1)
+ basic_machine=c1-convex
+ os=-bsd
+ ;;
+ convex-c2)
+ basic_machine=c2-convex
+ os=-bsd
+ ;;
+ convex-c32)
+ basic_machine=c32-convex
+ os=-bsd
+ ;;
+ convex-c34)
+ basic_machine=c34-convex
+ os=-bsd
+ ;;
+ convex-c38)
+ basic_machine=c38-convex
+ os=-bsd
+ ;;
+ cray | j90)
+ basic_machine=j90-cray
+ os=-unicos
+ ;;
+ craynv)
+ basic_machine=craynv-cray
+ os=-unicosmp
+ ;;
+ cr16)
+ basic_machine=cr16-unknown
+ os=-elf
+ ;;
+ crds | unos)
+ basic_machine=m68k-crds
+ ;;
+ crisv32 | crisv32-* | etraxfs*)
+ basic_machine=crisv32-axis
+ ;;
+ cris | cris-* | etrax*)
+ basic_machine=cris-axis
+ ;;
+ crx)
+ basic_machine=crx-unknown
+ os=-elf
+ ;;
+ da30 | da30-*)
+ basic_machine=m68k-da30
+ ;;
+ decstation | decstation-3100 | pmax | pmax-* | pmin | dec3100 | decstatn)
+ basic_machine=mips-dec
+ ;;
+ decsystem10* | dec10*)
+ basic_machine=pdp10-dec
+ os=-tops10
+ ;;
+ decsystem20* | dec20*)
+ basic_machine=pdp10-dec
+ os=-tops20
+ ;;
+ delta | 3300 | motorola-3300 | motorola-delta \
+ | 3300-motorola | delta-motorola)
+ basic_machine=m68k-motorola
+ ;;
+ delta88)
+ basic_machine=m88k-motorola
+ os=-sysv3
+ ;;
+ djgpp)
+ basic_machine=i586-pc
+ os=-msdosdjgpp
+ ;;
+ dpx20 | dpx20-*)
+ basic_machine=rs6000-bull
+ os=-bosx
+ ;;
+ dpx2* | dpx2*-bull)
+ basic_machine=m68k-bull
+ os=-sysv3
+ ;;
+ ebmon29k)
+ basic_machine=a29k-amd
+ os=-ebmon
+ ;;
+ elxsi)
+ basic_machine=elxsi-elxsi
+ os=-bsd
+ ;;
+ encore | umax | mmax)
+ basic_machine=ns32k-encore
+ ;;
+ es1800 | OSE68k | ose68k | ose | OSE)
+ basic_machine=m68k-ericsson
+ os=-ose
+ ;;
+ fx2800)
+ basic_machine=i860-alliant
+ ;;
+ genix)
+ basic_machine=ns32k-ns
+ ;;
+ gmicro)
+ basic_machine=tron-gmicro
+ os=-sysv
+ ;;
+ go32)
+ basic_machine=i386-pc
+ os=-go32
+ ;;
+ h3050r* | hiux*)
+ basic_machine=hppa1.1-hitachi
+ os=-hiuxwe2
+ ;;
+ h8300hms)
+ basic_machine=h8300-hitachi
+ os=-hms
+ ;;
+ h8300xray)
+ basic_machine=h8300-hitachi
+ os=-xray
+ ;;
+ h8500hms)
+ basic_machine=h8500-hitachi
+ os=-hms
+ ;;
+ harris)
+ basic_machine=m88k-harris
+ os=-sysv3
+ ;;
+ hp300-*)
+ basic_machine=m68k-hp
+ ;;
+ hp300bsd)
+ basic_machine=m68k-hp
+ os=-bsd
+ ;;
+ hp300hpux)
+ basic_machine=m68k-hp
+ os=-hpux
+ ;;
+ hp3k9[0-9][0-9] | hp9[0-9][0-9])
+ basic_machine=hppa1.0-hp
+ ;;
+ hp9k2[0-9][0-9] | hp9k31[0-9])
+ basic_machine=m68000-hp
+ ;;
+ hp9k3[2-9][0-9])
+ basic_machine=m68k-hp
+ ;;
+ hp9k6[0-9][0-9] | hp6[0-9][0-9])
+ basic_machine=hppa1.0-hp
+ ;;
+ hp9k7[0-79][0-9] | hp7[0-79][0-9])
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k78[0-9] | hp78[0-9])
+ # FIXME: really hppa2.0-hp
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k8[67]1 | hp8[67]1 | hp9k80[24] | hp80[24] | hp9k8[78]9 | hp8[78]9 | hp9k893 | hp893)
+ # FIXME: really hppa2.0-hp
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k8[0-9][13679] | hp8[0-9][13679])
+ basic_machine=hppa1.1-hp
+ ;;
+ hp9k8[0-9][0-9] | hp8[0-9][0-9])
+ basic_machine=hppa1.0-hp
+ ;;
+ hppa-next)
+ os=-nextstep3
+ ;;
+ hppaosf)
+ basic_machine=hppa1.1-hp
+ os=-osf
+ ;;
+ hppro)
+ basic_machine=hppa1.1-hp
+ os=-proelf
+ ;;
+ i370-ibm* | ibm*)
+ basic_machine=i370-ibm
+ ;;
+# I'm not sure what "Sysv32" means. Should this be sysv3.2?
+ i*86v32)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-sysv32
+ ;;
+ i*86v4*)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-sysv4
+ ;;
+ i*86v)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-sysv
+ ;;
+ i*86sol2)
+ basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
+ os=-solaris2
+ ;;
+ i386mach)
+ basic_machine=i386-mach
+ os=-mach
+ ;;
+ i386-vsta | vsta)
+ basic_machine=i386-unknown
+ os=-vsta
+ ;;
+ iris | iris4d)
+ basic_machine=mips-sgi
+ case $os in
+ -irix*)
+ ;;
+ *)
+ os=-irix4
+ ;;
+ esac
+ ;;
+ isi68 | isi)
+ basic_machine=m68k-isi
+ os=-sysv
+ ;;
+ m68knommu)
+ basic_machine=m68k-unknown
+ os=-linux
+ ;;
+ m68knommu-*)
+ basic_machine=m68k-`echo $basic_machine | sed 's/^[^-]*-//'`
+ os=-linux
+ ;;
+ m88k-omron*)
+ basic_machine=m88k-omron
+ ;;
+ magnum | m3230)
+ basic_machine=mips-mips
+ os=-sysv
+ ;;
+ merlin)
+ basic_machine=ns32k-utek
+ os=-sysv
+ ;;
+ mingw32)
+ basic_machine=i386-pc
+ os=-mingw32
+ ;;
+ mingw32ce)
+ basic_machine=arm-unknown
+ os=-mingw32ce
+ ;;
+ miniframe)
+ basic_machine=m68000-convergent
+ ;;
+ *mint | -mint[0-9]* | *MiNT | *MiNT[0-9]*)
+ basic_machine=m68k-atari
+ os=-mint
+ ;;
+ mips3*-*)
+ basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`
+ ;;
+ mips3*)
+ basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown
+ ;;
+ monitor)
+ basic_machine=m68k-rom68k
+ os=-coff
+ ;;
+ morphos)
+ basic_machine=powerpc-unknown
+ os=-morphos
+ ;;
+ msdos)
+ basic_machine=i386-pc
+ os=-msdos
+ ;;
+ ms1-*)
+ basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'`
+ ;;
+ mvs)
+ basic_machine=i370-ibm
+ os=-mvs
+ ;;
+ ncr3000)
+ basic_machine=i486-ncr
+ os=-sysv4
+ ;;
+ netbsd386)
+ basic_machine=i386-unknown
+ os=-netbsd
+ ;;
+ netwinder)
+ basic_machine=armv4l-rebel
+ os=-linux
+ ;;
+ news | news700 | news800 | news900)
+ basic_machine=m68k-sony
+ os=-newsos
+ ;;
+ news1000)
+ basic_machine=m68030-sony
+ os=-newsos
+ ;;
+ news-3600 | risc-news)
+ basic_machine=mips-sony
+ os=-newsos
+ ;;
+ necv70)
+ basic_machine=v70-nec
+ os=-sysv
+ ;;
+ next | m*-next )
+ basic_machine=m68k-next
+ case $os in
+ -nextstep* )
+ ;;
+ -ns2*)
+ os=-nextstep2
+ ;;
+ *)
+ os=-nextstep3
+ ;;
+ esac
+ ;;
+ nh3000)
+ basic_machine=m68k-harris
+ os=-cxux
+ ;;
+ nh[45]000)
+ basic_machine=m88k-harris
+ os=-cxux
+ ;;
+ nindy960)
+ basic_machine=i960-intel
+ os=-nindy
+ ;;
+ mon960)
+ basic_machine=i960-intel
+ os=-mon960
+ ;;
+ nonstopux)
+ basic_machine=mips-compaq
+ os=-nonstopux
+ ;;
+ np1)
+ basic_machine=np1-gould
+ ;;
+ nsr-tandem)
+ basic_machine=nsr-tandem
+ ;;
+ op50n-* | op60c-*)
+ basic_machine=hppa1.1-oki
+ os=-proelf
+ ;;
+ openrisc | openrisc-*)
+ basic_machine=or32-unknown
+ ;;
+ os400)
+ basic_machine=powerpc-ibm
+ os=-os400
+ ;;
+ OSE68000 | ose68000)
+ basic_machine=m68000-ericsson
+ os=-ose
+ ;;
+ os68k)
+ basic_machine=m68k-none
+ os=-os68k
+ ;;
+ pa-hitachi)
+ basic_machine=hppa1.1-hitachi
+ os=-hiuxwe2
+ ;;
+ paragon)
+ basic_machine=i860-intel
+ os=-osf
+ ;;
+ parisc)
+ basic_machine=hppa-unknown
+ os=-linux
+ ;;
+ parisc-*)
+ basic_machine=hppa-`echo $basic_machine | sed 's/^[^-]*-//'`
+ os=-linux
+ ;;
+ pbd)
+ basic_machine=sparc-tti
+ ;;
+ pbb)
+ basic_machine=m68k-tti
+ ;;
+ pc532 | pc532-*)
+ basic_machine=ns32k-pc532
+ ;;
+ pc98)
+ basic_machine=i386-pc
+ ;;
+ pc98-*)
+ basic_machine=i386-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentium | p5 | k5 | k6 | nexgen | viac3)
+ basic_machine=i586-pc
+ ;;
+ pentiumpro | p6 | 6x86 | athlon | athlon_*)
+ basic_machine=i686-pc
+ ;;
+ pentiumii | pentium2 | pentiumiii | pentium3)
+ basic_machine=i686-pc
+ ;;
+ pentium4)
+ basic_machine=i786-pc
+ ;;
+ pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*)
+ basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentiumpro-* | p6-* | 6x86-* | athlon-*)
+ basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*)
+ basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pentium4-*)
+ basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ pn)
+ basic_machine=pn-gould
+ ;;
+ power) basic_machine=power-ibm
+ ;;
+ ppc) basic_machine=powerpc-unknown
+ ;;
+ ppc-*) basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ppcle | powerpclittle | ppc-le | powerpc-little)
+ basic_machine=powerpcle-unknown
+ ;;
+ ppcle-* | powerpclittle-*)
+ basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ppc64) basic_machine=powerpc64-unknown
+ ;;
+ ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ppc64le | powerpc64little | ppc64-le | powerpc64-little)
+ basic_machine=powerpc64le-unknown
+ ;;
+ ppc64le-* | powerpc64little-*)
+ basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'`
+ ;;
+ ps2)
+ basic_machine=i386-ibm
+ ;;
+ pw32)
+ basic_machine=i586-unknown
+ os=-pw32
+ ;;
+ rdos)
+ basic_machine=i386-pc
+ os=-rdos
+ ;;
+ rom68k)
+ basic_machine=m68k-rom68k
+ os=-coff
+ ;;
+ rm[46]00)
+ basic_machine=mips-siemens
+ ;;
+ rtpc | rtpc-*)
+ basic_machine=romp-ibm
+ ;;
+ s390 | s390-*)
+ basic_machine=s390-ibm
+ ;;
+ s390x | s390x-*)
+ basic_machine=s390x-ibm
+ ;;
+ sa29200)
+ basic_machine=a29k-amd
+ os=-udi
+ ;;
+ sb1)
+ basic_machine=mipsisa64sb1-unknown
+ ;;
+ sb1el)
+ basic_machine=mipsisa64sb1el-unknown
+ ;;
+ sde)
+ basic_machine=mipsisa32-sde
+ os=-elf
+ ;;
+ sei)
+ basic_machine=mips-sei
+ os=-seiux
+ ;;
+ sequent)
+ basic_machine=i386-sequent
+ ;;
+ sh)
+ basic_machine=sh-hitachi
+ os=-hms
+ ;;
+ sh5el)
+ basic_machine=sh5le-unknown
+ ;;
+ sh64)
+ basic_machine=sh64-unknown
+ ;;
+ sparclite-wrs | simso-wrs)
+ basic_machine=sparclite-wrs
+ os=-vxworks
+ ;;
+ sps7)
+ basic_machine=m68k-bull
+ os=-sysv2
+ ;;
+ spur)
+ basic_machine=spur-unknown
+ ;;
+ st2000)
+ basic_machine=m68k-tandem
+ ;;
+ stratus)
+ basic_machine=i860-stratus
+ os=-sysv4
+ ;;
+ sun2)
+ basic_machine=m68000-sun
+ ;;
+ sun2os3)
+ basic_machine=m68000-sun
+ os=-sunos3
+ ;;
+ sun2os4)
+ basic_machine=m68000-sun
+ os=-sunos4
+ ;;
+ sun3os3)
+ basic_machine=m68k-sun
+ os=-sunos3
+ ;;
+ sun3os4)
+ basic_machine=m68k-sun
+ os=-sunos4
+ ;;
+ sun4os3)
+ basic_machine=sparc-sun
+ os=-sunos3
+ ;;
+ sun4os4)
+ basic_machine=sparc-sun
+ os=-sunos4
+ ;;
+ sun4sol2)
+ basic_machine=sparc-sun
+ os=-solaris2
+ ;;
+ sun3 | sun3-*)
+ basic_machine=m68k-sun
+ ;;
+ sun4)
+ basic_machine=sparc-sun
+ ;;
+ sun386 | sun386i | roadrunner)
+ basic_machine=i386-sun
+ ;;
+ sv1)
+ basic_machine=sv1-cray
+ os=-unicos
+ ;;
+ symmetry)
+ basic_machine=i386-sequent
+ os=-dynix
+ ;;
+ t3e)
+ basic_machine=alphaev5-cray
+ os=-unicos
+ ;;
+ t90)
+ basic_machine=t90-cray
+ os=-unicos
+ ;;
+ tic54x | c54x*)
+ basic_machine=tic54x-unknown
+ os=-coff
+ ;;
+ tic55x | c55x*)
+ basic_machine=tic55x-unknown
+ os=-coff
+ ;;
+ tic6x | c6x*)
+ basic_machine=tic6x-unknown
+ os=-coff
+ ;;
+ tile*)
+ basic_machine=tile-unknown
+ os=-linux-gnu
+ ;;
+ tx39)
+ basic_machine=mipstx39-unknown
+ ;;
+ tx39el)
+ basic_machine=mipstx39el-unknown
+ ;;
+ toad1)
+ basic_machine=pdp10-xkl
+ os=-tops20
+ ;;
+ tower | tower-32)
+ basic_machine=m68k-ncr
+ ;;
+ tpf)
+ basic_machine=s390x-ibm
+ os=-tpf
+ ;;
+ udi29k)
+ basic_machine=a29k-amd
+ os=-udi
+ ;;
+ ultra3)
+ basic_machine=a29k-nyu
+ os=-sym1
+ ;;
+ v810 | necv810)
+ basic_machine=v810-nec
+ os=-none
+ ;;
+ vaxv)
+ basic_machine=vax-dec
+ os=-sysv
+ ;;
+ vms)
+ basic_machine=vax-dec
+ os=-vms
+ ;;
+ vpp*|vx|vx-*)
+ basic_machine=f301-fujitsu
+ ;;
+ vxworks960)
+ basic_machine=i960-wrs
+ os=-vxworks
+ ;;
+ vxworks68)
+ basic_machine=m68k-wrs
+ os=-vxworks
+ ;;
+ vxworks29k)
+ basic_machine=a29k-wrs
+ os=-vxworks
+ ;;
+ w65*)
+ basic_machine=w65-wdc
+ os=-none
+ ;;
+ w89k-*)
+ basic_machine=hppa1.1-winbond
+ os=-proelf
+ ;;
+ xbox)
+ basic_machine=i686-pc
+ os=-mingw32
+ ;;
+ xps | xps100)
+ basic_machine=xps100-honeywell
+ ;;
+ ymp)
+ basic_machine=ymp-cray
+ os=-unicos
+ ;;
+ z8k-*-coff)
+ basic_machine=z8k-unknown
+ os=-sim
+ ;;
+ none)
+ basic_machine=none-none
+ os=-none
+ ;;
+
+# Here we handle the default manufacturer of certain CPU types. It is in
+# some cases the only manufacturer, in others, it is the most popular.
+ w89k)
+ basic_machine=hppa1.1-winbond
+ ;;
+ op50n)
+ basic_machine=hppa1.1-oki
+ ;;
+ op60c)
+ basic_machine=hppa1.1-oki
+ ;;
+ romp)
+ basic_machine=romp-ibm
+ ;;
+ mmix)
+ basic_machine=mmix-knuth
+ ;;
+ rs6000)
+ basic_machine=rs6000-ibm
+ ;;
+ vax)
+ basic_machine=vax-dec
+ ;;
+ pdp10)
+ # there are many clones, so DEC is not a safe bet
+ basic_machine=pdp10-unknown
+ ;;
+ pdp11)
+ basic_machine=pdp11-dec
+ ;;
+ we32k)
+ basic_machine=we32k-att
+ ;;
+ sh[1234] | sh[24]a | sh[34]eb | sh[1234]le | sh[23]ele)
+ basic_machine=sh-unknown
+ ;;
+ sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v)
+ basic_machine=sparc-sun
+ ;;
+ cydra)
+ basic_machine=cydra-cydrome
+ ;;
+ orion)
+ basic_machine=orion-highlevel
+ ;;
+ orion105)
+ basic_machine=clipper-highlevel
+ ;;
+ mac | mpw | mac-mpw)
+ basic_machine=m68k-apple
+ ;;
+ pmac | pmac-mpw)
+ basic_machine=powerpc-apple
+ ;;
+ *-unknown)
+ # Make sure to match an already-canonicalized machine name.
+ ;;
+ *)
+ echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
+ exit 1
+ ;;
+esac
+
+# Here we canonicalize certain aliases for manufacturers.
+case $basic_machine in
+ *-digital*)
+ basic_machine=`echo $basic_machine | sed 's/digital.*/dec/'`
+ ;;
+ *-commodore*)
+ basic_machine=`echo $basic_machine | sed 's/commodore.*/cbm/'`
+ ;;
+ *)
+ ;;
+esac
+
+# Decode manufacturer-specific aliases for certain operating systems.
+
+if [ x"$os" != x"" ]
+then
+case $os in
+ # First match some system type aliases
+ # that might get confused with valid system types.
+ # -solaris* is a basic system type, with this one exception.
+ -solaris1 | -solaris1.*)
+ os=`echo $os | sed -e 's|solaris1|sunos4|'`
+ ;;
+ -solaris)
+ os=-solaris2
+ ;;
+ -svr4*)
+ os=-sysv4
+ ;;
+ -unixware*)
+ os=-sysv4.2uw
+ ;;
+ -gnu/linux*)
+ os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'`
+ ;;
+ # First accept the basic system types.
+ # The portable systems comes first.
+ # Each alternative MUST END IN A *, to match a version number.
+ # -sysv* is not here because it comes later, after sysvr4.
+ -gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \
+ | -*vms* | -sco* | -esix* | -isc* | -aix* | -sunos | -sunos[34]*\
+ | -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \
+ | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \
+ | -aos* \
+ | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \
+ | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \
+ | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \
+ | -openbsd* | -solidbsd* \
+ | -ekkobsd* | -kfreebsd* | -freebsd* | -riscix* | -lynxos* \
+ | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \
+ | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
+ | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
+ | -chorusos* | -chorusrdb* \
+ | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
+ | -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \
+ | -uxpv* | -beos* | -mpeix* | -udk* \
+ | -interix* | -uwin* | -mks* | -rhapsody* | -darwin* | -opened* \
+ | -openstep* | -oskit* | -conix* | -pw32* | -nonstopux* \
+ | -storm-chaos* | -tops10* | -tenex* | -tops20* | -its* \
+ | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \
+ | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \
+ | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \
+ | -skyos* | -haiku* | -rdos* | -toppers* | -drops*)
+ # Remember, each alternative MUST END IN *, to match a version number.
+ ;;
+ -qnx*)
+ case $basic_machine in
+ x86-* | i*86-*)
+ ;;
+ *)
+ os=-nto$os
+ ;;
+ esac
+ ;;
+ -nto-qnx*)
+ ;;
+ -nto*)
+ os=`echo $os | sed -e 's|nto|nto-qnx|'`
+ ;;
+ -sim | -es1800* | -hms* | -xray | -os68k* | -none* | -v88r* \
+ | -windows* | -osx | -abug | -netware* | -os9* | -beos* | -haiku* \
+ | -macos* | -mpw* | -magic* | -mmixware* | -mon960* | -lnews*)
+ ;;
+ -mac*)
+ os=`echo $os | sed -e 's|mac|macos|'`
+ ;;
+ -linux-dietlibc)
+ os=-linux-dietlibc
+ ;;
+ -linux*)
+ os=`echo $os | sed -e 's|linux|linux-gnu|'`
+ ;;
+ -sunos5*)
+ os=`echo $os | sed -e 's|sunos5|solaris2|'`
+ ;;
+ -sunos6*)
+ os=`echo $os | sed -e 's|sunos6|solaris3|'`
+ ;;
+ -opened*)
+ os=-openedition
+ ;;
+ -os400*)
+ os=-os400
+ ;;
+ -wince*)
+ os=-wince
+ ;;
+ -osfrose*)
+ os=-osfrose
+ ;;
+ -osf*)
+ os=-osf
+ ;;
+ -utek*)
+ os=-bsd
+ ;;
+ -dynix*)
+ os=-bsd
+ ;;
+ -acis*)
+ os=-aos
+ ;;
+ -atheos*)
+ os=-atheos
+ ;;
+ -syllable*)
+ os=-syllable
+ ;;
+ -386bsd)
+ os=-bsd
+ ;;
+ -ctix* | -uts*)
+ os=-sysv
+ ;;
+ -nova*)
+ os=-rtmk-nova
+ ;;
+ -ns2 )
+ os=-nextstep2
+ ;;
+ -nsk*)
+ os=-nsk
+ ;;
+ # Preserve the version number of sinix5.
+ -sinix5.*)
+ os=`echo $os | sed -e 's|sinix|sysv|'`
+ ;;
+ -sinix*)
+ os=-sysv4
+ ;;
+ -tpf*)
+ os=-tpf
+ ;;
+ -triton*)
+ os=-sysv3
+ ;;
+ -oss*)
+ os=-sysv3
+ ;;
+ -svr4)
+ os=-sysv4
+ ;;
+ -svr3)
+ os=-sysv3
+ ;;
+ -sysvr4)
+ os=-sysv4
+ ;;
+ # This must come after -sysvr4.
+ -sysv*)
+ ;;
+ -ose*)
+ os=-ose
+ ;;
+ -es1800*)
+ os=-ose
+ ;;
+ -xenix)
+ os=-xenix
+ ;;
+ -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
+ os=-mint
+ ;;
+ -aros*)
+ os=-aros
+ ;;
+ -kaos*)
+ os=-kaos
+ ;;
+ -zvmoe)
+ os=-zvmoe
+ ;;
+ -none)
+ ;;
+ *)
+ # Get rid of the `-' at the beginning of $os.
+ os=`echo $os | sed 's/[^-]*-//'`
+ echo Invalid configuration \`$1\': system \`$os\' not recognized 1>&2
+ exit 1
+ ;;
+esac
+else
+
+# Here we handle the default operating systems that come with various machines.
+# The value should be what the vendor currently ships out the door with their
+# machine or put another way, the most popular os provided with the machine.
+
+# Note that if you're going to try to match "-MANUFACTURER" here (say,
+# "-sun"), then you have to tell the case statement up towards the top
+# that MANUFACTURER isn't an operating system. Otherwise, code above
+# will signal an error saying that MANUFACTURER isn't an operating
+# system, and we'll never get to this point.
+
+case $basic_machine in
+ score-*)
+ os=-elf
+ ;;
+ spu-*)
+ os=-elf
+ ;;
+ *-acorn)
+ os=-riscix1.2
+ ;;
+ arm*-rebel)
+ os=-linux
+ ;;
+ arm*-semi)
+ os=-aout
+ ;;
+ c4x-* | tic4x-*)
+ os=-coff
+ ;;
+ # This must come before the *-dec entry.
+ pdp10-*)
+ os=-tops20
+ ;;
+ pdp11-*)
+ os=-none
+ ;;
+ *-dec | vax-*)
+ os=-ultrix4.2
+ ;;
+ m68*-apollo)
+ os=-domain
+ ;;
+ i386-sun)
+ os=-sunos4.0.2
+ ;;
+ m68000-sun)
+ os=-sunos3
+ # This also exists in the configure program, but was not the
+ # default.
+ # os=-sunos4
+ ;;
+ m68*-cisco)
+ os=-aout
+ ;;
+ mep-*)
+ os=-elf
+ ;;
+ mips*-cisco)
+ os=-elf
+ ;;
+ mips*-*)
+ os=-elf
+ ;;
+ or32-*)
+ os=-coff
+ ;;
+ *-tti) # must be before sparc entry or we get the wrong os.
+ os=-sysv3
+ ;;
+ sparc-* | *-sun)
+ os=-sunos4.1.1
+ ;;
+ *-be)
+ os=-beos
+ ;;
+ *-haiku)
+ os=-haiku
+ ;;
+ *-ibm)
+ os=-aix
+ ;;
+ *-knuth)
+ os=-mmixware
+ ;;
+ *-wec)
+ os=-proelf
+ ;;
+ *-winbond)
+ os=-proelf
+ ;;
+ *-oki)
+ os=-proelf
+ ;;
+ *-hp)
+ os=-hpux
+ ;;
+ *-hitachi)
+ os=-hiux
+ ;;
+ i860-* | *-att | *-ncr | *-altos | *-motorola | *-convergent)
+ os=-sysv
+ ;;
+ *-cbm)
+ os=-amigaos
+ ;;
+ *-dg)
+ os=-dgux
+ ;;
+ *-dolphin)
+ os=-sysv3
+ ;;
+ m68k-ccur)
+ os=-rtu
+ ;;
+ m88k-omron*)
+ os=-luna
+ ;;
+ *-next )
+ os=-nextstep
+ ;;
+ *-sequent)
+ os=-ptx
+ ;;
+ *-crds)
+ os=-unos
+ ;;
+ *-ns)
+ os=-genix
+ ;;
+ i370-*)
+ os=-mvs
+ ;;
+ *-next)
+ os=-nextstep3
+ ;;
+ *-gould)
+ os=-sysv
+ ;;
+ *-highlevel)
+ os=-bsd
+ ;;
+ *-encore)
+ os=-bsd
+ ;;
+ *-sgi)
+ os=-irix
+ ;;
+ *-siemens)
+ os=-sysv4
+ ;;
+ *-masscomp)
+ os=-rtu
+ ;;
+ f30[01]-fujitsu | f700-fujitsu)
+ os=-uxpv
+ ;;
+ *-rom68k)
+ os=-coff
+ ;;
+ *-*bug)
+ os=-coff
+ ;;
+ *-apple)
+ os=-macos
+ ;;
+ *-atari*)
+ os=-mint
+ ;;
+ *)
+ os=-none
+ ;;
+esac
+fi
+
+# Here we handle the case where we know the os, and the CPU type, but not the
+# manufacturer. We pick the logical manufacturer.
+vendor=unknown
+case $basic_machine in
+ *-unknown)
+ case $os in
+ -riscix*)
+ vendor=acorn
+ ;;
+ -sunos*)
+ vendor=sun
+ ;;
+ -aix*)
+ vendor=ibm
+ ;;
+ -beos*)
+ vendor=be
+ ;;
+ -hpux*)
+ vendor=hp
+ ;;
+ -mpeix*)
+ vendor=hp
+ ;;
+ -hiux*)
+ vendor=hitachi
+ ;;
+ -unos*)
+ vendor=crds
+ ;;
+ -dgux*)
+ vendor=dg
+ ;;
+ -luna*)
+ vendor=omron
+ ;;
+ -genix*)
+ vendor=ns
+ ;;
+ -mvs* | -opened*)
+ vendor=ibm
+ ;;
+ -os400*)
+ vendor=ibm
+ ;;
+ -ptx*)
+ vendor=sequent
+ ;;
+ -tpf*)
+ vendor=ibm
+ ;;
+ -vxsim* | -vxworks* | -windiss*)
+ vendor=wrs
+ ;;
+ -aux*)
+ vendor=apple
+ ;;
+ -hms*)
+ vendor=hitachi
+ ;;
+ -mpw* | -macos*)
+ vendor=apple
+ ;;
+ -*mint | -mint[0-9]* | -*MiNT | -MiNT[0-9]*)
+ vendor=atari
+ ;;
+ -vos*)
+ vendor=stratus
+ ;;
+ esac
+ basic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"`
+ ;;
+esac
+
+echo $basic_machine$os
+exit
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "timestamp='"
+# time-stamp-format: "%:y-%02m-%02d"
+# time-stamp-end: "'"
+# End:
--- /dev/null
+#! /bin/sh
+# Guess values for system-dependent variables and create Makefiles.
+# Generated by GNU Autoconf 2.63 for Clustal Omega 1.0.2.
+#
+# Report bugs to <clustalw@ucd.ie>.
+#
+# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
+# 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+# This configure script is free software; the Free Software Foundation
+# gives unlimited permission to copy, distribute and modify it.
+## --------------------- ##
+## M4sh Initialization. ##
+## --------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in
+ *posix*) set -o posix ;;
+esac
+
+fi
+
+
+
+
+# PATH needs CR
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+as_nl='
+'
+export as_nl
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
+if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='printf %s\n'
+ as_echo_n='printf %s'
+else
+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
+ as_echo_n='/usr/ucb/echo -n'
+ else
+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
+ as_echo_n_body='eval
+ arg=$1;
+ case $arg in
+ *"$as_nl"*)
+ expr "X$arg" : "X\\(.*\\)$as_nl";
+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
+ esac;
+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
+ '
+ export as_echo_n_body
+ as_echo_n='sh -c $as_echo_n_body as_echo'
+ fi
+ export as_echo_body
+ as_echo='sh -c $as_echo_body as_echo'
+fi
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+# Support unset when possible.
+if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
+ as_unset=unset
+else
+ as_unset=false
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
+# splitting by setting IFS to empty value.)
+IFS=" "" $as_nl"
+
+# Find who we are. Look in the path if we contain no directory separator.
+case $0 in
+ *[\\/]* ) as_myself=$0 ;;
+ *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+done
+IFS=$as_save_IFS
+
+ ;;
+esac
+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+ as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ { (exit 1); exit 1; }
+fi
+
+# Work around bugs in pre-3.0 UWIN ksh.
+for as_var in ENV MAIL MAILPATH
+do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
+done
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
+
+# Required to use basename.
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+ as_basename=basename
+else
+ as_basename=false
+fi
+
+
+# Name of the executable.
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+
+# CDPATH.
+$as_unset CDPATH
+
+
+if test "x$CONFIG_SHELL" = x; then
+ if (eval ":") 2>/dev/null; then
+ as_have_required=yes
+else
+ as_have_required=no
+fi
+
+ if test $as_have_required = yes && (eval ":
+(as_func_return () {
+ (exit \$1)
+}
+as_func_success () {
+ as_func_return 0
+}
+as_func_failure () {
+ as_func_return 1
+}
+as_func_ret_success () {
+ return 0
+}
+as_func_ret_failure () {
+ return 1
+}
+
+exitcode=0
+if as_func_success; then
+ :
+else
+ exitcode=1
+ echo as_func_success failed.
+fi
+
+if as_func_failure; then
+ exitcode=1
+ echo as_func_failure succeeded.
+fi
+
+if as_func_ret_success; then
+ :
+else
+ exitcode=1
+ echo as_func_ret_success failed.
+fi
+
+if as_func_ret_failure; then
+ exitcode=1
+ echo as_func_ret_failure succeeded.
+fi
+
+if ( set x; as_func_ret_success y && test x = \"\$1\" ); then
+ :
+else
+ exitcode=1
+ echo positional parameters were not saved.
+fi
+
+test \$exitcode = 0) || { (exit 1); exit 1; }
+
+(
+ as_lineno_1=\$LINENO
+ as_lineno_2=\$LINENO
+ test \"x\$as_lineno_1\" != \"x\$as_lineno_2\" &&
+ test \"x\`expr \$as_lineno_1 + 1\`\" = \"x\$as_lineno_2\") || { (exit 1); exit 1; }
+") 2> /dev/null; then
+ :
+else
+ as_candidate_shells=
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ case $as_dir in
+ /*)
+ for as_base in sh bash ksh sh5; do
+ as_candidate_shells="$as_candidate_shells $as_dir/$as_base"
+ done;;
+ esac
+done
+IFS=$as_save_IFS
+
+
+ for as_shell in $as_candidate_shells $SHELL; do
+ # Try only shells that exist, to save several forks.
+ if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
+ { ("$as_shell") 2> /dev/null <<\_ASEOF
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in
+ *posix*) set -o posix ;;
+esac
+
+fi
+
+
+:
+_ASEOF
+}; then
+ CONFIG_SHELL=$as_shell
+ as_have_required=yes
+ if { "$as_shell" 2> /dev/null <<\_ASEOF
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in
+ *posix*) set -o posix ;;
+esac
+
+fi
+
+
+:
+(as_func_return () {
+ (exit $1)
+}
+as_func_success () {
+ as_func_return 0
+}
+as_func_failure () {
+ as_func_return 1
+}
+as_func_ret_success () {
+ return 0
+}
+as_func_ret_failure () {
+ return 1
+}
+
+exitcode=0
+if as_func_success; then
+ :
+else
+ exitcode=1
+ echo as_func_success failed.
+fi
+
+if as_func_failure; then
+ exitcode=1
+ echo as_func_failure succeeded.
+fi
+
+if as_func_ret_success; then
+ :
+else
+ exitcode=1
+ echo as_func_ret_success failed.
+fi
+
+if as_func_ret_failure; then
+ exitcode=1
+ echo as_func_ret_failure succeeded.
+fi
+
+if ( set x; as_func_ret_success y && test x = "$1" ); then
+ :
+else
+ exitcode=1
+ echo positional parameters were not saved.
+fi
+
+test $exitcode = 0) || { (exit 1); exit 1; }
+
+(
+ as_lineno_1=$LINENO
+ as_lineno_2=$LINENO
+ test "x$as_lineno_1" != "x$as_lineno_2" &&
+ test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2") || { (exit 1); exit 1; }
+
+_ASEOF
+}; then
+ break
+fi
+
+fi
+
+ done
+
+ if test "x$CONFIG_SHELL" != x; then
+ for as_var in BASH_ENV ENV
+ do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
+ done
+ export CONFIG_SHELL
+ exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"}
+fi
+
+
+ if test $as_have_required = no; then
+ echo This script requires a shell more modern than all the
+ echo shells that I found on your system. Please install a
+ echo modern shell, or manually run the script under such a
+ echo shell if you do have one.
+ { (exit 1); exit 1; }
+fi
+
+
+fi
+
+fi
+
+
+
+(eval "as_func_return () {
+ (exit \$1)
+}
+as_func_success () {
+ as_func_return 0
+}
+as_func_failure () {
+ as_func_return 1
+}
+as_func_ret_success () {
+ return 0
+}
+as_func_ret_failure () {
+ return 1
+}
+
+exitcode=0
+if as_func_success; then
+ :
+else
+ exitcode=1
+ echo as_func_success failed.
+fi
+
+if as_func_failure; then
+ exitcode=1
+ echo as_func_failure succeeded.
+fi
+
+if as_func_ret_success; then
+ :
+else
+ exitcode=1
+ echo as_func_ret_success failed.
+fi
+
+if as_func_ret_failure; then
+ exitcode=1
+ echo as_func_ret_failure succeeded.
+fi
+
+if ( set x; as_func_ret_success y && test x = \"\$1\" ); then
+ :
+else
+ exitcode=1
+ echo positional parameters were not saved.
+fi
+
+test \$exitcode = 0") || {
+ echo No shell found that supports shell functions.
+ echo Please tell bug-autoconf@gnu.org about your system,
+ echo including any error possibly output before this message.
+ echo This can help us improve future autoconf versions.
+ echo Configuration will now proceed without shell functions.
+}
+
+
+
+ as_lineno_1=$LINENO
+ as_lineno_2=$LINENO
+ test "x$as_lineno_1" != "x$as_lineno_2" &&
+ test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {
+
+ # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
+ # uniformly replaced by the line number. The first 'sed' inserts a
+ # line-number line after each line using $LINENO; the second 'sed'
+ # does the real work. The second script uses 'N' to pair each
+ # line-number line with the line containing $LINENO, and appends
+ # trailing '-' during substitution so that $LINENO is not a special
+ # case at line end.
+ # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
+ # scripts with optimization help from Paolo Bonzini. Blame Lee
+ # E. McMahon (1931-1989) for sed's syntax. :-)
+ sed -n '
+ p
+ /[$]LINENO/=
+ ' <$as_myself |
+ sed '
+ s/[$]LINENO.*/&-/
+ t lineno
+ b
+ :lineno
+ N
+ :loop
+ s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
+ t loop
+ s/-\n.*//
+ ' >$as_me.lineno &&
+ chmod +x "$as_me.lineno" ||
+ { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2
+ { (exit 1); exit 1; }; }
+
+ # Don't try to exec as it changes $[0], causing all sort of problems
+ # (the dirname of $[0] is not the place where we might find the
+ # original and so on. Autoconf is especially sensitive to this).
+ . "./$as_me.lineno"
+ # Exit status is that of the last command.
+ exit
+}
+
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
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+else
+ as_dirname=false
+fi
+
+ECHO_C= ECHO_N= ECHO_T=
+case `echo -n x` in
+-n*)
+ case `echo 'x\c'` in
+ *c*) ECHO_T=' ';; # ECHO_T is single tab character.
+ *) ECHO_C='\c';;
+ esac;;
+*)
+ ECHO_N='-n';;
+esac
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+rm -f conf$$ conf$$.exe conf$$.file
+if test -d conf$$.dir; then
+ rm -f conf$$.dir/conf$$.file
+else
+ rm -f conf$$.dir
+ mkdir conf$$.dir 2>/dev/null
+fi
+if (echo >conf$$.file) 2>/dev/null; then
+ if ln -s conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s='ln -s'
+ # ... but there are two gotchas:
+ # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+ # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+ # In both cases, we have to default to `cp -p'.
+ ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+ as_ln_s='cp -p'
+ elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+ else
+ as_ln_s='cp -p'
+ fi
+else
+ as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
+rmdir conf$$.dir 2>/dev/null
+
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p=:
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+if test -x / >/dev/null 2>&1; then
+ as_test_x='test -x'
+else
+ if ls -dL / >/dev/null 2>&1; then
+ as_ls_L_option=L
+ else
+ as_ls_L_option=
+ fi
+ as_test_x='
+ eval sh -c '\''
+ if test -d "$1"; then
+ test -d "$1/.";
+ else
+ case $1 in
+ -*)set "./$1";;
+ esac;
+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in
+ ???[sx]*):;;*)false;;esac;fi
+ '\'' sh
+ '
+fi
+as_executable_p=$as_test_x
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+
+
+# Check that we are running under the correct shell.
+SHELL=${CONFIG_SHELL-/bin/sh}
+
+case X$lt_ECHO in
+X*--fallback-echo)
+ # Remove one level of quotation (which was required for Make).
+ ECHO=`echo "$lt_ECHO" | sed 's,\\\\\$\\$0,'$0','`
+ ;;
+esac
+
+ECHO=${lt_ECHO-echo}
+if test "X$1" = X--no-reexec; then
+ # Discard the --no-reexec flag, and continue.
+ shift
+elif test "X$1" = X--fallback-echo; then
+ # Avoid inline document here, it may be left over
+ :
+elif test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' ; then
+ # Yippee, $ECHO works!
+ :
+else
+ # Restart under the correct shell.
+ exec $SHELL "$0" --no-reexec ${1+"$@"}
+fi
+
+if test "X$1" = X--fallback-echo; then
+ # used as fallback echo
+ shift
+ cat <<_LT_EOF
+$*
+_LT_EOF
+ exit 0
+fi
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+if test -z "$lt_ECHO"; then
+ if test "X${echo_test_string+set}" != Xset; then
+ # find a string as large as possible, as long as the shell can cope with it
+ for cmd in 'sed 50q "$0"' 'sed 20q "$0"' 'sed 10q "$0"' 'sed 2q "$0"' 'echo test'; do
+ # expected sizes: less than 2Kb, 1Kb, 512 bytes, 16 bytes, ...
+ if { echo_test_string=`eval $cmd`; } 2>/dev/null &&
+ { test "X$echo_test_string" = "X$echo_test_string"; } 2>/dev/null
+ then
+ break
+ fi
+ done
+ fi
+
+ if test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ $ECHO "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ :
+ else
+ # The Solaris, AIX, and Digital Unix default echo programs unquote
+ # backslashes. This makes it impossible to quote backslashes using
+ # echo "$something" | sed 's/\\/\\\\/g'
+ #
+ # So, first we look for a working echo in the user's PATH.
+
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for dir in $PATH /usr/ucb; do
+ IFS="$lt_save_ifs"
+ if (test -f $dir/echo || test -f $dir/echo$ac_exeext) &&
+ test "X`($dir/echo '\t') 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`($dir/echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ ECHO="$dir/echo"
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+
+ if test "X$ECHO" = Xecho; then
+ # We didn't find a better echo, so look for alternatives.
+ if test "X`{ print -r '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ print -r "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ # This shell has a builtin print -r that does the trick.
+ ECHO='print -r'
+ elif { test -f /bin/ksh || test -f /bin/ksh$ac_exeext; } &&
+ test "X$CONFIG_SHELL" != X/bin/ksh; then
+ # If we have ksh, try running configure again with it.
+ ORIGINAL_CONFIG_SHELL=${CONFIG_SHELL-/bin/sh}
+ export ORIGINAL_CONFIG_SHELL
+ CONFIG_SHELL=/bin/ksh
+ export CONFIG_SHELL
+ exec $CONFIG_SHELL "$0" --no-reexec ${1+"$@"}
+ else
+ # Try using printf.
+ ECHO='printf %s\n'
+ if test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ $ECHO "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ # Cool, printf works
+ :
+ elif echo_testing_string=`($ORIGINAL_CONFIG_SHELL "$0" --fallback-echo '\t') 2>/dev/null` &&
+ test "X$echo_testing_string" = 'X\t' &&
+ echo_testing_string=`($ORIGINAL_CONFIG_SHELL "$0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ CONFIG_SHELL=$ORIGINAL_CONFIG_SHELL
+ export CONFIG_SHELL
+ SHELL="$CONFIG_SHELL"
+ export SHELL
+ ECHO="$CONFIG_SHELL $0 --fallback-echo"
+ elif echo_testing_string=`($CONFIG_SHELL "$0" --fallback-echo '\t') 2>/dev/null` &&
+ test "X$echo_testing_string" = 'X\t' &&
+ echo_testing_string=`($CONFIG_SHELL "$0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ ECHO="$CONFIG_SHELL $0 --fallback-echo"
+ else
+ # maybe with a smaller string...
+ prev=:
+
+ for cmd in 'echo test' 'sed 2q "$0"' 'sed 10q "$0"' 'sed 20q "$0"' 'sed 50q "$0"'; do
+ if { test "X$echo_test_string" = "X`eval $cmd`"; } 2>/dev/null
+ then
+ break
+ fi
+ prev="$cmd"
+ done
+
+ if test "$prev" != 'sed 50q "$0"'; then
+ echo_test_string=`eval $prev`
+ export echo_test_string
+ exec ${ORIGINAL_CONFIG_SHELL-${CONFIG_SHELL-/bin/sh}} "$0" ${1+"$@"}
+ else
+ # Oops. We lost completely, so just stick with echo.
+ ECHO=echo
+ fi
+ fi
+ fi
+ fi
+ fi
+fi
+
+# Copy echo and quote the copy suitably for passing to libtool from
+# the Makefile, instead of quoting the original, which is used later.
+lt_ECHO=$ECHO
+if test "X$lt_ECHO" = "X$CONFIG_SHELL $0 --fallback-echo"; then
+ lt_ECHO="$CONFIG_SHELL \\\$\$0 --fallback-echo"
+fi
+
+
+
+
+exec 7<&0 </dev/null 6>&1
+
+# Name of the host.
+# hostname on some systems (SVR3.2, Linux) returns a bogus exit status,
+# so uname gets run too.
+ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`
+
+#
+# Initializations.
+#
+ac_default_prefix=/usr/local
+ac_clean_files=
+ac_config_libobj_dir=.
+LIBOBJS=
+cross_compiling=no
+subdirs=
+MFLAGS=
+MAKEFLAGS=
+SHELL=${CONFIG_SHELL-/bin/sh}
+
+# Identity of this package.
+PACKAGE_NAME='Clustal Omega'
+PACKAGE_TARNAME='clustal-omega'
+PACKAGE_VERSION='1.0.2'
+PACKAGE_STRING='Clustal Omega 1.0.2'
+PACKAGE_BUGREPORT='clustalw@ucd.ie'
+
+# Factoring default headers for most tests.
+ac_includes_default="\
+#include <stdio.h>
+#ifdef HAVE_SYS_TYPES_H
+# include <sys/types.h>
+#endif
+#ifdef HAVE_SYS_STAT_H
+# include <sys/stat.h>
+#endif
+#ifdef STDC_HEADERS
+# include <stdlib.h>
+# include <stddef.h>
+#else
+# ifdef HAVE_STDLIB_H
+# include <stdlib.h>
+# endif
+#endif
+#ifdef HAVE_STRING_H
+# if !defined STDC_HEADERS && defined HAVE_MEMORY_H
+# include <memory.h>
+# endif
+# include <string.h>
+#endif
+#ifdef HAVE_STRINGS_H
+# include <strings.h>
+#endif
+#ifdef HAVE_INTTYPES_H
+# include <inttypes.h>
+#endif
+#ifdef HAVE_STDINT_H
+# include <stdint.h>
+#endif
+#ifdef HAVE_UNISTD_H
+# include <unistd.h>
+#endif"
+
+ac_subst_vars='LTLIBOBJS
+LIBOBJS
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+AM_CXXFLAGS
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+CXXCPP
+am__fastdepCXX_FALSE
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+CXXDEPMODE
+ac_ct_CXX
+CXXFLAGS
+CXX
+OTOOL64
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+NMEDIT
+DSYMUTIL
+lt_ECHO
+RANLIB
+AR
+OBJDUMP
+LN_S
+NM
+ac_ct_DUMPBIN
+DUMPBIN
+LD
+FGREP
+SED
+LIBTOOL
+host_os
+host_vendor
+host_cpu
+host
+build_os
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+build_cpu
+build
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+GREP
+CPP
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+am__fastdepCC_TRUE
+CCDEPMODE
+AMDEPBACKSLASH
+AMDEP_FALSE
+AMDEP_TRUE
+am__quote
+am__include
+DEPDIR
+OBJEXT
+EXEEXT
+ac_ct_CC
+CPPFLAGS
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+CC
+am__untar
+am__tar
+AMTAR
+am__leading_dot
+SET_MAKE
+AWK
+mkdir_p
+MKDIR_P
+INSTALL_STRIP_PROGRAM
+STRIP
+install_sh
+MAKEINFO
+AUTOHEADER
+AUTOMAKE
+AUTOCONF
+ACLOCAL
+VERSION
+PACKAGE
+CYGPATH_W
+am__isrc
+INSTALL_DATA
+INSTALL_SCRIPT
+INSTALL_PROGRAM
+PACKAGE_CODENAME
+target_alias
+host_alias
+build_alias
+LIBS
+ECHO_T
+ECHO_N
+ECHO_C
+DEFS
+mandir
+localedir
+libdir
+psdir
+pdfdir
+dvidir
+htmldir
+infodir
+docdir
+oldincludedir
+includedir
+localstatedir
+sharedstatedir
+sysconfdir
+datadir
+datarootdir
+libexecdir
+sbindir
+bindir
+program_transform_name
+prefix
+exec_prefix
+PACKAGE_BUGREPORT
+PACKAGE_STRING
+PACKAGE_VERSION
+PACKAGE_TARNAME
+PACKAGE_NAME
+PATH_SEPARATOR
+SHELL'
+ac_subst_files=''
+ac_user_opts='
+enable_option_checking
+enable_dependency_tracking
+enable_shared
+enable_static
+with_pic
+enable_fast_install
+with_gnu_ld
+enable_libtool_lock
+with_openmp
+with_dmalloc
+enable_debug
+'
+ ac_precious_vars='build_alias
+host_alias
+target_alias
+CC
+CFLAGS
+LDFLAGS
+LIBS
+CPPFLAGS
+CPP
+CXX
+CXXFLAGS
+CCC
+CXXCPP'
+
+
+# Initialize some variables set by options.
+ac_init_help=
+ac_init_version=false
+ac_unrecognized_opts=
+ac_unrecognized_sep=
+# The variables have the same names as the options, with
+# dashes changed to underlines.
+cache_file=/dev/null
+exec_prefix=NONE
+no_create=
+no_recursion=
+prefix=NONE
+program_prefix=NONE
+program_suffix=NONE
+program_transform_name=s,x,x,
+silent=
+site=
+srcdir=
+verbose=
+x_includes=NONE
+x_libraries=NONE
+
+# Installation directory options.
+# These are left unexpanded so users can "make install exec_prefix=/foo"
+# and all the variables that are supposed to be based on exec_prefix
+# by default will actually change.
+# Use braces instead of parens because sh, perl, etc. also accept them.
+# (The list follows the same order as the GNU Coding Standards.)
+bindir='${exec_prefix}/bin'
+sbindir='${exec_prefix}/sbin'
+libexecdir='${exec_prefix}/libexec'
+datarootdir='${prefix}/share'
+datadir='${datarootdir}'
+sysconfdir='${prefix}/etc'
+sharedstatedir='${prefix}/com'
+localstatedir='${prefix}/var'
+includedir='${prefix}/include'
+oldincludedir='/usr/include'
+docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
+infodir='${datarootdir}/info'
+htmldir='${docdir}'
+dvidir='${docdir}'
+pdfdir='${docdir}'
+psdir='${docdir}'
+libdir='${exec_prefix}/lib'
+localedir='${datarootdir}/locale'
+mandir='${datarootdir}/man'
+
+ac_prev=
+ac_dashdash=
+for ac_option
+do
+ # If the previous option needs an argument, assign it.
+ if test -n "$ac_prev"; then
+ eval $ac_prev=\$ac_option
+ ac_prev=
+ continue
+ fi
+
+ case $ac_option in
+ *=*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
+ *) ac_optarg=yes ;;
+ esac
+
+ # Accept the important Cygnus configure options, so we can diagnose typos.
+
+ case $ac_dashdash$ac_option in
+ --)
+ ac_dashdash=yes ;;
+
+ -bindir | --bindir | --bindi | --bind | --bin | --bi)
+ ac_prev=bindir ;;
+ -bindir=* | --bindir=* | --bindi=* | --bind=* | --bin=* | --bi=*)
+ bindir=$ac_optarg ;;
+
+ -build | --build | --buil | --bui | --bu)
+ ac_prev=build_alias ;;
+ -build=* | --build=* | --buil=* | --bui=* | --bu=*)
+ build_alias=$ac_optarg ;;
+
+ -cache-file | --cache-file | --cache-fil | --cache-fi \
+ | --cache-f | --cache- | --cache | --cach | --cac | --ca | --c)
+ ac_prev=cache_file ;;
+ -cache-file=* | --cache-file=* | --cache-fil=* | --cache-fi=* \
+ | --cache-f=* | --cache-=* | --cache=* | --cach=* | --cac=* | --ca=* | --c=*)
+ cache_file=$ac_optarg ;;
+
+ --config-cache | -C)
+ cache_file=config.cache ;;
+
+ -datadir | --datadir | --datadi | --datad)
+ ac_prev=datadir ;;
+ -datadir=* | --datadir=* | --datadi=* | --datad=*)
+ datadir=$ac_optarg ;;
+
+ -datarootdir | --datarootdir | --datarootdi | --datarootd | --dataroot \
+ | --dataroo | --dataro | --datar)
+ ac_prev=datarootdir ;;
+ -datarootdir=* | --datarootdir=* | --datarootdi=* | --datarootd=* \
+ | --dataroot=* | --dataroo=* | --dataro=* | --datar=*)
+ datarootdir=$ac_optarg ;;
+
+ -disable-* | --disable-*)
+ ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ { $as_echo "$as_me: error: invalid feature name: $ac_useropt" >&2
+ { (exit 1); exit 1; }; }
+ ac_useropt_orig=$ac_useropt
+ ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
+ case $ac_user_opts in
+ *"
+"enable_$ac_useropt"
+"*) ;;
+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--disable-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
+ esac
+ eval enable_$ac_useropt=no ;;
+
+ -docdir | --docdir | --docdi | --doc | --do)
+ ac_prev=docdir ;;
+ -docdir=* | --docdir=* | --docdi=* | --doc=* | --do=*)
+ docdir=$ac_optarg ;;
+
+ -dvidir | --dvidir | --dvidi | --dvid | --dvi | --dv)
+ ac_prev=dvidir ;;
+ -dvidir=* | --dvidir=* | --dvidi=* | --dvid=* | --dvi=* | --dv=*)
+ dvidir=$ac_optarg ;;
+
+ -enable-* | --enable-*)
+ ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
+ # Reject names that are not valid shell variable names.
+ expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null &&
+ { $as_echo "$as_me: error: invalid feature name: $ac_useropt" >&2
+ { (exit 1); exit 1; }; }
+ ac_useropt_orig=$ac_useropt
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+
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+ -program-suffix | --program-suffix | --program-suffi | --program-suff \
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+ ac_prev=sbindir ;;
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+ -sharedstatedir | --sharedstatedir | --sharedstatedi \
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+ ac_prev=sharedstatedir ;;
+ -sharedstatedir=* | --sharedstatedir=* | --sharedstatedi=* \
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+ -sysconfdir | --sysconfdir | --sysconfdi | --sysconfd | --sysconf \
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+ ac_prev=sysconfdir ;;
+ -sysconfdir=* | --sysconfdir=* | --sysconfdi=* | --sysconfd=* | --sysconf=* \
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+ sysconfdir=$ac_optarg ;;
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+ *) ac_unrecognized_opts="$ac_unrecognized_opts$ac_unrecognized_sep--without-$ac_useropt_orig"
+ ac_unrecognized_sep=', ';;
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+ eval with_$ac_useropt=no ;;
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+ --x)
+ # Obsolete; use --with-x.
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+ x_includes=$ac_optarg ;;
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+ -x-libraries=* | --x-libraries=* | --x-librarie=* | --x-librari=* \
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+ { (exit 1); exit 1; }; }
+ eval $ac_envvar=\$ac_optarg
+ export $ac_envvar ;;
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+ *)
+ # FIXME: should be removed in autoconf 3.0.
+ $as_echo "$as_me: WARNING: you should use --build, --host, --target" >&2
+ expr "x$ac_option" : ".*[^-._$as_cr_alnum]" >/dev/null &&
+ $as_echo "$as_me: WARNING: invalid host type: $ac_option" >&2
+ : ${build_alias=$ac_option} ${host_alias=$ac_option} ${target_alias=$ac_option}
+ ;;
+
+ esac
+done
+
+if test -n "$ac_prev"; then
+ ac_option=--`echo $ac_prev | sed 's/_/-/g'`
+ { $as_echo "$as_me: error: missing argument to $ac_option" >&2
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+if test -n "$ac_unrecognized_opts"; then
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+ fatal) { $as_echo "$as_me: error: unrecognized options: $ac_unrecognized_opts" >&2
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+ *) $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;;
+ esac
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+
+# Check all directory arguments for consistency.
+for ac_var in exec_prefix prefix bindir sbindir libexecdir datarootdir \
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+ eval ac_val=\$$ac_var
+ # Remove trailing slashes.
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+
+# There might be people who depend on the old broken behavior: `$host'
+# used to hold the argument of --host etc.
+# FIXME: To remove some day.
+build=$build_alias
+host=$host_alias
+target=$target_alias
+
+# FIXME: To remove some day.
+if test "x$host_alias" != x; then
+ if test "x$build_alias" = x; then
+ cross_compiling=maybe
+ $as_echo "$as_me: WARNING: If you wanted to set the --build type, don't use --host.
+ If a cross compiler is detected then cross compile mode will be used." >&2
+ elif test "x$build_alias" != "x$host_alias"; then
+ cross_compiling=yes
+ fi
+fi
+
+ac_tool_prefix=
+test -n "$host_alias" && ac_tool_prefix=$host_alias-
+
+test "$silent" = yes && exec 6>/dev/null
+
+
+ac_pwd=`pwd` && test -n "$ac_pwd" &&
+ac_ls_di=`ls -di .` &&
+ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` ||
+ { $as_echo "$as_me: error: working directory cannot be determined" >&2
+ { (exit 1); exit 1; }; }
+test "X$ac_ls_di" = "X$ac_pwd_ls_di" ||
+ { $as_echo "$as_me: error: pwd does not report name of working directory" >&2
+ { (exit 1); exit 1; }; }
+
+
+# Find the source files, if location was not specified.
+if test -z "$srcdir"; then
+ ac_srcdir_defaulted=yes
+ # Try the directory containing this script, then the parent directory.
+ ac_confdir=`$as_dirname -- "$as_myself" ||
+$as_expr X"$as_myself" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
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+ X"$as_myself" : 'X\(//\)$' \| \
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+ s//\1/
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+ s/.*/./; q'`
+ srcdir=$ac_confdir
+ if test ! -r "$srcdir/$ac_unique_file"; then
+ srcdir=..
+ fi
+else
+ ac_srcdir_defaulted=no
+fi
+if test ! -r "$srcdir/$ac_unique_file"; then
+ test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .."
+ { $as_echo "$as_me: error: cannot find sources ($ac_unique_file) in $srcdir" >&2
+ { (exit 1); exit 1; }; }
+fi
+ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work"
+ac_abs_confdir=`(
+ cd "$srcdir" && test -r "./$ac_unique_file" || { $as_echo "$as_me: error: $ac_msg" >&2
+ { (exit 1); exit 1; }; }
+ pwd)`
+# When building in place, set srcdir=.
+if test "$ac_abs_confdir" = "$ac_pwd"; then
+ srcdir=.
+fi
+# Remove unnecessary trailing slashes from srcdir.
+# Double slashes in file names in object file debugging info
+# mess up M-x gdb in Emacs.
+case $srcdir in
+*/) srcdir=`expr "X$srcdir" : 'X\(.*[^/]\)' \| "X$srcdir" : 'X\(.*\)'`;;
+esac
+for ac_var in $ac_precious_vars; do
+ eval ac_env_${ac_var}_set=\${${ac_var}+set}
+ eval ac_env_${ac_var}_value=\$${ac_var}
+ eval ac_cv_env_${ac_var}_set=\${${ac_var}+set}
+ eval ac_cv_env_${ac_var}_value=\$${ac_var}
+done
+
+#
+# Report the --help message.
+#
+if test "$ac_init_help" = "long"; then
+ # Omit some internal or obsolete options to make the list less imposing.
+ # This message is too long to be a string in the A/UX 3.1 sh.
+ cat <<_ACEOF
+\`configure' configures Clustal Omega 1.0.2 to adapt to many kinds of systems.
+
+Usage: $0 [OPTION]... [VAR=VALUE]...
+
+To assign environment variables (e.g., CC, CFLAGS...), specify them as
+VAR=VALUE. See below for descriptions of some of the useful variables.
+
+Defaults for the options are specified in brackets.
+
+Configuration:
+ -h, --help display this help and exit
+ --help=short display options specific to this package
+ --help=recursive display the short help of all the included packages
+ -V, --version display version information and exit
+ -q, --quiet, --silent do not print \`checking...' messages
+ --cache-file=FILE cache test results in FILE [disabled]
+ -C, --config-cache alias for \`--cache-file=config.cache'
+ -n, --no-create do not create output files
+ --srcdir=DIR find the sources in DIR [configure dir or \`..']
+
+Installation directories:
+ --prefix=PREFIX install architecture-independent files in PREFIX
+ [$ac_default_prefix]
+ --exec-prefix=EPREFIX install architecture-dependent files in EPREFIX
+ [PREFIX]
+
+By default, \`make install' will install all the files in
+\`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc. You can specify
+an installation prefix other than \`$ac_default_prefix' using \`--prefix',
+for instance \`--prefix=\$HOME'.
+
+For better control, use the options below.
+
+Fine tuning of the installation directories:
+ --bindir=DIR user executables [EPREFIX/bin]
+ --sbindir=DIR system admin executables [EPREFIX/sbin]
+ --libexecdir=DIR program executables [EPREFIX/libexec]
+ --sysconfdir=DIR read-only single-machine data [PREFIX/etc]
+ --sharedstatedir=DIR modifiable architecture-independent data [PREFIX/com]
+ --localstatedir=DIR modifiable single-machine data [PREFIX/var]
+ --libdir=DIR object code libraries [EPREFIX/lib]
+ --includedir=DIR C header files [PREFIX/include]
+ --oldincludedir=DIR C header files for non-gcc [/usr/include]
+ --datarootdir=DIR read-only arch.-independent data root [PREFIX/share]
+ --datadir=DIR read-only architecture-independent data [DATAROOTDIR]
+ --infodir=DIR info documentation [DATAROOTDIR/info]
+ --localedir=DIR locale-dependent data [DATAROOTDIR/locale]
+ --mandir=DIR man documentation [DATAROOTDIR/man]
+ --docdir=DIR documentation root [DATAROOTDIR/doc/clustal-omega]
+ --htmldir=DIR html documentation [DOCDIR]
+ --dvidir=DIR dvi documentation [DOCDIR]
+ --pdfdir=DIR pdf documentation [DOCDIR]
+ --psdir=DIR ps documentation [DOCDIR]
+_ACEOF
+
+ cat <<\_ACEOF
+
+Program names:
+ --program-prefix=PREFIX prepend PREFIX to installed program names
+ --program-suffix=SUFFIX append SUFFIX to installed program names
+ --program-transform-name=PROGRAM run sed PROGRAM on installed program names
+
+System types:
+ --build=BUILD configure for building on BUILD [guessed]
+ --host=HOST cross-compile to build programs to run on HOST [BUILD]
+_ACEOF
+fi
+
+if test -n "$ac_init_help"; then
+ case $ac_init_help in
+ short | recursive ) echo "Configuration of Clustal Omega 1.0.2:";;
+ esac
+ cat <<\_ACEOF
+
+Optional Features:
+ --disable-option-checking ignore unrecognized --enable/--with options
+ --disable-FEATURE do not include FEATURE (same as --enable-FEATURE=no)
+ --enable-FEATURE[=ARG] include FEATURE [ARG=yes]
+ --disable-dependency-tracking speeds up one-time build
+ --enable-dependency-tracking do not reject slow dependency extractors
+ --enable-shared[=PKGS] build shared libraries [default=yes]
+ --enable-static[=PKGS] build static libraries [default=yes]
+ --enable-fast-install[=PKGS]
+ optimize for fast installation [default=yes]
+ --disable-libtool-lock avoid locking (might break parallel builds)
+ --enable-debug Enable debugging (default=no)
+
+Optional Packages:
+ --with-PACKAGE[=ARG] use PACKAGE [ARG=yes]
+ --without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no)
+ --with-pic try to use only PIC/non-PIC objects [default=use
+ both]
+ --with-gnu-ld assume the C compiler uses GNU ld [default=no]
+ --without-openmp Do not use OpenMP
+ --with-dmalloc use dmalloc, as in
+ http://www.dmalloc.com/dmalloc.tar.gz
+
+Some influential environment variables:
+ CC C compiler command
+ CFLAGS C compiler flags
+ LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries in a
+ nonstandard directory <lib dir>
+ LIBS libraries to pass to the linker, e.g. -l<library>
+ CPPFLAGS C/C++/Objective C preprocessor flags, e.g. -I<include dir> if
+ you have headers in a nonstandard directory <include dir>
+ CPP C preprocessor
+ CXX C++ compiler command
+ CXXFLAGS C++ compiler flags
+ CXXCPP C++ preprocessor
+
+Use these variables to override the choices made by `configure' or to help
+it to find libraries and programs with nonstandard names/locations.
+
+Report bugs to <clustalw@ucd.ie>.
+_ACEOF
+ac_status=$?
+fi
+
+if test "$ac_init_help" = "recursive"; then
+ # If there are subdirs, report their specific --help.
+ for ac_dir in : $ac_subdirs_all; do test "x$ac_dir" = x: && continue
+ test -d "$ac_dir" ||
+ { cd "$srcdir" && ac_pwd=`pwd` && srcdir=. && test -d "$ac_dir"; } ||
+ continue
+ ac_builddir=.
+
+case "$ac_dir" in
+.) ac_dir_suffix= ac_top_builddir_sub=. ac_top_build_prefix= ;;
+*)
+ ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
+ # A ".." for each directory in $ac_dir_suffix.
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+ case $ac_top_builddir_sub in
+ "") ac_top_builddir_sub=. ac_top_build_prefix= ;;
+ *) ac_top_build_prefix=$ac_top_builddir_sub/ ;;
+ esac ;;
+esac
+ac_abs_top_builddir=$ac_pwd
+ac_abs_builddir=$ac_pwd$ac_dir_suffix
+# for backward compatibility:
+ac_top_builddir=$ac_top_build_prefix
+
+case $srcdir in
+ .) # We are building in place.
+ ac_srcdir=.
+ ac_top_srcdir=$ac_top_builddir_sub
+ ac_abs_top_srcdir=$ac_pwd ;;
+ [\\/]* | ?:[\\/]* ) # Absolute name.
+ ac_srcdir=$srcdir$ac_dir_suffix;
+ ac_top_srcdir=$srcdir
+ ac_abs_top_srcdir=$srcdir ;;
+ *) # Relative name.
+ ac_srcdir=$ac_top_build_prefix$srcdir$ac_dir_suffix
+ ac_top_srcdir=$ac_top_build_prefix$srcdir
+ ac_abs_top_srcdir=$ac_pwd/$srcdir ;;
+esac
+ac_abs_srcdir=$ac_abs_top_srcdir$ac_dir_suffix
+
+ cd "$ac_dir" || { ac_status=$?; continue; }
+ # Check for guested configure.
+ if test -f "$ac_srcdir/configure.gnu"; then
+ echo &&
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+ elif test -f "$ac_srcdir/configure"; then
+ echo &&
+ $SHELL "$ac_srcdir/configure" --help=recursive
+ else
+ $as_echo "$as_me: WARNING: no configuration information is in $ac_dir" >&2
+ fi || ac_status=$?
+ cd "$ac_pwd" || { ac_status=$?; break; }
+ done
+fi
+
+test -n "$ac_init_help" && exit $ac_status
+if $ac_init_version; then
+ cat <<\_ACEOF
+Clustal Omega configure 1.0.2
+generated by GNU Autoconf 2.63
+
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
+2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+This configure script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it.
+_ACEOF
+ exit
+fi
+cat >config.log <<_ACEOF
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
+
+It was created by Clustal Omega $as_me 1.0.2, which was
+generated by GNU Autoconf 2.63. Invocation command line was
+
+ $ $0 $@
+
+_ACEOF
+exec 5>>config.log
+{
+cat <<_ASUNAME
+## --------- ##
+## Platform. ##
+## --------- ##
+
+hostname = `(hostname || uname -n) 2>/dev/null | sed 1q`
+uname -m = `(uname -m) 2>/dev/null || echo unknown`
+uname -r = `(uname -r) 2>/dev/null || echo unknown`
+uname -s = `(uname -s) 2>/dev/null || echo unknown`
+uname -v = `(uname -v) 2>/dev/null || echo unknown`
+
+/usr/bin/uname -p = `(/usr/bin/uname -p) 2>/dev/null || echo unknown`
+/bin/uname -X = `(/bin/uname -X) 2>/dev/null || echo unknown`
+
+/bin/arch = `(/bin/arch) 2>/dev/null || echo unknown`
+/usr/bin/arch -k = `(/usr/bin/arch -k) 2>/dev/null || echo unknown`
+/usr/convex/getsysinfo = `(/usr/convex/getsysinfo) 2>/dev/null || echo unknown`
+/usr/bin/hostinfo = `(/usr/bin/hostinfo) 2>/dev/null || echo unknown`
+/bin/machine = `(/bin/machine) 2>/dev/null || echo unknown`
+/usr/bin/oslevel = `(/usr/bin/oslevel) 2>/dev/null || echo unknown`
+/bin/universe = `(/bin/universe) 2>/dev/null || echo unknown`
+
+_ASUNAME
+
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ $as_echo "PATH: $as_dir"
+done
+IFS=$as_save_IFS
+
+} >&5
+
+cat >&5 <<_ACEOF
+
+
+## ----------- ##
+## Core tests. ##
+## ----------- ##
+
+_ACEOF
+
+
+# Keep a trace of the command line.
+# Strip out --no-create and --no-recursion so they do not pile up.
+# Strip out --silent because we don't want to record it for future runs.
+# Also quote any args containing shell meta-characters.
+# Make two passes to allow for proper duplicate-argument suppression.
+ac_configure_args=
+ac_configure_args0=
+ac_configure_args1=
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+for ac_pass in 1 2
+do
+ for ac_arg
+ do
+ case $ac_arg in
+ -no-create | --no-c* | -n | -no-recursion | --no-r*) continue ;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil)
+ continue ;;
+ *\'*)
+ ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ case $ac_pass in
+ 1) ac_configure_args0="$ac_configure_args0 '$ac_arg'" ;;
+ 2)
+ ac_configure_args1="$ac_configure_args1 '$ac_arg'"
+ if test $ac_must_keep_next = true; then
+ ac_must_keep_next=false # Got value, back to normal.
+ else
+ case $ac_arg in
+ *=* | --config-cache | -C | -disable-* | --disable-* \
+ | -enable-* | --enable-* | -gas | --g* | -nfp | --nf* \
+ | -q | -quiet | --q* | -silent | --sil* | -v | -verb* \
+ | -with-* | --with-* | -without-* | --without-* | --x)
+ case "$ac_configure_args0 " in
+ "$ac_configure_args1"*" '$ac_arg' "* ) continue ;;
+ esac
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+ -* ) ac_must_keep_next=true ;;
+ esac
+ fi
+ ac_configure_args="$ac_configure_args '$ac_arg'"
+ ;;
+ esac
+ done
+done
+$as_unset ac_configure_args0 || test "${ac_configure_args0+set}" != set || { ac_configure_args0=; export ac_configure_args0; }
+$as_unset ac_configure_args1 || test "${ac_configure_args1+set}" != set || { ac_configure_args1=; export ac_configure_args1; }
+
+# When interrupted or exit'd, cleanup temporary files, and complete
+# config.log. We remove comments because anyway the quotes in there
+# would cause problems or look ugly.
+# WARNING: Use '\'' to represent an apostrophe within the trap.
+# WARNING: Do not start the trap code with a newline, due to a FreeBSD 4.0 bug.
+trap 'exit_status=$?
+ # Save into config.log some information that might help in debugging.
+ {
+ echo
+
+ cat <<\_ASBOX
+## ---------------- ##
+## Cache variables. ##
+## ---------------- ##
+_ASBOX
+ echo
+ # The following way of writing the cache mishandles newlines in values,
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+ *${as_nl}*)
+ case $ac_var in #(
+ *_cv_*) { $as_echo "$as_me:$LINENO: WARNING: cache variable $ac_var contains a newline" >&5
+$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
+ esac
+ case $ac_var in #(
+ _ | IFS | as_nl) ;; #(
+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
+ *) $as_unset $ac_var ;;
+ esac ;;
+ esac
+ done
+ (set) 2>&1 |
+ case $as_nl`(ac_space='\'' '\''; set) 2>&1` in #(
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+ sed -n \
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+ ;; #(
+ *)
+ sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+ ;;
+ esac |
+ sort
+)
+ echo
+
+ cat <<\_ASBOX
+## ----------------- ##
+## Output variables. ##
+## ----------------- ##
+_ASBOX
+ echo
+ for ac_var in $ac_subst_vars
+ do
+ eval ac_val=\$$ac_var
+ case $ac_val in
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+ esac
+ $as_echo "$ac_var='\''$ac_val'\''"
+ done | sort
+ echo
+
+ if test -n "$ac_subst_files"; then
+ cat <<\_ASBOX
+## ------------------- ##
+## File substitutions. ##
+## ------------------- ##
+_ASBOX
+ echo
+ for ac_var in $ac_subst_files
+ do
+ eval ac_val=\$$ac_var
+ case $ac_val in
+ *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
+ esac
+ $as_echo "$ac_var='\''$ac_val'\''"
+ done | sort
+ echo
+ fi
+
+ if test -s confdefs.h; then
+ cat <<\_ASBOX
+## ----------- ##
+## confdefs.h. ##
+## ----------- ##
+_ASBOX
+ echo
+ cat confdefs.h
+ echo
+ fi
+ test "$ac_signal" != 0 &&
+ $as_echo "$as_me: caught signal $ac_signal"
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+' 0
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+ trap 'ac_signal='$ac_signal'; { (exit 1); exit 1; }' $ac_signal
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+ac_signal=0
+
+# confdefs.h avoids OS command line length limits that DEFS can exceed.
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+
+# Predefined preprocessor variables.
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_NAME "$PACKAGE_NAME"
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_TARNAME "$PACKAGE_TARNAME"
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_VERSION "$PACKAGE_VERSION"
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_STRING "$PACKAGE_STRING"
+_ACEOF
+
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT"
+_ACEOF
+
+
+# Let the site file select an alternate cache file if it wants to.
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+ac_site_file2=NONE
+if test -n "$CONFIG_SITE"; then
+ ac_site_file1=$CONFIG_SITE
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+ ac_site_file2=$prefix/etc/config.site
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+ ac_site_file1=$ac_default_prefix/share/config.site
+ ac_site_file2=$ac_default_prefix/etc/config.site
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+for ac_site_file in "$ac_site_file1" "$ac_site_file2"
+do
+ test "x$ac_site_file" = xNONE && continue
+ if test -r "$ac_site_file"; then
+ { $as_echo "$as_me:$LINENO: loading site script $ac_site_file" >&5
+$as_echo "$as_me: loading site script $ac_site_file" >&6;}
+ sed 's/^/| /' "$ac_site_file" >&5
+ . "$ac_site_file"
+ fi
+done
+
+if test -r "$cache_file"; then
+ # Some versions of bash will fail to source /dev/null (special
+ # files actually), so we avoid doing that.
+ if test -f "$cache_file"; then
+ { $as_echo "$as_me:$LINENO: loading cache $cache_file" >&5
+$as_echo "$as_me: loading cache $cache_file" >&6;}
+ case $cache_file in
+ [\\/]* | ?:[\\/]* ) . "$cache_file";;
+ *) . "./$cache_file";;
+ esac
+ fi
+else
+ { $as_echo "$as_me:$LINENO: creating cache $cache_file" >&5
+$as_echo "$as_me: creating cache $cache_file" >&6;}
+ >$cache_file
+fi
+
+# Check that the precious variables saved in the cache have kept the same
+# value.
+ac_cache_corrupted=false
+for ac_var in $ac_precious_vars; do
+ eval ac_old_set=\$ac_cv_env_${ac_var}_set
+ eval ac_new_set=\$ac_env_${ac_var}_set
+ eval ac_old_val=\$ac_cv_env_${ac_var}_value
+ eval ac_new_val=\$ac_env_${ac_var}_value
+ case $ac_old_set,$ac_new_set in
+ set,)
+ { $as_echo "$as_me:$LINENO: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
+$as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,set)
+ { $as_echo "$as_me:$LINENO: error: \`$ac_var' was not set in the previous run" >&5
+$as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;}
+ ac_cache_corrupted=: ;;
+ ,);;
+ *)
+ if test "x$ac_old_val" != "x$ac_new_val"; then
+ # differences in whitespace do not lead to failure.
+ ac_old_val_w=`echo x $ac_old_val`
+ ac_new_val_w=`echo x $ac_new_val`
+ if test "$ac_old_val_w" != "$ac_new_val_w"; then
+ { $as_echo "$as_me:$LINENO: error: \`$ac_var' has changed since the previous run:" >&5
+$as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;}
+ ac_cache_corrupted=:
+ else
+ { $as_echo "$as_me:$LINENO: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5
+$as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;}
+ eval $ac_var=\$ac_old_val
+ fi
+ { $as_echo "$as_me:$LINENO: former value: \`$ac_old_val'" >&5
+$as_echo "$as_me: former value: \`$ac_old_val'" >&2;}
+ { $as_echo "$as_me:$LINENO: current value: \`$ac_new_val'" >&5
+$as_echo "$as_me: current value: \`$ac_new_val'" >&2;}
+ fi;;
+ esac
+ # Pass precious variables to config.status.
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+ *\'*) ac_arg=$ac_var=`$as_echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;;
+ *) ac_arg=$ac_var=$ac_new_val ;;
+ esac
+ case " $ac_configure_args " in
+ *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy.
+ *) ac_configure_args="$ac_configure_args '$ac_arg'" ;;
+ esac
+ fi
+done
+if $ac_cache_corrupted; then
+ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+ { $as_echo "$as_me:$LINENO: error: changes in the environment can compromise the build" >&5
+$as_echo "$as_me: error: changes in the environment can compromise the build" >&2;}
+ { { $as_echo "$as_me:$LINENO: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&5
+$as_echo "$as_me: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&2;}
+ { (exit 1); exit 1; }; }
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
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+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+PACKAGE_CODENAME="DeshilHollesEamus"
+
+# The AC_INIT macro can take any source file as an argument. It just
+# checks that the file is there, which should, in turn, mean that the
+# source directory is there. AC_INIT generates the following m4
+# macros, output variables and preprocessor symbols:
+
+
+
+
+
+
+
+{ $as_echo "$as_me:$LINENO:
+
+ Welcome to $PACKAGE_NAME - version $PACKAGE_VERSION ($PACKAGE_CODENAME)
+
+ +NMMMMMMMMMS=
+ MMMMM? :MMMMM8
+ IMMMMS MMMMM,
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+ MMMMS MMMM,
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+ ,M7 M+ M+ :M8
+ ,MMMMMMMMMMMMI MMMMMMMMMMMM8
+ ,MMMMMMMMMMMM8 MMMMMMMMMMMM8
+ ,MMMMMMMMMMMMN MMMMMMMMMMMM8
+
+ " >&5
+$as_echo "$as_me:
+
+ Welcome to $PACKAGE_NAME - version $PACKAGE_VERSION ($PACKAGE_CODENAME)
+
+ +NMMMMMMMMMS=
+ MMMMM? :MMMMM8
+ IMMMMS MMMMM,
+ ~MMMMN ,MMMMM
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+ ,M7 M+ M+ :M8
+ ,MMMMMMMMMMMMI MMMMMMMMMMMM8
+ ,MMMMMMMMMMMM8 MMMMMMMMMMMM8
+ ,MMMMMMMMMMMMN MMMMMMMMMMMM8
+
+ " >&6;}
+#
+# Created with http://www.glassgiant.com/ascii/ and Wikipedia's Omega
+# Replaced all dollars with S's.
+#
+#
+# ,MMMMMMMMMD: MMMMM
+# NMMMMMMMMMMMMMM+ SMMMM
+# DMMMMMMMMMMMMMMMMMM, +MMMM
+# MMMMMMMMM8ZSO8MMMMMMMM +MMMM
+# MMMMM7 SMMMM +MMMM
+# MMMO MM? +MMMM
+# ?MMI NMIIMMMM
+# MMM MMMMMMM
+# MM
+# MN
+# MD
+# MM
+# MM? ,~+ISON
+# =MMI MMSOMMMM
+# MMMZ MMS +MMMM
+# MMMM8: :NMMM +MMMM
+# MMMMMMMMMDOODMMMMMMMMM +MMMM
+# MMMMMMMMMMMMMMMMMMMM +MMMM
+# OMMMMMMMMMMMMMMZ SMMMM
+# MMMMMMMMMM+ MMMMM
+#
+
+
+# AC_MSG_NOTICE([Configuring for your system...])
+
+ # 2.60 needed for AC_USE_SYSTEM_EXTENSIONS
+# consider 2.64 which allows to define a URL as well
+
+# The AM_INIT_AUTOMAKE line adds several standard checks.
+# This macro is always needed for automake
+# Obsolete: It takes the program name and version number as arguments.
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+
+ac_aux_dir=
+for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do
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+ break
+ elif test -f "$ac_dir/install.sh"; then
+ ac_aux_dir=$ac_dir
+ ac_install_sh="$ac_aux_dir/install.sh -c"
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+ elif test -f "$ac_dir/shtool"; then
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+ ac_install_sh="$ac_aux_dir/shtool install -c"
+ break
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+if test -z "$ac_aux_dir"; then
+ { { $as_echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" >&5
+$as_echo "$as_me: error: cannot find install-sh or install.sh in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" >&2;}
+ { (exit 1); exit 1; }; }
+fi
+
+# These three variables are undocumented and unsupported,
+# and are intended to be withdrawn in a future Autoconf release.
+# They can cause serious problems if a builder's source tree is in a directory
+# whose full name contains unusual characters.
+ac_config_guess="$SHELL $ac_aux_dir/config.guess" # Please don't use this var.
+ac_config_sub="$SHELL $ac_aux_dir/config.sub" # Please don't use this var.
+ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var.
+
+
+# Find a good install program. We prefer a C program (faster),
+# so one script is as good as another. But avoid the broken or
+# incompatible versions:
+# SysV /etc/install, /usr/sbin/install
+# SunOS /usr/etc/install
+# IRIX /sbin/install
+# AIX /bin/install
+# AmigaOS /C/install, which installs bootblocks on floppy discs
+# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
+# AFS /usr/afsws/bin/install, which mishandles nonexistent args
+# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
+# OS/2's system install, which has a completely different semantic
+# ./install, which can be erroneously created by make from ./install.sh.
+# Reject install programs that cannot install multiple files.
+{ $as_echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5
+$as_echo_n "checking for a BSD-compatible install... " >&6; }
+if test -z "$INSTALL"; then
+if test "${ac_cv_path_install+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ # Account for people who put trailing slashes in PATH elements.
+case $as_dir/ in
+ ./ | .// | /cC/* | \
+ /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
+ ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \
+ /usr/ucb/* ) ;;
+ *)
+ # OSF1 and SCO ODT 3.0 have their own names for install.
+ # Don't use installbsd from OSF since it installs stuff as root
+ # by default.
+ for ac_prog in ginstall scoinst install; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
+ if test $ac_prog = install &&
+ grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # AIX install. It has an incompatible calling convention.
+ :
+ elif test $ac_prog = install &&
+ grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # program-specific install script used by HP pwplus--don't use.
+ :
+ else
+ rm -rf conftest.one conftest.two conftest.dir
+ echo one > conftest.one
+ echo two > conftest.two
+ mkdir conftest.dir
+ if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" &&
+ test -s conftest.one && test -s conftest.two &&
+ test -s conftest.dir/conftest.one &&
+ test -s conftest.dir/conftest.two
+ then
+ ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
+ break 3
+ fi
+ fi
+ fi
+ done
+ done
+ ;;
+esac
+
+done
+IFS=$as_save_IFS
+
+rm -rf conftest.one conftest.two conftest.dir
+
+fi
+ if test "${ac_cv_path_install+set}" = set; then
+ INSTALL=$ac_cv_path_install
+ else
+ # As a last resort, use the slow shell script. Don't cache a
+ # value for INSTALL within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the value is a relative name.
+ INSTALL=$ac_install_sh
+ fi
+fi
+{ $as_echo "$as_me:$LINENO: result: $INSTALL" >&5
+$as_echo "$INSTALL" >&6; }
+
+# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
+# It thinks the first close brace ends the variable substitution.
+test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
+
+test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
+
+test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
+
+{ $as_echo "$as_me:$LINENO: checking whether build environment is sane" >&5
+$as_echo_n "checking whether build environment is sane... " >&6; }
+# Just in case
+sleep 1
+echo timestamp > conftest.file
+# Do `set' in a subshell so we don't clobber the current shell's
+# arguments. Must try -L first in case configure is actually a
+# symlink; some systems play weird games with the mod time of symlinks
+# (eg FreeBSD returns the mod time of the symlink's containing
+# directory).
+if (
+ set X `ls -Lt $srcdir/configure conftest.file 2> /dev/null`
+ if test "$*" = "X"; then
+ # -L didn't work.
+ set X `ls -t $srcdir/configure conftest.file`
+ fi
+ rm -f conftest.file
+ if test "$*" != "X $srcdir/configure conftest.file" \
+ && test "$*" != "X conftest.file $srcdir/configure"; then
+
+ # If neither matched, then we have a broken ls. This can happen
+ # if, for instance, CONFIG_SHELL is bash and it inherits a
+ # broken ls alias from the environment. This has actually
+ # happened. Such a system could not be considered "sane".
+ { { $as_echo "$as_me:$LINENO: error: ls -t appears to fail. Make sure there is not a broken
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+$as_echo "$as_me: error: ls -t appears to fail. Make sure there is not a broken
+alias in your environment" >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+
+ test "$2" = conftest.file
+ )
+then
+ # Ok.
+ :
+else
+ { { $as_echo "$as_me:$LINENO: error: newly created file is older than distributed files!
+Check your system clock" >&5
+$as_echo "$as_me: error: newly created file is older than distributed files!
+Check your system clock" >&2;}
+ { (exit 1); exit 1; }; }
+fi
+{ $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+test "$program_prefix" != NONE &&
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+# Use a double $ so make ignores it.
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+# Double any \ or $.
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+ac_script='s/[\\$]/&&/g;s/;s,x,x,$//'
+program_transform_name=`$as_echo "$program_transform_name" | sed "$ac_script"`
+
+# expand $ac_aux_dir to an absolute path
+am_aux_dir=`cd $ac_aux_dir && pwd`
+
+test x"${MISSING+set}" = xset || MISSING="\${SHELL} $am_aux_dir/missing"
+# Use eval to expand $SHELL
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+ am_missing_run="$MISSING --run "
+else
+ am_missing_run=
+ { $as_echo "$as_me:$LINENO: WARNING: \`missing' script is too old or missing" >&5
+$as_echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;}
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+
+{ $as_echo "$as_me:$LINENO: checking for a thread-safe mkdir -p" >&5
+$as_echo_n "checking for a thread-safe mkdir -p... " >&6; }
+if test -z "$MKDIR_P"; then
+ if test "${ac_cv_path_mkdir+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/opt/sfw/bin
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+ done
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+ if test "${ac_cv_path_mkdir+set}" = set; then
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+ # As a last resort, use the slow shell script. Don't cache a
+ # value for MKDIR_P within a source directory, because that will
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+ # removed, or if the value is a relative name.
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+ MKDIR_P="$ac_install_sh -d"
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+{ $as_echo "$as_me:$LINENO: result: $MKDIR_P" >&5
+$as_echo "$MKDIR_P" >&6; }
+
+mkdir_p="$MKDIR_P"
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+ */*) mkdir_p="\$(top_builddir)/$mkdir_p" ;;
+esac
+
+for ac_prog in gawk mawk nawk awk
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
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+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_AWK+set}" = set; then
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+else
+ if test -n "$AWK"; then
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+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+AWK=$ac_cv_prog_AWK
+if test -n "$AWK"; then
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+$as_echo "$AWK" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$AWK" && break
+done
+
+{ $as_echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5
+$as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
+set x ${MAKE-make}
+ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
+if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.make <<\_ACEOF
+SHELL = /bin/sh
+all:
+ @echo '@@@%%%=$(MAKE)=@@@%%%'
+_ACEOF
+# GNU make sometimes prints "make[1]: Entering...", which would confuse us.
+case `${MAKE-make} -f conftest.make 2>/dev/null` in
+ *@@@%%%=?*=@@@%%%*)
+ eval ac_cv_prog_make_${ac_make}_set=yes;;
+ *)
+ eval ac_cv_prog_make_${ac_make}_set=no;;
+esac
+rm -f conftest.make
+fi
+if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+ SET_MAKE=
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+ SET_MAKE="MAKE=${MAKE-make}"
+fi
+
+rm -rf .tst 2>/dev/null
+mkdir .tst 2>/dev/null
+if test -d .tst; then
+ am__leading_dot=.
+else
+ am__leading_dot=_
+fi
+rmdir .tst 2>/dev/null
+
+if test "`cd $srcdir && pwd`" != "`pwd`"; then
+ # Use -I$(srcdir) only when $(srcdir) != ., so that make's output
+ # is not polluted with repeated "-I."
+ am__isrc=' -I$(srcdir)'
+ # test to see if srcdir already configured
+ if test -f $srcdir/config.status; then
+ { { $as_echo "$as_me:$LINENO: error: source directory already configured; run \"make distclean\" there first" >&5
+$as_echo "$as_me: error: source directory already configured; run \"make distclean\" there first" >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+fi
+
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+ else
+ CYGPATH_W=echo
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+fi
+
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+# Define the identity of the package.
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+ VERSION='1.0.2'
+
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE "$PACKAGE"
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+
+
+cat >>confdefs.h <<_ACEOF
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+_ACEOF
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+
+
+AUTOCONF=${AUTOCONF-"${am_missing_run}autoconf"}
+
+
+AUTOMAKE=${AUTOMAKE-"${am_missing_run}automake-${am__api_version}"}
+
+
+AUTOHEADER=${AUTOHEADER-"${am_missing_run}autoheader"}
+
+
+MAKEINFO=${MAKEINFO-"${am_missing_run}makeinfo"}
+
+install_sh=${install_sh-"\$(SHELL) $am_aux_dir/install-sh"}
+
+# Installed binaries are usually stripped using `strip' when the user
+# run `make install-strip'. However `strip' might not be the right
+# tool to use in cross-compilation environments, therefore Automake
+# will honor the `STRIP' environment variable to overrule this program.
+if test "$cross_compiling" != no; then
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
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+$as_echo_n "checking for $ac_word... " >&6; }
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+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
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+IFS=$as_save_IFS
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+
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+if test -z "$ac_cv_prog_STRIP"; then
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+$as_echo_n "checking for $ac_word... " >&6; }
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+IFS=$as_save_IFS
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+$as_echo "$ac_ct_STRIP" >&6; }
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+$as_echo "no" >&6; }
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+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
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+ STRIP=$ac_ct_STRIP
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+
+fi
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+
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+
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+
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+# config header: provides a way for people to customise the
+# configuration for their platform, via #defines. config.h.in can be
+# generated automatically with the autoheader tool. However, you need
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+# config.h from config.h.in. Type 'touch stamp-h' to add this file to
+# your project.
+#
+ac_config_headers="$ac_config_headers src/config.h"
+
+
+# the following allows to install a copy config.h for libclustalo in a
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+
+ac_config_commands="$ac_config_commands src/clustal-omega-config.h"
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+
+# This macro was introduced in Autoconf 2.60. If possible, enable
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+$as_echo "$_am_result" >&6; }
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+ AMDEPBACKSLASH='\'
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+ac_compiler_gnu=$ac_cv_c_compiler_gnu
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+ break 2
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+IFS=$as_save_IFS
+
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+ac_ct_CC=$ac_cv_prog_ac_ct_CC
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+$as_echo "$ac_ct_CC" >&6; }
+else
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+$as_echo "no" >&6; }
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+ac_tool_warned=yes ;;
+esac
+ CC=$ac_ct_CC
+ fi
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+ CC="$ac_cv_prog_CC"
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+
+if test -z "$CC"; then
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+$as_echo_n "checking for $ac_word... " >&6; }
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+else
+ if test -n "$CC"; then
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+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
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+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:$LINENO: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ fi
+fi
+if test -z "$CC"; then
+ # Extract the first word of "cc", so it can be a program name with args.
+set dummy cc; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+ ac_prog_rejected=no
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
+ ac_prog_rejected=yes
+ continue
+ fi
+ ac_cv_prog_CC="cc"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+if test $ac_prog_rejected = yes; then
+ # We found a bogon in the path, so make sure we never use it.
+ set dummy $ac_cv_prog_CC
+ shift
+ if test $# != 0; then
+ # We chose a different compiler from the bogus one.
+ # However, it has the same basename, so the bogon will be chosen
+ # first if we set CC to just the basename; use the full file name.
+ shift
+ ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@"
+ fi
+fi
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:$LINENO: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in cl.exe
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:$LINENO: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CC" && break
+ done
+fi
+if test -z "$CC"; then
+ ac_ct_CC=$CC
+ for ac_prog in cl.exe
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CC="$ac_prog"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CC" && break
+done
+
+ if test "x$ac_ct_CC" = x; then
+ CC=""
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CC=$ac_ct_CC
+ fi
+fi
+
+fi
+
+
+test -z "$CC" && { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: no acceptable C compiler found in \$PATH
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
+
+# Provide some information about the compiler.
+$as_echo "$as_me:$LINENO: checking for C compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+{ (ac_try="$ac_compiler --version >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compiler --version >&5") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+{ (ac_try="$ac_compiler -v >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compiler -v >&5") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+{ (ac_try="$ac_compiler -V >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compiler -V >&5") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out"
+# Try to create an executable without -o first, disregard a.out.
+# It will help us diagnose broken compilers, and finding out an intuition
+# of exeext.
+{ $as_echo "$as_me:$LINENO: checking for C compiler default output file name" >&5
+$as_echo_n "checking for C compiler default output file name... " >&6; }
+ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
+
+# The possible output files:
+ac_files="a.out conftest.exe conftest a.exe a_out.exe b.out conftest.*"
+
+ac_rmfiles=
+for ac_file in $ac_files
+do
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
+ * ) ac_rmfiles="$ac_rmfiles $ac_file";;
+ esac
+done
+rm -f $ac_rmfiles
+
+if { (ac_try="$ac_link_default"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link_default") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
+ # Autoconf-2.13 could set the ac_cv_exeext variable to `no'.
+# So ignore a value of `no', otherwise this would lead to `EXEEXT = no'
+# in a Makefile. We should not override ac_cv_exeext if it was cached,
+# so that the user can short-circuit this test for compilers unknown to
+# Autoconf.
+for ac_file in $ac_files ''
+do
+ test -f "$ac_file" || continue
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj )
+ ;;
+ [ab].out )
+ # We found the default executable, but exeext='' is most
+ # certainly right.
+ break;;
+ *.* )
+ if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no;
+ then :; else
+ ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+ fi
+ # We set ac_cv_exeext here because the later test for it is not
+ # safe: cross compilers may not add the suffix if given an `-o'
+ # argument, so we may need to know it at that point already.
+ # Even if this section looks crufty: it has the advantage of
+ # actually working.
+ break;;
+ * )
+ break;;
+ esac
+done
+test "$ac_cv_exeext" = no && ac_cv_exeext=
+
+else
+ ac_file=''
+fi
+
+{ $as_echo "$as_me:$LINENO: result: $ac_file" >&5
+$as_echo "$ac_file" >&6; }
+if test -z "$ac_file"; then
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+{ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: C compiler cannot create executables
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: C compiler cannot create executables
+See \`config.log' for more details." >&2;}
+ { (exit 77); exit 77; }; }; }
+fi
+
+ac_exeext=$ac_cv_exeext
+
+# Check that the compiler produces executables we can run. If not, either
+# the compiler is broken, or we cross compile.
+{ $as_echo "$as_me:$LINENO: checking whether the C compiler works" >&5
+$as_echo_n "checking whether the C compiler works... " >&6; }
+# FIXME: These cross compiler hacks should be removed for Autoconf 3.0
+# If not cross compiling, check that we can run a simple program.
+if test "$cross_compiling" != yes; then
+ if { ac_try='./$ac_file'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ cross_compiling=no
+ else
+ if test "$cross_compiling" = maybe; then
+ cross_compiling=yes
+ else
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot run C compiled programs.
+If you meant to cross compile, use \`--host'.
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot run C compiled programs.
+If you meant to cross compile, use \`--host'.
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
+ fi
+ fi
+fi
+{ $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+
+rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out
+ac_clean_files=$ac_clean_files_save
+# Check that the compiler produces executables we can run. If not, either
+# the compiler is broken, or we cross compile.
+{ $as_echo "$as_me:$LINENO: checking whether we are cross compiling" >&5
+$as_echo_n "checking whether we are cross compiling... " >&6; }
+{ $as_echo "$as_me:$LINENO: result: $cross_compiling" >&5
+$as_echo "$cross_compiling" >&6; }
+
+{ $as_echo "$as_me:$LINENO: checking for suffix of executables" >&5
+$as_echo_n "checking for suffix of executables... " >&6; }
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
+ # If both `conftest.exe' and `conftest' are `present' (well, observable)
+# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will
+# work properly (i.e., refer to `conftest.exe'), while it won't with
+# `rm'.
+for ac_file in conftest.exe conftest conftest.*; do
+ test -f "$ac_file" || continue
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
+ *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
+ break;;
+ * ) break;;
+ esac
+done
+else
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot compute suffix of executables: cannot compile and link
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
+fi
+
+rm -f conftest$ac_cv_exeext
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5
+$as_echo "$ac_cv_exeext" >&6; }
+
+rm -f conftest.$ac_ext
+EXEEXT=$ac_cv_exeext
+ac_exeext=$EXEEXT
+{ $as_echo "$as_me:$LINENO: checking for suffix of object files" >&5
+$as_echo_n "checking for suffix of object files... " >&6; }
+if test "${ac_cv_objext+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.o conftest.obj
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
+ for ac_file in conftest.o conftest.obj conftest.*; do
+ test -f "$ac_file" || continue;
+ case $ac_file in
+ *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM ) ;;
+ *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'`
+ break;;
+ esac
+done
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+{ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot compute suffix of object files: cannot compile
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
+fi
+
+rm -f conftest.$ac_cv_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_objext" >&5
+$as_echo "$ac_cv_objext" >&6; }
+OBJEXT=$ac_cv_objext
+ac_objext=$OBJEXT
+{ $as_echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5
+$as_echo_n "checking whether we are using the GNU C compiler... " >&6; }
+if test "${ac_cv_c_compiler_gnu+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_compiler_gnu=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_compiler_gnu=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_c_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5
+$as_echo "$ac_cv_c_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+ GCC=yes
+else
+ GCC=
+fi
+ac_test_CFLAGS=${CFLAGS+set}
+ac_save_CFLAGS=$CFLAGS
+{ $as_echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5
+$as_echo_n "checking whether $CC accepts -g... " >&6; }
+if test "${ac_cv_prog_cc_g+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_save_c_werror_flag=$ac_c_werror_flag
+ ac_c_werror_flag=yes
+ ac_cv_prog_cc_g=no
+ CFLAGS="-g"
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_cv_prog_cc_g=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ CFLAGS=""
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ :
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_c_werror_flag=$ac_save_c_werror_flag
+ CFLAGS="-g"
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_cv_prog_cc_g=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_c_werror_flag=$ac_save_c_werror_flag
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5
+$as_echo "$ac_cv_prog_cc_g" >&6; }
+if test "$ac_test_CFLAGS" = set; then
+ CFLAGS=$ac_save_CFLAGS
+elif test $ac_cv_prog_cc_g = yes; then
+ if test "$GCC" = yes; then
+ CFLAGS="-g -O2"
+ else
+ CFLAGS="-g"
+ fi
+else
+ if test "$GCC" = yes; then
+ CFLAGS="-O2"
+ else
+ CFLAGS=
+ fi
+fi
+{ $as_echo "$as_me:$LINENO: checking for $CC option to accept ISO C89" >&5
+$as_echo_n "checking for $CC option to accept ISO C89... " >&6; }
+if test "${ac_cv_prog_cc_c89+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_prog_cc_c89=no
+ac_save_CC=$CC
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <stdarg.h>
+#include <stdio.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */
+struct buf { int x; };
+FILE * (*rcsopen) (struct buf *, struct stat *, int);
+static char *e (p, i)
+ char **p;
+ int i;
+{
+ return p[i];
+}
+static char *f (char * (*g) (char **, int), char **p, ...)
+{
+ char *s;
+ va_list v;
+ va_start (v,p);
+ s = g (p, va_arg (v,int));
+ va_end (v);
+ return s;
+}
+
+/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has
+ function prototypes and stuff, but not '\xHH' hex character constants.
+ These don't provoke an error unfortunately, instead are silently treated
+ as 'x'. The following induces an error, until -std is added to get
+ proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an
+ array size at least. It's necessary to write '\x00'==0 to get something
+ that's true only with -std. */
+int osf4_cc_array ['\x00' == 0 ? 1 : -1];
+
+/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters
+ inside strings and character constants. */
+#define FOO(x) 'x'
+int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1];
+
+int test (int i, double x);
+struct s1 {int (*f) (int a);};
+struct s2 {int (*f) (double a);};
+int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int);
+int argc;
+char **argv;
+int
+main ()
+{
+return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1];
+ ;
+ return 0;
+}
+_ACEOF
+for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \
+ -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
+do
+ CC="$ac_save_CC $ac_arg"
+ rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_cv_prog_cc_c89=$ac_arg
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext
+ test "x$ac_cv_prog_cc_c89" != "xno" && break
+done
+rm -f conftest.$ac_ext
+CC=$ac_save_CC
+
+fi
+# AC_CACHE_VAL
+case "x$ac_cv_prog_cc_c89" in
+ x)
+ { $as_echo "$as_me:$LINENO: result: none needed" >&5
+$as_echo "none needed" >&6; } ;;
+ xno)
+ { $as_echo "$as_me:$LINENO: result: unsupported" >&5
+$as_echo "unsupported" >&6; } ;;
+ *)
+ CC="$CC $ac_cv_prog_cc_c89"
+ { $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_c89" >&5
+$as_echo "$ac_cv_prog_cc_c89" >&6; } ;;
+esac
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+depcc="$CC" am_compiler_list=
+
+{ $as_echo "$as_me:$LINENO: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CC_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ case $depmode in
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ none) break ;;
+ esac
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this.
+ if depmode=$depmode \
+ source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CC_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CC_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $am_cv_CC_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CC_dependencies_compiler_type" >&6; }
+CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then
+ am__fastdepCC_TRUE=
+ am__fastdepCC_FALSE='#'
+else
+ am__fastdepCC_TRUE='#'
+ am__fastdepCC_FALSE=
+fi
+
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+{ $as_echo "$as_me:$LINENO: checking how to run the C preprocessor" >&5
+$as_echo_n "checking how to run the C preprocessor... " >&6; }
+# On Suns, sometimes $CPP names a directory.
+if test -n "$CPP" && test -d "$CPP"; then
+ CPP=
+fi
+if test -z "$CPP"; then
+ if test "${ac_cv_prog_CPP+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ # Double quotes because CPP needs to be expanded
+ for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp"
+ do
+ ac_preproc_ok=false
+for ac_c_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ :
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ # Broken: fails on valid input.
+continue
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ # Broken: success on invalid input.
+continue
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
+ break
+fi
+
+ done
+ ac_cv_prog_CPP=$CPP
+
+fi
+ CPP=$ac_cv_prog_CPP
+else
+ ac_cv_prog_CPP=$CPP
+fi
+{ $as_echo "$as_me:$LINENO: result: $CPP" >&5
+$as_echo "$CPP" >&6; }
+ac_preproc_ok=false
+for ac_c_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ :
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ # Broken: fails on valid input.
+continue
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ # Broken: success on invalid input.
+continue
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
+ :
+else
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: C preprocessor \"$CPP\" fails sanity check
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: C preprocessor \"$CPP\" fails sanity check
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+{ $as_echo "$as_me:$LINENO: checking for grep that handles long lines and -e" >&5
+$as_echo_n "checking for grep that handles long lines and -e... " >&6; }
+if test "${ac_cv_path_GREP+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$GREP"; then
+ ac_path_GREP_found=false
+ # Loop through the user's path and test for each of PROGNAME-LIST
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in grep ggrep; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext"
+ { test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } || continue
+# Check for GNU ac_path_GREP and select it if it is found.
+ # Check for GNU $ac_path_GREP
+case `"$ac_path_GREP" --version 2>&1` in
+*GNU*)
+ ac_cv_path_GREP="$ac_path_GREP" ac_path_GREP_found=:;;
+*)
+ ac_count=0
+ $as_echo_n 0123456789 >"conftest.in"
+ while :
+ do
+ cat "conftest.in" "conftest.in" >"conftest.tmp"
+ mv "conftest.tmp" "conftest.in"
+ cp "conftest.in" "conftest.nl"
+ $as_echo 'GREP' >> "conftest.nl"
+ "$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break
+ diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+ ac_count=`expr $ac_count + 1`
+ if test $ac_count -gt ${ac_path_GREP_max-0}; then
+ # Best one so far, save it but keep looking for a better one
+ ac_cv_path_GREP="$ac_path_GREP"
+ ac_path_GREP_max=$ac_count
+ fi
+ # 10*(2^10) chars as input seems more than enough
+ test $ac_count -gt 10 && break
+ done
+ rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+ $ac_path_GREP_found && break 3
+ done
+ done
+done
+IFS=$as_save_IFS
+ if test -z "$ac_cv_path_GREP"; then
+ { { $as_echo "$as_me:$LINENO: error: no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5
+$as_echo "$as_me: error: no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+else
+ ac_cv_path_GREP=$GREP
+fi
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_GREP" >&5
+$as_echo "$ac_cv_path_GREP" >&6; }
+ GREP="$ac_cv_path_GREP"
+
+
+{ $as_echo "$as_me:$LINENO: checking for egrep" >&5
+$as_echo_n "checking for egrep... " >&6; }
+if test "${ac_cv_path_EGREP+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if echo a | $GREP -E '(a|b)' >/dev/null 2>&1
+ then ac_cv_path_EGREP="$GREP -E"
+ else
+ if test -z "$EGREP"; then
+ ac_path_EGREP_found=false
+ # Loop through the user's path and test for each of PROGNAME-LIST
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in egrep; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext"
+ { test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } || continue
+# Check for GNU ac_path_EGREP and select it if it is found.
+ # Check for GNU $ac_path_EGREP
+case `"$ac_path_EGREP" --version 2>&1` in
+*GNU*)
+ ac_cv_path_EGREP="$ac_path_EGREP" ac_path_EGREP_found=:;;
+*)
+ ac_count=0
+ $as_echo_n 0123456789 >"conftest.in"
+ while :
+ do
+ cat "conftest.in" "conftest.in" >"conftest.tmp"
+ mv "conftest.tmp" "conftest.in"
+ cp "conftest.in" "conftest.nl"
+ $as_echo 'EGREP' >> "conftest.nl"
+ "$ac_path_EGREP" 'EGREP$' < "conftest.nl" >"conftest.out" 2>/dev/null || break
+ diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+ ac_count=`expr $ac_count + 1`
+ if test $ac_count -gt ${ac_path_EGREP_max-0}; then
+ # Best one so far, save it but keep looking for a better one
+ ac_cv_path_EGREP="$ac_path_EGREP"
+ ac_path_EGREP_max=$ac_count
+ fi
+ # 10*(2^10) chars as input seems more than enough
+ test $ac_count -gt 10 && break
+ done
+ rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+ $ac_path_EGREP_found && break 3
+ done
+ done
+done
+IFS=$as_save_IFS
+ if test -z "$ac_cv_path_EGREP"; then
+ { { $as_echo "$as_me:$LINENO: error: no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5
+$as_echo "$as_me: error: no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+else
+ ac_cv_path_EGREP=$EGREP
+fi
+
+ fi
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_EGREP" >&5
+$as_echo "$ac_cv_path_EGREP" >&6; }
+ EGREP="$ac_cv_path_EGREP"
+
+
+{ $as_echo "$as_me:$LINENO: checking for ANSI C header files" >&5
+$as_echo_n "checking for ANSI C header files... " >&6; }
+if test "${ac_cv_header_stdc+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <stdlib.h>
+#include <stdarg.h>
+#include <string.h>
+#include <float.h>
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_cv_header_stdc=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_header_stdc=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+
+if test $ac_cv_header_stdc = yes; then
+ # SunOS 4.x string.h does not declare mem*, contrary to ANSI.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <string.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ $EGREP "memchr" >/dev/null 2>&1; then
+ :
+else
+ ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+ # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <stdlib.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ $EGREP "free" >/dev/null 2>&1; then
+ :
+else
+ ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+ # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi.
+ if test "$cross_compiling" = yes; then
+ :
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <ctype.h>
+#include <stdlib.h>
+#if ((' ' & 0x0FF) == 0x020)
+# define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
+# define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c))
+#else
+# define ISLOWER(c) \
+ (('a' <= (c) && (c) <= 'i') \
+ || ('j' <= (c) && (c) <= 'r') \
+ || ('s' <= (c) && (c) <= 'z'))
+# define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c))
+#endif
+
+#define XOR(e, f) (((e) && !(f)) || (!(e) && (f)))
+int
+main ()
+{
+ int i;
+ for (i = 0; i < 256; i++)
+ if (XOR (islower (i), ISLOWER (i))
+ || toupper (i) != TOUPPER (i))
+ return 2;
+ return 0;
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ :
+else
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+ac_cv_header_stdc=no
+fi
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+
+
+fi
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5
+$as_echo "$ac_cv_header_stdc" >&6; }
+if test $ac_cv_header_stdc = yes; then
+
+cat >>confdefs.h <<\_ACEOF
+#define STDC_HEADERS 1
+_ACEOF
+
+fi
+
+# On IRIX 5.3, sys/types and inttypes.h are conflicting.
+
+
+
+
+
+
+
+
+
+for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \
+ inttypes.h stdint.h unistd.h
+do
+as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
+$as_echo_n "checking for $ac_header... " >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+
+#include <$ac_header>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ eval "$as_ac_Header=yes"
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ eval "$as_ac_Header=no"
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+ac_res=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+as_val=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ if test "x$as_val" = x""yes; then
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+
+done
+
+
+
+ if test "${ac_cv_header_minix_config_h+set}" = set; then
+ { $as_echo "$as_me:$LINENO: checking for minix/config.h" >&5
+$as_echo_n "checking for minix/config.h... " >&6; }
+if test "${ac_cv_header_minix_config_h+set}" = set; then
+ $as_echo_n "(cached) " >&6
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_minix_config_h" >&5
+$as_echo "$ac_cv_header_minix_config_h" >&6; }
+else
+ # Is the header compilable?
+{ $as_echo "$as_me:$LINENO: checking minix/config.h usability" >&5
+$as_echo_n "checking minix/config.h usability... " >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+#include <minix/config.h>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_header_compiler=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_header_compiler=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ $as_echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
+$as_echo "$ac_header_compiler" >&6; }
+
+# Is the header present?
+{ $as_echo "$as_me:$LINENO: checking minix/config.h presence" >&5
+$as_echo_n "checking minix/config.h presence... " >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <minix/config.h>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ ac_header_preproc=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_header_preproc=no
+fi
+
+rm -f conftest.err conftest.$ac_ext
+{ $as_echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
+$as_echo "$ac_header_preproc" >&6; }
+
+# So? What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
+ yes:no: )
+ { $as_echo "$as_me:$LINENO: WARNING: minix/config.h: accepted by the compiler, rejected by the preprocessor!" >&5
+$as_echo "$as_me: WARNING: minix/config.h: accepted by the compiler, rejected by the preprocessor!" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: minix/config.h: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: minix/config.h: proceeding with the compiler's result" >&2;}
+ ac_header_preproc=yes
+ ;;
+ no:yes:* )
+ { $as_echo "$as_me:$LINENO: WARNING: minix/config.h: present but cannot be compiled" >&5
+$as_echo "$as_me: WARNING: minix/config.h: present but cannot be compiled" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: minix/config.h: check for missing prerequisite headers?" >&5
+$as_echo "$as_me: WARNING: minix/config.h: check for missing prerequisite headers?" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: minix/config.h: see the Autoconf documentation" >&5
+$as_echo "$as_me: WARNING: minix/config.h: see the Autoconf documentation" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: minix/config.h: section \"Present But Cannot Be Compiled\"" >&5
+$as_echo "$as_me: WARNING: minix/config.h: section \"Present But Cannot Be Compiled\"" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: minix/config.h: proceeding with the preprocessor's result" >&5
+$as_echo "$as_me: WARNING: minix/config.h: proceeding with the preprocessor's result" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: minix/config.h: in the future, the compiler will take precedence" >&5
+$as_echo "$as_me: WARNING: minix/config.h: in the future, the compiler will take precedence" >&2;}
+ ( cat <<\_ASBOX
+## ------------------------------ ##
+## Report this to clustalw@ucd.ie ##
+## ------------------------------ ##
+_ASBOX
+ ) | sed "s/^/$as_me: WARNING: /" >&2
+ ;;
+esac
+{ $as_echo "$as_me:$LINENO: checking for minix/config.h" >&5
+$as_echo_n "checking for minix/config.h... " >&6; }
+if test "${ac_cv_header_minix_config_h+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_header_minix_config_h=$ac_header_preproc
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_minix_config_h" >&5
+$as_echo "$ac_cv_header_minix_config_h" >&6; }
+
+fi
+if test "x$ac_cv_header_minix_config_h" = x""yes; then
+ MINIX=yes
+else
+ MINIX=
+fi
+
+
+ if test "$MINIX" = yes; then
+
+cat >>confdefs.h <<\_ACEOF
+#define _POSIX_SOURCE 1
+_ACEOF
+
+
+cat >>confdefs.h <<\_ACEOF
+#define _POSIX_1_SOURCE 2
+_ACEOF
+
+
+cat >>confdefs.h <<\_ACEOF
+#define _MINIX 1
+_ACEOF
+
+ fi
+
+
+
+ { $as_echo "$as_me:$LINENO: checking whether it is safe to define __EXTENSIONS__" >&5
+$as_echo_n "checking whether it is safe to define __EXTENSIONS__... " >&6; }
+if test "${ac_cv_safe_to_define___extensions__+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+# define __EXTENSIONS__ 1
+ $ac_includes_default
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_cv_safe_to_define___extensions__=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_safe_to_define___extensions__=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_safe_to_define___extensions__" >&5
+$as_echo "$ac_cv_safe_to_define___extensions__" >&6; }
+ test $ac_cv_safe_to_define___extensions__ = yes &&
+ cat >>confdefs.h <<\_ACEOF
+#define __EXTENSIONS__ 1
+_ACEOF
+
+ cat >>confdefs.h <<\_ACEOF
+#define _ALL_SOURCE 1
+_ACEOF
+
+ cat >>confdefs.h <<\_ACEOF
+#define _GNU_SOURCE 1
+_ACEOF
+
+ cat >>confdefs.h <<\_ACEOF
+#define _POSIX_PTHREAD_SEMANTICS 1
+_ACEOF
+
+ cat >>confdefs.h <<\_ACEOF
+#define _TANDEM_SOURCE 1
+_ACEOF
+
+
+
+
+# for cross compilation
+#
+# Make sure we can run config.sub.
+$SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 ||
+ { { $as_echo "$as_me:$LINENO: error: cannot run $SHELL $ac_aux_dir/config.sub" >&5
+$as_echo "$as_me: error: cannot run $SHELL $ac_aux_dir/config.sub" >&2;}
+ { (exit 1); exit 1; }; }
+
+{ $as_echo "$as_me:$LINENO: checking build system type" >&5
+$as_echo_n "checking build system type... " >&6; }
+if test "${ac_cv_build+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_build_alias=$build_alias
+test "x$ac_build_alias" = x &&
+ ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"`
+test "x$ac_build_alias" = x &&
+ { { $as_echo "$as_me:$LINENO: error: cannot guess build type; you must specify one" >&5
+$as_echo "$as_me: error: cannot guess build type; you must specify one" >&2;}
+ { (exit 1); exit 1; }; }
+ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` ||
+ { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&5
+$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&2;}
+ { (exit 1); exit 1; }; }
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_build" >&5
+$as_echo "$ac_cv_build" >&6; }
+case $ac_cv_build in
+*-*-*) ;;
+*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical build" >&5
+$as_echo "$as_me: error: invalid value of canonical build" >&2;}
+ { (exit 1); exit 1; }; };;
+esac
+build=$ac_cv_build
+ac_save_IFS=$IFS; IFS='-'
+set x $ac_cv_build
+shift
+build_cpu=$1
+build_vendor=$2
+shift; shift
+# Remember, the first character of IFS is used to create $*,
+# except with old shells:
+build_os=$*
+IFS=$ac_save_IFS
+case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac
+
+
+{ $as_echo "$as_me:$LINENO: checking host system type" >&5
+$as_echo_n "checking host system type... " >&6; }
+if test "${ac_cv_host+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test "x$host_alias" = x; then
+ ac_cv_host=$ac_cv_build
+else
+ ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` ||
+ { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&5
+$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&2;}
+ { (exit 1); exit 1; }; }
+fi
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_host" >&5
+$as_echo "$ac_cv_host" >&6; }
+case $ac_cv_host in
+*-*-*) ;;
+*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical host" >&5
+$as_echo "$as_me: error: invalid value of canonical host" >&2;}
+ { (exit 1); exit 1; }; };;
+esac
+host=$ac_cv_host
+ac_save_IFS=$IFS; IFS='-'
+set x $ac_cv_host
+shift
+host_cpu=$1
+host_vendor=$2
+shift; shift
+# Remember, the first character of IFS is used to create $*,
+# except with old shells:
+host_os=$*
+IFS=$ac_save_IFS
+case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac
+
+
+## AC_CANONICAL_BUILD
+## AC_CANONICAL_TARGET
+
+# Set the @SET_MAKE@ variable=make if $(MAKE) not set
+{ $as_echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5
+$as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; }
+set x ${MAKE-make}
+ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'`
+if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.make <<\_ACEOF
+SHELL = /bin/sh
+all:
+ @echo '@@@%%%=$(MAKE)=@@@%%%'
+_ACEOF
+# GNU make sometimes prints "make[1]: Entering...", which would confuse us.
+case `${MAKE-make} -f conftest.make 2>/dev/null` in
+ *@@@%%%=?*=@@@%%%*)
+ eval ac_cv_prog_make_${ac_make}_set=yes;;
+ *)
+ eval ac_cv_prog_make_${ac_make}_set=no;;
+esac
+rm -f conftest.make
+fi
+if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+ SET_MAKE=
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+ SET_MAKE="MAKE=${MAKE-make}"
+fi
+
+
+# AC_PROG_RANLIB will allow you to build code in sub-directories into
+# temporary libraries, which make will then link in with the rest of
+# the code.
+# Rendered obsolte by LT_INIT: AC_PROG_RANLIB
+#AC_PROG_LIBTOOL
+case `pwd` in
+ *\ * | *\ *)
+ { $as_echo "$as_me:$LINENO: WARNING: Libtool does not cope well with whitespace in \`pwd\`" >&5
+$as_echo "$as_me: WARNING: Libtool does not cope well with whitespace in \`pwd\`" >&2;} ;;
+esac
+
+
+
+macro_version='2.2.6'
+macro_revision='1.3012'
+
+
+
+
+
+
+
+
+
+
+
+
+
+ltmain="$ac_aux_dir/ltmain.sh"
+
+{ $as_echo "$as_me:$LINENO: checking for a sed that does not truncate output" >&5
+$as_echo_n "checking for a sed that does not truncate output... " >&6; }
+if test "${ac_cv_path_SED+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_script=s/aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa/bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb/
+ for ac_i in 1 2 3 4 5 6 7; do
+ ac_script="$ac_script$as_nl$ac_script"
+ done
+ echo "$ac_script" 2>/dev/null | sed 99q >conftest.sed
+ $as_unset ac_script || ac_script=
+ if test -z "$SED"; then
+ ac_path_SED_found=false
+ # Loop through the user's path and test for each of PROGNAME-LIST
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in sed gsed; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ ac_path_SED="$as_dir/$ac_prog$ac_exec_ext"
+ { test -f "$ac_path_SED" && $as_test_x "$ac_path_SED"; } || continue
+# Check for GNU ac_path_SED and select it if it is found.
+ # Check for GNU $ac_path_SED
+case `"$ac_path_SED" --version 2>&1` in
+*GNU*)
+ ac_cv_path_SED="$ac_path_SED" ac_path_SED_found=:;;
+*)
+ ac_count=0
+ $as_echo_n 0123456789 >"conftest.in"
+ while :
+ do
+ cat "conftest.in" "conftest.in" >"conftest.tmp"
+ mv "conftest.tmp" "conftest.in"
+ cp "conftest.in" "conftest.nl"
+ $as_echo '' >> "conftest.nl"
+ "$ac_path_SED" -f conftest.sed < "conftest.nl" >"conftest.out" 2>/dev/null || break
+ diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+ ac_count=`expr $ac_count + 1`
+ if test $ac_count -gt ${ac_path_SED_max-0}; then
+ # Best one so far, save it but keep looking for a better one
+ ac_cv_path_SED="$ac_path_SED"
+ ac_path_SED_max=$ac_count
+ fi
+ # 10*(2^10) chars as input seems more than enough
+ test $ac_count -gt 10 && break
+ done
+ rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+ $ac_path_SED_found && break 3
+ done
+ done
+done
+IFS=$as_save_IFS
+ if test -z "$ac_cv_path_SED"; then
+ { { $as_echo "$as_me:$LINENO: error: no acceptable sed could be found in \$PATH" >&5
+$as_echo "$as_me: error: no acceptable sed could be found in \$PATH" >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+else
+ ac_cv_path_SED=$SED
+fi
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_SED" >&5
+$as_echo "$ac_cv_path_SED" >&6; }
+ SED="$ac_cv_path_SED"
+ rm -f conftest.sed
+
+test -z "$SED" && SED=sed
+Xsed="$SED -e 1s/^X//"
+
+
+
+
+
+
+
+
+
+
+
+{ $as_echo "$as_me:$LINENO: checking for fgrep" >&5
+$as_echo_n "checking for fgrep... " >&6; }
+if test "${ac_cv_path_FGREP+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if echo 'ab*c' | $GREP -F 'ab*c' >/dev/null 2>&1
+ then ac_cv_path_FGREP="$GREP -F"
+ else
+ if test -z "$FGREP"; then
+ ac_path_FGREP_found=false
+ # Loop through the user's path and test for each of PROGNAME-LIST
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_prog in fgrep; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ ac_path_FGREP="$as_dir/$ac_prog$ac_exec_ext"
+ { test -f "$ac_path_FGREP" && $as_test_x "$ac_path_FGREP"; } || continue
+# Check for GNU ac_path_FGREP and select it if it is found.
+ # Check for GNU $ac_path_FGREP
+case `"$ac_path_FGREP" --version 2>&1` in
+*GNU*)
+ ac_cv_path_FGREP="$ac_path_FGREP" ac_path_FGREP_found=:;;
+*)
+ ac_count=0
+ $as_echo_n 0123456789 >"conftest.in"
+ while :
+ do
+ cat "conftest.in" "conftest.in" >"conftest.tmp"
+ mv "conftest.tmp" "conftest.in"
+ cp "conftest.in" "conftest.nl"
+ $as_echo 'FGREP' >> "conftest.nl"
+ "$ac_path_FGREP" FGREP < "conftest.nl" >"conftest.out" 2>/dev/null || break
+ diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
+ ac_count=`expr $ac_count + 1`
+ if test $ac_count -gt ${ac_path_FGREP_max-0}; then
+ # Best one so far, save it but keep looking for a better one
+ ac_cv_path_FGREP="$ac_path_FGREP"
+ ac_path_FGREP_max=$ac_count
+ fi
+ # 10*(2^10) chars as input seems more than enough
+ test $ac_count -gt 10 && break
+ done
+ rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
+esac
+
+ $ac_path_FGREP_found && break 3
+ done
+ done
+done
+IFS=$as_save_IFS
+ if test -z "$ac_cv_path_FGREP"; then
+ { { $as_echo "$as_me:$LINENO: error: no acceptable fgrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5
+$as_echo "$as_me: error: no acceptable fgrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+else
+ ac_cv_path_FGREP=$FGREP
+fi
+
+ fi
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_FGREP" >&5
+$as_echo "$ac_cv_path_FGREP" >&6; }
+ FGREP="$ac_cv_path_FGREP"
+
+
+test -z "$GREP" && GREP=grep
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# Check whether --with-gnu-ld was given.
+if test "${with_gnu_ld+set}" = set; then
+ withval=$with_gnu_ld; test "$withval" = no || with_gnu_ld=yes
+else
+ with_gnu_ld=no
+fi
+
+ac_prog=ld
+if test "$GCC" = yes; then
+ # Check if gcc -print-prog-name=ld gives a path.
+ { $as_echo "$as_me:$LINENO: checking for ld used by $CC" >&5
+$as_echo_n "checking for ld used by $CC... " >&6; }
+ case $host in
+ *-*-mingw*)
+ # gcc leaves a trailing carriage return which upsets mingw
+ ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;;
+ *)
+ ac_prog=`($CC -print-prog-name=ld) 2>&5` ;;
+ esac
+ case $ac_prog in
+ # Accept absolute paths.
+ [\\/]* | ?:[\\/]*)
+ re_direlt='/[^/][^/]*/\.\./'
+ # Canonicalize the pathname of ld
+ ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'`
+ while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do
+ ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"`
+ done
+ test -z "$LD" && LD="$ac_prog"
+ ;;
+ "")
+ # If it fails, then pretend we aren't using GCC.
+ ac_prog=ld
+ ;;
+ *)
+ # If it is relative, then search for the first ld in PATH.
+ with_gnu_ld=unknown
+ ;;
+ esac
+elif test "$with_gnu_ld" = yes; then
+ { $as_echo "$as_me:$LINENO: checking for GNU ld" >&5
+$as_echo_n "checking for GNU ld... " >&6; }
+else
+ { $as_echo "$as_me:$LINENO: checking for non-GNU ld" >&5
+$as_echo_n "checking for non-GNU ld... " >&6; }
+fi
+if test "${lt_cv_path_LD+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$LD"; then
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then
+ lt_cv_path_LD="$ac_dir/$ac_prog"
+ # Check to see if the program is GNU ld. I'd rather use --version,
+ # but apparently some variants of GNU ld only accept -v.
+ # Break only if it was the GNU/non-GNU ld that we prefer.
+ case `"$lt_cv_path_LD" -v 2>&1 </dev/null` in
+ *GNU* | *'with BFD'*)
+ test "$with_gnu_ld" != no && break
+ ;;
+ *)
+ test "$with_gnu_ld" != yes && break
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+else
+ lt_cv_path_LD="$LD" # Let the user override the test with a path.
+fi
+fi
+
+LD="$lt_cv_path_LD"
+if test -n "$LD"; then
+ { $as_echo "$as_me:$LINENO: result: $LD" >&5
+$as_echo "$LD" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+test -z "$LD" && { { $as_echo "$as_me:$LINENO: error: no acceptable ld found in \$PATH" >&5
+$as_echo "$as_me: error: no acceptable ld found in \$PATH" >&2;}
+ { (exit 1); exit 1; }; }
+{ $as_echo "$as_me:$LINENO: checking if the linker ($LD) is GNU ld" >&5
+$as_echo_n "checking if the linker ($LD) is GNU ld... " >&6; }
+if test "${lt_cv_prog_gnu_ld+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ # I'd rather use --version here, but apparently some GNU lds only accept -v.
+case `$LD -v 2>&1 </dev/null` in
+*GNU* | *'with BFD'*)
+ lt_cv_prog_gnu_ld=yes
+ ;;
+*)
+ lt_cv_prog_gnu_ld=no
+ ;;
+esac
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_gnu_ld" >&5
+$as_echo "$lt_cv_prog_gnu_ld" >&6; }
+with_gnu_ld=$lt_cv_prog_gnu_ld
+
+
+
+
+
+
+
+
+
+{ $as_echo "$as_me:$LINENO: checking for BSD- or MS-compatible name lister (nm)" >&5
+$as_echo_n "checking for BSD- or MS-compatible name lister (nm)... " >&6; }
+if test "${lt_cv_path_NM+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$NM"; then
+ # Let the user override the test.
+ lt_cv_path_NM="$NM"
+else
+ lt_nm_to_check="${ac_tool_prefix}nm"
+ if test -n "$ac_tool_prefix" && test "$build" = "$host"; then
+ lt_nm_to_check="$lt_nm_to_check nm"
+ fi
+ for lt_tmp_nm in $lt_nm_to_check; do
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ tmp_nm="$ac_dir/$lt_tmp_nm"
+ if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then
+ # Check to see if the nm accepts a BSD-compat flag.
+ # Adding the `sed 1q' prevents false positives on HP-UX, which says:
+ # nm: unknown option "B" ignored
+ # Tru64's nm complains that /dev/null is an invalid object file
+ case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in
+ */dev/null* | *'Invalid file or object type'*)
+ lt_cv_path_NM="$tmp_nm -B"
+ break
+ ;;
+ *)
+ case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in
+ */dev/null*)
+ lt_cv_path_NM="$tmp_nm -p"
+ break
+ ;;
+ *)
+ lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but
+ continue # so that we can try to find one that supports BSD flags
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+ done
+ : ${lt_cv_path_NM=no}
+fi
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_path_NM" >&5
+$as_echo "$lt_cv_path_NM" >&6; }
+if test "$lt_cv_path_NM" != "no"; then
+ NM="$lt_cv_path_NM"
+else
+ # Didn't find any BSD compatible name lister, look for dumpbin.
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in "dumpbin -symbols" "link -dump -symbols"
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_DUMPBIN+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$DUMPBIN"; then
+ ac_cv_prog_DUMPBIN="$DUMPBIN" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_DUMPBIN="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+DUMPBIN=$ac_cv_prog_DUMPBIN
+if test -n "$DUMPBIN"; then
+ { $as_echo "$as_me:$LINENO: result: $DUMPBIN" >&5
+$as_echo "$DUMPBIN" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$DUMPBIN" && break
+ done
+fi
+if test -z "$DUMPBIN"; then
+ ac_ct_DUMPBIN=$DUMPBIN
+ for ac_prog in "dumpbin -symbols" "link -dump -symbols"
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_DUMPBIN+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_DUMPBIN"; then
+ ac_cv_prog_ac_ct_DUMPBIN="$ac_ct_DUMPBIN" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_DUMPBIN="$ac_prog"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_DUMPBIN=$ac_cv_prog_ac_ct_DUMPBIN
+if test -n "$ac_ct_DUMPBIN"; then
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_DUMPBIN" >&5
+$as_echo "$ac_ct_DUMPBIN" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_DUMPBIN" && break
+done
+
+ if test "x$ac_ct_DUMPBIN" = x; then
+ DUMPBIN=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ DUMPBIN=$ac_ct_DUMPBIN
+ fi
+fi
+
+
+ if test "$DUMPBIN" != ":"; then
+ NM="$DUMPBIN"
+ fi
+fi
+test -z "$NM" && NM=nm
+
+
+
+
+
+
+{ $as_echo "$as_me:$LINENO: checking the name lister ($NM) interface" >&5
+$as_echo_n "checking the name lister ($NM) interface... " >&6; }
+if test "${lt_cv_nm_interface+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_nm_interface="BSD nm"
+ echo "int some_variable = 0;" > conftest.$ac_ext
+ (eval echo "\"\$as_me:5230: $ac_compile\"" >&5)
+ (eval "$ac_compile" 2>conftest.err)
+ cat conftest.err >&5
+ (eval echo "\"\$as_me:5233: $NM \\\"conftest.$ac_objext\\\"\"" >&5)
+ (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out)
+ cat conftest.err >&5
+ (eval echo "\"\$as_me:5236: output\"" >&5)
+ cat conftest.out >&5
+ if $GREP 'External.*some_variable' conftest.out > /dev/null; then
+ lt_cv_nm_interface="MS dumpbin"
+ fi
+ rm -f conftest*
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_nm_interface" >&5
+$as_echo "$lt_cv_nm_interface" >&6; }
+
+{ $as_echo "$as_me:$LINENO: checking whether ln -s works" >&5
+$as_echo_n "checking whether ln -s works... " >&6; }
+LN_S=$as_ln_s
+if test "$LN_S" = "ln -s"; then
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no, using $LN_S" >&5
+$as_echo "no, using $LN_S" >&6; }
+fi
+
+# find the maximum length of command line arguments
+{ $as_echo "$as_me:$LINENO: checking the maximum length of command line arguments" >&5
+$as_echo_n "checking the maximum length of command line arguments... " >&6; }
+if test "${lt_cv_sys_max_cmd_len+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ i=0
+ teststring="ABCD"
+
+ case $build_os in
+ msdosdjgpp*)
+ # On DJGPP, this test can blow up pretty badly due to problems in libc
+ # (any single argument exceeding 2000 bytes causes a buffer overrun
+ # during glob expansion). Even if it were fixed, the result of this
+ # check would be larger than it should be.
+ lt_cv_sys_max_cmd_len=12288; # 12K is about right
+ ;;
+
+ gnu*)
+ # Under GNU Hurd, this test is not required because there is
+ # no limit to the length of command line arguments.
+ # Libtool will interpret -1 as no limit whatsoever
+ lt_cv_sys_max_cmd_len=-1;
+ ;;
+
+ cygwin* | mingw* | cegcc*)
+ # On Win9x/ME, this test blows up -- it succeeds, but takes
+ # about 5 minutes as the teststring grows exponentially.
+ # Worse, since 9x/ME are not pre-emptively multitasking,
+ # you end up with a "frozen" computer, even though with patience
+ # the test eventually succeeds (with a max line length of 256k).
+ # Instead, let's just punt: use the minimum linelength reported by
+ # all of the supported platforms: 8192 (on NT/2K/XP).
+ lt_cv_sys_max_cmd_len=8192;
+ ;;
+
+ amigaos*)
+ # On AmigaOS with pdksh, this test takes hours, literally.
+ # So we just punt and use a minimum line length of 8192.
+ lt_cv_sys_max_cmd_len=8192;
+ ;;
+
+ netbsd* | freebsd* | openbsd* | darwin* | dragonfly*)
+ # This has been around since 386BSD, at least. Likely further.
+ if test -x /sbin/sysctl; then
+ lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax`
+ elif test -x /usr/sbin/sysctl; then
+ lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax`
+ else
+ lt_cv_sys_max_cmd_len=65536 # usable default for all BSDs
+ fi
+ # And add a safety zone
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+ ;;
+
+ interix*)
+ # We know the value 262144 and hardcode it with a safety zone (like BSD)
+ lt_cv_sys_max_cmd_len=196608
+ ;;
+
+ osf*)
+ # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure
+ # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not
+ # nice to cause kernel panics so lets avoid the loop below.
+ # First set a reasonable default.
+ lt_cv_sys_max_cmd_len=16384
+ #
+ if test -x /sbin/sysconfig; then
+ case `/sbin/sysconfig -q proc exec_disable_arg_limit` in
+ *1*) lt_cv_sys_max_cmd_len=-1 ;;
+ esac
+ fi
+ ;;
+ sco3.2v5*)
+ lt_cv_sys_max_cmd_len=102400
+ ;;
+ sysv5* | sco5v6* | sysv4.2uw2*)
+ kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null`
+ if test -n "$kargmax"; then
+ lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[ ]//'`
+ else
+ lt_cv_sys_max_cmd_len=32768
+ fi
+ ;;
+ *)
+ lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null`
+ if test -n "$lt_cv_sys_max_cmd_len"; then
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+ else
+ # Make teststring a little bigger before we do anything with it.
+ # a 1K string should be a reasonable start.
+ for i in 1 2 3 4 5 6 7 8 ; do
+ teststring=$teststring$teststring
+ done
+ SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}}
+ # If test is not a shell built-in, we'll probably end up computing a
+ # maximum length that is only half of the actual maximum length, but
+ # we can't tell.
+ while { test "X"`$SHELL $0 --fallback-echo "X$teststring$teststring" 2>/dev/null` \
+ = "XX$teststring$teststring"; } >/dev/null 2>&1 &&
+ test $i != 17 # 1/2 MB should be enough
+ do
+ i=`expr $i + 1`
+ teststring=$teststring$teststring
+ done
+ # Only check the string length outside the loop.
+ lt_cv_sys_max_cmd_len=`expr "X$teststring" : ".*" 2>&1`
+ teststring=
+ # Add a significant safety factor because C++ compilers can tack on
+ # massive amounts of additional arguments before passing them to the
+ # linker. It appears as though 1/2 is a usable value.
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2`
+ fi
+ ;;
+ esac
+
+fi
+
+if test -n $lt_cv_sys_max_cmd_len ; then
+ { $as_echo "$as_me:$LINENO: result: $lt_cv_sys_max_cmd_len" >&5
+$as_echo "$lt_cv_sys_max_cmd_len" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: none" >&5
+$as_echo "none" >&6; }
+fi
+max_cmd_len=$lt_cv_sys_max_cmd_len
+
+
+
+
+
+
+: ${CP="cp -f"}
+: ${MV="mv -f"}
+: ${RM="rm -f"}
+
+{ $as_echo "$as_me:$LINENO: checking whether the shell understands some XSI constructs" >&5
+$as_echo_n "checking whether the shell understands some XSI constructs... " >&6; }
+# Try some XSI features
+xsi_shell=no
+( _lt_dummy="a/b/c"
+ test "${_lt_dummy##*/},${_lt_dummy%/*},"${_lt_dummy%"$_lt_dummy"}, \
+ = c,a/b,, \
+ && eval 'test $(( 1 + 1 )) -eq 2 \
+ && test "${#_lt_dummy}" -eq 5' ) >/dev/null 2>&1 \
+ && xsi_shell=yes
+{ $as_echo "$as_me:$LINENO: result: $xsi_shell" >&5
+$as_echo "$xsi_shell" >&6; }
+
+
+{ $as_echo "$as_me:$LINENO: checking whether the shell understands \"+=\"" >&5
+$as_echo_n "checking whether the shell understands \"+=\"... " >&6; }
+lt_shell_append=no
+( foo=bar; set foo baz; eval "$1+=\$2" && test "$foo" = barbaz ) \
+ >/dev/null 2>&1 \
+ && lt_shell_append=yes
+{ $as_echo "$as_me:$LINENO: result: $lt_shell_append" >&5
+$as_echo "$lt_shell_append" >&6; }
+
+
+if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
+ lt_unset=unset
+else
+ lt_unset=false
+fi
+
+
+
+
+
+# test EBCDIC or ASCII
+case `echo X|tr X '\101'` in
+ A) # ASCII based system
+ # \n is not interpreted correctly by Solaris 8 /usr/ucb/tr
+ lt_SP2NL='tr \040 \012'
+ lt_NL2SP='tr \015\012 \040\040'
+ ;;
+ *) # EBCDIC based system
+ lt_SP2NL='tr \100 \n'
+ lt_NL2SP='tr \r\n \100\100'
+ ;;
+esac
+
+
+
+
+
+
+
+
+
+{ $as_echo "$as_me:$LINENO: checking for $LD option to reload object files" >&5
+$as_echo_n "checking for $LD option to reload object files... " >&6; }
+if test "${lt_cv_ld_reload_flag+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_ld_reload_flag='-r'
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_ld_reload_flag" >&5
+$as_echo "$lt_cv_ld_reload_flag" >&6; }
+reload_flag=$lt_cv_ld_reload_flag
+case $reload_flag in
+"" | " "*) ;;
+*) reload_flag=" $reload_flag" ;;
+esac
+reload_cmds='$LD$reload_flag -o $output$reload_objs'
+case $host_os in
+ darwin*)
+ if test "$GCC" = yes; then
+ reload_cmds='$LTCC $LTCFLAGS -nostdlib ${wl}-r -o $output$reload_objs'
+ else
+ reload_cmds='$LD$reload_flag -o $output$reload_objs'
+ fi
+ ;;
+esac
+
+
+
+
+
+
+
+
+
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}objdump", so it can be a program name with args.
+set dummy ${ac_tool_prefix}objdump; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_OBJDUMP+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$OBJDUMP"; then
+ ac_cv_prog_OBJDUMP="$OBJDUMP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_OBJDUMP="${ac_tool_prefix}objdump"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+OBJDUMP=$ac_cv_prog_OBJDUMP
+if test -n "$OBJDUMP"; then
+ { $as_echo "$as_me:$LINENO: result: $OBJDUMP" >&5
+$as_echo "$OBJDUMP" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_OBJDUMP"; then
+ ac_ct_OBJDUMP=$OBJDUMP
+ # Extract the first word of "objdump", so it can be a program name with args.
+set dummy objdump; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_OBJDUMP+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_OBJDUMP"; then
+ ac_cv_prog_ac_ct_OBJDUMP="$ac_ct_OBJDUMP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_OBJDUMP="objdump"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_OBJDUMP=$ac_cv_prog_ac_ct_OBJDUMP
+if test -n "$ac_ct_OBJDUMP"; then
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_OBJDUMP" >&5
+$as_echo "$ac_ct_OBJDUMP" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_OBJDUMP" = x; then
+ OBJDUMP="false"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ OBJDUMP=$ac_ct_OBJDUMP
+ fi
+else
+ OBJDUMP="$ac_cv_prog_OBJDUMP"
+fi
+
+test -z "$OBJDUMP" && OBJDUMP=objdump
+
+
+
+
+
+
+
+
+
+{ $as_echo "$as_me:$LINENO: checking how to recognize dependent libraries" >&5
+$as_echo_n "checking how to recognize dependent libraries... " >&6; }
+if test "${lt_cv_deplibs_check_method+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_file_magic_cmd='$MAGIC_CMD'
+lt_cv_file_magic_test_file=
+lt_cv_deplibs_check_method='unknown'
+# Need to set the preceding variable on all platforms that support
+# interlibrary dependencies.
+# 'none' -- dependencies not supported.
+# `unknown' -- same as none, but documents that we really don't know.
+# 'pass_all' -- all dependencies passed with no checks.
+# 'test_compile' -- check by making test program.
+# 'file_magic [[regex]]' -- check by looking for files in library path
+# which responds to the $file_magic_cmd with a given extended regex.
+# If you have `file' or equivalent on your system and you're not sure
+# whether `pass_all' will *always* work, you probably want this one.
+
+case $host_os in
+aix[4-9]*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+beos*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+bsdi[45]*)
+ lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib)'
+ lt_cv_file_magic_cmd='/usr/bin/file -L'
+ lt_cv_file_magic_test_file=/shlib/libc.so
+ ;;
+
+cygwin*)
+ # func_win32_libid is a shell function defined in ltmain.sh
+ lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL'
+ lt_cv_file_magic_cmd='func_win32_libid'
+ ;;
+
+mingw* | pw32*)
+ # Base MSYS/MinGW do not provide the 'file' command needed by
+ # func_win32_libid shell function, so use a weaker test based on 'objdump',
+ # unless we find 'file', for example because we are cross-compiling.
+ if ( file / ) >/dev/null 2>&1; then
+ lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL'
+ lt_cv_file_magic_cmd='func_win32_libid'
+ else
+ lt_cv_deplibs_check_method='file_magic file format pei*-i386(.*architecture: i386)?'
+ lt_cv_file_magic_cmd='$OBJDUMP -f'
+ fi
+ ;;
+
+cegcc)
+ # use the weaker test based on 'objdump'. See mingw*.
+ lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?'
+ lt_cv_file_magic_cmd='$OBJDUMP -f'
+ ;;
+
+darwin* | rhapsody*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+freebsd* | dragonfly*)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
+ case $host_cpu in
+ i*86 )
+ # Not sure whether the presence of OpenBSD here was a mistake.
+ # Let's accept both of them until this is cleared up.
+ lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[3-9]86 (compact )?demand paged shared library'
+ lt_cv_file_magic_cmd=/usr/bin/file
+ lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*`
+ ;;
+ esac
+ else
+ lt_cv_deplibs_check_method=pass_all
+ fi
+ ;;
+
+gnu*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+hpux10.20* | hpux11*)
+ lt_cv_file_magic_cmd=/usr/bin/file
+ case $host_cpu in
+ ia64*)
+ lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - IA64'
+ lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so
+ ;;
+ hppa*64*)
+ lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]'
+ lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl
+ ;;
+ *)
+ lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|PA-RISC[0-9].[0-9]) shared library'
+ lt_cv_file_magic_test_file=/usr/lib/libc.sl
+ ;;
+ esac
+ ;;
+
+interix[3-9]*)
+ # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|\.a)$'
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $LD in
+ *-32|*"-32 ") libmagic=32-bit;;
+ *-n32|*"-n32 ") libmagic=N32;;
+ *-64|*"-64 ") libmagic=64-bit;;
+ *) libmagic=never-match;;
+ esac
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$'
+ else
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so|_pic\.a)$'
+ fi
+ ;;
+
+newos6*)
+ lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (executable|dynamic lib)'
+ lt_cv_file_magic_cmd=/usr/bin/file
+ lt_cv_file_magic_test_file=/usr/lib/libnls.so
+ ;;
+
+*nto* | *qnx*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+openbsd*)
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|\.so|_pic\.a)$'
+ else
+ lt_cv_deplibs_check_method='match_pattern /lib[^/]+(\.so\.[0-9]+\.[0-9]+|_pic\.a)$'
+ fi
+ ;;
+
+osf3* | osf4* | osf5*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+rdos*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+solaris*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+sysv4 | sysv4.3*)
+ case $host_vendor in
+ motorola)
+ lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [ML]SB (shared object|dynamic lib) M[0-9][0-9]* Version [0-9]'
+ lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*`
+ ;;
+ ncr)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ sequent)
+ lt_cv_file_magic_cmd='/bin/file'
+ lt_cv_deplibs_check_method='file_magic ELF [0-9][0-9]*-bit [LM]SB (shared object|dynamic lib )'
+ ;;
+ sni)
+ lt_cv_file_magic_cmd='/bin/file'
+ lt_cv_deplibs_check_method="file_magic ELF [0-9][0-9]*-bit [LM]SB dynamic lib"
+ lt_cv_file_magic_test_file=/lib/libc.so
+ ;;
+ siemens)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ pc)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ esac
+ ;;
+
+tpf*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+esac
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_deplibs_check_method" >&5
+$as_echo "$lt_cv_deplibs_check_method" >&6; }
+file_magic_cmd=$lt_cv_file_magic_cmd
+deplibs_check_method=$lt_cv_deplibs_check_method
+test -z "$deplibs_check_method" && deplibs_check_method=unknown
+
+
+
+
+
+
+
+
+
+
+
+
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}ar", so it can be a program name with args.
+set dummy ${ac_tool_prefix}ar; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_AR+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$AR"; then
+ ac_cv_prog_AR="$AR" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_AR="${ac_tool_prefix}ar"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+AR=$ac_cv_prog_AR
+if test -n "$AR"; then
+ { $as_echo "$as_me:$LINENO: result: $AR" >&5
+$as_echo "$AR" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_AR"; then
+ ac_ct_AR=$AR
+ # Extract the first word of "ar", so it can be a program name with args.
+set dummy ar; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_AR+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_AR"; then
+ ac_cv_prog_ac_ct_AR="$ac_ct_AR" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_AR="ar"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_AR=$ac_cv_prog_ac_ct_AR
+if test -n "$ac_ct_AR"; then
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_AR" >&5
+$as_echo "$ac_ct_AR" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_AR" = x; then
+ AR="false"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ AR=$ac_ct_AR
+ fi
+else
+ AR="$ac_cv_prog_AR"
+fi
+
+test -z "$AR" && AR=ar
+test -z "$AR_FLAGS" && AR_FLAGS=cru
+
+
+
+
+
+
+
+
+
+
+
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
+set dummy ${ac_tool_prefix}strip; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_STRIP+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$STRIP"; then
+ ac_cv_prog_STRIP="$STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_STRIP="${ac_tool_prefix}strip"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+STRIP=$ac_cv_prog_STRIP
+if test -n "$STRIP"; then
+ { $as_echo "$as_me:$LINENO: result: $STRIP" >&5
+$as_echo "$STRIP" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_STRIP"; then
+ ac_ct_STRIP=$STRIP
+ # Extract the first word of "strip", so it can be a program name with args.
+set dummy strip; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_STRIP"; then
+ ac_cv_prog_ac_ct_STRIP="$ac_ct_STRIP" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_STRIP="strip"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP
+if test -n "$ac_ct_STRIP"; then
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5
+$as_echo "$ac_ct_STRIP" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_STRIP" = x; then
+ STRIP=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ STRIP=$ac_ct_STRIP
+ fi
+else
+ STRIP="$ac_cv_prog_STRIP"
+fi
+
+test -z "$STRIP" && STRIP=:
+
+
+
+
+
+
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args.
+set dummy ${ac_tool_prefix}ranlib; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_RANLIB+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$RANLIB"; then
+ ac_cv_prog_RANLIB="$RANLIB" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_RANLIB="${ac_tool_prefix}ranlib"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+RANLIB=$ac_cv_prog_RANLIB
+if test -n "$RANLIB"; then
+ { $as_echo "$as_me:$LINENO: result: $RANLIB" >&5
+$as_echo "$RANLIB" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_RANLIB"; then
+ ac_ct_RANLIB=$RANLIB
+ # Extract the first word of "ranlib", so it can be a program name with args.
+set dummy ranlib; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_RANLIB+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_RANLIB"; then
+ ac_cv_prog_ac_ct_RANLIB="$ac_ct_RANLIB" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_RANLIB="ranlib"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_RANLIB=$ac_cv_prog_ac_ct_RANLIB
+if test -n "$ac_ct_RANLIB"; then
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_RANLIB" >&5
+$as_echo "$ac_ct_RANLIB" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_RANLIB" = x; then
+ RANLIB=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ RANLIB=$ac_ct_RANLIB
+ fi
+else
+ RANLIB="$ac_cv_prog_RANLIB"
+fi
+
+test -z "$RANLIB" && RANLIB=:
+
+
+
+
+
+
+# Determine commands to create old-style static archives.
+old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs'
+old_postinstall_cmds='chmod 644 $oldlib'
+old_postuninstall_cmds=
+
+if test -n "$RANLIB"; then
+ case $host_os in
+ openbsd*)
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib"
+ ;;
+ *)
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib"
+ ;;
+ esac
+ old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib"
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+
+
+# Check for command to grab the raw symbol name followed by C symbol from nm.
+{ $as_echo "$as_me:$LINENO: checking command to parse $NM output from $compiler object" >&5
+$as_echo_n "checking command to parse $NM output from $compiler object... " >&6; }
+if test "${lt_cv_sys_global_symbol_pipe+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+
+# These are sane defaults that work on at least a few old systems.
+# [They come from Ultrix. What could be older than Ultrix?!! ;)]
+
+# Character class describing NM global symbol codes.
+symcode='[BCDEGRST]'
+
+# Regexp to match symbols that can be accessed directly from C.
+sympat='\([_A-Za-z][_A-Za-z0-9]*\)'
+
+# Define system-specific variables.
+case $host_os in
+aix*)
+ symcode='[BCDT]'
+ ;;
+cygwin* | mingw* | pw32* | cegcc*)
+ symcode='[ABCDGISTW]'
+ ;;
+hpux*)
+ if test "$host_cpu" = ia64; then
+ symcode='[ABCDEGRST]'
+ fi
+ ;;
+irix* | nonstopux*)
+ symcode='[BCDEGRST]'
+ ;;
+osf*)
+ symcode='[BCDEGQRST]'
+ ;;
+solaris*)
+ symcode='[BDRT]'
+ ;;
+sco3.2v5*)
+ symcode='[DT]'
+ ;;
+sysv4.2uw2*)
+ symcode='[DT]'
+ ;;
+sysv5* | sco5v6* | unixware* | OpenUNIX*)
+ symcode='[ABDT]'
+ ;;
+sysv4)
+ symcode='[DFNSTU]'
+ ;;
+esac
+
+# If we're using GNU nm, then use its standard symbol codes.
+case `$NM -V 2>&1` in
+*GNU* | *'with BFD'*)
+ symcode='[ABCDGIRSTW]' ;;
+esac
+
+# Transform an extracted symbol line into a proper C declaration.
+# Some systems (esp. on ia64) link data and code symbols differently,
+# so use this general approach.
+lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'"
+
+# Transform an extracted symbol line into symbol name and symbol address
+lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"\2\", (void *) \&\2},/p'"
+lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([^ ]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([^ ]*\) \(lib[^ ]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([^ ]*\) \([^ ]*\)$/ {\"lib\2\", (void *) \&\2},/p'"
+
+# Handle CRLF in mingw tool chain
+opt_cr=
+case $build_os in
+mingw*)
+ opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp
+ ;;
+esac
+
+# Try without a prefix underscore, then with it.
+for ac_symprfx in "" "_"; do
+
+ # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol.
+ symxfrm="\\1 $ac_symprfx\\2 \\2"
+
+ # Write the raw and C identifiers.
+ if test "$lt_cv_nm_interface" = "MS dumpbin"; then
+ # Fake it for dumpbin and say T for any non-static function
+ # and D for any global variable.
+ # Also find C++ and __fastcall symbols from MSVC++,
+ # which start with @ or ?.
+ lt_cv_sys_global_symbol_pipe="$AWK '"\
+" {last_section=section; section=\$ 3};"\
+" /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\
+" \$ 0!~/External *\|/{next};"\
+" / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\
+" {if(hide[section]) next};"\
+" {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\
+" {split(\$ 0, a, /\||\r/); split(a[2], s)};"\
+" s[1]~/^[@?]/{print s[1], s[1]; next};"\
+" s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\
+" ' prfx=^$ac_symprfx"
+ else
+ lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[ ]\($symcode$symcode*\)[ ][ ]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'"
+ fi
+
+ # Check to see that the pipe works correctly.
+ pipe_works=no
+
+ rm -f conftest*
+ cat > conftest.$ac_ext <<_LT_EOF
+#ifdef __cplusplus
+extern "C" {
+#endif
+char nm_test_var;
+void nm_test_func(void);
+void nm_test_func(void){}
+#ifdef __cplusplus
+}
+#endif
+int main(){nm_test_var='a';nm_test_func();return(0);}
+_LT_EOF
+
+ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
+ # Now try to grab the symbols.
+ nlist=conftest.nm
+ if { (eval echo "$as_me:$LINENO: \"$NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist\"") >&5
+ (eval $NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && test -s "$nlist"; then
+ # Try sorting and uniquifying the output.
+ if sort "$nlist" | uniq > "$nlist"T; then
+ mv -f "$nlist"T "$nlist"
+ else
+ rm -f "$nlist"T
+ fi
+
+ # Make sure that we snagged all the symbols we need.
+ if $GREP ' nm_test_var$' "$nlist" >/dev/null; then
+ if $GREP ' nm_test_func$' "$nlist" >/dev/null; then
+ cat <<_LT_EOF > conftest.$ac_ext
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+_LT_EOF
+ # Now generate the symbol file.
+ eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext'
+
+ cat <<_LT_EOF >> conftest.$ac_ext
+
+/* The mapping between symbol names and symbols. */
+const struct {
+ const char *name;
+ void *address;
+}
+lt__PROGRAM__LTX_preloaded_symbols[] =
+{
+ { "@PROGRAM@", (void *) 0 },
+_LT_EOF
+ $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext
+ cat <<\_LT_EOF >> conftest.$ac_ext
+ {0, (void *) 0}
+};
+
+/* This works around a problem in FreeBSD linker */
+#ifdef FREEBSD_WORKAROUND
+static const void *lt_preloaded_setup() {
+ return lt__PROGRAM__LTX_preloaded_symbols;
+}
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+_LT_EOF
+ # Now try linking the two files.
+ mv conftest.$ac_objext conftstm.$ac_objext
+ lt_save_LIBS="$LIBS"
+ lt_save_CFLAGS="$CFLAGS"
+ LIBS="conftstm.$ac_objext"
+ CFLAGS="$CFLAGS$lt_prog_compiler_no_builtin_flag"
+ if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
+ (eval $ac_link) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && test -s conftest${ac_exeext}; then
+ pipe_works=yes
+ fi
+ LIBS="$lt_save_LIBS"
+ CFLAGS="$lt_save_CFLAGS"
+ else
+ echo "cannot find nm_test_func in $nlist" >&5
+ fi
+ else
+ echo "cannot find nm_test_var in $nlist" >&5
+ fi
+ else
+ echo "cannot run $lt_cv_sys_global_symbol_pipe" >&5
+ fi
+ else
+ echo "$progname: failed program was:" >&5
+ cat conftest.$ac_ext >&5
+ fi
+ rm -rf conftest* conftst*
+
+ # Do not use the global_symbol_pipe unless it works.
+ if test "$pipe_works" = yes; then
+ break
+ else
+ lt_cv_sys_global_symbol_pipe=
+ fi
+done
+
+fi
+
+if test -z "$lt_cv_sys_global_symbol_pipe"; then
+ lt_cv_sys_global_symbol_to_cdecl=
+fi
+if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then
+ { $as_echo "$as_me:$LINENO: result: failed" >&5
+$as_echo "failed" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: ok" >&5
+$as_echo "ok" >&6; }
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+# Check whether --enable-libtool-lock was given.
+if test "${enable_libtool_lock+set}" = set; then
+ enableval=$enable_libtool_lock;
+fi
+
+test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes
+
+# Some flags need to be propagated to the compiler or linker for good
+# libtool support.
+case $host in
+ia64-*-hpux*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *ELF-32*)
+ HPUX_IA64_MODE="32"
+ ;;
+ *ELF-64*)
+ HPUX_IA64_MODE="64"
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+*-*-irix6*)
+ # Find out which ABI we are using.
+ echo '#line 6441 "configure"' > conftest.$ac_ext
+ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *32-bit*)
+ LD="${LD-ld} -melf32bsmip"
+ ;;
+ *N32*)
+ LD="${LD-ld} -melf32bmipn32"
+ ;;
+ *64-bit*)
+ LD="${LD-ld} -melf64bmip"
+ ;;
+ esac
+ else
+ case `/usr/bin/file conftest.$ac_objext` in
+ *32-bit*)
+ LD="${LD-ld} -32"
+ ;;
+ *N32*)
+ LD="${LD-ld} -n32"
+ ;;
+ *64-bit*)
+ LD="${LD-ld} -64"
+ ;;
+ esac
+ fi
+ fi
+ rm -rf conftest*
+ ;;
+
+x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \
+s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
+ case `/usr/bin/file conftest.o` in
+ *32-bit*)
+ case $host in
+ x86_64-*kfreebsd*-gnu)
+ LD="${LD-ld} -m elf_i386_fbsd"
+ ;;
+ x86_64-*linux*)
+ LD="${LD-ld} -m elf_i386"
+ ;;
+ ppc64-*linux*|powerpc64-*linux*)
+ LD="${LD-ld} -m elf32ppclinux"
+ ;;
+ s390x-*linux*)
+ LD="${LD-ld} -m elf_s390"
+ ;;
+ sparc64-*linux*)
+ LD="${LD-ld} -m elf32_sparc"
+ ;;
+ esac
+ ;;
+ *64-bit*)
+ case $host in
+ x86_64-*kfreebsd*-gnu)
+ LD="${LD-ld} -m elf_x86_64_fbsd"
+ ;;
+ x86_64-*linux*)
+ LD="${LD-ld} -m elf_x86_64"
+ ;;
+ ppc*-*linux*|powerpc*-*linux*)
+ LD="${LD-ld} -m elf64ppc"
+ ;;
+ s390*-*linux*|s390*-*tpf*)
+ LD="${LD-ld} -m elf64_s390"
+ ;;
+ sparc*-*linux*)
+ LD="${LD-ld} -m elf64_sparc"
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+
+*-*-sco3.2v5*)
+ # On SCO OpenServer 5, we need -belf to get full-featured binaries.
+ SAVE_CFLAGS="$CFLAGS"
+ CFLAGS="$CFLAGS -belf"
+ { $as_echo "$as_me:$LINENO: checking whether the C compiler needs -belf" >&5
+$as_echo_n "checking whether the C compiler needs -belf... " >&6; }
+if test "${lt_cv_cc_needs_belf+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ lt_cv_cc_needs_belf=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ lt_cv_cc_needs_belf=no
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+ ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_cc_needs_belf" >&5
+$as_echo "$lt_cv_cc_needs_belf" >&6; }
+ if test x"$lt_cv_cc_needs_belf" != x"yes"; then
+ # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf
+ CFLAGS="$SAVE_CFLAGS"
+ fi
+ ;;
+sparc*-*solaris*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
+ case `/usr/bin/file conftest.o` in
+ *64-bit*)
+ case $lt_cv_prog_gnu_ld in
+ yes*) LD="${LD-ld} -m elf64_sparc" ;;
+ *)
+ if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then
+ LD="${LD-ld} -64"
+ fi
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+esac
+
+need_locks="$enable_libtool_lock"
+
+
+ case $host_os in
+ rhapsody* | darwin*)
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}dsymutil", so it can be a program name with args.
+set dummy ${ac_tool_prefix}dsymutil; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_DSYMUTIL+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$DSYMUTIL"; then
+ ac_cv_prog_DSYMUTIL="$DSYMUTIL" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_DSYMUTIL="${ac_tool_prefix}dsymutil"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+DSYMUTIL=$ac_cv_prog_DSYMUTIL
+if test -n "$DSYMUTIL"; then
+ { $as_echo "$as_me:$LINENO: result: $DSYMUTIL" >&5
+$as_echo "$DSYMUTIL" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_DSYMUTIL"; then
+ ac_ct_DSYMUTIL=$DSYMUTIL
+ # Extract the first word of "dsymutil", so it can be a program name with args.
+set dummy dsymutil; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_DSYMUTIL+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_DSYMUTIL"; then
+ ac_cv_prog_ac_ct_DSYMUTIL="$ac_ct_DSYMUTIL" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_DSYMUTIL="dsymutil"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_DSYMUTIL=$ac_cv_prog_ac_ct_DSYMUTIL
+if test -n "$ac_ct_DSYMUTIL"; then
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_DSYMUTIL" >&5
+$as_echo "$ac_ct_DSYMUTIL" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_DSYMUTIL" = x; then
+ DSYMUTIL=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ DSYMUTIL=$ac_ct_DSYMUTIL
+ fi
+else
+ DSYMUTIL="$ac_cv_prog_DSYMUTIL"
+fi
+
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}nmedit", so it can be a program name with args.
+set dummy ${ac_tool_prefix}nmedit; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_NMEDIT+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$NMEDIT"; then
+ ac_cv_prog_NMEDIT="$NMEDIT" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_NMEDIT="${ac_tool_prefix}nmedit"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+NMEDIT=$ac_cv_prog_NMEDIT
+if test -n "$NMEDIT"; then
+ { $as_echo "$as_me:$LINENO: result: $NMEDIT" >&5
+$as_echo "$NMEDIT" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_NMEDIT"; then
+ ac_ct_NMEDIT=$NMEDIT
+ # Extract the first word of "nmedit", so it can be a program name with args.
+set dummy nmedit; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_NMEDIT+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_NMEDIT"; then
+ ac_cv_prog_ac_ct_NMEDIT="$ac_ct_NMEDIT" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_NMEDIT="nmedit"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_NMEDIT=$ac_cv_prog_ac_ct_NMEDIT
+if test -n "$ac_ct_NMEDIT"; then
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_NMEDIT" >&5
+$as_echo "$ac_ct_NMEDIT" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_NMEDIT" = x; then
+ NMEDIT=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ NMEDIT=$ac_ct_NMEDIT
+ fi
+else
+ NMEDIT="$ac_cv_prog_NMEDIT"
+fi
+
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}lipo", so it can be a program name with args.
+set dummy ${ac_tool_prefix}lipo; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_LIPO+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$LIPO"; then
+ ac_cv_prog_LIPO="$LIPO" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_LIPO="${ac_tool_prefix}lipo"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+LIPO=$ac_cv_prog_LIPO
+if test -n "$LIPO"; then
+ { $as_echo "$as_me:$LINENO: result: $LIPO" >&5
+$as_echo "$LIPO" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_LIPO"; then
+ ac_ct_LIPO=$LIPO
+ # Extract the first word of "lipo", so it can be a program name with args.
+set dummy lipo; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_LIPO+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_LIPO"; then
+ ac_cv_prog_ac_ct_LIPO="$ac_ct_LIPO" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_LIPO="lipo"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_LIPO=$ac_cv_prog_ac_ct_LIPO
+if test -n "$ac_ct_LIPO"; then
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_LIPO" >&5
+$as_echo "$ac_ct_LIPO" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_LIPO" = x; then
+ LIPO=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ LIPO=$ac_ct_LIPO
+ fi
+else
+ LIPO="$ac_cv_prog_LIPO"
+fi
+
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}otool", so it can be a program name with args.
+set dummy ${ac_tool_prefix}otool; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_OTOOL+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$OTOOL"; then
+ ac_cv_prog_OTOOL="$OTOOL" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_OTOOL="${ac_tool_prefix}otool"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+OTOOL=$ac_cv_prog_OTOOL
+if test -n "$OTOOL"; then
+ { $as_echo "$as_me:$LINENO: result: $OTOOL" >&5
+$as_echo "$OTOOL" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_OTOOL"; then
+ ac_ct_OTOOL=$OTOOL
+ # Extract the first word of "otool", so it can be a program name with args.
+set dummy otool; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_OTOOL+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_OTOOL"; then
+ ac_cv_prog_ac_ct_OTOOL="$ac_ct_OTOOL" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_OTOOL="otool"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_OTOOL=$ac_cv_prog_ac_ct_OTOOL
+if test -n "$ac_ct_OTOOL"; then
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_OTOOL" >&5
+$as_echo "$ac_ct_OTOOL" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_OTOOL" = x; then
+ OTOOL=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ OTOOL=$ac_ct_OTOOL
+ fi
+else
+ OTOOL="$ac_cv_prog_OTOOL"
+fi
+
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}otool64", so it can be a program name with args.
+set dummy ${ac_tool_prefix}otool64; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_OTOOL64+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$OTOOL64"; then
+ ac_cv_prog_OTOOL64="$OTOOL64" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_OTOOL64="${ac_tool_prefix}otool64"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+OTOOL64=$ac_cv_prog_OTOOL64
+if test -n "$OTOOL64"; then
+ { $as_echo "$as_me:$LINENO: result: $OTOOL64" >&5
+$as_echo "$OTOOL64" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_OTOOL64"; then
+ ac_ct_OTOOL64=$OTOOL64
+ # Extract the first word of "otool64", so it can be a program name with args.
+set dummy otool64; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_OTOOL64+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_OTOOL64"; then
+ ac_cv_prog_ac_ct_OTOOL64="$ac_ct_OTOOL64" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_OTOOL64="otool64"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_OTOOL64=$ac_cv_prog_ac_ct_OTOOL64
+if test -n "$ac_ct_OTOOL64"; then
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_OTOOL64" >&5
+$as_echo "$ac_ct_OTOOL64" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_OTOOL64" = x; then
+ OTOOL64=":"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ OTOOL64=$ac_ct_OTOOL64
+ fi
+else
+ OTOOL64="$ac_cv_prog_OTOOL64"
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ { $as_echo "$as_me:$LINENO: checking for -single_module linker flag" >&5
+$as_echo_n "checking for -single_module linker flag... " >&6; }
+if test "${lt_cv_apple_cc_single_mod+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_apple_cc_single_mod=no
+ if test -z "${LT_MULTI_MODULE}"; then
+ # By default we will add the -single_module flag. You can override
+ # by either setting the environment variable LT_MULTI_MODULE
+ # non-empty at configure time, or by adding -multi_module to the
+ # link flags.
+ rm -rf libconftest.dylib*
+ echo "int foo(void){return 1;}" > conftest.c
+ echo "$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
+-dynamiclib -Wl,-single_module conftest.c" >&5
+ $LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
+ -dynamiclib -Wl,-single_module conftest.c 2>conftest.err
+ _lt_result=$?
+ if test -f libconftest.dylib && test ! -s conftest.err && test $_lt_result = 0; then
+ lt_cv_apple_cc_single_mod=yes
+ else
+ cat conftest.err >&5
+ fi
+ rm -rf libconftest.dylib*
+ rm -f conftest.*
+ fi
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_apple_cc_single_mod" >&5
+$as_echo "$lt_cv_apple_cc_single_mod" >&6; }
+ { $as_echo "$as_me:$LINENO: checking for -exported_symbols_list linker flag" >&5
+$as_echo_n "checking for -exported_symbols_list linker flag... " >&6; }
+if test "${lt_cv_ld_exported_symbols_list+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_ld_exported_symbols_list=no
+ save_LDFLAGS=$LDFLAGS
+ echo "_main" > conftest.sym
+ LDFLAGS="$LDFLAGS -Wl,-exported_symbols_list,conftest.sym"
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ lt_cv_ld_exported_symbols_list=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ lt_cv_ld_exported_symbols_list=no
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+ LDFLAGS="$save_LDFLAGS"
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_ld_exported_symbols_list" >&5
+$as_echo "$lt_cv_ld_exported_symbols_list" >&6; }
+ case $host_os in
+ rhapsody* | darwin1.[012])
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}suppress' ;;
+ darwin1.*)
+ _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;
+ darwin*) # darwin 5.x on
+ # if running on 10.5 or later, the deployment target defaults
+ # to the OS version, if on x86, and 10.4, the deployment
+ # target defaults to 10.4. Don't you love it?
+ case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in
+ 10.0,*86*-darwin8*|10.0,*-darwin[91]*)
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;
+ 10.[012]*)
+ _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;
+ 10.*)
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;
+ esac
+ ;;
+ esac
+ if test "$lt_cv_apple_cc_single_mod" = "yes"; then
+ _lt_dar_single_mod='$single_module'
+ fi
+ if test "$lt_cv_ld_exported_symbols_list" = "yes"; then
+ _lt_dar_export_syms=' ${wl}-exported_symbols_list,$output_objdir/${libname}-symbols.expsym'
+ else
+ _lt_dar_export_syms='~$NMEDIT -s $output_objdir/${libname}-symbols.expsym ${lib}'
+ fi
+ if test "$DSYMUTIL" != ":"; then
+ _lt_dsymutil='~$DSYMUTIL $lib || :'
+ else
+ _lt_dsymutil=
+ fi
+ ;;
+ esac
+
+
+for ac_header in dlfcn.h
+do
+as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
+$as_echo_n "checking for $ac_header... " >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+
+#include <$ac_header>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ eval "$as_ac_Header=yes"
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ eval "$as_ac_Header=no"
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+ac_res=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+as_val=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ if test "x$as_val" = x""yes; then
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+
+done
+
+
+
+# Set options
+
+
+
+ enable_dlopen=no
+
+
+ enable_win32_dll=no
+
+
+ # Check whether --enable-shared was given.
+if test "${enable_shared+set}" = set; then
+ enableval=$enable_shared; p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_shared=yes ;;
+ no) enable_shared=no ;;
+ *)
+ enable_shared=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_shared=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac
+else
+ enable_shared=yes
+fi
+
+
+
+
+
+
+
+
+
+ # Check whether --enable-static was given.
+if test "${enable_static+set}" = set; then
+ enableval=$enable_static; p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_static=yes ;;
+ no) enable_static=no ;;
+ *)
+ enable_static=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_static=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac
+else
+ enable_static=yes
+fi
+
+
+
+
+
+
+
+
+
+
+# Check whether --with-pic was given.
+if test "${with_pic+set}" = set; then
+ withval=$with_pic; pic_mode="$withval"
+else
+ pic_mode=default
+fi
+
+
+test -z "$pic_mode" && pic_mode=default
+
+
+
+
+
+
+
+ # Check whether --enable-fast-install was given.
+if test "${enable_fast_install+set}" = set; then
+ enableval=$enable_fast_install; p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_fast_install=yes ;;
+ no) enable_fast_install=no ;;
+ *)
+ enable_fast_install=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_fast_install=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac
+else
+ enable_fast_install=yes
+fi
+
+
+
+
+
+
+
+
+
+
+
+# This can be used to rebuild libtool when needed
+LIBTOOL_DEPS="$ltmain"
+
+# Always use our own libtool.
+LIBTOOL='$(SHELL) $(top_builddir)/libtool'
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+test -z "$LN_S" && LN_S="ln -s"
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+if test -n "${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+fi
+
+{ $as_echo "$as_me:$LINENO: checking for objdir" >&5
+$as_echo_n "checking for objdir... " >&6; }
+if test "${lt_cv_objdir+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ rm -f .libs 2>/dev/null
+mkdir .libs 2>/dev/null
+if test -d .libs; then
+ lt_cv_objdir=.libs
+else
+ # MS-DOS does not allow filenames that begin with a dot.
+ lt_cv_objdir=_libs
+fi
+rmdir .libs 2>/dev/null
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_objdir" >&5
+$as_echo "$lt_cv_objdir" >&6; }
+objdir=$lt_cv_objdir
+
+
+
+
+
+cat >>confdefs.h <<_ACEOF
+#define LT_OBJDIR "$lt_cv_objdir/"
+_ACEOF
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+case $host_os in
+aix3*)
+ # AIX sometimes has problems with the GCC collect2 program. For some
+ # reason, if we set the COLLECT_NAMES environment variable, the problems
+ # vanish in a puff of smoke.
+ if test "X${COLLECT_NAMES+set}" != Xset; then
+ COLLECT_NAMES=
+ export COLLECT_NAMES
+ fi
+ ;;
+esac
+
+# Sed substitution that helps us do robust quoting. It backslashifies
+# metacharacters that are still active within double-quoted strings.
+sed_quote_subst='s/\(["`$\\]\)/\\\1/g'
+
+# Same as above, but do not quote variable references.
+double_quote_subst='s/\(["`\\]\)/\\\1/g'
+
+# Sed substitution to delay expansion of an escaped shell variable in a
+# double_quote_subst'ed string.
+delay_variable_subst='s/\\\\\\\\\\\$/\\\\\\$/g'
+
+# Sed substitution to delay expansion of an escaped single quote.
+delay_single_quote_subst='s/'\''/'\'\\\\\\\'\''/g'
+
+# Sed substitution to avoid accidental globbing in evaled expressions
+no_glob_subst='s/\*/\\\*/g'
+
+# Global variables:
+ofile=libtool
+can_build_shared=yes
+
+# All known linkers require a `.a' archive for static linking (except MSVC,
+# which needs '.lib').
+libext=a
+
+with_gnu_ld="$lt_cv_prog_gnu_ld"
+
+old_CC="$CC"
+old_CFLAGS="$CFLAGS"
+
+# Set sane defaults for various variables
+test -z "$CC" && CC=cc
+test -z "$LTCC" && LTCC=$CC
+test -z "$LTCFLAGS" && LTCFLAGS=$CFLAGS
+test -z "$LD" && LD=ld
+test -z "$ac_objext" && ac_objext=o
+
+for cc_temp in $compiler""; do
+ case $cc_temp in
+ compile | *[\\/]compile | ccache | *[\\/]ccache ) ;;
+ distcc | *[\\/]distcc | purify | *[\\/]purify ) ;;
+ \-*) ;;
+ *) break;;
+ esac
+done
+cc_basename=`$ECHO "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+
+
+# Only perform the check for file, if the check method requires it
+test -z "$MAGIC_CMD" && MAGIC_CMD=file
+case $deplibs_check_method in
+file_magic*)
+ if test "$file_magic_cmd" = '$MAGIC_CMD'; then
+ { $as_echo "$as_me:$LINENO: checking for ${ac_tool_prefix}file" >&5
+$as_echo_n "checking for ${ac_tool_prefix}file... " >&6; }
+if test "${lt_cv_path_MAGIC_CMD+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ case $MAGIC_CMD in
+[\\/*] | ?:[\\/]*)
+ lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path.
+ ;;
+*)
+ lt_save_MAGIC_CMD="$MAGIC_CMD"
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ ac_dummy="/usr/bin$PATH_SEPARATOR$PATH"
+ for ac_dir in $ac_dummy; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f $ac_dir/${ac_tool_prefix}file; then
+ lt_cv_path_MAGIC_CMD="$ac_dir/${ac_tool_prefix}file"
+ if test -n "$file_magic_test_file"; then
+ case $deplibs_check_method in
+ "file_magic "*)
+ file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"`
+ MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+ if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null |
+ $EGREP "$file_magic_regex" > /dev/null; then
+ :
+ else
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the command libtool uses to detect shared libraries,
+*** $file_magic_cmd, produces output that libtool cannot recognize.
+*** The result is that libtool may fail to recognize shared libraries
+*** as such. This will affect the creation of libtool libraries that
+*** depend on shared libraries, but programs linked with such libtool
+*** libraries will work regardless of this problem. Nevertheless, you
+*** may want to report the problem to your system manager and/or to
+*** bug-libtool@gnu.org
+
+_LT_EOF
+ fi ;;
+ esac
+ fi
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+ MAGIC_CMD="$lt_save_MAGIC_CMD"
+ ;;
+esac
+fi
+
+MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+if test -n "$MAGIC_CMD"; then
+ { $as_echo "$as_me:$LINENO: result: $MAGIC_CMD" >&5
+$as_echo "$MAGIC_CMD" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+
+
+
+if test -z "$lt_cv_path_MAGIC_CMD"; then
+ if test -n "$ac_tool_prefix"; then
+ { $as_echo "$as_me:$LINENO: checking for file" >&5
+$as_echo_n "checking for file... " >&6; }
+if test "${lt_cv_path_MAGIC_CMD+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ case $MAGIC_CMD in
+[\\/*] | ?:[\\/]*)
+ lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path.
+ ;;
+*)
+ lt_save_MAGIC_CMD="$MAGIC_CMD"
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ ac_dummy="/usr/bin$PATH_SEPARATOR$PATH"
+ for ac_dir in $ac_dummy; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f $ac_dir/file; then
+ lt_cv_path_MAGIC_CMD="$ac_dir/file"
+ if test -n "$file_magic_test_file"; then
+ case $deplibs_check_method in
+ "file_magic "*)
+ file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"`
+ MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+ if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null |
+ $EGREP "$file_magic_regex" > /dev/null; then
+ :
+ else
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the command libtool uses to detect shared libraries,
+*** $file_magic_cmd, produces output that libtool cannot recognize.
+*** The result is that libtool may fail to recognize shared libraries
+*** as such. This will affect the creation of libtool libraries that
+*** depend on shared libraries, but programs linked with such libtool
+*** libraries will work regardless of this problem. Nevertheless, you
+*** may want to report the problem to your system manager and/or to
+*** bug-libtool@gnu.org
+
+_LT_EOF
+ fi ;;
+ esac
+ fi
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+ MAGIC_CMD="$lt_save_MAGIC_CMD"
+ ;;
+esac
+fi
+
+MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+if test -n "$MAGIC_CMD"; then
+ { $as_echo "$as_me:$LINENO: result: $MAGIC_CMD" >&5
+$as_echo "$MAGIC_CMD" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ else
+ MAGIC_CMD=:
+ fi
+fi
+
+ fi
+ ;;
+esac
+
+# Use C for the default configuration in the libtool script
+
+lt_save_CC="$CC"
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+# Source file extension for C test sources.
+ac_ext=c
+
+# Object file extension for compiled C test sources.
+objext=o
+objext=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="int some_variable = 0;"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='int main(){return(0);}'
+
+
+
+
+
+
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+
+# Save the default compiler, since it gets overwritten when the other
+# tags are being tested, and _LT_TAGVAR(compiler, []) is a NOP.
+compiler_DEFAULT=$CC
+
+# save warnings/boilerplate of simple test code
+ac_outfile=conftest.$ac_objext
+echo "$lt_simple_compile_test_code" >conftest.$ac_ext
+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_compiler_boilerplate=`cat conftest.err`
+$RM conftest*
+
+ac_outfile=conftest.$ac_objext
+echo "$lt_simple_link_test_code" >conftest.$ac_ext
+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_linker_boilerplate=`cat conftest.err`
+$RM -r conftest*
+
+
+## CAVEAT EMPTOR:
+## There is no encapsulation within the following macros, do not change
+## the running order or otherwise move them around unless you know exactly
+## what you are doing...
+if test -n "$compiler"; then
+
+lt_prog_compiler_no_builtin_flag=
+
+if test "$GCC" = yes; then
+ lt_prog_compiler_no_builtin_flag=' -fno-builtin'
+
+ { $as_echo "$as_me:$LINENO: checking if $compiler supports -fno-rtti -fno-exceptions" >&5
+$as_echo_n "checking if $compiler supports -fno-rtti -fno-exceptions... " >&6; }
+if test "${lt_cv_prog_compiler_rtti_exceptions+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_rtti_exceptions=no
+ ac_outfile=conftest.$ac_objext
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+ lt_compiler_flag="-fno-rtti -fno-exceptions"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ # The option is referenced via a variable to avoid confusing sed.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:7810: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>conftest.err)
+ ac_status=$?
+ cat conftest.err >&5
+ echo "$as_me:7814: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s "$ac_outfile"; then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings other than the usual output.
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_rtti_exceptions=yes
+ fi
+ fi
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_rtti_exceptions" >&5
+$as_echo "$lt_cv_prog_compiler_rtti_exceptions" >&6; }
+
+if test x"$lt_cv_prog_compiler_rtti_exceptions" = xyes; then
+ lt_prog_compiler_no_builtin_flag="$lt_prog_compiler_no_builtin_flag -fno-rtti -fno-exceptions"
+else
+ :
+fi
+
+fi
+
+
+
+
+
+
+ lt_prog_compiler_wl=
+lt_prog_compiler_pic=
+lt_prog_compiler_static=
+
+{ $as_echo "$as_me:$LINENO: checking for $compiler option to produce PIC" >&5
+$as_echo_n "checking for $compiler option to produce PIC... " >&6; }
+
+ if test "$GCC" = yes; then
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_static='-static'
+
+ case $host_os in
+ aix*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ lt_prog_compiler_static='-Bstatic'
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ lt_prog_compiler_pic='-fPIC'
+ ;;
+ m68k)
+ # FIXME: we need at least 68020 code to build shared libraries, but
+ # adding the `-m68020' flag to GCC prevents building anything better,
+ # like `-m68040'.
+ lt_prog_compiler_pic='-m68020 -resident32 -malways-restore-a4'
+ ;;
+ esac
+ ;;
+
+ beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+ # PIC is the default for these OSes.
+ ;;
+
+ mingw* | cygwin* | pw32* | os2* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ # Although the cygwin gcc ignores -fPIC, still need this for old-style
+ # (--disable-auto-import) libraries
+ lt_prog_compiler_pic='-DDLL_EXPORT'
+ ;;
+
+ darwin* | rhapsody*)
+ # PIC is the default on this platform
+ # Common symbols not allowed in MH_DYLIB files
+ lt_prog_compiler_pic='-fno-common'
+ ;;
+
+ hpux*)
+ # PIC is the default for 64-bit PA HP-UX, but not for 32-bit
+ # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag
+ # sets the default TLS model and affects inlining.
+ case $host_cpu in
+ hppa*64*)
+ # +Z the default
+ ;;
+ *)
+ lt_prog_compiler_pic='-fPIC'
+ ;;
+ esac
+ ;;
+
+ interix[3-9]*)
+ # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+ # Instead, we relocate shared libraries at runtime.
+ ;;
+
+ msdosdjgpp*)
+ # Just because we use GCC doesn't mean we suddenly get shared libraries
+ # on systems that don't support them.
+ lt_prog_compiler_can_build_shared=no
+ enable_shared=no
+ ;;
+
+ *nto* | *qnx*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ lt_prog_compiler_pic='-fPIC -shared'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ lt_prog_compiler_pic=-Kconform_pic
+ fi
+ ;;
+
+ *)
+ lt_prog_compiler_pic='-fPIC'
+ ;;
+ esac
+ else
+ # PORTME Check for flag to pass linker flags through the system compiler.
+ case $host_os in
+ aix*)
+ lt_prog_compiler_wl='-Wl,'
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ lt_prog_compiler_static='-Bstatic'
+ else
+ lt_prog_compiler_static='-bnso -bI:/lib/syscalls.exp'
+ fi
+ ;;
+
+ mingw* | cygwin* | pw32* | os2* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ lt_prog_compiler_pic='-DDLL_EXPORT'
+ ;;
+
+ hpux9* | hpux10* | hpux11*)
+ lt_prog_compiler_wl='-Wl,'
+ # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but
+ # not for PA HP-UX.
+ case $host_cpu in
+ hppa*64*|ia64*)
+ # +Z the default
+ ;;
+ *)
+ lt_prog_compiler_pic='+Z'
+ ;;
+ esac
+ # Is there a better lt_prog_compiler_static that works with the bundled CC?
+ lt_prog_compiler_static='${wl}-a ${wl}archive'
+ ;;
+
+ irix5* | irix6* | nonstopux*)
+ lt_prog_compiler_wl='-Wl,'
+ # PIC (with -KPIC) is the default.
+ lt_prog_compiler_static='-non_shared'
+ ;;
+
+ linux* | k*bsd*-gnu)
+ case $cc_basename in
+ # old Intel for x86_64 which still supported -KPIC.
+ ecc*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-static'
+ ;;
+ # icc used to be incompatible with GCC.
+ # ICC 10 doesn't accept -KPIC any more.
+ icc* | ifort*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-fPIC'
+ lt_prog_compiler_static='-static'
+ ;;
+ # Lahey Fortran 8.1.
+ lf95*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='--shared'
+ lt_prog_compiler_static='--static'
+ ;;
+ pgcc* | pgf77* | pgf90* | pgf95*)
+ # Portland Group compilers (*not* the Pentium gcc compiler,
+ # which looks to be a dead project)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-fpic'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+ ccc*)
+ lt_prog_compiler_wl='-Wl,'
+ # All Alpha code is PIC.
+ lt_prog_compiler_static='-non_shared'
+ ;;
+ xl*)
+ # IBM XL C 8.0/Fortran 10.1 on PPC
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-qpic'
+ lt_prog_compiler_static='-qstaticlink'
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C 5.9
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ lt_prog_compiler_wl='-Wl,'
+ ;;
+ *Sun\ F*)
+ # Sun Fortran 8.3 passes all unrecognized flags to the linker
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ lt_prog_compiler_wl=''
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+
+ newsos6)
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ *nto* | *qnx*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ lt_prog_compiler_pic='-fPIC -shared'
+ ;;
+
+ osf3* | osf4* | osf5*)
+ lt_prog_compiler_wl='-Wl,'
+ # All OSF/1 code is PIC.
+ lt_prog_compiler_static='-non_shared'
+ ;;
+
+ rdos*)
+ lt_prog_compiler_static='-non_shared'
+ ;;
+
+ solaris*)
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ case $cc_basename in
+ f77* | f90* | f95*)
+ lt_prog_compiler_wl='-Qoption ld ';;
+ *)
+ lt_prog_compiler_wl='-Wl,';;
+ esac
+ ;;
+
+ sunos4*)
+ lt_prog_compiler_wl='-Qoption ld '
+ lt_prog_compiler_pic='-PIC'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ sysv4 | sysv4.2uw2* | sysv4.3*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec ;then
+ lt_prog_compiler_pic='-Kconform_pic'
+ lt_prog_compiler_static='-Bstatic'
+ fi
+ ;;
+
+ sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_pic='-KPIC'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ unicos*)
+ lt_prog_compiler_wl='-Wl,'
+ lt_prog_compiler_can_build_shared=no
+ ;;
+
+ uts4*)
+ lt_prog_compiler_pic='-pic'
+ lt_prog_compiler_static='-Bstatic'
+ ;;
+
+ *)
+ lt_prog_compiler_can_build_shared=no
+ ;;
+ esac
+ fi
+
+case $host_os in
+ # For platforms which do not support PIC, -DPIC is meaningless:
+ *djgpp*)
+ lt_prog_compiler_pic=
+ ;;
+ *)
+ lt_prog_compiler_pic="$lt_prog_compiler_pic -DPIC"
+ ;;
+esac
+{ $as_echo "$as_me:$LINENO: result: $lt_prog_compiler_pic" >&5
+$as_echo "$lt_prog_compiler_pic" >&6; }
+
+
+
+
+
+
+#
+# Check to make sure the PIC flag actually works.
+#
+if test -n "$lt_prog_compiler_pic"; then
+ { $as_echo "$as_me:$LINENO: checking if $compiler PIC flag $lt_prog_compiler_pic works" >&5
+$as_echo_n "checking if $compiler PIC flag $lt_prog_compiler_pic works... " >&6; }
+if test "${lt_cv_prog_compiler_pic_works+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_pic_works=no
+ ac_outfile=conftest.$ac_objext
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+ lt_compiler_flag="$lt_prog_compiler_pic -DPIC"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ # The option is referenced via a variable to avoid confusing sed.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:8149: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>conftest.err)
+ ac_status=$?
+ cat conftest.err >&5
+ echo "$as_me:8153: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s "$ac_outfile"; then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings other than the usual output.
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_pic_works=yes
+ fi
+ fi
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_pic_works" >&5
+$as_echo "$lt_cv_prog_compiler_pic_works" >&6; }
+
+if test x"$lt_cv_prog_compiler_pic_works" = xyes; then
+ case $lt_prog_compiler_pic in
+ "" | " "*) ;;
+ *) lt_prog_compiler_pic=" $lt_prog_compiler_pic" ;;
+ esac
+else
+ lt_prog_compiler_pic=
+ lt_prog_compiler_can_build_shared=no
+fi
+
+fi
+
+
+
+
+
+
+#
+# Check to make sure the static flag actually works.
+#
+wl=$lt_prog_compiler_wl eval lt_tmp_static_flag=\"$lt_prog_compiler_static\"
+{ $as_echo "$as_me:$LINENO: checking if $compiler static flag $lt_tmp_static_flag works" >&5
+$as_echo_n "checking if $compiler static flag $lt_tmp_static_flag works... " >&6; }
+if test "${lt_cv_prog_compiler_static_works+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_static_works=no
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS $lt_tmp_static_flag"
+ echo "$lt_simple_link_test_code" > conftest.$ac_ext
+ if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then
+ # The linker can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ if test -s conftest.err; then
+ # Append any errors to the config.log.
+ cat conftest.err 1>&5
+ $ECHO "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_static_works=yes
+ fi
+ else
+ lt_cv_prog_compiler_static_works=yes
+ fi
+ fi
+ $RM -r conftest*
+ LDFLAGS="$save_LDFLAGS"
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_static_works" >&5
+$as_echo "$lt_cv_prog_compiler_static_works" >&6; }
+
+if test x"$lt_cv_prog_compiler_static_works" = xyes; then
+ :
+else
+ lt_prog_compiler_static=
+fi
+
+
+
+
+
+
+
+ { $as_echo "$as_me:$LINENO: checking if $compiler supports -c -o file.$ac_objext" >&5
+$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; }
+if test "${lt_cv_prog_compiler_c_o+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_c_o=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:8254: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&5
+ echo "$as_me:8258: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_c_o=yes
+ fi
+ fi
+ chmod u+w . 2>&5
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_c_o" >&5
+$as_echo "$lt_cv_prog_compiler_c_o" >&6; }
+
+
+
+
+
+
+ { $as_echo "$as_me:$LINENO: checking if $compiler supports -c -o file.$ac_objext" >&5
+$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; }
+if test "${lt_cv_prog_compiler_c_o+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_c_o=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:8309: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&5
+ echo "$as_me:8313: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_c_o=yes
+ fi
+ fi
+ chmod u+w . 2>&5
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_c_o" >&5
+$as_echo "$lt_cv_prog_compiler_c_o" >&6; }
+
+
+
+
+hard_links="nottested"
+if test "$lt_cv_prog_compiler_c_o" = no && test "$need_locks" != no; then
+ # do not overwrite the value of need_locks provided by the user
+ { $as_echo "$as_me:$LINENO: checking if we can lock with hard links" >&5
+$as_echo_n "checking if we can lock with hard links... " >&6; }
+ hard_links=yes
+ $RM conftest*
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ touch conftest.a
+ ln conftest.a conftest.b 2>&5 || hard_links=no
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ { $as_echo "$as_me:$LINENO: result: $hard_links" >&5
+$as_echo "$hard_links" >&6; }
+ if test "$hard_links" = no; then
+ { $as_echo "$as_me:$LINENO: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&5
+$as_echo "$as_me: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&2;}
+ need_locks=warn
+ fi
+else
+ need_locks=no
+fi
+
+
+
+
+
+
+ { $as_echo "$as_me:$LINENO: checking whether the $compiler linker ($LD) supports shared libraries" >&5
+$as_echo_n "checking whether the $compiler linker ($LD) supports shared libraries... " >&6; }
+
+ runpath_var=
+ allow_undefined_flag=
+ always_export_symbols=no
+ archive_cmds=
+ archive_expsym_cmds=
+ compiler_needs_object=no
+ enable_shared_with_static_runtimes=no
+ export_dynamic_flag_spec=
+ export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ hardcode_automatic=no
+ hardcode_direct=no
+ hardcode_direct_absolute=no
+ hardcode_libdir_flag_spec=
+ hardcode_libdir_flag_spec_ld=
+ hardcode_libdir_separator=
+ hardcode_minus_L=no
+ hardcode_shlibpath_var=unsupported
+ inherit_rpath=no
+ link_all_deplibs=unknown
+ module_cmds=
+ module_expsym_cmds=
+ old_archive_from_new_cmds=
+ old_archive_from_expsyms_cmds=
+ thread_safe_flag_spec=
+ whole_archive_flag_spec=
+ # include_expsyms should be a list of space-separated symbols to be *always*
+ # included in the symbol list
+ include_expsyms=
+ # exclude_expsyms can be an extended regexp of symbols to exclude
+ # it will be wrapped by ` (' and `)$', so one must not match beginning or
+ # end of line. Example: `a|bc|.*d.*' will exclude the symbols `a' and `bc',
+ # as well as any symbol that contains `d'.
+ exclude_expsyms='_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*'
+ # Although _GLOBAL_OFFSET_TABLE_ is a valid symbol C name, most a.out
+ # platforms (ab)use it in PIC code, but their linkers get confused if
+ # the symbol is explicitly referenced. Since portable code cannot
+ # rely on this symbol name, it's probably fine to never include it in
+ # preloaded symbol tables.
+ # Exclude shared library initialization/finalization symbols.
+ extract_expsyms_cmds=
+
+ case $host_os in
+ cygwin* | mingw* | pw32* | cegcc*)
+ # FIXME: the MSVC++ port hasn't been tested in a loooong time
+ # When not using gcc, we currently assume that we are using
+ # Microsoft Visual C++.
+ if test "$GCC" != yes; then
+ with_gnu_ld=no
+ fi
+ ;;
+ interix*)
+ # we just hope/assume this is gcc and not c89 (= MSVC++)
+ with_gnu_ld=yes
+ ;;
+ openbsd*)
+ with_gnu_ld=no
+ ;;
+ esac
+
+ ld_shlibs=yes
+ if test "$with_gnu_ld" = yes; then
+ # If archive_cmds runs LD, not CC, wlarc should be empty
+ wlarc='${wl}'
+
+ # Set some defaults for GNU ld with shared library support. These
+ # are reset later if shared libraries are not supported. Putting them
+ # here allows them to be overridden if necessary.
+ runpath_var=LD_RUN_PATH
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ export_dynamic_flag_spec='${wl}--export-dynamic'
+ # ancient GNU ld didn't support --whole-archive et. al.
+ if $LD --help 2>&1 | $GREP 'no-whole-archive' > /dev/null; then
+ whole_archive_flag_spec="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ else
+ whole_archive_flag_spec=
+ fi
+ supports_anon_versioning=no
+ case `$LD -v 2>&1` in
+ *\ [01].* | *\ 2.[0-9].* | *\ 2.10.*) ;; # catch versions < 2.11
+ *\ 2.11.93.0.2\ *) supports_anon_versioning=yes ;; # RH7.3 ...
+ *\ 2.11.92.0.12\ *) supports_anon_versioning=yes ;; # Mandrake 8.2 ...
+ *\ 2.11.*) ;; # other 2.11 versions
+ *) supports_anon_versioning=yes ;;
+ esac
+
+ # See if GNU ld supports shared libraries.
+ case $host_os in
+ aix[3-9]*)
+ # On AIX/PPC, the GNU linker is very broken
+ if test "$host_cpu" != ia64; then
+ ld_shlibs=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the GNU linker, at least up to release 2.9.1, is reported
+*** to be unable to reliably create shared libraries on AIX.
+*** Therefore, libtool is disabling shared libraries support. If you
+*** really care for shared libraries, you may want to modify your PATH
+*** so that a non-GNU linker is found, and then restart.
+
+_LT_EOF
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds=''
+ ;;
+ m68k)
+ archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_minus_L=yes
+ ;;
+ esac
+ ;;
+
+ beos*)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ allow_undefined_flag=unsupported
+ # Joseph Beckenbach <jrb3@best.com> says some releases of gcc
+ # support --undefined. This deserves some investigation. FIXME
+ archive_cmds='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # _LT_TAGVAR(hardcode_libdir_flag_spec, ) is actually meaningless,
+ # as there is no search path for DLLs.
+ hardcode_libdir_flag_spec='-L$libdir'
+ allow_undefined_flag=unsupported
+ always_export_symbols=no
+ enable_shared_with_static_runtimes=yes
+ export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS][ ]/s/.*[ ]\([^ ]*\)/\1 DATA/'\'' | $SED -e '\''/^[AITW][ ]/s/.*[ ]//'\'' | sort | uniq > $export_symbols'
+
+ if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ # If the export-symbols file already is a .def file (1st line
+ # is EXPORTS), use it as is; otherwise, prepend...
+ archive_expsym_cmds='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+ cp $export_symbols $output_objdir/$soname.def;
+ else
+ echo EXPORTS > $output_objdir/$soname.def;
+ cat $export_symbols >> $output_objdir/$soname.def;
+ fi~
+ $CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ interix[3-9]*)
+ hardcode_direct=no
+ hardcode_shlibpath_var=no
+ hardcode_libdir_flag_spec='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec='${wl}-E'
+ # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+ # Instead, shared libraries are loaded at an image base (0x10000000 by
+ # default) and relocated if they conflict, which is a slow very memory
+ # consuming and fragmenting process. To avoid this, we pick a random,
+ # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+ # time. Moving up from 0x10000000 also allows more sbrk(2) space.
+ archive_cmds='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ archive_expsym_cmds='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ ;;
+
+ gnu* | linux* | tpf* | k*bsd*-gnu)
+ tmp_diet=no
+ if test "$host_os" = linux-dietlibc; then
+ case $cc_basename in
+ diet\ *) tmp_diet=yes;; # linux-dietlibc with static linking (!diet-dyn)
+ esac
+ fi
+ if $LD --help 2>&1 | $EGREP ': supported targets:.* elf' > /dev/null \
+ && test "$tmp_diet" = no
+ then
+ tmp_addflag=
+ tmp_sharedflag='-shared'
+ case $cc_basename,$host_cpu in
+ pgcc*) # Portland Group C compiler
+ whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ tmp_addflag=' $pic_flag'
+ ;;
+ pgf77* | pgf90* | pgf95*) # Portland Group f77 and f90 compilers
+ whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ tmp_addflag=' $pic_flag -Mnomain' ;;
+ ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64
+ tmp_addflag=' -i_dynamic' ;;
+ efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64
+ tmp_addflag=' -i_dynamic -nofor_main' ;;
+ ifc* | ifort*) # Intel Fortran compiler
+ tmp_addflag=' -nofor_main' ;;
+ lf95*) # Lahey Fortran 8.1
+ whole_archive_flag_spec=
+ tmp_sharedflag='--shared' ;;
+ xl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ tmp_sharedflag='-qmkshrobj'
+ tmp_addflag= ;;
+ esac
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*) # Sun C 5.9
+ whole_archive_flag_spec='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ compiler_needs_object=yes
+ tmp_sharedflag='-G' ;;
+ *Sun\ F*) # Sun Fortran 8.3
+ tmp_sharedflag='-G' ;;
+ esac
+ archive_cmds='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+
+ if test "x$supports_anon_versioning" = xyes; then
+ archive_expsym_cmds='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+ fi
+
+ case $cc_basename in
+ xlf*)
+ # IBM XL Fortran 10.1 on PPC cannot create shared libs itself
+ whole_archive_flag_spec='--whole-archive$convenience --no-whole-archive'
+ hardcode_libdir_flag_spec=
+ hardcode_libdir_flag_spec_ld='-rpath $libdir'
+ archive_cmds='$LD -shared $libobjs $deplibs $compiler_flags -soname $soname -o $lib'
+ if test "x$supports_anon_versioning" = xyes; then
+ archive_expsym_cmds='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $LD -shared $libobjs $deplibs $compiler_flags -soname $soname -version-script $output_objdir/$libname.ver -o $lib'
+ fi
+ ;;
+ esac
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ archive_cmds='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib'
+ wlarc=
+ else
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ fi
+ ;;
+
+ solaris*)
+ if $LD -v 2>&1 | $GREP 'BFD 2\.8' > /dev/null; then
+ ld_shlibs=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: The releases 2.8.* of the GNU linker cannot reliably
+*** create shared libraries on Solaris systems. Therefore, libtool
+*** is disabling shared libraries support. We urge you to upgrade GNU
+*** binutils to release 2.9.1 or newer. Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+ elif $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*)
+ case `$LD -v 2>&1` in
+ *\ [01].* | *\ 2.[0-9].* | *\ 2.1[0-5].*)
+ ld_shlibs=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not
+*** reliably create shared libraries on SCO systems. Therefore, libtool
+*** is disabling shared libraries support. We urge you to upgrade GNU
+*** binutils to release 2.16.91.0.3 or newer. Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+ ;;
+ *)
+ # For security reasons, it is highly recommended that you always
+ # use absolute paths for naming shared libraries, and exclude the
+ # DT_RUNPATH tag from executables and libraries. But doing so
+ # requires that you compile everything twice, which is a pain.
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+ esac
+ ;;
+
+ sunos4*)
+ archive_cmds='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ wlarc=
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ *)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ ld_shlibs=no
+ fi
+ ;;
+ esac
+
+ if test "$ld_shlibs" = no; then
+ runpath_var=
+ hardcode_libdir_flag_spec=
+ export_dynamic_flag_spec=
+ whole_archive_flag_spec=
+ fi
+ else
+ # PORTME fill in a description of your system's linker (not GNU ld)
+ case $host_os in
+ aix3*)
+ allow_undefined_flag=unsupported
+ always_export_symbols=yes
+ archive_expsym_cmds='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname'
+ # Note: this linker hardcodes the directories in LIBPATH if there
+ # are no directories specified by -L.
+ hardcode_minus_L=yes
+ if test "$GCC" = yes && test -z "$lt_prog_compiler_static"; then
+ # Neither direct hardcoding nor static linking is supported with a
+ # broken collect2.
+ hardcode_direct=unsupported
+ fi
+ ;;
+
+ aix[4-9]*)
+ if test "$host_cpu" = ia64; then
+ # On IA64, the linker does run time linking by default, so we don't
+ # have to do anything special.
+ aix_use_runtimelinking=no
+ exp_sym_flag='-Bexport'
+ no_entry_flag=""
+ else
+ # If we're using GNU nm, then we don't want the "-C" option.
+ # -C means demangle to AIX nm, but means don't demangle with GNU nm
+ if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then
+ export_symbols_cmds='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ else
+ export_symbols_cmds='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ fi
+ aix_use_runtimelinking=no
+
+ # Test if we are trying to use run time linking or normal
+ # AIX style linking. If -brtl is somewhere in LDFLAGS, we
+ # need to do runtime linking.
+ case $host_os in aix4.[23]|aix4.[23].*|aix[5-9]*)
+ for ld_flag in $LDFLAGS; do
+ if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then
+ aix_use_runtimelinking=yes
+ break
+ fi
+ done
+ ;;
+ esac
+
+ exp_sym_flag='-bexport'
+ no_entry_flag='-bnoentry'
+ fi
+
+ # When large executables or shared objects are built, AIX ld can
+ # have problems creating the table of contents. If linking a library
+ # or program results in "error TOC overflow" add -mminimal-toc to
+ # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not
+ # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+ archive_cmds=''
+ hardcode_direct=yes
+ hardcode_direct_absolute=yes
+ hardcode_libdir_separator=':'
+ link_all_deplibs=yes
+ file_list_spec='${wl}-f,'
+
+ if test "$GCC" = yes; then
+ case $host_os in aix4.[012]|aix4.[012].*)
+ # We only want to do this on AIX 4.2 and lower, the check
+ # below for broken collect2 doesn't work under 4.3+
+ collect2name=`${CC} -print-prog-name=collect2`
+ if test -f "$collect2name" &&
+ strings "$collect2name" | $GREP resolve_lib_name >/dev/null
+ then
+ # We have reworked collect2
+ :
+ else
+ # We have old collect2
+ hardcode_direct=unsupported
+ # It fails to find uninstalled libraries when the uninstalled
+ # path is not listed in the libpath. Setting hardcode_minus_L
+ # to unsupported forces relinking
+ hardcode_minus_L=yes
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_libdir_separator=
+ fi
+ ;;
+ esac
+ shared_flag='-shared'
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag="$shared_flag "'${wl}-G'
+ fi
+ link_all_deplibs=no
+ else
+ # not using gcc
+ if test "$host_cpu" = ia64; then
+ # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+ # chokes on -Wl,-G. The following line is correct:
+ shared_flag='-G'
+ else
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag='${wl}-G'
+ else
+ shared_flag='${wl}-bM:SRE'
+ fi
+ fi
+ fi
+
+ export_dynamic_flag_spec='${wl}-bexpall'
+ # It seems that -bexpall does not export symbols beginning with
+ # underscore (_), so it is better to generate a list of symbols to export.
+ always_export_symbols=yes
+ if test "$aix_use_runtimelinking" = yes; then
+ # Warning - without using the other runtime loading flags (-brtl),
+ # -berok will link without error, but may produce a broken library.
+ allow_undefined_flag='-berok'
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+ hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath"
+ archive_expsym_cmds='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+ else
+ if test "$host_cpu" = ia64; then
+ hardcode_libdir_flag_spec='${wl}-R $libdir:/usr/lib:/lib'
+ allow_undefined_flag="-z nodefs"
+ archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+ else
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+ hardcode_libdir_flag_spec='${wl}-blibpath:$libdir:'"$aix_libpath"
+ # Warning - without using the other run time loading flags,
+ # -berok will link without error, but may produce a broken library.
+ no_undefined_flag=' ${wl}-bernotok'
+ allow_undefined_flag=' ${wl}-berok'
+ # Exported symbols can be pulled into shared objects from archives
+ whole_archive_flag_spec='$convenience'
+ archive_cmds_need_lc=yes
+ # This is similar to how AIX traditionally builds its shared libraries.
+ archive_expsym_cmds="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+ fi
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds=''
+ ;;
+ m68k)
+ archive_cmds='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_minus_L=yes
+ ;;
+ esac
+ ;;
+
+ bsdi[45]*)
+ export_dynamic_flag_spec=-rdynamic
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # When not using gcc, we currently assume that we are using
+ # Microsoft Visual C++.
+ # hardcode_libdir_flag_spec is actually meaningless, as there is
+ # no search path for DLLs.
+ hardcode_libdir_flag_spec=' '
+ allow_undefined_flag=unsupported
+ # Tell ltmain to make .lib files, not .a files.
+ libext=lib
+ # Tell ltmain to make .dll files, not .so files.
+ shrext_cmds=".dll"
+ # FIXME: Setting linknames here is a bad hack.
+ archive_cmds='$CC -o $lib $libobjs $compiler_flags `$ECHO "X$deplibs" | $Xsed -e '\''s/ -lc$//'\''` -link -dll~linknames='
+ # The linker will automatically build a .lib file if we build a DLL.
+ old_archive_from_new_cmds='true'
+ # FIXME: Should let the user specify the lib program.
+ old_archive_cmds='lib -OUT:$oldlib$oldobjs$old_deplibs'
+ fix_srcfile_path='`cygpath -w "$srcfile"`'
+ enable_shared_with_static_runtimes=yes
+ ;;
+
+ darwin* | rhapsody*)
+
+
+ archive_cmds_need_lc=no
+ hardcode_direct=no
+ hardcode_automatic=yes
+ hardcode_shlibpath_var=unsupported
+ whole_archive_flag_spec=''
+ link_all_deplibs=yes
+ allow_undefined_flag="$_lt_dar_allow_undefined"
+ case $cc_basename in
+ ifort*) _lt_dar_can_shared=yes ;;
+ *) _lt_dar_can_shared=$GCC ;;
+ esac
+ if test "$_lt_dar_can_shared" = "yes"; then
+ output_verbose_link_cmd=echo
+ archive_cmds="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}"
+ module_cmds="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}"
+ archive_expsym_cmds="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}"
+ module_expsym_cmds="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}"
+
+ else
+ ld_shlibs=no
+ fi
+
+ ;;
+
+ dgux*)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_shlibpath_var=no
+ ;;
+
+ freebsd1*)
+ ld_shlibs=no
+ ;;
+
+ # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor
+ # support. Future versions do this automatically, but an explicit c++rt0.o
+ # does not break anything, and helps significantly (at the cost of a little
+ # extra space).
+ freebsd2.2*)
+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o'
+ hardcode_libdir_flag_spec='-R$libdir'
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ # Unfortunately, older versions of FreeBSD 2 do not have this feature.
+ freebsd2*)
+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_direct=yes
+ hardcode_minus_L=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ # FreeBSD 3 and greater uses gcc -shared to do shared libraries.
+ freebsd* | dragonfly*)
+ archive_cmds='$CC -shared -o $lib $libobjs $deplibs $compiler_flags'
+ hardcode_libdir_flag_spec='-R$libdir'
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ hpux9*)
+ if test "$GCC" = yes; then
+ archive_cmds='$RM $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ else
+ archive_cmds='$RM $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ fi
+ hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir'
+ hardcode_libdir_separator=:
+ hardcode_direct=yes
+
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ hardcode_minus_L=yes
+ export_dynamic_flag_spec='${wl}-E'
+ ;;
+
+ hpux10*)
+ if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+ archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ archive_cmds='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags'
+ fi
+ if test "$with_gnu_ld" = no; then
+ hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir'
+ hardcode_libdir_flag_spec_ld='+b $libdir'
+ hardcode_libdir_separator=:
+ hardcode_direct=yes
+ hardcode_direct_absolute=yes
+ export_dynamic_flag_spec='${wl}-E'
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ hardcode_minus_L=yes
+ fi
+ ;;
+
+ hpux11*)
+ if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+ case $host_cpu in
+ hppa*64*)
+ archive_cmds='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ ia64*)
+ archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ archive_cmds='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ else
+ case $host_cpu in
+ hppa*64*)
+ archive_cmds='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ ia64*)
+ archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ archive_cmds='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ fi
+ if test "$with_gnu_ld" = no; then
+ hardcode_libdir_flag_spec='${wl}+b ${wl}$libdir'
+ hardcode_libdir_separator=:
+
+ case $host_cpu in
+ hppa*64*|ia64*)
+ hardcode_direct=no
+ hardcode_shlibpath_var=no
+ ;;
+ *)
+ hardcode_direct=yes
+ hardcode_direct_absolute=yes
+ export_dynamic_flag_spec='${wl}-E'
+
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ hardcode_minus_L=yes
+ ;;
+ esac
+ fi
+ ;;
+
+ irix5* | irix6* | nonstopux*)
+ if test "$GCC" = yes; then
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ # Try to use the -exported_symbol ld option, if it does not
+ # work, assume that -exports_file does not work either and
+ # implicitly export all symbols.
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS -shared ${wl}-exported_symbol ${wl}foo ${wl}-update_registry ${wl}/dev/null"
+ cat >conftest.$ac_ext <<_ACEOF
+int foo(void) {}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations ${wl}-exports_file ${wl}$export_symbols -o $lib'
+
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+ LDFLAGS="$save_LDFLAGS"
+ else
+ archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ archive_expsym_cmds='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -exports_file $export_symbols -o $lib'
+ fi
+ archive_cmds_need_lc='no'
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator=:
+ inherit_rpath=yes
+ link_all_deplibs=yes
+ ;;
+
+ netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out
+ else
+ archive_cmds='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF
+ fi
+ hardcode_libdir_flag_spec='-R$libdir'
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ newsos6)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_direct=yes
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator=:
+ hardcode_shlibpath_var=no
+ ;;
+
+ *nto* | *qnx*)
+ ;;
+
+ openbsd*)
+ if test -f /usr/libexec/ld.so; then
+ hardcode_direct=yes
+ hardcode_shlibpath_var=no
+ hardcode_direct_absolute=yes
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols'
+ hardcode_libdir_flag_spec='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec='${wl}-E'
+ else
+ case $host_os in
+ openbsd[01].* | openbsd2.[0-7] | openbsd2.[0-7].*)
+ archive_cmds='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_libdir_flag_spec='-R$libdir'
+ ;;
+ *)
+ archive_cmds='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+ hardcode_libdir_flag_spec='${wl}-rpath,$libdir'
+ ;;
+ esac
+ fi
+ else
+ ld_shlibs=no
+ fi
+ ;;
+
+ os2*)
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_minus_L=yes
+ allow_undefined_flag=unsupported
+ archive_cmds='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$ECHO DATA >> $output_objdir/$libname.def~$ECHO " SINGLE NONSHARED" >> $output_objdir/$libname.def~$ECHO EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def'
+ old_archive_from_new_cmds='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def'
+ ;;
+
+ osf3*)
+ if test "$GCC" = yes; then
+ allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*'
+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ else
+ allow_undefined_flag=' -expect_unresolved \*'
+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ fi
+ archive_cmds_need_lc='no'
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator=:
+ ;;
+
+ osf4* | osf5*) # as osf3* with the addition of -msym flag
+ if test "$GCC" = yes; then
+ allow_undefined_flag=' ${wl}-expect_unresolved ${wl}\*'
+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+ else
+ allow_undefined_flag=' -expect_unresolved \*'
+ archive_cmds='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ archive_expsym_cmds='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~
+ $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp'
+
+ # Both c and cxx compiler support -rpath directly
+ hardcode_libdir_flag_spec='-rpath $libdir'
+ fi
+ archive_cmds_need_lc='no'
+ hardcode_libdir_separator=:
+ ;;
+
+ solaris*)
+ no_undefined_flag=' -z defs'
+ if test "$GCC" = yes; then
+ wlarc='${wl}'
+ archive_cmds='$CC -shared ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -shared ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp'
+ else
+ case `$CC -V 2>&1` in
+ *"Compilers 5.0"*)
+ wlarc=''
+ archive_cmds='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$RM $lib.exp'
+ ;;
+ *)
+ wlarc='${wl}'
+ archive_cmds='$CC -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp'
+ ;;
+ esac
+ fi
+ hardcode_libdir_flag_spec='-R$libdir'
+ hardcode_shlibpath_var=no
+ case $host_os in
+ solaris2.[0-5] | solaris2.[0-5].*) ;;
+ *)
+ # The compiler driver will combine and reorder linker options,
+ # but understands `-z linker_flag'. GCC discards it without `$wl',
+ # but is careful enough not to reorder.
+ # Supported since Solaris 2.6 (maybe 2.5.1?)
+ if test "$GCC" = yes; then
+ whole_archive_flag_spec='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract'
+ else
+ whole_archive_flag_spec='-z allextract$convenience -z defaultextract'
+ fi
+ ;;
+ esac
+ link_all_deplibs=yes
+ ;;
+
+ sunos4*)
+ if test "x$host_vendor" = xsequent; then
+ # Use $CC to link under sequent, because it throws in some extra .o
+ # files that make .init and .fini sections work.
+ archive_cmds='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ archive_cmds='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags'
+ fi
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_direct=yes
+ hardcode_minus_L=yes
+ hardcode_shlibpath_var=no
+ ;;
+
+ sysv4)
+ case $host_vendor in
+ sni)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_direct=yes # is this really true???
+ ;;
+ siemens)
+ ## LD is ld it makes a PLAMLIB
+ ## CC just makes a GrossModule.
+ archive_cmds='$LD -G -o $lib $libobjs $deplibs $linker_flags'
+ reload_cmds='$CC -r -o $output$reload_objs'
+ hardcode_direct=no
+ ;;
+ motorola)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_direct=no #Motorola manual says yes, but my tests say they lie
+ ;;
+ esac
+ runpath_var='LD_RUN_PATH'
+ hardcode_shlibpath_var=no
+ ;;
+
+ sysv4.3*)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_shlibpath_var=no
+ export_dynamic_flag_spec='-Bexport'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_shlibpath_var=no
+ runpath_var=LD_RUN_PATH
+ hardcode_runpath_var=yes
+ ld_shlibs=yes
+ fi
+ ;;
+
+ sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7* | sco3.2v5.0.[024]*)
+ no_undefined_flag='${wl}-z,text'
+ archive_cmds_need_lc=no
+ hardcode_shlibpath_var=no
+ runpath_var='LD_RUN_PATH'
+
+ if test "$GCC" = yes; then
+ archive_cmds='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ archive_cmds='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ fi
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6*)
+ # Note: We can NOT use -z defs as we might desire, because we do not
+ # link with -lc, and that would cause any symbols used from libc to
+ # always be unresolved, which means just about no library would
+ # ever link correctly. If we're not using GNU ld we use -z text
+ # though, which does catch some bad symbols but isn't as heavy-handed
+ # as -z defs.
+ no_undefined_flag='${wl}-z,text'
+ allow_undefined_flag='${wl}-z,nodefs'
+ archive_cmds_need_lc=no
+ hardcode_shlibpath_var=no
+ hardcode_libdir_flag_spec='${wl}-R,$libdir'
+ hardcode_libdir_separator=':'
+ link_all_deplibs=yes
+ export_dynamic_flag_spec='${wl}-Bexport'
+ runpath_var='LD_RUN_PATH'
+
+ if test "$GCC" = yes; then
+ archive_cmds='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ archive_cmds='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ fi
+ ;;
+
+ uts4*)
+ archive_cmds='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ hardcode_libdir_flag_spec='-L$libdir'
+ hardcode_shlibpath_var=no
+ ;;
+
+ *)
+ ld_shlibs=no
+ ;;
+ esac
+
+ if test x$host_vendor = xsni; then
+ case $host in
+ sysv4 | sysv4.2uw2* | sysv4.3* | sysv5*)
+ export_dynamic_flag_spec='${wl}-Blargedynsym'
+ ;;
+ esac
+ fi
+ fi
+
+{ $as_echo "$as_me:$LINENO: result: $ld_shlibs" >&5
+$as_echo "$ld_shlibs" >&6; }
+test "$ld_shlibs" = no && can_build_shared=no
+
+with_gnu_ld=$with_gnu_ld
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+#
+# Do we need to explicitly link libc?
+#
+case "x$archive_cmds_need_lc" in
+x|xyes)
+ # Assume -lc should be added
+ archive_cmds_need_lc=yes
+
+ if test "$enable_shared" = yes && test "$GCC" = yes; then
+ case $archive_cmds in
+ *'~'*)
+ # FIXME: we may have to deal with multi-command sequences.
+ ;;
+ '$CC '*)
+ # Test whether the compiler implicitly links with -lc since on some
+ # systems, -lgcc has to come before -lc. If gcc already passes -lc
+ # to ld, don't add -lc before -lgcc.
+ { $as_echo "$as_me:$LINENO: checking whether -lc should be explicitly linked in" >&5
+$as_echo_n "checking whether -lc should be explicitly linked in... " >&6; }
+ $RM conftest*
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } 2>conftest.err; then
+ soname=conftest
+ lib=conftest
+ libobjs=conftest.$ac_objext
+ deplibs=
+ wl=$lt_prog_compiler_wl
+ pic_flag=$lt_prog_compiler_pic
+ compiler_flags=-v
+ linker_flags=-v
+ verstring=
+ output_objdir=.
+ libname=conftest
+ lt_save_allow_undefined_flag=$allow_undefined_flag
+ allow_undefined_flag=
+ if { (eval echo "$as_me:$LINENO: \"$archive_cmds 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1\"") >&5
+ (eval $archive_cmds 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+ then
+ archive_cmds_need_lc=no
+ else
+ archive_cmds_need_lc=yes
+ fi
+ allow_undefined_flag=$lt_save_allow_undefined_flag
+ else
+ cat conftest.err 1>&5
+ fi
+ $RM conftest*
+ { $as_echo "$as_me:$LINENO: result: $archive_cmds_need_lc" >&5
+$as_echo "$archive_cmds_need_lc" >&6; }
+ ;;
+ esac
+ fi
+ ;;
+esac
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
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+
+
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+
+
+
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+
+
+
+
+
+
+
+
+
+
+ { $as_echo "$as_me:$LINENO: checking dynamic linker characteristics" >&5
+$as_echo_n "checking dynamic linker characteristics... " >&6; }
+
+if test "$GCC" = yes; then
+ case $host_os in
+ darwin*) lt_awk_arg="/^libraries:/,/LR/" ;;
+ *) lt_awk_arg="/^libraries:/" ;;
+ esac
+ lt_search_path_spec=`$CC -print-search-dirs | awk $lt_awk_arg | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$lt_search_path_spec" | $GREP ';' >/dev/null ; then
+ # if the path contains ";" then we assume it to be the separator
+ # otherwise default to the standard path separator (i.e. ":") - it is
+ # assumed that no part of a normal pathname contains ";" but that should
+ # okay in the real world where ";" in dirpaths is itself problematic.
+ lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ # Ok, now we have the path, separated by spaces, we can step through it
+ # and add multilib dir if necessary.
+ lt_tmp_lt_search_path_spec=
+ lt_multi_os_dir=`$CC $CPPFLAGS $CFLAGS $LDFLAGS -print-multi-os-directory 2>/dev/null`
+ for lt_sys_path in $lt_search_path_spec; do
+ if test -d "$lt_sys_path/$lt_multi_os_dir"; then
+ lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path/$lt_multi_os_dir"
+ else
+ test -d "$lt_sys_path" && \
+ lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path"
+ fi
+ done
+ lt_search_path_spec=`$ECHO $lt_tmp_lt_search_path_spec | awk '
+BEGIN {RS=" "; FS="/|\n";} {
+ lt_foo="";
+ lt_count=0;
+ for (lt_i = NF; lt_i > 0; lt_i--) {
+ if ($lt_i != "" && $lt_i != ".") {
+ if ($lt_i == "..") {
+ lt_count++;
+ } else {
+ if (lt_count == 0) {
+ lt_foo="/" $lt_i lt_foo;
+ } else {
+ lt_count--;
+ }
+ }
+ }
+ }
+ if (lt_foo != "") { lt_freq[lt_foo]++; }
+ if (lt_freq[lt_foo] == 1) { print lt_foo; }
+}'`
+ sys_lib_search_path_spec=`$ECHO $lt_search_path_spec`
+else
+ sys_lib_search_path_spec="/lib /usr/lib /usr/local/lib"
+fi
+library_names_spec=
+libname_spec='lib$name'
+soname_spec=
+shrext_cmds=".so"
+postinstall_cmds=
+postuninstall_cmds=
+finish_cmds=
+finish_eval=
+shlibpath_var=
+shlibpath_overrides_runpath=unknown
+version_type=none
+dynamic_linker="$host_os ld.so"
+sys_lib_dlsearch_path_spec="/lib /usr/lib"
+need_lib_prefix=unknown
+hardcode_into_libs=no
+
+# when you set need_version to no, make sure it does not cause -set_version
+# flags to be left without arguments
+need_version=unknown
+
+case $host_os in
+aix3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
+ shlibpath_var=LIBPATH
+
+ # AIX 3 has no versioning support, so we append a major version to the name.
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+
+aix[4-9]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ hardcode_into_libs=yes
+ if test "$host_cpu" = ia64; then
+ # AIX 5 supports IA64
+ library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ else
+ # With GCC up to 2.95.x, collect2 would create an import file
+ # for dependence libraries. The import file would start with
+ # the line `#! .'. This would cause the generated library to
+ # depend on `.', always an invalid library. This was fixed in
+ # development snapshots of GCC prior to 3.0.
+ case $host_os in
+ aix4 | aix4.[01] | aix4.[01].*)
+ if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)'
+ echo ' yes '
+ echo '#endif'; } | ${CC} -E - | $GREP yes > /dev/null; then
+ :
+ else
+ can_build_shared=no
+ fi
+ ;;
+ esac
+ # AIX (on Power*) has no versioning support, so currently we can not hardcode correct
+ # soname into executable. Probably we can add versioning support to
+ # collect2, so additional links can be useful in future.
+ if test "$aix_use_runtimelinking" = yes; then
+ # If using run time linking (on AIX 4.2 or later) use lib<name>.so
+ # instead of lib<name>.a to let people know that these are not
+ # typical AIX shared libraries.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ else
+ # We preserve .a as extension for shared libraries through AIX4.2
+ # and later when we are not doing run time linking.
+ library_names_spec='${libname}${release}.a $libname.a'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ fi
+ shlibpath_var=LIBPATH
+ fi
+ ;;
+
+amigaos*)
+ case $host_cpu in
+ powerpc)
+ # Since July 2007 AmigaOS4 officially supports .so libraries.
+ # When compiling the executable, add -use-dynld -Lsobjs: to the compileline.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ ;;
+ m68k)
+ library_names_spec='$libname.ixlibrary $libname.a'
+ # Create ${libname}_ixlibrary.a entries in /sys/libs.
+ finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$ECHO "X$lib" | $Xsed -e '\''s%^.*/\([^/]*\)\.ixlibrary$%\1%'\''`; test $RM /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done'
+ ;;
+ esac
+ ;;
+
+beos*)
+ library_names_spec='${libname}${shared_ext}'
+ dynamic_linker="$host_os ld.so"
+ shlibpath_var=LIBRARY_PATH
+ ;;
+
+bsdi[45]*)
+ version_type=linux
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib"
+ sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib"
+ # the default ld.so.conf also contains /usr/contrib/lib and
+ # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow
+ # libtool to hard-code these into programs
+ ;;
+
+cygwin* | mingw* | pw32* | cegcc*)
+ version_type=windows
+ shrext_cmds=".dll"
+ need_version=no
+ need_lib_prefix=no
+
+ case $GCC,$host_os in
+ yes,cygwin* | yes,mingw* | yes,pw32* | yes,cegcc*)
+ library_names_spec='$libname.dll.a'
+ # DLL is installed to $(libdir)/../bin by postinstall_cmds
+ postinstall_cmds='base_file=`basename \${file}`~
+ dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i; echo \$dlname'\''`~
+ dldir=$destdir/`dirname \$dlpath`~
+ test -d \$dldir || mkdir -p \$dldir~
+ $install_prog $dir/$dlname \$dldir/$dlname~
+ chmod a+x \$dldir/$dlname~
+ if test -n '\''$stripme'\'' && test -n '\''$striplib'\''; then
+ eval '\''$striplib \$dldir/$dlname'\'' || exit \$?;
+ fi'
+ postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~
+ dlpath=$dir/\$dldll~
+ $RM \$dlpath'
+ shlibpath_overrides_runpath=yes
+
+ case $host_os in
+ cygwin*)
+ # Cygwin DLLs use 'cyg' prefix rather than 'lib'
+ soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib"
+ ;;
+ mingw* | cegcc*)
+ # MinGW DLLs use traditional 'lib' prefix
+ soname_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec=`$CC -print-search-dirs | $GREP "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$sys_lib_search_path_spec" | $GREP ';[c-zC-Z]:/' >/dev/null; then
+ # It is most probably a Windows format PATH printed by
+ # mingw gcc, but we are running on Cygwin. Gcc prints its search
+ # path with ; separators, and with drive letters. We can handle the
+ # drive letters (cygwin fileutils understands them), so leave them,
+ # especially as we might pass files found there to a mingw objdump,
+ # which wouldn't understand a cygwinified path. Ahh.
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ ;;
+ pw32*)
+ # pw32 DLLs use 'pw' prefix rather than 'lib'
+ library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ ;;
+ esac
+ ;;
+
+ *)
+ library_names_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext} $libname.lib'
+ ;;
+ esac
+ dynamic_linker='Win32 ld.exe'
+ # FIXME: first we should search . and the directory the executable is in
+ shlibpath_var=PATH
+ ;;
+
+darwin* | rhapsody*)
+ dynamic_linker="$host_os dyld"
+ version_type=darwin
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${major}$shared_ext ${libname}$shared_ext'
+ soname_spec='${libname}${release}${major}$shared_ext'
+ shlibpath_overrides_runpath=yes
+ shlibpath_var=DYLD_LIBRARY_PATH
+ shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /usr/local/lib"
+ sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib'
+ ;;
+
+dgux*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+freebsd1*)
+ dynamic_linker=no
+ ;;
+
+freebsd* | dragonfly*)
+ # DragonFly does not have aout. When/if they implement a new
+ # versioning mechanism, adjust this.
+ if test -x /usr/bin/objformat; then
+ objformat=`/usr/bin/objformat`
+ else
+ case $host_os in
+ freebsd[123]*) objformat=aout ;;
+ *) objformat=elf ;;
+ esac
+ fi
+ version_type=freebsd-$objformat
+ case $version_type in
+ freebsd-elf*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ need_version=no
+ need_lib_prefix=no
+ ;;
+ freebsd-*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix'
+ need_version=yes
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_os in
+ freebsd2*)
+ shlibpath_overrides_runpath=yes
+ ;;
+ freebsd3.[01]* | freebsdelf3.[01]*)
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ freebsd3.[2-9]* | freebsdelf3.[2-9]* | \
+ freebsd4.[0-5] | freebsdelf4.[0-5] | freebsd4.1.1 | freebsdelf4.1.1)
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+ *) # from 4.6 on, and DragonFly
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ esac
+ ;;
+
+gnu*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ hardcode_into_libs=yes
+ ;;
+
+hpux9* | hpux10* | hpux11*)
+ # Give a soname corresponding to the major version so that dld.sl refuses to
+ # link against other versions.
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ case $host_cpu in
+ ia64*)
+ shrext_cmds='.so'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.so"
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ if test "X$HPUX_IA64_MODE" = X32; then
+ sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib"
+ else
+ sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64"
+ fi
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ hppa*64*)
+ shrext_cmds='.sl'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64"
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ *)
+ shrext_cmds='.sl'
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=SHLIB_PATH
+ shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+ esac
+ # HP-UX runs *really* slowly unless shared libraries are mode 555.
+ postinstall_cmds='chmod 555 $lib'
+ ;;
+
+interix[3-9]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $host_os in
+ nonstopux*) version_type=nonstopux ;;
+ *)
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ version_type=linux
+ else
+ version_type=irix
+ fi ;;
+ esac
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}'
+ case $host_os in
+ irix5* | nonstopux*)
+ libsuff= shlibsuff=
+ ;;
+ *)
+ case $LD in # libtool.m4 will add one of these switches to LD
+ *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ")
+ libsuff= shlibsuff= libmagic=32-bit;;
+ *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ")
+ libsuff=32 shlibsuff=N32 libmagic=N32;;
+ *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ")
+ libsuff=64 shlibsuff=64 libmagic=64-bit;;
+ *) libsuff= shlibsuff= libmagic=never-match;;
+ esac
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY${shlibsuff}_PATH
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}"
+ sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}"
+ hardcode_into_libs=yes
+ ;;
+
+# No shared lib support for Linux oldld, aout, or coff.
+linux*oldld* | linux*aout* | linux*coff*)
+ dynamic_linker=no
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ # Some binutils ld are patched to set DT_RUNPATH
+ save_LDFLAGS=$LDFLAGS
+ save_libdir=$libdir
+ eval "libdir=/foo; wl=\"$lt_prog_compiler_wl\"; \
+ LDFLAGS=\"\$LDFLAGS $hardcode_libdir_flag_spec\""
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ if ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null; then
+ shlibpath_overrides_runpath=yes
+fi
+
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+ LDFLAGS=$save_LDFLAGS
+ libdir=$save_libdir
+
+ # This implies no fast_install, which is unacceptable.
+ # Some rework will be needed to allow for fast_install
+ # before this can be enabled.
+ hardcode_into_libs=yes
+
+ # Append ld.so.conf contents to the search path
+ if test -f /etc/ld.so.conf; then
+ lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+ sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+ fi
+
+ # We used to test for /lib/ld.so.1 and disable shared libraries on
+ # powerpc, because MkLinux only supported shared libraries with the
+ # GNU dynamic linker. Since this was broken with cross compilers,
+ # most powerpc-linux boxes support dynamic linking these days and
+ # people can always --disable-shared, the test was removed, and we
+ # assume the GNU/Linux dynamic linker is in use.
+ dynamic_linker='GNU/Linux ld.so'
+ ;;
+
+netbsdelf*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='NetBSD ld.elf_so'
+ ;;
+
+netbsd*)
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ dynamic_linker='NetBSD (a.out) ld.so'
+ else
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='NetBSD ld.elf_so'
+ fi
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+
+newsos6)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ ;;
+
+*nto* | *qnx*)
+ version_type=qnx
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='ldqnx.so'
+ ;;
+
+openbsd*)
+ version_type=sunos
+ sys_lib_dlsearch_path_spec="/usr/lib"
+ need_lib_prefix=no
+ # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs.
+ case $host_os in
+ openbsd3.3 | openbsd3.3.*) need_version=yes ;;
+ *) need_version=no ;;
+ esac
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ case $host_os in
+ openbsd2.[89] | openbsd2.[89].*)
+ shlibpath_overrides_runpath=no
+ ;;
+ *)
+ shlibpath_overrides_runpath=yes
+ ;;
+ esac
+ else
+ shlibpath_overrides_runpath=yes
+ fi
+ ;;
+
+os2*)
+ libname_spec='$name'
+ shrext_cmds=".dll"
+ need_lib_prefix=no
+ library_names_spec='$libname${shared_ext} $libname.a'
+ dynamic_linker='OS/2 ld.exe'
+ shlibpath_var=LIBPATH
+ ;;
+
+osf3* | osf4* | osf5*)
+ version_type=osf
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib"
+ sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec"
+ ;;
+
+rdos*)
+ dynamic_linker=no
+ ;;
+
+solaris*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ # ldd complains unless libraries are executable
+ postinstall_cmds='chmod +x $lib'
+ ;;
+
+sunos4*)
+ version_type=sunos
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ if test "$with_gnu_ld" = yes; then
+ need_lib_prefix=no
+ fi
+ need_version=yes
+ ;;
+
+sysv4 | sysv4.3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_vendor in
+ sni)
+ shlibpath_overrides_runpath=no
+ need_lib_prefix=no
+ runpath_var=LD_RUN_PATH
+ ;;
+ siemens)
+ need_lib_prefix=no
+ ;;
+ motorola)
+ need_lib_prefix=no
+ need_version=no
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib'
+ ;;
+ esac
+ ;;
+
+sysv4*MP*)
+ if test -d /usr/nec ;then
+ version_type=linux
+ library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
+ soname_spec='$libname${shared_ext}.$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ fi
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ version_type=freebsd-elf
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ if test "$with_gnu_ld" = yes; then
+ sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib'
+ else
+ sys_lib_search_path_spec='/usr/ccs/lib /usr/lib'
+ case $host_os in
+ sco3.2v5*)
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /lib"
+ ;;
+ esac
+ fi
+ sys_lib_dlsearch_path_spec='/usr/lib'
+ ;;
+
+tpf*)
+ # TPF is a cross-target only. Preferred cross-host = GNU/Linux.
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+uts4*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+*)
+ dynamic_linker=no
+ ;;
+esac
+{ $as_echo "$as_me:$LINENO: result: $dynamic_linker" >&5
+$as_echo "$dynamic_linker" >&6; }
+test "$dynamic_linker" = no && can_build_shared=no
+
+variables_saved_for_relink="PATH $shlibpath_var $runpath_var"
+if test "$GCC" = yes; then
+ variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+fi
+
+if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then
+ sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec"
+fi
+if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then
+ sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec"
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ { $as_echo "$as_me:$LINENO: checking how to hardcode library paths into programs" >&5
+$as_echo_n "checking how to hardcode library paths into programs... " >&6; }
+hardcode_action=
+if test -n "$hardcode_libdir_flag_spec" ||
+ test -n "$runpath_var" ||
+ test "X$hardcode_automatic" = "Xyes" ; then
+
+ # We can hardcode non-existent directories.
+ if test "$hardcode_direct" != no &&
+ # If the only mechanism to avoid hardcoding is shlibpath_var, we
+ # have to relink, otherwise we might link with an installed library
+ # when we should be linking with a yet-to-be-installed one
+ ## test "$_LT_TAGVAR(hardcode_shlibpath_var, )" != no &&
+ test "$hardcode_minus_L" != no; then
+ # Linking always hardcodes the temporary library directory.
+ hardcode_action=relink
+ else
+ # We can link without hardcoding, and we can hardcode nonexisting dirs.
+ hardcode_action=immediate
+ fi
+else
+ # We cannot hardcode anything, or else we can only hardcode existing
+ # directories.
+ hardcode_action=unsupported
+fi
+{ $as_echo "$as_me:$LINENO: result: $hardcode_action" >&5
+$as_echo "$hardcode_action" >&6; }
+
+if test "$hardcode_action" = relink ||
+ test "$inherit_rpath" = yes; then
+ # Fast installation is not supported
+ enable_fast_install=no
+elif test "$shlibpath_overrides_runpath" = yes ||
+ test "$enable_shared" = no; then
+ # Fast installation is not necessary
+ enable_fast_install=needless
+fi
+
+
+
+
+
+
+ if test "x$enable_dlopen" != xyes; then
+ enable_dlopen=unknown
+ enable_dlopen_self=unknown
+ enable_dlopen_self_static=unknown
+else
+ lt_cv_dlopen=no
+ lt_cv_dlopen_libs=
+
+ case $host_os in
+ beos*)
+ lt_cv_dlopen="load_add_on"
+ lt_cv_dlopen_libs=
+ lt_cv_dlopen_self=yes
+ ;;
+
+ mingw* | pw32* | cegcc*)
+ lt_cv_dlopen="LoadLibrary"
+ lt_cv_dlopen_libs=
+ ;;
+
+ cygwin*)
+ lt_cv_dlopen="dlopen"
+ lt_cv_dlopen_libs=
+ ;;
+
+ darwin*)
+ # if libdl is installed we need to link against it
+ { $as_echo "$as_me:$LINENO: checking for dlopen in -ldl" >&5
+$as_echo_n "checking for dlopen in -ldl... " >&6; }
+if test "${ac_cv_lib_dl_dlopen+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldl $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dlopen ();
+int
+main ()
+{
+return dlopen ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ ac_cv_lib_dl_dlopen=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_lib_dl_dlopen=no
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_dl_dlopen" >&5
+$as_echo "$ac_cv_lib_dl_dlopen" >&6; }
+if test "x$ac_cv_lib_dl_dlopen" = x""yes; then
+ lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"
+else
+
+ lt_cv_dlopen="dyld"
+ lt_cv_dlopen_libs=
+ lt_cv_dlopen_self=yes
+
+fi
+
+ ;;
+
+ *)
+ { $as_echo "$as_me:$LINENO: checking for shl_load" >&5
+$as_echo_n "checking for shl_load... " >&6; }
+if test "${ac_cv_func_shl_load+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+/* Define shl_load to an innocuous variant, in case <limits.h> declares shl_load.
+ For example, HP-UX 11i <limits.h> declares gettimeofday. */
+#define shl_load innocuous_shl_load
+
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char shl_load (); below.
+ Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ <limits.h> exists even on freestanding compilers. */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef shl_load
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char shl_load ();
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined __stub_shl_load || defined __stub___shl_load
+choke me
+#endif
+
+int
+main ()
+{
+return shl_load ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ ac_cv_func_shl_load=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_func_shl_load=no
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_func_shl_load" >&5
+$as_echo "$ac_cv_func_shl_load" >&6; }
+if test "x$ac_cv_func_shl_load" = x""yes; then
+ lt_cv_dlopen="shl_load"
+else
+ { $as_echo "$as_me:$LINENO: checking for shl_load in -ldld" >&5
+$as_echo_n "checking for shl_load in -ldld... " >&6; }
+if test "${ac_cv_lib_dld_shl_load+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldld $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char shl_load ();
+int
+main ()
+{
+return shl_load ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ ac_cv_lib_dld_shl_load=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_lib_dld_shl_load=no
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_dld_shl_load" >&5
+$as_echo "$ac_cv_lib_dld_shl_load" >&6; }
+if test "x$ac_cv_lib_dld_shl_load" = x""yes; then
+ lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-ldld"
+else
+ { $as_echo "$as_me:$LINENO: checking for dlopen" >&5
+$as_echo_n "checking for dlopen... " >&6; }
+if test "${ac_cv_func_dlopen+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+/* Define dlopen to an innocuous variant, in case <limits.h> declares dlopen.
+ For example, HP-UX 11i <limits.h> declares gettimeofday. */
+#define dlopen innocuous_dlopen
+
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char dlopen (); below.
+ Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ <limits.h> exists even on freestanding compilers. */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef dlopen
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dlopen ();
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined __stub_dlopen || defined __stub___dlopen
+choke me
+#endif
+
+int
+main ()
+{
+return dlopen ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ ac_cv_func_dlopen=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_func_dlopen=no
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_func_dlopen" >&5
+$as_echo "$ac_cv_func_dlopen" >&6; }
+if test "x$ac_cv_func_dlopen" = x""yes; then
+ lt_cv_dlopen="dlopen"
+else
+ { $as_echo "$as_me:$LINENO: checking for dlopen in -ldl" >&5
+$as_echo_n "checking for dlopen in -ldl... " >&6; }
+if test "${ac_cv_lib_dl_dlopen+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldl $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dlopen ();
+int
+main ()
+{
+return dlopen ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ ac_cv_lib_dl_dlopen=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_lib_dl_dlopen=no
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_dl_dlopen" >&5
+$as_echo "$ac_cv_lib_dl_dlopen" >&6; }
+if test "x$ac_cv_lib_dl_dlopen" = x""yes; then
+ lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"
+else
+ { $as_echo "$as_me:$LINENO: checking for dlopen in -lsvld" >&5
+$as_echo_n "checking for dlopen in -lsvld... " >&6; }
+if test "${ac_cv_lib_svld_dlopen+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lsvld $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dlopen ();
+int
+main ()
+{
+return dlopen ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ ac_cv_lib_svld_dlopen=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_lib_svld_dlopen=no
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_svld_dlopen" >&5
+$as_echo "$ac_cv_lib_svld_dlopen" >&6; }
+if test "x$ac_cv_lib_svld_dlopen" = x""yes; then
+ lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld"
+else
+ { $as_echo "$as_me:$LINENO: checking for dld_link in -ldld" >&5
+$as_echo_n "checking for dld_link in -ldld... " >&6; }
+if test "${ac_cv_lib_dld_dld_link+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-ldld $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char dld_link ();
+int
+main ()
+{
+return dld_link ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ ac_cv_lib_dld_dld_link=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_lib_dld_dld_link=no
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_dld_dld_link" >&5
+$as_echo "$ac_cv_lib_dld_dld_link" >&6; }
+if test "x$ac_cv_lib_dld_dld_link" = x""yes; then
+ lt_cv_dlopen="dld_link" lt_cv_dlopen_libs="-ldld"
+fi
+
+
+fi
+
+
+fi
+
+
+fi
+
+
+fi
+
+
+fi
+
+ ;;
+ esac
+
+ if test "x$lt_cv_dlopen" != xno; then
+ enable_dlopen=yes
+ else
+ enable_dlopen=no
+ fi
+
+ case $lt_cv_dlopen in
+ dlopen)
+ save_CPPFLAGS="$CPPFLAGS"
+ test "x$ac_cv_header_dlfcn_h" = xyes && CPPFLAGS="$CPPFLAGS -DHAVE_DLFCN_H"
+
+ save_LDFLAGS="$LDFLAGS"
+ wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $export_dynamic_flag_spec\"
+
+ save_LIBS="$LIBS"
+ LIBS="$lt_cv_dlopen_libs $LIBS"
+
+ { $as_echo "$as_me:$LINENO: checking whether a program can dlopen itself" >&5
+$as_echo_n "checking whether a program can dlopen itself... " >&6; }
+if test "${lt_cv_dlopen_self+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then :
+ lt_cv_dlopen_self=cross
+else
+ lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
+ lt_status=$lt_dlunknown
+ cat > conftest.$ac_ext <<_LT_EOF
+#line 11122 "configure"
+#include "confdefs.h"
+
+#if HAVE_DLFCN_H
+#include <dlfcn.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef RTLD_GLOBAL
+# define LT_DLGLOBAL RTLD_GLOBAL
+#else
+# ifdef DL_GLOBAL
+# define LT_DLGLOBAL DL_GLOBAL
+# else
+# define LT_DLGLOBAL 0
+# endif
+#endif
+
+/* We may have to define LT_DLLAZY_OR_NOW in the command line if we
+ find out it does not work in some platform. */
+#ifndef LT_DLLAZY_OR_NOW
+# ifdef RTLD_LAZY
+# define LT_DLLAZY_OR_NOW RTLD_LAZY
+# else
+# ifdef DL_LAZY
+# define LT_DLLAZY_OR_NOW DL_LAZY
+# else
+# ifdef RTLD_NOW
+# define LT_DLLAZY_OR_NOW RTLD_NOW
+# else
+# ifdef DL_NOW
+# define LT_DLLAZY_OR_NOW DL_NOW
+# else
+# define LT_DLLAZY_OR_NOW 0
+# endif
+# endif
+# endif
+# endif
+#endif
+
+void fnord() { int i=42;}
+int main ()
+{
+ void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW);
+ int status = $lt_dlunknown;
+
+ if (self)
+ {
+ if (dlsym (self,"fnord")) status = $lt_dlno_uscore;
+ else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore;
+ /* dlclose (self); */
+ }
+ else
+ puts (dlerror ());
+
+ return status;
+}
+_LT_EOF
+ if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
+ (eval $ac_link) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && test -s conftest${ac_exeext} 2>/dev/null; then
+ (./conftest; exit; ) >&5 2>/dev/null
+ lt_status=$?
+ case x$lt_status in
+ x$lt_dlno_uscore) lt_cv_dlopen_self=yes ;;
+ x$lt_dlneed_uscore) lt_cv_dlopen_self=yes ;;
+ x$lt_dlunknown|x*) lt_cv_dlopen_self=no ;;
+ esac
+ else :
+ # compilation failed
+ lt_cv_dlopen_self=no
+ fi
+fi
+rm -fr conftest*
+
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_dlopen_self" >&5
+$as_echo "$lt_cv_dlopen_self" >&6; }
+
+ if test "x$lt_cv_dlopen_self" = xyes; then
+ wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $lt_prog_compiler_static\"
+ { $as_echo "$as_me:$LINENO: checking whether a statically linked program can dlopen itself" >&5
+$as_echo_n "checking whether a statically linked program can dlopen itself... " >&6; }
+if test "${lt_cv_dlopen_self_static+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then :
+ lt_cv_dlopen_self_static=cross
+else
+ lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
+ lt_status=$lt_dlunknown
+ cat > conftest.$ac_ext <<_LT_EOF
+#line 11218 "configure"
+#include "confdefs.h"
+
+#if HAVE_DLFCN_H
+#include <dlfcn.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef RTLD_GLOBAL
+# define LT_DLGLOBAL RTLD_GLOBAL
+#else
+# ifdef DL_GLOBAL
+# define LT_DLGLOBAL DL_GLOBAL
+# else
+# define LT_DLGLOBAL 0
+# endif
+#endif
+
+/* We may have to define LT_DLLAZY_OR_NOW in the command line if we
+ find out it does not work in some platform. */
+#ifndef LT_DLLAZY_OR_NOW
+# ifdef RTLD_LAZY
+# define LT_DLLAZY_OR_NOW RTLD_LAZY
+# else
+# ifdef DL_LAZY
+# define LT_DLLAZY_OR_NOW DL_LAZY
+# else
+# ifdef RTLD_NOW
+# define LT_DLLAZY_OR_NOW RTLD_NOW
+# else
+# ifdef DL_NOW
+# define LT_DLLAZY_OR_NOW DL_NOW
+# else
+# define LT_DLLAZY_OR_NOW 0
+# endif
+# endif
+# endif
+# endif
+#endif
+
+void fnord() { int i=42;}
+int main ()
+{
+ void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW);
+ int status = $lt_dlunknown;
+
+ if (self)
+ {
+ if (dlsym (self,"fnord")) status = $lt_dlno_uscore;
+ else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore;
+ /* dlclose (self); */
+ }
+ else
+ puts (dlerror ());
+
+ return status;
+}
+_LT_EOF
+ if { (eval echo "$as_me:$LINENO: \"$ac_link\"") >&5
+ (eval $ac_link) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && test -s conftest${ac_exeext} 2>/dev/null; then
+ (./conftest; exit; ) >&5 2>/dev/null
+ lt_status=$?
+ case x$lt_status in
+ x$lt_dlno_uscore) lt_cv_dlopen_self_static=yes ;;
+ x$lt_dlneed_uscore) lt_cv_dlopen_self_static=yes ;;
+ x$lt_dlunknown|x*) lt_cv_dlopen_self_static=no ;;
+ esac
+ else :
+ # compilation failed
+ lt_cv_dlopen_self_static=no
+ fi
+fi
+rm -fr conftest*
+
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_dlopen_self_static" >&5
+$as_echo "$lt_cv_dlopen_self_static" >&6; }
+ fi
+
+ CPPFLAGS="$save_CPPFLAGS"
+ LDFLAGS="$save_LDFLAGS"
+ LIBS="$save_LIBS"
+ ;;
+ esac
+
+ case $lt_cv_dlopen_self in
+ yes|no) enable_dlopen_self=$lt_cv_dlopen_self ;;
+ *) enable_dlopen_self=unknown ;;
+ esac
+
+ case $lt_cv_dlopen_self_static in
+ yes|no) enable_dlopen_self_static=$lt_cv_dlopen_self_static ;;
+ *) enable_dlopen_self_static=unknown ;;
+ esac
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+striplib=
+old_striplib=
+{ $as_echo "$as_me:$LINENO: checking whether stripping libraries is possible" >&5
+$as_echo_n "checking whether stripping libraries is possible... " >&6; }
+if test -n "$STRIP" && $STRIP -V 2>&1 | $GREP "GNU strip" >/dev/null; then
+ test -z "$old_striplib" && old_striplib="$STRIP --strip-debug"
+ test -z "$striplib" && striplib="$STRIP --strip-unneeded"
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+else
+# FIXME - insert some real tests, host_os isn't really good enough
+ case $host_os in
+ darwin*)
+ if test -n "$STRIP" ; then
+ striplib="$STRIP -x"
+ old_striplib="$STRIP -S"
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+ else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+ fi
+ ;;
+ *)
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+ ;;
+ esac
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+ # Report which library types will actually be built
+ { $as_echo "$as_me:$LINENO: checking if libtool supports shared libraries" >&5
+$as_echo_n "checking if libtool supports shared libraries... " >&6; }
+ { $as_echo "$as_me:$LINENO: result: $can_build_shared" >&5
+$as_echo "$can_build_shared" >&6; }
+
+ { $as_echo "$as_me:$LINENO: checking whether to build shared libraries" >&5
+$as_echo_n "checking whether to build shared libraries... " >&6; }
+ test "$can_build_shared" = "no" && enable_shared=no
+
+ # On AIX, shared libraries and static libraries use the same namespace, and
+ # are all built from PIC.
+ case $host_os in
+ aix3*)
+ test "$enable_shared" = yes && enable_static=no
+ if test -n "$RANLIB"; then
+ archive_cmds="$archive_cmds~\$RANLIB \$lib"
+ postinstall_cmds='$RANLIB $lib'
+ fi
+ ;;
+
+ aix[4-9]*)
+ if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+ test "$enable_shared" = yes && enable_static=no
+ fi
+ ;;
+ esac
+ { $as_echo "$as_me:$LINENO: result: $enable_shared" >&5
+$as_echo "$enable_shared" >&6; }
+
+ { $as_echo "$as_me:$LINENO: checking whether to build static libraries" >&5
+$as_echo_n "checking whether to build static libraries... " >&6; }
+ # Make sure either enable_shared or enable_static is yes.
+ test "$enable_shared" = yes || enable_static=yes
+ { $as_echo "$as_me:$LINENO: result: $enable_static" >&5
+$as_echo "$enable_static" >&6; }
+
+
+
+
+fi
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+CC="$lt_save_CC"
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ac_config_commands="$ac_config_commands libtool"
+
+
+
+
+# Only expand once:
+
+
+
+# AC_PROG_INSTALL will generate an install target so that users may
+# just type 'make install' to install the software.
+# Find a good install program. We prefer a C program (faster),
+# so one script is as good as another. But avoid the broken or
+# incompatible versions:
+# SysV /etc/install, /usr/sbin/install
+# SunOS /usr/etc/install
+# IRIX /sbin/install
+# AIX /bin/install
+# AmigaOS /C/install, which installs bootblocks on floppy discs
+# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag
+# AFS /usr/afsws/bin/install, which mishandles nonexistent args
+# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
+# OS/2's system install, which has a completely different semantic
+# ./install, which can be erroneously created by make from ./install.sh.
+# Reject install programs that cannot install multiple files.
+{ $as_echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5
+$as_echo_n "checking for a BSD-compatible install... " >&6; }
+if test -z "$INSTALL"; then
+if test "${ac_cv_path_install+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ # Account for people who put trailing slashes in PATH elements.
+case $as_dir/ in
+ ./ | .// | /cC/* | \
+ /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \
+ ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \
+ /usr/ucb/* ) ;;
+ *)
+ # OSF1 and SCO ODT 3.0 have their own names for install.
+ # Don't use installbsd from OSF since it installs stuff as root
+ # by default.
+ for ac_prog in ginstall scoinst install; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then
+ if test $ac_prog = install &&
+ grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # AIX install. It has an incompatible calling convention.
+ :
+ elif test $ac_prog = install &&
+ grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then
+ # program-specific install script used by HP pwplus--don't use.
+ :
+ else
+ rm -rf conftest.one conftest.two conftest.dir
+ echo one > conftest.one
+ echo two > conftest.two
+ mkdir conftest.dir
+ if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" &&
+ test -s conftest.one && test -s conftest.two &&
+ test -s conftest.dir/conftest.one &&
+ test -s conftest.dir/conftest.two
+ then
+ ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c"
+ break 3
+ fi
+ fi
+ fi
+ done
+ done
+ ;;
+esac
+
+done
+IFS=$as_save_IFS
+
+rm -rf conftest.one conftest.two conftest.dir
+
+fi
+ if test "${ac_cv_path_install+set}" = set; then
+ INSTALL=$ac_cv_path_install
+ else
+ # As a last resort, use the slow shell script. Don't cache a
+ # value for INSTALL within a source directory, because that will
+ # break other packages using the cache if that directory is
+ # removed, or if the value is a relative name.
+ INSTALL=$ac_install_sh
+ fi
+fi
+{ $as_echo "$as_me:$LINENO: result: $INSTALL" >&5
+$as_echo "$INSTALL" >&6; }
+
+# Use test -z because SunOS4 sh mishandles braces in ${var-val}.
+# It thinks the first close brace ends the variable substitution.
+test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}'
+
+test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}'
+
+test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
+
+
+# check for C++ preprocessor and compiler and the library compiler
+# (might change the compiler flags)
+#
+# Determine a C compiler to use. If using the GNU C compiler, set
+# shell variable GCC to `yes'. If output variable CFLAGS was not
+# already set, set it to `-g -O2' for the GNU C compiler (`-O2' on
+# systems where GCC does not accept `-g'), or `-g' for other
+# compilers.
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}gcc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}gcc; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="${ac_tool_prefix}gcc"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:$LINENO: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$ac_cv_prog_CC"; then
+ ac_ct_CC=$CC
+ # Extract the first word of "gcc", so it can be a program name with args.
+set dummy gcc; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CC="gcc"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+ if test "x$ac_ct_CC" = x; then
+ CC=""
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CC=$ac_ct_CC
+ fi
+else
+ CC="$ac_cv_prog_CC"
+fi
+
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ # Extract the first word of "${ac_tool_prefix}cc", so it can be a program name with args.
+set dummy ${ac_tool_prefix}cc; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="${ac_tool_prefix}cc"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:$LINENO: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ fi
+fi
+if test -z "$CC"; then
+ # Extract the first word of "cc", so it can be a program name with args.
+set dummy cc; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+ ac_prog_rejected=no
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ if test "$as_dir/$ac_word$ac_exec_ext" = "/usr/ucb/cc"; then
+ ac_prog_rejected=yes
+ continue
+ fi
+ ac_cv_prog_CC="cc"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+if test $ac_prog_rejected = yes; then
+ # We found a bogon in the path, so make sure we never use it.
+ set dummy $ac_cv_prog_CC
+ shift
+ if test $# != 0; then
+ # We chose a different compiler from the bogus one.
+ # However, it has the same basename, so the bogon will be chosen
+ # first if we set CC to just the basename; use the full file name.
+ shift
+ ac_cv_prog_CC="$as_dir/$ac_word${1+' '}$@"
+ fi
+fi
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:$LINENO: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+fi
+if test -z "$CC"; then
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in cl.exe
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CC+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CC"; then
+ ac_cv_prog_CC="$CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CC="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+CC=$ac_cv_prog_CC
+if test -n "$CC"; then
+ { $as_echo "$as_me:$LINENO: result: $CC" >&5
+$as_echo "$CC" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CC" && break
+ done
+fi
+if test -z "$CC"; then
+ ac_ct_CC=$CC
+ for ac_prog in cl.exe
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_CC+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CC"; then
+ ac_cv_prog_ac_ct_CC="$ac_ct_CC" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CC="$ac_prog"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CC=$ac_cv_prog_ac_ct_CC
+if test -n "$ac_ct_CC"; then
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_CC" >&5
+$as_echo "$ac_ct_CC" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CC" && break
+done
+
+ if test "x$ac_ct_CC" = x; then
+ CC=""
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CC=$ac_ct_CC
+ fi
+fi
+
+fi
+
+
+test -z "$CC" && { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: no acceptable C compiler found in \$PATH
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
+
+# Provide some information about the compiler.
+$as_echo "$as_me:$LINENO: checking for C compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+{ (ac_try="$ac_compiler --version >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compiler --version >&5") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+{ (ac_try="$ac_compiler -v >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compiler -v >&5") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+{ (ac_try="$ac_compiler -V >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compiler -V >&5") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+
+{ $as_echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5
+$as_echo_n "checking whether we are using the GNU C compiler... " >&6; }
+if test "${ac_cv_c_compiler_gnu+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_compiler_gnu=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_compiler_gnu=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_c_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5
+$as_echo "$ac_cv_c_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+ GCC=yes
+else
+ GCC=
+fi
+ac_test_CFLAGS=${CFLAGS+set}
+ac_save_CFLAGS=$CFLAGS
+{ $as_echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5
+$as_echo_n "checking whether $CC accepts -g... " >&6; }
+if test "${ac_cv_prog_cc_g+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_save_c_werror_flag=$ac_c_werror_flag
+ ac_c_werror_flag=yes
+ ac_cv_prog_cc_g=no
+ CFLAGS="-g"
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_cv_prog_cc_g=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ CFLAGS=""
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ :
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_c_werror_flag=$ac_save_c_werror_flag
+ CFLAGS="-g"
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_cv_prog_cc_g=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_c_werror_flag=$ac_save_c_werror_flag
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5
+$as_echo "$ac_cv_prog_cc_g" >&6; }
+if test "$ac_test_CFLAGS" = set; then
+ CFLAGS=$ac_save_CFLAGS
+elif test $ac_cv_prog_cc_g = yes; then
+ if test "$GCC" = yes; then
+ CFLAGS="-g -O2"
+ else
+ CFLAGS="-g"
+ fi
+else
+ if test "$GCC" = yes; then
+ CFLAGS="-O2"
+ else
+ CFLAGS=
+ fi
+fi
+{ $as_echo "$as_me:$LINENO: checking for $CC option to accept ISO C89" >&5
+$as_echo_n "checking for $CC option to accept ISO C89... " >&6; }
+if test "${ac_cv_prog_cc_c89+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_prog_cc_c89=no
+ac_save_CC=$CC
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <stdarg.h>
+#include <stdio.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+/* Most of the following tests are stolen from RCS 5.7's src/conf.sh. */
+struct buf { int x; };
+FILE * (*rcsopen) (struct buf *, struct stat *, int);
+static char *e (p, i)
+ char **p;
+ int i;
+{
+ return p[i];
+}
+static char *f (char * (*g) (char **, int), char **p, ...)
+{
+ char *s;
+ va_list v;
+ va_start (v,p);
+ s = g (p, va_arg (v,int));
+ va_end (v);
+ return s;
+}
+
+/* OSF 4.0 Compaq cc is some sort of almost-ANSI by default. It has
+ function prototypes and stuff, but not '\xHH' hex character constants.
+ These don't provoke an error unfortunately, instead are silently treated
+ as 'x'. The following induces an error, until -std is added to get
+ proper ANSI mode. Curiously '\x00'!='x' always comes out true, for an
+ array size at least. It's necessary to write '\x00'==0 to get something
+ that's true only with -std. */
+int osf4_cc_array ['\x00' == 0 ? 1 : -1];
+
+/* IBM C 6 for AIX is almost-ANSI by default, but it replaces macro parameters
+ inside strings and character constants. */
+#define FOO(x) 'x'
+int xlc6_cc_array[FOO(a) == 'x' ? 1 : -1];
+
+int test (int i, double x);
+struct s1 {int (*f) (int a);};
+struct s2 {int (*f) (double a);};
+int pairnames (int, char **, FILE *(*)(struct buf *, struct stat *, int), int, int);
+int argc;
+char **argv;
+int
+main ()
+{
+return f (e, argv, 0) != argv[0] || f (e, argv, 1) != argv[1];
+ ;
+ return 0;
+}
+_ACEOF
+for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \
+ -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__"
+do
+ CC="$ac_save_CC $ac_arg"
+ rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_cv_prog_cc_c89=$ac_arg
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext
+ test "x$ac_cv_prog_cc_c89" != "xno" && break
+done
+rm -f conftest.$ac_ext
+CC=$ac_save_CC
+
+fi
+# AC_CACHE_VAL
+case "x$ac_cv_prog_cc_c89" in
+ x)
+ { $as_echo "$as_me:$LINENO: result: none needed" >&5
+$as_echo "none needed" >&6; } ;;
+ xno)
+ { $as_echo "$as_me:$LINENO: result: unsupported" >&5
+$as_echo "unsupported" >&6; } ;;
+ *)
+ CC="$CC $ac_cv_prog_cc_c89"
+ { $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_c89" >&5
+$as_echo "$ac_cv_prog_cc_c89" >&6; } ;;
+esac
+
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+depcc="$CC" am_compiler_list=
+
+{ $as_echo "$as_me:$LINENO: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CC_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ case $depmode in
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ none) break ;;
+ esac
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this.
+ if depmode=$depmode \
+ source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CC_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CC_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $am_cv_CC_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CC_dependencies_compiler_type" >&6; }
+CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CC_dependencies_compiler_type" = gcc3; then
+ am__fastdepCC_TRUE=
+ am__fastdepCC_FALSE='#'
+else
+ am__fastdepCC_TRUE='#'
+ am__fastdepCC_FALSE=
+fi
+
+
+# Set output variable CPP to a command that runs the C preprocessor.
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+{ $as_echo "$as_me:$LINENO: checking how to run the C preprocessor" >&5
+$as_echo_n "checking how to run the C preprocessor... " >&6; }
+# On Suns, sometimes $CPP names a directory.
+if test -n "$CPP" && test -d "$CPP"; then
+ CPP=
+fi
+if test -z "$CPP"; then
+ if test "${ac_cv_prog_CPP+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ # Double quotes because CPP needs to be expanded
+ for CPP in "$CC -E" "$CC -E -traditional-cpp" "/lib/cpp"
+ do
+ ac_preproc_ok=false
+for ac_c_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ :
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ # Broken: fails on valid input.
+continue
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ # Broken: success on invalid input.
+continue
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
+ break
+fi
+
+ done
+ ac_cv_prog_CPP=$CPP
+
+fi
+ CPP=$ac_cv_prog_CPP
+else
+ ac_cv_prog_CPP=$CPP
+fi
+{ $as_echo "$as_me:$LINENO: result: $CPP" >&5
+$as_echo "$CPP" >&6; }
+ac_preproc_ok=false
+for ac_c_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ :
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ # Broken: fails on valid input.
+continue
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ # Broken: success on invalid input.
+continue
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
+ :
+else
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: C preprocessor \"$CPP\" fails sanity check
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: C preprocessor \"$CPP\" fails sanity check
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+#
+# Determine a C++ compiler to use. If output variable CXXFLAGS was not
+# already set, set it to `-g -O2' for the GNU C++ compiler (`-O2' on
+# systems where G++ does not accept `-g'), or `-g' for other
+# compilers.
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+if test -z "$CXX"; then
+ if test -n "$CCC"; then
+ CXX=$CCC
+ else
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CXX+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CXX"; then
+ ac_cv_prog_CXX="$CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+CXX=$ac_cv_prog_CXX
+if test -n "$CXX"; then
+ { $as_echo "$as_me:$LINENO: result: $CXX" >&5
+$as_echo "$CXX" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CXX" && break
+ done
+fi
+if test -z "$CXX"; then
+ ac_ct_CXX=$CXX
+ for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CXX"; then
+ ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CXX="$ac_prog"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CXX=$ac_cv_prog_ac_ct_CXX
+if test -n "$ac_ct_CXX"; then
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5
+$as_echo "$ac_ct_CXX" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CXX" && break
+done
+
+ if test "x$ac_ct_CXX" = x; then
+ CXX="g++"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CXX=$ac_ct_CXX
+ fi
+fi
+
+ fi
+fi
+# Provide some information about the compiler.
+$as_echo "$as_me:$LINENO: checking for C++ compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+{ (ac_try="$ac_compiler --version >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compiler --version >&5") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+{ (ac_try="$ac_compiler -v >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compiler -v >&5") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+{ (ac_try="$ac_compiler -V >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compiler -V >&5") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+
+{ $as_echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5
+$as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; }
+if test "${ac_cv_cxx_compiler_gnu+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_compiler_gnu=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_compiler_gnu=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_cxx_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_cxx_compiler_gnu" >&5
+$as_echo "$ac_cv_cxx_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+ GXX=yes
+else
+ GXX=
+fi
+ac_test_CXXFLAGS=${CXXFLAGS+set}
+ac_save_CXXFLAGS=$CXXFLAGS
+{ $as_echo "$as_me:$LINENO: checking whether $CXX accepts -g" >&5
+$as_echo_n "checking whether $CXX accepts -g... " >&6; }
+if test "${ac_cv_prog_cxx_g+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_save_cxx_werror_flag=$ac_cxx_werror_flag
+ ac_cxx_werror_flag=yes
+ ac_cv_prog_cxx_g=no
+ CXXFLAGS="-g"
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_cv_prog_cxx_g=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ CXXFLAGS=""
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ :
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+ CXXFLAGS="-g"
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_cv_prog_cxx_g=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cxx_g" >&5
+$as_echo "$ac_cv_prog_cxx_g" >&6; }
+if test "$ac_test_CXXFLAGS" = set; then
+ CXXFLAGS=$ac_save_CXXFLAGS
+elif test $ac_cv_prog_cxx_g = yes; then
+ if test "$GXX" = yes; then
+ CXXFLAGS="-g -O2"
+ else
+ CXXFLAGS="-g"
+ fi
+else
+ if test "$GXX" = yes; then
+ CXXFLAGS="-O2"
+ else
+ CXXFLAGS=
+ fi
+fi
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+depcc="$CXX" am_compiler_list=
+
+{ $as_echo "$as_me:$LINENO: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CXX_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ case $depmode in
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ none) break ;;
+ esac
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this.
+ if depmode=$depmode \
+ source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CXX_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CXX_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $am_cv_CXX_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CXX_dependencies_compiler_type" >&6; }
+CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CXX_dependencies_compiler_type" = gcc3; then
+ am__fastdepCXX_TRUE=
+ am__fastdepCXX_FALSE='#'
+else
+ am__fastdepCXX_TRUE='#'
+ am__fastdepCXX_FALSE=
+fi
+
+
+
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+if test -z "$CXX"; then
+ if test -n "$CCC"; then
+ CXX=$CCC
+ else
+ if test -n "$ac_tool_prefix"; then
+ for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+ do
+ # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args.
+set dummy $ac_tool_prefix$ac_prog; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_CXX+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$CXX"; then
+ ac_cv_prog_CXX="$CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_CXX="$ac_tool_prefix$ac_prog"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+CXX=$ac_cv_prog_CXX
+if test -n "$CXX"; then
+ { $as_echo "$as_me:$LINENO: result: $CXX" >&5
+$as_echo "$CXX" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$CXX" && break
+ done
+fi
+if test -z "$CXX"; then
+ ac_ct_CXX=$CXX
+ for ac_prog in g++ c++ gpp aCC CC cxx cc++ cl.exe FCC KCC RCC xlC_r xlC
+do
+ # Extract the first word of "$ac_prog", so it can be a program name with args.
+set dummy $ac_prog; ac_word=$2
+{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5
+$as_echo_n "checking for $ac_word... " >&6; }
+if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -n "$ac_ct_CXX"; then
+ ac_cv_prog_ac_ct_CXX="$ac_ct_CXX" # Let the user override the test.
+else
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then
+ ac_cv_prog_ac_ct_CXX="$ac_prog"
+ $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5
+ break 2
+ fi
+done
+done
+IFS=$as_save_IFS
+
+fi
+fi
+ac_ct_CXX=$ac_cv_prog_ac_ct_CXX
+if test -n "$ac_ct_CXX"; then
+ { $as_echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5
+$as_echo "$ac_ct_CXX" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+ test -n "$ac_ct_CXX" && break
+done
+
+ if test "x$ac_ct_CXX" = x; then
+ CXX="g++"
+ else
+ case $cross_compiling:$ac_tool_warned in
+yes:)
+{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5
+$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
+ac_tool_warned=yes ;;
+esac
+ CXX=$ac_ct_CXX
+ fi
+fi
+
+ fi
+fi
+# Provide some information about the compiler.
+$as_echo "$as_me:$LINENO: checking for C++ compiler version" >&5
+set X $ac_compile
+ac_compiler=$2
+{ (ac_try="$ac_compiler --version >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compiler --version >&5") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+{ (ac_try="$ac_compiler -v >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compiler -v >&5") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+{ (ac_try="$ac_compiler -V >&5"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compiler -V >&5") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+
+{ $as_echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5
+$as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; }
+if test "${ac_cv_cxx_compiler_gnu+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+#ifndef __GNUC__
+ choke me
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_compiler_gnu=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_compiler_gnu=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ac_cv_cxx_compiler_gnu=$ac_compiler_gnu
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_cxx_compiler_gnu" >&5
+$as_echo "$ac_cv_cxx_compiler_gnu" >&6; }
+if test $ac_compiler_gnu = yes; then
+ GXX=yes
+else
+ GXX=
+fi
+ac_test_CXXFLAGS=${CXXFLAGS+set}
+ac_save_CXXFLAGS=$CXXFLAGS
+{ $as_echo "$as_me:$LINENO: checking whether $CXX accepts -g" >&5
+$as_echo_n "checking whether $CXX accepts -g... " >&6; }
+if test "${ac_cv_prog_cxx_g+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_save_cxx_werror_flag=$ac_cxx_werror_flag
+ ac_cxx_werror_flag=yes
+ ac_cv_prog_cxx_g=no
+ CXXFLAGS="-g"
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_cv_prog_cxx_g=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ CXXFLAGS=""
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ :
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+ CXXFLAGS="-g"
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_cv_prog_cxx_g=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ ac_cxx_werror_flag=$ac_save_cxx_werror_flag
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cxx_g" >&5
+$as_echo "$ac_cv_prog_cxx_g" >&6; }
+if test "$ac_test_CXXFLAGS" = set; then
+ CXXFLAGS=$ac_save_CXXFLAGS
+elif test $ac_cv_prog_cxx_g = yes; then
+ if test "$GXX" = yes; then
+ CXXFLAGS="-g -O2"
+ else
+ CXXFLAGS="-g"
+ fi
+else
+ if test "$GXX" = yes; then
+ CXXFLAGS="-O2"
+ else
+ CXXFLAGS=
+ fi
+fi
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+depcc="$CXX" am_compiler_list=
+
+{ $as_echo "$as_me:$LINENO: checking dependency style of $depcc" >&5
+$as_echo_n "checking dependency style of $depcc... " >&6; }
+if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then
+ # We make a subdir and do the tests there. Otherwise we can end up
+ # making bogus files that we don't know about and never remove. For
+ # instance it was reported that on HP-UX the gcc test will end up
+ # making a dummy file named `D' -- because `-MD' means `put the output
+ # in D'.
+ mkdir conftest.dir
+ # Copy depcomp to subdir because otherwise we won't find it if we're
+ # using a relative directory.
+ cp "$am_depcomp" conftest.dir
+ cd conftest.dir
+ # We will build objects and dependencies in a subdirectory because
+ # it helps to detect inapplicable dependency modes. For instance
+ # both Tru64's cc and ICC support -MD to output dependencies as a
+ # side effect of compilation, but ICC will put the dependencies in
+ # the current directory while Tru64 will put them in the object
+ # directory.
+ mkdir sub
+
+ am_cv_CXX_dependencies_compiler_type=none
+ if test "$am_compiler_list" = ""; then
+ am_compiler_list=`sed -n 's/^#*\([a-zA-Z0-9]*\))$/\1/p' < ./depcomp`
+ fi
+ for depmode in $am_compiler_list; do
+ # Setup a source with many dependencies, because some compilers
+ # like to wrap large dependency lists on column 80 (with \), and
+ # we should not choose a depcomp mode which is confused by this.
+ #
+ # We need to recreate these files for each test, as the compiler may
+ # overwrite some of them when testing with obscure command lines.
+ # This happens at least with the AIX C compiler.
+ : > sub/conftest.c
+ for i in 1 2 3 4 5 6; do
+ echo '#include "conftst'$i'.h"' >> sub/conftest.c
+ # Using `: > sub/conftst$i.h' creates only sub/conftst1.h with
+ # Solaris 8's {/usr,}/bin/sh.
+ touch sub/conftst$i.h
+ done
+ echo "${am__include} ${am__quote}sub/conftest.Po${am__quote}" > confmf
+
+ case $depmode in
+ nosideeffect)
+ # after this tag, mechanisms are not by side-effect, so they'll
+ # only be used when explicitly requested
+ if test "x$enable_dependency_tracking" = xyes; then
+ continue
+ else
+ break
+ fi
+ ;;
+ none) break ;;
+ esac
+ # We check with `-c' and `-o' for the sake of the "dashmstdout"
+ # mode. It turns out that the SunPro C++ compiler does not properly
+ # handle `-M -o', and we need to detect this.
+ if depmode=$depmode \
+ source=sub/conftest.c object=sub/conftest.${OBJEXT-o} \
+ depfile=sub/conftest.Po tmpdepfile=sub/conftest.TPo \
+ $SHELL ./depcomp $depcc -c -o sub/conftest.${OBJEXT-o} sub/conftest.c \
+ >/dev/null 2>conftest.err &&
+ grep sub/conftst1.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftst6.h sub/conftest.Po > /dev/null 2>&1 &&
+ grep sub/conftest.${OBJEXT-o} sub/conftest.Po > /dev/null 2>&1 &&
+ ${MAKE-make} -s -f confmf > /dev/null 2>&1; then
+ # icc doesn't choke on unknown options, it will just issue warnings
+ # or remarks (even with -Werror). So we grep stderr for any message
+ # that says an option was ignored or not supported.
+ # When given -MP, icc 7.0 and 7.1 complain thusly:
+ # icc: Command line warning: ignoring option '-M'; no argument required
+ # The diagnosis changed in icc 8.0:
+ # icc: Command line remark: option '-MP' not supported
+ if (grep 'ignoring option' conftest.err ||
+ grep 'not supported' conftest.err) >/dev/null 2>&1; then :; else
+ am_cv_CXX_dependencies_compiler_type=$depmode
+ break
+ fi
+ fi
+ done
+
+ cd ..
+ rm -rf conftest.dir
+else
+ am_cv_CXX_dependencies_compiler_type=none
+fi
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $am_cv_CXX_dependencies_compiler_type" >&5
+$as_echo "$am_cv_CXX_dependencies_compiler_type" >&6; }
+CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type
+
+ if
+ test "x$enable_dependency_tracking" != xno \
+ && test "$am_cv_CXX_dependencies_compiler_type" = gcc3; then
+ am__fastdepCXX_TRUE=
+ am__fastdepCXX_FALSE='#'
+else
+ am__fastdepCXX_TRUE='#'
+ am__fastdepCXX_FALSE=
+fi
+
+
+if test -n "$CXX" && ( test "X$CXX" != "Xno" &&
+ ( (test "X$CXX" = "Xg++" && `g++ -v >/dev/null 2>&1` ) ||
+ (test "X$CXX" != "Xg++"))) ; then
+ ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+{ $as_echo "$as_me:$LINENO: checking how to run the C++ preprocessor" >&5
+$as_echo_n "checking how to run the C++ preprocessor... " >&6; }
+if test -z "$CXXCPP"; then
+ if test "${ac_cv_prog_CXXCPP+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ # Double quotes because CXXCPP needs to be expanded
+ for CXXCPP in "$CXX -E" "/lib/cpp"
+ do
+ ac_preproc_ok=false
+for ac_cxx_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ :
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ # Broken: fails on valid input.
+continue
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ # Broken: success on invalid input.
+continue
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
+ break
+fi
+
+ done
+ ac_cv_prog_CXXCPP=$CXXCPP
+
+fi
+ CXXCPP=$ac_cv_prog_CXXCPP
+else
+ ac_cv_prog_CXXCPP=$CXXCPP
+fi
+{ $as_echo "$as_me:$LINENO: result: $CXXCPP" >&5
+$as_echo "$CXXCPP" >&6; }
+ac_preproc_ok=false
+for ac_cxx_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ :
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ # Broken: fails on valid input.
+continue
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ # Broken: success on invalid input.
+continue
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
+ :
+else
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+_lt_caught_CXX_error=yes; }
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+else
+ _lt_caught_CXX_error=yes
+fi
+
+
+
+
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+archive_cmds_need_lc_CXX=no
+allow_undefined_flag_CXX=
+always_export_symbols_CXX=no
+archive_expsym_cmds_CXX=
+compiler_needs_object_CXX=no
+export_dynamic_flag_spec_CXX=
+hardcode_direct_CXX=no
+hardcode_direct_absolute_CXX=no
+hardcode_libdir_flag_spec_CXX=
+hardcode_libdir_flag_spec_ld_CXX=
+hardcode_libdir_separator_CXX=
+hardcode_minus_L_CXX=no
+hardcode_shlibpath_var_CXX=unsupported
+hardcode_automatic_CXX=no
+inherit_rpath_CXX=no
+module_cmds_CXX=
+module_expsym_cmds_CXX=
+link_all_deplibs_CXX=unknown
+old_archive_cmds_CXX=$old_archive_cmds
+no_undefined_flag_CXX=
+whole_archive_flag_spec_CXX=
+enable_shared_with_static_runtimes_CXX=no
+
+# Source file extension for C++ test sources.
+ac_ext=cpp
+
+# Object file extension for compiled C++ test sources.
+objext=o
+objext_CXX=$objext
+
+# No sense in running all these tests if we already determined that
+# the CXX compiler isn't working. Some variables (like enable_shared)
+# are currently assumed to apply to all compilers on this platform,
+# and will be corrupted by setting them based on a non-working compiler.
+if test "$_lt_caught_CXX_error" != yes; then
+ # Code to be used in simple compile tests
+ lt_simple_compile_test_code="int some_variable = 0;"
+
+ # Code to be used in simple link tests
+ lt_simple_link_test_code='int main(int, char *[]) { return(0); }'
+
+ # ltmain only uses $CC for tagged configurations so make sure $CC is set.
+
+
+
+
+
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+
+
+ # save warnings/boilerplate of simple test code
+ ac_outfile=conftest.$ac_objext
+echo "$lt_simple_compile_test_code" >conftest.$ac_ext
+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_compiler_boilerplate=`cat conftest.err`
+$RM conftest*
+
+ ac_outfile=conftest.$ac_objext
+echo "$lt_simple_link_test_code" >conftest.$ac_ext
+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_linker_boilerplate=`cat conftest.err`
+$RM -r conftest*
+
+
+ # Allow CC to be a program name with arguments.
+ lt_save_CC=$CC
+ lt_save_LD=$LD
+ lt_save_GCC=$GCC
+ GCC=$GXX
+ lt_save_with_gnu_ld=$with_gnu_ld
+ lt_save_path_LD=$lt_cv_path_LD
+ if test -n "${lt_cv_prog_gnu_ldcxx+set}"; then
+ lt_cv_prog_gnu_ld=$lt_cv_prog_gnu_ldcxx
+ else
+ $as_unset lt_cv_prog_gnu_ld
+ fi
+ if test -n "${lt_cv_path_LDCXX+set}"; then
+ lt_cv_path_LD=$lt_cv_path_LDCXX
+ else
+ $as_unset lt_cv_path_LD
+ fi
+ test -z "${LDCXX+set}" || LD=$LDCXX
+ CC=${CXX-"c++"}
+ compiler=$CC
+ compiler_CXX=$CC
+ for cc_temp in $compiler""; do
+ case $cc_temp in
+ compile | *[\\/]compile | ccache | *[\\/]ccache ) ;;
+ distcc | *[\\/]distcc | purify | *[\\/]purify ) ;;
+ \-*) ;;
+ *) break;;
+ esac
+done
+cc_basename=`$ECHO "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+
+
+ if test -n "$compiler"; then
+ # We don't want -fno-exception when compiling C++ code, so set the
+ # no_builtin_flag separately
+ if test "$GXX" = yes; then
+ lt_prog_compiler_no_builtin_flag_CXX=' -fno-builtin'
+ else
+ lt_prog_compiler_no_builtin_flag_CXX=
+ fi
+
+ if test "$GXX" = yes; then
+ # Set up default GNU C++ configuration
+
+
+
+# Check whether --with-gnu-ld was given.
+if test "${with_gnu_ld+set}" = set; then
+ withval=$with_gnu_ld; test "$withval" = no || with_gnu_ld=yes
+else
+ with_gnu_ld=no
+fi
+
+ac_prog=ld
+if test "$GCC" = yes; then
+ # Check if gcc -print-prog-name=ld gives a path.
+ { $as_echo "$as_me:$LINENO: checking for ld used by $CC" >&5
+$as_echo_n "checking for ld used by $CC... " >&6; }
+ case $host in
+ *-*-mingw*)
+ # gcc leaves a trailing carriage return which upsets mingw
+ ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;;
+ *)
+ ac_prog=`($CC -print-prog-name=ld) 2>&5` ;;
+ esac
+ case $ac_prog in
+ # Accept absolute paths.
+ [\\/]* | ?:[\\/]*)
+ re_direlt='/[^/][^/]*/\.\./'
+ # Canonicalize the pathname of ld
+ ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'`
+ while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do
+ ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"`
+ done
+ test -z "$LD" && LD="$ac_prog"
+ ;;
+ "")
+ # If it fails, then pretend we aren't using GCC.
+ ac_prog=ld
+ ;;
+ *)
+ # If it is relative, then search for the first ld in PATH.
+ with_gnu_ld=unknown
+ ;;
+ esac
+elif test "$with_gnu_ld" = yes; then
+ { $as_echo "$as_me:$LINENO: checking for GNU ld" >&5
+$as_echo_n "checking for GNU ld... " >&6; }
+else
+ { $as_echo "$as_me:$LINENO: checking for non-GNU ld" >&5
+$as_echo_n "checking for non-GNU ld... " >&6; }
+fi
+if test "${lt_cv_path_LD+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test -z "$LD"; then
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then
+ lt_cv_path_LD="$ac_dir/$ac_prog"
+ # Check to see if the program is GNU ld. I'd rather use --version,
+ # but apparently some variants of GNU ld only accept -v.
+ # Break only if it was the GNU/non-GNU ld that we prefer.
+ case `"$lt_cv_path_LD" -v 2>&1 </dev/null` in
+ *GNU* | *'with BFD'*)
+ test "$with_gnu_ld" != no && break
+ ;;
+ *)
+ test "$with_gnu_ld" != yes && break
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+else
+ lt_cv_path_LD="$LD" # Let the user override the test with a path.
+fi
+fi
+
+LD="$lt_cv_path_LD"
+if test -n "$LD"; then
+ { $as_echo "$as_me:$LINENO: result: $LD" >&5
+$as_echo "$LD" >&6; }
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+test -z "$LD" && { { $as_echo "$as_me:$LINENO: error: no acceptable ld found in \$PATH" >&5
+$as_echo "$as_me: error: no acceptable ld found in \$PATH" >&2;}
+ { (exit 1); exit 1; }; }
+{ $as_echo "$as_me:$LINENO: checking if the linker ($LD) is GNU ld" >&5
+$as_echo_n "checking if the linker ($LD) is GNU ld... " >&6; }
+if test "${lt_cv_prog_gnu_ld+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ # I'd rather use --version here, but apparently some GNU lds only accept -v.
+case `$LD -v 2>&1 </dev/null` in
+*GNU* | *'with BFD'*)
+ lt_cv_prog_gnu_ld=yes
+ ;;
+*)
+ lt_cv_prog_gnu_ld=no
+ ;;
+esac
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_gnu_ld" >&5
+$as_echo "$lt_cv_prog_gnu_ld" >&6; }
+with_gnu_ld=$lt_cv_prog_gnu_ld
+
+
+
+
+
+
+
+ # Check if GNU C++ uses GNU ld as the underlying linker, since the
+ # archiving commands below assume that GNU ld is being used.
+ if test "$with_gnu_ld" = yes; then
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+
+ # If archive_cmds runs LD, not CC, wlarc should be empty
+ # XXX I think wlarc can be eliminated in ltcf-cxx, but I need to
+ # investigate it a little bit more. (MM)
+ wlarc='${wl}'
+
+ # ancient GNU ld didn't support --whole-archive et. al.
+ if eval "`$CC -print-prog-name=ld` --help 2>&1" |
+ $GREP 'no-whole-archive' > /dev/null; then
+ whole_archive_flag_spec_CXX="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ else
+ whole_archive_flag_spec_CXX=
+ fi
+ else
+ with_gnu_ld=no
+ wlarc=
+
+ # A generic and very simple default shared library creation
+ # command for GNU C++ for the case where it uses the native
+ # linker, instead of GNU ld. If possible, this setting should
+ # overridden to take advantage of the native linker features on
+ # the platform it is being used on.
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+ fi
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+
+ else
+ GXX=no
+ with_gnu_ld=no
+ wlarc=
+ fi
+
+ # PORTME: fill in a description of your system's C++ link characteristics
+ { $as_echo "$as_me:$LINENO: checking whether the $compiler linker ($LD) supports shared libraries" >&5
+$as_echo_n "checking whether the $compiler linker ($LD) supports shared libraries... " >&6; }
+ ld_shlibs_CXX=yes
+ case $host_os in
+ aix3*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ aix[4-9]*)
+ if test "$host_cpu" = ia64; then
+ # On IA64, the linker does run time linking by default, so we don't
+ # have to do anything special.
+ aix_use_runtimelinking=no
+ exp_sym_flag='-Bexport'
+ no_entry_flag=""
+ else
+ aix_use_runtimelinking=no
+
+ # Test if we are trying to use run time linking or normal
+ # AIX style linking. If -brtl is somewhere in LDFLAGS, we
+ # need to do runtime linking.
+ case $host_os in aix4.[23]|aix4.[23].*|aix[5-9]*)
+ for ld_flag in $LDFLAGS; do
+ case $ld_flag in
+ *-brtl*)
+ aix_use_runtimelinking=yes
+ break
+ ;;
+ esac
+ done
+ ;;
+ esac
+
+ exp_sym_flag='-bexport'
+ no_entry_flag='-bnoentry'
+ fi
+
+ # When large executables or shared objects are built, AIX ld can
+ # have problems creating the table of contents. If linking a library
+ # or program results in "error TOC overflow" add -mminimal-toc to
+ # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not
+ # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+ archive_cmds_CXX=''
+ hardcode_direct_CXX=yes
+ hardcode_direct_absolute_CXX=yes
+ hardcode_libdir_separator_CXX=':'
+ link_all_deplibs_CXX=yes
+ file_list_spec_CXX='${wl}-f,'
+
+ if test "$GXX" = yes; then
+ case $host_os in aix4.[012]|aix4.[012].*)
+ # We only want to do this on AIX 4.2 and lower, the check
+ # below for broken collect2 doesn't work under 4.3+
+ collect2name=`${CC} -print-prog-name=collect2`
+ if test -f "$collect2name" &&
+ strings "$collect2name" | $GREP resolve_lib_name >/dev/null
+ then
+ # We have reworked collect2
+ :
+ else
+ # We have old collect2
+ hardcode_direct_CXX=unsupported
+ # It fails to find uninstalled libraries when the uninstalled
+ # path is not listed in the libpath. Setting hardcode_minus_L
+ # to unsupported forces relinking
+ hardcode_minus_L_CXX=yes
+ hardcode_libdir_flag_spec_CXX='-L$libdir'
+ hardcode_libdir_separator_CXX=
+ fi
+ esac
+ shared_flag='-shared'
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag="$shared_flag "'${wl}-G'
+ fi
+ else
+ # not using gcc
+ if test "$host_cpu" = ia64; then
+ # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+ # chokes on -Wl,-G. The following line is correct:
+ shared_flag='-G'
+ else
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag='${wl}-G'
+ else
+ shared_flag='${wl}-bM:SRE'
+ fi
+ fi
+ fi
+
+ export_dynamic_flag_spec_CXX='${wl}-bexpall'
+ # It seems that -bexpall does not export symbols beginning with
+ # underscore (_), so it is better to generate a list of symbols to
+ # export.
+ always_export_symbols_CXX=yes
+ if test "$aix_use_runtimelinking" = yes; then
+ # Warning - without using the other runtime loading flags (-brtl),
+ # -berok will link without error, but may produce a broken library.
+ allow_undefined_flag_CXX='-berok'
+ # Determine the default libpath from the value encoded in an empty
+ # executable.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+ hardcode_libdir_flag_spec_CXX='${wl}-blibpath:$libdir:'"$aix_libpath"
+
+ archive_expsym_cmds_CXX='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+ else
+ if test "$host_cpu" = ia64; then
+ hardcode_libdir_flag_spec_CXX='${wl}-R $libdir:/usr/lib:/lib'
+ allow_undefined_flag_CXX="-z nodefs"
+ archive_expsym_cmds_CXX="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+ else
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+
+ hardcode_libdir_flag_spec_CXX='${wl}-blibpath:$libdir:'"$aix_libpath"
+ # Warning - without using the other run time loading flags,
+ # -berok will link without error, but may produce a broken library.
+ no_undefined_flag_CXX=' ${wl}-bernotok'
+ allow_undefined_flag_CXX=' ${wl}-berok'
+ # Exported symbols can be pulled into shared objects from archives
+ whole_archive_flag_spec_CXX='$convenience'
+ archive_cmds_need_lc_CXX=yes
+ # This is similar to how AIX traditionally builds its shared
+ # libraries.
+ archive_expsym_cmds_CXX="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+ fi
+ fi
+ ;;
+
+ beos*)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ allow_undefined_flag_CXX=unsupported
+ # Joseph Beckenbach <jrb3@best.com> says some releases of gcc
+ # support --undefined. This deserves some investigation. FIXME
+ archive_cmds_CXX='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ else
+ ld_shlibs_CXX=no
+ fi
+ ;;
+
+ chorus*)
+ case $cc_basename in
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # _LT_TAGVAR(hardcode_libdir_flag_spec, CXX) is actually meaningless,
+ # as there is no search path for DLLs.
+ hardcode_libdir_flag_spec_CXX='-L$libdir'
+ allow_undefined_flag_CXX=unsupported
+ always_export_symbols_CXX=no
+ enable_shared_with_static_runtimes_CXX=yes
+
+ if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ # If the export-symbols file already is a .def file (1st line
+ # is EXPORTS), use it as is; otherwise, prepend...
+ archive_expsym_cmds_CXX='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+ cp $export_symbols $output_objdir/$soname.def;
+ else
+ echo EXPORTS > $output_objdir/$soname.def;
+ cat $export_symbols >> $output_objdir/$soname.def;
+ fi~
+ $CC -shared -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ else
+ ld_shlibs_CXX=no
+ fi
+ ;;
+ darwin* | rhapsody*)
+
+
+ archive_cmds_need_lc_CXX=no
+ hardcode_direct_CXX=no
+ hardcode_automatic_CXX=yes
+ hardcode_shlibpath_var_CXX=unsupported
+ whole_archive_flag_spec_CXX=''
+ link_all_deplibs_CXX=yes
+ allow_undefined_flag_CXX="$_lt_dar_allow_undefined"
+ case $cc_basename in
+ ifort*) _lt_dar_can_shared=yes ;;
+ *) _lt_dar_can_shared=$GCC ;;
+ esac
+ if test "$_lt_dar_can_shared" = "yes"; then
+ output_verbose_link_cmd=echo
+ archive_cmds_CXX="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}"
+ module_cmds_CXX="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}"
+ archive_expsym_cmds_CXX="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}"
+ module_expsym_cmds_CXX="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}"
+ if test "$lt_cv_apple_cc_single_mod" != "yes"; then
+ archive_cmds_CXX="\$CC -r -keep_private_externs -nostdlib -o \${lib}-master.o \$libobjs~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \${lib}-master.o \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring${_lt_dsymutil}"
+ archive_expsym_cmds_CXX="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -r -keep_private_externs -nostdlib -o \${lib}-master.o \$libobjs~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \${lib}-master.o \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring${_lt_dar_export_syms}${_lt_dsymutil}"
+ fi
+
+ else
+ ld_shlibs_CXX=no
+ fi
+
+ ;;
+
+ dgux*)
+ case $cc_basename in
+ ec++*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ ghcx*)
+ # Green Hills C++ Compiler
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ freebsd[12]*)
+ # C++ shared libraries reported to be fairly broken before
+ # switch to ELF
+ ld_shlibs_CXX=no
+ ;;
+
+ freebsd-elf*)
+ archive_cmds_need_lc_CXX=no
+ ;;
+
+ freebsd* | dragonfly*)
+ # FreeBSD 3 and later use GNU C++ and GNU ld with standard ELF
+ # conventions
+ ld_shlibs_CXX=yes
+ ;;
+
+ gnu*)
+ ;;
+
+ hpux9*)
+ hardcode_libdir_flag_spec_CXX='${wl}+b ${wl}$libdir'
+ hardcode_libdir_separator_CXX=:
+ export_dynamic_flag_spec_CXX='${wl}-E'
+ hardcode_direct_CXX=yes
+ hardcode_minus_L_CXX=yes # Not in the search PATH,
+ # but as the default
+ # location of the library.
+
+ case $cc_basename in
+ CC*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ aCC*)
+ archive_cmds_CXX='$RM $output_objdir/$soname~$CC -b ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | $EGREP "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ archive_cmds_CXX='$RM $output_objdir/$soname~$CC -shared -nostdlib -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ else
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ fi
+ ;;
+ esac
+ ;;
+
+ hpux10*|hpux11*)
+ if test $with_gnu_ld = no; then
+ hardcode_libdir_flag_spec_CXX='${wl}+b ${wl}$libdir'
+ hardcode_libdir_separator_CXX=:
+
+ case $host_cpu in
+ hppa*64*|ia64*)
+ ;;
+ *)
+ export_dynamic_flag_spec_CXX='${wl}-E'
+ ;;
+ esac
+ fi
+ case $host_cpu in
+ hppa*64*|ia64*)
+ hardcode_direct_CXX=no
+ hardcode_shlibpath_var_CXX=no
+ ;;
+ *)
+ hardcode_direct_CXX=yes
+ hardcode_direct_absolute_CXX=yes
+ hardcode_minus_L_CXX=yes # Not in the search PATH,
+ # but as the default
+ # location of the library.
+ ;;
+ esac
+
+ case $cc_basename in
+ CC*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ aCC*)
+ case $host_cpu in
+ hppa*64*)
+ archive_cmds_CXX='$CC -b ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ ia64*)
+ archive_cmds_CXX='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ esac
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | $GREP "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ if test $with_gnu_ld = no; then
+ case $host_cpu in
+ hppa*64*)
+ archive_cmds_CXX='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ ia64*)
+ archive_cmds_CXX='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ esac
+ fi
+ else
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ fi
+ ;;
+ esac
+ ;;
+
+ interix[3-9]*)
+ hardcode_direct_CXX=no
+ hardcode_shlibpath_var_CXX=no
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec_CXX='${wl}-E'
+ # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+ # Instead, shared libraries are loaded at an image base (0x10000000 by
+ # default) and relocated if they conflict, which is a slow very memory
+ # consuming and fragmenting process. To avoid this, we pick a random,
+ # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+ # time. Moving up from 0x10000000 also allows more sbrk(2) space.
+ archive_cmds_CXX='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ archive_expsym_cmds_CXX='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ ;;
+ irix5* | irix6*)
+ case $cc_basename in
+ CC*)
+ # SGI C++
+ archive_cmds_CXX='$CC -shared -all -multigot $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+
+ # Archives containing C++ object files must be created using
+ # "CC -ar", where "CC" is the IRIX C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ old_archive_cmds_CXX='$CC -ar -WR,-u -o $oldlib $oldobjs'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ if test "$with_gnu_ld" = no; then
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ else
+ archive_cmds_CXX='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` -o $lib'
+ fi
+ fi
+ link_all_deplibs_CXX=yes
+ ;;
+ esac
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator_CXX=:
+ inherit_rpath_CXX=yes
+ ;;
+
+ linux* | k*bsd*-gnu)
+ case $cc_basename in
+ KCC*)
+ # Kuck and Associates, Inc. (KAI) C++ Compiler
+
+ # KCC will only create a shared library if the output file
+ # ends with ".so" (or ".sl" for HP-UX), so rename the library
+ # to its proper name (with version) after linking.
+ archive_cmds_CXX='tempext=`echo $shared_ext | $SED -e '\''s/\([^()0-9A-Za-z{}]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+ archive_expsym_cmds_CXX='tempext=`echo $shared_ext | $SED -e '\''s/\([^()0-9A-Za-z{}]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib ${wl}-retain-symbols-file,$export_symbols; mv \$templib $lib'
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1 | $GREP "ld"`; rm -f libconftest$shared_ext; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+
+ # Archives containing C++ object files must be created using
+ # "CC -Bstatic", where "CC" is the KAI C++ compiler.
+ old_archive_cmds_CXX='$CC -Bstatic -o $oldlib $oldobjs'
+ ;;
+ icpc* | ecpc* )
+ # Intel C++
+ with_gnu_ld=yes
+ # version 8.0 and above of icpc choke on multiply defined symbols
+ # if we add $predep_objects and $postdep_objects, however 7.1 and
+ # earlier do not add the objects themselves.
+ case `$CC -V 2>&1` in
+ *"Version 7."*)
+ archive_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ ;;
+ *) # Version 8.0 or newer
+ tmp_idyn=
+ case $host_cpu in
+ ia64*) tmp_idyn=' -i_dynamic';;
+ esac
+ archive_cmds_CXX='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ ;;
+ esac
+ archive_cmds_need_lc_CXX=no
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+ whole_archive_flag_spec_CXX='${wl}--whole-archive$convenience ${wl}--no-whole-archive'
+ ;;
+ pgCC* | pgcpp*)
+ # Portland Group C++ compiler
+ case `$CC -V` in
+ *pgCC\ [1-5]* | *pgcpp\ [1-5]*)
+ prelink_cmds_CXX='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $objs $libobjs $compile_deplibs~
+ compile_command="$compile_command `find $tpldir -name \*.o | $NL2SP`"'
+ old_archive_cmds_CXX='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $oldobjs$old_deplibs~
+ $AR $AR_FLAGS $oldlib$oldobjs$old_deplibs `find $tpldir -name \*.o | $NL2SP`~
+ $RANLIB $oldlib'
+ archive_cmds_CXX='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $predep_objects $libobjs $deplibs $convenience $postdep_objects~
+ $CC -shared $pic_flag $predep_objects $libobjs $deplibs `find $tpldir -name \*.o | $NL2SP` $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib'
+ archive_expsym_cmds_CXX='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $predep_objects $libobjs $deplibs $convenience $postdep_objects~
+ $CC -shared $pic_flag $predep_objects $libobjs $deplibs `find $tpldir -name \*.o | $NL2SP` $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib'
+ ;;
+ *) # Version 6 will use weak symbols
+ archive_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib'
+ ;;
+ esac
+
+ hardcode_libdir_flag_spec_CXX='${wl}--rpath ${wl}$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+ whole_archive_flag_spec_CXX='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ ;;
+ cxx*)
+ # Compaq C++
+ archive_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib ${wl}-retain-symbols-file $wl$export_symbols'
+
+ runpath_var=LD_RUN_PATH
+ hardcode_libdir_flag_spec_CXX='-rpath $libdir'
+ hardcode_libdir_separator_CXX=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld .*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ xl*)
+ # IBM XL 8.0 on PPC, with GNU ld
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+ archive_cmds_CXX='$CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ if test "x$supports_anon_versioning" = xyes; then
+ archive_expsym_cmds_CXX='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+ fi
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+ no_undefined_flag_CXX=' -zdefs'
+ archive_cmds_CXX='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file ${wl}$export_symbols'
+ hardcode_libdir_flag_spec_CXX='-R$libdir'
+ whole_archive_flag_spec_CXX='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ compiler_needs_object_CXX=yes
+
+ # Not sure whether something based on
+ # $CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1
+ # would be better.
+ output_verbose_link_cmd='echo'
+
+ # Archives containing C++ object files must be created using
+ # "CC -xar", where "CC" is the Sun C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ old_archive_cmds_CXX='$CC -xar -o $oldlib $oldobjs'
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+
+ lynxos*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+
+ m88k*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+
+ mvs*)
+ case $cc_basename in
+ cxx*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ netbsd*)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ archive_cmds_CXX='$LD -Bshareable -o $lib $predep_objects $libobjs $deplibs $postdep_objects $linker_flags'
+ wlarc=
+ hardcode_libdir_flag_spec_CXX='-R$libdir'
+ hardcode_direct_CXX=yes
+ hardcode_shlibpath_var_CXX=no
+ fi
+ # Workaround some broken pre-1.5 toolchains
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP conftest.$objext | $SED -e "s:-lgcc -lc -lgcc::"'
+ ;;
+
+ *nto* | *qnx*)
+ ld_shlibs_CXX=yes
+ ;;
+
+ openbsd2*)
+ # C++ shared libraries are fairly broken
+ ld_shlibs_CXX=no
+ ;;
+
+ openbsd*)
+ if test -f /usr/libexec/ld.so; then
+ hardcode_direct_CXX=yes
+ hardcode_shlibpath_var_CXX=no
+ hardcode_direct_absolute_CXX=yes
+ archive_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ archive_expsym_cmds_CXX='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file,$export_symbols -o $lib'
+ export_dynamic_flag_spec_CXX='${wl}-E'
+ whole_archive_flag_spec_CXX="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ fi
+ output_verbose_link_cmd=echo
+ else
+ ld_shlibs_CXX=no
+ fi
+ ;;
+
+ osf3* | osf4* | osf5*)
+ case $cc_basename in
+ KCC*)
+ # Kuck and Associates, Inc. (KAI) C++ Compiler
+
+ # KCC will only create a shared library if the output file
+ # ends with ".so" (or ".sl" for HP-UX), so rename the library
+ # to its proper name (with version) after linking.
+ archive_cmds_CXX='tempext=`echo $shared_ext | $SED -e '\''s/\([^()0-9A-Za-z{}]\)/\\\\\1/g'\''`; templib=`echo "$lib" | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath,$libdir'
+ hardcode_libdir_separator_CXX=:
+
+ # Archives containing C++ object files must be created using
+ # the KAI C++ compiler.
+ case $host in
+ osf3*) old_archive_cmds_CXX='$CC -Bstatic -o $oldlib $oldobjs' ;;
+ *) old_archive_cmds_CXX='$CC -o $oldlib $oldobjs' ;;
+ esac
+ ;;
+ RCC*)
+ # Rational C++ 2.4.1
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ cxx*)
+ case $host in
+ osf3*)
+ allow_undefined_flag_CXX=' ${wl}-expect_unresolved ${wl}\*'
+ archive_cmds_CXX='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $soname `test -n "$verstring" && $ECHO "X${wl}-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ ;;
+ *)
+ allow_undefined_flag_CXX=' -expect_unresolved \*'
+ archive_cmds_CXX='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ archive_expsym_cmds_CXX='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done~
+ echo "-hidden">> $lib.exp~
+ $CC -shared$allow_undefined_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname ${wl}-input ${wl}$lib.exp `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~
+ $RM $lib.exp'
+ hardcode_libdir_flag_spec_CXX='-rpath $libdir'
+ ;;
+ esac
+
+ hardcode_libdir_separator_CXX=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld" | $GREP -v "ld:"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld.*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+ allow_undefined_flag_CXX=' ${wl}-expect_unresolved ${wl}\*'
+ case $host in
+ osf3*)
+ archive_cmds_CXX='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ ;;
+ esac
+
+ hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+ hardcode_libdir_separator_CXX=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+
+ else
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ fi
+ ;;
+ esac
+ ;;
+
+ psos*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+
+ sunos4*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.x
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ lcc*)
+ # Lucid
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ solaris*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.2, 5.x and Centerline C++
+ archive_cmds_need_lc_CXX=yes
+ no_undefined_flag_CXX=' -zdefs'
+ archive_cmds_CXX='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ archive_expsym_cmds_CXX='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G${allow_undefined_flag} ${wl}-M ${wl}$lib.exp -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ hardcode_libdir_flag_spec_CXX='-R$libdir'
+ hardcode_shlibpath_var_CXX=no
+ case $host_os in
+ solaris2.[0-5] | solaris2.[0-5].*) ;;
+ *)
+ # The compiler driver will combine and reorder linker options,
+ # but understands `-z linker_flag'.
+ # Supported since Solaris 2.6 (maybe 2.5.1?)
+ whole_archive_flag_spec_CXX='-z allextract$convenience -z defaultextract'
+ ;;
+ esac
+ link_all_deplibs_CXX=yes
+
+ output_verbose_link_cmd='echo'
+
+ # Archives containing C++ object files must be created using
+ # "CC -xar", where "CC" is the Sun C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ old_archive_cmds_CXX='$CC -xar -o $oldlib $oldobjs'
+ ;;
+ gcx*)
+ # Green Hills C++ Compiler
+ archive_cmds_CXX='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+
+ # The C++ compiler must be used to create the archive.
+ old_archive_cmds_CXX='$CC $LDFLAGS -archive -o $oldlib $oldobjs'
+ ;;
+ *)
+ # GNU C++ compiler with Solaris linker
+ if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+ no_undefined_flag_CXX=' ${wl}-z ${wl}defs'
+ if $CC --version | $GREP -v '^2\.7' > /dev/null; then
+ archive_cmds_CXX='$CC -shared -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -shared -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+ else
+ # g++ 2.7 appears to require `-G' NOT `-shared' on this
+ # platform.
+ archive_cmds_CXX='$CC -G -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+ archive_expsym_cmds_CXX='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -G $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+ fi
+
+ hardcode_libdir_flag_spec_CXX='${wl}-R $wl$libdir'
+ case $host_os in
+ solaris2.[0-5] | solaris2.[0-5].*) ;;
+ *)
+ whole_archive_flag_spec_CXX='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract'
+ ;;
+ esac
+ fi
+ ;;
+ esac
+ ;;
+
+ sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[01].[10]* | unixware7* | sco3.2v5.0.[024]*)
+ no_undefined_flag_CXX='${wl}-z,text'
+ archive_cmds_need_lc_CXX=no
+ hardcode_shlibpath_var_CXX=no
+ runpath_var='LD_RUN_PATH'
+
+ case $cc_basename in
+ CC*)
+ archive_cmds_CXX='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6*)
+ # Note: We can NOT use -z defs as we might desire, because we do not
+ # link with -lc, and that would cause any symbols used from libc to
+ # always be unresolved, which means just about no library would
+ # ever link correctly. If we're not using GNU ld we use -z text
+ # though, which does catch some bad symbols but isn't as heavy-handed
+ # as -z defs.
+ no_undefined_flag_CXX='${wl}-z,text'
+ allow_undefined_flag_CXX='${wl}-z,nodefs'
+ archive_cmds_need_lc_CXX=no
+ hardcode_shlibpath_var_CXX=no
+ hardcode_libdir_flag_spec_CXX='${wl}-R,$libdir'
+ hardcode_libdir_separator_CXX=':'
+ link_all_deplibs_CXX=yes
+ export_dynamic_flag_spec_CXX='${wl}-Bexport'
+ runpath_var='LD_RUN_PATH'
+
+ case $cc_basename in
+ CC*)
+ archive_cmds_CXX='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ archive_cmds_CXX='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ archive_expsym_cmds_CXX='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ ;;
+
+ tandem*)
+ case $cc_basename in
+ NCC*)
+ # NonStop-UX NCC 3.20
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+ ;;
+
+ vxworks*)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+
+ *)
+ # FIXME: insert proper C++ library support
+ ld_shlibs_CXX=no
+ ;;
+ esac
+
+ { $as_echo "$as_me:$LINENO: result: $ld_shlibs_CXX" >&5
+$as_echo "$ld_shlibs_CXX" >&6; }
+ test "$ld_shlibs_CXX" = no && can_build_shared=no
+
+ GCC_CXX="$GXX"
+ LD_CXX="$LD"
+
+ ## CAVEAT EMPTOR:
+ ## There is no encapsulation within the following macros, do not change
+ ## the running order or otherwise move them around unless you know exactly
+ ## what you are doing...
+ # Dependencies to place before and after the object being linked:
+predep_objects_CXX=
+postdep_objects_CXX=
+predeps_CXX=
+postdeps_CXX=
+compiler_lib_search_path_CXX=
+
+cat > conftest.$ac_ext <<_LT_EOF
+class Foo
+{
+public:
+ Foo (void) { a = 0; }
+private:
+ int a;
+};
+_LT_EOF
+
+if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; then
+ # Parse the compiler output and extract the necessary
+ # objects, libraries and library flags.
+
+ # Sentinel used to keep track of whether or not we are before
+ # the conftest object file.
+ pre_test_object_deps_done=no
+
+ for p in `eval "$output_verbose_link_cmd"`; do
+ case $p in
+
+ -L* | -R* | -l*)
+ # Some compilers place space between "-{L,R}" and the path.
+ # Remove the space.
+ if test $p = "-L" ||
+ test $p = "-R"; then
+ prev=$p
+ continue
+ else
+ prev=
+ fi
+
+ if test "$pre_test_object_deps_done" = no; then
+ case $p in
+ -L* | -R*)
+ # Internal compiler library paths should come after those
+ # provided the user. The postdeps already come after the
+ # user supplied libs so there is no need to process them.
+ if test -z "$compiler_lib_search_path_CXX"; then
+ compiler_lib_search_path_CXX="${prev}${p}"
+ else
+ compiler_lib_search_path_CXX="${compiler_lib_search_path_CXX} ${prev}${p}"
+ fi
+ ;;
+ # The "-l" case would never come before the object being
+ # linked, so don't bother handling this case.
+ esac
+ else
+ if test -z "$postdeps_CXX"; then
+ postdeps_CXX="${prev}${p}"
+ else
+ postdeps_CXX="${postdeps_CXX} ${prev}${p}"
+ fi
+ fi
+ ;;
+
+ *.$objext)
+ # This assumes that the test object file only shows up
+ # once in the compiler output.
+ if test "$p" = "conftest.$objext"; then
+ pre_test_object_deps_done=yes
+ continue
+ fi
+
+ if test "$pre_test_object_deps_done" = no; then
+ if test -z "$predep_objects_CXX"; then
+ predep_objects_CXX="$p"
+ else
+ predep_objects_CXX="$predep_objects_CXX $p"
+ fi
+ else
+ if test -z "$postdep_objects_CXX"; then
+ postdep_objects_CXX="$p"
+ else
+ postdep_objects_CXX="$postdep_objects_CXX $p"
+ fi
+ fi
+ ;;
+
+ *) ;; # Ignore the rest.
+
+ esac
+ done
+
+ # Clean up.
+ rm -f a.out a.exe
+else
+ echo "libtool.m4: error: problem compiling CXX test program"
+fi
+
+$RM -f confest.$objext
+
+# PORTME: override above test on systems where it is broken
+case $host_os in
+interix[3-9]*)
+ # Interix 3.5 installs completely hosed .la files for C++, so rather than
+ # hack all around it, let's just trust "g++" to DTRT.
+ predep_objects_CXX=
+ postdep_objects_CXX=
+ postdeps_CXX=
+ ;;
+
+linux*)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+
+ # The more standards-conforming stlport4 library is
+ # incompatible with the Cstd library. Avoid specifying
+ # it if it's in CXXFLAGS. Ignore libCrun as
+ # -library=stlport4 depends on it.
+ case " $CXX $CXXFLAGS " in
+ *" -library=stlport4 "*)
+ solaris_use_stlport4=yes
+ ;;
+ esac
+
+ if test "$solaris_use_stlport4" != yes; then
+ postdeps_CXX='-library=Cstd -library=Crun'
+ fi
+ ;;
+ esac
+ ;;
+
+solaris*)
+ case $cc_basename in
+ CC*)
+ # The more standards-conforming stlport4 library is
+ # incompatible with the Cstd library. Avoid specifying
+ # it if it's in CXXFLAGS. Ignore libCrun as
+ # -library=stlport4 depends on it.
+ case " $CXX $CXXFLAGS " in
+ *" -library=stlport4 "*)
+ solaris_use_stlport4=yes
+ ;;
+ esac
+
+ # Adding this requires a known-good setup of shared libraries for
+ # Sun compiler versions before 5.6, else PIC objects from an old
+ # archive will be linked into the output, leading to subtle bugs.
+ if test "$solaris_use_stlport4" != yes; then
+ postdeps_CXX='-library=Cstd -library=Crun'
+ fi
+ ;;
+ esac
+ ;;
+esac
+
+
+case " $postdeps_CXX " in
+*" -lc "*) archive_cmds_need_lc_CXX=no ;;
+esac
+ compiler_lib_search_dirs_CXX=
+if test -n "${compiler_lib_search_path_CXX}"; then
+ compiler_lib_search_dirs_CXX=`echo " ${compiler_lib_search_path_CXX}" | ${SED} -e 's! -L! !g' -e 's!^ !!'`
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ lt_prog_compiler_wl_CXX=
+lt_prog_compiler_pic_CXX=
+lt_prog_compiler_static_CXX=
+
+{ $as_echo "$as_me:$LINENO: checking for $compiler option to produce PIC" >&5
+$as_echo_n "checking for $compiler option to produce PIC... " >&6; }
+
+ # C++ specific cases for pic, static, wl, etc.
+ if test "$GXX" = yes; then
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_static_CXX='-static'
+
+ case $host_os in
+ aix*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ lt_prog_compiler_static_CXX='-Bstatic'
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ lt_prog_compiler_pic_CXX='-fPIC'
+ ;;
+ m68k)
+ # FIXME: we need at least 68020 code to build shared libraries, but
+ # adding the `-m68020' flag to GCC prevents building anything better,
+ # like `-m68040'.
+ lt_prog_compiler_pic_CXX='-m68020 -resident32 -malways-restore-a4'
+ ;;
+ esac
+ ;;
+
+ beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+ # PIC is the default for these OSes.
+ ;;
+ mingw* | cygwin* | os2* | pw32* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ # Although the cygwin gcc ignores -fPIC, still need this for old-style
+ # (--disable-auto-import) libraries
+ lt_prog_compiler_pic_CXX='-DDLL_EXPORT'
+ ;;
+ darwin* | rhapsody*)
+ # PIC is the default on this platform
+ # Common symbols not allowed in MH_DYLIB files
+ lt_prog_compiler_pic_CXX='-fno-common'
+ ;;
+ *djgpp*)
+ # DJGPP does not support shared libraries at all
+ lt_prog_compiler_pic_CXX=
+ ;;
+ interix[3-9]*)
+ # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+ # Instead, we relocate shared libraries at runtime.
+ ;;
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ lt_prog_compiler_pic_CXX=-Kconform_pic
+ fi
+ ;;
+ hpux*)
+ # PIC is the default for 64-bit PA HP-UX, but not for 32-bit
+ # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag
+ # sets the default TLS model and affects inlining.
+ case $host_cpu in
+ hppa*64*)
+ ;;
+ *)
+ lt_prog_compiler_pic_CXX='-fPIC'
+ ;;
+ esac
+ ;;
+ *qnx* | *nto*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ lt_prog_compiler_pic_CXX='-fPIC -shared'
+ ;;
+ *)
+ lt_prog_compiler_pic_CXX='-fPIC'
+ ;;
+ esac
+ else
+ case $host_os in
+ aix[4-9]*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ lt_prog_compiler_static_CXX='-Bstatic'
+ else
+ lt_prog_compiler_static_CXX='-bnso -bI:/lib/syscalls.exp'
+ fi
+ ;;
+ chorus*)
+ case $cc_basename in
+ cxch68*)
+ # Green Hills C++ Compiler
+ # _LT_TAGVAR(lt_prog_compiler_static, CXX)="--no_auto_instantiation -u __main -u __premain -u _abort -r $COOL_DIR/lib/libOrb.a $MVME_DIR/lib/CC/libC.a $MVME_DIR/lib/classix/libcx.s.a"
+ ;;
+ esac
+ ;;
+ dgux*)
+ case $cc_basename in
+ ec++*)
+ lt_prog_compiler_pic_CXX='-KPIC'
+ ;;
+ ghcx*)
+ # Green Hills C++ Compiler
+ lt_prog_compiler_pic_CXX='-pic'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ freebsd* | dragonfly*)
+ # FreeBSD uses GNU C++
+ ;;
+ hpux9* | hpux10* | hpux11*)
+ case $cc_basename in
+ CC*)
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_static_CXX='${wl}-a ${wl}archive'
+ if test "$host_cpu" != ia64; then
+ lt_prog_compiler_pic_CXX='+Z'
+ fi
+ ;;
+ aCC*)
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_static_CXX='${wl}-a ${wl}archive'
+ case $host_cpu in
+ hppa*64*|ia64*)
+ # +Z the default
+ ;;
+ *)
+ lt_prog_compiler_pic_CXX='+Z'
+ ;;
+ esac
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ interix*)
+ # This is c89, which is MS Visual C++ (no shared libs)
+ # Anyone wants to do a port?
+ ;;
+ irix5* | irix6* | nonstopux*)
+ case $cc_basename in
+ CC*)
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_static_CXX='-non_shared'
+ # CC pic flag -KPIC is the default.
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ linux* | k*bsd*-gnu)
+ case $cc_basename in
+ KCC*)
+ # KAI C++ Compiler
+ lt_prog_compiler_wl_CXX='--backend -Wl,'
+ lt_prog_compiler_pic_CXX='-fPIC'
+ ;;
+ ecpc* )
+ # old Intel C++ for x86_64 which still supported -KPIC.
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-KPIC'
+ lt_prog_compiler_static_CXX='-static'
+ ;;
+ icpc* )
+ # Intel C++, used to be incompatible with GCC.
+ # ICC 10 doesn't accept -KPIC any more.
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-fPIC'
+ lt_prog_compiler_static_CXX='-static'
+ ;;
+ pgCC* | pgcpp*)
+ # Portland Group C++ compiler
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-fpic'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ ;;
+ cxx*)
+ # Compaq C++
+ # Make sure the PIC flag is empty. It appears that all Alpha
+ # Linux and Compaq Tru64 Unix objects are PIC.
+ lt_prog_compiler_pic_CXX=
+ lt_prog_compiler_static_CXX='-non_shared'
+ ;;
+ xlc* | xlC*)
+ # IBM XL 8.0 on PPC
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-qpic'
+ lt_prog_compiler_static_CXX='-qstaticlink'
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+ lt_prog_compiler_pic_CXX='-KPIC'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ lt_prog_compiler_wl_CXX='-Qoption ld '
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+ lynxos*)
+ ;;
+ m88k*)
+ ;;
+ mvs*)
+ case $cc_basename in
+ cxx*)
+ lt_prog_compiler_pic_CXX='-W c,exportall'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ netbsd* | netbsdelf*-gnu)
+ ;;
+ *qnx* | *nto*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ lt_prog_compiler_pic_CXX='-fPIC -shared'
+ ;;
+ osf3* | osf4* | osf5*)
+ case $cc_basename in
+ KCC*)
+ lt_prog_compiler_wl_CXX='--backend -Wl,'
+ ;;
+ RCC*)
+ # Rational C++ 2.4.1
+ lt_prog_compiler_pic_CXX='-pic'
+ ;;
+ cxx*)
+ # Digital/Compaq C++
+ lt_prog_compiler_wl_CXX='-Wl,'
+ # Make sure the PIC flag is empty. It appears that all Alpha
+ # Linux and Compaq Tru64 Unix objects are PIC.
+ lt_prog_compiler_pic_CXX=
+ lt_prog_compiler_static_CXX='-non_shared'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ psos*)
+ ;;
+ solaris*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.2, 5.x and Centerline C++
+ lt_prog_compiler_pic_CXX='-KPIC'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ lt_prog_compiler_wl_CXX='-Qoption ld '
+ ;;
+ gcx*)
+ # Green Hills C++ Compiler
+ lt_prog_compiler_pic_CXX='-PIC'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ sunos4*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.x
+ lt_prog_compiler_pic_CXX='-pic'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ ;;
+ lcc*)
+ # Lucid
+ lt_prog_compiler_pic_CXX='-pic'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+ case $cc_basename in
+ CC*)
+ lt_prog_compiler_wl_CXX='-Wl,'
+ lt_prog_compiler_pic_CXX='-KPIC'
+ lt_prog_compiler_static_CXX='-Bstatic'
+ ;;
+ esac
+ ;;
+ tandem*)
+ case $cc_basename in
+ NCC*)
+ # NonStop-UX NCC 3.20
+ lt_prog_compiler_pic_CXX='-KPIC'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ vxworks*)
+ ;;
+ *)
+ lt_prog_compiler_can_build_shared_CXX=no
+ ;;
+ esac
+ fi
+
+case $host_os in
+ # For platforms which do not support PIC, -DPIC is meaningless:
+ *djgpp*)
+ lt_prog_compiler_pic_CXX=
+ ;;
+ *)
+ lt_prog_compiler_pic_CXX="$lt_prog_compiler_pic_CXX -DPIC"
+ ;;
+esac
+{ $as_echo "$as_me:$LINENO: result: $lt_prog_compiler_pic_CXX" >&5
+$as_echo "$lt_prog_compiler_pic_CXX" >&6; }
+
+
+
+#
+# Check to make sure the PIC flag actually works.
+#
+if test -n "$lt_prog_compiler_pic_CXX"; then
+ { $as_echo "$as_me:$LINENO: checking if $compiler PIC flag $lt_prog_compiler_pic_CXX works" >&5
+$as_echo_n "checking if $compiler PIC flag $lt_prog_compiler_pic_CXX works... " >&6; }
+if test "${lt_cv_prog_compiler_pic_works_CXX+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_pic_works_CXX=no
+ ac_outfile=conftest.$ac_objext
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+ lt_compiler_flag="$lt_prog_compiler_pic_CXX -DPIC"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ # The option is referenced via a variable to avoid confusing sed.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:15594: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>conftest.err)
+ ac_status=$?
+ cat conftest.err >&5
+ echo "$as_me:15598: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s "$ac_outfile"; then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings other than the usual output.
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_pic_works_CXX=yes
+ fi
+ fi
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_pic_works_CXX" >&5
+$as_echo "$lt_cv_prog_compiler_pic_works_CXX" >&6; }
+
+if test x"$lt_cv_prog_compiler_pic_works_CXX" = xyes; then
+ case $lt_prog_compiler_pic_CXX in
+ "" | " "*) ;;
+ *) lt_prog_compiler_pic_CXX=" $lt_prog_compiler_pic_CXX" ;;
+ esac
+else
+ lt_prog_compiler_pic_CXX=
+ lt_prog_compiler_can_build_shared_CXX=no
+fi
+
+fi
+
+
+
+#
+# Check to make sure the static flag actually works.
+#
+wl=$lt_prog_compiler_wl_CXX eval lt_tmp_static_flag=\"$lt_prog_compiler_static_CXX\"
+{ $as_echo "$as_me:$LINENO: checking if $compiler static flag $lt_tmp_static_flag works" >&5
+$as_echo_n "checking if $compiler static flag $lt_tmp_static_flag works... " >&6; }
+if test "${lt_cv_prog_compiler_static_works_CXX+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_static_works_CXX=no
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS $lt_tmp_static_flag"
+ echo "$lt_simple_link_test_code" > conftest.$ac_ext
+ if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then
+ # The linker can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ if test -s conftest.err; then
+ # Append any errors to the config.log.
+ cat conftest.err 1>&5
+ $ECHO "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if diff conftest.exp conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_static_works_CXX=yes
+ fi
+ else
+ lt_cv_prog_compiler_static_works_CXX=yes
+ fi
+ fi
+ $RM -r conftest*
+ LDFLAGS="$save_LDFLAGS"
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_static_works_CXX" >&5
+$as_echo "$lt_cv_prog_compiler_static_works_CXX" >&6; }
+
+if test x"$lt_cv_prog_compiler_static_works_CXX" = xyes; then
+ :
+else
+ lt_prog_compiler_static_CXX=
+fi
+
+
+
+
+ { $as_echo "$as_me:$LINENO: checking if $compiler supports -c -o file.$ac_objext" >&5
+$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; }
+if test "${lt_cv_prog_compiler_c_o_CXX+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_c_o_CXX=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:15693: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&5
+ echo "$as_me:15697: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_c_o_CXX=yes
+ fi
+ fi
+ chmod u+w . 2>&5
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_c_o_CXX" >&5
+$as_echo "$lt_cv_prog_compiler_c_o_CXX" >&6; }
+
+
+
+ { $as_echo "$as_me:$LINENO: checking if $compiler supports -c -o file.$ac_objext" >&5
+$as_echo_n "checking if $compiler supports -c -o file.$ac_objext... " >&6; }
+if test "${lt_cv_prog_compiler_c_o_CXX+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ lt_cv_prog_compiler_c_o_CXX=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [^ ]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:15745: $lt_compile\"" >&5)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&5
+ echo "$as_me:15749: \$? = $ac_status" >&5
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ lt_cv_prog_compiler_c_o_CXX=yes
+ fi
+ fi
+ chmod u+w . 2>&5
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $lt_cv_prog_compiler_c_o_CXX" >&5
+$as_echo "$lt_cv_prog_compiler_c_o_CXX" >&6; }
+
+
+
+
+hard_links="nottested"
+if test "$lt_cv_prog_compiler_c_o_CXX" = no && test "$need_locks" != no; then
+ # do not overwrite the value of need_locks provided by the user
+ { $as_echo "$as_me:$LINENO: checking if we can lock with hard links" >&5
+$as_echo_n "checking if we can lock with hard links... " >&6; }
+ hard_links=yes
+ $RM conftest*
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ touch conftest.a
+ ln conftest.a conftest.b 2>&5 || hard_links=no
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ { $as_echo "$as_me:$LINENO: result: $hard_links" >&5
+$as_echo "$hard_links" >&6; }
+ if test "$hard_links" = no; then
+ { $as_echo "$as_me:$LINENO: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&5
+$as_echo "$as_me: WARNING: \`$CC' does not support \`-c -o', so \`make -j' may be unsafe" >&2;}
+ need_locks=warn
+ fi
+else
+ need_locks=no
+fi
+
+
+
+ { $as_echo "$as_me:$LINENO: checking whether the $compiler linker ($LD) supports shared libraries" >&5
+$as_echo_n "checking whether the $compiler linker ($LD) supports shared libraries... " >&6; }
+
+ export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ case $host_os in
+ aix[4-9]*)
+ # If we're using GNU nm, then we don't want the "-C" option.
+ # -C means demangle to AIX nm, but means don't demangle with GNU nm
+ if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then
+ export_symbols_cmds_CXX='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ else
+ export_symbols_cmds_CXX='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && (substr(\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ fi
+ ;;
+ pw32*)
+ export_symbols_cmds_CXX="$ltdll_cmds"
+ ;;
+ cygwin* | mingw* | cegcc*)
+ export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[BCDGRS][ ]/s/.*[ ]\([^ ]*\)/\1 DATA/;/^.*[ ]__nm__/s/^.*[ ]__nm__\([^ ]*\)[ ][^ ]*/\1 DATA/;/^I[ ]/d;/^[AITW][ ]/s/.* //'\'' | sort | uniq > $export_symbols'
+ ;;
+ linux* | k*bsd*-gnu)
+ link_all_deplibs_CXX=no
+ ;;
+ *)
+ export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ ;;
+ esac
+ exclude_expsyms_CXX='_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*'
+
+{ $as_echo "$as_me:$LINENO: result: $ld_shlibs_CXX" >&5
+$as_echo "$ld_shlibs_CXX" >&6; }
+test "$ld_shlibs_CXX" = no && can_build_shared=no
+
+with_gnu_ld_CXX=$with_gnu_ld
+
+
+
+
+
+
+#
+# Do we need to explicitly link libc?
+#
+case "x$archive_cmds_need_lc_CXX" in
+x|xyes)
+ # Assume -lc should be added
+ archive_cmds_need_lc_CXX=yes
+
+ if test "$enable_shared" = yes && test "$GCC" = yes; then
+ case $archive_cmds_CXX in
+ *'~'*)
+ # FIXME: we may have to deal with multi-command sequences.
+ ;;
+ '$CC '*)
+ # Test whether the compiler implicitly links with -lc since on some
+ # systems, -lgcc has to come before -lc. If gcc already passes -lc
+ # to ld, don't add -lc before -lgcc.
+ { $as_echo "$as_me:$LINENO: checking whether -lc should be explicitly linked in" >&5
+$as_echo_n "checking whether -lc should be explicitly linked in... " >&6; }
+ $RM conftest*
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5
+ (eval $ac_compile) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } 2>conftest.err; then
+ soname=conftest
+ lib=conftest
+ libobjs=conftest.$ac_objext
+ deplibs=
+ wl=$lt_prog_compiler_wl_CXX
+ pic_flag=$lt_prog_compiler_pic_CXX
+ compiler_flags=-v
+ linker_flags=-v
+ verstring=
+ output_objdir=.
+ libname=conftest
+ lt_save_allow_undefined_flag=$allow_undefined_flag_CXX
+ allow_undefined_flag_CXX=
+ if { (eval echo "$as_me:$LINENO: \"$archive_cmds_CXX 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1\"") >&5
+ (eval $archive_cmds_CXX 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1) 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }
+ then
+ archive_cmds_need_lc_CXX=no
+ else
+ archive_cmds_need_lc_CXX=yes
+ fi
+ allow_undefined_flag_CXX=$lt_save_allow_undefined_flag
+ else
+ cat conftest.err 1>&5
+ fi
+ $RM conftest*
+ { $as_echo "$as_me:$LINENO: result: $archive_cmds_need_lc_CXX" >&5
+$as_echo "$archive_cmds_need_lc_CXX" >&6; }
+ ;;
+ esac
+ fi
+ ;;
+esac
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ { $as_echo "$as_me:$LINENO: checking dynamic linker characteristics" >&5
+$as_echo_n "checking dynamic linker characteristics... " >&6; }
+
+library_names_spec=
+libname_spec='lib$name'
+soname_spec=
+shrext_cmds=".so"
+postinstall_cmds=
+postuninstall_cmds=
+finish_cmds=
+finish_eval=
+shlibpath_var=
+shlibpath_overrides_runpath=unknown
+version_type=none
+dynamic_linker="$host_os ld.so"
+sys_lib_dlsearch_path_spec="/lib /usr/lib"
+need_lib_prefix=unknown
+hardcode_into_libs=no
+
+# when you set need_version to no, make sure it does not cause -set_version
+# flags to be left without arguments
+need_version=unknown
+
+case $host_os in
+aix3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
+ shlibpath_var=LIBPATH
+
+ # AIX 3 has no versioning support, so we append a major version to the name.
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+
+aix[4-9]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ hardcode_into_libs=yes
+ if test "$host_cpu" = ia64; then
+ # AIX 5 supports IA64
+ library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ else
+ # With GCC up to 2.95.x, collect2 would create an import file
+ # for dependence libraries. The import file would start with
+ # the line `#! .'. This would cause the generated library to
+ # depend on `.', always an invalid library. This was fixed in
+ # development snapshots of GCC prior to 3.0.
+ case $host_os in
+ aix4 | aix4.[01] | aix4.[01].*)
+ if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)'
+ echo ' yes '
+ echo '#endif'; } | ${CC} -E - | $GREP yes > /dev/null; then
+ :
+ else
+ can_build_shared=no
+ fi
+ ;;
+ esac
+ # AIX (on Power*) has no versioning support, so currently we can not hardcode correct
+ # soname into executable. Probably we can add versioning support to
+ # collect2, so additional links can be useful in future.
+ if test "$aix_use_runtimelinking" = yes; then
+ # If using run time linking (on AIX 4.2 or later) use lib<name>.so
+ # instead of lib<name>.a to let people know that these are not
+ # typical AIX shared libraries.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ else
+ # We preserve .a as extension for shared libraries through AIX4.2
+ # and later when we are not doing run time linking.
+ library_names_spec='${libname}${release}.a $libname.a'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ fi
+ shlibpath_var=LIBPATH
+ fi
+ ;;
+
+amigaos*)
+ case $host_cpu in
+ powerpc)
+ # Since July 2007 AmigaOS4 officially supports .so libraries.
+ # When compiling the executable, add -use-dynld -Lsobjs: to the compileline.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ ;;
+ m68k)
+ library_names_spec='$libname.ixlibrary $libname.a'
+ # Create ${libname}_ixlibrary.a entries in /sys/libs.
+ finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$ECHO "X$lib" | $Xsed -e '\''s%^.*/\([^/]*\)\.ixlibrary$%\1%'\''`; test $RM /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done'
+ ;;
+ esac
+ ;;
+
+beos*)
+ library_names_spec='${libname}${shared_ext}'
+ dynamic_linker="$host_os ld.so"
+ shlibpath_var=LIBRARY_PATH
+ ;;
+
+bsdi[45]*)
+ version_type=linux
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib"
+ sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib"
+ # the default ld.so.conf also contains /usr/contrib/lib and
+ # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow
+ # libtool to hard-code these into programs
+ ;;
+
+cygwin* | mingw* | pw32* | cegcc*)
+ version_type=windows
+ shrext_cmds=".dll"
+ need_version=no
+ need_lib_prefix=no
+
+ case $GCC,$host_os in
+ yes,cygwin* | yes,mingw* | yes,pw32* | yes,cegcc*)
+ library_names_spec='$libname.dll.a'
+ # DLL is installed to $(libdir)/../bin by postinstall_cmds
+ postinstall_cmds='base_file=`basename \${file}`~
+ dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i; echo \$dlname'\''`~
+ dldir=$destdir/`dirname \$dlpath`~
+ test -d \$dldir || mkdir -p \$dldir~
+ $install_prog $dir/$dlname \$dldir/$dlname~
+ chmod a+x \$dldir/$dlname~
+ if test -n '\''$stripme'\'' && test -n '\''$striplib'\''; then
+ eval '\''$striplib \$dldir/$dlname'\'' || exit \$?;
+ fi'
+ postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~
+ dlpath=$dir/\$dldll~
+ $RM \$dlpath'
+ shlibpath_overrides_runpath=yes
+
+ case $host_os in
+ cygwin*)
+ # Cygwin DLLs use 'cyg' prefix rather than 'lib'
+ soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib"
+ ;;
+ mingw* | cegcc*)
+ # MinGW DLLs use traditional 'lib' prefix
+ soname_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec=`$CC -print-search-dirs | $GREP "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$sys_lib_search_path_spec" | $GREP ';[c-zC-Z]:/' >/dev/null; then
+ # It is most probably a Windows format PATH printed by
+ # mingw gcc, but we are running on Cygwin. Gcc prints its search
+ # path with ; separators, and with drive letters. We can handle the
+ # drive letters (cygwin fileutils understands them), so leave them,
+ # especially as we might pass files found there to a mingw objdump,
+ # which wouldn't understand a cygwinified path. Ahh.
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ ;;
+ pw32*)
+ # pw32 DLLs use 'pw' prefix rather than 'lib'
+ library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext}'
+ ;;
+ esac
+ ;;
+
+ *)
+ library_names_spec='${libname}`echo ${release} | $SED -e 's/[.]/-/g'`${versuffix}${shared_ext} $libname.lib'
+ ;;
+ esac
+ dynamic_linker='Win32 ld.exe'
+ # FIXME: first we should search . and the directory the executable is in
+ shlibpath_var=PATH
+ ;;
+
+darwin* | rhapsody*)
+ dynamic_linker="$host_os dyld"
+ version_type=darwin
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${major}$shared_ext ${libname}$shared_ext'
+ soname_spec='${libname}${release}${major}$shared_ext'
+ shlibpath_overrides_runpath=yes
+ shlibpath_var=DYLD_LIBRARY_PATH
+ shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+
+ sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib'
+ ;;
+
+dgux*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+freebsd1*)
+ dynamic_linker=no
+ ;;
+
+freebsd* | dragonfly*)
+ # DragonFly does not have aout. When/if they implement a new
+ # versioning mechanism, adjust this.
+ if test -x /usr/bin/objformat; then
+ objformat=`/usr/bin/objformat`
+ else
+ case $host_os in
+ freebsd[123]*) objformat=aout ;;
+ *) objformat=elf ;;
+ esac
+ fi
+ version_type=freebsd-$objformat
+ case $version_type in
+ freebsd-elf*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ need_version=no
+ need_lib_prefix=no
+ ;;
+ freebsd-*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix'
+ need_version=yes
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_os in
+ freebsd2*)
+ shlibpath_overrides_runpath=yes
+ ;;
+ freebsd3.[01]* | freebsdelf3.[01]*)
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ freebsd3.[2-9]* | freebsdelf3.[2-9]* | \
+ freebsd4.[0-5] | freebsdelf4.[0-5] | freebsd4.1.1 | freebsdelf4.1.1)
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+ *) # from 4.6 on, and DragonFly
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ esac
+ ;;
+
+gnu*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ hardcode_into_libs=yes
+ ;;
+
+hpux9* | hpux10* | hpux11*)
+ # Give a soname corresponding to the major version so that dld.sl refuses to
+ # link against other versions.
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ case $host_cpu in
+ ia64*)
+ shrext_cmds='.so'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.so"
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ if test "X$HPUX_IA64_MODE" = X32; then
+ sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib"
+ else
+ sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64"
+ fi
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ hppa*64*)
+ shrext_cmds='.sl'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64"
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ *)
+ shrext_cmds='.sl'
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=SHLIB_PATH
+ shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+ esac
+ # HP-UX runs *really* slowly unless shared libraries are mode 555.
+ postinstall_cmds='chmod 555 $lib'
+ ;;
+
+interix[3-9]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $host_os in
+ nonstopux*) version_type=nonstopux ;;
+ *)
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ version_type=linux
+ else
+ version_type=irix
+ fi ;;
+ esac
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}'
+ case $host_os in
+ irix5* | nonstopux*)
+ libsuff= shlibsuff=
+ ;;
+ *)
+ case $LD in # libtool.m4 will add one of these switches to LD
+ *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ")
+ libsuff= shlibsuff= libmagic=32-bit;;
+ *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ")
+ libsuff=32 shlibsuff=N32 libmagic=N32;;
+ *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ")
+ libsuff=64 shlibsuff=64 libmagic=64-bit;;
+ *) libsuff= shlibsuff= libmagic=never-match;;
+ esac
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY${shlibsuff}_PATH
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}"
+ sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}"
+ hardcode_into_libs=yes
+ ;;
+
+# No shared lib support for Linux oldld, aout, or coff.
+linux*oldld* | linux*aout* | linux*coff*)
+ dynamic_linker=no
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ # Some binutils ld are patched to set DT_RUNPATH
+ save_LDFLAGS=$LDFLAGS
+ save_libdir=$libdir
+ eval "libdir=/foo; wl=\"$lt_prog_compiler_wl_CXX\"; \
+ LDFLAGS=\"\$LDFLAGS $hardcode_libdir_flag_spec_CXX\""
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ if ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null; then
+ shlibpath_overrides_runpath=yes
+fi
+
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+ LDFLAGS=$save_LDFLAGS
+ libdir=$save_libdir
+
+ # This implies no fast_install, which is unacceptable.
+ # Some rework will be needed to allow for fast_install
+ # before this can be enabled.
+ hardcode_into_libs=yes
+
+ # Append ld.so.conf contents to the search path
+ if test -f /etc/ld.so.conf; then
+ lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \$2)); skip = 1; } { if (!skip) print \$0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+ sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+ fi
+
+ # We used to test for /lib/ld.so.1 and disable shared libraries on
+ # powerpc, because MkLinux only supported shared libraries with the
+ # GNU dynamic linker. Since this was broken with cross compilers,
+ # most powerpc-linux boxes support dynamic linking these days and
+ # people can always --disable-shared, the test was removed, and we
+ # assume the GNU/Linux dynamic linker is in use.
+ dynamic_linker='GNU/Linux ld.so'
+ ;;
+
+netbsdelf*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='NetBSD ld.elf_so'
+ ;;
+
+netbsd*)
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ dynamic_linker='NetBSD (a.out) ld.so'
+ else
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='NetBSD ld.elf_so'
+ fi
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+
+newsos6)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ ;;
+
+*nto* | *qnx*)
+ version_type=qnx
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='ldqnx.so'
+ ;;
+
+openbsd*)
+ version_type=sunos
+ sys_lib_dlsearch_path_spec="/usr/lib"
+ need_lib_prefix=no
+ # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs.
+ case $host_os in
+ openbsd3.3 | openbsd3.3.*) need_version=yes ;;
+ *) need_version=no ;;
+ esac
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ case $host_os in
+ openbsd2.[89] | openbsd2.[89].*)
+ shlibpath_overrides_runpath=no
+ ;;
+ *)
+ shlibpath_overrides_runpath=yes
+ ;;
+ esac
+ else
+ shlibpath_overrides_runpath=yes
+ fi
+ ;;
+
+os2*)
+ libname_spec='$name'
+ shrext_cmds=".dll"
+ need_lib_prefix=no
+ library_names_spec='$libname${shared_ext} $libname.a'
+ dynamic_linker='OS/2 ld.exe'
+ shlibpath_var=LIBPATH
+ ;;
+
+osf3* | osf4* | osf5*)
+ version_type=osf
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib"
+ sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec"
+ ;;
+
+rdos*)
+ dynamic_linker=no
+ ;;
+
+solaris*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ # ldd complains unless libraries are executable
+ postinstall_cmds='chmod +x $lib'
+ ;;
+
+sunos4*)
+ version_type=sunos
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ if test "$with_gnu_ld" = yes; then
+ need_lib_prefix=no
+ fi
+ need_version=yes
+ ;;
+
+sysv4 | sysv4.3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_vendor in
+ sni)
+ shlibpath_overrides_runpath=no
+ need_lib_prefix=no
+ runpath_var=LD_RUN_PATH
+ ;;
+ siemens)
+ need_lib_prefix=no
+ ;;
+ motorola)
+ need_lib_prefix=no
+ need_version=no
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib'
+ ;;
+ esac
+ ;;
+
+sysv4*MP*)
+ if test -d /usr/nec ;then
+ version_type=linux
+ library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
+ soname_spec='$libname${shared_ext}.$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ fi
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ version_type=freebsd-elf
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ if test "$with_gnu_ld" = yes; then
+ sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib'
+ else
+ sys_lib_search_path_spec='/usr/ccs/lib /usr/lib'
+ case $host_os in
+ sco3.2v5*)
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /lib"
+ ;;
+ esac
+ fi
+ sys_lib_dlsearch_path_spec='/usr/lib'
+ ;;
+
+tpf*)
+ # TPF is a cross-target only. Preferred cross-host = GNU/Linux.
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+uts4*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+*)
+ dynamic_linker=no
+ ;;
+esac
+{ $as_echo "$as_me:$LINENO: result: $dynamic_linker" >&5
+$as_echo "$dynamic_linker" >&6; }
+test "$dynamic_linker" = no && can_build_shared=no
+
+variables_saved_for_relink="PATH $shlibpath_var $runpath_var"
+if test "$GCC" = yes; then
+ variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+fi
+
+if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then
+ sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec"
+fi
+if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then
+ sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec"
+fi
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ { $as_echo "$as_me:$LINENO: checking how to hardcode library paths into programs" >&5
+$as_echo_n "checking how to hardcode library paths into programs... " >&6; }
+hardcode_action_CXX=
+if test -n "$hardcode_libdir_flag_spec_CXX" ||
+ test -n "$runpath_var_CXX" ||
+ test "X$hardcode_automatic_CXX" = "Xyes" ; then
+
+ # We can hardcode non-existent directories.
+ if test "$hardcode_direct_CXX" != no &&
+ # If the only mechanism to avoid hardcoding is shlibpath_var, we
+ # have to relink, otherwise we might link with an installed library
+ # when we should be linking with a yet-to-be-installed one
+ ## test "$_LT_TAGVAR(hardcode_shlibpath_var, CXX)" != no &&
+ test "$hardcode_minus_L_CXX" != no; then
+ # Linking always hardcodes the temporary library directory.
+ hardcode_action_CXX=relink
+ else
+ # We can link without hardcoding, and we can hardcode nonexisting dirs.
+ hardcode_action_CXX=immediate
+ fi
+else
+ # We cannot hardcode anything, or else we can only hardcode existing
+ # directories.
+ hardcode_action_CXX=unsupported
+fi
+{ $as_echo "$as_me:$LINENO: result: $hardcode_action_CXX" >&5
+$as_echo "$hardcode_action_CXX" >&6; }
+
+if test "$hardcode_action_CXX" = relink ||
+ test "$inherit_rpath_CXX" = yes; then
+ # Fast installation is not supported
+ enable_fast_install=no
+elif test "$shlibpath_overrides_runpath" = yes ||
+ test "$enable_shared" = no; then
+ # Fast installation is not necessary
+ enable_fast_install=needless
+fi
+
+
+
+
+
+
+
+ fi # test -n "$compiler"
+
+ CC=$lt_save_CC
+ LDCXX=$LD
+ LD=$lt_save_LD
+ GCC=$lt_save_GCC
+ with_gnu_ld=$lt_save_with_gnu_ld
+ lt_cv_path_LDCXX=$lt_cv_path_LD
+ lt_cv_path_LD=$lt_save_path_LD
+ lt_cv_prog_gnu_ldcxx=$lt_cv_prog_gnu_ld
+ lt_cv_prog_gnu_ld=$lt_save_with_gnu_ld
+fi # test "$_lt_caught_CXX_error" != yes
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+
+# Set CXXCPP to a command that runs the C++ preprocessor
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+{ $as_echo "$as_me:$LINENO: checking how to run the C++ preprocessor" >&5
+$as_echo_n "checking how to run the C++ preprocessor... " >&6; }
+if test -z "$CXXCPP"; then
+ if test "${ac_cv_prog_CXXCPP+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ # Double quotes because CXXCPP needs to be expanded
+ for CXXCPP in "$CXX -E" "/lib/cpp"
+ do
+ ac_preproc_ok=false
+for ac_cxx_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ :
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ # Broken: fails on valid input.
+continue
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ # Broken: success on invalid input.
+continue
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
+ break
+fi
+
+ done
+ ac_cv_prog_CXXCPP=$CXXCPP
+
+fi
+ CXXCPP=$ac_cv_prog_CXXCPP
+else
+ ac_cv_prog_CXXCPP=$CXXCPP
+fi
+{ $as_echo "$as_me:$LINENO: result: $CXXCPP" >&5
+$as_echo "$CXXCPP" >&6; }
+ac_preproc_ok=false
+for ac_cxx_preproc_warn_flag in '' yes
+do
+ # Use a header file that comes with gcc, so configuring glibc
+ # with a fresh cross-compiler works.
+ # Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ # <limits.h> exists even on freestanding compilers.
+ # On the NeXT, cc -E runs the code through the compiler's parser,
+ # not just through cpp. "Syntax error" is here to catch this case.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+ Syntax error
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ :
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ # Broken: fails on valid input.
+continue
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+ # OK, works on sane cases. Now check whether nonexistent headers
+ # can be detected and how.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <ac_nonexistent.h>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_cxx_preproc_warn_flag$ac_cxx_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ # Broken: success on invalid input.
+continue
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ # Passes both tests.
+ac_preproc_ok=:
+break
+fi
+
+rm -f conftest.err conftest.$ac_ext
+
+done
+# Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped.
+rm -f conftest.err conftest.$ac_ext
+if $ac_preproc_ok; then
+ :
+else
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: C++ preprocessor \"$CXXCPP\" fails sanity check
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: C++ preprocessor \"$CXXCPP\" fails sanity check
+See \`config.log' for more details." >&2;}
+ { (exit 1); exit 1; }; }; }
+fi
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
+#
+# reset compiler flags to initial flags
+#CXXFLAGS=$OLD_CXXFLAGS
+
+
+
+
+# safety check: AC_CONFIG_SRCDIR([src/clustal.h])
+
+# Let source files know in which context they are being used
+
+cat >>confdefs.h <<\_ACEOF
+#define CLUSTALO 1
+_ACEOF
+
+
+
+cat >>confdefs.h <<_ACEOF
+#define PACKAGE_CODENAME "$PACKAGE_CODENAME"
+_ACEOF
+
+
+
+# Get svn revision
+#AC_PATH_PROG(svnversioncommand, svnversion)
+#if test "X$svnversioncommand" = "X" || test `$svnversioncommand -n '.'` = "exported"; then
+#AC_DEFINE_UNQUOTED(SVN_VERSION, ["`cat saved_svn_version.txt`"], [repository svn version])
+#else
+#AC_DEFINE_UNQUOTED(SVN_VERSION, ["`svnversion -n`"], [repository svn version])
+#`svnversion -n > saved_svn_version.txt`
+#fi
+
+
+
+
+# AW: we might need this in the future
+#
+case "$host_os" in
+linux*)
+# AC_DEFINE(LINUX,1,[This is a Linux system])
+
+cat >>confdefs.h <<_ACEOF
+#define LINUX 1
+_ACEOF
+
+# AM_CONDITIONAL(HAVE_GNU_LD, true)
+# AM_CONDITIONAL(SOMEBSD, false)
+# XTRA_CPPLIBS=-lstdc++
+# LIBEXT=.so
+ ;;
+freebsd*)
+
+cat >>confdefs.h <<_ACEOF
+#define SOMEBSD 1
+_ACEOF
+
+# AC_CHECK_LIB(c_r, pthread_create)
+# AM_CONDITIONAL(HAVE_GNU_LD, true)
+# AM_CONDITIONAL(SOMEBSD, true)
+# XTRA_CPPLIBS=-lstdc++
+# LIBEXT=.so
+ ;;
+openbsd*)
+
+cat >>confdefs.h <<_ACEOF
+#define SOMEBSD 1
+_ACEOF
+
+# AC_CHECK_LIB(c_r, pthread_create)
+# AM_CONDITIONAL(HAVE_GNU_LD, true)
+# AM_CONDITIONAL(SOMEBSD, true)
+# XTRA_CPPLIBS=-lstdc++
+# LIBEXT=.so
+ ;;
+netbsd*)
+
+cat >>confdefs.h <<_ACEOF
+#define SOMEBSD 1
+_ACEOF
+
+# AC_CHECK_LIB(c_r, pthread_create)
+# AM_CONDITIONAL(HAVE_GNU_LD, true)
+# AM_CONDITIONAL(SOMEBSD, true)
+# XTRA_CPPLIBS=-lstdc++
+# LIBEXT=.so
+ ;;
+*solaris*)
+
+cat >>confdefs.h <<_ACEOF
+#define SOLARIS 1
+_ACEOF
+
+# AC_CHECK_LIB(resolv, res_init)
+# XTRA_CPPLIBS=-lstdc++
+# AM_CONDITIONAL(HAVE_GNU_LD, false)
+# AM_CONDITIONAL(SOMEBSD, false)
+# CFLAGS="-D_POSIX_PTHREAD_SEMANTICS $CFLAGS"
+# LIBEXT=.so
+ ;;
+darwin*)
+
+cat >>confdefs.h <<_ACEOF
+#define DARWIN 1
+_ACEOF
+
+# AM_CONDITIONAL(HAVE_GNU_LD, false)
+# AM_CONDITIONAL(SOMEBSD, false)
+# CFLAGS="-fno-common $CFLAGS"
+# LIBEXT=.so
+ ;;
+cygwin*)
+
+cat >>confdefs.h <<_ACEOF
+#define CYGWIN 1
+_ACEOF
+
+# LDFLAGS="$LDFLAGS -no-undefined"
+# AM_CONDITIONAL(SOMEBSD, false)
+# AM_CONDITIONAL(HAVE_GNU_LD, false)
+# LIBEXT=.dll
+ ;;
+mingw*)
+
+cat >>confdefs.h <<_ACEOF
+#define MINGW 1
+_ACEOF
+
+# AC_DEFINE_UNQUOTED(WINDOWS,1,[This is a Windows system])
+# AC_CHECK_LIB(intl, gettext)
+# AC_CHECK_LIB(ws2_32, _head_libws2_32_a,,[AC_MSG_ERROR([libextractor requires Winsock2])])
+# AC_CHECK_LIB(plibc, plibc_init,,[AC_MSG_ERROR([libextractor requires PlibC])])
+# LDFLAGS="$LDFLAGS -no-undefined -Wl,--export-all-symbols"
+# LIBSOLD=$LIBS
+# AM_CONDITIONAL(HAVE_GNU_LD, true)
+# AM_CONDITIONAL(SOMEBSD, false)
+# LIBEXT=.dll
+ ;;
+*)
+# AC_MSG_RESULT(Unrecognised OS $host_os)
+
+cat >>confdefs.h <<_ACEOF
+#define OTHEROS 1
+_ACEOF
+
+# AC_MSG_RESULT(otheros)
+# AM_CONDITIONAL(HAVE_GNU_LD, false)
+# AM_CONDITIONAL(SOMEBSD, false)
+# LIBEXT=.so
+ ;;
+esac
+
+
+
+# Checks for standard header files.
+# obsolescent according to http://www.gnu.org/software/hello/manual/autoconf/Particular-Headers.html
+{ $as_echo "$as_me:$LINENO: checking for ANSI C header files" >&5
+$as_echo_n "checking for ANSI C header files... " >&6; }
+if test "${ac_cv_header_stdc+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <stdlib.h>
+#include <stdarg.h>
+#include <string.h>
+#include <float.h>
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_cv_header_stdc=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_header_stdc=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+
+if test $ac_cv_header_stdc = yes; then
+ # SunOS 4.x string.h does not declare mem*, contrary to ANSI.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <string.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ $EGREP "memchr" >/dev/null 2>&1; then
+ :
+else
+ ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+ # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <stdlib.h>
+
+_ACEOF
+if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
+ $EGREP "free" >/dev/null 2>&1; then
+ :
+else
+ ac_cv_header_stdc=no
+fi
+rm -f conftest*
+
+fi
+
+if test $ac_cv_header_stdc = yes; then
+ # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi.
+ if test "$cross_compiling" = yes; then
+ :
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <ctype.h>
+#include <stdlib.h>
+#if ((' ' & 0x0FF) == 0x020)
+# define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
+# define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c))
+#else
+# define ISLOWER(c) \
+ (('a' <= (c) && (c) <= 'i') \
+ || ('j' <= (c) && (c) <= 'r') \
+ || ('s' <= (c) && (c) <= 'z'))
+# define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c))
+#endif
+
+#define XOR(e, f) (((e) && !(f)) || (!(e) && (f)))
+int
+main ()
+{
+ int i;
+ for (i = 0; i < 256; i++)
+ if (XOR (islower (i), ISLOWER (i))
+ || toupper (i) != TOUPPER (i))
+ return 2;
+ return 0;
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ :
+else
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+ac_cv_header_stdc=no
+fi
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+
+
+fi
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5
+$as_echo "$ac_cv_header_stdc" >&6; }
+if test $ac_cv_header_stdc = yes; then
+
+cat >>confdefs.h <<\_ACEOF
+#define STDC_HEADERS 1
+_ACEOF
+
+fi
+
+# Guess the next one is obsolete as well then?
+
+
+
+
+
+
+
+
+
+
+
+
+for ac_header in assert.h ctype.h float.h limits.h math.h memory.h stdarg.h stdio.h stdlib.h string.h time.h unistd.h
+do
+as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+ { $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
+$as_echo_n "checking for $ac_header... " >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+fi
+ac_res=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+else
+ # Is the header compilable?
+{ $as_echo "$as_me:$LINENO: checking $ac_header usability" >&5
+$as_echo_n "checking $ac_header usability... " >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+#include <$ac_header>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_header_compiler=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_header_compiler=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ $as_echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
+$as_echo "$ac_header_compiler" >&6; }
+
+# Is the header present?
+{ $as_echo "$as_me:$LINENO: checking $ac_header presence" >&5
+$as_echo_n "checking $ac_header presence... " >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <$ac_header>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ ac_header_preproc=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_header_preproc=no
+fi
+
+rm -f conftest.err conftest.$ac_ext
+{ $as_echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
+$as_echo "$ac_header_preproc" >&6; }
+
+# So? What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
+ yes:no: )
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5
+$as_echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;}
+ ac_header_preproc=yes
+ ;;
+ no:yes:* )
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5
+$as_echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5
+$as_echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5
+$as_echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5
+$as_echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5
+$as_echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5
+$as_echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;}
+ ( cat <<\_ASBOX
+## ------------------------------ ##
+## Report this to clustalw@ucd.ie ##
+## ------------------------------ ##
+_ASBOX
+ ) | sed "s/^/$as_me: WARNING: /" >&2
+ ;;
+esac
+{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
+$as_echo_n "checking for $ac_header... " >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+else
+ eval "$as_ac_Header=\$ac_header_preproc"
+fi
+ac_res=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+
+fi
+as_val=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ if test "x$as_val" = x""yes; then
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+
+done
+
+# awk '/^#include *</ {print $2}' $(find src/ -name \*.[ch] -or -name \*.cpp) | grep -v argtable2.h | sort -u | tr -d '<>'
+
+# Checks for typedefs, structures, and compiler characteristics.
+{ $as_echo "$as_me:$LINENO: checking for an ANSI C-conforming const" >&5
+$as_echo_n "checking for an ANSI C-conforming const... " >&6; }
+if test "${ac_cv_c_const+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+int
+main ()
+{
+/* FIXME: Include the comments suggested by Paul. */
+#ifndef __cplusplus
+ /* Ultrix mips cc rejects this. */
+ typedef int charset[2];
+ const charset cs;
+ /* SunOS 4.1.1 cc rejects this. */
+ char const *const *pcpcc;
+ char **ppc;
+ /* NEC SVR4.0.2 mips cc rejects this. */
+ struct point {int x, y;};
+ static struct point const zero = {0,0};
+ /* AIX XL C 1.02.0.0 rejects this.
+ It does not let you subtract one const X* pointer from another in
+ an arm of an if-expression whose if-part is not a constant
+ expression */
+ const char *g = "string";
+ pcpcc = &g + (g ? g-g : 0);
+ /* HPUX 7.0 cc rejects these. */
+ ++pcpcc;
+ ppc = (char**) pcpcc;
+ pcpcc = (char const *const *) ppc;
+ { /* SCO 3.2v4 cc rejects this. */
+ char *t;
+ char const *s = 0 ? (char *) 0 : (char const *) 0;
+
+ *t++ = 0;
+ if (s) return 0;
+ }
+ { /* Someone thinks the Sun supposedly-ANSI compiler will reject this. */
+ int x[] = {25, 17};
+ const int *foo = &x[0];
+ ++foo;
+ }
+ { /* Sun SC1.0 ANSI compiler rejects this -- but not the above. */
+ typedef const int *iptr;
+ iptr p = 0;
+ ++p;
+ }
+ { /* AIX XL C 1.02.0.0 rejects this saying
+ "k.c", line 2.27: 1506-025 (S) Operand must be a modifiable lvalue. */
+ struct s { int j; const int *ap[3]; };
+ struct s *b; b->j = 5;
+ }
+ { /* ULTRIX-32 V3.1 (Rev 9) vcc rejects this */
+ const int foo = 10;
+ if (!foo) return 0;
+ }
+ return !cs[0] && !zero.x;
+#endif
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_cv_c_const=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_c_const=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_const" >&5
+$as_echo "$ac_cv_c_const" >&6; }
+if test $ac_cv_c_const = no; then
+
+cat >>confdefs.h <<\_ACEOF
+#define const /**/
+_ACEOF
+
+fi
+
+{ $as_echo "$as_me:$LINENO: checking for size_t" >&5
+$as_echo_n "checking for size_t... " >&6; }
+if test "${ac_cv_type_size_t+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_type_size_t=no
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+if (sizeof (size_t))
+ return 0;
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+if (sizeof ((size_t)))
+ return 0;
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ :
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_type_size_t=yes
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_type_size_t" >&5
+$as_echo "$ac_cv_type_size_t" >&6; }
+if test "x$ac_cv_type_size_t" = x""yes; then
+ :
+else
+
+cat >>confdefs.h <<_ACEOF
+#define size_t unsigned int
+_ACEOF
+
+fi
+
+{ $as_echo "$as_me:$LINENO: checking for inline" >&5
+$as_echo_n "checking for inline... " >&6; }
+if test "${ac_cv_c_inline+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_c_inline=no
+for ac_kw in inline __inline__ __inline; do
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#ifndef __cplusplus
+typedef int foo_t;
+static $ac_kw foo_t static_foo () {return 0; }
+$ac_kw foo_t foo () {return 0; }
+#endif
+
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_cv_c_inline=$ac_kw
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ test "$ac_cv_c_inline" != no && break
+done
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_inline" >&5
+$as_echo "$ac_cv_c_inline" >&6; }
+
+
+case $ac_cv_c_inline in
+ inline | yes) ;;
+ *)
+ case $ac_cv_c_inline in
+ no) ac_val=;;
+ *) ac_val=$ac_cv_c_inline;;
+ esac
+ cat >>confdefs.h <<_ACEOF
+#ifndef __cplusplus
+#define inline $ac_val
+#endif
+_ACEOF
+ ;;
+esac
+
+
+# Checks for library functions.
+# AC_CHECK_FUNCS(strdup strstr strchr erand48)
+# AW is there an automatic way to extract library functions used in the program?
+
+
+# explicit libm check
+
+{ $as_echo "$as_me:$LINENO: checking for log in -lm" >&5
+$as_echo_n "checking for log in -lm... " >&6; }
+if test "${ac_cv_lib_m_log+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lm $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char log ();
+int
+main ()
+{
+return log ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ ac_cv_lib_m_log=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_lib_m_log=no
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_m_log" >&5
+$as_echo "$ac_cv_lib_m_log" >&6; }
+if test "x$ac_cv_lib_m_log" = x""yes; then
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_LIBM 1
+_ACEOF
+
+ LIBS="-lm $LIBS"
+
+else
+ { { $as_echo "$as_me:$LINENO: error: Could not find libm" >&5
+$as_echo "$as_me: error: Could not find libm" >&2;}
+ { (exit 1); exit 1; }; }
+fi
+
+{ $as_echo "$as_me:$LINENO: checking for log2 in -lm" >&5
+$as_echo_n "checking for log2 in -lm... " >&6; }
+if test "${ac_cv_lib_m_log2+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-lm $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char log2 ();
+int
+main ()
+{
+return log2 ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ ac_cv_lib_m_log2=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_lib_m_log2=no
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_m_log2" >&5
+$as_echo "$ac_cv_lib_m_log2" >&6; }
+if test "x$ac_cv_lib_m_log2" = x""yes; then
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_LOG2 1
+_ACEOF
+
+fi
+
+
+
+# --- argtable header and library check
+#
+#
+
+for ac_header in argtable2.h
+do
+as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+ { $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
+$as_echo_n "checking for $ac_header... " >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+fi
+ac_res=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+else
+ # Is the header compilable?
+{ $as_echo "$as_me:$LINENO: checking $ac_header usability" >&5
+$as_echo_n "checking $ac_header usability... " >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+#include <$ac_header>
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_header_compiler=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_header_compiler=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+{ $as_echo "$as_me:$LINENO: result: $ac_header_compiler" >&5
+$as_echo "$ac_header_compiler" >&6; }
+
+# Is the header present?
+{ $as_echo "$as_me:$LINENO: checking $ac_header presence" >&5
+$as_echo_n "checking $ac_header presence... " >&6; }
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <$ac_header>
+_ACEOF
+if { (ac_try="$ac_cpp conftest.$ac_ext"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } >/dev/null && {
+ test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ }; then
+ ac_header_preproc=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_header_preproc=no
+fi
+
+rm -f conftest.err conftest.$ac_ext
+{ $as_echo "$as_me:$LINENO: result: $ac_header_preproc" >&5
+$as_echo "$ac_header_preproc" >&6; }
+
+# So? What about this header?
+case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in
+ yes:no: )
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5
+$as_echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5
+$as_echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;}
+ ac_header_preproc=yes
+ ;;
+ no:yes:* )
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5
+$as_echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5
+$as_echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5
+$as_echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5
+$as_echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5
+$as_echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;}
+ { $as_echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5
+$as_echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;}
+ ( cat <<\_ASBOX
+## ------------------------------ ##
+## Report this to clustalw@ucd.ie ##
+## ------------------------------ ##
+_ASBOX
+ ) | sed "s/^/$as_me: WARNING: /" >&2
+ ;;
+esac
+{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5
+$as_echo_n "checking for $ac_header... " >&6; }
+if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+else
+ eval "$as_ac_Header=\$ac_header_preproc"
+fi
+ac_res=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+
+fi
+as_val=`eval 'as_val=${'$as_ac_Header'}
+ $as_echo "$as_val"'`
+ if test "x$as_val" = x""yes; then
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
+_ACEOF
+
+else
+ { { $as_echo "$as_me:$LINENO: error: Could not find argtable2.h. Try $ ./configure CFLAGS='-Iyour-argtable2-include-path" >&5
+$as_echo "$as_me: error: Could not find argtable2.h. Try $ ./configure CFLAGS='-Iyour-argtable2-include-path" >&2;}
+ { (exit 1); exit 1; }; }
+fi
+
+done
+
+
+{ $as_echo "$as_me:$LINENO: checking for arg_parse in -largtable2" >&5
+$as_echo_n "checking for arg_parse in -largtable2... " >&6; }
+if test "${ac_cv_lib_argtable2_arg_parse+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_check_lib_save_LIBS=$LIBS
+LIBS="-largtable2 $LIBS"
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char arg_parse ();
+int
+main ()
+{
+return arg_parse ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ ac_cv_lib_argtable2_arg_parse=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_lib_argtable2_arg_parse=no
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+LIBS=$ac_check_lib_save_LIBS
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_argtable2_arg_parse" >&5
+$as_echo "$ac_cv_lib_argtable2_arg_parse" >&6; }
+if test "x$ac_cv_lib_argtable2_arg_parse" = x""yes; then
+ cat >>confdefs.h <<_ACEOF
+#define HAVE_LIBARGTABLE2 1
+_ACEOF
+
+ LIBS="-largtable2 $LIBS"
+
+else
+ { { $as_echo "$as_me:$LINENO: error: Could not find libargtable2. Try $ ./configure LDFLAGS=\"-Lyour-argtable2-lib-path'" >&5
+$as_echo "$as_me: error: Could not find libargtable2. Try $ ./configure LDFLAGS=\"-Lyour-argtable2-lib-path'" >&2;}
+ { (exit 1); exit 1; }; }
+fi
+
+
+
+# enable python if requested (--with-python)
+#
+#AC_ARG_WITH([python],
+# [AS_HELP_STRING([--with-python],
+# [Enable Python Interface])],
+# [with_python=$withval],
+# [with_python=no])
+#if test "$with_python" = "yes"; then
+# AC_MSG_CHECKING([for python-config to get compiler flags])
+# AC_CHECK_PROG(python_config, 'python-config', yes)
+# if test "${python_config}" != "yes"; then
+# AC_MSG_ERROR("Could not run python-config.")
+# fi
+# PYTHON_CFLAGS=`python-config --cflags`
+# PYTHON_LDFLAGS=`python-config --ldflags`
+# AC_DEFINE([PYTHON_ENABLED], [1], [define for python usage])
+#fi
+#AC_SUBST(PYTHON_CFLAGS)
+#AC_SUBST(PYTHON_LDFLAGS)
+
+
+# --- SSE support
+# "One instruction to do the same operation on 4 packed elements simultaneously."
+#
+# http://www.codeproject.com/KB/recipes/sseintro.aspx?msg=568491
+# http://www.drdobbs.com/go-parallel/blog/archives/2010/03/getting_amazing.html
+# http://software.intel.com/file/1000
+#
+# AC_MSG_CHECKING(for SSE in current arch/CFLAGS)
+# AC_LINK_IFELSE([
+# AC_LANG_PROGRAM([[
+# #include <xmmintrin.h>
+# __m128 testfunc(float *a, float *b) {
+# return _mm_add_ps(_mm_loadu_ps(a), _mm_loadu_ps(b));
+# }
+# ]])],
+# [has_sse=yes], [has_sse=no]
+# )
+# AC_MSG_RESULT($has_sse)
+#
+# AC_ARG_ENABLE([sse],
+# [AS_HELP_STRING([--enable-sse],
+# [Enable SSE support])],
+# [has_sse="$enableval"],
+# [has_sse=no])
+#
+# if test x"$has_sse" = x"yes"; then
+# AC_DEFINE([USE_SSE], , [Enable SSE support])
+# CFLAGS="${CFLAGS} -msse"
+# fi
+
+
+# --- openmp
+#
+
+# ===========================================================================
+# http://www.gnu.org/software/autoconf-archive/ax_openmp.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+# AX_OPENMP([ACTION-IF-FOUND[, ACTION-IF-NOT-FOUND]])
+#
+# DESCRIPTION
+#
+# This macro tries to find out how to compile programs that use OpenMP a
+# standard API and set of compiler directives for parallel programming
+# (see http://www-unix.mcs/)
+#
+# On success, it sets the OPENMP_CFLAGS/OPENMP_CXXFLAGS/OPENMP_F77FLAGS
+# output variable to the flag (e.g. -omp) used both to compile *and* link
+# OpenMP programs in the current language.
+#
+# NOTE: You are assumed to not only compile your program with these flags,
+# but also link it with them as well.
+#
+# If you want to compile everything with OpenMP, you should set:
+#
+# CFLAGS="$CFLAGS $OPENMP_CFLAGS"
+# #OR# CXXFLAGS="$CXXFLAGS $OPENMP_CXXFLAGS"
+# #OR# FFLAGS="$FFLAGS $OPENMP_FFLAGS"
+#
+# (depending on the selected language).
+#
+# The user can override the default choice by setting the corresponding
+# environment variable (e.g. OPENMP_CFLAGS).
+#
+# ACTION-IF-FOUND is a list of shell commands to run if an OpenMP flag is
+# found, and ACTION-IF-NOT-FOUND is a list of commands to run it if it is
+# not found. If ACTION-IF-FOUND is not specified, the default action will
+# define HAVE_OPENMP.
+#
+# LICENSE
+#
+# Copyright (c) 2008 Steven G. Johnson <stevenj@alum.mit.edu>
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
+# Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program. If not, see <http://www.gnu.org/licenses/>.
+#
+# As a special exception, the respective Autoconf Macro's copyright owner
+# gives unlimited permission to copy, distribute and modify the configure
+# scripts that are the output of Autoconf when processing the Macro. You
+# need not follow the terms of the GNU General Public License when using
+# or distributing such scripts, even though portions of the text of the
+# Macro appear in them. The GNU General Public License (GPL) does govern
+# all other use of the material that constitutes the Autoconf Macro.
+#
+# This special exception to the GPL applies to versions of the Autoconf
+# Macro released by the Autoconf Archive. When you make and distribute a
+# modified version of the Autoconf Macro, you may extend this special
+# exception to the GPL to apply to your modified version as well.
+
+#serial 8
+
+
+
+# Check whether --with-openmp was given.
+if test "${with_openmp+set}" = set; then
+ withval=$with_openmp;
+fi
+
+if test "x$with_openmp" = "xno"; then
+ :
+else
+
+
+{ $as_echo "$as_me:$LINENO: checking for OpenMP flag of C compiler" >&5
+$as_echo_n "checking for OpenMP flag of C compiler... " >&6; }
+if test "${ax_cv_c_openmp+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ saveCFLAGS=$CFLAGS
+ax_cv_c_openmp=unknown
+# Flags to try: -fopenmp (gcc), -openmp (icc), -mp (SGI & PGI),
+# -xopenmp (Sun), -omp (Tru64), -qsmp=omp (AIX), none
+ax_openmp_flags="-fopenmp -openmp -mp -xopenmp -omp -qsmp=omp none"
+if test "x$OPENMP_CFLAGS" != x; then
+ ax_openmp_flags="$OPENMP_CFLAGS $ax_openmp_flags"
+fi
+for ax_openmp_flag in $ax_openmp_flags; do
+ case $ax_openmp_flag in
+ none) CFLAGS=$saveC ;;
+ *) CFLAGS="$saveCFLAGS $ax_openmp_flag" ;;
+ esac
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char omp_set_num_threads ();
+int
+main ()
+{
+return omp_set_num_threads ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ ax_cv_c_openmp=$ax_openmp_flag; break
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+done
+CFLAGS=$saveCFLAGS
+
+fi
+{ $as_echo "$as_me:$LINENO: result: $ax_cv_c_openmp" >&5
+$as_echo "$ax_cv_c_openmp" >&6; }
+if test "x$ax_cv_c_openmp" = "xunknown"; then
+ :
+else
+ if test "x$ax_cv_c_openmp" != "xnone"; then
+ OPENMP_CFLAGS=$ax_cv_c_openmp
+ fi
+
+cat >>confdefs.h <<\_ACEOF
+#define HAVE_OPENMP 1
+_ACEOF
+
+
+fi
+
+
+fi
+
+
+# according to http://beagle-lib.googlecode.com/svn-history/r824/trunk/configure.ac:
+# "OpenMP checker only defines for C when compiling both C and C++"
+OPENMP_CXXFLAGS=$OPENMP_CFLAGS
+
+
+# version 2: enable openmp only if explicitely asked for it
+#AC_ARG_ENABLE(openmp, AS_HELP_STRING([--enable-openmp], [Multi-threaded parallel version using OpenMP]))
+#if test -n "${enable_openmp}" -a x"${enable_openmp}" != x"no"; then
+# m4_include([m4/ax_openmp.m4])
+# AX_OPENMP(AC_DEFINE(HAVE_OPENMP, 1, [enable OpenMP support]),
+# AC_MSG_ERROR([Compiler does not seem to support OpenMP]))
+# AC_SUBST(OPENMP_CFLAGS)
+# AC_SUBST(OPENMP_CXXFLAGS)
+#fi
+
+# --- squid
+#
+#
+# Extra checks for squid; see their configure, config.log, squidconf.h
+# etc. For example, I'm not sure about USE_HOST_BYTESWAP_FUNCTIONS,
+# SIZEOF_UNSIGNED_LONG, HAVE_STRTOUL and HAVE_STRTOULL
+#
+# Might not just have to set compiler flags but create use squidconf.h.in
+#
+# The following hopefully takes about byte ordering (big-endian...).
+# My hope is that it will set WORDS_BIGENDIAN and
+# USE_HOST_BYTESWAP_FUNCTIONS (as used by squid) if necessary:
+#
+
+ { $as_echo "$as_me:$LINENO: checking whether byte ordering is bigendian" >&5
+$as_echo_n "checking whether byte ordering is bigendian... " >&6; }
+if test "${ac_cv_c_bigendian+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_c_bigendian=unknown
+ # See if we're dealing with a universal compiler.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#ifndef __APPLE_CC__
+ not a universal capable compiler
+ #endif
+ typedef int dummy;
+
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+
+ # Check for potential -arch flags. It is not universal unless
+ # there are some -arch flags. Note that *ppc* also matches
+ # ppc64. This check is also rather less than ideal.
+ case "${CC} ${CFLAGS} ${CPPFLAGS} ${LDFLAGS}" in #(
+ *-arch*ppc*|*-arch*i386*|*-arch*x86_64*) ac_cv_c_bigendian=universal;;
+ esac
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ if test $ac_cv_c_bigendian = unknown; then
+ # See if sys/param.h defines the BYTE_ORDER macro.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <sys/types.h>
+ #include <sys/param.h>
+
+int
+main ()
+{
+#if ! (defined BYTE_ORDER && defined BIG_ENDIAN \
+ && defined LITTLE_ENDIAN && BYTE_ORDER && BIG_ENDIAN \
+ && LITTLE_ENDIAN)
+ bogus endian macros
+ #endif
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ # It does; now see whether it defined to BIG_ENDIAN or not.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <sys/types.h>
+ #include <sys/param.h>
+
+int
+main ()
+{
+#if BYTE_ORDER != BIG_ENDIAN
+ not big endian
+ #endif
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_cv_c_bigendian=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_c_bigendian=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ fi
+ if test $ac_cv_c_bigendian = unknown; then
+ # See if <limits.h> defines _LITTLE_ENDIAN or _BIG_ENDIAN (e.g., Solaris).
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <limits.h>
+
+int
+main ()
+{
+#if ! (defined _LITTLE_ENDIAN || defined _BIG_ENDIAN)
+ bogus endian macros
+ #endif
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ # It does; now see whether it defined to _BIG_ENDIAN or not.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+#include <limits.h>
+
+int
+main ()
+{
+#ifndef _BIG_ENDIAN
+ not big endian
+ #endif
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_cv_c_bigendian=yes
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_c_bigendian=no
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ fi
+ if test $ac_cv_c_bigendian = unknown; then
+ # Compile a test program.
+ if test "$cross_compiling" = yes; then
+ # Try to guess by grepping values from an object file.
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+short int ascii_mm[] =
+ { 0x4249, 0x4765, 0x6E44, 0x6961, 0x6E53, 0x7953, 0 };
+ short int ascii_ii[] =
+ { 0x694C, 0x5454, 0x656C, 0x6E45, 0x6944, 0x6E61, 0 };
+ int use_ascii (int i) {
+ return ascii_mm[i] + ascii_ii[i];
+ }
+ short int ebcdic_ii[] =
+ { 0x89D3, 0xE3E3, 0x8593, 0x95C5, 0x89C4, 0x9581, 0 };
+ short int ebcdic_mm[] =
+ { 0xC2C9, 0xC785, 0x95C4, 0x8981, 0x95E2, 0xA8E2, 0 };
+ int use_ebcdic (int i) {
+ return ebcdic_mm[i] + ebcdic_ii[i];
+ }
+ extern int foo;
+
+int
+main ()
+{
+return use_ascii (foo) == use_ebcdic (foo);
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ if grep BIGenDianSyS conftest.$ac_objext >/dev/null; then
+ ac_cv_c_bigendian=yes
+ fi
+ if grep LiTTleEnDian conftest.$ac_objext >/dev/null ; then
+ if test "$ac_cv_c_bigendian" = unknown; then
+ ac_cv_c_bigendian=no
+ else
+ # finding both strings is unlikely to happen, but who knows?
+ ac_cv_c_bigendian=unknown
+ fi
+ fi
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+
+ /* Are we little or big endian? From Harbison&Steele. */
+ union
+ {
+ long int l;
+ char c[sizeof (long int)];
+ } u;
+ u.l = 1;
+ return u.c[sizeof (long int) - 1] == 1;
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_cv_c_bigendian=no
+else
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+ac_cv_c_bigendian=yes
+fi
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+
+
+ fi
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_bigendian" >&5
+$as_echo "$ac_cv_c_bigendian" >&6; }
+ case $ac_cv_c_bigendian in #(
+ yes)
+ { $as_echo "$as_me:$LINENO: WARNING: $PACKAGE_NAME hasn't been tested on Big-Endian machines...expecting trouble!" >&5
+$as_echo "$as_me: WARNING: $PACKAGE_NAME hasn't been tested on Big-Endian machines...expecting trouble!" >&2;};; #(
+ no)
+ ;; #(
+ universal)
+
+cat >>confdefs.h <<\_ACEOF
+#define AC_APPLE_UNIVERSAL_BUILD 1
+_ACEOF
+
+ ;; #(
+ *)
+ { { $as_echo "$as_me:$LINENO: error: unknown endianness
+ presetting ac_cv_c_bigendian=no (or yes) will help" >&5
+$as_echo "$as_me: error: unknown endianness
+ presetting ac_cv_c_bigendian=no (or yes) will help" >&2;}
+ { (exit 1); exit 1; }; } ;;
+ esac
+
+
+
+
+
+for ac_func in ntohs ntohl ntons ntonl
+do
+as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking for $ac_func" >&5
+$as_echo_n "checking for $ac_func... " >&6; }
+if { as_var=$as_ac_var; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+/* Define $ac_func to an innocuous variant, in case <limits.h> declares $ac_func.
+ For example, HP-UX 11i <limits.h> declares gettimeofday. */
+#define $ac_func innocuous_$ac_func
+
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char $ac_func (); below.
+ Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ <limits.h> exists even on freestanding compilers. */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $ac_func
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $ac_func ();
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined __stub_$ac_func || defined __stub___$ac_func
+choke me
+#endif
+
+int
+main ()
+{
+return $ac_func ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ eval "$as_ac_var=yes"
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ eval "$as_ac_var=no"
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+ac_res=`eval 'as_val=${'$as_ac_var'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+as_val=`eval 'as_val=${'$as_ac_var'}
+ $as_echo "$as_val"'`
+ if test "x$as_val" = x""yes; then
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+done
+
+#
+# The cast to long int works around a bug in the HP C Compiler
+# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects
+# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'.
+# This bug is HP SR number 8606223364.
+{ $as_echo "$as_me:$LINENO: checking size of unsigned short" >&5
+$as_echo_n "checking size of unsigned short... " >&6; }
+if test "${ac_cv_sizeof_unsigned_short+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then
+ # Depending upon the size, compute the lo and hi bounds.
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned short))) >= 0)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_lo=0 ac_mid=0
+ while :; do
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned short))) <= $ac_mid)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_hi=$ac_mid; break
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_lo=`expr $ac_mid + 1`
+ if test $ac_lo -le $ac_mid; then
+ ac_lo= ac_hi=
+ break
+ fi
+ ac_mid=`expr 2 '*' $ac_mid + 1`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ done
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned short))) < 0)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_hi=-1 ac_mid=-1
+ while :; do
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned short))) >= $ac_mid)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_lo=$ac_mid; break
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_hi=`expr '(' $ac_mid ')' - 1`
+ if test $ac_mid -le $ac_hi; then
+ ac_lo= ac_hi=
+ break
+ fi
+ ac_mid=`expr 2 '*' $ac_mid`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ done
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_lo= ac_hi=
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+# Binary search between lo and hi bounds.
+while test "x$ac_lo" != "x$ac_hi"; do
+ ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo`
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned short))) <= $ac_mid)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_hi=$ac_mid
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_lo=`expr '(' $ac_mid ')' + 1`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+done
+case $ac_lo in
+?*) ac_cv_sizeof_unsigned_short=$ac_lo;;
+'') if test "$ac_cv_type_unsigned_short" = yes; then
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (unsigned short)
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot compute sizeof (unsigned short)
+See \`config.log' for more details." >&2;}
+ { (exit 77); exit 77; }; }; }
+ else
+ ac_cv_sizeof_unsigned_short=0
+ fi ;;
+esac
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+static long int longval () { return (long int) (sizeof (unsigned short)); }
+static unsigned long int ulongval () { return (long int) (sizeof (unsigned short)); }
+#include <stdio.h>
+#include <stdlib.h>
+int
+main ()
+{
+
+ FILE *f = fopen ("conftest.val", "w");
+ if (! f)
+ return 1;
+ if (((long int) (sizeof (unsigned short))) < 0)
+ {
+ long int i = longval ();
+ if (i != ((long int) (sizeof (unsigned short))))
+ return 1;
+ fprintf (f, "%ld", i);
+ }
+ else
+ {
+ unsigned long int i = ulongval ();
+ if (i != ((long int) (sizeof (unsigned short))))
+ return 1;
+ fprintf (f, "%lu", i);
+ }
+ /* Do not output a trailing newline, as this causes \r\n confusion
+ on some platforms. */
+ return ferror (f) || fclose (f) != 0;
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_cv_sizeof_unsigned_short=`cat conftest.val`
+else
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+if test "$ac_cv_type_unsigned_short" = yes; then
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (unsigned short)
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot compute sizeof (unsigned short)
+See \`config.log' for more details." >&2;}
+ { (exit 77); exit 77; }; }; }
+ else
+ ac_cv_sizeof_unsigned_short=0
+ fi
+fi
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f conftest.val
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_sizeof_unsigned_short" >&5
+$as_echo "$ac_cv_sizeof_unsigned_short" >&6; }
+
+
+
+cat >>confdefs.h <<_ACEOF
+#define SIZEOF_UNSIGNED_SHORT $ac_cv_sizeof_unsigned_short
+_ACEOF
+
+
+# The cast to long int works around a bug in the HP C Compiler
+# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects
+# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'.
+# This bug is HP SR number 8606223364.
+{ $as_echo "$as_me:$LINENO: checking size of unsigned int" >&5
+$as_echo_n "checking size of unsigned int... " >&6; }
+if test "${ac_cv_sizeof_unsigned_int+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then
+ # Depending upon the size, compute the lo and hi bounds.
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned int))) >= 0)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_lo=0 ac_mid=0
+ while :; do
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned int))) <= $ac_mid)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_hi=$ac_mid; break
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_lo=`expr $ac_mid + 1`
+ if test $ac_lo -le $ac_mid; then
+ ac_lo= ac_hi=
+ break
+ fi
+ ac_mid=`expr 2 '*' $ac_mid + 1`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ done
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned int))) < 0)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_hi=-1 ac_mid=-1
+ while :; do
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned int))) >= $ac_mid)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_lo=$ac_mid; break
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_hi=`expr '(' $ac_mid ')' - 1`
+ if test $ac_mid -le $ac_hi; then
+ ac_lo= ac_hi=
+ break
+ fi
+ ac_mid=`expr 2 '*' $ac_mid`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ done
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_lo= ac_hi=
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+# Binary search between lo and hi bounds.
+while test "x$ac_lo" != "x$ac_hi"; do
+ ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo`
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned int))) <= $ac_mid)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_hi=$ac_mid
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_lo=`expr '(' $ac_mid ')' + 1`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+done
+case $ac_lo in
+?*) ac_cv_sizeof_unsigned_int=$ac_lo;;
+'') if test "$ac_cv_type_unsigned_int" = yes; then
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (unsigned int)
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot compute sizeof (unsigned int)
+See \`config.log' for more details." >&2;}
+ { (exit 77); exit 77; }; }; }
+ else
+ ac_cv_sizeof_unsigned_int=0
+ fi ;;
+esac
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+static long int longval () { return (long int) (sizeof (unsigned int)); }
+static unsigned long int ulongval () { return (long int) (sizeof (unsigned int)); }
+#include <stdio.h>
+#include <stdlib.h>
+int
+main ()
+{
+
+ FILE *f = fopen ("conftest.val", "w");
+ if (! f)
+ return 1;
+ if (((long int) (sizeof (unsigned int))) < 0)
+ {
+ long int i = longval ();
+ if (i != ((long int) (sizeof (unsigned int))))
+ return 1;
+ fprintf (f, "%ld", i);
+ }
+ else
+ {
+ unsigned long int i = ulongval ();
+ if (i != ((long int) (sizeof (unsigned int))))
+ return 1;
+ fprintf (f, "%lu", i);
+ }
+ /* Do not output a trailing newline, as this causes \r\n confusion
+ on some platforms. */
+ return ferror (f) || fclose (f) != 0;
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_cv_sizeof_unsigned_int=`cat conftest.val`
+else
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+if test "$ac_cv_type_unsigned_int" = yes; then
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (unsigned int)
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot compute sizeof (unsigned int)
+See \`config.log' for more details." >&2;}
+ { (exit 77); exit 77; }; }; }
+ else
+ ac_cv_sizeof_unsigned_int=0
+ fi
+fi
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f conftest.val
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_sizeof_unsigned_int" >&5
+$as_echo "$ac_cv_sizeof_unsigned_int" >&6; }
+
+
+
+cat >>confdefs.h <<_ACEOF
+#define SIZEOF_UNSIGNED_INT $ac_cv_sizeof_unsigned_int
+_ACEOF
+
+
+# The cast to long int works around a bug in the HP C Compiler
+# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects
+# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'.
+# This bug is HP SR number 8606223364.
+{ $as_echo "$as_me:$LINENO: checking size of unsigned long" >&5
+$as_echo_n "checking size of unsigned long... " >&6; }
+if test "${ac_cv_sizeof_unsigned_long+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then
+ # Depending upon the size, compute the lo and hi bounds.
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long))) >= 0)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_lo=0 ac_mid=0
+ while :; do
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long))) <= $ac_mid)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_hi=$ac_mid; break
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_lo=`expr $ac_mid + 1`
+ if test $ac_lo -le $ac_mid; then
+ ac_lo= ac_hi=
+ break
+ fi
+ ac_mid=`expr 2 '*' $ac_mid + 1`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ done
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long))) < 0)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_hi=-1 ac_mid=-1
+ while :; do
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long))) >= $ac_mid)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_lo=$ac_mid; break
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_hi=`expr '(' $ac_mid ')' - 1`
+ if test $ac_mid -le $ac_hi; then
+ ac_lo= ac_hi=
+ break
+ fi
+ ac_mid=`expr 2 '*' $ac_mid`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ done
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_lo= ac_hi=
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+# Binary search between lo and hi bounds.
+while test "x$ac_lo" != "x$ac_hi"; do
+ ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo`
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long))) <= $ac_mid)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_hi=$ac_mid
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_lo=`expr '(' $ac_mid ')' + 1`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+done
+case $ac_lo in
+?*) ac_cv_sizeof_unsigned_long=$ac_lo;;
+'') if test "$ac_cv_type_unsigned_long" = yes; then
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (unsigned long)
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot compute sizeof (unsigned long)
+See \`config.log' for more details." >&2;}
+ { (exit 77); exit 77; }; }; }
+ else
+ ac_cv_sizeof_unsigned_long=0
+ fi ;;
+esac
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+static long int longval () { return (long int) (sizeof (unsigned long)); }
+static unsigned long int ulongval () { return (long int) (sizeof (unsigned long)); }
+#include <stdio.h>
+#include <stdlib.h>
+int
+main ()
+{
+
+ FILE *f = fopen ("conftest.val", "w");
+ if (! f)
+ return 1;
+ if (((long int) (sizeof (unsigned long))) < 0)
+ {
+ long int i = longval ();
+ if (i != ((long int) (sizeof (unsigned long))))
+ return 1;
+ fprintf (f, "%ld", i);
+ }
+ else
+ {
+ unsigned long int i = ulongval ();
+ if (i != ((long int) (sizeof (unsigned long))))
+ return 1;
+ fprintf (f, "%lu", i);
+ }
+ /* Do not output a trailing newline, as this causes \r\n confusion
+ on some platforms. */
+ return ferror (f) || fclose (f) != 0;
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_cv_sizeof_unsigned_long=`cat conftest.val`
+else
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+if test "$ac_cv_type_unsigned_long" = yes; then
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (unsigned long)
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot compute sizeof (unsigned long)
+See \`config.log' for more details." >&2;}
+ { (exit 77); exit 77; }; }; }
+ else
+ ac_cv_sizeof_unsigned_long=0
+ fi
+fi
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f conftest.val
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_sizeof_unsigned_long" >&5
+$as_echo "$ac_cv_sizeof_unsigned_long" >&6; }
+
+
+
+cat >>confdefs.h <<_ACEOF
+#define SIZEOF_UNSIGNED_LONG $ac_cv_sizeof_unsigned_long
+_ACEOF
+
+
+# The cast to long int works around a bug in the HP C Compiler
+# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects
+# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'.
+# This bug is HP SR number 8606223364.
+{ $as_echo "$as_me:$LINENO: checking size of unsigned long long" >&5
+$as_echo_n "checking size of unsigned long long... " >&6; }
+if test "${ac_cv_sizeof_unsigned_long_long+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then
+ # Depending upon the size, compute the lo and hi bounds.
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long long))) >= 0)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_lo=0 ac_mid=0
+ while :; do
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long long))) <= $ac_mid)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_hi=$ac_mid; break
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_lo=`expr $ac_mid + 1`
+ if test $ac_lo -le $ac_mid; then
+ ac_lo= ac_hi=
+ break
+ fi
+ ac_mid=`expr 2 '*' $ac_mid + 1`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ done
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long long))) < 0)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_hi=-1 ac_mid=-1
+ while :; do
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long long))) >= $ac_mid)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_lo=$ac_mid; break
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_hi=`expr '(' $ac_mid ')' - 1`
+ if test $ac_mid -le $ac_hi; then
+ ac_lo= ac_hi=
+ break
+ fi
+ ac_mid=`expr 2 '*' $ac_mid`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ done
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_lo= ac_hi=
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+# Binary search between lo and hi bounds.
+while test "x$ac_lo" != "x$ac_hi"; do
+ ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo`
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (unsigned long long))) <= $ac_mid)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_hi=$ac_mid
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_lo=`expr '(' $ac_mid ')' + 1`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+done
+case $ac_lo in
+?*) ac_cv_sizeof_unsigned_long_long=$ac_lo;;
+'') if test "$ac_cv_type_unsigned_long_long" = yes; then
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (unsigned long long)
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot compute sizeof (unsigned long long)
+See \`config.log' for more details." >&2;}
+ { (exit 77); exit 77; }; }; }
+ else
+ ac_cv_sizeof_unsigned_long_long=0
+ fi ;;
+esac
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+static long int longval () { return (long int) (sizeof (unsigned long long)); }
+static unsigned long int ulongval () { return (long int) (sizeof (unsigned long long)); }
+#include <stdio.h>
+#include <stdlib.h>
+int
+main ()
+{
+
+ FILE *f = fopen ("conftest.val", "w");
+ if (! f)
+ return 1;
+ if (((long int) (sizeof (unsigned long long))) < 0)
+ {
+ long int i = longval ();
+ if (i != ((long int) (sizeof (unsigned long long))))
+ return 1;
+ fprintf (f, "%ld", i);
+ }
+ else
+ {
+ unsigned long int i = ulongval ();
+ if (i != ((long int) (sizeof (unsigned long long))))
+ return 1;
+ fprintf (f, "%lu", i);
+ }
+ /* Do not output a trailing newline, as this causes \r\n confusion
+ on some platforms. */
+ return ferror (f) || fclose (f) != 0;
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_cv_sizeof_unsigned_long_long=`cat conftest.val`
+else
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+if test "$ac_cv_type_unsigned_long_long" = yes; then
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (unsigned long long)
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot compute sizeof (unsigned long long)
+See \`config.log' for more details." >&2;}
+ { (exit 77); exit 77; }; }; }
+ else
+ ac_cv_sizeof_unsigned_long_long=0
+ fi
+fi
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f conftest.val
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_sizeof_unsigned_long_long" >&5
+$as_echo "$ac_cv_sizeof_unsigned_long_long" >&6; }
+
+
+
+cat >>confdefs.h <<_ACEOF
+#define SIZEOF_UNSIGNED_LONG_LONG $ac_cv_sizeof_unsigned_long_long
+_ACEOF
+
+
+#
+
+
+for ac_func in stroul strtoull
+do
+as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking for $ac_func" >&5
+$as_echo_n "checking for $ac_func... " >&6; }
+if { as_var=$as_ac_var; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+/* Define $ac_func to an innocuous variant, in case <limits.h> declares $ac_func.
+ For example, HP-UX 11i <limits.h> declares gettimeofday. */
+#define $ac_func innocuous_$ac_func
+
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char $ac_func (); below.
+ Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ <limits.h> exists even on freestanding compilers. */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $ac_func
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $ac_func ();
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined __stub_$ac_func || defined __stub___$ac_func
+choke me
+#endif
+
+int
+main ()
+{
+return $ac_func ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ eval "$as_ac_var=yes"
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ eval "$as_ac_var=no"
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+ac_res=`eval 'as_val=${'$as_ac_var'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+as_val=`eval 'as_val=${'$as_ac_var'}
+ $as_echo "$as_val"'`
+ if test "x$as_val" = x""yes; then
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+done
+
+
+
+for ac_func in ftello fseeko
+do
+as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking for $ac_func" >&5
+$as_echo_n "checking for $ac_func... " >&6; }
+if { as_var=$as_ac_var; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+/* Define $ac_func to an innocuous variant, in case <limits.h> declares $ac_func.
+ For example, HP-UX 11i <limits.h> declares gettimeofday. */
+#define $ac_func innocuous_$ac_func
+
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char $ac_func (); below.
+ Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ <limits.h> exists even on freestanding compilers. */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $ac_func
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $ac_func ();
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined __stub_$ac_func || defined __stub___$ac_func
+choke me
+#endif
+
+int
+main ()
+{
+return $ac_func ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ eval "$as_ac_var=yes"
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ eval "$as_ac_var=no"
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+ac_res=`eval 'as_val=${'$as_ac_var'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+as_val=`eval 'as_val=${'$as_ac_var'}
+ $as_echo "$as_val"'`
+ if test "x$as_val" = x""yes; then
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+done
+
+
+
+for ac_func in ftello64 fseeko64
+do
+as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking for $ac_func" >&5
+$as_echo_n "checking for $ac_func... " >&6; }
+if { as_var=$as_ac_var; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+/* Define $ac_func to an innocuous variant, in case <limits.h> declares $ac_func.
+ For example, HP-UX 11i <limits.h> declares gettimeofday. */
+#define $ac_func innocuous_$ac_func
+
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char $ac_func (); below.
+ Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ <limits.h> exists even on freestanding compilers. */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $ac_func
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $ac_func ();
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined __stub_$ac_func || defined __stub___$ac_func
+choke me
+#endif
+
+int
+main ()
+{
+return $ac_func ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ eval "$as_ac_var=yes"
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ eval "$as_ac_var=no"
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+ac_res=`eval 'as_val=${'$as_ac_var'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+as_val=`eval 'as_val=${'$as_ac_var'}
+ $as_echo "$as_val"'`
+ if test "x$as_val" = x""yes; then
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+done
+
+
+
+for ac_func in ftell64 fseek64
+do
+as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
+{ $as_echo "$as_me:$LINENO: checking for $ac_func" >&5
+$as_echo_n "checking for $ac_func... " >&6; }
+if { as_var=$as_ac_var; eval "test \"\${$as_var+set}\" = set"; }; then
+ $as_echo_n "(cached) " >&6
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+/* Define $ac_func to an innocuous variant, in case <limits.h> declares $ac_func.
+ For example, HP-UX 11i <limits.h> declares gettimeofday. */
+#define $ac_func innocuous_$ac_func
+
+/* System header to define __stub macros and hopefully few prototypes,
+ which can conflict with char $ac_func (); below.
+ Prefer <limits.h> to <assert.h> if __STDC__ is defined, since
+ <limits.h> exists even on freestanding compilers. */
+
+#ifdef __STDC__
+# include <limits.h>
+#else
+# include <assert.h>
+#endif
+
+#undef $ac_func
+
+/* Override any GCC internal prototype to avoid an error.
+ Use char because int might match the return type of a GCC
+ builtin and then its argument prototype would still apply. */
+#ifdef __cplusplus
+extern "C"
+#endif
+char $ac_func ();
+/* The GNU C library defines this for functions which it implements
+ to always fail with ENOSYS. Some functions are actually named
+ something starting with __ and the normal name is an alias. */
+#if defined __stub_$ac_func || defined __stub___$ac_func
+choke me
+#endif
+
+int
+main ()
+{
+return $ac_func ();
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest$ac_exeext && {
+ test "$cross_compiling" = yes ||
+ $as_test_x conftest$ac_exeext
+ }; then
+ eval "$as_ac_var=yes"
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ eval "$as_ac_var=no"
+fi
+
+rm -rf conftest.dSYM
+rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \
+ conftest$ac_exeext conftest.$ac_ext
+fi
+ac_res=`eval 'as_val=${'$as_ac_var'}
+ $as_echo "$as_val"'`
+ { $as_echo "$as_me:$LINENO: result: $ac_res" >&5
+$as_echo "$ac_res" >&6; }
+as_val=`eval 'as_val=${'$as_ac_var'}
+ $as_echo "$as_val"'`
+ if test "x$as_val" = x""yes; then
+ cat >>confdefs.h <<_ACEOF
+#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
+_ACEOF
+
+fi
+done
+
+#
+{ $as_echo "$as_me:$LINENO: checking for off_t" >&5
+$as_echo_n "checking for off_t... " >&6; }
+if test "${ac_cv_type_off_t+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ ac_cv_type_off_t=no
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+if (sizeof (off_t))
+ return 0;
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+if (sizeof ((off_t)))
+ return 0;
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ :
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_cv_type_off_t=yes
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_type_off_t" >&5
+$as_echo "$ac_cv_type_off_t" >&6; }
+if test "x$ac_cv_type_off_t" = x""yes; then
+ :
+else
+
+cat >>confdefs.h <<_ACEOF
+#define off_t long int
+_ACEOF
+
+fi
+
+# The cast to long int works around a bug in the HP C Compiler
+# version HP92453-01 B.11.11.23709.GP, which incorrectly rejects
+# declarations like `int a3[[(sizeof (unsigned char)) >= 0]];'.
+# This bug is HP SR number 8606223364.
+{ $as_echo "$as_me:$LINENO: checking size of fpos_t" >&5
+$as_echo_n "checking size of fpos_t... " >&6; }
+if test "${ac_cv_sizeof_fpos_t+set}" = set; then
+ $as_echo_n "(cached) " >&6
+else
+ if test "$cross_compiling" = yes; then
+ # Depending upon the size, compute the lo and hi bounds.
+cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (fpos_t))) >= 0)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_lo=0 ac_mid=0
+ while :; do
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (fpos_t))) <= $ac_mid)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_hi=$ac_mid; break
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_lo=`expr $ac_mid + 1`
+ if test $ac_lo -le $ac_mid; then
+ ac_lo= ac_hi=
+ break
+ fi
+ ac_mid=`expr 2 '*' $ac_mid + 1`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ done
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (fpos_t))) < 0)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_hi=-1 ac_mid=-1
+ while :; do
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (fpos_t))) >= $ac_mid)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_lo=$ac_mid; break
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_hi=`expr '(' $ac_mid ')' - 1`
+ if test $ac_mid -le $ac_hi; then
+ ac_lo= ac_hi=
+ break
+ fi
+ ac_mid=`expr 2 '*' $ac_mid`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ done
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_lo= ac_hi=
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+# Binary search between lo and hi bounds.
+while test "x$ac_lo" != "x$ac_hi"; do
+ ac_mid=`expr '(' $ac_hi - $ac_lo ')' / 2 + $ac_lo`
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+int
+main ()
+{
+static int test_array [1 - 2 * !(((long int) (sizeof (fpos_t))) <= $ac_mid)];
+test_array [0] = 0
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest.$ac_objext
+if { (ac_try="$ac_compile"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_compile") 2>conftest.er1
+ ac_status=$?
+ grep -v '^ *+' conftest.er1 >conftest.err
+ rm -f conftest.er1
+ cat conftest.err >&5
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && {
+ test -z "$ac_c_werror_flag" ||
+ test ! -s conftest.err
+ } && test -s conftest.$ac_objext; then
+ ac_hi=$ac_mid
+else
+ $as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+ ac_lo=`expr '(' $ac_mid ')' + 1`
+fi
+
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+done
+case $ac_lo in
+?*) ac_cv_sizeof_fpos_t=$ac_lo;;
+'') if test "$ac_cv_type_fpos_t" = yes; then
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (fpos_t)
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot compute sizeof (fpos_t)
+See \`config.log' for more details." >&2;}
+ { (exit 77); exit 77; }; }; }
+ else
+ ac_cv_sizeof_fpos_t=0
+ fi ;;
+esac
+else
+ cat >conftest.$ac_ext <<_ACEOF
+/* confdefs.h. */
+_ACEOF
+cat confdefs.h >>conftest.$ac_ext
+cat >>conftest.$ac_ext <<_ACEOF
+/* end confdefs.h. */
+$ac_includes_default
+static long int longval () { return (long int) (sizeof (fpos_t)); }
+static unsigned long int ulongval () { return (long int) (sizeof (fpos_t)); }
+#include <stdio.h>
+#include <stdlib.h>
+int
+main ()
+{
+
+ FILE *f = fopen ("conftest.val", "w");
+ if (! f)
+ return 1;
+ if (((long int) (sizeof (fpos_t))) < 0)
+ {
+ long int i = longval ();
+ if (i != ((long int) (sizeof (fpos_t))))
+ return 1;
+ fprintf (f, "%ld", i);
+ }
+ else
+ {
+ unsigned long int i = ulongval ();
+ if (i != ((long int) (sizeof (fpos_t))))
+ return 1;
+ fprintf (f, "%lu", i);
+ }
+ /* Do not output a trailing newline, as this causes \r\n confusion
+ on some platforms. */
+ return ferror (f) || fclose (f) != 0;
+
+ ;
+ return 0;
+}
+_ACEOF
+rm -f conftest$ac_exeext
+if { (ac_try="$ac_link"
+case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_link") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); } && { ac_try='./conftest$ac_exeext'
+ { (case "(($ac_try" in
+ *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+ *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\""
+$as_echo "$ac_try_echo") >&5
+ (eval "$ac_try") 2>&5
+ ac_status=$?
+ $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5
+ (exit $ac_status); }; }; then
+ ac_cv_sizeof_fpos_t=`cat conftest.val`
+else
+ $as_echo "$as_me: program exited with status $ac_status" >&5
+$as_echo "$as_me: failed program was:" >&5
+sed 's/^/| /' conftest.$ac_ext >&5
+
+( exit $ac_status )
+if test "$ac_cv_type_fpos_t" = yes; then
+ { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+{ { $as_echo "$as_me:$LINENO: error: cannot compute sizeof (fpos_t)
+See \`config.log' for more details." >&5
+$as_echo "$as_me: error: cannot compute sizeof (fpos_t)
+See \`config.log' for more details." >&2;}
+ { (exit 77); exit 77; }; }; }
+ else
+ ac_cv_sizeof_fpos_t=0
+ fi
+fi
+rm -rf conftest.dSYM
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext
+fi
+rm -f conftest.val
+fi
+{ $as_echo "$as_me:$LINENO: result: $ac_cv_sizeof_fpos_t" >&5
+$as_echo "$ac_cv_sizeof_fpos_t" >&6; }
+
+
+
+cat >>confdefs.h <<_ACEOF
+#define SIZEOF_FPOS_T $ac_cv_sizeof_fpos_t
+_ACEOF
+
+
+#
+# struct stat64 and stat64 test:
+# version 1:
+#AC_CHECK_TYPE(struct stat64,
+# [AC_CHECK_FUNC([stat64],
+# AC_DEFINE([HAVE_STAT64], [1], [Define if you have the stat64 function]))])
+# version 2:
+#AC_MSG_CHECKING(for struct stat64)
+#AC_CACHE_VAL(sc_cv_type_stat64,
+#[AC_TRY_COMPILE([#include <sys/stat.h>],[struct stat64 s;],
+#[sc_cv_type_stat64=yes],
+#[sc_cv_type_stat64=no])])
+#if test $sc_cv_type_stat64 = yes; then
+# AC_MSG_RESULT($sc_cv_type_stat64)
+# AC_CHECK_FUNC([stat64], AC_DEFINE([HAVE_STAT64], [1], [Define if you have the stat64 function]))
+# #AC_DEFINE(HAVE_STAT64, [1], [Define if you have the stat64 function])
+#fi
+#
+#
+# Above fails on myosin because storage size of struct 64 is unknown:
+# ssi.c:480: error: storage size of ‘s1’ isn’t known
+#
+# On my MacBook OS X 10.6 I get:
+# ssi.c:481: warning: ‘stat64’ is deprecated (declared at /usr/include/sys/stat.h:465)
+#
+# So forget about it: we won't use stat64 or define HAVE_STAT64 and
+# consequently do no tests here
+#
+
+
+
+# Add support for the Dmalloc package. If the user runs configure with
+# --with-dmalloc, then define WITH_DMALLOC and add -ldmalloc to LIBS.
+{ $as_echo "$as_me:$LINENO: checking if malloc debugging is wanted" >&5
+$as_echo_n "checking if malloc debugging is wanted... " >&6; }
+
+# Check whether --with-dmalloc was given.
+if test "${with_dmalloc+set}" = set; then
+ withval=$with_dmalloc; if test "$withval" = yes; then
+ { $as_echo "$as_me:$LINENO: result: yes" >&5
+$as_echo "yes" >&6; }
+
+cat >>confdefs.h <<\_ACEOF
+#define WITH_DMALLOC 1
+_ACEOF
+
+ LIBS="$LIBS -ldmalloc"
+ LDFLAGS="$LDFLAGS -g"
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+else
+ { $as_echo "$as_me:$LINENO: result: no" >&5
+$as_echo "no" >&6; }
+fi
+
+
+
+
+# Check if svnversion is installed
+#AC_PATH_PROG([SVNVERSION_BIN], [svnversionFIXME], [no])
+## checking if we build in a subversion WC
+#wc_found="no";
+#if test "$SVNVERSION_BIN" != "no"; then
+# SVNVERSION=`$SVNVERSION_BIN -n $srcdir`
+# if test $SVNVERSION != "exported";
+# then
+# AC_MSG_NOTICE($SVNVERSION);
+# fi
+#fi
+
+
+# --- debugging
+#
+#
+#
+{ $as_echo "$as_me:$LINENO: checking whether to build with debug information" >&5
+$as_echo_n "checking whether to build with debug information... " >&6; }
+# Check whether --enable-debug was given.
+if test "${enable_debug+set}" = set; then
+ enableval=$enable_debug; debugit="$enableval"
+else
+ debugit=no
+fi
+
+{ $as_echo "$as_me:$LINENO: result: $debugit" >&5
+$as_echo "$debugit" >&6; }
+
+if test x"$debugit" = x"yes"; then
+ # User variables CFLAGS/CXXFLAGS are used last during compilation and
+ # can therefore overwrite system settings.
+ #
+ # if debugging was requested, add debugging info at the end of
+ # C[XX]FLAGS, which makes sure previous optimisation flags are
+ # overwritten (normally C[XX]FLAGS should not be modified as they
+ # are user variables):
+ # switch off assert etc
+ # AC_DEFINE([DEBUG],[],[Debug Mode])
+ CFLAGS="${CFLAGS} -g -ansi -Wall -O0"
+ CXXFLAGS="${CXXFLAGS} -g -ansi -Wall -O0"
+else
+ # switch off assert etc
+
+cat >>confdefs.h <<\_ACEOF
+#define NDEBUG /**/
+_ACEOF
+
+ # if no debugging is requested, we make optimisation explicit
+ AM_CXXFLAGS="${AM_CXXFLAGS} -O3"
+ AM_CFLAGS="${AM_CFLAGS} -O3"
+fi
+
+
+
+
+
+
+
+
+ac_config_files="$ac_config_files Makefile src/Makefile clustalo.pc Doxyfile src/clustal/Makefile src/hhalign/Makefile src/kmpp/Makefile src/squid/Makefile"
+
+cat >confcache <<\_ACEOF
+# This file is a shell script that caches the results of configure
+# tests run on this system so they can be shared between configure
+# scripts and configure runs, see configure's option --config-cache.
+# It is not useful on other systems. If it contains results you don't
+# want to keep, you may remove or edit it.
+#
+# config.status only pays attention to the cache file if you give it
+# the --recheck option to rerun configure.
+#
+# `ac_cv_env_foo' variables (set or unset) will be overridden when
+# loading this file, other *unset* `ac_cv_foo' will be assigned the
+# following values.
+
+_ACEOF
+
+# The following way of writing the cache mishandles newlines in values,
+# but we know of no workaround that is simple, portable, and efficient.
+# So, we kill variables containing newlines.
+# Ultrix sh set writes to stderr and can't be redirected directly,
+# and sets the high bit in the cache file unless we assign to the vars.
+(
+ for ac_var in `(set) 2>&1 | sed -n 's/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'`; do
+ eval ac_val=\$$ac_var
+ case $ac_val in #(
+ *${as_nl}*)
+ case $ac_var in #(
+ *_cv_*) { $as_echo "$as_me:$LINENO: WARNING: cache variable $ac_var contains a newline" >&5
+$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
+ esac
+ case $ac_var in #(
+ _ | IFS | as_nl) ;; #(
+ BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
+ *) $as_unset $ac_var ;;
+ esac ;;
+ esac
+ done
+
+ (set) 2>&1 |
+ case $as_nl`(ac_space=' '; set) 2>&1` in #(
+ *${as_nl}ac_space=\ *)
+ # `set' does not quote correctly, so add quotes (double-quote
+ # substitution turns \\\\ into \\, and sed turns \\ into \).
+ sed -n \
+ "s/'/'\\\\''/g;
+ s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p"
+ ;; #(
+ *)
+ # `set' quotes correctly as required by POSIX, so do not add quotes.
+ sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
+ ;;
+ esac |
+ sort
+) |
+ sed '
+ /^ac_cv_env_/b end
+ t clear
+ :clear
+ s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/
+ t end
+ s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/
+ :end' >>confcache
+if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
+ if test -w "$cache_file"; then
+ test "x$cache_file" != "x/dev/null" &&
+ { $as_echo "$as_me:$LINENO: updating cache $cache_file" >&5
+$as_echo "$as_me: updating cache $cache_file" >&6;}
+ cat confcache >$cache_file
+ else
+ { $as_echo "$as_me:$LINENO: not updating unwritable cache $cache_file" >&5
+$as_echo "$as_me: not updating unwritable cache $cache_file" >&6;}
+ fi
+fi
+rm -f confcache
+
+test "x$prefix" = xNONE && prefix=$ac_default_prefix
+# Let make expand exec_prefix.
+test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'
+
+DEFS=-DHAVE_CONFIG_H
+
+ac_libobjs=
+ac_ltlibobjs=
+for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
+ # 1. Remove the extension, and $U if already installed.
+ ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
+ ac_i=`$as_echo "$ac_i" | sed "$ac_script"`
+ # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR
+ # will be set to the directory where LIBOBJS objects are built.
+ ac_libobjs="$ac_libobjs \${LIBOBJDIR}$ac_i\$U.$ac_objext"
+ ac_ltlibobjs="$ac_ltlibobjs \${LIBOBJDIR}$ac_i"'$U.lo'
+done
+LIBOBJS=$ac_libobjs
+
+LTLIBOBJS=$ac_ltlibobjs
+
+
+if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
+ { { $as_echo "$as_me:$LINENO: error: conditional \"AMDEP\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+$as_echo "$as_me: error: conditional \"AMDEP\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+ { (exit 1); exit 1; }; }
+fi
+if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
+ { { $as_echo "$as_me:$LINENO: error: conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+$as_echo "$as_me: error: conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+ { (exit 1); exit 1; }; }
+fi
+if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
+ { { $as_echo "$as_me:$LINENO: error: conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+$as_echo "$as_me: error: conditional \"am__fastdepCC\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+ { (exit 1); exit 1; }; }
+fi
+if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then
+ { { $as_echo "$as_me:$LINENO: error: conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+$as_echo "$as_me: error: conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+ { (exit 1); exit 1; }; }
+fi
+if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then
+ { { $as_echo "$as_me:$LINENO: error: conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." >&5
+$as_echo "$as_me: error: conditional \"am__fastdepCXX\" was never defined.
+Usually this means the macro was only invoked conditionally." >&2;}
+ { (exit 1); exit 1; }; }
+fi
+
+
+: ${CONFIG_STATUS=./config.status}
+ac_write_fail=0
+ac_clean_files_save=$ac_clean_files
+ac_clean_files="$ac_clean_files $CONFIG_STATUS"
+{ $as_echo "$as_me:$LINENO: creating $CONFIG_STATUS" >&5
+$as_echo "$as_me: creating $CONFIG_STATUS" >&6;}
+cat >$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+#! $SHELL
+# Generated by $as_me.
+# Run this file to recreate the current configuration.
+# Compiler output produced by configure, useful for debugging
+# configure, is in config.log if it exists.
+
+debug=false
+ac_cs_recheck=false
+ac_cs_silent=false
+SHELL=\${CONFIG_SHELL-$SHELL}
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+## --------------------- ##
+## M4sh Initialization. ##
+## --------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+ emulate sh
+ NULLCMD=:
+ # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in
+ *posix*) set -o posix ;;
+esac
+
+fi
+
+
+
+
+# PATH needs CR
+# Avoid depending upon Character Ranges.
+as_cr_letters='abcdefghijklmnopqrstuvwxyz'
+as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
+as_cr_Letters=$as_cr_letters$as_cr_LETTERS
+as_cr_digits='0123456789'
+as_cr_alnum=$as_cr_Letters$as_cr_digits
+
+as_nl='
+'
+export as_nl
+# Printing a long string crashes Solaris 7 /usr/bin/printf.
+as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
+as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
+if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
+ as_echo='printf %s\n'
+ as_echo_n='printf %s'
+else
+ if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
+ as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
+ as_echo_n='/usr/ucb/echo -n'
+ else
+ as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
+ as_echo_n_body='eval
+ arg=$1;
+ case $arg in
+ *"$as_nl"*)
+ expr "X$arg" : "X\\(.*\\)$as_nl";
+ arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
+ esac;
+ expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
+ '
+ export as_echo_n_body
+ as_echo_n='sh -c $as_echo_n_body as_echo'
+ fi
+ export as_echo_body
+ as_echo='sh -c $as_echo_body as_echo'
+fi
+
+# The user is always right.
+if test "${PATH_SEPARATOR+set}" != set; then
+ PATH_SEPARATOR=:
+ (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
+ (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
+ PATH_SEPARATOR=';'
+ }
+fi
+
+# Support unset when possible.
+if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
+ as_unset=unset
+else
+ as_unset=false
+fi
+
+
+# IFS
+# We need space, tab and new line, in precisely that order. Quoting is
+# there to prevent editors from complaining about space-tab.
+# (If _AS_PATH_WALK were called with IFS unset, it would disable word
+# splitting by setting IFS to empty value.)
+IFS=" "" $as_nl"
+
+# Find who we are. Look in the path if we contain no directory separator.
+case $0 in
+ *[\\/]* ) as_myself=$0 ;;
+ *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
+done
+IFS=$as_save_IFS
+
+ ;;
+esac
+# We did not find ourselves, most probably we were run as `sh COMMAND'
+# in which case we are not to be found in the path.
+if test "x$as_myself" = x; then
+ as_myself=$0
+fi
+if test ! -f "$as_myself"; then
+ $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
+ { (exit 1); exit 1; }
+fi
+
+# Work around bugs in pre-3.0 UWIN ksh.
+for as_var in ENV MAIL MAILPATH
+do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var
+done
+PS1='$ '
+PS2='> '
+PS4='+ '
+
+# NLS nuisances.
+LC_ALL=C
+export LC_ALL
+LANGUAGE=C
+export LANGUAGE
+
+# Required to use basename.
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
+ as_basename=basename
+else
+ as_basename=false
+fi
+
+
+# Name of the executable.
+as_me=`$as_basename -- "$0" ||
+$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
+ X"$0" : 'X\(//\)$' \| \
+ X"$0" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X/"$0" |
+ sed '/^.*\/\([^/][^/]*\)\/*$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\/\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+
+# CDPATH.
+$as_unset CDPATH
+
+
+
+ as_lineno_1=$LINENO
+ as_lineno_2=$LINENO
+ test "x$as_lineno_1" != "x$as_lineno_2" &&
+ test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || {
+
+ # Create $as_me.lineno as a copy of $as_myself, but with $LINENO
+ # uniformly replaced by the line number. The first 'sed' inserts a
+ # line-number line after each line using $LINENO; the second 'sed'
+ # does the real work. The second script uses 'N' to pair each
+ # line-number line with the line containing $LINENO, and appends
+ # trailing '-' during substitution so that $LINENO is not a special
+ # case at line end.
+ # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the
+ # scripts with optimization help from Paolo Bonzini. Blame Lee
+ # E. McMahon (1931-1989) for sed's syntax. :-)
+ sed -n '
+ p
+ /[$]LINENO/=
+ ' <$as_myself |
+ sed '
+ s/[$]LINENO.*/&-/
+ t lineno
+ b
+ :lineno
+ N
+ :loop
+ s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
+ t loop
+ s/-\n.*//
+ ' >$as_me.lineno &&
+ chmod +x "$as_me.lineno" ||
+ { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2
+ { (exit 1); exit 1; }; }
+
+ # Don't try to exec as it changes $[0], causing all sort of problems
+ # (the dirname of $[0] is not the place where we might find the
+ # original and so on. Autoconf is especially sensitive to this).
+ . "./$as_me.lineno"
+ # Exit status is that of the last command.
+ exit
+}
+
+
+if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
+ as_dirname=dirname
+else
+ as_dirname=false
+fi
+
+ECHO_C= ECHO_N= ECHO_T=
+case `echo -n x` in
+-n*)
+ case `echo 'x\c'` in
+ *c*) ECHO_T=' ';; # ECHO_T is single tab character.
+ *) ECHO_C='\c';;
+ esac;;
+*)
+ ECHO_N='-n';;
+esac
+if expr a : '\(a\)' >/dev/null 2>&1 &&
+ test "X`expr 00001 : '.*\(...\)'`" = X001; then
+ as_expr=expr
+else
+ as_expr=false
+fi
+
+rm -f conf$$ conf$$.exe conf$$.file
+if test -d conf$$.dir; then
+ rm -f conf$$.dir/conf$$.file
+else
+ rm -f conf$$.dir
+ mkdir conf$$.dir 2>/dev/null
+fi
+if (echo >conf$$.file) 2>/dev/null; then
+ if ln -s conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s='ln -s'
+ # ... but there are two gotchas:
+ # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
+ # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
+ # In both cases, we have to default to `cp -p'.
+ ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
+ as_ln_s='cp -p'
+ elif ln conf$$.file conf$$ 2>/dev/null; then
+ as_ln_s=ln
+ else
+ as_ln_s='cp -p'
+ fi
+else
+ as_ln_s='cp -p'
+fi
+rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
+rmdir conf$$.dir 2>/dev/null
+
+if mkdir -p . 2>/dev/null; then
+ as_mkdir_p=:
+else
+ test -d ./-p && rmdir ./-p
+ as_mkdir_p=false
+fi
+
+if test -x / >/dev/null 2>&1; then
+ as_test_x='test -x'
+else
+ if ls -dL / >/dev/null 2>&1; then
+ as_ls_L_option=L
+ else
+ as_ls_L_option=
+ fi
+ as_test_x='
+ eval sh -c '\''
+ if test -d "$1"; then
+ test -d "$1/.";
+ else
+ case $1 in
+ -*)set "./$1";;
+ esac;
+ case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in
+ ???[sx]*):;;*)false;;esac;fi
+ '\'' sh
+ '
+fi
+as_executable_p=$as_test_x
+
+# Sed expression to map a string onto a valid CPP name.
+as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
+
+# Sed expression to map a string onto a valid variable name.
+as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
+
+
+exec 6>&1
+
+# Save the log message, to keep $[0] and so on meaningful, and to
+# report actual input values of CONFIG_FILES etc. instead of their
+# values after options handling.
+ac_log="
+This file was extended by Clustal Omega $as_me 1.0.2, which was
+generated by GNU Autoconf 2.63. Invocation command line was
+
+ CONFIG_FILES = $CONFIG_FILES
+ CONFIG_HEADERS = $CONFIG_HEADERS
+ CONFIG_LINKS = $CONFIG_LINKS
+ CONFIG_COMMANDS = $CONFIG_COMMANDS
+ $ $0 $@
+
+on `(hostname || uname -n) 2>/dev/null | sed 1q`
+"
+
+_ACEOF
+
+case $ac_config_files in *"
+"*) set x $ac_config_files; shift; ac_config_files=$*;;
+esac
+
+case $ac_config_headers in *"
+"*) set x $ac_config_headers; shift; ac_config_headers=$*;;
+esac
+
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+# Files that config.status was made for.
+config_files="$ac_config_files"
+config_headers="$ac_config_headers"
+config_commands="$ac_config_commands"
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+ac_cs_usage="\
+\`$as_me' instantiates files from templates according to the
+current configuration.
+
+Usage: $0 [OPTION]... [FILE]...
+
+ -h, --help print this help, then exit
+ -V, --version print version number and configuration settings, then exit
+ -q, --quiet, --silent
+ do not print progress messages
+ -d, --debug don't remove temporary files
+ --recheck update $as_me by reconfiguring in the same conditions
+ --file=FILE[:TEMPLATE]
+ instantiate the configuration file FILE
+ --header=FILE[:TEMPLATE]
+ instantiate the configuration header FILE
+
+Configuration files:
+$config_files
+
+Configuration headers:
+$config_headers
+
+Configuration commands:
+$config_commands
+
+Report bugs to <bug-autoconf@gnu.org>."
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ac_cs_version="\\
+Clustal Omega config.status 1.0.2
+configured by $0, generated by GNU Autoconf 2.63,
+ with options \\"`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\"
+
+Copyright (C) 2008 Free Software Foundation, Inc.
+This config.status script is free software; the Free Software Foundation
+gives unlimited permission to copy, distribute and modify it."
+
+ac_pwd='$ac_pwd'
+srcdir='$srcdir'
+INSTALL='$INSTALL'
+MKDIR_P='$MKDIR_P'
+AWK='$AWK'
+test -n "\$AWK" || AWK=awk
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+# The default lists apply if the user does not specify any file.
+ac_need_defaults=:
+while test $# != 0
+do
+ case $1 in
+ --*=*)
+ ac_option=`expr "X$1" : 'X\([^=]*\)='`
+ ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
+ ac_shift=:
+ ;;
+ *)
+ ac_option=$1
+ ac_optarg=$2
+ ac_shift=shift
+ ;;
+ esac
+
+ case $ac_option in
+ # Handling of the options.
+ -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
+ ac_cs_recheck=: ;;
+ --version | --versio | --versi | --vers | --ver | --ve | --v | -V )
+ $as_echo "$ac_cs_version"; exit ;;
+ --debug | --debu | --deb | --de | --d | -d )
+ debug=: ;;
+ --file | --fil | --fi | --f )
+ $ac_shift
+ case $ac_optarg in
+ *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ CONFIG_FILES="$CONFIG_FILES '$ac_optarg'"
+ ac_need_defaults=false;;
+ --header | --heade | --head | --hea )
+ $ac_shift
+ case $ac_optarg in
+ *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
+ esac
+ CONFIG_HEADERS="$CONFIG_HEADERS '$ac_optarg'"
+ ac_need_defaults=false;;
+ --he | --h)
+ # Conflict between --help and --header
+ { $as_echo "$as_me: error: ambiguous option: $1
+Try \`$0 --help' for more information." >&2
+ { (exit 1); exit 1; }; };;
+ --help | --hel | -h )
+ $as_echo "$ac_cs_usage"; exit ;;
+ -q | -quiet | --quiet | --quie | --qui | --qu | --q \
+ | -silent | --silent | --silen | --sile | --sil | --si | --s)
+ ac_cs_silent=: ;;
+
+ # This is an error.
+ -*) { $as_echo "$as_me: error: unrecognized option: $1
+Try \`$0 --help' for more information." >&2
+ { (exit 1); exit 1; }; } ;;
+
+ *) ac_config_targets="$ac_config_targets $1"
+ ac_need_defaults=false ;;
+
+ esac
+ shift
+done
+
+ac_configure_extra_args=
+
+if $ac_cs_silent; then
+ exec 6>/dev/null
+ ac_configure_extra_args="$ac_configure_extra_args --silent"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+if \$ac_cs_recheck; then
+ set X '$SHELL' '$0' $ac_configure_args \$ac_configure_extra_args --no-create --no-recursion
+ shift
+ \$as_echo "running CONFIG_SHELL=$SHELL \$*" >&6
+ CONFIG_SHELL='$SHELL'
+ export CONFIG_SHELL
+ exec "\$@"
+fi
+
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+exec 5>>config.log
+{
+ echo
+ sed 'h;s/./-/g;s/^.../## /;s/...$/ ##/;p;x;p;x' <<_ASBOX
+## Running $as_me. ##
+_ASBOX
+ $as_echo "$ac_log"
+} >&5
+
+_ACEOF
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+#
+# INIT-COMMANDS
+#
+PACKAGE="$PACKAGE"
+AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"
+
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+sed_quote_subst='$sed_quote_subst'
+double_quote_subst='$double_quote_subst'
+delay_variable_subst='$delay_variable_subst'
+macro_version='`$ECHO "X$macro_version" | $Xsed -e "$delay_single_quote_subst"`'
+macro_revision='`$ECHO "X$macro_revision" | $Xsed -e "$delay_single_quote_subst"`'
+enable_shared='`$ECHO "X$enable_shared" | $Xsed -e "$delay_single_quote_subst"`'
+enable_static='`$ECHO "X$enable_static" | $Xsed -e "$delay_single_quote_subst"`'
+pic_mode='`$ECHO "X$pic_mode" | $Xsed -e "$delay_single_quote_subst"`'
+enable_fast_install='`$ECHO "X$enable_fast_install" | $Xsed -e "$delay_single_quote_subst"`'
+host_alias='`$ECHO "X$host_alias" | $Xsed -e "$delay_single_quote_subst"`'
+host='`$ECHO "X$host" | $Xsed -e "$delay_single_quote_subst"`'
+host_os='`$ECHO "X$host_os" | $Xsed -e "$delay_single_quote_subst"`'
+build_alias='`$ECHO "X$build_alias" | $Xsed -e "$delay_single_quote_subst"`'
+build='`$ECHO "X$build" | $Xsed -e "$delay_single_quote_subst"`'
+build_os='`$ECHO "X$build_os" | $Xsed -e "$delay_single_quote_subst"`'
+SED='`$ECHO "X$SED" | $Xsed -e "$delay_single_quote_subst"`'
+Xsed='`$ECHO "X$Xsed" | $Xsed -e "$delay_single_quote_subst"`'
+GREP='`$ECHO "X$GREP" | $Xsed -e "$delay_single_quote_subst"`'
+EGREP='`$ECHO "X$EGREP" | $Xsed -e "$delay_single_quote_subst"`'
+FGREP='`$ECHO "X$FGREP" | $Xsed -e "$delay_single_quote_subst"`'
+LD='`$ECHO "X$LD" | $Xsed -e "$delay_single_quote_subst"`'
+NM='`$ECHO "X$NM" | $Xsed -e "$delay_single_quote_subst"`'
+LN_S='`$ECHO "X$LN_S" | $Xsed -e "$delay_single_quote_subst"`'
+max_cmd_len='`$ECHO "X$max_cmd_len" | $Xsed -e "$delay_single_quote_subst"`'
+ac_objext='`$ECHO "X$ac_objext" | $Xsed -e "$delay_single_quote_subst"`'
+exeext='`$ECHO "X$exeext" | $Xsed -e "$delay_single_quote_subst"`'
+lt_unset='`$ECHO "X$lt_unset" | $Xsed -e "$delay_single_quote_subst"`'
+lt_SP2NL='`$ECHO "X$lt_SP2NL" | $Xsed -e "$delay_single_quote_subst"`'
+lt_NL2SP='`$ECHO "X$lt_NL2SP" | $Xsed -e "$delay_single_quote_subst"`'
+reload_flag='`$ECHO "X$reload_flag" | $Xsed -e "$delay_single_quote_subst"`'
+reload_cmds='`$ECHO "X$reload_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+OBJDUMP='`$ECHO "X$OBJDUMP" | $Xsed -e "$delay_single_quote_subst"`'
+deplibs_check_method='`$ECHO "X$deplibs_check_method" | $Xsed -e "$delay_single_quote_subst"`'
+file_magic_cmd='`$ECHO "X$file_magic_cmd" | $Xsed -e "$delay_single_quote_subst"`'
+AR='`$ECHO "X$AR" | $Xsed -e "$delay_single_quote_subst"`'
+AR_FLAGS='`$ECHO "X$AR_FLAGS" | $Xsed -e "$delay_single_quote_subst"`'
+STRIP='`$ECHO "X$STRIP" | $Xsed -e "$delay_single_quote_subst"`'
+RANLIB='`$ECHO "X$RANLIB" | $Xsed -e "$delay_single_quote_subst"`'
+old_postinstall_cmds='`$ECHO "X$old_postinstall_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+old_postuninstall_cmds='`$ECHO "X$old_postuninstall_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_cmds='`$ECHO "X$old_archive_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+CC='`$ECHO "X$CC" | $Xsed -e "$delay_single_quote_subst"`'
+CFLAGS='`$ECHO "X$CFLAGS" | $Xsed -e "$delay_single_quote_subst"`'
+compiler='`$ECHO "X$compiler" | $Xsed -e "$delay_single_quote_subst"`'
+GCC='`$ECHO "X$GCC" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_sys_global_symbol_pipe='`$ECHO "X$lt_cv_sys_global_symbol_pipe" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_sys_global_symbol_to_cdecl='`$ECHO "X$lt_cv_sys_global_symbol_to_cdecl" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_sys_global_symbol_to_c_name_address='`$ECHO "X$lt_cv_sys_global_symbol_to_c_name_address" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='`$ECHO "X$lt_cv_sys_global_symbol_to_c_name_address_lib_prefix" | $Xsed -e "$delay_single_quote_subst"`'
+objdir='`$ECHO "X$objdir" | $Xsed -e "$delay_single_quote_subst"`'
+SHELL='`$ECHO "X$SHELL" | $Xsed -e "$delay_single_quote_subst"`'
+ECHO='`$ECHO "X$ECHO" | $Xsed -e "$delay_single_quote_subst"`'
+MAGIC_CMD='`$ECHO "X$MAGIC_CMD" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_no_builtin_flag='`$ECHO "X$lt_prog_compiler_no_builtin_flag" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_wl='`$ECHO "X$lt_prog_compiler_wl" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_pic='`$ECHO "X$lt_prog_compiler_pic" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_static='`$ECHO "X$lt_prog_compiler_static" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_prog_compiler_c_o='`$ECHO "X$lt_cv_prog_compiler_c_o" | $Xsed -e "$delay_single_quote_subst"`'
+need_locks='`$ECHO "X$need_locks" | $Xsed -e "$delay_single_quote_subst"`'
+DSYMUTIL='`$ECHO "X$DSYMUTIL" | $Xsed -e "$delay_single_quote_subst"`'
+NMEDIT='`$ECHO "X$NMEDIT" | $Xsed -e "$delay_single_quote_subst"`'
+LIPO='`$ECHO "X$LIPO" | $Xsed -e "$delay_single_quote_subst"`'
+OTOOL='`$ECHO "X$OTOOL" | $Xsed -e "$delay_single_quote_subst"`'
+OTOOL64='`$ECHO "X$OTOOL64" | $Xsed -e "$delay_single_quote_subst"`'
+libext='`$ECHO "X$libext" | $Xsed -e "$delay_single_quote_subst"`'
+shrext_cmds='`$ECHO "X$shrext_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+extract_expsyms_cmds='`$ECHO "X$extract_expsyms_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+archive_cmds_need_lc='`$ECHO "X$archive_cmds_need_lc" | $Xsed -e "$delay_single_quote_subst"`'
+enable_shared_with_static_runtimes='`$ECHO "X$enable_shared_with_static_runtimes" | $Xsed -e "$delay_single_quote_subst"`'
+export_dynamic_flag_spec='`$ECHO "X$export_dynamic_flag_spec" | $Xsed -e "$delay_single_quote_subst"`'
+whole_archive_flag_spec='`$ECHO "X$whole_archive_flag_spec" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_needs_object='`$ECHO "X$compiler_needs_object" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_from_new_cmds='`$ECHO "X$old_archive_from_new_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_from_expsyms_cmds='`$ECHO "X$old_archive_from_expsyms_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+archive_cmds='`$ECHO "X$archive_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+archive_expsym_cmds='`$ECHO "X$archive_expsym_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+module_cmds='`$ECHO "X$module_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+module_expsym_cmds='`$ECHO "X$module_expsym_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+with_gnu_ld='`$ECHO "X$with_gnu_ld" | $Xsed -e "$delay_single_quote_subst"`'
+allow_undefined_flag='`$ECHO "X$allow_undefined_flag" | $Xsed -e "$delay_single_quote_subst"`'
+no_undefined_flag='`$ECHO "X$no_undefined_flag" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_flag_spec='`$ECHO "X$hardcode_libdir_flag_spec" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_flag_spec_ld='`$ECHO "X$hardcode_libdir_flag_spec_ld" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_separator='`$ECHO "X$hardcode_libdir_separator" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_direct='`$ECHO "X$hardcode_direct" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_direct_absolute='`$ECHO "X$hardcode_direct_absolute" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_minus_L='`$ECHO "X$hardcode_minus_L" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_shlibpath_var='`$ECHO "X$hardcode_shlibpath_var" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_automatic='`$ECHO "X$hardcode_automatic" | $Xsed -e "$delay_single_quote_subst"`'
+inherit_rpath='`$ECHO "X$inherit_rpath" | $Xsed -e "$delay_single_quote_subst"`'
+link_all_deplibs='`$ECHO "X$link_all_deplibs" | $Xsed -e "$delay_single_quote_subst"`'
+fix_srcfile_path='`$ECHO "X$fix_srcfile_path" | $Xsed -e "$delay_single_quote_subst"`'
+always_export_symbols='`$ECHO "X$always_export_symbols" | $Xsed -e "$delay_single_quote_subst"`'
+export_symbols_cmds='`$ECHO "X$export_symbols_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+exclude_expsyms='`$ECHO "X$exclude_expsyms" | $Xsed -e "$delay_single_quote_subst"`'
+include_expsyms='`$ECHO "X$include_expsyms" | $Xsed -e "$delay_single_quote_subst"`'
+prelink_cmds='`$ECHO "X$prelink_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+file_list_spec='`$ECHO "X$file_list_spec" | $Xsed -e "$delay_single_quote_subst"`'
+variables_saved_for_relink='`$ECHO "X$variables_saved_for_relink" | $Xsed -e "$delay_single_quote_subst"`'
+need_lib_prefix='`$ECHO "X$need_lib_prefix" | $Xsed -e "$delay_single_quote_subst"`'
+need_version='`$ECHO "X$need_version" | $Xsed -e "$delay_single_quote_subst"`'
+version_type='`$ECHO "X$version_type" | $Xsed -e "$delay_single_quote_subst"`'
+runpath_var='`$ECHO "X$runpath_var" | $Xsed -e "$delay_single_quote_subst"`'
+shlibpath_var='`$ECHO "X$shlibpath_var" | $Xsed -e "$delay_single_quote_subst"`'
+shlibpath_overrides_runpath='`$ECHO "X$shlibpath_overrides_runpath" | $Xsed -e "$delay_single_quote_subst"`'
+libname_spec='`$ECHO "X$libname_spec" | $Xsed -e "$delay_single_quote_subst"`'
+library_names_spec='`$ECHO "X$library_names_spec" | $Xsed -e "$delay_single_quote_subst"`'
+soname_spec='`$ECHO "X$soname_spec" | $Xsed -e "$delay_single_quote_subst"`'
+postinstall_cmds='`$ECHO "X$postinstall_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+postuninstall_cmds='`$ECHO "X$postuninstall_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+finish_cmds='`$ECHO "X$finish_cmds" | $Xsed -e "$delay_single_quote_subst"`'
+finish_eval='`$ECHO "X$finish_eval" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_into_libs='`$ECHO "X$hardcode_into_libs" | $Xsed -e "$delay_single_quote_subst"`'
+sys_lib_search_path_spec='`$ECHO "X$sys_lib_search_path_spec" | $Xsed -e "$delay_single_quote_subst"`'
+sys_lib_dlsearch_path_spec='`$ECHO "X$sys_lib_dlsearch_path_spec" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_action='`$ECHO "X$hardcode_action" | $Xsed -e "$delay_single_quote_subst"`'
+enable_dlopen='`$ECHO "X$enable_dlopen" | $Xsed -e "$delay_single_quote_subst"`'
+enable_dlopen_self='`$ECHO "X$enable_dlopen_self" | $Xsed -e "$delay_single_quote_subst"`'
+enable_dlopen_self_static='`$ECHO "X$enable_dlopen_self_static" | $Xsed -e "$delay_single_quote_subst"`'
+old_striplib='`$ECHO "X$old_striplib" | $Xsed -e "$delay_single_quote_subst"`'
+striplib='`$ECHO "X$striplib" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_lib_search_dirs='`$ECHO "X$compiler_lib_search_dirs" | $Xsed -e "$delay_single_quote_subst"`'
+predep_objects='`$ECHO "X$predep_objects" | $Xsed -e "$delay_single_quote_subst"`'
+postdep_objects='`$ECHO "X$postdep_objects" | $Xsed -e "$delay_single_quote_subst"`'
+predeps='`$ECHO "X$predeps" | $Xsed -e "$delay_single_quote_subst"`'
+postdeps='`$ECHO "X$postdeps" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_lib_search_path='`$ECHO "X$compiler_lib_search_path" | $Xsed -e "$delay_single_quote_subst"`'
+LD_CXX='`$ECHO "X$LD_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_cmds_CXX='`$ECHO "X$old_archive_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_CXX='`$ECHO "X$compiler_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+GCC_CXX='`$ECHO "X$GCC_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_no_builtin_flag_CXX='`$ECHO "X$lt_prog_compiler_no_builtin_flag_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_wl_CXX='`$ECHO "X$lt_prog_compiler_wl_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_pic_CXX='`$ECHO "X$lt_prog_compiler_pic_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_prog_compiler_static_CXX='`$ECHO "X$lt_prog_compiler_static_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+lt_cv_prog_compiler_c_o_CXX='`$ECHO "X$lt_cv_prog_compiler_c_o_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+archive_cmds_need_lc_CXX='`$ECHO "X$archive_cmds_need_lc_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+enable_shared_with_static_runtimes_CXX='`$ECHO "X$enable_shared_with_static_runtimes_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+export_dynamic_flag_spec_CXX='`$ECHO "X$export_dynamic_flag_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+whole_archive_flag_spec_CXX='`$ECHO "X$whole_archive_flag_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_needs_object_CXX='`$ECHO "X$compiler_needs_object_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_from_new_cmds_CXX='`$ECHO "X$old_archive_from_new_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+old_archive_from_expsyms_cmds_CXX='`$ECHO "X$old_archive_from_expsyms_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+archive_cmds_CXX='`$ECHO "X$archive_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+archive_expsym_cmds_CXX='`$ECHO "X$archive_expsym_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+module_cmds_CXX='`$ECHO "X$module_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+module_expsym_cmds_CXX='`$ECHO "X$module_expsym_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+with_gnu_ld_CXX='`$ECHO "X$with_gnu_ld_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+allow_undefined_flag_CXX='`$ECHO "X$allow_undefined_flag_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+no_undefined_flag_CXX='`$ECHO "X$no_undefined_flag_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_flag_spec_CXX='`$ECHO "X$hardcode_libdir_flag_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_flag_spec_ld_CXX='`$ECHO "X$hardcode_libdir_flag_spec_ld_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_libdir_separator_CXX='`$ECHO "X$hardcode_libdir_separator_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_direct_CXX='`$ECHO "X$hardcode_direct_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_direct_absolute_CXX='`$ECHO "X$hardcode_direct_absolute_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_minus_L_CXX='`$ECHO "X$hardcode_minus_L_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_shlibpath_var_CXX='`$ECHO "X$hardcode_shlibpath_var_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_automatic_CXX='`$ECHO "X$hardcode_automatic_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+inherit_rpath_CXX='`$ECHO "X$inherit_rpath_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+link_all_deplibs_CXX='`$ECHO "X$link_all_deplibs_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+fix_srcfile_path_CXX='`$ECHO "X$fix_srcfile_path_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+always_export_symbols_CXX='`$ECHO "X$always_export_symbols_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+export_symbols_cmds_CXX='`$ECHO "X$export_symbols_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+exclude_expsyms_CXX='`$ECHO "X$exclude_expsyms_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+include_expsyms_CXX='`$ECHO "X$include_expsyms_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+prelink_cmds_CXX='`$ECHO "X$prelink_cmds_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+file_list_spec_CXX='`$ECHO "X$file_list_spec_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+hardcode_action_CXX='`$ECHO "X$hardcode_action_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_lib_search_dirs_CXX='`$ECHO "X$compiler_lib_search_dirs_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+predep_objects_CXX='`$ECHO "X$predep_objects_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+postdep_objects_CXX='`$ECHO "X$postdep_objects_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+predeps_CXX='`$ECHO "X$predeps_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+postdeps_CXX='`$ECHO "X$postdeps_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+compiler_lib_search_path_CXX='`$ECHO "X$compiler_lib_search_path_CXX" | $Xsed -e "$delay_single_quote_subst"`'
+
+LTCC='$LTCC'
+LTCFLAGS='$LTCFLAGS'
+compiler='$compiler_DEFAULT'
+
+# Quote evaled strings.
+for var in SED \
+GREP \
+EGREP \
+FGREP \
+LD \
+NM \
+LN_S \
+lt_SP2NL \
+lt_NL2SP \
+reload_flag \
+OBJDUMP \
+deplibs_check_method \
+file_magic_cmd \
+AR \
+AR_FLAGS \
+STRIP \
+RANLIB \
+CC \
+CFLAGS \
+compiler \
+lt_cv_sys_global_symbol_pipe \
+lt_cv_sys_global_symbol_to_cdecl \
+lt_cv_sys_global_symbol_to_c_name_address \
+lt_cv_sys_global_symbol_to_c_name_address_lib_prefix \
+SHELL \
+ECHO \
+lt_prog_compiler_no_builtin_flag \
+lt_prog_compiler_wl \
+lt_prog_compiler_pic \
+lt_prog_compiler_static \
+lt_cv_prog_compiler_c_o \
+need_locks \
+DSYMUTIL \
+NMEDIT \
+LIPO \
+OTOOL \
+OTOOL64 \
+shrext_cmds \
+export_dynamic_flag_spec \
+whole_archive_flag_spec \
+compiler_needs_object \
+with_gnu_ld \
+allow_undefined_flag \
+no_undefined_flag \
+hardcode_libdir_flag_spec \
+hardcode_libdir_flag_spec_ld \
+hardcode_libdir_separator \
+fix_srcfile_path \
+exclude_expsyms \
+include_expsyms \
+file_list_spec \
+variables_saved_for_relink \
+libname_spec \
+library_names_spec \
+soname_spec \
+finish_eval \
+old_striplib \
+striplib \
+compiler_lib_search_dirs \
+predep_objects \
+postdep_objects \
+predeps \
+postdeps \
+compiler_lib_search_path \
+LD_CXX \
+compiler_CXX \
+lt_prog_compiler_no_builtin_flag_CXX \
+lt_prog_compiler_wl_CXX \
+lt_prog_compiler_pic_CXX \
+lt_prog_compiler_static_CXX \
+lt_cv_prog_compiler_c_o_CXX \
+export_dynamic_flag_spec_CXX \
+whole_archive_flag_spec_CXX \
+compiler_needs_object_CXX \
+with_gnu_ld_CXX \
+allow_undefined_flag_CXX \
+no_undefined_flag_CXX \
+hardcode_libdir_flag_spec_CXX \
+hardcode_libdir_flag_spec_ld_CXX \
+hardcode_libdir_separator_CXX \
+fix_srcfile_path_CXX \
+exclude_expsyms_CXX \
+include_expsyms_CXX \
+file_list_spec_CXX \
+compiler_lib_search_dirs_CXX \
+predep_objects_CXX \
+postdep_objects_CXX \
+predeps_CXX \
+postdeps_CXX \
+compiler_lib_search_path_CXX; do
+ case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in
+ *[\\\\\\\`\\"\\\$]*)
+ eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$sed_quote_subst\\"\\\`\\\\\\""
+ ;;
+ *)
+ eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\""
+ ;;
+ esac
+done
+
+# Double-quote double-evaled strings.
+for var in reload_cmds \
+old_postinstall_cmds \
+old_postuninstall_cmds \
+old_archive_cmds \
+extract_expsyms_cmds \
+old_archive_from_new_cmds \
+old_archive_from_expsyms_cmds \
+archive_cmds \
+archive_expsym_cmds \
+module_cmds \
+module_expsym_cmds \
+export_symbols_cmds \
+prelink_cmds \
+postinstall_cmds \
+postuninstall_cmds \
+finish_cmds \
+sys_lib_search_path_spec \
+sys_lib_dlsearch_path_spec \
+old_archive_cmds_CXX \
+old_archive_from_new_cmds_CXX \
+old_archive_from_expsyms_cmds_CXX \
+archive_cmds_CXX \
+archive_expsym_cmds_CXX \
+module_cmds_CXX \
+module_expsym_cmds_CXX \
+export_symbols_cmds_CXX \
+prelink_cmds_CXX; do
+ case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in
+ *[\\\\\\\`\\"\\\$]*)
+ eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$double_quote_subst\\" -e \\"\\\$sed_quote_subst\\" -e \\"\\\$delay_variable_subst\\"\\\`\\\\\\""
+ ;;
+ *)
+ eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\""
+ ;;
+ esac
+done
+
+# Fix-up fallback echo if it was mangled by the above quoting rules.
+case \$lt_ECHO in
+*'\\\$0 --fallback-echo"') lt_ECHO=\`\$ECHO "X\$lt_ECHO" | \$Xsed -e 's/\\\\\\\\\\\\\\\$0 --fallback-echo"\$/\$0 --fallback-echo"/'\`
+ ;;
+esac
+
+ac_aux_dir='$ac_aux_dir'
+xsi_shell='$xsi_shell'
+lt_shell_append='$lt_shell_append'
+
+# See if we are running on zsh, and set the options which allow our
+# commands through without removal of \ escapes INIT.
+if test -n "\${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+fi
+
+
+ PACKAGE='$PACKAGE'
+ VERSION='$VERSION'
+ TIMESTAMP='$TIMESTAMP'
+ RM='$RM'
+ ofile='$ofile'
+
+
+
+
+
+
+_ACEOF
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+
+# Handling of arguments.
+for ac_config_target in $ac_config_targets
+do
+ case $ac_config_target in
+ "src/config.h") CONFIG_HEADERS="$CONFIG_HEADERS src/config.h" ;;
+ "src/clustal-omega-config.h") CONFIG_COMMANDS="$CONFIG_COMMANDS src/clustal-omega-config.h" ;;
+ "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
+ "libtool") CONFIG_COMMANDS="$CONFIG_COMMANDS libtool" ;;
+ "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
+ "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
+ "clustalo.pc") CONFIG_FILES="$CONFIG_FILES clustalo.pc" ;;
+ "Doxyfile") CONFIG_FILES="$CONFIG_FILES Doxyfile" ;;
+ "src/clustal/Makefile") CONFIG_FILES="$CONFIG_FILES src/clustal/Makefile" ;;
+ "src/hhalign/Makefile") CONFIG_FILES="$CONFIG_FILES src/hhalign/Makefile" ;;
+ "src/kmpp/Makefile") CONFIG_FILES="$CONFIG_FILES src/kmpp/Makefile" ;;
+ "src/squid/Makefile") CONFIG_FILES="$CONFIG_FILES src/squid/Makefile" ;;
+
+ *) { { $as_echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5
+$as_echo "$as_me: error: invalid argument: $ac_config_target" >&2;}
+ { (exit 1); exit 1; }; };;
+ esac
+done
+
+
+# If the user did not use the arguments to specify the items to instantiate,
+# then the envvar interface is used. Set only those that are not.
+# We use the long form for the default assignment because of an extremely
+# bizarre bug on SunOS 4.1.3.
+if $ac_need_defaults; then
+ test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files
+ test "${CONFIG_HEADERS+set}" = set || CONFIG_HEADERS=$config_headers
+ test "${CONFIG_COMMANDS+set}" = set || CONFIG_COMMANDS=$config_commands
+fi
+
+# Have a temporary directory for convenience. Make it in the build tree
+# simply because there is no reason against having it here, and in addition,
+# creating and moving files from /tmp can sometimes cause problems.
+# Hook for its removal unless debugging.
+# Note that there is a small window in which the directory will not be cleaned:
+# after its creation but before its name has been assigned to `$tmp'.
+$debug ||
+{
+ tmp=
+ trap 'exit_status=$?
+ { test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status
+' 0
+ trap '{ (exit 1); exit 1; }' 1 2 13 15
+}
+# Create a (secure) tmp directory for tmp files.
+
+{
+ tmp=`(umask 077 && mktemp -d "./confXXXXXX") 2>/dev/null` &&
+ test -n "$tmp" && test -d "$tmp"
+} ||
+{
+ tmp=./conf$$-$RANDOM
+ (umask 077 && mkdir "$tmp")
+} ||
+{
+ $as_echo "$as_me: cannot create a temporary directory in ." >&2
+ { (exit 1); exit 1; }
+}
+
+# Set up the scripts for CONFIG_FILES section.
+# No need to generate them if there are no CONFIG_FILES.
+# This happens for instance with `./config.status config.h'.
+if test -n "$CONFIG_FILES"; then
+
+
+ac_cr='\r'
+ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
+if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
+ ac_cs_awk_cr='\\r'
+else
+ ac_cs_awk_cr=$ac_cr
+fi
+
+echo 'BEGIN {' >"$tmp/subs1.awk" &&
+_ACEOF
+
+
+{
+ echo "cat >conf$$subs.awk <<_ACEOF" &&
+ echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' &&
+ echo "_ACEOF"
+} >conf$$subs.sh ||
+ { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
+$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;}
+ { (exit 1); exit 1; }; }
+ac_delim_num=`echo "$ac_subst_vars" | grep -c '$'`
+ac_delim='%!_!# '
+for ac_last_try in false false false false false :; do
+ . ./conf$$subs.sh ||
+ { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
+$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;}
+ { (exit 1); exit 1; }; }
+
+ ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
+ if test $ac_delim_n = $ac_delim_num; then
+ break
+ elif $ac_last_try; then
+ { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5
+$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;}
+ { (exit 1); exit 1; }; }
+ else
+ ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
+ fi
+done
+rm -f conf$$subs.sh
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+cat >>"\$tmp/subs1.awk" <<\\_ACAWK &&
+_ACEOF
+sed -n '
+h
+s/^/S["/; s/!.*/"]=/
+p
+g
+s/^[^!]*!//
+:repl
+t repl
+s/'"$ac_delim"'$//
+t delim
+:nl
+h
+s/\(.\{148\}\).*/\1/
+t more1
+s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/
+p
+n
+b repl
+:more1
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t nl
+:delim
+h
+s/\(.\{148\}\).*/\1/
+t more2
+s/["\\]/\\&/g; s/^/"/; s/$/"/
+p
+b
+:more2
+s/["\\]/\\&/g; s/^/"/; s/$/"\\/
+p
+g
+s/.\{148\}//
+t delim
+' <conf$$subs.awk | sed '
+/^[^""]/{
+ N
+ s/\n//
+}
+' >>$CONFIG_STATUS || ac_write_fail=1
+rm -f conf$$subs.awk
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+_ACAWK
+cat >>"\$tmp/subs1.awk" <<_ACAWK &&
+ for (key in S) S_is_set[key] = 1
+ FS = "\a"
+
+}
+{
+ line = $ 0
+ nfields = split(line, field, "@")
+ substed = 0
+ len = length(field[1])
+ for (i = 2; i < nfields; i++) {
+ key = field[i]
+ keylen = length(key)
+ if (S_is_set[key]) {
+ value = S[key]
+ line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3)
+ len += length(value) + length(field[++i])
+ substed = 1
+ } else
+ len += 1 + keylen
+ }
+
+ print line
+}
+
+_ACAWK
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then
+ sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g"
+else
+ cat
+fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \
+ || { { $as_echo "$as_me:$LINENO: error: could not setup config files machinery" >&5
+$as_echo "$as_me: error: could not setup config files machinery" >&2;}
+ { (exit 1); exit 1; }; }
+_ACEOF
+
+# VPATH may cause trouble with some makes, so we remove $(srcdir),
+# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and
+# trailing colons and then remove the whole line if VPATH becomes empty
+# (actually we leave an empty line to preserve line numbers).
+if test "x$srcdir" = x.; then
+ ac_vpsub='/^[ ]*VPATH[ ]*=/{
+s/:*\$(srcdir):*/:/
+s/:*\${srcdir}:*/:/
+s/:*@srcdir@:*/:/
+s/^\([^=]*=[ ]*\):*/\1/
+s/:*$//
+s/^[^=]*=[ ]*$//
+}'
+fi
+
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+fi # test -n "$CONFIG_FILES"
+
+# Set up the scripts for CONFIG_HEADERS section.
+# No need to generate them if there are no CONFIG_HEADERS.
+# This happens for instance with `./config.status Makefile'.
+if test -n "$CONFIG_HEADERS"; then
+cat >"$tmp/defines.awk" <<\_ACAWK ||
+BEGIN {
+_ACEOF
+
+# Transform confdefs.h into an awk script `defines.awk', embedded as
+# here-document in config.status, that substitutes the proper values into
+# config.h.in to produce config.h.
+
+# Create a delimiter string that does not exist in confdefs.h, to ease
+# handling of long lines.
+ac_delim='%!_!# '
+for ac_last_try in false false :; do
+ ac_t=`sed -n "/$ac_delim/p" confdefs.h`
+ if test -z "$ac_t"; then
+ break
+ elif $ac_last_try; then
+ { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_HEADERS" >&5
+$as_echo "$as_me: error: could not make $CONFIG_HEADERS" >&2;}
+ { (exit 1); exit 1; }; }
+ else
+ ac_delim="$ac_delim!$ac_delim _$ac_delim!! "
+ fi
+done
+
+# For the awk script, D is an array of macro values keyed by name,
+# likewise P contains macro parameters if any. Preserve backslash
+# newline sequences.
+
+ac_word_re=[_$as_cr_Letters][_$as_cr_alnum]*
+sed -n '
+s/.\{148\}/&'"$ac_delim"'/g
+t rset
+:rset
+s/^[ ]*#[ ]*define[ ][ ]*/ /
+t def
+d
+:def
+s/\\$//
+t bsnl
+s/["\\]/\\&/g
+s/^ \('"$ac_word_re"'\)\(([^()]*)\)[ ]*\(.*\)/P["\1"]="\2"\
+D["\1"]=" \3"/p
+s/^ \('"$ac_word_re"'\)[ ]*\(.*\)/D["\1"]=" \2"/p
+d
+:bsnl
+s/["\\]/\\&/g
+s/^ \('"$ac_word_re"'\)\(([^()]*)\)[ ]*\(.*\)/P["\1"]="\2"\
+D["\1"]=" \3\\\\\\n"\\/p
+t cont
+s/^ \('"$ac_word_re"'\)[ ]*\(.*\)/D["\1"]=" \2\\\\\\n"\\/p
+t cont
+d
+:cont
+n
+s/.\{148\}/&'"$ac_delim"'/g
+t clear
+:clear
+s/\\$//
+t bsnlc
+s/["\\]/\\&/g; s/^/"/; s/$/"/p
+d
+:bsnlc
+s/["\\]/\\&/g; s/^/"/; s/$/\\\\\\n"\\/p
+b cont
+' <confdefs.h | sed '
+s/'"$ac_delim"'/"\\\
+"/g' >>$CONFIG_STATUS || ac_write_fail=1
+
+cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
+ for (key in D) D_is_set[key] = 1
+ FS = "\a"
+}
+/^[\t ]*#[\t ]*(define|undef)[\t ]+$ac_word_re([\t (]|\$)/ {
+ line = \$ 0
+ split(line, arg, " ")
+ if (arg[1] == "#") {
+ defundef = arg[2]
+ mac1 = arg[3]
+ } else {
+ defundef = substr(arg[1], 2)
+ mac1 = arg[2]
+ }
+ split(mac1, mac2, "(") #)
+ macro = mac2[1]
+ prefix = substr(line, 1, index(line, defundef) - 1)
+ if (D_is_set[macro]) {
+ # Preserve the white space surrounding the "#".
+ print prefix "define", macro P[macro] D[macro]
+ next
+ } else {
+ # Replace #undef with comments. This is necessary, for example,
+ # in the case of _POSIX_SOURCE, which is predefined and required
+ # on some systems where configure will not decide to define it.
+ if (defundef == "undef") {
+ print "/*", prefix defundef, macro, "*/"
+ next
+ }
+ }
+}
+{ print }
+_ACAWK
+_ACEOF
+cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
+ { { $as_echo "$as_me:$LINENO: error: could not setup config headers machinery" >&5
+$as_echo "$as_me: error: could not setup config headers machinery" >&2;}
+ { (exit 1); exit 1; }; }
+fi # test -n "$CONFIG_HEADERS"
+
+
+eval set X " :F $CONFIG_FILES :H $CONFIG_HEADERS :C $CONFIG_COMMANDS"
+shift
+for ac_tag
+do
+ case $ac_tag in
+ :[FHLC]) ac_mode=$ac_tag; continue;;
+ esac
+ case $ac_mode$ac_tag in
+ :[FHL]*:*);;
+ :L* | :C*:*) { { $as_echo "$as_me:$LINENO: error: invalid tag $ac_tag" >&5
+$as_echo "$as_me: error: invalid tag $ac_tag" >&2;}
+ { (exit 1); exit 1; }; };;
+ :[FH]-) ac_tag=-:-;;
+ :[FH]*) ac_tag=$ac_tag:$ac_tag.in;;
+ esac
+ ac_save_IFS=$IFS
+ IFS=:
+ set x $ac_tag
+ IFS=$ac_save_IFS
+ shift
+ ac_file=$1
+ shift
+
+ case $ac_mode in
+ :L) ac_source=$1;;
+ :[FH])
+ ac_file_inputs=
+ for ac_f
+ do
+ case $ac_f in
+ -) ac_f="$tmp/stdin";;
+ *) # Look for the file first in the build tree, then in the source tree
+ # (if the path is not absolute). The absolute path cannot be DOS-style,
+ # because $ac_f cannot contain `:'.
+ test -f "$ac_f" ||
+ case $ac_f in
+ [\\/$]*) false;;
+ *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
+ esac ||
+ { { $as_echo "$as_me:$LINENO: error: cannot find input file: $ac_f" >&5
+$as_echo "$as_me: error: cannot find input file: $ac_f" >&2;}
+ { (exit 1); exit 1; }; };;
+ esac
+ case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
+ ac_file_inputs="$ac_file_inputs '$ac_f'"
+ done
+
+ # Let's still pretend it is `configure' which instantiates (i.e., don't
+ # use $as_me), people would be surprised to read:
+ # /* config.h. Generated by config.status. */
+ configure_input='Generated from '`
+ $as_echo "$*" | sed 's|^[^:]*/||;s|:[^:]*/|, |g'
+ `' by configure.'
+ if test x"$ac_file" != x-; then
+ configure_input="$ac_file. $configure_input"
+ { $as_echo "$as_me:$LINENO: creating $ac_file" >&5
+$as_echo "$as_me: creating $ac_file" >&6;}
+ fi
+ # Neutralize special characters interpreted by sed in replacement strings.
+ case $configure_input in #(
+ *\&* | *\|* | *\\* )
+ ac_sed_conf_input=`$as_echo "$configure_input" |
+ sed 's/[\\\\&|]/\\\\&/g'`;; #(
+ *) ac_sed_conf_input=$configure_input;;
+ esac
+
+ case $ac_tag in
+ *:-:* | *:-) cat >"$tmp/stdin" \
+ || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5
+$as_echo "$as_me: error: could not create $ac_file" >&2;}
+ { (exit 1); exit 1; }; } ;;
+ esac
+ ;;
+ esac
+
+ ac_dir=`$as_dirname -- "$ac_file" ||
+$as_expr X"$ac_file" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$ac_file" : 'X\(//\)[^/]' \| \
+ X"$ac_file" : 'X\(//\)$' \| \
+ X"$ac_file" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$ac_file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'`
+ { as_dir="$ac_dir"
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+
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+_ACEOF
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+ac_sed_dataroot='
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+ :H)
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+ac_prefix_conf_PKG=`echo $PACKAGE`
+ac_prefix_conf_LOW=`echo _$ac_prefix_conf_PKG | sed -e "y:ABCDEFGHIJKLMNOPQRSTUVWXYZ-:abcdefghijklmnopqrstuvwxyz_:"`
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+ac_prefix_conf_INP=`echo "" | sed -e 's/ *//'`
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+ *) ac_prefix_conf_INP=config.h
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+ { (exit 1); exit 1; }; }
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+ if test ! -f "$ac_prefix_conf_INP" ; then if test -f "$srcdir/$ac_prefix_conf_INP" ; then
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+$as_echo "$as_me: creating $ac_prefix_conf_OUT - prefix $ac_prefix_conf_UPP for $ac_prefix_conf_INP defines" >&6;}
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+ $as_echo "#define $ac_prefix_conf_UPP""_\\1\\2\\" >> conftest.prefix
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+ $as_echo "#define $ac_prefix_conf_LOW""_\\1\\2\\" >> conftest.prefix
+ $as_echo "#endif/" >> conftest.prefix
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+ echo "#define $ac_prefix_conf_DEF 1" >>$tmp/pconfig.h
+ echo ' ' >>$tmp/pconfig.h
+ echo /'*' $ac_prefix_conf_OUT. Generated automatically at end of configure. '*'/ >>$tmp/pconfig.h
+
+ sed -f conftest.prefix $ac_prefix_conf_INP >>$tmp/pconfig.h
+ echo ' ' >>$tmp/pconfig.h
+ echo '/* once:' $ac_prefix_conf_DEF '*/' >>$tmp/pconfig.h
+ echo "#endif" >>$tmp/pconfig.h
+ if cmp -s $ac_prefix_conf_OUT $tmp/pconfig.h 2>/dev/null; then
+ { $as_echo "$as_me:$LINENO: $ac_prefix_conf_OUT is unchanged" >&5
+$as_echo "$as_me: $ac_prefix_conf_OUT is unchanged" >&6;}
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+ s/.*/./; q'`
+ { as_dir="$ac_dir"
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+ esac
+ test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || {
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+ *) as_qdir=$as_dir;;
+ esac
+ as_dirs="'$as_qdir' $as_dirs"
+ as_dir=`$as_dirname -- "$as_dir" ||
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+$as_echo "$as_me: error: cannot create directory $as_dir" >&2;}
+ { (exit 1); exit 1; }; }; }
+ rm -f "$ac_prefix_conf_OUT"
+ mv $tmp/pconfig.h "$ac_prefix_conf_OUT"
+ fi
+ cp conftest.prefix _configs.sed
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+ { { $as_echo "$as_me:$LINENO: error: input file $ac_prefix_conf_INP does not exist - skip generating $ac_prefix_conf_OUT" >&5
+$as_echo "$as_me: error: input file $ac_prefix_conf_INP does not exist - skip generating $ac_prefix_conf_OUT" >&2;}
+ { (exit 1); exit 1; }; }
+ fi
+ rm -f conftest.*
+fi
+ ;;
+ "depfiles":C) test x"$AMDEP_TRUE" != x"" || {
+ # Autoconf 2.62 quotes --file arguments for eval, but not when files
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+ # if we detect the quoting.
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+ shift
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+ # Check whether this is an Automake generated Makefile or not.
+ # We used to match only the files named `Makefile.in', but
+ # some people rename them; so instead we look at the file content.
+ # Grep'ing the first line is not enough: some people post-process
+ # each Makefile.in and add a new line on top of each file to say so.
+ # Grep'ing the whole file is not good either: AIX grep has a line
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+ X"$mf" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$mf" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
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+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
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+ q
+ }
+ s/.*/./; q'`
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+ # Extract the definition of DEPDIR, am__include, and am__quote
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+ test -z "$DEPDIR" && continue
+ am__include=`sed -n 's/^am__include = //p' < "$mf"`
+ test -z "am__include" && continue
+ am__quote=`sed -n 's/^am__quote = //p' < "$mf"`
+ # When using ansi2knr, U may be empty or an underscore; expand it
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+ # Find all dependency output files, they are included files with
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+ # simplest approach to changing $(DEPDIR) to its actual value in the
+ # expansion.
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+ sed -e 's/\$(DEPDIR)/'"$DEPDIR"'/g' -e 's/\$U/'"$U"'/g'`; do
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+ X"$file" : 'X\(/\)' \| . 2>/dev/null ||
+$as_echo X"$file" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
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+ /^X\(\/\/\)$/{
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+ /^X\(\/\).*/{
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+ s/.*/./; q'`
+ { as_dir=$dirpart/$fdir
+ case $as_dir in #(
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+ test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || {
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+ /^X\(\/\/\)$/{
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+ { (exit 1); exit 1; }; }; }
+ # echo "creating $dirpart/$file"
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+ done
+}
+ ;;
+ "libtool":C)
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+ fi
+
+ cfgfile="${ofile}T"
+ trap "$RM \"$cfgfile\"; exit 1" 1 2 15
+ $RM "$cfgfile"
+
+ cat <<_LT_EOF >> "$cfgfile"
+#! $SHELL
+
+# `$ECHO "$ofile" | sed 's%^.*/%%'` - Provide generalized library-building support services.
+# Generated automatically by $as_me ($PACKAGE$TIMESTAMP) $VERSION
+# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
+# NOTE: Changes made to this file will be lost: look at ltmain.sh.
+#
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005,
+# 2006, 2007, 2008 Free Software Foundation, Inc.
+# Written by Gordon Matzigkeit, 1996
+#
+# This file is part of GNU Libtool.
+#
+# GNU Libtool is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License as
+# published by the Free Software Foundation; either version 2 of
+# the License, or (at your option) any later version.
+#
+# As a special exception to the GNU General Public License,
+# if you distribute this file as part of a program or library that
+# is built using GNU Libtool, you may include this file under the
+# same distribution terms that you use for the rest of that program.
+#
+# GNU Libtool is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GNU Libtool; see the file COPYING. If not, a copy
+# can be downloaded from http://www.gnu.org/licenses/gpl.html, or
+# obtained by writing to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+
+# The names of the tagged configurations supported by this script.
+available_tags="CXX "
+
+# ### BEGIN LIBTOOL CONFIG
+
+# Which release of libtool.m4 was used?
+macro_version=$macro_version
+macro_revision=$macro_revision
+
+# Whether or not to build shared libraries.
+build_libtool_libs=$enable_shared
+
+# Whether or not to build static libraries.
+build_old_libs=$enable_static
+
+# What type of objects to build.
+pic_mode=$pic_mode
+
+# Whether or not to optimize for fast installation.
+fast_install=$enable_fast_install
+
+# The host system.
+host_alias=$host_alias
+host=$host
+host_os=$host_os
+
+# The build system.
+build_alias=$build_alias
+build=$build
+build_os=$build_os
+
+# A sed program that does not truncate output.
+SED=$lt_SED
+
+# Sed that helps us avoid accidentally triggering echo(1) options like -n.
+Xsed="\$SED -e 1s/^X//"
+
+# A grep program that handles long lines.
+GREP=$lt_GREP
+
+# An ERE matcher.
+EGREP=$lt_EGREP
+
+# A literal string matcher.
+FGREP=$lt_FGREP
+
+# A BSD- or MS-compatible name lister.
+NM=$lt_NM
+
+# Whether we need soft or hard links.
+LN_S=$lt_LN_S
+
+# What is the maximum length of a command?
+max_cmd_len=$max_cmd_len
+
+# Object file suffix (normally "o").
+objext=$ac_objext
+
+# Executable file suffix (normally "").
+exeext=$exeext
+
+# whether the shell understands "unset".
+lt_unset=$lt_unset
+
+# turn spaces into newlines.
+SP2NL=$lt_lt_SP2NL
+
+# turn newlines into spaces.
+NL2SP=$lt_lt_NL2SP
+
+# How to create reloadable object files.
+reload_flag=$lt_reload_flag
+reload_cmds=$lt_reload_cmds
+
+# An object symbol dumper.
+OBJDUMP=$lt_OBJDUMP
+
+# Method to check whether dependent libraries are shared objects.
+deplibs_check_method=$lt_deplibs_check_method
+
+# Command to use when deplibs_check_method == "file_magic".
+file_magic_cmd=$lt_file_magic_cmd
+
+# The archiver.
+AR=$lt_AR
+AR_FLAGS=$lt_AR_FLAGS
+
+# A symbol stripping program.
+STRIP=$lt_STRIP
+
+# Commands used to install an old-style archive.
+RANLIB=$lt_RANLIB
+old_postinstall_cmds=$lt_old_postinstall_cmds
+old_postuninstall_cmds=$lt_old_postuninstall_cmds
+
+# A C compiler.
+LTCC=$lt_CC
+
+# LTCC compiler flags.
+LTCFLAGS=$lt_CFLAGS
+
+# Take the output of nm and produce a listing of raw symbols and C names.
+global_symbol_pipe=$lt_lt_cv_sys_global_symbol_pipe
+
+# Transform the output of nm in a proper C declaration.
+global_symbol_to_cdecl=$lt_lt_cv_sys_global_symbol_to_cdecl
+
+# Transform the output of nm in a C name address pair.
+global_symbol_to_c_name_address=$lt_lt_cv_sys_global_symbol_to_c_name_address
+
+# Transform the output of nm in a C name address pair when lib prefix is needed.
+global_symbol_to_c_name_address_lib_prefix=$lt_lt_cv_sys_global_symbol_to_c_name_address_lib_prefix
+
+# The name of the directory that contains temporary libtool files.
+objdir=$objdir
+
+# Shell to use when invoking shell scripts.
+SHELL=$lt_SHELL
+
+# An echo program that does not interpret backslashes.
+ECHO=$lt_ECHO
+
+# Used to examine libraries when file_magic_cmd begins with "file".
+MAGIC_CMD=$MAGIC_CMD
+
+# Must we lock files when doing compilation?
+need_locks=$lt_need_locks
+
+# Tool to manipulate archived DWARF debug symbol files on Mac OS X.
+DSYMUTIL=$lt_DSYMUTIL
+
+# Tool to change global to local symbols on Mac OS X.
+NMEDIT=$lt_NMEDIT
+
+# Tool to manipulate fat objects and archives on Mac OS X.
+LIPO=$lt_LIPO
+
+# ldd/readelf like tool for Mach-O binaries on Mac OS X.
+OTOOL=$lt_OTOOL
+
+# ldd/readelf like tool for 64 bit Mach-O binaries on Mac OS X 10.4.
+OTOOL64=$lt_OTOOL64
+
+# Old archive suffix (normally "a").
+libext=$libext
+
+# Shared library suffix (normally ".so").
+shrext_cmds=$lt_shrext_cmds
+
+# The commands to extract the exported symbol list from a shared archive.
+extract_expsyms_cmds=$lt_extract_expsyms_cmds
+
+# Variables whose values should be saved in libtool wrapper scripts and
+# restored at link time.
+variables_saved_for_relink=$lt_variables_saved_for_relink
+
+# Do we need the "lib" prefix for modules?
+need_lib_prefix=$need_lib_prefix
+
+# Do we need a version for libraries?
+need_version=$need_version
+
+# Library versioning type.
+version_type=$version_type
+
+# Shared library runtime path variable.
+runpath_var=$runpath_var
+
+# Shared library path variable.
+shlibpath_var=$shlibpath_var
+
+# Is shlibpath searched before the hard-coded library search path?
+shlibpath_overrides_runpath=$shlibpath_overrides_runpath
+
+# Format of library name prefix.
+libname_spec=$lt_libname_spec
+
+# List of archive names. First name is the real one, the rest are links.
+# The last name is the one that the linker finds with -lNAME
+library_names_spec=$lt_library_names_spec
+
+# The coded name of the library, if different from the real name.
+soname_spec=$lt_soname_spec
+
+# Command to use after installation of a shared archive.
+postinstall_cmds=$lt_postinstall_cmds
+
+# Command to use after uninstallation of a shared archive.
+postuninstall_cmds=$lt_postuninstall_cmds
+
+# Commands used to finish a libtool library installation in a directory.
+finish_cmds=$lt_finish_cmds
+
+# As "finish_cmds", except a single script fragment to be evaled but
+# not shown.
+finish_eval=$lt_finish_eval
+
+# Whether we should hardcode library paths into libraries.
+hardcode_into_libs=$hardcode_into_libs
+
+# Compile-time system search path for libraries.
+sys_lib_search_path_spec=$lt_sys_lib_search_path_spec
+
+# Run-time system search path for libraries.
+sys_lib_dlsearch_path_spec=$lt_sys_lib_dlsearch_path_spec
+
+# Whether dlopen is supported.
+dlopen_support=$enable_dlopen
+
+# Whether dlopen of programs is supported.
+dlopen_self=$enable_dlopen_self
+
+# Whether dlopen of statically linked programs is supported.
+dlopen_self_static=$enable_dlopen_self_static
+
+# Commands to strip libraries.
+old_striplib=$lt_old_striplib
+striplib=$lt_striplib
+
+
+# The linker used to build libraries.
+LD=$lt_LD
+
+# Commands used to build an old-style archive.
+old_archive_cmds=$lt_old_archive_cmds
+
+# A language specific compiler.
+CC=$lt_compiler
+
+# Is the compiler the GNU compiler?
+with_gcc=$GCC
+
+# Compiler flag to turn off builtin functions.
+no_builtin_flag=$lt_lt_prog_compiler_no_builtin_flag
+
+# How to pass a linker flag through the compiler.
+wl=$lt_lt_prog_compiler_wl
+
+# Additional compiler flags for building library objects.
+pic_flag=$lt_lt_prog_compiler_pic
+
+# Compiler flag to prevent dynamic linking.
+link_static_flag=$lt_lt_prog_compiler_static
+
+# Does compiler simultaneously support -c and -o options?
+compiler_c_o=$lt_lt_cv_prog_compiler_c_o
+
+# Whether or not to add -lc for building shared libraries.
+build_libtool_need_lc=$archive_cmds_need_lc
+
+# Whether or not to disallow shared libs when runtime libs are static.
+allow_libtool_libs_with_static_runtimes=$enable_shared_with_static_runtimes
+
+# Compiler flag to allow reflexive dlopens.
+export_dynamic_flag_spec=$lt_export_dynamic_flag_spec
+
+# Compiler flag to generate shared objects directly from archives.
+whole_archive_flag_spec=$lt_whole_archive_flag_spec
+
+# Whether the compiler copes with passing no objects directly.
+compiler_needs_object=$lt_compiler_needs_object
+
+# Create an old-style archive from a shared archive.
+old_archive_from_new_cmds=$lt_old_archive_from_new_cmds
+
+# Create a temporary old-style archive to link instead of a shared archive.
+old_archive_from_expsyms_cmds=$lt_old_archive_from_expsyms_cmds
+
+# Commands used to build a shared archive.
+archive_cmds=$lt_archive_cmds
+archive_expsym_cmds=$lt_archive_expsym_cmds
+
+# Commands used to build a loadable module if different from building
+# a shared archive.
+module_cmds=$lt_module_cmds
+module_expsym_cmds=$lt_module_expsym_cmds
+
+# Whether we are building with GNU ld or not.
+with_gnu_ld=$lt_with_gnu_ld
+
+# Flag that allows shared libraries with undefined symbols to be built.
+allow_undefined_flag=$lt_allow_undefined_flag
+
+# Flag that enforces no undefined symbols.
+no_undefined_flag=$lt_no_undefined_flag
+
+# Flag to hardcode \$libdir into a binary during linking.
+# This must work even if \$libdir does not exist
+hardcode_libdir_flag_spec=$lt_hardcode_libdir_flag_spec
+
+# If ld is used when linking, flag to hardcode \$libdir into a binary
+# during linking. This must work even if \$libdir does not exist.
+hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld
+
+# Whether we need a single "-rpath" flag with a separated argument.
+hardcode_libdir_separator=$lt_hardcode_libdir_separator
+
+# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes
+# DIR into the resulting binary.
+hardcode_direct=$hardcode_direct
+
+# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes
+# DIR into the resulting binary and the resulting library dependency is
+# "absolute",i.e impossible to change by setting \${shlibpath_var} if the
+# library is relocated.
+hardcode_direct_absolute=$hardcode_direct_absolute
+
+# Set to "yes" if using the -LDIR flag during linking hardcodes DIR
+# into the resulting binary.
+hardcode_minus_L=$hardcode_minus_L
+
+# Set to "yes" if using SHLIBPATH_VAR=DIR during linking hardcodes DIR
+# into the resulting binary.
+hardcode_shlibpath_var=$hardcode_shlibpath_var
+
+# Set to "yes" if building a shared library automatically hardcodes DIR
+# into the library and all subsequent libraries and executables linked
+# against it.
+hardcode_automatic=$hardcode_automatic
+
+# Set to yes if linker adds runtime paths of dependent libraries
+# to runtime path list.
+inherit_rpath=$inherit_rpath
+
+# Whether libtool must link a program against all its dependency libraries.
+link_all_deplibs=$link_all_deplibs
+
+# Fix the shell variable \$srcfile for the compiler.
+fix_srcfile_path=$lt_fix_srcfile_path
+
+# Set to "yes" if exported symbols are required.
+always_export_symbols=$always_export_symbols
+
+# The commands to list exported symbols.
+export_symbols_cmds=$lt_export_symbols_cmds
+
+# Symbols that should not be listed in the preloaded symbols.
+exclude_expsyms=$lt_exclude_expsyms
+
+# Symbols that must always be exported.
+include_expsyms=$lt_include_expsyms
+
+# Commands necessary for linking programs (against libraries) with templates.
+prelink_cmds=$lt_prelink_cmds
+
+# Specify filename containing input files.
+file_list_spec=$lt_file_list_spec
+
+# How to hardcode a shared library path into an executable.
+hardcode_action=$hardcode_action
+
+# The directories searched by this compiler when creating a shared library.
+compiler_lib_search_dirs=$lt_compiler_lib_search_dirs
+
+# Dependencies to place before and after the objects being linked to
+# create a shared library.
+predep_objects=$lt_predep_objects
+postdep_objects=$lt_postdep_objects
+predeps=$lt_predeps
+postdeps=$lt_postdeps
+
+# The library search path used internally by the compiler when linking
+# a shared library.
+compiler_lib_search_path=$lt_compiler_lib_search_path
+
+# ### END LIBTOOL CONFIG
+
+_LT_EOF
+
+ case $host_os in
+ aix3*)
+ cat <<\_LT_EOF >> "$cfgfile"
+# AIX sometimes has problems with the GCC collect2 program. For some
+# reason, if we set the COLLECT_NAMES environment variable, the problems
+# vanish in a puff of smoke.
+if test "X${COLLECT_NAMES+set}" != Xset; then
+ COLLECT_NAMES=
+ export COLLECT_NAMES
+fi
+_LT_EOF
+ ;;
+ esac
+
+
+ltmain="$ac_aux_dir/ltmain.sh"
+
+
+ # We use sed instead of cat because bash on DJGPP gets confused if
+ # if finds mixed CR/LF and LF-only lines. Since sed operates in
+ # text mode, it properly converts lines to CR/LF. This bash problem
+ # is reportedly fixed, but why not run on old versions too?
+ sed '/^# Generated shell functions inserted here/q' "$ltmain" >> "$cfgfile" \
+ || (rm -f "$cfgfile"; exit 1)
+
+ case $xsi_shell in
+ yes)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_dirname file append nondir_replacement
+# Compute the dirname of FILE. If nonempty, add APPEND to the result,
+# otherwise set result to NONDIR_REPLACEMENT.
+func_dirname ()
+{
+ case ${1} in
+ */*) func_dirname_result="${1%/*}${2}" ;;
+ * ) func_dirname_result="${3}" ;;
+ esac
+}
+
+# func_basename file
+func_basename ()
+{
+ func_basename_result="${1##*/}"
+}
+
+# func_dirname_and_basename file append nondir_replacement
+# perform func_basename and func_dirname in a single function
+# call:
+# dirname: Compute the dirname of FILE. If nonempty,
+# add APPEND to the result, otherwise set result
+# to NONDIR_REPLACEMENT.
+# value returned in "$func_dirname_result"
+# basename: Compute filename of FILE.
+# value retuned in "$func_basename_result"
+# Implementation must be kept synchronized with func_dirname
+# and func_basename. For efficiency, we do not delegate to
+# those functions but instead duplicate the functionality here.
+func_dirname_and_basename ()
+{
+ case ${1} in
+ */*) func_dirname_result="${1%/*}${2}" ;;
+ * ) func_dirname_result="${3}" ;;
+ esac
+ func_basename_result="${1##*/}"
+}
+
+# func_stripname prefix suffix name
+# strip PREFIX and SUFFIX off of NAME.
+# PREFIX and SUFFIX must not contain globbing or regex special
+# characters, hashes, percent signs, but SUFFIX may contain a leading
+# dot (in which case that matches only a dot).
+func_stripname ()
+{
+ # pdksh 5.2.14 does not do ${X%$Y} correctly if both X and Y are
+ # positional parameters, so assign one to ordinary parameter first.
+ func_stripname_result=${3}
+ func_stripname_result=${func_stripname_result#"${1}"}
+ func_stripname_result=${func_stripname_result%"${2}"}
+}
+
+# func_opt_split
+func_opt_split ()
+{
+ func_opt_split_opt=${1%%=*}
+ func_opt_split_arg=${1#*=}
+}
+
+# func_lo2o object
+func_lo2o ()
+{
+ case ${1} in
+ *.lo) func_lo2o_result=${1%.lo}.${objext} ;;
+ *) func_lo2o_result=${1} ;;
+ esac
+}
+
+# func_xform libobj-or-source
+func_xform ()
+{
+ func_xform_result=${1%.*}.lo
+}
+
+# func_arith arithmetic-term...
+func_arith ()
+{
+ func_arith_result=$(( $* ))
+}
+
+# func_len string
+# STRING may not start with a hyphen.
+func_len ()
+{
+ func_len_result=${#1}
+}
+
+_LT_EOF
+ ;;
+ *) # Bourne compatible functions.
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_dirname file append nondir_replacement
+# Compute the dirname of FILE. If nonempty, add APPEND to the result,
+# otherwise set result to NONDIR_REPLACEMENT.
+func_dirname ()
+{
+ # Extract subdirectory from the argument.
+ func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"`
+ if test "X$func_dirname_result" = "X${1}"; then
+ func_dirname_result="${3}"
+ else
+ func_dirname_result="$func_dirname_result${2}"
+ fi
+}
+
+# func_basename file
+func_basename ()
+{
+ func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"`
+}
+
+
+# func_stripname prefix suffix name
+# strip PREFIX and SUFFIX off of NAME.
+# PREFIX and SUFFIX must not contain globbing or regex special
+# characters, hashes, percent signs, but SUFFIX may contain a leading
+# dot (in which case that matches only a dot).
+# func_strip_suffix prefix name
+func_stripname ()
+{
+ case ${2} in
+ .*) func_stripname_result=`$ECHO "X${3}" \
+ | $Xsed -e "s%^${1}%%" -e "s%\\\\${2}\$%%"`;;
+ *) func_stripname_result=`$ECHO "X${3}" \
+ | $Xsed -e "s%^${1}%%" -e "s%${2}\$%%"`;;
+ esac
+}
+
+# sed scripts:
+my_sed_long_opt='1s/^\(-[^=]*\)=.*/\1/;q'
+my_sed_long_arg='1s/^-[^=]*=//'
+
+# func_opt_split
+func_opt_split ()
+{
+ func_opt_split_opt=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_opt"`
+ func_opt_split_arg=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_arg"`
+}
+
+# func_lo2o object
+func_lo2o ()
+{
+ func_lo2o_result=`$ECHO "X${1}" | $Xsed -e "$lo2o"`
+}
+
+# func_xform libobj-or-source
+func_xform ()
+{
+ func_xform_result=`$ECHO "X${1}" | $Xsed -e 's/\.[^.]*$/.lo/'`
+}
+
+# func_arith arithmetic-term...
+func_arith ()
+{
+ func_arith_result=`expr "$@"`
+}
+
+# func_len string
+# STRING may not start with a hyphen.
+func_len ()
+{
+ func_len_result=`expr "$1" : ".*" 2>/dev/null || echo $max_cmd_len`
+}
+
+_LT_EOF
+esac
+
+case $lt_shell_append in
+ yes)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_append var value
+# Append VALUE to the end of shell variable VAR.
+func_append ()
+{
+ eval "$1+=\$2"
+}
+_LT_EOF
+ ;;
+ *)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_append var value
+# Append VALUE to the end of shell variable VAR.
+func_append ()
+{
+ eval "$1=\$$1\$2"
+}
+
+_LT_EOF
+ ;;
+ esac
+
+
+ sed -n '/^# Generated shell functions inserted here/,$p' "$ltmain" >> "$cfgfile" \
+ || (rm -f "$cfgfile"; exit 1)
+
+ mv -f "$cfgfile" "$ofile" ||
+ (rm -f "$ofile" && cp "$cfgfile" "$ofile" && rm -f "$cfgfile")
+ chmod +x "$ofile"
+
+
+ cat <<_LT_EOF >> "$ofile"
+
+# ### BEGIN LIBTOOL TAG CONFIG: CXX
+
+# The linker used to build libraries.
+LD=$lt_LD_CXX
+
+# Commands used to build an old-style archive.
+old_archive_cmds=$lt_old_archive_cmds_CXX
+
+# A language specific compiler.
+CC=$lt_compiler_CXX
+
+# Is the compiler the GNU compiler?
+with_gcc=$GCC_CXX
+
+# Compiler flag to turn off builtin functions.
+no_builtin_flag=$lt_lt_prog_compiler_no_builtin_flag_CXX
+
+# How to pass a linker flag through the compiler.
+wl=$lt_lt_prog_compiler_wl_CXX
+
+# Additional compiler flags for building library objects.
+pic_flag=$lt_lt_prog_compiler_pic_CXX
+
+# Compiler flag to prevent dynamic linking.
+link_static_flag=$lt_lt_prog_compiler_static_CXX
+
+# Does compiler simultaneously support -c and -o options?
+compiler_c_o=$lt_lt_cv_prog_compiler_c_o_CXX
+
+# Whether or not to add -lc for building shared libraries.
+build_libtool_need_lc=$archive_cmds_need_lc_CXX
+
+# Whether or not to disallow shared libs when runtime libs are static.
+allow_libtool_libs_with_static_runtimes=$enable_shared_with_static_runtimes_CXX
+
+# Compiler flag to allow reflexive dlopens.
+export_dynamic_flag_spec=$lt_export_dynamic_flag_spec_CXX
+
+# Compiler flag to generate shared objects directly from archives.
+whole_archive_flag_spec=$lt_whole_archive_flag_spec_CXX
+
+# Whether the compiler copes with passing no objects directly.
+compiler_needs_object=$lt_compiler_needs_object_CXX
+
+# Create an old-style archive from a shared archive.
+old_archive_from_new_cmds=$lt_old_archive_from_new_cmds_CXX
+
+# Create a temporary old-style archive to link instead of a shared archive.
+old_archive_from_expsyms_cmds=$lt_old_archive_from_expsyms_cmds_CXX
+
+# Commands used to build a shared archive.
+archive_cmds=$lt_archive_cmds_CXX
+archive_expsym_cmds=$lt_archive_expsym_cmds_CXX
+
+# Commands used to build a loadable module if different from building
+# a shared archive.
+module_cmds=$lt_module_cmds_CXX
+module_expsym_cmds=$lt_module_expsym_cmds_CXX
+
+# Whether we are building with GNU ld or not.
+with_gnu_ld=$lt_with_gnu_ld_CXX
+
+# Flag that allows shared libraries with undefined symbols to be built.
+allow_undefined_flag=$lt_allow_undefined_flag_CXX
+
+# Flag that enforces no undefined symbols.
+no_undefined_flag=$lt_no_undefined_flag_CXX
+
+# Flag to hardcode \$libdir into a binary during linking.
+# This must work even if \$libdir does not exist
+hardcode_libdir_flag_spec=$lt_hardcode_libdir_flag_spec_CXX
+
+# If ld is used when linking, flag to hardcode \$libdir into a binary
+# during linking. This must work even if \$libdir does not exist.
+hardcode_libdir_flag_spec_ld=$lt_hardcode_libdir_flag_spec_ld_CXX
+
+# Whether we need a single "-rpath" flag with a separated argument.
+hardcode_libdir_separator=$lt_hardcode_libdir_separator_CXX
+
+# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes
+# DIR into the resulting binary.
+hardcode_direct=$hardcode_direct_CXX
+
+# Set to "yes" if using DIR/libNAME\${shared_ext} during linking hardcodes
+# DIR into the resulting binary and the resulting library dependency is
+# "absolute",i.e impossible to change by setting \${shlibpath_var} if the
+# library is relocated.
+hardcode_direct_absolute=$hardcode_direct_absolute_CXX
+
+# Set to "yes" if using the -LDIR flag during linking hardcodes DIR
+# into the resulting binary.
+hardcode_minus_L=$hardcode_minus_L_CXX
+
+# Set to "yes" if using SHLIBPATH_VAR=DIR during linking hardcodes DIR
+# into the resulting binary.
+hardcode_shlibpath_var=$hardcode_shlibpath_var_CXX
+
+# Set to "yes" if building a shared library automatically hardcodes DIR
+# into the library and all subsequent libraries and executables linked
+# against it.
+hardcode_automatic=$hardcode_automatic_CXX
+
+# Set to yes if linker adds runtime paths of dependent libraries
+# to runtime path list.
+inherit_rpath=$inherit_rpath_CXX
+
+# Whether libtool must link a program against all its dependency libraries.
+link_all_deplibs=$link_all_deplibs_CXX
+
+# Fix the shell variable \$srcfile for the compiler.
+fix_srcfile_path=$lt_fix_srcfile_path_CXX
+
+# Set to "yes" if exported symbols are required.
+always_export_symbols=$always_export_symbols_CXX
+
+# The commands to list exported symbols.
+export_symbols_cmds=$lt_export_symbols_cmds_CXX
+
+# Symbols that should not be listed in the preloaded symbols.
+exclude_expsyms=$lt_exclude_expsyms_CXX
+
+# Symbols that must always be exported.
+include_expsyms=$lt_include_expsyms_CXX
+
+# Commands necessary for linking programs (against libraries) with templates.
+prelink_cmds=$lt_prelink_cmds_CXX
+
+# Specify filename containing input files.
+file_list_spec=$lt_file_list_spec_CXX
+
+# How to hardcode a shared library path into an executable.
+hardcode_action=$hardcode_action_CXX
+
+# The directories searched by this compiler when creating a shared library.
+compiler_lib_search_dirs=$lt_compiler_lib_search_dirs_CXX
+
+# Dependencies to place before and after the objects being linked to
+# create a shared library.
+predep_objects=$lt_predep_objects_CXX
+postdep_objects=$lt_postdep_objects_CXX
+predeps=$lt_predeps_CXX
+postdeps=$lt_postdeps_CXX
+
+# The library search path used internally by the compiler when linking
+# a shared library.
+compiler_lib_search_path=$lt_compiler_lib_search_path_CXX
+
+# ### END LIBTOOL TAG CONFIG: CXX
+_LT_EOF
+
+ ;;
+
+ esac
+done # for ac_tag
+
+
+{ (exit 0); exit 0; }
+_ACEOF
+chmod +x $CONFIG_STATUS
+ac_clean_files=$ac_clean_files_save
+
+test $ac_write_fail = 0 ||
+ { { $as_echo "$as_me:$LINENO: error: write failure creating $CONFIG_STATUS" >&5
+$as_echo "$as_me: error: write failure creating $CONFIG_STATUS" >&2;}
+ { (exit 1); exit 1; }; }
+
+
+# configure is writing to config.log, and then calls config.status.
+# config.status does its own redirection, appending to config.log.
+# Unfortunately, on DOS this fails, as config.log is still kept open
+# by configure, so config.status won't be able to write to it; its
+# output is simply discarded. So we exec the FD to /dev/null,
+# effectively closing config.log, so it can be properly (re)opened and
+# appended to by config.status. When coming back to configure, we
+# need to make the FD available again.
+if test "$no_create" != yes; then
+ ac_cs_success=:
+ ac_config_status_args=
+ test "$silent" = yes &&
+ ac_config_status_args="$ac_config_status_args --quiet"
+ exec 5>/dev/null
+ $SHELL $CONFIG_STATUS $ac_config_status_args || ac_cs_success=false
+ exec 5>>config.log
+ # Use ||, not &&, to avoid exiting from the if with $? = 1, which
+ # would make configure fail if this is the last instruction.
+ $ac_cs_success || { (exit 1); exit 1; }
+fi
+if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then
+ { $as_echo "$as_me:$LINENO: WARNING: unrecognized options: $ac_unrecognized_opts" >&5
+$as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;}
+fi
+
--- /dev/null
+# configure.ac for Clustal Omega
+#
+# RCS $Id: configure.ac 256 2011-06-23 13:57:28Z fabian $
+
+
+# release
+#
+#AC_INIT([Clustal Omega], [0.1.1], [clustalw@ucd.ie])
+#PACKAGE_CODENAME="OppidumLeonis"
+#r238
+#AC_INIT([Clustal Omega], [0.2.0], [clustalw@ucd.ie])
+#PACKAGE_CODENAME="IbiMeVidebunt"
+#r250
+#AC_INIT([Clustal Omega], [1.0.1], [clustalw@ucd.ie])
+#PACKAGE_CODENAME="DeshilHollesEamus"
+#r255
+AC_INIT([Clustal Omega], [1.0.2], [clustalw@ucd.ie])
+PACKAGE_CODENAME="DeshilHollesEamus"
+
+# The AC_INIT macro can take any source file as an argument. It just
+# checks that the file is there, which should, in turn, mean that the
+# source directory is there. AC_INIT generates the following m4
+# macros, output variables and preprocessor symbols:
+AC_SUBST(PACKAGE_NAME)
+AC_SUBST(PACKAGE_TARNAME)
+AC_SUBST(PACKAGE_VERSION)
+AC_SUBST(PACKAGE_STRING)
+AC_SUBST(PACKAGE_BUGREPORT)
+AC_SUBST(PACKAGE_CODENAME)
+
+AC_MSG_NOTICE([
+
+ Welcome to $PACKAGE_NAME - version $PACKAGE_VERSION ($PACKAGE_CODENAME)
+
+ +NMMMMMMMMMS=
+ MMMMM? :MMMMM8
+ IMMMMS MMMMM,
+ ~MMMMN ,MMMMM
+ =MMMMM MMMMM
+ ?MMMMM +MMMMM
+ MMMMMS MMMMM
+ MMMMM MMMMM:
+ MMMMM MMMMM+
+ MMMMM MMMMM~
+ MMMMM MMMMM
+ MMMMMZ MMMMM
+ MMMMM ,MMMMZ
+ MMMM8 MMMM+
+ MMMMS MMMM,
+ MMMMO MMMM
+ ,N SMMM MMM8 +8
+ ,M7 M+ M+ :M8
+ ,MMMMMMMMMMMMI MMMMMMMMMMMM8
+ ,MMMMMMMMMMMM8 MMMMMMMMMMMM8
+ ,MMMMMMMMMMMMN MMMMMMMMMMMM8
+
+ ])
+#
+# Created with http://www.glassgiant.com/ascii/ and Wikipedia's Omega
+# Replaced all dollars with S's.
+#
+#
+# ,MMMMMMMMMD: MMMMM
+# NMMMMMMMMMMMMMM+ SMMMM
+# DMMMMMMMMMMMMMMMMMM, +MMMM
+# MMMMMMMMM8ZSO8MMMMMMMM +MMMM
+# MMMMM7 SMMMM +MMMM
+# MMMO MM? +MMMM
+# ?MMI NMIIMMMM
+# MMM MMMMMMM
+# MM
+# MN
+# MD
+# MM
+# MM? ,~+ISON
+# =MMI MMSOMMMM
+# MMMZ MMS +MMMM
+# MMMM8: :NMMM +MMMM
+# MMMMMMMMMDOODMMMMMMMMM +MMMM
+# MMMMMMMMMMMMMMMMMMMM +MMMM
+# OMMMMMMMMMMMMMMZ SMMMM
+# MMMMMMMMMM+ MMMMM
+#
+
+
+# AC_MSG_NOTICE([Configuring for your system...])
+
+AC_PREREQ(2.6) # 2.60 needed for AC_USE_SYSTEM_EXTENSIONS
+# consider 2.64 which allows to define a URL as well
+
+# The AM_INIT_AUTOMAKE line adds several standard checks.
+# This macro is always needed for automake
+# Obsolete: It takes the program name and version number as arguments.
+AM_INIT_AUTOMAKE
+
+# config header: provides a way for people to customise the
+# configuration for their platform, via #defines. config.h.in can be
+# generated automatically with the autoheader tool. However, you need
+# a stamp-h file in your project to ensure that automake regenerates
+# config.h from config.h.in. Type 'touch stamp-h' to add this file to
+# your project.
+#
+AM_CONFIG_HEADER(src/config.h)
+
+# the following allows to install a copy config.h for libclustalo in a
+# namespace like way, i.e. no name clash with your own config.h
+AX_PREFIX_CONFIG_H(src/clustal-omega-config.h)
+
+# This macro was introduced in Autoconf 2.60. If possible, enable
+# extensions to C or Posix on hosts that normally disable the
+# extensions.
+AC_USE_SYSTEM_EXTENSIONS
+
+
+# for cross compilation
+#
+AC_CANONICAL_HOST
+## AC_CANONICAL_BUILD
+## AC_CANONICAL_TARGET
+
+# Set the @SET_MAKE@ variable=make if $(MAKE) not set
+AC_PROG_MAKE_SET
+
+# AC_PROG_RANLIB will allow you to build code in sub-directories into
+# temporary libraries, which make will then link in with the rest of
+# the code.
+# Rendered obsolte by LT_INIT: AC_PROG_RANLIB
+#AC_PROG_LIBTOOL
+LT_INIT
+
+# AC_PROG_INSTALL will generate an install target so that users may
+# just type 'make install' to install the software.
+AC_PROG_INSTALL
+
+# check for C++ preprocessor and compiler and the library compiler
+# (might change the compiler flags)
+#
+# Determine a C compiler to use. If using the GNU C compiler, set
+# shell variable GCC to `yes'. If output variable CFLAGS was not
+# already set, set it to `-g -O2' for the GNU C compiler (`-O2' on
+# systems where GCC does not accept `-g'), or `-g' for other
+# compilers.
+AC_PROG_CC
+# Set output variable CPP to a command that runs the C preprocessor.
+AC_PROG_CPP
+#
+# Determine a C++ compiler to use. If output variable CXXFLAGS was not
+# already set, set it to `-g -O2' for the GNU C++ compiler (`-O2' on
+# systems where G++ does not accept `-g'), or `-g' for other
+# compilers.
+AC_PROG_CXX
+# Set CXXCPP to a command that runs the C++ preprocessor
+AC_PROG_CXXCPP
+#
+# reset compiler flags to initial flags
+#CXXFLAGS=$OLD_CXXFLAGS
+
+
+
+
+# safety check: AC_CONFIG_SRCDIR([src/clustal.h])
+
+# Let source files know in which context they are being used
+AC_DEFINE([CLUSTALO], [1],
+ [Let all files know they are being used inside Clustal Omega])
+
+AC_DEFINE_UNQUOTED(PACKAGE_CODENAME, "$PACKAGE_CODENAME", [The package code name])
+
+
+# Get svn revision
+#AC_PATH_PROG(svnversioncommand, svnversion)
+#if test "X$svnversioncommand" = "X" || test `$svnversioncommand -n '.'` = "exported"; then
+#AC_DEFINE_UNQUOTED(SVN_VERSION, ["`cat saved_svn_version.txt`"], [repository svn version])
+#else
+#AC_DEFINE_UNQUOTED(SVN_VERSION, ["`svnversion -n`"], [repository svn version])
+#`svnversion -n > saved_svn_version.txt`
+#fi
+
+
+
+
+# AW: we might need this in the future
+#
+case "$host_os" in
+linux*)
+# AC_DEFINE(LINUX,1,[This is a Linux system])
+ AC_DEFINE_UNQUOTED(LINUX,1,[This is a LINUX system])
+# AM_CONDITIONAL(HAVE_GNU_LD, true)
+# AM_CONDITIONAL(SOMEBSD, false)
+# XTRA_CPPLIBS=-lstdc++
+# LIBEXT=.so
+ ;;
+freebsd*)
+ AC_DEFINE_UNQUOTED(SOMEBSD,1,[This is a BSD system])
+# AC_CHECK_LIB(c_r, pthread_create)
+# AM_CONDITIONAL(HAVE_GNU_LD, true)
+# AM_CONDITIONAL(SOMEBSD, true)
+# XTRA_CPPLIBS=-lstdc++
+# LIBEXT=.so
+ ;;
+openbsd*)
+ AC_DEFINE_UNQUOTED(SOMEBSD,1,[This is a BSD system])
+# AC_CHECK_LIB(c_r, pthread_create)
+# AM_CONDITIONAL(HAVE_GNU_LD, true)
+# AM_CONDITIONAL(SOMEBSD, true)
+# XTRA_CPPLIBS=-lstdc++
+# LIBEXT=.so
+ ;;
+netbsd*)
+ AC_DEFINE_UNQUOTED(SOMEBSD,1,[This is a BSD system])
+# AC_CHECK_LIB(c_r, pthread_create)
+# AM_CONDITIONAL(HAVE_GNU_LD, true)
+# AM_CONDITIONAL(SOMEBSD, true)
+# XTRA_CPPLIBS=-lstdc++
+# LIBEXT=.so
+ ;;
+*solaris*)
+ AC_DEFINE_UNQUOTED(SOLARIS,1,[This is a Solaris system])
+# AC_CHECK_LIB(resolv, res_init)
+# XTRA_CPPLIBS=-lstdc++
+# AM_CONDITIONAL(HAVE_GNU_LD, false)
+# AM_CONDITIONAL(SOMEBSD, false)
+# CFLAGS="-D_POSIX_PTHREAD_SEMANTICS $CFLAGS"
+# LIBEXT=.so
+ ;;
+darwin*)
+ AC_DEFINE_UNQUOTED(DARWIN,1,[This is a Darwin system])
+# AM_CONDITIONAL(HAVE_GNU_LD, false)
+# AM_CONDITIONAL(SOMEBSD, false)
+# CFLAGS="-fno-common $CFLAGS"
+# LIBEXT=.so
+ ;;
+cygwin*)
+ AC_DEFINE_UNQUOTED(CYGWIN,1,[This is a CYGWIN system])
+# LDFLAGS="$LDFLAGS -no-undefined"
+# AM_CONDITIONAL(SOMEBSD, false)
+# AM_CONDITIONAL(HAVE_GNU_LD, false)
+# LIBEXT=.dll
+ ;;
+mingw*)
+ AC_DEFINE_UNQUOTED(MINGW,1,[This is a MinGW system])
+# AC_DEFINE_UNQUOTED(WINDOWS,1,[This is a Windows system])
+# AC_CHECK_LIB(intl, gettext)
+# AC_CHECK_LIB(ws2_32, _head_libws2_32_a,,[AC_MSG_ERROR([libextractor requires Winsock2])])
+# AC_CHECK_LIB(plibc, plibc_init,,[AC_MSG_ERROR([libextractor requires PlibC])])
+# LDFLAGS="$LDFLAGS -no-undefined -Wl,--export-all-symbols"
+# LIBSOLD=$LIBS
+# AM_CONDITIONAL(HAVE_GNU_LD, true)
+# AM_CONDITIONAL(SOMEBSD, false)
+# LIBEXT=.dll
+ ;;
+*)
+# AC_MSG_RESULT(Unrecognised OS $host_os)
+ AC_DEFINE_UNQUOTED(OTHEROS,1,[Some strange OS])
+# AC_MSG_RESULT(otheros)
+# AM_CONDITIONAL(HAVE_GNU_LD, false)
+# AM_CONDITIONAL(SOMEBSD, false)
+# LIBEXT=.so
+ ;;
+esac
+
+
+
+# Checks for standard header files.
+# obsolescent according to http://www.gnu.org/software/hello/manual/autoconf/Particular-Headers.html
+AC_HEADER_STDC
+# Guess the next one is obsolete as well then?
+AC_CHECK_HEADERS(assert.h ctype.h float.h limits.h math.h memory.h stdarg.h stdio.h stdlib.h string.h time.h unistd.h)
+# awk '/^#include *</ {print $2}' $(find src/ -name \*.[ch] -or -name \*.cpp) | grep -v argtable2.h | sort -u | tr -d '<>'
+
+# Checks for typedefs, structures, and compiler characteristics.
+AC_C_CONST
+AC_TYPE_SIZE_T
+AC_C_INLINE
+
+# Checks for library functions.
+# AC_CHECK_FUNCS(strdup strstr strchr erand48)
+# AW is there an automatic way to extract library functions used in the program?
+
+
+# explicit libm check
+AC_CHECK_LIB(m, log,, AC_MSG_ERROR([Could not find libm]))
+AC_CHECK_LIB(m, log2, AC_DEFINE(HAVE_LOG2, 1, [Has log2()]))
+
+
+# --- argtable header and library check
+#
+#
+AC_CHECK_HEADERS([argtable2.h], [],
+ AC_MSG_ERROR([Could not find argtable2.h. Try $ ./configure CFLAGS='-Iyour-argtable2-include-path]))
+AC_CHECK_LIB(argtable2, arg_parse, [],
+ AC_MSG_ERROR([Could not find libargtable2. Try $ ./configure LDFLAGS="-Lyour-argtable2-lib-path']))
+
+
+# enable python if requested (--with-python)
+#
+#AC_ARG_WITH([python],
+# [AS_HELP_STRING([--with-python],
+# [Enable Python Interface])],
+# [with_python=$withval],
+# [with_python=no])
+#if test "$with_python" = "yes"; then
+# AC_MSG_CHECKING([for python-config to get compiler flags])
+# AC_CHECK_PROG(python_config, 'python-config', yes)
+# if test "${python_config}" != "yes"; then
+# AC_MSG_ERROR("Could not run python-config.")
+# fi
+# PYTHON_CFLAGS=`python-config --cflags`
+# PYTHON_LDFLAGS=`python-config --ldflags`
+# AC_DEFINE([PYTHON_ENABLED], [1], [define for python usage])
+#fi
+#AC_SUBST(PYTHON_CFLAGS)
+#AC_SUBST(PYTHON_LDFLAGS)
+
+
+# --- SSE support
+# "One instruction to do the same operation on 4 packed elements simultaneously."
+#
+# http://www.codeproject.com/KB/recipes/sseintro.aspx?msg=568491
+# http://www.drdobbs.com/go-parallel/blog/archives/2010/03/getting_amazing.html
+# http://software.intel.com/file/1000
+#
+# AC_MSG_CHECKING(for SSE in current arch/CFLAGS)
+# AC_LINK_IFELSE([
+# AC_LANG_PROGRAM([[
+# #include <xmmintrin.h>
+# __m128 testfunc(float *a, float *b) {
+# return _mm_add_ps(_mm_loadu_ps(a), _mm_loadu_ps(b));
+# }
+# ]])],
+# [has_sse=yes], [has_sse=no]
+# )
+# AC_MSG_RESULT($has_sse)
+#
+# AC_ARG_ENABLE([sse],
+# [AS_HELP_STRING([--enable-sse],
+# [Enable SSE support])],
+# [has_sse="$enableval"],
+# [has_sse=no])
+#
+# if test x"$has_sse" = x"yes"; then
+# AC_DEFINE([USE_SSE], , [Enable SSE support])
+# CFLAGS="${CFLAGS} -msse"
+# fi
+
+
+# --- openmp
+#
+AC_CONFIG_MACRO_DIR([m4])
+m4_include([m4/ax_openmp.m4])
+AC_ARG_WITH([openmp],
+ AS_HELP_STRING([--without-openmp], [Do not use OpenMP]))
+AS_IF([test "x$with_openmp" = "xno"],
+ [],
+ [AX_OPENMP(
+ AC_DEFINE([HAVE_OPENMP],[1],[Defined if OpenMP should and can be used])
+ )]
+ )
+AC_SUBST(OPENMP_CFLAGS)
+# according to http://beagle-lib.googlecode.com/svn-history/r824/trunk/configure.ac:
+# "OpenMP checker only defines for C when compiling both C and C++"
+OPENMP_CXXFLAGS=$OPENMP_CFLAGS
+AC_SUBST(OPENMP_CXXFLAGS)
+
+# version 2: enable openmp only if explicitely asked for it
+#AC_ARG_ENABLE(openmp, AS_HELP_STRING([--enable-openmp], [Multi-threaded parallel version using OpenMP]))
+#if test -n "${enable_openmp}" -a x"${enable_openmp}" != x"no"; then
+# m4_include([m4/ax_openmp.m4])
+# AX_OPENMP(AC_DEFINE(HAVE_OPENMP, 1, [enable OpenMP support]),
+# AC_MSG_ERROR([Compiler does not seem to support OpenMP]))
+# AC_SUBST(OPENMP_CFLAGS)
+# AC_SUBST(OPENMP_CXXFLAGS)
+#fi
+
+# --- squid
+#
+#
+# Extra checks for squid; see their configure, config.log, squidconf.h
+# etc. For example, I'm not sure about USE_HOST_BYTESWAP_FUNCTIONS,
+# SIZEOF_UNSIGNED_LONG, HAVE_STRTOUL and HAVE_STRTOULL
+#
+# Might not just have to set compiler flags but create use squidconf.h.in
+#
+# The following hopefully takes about byte ordering (big-endian...).
+# My hope is that it will set WORDS_BIGENDIAN and
+# USE_HOST_BYTESWAP_FUNCTIONS (as used by squid) if necessary:
+#
+AC_C_BIGENDIAN(AC_MSG_WARN([$PACKAGE_NAME hasn't been tested on Big-Endian machines...expecting trouble!]))
+AC_CHECK_FUNCS([ntohs ntohl ntons ntonl])
+#
+AC_CHECK_SIZEOF(unsigned short)
+AC_CHECK_SIZEOF(unsigned int)
+AC_CHECK_SIZEOF(unsigned long)
+AC_CHECK_SIZEOF(unsigned long long)
+#
+AC_CHECK_FUNCS([stroul strtoull])
+AC_CHECK_FUNCS([ftello fseeko])
+AC_CHECK_FUNCS([ftello64 fseeko64])
+AC_CHECK_FUNCS([ftell64 fseek64])
+#
+AC_TYPE_OFF_T
+AC_CHECK_SIZEOF(fpos_t)
+#
+# struct stat64 and stat64 test:
+# version 1:
+#AC_CHECK_TYPE(struct stat64,
+# [AC_CHECK_FUNC([stat64],
+# AC_DEFINE([HAVE_STAT64], [1], [Define if you have the stat64 function]))])
+# version 2:
+#AC_MSG_CHECKING(for struct stat64)
+#AC_CACHE_VAL(sc_cv_type_stat64,
+#[AC_TRY_COMPILE([#include <sys/stat.h>],[struct stat64 s;],
+#[sc_cv_type_stat64=yes],
+#[sc_cv_type_stat64=no])])
+#if test $sc_cv_type_stat64 = yes; then
+# AC_MSG_RESULT($sc_cv_type_stat64)
+# AC_CHECK_FUNC([stat64], AC_DEFINE([HAVE_STAT64], [1], [Define if you have the stat64 function]))
+# #AC_DEFINE(HAVE_STAT64, [1], [Define if you have the stat64 function])
+#fi
+#
+#
+# Above fails on myosin because storage size of struct 64 is unknown:
+# ssi.c:480: error: storage size of ‘s1’ isn’t known
+#
+# On my MacBook OS X 10.6 I get:
+# ssi.c:481: warning: ‘stat64’ is deprecated (declared at /usr/include/sys/stat.h:465)
+#
+# So forget about it: we won't use stat64 or define HAVE_STAT64 and
+# consequently do no tests here
+#
+
+
+
+# Add support for the Dmalloc package. If the user runs configure with
+# --with-dmalloc, then define WITH_DMALLOC and add -ldmalloc to LIBS.
+AM_WITH_DMALLOC
+
+
+# Check if svnversion is installed
+#AC_PATH_PROG([SVNVERSION_BIN], [svnversionFIXME], [no])
+## checking if we build in a subversion WC
+#wc_found="no";
+#if test "$SVNVERSION_BIN" != "no"; then
+# SVNVERSION=`$SVNVERSION_BIN -n $srcdir`
+# if test $SVNVERSION != "exported";
+# then
+# AC_MSG_NOTICE($SVNVERSION);
+# fi
+#fi
+
+
+# --- debugging
+#
+#
+#
+AC_MSG_CHECKING([whether to build with debug information])
+AC_ARG_ENABLE([debug],
+ [AS_HELP_STRING([--enable-debug],
+ [Enable debugging (default=no)])],
+ [debugit="$enableval"],
+ [debugit=no])
+AC_MSG_RESULT([$debugit])
+
+if test x"$debugit" = x"yes"; then
+ # User variables CFLAGS/CXXFLAGS are used last during compilation and
+ # can therefore overwrite system settings.
+ #
+ # if debugging was requested, add debugging info at the end of
+ # C[XX]FLAGS, which makes sure previous optimisation flags are
+ # overwritten (normally C[XX]FLAGS should not be modified as they
+ # are user variables):
+ # switch off assert etc
+ # AC_DEFINE([DEBUG],[],[Debug Mode])
+ CFLAGS="${CFLAGS} -g -ansi -Wall -O0"
+ CXXFLAGS="${CXXFLAGS} -g -ansi -Wall -O0"
+else
+ # switch off assert etc
+ AC_DEFINE([NDEBUG],[],[No-debug Mode])
+ # if no debugging is requested, we make optimisation explicit
+ AM_CXXFLAGS="${AM_CXXFLAGS} -O3"
+ AM_CFLAGS="${AM_CFLAGS} -O3"
+fi
+
+
+
+AC_SUBST([AM_CXXFLAGS])
+AC_SUBST([AM_CFLAGS])
+AC_SUBST([AM_LDFLAGS])
+
+
+AC_CONFIG_FILES(Makefile
+ src/Makefile
+ clustalo.pc
+ Doxyfile
+ src/clustal/Makefile
+ src/hhalign/Makefile
+ src/kmpp/Makefile
+ src/squid/Makefile)
+AC_OUTPUT
--- /dev/null
+#! /bin/sh
+# depcomp - compile a program generating dependencies as side-effects
+
+scriptversion=2009-04-28.21; # UTC
+
+# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free
+# Software Foundation, Inc.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# Originally written by Alexandre Oliva <oliva@dcc.unicamp.br>.
+
+case $1 in
+ '')
+ echo "$0: No command. Try \`$0 --help' for more information." 1>&2
+ exit 1;
+ ;;
+ -h | --h*)
+ cat <<\EOF
+Usage: depcomp [--help] [--version] PROGRAM [ARGS]
+
+Run PROGRAMS ARGS to compile a file, generating dependencies
+as side-effects.
+
+Environment variables:
+ depmode Dependency tracking mode.
+ source Source file read by `PROGRAMS ARGS'.
+ object Object file output by `PROGRAMS ARGS'.
+ DEPDIR directory where to store dependencies.
+ depfile Dependency file to output.
+ tmpdepfile Temporary file to use when outputing dependencies.
+ libtool Whether libtool is used (yes/no).
+
+Report bugs to <bug-automake@gnu.org>.
+EOF
+ exit $?
+ ;;
+ -v | --v*)
+ echo "depcomp $scriptversion"
+ exit $?
+ ;;
+esac
+
+if test -z "$depmode" || test -z "$source" || test -z "$object"; then
+ echo "depcomp: Variables source, object and depmode must be set" 1>&2
+ exit 1
+fi
+
+# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
+depfile=${depfile-`echo "$object" |
+ sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
+tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
+
+rm -f "$tmpdepfile"
+
+# Some modes work just like other modes, but use different flags. We
+# parameterize here, but still list the modes in the big case below,
+# to make depend.m4 easier to write. Note that we *cannot* use a case
+# here, because this file can only contain one case statement.
+if test "$depmode" = hp; then
+ # HP compiler uses -M and no extra arg.
+ gccflag=-M
+ depmode=gcc
+fi
+
+if test "$depmode" = dashXmstdout; then
+ # This is just like dashmstdout with a different argument.
+ dashmflag=-xM
+ depmode=dashmstdout
+fi
+
+cygpath_u="cygpath -u -f -"
+if test "$depmode" = msvcmsys; then
+ # This is just like msvisualcpp but w/o cygpath translation.
+ # Just convert the backslash-escaped backslashes to single forward
+ # slashes to satisfy depend.m4
+ cygpath_u="sed s,\\\\\\\\,/,g"
+ depmode=msvisualcpp
+fi
+
+case "$depmode" in
+gcc3)
+## gcc 3 implements dependency tracking that does exactly what
+## we want. Yay! Note: for some reason libtool 1.4 doesn't like
+## it if -MD -MP comes after the -MF stuff. Hmm.
+## Unfortunately, FreeBSD c89 acceptance of flags depends upon
+## the command line argument order; so add the flags where they
+## appear in depend2.am. Note that the slowdown incurred here
+## affects only configure: in makefiles, %FASTDEP% shortcuts this.
+ for arg
+ do
+ case $arg in
+ -c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;;
+ *) set fnord "$@" "$arg" ;;
+ esac
+ shift # fnord
+ shift # $arg
+ done
+ "$@"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ mv "$tmpdepfile" "$depfile"
+ ;;
+
+gcc)
+## There are various ways to get dependency output from gcc. Here's
+## why we pick this rather obscure method:
+## - Don't want to use -MD because we'd like the dependencies to end
+## up in a subdir. Having to rename by hand is ugly.
+## (We might end up doing this anyway to support other compilers.)
+## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
+## -MM, not -M (despite what the docs say).
+## - Using -M directly means running the compiler twice (even worse
+## than renaming).
+ if test -z "$gccflag"; then
+ gccflag=-MD,
+ fi
+ "$@" -Wp,"$gccflag$tmpdepfile"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
+## The second -e expression handles DOS-style file names with drive letters.
+ sed -e 's/^[^:]*: / /' \
+ -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
+## This next piece of magic avoids the `deleted header file' problem.
+## The problem is that when a header file which appears in a .P file
+## is deleted, the dependency causes make to die (because there is
+## typically no way to rebuild the header). We avoid this by adding
+## dummy dependencies for each header file. Too bad gcc doesn't do
+## this for us directly.
+ tr ' ' '
+' < "$tmpdepfile" |
+## Some versions of gcc put a space before the `:'. On the theory
+## that the space means something, we add a space to the output as
+## well.
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+hp)
+ # This case exists only to let depend.m4 do its work. It works by
+ # looking at the text of this script. This case will never be run,
+ # since it is checked for above.
+ exit 1
+ ;;
+
+sgi)
+ if test "$libtool" = yes; then
+ "$@" "-Wp,-MDupdate,$tmpdepfile"
+ else
+ "$@" -MDupdate "$tmpdepfile"
+ fi
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+
+ if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
+ echo "$object : \\" > "$depfile"
+
+ # Clip off the initial element (the dependent). Don't try to be
+ # clever and replace this with sed code, as IRIX sed won't handle
+ # lines with more than a fixed number of characters (4096 in
+ # IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
+ # the IRIX cc adds comments like `#:fec' to the end of the
+ # dependency line.
+ tr ' ' '
+' < "$tmpdepfile" \
+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \
+ tr '
+' ' ' >> "$depfile"
+ echo >> "$depfile"
+
+ # The second pass generates a dummy entry for each header file.
+ tr ' ' '
+' < "$tmpdepfile" \
+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
+ >> "$depfile"
+ else
+ # The sourcefile does not contain any dependencies, so just
+ # store a dummy comment line, to avoid errors with the Makefile
+ # "include basename.Plo" scheme.
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile"
+ ;;
+
+aix)
+ # The C for AIX Compiler uses -M and outputs the dependencies
+ # in a .u file. In older versions, this file always lives in the
+ # current directory. Also, the AIX compiler puts `$object:' at the
+ # start of each line; $object doesn't have directory information.
+ # Version 6 uses the directory in both cases.
+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+ test "x$dir" = "x$object" && dir=
+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+ if test "$libtool" = yes; then
+ tmpdepfile1=$dir$base.u
+ tmpdepfile2=$base.u
+ tmpdepfile3=$dir.libs/$base.u
+ "$@" -Wc,-M
+ else
+ tmpdepfile1=$dir$base.u
+ tmpdepfile2=$dir$base.u
+ tmpdepfile3=$dir$base.u
+ "$@" -M
+ fi
+ stat=$?
+
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
+ exit $stat
+ fi
+
+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
+ do
+ test -f "$tmpdepfile" && break
+ done
+ if test -f "$tmpdepfile"; then
+ # Each line is of the form `foo.o: dependent.h'.
+ # Do two passes, one to just change these to
+ # `$object: dependent.h' and one to simply `dependent.h:'.
+ sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
+ # That's a tab and a space in the [].
+ sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
+ else
+ # The sourcefile does not contain any dependencies, so just
+ # store a dummy comment line, to avoid errors with the Makefile
+ # "include basename.Plo" scheme.
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile"
+ ;;
+
+icc)
+ # Intel's C compiler understands `-MD -MF file'. However on
+ # icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
+ # ICC 7.0 will fill foo.d with something like
+ # foo.o: sub/foo.c
+ # foo.o: sub/foo.h
+ # which is wrong. We want:
+ # sub/foo.o: sub/foo.c
+ # sub/foo.o: sub/foo.h
+ # sub/foo.c:
+ # sub/foo.h:
+ # ICC 7.1 will output
+ # foo.o: sub/foo.c sub/foo.h
+ # and will wrap long lines using \ :
+ # foo.o: sub/foo.c ... \
+ # sub/foo.h ... \
+ # ...
+
+ "$@" -MD -MF "$tmpdepfile"
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+ # Each line is of the form `foo.o: dependent.h',
+ # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
+ # Do two passes, one to just change these to
+ # `$object: dependent.h' and one to simply `dependent.h:'.
+ sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
+ # Some versions of the HPUX 10.20 sed can't process this invocation
+ # correctly. Breaking it into two sed invocations is a workaround.
+ sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" |
+ sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+hp2)
+ # The "hp" stanza above does not work with aCC (C++) and HP's ia64
+ # compilers, which have integrated preprocessors. The correct option
+ # to use with these is +Maked; it writes dependencies to a file named
+ # 'foo.d', which lands next to the object file, wherever that
+ # happens to be.
+ # Much of this is similar to the tru64 case; see comments there.
+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+ test "x$dir" = "x$object" && dir=
+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+ if test "$libtool" = yes; then
+ tmpdepfile1=$dir$base.d
+ tmpdepfile2=$dir.libs/$base.d
+ "$@" -Wc,+Maked
+ else
+ tmpdepfile1=$dir$base.d
+ tmpdepfile2=$dir$base.d
+ "$@" +Maked
+ fi
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile1" "$tmpdepfile2"
+ exit $stat
+ fi
+
+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2"
+ do
+ test -f "$tmpdepfile" && break
+ done
+ if test -f "$tmpdepfile"; then
+ sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile"
+ # Add `dependent.h:' lines.
+ sed -ne '2,${
+ s/^ *//
+ s/ \\*$//
+ s/$/:/
+ p
+ }' "$tmpdepfile" >> "$depfile"
+ else
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile" "$tmpdepfile2"
+ ;;
+
+tru64)
+ # The Tru64 compiler uses -MD to generate dependencies as a side
+ # effect. `cc -MD -o foo.o ...' puts the dependencies into `foo.o.d'.
+ # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
+ # dependencies in `foo.d' instead, so we check for that too.
+ # Subdirectories are respected.
+ dir=`echo "$object" | sed -e 's|/[^/]*$|/|'`
+ test "x$dir" = "x$object" && dir=
+ base=`echo "$object" | sed -e 's|^.*/||' -e 's/\.o$//' -e 's/\.lo$//'`
+
+ if test "$libtool" = yes; then
+ # With Tru64 cc, shared objects can also be used to make a
+ # static library. This mechanism is used in libtool 1.4 series to
+ # handle both shared and static libraries in a single compilation.
+ # With libtool 1.4, dependencies were output in $dir.libs/$base.lo.d.
+ #
+ # With libtool 1.5 this exception was removed, and libtool now
+ # generates 2 separate objects for the 2 libraries. These two
+ # compilations output dependencies in $dir.libs/$base.o.d and
+ # in $dir$base.o.d. We have to check for both files, because
+ # one of the two compilations can be disabled. We should prefer
+ # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
+ # automatically cleaned when .libs/ is deleted, while ignoring
+ # the former would cause a distcleancheck panic.
+ tmpdepfile1=$dir.libs/$base.lo.d # libtool 1.4
+ tmpdepfile2=$dir$base.o.d # libtool 1.5
+ tmpdepfile3=$dir.libs/$base.o.d # libtool 1.5
+ tmpdepfile4=$dir.libs/$base.d # Compaq CCC V6.2-504
+ "$@" -Wc,-MD
+ else
+ tmpdepfile1=$dir$base.o.d
+ tmpdepfile2=$dir$base.d
+ tmpdepfile3=$dir$base.d
+ tmpdepfile4=$dir$base.d
+ "$@" -MD
+ fi
+
+ stat=$?
+ if test $stat -eq 0; then :
+ else
+ rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
+ exit $stat
+ fi
+
+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3" "$tmpdepfile4"
+ do
+ test -f "$tmpdepfile" && break
+ done
+ if test -f "$tmpdepfile"; then
+ sed -e "s,^.*\.[a-z]*:,$object:," < "$tmpdepfile" > "$depfile"
+ # That's a tab and a space in the [].
+ sed -e 's,^.*\.[a-z]*:[ ]*,,' -e 's,$,:,' < "$tmpdepfile" >> "$depfile"
+ else
+ echo "#dummy" > "$depfile"
+ fi
+ rm -f "$tmpdepfile"
+ ;;
+
+#nosideeffect)
+ # This comment above is used by automake to tell side-effect
+ # dependency tracking mechanisms from slower ones.
+
+dashmstdout)
+ # Important note: in order to support this mode, a compiler *must*
+ # always write the preprocessed file to stdout, regardless of -o.
+ "$@" || exit $?
+
+ # Remove the call to Libtool.
+ if test "$libtool" = yes; then
+ while test "X$1" != 'X--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+
+ # Remove `-o $object'.
+ IFS=" "
+ for arg
+ do
+ case $arg in
+ -o)
+ shift
+ ;;
+ $object)
+ shift
+ ;;
+ *)
+ set fnord "$@" "$arg"
+ shift # fnord
+ shift # $arg
+ ;;
+ esac
+ done
+
+ test -z "$dashmflag" && dashmflag=-M
+ # Require at least two characters before searching for `:'
+ # in the target name. This is to cope with DOS-style filenames:
+ # a dependency such as `c:/foo/bar' could be seen as target `c' otherwise.
+ "$@" $dashmflag |
+ sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile"
+ rm -f "$depfile"
+ cat < "$tmpdepfile" > "$depfile"
+ tr ' ' '
+' < "$tmpdepfile" | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+dashXmstdout)
+ # This case only exists to satisfy depend.m4. It is never actually
+ # run, as this mode is specially recognized in the preamble.
+ exit 1
+ ;;
+
+makedepend)
+ "$@" || exit $?
+ # Remove any Libtool call
+ if test "$libtool" = yes; then
+ while test "X$1" != 'X--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+ # X makedepend
+ shift
+ cleared=no eat=no
+ for arg
+ do
+ case $cleared in
+ no)
+ set ""; shift
+ cleared=yes ;;
+ esac
+ if test $eat = yes; then
+ eat=no
+ continue
+ fi
+ case "$arg" in
+ -D*|-I*)
+ set fnord "$@" "$arg"; shift ;;
+ # Strip any option that makedepend may not understand. Remove
+ # the object too, otherwise makedepend will parse it as a source file.
+ -arch)
+ eat=yes ;;
+ -*|$object)
+ ;;
+ *)
+ set fnord "$@" "$arg"; shift ;;
+ esac
+ done
+ obj_suffix=`echo "$object" | sed 's/^.*\././'`
+ touch "$tmpdepfile"
+ ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
+ rm -f "$depfile"
+ cat < "$tmpdepfile" > "$depfile"
+ sed '1,2d' "$tmpdepfile" | tr ' ' '
+' | \
+## Some versions of the HPUX 10.20 sed can't process this invocation
+## correctly. Breaking it into two sed invocations is a workaround.
+ sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' | sed -e 's/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile" "$tmpdepfile".bak
+ ;;
+
+cpp)
+ # Important note: in order to support this mode, a compiler *must*
+ # always write the preprocessed file to stdout.
+ "$@" || exit $?
+
+ # Remove the call to Libtool.
+ if test "$libtool" = yes; then
+ while test "X$1" != 'X--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+
+ # Remove `-o $object'.
+ IFS=" "
+ for arg
+ do
+ case $arg in
+ -o)
+ shift
+ ;;
+ $object)
+ shift
+ ;;
+ *)
+ set fnord "$@" "$arg"
+ shift # fnord
+ shift # $arg
+ ;;
+ esac
+ done
+
+ "$@" -E |
+ sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
+ -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
+ sed '$ s: \\$::' > "$tmpdepfile"
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ cat < "$tmpdepfile" >> "$depfile"
+ sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+msvisualcpp)
+ # Important note: in order to support this mode, a compiler *must*
+ # always write the preprocessed file to stdout.
+ "$@" || exit $?
+
+ # Remove the call to Libtool.
+ if test "$libtool" = yes; then
+ while test "X$1" != 'X--mode=compile'; do
+ shift
+ done
+ shift
+ fi
+
+ IFS=" "
+ for arg
+ do
+ case "$arg" in
+ -o)
+ shift
+ ;;
+ $object)
+ shift
+ ;;
+ "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
+ set fnord "$@"
+ shift
+ shift
+ ;;
+ *)
+ set fnord "$@" "$arg"
+ shift
+ shift
+ ;;
+ esac
+ done
+ "$@" -E 2>/dev/null |
+ sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile"
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile"
+ echo " " >> "$depfile"
+ sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"
+ rm -f "$tmpdepfile"
+ ;;
+
+msvcmsys)
+ # This case exists only to let depend.m4 do its work. It works by
+ # looking at the text of this script. This case will never be run,
+ # since it is checked for above.
+ exit 1
+ ;;
+
+none)
+ exec "$@"
+ ;;
+
+*)
+ echo "Unknown depmode $depmode" 1>&2
+ exit 1
+ ;;
+esac
+
+exit 0
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
--- /dev/null
+#!/bin/sh
+# install - install a program, script, or datafile
+
+scriptversion=2009-04-28.21; # UTC
+
+# This originates from X11R5 (mit/util/scripts/install.sh), which was
+# later released in X11R6 (xc/config/util/install.sh) with the
+# following copyright and license.
+#
+# Copyright (C) 1994 X Consortium
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to
+# deal in the Software without restriction, including without limitation the
+# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+# sell copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
+# AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
+# TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# Except as contained in this notice, the name of the X Consortium shall not
+# be used in advertising or otherwise to promote the sale, use or other deal-
+# ings in this Software without prior written authorization from the X Consor-
+# tium.
+#
+#
+# FSF changes to this file are in the public domain.
+#
+# Calling this script install-sh is preferred over install.sh, to prevent
+# `make' implicit rules from creating a file called install from it
+# when there is no Makefile.
+#
+# This script is compatible with the BSD install script, but was written
+# from scratch.
+
+nl='
+'
+IFS=" "" $nl"
+
+# set DOITPROG to echo to test this script
+
+# Don't use :- since 4.3BSD and earlier shells don't like it.
+doit=${DOITPROG-}
+if test -z "$doit"; then
+ doit_exec=exec
+else
+ doit_exec=$doit
+fi
+
+# Put in absolute file names if you don't have them in your path;
+# or use environment vars.
+
+chgrpprog=${CHGRPPROG-chgrp}
+chmodprog=${CHMODPROG-chmod}
+chownprog=${CHOWNPROG-chown}
+cmpprog=${CMPPROG-cmp}
+cpprog=${CPPROG-cp}
+mkdirprog=${MKDIRPROG-mkdir}
+mvprog=${MVPROG-mv}
+rmprog=${RMPROG-rm}
+stripprog=${STRIPPROG-strip}
+
+posix_glob='?'
+initialize_posix_glob='
+ test "$posix_glob" != "?" || {
+ if (set -f) 2>/dev/null; then
+ posix_glob=
+ else
+ posix_glob=:
+ fi
+ }
+'
+
+posix_mkdir=
+
+# Desired mode of installed file.
+mode=0755
+
+chgrpcmd=
+chmodcmd=$chmodprog
+chowncmd=
+mvcmd=$mvprog
+rmcmd="$rmprog -f"
+stripcmd=
+
+src=
+dst=
+dir_arg=
+dst_arg=
+
+copy_on_change=false
+no_target_directory=
+
+usage="\
+Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
+ or: $0 [OPTION]... SRCFILES... DIRECTORY
+ or: $0 [OPTION]... -t DIRECTORY SRCFILES...
+ or: $0 [OPTION]... -d DIRECTORIES...
+
+In the 1st form, copy SRCFILE to DSTFILE.
+In the 2nd and 3rd, copy all SRCFILES to DIRECTORY.
+In the 4th, create DIRECTORIES.
+
+Options:
+ --help display this help and exit.
+ --version display version info and exit.
+
+ -c (ignored)
+ -C install only if different (preserve the last data modification time)
+ -d create directories instead of installing files.
+ -g GROUP $chgrpprog installed files to GROUP.
+ -m MODE $chmodprog installed files to MODE.
+ -o USER $chownprog installed files to USER.
+ -s $stripprog installed files.
+ -t DIRECTORY install into DIRECTORY.
+ -T report an error if DSTFILE is a directory.
+
+Environment variables override the default commands:
+ CHGRPPROG CHMODPROG CHOWNPROG CMPPROG CPPROG MKDIRPROG MVPROG
+ RMPROG STRIPPROG
+"
+
+while test $# -ne 0; do
+ case $1 in
+ -c) ;;
+
+ -C) copy_on_change=true;;
+
+ -d) dir_arg=true;;
+
+ -g) chgrpcmd="$chgrpprog $2"
+ shift;;
+
+ --help) echo "$usage"; exit $?;;
+
+ -m) mode=$2
+ case $mode in
+ *' '* | *' '* | *'
+'* | *'*'* | *'?'* | *'['*)
+ echo "$0: invalid mode: $mode" >&2
+ exit 1;;
+ esac
+ shift;;
+
+ -o) chowncmd="$chownprog $2"
+ shift;;
+
+ -s) stripcmd=$stripprog;;
+
+ -t) dst_arg=$2
+ shift;;
+
+ -T) no_target_directory=true;;
+
+ --version) echo "$0 $scriptversion"; exit $?;;
+
+ --) shift
+ break;;
+
+ -*) echo "$0: invalid option: $1" >&2
+ exit 1;;
+
+ *) break;;
+ esac
+ shift
+done
+
+if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
+ # When -d is used, all remaining arguments are directories to create.
+ # When -t is used, the destination is already specified.
+ # Otherwise, the last argument is the destination. Remove it from $@.
+ for arg
+ do
+ if test -n "$dst_arg"; then
+ # $@ is not empty: it contains at least $arg.
+ set fnord "$@" "$dst_arg"
+ shift # fnord
+ fi
+ shift # arg
+ dst_arg=$arg
+ done
+fi
+
+if test $# -eq 0; then
+ if test -z "$dir_arg"; then
+ echo "$0: no input file specified." >&2
+ exit 1
+ fi
+ # It's OK to call `install-sh -d' without argument.
+ # This can happen when creating conditional directories.
+ exit 0
+fi
+
+if test -z "$dir_arg"; then
+ trap '(exit $?); exit' 1 2 13 15
+
+ # Set umask so as not to create temps with too-generous modes.
+ # However, 'strip' requires both read and write access to temps.
+ case $mode in
+ # Optimize common cases.
+ *644) cp_umask=133;;
+ *755) cp_umask=22;;
+
+ *[0-7])
+ if test -z "$stripcmd"; then
+ u_plus_rw=
+ else
+ u_plus_rw='% 200'
+ fi
+ cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
+ *)
+ if test -z "$stripcmd"; then
+ u_plus_rw=
+ else
+ u_plus_rw=,u+rw
+ fi
+ cp_umask=$mode$u_plus_rw;;
+ esac
+fi
+
+for src
+do
+ # Protect names starting with `-'.
+ case $src in
+ -*) src=./$src;;
+ esac
+
+ if test -n "$dir_arg"; then
+ dst=$src
+ dstdir=$dst
+ test -d "$dstdir"
+ dstdir_status=$?
+ else
+
+ # Waiting for this to be detected by the "$cpprog $src $dsttmp" command
+ # might cause directories to be created, which would be especially bad
+ # if $src (and thus $dsttmp) contains '*'.
+ if test ! -f "$src" && test ! -d "$src"; then
+ echo "$0: $src does not exist." >&2
+ exit 1
+ fi
+
+ if test -z "$dst_arg"; then
+ echo "$0: no destination specified." >&2
+ exit 1
+ fi
+
+ dst=$dst_arg
+ # Protect names starting with `-'.
+ case $dst in
+ -*) dst=./$dst;;
+ esac
+
+ # If destination is a directory, append the input filename; won't work
+ # if double slashes aren't ignored.
+ if test -d "$dst"; then
+ if test -n "$no_target_directory"; then
+ echo "$0: $dst_arg: Is a directory" >&2
+ exit 1
+ fi
+ dstdir=$dst
+ dst=$dstdir/`basename "$src"`
+ dstdir_status=0
+ else
+ # Prefer dirname, but fall back on a substitute if dirname fails.
+ dstdir=`
+ (dirname "$dst") 2>/dev/null ||
+ expr X"$dst" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
+ X"$dst" : 'X\(//\)[^/]' \| \
+ X"$dst" : 'X\(//\)$' \| \
+ X"$dst" : 'X\(/\)' \| . 2>/dev/null ||
+ echo X"$dst" |
+ sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)[^/].*/{
+ s//\1/
+ q
+ }
+ /^X\(\/\/\)$/{
+ s//\1/
+ q
+ }
+ /^X\(\/\).*/{
+ s//\1/
+ q
+ }
+ s/.*/./; q'
+ `
+
+ test -d "$dstdir"
+ dstdir_status=$?
+ fi
+ fi
+
+ obsolete_mkdir_used=false
+
+ if test $dstdir_status != 0; then
+ case $posix_mkdir in
+ '')
+ # Create intermediate dirs using mode 755 as modified by the umask.
+ # This is like FreeBSD 'install' as of 1997-10-28.
+ umask=`umask`
+ case $stripcmd.$umask in
+ # Optimize common cases.
+ *[2367][2367]) mkdir_umask=$umask;;
+ .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
+
+ *[0-7])
+ mkdir_umask=`expr $umask + 22 \
+ - $umask % 100 % 40 + $umask % 20 \
+ - $umask % 10 % 4 + $umask % 2
+ `;;
+ *) mkdir_umask=$umask,go-w;;
+ esac
+
+ # With -d, create the new directory with the user-specified mode.
+ # Otherwise, rely on $mkdir_umask.
+ if test -n "$dir_arg"; then
+ mkdir_mode=-m$mode
+ else
+ mkdir_mode=
+ fi
+
+ posix_mkdir=false
+ case $umask in
+ *[123567][0-7][0-7])
+ # POSIX mkdir -p sets u+wx bits regardless of umask, which
+ # is incompatible with FreeBSD 'install' when (umask & 300) != 0.
+ ;;
+ *)
+ tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
+ trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
+
+ if (umask $mkdir_umask &&
+ exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
+ then
+ if test -z "$dir_arg" || {
+ # Check for POSIX incompatibilities with -m.
+ # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
+ # other-writeable bit of parent directory when it shouldn't.
+ # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
+ ls_ld_tmpdir=`ls -ld "$tmpdir"`
+ case $ls_ld_tmpdir in
+ d????-?r-*) different_mode=700;;
+ d????-?--*) different_mode=755;;
+ *) false;;
+ esac &&
+ $mkdirprog -m$different_mode -p -- "$tmpdir" && {
+ ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
+ test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
+ }
+ }
+ then posix_mkdir=:
+ fi
+ rmdir "$tmpdir/d" "$tmpdir"
+ else
+ # Remove any dirs left behind by ancient mkdir implementations.
+ rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
+ fi
+ trap '' 0;;
+ esac;;
+ esac
+
+ if
+ $posix_mkdir && (
+ umask $mkdir_umask &&
+ $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
+ )
+ then :
+ else
+
+ # The umask is ridiculous, or mkdir does not conform to POSIX,
+ # or it failed possibly due to a race condition. Create the
+ # directory the slow way, step by step, checking for races as we go.
+
+ case $dstdir in
+ /*) prefix='/';;
+ -*) prefix='./';;
+ *) prefix='';;
+ esac
+
+ eval "$initialize_posix_glob"
+
+ oIFS=$IFS
+ IFS=/
+ $posix_glob set -f
+ set fnord $dstdir
+ shift
+ $posix_glob set +f
+ IFS=$oIFS
+
+ prefixes=
+
+ for d
+ do
+ test -z "$d" && continue
+
+ prefix=$prefix$d
+ if test -d "$prefix"; then
+ prefixes=
+ else
+ if $posix_mkdir; then
+ (umask=$mkdir_umask &&
+ $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir") && break
+ # Don't fail if two instances are running concurrently.
+ test -d "$prefix" || exit 1
+ else
+ case $prefix in
+ *\'*) qprefix=`echo "$prefix" | sed "s/'/'\\\\\\\\''/g"`;;
+ *) qprefix=$prefix;;
+ esac
+ prefixes="$prefixes '$qprefix'"
+ fi
+ fi
+ prefix=$prefix/
+ done
+
+ if test -n "$prefixes"; then
+ # Don't fail if two instances are running concurrently.
+ (umask $mkdir_umask &&
+ eval "\$doit_exec \$mkdirprog $prefixes") ||
+ test -d "$dstdir" || exit 1
+ obsolete_mkdir_used=true
+ fi
+ fi
+ fi
+
+ if test -n "$dir_arg"; then
+ { test -z "$chowncmd" || $doit $chowncmd "$dst"; } &&
+ { test -z "$chgrpcmd" || $doit $chgrpcmd "$dst"; } &&
+ { test "$obsolete_mkdir_used$chowncmd$chgrpcmd" = false ||
+ test -z "$chmodcmd" || $doit $chmodcmd $mode "$dst"; } || exit 1
+ else
+
+ # Make a couple of temp file names in the proper directory.
+ dsttmp=$dstdir/_inst.$$_
+ rmtmp=$dstdir/_rm.$$_
+
+ # Trap to clean up those temp files at exit.
+ trap 'ret=$?; rm -f "$dsttmp" "$rmtmp" && exit $ret' 0
+
+ # Copy the file name to the temp name.
+ (umask $cp_umask && $doit_exec $cpprog "$src" "$dsttmp") &&
+
+ # and set any options; do chmod last to preserve setuid bits.
+ #
+ # If any of these fail, we abort the whole thing. If we want to
+ # ignore errors from any of these, just make sure not to ignore
+ # errors from the above "$doit $cpprog $src $dsttmp" command.
+ #
+ { test -z "$chowncmd" || $doit $chowncmd "$dsttmp"; } &&
+ { test -z "$chgrpcmd" || $doit $chgrpcmd "$dsttmp"; } &&
+ { test -z "$stripcmd" || $doit $stripcmd "$dsttmp"; } &&
+ { test -z "$chmodcmd" || $doit $chmodcmd $mode "$dsttmp"; } &&
+
+ # If -C, don't bother to copy if it wouldn't change the file.
+ if $copy_on_change &&
+ old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&
+ new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&
+
+ eval "$initialize_posix_glob" &&
+ $posix_glob set -f &&
+ set X $old && old=:$2:$4:$5:$6 &&
+ set X $new && new=:$2:$4:$5:$6 &&
+ $posix_glob set +f &&
+
+ test "$old" = "$new" &&
+ $cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
+ then
+ rm -f "$dsttmp"
+ else
+ # Rename the file to the real destination.
+ $doit $mvcmd -f "$dsttmp" "$dst" 2>/dev/null ||
+
+ # The rename failed, perhaps because mv can't rename something else
+ # to itself, or perhaps because mv is so ancient that it does not
+ # support -f.
+ {
+ # Now remove or move aside any old file at destination location.
+ # We try this two ways since rm can't unlink itself on some
+ # systems and the destination file might be busy for other
+ # reasons. In this case, the final cleanup might fail but the new
+ # file should still install successfully.
+ {
+ test ! -f "$dst" ||
+ $doit $rmcmd -f "$dst" 2>/dev/null ||
+ { $doit $mvcmd -f "$dst" "$rmtmp" 2>/dev/null &&
+ { $doit $rmcmd -f "$rmtmp" 2>/dev/null; :; }
+ } ||
+ { echo "$0: cannot unlink or rename $dst" >&2
+ (exit 1); exit 1
+ }
+ } &&
+
+ # Now rename the file to the real destination.
+ $doit $mvcmd "$dsttmp" "$dst"
+ }
+ fi || exit 1
+
+ trap '' 0
+ fi
+done
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
--- /dev/null
+# Generated from ltmain.m4sh.
+
+# ltmain.sh (GNU libtool) 2.2.6
+# Written by Gordon Matzigkeit <gord@gnu.ai.mit.edu>, 1996
+
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, 2006, 2007 2008 Free Software Foundation, Inc.
+# This is free software; see the source for copying conditions. There is NO
+# warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+# GNU Libtool is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# As a special exception to the GNU General Public License,
+# if you distribute this file as part of a program or library that
+# is built using GNU Libtool, you may include this file under the
+# same distribution terms that you use for the rest of that program.
+#
+# GNU Libtool is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GNU Libtool; see the file COPYING. If not, a copy
+# can be downloaded from http://www.gnu.org/licenses/gpl.html,
+# or obtained by writing to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# Usage: $progname [OPTION]... [MODE-ARG]...
+#
+# Provide generalized library-building support services.
+#
+# --config show all configuration variables
+# --debug enable verbose shell tracing
+# -n, --dry-run display commands without modifying any files
+# --features display basic configuration information and exit
+# --mode=MODE use operation mode MODE
+# --preserve-dup-deps don't remove duplicate dependency libraries
+# --quiet, --silent don't print informational messages
+# --tag=TAG use configuration variables from tag TAG
+# -v, --verbose print informational messages (default)
+# --version print version information
+# -h, --help print short or long help message
+#
+# MODE must be one of the following:
+#
+# clean remove files from the build directory
+# compile compile a source file into a libtool object
+# execute automatically set library path, then run a program
+# finish complete the installation of libtool libraries
+# install install libraries or executables
+# link create a library or an executable
+# uninstall remove libraries from an installed directory
+#
+# MODE-ARGS vary depending on the MODE.
+# Try `$progname --help --mode=MODE' for a more detailed description of MODE.
+#
+# When reporting a bug, please describe a test case to reproduce it and
+# include the following information:
+#
+# host-triplet: $host
+# shell: $SHELL
+# compiler: $LTCC
+# compiler flags: $LTCFLAGS
+# linker: $LD (gnu? $with_gnu_ld)
+# $progname: (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+# automake: $automake_version
+# autoconf: $autoconf_version
+#
+# Report bugs to <bug-libtool@gnu.org>.
+
+PROGRAM=ltmain.sh
+PACKAGE=libtool
+VERSION="2.2.6 Debian-2.2.6a-1ubuntu1"
+TIMESTAMP=""
+package_revision=1.3012
+
+# Be Bourne compatible
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+ emulate sh
+ NULLCMD=:
+ # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
+ setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in *posix*) set -o posix;; esac
+fi
+BIN_SH=xpg4; export BIN_SH # for Tru64
+DUALCASE=1; export DUALCASE # for MKS sh
+
+# NLS nuisances: We save the old values to restore during execute mode.
+# Only set LANG and LC_ALL to C if already set.
+# These must not be set unconditionally because not all systems understand
+# e.g. LANG=C (notably SCO).
+lt_user_locale=
+lt_safe_locale=
+for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES
+do
+ eval "if test \"\${$lt_var+set}\" = set; then
+ save_$lt_var=\$$lt_var
+ $lt_var=C
+ export $lt_var
+ lt_user_locale=\"$lt_var=\\\$save_\$lt_var; \$lt_user_locale\"
+ lt_safe_locale=\"$lt_var=C; \$lt_safe_locale\"
+ fi"
+done
+
+$lt_unset CDPATH
+
+
+
+
+
+: ${CP="cp -f"}
+: ${ECHO="echo"}
+: ${EGREP="/bin/grep -E"}
+: ${FGREP="/bin/grep -F"}
+: ${GREP="/bin/grep"}
+: ${LN_S="ln -s"}
+: ${MAKE="make"}
+: ${MKDIR="mkdir"}
+: ${MV="mv -f"}
+: ${RM="rm -f"}
+: ${SED="/bin/sed"}
+: ${SHELL="${CONFIG_SHELL-/bin/sh}"}
+: ${Xsed="$SED -e 1s/^X//"}
+
+# Global variables:
+EXIT_SUCCESS=0
+EXIT_FAILURE=1
+EXIT_MISMATCH=63 # $? = 63 is used to indicate version mismatch to missing.
+EXIT_SKIP=77 # $? = 77 is used to indicate a skipped test to automake.
+
+exit_status=$EXIT_SUCCESS
+
+# Make sure IFS has a sensible default
+lt_nl='
+'
+IFS=" $lt_nl"
+
+dirname="s,/[^/]*$,,"
+basename="s,^.*/,,"
+
+# func_dirname_and_basename file append nondir_replacement
+# perform func_basename and func_dirname in a single function
+# call:
+# dirname: Compute the dirname of FILE. If nonempty,
+# add APPEND to the result, otherwise set result
+# to NONDIR_REPLACEMENT.
+# value returned in "$func_dirname_result"
+# basename: Compute filename of FILE.
+# value retuned in "$func_basename_result"
+# Implementation must be kept synchronized with func_dirname
+# and func_basename. For efficiency, we do not delegate to
+# those functions but instead duplicate the functionality here.
+func_dirname_and_basename ()
+{
+ # Extract subdirectory from the argument.
+ func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"`
+ if test "X$func_dirname_result" = "X${1}"; then
+ func_dirname_result="${3}"
+ else
+ func_dirname_result="$func_dirname_result${2}"
+ fi
+ func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"`
+}
+
+# Generated shell functions inserted here.
+
+# Work around backward compatibility issue on IRIX 6.5. On IRIX 6.4+, sh
+# is ksh but when the shell is invoked as "sh" and the current value of
+# the _XPG environment variable is not equal to 1 (one), the special
+# positional parameter $0, within a function call, is the name of the
+# function.
+progpath="$0"
+
+# The name of this program:
+# In the unlikely event $progname began with a '-', it would play havoc with
+# func_echo (imagine progname=-n), so we prepend ./ in that case:
+func_dirname_and_basename "$progpath"
+progname=$func_basename_result
+case $progname in
+ -*) progname=./$progname ;;
+esac
+
+# Make sure we have an absolute path for reexecution:
+case $progpath in
+ [\\/]*|[A-Za-z]:\\*) ;;
+ *[\\/]*)
+ progdir=$func_dirname_result
+ progdir=`cd "$progdir" && pwd`
+ progpath="$progdir/$progname"
+ ;;
+ *)
+ save_IFS="$IFS"
+ IFS=:
+ for progdir in $PATH; do
+ IFS="$save_IFS"
+ test -x "$progdir/$progname" && break
+ done
+ IFS="$save_IFS"
+ test -n "$progdir" || progdir=`pwd`
+ progpath="$progdir/$progname"
+ ;;
+esac
+
+# Sed substitution that helps us do robust quoting. It backslashifies
+# metacharacters that are still active within double-quoted strings.
+Xsed="${SED}"' -e 1s/^X//'
+sed_quote_subst='s/\([`"$\\]\)/\\\1/g'
+
+# Same as above, but do not quote variable references.
+double_quote_subst='s/\(["`\\]\)/\\\1/g'
+
+# Re-`\' parameter expansions in output of double_quote_subst that were
+# `\'-ed in input to the same. If an odd number of `\' preceded a '$'
+# in input to double_quote_subst, that '$' was protected from expansion.
+# Since each input `\' is now two `\'s, look for any number of runs of
+# four `\'s followed by two `\'s and then a '$'. `\' that '$'.
+bs='\\'
+bs2='\\\\'
+bs4='\\\\\\\\'
+dollar='\$'
+sed_double_backslash="\
+ s/$bs4/&\\
+/g
+ s/^$bs2$dollar/$bs&/
+ s/\\([^$bs]\\)$bs2$dollar/\\1$bs2$bs$dollar/g
+ s/\n//g"
+
+# Standard options:
+opt_dry_run=false
+opt_help=false
+opt_quiet=false
+opt_verbose=false
+opt_warning=:
+
+# func_echo arg...
+# Echo program name prefixed message, along with the current mode
+# name if it has been set yet.
+func_echo ()
+{
+ $ECHO "$progname${mode+: }$mode: $*"
+}
+
+# func_verbose arg...
+# Echo program name prefixed message in verbose mode only.
+func_verbose ()
+{
+ $opt_verbose && func_echo ${1+"$@"}
+
+ # A bug in bash halts the script if the last line of a function
+ # fails when set -e is in force, so we need another command to
+ # work around that:
+ :
+}
+
+# func_error arg...
+# Echo program name prefixed message to standard error.
+func_error ()
+{
+ $ECHO "$progname${mode+: }$mode: "${1+"$@"} 1>&2
+}
+
+# func_warning arg...
+# Echo program name prefixed warning message to standard error.
+func_warning ()
+{
+ $opt_warning && $ECHO "$progname${mode+: }$mode: warning: "${1+"$@"} 1>&2
+
+ # bash bug again:
+ :
+}
+
+# func_fatal_error arg...
+# Echo program name prefixed message to standard error, and exit.
+func_fatal_error ()
+{
+ func_error ${1+"$@"}
+ exit $EXIT_FAILURE
+}
+
+# func_fatal_help arg...
+# Echo program name prefixed message to standard error, followed by
+# a help hint, and exit.
+func_fatal_help ()
+{
+ func_error ${1+"$@"}
+ func_fatal_error "$help"
+}
+help="Try \`$progname --help' for more information." ## default
+
+
+# func_grep expression filename
+# Check whether EXPRESSION matches any line of FILENAME, without output.
+func_grep ()
+{
+ $GREP "$1" "$2" >/dev/null 2>&1
+}
+
+
+# func_mkdir_p directory-path
+# Make sure the entire path to DIRECTORY-PATH is available.
+func_mkdir_p ()
+{
+ my_directory_path="$1"
+ my_dir_list=
+
+ if test -n "$my_directory_path" && test "$opt_dry_run" != ":"; then
+
+ # Protect directory names starting with `-'
+ case $my_directory_path in
+ -*) my_directory_path="./$my_directory_path" ;;
+ esac
+
+ # While some portion of DIR does not yet exist...
+ while test ! -d "$my_directory_path"; do
+ # ...make a list in topmost first order. Use a colon delimited
+ # list incase some portion of path contains whitespace.
+ my_dir_list="$my_directory_path:$my_dir_list"
+
+ # If the last portion added has no slash in it, the list is done
+ case $my_directory_path in */*) ;; *) break ;; esac
+
+ # ...otherwise throw away the child directory and loop
+ my_directory_path=`$ECHO "X$my_directory_path" | $Xsed -e "$dirname"`
+ done
+ my_dir_list=`$ECHO "X$my_dir_list" | $Xsed -e 's,:*$,,'`
+
+ save_mkdir_p_IFS="$IFS"; IFS=':'
+ for my_dir in $my_dir_list; do
+ IFS="$save_mkdir_p_IFS"
+ # mkdir can fail with a `File exist' error if two processes
+ # try to create one of the directories concurrently. Don't
+ # stop in that case!
+ $MKDIR "$my_dir" 2>/dev/null || :
+ done
+ IFS="$save_mkdir_p_IFS"
+
+ # Bail out if we (or some other process) failed to create a directory.
+ test -d "$my_directory_path" || \
+ func_fatal_error "Failed to create \`$1'"
+ fi
+}
+
+
+# func_mktempdir [string]
+# Make a temporary directory that won't clash with other running
+# libtool processes, and avoids race conditions if possible. If
+# given, STRING is the basename for that directory.
+func_mktempdir ()
+{
+ my_template="${TMPDIR-/tmp}/${1-$progname}"
+
+ if test "$opt_dry_run" = ":"; then
+ # Return a directory name, but don't create it in dry-run mode
+ my_tmpdir="${my_template}-$$"
+ else
+
+ # If mktemp works, use that first and foremost
+ my_tmpdir=`mktemp -d "${my_template}-XXXXXXXX" 2>/dev/null`
+
+ if test ! -d "$my_tmpdir"; then
+ # Failing that, at least try and use $RANDOM to avoid a race
+ my_tmpdir="${my_template}-${RANDOM-0}$$"
+
+ save_mktempdir_umask=`umask`
+ umask 0077
+ $MKDIR "$my_tmpdir"
+ umask $save_mktempdir_umask
+ fi
+
+ # If we're not in dry-run mode, bomb out on failure
+ test -d "$my_tmpdir" || \
+ func_fatal_error "cannot create temporary directory \`$my_tmpdir'"
+ fi
+
+ $ECHO "X$my_tmpdir" | $Xsed
+}
+
+
+# func_quote_for_eval arg
+# Aesthetically quote ARG to be evaled later.
+# This function returns two values: FUNC_QUOTE_FOR_EVAL_RESULT
+# is double-quoted, suitable for a subsequent eval, whereas
+# FUNC_QUOTE_FOR_EVAL_UNQUOTED_RESULT has merely all characters
+# which are still active within double quotes backslashified.
+func_quote_for_eval ()
+{
+ case $1 in
+ *[\\\`\"\$]*)
+ func_quote_for_eval_unquoted_result=`$ECHO "X$1" | $Xsed -e "$sed_quote_subst"` ;;
+ *)
+ func_quote_for_eval_unquoted_result="$1" ;;
+ esac
+
+ case $func_quote_for_eval_unquoted_result in
+ # Double-quote args containing shell metacharacters to delay
+ # word splitting, command substitution and and variable
+ # expansion for a subsequent eval.
+ # Many Bourne shells cannot handle close brackets correctly
+ # in scan sets, so we specify it separately.
+ *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"")
+ func_quote_for_eval_result="\"$func_quote_for_eval_unquoted_result\""
+ ;;
+ *)
+ func_quote_for_eval_result="$func_quote_for_eval_unquoted_result"
+ esac
+}
+
+
+# func_quote_for_expand arg
+# Aesthetically quote ARG to be evaled later; same as above,
+# but do not quote variable references.
+func_quote_for_expand ()
+{
+ case $1 in
+ *[\\\`\"]*)
+ my_arg=`$ECHO "X$1" | $Xsed \
+ -e "$double_quote_subst" -e "$sed_double_backslash"` ;;
+ *)
+ my_arg="$1" ;;
+ esac
+
+ case $my_arg in
+ # Double-quote args containing shell metacharacters to delay
+ # word splitting and command substitution for a subsequent eval.
+ # Many Bourne shells cannot handle close brackets correctly
+ # in scan sets, so we specify it separately.
+ *[\[\~\#\^\&\*\(\)\{\}\|\;\<\>\?\'\ \ ]*|*]*|"")
+ my_arg="\"$my_arg\""
+ ;;
+ esac
+
+ func_quote_for_expand_result="$my_arg"
+}
+
+
+# func_show_eval cmd [fail_exp]
+# Unless opt_silent is true, then output CMD. Then, if opt_dryrun is
+# not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP
+# is given, then evaluate it.
+func_show_eval ()
+{
+ my_cmd="$1"
+ my_fail_exp="${2-:}"
+
+ ${opt_silent-false} || {
+ func_quote_for_expand "$my_cmd"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+
+ if ${opt_dry_run-false}; then :; else
+ eval "$my_cmd"
+ my_status=$?
+ if test "$my_status" -eq 0; then :; else
+ eval "(exit $my_status); $my_fail_exp"
+ fi
+ fi
+}
+
+
+# func_show_eval_locale cmd [fail_exp]
+# Unless opt_silent is true, then output CMD. Then, if opt_dryrun is
+# not true, evaluate CMD. If the evaluation of CMD fails, and FAIL_EXP
+# is given, then evaluate it. Use the saved locale for evaluation.
+func_show_eval_locale ()
+{
+ my_cmd="$1"
+ my_fail_exp="${2-:}"
+
+ ${opt_silent-false} || {
+ func_quote_for_expand "$my_cmd"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+
+ if ${opt_dry_run-false}; then :; else
+ eval "$lt_user_locale
+ $my_cmd"
+ my_status=$?
+ eval "$lt_safe_locale"
+ if test "$my_status" -eq 0; then :; else
+ eval "(exit $my_status); $my_fail_exp"
+ fi
+ fi
+}
+
+
+
+
+
+# func_version
+# Echo version message to standard output and exit.
+func_version ()
+{
+ $SED -n '/^# '$PROGRAM' (GNU /,/# warranty; / {
+ s/^# //
+ s/^# *$//
+ s/\((C)\)[ 0-9,-]*\( [1-9][0-9]*\)/\1\2/
+ p
+ }' < "$progpath"
+ exit $?
+}
+
+# func_usage
+# Echo short help message to standard output and exit.
+func_usage ()
+{
+ $SED -n '/^# Usage:/,/# -h/ {
+ s/^# //
+ s/^# *$//
+ s/\$progname/'$progname'/
+ p
+ }' < "$progpath"
+ $ECHO
+ $ECHO "run \`$progname --help | more' for full usage"
+ exit $?
+}
+
+# func_help
+# Echo long help message to standard output and exit.
+func_help ()
+{
+ $SED -n '/^# Usage:/,/# Report bugs to/ {
+ s/^# //
+ s/^# *$//
+ s*\$progname*'$progname'*
+ s*\$host*'"$host"'*
+ s*\$SHELL*'"$SHELL"'*
+ s*\$LTCC*'"$LTCC"'*
+ s*\$LTCFLAGS*'"$LTCFLAGS"'*
+ s*\$LD*'"$LD"'*
+ s/\$with_gnu_ld/'"$with_gnu_ld"'/
+ s/\$automake_version/'"`(automake --version) 2>/dev/null |$SED 1q`"'/
+ s/\$autoconf_version/'"`(autoconf --version) 2>/dev/null |$SED 1q`"'/
+ p
+ }' < "$progpath"
+ exit $?
+}
+
+# func_missing_arg argname
+# Echo program name prefixed message to standard error and set global
+# exit_cmd.
+func_missing_arg ()
+{
+ func_error "missing argument for $1"
+ exit_cmd=exit
+}
+
+exit_cmd=:
+
+
+
+
+
+# Check that we have a working $ECHO.
+if test "X$1" = X--no-reexec; then
+ # Discard the --no-reexec flag, and continue.
+ shift
+elif test "X$1" = X--fallback-echo; then
+ # Avoid inline document here, it may be left over
+ :
+elif test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t'; then
+ # Yippee, $ECHO works!
+ :
+else
+ # Restart under the correct shell, and then maybe $ECHO will work.
+ exec $SHELL "$progpath" --no-reexec ${1+"$@"}
+fi
+
+if test "X$1" = X--fallback-echo; then
+ # used as fallback echo
+ shift
+ cat <<EOF
+$*
+EOF
+ exit $EXIT_SUCCESS
+fi
+
+magic="%%%MAGIC variable%%%"
+magic_exe="%%%MAGIC EXE variable%%%"
+
+# Global variables.
+# $mode is unset
+nonopt=
+execute_dlfiles=
+preserve_args=
+lo2o="s/\\.lo\$/.${objext}/"
+o2lo="s/\\.${objext}\$/.lo/"
+extracted_archives=
+extracted_serial=0
+
+opt_dry_run=false
+opt_duplicate_deps=false
+opt_silent=false
+opt_debug=:
+
+# If this variable is set in any of the actions, the command in it
+# will be execed at the end. This prevents here-documents from being
+# left over by shells.
+exec_cmd=
+
+# func_fatal_configuration arg...
+# Echo program name prefixed message to standard error, followed by
+# a configuration failure hint, and exit.
+func_fatal_configuration ()
+{
+ func_error ${1+"$@"}
+ func_error "See the $PACKAGE documentation for more information."
+ func_fatal_error "Fatal configuration error."
+}
+
+
+# func_config
+# Display the configuration for all the tags in this script.
+func_config ()
+{
+ re_begincf='^# ### BEGIN LIBTOOL'
+ re_endcf='^# ### END LIBTOOL'
+
+ # Default configuration.
+ $SED "1,/$re_begincf CONFIG/d;/$re_endcf CONFIG/,\$d" < "$progpath"
+
+ # Now print the configurations for the tags.
+ for tagname in $taglist; do
+ $SED -n "/$re_begincf TAG CONFIG: $tagname\$/,/$re_endcf TAG CONFIG: $tagname\$/p" < "$progpath"
+ done
+
+ exit $?
+}
+
+# func_features
+# Display the features supported by this script.
+func_features ()
+{
+ $ECHO "host: $host"
+ if test "$build_libtool_libs" = yes; then
+ $ECHO "enable shared libraries"
+ else
+ $ECHO "disable shared libraries"
+ fi
+ if test "$build_old_libs" = yes; then
+ $ECHO "enable static libraries"
+ else
+ $ECHO "disable static libraries"
+ fi
+
+ exit $?
+}
+
+# func_enable_tag tagname
+# Verify that TAGNAME is valid, and either flag an error and exit, or
+# enable the TAGNAME tag. We also add TAGNAME to the global $taglist
+# variable here.
+func_enable_tag ()
+{
+ # Global variable:
+ tagname="$1"
+
+ re_begincf="^# ### BEGIN LIBTOOL TAG CONFIG: $tagname\$"
+ re_endcf="^# ### END LIBTOOL TAG CONFIG: $tagname\$"
+ sed_extractcf="/$re_begincf/,/$re_endcf/p"
+
+ # Validate tagname.
+ case $tagname in
+ *[!-_A-Za-z0-9,/]*)
+ func_fatal_error "invalid tag name: $tagname"
+ ;;
+ esac
+
+ # Don't test for the "default" C tag, as we know it's
+ # there but not specially marked.
+ case $tagname in
+ CC) ;;
+ *)
+ if $GREP "$re_begincf" "$progpath" >/dev/null 2>&1; then
+ taglist="$taglist $tagname"
+
+ # Evaluate the configuration. Be careful to quote the path
+ # and the sed script, to avoid splitting on whitespace, but
+ # also don't use non-portable quotes within backquotes within
+ # quotes we have to do it in 2 steps:
+ extractedcf=`$SED -n -e "$sed_extractcf" < "$progpath"`
+ eval "$extractedcf"
+ else
+ func_error "ignoring unknown tag $tagname"
+ fi
+ ;;
+ esac
+}
+
+# Parse options once, thoroughly. This comes as soon as possible in
+# the script to make things like `libtool --version' happen quickly.
+{
+
+ # Shorthand for --mode=foo, only valid as the first argument
+ case $1 in
+ clean|clea|cle|cl)
+ shift; set dummy --mode clean ${1+"$@"}; shift
+ ;;
+ compile|compil|compi|comp|com|co|c)
+ shift; set dummy --mode compile ${1+"$@"}; shift
+ ;;
+ execute|execut|execu|exec|exe|ex|e)
+ shift; set dummy --mode execute ${1+"$@"}; shift
+ ;;
+ finish|finis|fini|fin|fi|f)
+ shift; set dummy --mode finish ${1+"$@"}; shift
+ ;;
+ install|instal|insta|inst|ins|in|i)
+ shift; set dummy --mode install ${1+"$@"}; shift
+ ;;
+ link|lin|li|l)
+ shift; set dummy --mode link ${1+"$@"}; shift
+ ;;
+ uninstall|uninstal|uninsta|uninst|unins|unin|uni|un|u)
+ shift; set dummy --mode uninstall ${1+"$@"}; shift
+ ;;
+ esac
+
+ # Parse non-mode specific arguments:
+ while test "$#" -gt 0; do
+ opt="$1"
+ shift
+
+ case $opt in
+ --config) func_config ;;
+
+ --debug) preserve_args="$preserve_args $opt"
+ func_echo "enabling shell trace mode"
+ opt_debug='set -x'
+ $opt_debug
+ ;;
+
+ -dlopen) test "$#" -eq 0 && func_missing_arg "$opt" && break
+ execute_dlfiles="$execute_dlfiles $1"
+ shift
+ ;;
+
+ --dry-run | -n) opt_dry_run=: ;;
+ --features) func_features ;;
+ --finish) mode="finish" ;;
+
+ --mode) test "$#" -eq 0 && func_missing_arg "$opt" && break
+ case $1 in
+ # Valid mode arguments:
+ clean) ;;
+ compile) ;;
+ execute) ;;
+ finish) ;;
+ install) ;;
+ link) ;;
+ relink) ;;
+ uninstall) ;;
+
+ # Catch anything else as an error
+ *) func_error "invalid argument for $opt"
+ exit_cmd=exit
+ break
+ ;;
+ esac
+
+ mode="$1"
+ shift
+ ;;
+
+ --preserve-dup-deps)
+ opt_duplicate_deps=: ;;
+
+ --quiet|--silent) preserve_args="$preserve_args $opt"
+ opt_silent=:
+ ;;
+
+ --verbose| -v) preserve_args="$preserve_args $opt"
+ opt_silent=false
+ ;;
+
+ --tag) test "$#" -eq 0 && func_missing_arg "$opt" && break
+ preserve_args="$preserve_args $opt $1"
+ func_enable_tag "$1" # tagname is set here
+ shift
+ ;;
+
+ # Separate optargs to long options:
+ -dlopen=*|--mode=*|--tag=*)
+ func_opt_split "$opt"
+ set dummy "$func_opt_split_opt" "$func_opt_split_arg" ${1+"$@"}
+ shift
+ ;;
+
+ -\?|-h) func_usage ;;
+ --help) opt_help=: ;;
+ --version) func_version ;;
+
+ -*) func_fatal_help "unrecognized option \`$opt'" ;;
+
+ *) nonopt="$opt"
+ break
+ ;;
+ esac
+ done
+
+
+ case $host in
+ *cygwin* | *mingw* | *pw32* | *cegcc*)
+ # don't eliminate duplications in $postdeps and $predeps
+ opt_duplicate_compiler_generated_deps=:
+ ;;
+ *)
+ opt_duplicate_compiler_generated_deps=$opt_duplicate_deps
+ ;;
+ esac
+
+ # Having warned about all mis-specified options, bail out if
+ # anything was wrong.
+ $exit_cmd $EXIT_FAILURE
+}
+
+# func_check_version_match
+# Ensure that we are using m4 macros, and libtool script from the same
+# release of libtool.
+func_check_version_match ()
+{
+ if test "$package_revision" != "$macro_revision"; then
+ if test "$VERSION" != "$macro_version"; then
+ if test -z "$macro_version"; then
+ cat >&2 <<_LT_EOF
+$progname: Version mismatch error. This is $PACKAGE $VERSION, but the
+$progname: definition of this LT_INIT comes from an older release.
+$progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION
+$progname: and run autoconf again.
+_LT_EOF
+ else
+ cat >&2 <<_LT_EOF
+$progname: Version mismatch error. This is $PACKAGE $VERSION, but the
+$progname: definition of this LT_INIT comes from $PACKAGE $macro_version.
+$progname: You should recreate aclocal.m4 with macros from $PACKAGE $VERSION
+$progname: and run autoconf again.
+_LT_EOF
+ fi
+ else
+ cat >&2 <<_LT_EOF
+$progname: Version mismatch error. This is $PACKAGE $VERSION, revision $package_revision,
+$progname: but the definition of this LT_INIT comes from revision $macro_revision.
+$progname: You should recreate aclocal.m4 with macros from revision $package_revision
+$progname: of $PACKAGE $VERSION and run autoconf again.
+_LT_EOF
+ fi
+
+ exit $EXIT_MISMATCH
+ fi
+}
+
+
+## ----------- ##
+## Main. ##
+## ----------- ##
+
+$opt_help || {
+ # Sanity checks first:
+ func_check_version_match
+
+ if test "$build_libtool_libs" != yes && test "$build_old_libs" != yes; then
+ func_fatal_configuration "not configured to build any kind of library"
+ fi
+
+ test -z "$mode" && func_fatal_error "error: you must specify a MODE."
+
+
+ # Darwin sucks
+ eval std_shrext=\"$shrext_cmds\"
+
+
+ # Only execute mode is allowed to have -dlopen flags.
+ if test -n "$execute_dlfiles" && test "$mode" != execute; then
+ func_error "unrecognized option \`-dlopen'"
+ $ECHO "$help" 1>&2
+ exit $EXIT_FAILURE
+ fi
+
+ # Change the help message to a mode-specific one.
+ generic_help="$help"
+ help="Try \`$progname --help --mode=$mode' for more information."
+}
+
+
+# func_lalib_p file
+# True iff FILE is a libtool `.la' library or `.lo' object file.
+# This function is only a basic sanity check; it will hardly flush out
+# determined imposters.
+func_lalib_p ()
+{
+ test -f "$1" &&
+ $SED -e 4q "$1" 2>/dev/null \
+ | $GREP "^# Generated by .*$PACKAGE" > /dev/null 2>&1
+}
+
+# func_lalib_unsafe_p file
+# True iff FILE is a libtool `.la' library or `.lo' object file.
+# This function implements the same check as func_lalib_p without
+# resorting to external programs. To this end, it redirects stdin and
+# closes it afterwards, without saving the original file descriptor.
+# As a safety measure, use it only where a negative result would be
+# fatal anyway. Works if `file' does not exist.
+func_lalib_unsafe_p ()
+{
+ lalib_p=no
+ if test -f "$1" && test -r "$1" && exec 5<&0 <"$1"; then
+ for lalib_p_l in 1 2 3 4
+ do
+ read lalib_p_line
+ case "$lalib_p_line" in
+ \#\ Generated\ by\ *$PACKAGE* ) lalib_p=yes; break;;
+ esac
+ done
+ exec 0<&5 5<&-
+ fi
+ test "$lalib_p" = yes
+}
+
+# func_ltwrapper_script_p file
+# True iff FILE is a libtool wrapper script
+# This function is only a basic sanity check; it will hardly flush out
+# determined imposters.
+func_ltwrapper_script_p ()
+{
+ func_lalib_p "$1"
+}
+
+# func_ltwrapper_executable_p file
+# True iff FILE is a libtool wrapper executable
+# This function is only a basic sanity check; it will hardly flush out
+# determined imposters.
+func_ltwrapper_executable_p ()
+{
+ func_ltwrapper_exec_suffix=
+ case $1 in
+ *.exe) ;;
+ *) func_ltwrapper_exec_suffix=.exe ;;
+ esac
+ $GREP "$magic_exe" "$1$func_ltwrapper_exec_suffix" >/dev/null 2>&1
+}
+
+# func_ltwrapper_scriptname file
+# Assumes file is an ltwrapper_executable
+# uses $file to determine the appropriate filename for a
+# temporary ltwrapper_script.
+func_ltwrapper_scriptname ()
+{
+ func_ltwrapper_scriptname_result=""
+ if func_ltwrapper_executable_p "$1"; then
+ func_dirname_and_basename "$1" "" "."
+ func_stripname '' '.exe' "$func_basename_result"
+ func_ltwrapper_scriptname_result="$func_dirname_result/$objdir/${func_stripname_result}_ltshwrapper"
+ fi
+}
+
+# func_ltwrapper_p file
+# True iff FILE is a libtool wrapper script or wrapper executable
+# This function is only a basic sanity check; it will hardly flush out
+# determined imposters.
+func_ltwrapper_p ()
+{
+ func_ltwrapper_script_p "$1" || func_ltwrapper_executable_p "$1"
+}
+
+
+# func_execute_cmds commands fail_cmd
+# Execute tilde-delimited COMMANDS.
+# If FAIL_CMD is given, eval that upon failure.
+# FAIL_CMD may read-access the current command in variable CMD!
+func_execute_cmds ()
+{
+ $opt_debug
+ save_ifs=$IFS; IFS='~'
+ for cmd in $1; do
+ IFS=$save_ifs
+ eval cmd=\"$cmd\"
+ func_show_eval "$cmd" "${2-:}"
+ done
+ IFS=$save_ifs
+}
+
+
+# func_source file
+# Source FILE, adding directory component if necessary.
+# Note that it is not necessary on cygwin/mingw to append a dot to
+# FILE even if both FILE and FILE.exe exist: automatic-append-.exe
+# behavior happens only for exec(3), not for open(2)! Also, sourcing
+# `FILE.' does not work on cygwin managed mounts.
+func_source ()
+{
+ $opt_debug
+ case $1 in
+ */* | *\\*) . "$1" ;;
+ *) . "./$1" ;;
+ esac
+}
+
+
+# func_infer_tag arg
+# Infer tagged configuration to use if any are available and
+# if one wasn't chosen via the "--tag" command line option.
+# Only attempt this if the compiler in the base compile
+# command doesn't match the default compiler.
+# arg is usually of the form 'gcc ...'
+func_infer_tag ()
+{
+ $opt_debug
+ if test -n "$available_tags" && test -z "$tagname"; then
+ CC_quoted=
+ for arg in $CC; do
+ func_quote_for_eval "$arg"
+ CC_quoted="$CC_quoted $func_quote_for_eval_result"
+ done
+ case $@ in
+ # Blanks in the command may have been stripped by the calling shell,
+ # but not from the CC environment variable when configure was run.
+ " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*) ;;
+ # Blanks at the start of $base_compile will cause this to fail
+ # if we don't check for them as well.
+ *)
+ for z in $available_tags; do
+ if $GREP "^# ### BEGIN LIBTOOL TAG CONFIG: $z$" < "$progpath" > /dev/null; then
+ # Evaluate the configuration.
+ eval "`${SED} -n -e '/^# ### BEGIN LIBTOOL TAG CONFIG: '$z'$/,/^# ### END LIBTOOL TAG CONFIG: '$z'$/p' < $progpath`"
+ CC_quoted=
+ for arg in $CC; do
+ # Double-quote args containing other shell metacharacters.
+ func_quote_for_eval "$arg"
+ CC_quoted="$CC_quoted $func_quote_for_eval_result"
+ done
+ case "$@ " in
+ " $CC "* | "$CC "* | " `$ECHO $CC` "* | "`$ECHO $CC` "* | " $CC_quoted"* | "$CC_quoted "* | " `$ECHO $CC_quoted` "* | "`$ECHO $CC_quoted` "*)
+ # The compiler in the base compile command matches
+ # the one in the tagged configuration.
+ # Assume this is the tagged configuration we want.
+ tagname=$z
+ break
+ ;;
+ esac
+ fi
+ done
+ # If $tagname still isn't set, then no tagged configuration
+ # was found and let the user know that the "--tag" command
+ # line option must be used.
+ if test -z "$tagname"; then
+ func_echo "unable to infer tagged configuration"
+ func_fatal_error "specify a tag with \`--tag'"
+# else
+# func_verbose "using $tagname tagged configuration"
+ fi
+ ;;
+ esac
+ fi
+}
+
+
+
+# func_write_libtool_object output_name pic_name nonpic_name
+# Create a libtool object file (analogous to a ".la" file),
+# but don't create it if we're doing a dry run.
+func_write_libtool_object ()
+{
+ write_libobj=${1}
+ if test "$build_libtool_libs" = yes; then
+ write_lobj=\'${2}\'
+ else
+ write_lobj=none
+ fi
+
+ if test "$build_old_libs" = yes; then
+ write_oldobj=\'${3}\'
+ else
+ write_oldobj=none
+ fi
+
+ $opt_dry_run || {
+ cat >${write_libobj}T <<EOF
+# $write_libobj - a libtool object file
+# Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object=$write_lobj
+
+# Name of the non-PIC object
+non_pic_object=$write_oldobj
+
+EOF
+ $MV "${write_libobj}T" "${write_libobj}"
+ }
+}
+
+# func_mode_compile arg...
+func_mode_compile ()
+{
+ $opt_debug
+ # Get the compilation command and the source file.
+ base_compile=
+ srcfile="$nonopt" # always keep a non-empty value in "srcfile"
+ suppress_opt=yes
+ suppress_output=
+ arg_mode=normal
+ libobj=
+ later=
+ pie_flag=
+
+ for arg
+ do
+ case $arg_mode in
+ arg )
+ # do not "continue". Instead, add this to base_compile
+ lastarg="$arg"
+ arg_mode=normal
+ ;;
+
+ target )
+ libobj="$arg"
+ arg_mode=normal
+ continue
+ ;;
+
+ normal )
+ # Accept any command-line options.
+ case $arg in
+ -o)
+ test -n "$libobj" && \
+ func_fatal_error "you cannot specify \`-o' more than once"
+ arg_mode=target
+ continue
+ ;;
+
+ -pie | -fpie | -fPIE)
+ pie_flag="$pie_flag $arg"
+ continue
+ ;;
+
+ -shared | -static | -prefer-pic | -prefer-non-pic)
+ later="$later $arg"
+ continue
+ ;;
+
+ -no-suppress)
+ suppress_opt=no
+ continue
+ ;;
+
+ -Xcompiler)
+ arg_mode=arg # the next one goes into the "base_compile" arg list
+ continue # The current "srcfile" will either be retained or
+ ;; # replaced later. I would guess that would be a bug.
+
+ -Wc,*)
+ func_stripname '-Wc,' '' "$arg"
+ args=$func_stripname_result
+ lastarg=
+ save_ifs="$IFS"; IFS=','
+ for arg in $args; do
+ IFS="$save_ifs"
+ func_quote_for_eval "$arg"
+ lastarg="$lastarg $func_quote_for_eval_result"
+ done
+ IFS="$save_ifs"
+ func_stripname ' ' '' "$lastarg"
+ lastarg=$func_stripname_result
+
+ # Add the arguments to base_compile.
+ base_compile="$base_compile $lastarg"
+ continue
+ ;;
+
+ *)
+ # Accept the current argument as the source file.
+ # The previous "srcfile" becomes the current argument.
+ #
+ lastarg="$srcfile"
+ srcfile="$arg"
+ ;;
+ esac # case $arg
+ ;;
+ esac # case $arg_mode
+
+ # Aesthetically quote the previous argument.
+ func_quote_for_eval "$lastarg"
+ base_compile="$base_compile $func_quote_for_eval_result"
+ done # for arg
+
+ case $arg_mode in
+ arg)
+ func_fatal_error "you must specify an argument for -Xcompile"
+ ;;
+ target)
+ func_fatal_error "you must specify a target with \`-o'"
+ ;;
+ *)
+ # Get the name of the library object.
+ test -z "$libobj" && {
+ func_basename "$srcfile"
+ libobj="$func_basename_result"
+ }
+ ;;
+ esac
+
+ # Recognize several different file suffixes.
+ # If the user specifies -o file.o, it is replaced with file.lo
+ case $libobj in
+ *.[cCFSifmso] | \
+ *.ada | *.adb | *.ads | *.asm | \
+ *.c++ | *.cc | *.ii | *.class | *.cpp | *.cxx | \
+ *.[fF][09]? | *.for | *.java | *.obj | *.sx)
+ func_xform "$libobj"
+ libobj=$func_xform_result
+ ;;
+ esac
+
+ case $libobj in
+ *.lo) func_lo2o "$libobj"; obj=$func_lo2o_result ;;
+ *)
+ func_fatal_error "cannot determine name of library object from \`$libobj'"
+ ;;
+ esac
+
+ func_infer_tag $base_compile
+
+ for arg in $later; do
+ case $arg in
+ -shared)
+ test "$build_libtool_libs" != yes && \
+ func_fatal_configuration "can not build a shared library"
+ build_old_libs=no
+ continue
+ ;;
+
+ -static)
+ build_libtool_libs=no
+ build_old_libs=yes
+ continue
+ ;;
+
+ -prefer-pic)
+ pic_mode=yes
+ continue
+ ;;
+
+ -prefer-non-pic)
+ pic_mode=no
+ continue
+ ;;
+ esac
+ done
+
+ func_quote_for_eval "$libobj"
+ test "X$libobj" != "X$func_quote_for_eval_result" \
+ && $ECHO "X$libobj" | $GREP '[]~#^*{};<>?"'"'"' &()|`$[]' \
+ && func_warning "libobj name \`$libobj' may not contain shell special characters."
+ func_dirname_and_basename "$obj" "/" ""
+ objname="$func_basename_result"
+ xdir="$func_dirname_result"
+ lobj=${xdir}$objdir/$objname
+
+ test -z "$base_compile" && \
+ func_fatal_help "you must specify a compilation command"
+
+ # Delete any leftover library objects.
+ if test "$build_old_libs" = yes; then
+ removelist="$obj $lobj $libobj ${libobj}T"
+ else
+ removelist="$lobj $libobj ${libobj}T"
+ fi
+
+ # On Cygwin there's no "real" PIC flag so we must build both object types
+ case $host_os in
+ cygwin* | mingw* | pw32* | os2* | cegcc*)
+ pic_mode=default
+ ;;
+ esac
+ if test "$pic_mode" = no && test "$deplibs_check_method" != pass_all; then
+ # non-PIC code in shared libraries is not supported
+ pic_mode=default
+ fi
+
+ # Calculate the filename of the output object if compiler does
+ # not support -o with -c
+ if test "$compiler_c_o" = no; then
+ output_obj=`$ECHO "X$srcfile" | $Xsed -e 's%^.*/%%' -e 's%\.[^.]*$%%'`.${objext}
+ lockfile="$output_obj.lock"
+ else
+ output_obj=
+ need_locks=no
+ lockfile=
+ fi
+
+ # Lock this critical section if it is needed
+ # We use this script file to make the link, it avoids creating a new file
+ if test "$need_locks" = yes; then
+ until $opt_dry_run || ln "$progpath" "$lockfile" 2>/dev/null; do
+ func_echo "Waiting for $lockfile to be removed"
+ sleep 2
+ done
+ elif test "$need_locks" = warn; then
+ if test -f "$lockfile"; then
+ $ECHO "\
+*** ERROR, $lockfile exists and contains:
+`cat $lockfile 2>/dev/null`
+
+This indicates that another process is trying to use the same
+temporary object file, and libtool could not work around it because
+your compiler does not support \`-c' and \`-o' together. If you
+repeat this compilation, it may succeed, by chance, but you had better
+avoid parallel builds (make -j) in this platform, or get a better
+compiler."
+
+ $opt_dry_run || $RM $removelist
+ exit $EXIT_FAILURE
+ fi
+ removelist="$removelist $output_obj"
+ $ECHO "$srcfile" > "$lockfile"
+ fi
+
+ $opt_dry_run || $RM $removelist
+ removelist="$removelist $lockfile"
+ trap '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE' 1 2 15
+
+ if test -n "$fix_srcfile_path"; then
+ eval srcfile=\"$fix_srcfile_path\"
+ fi
+ func_quote_for_eval "$srcfile"
+ qsrcfile=$func_quote_for_eval_result
+
+ # Only build a PIC object if we are building libtool libraries.
+ if test "$build_libtool_libs" = yes; then
+ # Without this assignment, base_compile gets emptied.
+ fbsd_hideous_sh_bug=$base_compile
+
+ if test "$pic_mode" != no; then
+ command="$base_compile $qsrcfile $pic_flag"
+ else
+ # Don't build PIC code
+ command="$base_compile $qsrcfile"
+ fi
+
+ func_mkdir_p "$xdir$objdir"
+
+ if test -z "$output_obj"; then
+ # Place PIC objects in $objdir
+ command="$command -o $lobj"
+ fi
+
+ func_show_eval_locale "$command" \
+ 'test -n "$output_obj" && $RM $removelist; exit $EXIT_FAILURE'
+
+ if test "$need_locks" = warn &&
+ test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then
+ $ECHO "\
+*** ERROR, $lockfile contains:
+`cat $lockfile 2>/dev/null`
+
+but it should contain:
+$srcfile
+
+This indicates that another process is trying to use the same
+temporary object file, and libtool could not work around it because
+your compiler does not support \`-c' and \`-o' together. If you
+repeat this compilation, it may succeed, by chance, but you had better
+avoid parallel builds (make -j) in this platform, or get a better
+compiler."
+
+ $opt_dry_run || $RM $removelist
+ exit $EXIT_FAILURE
+ fi
+
+ # Just move the object if needed, then go on to compile the next one
+ if test -n "$output_obj" && test "X$output_obj" != "X$lobj"; then
+ func_show_eval '$MV "$output_obj" "$lobj"' \
+ 'error=$?; $opt_dry_run || $RM $removelist; exit $error'
+ fi
+
+ # Allow error messages only from the first compilation.
+ if test "$suppress_opt" = yes; then
+ suppress_output=' >/dev/null 2>&1'
+ fi
+ fi
+
+ # Only build a position-dependent object if we build old libraries.
+ if test "$build_old_libs" = yes; then
+ if test "$pic_mode" != yes; then
+ # Don't build PIC code
+ command="$base_compile $qsrcfile$pie_flag"
+ else
+ command="$base_compile $qsrcfile $pic_flag"
+ fi
+ if test "$compiler_c_o" = yes; then
+ command="$command -o $obj"
+ fi
+
+ # Suppress compiler output if we already did a PIC compilation.
+ command="$command$suppress_output"
+ func_show_eval_locale "$command" \
+ '$opt_dry_run || $RM $removelist; exit $EXIT_FAILURE'
+
+ if test "$need_locks" = warn &&
+ test "X`cat $lockfile 2>/dev/null`" != "X$srcfile"; then
+ $ECHO "\
+*** ERROR, $lockfile contains:
+`cat $lockfile 2>/dev/null`
+
+but it should contain:
+$srcfile
+
+This indicates that another process is trying to use the same
+temporary object file, and libtool could not work around it because
+your compiler does not support \`-c' and \`-o' together. If you
+repeat this compilation, it may succeed, by chance, but you had better
+avoid parallel builds (make -j) in this platform, or get a better
+compiler."
+
+ $opt_dry_run || $RM $removelist
+ exit $EXIT_FAILURE
+ fi
+
+ # Just move the object if needed
+ if test -n "$output_obj" && test "X$output_obj" != "X$obj"; then
+ func_show_eval '$MV "$output_obj" "$obj"' \
+ 'error=$?; $opt_dry_run || $RM $removelist; exit $error'
+ fi
+ fi
+
+ $opt_dry_run || {
+ func_write_libtool_object "$libobj" "$objdir/$objname" "$objname"
+
+ # Unlock the critical section if it was locked
+ if test "$need_locks" != no; then
+ removelist=$lockfile
+ $RM "$lockfile"
+ fi
+ }
+
+ exit $EXIT_SUCCESS
+}
+
+$opt_help || {
+test "$mode" = compile && func_mode_compile ${1+"$@"}
+}
+
+func_mode_help ()
+{
+ # We need to display help for each of the modes.
+ case $mode in
+ "")
+ # Generic help is extracted from the usage comments
+ # at the start of this file.
+ func_help
+ ;;
+
+ clean)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=clean RM [RM-OPTION]... FILE...
+
+Remove files from the build directory.
+
+RM is the name of the program to use to delete files associated with each FILE
+(typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed
+to RM.
+
+If FILE is a libtool library, object or program, all the files associated
+with it are deleted. Otherwise, only FILE itself is deleted using RM."
+ ;;
+
+ compile)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=compile COMPILE-COMMAND... SOURCEFILE
+
+Compile a source file into a libtool library object.
+
+This mode accepts the following additional options:
+
+ -o OUTPUT-FILE set the output file name to OUTPUT-FILE
+ -no-suppress do not suppress compiler output for multiple passes
+ -prefer-pic try to building PIC objects only
+ -prefer-non-pic try to building non-PIC objects only
+ -shared do not build a \`.o' file suitable for static linking
+ -static only build a \`.o' file suitable for static linking
+
+COMPILE-COMMAND is a command to be used in creating a \`standard' object file
+from the given SOURCEFILE.
+
+The output file name is determined by removing the directory component from
+SOURCEFILE, then substituting the C source code suffix \`.c' with the
+library object suffix, \`.lo'."
+ ;;
+
+ execute)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=execute COMMAND [ARGS]...
+
+Automatically set library path, then run a program.
+
+This mode accepts the following additional options:
+
+ -dlopen FILE add the directory containing FILE to the library path
+
+This mode sets the library path environment variable according to \`-dlopen'
+flags.
+
+If any of the ARGS are libtool executable wrappers, then they are translated
+into their corresponding uninstalled binary, and any of their required library
+directories are added to the library path.
+
+Then, COMMAND is executed, with ARGS as arguments."
+ ;;
+
+ finish)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=finish [LIBDIR]...
+
+Complete the installation of libtool libraries.
+
+Each LIBDIR is a directory that contains libtool libraries.
+
+The commands that this mode executes may require superuser privileges. Use
+the \`--dry-run' option if you just want to see what would be executed."
+ ;;
+
+ install)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=install INSTALL-COMMAND...
+
+Install executables or libraries.
+
+INSTALL-COMMAND is the installation command. The first component should be
+either the \`install' or \`cp' program.
+
+The following components of INSTALL-COMMAND are treated specially:
+
+ -inst-prefix PREFIX-DIR Use PREFIX-DIR as a staging area for installation
+
+The rest of the components are interpreted as arguments to that command (only
+BSD-compatible install options are recognized)."
+ ;;
+
+ link)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=link LINK-COMMAND...
+
+Link object files or libraries together to form another library, or to
+create an executable program.
+
+LINK-COMMAND is a command using the C compiler that you would use to create
+a program from several object files.
+
+The following components of LINK-COMMAND are treated specially:
+
+ -all-static do not do any dynamic linking at all
+ -avoid-version do not add a version suffix if possible
+ -dlopen FILE \`-dlpreopen' FILE if it cannot be dlopened at runtime
+ -dlpreopen FILE link in FILE and add its symbols to lt_preloaded_symbols
+ -export-dynamic allow symbols from OUTPUT-FILE to be resolved with dlsym(3)
+ -export-symbols SYMFILE
+ try to export only the symbols listed in SYMFILE
+ -export-symbols-regex REGEX
+ try to export only the symbols matching REGEX
+ -LLIBDIR search LIBDIR for required installed libraries
+ -lNAME OUTPUT-FILE requires the installed library libNAME
+ -module build a library that can dlopened
+ -no-fast-install disable the fast-install mode
+ -no-install link a not-installable executable
+ -no-undefined declare that a library does not refer to external symbols
+ -o OUTPUT-FILE create OUTPUT-FILE from the specified objects
+ -objectlist FILE Use a list of object files found in FILE to specify objects
+ -precious-files-regex REGEX
+ don't remove output files matching REGEX
+ -release RELEASE specify package release information
+ -rpath LIBDIR the created library will eventually be installed in LIBDIR
+ -R[ ]LIBDIR add LIBDIR to the runtime path of programs and libraries
+ -shared only do dynamic linking of libtool libraries
+ -shrext SUFFIX override the standard shared library file extension
+ -static do not do any dynamic linking of uninstalled libtool libraries
+ -static-libtool-libs
+ do not do any dynamic linking of libtool libraries
+ -version-info CURRENT[:REVISION[:AGE]]
+ specify library version info [each variable defaults to 0]
+ -weak LIBNAME declare that the target provides the LIBNAME interface
+
+All other options (arguments beginning with \`-') are ignored.
+
+Every other argument is treated as a filename. Files ending in \`.la' are
+treated as uninstalled libtool libraries, other files are standard or library
+object files.
+
+If the OUTPUT-FILE ends in \`.la', then a libtool library is created,
+only library objects (\`.lo' files) may be specified, and \`-rpath' is
+required, except when creating a convenience library.
+
+If OUTPUT-FILE ends in \`.a' or \`.lib', then a standard library is created
+using \`ar' and \`ranlib', or on Windows using \`lib'.
+
+If OUTPUT-FILE ends in \`.lo' or \`.${objext}', then a reloadable object file
+is created, otherwise an executable program is created."
+ ;;
+
+ uninstall)
+ $ECHO \
+"Usage: $progname [OPTION]... --mode=uninstall RM [RM-OPTION]... FILE...
+
+Remove libraries from an installation directory.
+
+RM is the name of the program to use to delete files associated with each FILE
+(typically \`/bin/rm'). RM-OPTIONS are options (such as \`-f') to be passed
+to RM.
+
+If FILE is a libtool library, all the files associated with it are deleted.
+Otherwise, only FILE itself is deleted using RM."
+ ;;
+
+ *)
+ func_fatal_help "invalid operation mode \`$mode'"
+ ;;
+ esac
+
+ $ECHO
+ $ECHO "Try \`$progname --help' for more information about other modes."
+
+ exit $?
+}
+
+ # Now that we've collected a possible --mode arg, show help if necessary
+ $opt_help && func_mode_help
+
+
+# func_mode_execute arg...
+func_mode_execute ()
+{
+ $opt_debug
+ # The first argument is the command name.
+ cmd="$nonopt"
+ test -z "$cmd" && \
+ func_fatal_help "you must specify a COMMAND"
+
+ # Handle -dlopen flags immediately.
+ for file in $execute_dlfiles; do
+ test -f "$file" \
+ || func_fatal_help "\`$file' is not a file"
+
+ dir=
+ case $file in
+ *.la)
+ # Check to see that this really is a libtool archive.
+ func_lalib_unsafe_p "$file" \
+ || func_fatal_help "\`$lib' is not a valid libtool archive"
+
+ # Read the libtool library.
+ dlname=
+ library_names=
+ func_source "$file"
+
+ # Skip this library if it cannot be dlopened.
+ if test -z "$dlname"; then
+ # Warn if it was a shared library.
+ test -n "$library_names" && \
+ func_warning "\`$file' was not linked with \`-export-dynamic'"
+ continue
+ fi
+
+ func_dirname "$file" "" "."
+ dir="$func_dirname_result"
+
+ if test -f "$dir/$objdir/$dlname"; then
+ dir="$dir/$objdir"
+ else
+ if test ! -f "$dir/$dlname"; then
+ func_fatal_error "cannot find \`$dlname' in \`$dir' or \`$dir/$objdir'"
+ fi
+ fi
+ ;;
+
+ *.lo)
+ # Just add the directory containing the .lo file.
+ func_dirname "$file" "" "."
+ dir="$func_dirname_result"
+ ;;
+
+ *)
+ func_warning "\`-dlopen' is ignored for non-libtool libraries and objects"
+ continue
+ ;;
+ esac
+
+ # Get the absolute pathname.
+ absdir=`cd "$dir" && pwd`
+ test -n "$absdir" && dir="$absdir"
+
+ # Now add the directory to shlibpath_var.
+ if eval "test -z \"\$$shlibpath_var\""; then
+ eval "$shlibpath_var=\"\$dir\""
+ else
+ eval "$shlibpath_var=\"\$dir:\$$shlibpath_var\""
+ fi
+ done
+
+ # This variable tells wrapper scripts just to set shlibpath_var
+ # rather than running their programs.
+ libtool_execute_magic="$magic"
+
+ # Check if any of the arguments is a wrapper script.
+ args=
+ for file
+ do
+ case $file in
+ -*) ;;
+ *)
+ # Do a test to see if this is really a libtool program.
+ if func_ltwrapper_script_p "$file"; then
+ func_source "$file"
+ # Transform arg to wrapped name.
+ file="$progdir/$program"
+ elif func_ltwrapper_executable_p "$file"; then
+ func_ltwrapper_scriptname "$file"
+ func_source "$func_ltwrapper_scriptname_result"
+ # Transform arg to wrapped name.
+ file="$progdir/$program"
+ fi
+ ;;
+ esac
+ # Quote arguments (to preserve shell metacharacters).
+ func_quote_for_eval "$file"
+ args="$args $func_quote_for_eval_result"
+ done
+
+ if test "X$opt_dry_run" = Xfalse; then
+ if test -n "$shlibpath_var"; then
+ # Export the shlibpath_var.
+ eval "export $shlibpath_var"
+ fi
+
+ # Restore saved environment variables
+ for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES
+ do
+ eval "if test \"\${save_$lt_var+set}\" = set; then
+ $lt_var=\$save_$lt_var; export $lt_var
+ else
+ $lt_unset $lt_var
+ fi"
+ done
+
+ # Now prepare to actually exec the command.
+ exec_cmd="\$cmd$args"
+ else
+ # Display what would be done.
+ if test -n "$shlibpath_var"; then
+ eval "\$ECHO \"\$shlibpath_var=\$$shlibpath_var\""
+ $ECHO "export $shlibpath_var"
+ fi
+ $ECHO "$cmd$args"
+ exit $EXIT_SUCCESS
+ fi
+}
+
+test "$mode" = execute && func_mode_execute ${1+"$@"}
+
+
+# func_mode_finish arg...
+func_mode_finish ()
+{
+ $opt_debug
+ libdirs="$nonopt"
+ admincmds=
+
+ if test -n "$finish_cmds$finish_eval" && test -n "$libdirs"; then
+ for dir
+ do
+ libdirs="$libdirs $dir"
+ done
+
+ for libdir in $libdirs; do
+ if test -n "$finish_cmds"; then
+ # Do each command in the finish commands.
+ func_execute_cmds "$finish_cmds" 'admincmds="$admincmds
+'"$cmd"'"'
+ fi
+ if test -n "$finish_eval"; then
+ # Do the single finish_eval.
+ eval cmds=\"$finish_eval\"
+ $opt_dry_run || eval "$cmds" || admincmds="$admincmds
+ $cmds"
+ fi
+ done
+ fi
+
+ # Exit here if they wanted silent mode.
+ $opt_silent && exit $EXIT_SUCCESS
+
+ $ECHO "X----------------------------------------------------------------------" | $Xsed
+ $ECHO "Libraries have been installed in:"
+ for libdir in $libdirs; do
+ $ECHO " $libdir"
+ done
+ $ECHO
+ $ECHO "If you ever happen to want to link against installed libraries"
+ $ECHO "in a given directory, LIBDIR, you must either use libtool, and"
+ $ECHO "specify the full pathname of the library, or use the \`-LLIBDIR'"
+ $ECHO "flag during linking and do at least one of the following:"
+ if test -n "$shlibpath_var"; then
+ $ECHO " - add LIBDIR to the \`$shlibpath_var' environment variable"
+ $ECHO " during execution"
+ fi
+ if test -n "$runpath_var"; then
+ $ECHO " - add LIBDIR to the \`$runpath_var' environment variable"
+ $ECHO " during linking"
+ fi
+ if test -n "$hardcode_libdir_flag_spec"; then
+ libdir=LIBDIR
+ eval flag=\"$hardcode_libdir_flag_spec\"
+
+ $ECHO " - use the \`$flag' linker flag"
+ fi
+ if test -n "$admincmds"; then
+ $ECHO " - have your system administrator run these commands:$admincmds"
+ fi
+ if test -f /etc/ld.so.conf; then
+ $ECHO " - have your system administrator add LIBDIR to \`/etc/ld.so.conf'"
+ fi
+ $ECHO
+
+ $ECHO "See any operating system documentation about shared libraries for"
+ case $host in
+ solaris2.[6789]|solaris2.1[0-9])
+ $ECHO "more information, such as the ld(1), crle(1) and ld.so(8) manual"
+ $ECHO "pages."
+ ;;
+ *)
+ $ECHO "more information, such as the ld(1) and ld.so(8) manual pages."
+ ;;
+ esac
+ $ECHO "X----------------------------------------------------------------------" | $Xsed
+ exit $EXIT_SUCCESS
+}
+
+test "$mode" = finish && func_mode_finish ${1+"$@"}
+
+
+# func_mode_install arg...
+func_mode_install ()
+{
+ $opt_debug
+ # There may be an optional sh(1) argument at the beginning of
+ # install_prog (especially on Windows NT).
+ if test "$nonopt" = "$SHELL" || test "$nonopt" = /bin/sh ||
+ # Allow the use of GNU shtool's install command.
+ $ECHO "X$nonopt" | $GREP shtool >/dev/null; then
+ # Aesthetically quote it.
+ func_quote_for_eval "$nonopt"
+ install_prog="$func_quote_for_eval_result "
+ arg=$1
+ shift
+ else
+ install_prog=
+ arg=$nonopt
+ fi
+
+ # The real first argument should be the name of the installation program.
+ # Aesthetically quote it.
+ func_quote_for_eval "$arg"
+ install_prog="$install_prog$func_quote_for_eval_result"
+
+ # We need to accept at least all the BSD install flags.
+ dest=
+ files=
+ opts=
+ prev=
+ install_type=
+ isdir=no
+ stripme=
+ for arg
+ do
+ if test -n "$dest"; then
+ files="$files $dest"
+ dest=$arg
+ continue
+ fi
+
+ case $arg in
+ -d) isdir=yes ;;
+ -f)
+ case " $install_prog " in
+ *[\\\ /]cp\ *) ;;
+ *) prev=$arg ;;
+ esac
+ ;;
+ -g | -m | -o)
+ prev=$arg
+ ;;
+ -s)
+ stripme=" -s"
+ continue
+ ;;
+ -*)
+ ;;
+ *)
+ # If the previous option needed an argument, then skip it.
+ if test -n "$prev"; then
+ prev=
+ else
+ dest=$arg
+ continue
+ fi
+ ;;
+ esac
+
+ # Aesthetically quote the argument.
+ func_quote_for_eval "$arg"
+ install_prog="$install_prog $func_quote_for_eval_result"
+ done
+
+ test -z "$install_prog" && \
+ func_fatal_help "you must specify an install program"
+
+ test -n "$prev" && \
+ func_fatal_help "the \`$prev' option requires an argument"
+
+ if test -z "$files"; then
+ if test -z "$dest"; then
+ func_fatal_help "no file or destination specified"
+ else
+ func_fatal_help "you must specify a destination"
+ fi
+ fi
+
+ # Strip any trailing slash from the destination.
+ func_stripname '' '/' "$dest"
+ dest=$func_stripname_result
+
+ # Check to see that the destination is a directory.
+ test -d "$dest" && isdir=yes
+ if test "$isdir" = yes; then
+ destdir="$dest"
+ destname=
+ else
+ func_dirname_and_basename "$dest" "" "."
+ destdir="$func_dirname_result"
+ destname="$func_basename_result"
+
+ # Not a directory, so check to see that there is only one file specified.
+ set dummy $files; shift
+ test "$#" -gt 1 && \
+ func_fatal_help "\`$dest' is not a directory"
+ fi
+ case $destdir in
+ [\\/]* | [A-Za-z]:[\\/]*) ;;
+ *)
+ for file in $files; do
+ case $file in
+ *.lo) ;;
+ *)
+ func_fatal_help "\`$destdir' must be an absolute directory name"
+ ;;
+ esac
+ done
+ ;;
+ esac
+
+ # This variable tells wrapper scripts just to set variables rather
+ # than running their programs.
+ libtool_install_magic="$magic"
+
+ staticlibs=
+ future_libdirs=
+ current_libdirs=
+ for file in $files; do
+
+ # Do each installation.
+ case $file in
+ *.$libext)
+ # Do the static libraries later.
+ staticlibs="$staticlibs $file"
+ ;;
+
+ *.la)
+ # Check to see that this really is a libtool archive.
+ func_lalib_unsafe_p "$file" \
+ || func_fatal_help "\`$file' is not a valid libtool archive"
+
+ library_names=
+ old_library=
+ relink_command=
+ func_source "$file"
+
+ # Add the libdir to current_libdirs if it is the destination.
+ if test "X$destdir" = "X$libdir"; then
+ case "$current_libdirs " in
+ *" $libdir "*) ;;
+ *) current_libdirs="$current_libdirs $libdir" ;;
+ esac
+ else
+ # Note the libdir as a future libdir.
+ case "$future_libdirs " in
+ *" $libdir "*) ;;
+ *) future_libdirs="$future_libdirs $libdir" ;;
+ esac
+ fi
+
+ func_dirname "$file" "/" ""
+ dir="$func_dirname_result"
+ dir="$dir$objdir"
+
+ if test -n "$relink_command"; then
+ # Determine the prefix the user has applied to our future dir.
+ inst_prefix_dir=`$ECHO "X$destdir" | $Xsed -e "s%$libdir\$%%"`
+
+ # Don't allow the user to place us outside of our expected
+ # location b/c this prevents finding dependent libraries that
+ # are installed to the same prefix.
+ # At present, this check doesn't affect windows .dll's that
+ # are installed into $libdir/../bin (currently, that works fine)
+ # but it's something to keep an eye on.
+ test "$inst_prefix_dir" = "$destdir" && \
+ func_fatal_error "error: cannot install \`$file' to a directory not ending in $libdir"
+
+ if test -n "$inst_prefix_dir"; then
+ # Stick the inst_prefix_dir data into the link command.
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%-inst-prefix-dir $inst_prefix_dir%"`
+ else
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e "s%@inst_prefix_dir@%%"`
+ fi
+
+ func_warning "relinking \`$file'"
+ func_show_eval "$relink_command" \
+ 'func_fatal_error "error: relink \`$file'\'' with the above command before installing it"'
+ fi
+
+ # See the names of the shared library.
+ set dummy $library_names; shift
+ if test -n "$1"; then
+ realname="$1"
+ shift
+
+ srcname="$realname"
+ test -n "$relink_command" && srcname="$realname"T
+
+ # Install the shared library and build the symlinks.
+ func_show_eval "$install_prog $dir/$srcname $destdir/$realname" \
+ 'exit $?'
+ tstripme="$stripme"
+ case $host_os in
+ cygwin* | mingw* | pw32* | cegcc*)
+ case $realname in
+ *.dll.a)
+ tstripme=""
+ ;;
+ esac
+ ;;
+ esac
+ if test -n "$tstripme" && test -n "$striplib"; then
+ func_show_eval "$striplib $destdir/$realname" 'exit $?'
+ fi
+
+ if test "$#" -gt 0; then
+ # Delete the old symlinks, and create new ones.
+ # Try `ln -sf' first, because the `ln' binary might depend on
+ # the symlink we replace! Solaris /bin/ln does not understand -f,
+ # so we also need to try rm && ln -s.
+ for linkname
+ do
+ test "$linkname" != "$realname" \
+ && func_show_eval "(cd $destdir && { $LN_S -f $realname $linkname || { $RM $linkname && $LN_S $realname $linkname; }; })"
+ done
+ fi
+
+ # Do each command in the postinstall commands.
+ lib="$destdir/$realname"
+ func_execute_cmds "$postinstall_cmds" 'exit $?'
+ fi
+
+ # Install the pseudo-library for information purposes.
+ func_basename "$file"
+ name="$func_basename_result"
+ instname="$dir/$name"i
+ func_show_eval "$install_prog $instname $destdir/$name" 'exit $?'
+
+ # Maybe install the static library, too.
+ test -n "$old_library" && staticlibs="$staticlibs $dir/$old_library"
+ ;;
+
+ *.lo)
+ # Install (i.e. copy) a libtool object.
+
+ # Figure out destination file name, if it wasn't already specified.
+ if test -n "$destname"; then
+ destfile="$destdir/$destname"
+ else
+ func_basename "$file"
+ destfile="$func_basename_result"
+ destfile="$destdir/$destfile"
+ fi
+
+ # Deduce the name of the destination old-style object file.
+ case $destfile in
+ *.lo)
+ func_lo2o "$destfile"
+ staticdest=$func_lo2o_result
+ ;;
+ *.$objext)
+ staticdest="$destfile"
+ destfile=
+ ;;
+ *)
+ func_fatal_help "cannot copy a libtool object to \`$destfile'"
+ ;;
+ esac
+
+ # Install the libtool object if requested.
+ test -n "$destfile" && \
+ func_show_eval "$install_prog $file $destfile" 'exit $?'
+
+ # Install the old object if enabled.
+ if test "$build_old_libs" = yes; then
+ # Deduce the name of the old-style object file.
+ func_lo2o "$file"
+ staticobj=$func_lo2o_result
+ func_show_eval "$install_prog \$staticobj \$staticdest" 'exit $?'
+ fi
+ exit $EXIT_SUCCESS
+ ;;
+
+ *)
+ # Figure out destination file name, if it wasn't already specified.
+ if test -n "$destname"; then
+ destfile="$destdir/$destname"
+ else
+ func_basename "$file"
+ destfile="$func_basename_result"
+ destfile="$destdir/$destfile"
+ fi
+
+ # If the file is missing, and there is a .exe on the end, strip it
+ # because it is most likely a libtool script we actually want to
+ # install
+ stripped_ext=""
+ case $file in
+ *.exe)
+ if test ! -f "$file"; then
+ func_stripname '' '.exe' "$file"
+ file=$func_stripname_result
+ stripped_ext=".exe"
+ fi
+ ;;
+ esac
+
+ # Do a test to see if this is really a libtool program.
+ case $host in
+ *cygwin* | *mingw*)
+ if func_ltwrapper_executable_p "$file"; then
+ func_ltwrapper_scriptname "$file"
+ wrapper=$func_ltwrapper_scriptname_result
+ else
+ func_stripname '' '.exe' "$file"
+ wrapper=$func_stripname_result
+ fi
+ ;;
+ *)
+ wrapper=$file
+ ;;
+ esac
+ if func_ltwrapper_script_p "$wrapper"; then
+ notinst_deplibs=
+ relink_command=
+
+ func_source "$wrapper"
+
+ # Check the variables that should have been set.
+ test -z "$generated_by_libtool_version" && \
+ func_fatal_error "invalid libtool wrapper script \`$wrapper'"
+
+ finalize=yes
+ for lib in $notinst_deplibs; do
+ # Check to see that each library is installed.
+ libdir=
+ if test -f "$lib"; then
+ func_source "$lib"
+ fi
+ libfile="$libdir/"`$ECHO "X$lib" | $Xsed -e 's%^.*/%%g'` ### testsuite: skip nested quoting test
+ if test -n "$libdir" && test ! -f "$libfile"; then
+ func_warning "\`$lib' has not been installed in \`$libdir'"
+ finalize=no
+ fi
+ done
+
+ relink_command=
+ func_source "$wrapper"
+
+ outputname=
+ if test "$fast_install" = no && test -n "$relink_command"; then
+ $opt_dry_run || {
+ if test "$finalize" = yes; then
+ tmpdir=`func_mktempdir`
+ func_basename "$file$stripped_ext"
+ file="$func_basename_result"
+ outputname="$tmpdir/$file"
+ # Replace the output file specification.
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e 's%@OUTPUT@%'"$outputname"'%g'`
+
+ $opt_silent || {
+ func_quote_for_expand "$relink_command"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+ if eval "$relink_command"; then :
+ else
+ func_error "error: relink \`$file' with the above command before installing it"
+ $opt_dry_run || ${RM}r "$tmpdir"
+ continue
+ fi
+ file="$outputname"
+ else
+ func_warning "cannot relink \`$file'"
+ fi
+ }
+ else
+ # Install the binary that we compiled earlier.
+ file=`$ECHO "X$file$stripped_ext" | $Xsed -e "s%\([^/]*\)$%$objdir/\1%"`
+ fi
+ fi
+
+ # remove .exe since cygwin /usr/bin/install will append another
+ # one anyway
+ case $install_prog,$host in
+ */usr/bin/install*,*cygwin*)
+ case $file:$destfile in
+ *.exe:*.exe)
+ # this is ok
+ ;;
+ *.exe:*)
+ destfile=$destfile.exe
+ ;;
+ *:*.exe)
+ func_stripname '' '.exe' "$destfile"
+ destfile=$func_stripname_result
+ ;;
+ esac
+ ;;
+ esac
+ func_show_eval "$install_prog\$stripme \$file \$destfile" 'exit $?'
+ $opt_dry_run || if test -n "$outputname"; then
+ ${RM}r "$tmpdir"
+ fi
+ ;;
+ esac
+ done
+
+ for file in $staticlibs; do
+ func_basename "$file"
+ name="$func_basename_result"
+
+ # Set up the ranlib parameters.
+ oldlib="$destdir/$name"
+
+ func_show_eval "$install_prog \$file \$oldlib" 'exit $?'
+
+ if test -n "$stripme" && test -n "$old_striplib"; then
+ func_show_eval "$old_striplib $oldlib" 'exit $?'
+ fi
+
+ # Do each command in the postinstall commands.
+ func_execute_cmds "$old_postinstall_cmds" 'exit $?'
+ done
+
+ test -n "$future_libdirs" && \
+ func_warning "remember to run \`$progname --finish$future_libdirs'"
+
+ if test -n "$current_libdirs"; then
+ # Maybe just do a dry run.
+ $opt_dry_run && current_libdirs=" -n$current_libdirs"
+ exec_cmd='$SHELL $progpath $preserve_args --finish$current_libdirs'
+ else
+ exit $EXIT_SUCCESS
+ fi
+}
+
+test "$mode" = install && func_mode_install ${1+"$@"}
+
+
+# func_generate_dlsyms outputname originator pic_p
+# Extract symbols from dlprefiles and create ${outputname}S.o with
+# a dlpreopen symbol table.
+func_generate_dlsyms ()
+{
+ $opt_debug
+ my_outputname="$1"
+ my_originator="$2"
+ my_pic_p="${3-no}"
+ my_prefix=`$ECHO "$my_originator" | sed 's%[^a-zA-Z0-9]%_%g'`
+ my_dlsyms=
+
+ if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
+ if test -n "$NM" && test -n "$global_symbol_pipe"; then
+ my_dlsyms="${my_outputname}S.c"
+ else
+ func_error "not configured to extract global symbols from dlpreopened files"
+ fi
+ fi
+
+ if test -n "$my_dlsyms"; then
+ case $my_dlsyms in
+ "") ;;
+ *.c)
+ # Discover the nlist of each of the dlfiles.
+ nlist="$output_objdir/${my_outputname}.nm"
+
+ func_show_eval "$RM $nlist ${nlist}S ${nlist}T"
+
+ # Parse the name list into a source file.
+ func_verbose "creating $output_objdir/$my_dlsyms"
+
+ $opt_dry_run || $ECHO > "$output_objdir/$my_dlsyms" "\
+/* $my_dlsyms - symbol resolution table for \`$my_outputname' dlsym emulation. */
+/* Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION */
+
+#ifdef __cplusplus
+extern \"C\" {
+#endif
+
+/* External symbol declarations for the compiler. */\
+"
+
+ if test "$dlself" = yes; then
+ func_verbose "generating symbol list for \`$output'"
+
+ $opt_dry_run || echo ': @PROGRAM@ ' > "$nlist"
+
+ # Add our own program objects to the symbol list.
+ progfiles=`$ECHO "X$objs$old_deplibs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+ for progfile in $progfiles; do
+ func_verbose "extracting global C symbols from \`$progfile'"
+ $opt_dry_run || eval "$NM $progfile | $global_symbol_pipe >> '$nlist'"
+ done
+
+ if test -n "$exclude_expsyms"; then
+ $opt_dry_run || {
+ eval '$EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T'
+ eval '$MV "$nlist"T "$nlist"'
+ }
+ fi
+
+ if test -n "$export_symbols_regex"; then
+ $opt_dry_run || {
+ eval '$EGREP -e "$export_symbols_regex" "$nlist" > "$nlist"T'
+ eval '$MV "$nlist"T "$nlist"'
+ }
+ fi
+
+ # Prepare the list of exported symbols
+ if test -z "$export_symbols"; then
+ export_symbols="$output_objdir/$outputname.exp"
+ $opt_dry_run || {
+ $RM $export_symbols
+ eval "${SED} -n -e '/^: @PROGRAM@ $/d' -e 's/^.* \(.*\)$/\1/p' "'< "$nlist" > "$export_symbols"'
+ case $host in
+ *cygwin* | *mingw* | *cegcc* )
+ eval "echo EXPORTS "'> "$output_objdir/$outputname.def"'
+ eval 'cat "$export_symbols" >> "$output_objdir/$outputname.def"'
+ ;;
+ esac
+ }
+ else
+ $opt_dry_run || {
+ eval "${SED} -e 's/\([].[*^$]\)/\\\\\1/g' -e 's/^/ /' -e 's/$/$/'"' < "$export_symbols" > "$output_objdir/$outputname.exp"'
+ eval '$GREP -f "$output_objdir/$outputname.exp" < "$nlist" > "$nlist"T'
+ eval '$MV "$nlist"T "$nlist"'
+ case $host in
+ *cygwin | *mingw* | *cegcc* )
+ eval "echo EXPORTS "'> "$output_objdir/$outputname.def"'
+ eval 'cat "$nlist" >> "$output_objdir/$outputname.def"'
+ ;;
+ esac
+ }
+ fi
+ fi
+
+ for dlprefile in $dlprefiles; do
+ func_verbose "extracting global C symbols from \`$dlprefile'"
+ func_basename "$dlprefile"
+ name="$func_basename_result"
+ $opt_dry_run || {
+ eval '$ECHO ": $name " >> "$nlist"'
+ eval "$NM $dlprefile 2>/dev/null | $global_symbol_pipe >> '$nlist'"
+ }
+ done
+
+ $opt_dry_run || {
+ # Make sure we have at least an empty file.
+ test -f "$nlist" || : > "$nlist"
+
+ if test -n "$exclude_expsyms"; then
+ $EGREP -v " ($exclude_expsyms)$" "$nlist" > "$nlist"T
+ $MV "$nlist"T "$nlist"
+ fi
+
+ # Try sorting and uniquifying the output.
+ if $GREP -v "^: " < "$nlist" |
+ if sort -k 3 </dev/null >/dev/null 2>&1; then
+ sort -k 3
+ else
+ sort +2
+ fi |
+ uniq > "$nlist"S; then
+ :
+ else
+ $GREP -v "^: " < "$nlist" > "$nlist"S
+ fi
+
+ if test -f "$nlist"S; then
+ eval "$global_symbol_to_cdecl"' < "$nlist"S >> "$output_objdir/$my_dlsyms"'
+ else
+ $ECHO '/* NONE */' >> "$output_objdir/$my_dlsyms"
+ fi
+
+ $ECHO >> "$output_objdir/$my_dlsyms" "\
+
+/* The mapping between symbol names and symbols. */
+typedef struct {
+ const char *name;
+ void *address;
+} lt_dlsymlist;
+"
+ case $host in
+ *cygwin* | *mingw* | *cegcc* )
+ $ECHO >> "$output_objdir/$my_dlsyms" "\
+/* DATA imports from DLLs on WIN32 con't be const, because
+ runtime relocations are performed -- see ld's documentation
+ on pseudo-relocs. */"
+ lt_dlsym_const= ;;
+ *osf5*)
+ echo >> "$output_objdir/$my_dlsyms" "\
+/* This system does not cope well with relocations in const data */"
+ lt_dlsym_const= ;;
+ *)
+ lt_dlsym_const=const ;;
+ esac
+
+ $ECHO >> "$output_objdir/$my_dlsyms" "\
+extern $lt_dlsym_const lt_dlsymlist
+lt_${my_prefix}_LTX_preloaded_symbols[];
+$lt_dlsym_const lt_dlsymlist
+lt_${my_prefix}_LTX_preloaded_symbols[] =
+{\
+ { \"$my_originator\", (void *) 0 },"
+
+ case $need_lib_prefix in
+ no)
+ eval "$global_symbol_to_c_name_address" < "$nlist" >> "$output_objdir/$my_dlsyms"
+ ;;
+ *)
+ eval "$global_symbol_to_c_name_address_lib_prefix" < "$nlist" >> "$output_objdir/$my_dlsyms"
+ ;;
+ esac
+ $ECHO >> "$output_objdir/$my_dlsyms" "\
+ {0, (void *) 0}
+};
+
+/* This works around a problem in FreeBSD linker */
+#ifdef FREEBSD_WORKAROUND
+static const void *lt_preloaded_setup() {
+ return lt_${my_prefix}_LTX_preloaded_symbols;
+}
+#endif
+
+#ifdef __cplusplus
+}
+#endif\
+"
+ } # !$opt_dry_run
+
+ pic_flag_for_symtable=
+ case "$compile_command " in
+ *" -static "*) ;;
+ *)
+ case $host in
+ # compiling the symbol table file with pic_flag works around
+ # a FreeBSD bug that causes programs to crash when -lm is
+ # linked before any other PIC object. But we must not use
+ # pic_flag when linking with -static. The problem exists in
+ # FreeBSD 2.2.6 and is fixed in FreeBSD 3.1.
+ *-*-freebsd2*|*-*-freebsd3.0*|*-*-freebsdelf3.0*)
+ pic_flag_for_symtable=" $pic_flag -DFREEBSD_WORKAROUND" ;;
+ *-*-hpux*)
+ pic_flag_for_symtable=" $pic_flag" ;;
+ *)
+ if test "X$my_pic_p" != Xno; then
+ pic_flag_for_symtable=" $pic_flag"
+ fi
+ ;;
+ esac
+ ;;
+ esac
+ symtab_cflags=
+ for arg in $LTCFLAGS; do
+ case $arg in
+ -pie | -fpie | -fPIE) ;;
+ *) symtab_cflags="$symtab_cflags $arg" ;;
+ esac
+ done
+
+ # Now compile the dynamic symbol file.
+ func_show_eval '(cd $output_objdir && $LTCC$symtab_cflags -c$no_builtin_flag$pic_flag_for_symtable "$my_dlsyms")' 'exit $?'
+
+ # Clean up the generated files.
+ func_show_eval '$RM "$output_objdir/$my_dlsyms" "$nlist" "${nlist}S" "${nlist}T"'
+
+ # Transform the symbol file into the correct name.
+ symfileobj="$output_objdir/${my_outputname}S.$objext"
+ case $host in
+ *cygwin* | *mingw* | *cegcc* )
+ if test -f "$output_objdir/$my_outputname.def"; then
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"`
+ finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/$my_outputname.def $symfileobj%"`
+ else
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"`
+ finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"`
+ fi
+ ;;
+ *)
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"`
+ finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$symfileobj%"`
+ ;;
+ esac
+ ;;
+ *)
+ func_fatal_error "unknown suffix for \`$my_dlsyms'"
+ ;;
+ esac
+ else
+ # We keep going just in case the user didn't refer to
+ # lt_preloaded_symbols. The linker will fail if global_symbol_pipe
+ # really was required.
+
+ # Nullify the symbol file.
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e "s% @SYMFILE@%%"`
+ finalize_command=`$ECHO "X$finalize_command" | $Xsed -e "s% @SYMFILE@%%"`
+ fi
+}
+
+# func_win32_libid arg
+# return the library type of file 'arg'
+#
+# Need a lot of goo to handle *both* DLLs and import libs
+# Has to be a shell function in order to 'eat' the argument
+# that is supplied when $file_magic_command is called.
+func_win32_libid ()
+{
+ $opt_debug
+ win32_libid_type="unknown"
+ win32_fileres=`file -L $1 2>/dev/null`
+ case $win32_fileres in
+ *ar\ archive\ import\ library*) # definitely import
+ win32_libid_type="x86 archive import"
+ ;;
+ *ar\ archive*) # could be an import, or static
+ if eval $OBJDUMP -f $1 | $SED -e '10q' 2>/dev/null |
+ $EGREP 'file format pe-i386(.*architecture: i386)?' >/dev/null ; then
+ win32_nmres=`eval $NM -f posix -A $1 |
+ $SED -n -e '
+ 1,100{
+ / I /{
+ s,.*,import,
+ p
+ q
+ }
+ }'`
+ case $win32_nmres in
+ import*) win32_libid_type="x86 archive import";;
+ *) win32_libid_type="x86 archive static";;
+ esac
+ fi
+ ;;
+ *DLL*)
+ win32_libid_type="x86 DLL"
+ ;;
+ *executable*) # but shell scripts are "executable" too...
+ case $win32_fileres in
+ *MS\ Windows\ PE\ Intel*)
+ win32_libid_type="x86 DLL"
+ ;;
+ esac
+ ;;
+ esac
+ $ECHO "$win32_libid_type"
+}
+
+
+
+# func_extract_an_archive dir oldlib
+func_extract_an_archive ()
+{
+ $opt_debug
+ f_ex_an_ar_dir="$1"; shift
+ f_ex_an_ar_oldlib="$1"
+ func_show_eval "(cd \$f_ex_an_ar_dir && $AR x \"\$f_ex_an_ar_oldlib\")" 'exit $?'
+ if ($AR t "$f_ex_an_ar_oldlib" | sort | sort -uc >/dev/null 2>&1); then
+ :
+ else
+ func_fatal_error "object name conflicts in archive: $f_ex_an_ar_dir/$f_ex_an_ar_oldlib"
+ fi
+}
+
+
+# func_extract_archives gentop oldlib ...
+func_extract_archives ()
+{
+ $opt_debug
+ my_gentop="$1"; shift
+ my_oldlibs=${1+"$@"}
+ my_oldobjs=""
+ my_xlib=""
+ my_xabs=""
+ my_xdir=""
+
+ for my_xlib in $my_oldlibs; do
+ # Extract the objects.
+ case $my_xlib in
+ [\\/]* | [A-Za-z]:[\\/]*) my_xabs="$my_xlib" ;;
+ *) my_xabs=`pwd`"/$my_xlib" ;;
+ esac
+ func_basename "$my_xlib"
+ my_xlib="$func_basename_result"
+ my_xlib_u=$my_xlib
+ while :; do
+ case " $extracted_archives " in
+ *" $my_xlib_u "*)
+ func_arith $extracted_serial + 1
+ extracted_serial=$func_arith_result
+ my_xlib_u=lt$extracted_serial-$my_xlib ;;
+ *) break ;;
+ esac
+ done
+ extracted_archives="$extracted_archives $my_xlib_u"
+ my_xdir="$my_gentop/$my_xlib_u"
+
+ func_mkdir_p "$my_xdir"
+
+ case $host in
+ *-darwin*)
+ func_verbose "Extracting $my_xabs"
+ # Do not bother doing anything if just a dry run
+ $opt_dry_run || {
+ darwin_orig_dir=`pwd`
+ cd $my_xdir || exit $?
+ darwin_archive=$my_xabs
+ darwin_curdir=`pwd`
+ darwin_base_archive=`basename "$darwin_archive"`
+ darwin_arches=`$LIPO -info "$darwin_archive" 2>/dev/null | $GREP Architectures 2>/dev/null || true`
+ if test -n "$darwin_arches"; then
+ darwin_arches=`$ECHO "$darwin_arches" | $SED -e 's/.*are://'`
+ darwin_arch=
+ func_verbose "$darwin_base_archive has multiple architectures $darwin_arches"
+ for darwin_arch in $darwin_arches ; do
+ func_mkdir_p "unfat-$$/${darwin_base_archive}-${darwin_arch}"
+ $LIPO -thin $darwin_arch -output "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}" "${darwin_archive}"
+ cd "unfat-$$/${darwin_base_archive}-${darwin_arch}"
+ func_extract_an_archive "`pwd`" "${darwin_base_archive}"
+ cd "$darwin_curdir"
+ $RM "unfat-$$/${darwin_base_archive}-${darwin_arch}/${darwin_base_archive}"
+ done # $darwin_arches
+ ## Okay now we've a bunch of thin objects, gotta fatten them up :)
+ darwin_filelist=`find unfat-$$ -type f -name \*.o -print -o -name \*.lo -print | $SED -e "$basename" | sort -u`
+ darwin_file=
+ darwin_files=
+ for darwin_file in $darwin_filelist; do
+ darwin_files=`find unfat-$$ -name $darwin_file -print | $NL2SP`
+ $LIPO -create -output "$darwin_file" $darwin_files
+ done # $darwin_filelist
+ $RM -rf unfat-$$
+ cd "$darwin_orig_dir"
+ else
+ cd $darwin_orig_dir
+ func_extract_an_archive "$my_xdir" "$my_xabs"
+ fi # $darwin_arches
+ } # !$opt_dry_run
+ ;;
+ *)
+ func_extract_an_archive "$my_xdir" "$my_xabs"
+ ;;
+ esac
+ my_oldobjs="$my_oldobjs "`find $my_xdir -name \*.$objext -print -o -name \*.lo -print | $NL2SP`
+ done
+
+ func_extract_archives_result="$my_oldobjs"
+}
+
+
+
+# func_emit_wrapper_part1 [arg=no]
+#
+# Emit the first part of a libtool wrapper script on stdout.
+# For more information, see the description associated with
+# func_emit_wrapper(), below.
+func_emit_wrapper_part1 ()
+{
+ func_emit_wrapper_part1_arg1=no
+ if test -n "$1" ; then
+ func_emit_wrapper_part1_arg1=$1
+ fi
+
+ $ECHO "\
+#! $SHELL
+
+# $output - temporary wrapper script for $objdir/$outputname
+# Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
+#
+# The $output program cannot be directly executed until all the libtool
+# libraries that it depends on are installed.
+#
+# This wrapper script should never be moved out of the build directory.
+# If it is, it will not operate correctly.
+
+# Sed substitution that helps us do robust quoting. It backslashifies
+# metacharacters that are still active within double-quoted strings.
+Xsed='${SED} -e 1s/^X//'
+sed_quote_subst='$sed_quote_subst'
+
+# Be Bourne compatible
+if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then
+ emulate sh
+ NULLCMD=:
+ # Zsh 3.x and 4.x performs word splitting on \${1+\"\$@\"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '\${1+\"\$@\"}'='\"\$@\"'
+ setopt NO_GLOB_SUBST
+else
+ case \`(set -o) 2>/dev/null\` in *posix*) set -o posix;; esac
+fi
+BIN_SH=xpg4; export BIN_SH # for Tru64
+DUALCASE=1; export DUALCASE # for MKS sh
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+relink_command=\"$relink_command\"
+
+# This environment variable determines our operation mode.
+if test \"\$libtool_install_magic\" = \"$magic\"; then
+ # install mode needs the following variables:
+ generated_by_libtool_version='$macro_version'
+ notinst_deplibs='$notinst_deplibs'
+else
+ # When we are sourced in execute mode, \$file and \$ECHO are already set.
+ if test \"\$libtool_execute_magic\" != \"$magic\"; then
+ ECHO=\"$qecho\"
+ file=\"\$0\"
+ # Make sure echo works.
+ if test \"X\$1\" = X--no-reexec; then
+ # Discard the --no-reexec flag, and continue.
+ shift
+ elif test \"X\`{ \$ECHO '\t'; } 2>/dev/null\`\" = 'X\t'; then
+ # Yippee, \$ECHO works!
+ :
+ else
+ # Restart under the correct shell, and then maybe \$ECHO will work.
+ exec $SHELL \"\$0\" --no-reexec \${1+\"\$@\"}
+ fi
+ fi\
+"
+ $ECHO "\
+
+ # Find the directory that this script lives in.
+ thisdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*$%%'\`
+ test \"x\$thisdir\" = \"x\$file\" && thisdir=.
+
+ # Follow symbolic links until we get to the real thisdir.
+ file=\`ls -ld \"\$file\" | ${SED} -n 's/.*-> //p'\`
+ while test -n \"\$file\"; do
+ destdir=\`\$ECHO \"X\$file\" | \$Xsed -e 's%/[^/]*\$%%'\`
+
+ # If there was a directory component, then change thisdir.
+ if test \"x\$destdir\" != \"x\$file\"; then
+ case \"\$destdir\" in
+ [\\\\/]* | [A-Za-z]:[\\\\/]*) thisdir=\"\$destdir\" ;;
+ *) thisdir=\"\$thisdir/\$destdir\" ;;
+ esac
+ fi
+
+ file=\`\$ECHO \"X\$file\" | \$Xsed -e 's%^.*/%%'\`
+ file=\`ls -ld \"\$thisdir/\$file\" | ${SED} -n 's/.*-> //p'\`
+ done
+"
+}
+# end: func_emit_wrapper_part1
+
+# func_emit_wrapper_part2 [arg=no]
+#
+# Emit the second part of a libtool wrapper script on stdout.
+# For more information, see the description associated with
+# func_emit_wrapper(), below.
+func_emit_wrapper_part2 ()
+{
+ func_emit_wrapper_part2_arg1=no
+ if test -n "$1" ; then
+ func_emit_wrapper_part2_arg1=$1
+ fi
+
+ $ECHO "\
+
+ # Usually 'no', except on cygwin/mingw when embedded into
+ # the cwrapper.
+ WRAPPER_SCRIPT_BELONGS_IN_OBJDIR=$func_emit_wrapper_part2_arg1
+ if test \"\$WRAPPER_SCRIPT_BELONGS_IN_OBJDIR\" = \"yes\"; then
+ # special case for '.'
+ if test \"\$thisdir\" = \".\"; then
+ thisdir=\`pwd\`
+ fi
+ # remove .libs from thisdir
+ case \"\$thisdir\" in
+ *[\\\\/]$objdir ) thisdir=\`\$ECHO \"X\$thisdir\" | \$Xsed -e 's%[\\\\/][^\\\\/]*$%%'\` ;;
+ $objdir ) thisdir=. ;;
+ esac
+ fi
+
+ # Try to get the absolute directory name.
+ absdir=\`cd \"\$thisdir\" && pwd\`
+ test -n \"\$absdir\" && thisdir=\"\$absdir\"
+"
+
+ if test "$fast_install" = yes; then
+ $ECHO "\
+ program=lt-'$outputname'$exeext
+ progdir=\"\$thisdir/$objdir\"
+
+ if test ! -f \"\$progdir/\$program\" ||
+ { file=\`ls -1dt \"\$progdir/\$program\" \"\$progdir/../\$program\" 2>/dev/null | ${SED} 1q\`; \\
+ test \"X\$file\" != \"X\$progdir/\$program\"; }; then
+
+ file=\"\$\$-\$program\"
+
+ if test ! -d \"\$progdir\"; then
+ $MKDIR \"\$progdir\"
+ else
+ $RM \"\$progdir/\$file\"
+ fi"
+
+ $ECHO "\
+
+ # relink executable if necessary
+ if test -n \"\$relink_command\"; then
+ if relink_command_output=\`eval \$relink_command 2>&1\`; then :
+ else
+ $ECHO \"\$relink_command_output\" >&2
+ $RM \"\$progdir/\$file\"
+ exit 1
+ fi
+ fi
+
+ $MV \"\$progdir/\$file\" \"\$progdir/\$program\" 2>/dev/null ||
+ { $RM \"\$progdir/\$program\";
+ $MV \"\$progdir/\$file\" \"\$progdir/\$program\"; }
+ $RM \"\$progdir/\$file\"
+ fi"
+ else
+ $ECHO "\
+ program='$outputname'
+ progdir=\"\$thisdir/$objdir\"
+"
+ fi
+
+ $ECHO "\
+
+ if test -f \"\$progdir/\$program\"; then"
+
+ # Export our shlibpath_var if we have one.
+ if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then
+ $ECHO "\
+ # Add our own library path to $shlibpath_var
+ $shlibpath_var=\"$temp_rpath\$$shlibpath_var\"
+
+ # Some systems cannot cope with colon-terminated $shlibpath_var
+ # The second colon is a workaround for a bug in BeOS R4 sed
+ $shlibpath_var=\`\$ECHO \"X\$$shlibpath_var\" | \$Xsed -e 's/::*\$//'\`
+
+ export $shlibpath_var
+"
+ fi
+
+ # fixup the dll searchpath if we need to.
+ if test -n "$dllsearchpath"; then
+ $ECHO "\
+ # Add the dll search path components to the executable PATH
+ PATH=$dllsearchpath:\$PATH
+"
+ fi
+
+ $ECHO "\
+ if test \"\$libtool_execute_magic\" != \"$magic\"; then
+ # Run the actual program with our arguments.
+"
+ case $host in
+ # Backslashes separate directories on plain windows
+ *-*-mingw | *-*-os2* | *-cegcc*)
+ $ECHO "\
+ exec \"\$progdir\\\\\$program\" \${1+\"\$@\"}
+"
+ ;;
+
+ *)
+ $ECHO "\
+ exec \"\$progdir/\$program\" \${1+\"\$@\"}
+"
+ ;;
+ esac
+ $ECHO "\
+ \$ECHO \"\$0: cannot exec \$program \$*\" 1>&2
+ exit 1
+ fi
+ else
+ # The program doesn't exist.
+ \$ECHO \"\$0: error: \\\`\$progdir/\$program' does not exist\" 1>&2
+ \$ECHO \"This script is just a wrapper for \$program.\" 1>&2
+ $ECHO \"See the $PACKAGE documentation for more information.\" 1>&2
+ exit 1
+ fi
+fi\
+"
+}
+# end: func_emit_wrapper_part2
+
+
+# func_emit_wrapper [arg=no]
+#
+# Emit a libtool wrapper script on stdout.
+# Don't directly open a file because we may want to
+# incorporate the script contents within a cygwin/mingw
+# wrapper executable. Must ONLY be called from within
+# func_mode_link because it depends on a number of variables
+# set therein.
+#
+# ARG is the value that the WRAPPER_SCRIPT_BELONGS_IN_OBJDIR
+# variable will take. If 'yes', then the emitted script
+# will assume that the directory in which it is stored is
+# the $objdir directory. This is a cygwin/mingw-specific
+# behavior.
+func_emit_wrapper ()
+{
+ func_emit_wrapper_arg1=no
+ if test -n "$1" ; then
+ func_emit_wrapper_arg1=$1
+ fi
+
+ # split this up so that func_emit_cwrapperexe_src
+ # can call each part independently.
+ func_emit_wrapper_part1 "${func_emit_wrapper_arg1}"
+ func_emit_wrapper_part2 "${func_emit_wrapper_arg1}"
+}
+
+
+# func_to_host_path arg
+#
+# Convert paths to host format when used with build tools.
+# Intended for use with "native" mingw (where libtool itself
+# is running under the msys shell), or in the following cross-
+# build environments:
+# $build $host
+# mingw (msys) mingw [e.g. native]
+# cygwin mingw
+# *nix + wine mingw
+# where wine is equipped with the `winepath' executable.
+# In the native mingw case, the (msys) shell automatically
+# converts paths for any non-msys applications it launches,
+# but that facility isn't available from inside the cwrapper.
+# Similar accommodations are necessary for $host mingw and
+# $build cygwin. Calling this function does no harm for other
+# $host/$build combinations not listed above.
+#
+# ARG is the path (on $build) that should be converted to
+# the proper representation for $host. The result is stored
+# in $func_to_host_path_result.
+func_to_host_path ()
+{
+ func_to_host_path_result="$1"
+ if test -n "$1" ; then
+ case $host in
+ *mingw* )
+ lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g'
+ case $build in
+ *mingw* ) # actually, msys
+ # awkward: cmd appends spaces to result
+ lt_sed_strip_trailing_spaces="s/[ ]*\$//"
+ func_to_host_path_tmp1=`( cmd //c echo "$1" |\
+ $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""`
+ func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ ;;
+ *cygwin* )
+ func_to_host_path_tmp1=`cygpath -w "$1"`
+ func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ ;;
+ * )
+ # Unfortunately, winepath does not exit with a non-zero
+ # error code, so we are forced to check the contents of
+ # stdout. On the other hand, if the command is not
+ # found, the shell will set an exit code of 127 and print
+ # *an error message* to stdout. So we must check for both
+ # error code of zero AND non-empty stdout, which explains
+ # the odd construction:
+ func_to_host_path_tmp1=`winepath -w "$1" 2>/dev/null`
+ if test "$?" -eq 0 && test -n "${func_to_host_path_tmp1}"; then
+ func_to_host_path_result=`echo "$func_to_host_path_tmp1" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ else
+ # Allow warning below.
+ func_to_host_path_result=""
+ fi
+ ;;
+ esac
+ if test -z "$func_to_host_path_result" ; then
+ func_error "Could not determine host path corresponding to"
+ func_error " '$1'"
+ func_error "Continuing, but uninstalled executables may not work."
+ # Fallback:
+ func_to_host_path_result="$1"
+ fi
+ ;;
+ esac
+ fi
+}
+# end: func_to_host_path
+
+# func_to_host_pathlist arg
+#
+# Convert pathlists to host format when used with build tools.
+# See func_to_host_path(), above. This function supports the
+# following $build/$host combinations (but does no harm for
+# combinations not listed here):
+# $build $host
+# mingw (msys) mingw [e.g. native]
+# cygwin mingw
+# *nix + wine mingw
+#
+# Path separators are also converted from $build format to
+# $host format. If ARG begins or ends with a path separator
+# character, it is preserved (but converted to $host format)
+# on output.
+#
+# ARG is a pathlist (on $build) that should be converted to
+# the proper representation on $host. The result is stored
+# in $func_to_host_pathlist_result.
+func_to_host_pathlist ()
+{
+ func_to_host_pathlist_result="$1"
+ if test -n "$1" ; then
+ case $host in
+ *mingw* )
+ lt_sed_naive_backslashify='s|\\\\*|\\|g;s|/|\\|g;s|\\|\\\\|g'
+ # Remove leading and trailing path separator characters from
+ # ARG. msys behavior is inconsistent here, cygpath turns them
+ # into '.;' and ';.', and winepath ignores them completely.
+ func_to_host_pathlist_tmp2="$1"
+ # Once set for this call, this variable should not be
+ # reassigned. It is used in tha fallback case.
+ func_to_host_pathlist_tmp1=`echo "$func_to_host_pathlist_tmp2" |\
+ $SED -e 's|^:*||' -e 's|:*$||'`
+ case $build in
+ *mingw* ) # Actually, msys.
+ # Awkward: cmd appends spaces to result.
+ lt_sed_strip_trailing_spaces="s/[ ]*\$//"
+ func_to_host_pathlist_tmp2=`( cmd //c echo "$func_to_host_pathlist_tmp1" |\
+ $SED -e "$lt_sed_strip_trailing_spaces" ) 2>/dev/null || echo ""`
+ func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ ;;
+ *cygwin* )
+ func_to_host_pathlist_tmp2=`cygpath -w -p "$func_to_host_pathlist_tmp1"`
+ func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp2" |\
+ $SED -e "$lt_sed_naive_backslashify"`
+ ;;
+ * )
+ # unfortunately, winepath doesn't convert pathlists
+ func_to_host_pathlist_result=""
+ func_to_host_pathlist_oldIFS=$IFS
+ IFS=:
+ for func_to_host_pathlist_f in $func_to_host_pathlist_tmp1 ; do
+ IFS=$func_to_host_pathlist_oldIFS
+ if test -n "$func_to_host_pathlist_f" ; then
+ func_to_host_path "$func_to_host_pathlist_f"
+ if test -n "$func_to_host_path_result" ; then
+ if test -z "$func_to_host_pathlist_result" ; then
+ func_to_host_pathlist_result="$func_to_host_path_result"
+ else
+ func_to_host_pathlist_result="$func_to_host_pathlist_result;$func_to_host_path_result"
+ fi
+ fi
+ fi
+ IFS=:
+ done
+ IFS=$func_to_host_pathlist_oldIFS
+ ;;
+ esac
+ if test -z "$func_to_host_pathlist_result" ; then
+ func_error "Could not determine the host path(s) corresponding to"
+ func_error " '$1'"
+ func_error "Continuing, but uninstalled executables may not work."
+ # Fallback. This may break if $1 contains DOS-style drive
+ # specifications. The fix is not to complicate the expression
+ # below, but for the user to provide a working wine installation
+ # with winepath so that path translation in the cross-to-mingw
+ # case works properly.
+ lt_replace_pathsep_nix_to_dos="s|:|;|g"
+ func_to_host_pathlist_result=`echo "$func_to_host_pathlist_tmp1" |\
+ $SED -e "$lt_replace_pathsep_nix_to_dos"`
+ fi
+ # Now, add the leading and trailing path separators back
+ case "$1" in
+ :* ) func_to_host_pathlist_result=";$func_to_host_pathlist_result"
+ ;;
+ esac
+ case "$1" in
+ *: ) func_to_host_pathlist_result="$func_to_host_pathlist_result;"
+ ;;
+ esac
+ ;;
+ esac
+ fi
+}
+# end: func_to_host_pathlist
+
+# func_emit_cwrapperexe_src
+# emit the source code for a wrapper executable on stdout
+# Must ONLY be called from within func_mode_link because
+# it depends on a number of variable set therein.
+func_emit_cwrapperexe_src ()
+{
+ cat <<EOF
+
+/* $cwrappersource - temporary wrapper executable for $objdir/$outputname
+ Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
+
+ The $output program cannot be directly executed until all the libtool
+ libraries that it depends on are installed.
+
+ This wrapper executable should never be moved out of the build directory.
+ If it is, it will not operate correctly.
+
+ Currently, it simply execs the wrapper *script* "$SHELL $output",
+ but could eventually absorb all of the scripts functionality and
+ exec $objdir/$outputname directly.
+*/
+EOF
+ cat <<"EOF"
+#include <stdio.h>
+#include <stdlib.h>
+#ifdef _MSC_VER
+# include <direct.h>
+# include <process.h>
+# include <io.h>
+# define setmode _setmode
+#else
+# include <unistd.h>
+# include <stdint.h>
+# ifdef __CYGWIN__
+# include <io.h>
+# define HAVE_SETENV
+# ifdef __STRICT_ANSI__
+char *realpath (const char *, char *);
+int putenv (char *);
+int setenv (const char *, const char *, int);
+# endif
+# endif
+#endif
+#include <malloc.h>
+#include <stdarg.h>
+#include <assert.h>
+#include <string.h>
+#include <ctype.h>
+#include <errno.h>
+#include <fcntl.h>
+#include <sys/stat.h>
+
+#if defined(PATH_MAX)
+# define LT_PATHMAX PATH_MAX
+#elif defined(MAXPATHLEN)
+# define LT_PATHMAX MAXPATHLEN
+#else
+# define LT_PATHMAX 1024
+#endif
+
+#ifndef S_IXOTH
+# define S_IXOTH 0
+#endif
+#ifndef S_IXGRP
+# define S_IXGRP 0
+#endif
+
+#ifdef _MSC_VER
+# define S_IXUSR _S_IEXEC
+# define stat _stat
+# ifndef _INTPTR_T_DEFINED
+# define intptr_t int
+# endif
+#endif
+
+#ifndef DIR_SEPARATOR
+# define DIR_SEPARATOR '/'
+# define PATH_SEPARATOR ':'
+#endif
+
+#if defined (_WIN32) || defined (__MSDOS__) || defined (__DJGPP__) || \
+ defined (__OS2__)
+# define HAVE_DOS_BASED_FILE_SYSTEM
+# define FOPEN_WB "wb"
+# ifndef DIR_SEPARATOR_2
+# define DIR_SEPARATOR_2 '\\'
+# endif
+# ifndef PATH_SEPARATOR_2
+# define PATH_SEPARATOR_2 ';'
+# endif
+#endif
+
+#ifndef DIR_SEPARATOR_2
+# define IS_DIR_SEPARATOR(ch) ((ch) == DIR_SEPARATOR)
+#else /* DIR_SEPARATOR_2 */
+# define IS_DIR_SEPARATOR(ch) \
+ (((ch) == DIR_SEPARATOR) || ((ch) == DIR_SEPARATOR_2))
+#endif /* DIR_SEPARATOR_2 */
+
+#ifndef PATH_SEPARATOR_2
+# define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR)
+#else /* PATH_SEPARATOR_2 */
+# define IS_PATH_SEPARATOR(ch) ((ch) == PATH_SEPARATOR_2)
+#endif /* PATH_SEPARATOR_2 */
+
+#ifdef __CYGWIN__
+# define FOPEN_WB "wb"
+#endif
+
+#ifndef FOPEN_WB
+# define FOPEN_WB "w"
+#endif
+#ifndef _O_BINARY
+# define _O_BINARY 0
+#endif
+
+#define XMALLOC(type, num) ((type *) xmalloc ((num) * sizeof(type)))
+#define XFREE(stale) do { \
+ if (stale) { free ((void *) stale); stale = 0; } \
+} while (0)
+
+#undef LTWRAPPER_DEBUGPRINTF
+#if defined DEBUGWRAPPER
+# define LTWRAPPER_DEBUGPRINTF(args) ltwrapper_debugprintf args
+static void
+ltwrapper_debugprintf (const char *fmt, ...)
+{
+ va_list args;
+ va_start (args, fmt);
+ (void) vfprintf (stderr, fmt, args);
+ va_end (args);
+}
+#else
+# define LTWRAPPER_DEBUGPRINTF(args)
+#endif
+
+const char *program_name = NULL;
+
+void *xmalloc (size_t num);
+char *xstrdup (const char *string);
+const char *base_name (const char *name);
+char *find_executable (const char *wrapper);
+char *chase_symlinks (const char *pathspec);
+int make_executable (const char *path);
+int check_executable (const char *path);
+char *strendzap (char *str, const char *pat);
+void lt_fatal (const char *message, ...);
+void lt_setenv (const char *name, const char *value);
+char *lt_extend_str (const char *orig_value, const char *add, int to_end);
+void lt_opt_process_env_set (const char *arg);
+void lt_opt_process_env_prepend (const char *arg);
+void lt_opt_process_env_append (const char *arg);
+int lt_split_name_value (const char *arg, char** name, char** value);
+void lt_update_exe_path (const char *name, const char *value);
+void lt_update_lib_path (const char *name, const char *value);
+
+static const char *script_text_part1 =
+EOF
+
+ func_emit_wrapper_part1 yes |
+ $SED -e 's/\([\\"]\)/\\\1/g' \
+ -e 's/^/ "/' -e 's/$/\\n"/'
+ echo ";"
+ cat <<EOF
+
+static const char *script_text_part2 =
+EOF
+ func_emit_wrapper_part2 yes |
+ $SED -e 's/\([\\"]\)/\\\1/g' \
+ -e 's/^/ "/' -e 's/$/\\n"/'
+ echo ";"
+
+ cat <<EOF
+const char * MAGIC_EXE = "$magic_exe";
+const char * LIB_PATH_VARNAME = "$shlibpath_var";
+EOF
+
+ if test "$shlibpath_overrides_runpath" = yes && test -n "$shlibpath_var" && test -n "$temp_rpath"; then
+ func_to_host_pathlist "$temp_rpath"
+ cat <<EOF
+const char * LIB_PATH_VALUE = "$func_to_host_pathlist_result";
+EOF
+ else
+ cat <<"EOF"
+const char * LIB_PATH_VALUE = "";
+EOF
+ fi
+
+ if test -n "$dllsearchpath"; then
+ func_to_host_pathlist "$dllsearchpath:"
+ cat <<EOF
+const char * EXE_PATH_VARNAME = "PATH";
+const char * EXE_PATH_VALUE = "$func_to_host_pathlist_result";
+EOF
+ else
+ cat <<"EOF"
+const char * EXE_PATH_VARNAME = "";
+const char * EXE_PATH_VALUE = "";
+EOF
+ fi
+
+ if test "$fast_install" = yes; then
+ cat <<EOF
+const char * TARGET_PROGRAM_NAME = "lt-$outputname"; /* hopefully, no .exe */
+EOF
+ else
+ cat <<EOF
+const char * TARGET_PROGRAM_NAME = "$outputname"; /* hopefully, no .exe */
+EOF
+ fi
+
+
+ cat <<"EOF"
+
+#define LTWRAPPER_OPTION_PREFIX "--lt-"
+#define LTWRAPPER_OPTION_PREFIX_LENGTH 5
+
+static const size_t opt_prefix_len = LTWRAPPER_OPTION_PREFIX_LENGTH;
+static const char *ltwrapper_option_prefix = LTWRAPPER_OPTION_PREFIX;
+
+static const char *dumpscript_opt = LTWRAPPER_OPTION_PREFIX "dump-script";
+
+static const size_t env_set_opt_len = LTWRAPPER_OPTION_PREFIX_LENGTH + 7;
+static const char *env_set_opt = LTWRAPPER_OPTION_PREFIX "env-set";
+ /* argument is putenv-style "foo=bar", value of foo is set to bar */
+
+static const size_t env_prepend_opt_len = LTWRAPPER_OPTION_PREFIX_LENGTH + 11;
+static const char *env_prepend_opt = LTWRAPPER_OPTION_PREFIX "env-prepend";
+ /* argument is putenv-style "foo=bar", new value of foo is bar${foo} */
+
+static const size_t env_append_opt_len = LTWRAPPER_OPTION_PREFIX_LENGTH + 10;
+static const char *env_append_opt = LTWRAPPER_OPTION_PREFIX "env-append";
+ /* argument is putenv-style "foo=bar", new value of foo is ${foo}bar */
+
+int
+main (int argc, char *argv[])
+{
+ char **newargz;
+ int newargc;
+ char *tmp_pathspec;
+ char *actual_cwrapper_path;
+ char *actual_cwrapper_name;
+ char *target_name;
+ char *lt_argv_zero;
+ intptr_t rval = 127;
+
+ int i;
+
+ program_name = (char *) xstrdup (base_name (argv[0]));
+ LTWRAPPER_DEBUGPRINTF (("(main) argv[0] : %s\n", argv[0]));
+ LTWRAPPER_DEBUGPRINTF (("(main) program_name : %s\n", program_name));
+
+ /* very simple arg parsing; don't want to rely on getopt */
+ for (i = 1; i < argc; i++)
+ {
+ if (strcmp (argv[i], dumpscript_opt) == 0)
+ {
+EOF
+ case "$host" in
+ *mingw* | *cygwin* )
+ # make stdout use "unix" line endings
+ echo " setmode(1,_O_BINARY);"
+ ;;
+ esac
+
+ cat <<"EOF"
+ printf ("%s", script_text_part1);
+ printf ("%s", script_text_part2);
+ return 0;
+ }
+ }
+
+ newargz = XMALLOC (char *, argc + 1);
+ tmp_pathspec = find_executable (argv[0]);
+ if (tmp_pathspec == NULL)
+ lt_fatal ("Couldn't find %s", argv[0]);
+ LTWRAPPER_DEBUGPRINTF (("(main) found exe (before symlink chase) at : %s\n",
+ tmp_pathspec));
+
+ actual_cwrapper_path = chase_symlinks (tmp_pathspec);
+ LTWRAPPER_DEBUGPRINTF (("(main) found exe (after symlink chase) at : %s\n",
+ actual_cwrapper_path));
+ XFREE (tmp_pathspec);
+
+ actual_cwrapper_name = xstrdup( base_name (actual_cwrapper_path));
+ strendzap (actual_cwrapper_path, actual_cwrapper_name);
+
+ /* wrapper name transforms */
+ strendzap (actual_cwrapper_name, ".exe");
+ tmp_pathspec = lt_extend_str (actual_cwrapper_name, ".exe", 1);
+ XFREE (actual_cwrapper_name);
+ actual_cwrapper_name = tmp_pathspec;
+ tmp_pathspec = 0;
+
+ /* target_name transforms -- use actual target program name; might have lt- prefix */
+ target_name = xstrdup (base_name (TARGET_PROGRAM_NAME));
+ strendzap (target_name, ".exe");
+ tmp_pathspec = lt_extend_str (target_name, ".exe", 1);
+ XFREE (target_name);
+ target_name = tmp_pathspec;
+ tmp_pathspec = 0;
+
+ LTWRAPPER_DEBUGPRINTF (("(main) libtool target name: %s\n",
+ target_name));
+EOF
+
+ cat <<EOF
+ newargz[0] =
+ XMALLOC (char, (strlen (actual_cwrapper_path) +
+ strlen ("$objdir") + 1 + strlen (actual_cwrapper_name) + 1));
+ strcpy (newargz[0], actual_cwrapper_path);
+ strcat (newargz[0], "$objdir");
+ strcat (newargz[0], "/");
+EOF
+
+ cat <<"EOF"
+ /* stop here, and copy so we don't have to do this twice */
+ tmp_pathspec = xstrdup (newargz[0]);
+
+ /* do NOT want the lt- prefix here, so use actual_cwrapper_name */
+ strcat (newargz[0], actual_cwrapper_name);
+
+ /* DO want the lt- prefix here if it exists, so use target_name */
+ lt_argv_zero = lt_extend_str (tmp_pathspec, target_name, 1);
+ XFREE (tmp_pathspec);
+ tmp_pathspec = NULL;
+EOF
+
+ case $host_os in
+ mingw*)
+ cat <<"EOF"
+ {
+ char* p;
+ while ((p = strchr (newargz[0], '\\')) != NULL)
+ {
+ *p = '/';
+ }
+ while ((p = strchr (lt_argv_zero, '\\')) != NULL)
+ {
+ *p = '/';
+ }
+ }
+EOF
+ ;;
+ esac
+
+ cat <<"EOF"
+ XFREE (target_name);
+ XFREE (actual_cwrapper_path);
+ XFREE (actual_cwrapper_name);
+
+ lt_setenv ("BIN_SH", "xpg4"); /* for Tru64 */
+ lt_setenv ("DUALCASE", "1"); /* for MSK sh */
+ lt_update_lib_path (LIB_PATH_VARNAME, LIB_PATH_VALUE);
+ lt_update_exe_path (EXE_PATH_VARNAME, EXE_PATH_VALUE);
+
+ newargc=0;
+ for (i = 1; i < argc; i++)
+ {
+ if (strncmp (argv[i], env_set_opt, env_set_opt_len) == 0)
+ {
+ if (argv[i][env_set_opt_len] == '=')
+ {
+ const char *p = argv[i] + env_set_opt_len + 1;
+ lt_opt_process_env_set (p);
+ }
+ else if (argv[i][env_set_opt_len] == '\0' && i + 1 < argc)
+ {
+ lt_opt_process_env_set (argv[++i]); /* don't copy */
+ }
+ else
+ lt_fatal ("%s missing required argument", env_set_opt);
+ continue;
+ }
+ if (strncmp (argv[i], env_prepend_opt, env_prepend_opt_len) == 0)
+ {
+ if (argv[i][env_prepend_opt_len] == '=')
+ {
+ const char *p = argv[i] + env_prepend_opt_len + 1;
+ lt_opt_process_env_prepend (p);
+ }
+ else if (argv[i][env_prepend_opt_len] == '\0' && i + 1 < argc)
+ {
+ lt_opt_process_env_prepend (argv[++i]); /* don't copy */
+ }
+ else
+ lt_fatal ("%s missing required argument", env_prepend_opt);
+ continue;
+ }
+ if (strncmp (argv[i], env_append_opt, env_append_opt_len) == 0)
+ {
+ if (argv[i][env_append_opt_len] == '=')
+ {
+ const char *p = argv[i] + env_append_opt_len + 1;
+ lt_opt_process_env_append (p);
+ }
+ else if (argv[i][env_append_opt_len] == '\0' && i + 1 < argc)
+ {
+ lt_opt_process_env_append (argv[++i]); /* don't copy */
+ }
+ else
+ lt_fatal ("%s missing required argument", env_append_opt);
+ continue;
+ }
+ if (strncmp (argv[i], ltwrapper_option_prefix, opt_prefix_len) == 0)
+ {
+ /* however, if there is an option in the LTWRAPPER_OPTION_PREFIX
+ namespace, but it is not one of the ones we know about and
+ have already dealt with, above (inluding dump-script), then
+ report an error. Otherwise, targets might begin to believe
+ they are allowed to use options in the LTWRAPPER_OPTION_PREFIX
+ namespace. The first time any user complains about this, we'll
+ need to make LTWRAPPER_OPTION_PREFIX a configure-time option
+ or a configure.ac-settable value.
+ */
+ lt_fatal ("Unrecognized option in %s namespace: '%s'",
+ ltwrapper_option_prefix, argv[i]);
+ }
+ /* otherwise ... */
+ newargz[++newargc] = xstrdup (argv[i]);
+ }
+ newargz[++newargc] = NULL;
+
+ LTWRAPPER_DEBUGPRINTF (("(main) lt_argv_zero : %s\n", (lt_argv_zero ? lt_argv_zero : "<NULL>")));
+ for (i = 0; i < newargc; i++)
+ {
+ LTWRAPPER_DEBUGPRINTF (("(main) newargz[%d] : %s\n", i, (newargz[i] ? newargz[i] : "<NULL>")));
+ }
+
+EOF
+
+ case $host_os in
+ mingw*)
+ cat <<"EOF"
+ /* execv doesn't actually work on mingw as expected on unix */
+ rval = _spawnv (_P_WAIT, lt_argv_zero, (const char * const *) newargz);
+ if (rval == -1)
+ {
+ /* failed to start process */
+ LTWRAPPER_DEBUGPRINTF (("(main) failed to launch target \"%s\": errno = %d\n", lt_argv_zero, errno));
+ return 127;
+ }
+ return rval;
+EOF
+ ;;
+ *)
+ cat <<"EOF"
+ execv (lt_argv_zero, newargz);
+ return rval; /* =127, but avoids unused variable warning */
+EOF
+ ;;
+ esac
+
+ cat <<"EOF"
+}
+
+void *
+xmalloc (size_t num)
+{
+ void *p = (void *) malloc (num);
+ if (!p)
+ lt_fatal ("Memory exhausted");
+
+ return p;
+}
+
+char *
+xstrdup (const char *string)
+{
+ return string ? strcpy ((char *) xmalloc (strlen (string) + 1),
+ string) : NULL;
+}
+
+const char *
+base_name (const char *name)
+{
+ const char *base;
+
+#if defined (HAVE_DOS_BASED_FILE_SYSTEM)
+ /* Skip over the disk name in MSDOS pathnames. */
+ if (isalpha ((unsigned char) name[0]) && name[1] == ':')
+ name += 2;
+#endif
+
+ for (base = name; *name; name++)
+ if (IS_DIR_SEPARATOR (*name))
+ base = name + 1;
+ return base;
+}
+
+int
+check_executable (const char *path)
+{
+ struct stat st;
+
+ LTWRAPPER_DEBUGPRINTF (("(check_executable) : %s\n",
+ path ? (*path ? path : "EMPTY!") : "NULL!"));
+ if ((!path) || (!*path))
+ return 0;
+
+ if ((stat (path, &st) >= 0)
+ && (st.st_mode & (S_IXUSR | S_IXGRP | S_IXOTH)))
+ return 1;
+ else
+ return 0;
+}
+
+int
+make_executable (const char *path)
+{
+ int rval = 0;
+ struct stat st;
+
+ LTWRAPPER_DEBUGPRINTF (("(make_executable) : %s\n",
+ path ? (*path ? path : "EMPTY!") : "NULL!"));
+ if ((!path) || (!*path))
+ return 0;
+
+ if (stat (path, &st) >= 0)
+ {
+ rval = chmod (path, st.st_mode | S_IXOTH | S_IXGRP | S_IXUSR);
+ }
+ return rval;
+}
+
+/* Searches for the full path of the wrapper. Returns
+ newly allocated full path name if found, NULL otherwise
+ Does not chase symlinks, even on platforms that support them.
+*/
+char *
+find_executable (const char *wrapper)
+{
+ int has_slash = 0;
+ const char *p;
+ const char *p_next;
+ /* static buffer for getcwd */
+ char tmp[LT_PATHMAX + 1];
+ int tmp_len;
+ char *concat_name;
+
+ LTWRAPPER_DEBUGPRINTF (("(find_executable) : %s\n",
+ wrapper ? (*wrapper ? wrapper : "EMPTY!") : "NULL!"));
+
+ if ((wrapper == NULL) || (*wrapper == '\0'))
+ return NULL;
+
+ /* Absolute path? */
+#if defined (HAVE_DOS_BASED_FILE_SYSTEM)
+ if (isalpha ((unsigned char) wrapper[0]) && wrapper[1] == ':')
+ {
+ concat_name = xstrdup (wrapper);
+ if (check_executable (concat_name))
+ return concat_name;
+ XFREE (concat_name);
+ }
+ else
+ {
+#endif
+ if (IS_DIR_SEPARATOR (wrapper[0]))
+ {
+ concat_name = xstrdup (wrapper);
+ if (check_executable (concat_name))
+ return concat_name;
+ XFREE (concat_name);
+ }
+#if defined (HAVE_DOS_BASED_FILE_SYSTEM)
+ }
+#endif
+
+ for (p = wrapper; *p; p++)
+ if (*p == '/')
+ {
+ has_slash = 1;
+ break;
+ }
+ if (!has_slash)
+ {
+ /* no slashes; search PATH */
+ const char *path = getenv ("PATH");
+ if (path != NULL)
+ {
+ for (p = path; *p; p = p_next)
+ {
+ const char *q;
+ size_t p_len;
+ for (q = p; *q; q++)
+ if (IS_PATH_SEPARATOR (*q))
+ break;
+ p_len = q - p;
+ p_next = (*q == '\0' ? q : q + 1);
+ if (p_len == 0)
+ {
+ /* empty path: current directory */
+ if (getcwd (tmp, LT_PATHMAX) == NULL)
+ lt_fatal ("getcwd failed");
+ tmp_len = strlen (tmp);
+ concat_name =
+ XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1);
+ memcpy (concat_name, tmp, tmp_len);
+ concat_name[tmp_len] = '/';
+ strcpy (concat_name + tmp_len + 1, wrapper);
+ }
+ else
+ {
+ concat_name =
+ XMALLOC (char, p_len + 1 + strlen (wrapper) + 1);
+ memcpy (concat_name, p, p_len);
+ concat_name[p_len] = '/';
+ strcpy (concat_name + p_len + 1, wrapper);
+ }
+ if (check_executable (concat_name))
+ return concat_name;
+ XFREE (concat_name);
+ }
+ }
+ /* not found in PATH; assume curdir */
+ }
+ /* Relative path | not found in path: prepend cwd */
+ if (getcwd (tmp, LT_PATHMAX) == NULL)
+ lt_fatal ("getcwd failed");
+ tmp_len = strlen (tmp);
+ concat_name = XMALLOC (char, tmp_len + 1 + strlen (wrapper) + 1);
+ memcpy (concat_name, tmp, tmp_len);
+ concat_name[tmp_len] = '/';
+ strcpy (concat_name + tmp_len + 1, wrapper);
+
+ if (check_executable (concat_name))
+ return concat_name;
+ XFREE (concat_name);
+ return NULL;
+}
+
+char *
+chase_symlinks (const char *pathspec)
+{
+#ifndef S_ISLNK
+ return xstrdup (pathspec);
+#else
+ char buf[LT_PATHMAX];
+ struct stat s;
+ char *tmp_pathspec = xstrdup (pathspec);
+ char *p;
+ int has_symlinks = 0;
+ while (strlen (tmp_pathspec) && !has_symlinks)
+ {
+ LTWRAPPER_DEBUGPRINTF (("checking path component for symlinks: %s\n",
+ tmp_pathspec));
+ if (lstat (tmp_pathspec, &s) == 0)
+ {
+ if (S_ISLNK (s.st_mode) != 0)
+ {
+ has_symlinks = 1;
+ break;
+ }
+
+ /* search backwards for last DIR_SEPARATOR */
+ p = tmp_pathspec + strlen (tmp_pathspec) - 1;
+ while ((p > tmp_pathspec) && (!IS_DIR_SEPARATOR (*p)))
+ p--;
+ if ((p == tmp_pathspec) && (!IS_DIR_SEPARATOR (*p)))
+ {
+ /* no more DIR_SEPARATORS left */
+ break;
+ }
+ *p = '\0';
+ }
+ else
+ {
+ char *errstr = strerror (errno);
+ lt_fatal ("Error accessing file %s (%s)", tmp_pathspec, errstr);
+ }
+ }
+ XFREE (tmp_pathspec);
+
+ if (!has_symlinks)
+ {
+ return xstrdup (pathspec);
+ }
+
+ tmp_pathspec = realpath (pathspec, buf);
+ if (tmp_pathspec == 0)
+ {
+ lt_fatal ("Could not follow symlinks for %s", pathspec);
+ }
+ return xstrdup (tmp_pathspec);
+#endif
+}
+
+char *
+strendzap (char *str, const char *pat)
+{
+ size_t len, patlen;
+
+ assert (str != NULL);
+ assert (pat != NULL);
+
+ len = strlen (str);
+ patlen = strlen (pat);
+
+ if (patlen <= len)
+ {
+ str += len - patlen;
+ if (strcmp (str, pat) == 0)
+ *str = '\0';
+ }
+ return str;
+}
+
+static void
+lt_error_core (int exit_status, const char *mode,
+ const char *message, va_list ap)
+{
+ fprintf (stderr, "%s: %s: ", program_name, mode);
+ vfprintf (stderr, message, ap);
+ fprintf (stderr, ".\n");
+
+ if (exit_status >= 0)
+ exit (exit_status);
+}
+
+void
+lt_fatal (const char *message, ...)
+{
+ va_list ap;
+ va_start (ap, message);
+ lt_error_core (EXIT_FAILURE, "FATAL", message, ap);
+ va_end (ap);
+}
+
+void
+lt_setenv (const char *name, const char *value)
+{
+ LTWRAPPER_DEBUGPRINTF (("(lt_setenv) setting '%s' to '%s'\n",
+ (name ? name : "<NULL>"),
+ (value ? value : "<NULL>")));
+ {
+#ifdef HAVE_SETENV
+ /* always make a copy, for consistency with !HAVE_SETENV */
+ char *str = xstrdup (value);
+ setenv (name, str, 1);
+#else
+ int len = strlen (name) + 1 + strlen (value) + 1;
+ char *str = XMALLOC (char, len);
+ sprintf (str, "%s=%s", name, value);
+ if (putenv (str) != EXIT_SUCCESS)
+ {
+ XFREE (str);
+ }
+#endif
+ }
+}
+
+char *
+lt_extend_str (const char *orig_value, const char *add, int to_end)
+{
+ char *new_value;
+ if (orig_value && *orig_value)
+ {
+ int orig_value_len = strlen (orig_value);
+ int add_len = strlen (add);
+ new_value = XMALLOC (char, add_len + orig_value_len + 1);
+ if (to_end)
+ {
+ strcpy (new_value, orig_value);
+ strcpy (new_value + orig_value_len, add);
+ }
+ else
+ {
+ strcpy (new_value, add);
+ strcpy (new_value + add_len, orig_value);
+ }
+ }
+ else
+ {
+ new_value = xstrdup (add);
+ }
+ return new_value;
+}
+
+int
+lt_split_name_value (const char *arg, char** name, char** value)
+{
+ const char *p;
+ int len;
+ if (!arg || !*arg)
+ return 1;
+
+ p = strchr (arg, (int)'=');
+
+ if (!p)
+ return 1;
+
+ *value = xstrdup (++p);
+
+ len = strlen (arg) - strlen (*value);
+ *name = XMALLOC (char, len);
+ strncpy (*name, arg, len-1);
+ (*name)[len - 1] = '\0';
+
+ return 0;
+}
+
+void
+lt_opt_process_env_set (const char *arg)
+{
+ char *name = NULL;
+ char *value = NULL;
+
+ if (lt_split_name_value (arg, &name, &value) != 0)
+ {
+ XFREE (name);
+ XFREE (value);
+ lt_fatal ("bad argument for %s: '%s'", env_set_opt, arg);
+ }
+
+ lt_setenv (name, value);
+ XFREE (name);
+ XFREE (value);
+}
+
+void
+lt_opt_process_env_prepend (const char *arg)
+{
+ char *name = NULL;
+ char *value = NULL;
+ char *new_value = NULL;
+
+ if (lt_split_name_value (arg, &name, &value) != 0)
+ {
+ XFREE (name);
+ XFREE (value);
+ lt_fatal ("bad argument for %s: '%s'", env_prepend_opt, arg);
+ }
+
+ new_value = lt_extend_str (getenv (name), value, 0);
+ lt_setenv (name, new_value);
+ XFREE (new_value);
+ XFREE (name);
+ XFREE (value);
+}
+
+void
+lt_opt_process_env_append (const char *arg)
+{
+ char *name = NULL;
+ char *value = NULL;
+ char *new_value = NULL;
+
+ if (lt_split_name_value (arg, &name, &value) != 0)
+ {
+ XFREE (name);
+ XFREE (value);
+ lt_fatal ("bad argument for %s: '%s'", env_append_opt, arg);
+ }
+
+ new_value = lt_extend_str (getenv (name), value, 1);
+ lt_setenv (name, new_value);
+ XFREE (new_value);
+ XFREE (name);
+ XFREE (value);
+}
+
+void
+lt_update_exe_path (const char *name, const char *value)
+{
+ LTWRAPPER_DEBUGPRINTF (("(lt_update_exe_path) modifying '%s' by prepending '%s'\n",
+ (name ? name : "<NULL>"),
+ (value ? value : "<NULL>")));
+
+ if (name && *name && value && *value)
+ {
+ char *new_value = lt_extend_str (getenv (name), value, 0);
+ /* some systems can't cope with a ':'-terminated path #' */
+ int len = strlen (new_value);
+ while (((len = strlen (new_value)) > 0) && IS_PATH_SEPARATOR (new_value[len-1]))
+ {
+ new_value[len-1] = '\0';
+ }
+ lt_setenv (name, new_value);
+ XFREE (new_value);
+ }
+}
+
+void
+lt_update_lib_path (const char *name, const char *value)
+{
+ LTWRAPPER_DEBUGPRINTF (("(lt_update_lib_path) modifying '%s' by prepending '%s'\n",
+ (name ? name : "<NULL>"),
+ (value ? value : "<NULL>")));
+
+ if (name && *name && value && *value)
+ {
+ char *new_value = lt_extend_str (getenv (name), value, 0);
+ lt_setenv (name, new_value);
+ XFREE (new_value);
+ }
+}
+
+
+EOF
+}
+# end: func_emit_cwrapperexe_src
+
+# func_mode_link arg...
+func_mode_link ()
+{
+ $opt_debug
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*)
+ # It is impossible to link a dll without this setting, and
+ # we shouldn't force the makefile maintainer to figure out
+ # which system we are compiling for in order to pass an extra
+ # flag for every libtool invocation.
+ # allow_undefined=no
+
+ # FIXME: Unfortunately, there are problems with the above when trying
+ # to make a dll which has undefined symbols, in which case not
+ # even a static library is built. For now, we need to specify
+ # -no-undefined on the libtool link line when we can be certain
+ # that all symbols are satisfied, otherwise we get a static library.
+ allow_undefined=yes
+ ;;
+ *)
+ allow_undefined=yes
+ ;;
+ esac
+ libtool_args=$nonopt
+ base_compile="$nonopt $@"
+ compile_command=$nonopt
+ finalize_command=$nonopt
+
+ compile_rpath=
+ finalize_rpath=
+ compile_shlibpath=
+ finalize_shlibpath=
+ convenience=
+ old_convenience=
+ deplibs=
+ old_deplibs=
+ compiler_flags=
+ linker_flags=
+ dllsearchpath=
+ lib_search_path=`pwd`
+ inst_prefix_dir=
+ new_inherited_linker_flags=
+
+ avoid_version=no
+ dlfiles=
+ dlprefiles=
+ dlself=no
+ export_dynamic=no
+ export_symbols=
+ export_symbols_regex=
+ generated=
+ libobjs=
+ ltlibs=
+ module=no
+ no_install=no
+ objs=
+ non_pic_objects=
+ precious_files_regex=
+ prefer_static_libs=no
+ preload=no
+ prev=
+ prevarg=
+ release=
+ rpath=
+ xrpath=
+ perm_rpath=
+ temp_rpath=
+ thread_safe=no
+ vinfo=
+ vinfo_number=no
+ weak_libs=
+ single_module="${wl}-single_module"
+ func_infer_tag $base_compile
+
+ # We need to know -static, to get the right output filenames.
+ for arg
+ do
+ case $arg in
+ -shared)
+ test "$build_libtool_libs" != yes && \
+ func_fatal_configuration "can not build a shared library"
+ build_old_libs=no
+ break
+ ;;
+ -all-static | -static | -static-libtool-libs)
+ case $arg in
+ -all-static)
+ if test "$build_libtool_libs" = yes && test -z "$link_static_flag"; then
+ func_warning "complete static linking is impossible in this configuration"
+ fi
+ if test -n "$link_static_flag"; then
+ dlopen_self=$dlopen_self_static
+ fi
+ prefer_static_libs=yes
+ ;;
+ -static)
+ if test -z "$pic_flag" && test -n "$link_static_flag"; then
+ dlopen_self=$dlopen_self_static
+ fi
+ prefer_static_libs=built
+ ;;
+ -static-libtool-libs)
+ if test -z "$pic_flag" && test -n "$link_static_flag"; then
+ dlopen_self=$dlopen_self_static
+ fi
+ prefer_static_libs=yes
+ ;;
+ esac
+ build_libtool_libs=no
+ build_old_libs=yes
+ break
+ ;;
+ esac
+ done
+
+ # See if our shared archives depend on static archives.
+ test -n "$old_archive_from_new_cmds" && build_old_libs=yes
+
+ # Go through the arguments, transforming them on the way.
+ while test "$#" -gt 0; do
+ arg="$1"
+ shift
+ func_quote_for_eval "$arg"
+ qarg=$func_quote_for_eval_unquoted_result
+ func_append libtool_args " $func_quote_for_eval_result"
+
+ # If the previous option needs an argument, assign it.
+ if test -n "$prev"; then
+ case $prev in
+ output)
+ func_append compile_command " @OUTPUT@"
+ func_append finalize_command " @OUTPUT@"
+ ;;
+ esac
+
+ case $prev in
+ dlfiles|dlprefiles)
+ if test "$preload" = no; then
+ # Add the symbol object into the linking commands.
+ func_append compile_command " @SYMFILE@"
+ func_append finalize_command " @SYMFILE@"
+ preload=yes
+ fi
+ case $arg in
+ *.la | *.lo) ;; # We handle these cases below.
+ force)
+ if test "$dlself" = no; then
+ dlself=needless
+ export_dynamic=yes
+ fi
+ prev=
+ continue
+ ;;
+ self)
+ if test "$prev" = dlprefiles; then
+ dlself=yes
+ elif test "$prev" = dlfiles && test "$dlopen_self" != yes; then
+ dlself=yes
+ else
+ dlself=needless
+ export_dynamic=yes
+ fi
+ prev=
+ continue
+ ;;
+ *)
+ if test "$prev" = dlfiles; then
+ dlfiles="$dlfiles $arg"
+ else
+ dlprefiles="$dlprefiles $arg"
+ fi
+ prev=
+ continue
+ ;;
+ esac
+ ;;
+ expsyms)
+ export_symbols="$arg"
+ test -f "$arg" \
+ || func_fatal_error "symbol file \`$arg' does not exist"
+ prev=
+ continue
+ ;;
+ expsyms_regex)
+ export_symbols_regex="$arg"
+ prev=
+ continue
+ ;;
+ framework)
+ case $host in
+ *-*-darwin*)
+ case "$deplibs " in
+ *" $qarg.ltframework "*) ;;
+ *) deplibs="$deplibs $qarg.ltframework" # this is fixed later
+ ;;
+ esac
+ ;;
+ esac
+ prev=
+ continue
+ ;;
+ inst_prefix)
+ inst_prefix_dir="$arg"
+ prev=
+ continue
+ ;;
+ objectlist)
+ if test -f "$arg"; then
+ save_arg=$arg
+ moreargs=
+ for fil in `cat "$save_arg"`
+ do
+# moreargs="$moreargs $fil"
+ arg=$fil
+ # A libtool-controlled object.
+
+ # Check to see that this really is a libtool object.
+ if func_lalib_unsafe_p "$arg"; then
+ pic_object=
+ non_pic_object=
+
+ # Read the .lo file
+ func_source "$arg"
+
+ if test -z "$pic_object" ||
+ test -z "$non_pic_object" ||
+ test "$pic_object" = none &&
+ test "$non_pic_object" = none; then
+ func_fatal_error "cannot find name of object for \`$arg'"
+ fi
+
+ # Extract subdirectory from the argument.
+ func_dirname "$arg" "/" ""
+ xdir="$func_dirname_result"
+
+ if test "$pic_object" != none; then
+ # Prepend the subdirectory the object is found in.
+ pic_object="$xdir$pic_object"
+
+ if test "$prev" = dlfiles; then
+ if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then
+ dlfiles="$dlfiles $pic_object"
+ prev=
+ continue
+ else
+ # If libtool objects are unsupported, then we need to preload.
+ prev=dlprefiles
+ fi
+ fi
+
+ # CHECK ME: I think I busted this. -Ossama
+ if test "$prev" = dlprefiles; then
+ # Preload the old-style object.
+ dlprefiles="$dlprefiles $pic_object"
+ prev=
+ fi
+
+ # A PIC object.
+ func_append libobjs " $pic_object"
+ arg="$pic_object"
+ fi
+
+ # Non-PIC object.
+ if test "$non_pic_object" != none; then
+ # Prepend the subdirectory the object is found in.
+ non_pic_object="$xdir$non_pic_object"
+
+ # A standard non-PIC object
+ func_append non_pic_objects " $non_pic_object"
+ if test -z "$pic_object" || test "$pic_object" = none ; then
+ arg="$non_pic_object"
+ fi
+ else
+ # If the PIC object exists, use it instead.
+ # $xdir was prepended to $pic_object above.
+ non_pic_object="$pic_object"
+ func_append non_pic_objects " $non_pic_object"
+ fi
+ else
+ # Only an error if not doing a dry-run.
+ if $opt_dry_run; then
+ # Extract subdirectory from the argument.
+ func_dirname "$arg" "/" ""
+ xdir="$func_dirname_result"
+
+ func_lo2o "$arg"
+ pic_object=$xdir$objdir/$func_lo2o_result
+ non_pic_object=$xdir$func_lo2o_result
+ func_append libobjs " $pic_object"
+ func_append non_pic_objects " $non_pic_object"
+ else
+ func_fatal_error "\`$arg' is not a valid libtool object"
+ fi
+ fi
+ done
+ else
+ func_fatal_error "link input file \`$arg' does not exist"
+ fi
+ arg=$save_arg
+ prev=
+ continue
+ ;;
+ precious_regex)
+ precious_files_regex="$arg"
+ prev=
+ continue
+ ;;
+ release)
+ release="-$arg"
+ prev=
+ continue
+ ;;
+ rpath | xrpath)
+ # We need an absolute path.
+ case $arg in
+ [\\/]* | [A-Za-z]:[\\/]*) ;;
+ *)
+ func_fatal_error "only absolute run-paths are allowed"
+ ;;
+ esac
+ if test "$prev" = rpath; then
+ case "$rpath " in
+ *" $arg "*) ;;
+ *) rpath="$rpath $arg" ;;
+ esac
+ else
+ case "$xrpath " in
+ *" $arg "*) ;;
+ *) xrpath="$xrpath $arg" ;;
+ esac
+ fi
+ prev=
+ continue
+ ;;
+ shrext)
+ shrext_cmds="$arg"
+ prev=
+ continue
+ ;;
+ weak)
+ weak_libs="$weak_libs $arg"
+ prev=
+ continue
+ ;;
+ xcclinker)
+ linker_flags="$linker_flags $qarg"
+ compiler_flags="$compiler_flags $qarg"
+ prev=
+ func_append compile_command " $qarg"
+ func_append finalize_command " $qarg"
+ continue
+ ;;
+ xcompiler)
+ compiler_flags="$compiler_flags $qarg"
+ prev=
+ func_append compile_command " $qarg"
+ func_append finalize_command " $qarg"
+ continue
+ ;;
+ xlinker)
+ linker_flags="$linker_flags $qarg"
+ compiler_flags="$compiler_flags $wl$qarg"
+ prev=
+ func_append compile_command " $wl$qarg"
+ func_append finalize_command " $wl$qarg"
+ continue
+ ;;
+ *)
+ eval "$prev=\"\$arg\""
+ prev=
+ continue
+ ;;
+ esac
+ fi # test -n "$prev"
+
+ prevarg="$arg"
+
+ case $arg in
+ -all-static)
+ if test -n "$link_static_flag"; then
+ # See comment for -static flag below, for more details.
+ func_append compile_command " $link_static_flag"
+ func_append finalize_command " $link_static_flag"
+ fi
+ continue
+ ;;
+
+ -allow-undefined)
+ # FIXME: remove this flag sometime in the future.
+ func_fatal_error "\`-allow-undefined' must not be used because it is the default"
+ ;;
+
+ -avoid-version)
+ avoid_version=yes
+ continue
+ ;;
+
+ -dlopen)
+ prev=dlfiles
+ continue
+ ;;
+
+ -dlpreopen)
+ prev=dlprefiles
+ continue
+ ;;
+
+ -export-dynamic)
+ export_dynamic=yes
+ continue
+ ;;
+
+ -export-symbols | -export-symbols-regex)
+ if test -n "$export_symbols" || test -n "$export_symbols_regex"; then
+ func_fatal_error "more than one -exported-symbols argument is not allowed"
+ fi
+ if test "X$arg" = "X-export-symbols"; then
+ prev=expsyms
+ else
+ prev=expsyms_regex
+ fi
+ continue
+ ;;
+
+ -framework)
+ prev=framework
+ continue
+ ;;
+
+ -inst-prefix-dir)
+ prev=inst_prefix
+ continue
+ ;;
+
+ # The native IRIX linker understands -LANG:*, -LIST:* and -LNO:*
+ # so, if we see these flags be careful not to treat them like -L
+ -L[A-Z][A-Z]*:*)
+ case $with_gcc/$host in
+ no/*-*-irix* | /*-*-irix*)
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ ;;
+ esac
+ continue
+ ;;
+
+ -L*)
+ func_stripname '-L' '' "$arg"
+ dir=$func_stripname_result
+ if test -z "$dir"; then
+ if test "$#" -gt 0; then
+ func_fatal_error "require no space between \`-L' and \`$1'"
+ else
+ func_fatal_error "need path for \`-L' option"
+ fi
+ fi
+ # We need an absolute path.
+ case $dir in
+ [\\/]* | [A-Za-z]:[\\/]*) ;;
+ *)
+ absdir=`cd "$dir" && pwd`
+ test -z "$absdir" && \
+ func_fatal_error "cannot determine absolute directory name of \`$dir'"
+ dir="$absdir"
+ ;;
+ esac
+ case "$deplibs " in
+ *" -L$dir "*) ;;
+ *)
+ deplibs="$deplibs -L$dir"
+ lib_search_path="$lib_search_path $dir"
+ ;;
+ esac
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*)
+ testbindir=`$ECHO "X$dir" | $Xsed -e 's*/lib$*/bin*'`
+ case :$dllsearchpath: in
+ *":$dir:"*) ;;
+ ::) dllsearchpath=$dir;;
+ *) dllsearchpath="$dllsearchpath:$dir";;
+ esac
+ case :$dllsearchpath: in
+ *":$testbindir:"*) ;;
+ ::) dllsearchpath=$testbindir;;
+ *) dllsearchpath="$dllsearchpath:$testbindir";;
+ esac
+ ;;
+ esac
+ continue
+ ;;
+
+ -l*)
+ if test "X$arg" = "X-lc" || test "X$arg" = "X-lm"; then
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-beos* | *-cegcc*)
+ # These systems don't actually have a C or math library (as such)
+ continue
+ ;;
+ *-*-os2*)
+ # These systems don't actually have a C library (as such)
+ test "X$arg" = "X-lc" && continue
+ ;;
+ *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*)
+ # Do not include libc due to us having libc/libc_r.
+ test "X$arg" = "X-lc" && continue
+ ;;
+ *-*-rhapsody* | *-*-darwin1.[012])
+ # Rhapsody C and math libraries are in the System framework
+ deplibs="$deplibs System.ltframework"
+ continue
+ ;;
+ *-*-sco3.2v5* | *-*-sco5v6*)
+ # Causes problems with __ctype
+ test "X$arg" = "X-lc" && continue
+ ;;
+ *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*)
+ # Compiler inserts libc in the correct place for threads to work
+ test "X$arg" = "X-lc" && continue
+ ;;
+ esac
+ elif test "X$arg" = "X-lc_r"; then
+ case $host in
+ *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*)
+ # Do not include libc_r directly, use -pthread flag.
+ continue
+ ;;
+ esac
+ fi
+ deplibs="$deplibs $arg"
+ continue
+ ;;
+
+ -module)
+ module=yes
+ continue
+ ;;
+
+ # Tru64 UNIX uses -model [arg] to determine the layout of C++
+ # classes, name mangling, and exception handling.
+ # Darwin uses the -arch flag to determine output architecture.
+ -model|-arch|-isysroot)
+ compiler_flags="$compiler_flags $arg"
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ prev=xcompiler
+ continue
+ ;;
+
+ -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads)
+ compiler_flags="$compiler_flags $arg"
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ case "$new_inherited_linker_flags " in
+ *" $arg "*) ;;
+ * ) new_inherited_linker_flags="$new_inherited_linker_flags $arg" ;;
+ esac
+ continue
+ ;;
+
+ -multi_module)
+ single_module="${wl}-multi_module"
+ continue
+ ;;
+
+ -no-fast-install)
+ fast_install=no
+ continue
+ ;;
+
+ -no-install)
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-darwin* | *-cegcc*)
+ # The PATH hackery in wrapper scripts is required on Windows
+ # and Darwin in order for the loader to find any dlls it needs.
+ func_warning "\`-no-install' is ignored for $host"
+ func_warning "assuming \`-no-fast-install' instead"
+ fast_install=no
+ ;;
+ *) no_install=yes ;;
+ esac
+ continue
+ ;;
+
+ -no-undefined)
+ allow_undefined=no
+ continue
+ ;;
+
+ -objectlist)
+ prev=objectlist
+ continue
+ ;;
+
+ -o) prev=output ;;
+
+ -precious-files-regex)
+ prev=precious_regex
+ continue
+ ;;
+
+ -release)
+ prev=release
+ continue
+ ;;
+
+ -rpath)
+ prev=rpath
+ continue
+ ;;
+
+ -R)
+ prev=xrpath
+ continue
+ ;;
+
+ -R*)
+ func_stripname '-R' '' "$arg"
+ dir=$func_stripname_result
+ # We need an absolute path.
+ case $dir in
+ [\\/]* | [A-Za-z]:[\\/]*) ;;
+ *)
+ func_fatal_error "only absolute run-paths are allowed"
+ ;;
+ esac
+ case "$xrpath " in
+ *" $dir "*) ;;
+ *) xrpath="$xrpath $dir" ;;
+ esac
+ continue
+ ;;
+
+ -shared)
+ # The effects of -shared are defined in a previous loop.
+ continue
+ ;;
+
+ -shrext)
+ prev=shrext
+ continue
+ ;;
+
+ -static | -static-libtool-libs)
+ # The effects of -static are defined in a previous loop.
+ # We used to do the same as -all-static on platforms that
+ # didn't have a PIC flag, but the assumption that the effects
+ # would be equivalent was wrong. It would break on at least
+ # Digital Unix and AIX.
+ continue
+ ;;
+
+ -thread-safe)
+ thread_safe=yes
+ continue
+ ;;
+
+ -version-info)
+ prev=vinfo
+ continue
+ ;;
+
+ -version-number)
+ prev=vinfo
+ vinfo_number=yes
+ continue
+ ;;
+
+ -weak)
+ prev=weak
+ continue
+ ;;
+
+ -Wc,*)
+ func_stripname '-Wc,' '' "$arg"
+ args=$func_stripname_result
+ arg=
+ save_ifs="$IFS"; IFS=','
+ for flag in $args; do
+ IFS="$save_ifs"
+ func_quote_for_eval "$flag"
+ arg="$arg $wl$func_quote_for_eval_result"
+ compiler_flags="$compiler_flags $func_quote_for_eval_result"
+ done
+ IFS="$save_ifs"
+ func_stripname ' ' '' "$arg"
+ arg=$func_stripname_result
+ ;;
+
+ -Wl,*)
+ func_stripname '-Wl,' '' "$arg"
+ args=$func_stripname_result
+ arg=
+ save_ifs="$IFS"; IFS=','
+ for flag in $args; do
+ IFS="$save_ifs"
+ func_quote_for_eval "$flag"
+ arg="$arg $wl$func_quote_for_eval_result"
+ compiler_flags="$compiler_flags $wl$func_quote_for_eval_result"
+ linker_flags="$linker_flags $func_quote_for_eval_result"
+ done
+ IFS="$save_ifs"
+ func_stripname ' ' '' "$arg"
+ arg=$func_stripname_result
+ ;;
+
+ -Xcompiler)
+ prev=xcompiler
+ continue
+ ;;
+
+ -Xlinker)
+ prev=xlinker
+ continue
+ ;;
+
+ -XCClinker)
+ prev=xcclinker
+ continue
+ ;;
+
+ # -msg_* for osf cc
+ -msg_*)
+ func_quote_for_eval "$arg"
+ arg="$func_quote_for_eval_result"
+ ;;
+
+ # -64, -mips[0-9] enable 64-bit mode on the SGI compiler
+ # -r[0-9][0-9]* specifies the processor on the SGI compiler
+ # -xarch=*, -xtarget=* enable 64-bit mode on the Sun compiler
+ # +DA*, +DD* enable 64-bit mode on the HP compiler
+ # -q* pass through compiler args for the IBM compiler
+ # -m*, -t[45]*, -txscale* pass through architecture-specific
+ # compiler args for GCC
+ # -F/path gives path to uninstalled frameworks, gcc on darwin
+ # -p, -pg, --coverage, -fprofile-* pass through profiling flag for GCC
+ # @file GCC response files
+ -64|-mips[0-9]|-r[0-9][0-9]*|-xarch=*|-xtarget=*|+DA*|+DD*|-q*|-m*| \
+ -t[45]*|-txscale*|-p|-pg|--coverage|-fprofile-*|-F*|@*)
+ func_quote_for_eval "$arg"
+ arg="$func_quote_for_eval_result"
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ compiler_flags="$compiler_flags $arg"
+ continue
+ ;;
+
+ # Some other compiler flag.
+ -* | +*)
+ func_quote_for_eval "$arg"
+ arg="$func_quote_for_eval_result"
+ ;;
+
+ *.$objext)
+ # A standard object.
+ objs="$objs $arg"
+ ;;
+
+ *.lo)
+ # A libtool-controlled object.
+
+ # Check to see that this really is a libtool object.
+ if func_lalib_unsafe_p "$arg"; then
+ pic_object=
+ non_pic_object=
+
+ # Read the .lo file
+ func_source "$arg"
+
+ if test -z "$pic_object" ||
+ test -z "$non_pic_object" ||
+ test "$pic_object" = none &&
+ test "$non_pic_object" = none; then
+ func_fatal_error "cannot find name of object for \`$arg'"
+ fi
+
+ # Extract subdirectory from the argument.
+ func_dirname "$arg" "/" ""
+ xdir="$func_dirname_result"
+
+ if test "$pic_object" != none; then
+ # Prepend the subdirectory the object is found in.
+ pic_object="$xdir$pic_object"
+
+ if test "$prev" = dlfiles; then
+ if test "$build_libtool_libs" = yes && test "$dlopen_support" = yes; then
+ dlfiles="$dlfiles $pic_object"
+ prev=
+ continue
+ else
+ # If libtool objects are unsupported, then we need to preload.
+ prev=dlprefiles
+ fi
+ fi
+
+ # CHECK ME: I think I busted this. -Ossama
+ if test "$prev" = dlprefiles; then
+ # Preload the old-style object.
+ dlprefiles="$dlprefiles $pic_object"
+ prev=
+ fi
+
+ # A PIC object.
+ func_append libobjs " $pic_object"
+ arg="$pic_object"
+ fi
+
+ # Non-PIC object.
+ if test "$non_pic_object" != none; then
+ # Prepend the subdirectory the object is found in.
+ non_pic_object="$xdir$non_pic_object"
+
+ # A standard non-PIC object
+ func_append non_pic_objects " $non_pic_object"
+ if test -z "$pic_object" || test "$pic_object" = none ; then
+ arg="$non_pic_object"
+ fi
+ else
+ # If the PIC object exists, use it instead.
+ # $xdir was prepended to $pic_object above.
+ non_pic_object="$pic_object"
+ func_append non_pic_objects " $non_pic_object"
+ fi
+ else
+ # Only an error if not doing a dry-run.
+ if $opt_dry_run; then
+ # Extract subdirectory from the argument.
+ func_dirname "$arg" "/" ""
+ xdir="$func_dirname_result"
+
+ func_lo2o "$arg"
+ pic_object=$xdir$objdir/$func_lo2o_result
+ non_pic_object=$xdir$func_lo2o_result
+ func_append libobjs " $pic_object"
+ func_append non_pic_objects " $non_pic_object"
+ else
+ func_fatal_error "\`$arg' is not a valid libtool object"
+ fi
+ fi
+ ;;
+
+ *.$libext)
+ # An archive.
+ deplibs="$deplibs $arg"
+ old_deplibs="$old_deplibs $arg"
+ continue
+ ;;
+
+ *.la)
+ # A libtool-controlled library.
+
+ if test "$prev" = dlfiles; then
+ # This library was specified with -dlopen.
+ dlfiles="$dlfiles $arg"
+ prev=
+ elif test "$prev" = dlprefiles; then
+ # The library was specified with -dlpreopen.
+ dlprefiles="$dlprefiles $arg"
+ prev=
+ else
+ deplibs="$deplibs $arg"
+ fi
+ continue
+ ;;
+
+ # Some other compiler argument.
+ *)
+ # Unknown arguments in both finalize_command and compile_command need
+ # to be aesthetically quoted because they are evaled later.
+ func_quote_for_eval "$arg"
+ arg="$func_quote_for_eval_result"
+ ;;
+ esac # arg
+
+ # Now actually substitute the argument into the commands.
+ if test -n "$arg"; then
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ fi
+ done # argument parsing loop
+
+ test -n "$prev" && \
+ func_fatal_help "the \`$prevarg' option requires an argument"
+
+ if test "$export_dynamic" = yes && test -n "$export_dynamic_flag_spec"; then
+ eval arg=\"$export_dynamic_flag_spec\"
+ func_append compile_command " $arg"
+ func_append finalize_command " $arg"
+ fi
+
+ oldlibs=
+ # calculate the name of the file, without its directory
+ func_basename "$output"
+ outputname="$func_basename_result"
+ libobjs_save="$libobjs"
+
+ if test -n "$shlibpath_var"; then
+ # get the directories listed in $shlibpath_var
+ eval shlib_search_path=\`\$ECHO \"X\${$shlibpath_var}\" \| \$Xsed -e \'s/:/ /g\'\`
+ else
+ shlib_search_path=
+ fi
+ eval sys_lib_search_path=\"$sys_lib_search_path_spec\"
+ eval sys_lib_dlsearch_path=\"$sys_lib_dlsearch_path_spec\"
+
+ func_dirname "$output" "/" ""
+ output_objdir="$func_dirname_result$objdir"
+ # Create the object directory.
+ func_mkdir_p "$output_objdir"
+
+ # Determine the type of output
+ case $output in
+ "")
+ func_fatal_help "you must specify an output file"
+ ;;
+ *.$libext) linkmode=oldlib ;;
+ *.lo | *.$objext) linkmode=obj ;;
+ *.la) linkmode=lib ;;
+ *) linkmode=prog ;; # Anything else should be a program.
+ esac
+
+ specialdeplibs=
+
+ libs=
+ # Find all interdependent deplibs by searching for libraries
+ # that are linked more than once (e.g. -la -lb -la)
+ for deplib in $deplibs; do
+ if $opt_duplicate_deps ; then
+ case "$libs " in
+ *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+ esac
+ fi
+ libs="$libs $deplib"
+ done
+
+ if test "$linkmode" = lib; then
+ libs="$predeps $libs $compiler_lib_search_path $postdeps"
+
+ # Compute libraries that are listed more than once in $predeps
+ # $postdeps and mark them as special (i.e., whose duplicates are
+ # not to be eliminated).
+ pre_post_deps=
+ if $opt_duplicate_compiler_generated_deps; then
+ for pre_post_dep in $predeps $postdeps; do
+ case "$pre_post_deps " in
+ *" $pre_post_dep "*) specialdeplibs="$specialdeplibs $pre_post_deps" ;;
+ esac
+ pre_post_deps="$pre_post_deps $pre_post_dep"
+ done
+ fi
+ pre_post_deps=
+ fi
+
+ deplibs=
+ newdependency_libs=
+ newlib_search_path=
+ need_relink=no # whether we're linking any uninstalled libtool libraries
+ notinst_deplibs= # not-installed libtool libraries
+ notinst_path= # paths that contain not-installed libtool libraries
+
+ case $linkmode in
+ lib)
+ passes="conv dlpreopen link"
+ for file in $dlfiles $dlprefiles; do
+ case $file in
+ *.la) ;;
+ *)
+ func_fatal_help "libraries can \`-dlopen' only libtool libraries: $file"
+ ;;
+ esac
+ done
+ ;;
+ prog)
+ compile_deplibs=
+ finalize_deplibs=
+ alldeplibs=no
+ newdlfiles=
+ newdlprefiles=
+ passes="conv scan dlopen dlpreopen link"
+ ;;
+ *) passes="conv"
+ ;;
+ esac
+
+ for pass in $passes; do
+ # The preopen pass in lib mode reverses $deplibs; put it back here
+ # so that -L comes before libs that need it for instance...
+ if test "$linkmode,$pass" = "lib,link"; then
+ ## FIXME: Find the place where the list is rebuilt in the wrong
+ ## order, and fix it there properly
+ tmp_deplibs=
+ for deplib in $deplibs; do
+ tmp_deplibs="$deplib $tmp_deplibs"
+ done
+ deplibs="$tmp_deplibs"
+ fi
+
+ if test "$linkmode,$pass" = "lib,link" ||
+ test "$linkmode,$pass" = "prog,scan"; then
+ libs="$deplibs"
+ deplibs=
+ fi
+ if test "$linkmode" = prog; then
+ case $pass in
+ dlopen) libs="$dlfiles" ;;
+ dlpreopen) libs="$dlprefiles" ;;
+ link)
+ libs="$deplibs %DEPLIBS%"
+ test "X$link_all_deplibs" != Xno && libs="$libs $dependency_libs"
+ ;;
+ esac
+ fi
+ if test "$linkmode,$pass" = "lib,dlpreopen"; then
+ # Collect and forward deplibs of preopened libtool libs
+ for lib in $dlprefiles; do
+ # Ignore non-libtool-libs
+ dependency_libs=
+ case $lib in
+ *.la) func_source "$lib" ;;
+ esac
+
+ # Collect preopened libtool deplibs, except any this library
+ # has declared as weak libs
+ for deplib in $dependency_libs; do
+ deplib_base=`$ECHO "X$deplib" | $Xsed -e "$basename"`
+ case " $weak_libs " in
+ *" $deplib_base "*) ;;
+ *) deplibs="$deplibs $deplib" ;;
+ esac
+ done
+ done
+ libs="$dlprefiles"
+ fi
+ if test "$pass" = dlopen; then
+ # Collect dlpreopened libraries
+ save_deplibs="$deplibs"
+ deplibs=
+ fi
+
+ for deplib in $libs; do
+ lib=
+ found=no
+ case $deplib in
+ -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads)
+ if test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ compiler_flags="$compiler_flags $deplib"
+ if test "$linkmode" = lib ; then
+ case "$new_inherited_linker_flags " in
+ *" $deplib "*) ;;
+ * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;;
+ esac
+ fi
+ fi
+ continue
+ ;;
+ -l*)
+ if test "$linkmode" != lib && test "$linkmode" != prog; then
+ func_warning "\`-l' is ignored for archives/objects"
+ continue
+ fi
+ func_stripname '-l' '' "$deplib"
+ name=$func_stripname_result
+ if test "$linkmode" = lib; then
+ searchdirs="$newlib_search_path $lib_search_path $compiler_lib_search_dirs $sys_lib_search_path $shlib_search_path"
+ else
+ searchdirs="$newlib_search_path $lib_search_path $sys_lib_search_path $shlib_search_path"
+ fi
+ for searchdir in $searchdirs; do
+ for search_ext in .la $std_shrext .so .a; do
+ # Search the libtool library
+ lib="$searchdir/lib${name}${search_ext}"
+ if test -f "$lib"; then
+ if test "$search_ext" = ".la"; then
+ found=yes
+ else
+ found=no
+ fi
+ break 2
+ fi
+ done
+ done
+ if test "$found" != yes; then
+ # deplib doesn't seem to be a libtool library
+ if test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ deplibs="$deplib $deplibs"
+ test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs"
+ fi
+ continue
+ else # deplib is a libtool library
+ # If $allow_libtool_libs_with_static_runtimes && $deplib is a stdlib,
+ # We need to do some special things here, and not later.
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $deplib "*)
+ if func_lalib_p "$lib"; then
+ library_names=
+ old_library=
+ func_source "$lib"
+ for l in $old_library $library_names; do
+ ll="$l"
+ done
+ if test "X$ll" = "X$old_library" ; then # only static version available
+ found=no
+ func_dirname "$lib" "" "."
+ ladir="$func_dirname_result"
+ lib=$ladir/$old_library
+ if test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ deplibs="$deplib $deplibs"
+ test "$linkmode" = lib && newdependency_libs="$deplib $newdependency_libs"
+ fi
+ continue
+ fi
+ fi
+ ;;
+ *) ;;
+ esac
+ fi
+ fi
+ ;; # -l
+ *.ltframework)
+ if test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ deplibs="$deplib $deplibs"
+ if test "$linkmode" = lib ; then
+ case "$new_inherited_linker_flags " in
+ *" $deplib "*) ;;
+ * ) new_inherited_linker_flags="$new_inherited_linker_flags $deplib" ;;
+ esac
+ fi
+ fi
+ continue
+ ;;
+ -L*)
+ case $linkmode in
+ lib)
+ deplibs="$deplib $deplibs"
+ test "$pass" = conv && continue
+ newdependency_libs="$deplib $newdependency_libs"
+ func_stripname '-L' '' "$deplib"
+ newlib_search_path="$newlib_search_path $func_stripname_result"
+ ;;
+ prog)
+ if test "$pass" = conv; then
+ deplibs="$deplib $deplibs"
+ continue
+ fi
+ if test "$pass" = scan; then
+ deplibs="$deplib $deplibs"
+ else
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ fi
+ func_stripname '-L' '' "$deplib"
+ newlib_search_path="$newlib_search_path $func_stripname_result"
+ ;;
+ *)
+ func_warning "\`-L' is ignored for archives/objects"
+ ;;
+ esac # linkmode
+ continue
+ ;; # -L
+ -R*)
+ if test "$pass" = link; then
+ func_stripname '-R' '' "$deplib"
+ dir=$func_stripname_result
+ # Make sure the xrpath contains only unique directories.
+ case "$xrpath " in
+ *" $dir "*) ;;
+ *) xrpath="$xrpath $dir" ;;
+ esac
+ fi
+ deplibs="$deplib $deplibs"
+ continue
+ ;;
+ *.la) lib="$deplib" ;;
+ *.$libext)
+ if test "$pass" = conv; then
+ deplibs="$deplib $deplibs"
+ continue
+ fi
+ case $linkmode in
+ lib)
+ # Linking convenience modules into shared libraries is allowed,
+ # but linking other static libraries is non-portable.
+ case " $dlpreconveniencelibs " in
+ *" $deplib "*) ;;
+ *)
+ valid_a_lib=no
+ case $deplibs_check_method in
+ match_pattern*)
+ set dummy $deplibs_check_method; shift
+ match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"`
+ if eval "\$ECHO \"X$deplib\"" 2>/dev/null | $Xsed -e 10q \
+ | $EGREP "$match_pattern_regex" > /dev/null; then
+ valid_a_lib=yes
+ fi
+ ;;
+ pass_all)
+ valid_a_lib=yes
+ ;;
+ esac
+ if test "$valid_a_lib" != yes; then
+ $ECHO
+ $ECHO "*** Warning: Trying to link with static lib archive $deplib."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have"
+ $ECHO "*** because the file extensions .$libext of this argument makes me believe"
+ $ECHO "*** that it is just a static archive that I should not use here."
+ else
+ $ECHO
+ $ECHO "*** Warning: Linking the shared library $output against the"
+ $ECHO "*** static library $deplib is not portable!"
+ deplibs="$deplib $deplibs"
+ fi
+ ;;
+ esac
+ continue
+ ;;
+ prog)
+ if test "$pass" != link; then
+ deplibs="$deplib $deplibs"
+ else
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ fi
+ continue
+ ;;
+ esac # linkmode
+ ;; # *.$libext
+ *.lo | *.$objext)
+ if test "$pass" = conv; then
+ deplibs="$deplib $deplibs"
+ elif test "$linkmode" = prog; then
+ if test "$pass" = dlpreopen || test "$dlopen_support" != yes || test "$build_libtool_libs" = no; then
+ # If there is no dlopen support or we're linking statically,
+ # we need to preload.
+ newdlprefiles="$newdlprefiles $deplib"
+ compile_deplibs="$deplib $compile_deplibs"
+ finalize_deplibs="$deplib $finalize_deplibs"
+ else
+ newdlfiles="$newdlfiles $deplib"
+ fi
+ fi
+ continue
+ ;;
+ %DEPLIBS%)
+ alldeplibs=yes
+ continue
+ ;;
+ esac # case $deplib
+
+ if test "$found" = yes || test -f "$lib"; then :
+ else
+ func_fatal_error "cannot find the library \`$lib' or unhandled argument \`$deplib'"
+ fi
+
+ # Check to see that this really is a libtool archive.
+ func_lalib_unsafe_p "$lib" \
+ || func_fatal_error "\`$lib' is not a valid libtool archive"
+
+ func_dirname "$lib" "" "."
+ ladir="$func_dirname_result"
+
+ dlname=
+ dlopen=
+ dlpreopen=
+ libdir=
+ library_names=
+ old_library=
+ inherited_linker_flags=
+ # If the library was installed with an old release of libtool,
+ # it will not redefine variables installed, or shouldnotlink
+ installed=yes
+ shouldnotlink=no
+ avoidtemprpath=
+
+
+ # Read the .la file
+ func_source "$lib"
+
+ # Convert "-framework foo" to "foo.ltframework"
+ if test -n "$inherited_linker_flags"; then
+ tmp_inherited_linker_flags=`$ECHO "X$inherited_linker_flags" | $Xsed -e 's/-framework \([^ $]*\)/\1.ltframework/g'`
+ for tmp_inherited_linker_flag in $tmp_inherited_linker_flags; do
+ case " $new_inherited_linker_flags " in
+ *" $tmp_inherited_linker_flag "*) ;;
+ *) new_inherited_linker_flags="$new_inherited_linker_flags $tmp_inherited_linker_flag";;
+ esac
+ done
+ fi
+ dependency_libs=`$ECHO "X $dependency_libs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ if test "$linkmode,$pass" = "lib,link" ||
+ test "$linkmode,$pass" = "prog,scan" ||
+ { test "$linkmode" != prog && test "$linkmode" != lib; }; then
+ test -n "$dlopen" && dlfiles="$dlfiles $dlopen"
+ test -n "$dlpreopen" && dlprefiles="$dlprefiles $dlpreopen"
+ fi
+
+ if test "$pass" = conv; then
+ # Only check for convenience libraries
+ deplibs="$lib $deplibs"
+ if test -z "$libdir"; then
+ if test -z "$old_library"; then
+ func_fatal_error "cannot find name of link library for \`$lib'"
+ fi
+ # It is a libtool convenience library, so add in its objects.
+ convenience="$convenience $ladir/$objdir/$old_library"
+ old_convenience="$old_convenience $ladir/$objdir/$old_library"
+ elif test "$linkmode" != prog && test "$linkmode" != lib; then
+ func_fatal_error "\`$lib' is not a convenience library"
+ fi
+ tmp_libs=
+ for deplib in $dependency_libs; do
+ deplibs="$deplib $deplibs"
+ if $opt_duplicate_deps ; then
+ case "$tmp_libs " in
+ *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+ esac
+ fi
+ tmp_libs="$tmp_libs $deplib"
+ done
+ continue
+ fi # $pass = conv
+
+
+ # Get the name of the library we link against.
+ linklib=
+ for l in $old_library $library_names; do
+ linklib="$l"
+ done
+ if test -z "$linklib"; then
+ func_fatal_error "cannot find name of link library for \`$lib'"
+ fi
+
+ # This library was specified with -dlopen.
+ if test "$pass" = dlopen; then
+ if test -z "$libdir"; then
+ func_fatal_error "cannot -dlopen a convenience library: \`$lib'"
+ fi
+ if test -z "$dlname" ||
+ test "$dlopen_support" != yes ||
+ test "$build_libtool_libs" = no; then
+ # If there is no dlname, no dlopen support or we're linking
+ # statically, we need to preload. We also need to preload any
+ # dependent libraries so libltdl's deplib preloader doesn't
+ # bomb out in the load deplibs phase.
+ dlprefiles="$dlprefiles $lib $dependency_libs"
+ else
+ newdlfiles="$newdlfiles $lib"
+ fi
+ continue
+ fi # $pass = dlopen
+
+ # We need an absolute path.
+ case $ladir in
+ [\\/]* | [A-Za-z]:[\\/]*) abs_ladir="$ladir" ;;
+ *)
+ abs_ladir=`cd "$ladir" && pwd`
+ if test -z "$abs_ladir"; then
+ func_warning "cannot determine absolute directory name of \`$ladir'"
+ func_warning "passing it literally to the linker, although it might fail"
+ abs_ladir="$ladir"
+ fi
+ ;;
+ esac
+ func_basename "$lib"
+ laname="$func_basename_result"
+
+ # Find the relevant object directory and library name.
+ if test "X$installed" = Xyes; then
+ if test ! -f "$libdir/$linklib" && test -f "$abs_ladir/$linklib"; then
+ func_warning "library \`$lib' was moved."
+ dir="$ladir"
+ absdir="$abs_ladir"
+ libdir="$abs_ladir"
+ else
+ dir="$libdir"
+ absdir="$libdir"
+ fi
+ test "X$hardcode_automatic" = Xyes && avoidtemprpath=yes
+ else
+ if test ! -f "$ladir/$objdir/$linklib" && test -f "$abs_ladir/$linklib"; then
+ dir="$ladir"
+ absdir="$abs_ladir"
+ # Remove this search path later
+ notinst_path="$notinst_path $abs_ladir"
+ else
+ dir="$ladir/$objdir"
+ absdir="$abs_ladir/$objdir"
+ # Remove this search path later
+ notinst_path="$notinst_path $abs_ladir"
+ fi
+ fi # $installed = yes
+ func_stripname 'lib' '.la' "$laname"
+ name=$func_stripname_result
+
+ # This library was specified with -dlpreopen.
+ if test "$pass" = dlpreopen; then
+ if test -z "$libdir" && test "$linkmode" = prog; then
+ func_fatal_error "only libraries may -dlpreopen a convenience library: \`$lib'"
+ fi
+ # Prefer using a static library (so that no silly _DYNAMIC symbols
+ # are required to link).
+ if test -n "$old_library"; then
+ newdlprefiles="$newdlprefiles $dir/$old_library"
+ # Keep a list of preopened convenience libraries to check
+ # that they are being used correctly in the link pass.
+ test -z "$libdir" && \
+ dlpreconveniencelibs="$dlpreconveniencelibs $dir/$old_library"
+ # Otherwise, use the dlname, so that lt_dlopen finds it.
+ elif test -n "$dlname"; then
+ newdlprefiles="$newdlprefiles $dir/$dlname"
+ else
+ newdlprefiles="$newdlprefiles $dir/$linklib"
+ fi
+ fi # $pass = dlpreopen
+
+ if test -z "$libdir"; then
+ # Link the convenience library
+ if test "$linkmode" = lib; then
+ deplibs="$dir/$old_library $deplibs"
+ elif test "$linkmode,$pass" = "prog,link"; then
+ compile_deplibs="$dir/$old_library $compile_deplibs"
+ finalize_deplibs="$dir/$old_library $finalize_deplibs"
+ else
+ deplibs="$lib $deplibs" # used for prog,scan pass
+ fi
+ continue
+ fi
+
+
+ if test "$linkmode" = prog && test "$pass" != link; then
+ newlib_search_path="$newlib_search_path $ladir"
+ deplibs="$lib $deplibs"
+
+ linkalldeplibs=no
+ if test "$link_all_deplibs" != no || test -z "$library_names" ||
+ test "$build_libtool_libs" = no; then
+ linkalldeplibs=yes
+ fi
+
+ tmp_libs=
+ for deplib in $dependency_libs; do
+ case $deplib in
+ -L*) func_stripname '-L' '' "$deplib"
+ newlib_search_path="$newlib_search_path $func_stripname_result"
+ ;;
+ esac
+ # Need to link against all dependency_libs?
+ if test "$linkalldeplibs" = yes; then
+ deplibs="$deplib $deplibs"
+ else
+ # Need to hardcode shared library paths
+ # or/and link against static libraries
+ newdependency_libs="$deplib $newdependency_libs"
+ fi
+ if $opt_duplicate_deps ; then
+ case "$tmp_libs " in
+ *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+ esac
+ fi
+ tmp_libs="$tmp_libs $deplib"
+ done # for deplib
+ continue
+ fi # $linkmode = prog...
+
+ if test "$linkmode,$pass" = "prog,link"; then
+ if test -n "$library_names" &&
+ { { test "$prefer_static_libs" = no ||
+ test "$prefer_static_libs,$installed" = "built,yes"; } ||
+ test -z "$old_library"; }; then
+ # We need to hardcode the library path
+ if test -n "$shlibpath_var" && test -z "$avoidtemprpath" ; then
+ # Make sure the rpath contains only unique directories.
+ case "$temp_rpath:" in
+ *"$absdir:"*) ;;
+ *) temp_rpath="$temp_rpath$absdir:" ;;
+ esac
+ fi
+
+ # Hardcode the library path.
+ # Skip directories that are in the system default run-time
+ # search path.
+ case " $sys_lib_dlsearch_path " in
+ *" $absdir "*) ;;
+ *)
+ case "$compile_rpath " in
+ *" $absdir "*) ;;
+ *) compile_rpath="$compile_rpath $absdir"
+ esac
+ ;;
+ esac
+ case " $sys_lib_dlsearch_path " in
+ *" $libdir "*) ;;
+ *)
+ case "$finalize_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_rpath="$finalize_rpath $libdir"
+ esac
+ ;;
+ esac
+ fi # $linkmode,$pass = prog,link...
+
+ if test "$alldeplibs" = yes &&
+ { test "$deplibs_check_method" = pass_all ||
+ { test "$build_libtool_libs" = yes &&
+ test -n "$library_names"; }; }; then
+ # We only need to search for static libraries
+ continue
+ fi
+ fi
+
+ link_static=no # Whether the deplib will be linked statically
+ use_static_libs=$prefer_static_libs
+ if test "$use_static_libs" = built && test "$installed" = yes; then
+ use_static_libs=no
+ fi
+ if test -n "$library_names" &&
+ { test "$use_static_libs" = no || test -z "$old_library"; }; then
+ case $host in
+ *cygwin* | *mingw* | *cegcc*)
+ # No point in relinking DLLs because paths are not encoded
+ notinst_deplibs="$notinst_deplibs $lib"
+ need_relink=no
+ ;;
+ *)
+ if test "$installed" = no; then
+ notinst_deplibs="$notinst_deplibs $lib"
+ need_relink=yes
+ fi
+ ;;
+ esac
+ # This is a shared library
+
+ # Warn about portability, can't link against -module's on some
+ # systems (darwin). Don't bleat about dlopened modules though!
+ dlopenmodule=""
+ for dlpremoduletest in $dlprefiles; do
+ if test "X$dlpremoduletest" = "X$lib"; then
+ dlopenmodule="$dlpremoduletest"
+ break
+ fi
+ done
+ if test -z "$dlopenmodule" && test "$shouldnotlink" = yes && test "$pass" = link; then
+ $ECHO
+ if test "$linkmode" = prog; then
+ $ECHO "*** Warning: Linking the executable $output against the loadable module"
+ else
+ $ECHO "*** Warning: Linking the shared library $output against the loadable module"
+ fi
+ $ECHO "*** $linklib is not portable!"
+ fi
+ if test "$linkmode" = lib &&
+ test "$hardcode_into_libs" = yes; then
+ # Hardcode the library path.
+ # Skip directories that are in the system default run-time
+ # search path.
+ case " $sys_lib_dlsearch_path " in
+ *" $absdir "*) ;;
+ *)
+ case "$compile_rpath " in
+ *" $absdir "*) ;;
+ *) compile_rpath="$compile_rpath $absdir"
+ esac
+ ;;
+ esac
+ case " $sys_lib_dlsearch_path " in
+ *" $libdir "*) ;;
+ *)
+ case "$finalize_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_rpath="$finalize_rpath $libdir"
+ esac
+ ;;
+ esac
+ fi
+
+ if test -n "$old_archive_from_expsyms_cmds"; then
+ # figure out the soname
+ set dummy $library_names
+ shift
+ realname="$1"
+ shift
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ # use dlname if we got it. it's perfectly good, no?
+ if test -n "$dlname"; then
+ soname="$dlname"
+ elif test -n "$soname_spec"; then
+ # bleh windows
+ case $host in
+ *cygwin* | mingw* | *cegcc*)
+ func_arith $current - $age
+ major=$func_arith_result
+ versuffix="-$major"
+ ;;
+ esac
+ eval soname=\"$soname_spec\"
+ else
+ soname="$realname"
+ fi
+
+ # Make a new name for the extract_expsyms_cmds to use
+ soroot="$soname"
+ func_basename "$soroot"
+ soname="$func_basename_result"
+ func_stripname 'lib' '.dll' "$soname"
+ newlib=libimp-$func_stripname_result.a
+
+ # If the library has no export list, then create one now
+ if test -f "$output_objdir/$soname-def"; then :
+ else
+ func_verbose "extracting exported symbol list from \`$soname'"
+ func_execute_cmds "$extract_expsyms_cmds" 'exit $?'
+ fi
+
+ # Create $newlib
+ if test -f "$output_objdir/$newlib"; then :; else
+ func_verbose "generating import library for \`$soname'"
+ func_execute_cmds "$old_archive_from_expsyms_cmds" 'exit $?'
+ fi
+ # make sure the library variables are pointing to the new library
+ dir=$output_objdir
+ linklib=$newlib
+ fi # test -n "$old_archive_from_expsyms_cmds"
+
+ if test "$linkmode" = prog || test "$mode" != relink; then
+ add_shlibpath=
+ add_dir=
+ add=
+ lib_linked=yes
+ case $hardcode_action in
+ immediate | unsupported)
+ if test "$hardcode_direct" = no; then
+ add="$dir/$linklib"
+ case $host in
+ *-*-sco3.2v5.0.[024]*) add_dir="-L$dir" ;;
+ *-*-sysv4*uw2*) add_dir="-L$dir" ;;
+ *-*-sysv5OpenUNIX* | *-*-sysv5UnixWare7.[01].[10]* | \
+ *-*-unixware7*) add_dir="-L$dir" ;;
+ *-*-darwin* )
+ # if the lib is a (non-dlopened) module then we can not
+ # link against it, someone is ignoring the earlier warnings
+ if /usr/bin/file -L $add 2> /dev/null |
+ $GREP ": [^:]* bundle" >/dev/null ; then
+ if test "X$dlopenmodule" != "X$lib"; then
+ $ECHO "*** Warning: lib $linklib is a module, not a shared library"
+ if test -z "$old_library" ; then
+ $ECHO
+ $ECHO "*** And there doesn't seem to be a static archive available"
+ $ECHO "*** The link will probably fail, sorry"
+ else
+ add="$dir/$old_library"
+ fi
+ elif test -n "$old_library"; then
+ add="$dir/$old_library"
+ fi
+ fi
+ esac
+ elif test "$hardcode_minus_L" = no; then
+ case $host in
+ *-*-sunos*) add_shlibpath="$dir" ;;
+ esac
+ add_dir="-L$dir"
+ add="-l$name"
+ elif test "$hardcode_shlibpath_var" = no; then
+ add_shlibpath="$dir"
+ add="-l$name"
+ else
+ lib_linked=no
+ fi
+ ;;
+ relink)
+ if test "$hardcode_direct" = yes &&
+ test "$hardcode_direct_absolute" = no; then
+ add="$dir/$linklib"
+ elif test "$hardcode_minus_L" = yes; then
+ add_dir="-L$dir"
+ # Try looking first in the location we're being installed to.
+ if test -n "$inst_prefix_dir"; then
+ case $libdir in
+ [\\/]*)
+ add_dir="$add_dir -L$inst_prefix_dir$libdir"
+ ;;
+ esac
+ fi
+ add="-l$name"
+ elif test "$hardcode_shlibpath_var" = yes; then
+ add_shlibpath="$dir"
+ add="-l$name"
+ else
+ lib_linked=no
+ fi
+ ;;
+ *) lib_linked=no ;;
+ esac
+
+ if test "$lib_linked" != yes; then
+ func_fatal_configuration "unsupported hardcode properties"
+ fi
+
+ if test -n "$add_shlibpath"; then
+ case :$compile_shlibpath: in
+ *":$add_shlibpath:"*) ;;
+ *) compile_shlibpath="$compile_shlibpath$add_shlibpath:" ;;
+ esac
+ fi
+ if test "$linkmode" = prog; then
+ test -n "$add_dir" && compile_deplibs="$add_dir $compile_deplibs"
+ test -n "$add" && compile_deplibs="$add $compile_deplibs"
+ else
+ test -n "$add_dir" && deplibs="$add_dir $deplibs"
+ test -n "$add" && deplibs="$add $deplibs"
+ if test "$hardcode_direct" != yes &&
+ test "$hardcode_minus_L" != yes &&
+ test "$hardcode_shlibpath_var" = yes; then
+ case :$finalize_shlibpath: in
+ *":$libdir:"*) ;;
+ *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;;
+ esac
+ fi
+ fi
+ fi
+
+ if test "$linkmode" = prog || test "$mode" = relink; then
+ add_shlibpath=
+ add_dir=
+ add=
+ # Finalize command for both is simple: just hardcode it.
+ if test "$hardcode_direct" = yes &&
+ test "$hardcode_direct_absolute" = no; then
+ add="$libdir/$linklib"
+ elif test "$hardcode_minus_L" = yes; then
+ add_dir="-L$libdir"
+ add="-l$name"
+ elif test "$hardcode_shlibpath_var" = yes; then
+ case :$finalize_shlibpath: in
+ *":$libdir:"*) ;;
+ *) finalize_shlibpath="$finalize_shlibpath$libdir:" ;;
+ esac
+ add="-l$name"
+ elif test "$hardcode_automatic" = yes; then
+ if test -n "$inst_prefix_dir" &&
+ test -f "$inst_prefix_dir$libdir/$linklib" ; then
+ add="$inst_prefix_dir$libdir/$linklib"
+ else
+ add="$libdir/$linklib"
+ fi
+ else
+ # We cannot seem to hardcode it, guess we'll fake it.
+ add_dir="-L$libdir"
+ # Try looking first in the location we're being installed to.
+ if test -n "$inst_prefix_dir"; then
+ case $libdir in
+ [\\/]*)
+ add_dir="$add_dir -L$inst_prefix_dir$libdir"
+ ;;
+ esac
+ fi
+ add="-l$name"
+ fi
+
+ if test "$linkmode" = prog; then
+ test -n "$add_dir" && finalize_deplibs="$add_dir $finalize_deplibs"
+ test -n "$add" && finalize_deplibs="$add $finalize_deplibs"
+ else
+ test -n "$add_dir" && deplibs="$add_dir $deplibs"
+ test -n "$add" && deplibs="$add $deplibs"
+ fi
+ fi
+ elif test "$linkmode" = prog; then
+ # Here we assume that one of hardcode_direct or hardcode_minus_L
+ # is not unsupported. This is valid on all known static and
+ # shared platforms.
+ if test "$hardcode_direct" != unsupported; then
+ test -n "$old_library" && linklib="$old_library"
+ compile_deplibs="$dir/$linklib $compile_deplibs"
+ finalize_deplibs="$dir/$linklib $finalize_deplibs"
+ else
+ compile_deplibs="-l$name -L$dir $compile_deplibs"
+ finalize_deplibs="-l$name -L$dir $finalize_deplibs"
+ fi
+ elif test "$build_libtool_libs" = yes; then
+ # Not a shared library
+ if test "$deplibs_check_method" != pass_all; then
+ # We're trying link a shared library against a static one
+ # but the system doesn't support it.
+
+ # Just print a warning and add the library to dependency_libs so
+ # that the program can be linked against the static library.
+ $ECHO
+ $ECHO "*** Warning: This system can not link to static lib archive $lib."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have."
+ if test "$module" = yes; then
+ $ECHO "*** But as you try to build a module library, libtool will still create "
+ $ECHO "*** a static module, that should work as long as the dlopening application"
+ $ECHO "*** is linked with the -dlopen flag to resolve symbols at runtime."
+ if test -z "$global_symbol_pipe"; then
+ $ECHO
+ $ECHO "*** However, this would only work if libtool was able to extract symbol"
+ $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could"
+ $ECHO "*** not find such a program. So, this module is probably useless."
+ $ECHO "*** \`nm' from GNU binutils and a full rebuild may help."
+ fi
+ if test "$build_old_libs" = no; then
+ build_libtool_libs=module
+ build_old_libs=yes
+ else
+ build_libtool_libs=no
+ fi
+ fi
+ else
+ deplibs="$dir/$old_library $deplibs"
+ link_static=yes
+ fi
+ fi # link shared/static library?
+
+ if test "$linkmode" = lib; then
+ if test -n "$dependency_libs" &&
+ { test "$hardcode_into_libs" != yes ||
+ test "$build_old_libs" = yes ||
+ test "$link_static" = yes; }; then
+ # Extract -R from dependency_libs
+ temp_deplibs=
+ for libdir in $dependency_libs; do
+ case $libdir in
+ -R*) func_stripname '-R' '' "$libdir"
+ temp_xrpath=$func_stripname_result
+ case " $xrpath " in
+ *" $temp_xrpath "*) ;;
+ *) xrpath="$xrpath $temp_xrpath";;
+ esac;;
+ *) temp_deplibs="$temp_deplibs $libdir";;
+ esac
+ done
+ dependency_libs="$temp_deplibs"
+ fi
+
+ newlib_search_path="$newlib_search_path $absdir"
+ # Link against this library
+ test "$link_static" = no && newdependency_libs="$abs_ladir/$laname $newdependency_libs"
+ # ... and its dependency_libs
+ tmp_libs=
+ for deplib in $dependency_libs; do
+ newdependency_libs="$deplib $newdependency_libs"
+ if $opt_duplicate_deps ; then
+ case "$tmp_libs " in
+ *" $deplib "*) specialdeplibs="$specialdeplibs $deplib" ;;
+ esac
+ fi
+ tmp_libs="$tmp_libs $deplib"
+ done
+
+ if test "$link_all_deplibs" != no; then
+ # Add the search paths of all dependency libraries
+ for deplib in $dependency_libs; do
+ case $deplib in
+ -L*) path="$deplib" ;;
+ *.la)
+ func_dirname "$deplib" "" "."
+ dir="$func_dirname_result"
+ # We need an absolute path.
+ case $dir in
+ [\\/]* | [A-Za-z]:[\\/]*) absdir="$dir" ;;
+ *)
+ absdir=`cd "$dir" && pwd`
+ if test -z "$absdir"; then
+ func_warning "cannot determine absolute directory name of \`$dir'"
+ absdir="$dir"
+ fi
+ ;;
+ esac
+ if $GREP "^installed=no" $deplib > /dev/null; then
+ case $host in
+ *-*-darwin*)
+ depdepl=
+ eval deplibrary_names=`${SED} -n -e 's/^library_names=\(.*\)$/\1/p' $deplib`
+ if test -n "$deplibrary_names" ; then
+ for tmp in $deplibrary_names ; do
+ depdepl=$tmp
+ done
+ if test -f "$absdir/$objdir/$depdepl" ; then
+ depdepl="$absdir/$objdir/$depdepl"
+ darwin_install_name=`${OTOOL} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'`
+ if test -z "$darwin_install_name"; then
+ darwin_install_name=`${OTOOL64} -L $depdepl | awk '{if (NR == 2) {print $1;exit}}'`
+ fi
+ compiler_flags="$compiler_flags ${wl}-dylib_file ${wl}${darwin_install_name}:${depdepl}"
+ linker_flags="$linker_flags -dylib_file ${darwin_install_name}:${depdepl}"
+ path=
+ fi
+ fi
+ ;;
+ *)
+ path="-L$absdir/$objdir"
+ ;;
+ esac
+ else
+ eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib`
+ test -z "$libdir" && \
+ func_fatal_error "\`$deplib' is not a valid libtool archive"
+ test "$absdir" != "$libdir" && \
+ func_warning "\`$deplib' seems to be moved"
+
+ path="-L$absdir"
+ fi
+ ;;
+ esac
+ case " $deplibs " in
+ *" $path "*) ;;
+ *) deplibs="$path $deplibs" ;;
+ esac
+ done
+ fi # link_all_deplibs != no
+ fi # linkmode = lib
+ done # for deplib in $libs
+ if test "$pass" = link; then
+ if test "$linkmode" = "prog"; then
+ compile_deplibs="$new_inherited_linker_flags $compile_deplibs"
+ finalize_deplibs="$new_inherited_linker_flags $finalize_deplibs"
+ else
+ compiler_flags="$compiler_flags "`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ fi
+ fi
+ dependency_libs="$newdependency_libs"
+ if test "$pass" = dlpreopen; then
+ # Link the dlpreopened libraries before other libraries
+ for deplib in $save_deplibs; do
+ deplibs="$deplib $deplibs"
+ done
+ fi
+ if test "$pass" != dlopen; then
+ if test "$pass" != conv; then
+ # Make sure lib_search_path contains only unique directories.
+ lib_search_path=
+ for dir in $newlib_search_path; do
+ case "$lib_search_path " in
+ *" $dir "*) ;;
+ *) lib_search_path="$lib_search_path $dir" ;;
+ esac
+ done
+ newlib_search_path=
+ fi
+
+ if test "$linkmode,$pass" != "prog,link"; then
+ vars="deplibs"
+ else
+ vars="compile_deplibs finalize_deplibs"
+ fi
+ for var in $vars dependency_libs; do
+ # Add libraries to $var in reverse order
+ eval tmp_libs=\"\$$var\"
+ new_libs=
+ for deplib in $tmp_libs; do
+ # FIXME: Pedantically, this is the right thing to do, so
+ # that some nasty dependency loop isn't accidentally
+ # broken:
+ #new_libs="$deplib $new_libs"
+ # Pragmatically, this seems to cause very few problems in
+ # practice:
+ case $deplib in
+ -L*) new_libs="$deplib $new_libs" ;;
+ -R*) ;;
+ *)
+ # And here is the reason: when a library appears more
+ # than once as an explicit dependence of a library, or
+ # is implicitly linked in more than once by the
+ # compiler, it is considered special, and multiple
+ # occurrences thereof are not removed. Compare this
+ # with having the same library being listed as a
+ # dependency of multiple other libraries: in this case,
+ # we know (pedantically, we assume) the library does not
+ # need to be listed more than once, so we keep only the
+ # last copy. This is not always right, but it is rare
+ # enough that we require users that really mean to play
+ # such unportable linking tricks to link the library
+ # using -Wl,-lname, so that libtool does not consider it
+ # for duplicate removal.
+ case " $specialdeplibs " in
+ *" $deplib "*) new_libs="$deplib $new_libs" ;;
+ *)
+ case " $new_libs " in
+ *" $deplib "*) ;;
+ *) new_libs="$deplib $new_libs" ;;
+ esac
+ ;;
+ esac
+ ;;
+ esac
+ done
+ tmp_libs=
+ for deplib in $new_libs; do
+ case $deplib in
+ -L*)
+ case " $tmp_libs " in
+ *" $deplib "*) ;;
+ *) tmp_libs="$tmp_libs $deplib" ;;
+ esac
+ ;;
+ *) tmp_libs="$tmp_libs $deplib" ;;
+ esac
+ done
+ eval $var=\"$tmp_libs\"
+ done # for var
+ fi
+ # Last step: remove runtime libs from dependency_libs
+ # (they stay in deplibs)
+ tmp_libs=
+ for i in $dependency_libs ; do
+ case " $predeps $postdeps $compiler_lib_search_path " in
+ *" $i "*)
+ i=""
+ ;;
+ esac
+ if test -n "$i" ; then
+ tmp_libs="$tmp_libs $i"
+ fi
+ done
+ dependency_libs=$tmp_libs
+ done # for pass
+ if test "$linkmode" = prog; then
+ dlfiles="$newdlfiles"
+ fi
+ if test "$linkmode" = prog || test "$linkmode" = lib; then
+ dlprefiles="$newdlprefiles"
+ fi
+
+ case $linkmode in
+ oldlib)
+ if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
+ func_warning "\`-dlopen' is ignored for archives"
+ fi
+
+ case " $deplibs" in
+ *\ -l* | *\ -L*)
+ func_warning "\`-l' and \`-L' are ignored for archives" ;;
+ esac
+
+ test -n "$rpath" && \
+ func_warning "\`-rpath' is ignored for archives"
+
+ test -n "$xrpath" && \
+ func_warning "\`-R' is ignored for archives"
+
+ test -n "$vinfo" && \
+ func_warning "\`-version-info/-version-number' is ignored for archives"
+
+ test -n "$release" && \
+ func_warning "\`-release' is ignored for archives"
+
+ test -n "$export_symbols$export_symbols_regex" && \
+ func_warning "\`-export-symbols' is ignored for archives"
+
+ # Now set the variables for building old libraries.
+ build_libtool_libs=no
+ oldlibs="$output"
+ objs="$objs$old_deplibs"
+ ;;
+
+ lib)
+ # Make sure we only generate libraries of the form `libNAME.la'.
+ case $outputname in
+ lib*)
+ func_stripname 'lib' '.la' "$outputname"
+ name=$func_stripname_result
+ eval shared_ext=\"$shrext_cmds\"
+ eval libname=\"$libname_spec\"
+ ;;
+ *)
+ test "$module" = no && \
+ func_fatal_help "libtool library \`$output' must begin with \`lib'"
+
+ if test "$need_lib_prefix" != no; then
+ # Add the "lib" prefix for modules if required
+ func_stripname '' '.la' "$outputname"
+ name=$func_stripname_result
+ eval shared_ext=\"$shrext_cmds\"
+ eval libname=\"$libname_spec\"
+ else
+ func_stripname '' '.la' "$outputname"
+ libname=$func_stripname_result
+ fi
+ ;;
+ esac
+
+ if test -n "$objs"; then
+ if test "$deplibs_check_method" != pass_all; then
+ func_fatal_error "cannot build libtool library \`$output' from non-libtool objects on this host:$objs"
+ else
+ $ECHO
+ $ECHO "*** Warning: Linking the shared library $output against the non-libtool"
+ $ECHO "*** objects $objs is not portable!"
+ libobjs="$libobjs $objs"
+ fi
+ fi
+
+ test "$dlself" != no && \
+ func_warning "\`-dlopen self' is ignored for libtool libraries"
+
+ set dummy $rpath
+ shift
+ test "$#" -gt 1 && \
+ func_warning "ignoring multiple \`-rpath's for a libtool library"
+
+ install_libdir="$1"
+
+ oldlibs=
+ if test -z "$rpath"; then
+ if test "$build_libtool_libs" = yes; then
+ # Building a libtool convenience library.
+ # Some compilers have problems with a `.al' extension so
+ # convenience libraries should have the same extension an
+ # archive normally would.
+ oldlibs="$output_objdir/$libname.$libext $oldlibs"
+ build_libtool_libs=convenience
+ build_old_libs=yes
+ fi
+
+ test -n "$vinfo" && \
+ func_warning "\`-version-info/-version-number' is ignored for convenience libraries"
+
+ test -n "$release" && \
+ func_warning "\`-release' is ignored for convenience libraries"
+ else
+
+ # Parse the version information argument.
+ save_ifs="$IFS"; IFS=':'
+ set dummy $vinfo 0 0 0
+ shift
+ IFS="$save_ifs"
+
+ test -n "$7" && \
+ func_fatal_help "too many parameters to \`-version-info'"
+
+ # convert absolute version numbers to libtool ages
+ # this retains compatibility with .la files and attempts
+ # to make the code below a bit more comprehensible
+
+ case $vinfo_number in
+ yes)
+ number_major="$1"
+ number_minor="$2"
+ number_revision="$3"
+ #
+ # There are really only two kinds -- those that
+ # use the current revision as the major version
+ # and those that subtract age and use age as
+ # a minor version. But, then there is irix
+ # which has an extra 1 added just for fun
+ #
+ case $version_type in
+ darwin|linux|osf|windows|none)
+ func_arith $number_major + $number_minor
+ current=$func_arith_result
+ age="$number_minor"
+ revision="$number_revision"
+ ;;
+ freebsd-aout|freebsd-elf|sunos)
+ current="$number_major"
+ revision="$number_minor"
+ age="0"
+ ;;
+ irix|nonstopux)
+ func_arith $number_major + $number_minor
+ current=$func_arith_result
+ age="$number_minor"
+ revision="$number_minor"
+ lt_irix_increment=no
+ ;;
+ *)
+ func_fatal_configuration "$modename: unknown library version type \`$version_type'"
+ ;;
+ esac
+ ;;
+ no)
+ current="$1"
+ revision="$2"
+ age="$3"
+ ;;
+ esac
+
+ # Check that each of the things are valid numbers.
+ case $current in
+ 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;;
+ *)
+ func_error "CURRENT \`$current' must be a nonnegative integer"
+ func_fatal_error "\`$vinfo' is not valid version information"
+ ;;
+ esac
+
+ case $revision in
+ 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;;
+ *)
+ func_error "REVISION \`$revision' must be a nonnegative integer"
+ func_fatal_error "\`$vinfo' is not valid version information"
+ ;;
+ esac
+
+ case $age in
+ 0|[1-9]|[1-9][0-9]|[1-9][0-9][0-9]|[1-9][0-9][0-9][0-9]|[1-9][0-9][0-9][0-9][0-9]) ;;
+ *)
+ func_error "AGE \`$age' must be a nonnegative integer"
+ func_fatal_error "\`$vinfo' is not valid version information"
+ ;;
+ esac
+
+ if test "$age" -gt "$current"; then
+ func_error "AGE \`$age' is greater than the current interface number \`$current'"
+ func_fatal_error "\`$vinfo' is not valid version information"
+ fi
+
+ # Calculate the version variables.
+ major=
+ versuffix=
+ verstring=
+ case $version_type in
+ none) ;;
+
+ darwin)
+ # Like Linux, but with the current version available in
+ # verstring for coding it into the library header
+ func_arith $current - $age
+ major=.$func_arith_result
+ versuffix="$major.$age.$revision"
+ # Darwin ld doesn't like 0 for these options...
+ func_arith $current + 1
+ minor_current=$func_arith_result
+ xlcverstring="${wl}-compatibility_version ${wl}$minor_current ${wl}-current_version ${wl}$minor_current.$revision"
+ verstring="-compatibility_version $minor_current -current_version $minor_current.$revision"
+ ;;
+
+ freebsd-aout)
+ major=".$current"
+ versuffix=".$current.$revision";
+ ;;
+
+ freebsd-elf)
+ major=".$current"
+ versuffix=".$current"
+ ;;
+
+ irix | nonstopux)
+ if test "X$lt_irix_increment" = "Xno"; then
+ func_arith $current - $age
+ else
+ func_arith $current - $age + 1
+ fi
+ major=$func_arith_result
+
+ case $version_type in
+ nonstopux) verstring_prefix=nonstopux ;;
+ *) verstring_prefix=sgi ;;
+ esac
+ verstring="$verstring_prefix$major.$revision"
+
+ # Add in all the interfaces that we are compatible with.
+ loop=$revision
+ while test "$loop" -ne 0; do
+ func_arith $revision - $loop
+ iface=$func_arith_result
+ func_arith $loop - 1
+ loop=$func_arith_result
+ verstring="$verstring_prefix$major.$iface:$verstring"
+ done
+
+ # Before this point, $major must not contain `.'.
+ major=.$major
+ versuffix="$major.$revision"
+ ;;
+
+ linux)
+ func_arith $current - $age
+ major=.$func_arith_result
+ versuffix="$major.$age.$revision"
+ ;;
+
+ osf)
+ func_arith $current - $age
+ major=.$func_arith_result
+ versuffix=".$current.$age.$revision"
+ verstring="$current.$age.$revision"
+
+ # Add in all the interfaces that we are compatible with.
+ loop=$age
+ while test "$loop" -ne 0; do
+ func_arith $current - $loop
+ iface=$func_arith_result
+ func_arith $loop - 1
+ loop=$func_arith_result
+ verstring="$verstring:${iface}.0"
+ done
+
+ # Make executables depend on our current version.
+ verstring="$verstring:${current}.0"
+ ;;
+
+ qnx)
+ major=".$current"
+ versuffix=".$current"
+ ;;
+
+ sunos)
+ major=".$current"
+ versuffix=".$current.$revision"
+ ;;
+
+ windows)
+ # Use '-' rather than '.', since we only want one
+ # extension on DOS 8.3 filesystems.
+ func_arith $current - $age
+ major=$func_arith_result
+ versuffix="-$major"
+ ;;
+
+ *)
+ func_fatal_configuration "unknown library version type \`$version_type'"
+ ;;
+ esac
+
+ # Clear the version info if we defaulted, and they specified a release.
+ if test -z "$vinfo" && test -n "$release"; then
+ major=
+ case $version_type in
+ darwin)
+ # we can't check for "0.0" in archive_cmds due to quoting
+ # problems, so we reset it completely
+ verstring=
+ ;;
+ *)
+ verstring="0.0"
+ ;;
+ esac
+ if test "$need_version" = no; then
+ versuffix=
+ else
+ versuffix=".0.0"
+ fi
+ fi
+
+ # Remove version info from name if versioning should be avoided
+ if test "$avoid_version" = yes && test "$need_version" = no; then
+ major=
+ versuffix=
+ verstring=""
+ fi
+
+ # Check to see if the archive will have undefined symbols.
+ if test "$allow_undefined" = yes; then
+ if test "$allow_undefined_flag" = unsupported; then
+ func_warning "undefined symbols not allowed in $host shared libraries"
+ build_libtool_libs=no
+ build_old_libs=yes
+ fi
+ else
+ # Don't allow undefined symbols.
+ allow_undefined_flag="$no_undefined_flag"
+ fi
+
+ fi
+
+ func_generate_dlsyms "$libname" "$libname" "yes"
+ libobjs="$libobjs $symfileobj"
+ test "X$libobjs" = "X " && libobjs=
+
+ if test "$mode" != relink; then
+ # Remove our outputs, but don't remove object files since they
+ # may have been created when compiling PIC objects.
+ removelist=
+ tempremovelist=`$ECHO "$output_objdir/*"`
+ for p in $tempremovelist; do
+ case $p in
+ *.$objext | *.gcno)
+ ;;
+ $output_objdir/$outputname | $output_objdir/$libname.* | $output_objdir/${libname}${release}.*)
+ if test "X$precious_files_regex" != "X"; then
+ if $ECHO "$p" | $EGREP -e "$precious_files_regex" >/dev/null 2>&1
+ then
+ continue
+ fi
+ fi
+ removelist="$removelist $p"
+ ;;
+ *) ;;
+ esac
+ done
+ test -n "$removelist" && \
+ func_show_eval "${RM}r \$removelist"
+ fi
+
+ # Now set the variables for building old libraries.
+ if test "$build_old_libs" = yes && test "$build_libtool_libs" != convenience ; then
+ oldlibs="$oldlibs $output_objdir/$libname.$libext"
+
+ # Transform .lo files to .o files.
+ oldobjs="$objs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}'$/d' -e "$lo2o" | $NL2SP`
+ fi
+
+ # Eliminate all temporary directories.
+ #for path in $notinst_path; do
+ # lib_search_path=`$ECHO "X$lib_search_path " | $Xsed -e "s% $path % %g"`
+ # deplibs=`$ECHO "X$deplibs " | $Xsed -e "s% -L$path % %g"`
+ # dependency_libs=`$ECHO "X$dependency_libs " | $Xsed -e "s% -L$path % %g"`
+ #done
+
+ if test -n "$xrpath"; then
+ # If the user specified any rpath flags, then add them.
+ temp_xrpath=
+ for libdir in $xrpath; do
+ temp_xrpath="$temp_xrpath -R$libdir"
+ case "$finalize_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_rpath="$finalize_rpath $libdir" ;;
+ esac
+ done
+ if test "$hardcode_into_libs" != yes || test "$build_old_libs" = yes; then
+ dependency_libs="$temp_xrpath $dependency_libs"
+ fi
+ fi
+
+ # Make sure dlfiles contains only unique files that won't be dlpreopened
+ old_dlfiles="$dlfiles"
+ dlfiles=
+ for lib in $old_dlfiles; do
+ case " $dlprefiles $dlfiles " in
+ *" $lib "*) ;;
+ *) dlfiles="$dlfiles $lib" ;;
+ esac
+ done
+
+ # Make sure dlprefiles contains only unique files
+ old_dlprefiles="$dlprefiles"
+ dlprefiles=
+ for lib in $old_dlprefiles; do
+ case "$dlprefiles " in
+ *" $lib "*) ;;
+ *) dlprefiles="$dlprefiles $lib" ;;
+ esac
+ done
+
+ if test "$build_libtool_libs" = yes; then
+ if test -n "$rpath"; then
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-beos* | *-cegcc*)
+ # these systems don't actually have a c library (as such)!
+ ;;
+ *-*-rhapsody* | *-*-darwin1.[012])
+ # Rhapsody C library is in the System framework
+ deplibs="$deplibs System.ltframework"
+ ;;
+ *-*-netbsd*)
+ # Don't link with libc until the a.out ld.so is fixed.
+ ;;
+ *-*-openbsd* | *-*-freebsd* | *-*-dragonfly*)
+ # Do not include libc due to us having libc/libc_r.
+ ;;
+ *-*-sco3.2v5* | *-*-sco5v6*)
+ # Causes problems with __ctype
+ ;;
+ *-*-sysv4.2uw2* | *-*-sysv5* | *-*-unixware* | *-*-OpenUNIX*)
+ # Compiler inserts libc in the correct place for threads to work
+ ;;
+ *)
+ # Add libc to deplibs on all other systems if necessary.
+ if test "$build_libtool_need_lc" = "yes"; then
+ deplibs="$deplibs -lc"
+ fi
+ ;;
+ esac
+ fi
+
+ # Transform deplibs into only deplibs that can be linked in shared.
+ name_save=$name
+ libname_save=$libname
+ release_save=$release
+ versuffix_save=$versuffix
+ major_save=$major
+ # I'm not sure if I'm treating the release correctly. I think
+ # release should show up in the -l (ie -lgmp5) so we don't want to
+ # add it in twice. Is that correct?
+ release=""
+ versuffix=""
+ major=""
+ newdeplibs=
+ droppeddeps=no
+ case $deplibs_check_method in
+ pass_all)
+ # Don't check for shared/static. Everything works.
+ # This might be a little naive. We might want to check
+ # whether the library exists or not. But this is on
+ # osf3 & osf4 and I'm not really sure... Just
+ # implementing what was already the behavior.
+ newdeplibs=$deplibs
+ ;;
+ test_compile)
+ # This code stresses the "libraries are programs" paradigm to its
+ # limits. Maybe even breaks it. We compile a program, linking it
+ # against the deplibs as a proxy for the library. Then we can check
+ # whether they linked in statically or dynamically with ldd.
+ $opt_dry_run || $RM conftest.c
+ cat > conftest.c <<EOF
+ int main() { return 0; }
+EOF
+ $opt_dry_run || $RM conftest
+ if $LTCC $LTCFLAGS -o conftest conftest.c $deplibs; then
+ ldd_output=`ldd conftest`
+ for i in $deplibs; do
+ case $i in
+ -l*)
+ func_stripname -l '' "$i"
+ name=$func_stripname_result
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $i "*)
+ newdeplibs="$newdeplibs $i"
+ i=""
+ ;;
+ esac
+ fi
+ if test -n "$i" ; then
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ deplib_matches=`eval "\\$ECHO \"$library_names_spec\""`
+ set dummy $deplib_matches; shift
+ deplib_match=$1
+ if test `expr "$ldd_output" : ".*$deplib_match"` -ne 0 ; then
+ newdeplibs="$newdeplibs $i"
+ else
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning: dynamic linker does not accept needed library $i."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which I believe you do not have"
+ $ECHO "*** because a test_compile did reveal that the linker did not use it for"
+ $ECHO "*** its dynamic dependency list that programs get resolved with at runtime."
+ fi
+ fi
+ ;;
+ *)
+ newdeplibs="$newdeplibs $i"
+ ;;
+ esac
+ done
+ else
+ # Error occurred in the first compile. Let's try to salvage
+ # the situation: Compile a separate program for each library.
+ for i in $deplibs; do
+ case $i in
+ -l*)
+ func_stripname -l '' "$i"
+ name=$func_stripname_result
+ $opt_dry_run || $RM conftest
+ if $LTCC $LTCFLAGS -o conftest conftest.c $i; then
+ ldd_output=`ldd conftest`
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $i "*)
+ newdeplibs="$newdeplibs $i"
+ i=""
+ ;;
+ esac
+ fi
+ if test -n "$i" ; then
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ deplib_matches=`eval "\\$ECHO \"$library_names_spec\""`
+ set dummy $deplib_matches; shift
+ deplib_match=$1
+ if test `expr "$ldd_output" : ".*$deplib_match"` -ne 0 ; then
+ newdeplibs="$newdeplibs $i"
+ else
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning: dynamic linker does not accept needed library $i."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have"
+ $ECHO "*** because a test_compile did reveal that the linker did not use this one"
+ $ECHO "*** as a dynamic dependency that programs can get resolved with at runtime."
+ fi
+ fi
+ else
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning! Library $i is needed by this library but I was not able to"
+ $ECHO "*** make it link in! You will probably need to install it or some"
+ $ECHO "*** library that it depends on before this library will be fully"
+ $ECHO "*** functional. Installing it before continuing would be even better."
+ fi
+ ;;
+ *)
+ newdeplibs="$newdeplibs $i"
+ ;;
+ esac
+ done
+ fi
+ ;;
+ file_magic*)
+ set dummy $deplibs_check_method; shift
+ file_magic_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"`
+ for a_deplib in $deplibs; do
+ case $a_deplib in
+ -l*)
+ func_stripname -l '' "$a_deplib"
+ name=$func_stripname_result
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $a_deplib "*)
+ newdeplibs="$newdeplibs $a_deplib"
+ a_deplib=""
+ ;;
+ esac
+ fi
+ if test -n "$a_deplib" ; then
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ for i in $lib_search_path $sys_lib_search_path $shlib_search_path; do
+ potential_libs=`ls $i/$libname[.-]* 2>/dev/null`
+ for potent_lib in $potential_libs; do
+ # Follow soft links.
+ if ls -lLd "$potent_lib" 2>/dev/null |
+ $GREP " -> " >/dev/null; then
+ continue
+ fi
+ # The statement above tries to avoid entering an
+ # endless loop below, in case of cyclic links.
+ # We might still enter an endless loop, since a link
+ # loop can be closed while we follow links,
+ # but so what?
+ potlib="$potent_lib"
+ while test -h "$potlib" 2>/dev/null; do
+ potliblink=`ls -ld $potlib | ${SED} 's/.* -> //'`
+ case $potliblink in
+ [\\/]* | [A-Za-z]:[\\/]*) potlib="$potliblink";;
+ *) potlib=`$ECHO "X$potlib" | $Xsed -e 's,[^/]*$,,'`"$potliblink";;
+ esac
+ done
+ if eval $file_magic_cmd \"\$potlib\" 2>/dev/null |
+ $SED -e 10q |
+ $EGREP "$file_magic_regex" > /dev/null; then
+ newdeplibs="$newdeplibs $a_deplib"
+ a_deplib=""
+ break 2
+ fi
+ done
+ done
+ fi
+ if test -n "$a_deplib" ; then
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning: linker path does not have real file for library $a_deplib."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have"
+ $ECHO "*** because I did check the linker path looking for a file starting"
+ if test -z "$potlib" ; then
+ $ECHO "*** with $libname but no candidates were found. (...for file magic test)"
+ else
+ $ECHO "*** with $libname and none of the candidates passed a file format test"
+ $ECHO "*** using a file magic. Last file checked: $potlib"
+ fi
+ fi
+ ;;
+ *)
+ # Add a -L argument.
+ newdeplibs="$newdeplibs $a_deplib"
+ ;;
+ esac
+ done # Gone through all deplibs.
+ ;;
+ match_pattern*)
+ set dummy $deplibs_check_method; shift
+ match_pattern_regex=`expr "$deplibs_check_method" : "$1 \(.*\)"`
+ for a_deplib in $deplibs; do
+ case $a_deplib in
+ -l*)
+ func_stripname -l '' "$a_deplib"
+ name=$func_stripname_result
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ case " $predeps $postdeps " in
+ *" $a_deplib "*)
+ newdeplibs="$newdeplibs $a_deplib"
+ a_deplib=""
+ ;;
+ esac
+ fi
+ if test -n "$a_deplib" ; then
+ libname=`eval "\\$ECHO \"$libname_spec\""`
+ for i in $lib_search_path $sys_lib_search_path $shlib_search_path; do
+ potential_libs=`ls $i/$libname[.-]* 2>/dev/null`
+ for potent_lib in $potential_libs; do
+ potlib="$potent_lib" # see symlink-check above in file_magic test
+ if eval "\$ECHO \"X$potent_lib\"" 2>/dev/null | $Xsed -e 10q | \
+ $EGREP "$match_pattern_regex" > /dev/null; then
+ newdeplibs="$newdeplibs $a_deplib"
+ a_deplib=""
+ break 2
+ fi
+ done
+ done
+ fi
+ if test -n "$a_deplib" ; then
+ droppeddeps=yes
+ $ECHO
+ $ECHO "*** Warning: linker path does not have real file for library $a_deplib."
+ $ECHO "*** I have the capability to make that library automatically link in when"
+ $ECHO "*** you link to this library. But I can only do this if you have a"
+ $ECHO "*** shared version of the library, which you do not appear to have"
+ $ECHO "*** because I did check the linker path looking for a file starting"
+ if test -z "$potlib" ; then
+ $ECHO "*** with $libname but no candidates were found. (...for regex pattern test)"
+ else
+ $ECHO "*** with $libname and none of the candidates passed a file format test"
+ $ECHO "*** using a regex pattern. Last file checked: $potlib"
+ fi
+ fi
+ ;;
+ *)
+ # Add a -L argument.
+ newdeplibs="$newdeplibs $a_deplib"
+ ;;
+ esac
+ done # Gone through all deplibs.
+ ;;
+ none | unknown | *)
+ newdeplibs=""
+ tmp_deplibs=`$ECHO "X $deplibs" | $Xsed \
+ -e 's/ -lc$//' -e 's/ -[LR][^ ]*//g'`
+ if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
+ for i in $predeps $postdeps ; do
+ # can't use Xsed below, because $i might contain '/'
+ tmp_deplibs=`$ECHO "X $tmp_deplibs" | $Xsed -e "s,$i,,"`
+ done
+ fi
+ if $ECHO "X $tmp_deplibs" | $Xsed -e 's/[ ]//g' |
+ $GREP . >/dev/null; then
+ $ECHO
+ if test "X$deplibs_check_method" = "Xnone"; then
+ $ECHO "*** Warning: inter-library dependencies are not supported in this platform."
+ else
+ $ECHO "*** Warning: inter-library dependencies are not known to be supported."
+ fi
+ $ECHO "*** All declared inter-library dependencies are being dropped."
+ droppeddeps=yes
+ fi
+ ;;
+ esac
+ versuffix=$versuffix_save
+ major=$major_save
+ release=$release_save
+ libname=$libname_save
+ name=$name_save
+
+ case $host in
+ *-*-rhapsody* | *-*-darwin1.[012])
+ # On Rhapsody replace the C library with the System framework
+ newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's/ -lc / System.ltframework /'`
+ ;;
+ esac
+
+ if test "$droppeddeps" = yes; then
+ if test "$module" = yes; then
+ $ECHO
+ $ECHO "*** Warning: libtool could not satisfy all declared inter-library"
+ $ECHO "*** dependencies of module $libname. Therefore, libtool will create"
+ $ECHO "*** a static module, that should work as long as the dlopening"
+ $ECHO "*** application is linked with the -dlopen flag."
+ if test -z "$global_symbol_pipe"; then
+ $ECHO
+ $ECHO "*** However, this would only work if libtool was able to extract symbol"
+ $ECHO "*** lists from a program, using \`nm' or equivalent, but libtool could"
+ $ECHO "*** not find such a program. So, this module is probably useless."
+ $ECHO "*** \`nm' from GNU binutils and a full rebuild may help."
+ fi
+ if test "$build_old_libs" = no; then
+ oldlibs="$output_objdir/$libname.$libext"
+ build_libtool_libs=module
+ build_old_libs=yes
+ else
+ build_libtool_libs=no
+ fi
+ else
+ $ECHO "*** The inter-library dependencies that have been dropped here will be"
+ $ECHO "*** automatically added whenever a program is linked with this library"
+ $ECHO "*** or is declared to -dlopen it."
+
+ if test "$allow_undefined" = no; then
+ $ECHO
+ $ECHO "*** Since this library must not contain undefined symbols,"
+ $ECHO "*** because either the platform does not support them or"
+ $ECHO "*** it was explicitly requested with -no-undefined,"
+ $ECHO "*** libtool will only create a static version of it."
+ if test "$build_old_libs" = no; then
+ oldlibs="$output_objdir/$libname.$libext"
+ build_libtool_libs=module
+ build_old_libs=yes
+ else
+ build_libtool_libs=no
+ fi
+ fi
+ fi
+ fi
+ # Done checking deplibs!
+ deplibs=$newdeplibs
+ fi
+ # Time to change all our "foo.ltframework" stuff back to "-framework foo"
+ case $host in
+ *-*-darwin*)
+ newdeplibs=`$ECHO "X $newdeplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ new_inherited_linker_flags=`$ECHO "X $new_inherited_linker_flags" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ deplibs=`$ECHO "X $deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ ;;
+ esac
+
+ # move library search paths that coincide with paths to not yet
+ # installed libraries to the beginning of the library search list
+ new_libs=
+ for path in $notinst_path; do
+ case " $new_libs " in
+ *" -L$path/$objdir "*) ;;
+ *)
+ case " $deplibs " in
+ *" -L$path/$objdir "*)
+ new_libs="$new_libs -L$path/$objdir" ;;
+ esac
+ ;;
+ esac
+ done
+ for deplib in $deplibs; do
+ case $deplib in
+ -L*)
+ case " $new_libs " in
+ *" $deplib "*) ;;
+ *) new_libs="$new_libs $deplib" ;;
+ esac
+ ;;
+ *) new_libs="$new_libs $deplib" ;;
+ esac
+ done
+ deplibs="$new_libs"
+
+ # All the library-specific variables (install_libdir is set above).
+ library_names=
+ old_library=
+ dlname=
+
+ # Test again, we may have decided not to build it any more
+ if test "$build_libtool_libs" = yes; then
+ if test "$hardcode_into_libs" = yes; then
+ # Hardcode the library paths
+ hardcode_libdirs=
+ dep_rpath=
+ rpath="$finalize_rpath"
+ test "$mode" != relink && rpath="$compile_rpath$rpath"
+ for libdir in $rpath; do
+ if test -n "$hardcode_libdir_flag_spec"; then
+ if test -n "$hardcode_libdir_separator"; then
+ if test -z "$hardcode_libdirs"; then
+ hardcode_libdirs="$libdir"
+ else
+ # Just accumulate the unique libdirs.
+ case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in
+ *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*)
+ ;;
+ *)
+ hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir"
+ ;;
+ esac
+ fi
+ else
+ eval flag=\"$hardcode_libdir_flag_spec\"
+ dep_rpath="$dep_rpath $flag"
+ fi
+ elif test -n "$runpath_var"; then
+ case "$perm_rpath " in
+ *" $libdir "*) ;;
+ *) perm_rpath="$perm_rpath $libdir" ;;
+ esac
+ fi
+ done
+ # Substitute the hardcoded libdirs into the rpath.
+ if test -n "$hardcode_libdir_separator" &&
+ test -n "$hardcode_libdirs"; then
+ libdir="$hardcode_libdirs"
+ if test -n "$hardcode_libdir_flag_spec_ld"; then
+ eval dep_rpath=\"$hardcode_libdir_flag_spec_ld\"
+ else
+ eval dep_rpath=\"$hardcode_libdir_flag_spec\"
+ fi
+ fi
+ if test -n "$runpath_var" && test -n "$perm_rpath"; then
+ # We should set the runpath_var.
+ rpath=
+ for dir in $perm_rpath; do
+ rpath="$rpath$dir:"
+ done
+ eval "$runpath_var='$rpath\$$runpath_var'; export $runpath_var"
+ fi
+ test -n "$dep_rpath" && deplibs="$dep_rpath $deplibs"
+ fi
+
+ shlibpath="$finalize_shlibpath"
+ test "$mode" != relink && shlibpath="$compile_shlibpath$shlibpath"
+ if test -n "$shlibpath"; then
+ eval "$shlibpath_var='$shlibpath\$$shlibpath_var'; export $shlibpath_var"
+ fi
+
+ # Get the real and link names of the library.
+ eval shared_ext=\"$shrext_cmds\"
+ eval library_names=\"$library_names_spec\"
+ set dummy $library_names
+ shift
+ realname="$1"
+ shift
+
+ if test -n "$soname_spec"; then
+ eval soname=\"$soname_spec\"
+ else
+ soname="$realname"
+ fi
+ if test -z "$dlname"; then
+ dlname=$soname
+ fi
+
+ lib="$output_objdir/$realname"
+ linknames=
+ for link
+ do
+ linknames="$linknames $link"
+ done
+
+ # Use standard objects if they are pic
+ test -z "$pic_flag" && libobjs=`$ECHO "X$libobjs" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+ test "X$libobjs" = "X " && libobjs=
+
+ delfiles=
+ if test -n "$export_symbols" && test -n "$include_expsyms"; then
+ $opt_dry_run || cp "$export_symbols" "$output_objdir/$libname.uexp"
+ export_symbols="$output_objdir/$libname.uexp"
+ delfiles="$delfiles $export_symbols"
+ fi
+
+ orig_export_symbols=
+ case $host_os in
+ cygwin* | mingw* | cegcc*)
+ if test -n "$export_symbols" && test -z "$export_symbols_regex"; then
+ # exporting using user supplied symfile
+ if test "x`$SED 1q $export_symbols`" != xEXPORTS; then
+ # and it's NOT already a .def file. Must figure out
+ # which of the given symbols are data symbols and tag
+ # them as such. So, trigger use of export_symbols_cmds.
+ # export_symbols gets reassigned inside the "prepare
+ # the list of exported symbols" if statement, so the
+ # include_expsyms logic still works.
+ orig_export_symbols="$export_symbols"
+ export_symbols=
+ always_export_symbols=yes
+ fi
+ fi
+ ;;
+ esac
+
+ # Prepare the list of exported symbols
+ if test -z "$export_symbols"; then
+ if test "$always_export_symbols" = yes || test -n "$export_symbols_regex"; then
+ func_verbose "generating symbol list for \`$libname.la'"
+ export_symbols="$output_objdir/$libname.exp"
+ $opt_dry_run || $RM $export_symbols
+ cmds=$export_symbols_cmds
+ save_ifs="$IFS"; IFS='~'
+ for cmd in $cmds; do
+ IFS="$save_ifs"
+ eval cmd=\"$cmd\"
+ func_len " $cmd"
+ len=$func_len_result
+ if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then
+ func_show_eval "$cmd" 'exit $?'
+ skipped_export=false
+ else
+ # The command line is too long to execute in one step.
+ func_verbose "using reloadable object file for export list..."
+ skipped_export=:
+ # Break out early, otherwise skipped_export may be
+ # set to false by a later but shorter cmd.
+ break
+ fi
+ done
+ IFS="$save_ifs"
+ if test -n "$export_symbols_regex" && test "X$skipped_export" != "X:"; then
+ func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"'
+ func_show_eval '$MV "${export_symbols}T" "$export_symbols"'
+ fi
+ fi
+ fi
+
+ if test -n "$export_symbols" && test -n "$include_expsyms"; then
+ tmp_export_symbols="$export_symbols"
+ test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols"
+ $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"'
+ fi
+
+ if test "X$skipped_export" != "X:" && test -n "$orig_export_symbols"; then
+ # The given exports_symbols file has to be filtered, so filter it.
+ func_verbose "filter symbol list for \`$libname.la' to tag DATA exports"
+ # FIXME: $output_objdir/$libname.filter potentially contains lots of
+ # 's' commands which not all seds can handle. GNU sed should be fine
+ # though. Also, the filter scales superlinearly with the number of
+ # global variables. join(1) would be nice here, but unfortunately
+ # isn't a blessed tool.
+ $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter
+ delfiles="$delfiles $export_symbols $output_objdir/$libname.filter"
+ export_symbols=$output_objdir/$libname.def
+ $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols
+ fi
+
+ tmp_deplibs=
+ for test_deplib in $deplibs; do
+ case " $convenience " in
+ *" $test_deplib "*) ;;
+ *)
+ tmp_deplibs="$tmp_deplibs $test_deplib"
+ ;;
+ esac
+ done
+ deplibs="$tmp_deplibs"
+
+ if test -n "$convenience"; then
+ if test -n "$whole_archive_flag_spec" &&
+ test "$compiler_needs_object" = yes &&
+ test -z "$libobjs"; then
+ # extract the archives, so we have objects to list.
+ # TODO: could optimize this to just extract one archive.
+ whole_archive_flag_spec=
+ fi
+ if test -n "$whole_archive_flag_spec"; then
+ save_libobjs=$libobjs
+ eval libobjs=\"\$libobjs $whole_archive_flag_spec\"
+ test "X$libobjs" = "X " && libobjs=
+ else
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $convenience
+ libobjs="$libobjs $func_extract_archives_result"
+ test "X$libobjs" = "X " && libobjs=
+ fi
+ fi
+
+ if test "$thread_safe" = yes && test -n "$thread_safe_flag_spec"; then
+ eval flag=\"$thread_safe_flag_spec\"
+ linker_flags="$linker_flags $flag"
+ fi
+
+ # Make a backup of the uninstalled library when relinking
+ if test "$mode" = relink; then
+ $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}U && $MV $realname ${realname}U)' || exit $?
+ fi
+
+ # Do each of the archive commands.
+ if test "$module" = yes && test -n "$module_cmds" ; then
+ if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then
+ eval test_cmds=\"$module_expsym_cmds\"
+ cmds=$module_expsym_cmds
+ else
+ eval test_cmds=\"$module_cmds\"
+ cmds=$module_cmds
+ fi
+ else
+ if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then
+ eval test_cmds=\"$archive_expsym_cmds\"
+ cmds=$archive_expsym_cmds
+ else
+ eval test_cmds=\"$archive_cmds\"
+ cmds=$archive_cmds
+ fi
+ fi
+
+ if test "X$skipped_export" != "X:" &&
+ func_len " $test_cmds" &&
+ len=$func_len_result &&
+ test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then
+ :
+ else
+ # The command line is too long to link in one step, link piecewise
+ # or, if using GNU ld and skipped_export is not :, use a linker
+ # script.
+
+ # Save the value of $output and $libobjs because we want to
+ # use them later. If we have whole_archive_flag_spec, we
+ # want to use save_libobjs as it was before
+ # whole_archive_flag_spec was expanded, because we can't
+ # assume the linker understands whole_archive_flag_spec.
+ # This may have to be revisited, in case too many
+ # convenience libraries get linked in and end up exceeding
+ # the spec.
+ if test -z "$convenience" || test -z "$whole_archive_flag_spec"; then
+ save_libobjs=$libobjs
+ fi
+ save_output=$output
+ output_la=`$ECHO "X$output" | $Xsed -e "$basename"`
+
+ # Clear the reloadable object creation command queue and
+ # initialize k to one.
+ test_cmds=
+ concat_cmds=
+ objlist=
+ last_robj=
+ k=1
+
+ if test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "$with_gnu_ld" = yes; then
+ output=${output_objdir}/${output_la}.lnkscript
+ func_verbose "creating GNU ld script: $output"
+ $ECHO 'INPUT (' > $output
+ for obj in $save_libobjs
+ do
+ $ECHO "$obj" >> $output
+ done
+ $ECHO ')' >> $output
+ delfiles="$delfiles $output"
+ elif test -n "$save_libobjs" && test "X$skipped_export" != "X:" && test "X$file_list_spec" != X; then
+ output=${output_objdir}/${output_la}.lnk
+ func_verbose "creating linker input file list: $output"
+ : > $output
+ set x $save_libobjs
+ shift
+ firstobj=
+ if test "$compiler_needs_object" = yes; then
+ firstobj="$1 "
+ shift
+ fi
+ for obj
+ do
+ $ECHO "$obj" >> $output
+ done
+ delfiles="$delfiles $output"
+ output=$firstobj\"$file_list_spec$output\"
+ else
+ if test -n "$save_libobjs"; then
+ func_verbose "creating reloadable object files..."
+ output=$output_objdir/$output_la-${k}.$objext
+ eval test_cmds=\"$reload_cmds\"
+ func_len " $test_cmds"
+ len0=$func_len_result
+ len=$len0
+
+ # Loop over the list of objects to be linked.
+ for obj in $save_libobjs
+ do
+ func_len " $obj"
+ func_arith $len + $func_len_result
+ len=$func_arith_result
+ if test "X$objlist" = X ||
+ test "$len" -lt "$max_cmd_len"; then
+ func_append objlist " $obj"
+ else
+ # The command $test_cmds is almost too long, add a
+ # command to the queue.
+ if test "$k" -eq 1 ; then
+ # The first file doesn't have a previous command to add.
+ eval concat_cmds=\"$reload_cmds $objlist $last_robj\"
+ else
+ # All subsequent reloadable object files will link in
+ # the last one created.
+ eval concat_cmds=\"\$concat_cmds~$reload_cmds $objlist $last_robj~\$RM $last_robj\"
+ fi
+ last_robj=$output_objdir/$output_la-${k}.$objext
+ func_arith $k + 1
+ k=$func_arith_result
+ output=$output_objdir/$output_la-${k}.$objext
+ objlist=$obj
+ func_len " $last_robj"
+ func_arith $len0 + $func_len_result
+ len=$func_arith_result
+ fi
+ done
+ # Handle the remaining objects by creating one last
+ # reloadable object file. All subsequent reloadable object
+ # files will link in the last one created.
+ test -z "$concat_cmds" || concat_cmds=$concat_cmds~
+ eval concat_cmds=\"\${concat_cmds}$reload_cmds $objlist $last_robj\"
+ if test -n "$last_robj"; then
+ eval concat_cmds=\"\${concat_cmds}~\$RM $last_robj\"
+ fi
+ delfiles="$delfiles $output"
+
+ else
+ output=
+ fi
+
+ if ${skipped_export-false}; then
+ func_verbose "generating symbol list for \`$libname.la'"
+ export_symbols="$output_objdir/$libname.exp"
+ $opt_dry_run || $RM $export_symbols
+ libobjs=$output
+ # Append the command to create the export file.
+ test -z "$concat_cmds" || concat_cmds=$concat_cmds~
+ eval concat_cmds=\"\$concat_cmds$export_symbols_cmds\"
+ if test -n "$last_robj"; then
+ eval concat_cmds=\"\$concat_cmds~\$RM $last_robj\"
+ fi
+ fi
+
+ test -n "$save_libobjs" &&
+ func_verbose "creating a temporary reloadable object file: $output"
+
+ # Loop through the commands generated above and execute them.
+ save_ifs="$IFS"; IFS='~'
+ for cmd in $concat_cmds; do
+ IFS="$save_ifs"
+ $opt_silent || {
+ func_quote_for_expand "$cmd"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+ $opt_dry_run || eval "$cmd" || {
+ lt_exit=$?
+
+ # Restore the uninstalled library and exit
+ if test "$mode" = relink; then
+ ( cd "$output_objdir" && \
+ $RM "${realname}T" && \
+ $MV "${realname}U" "$realname" )
+ fi
+
+ exit $lt_exit
+ }
+ done
+ IFS="$save_ifs"
+
+ if test -n "$export_symbols_regex" && ${skipped_export-false}; then
+ func_show_eval '$EGREP -e "$export_symbols_regex" "$export_symbols" > "${export_symbols}T"'
+ func_show_eval '$MV "${export_symbols}T" "$export_symbols"'
+ fi
+ fi
+
+ if ${skipped_export-false}; then
+ if test -n "$export_symbols" && test -n "$include_expsyms"; then
+ tmp_export_symbols="$export_symbols"
+ test -n "$orig_export_symbols" && tmp_export_symbols="$orig_export_symbols"
+ $opt_dry_run || eval '$ECHO "X$include_expsyms" | $Xsed | $SP2NL >> "$tmp_export_symbols"'
+ fi
+
+ if test -n "$orig_export_symbols"; then
+ # The given exports_symbols file has to be filtered, so filter it.
+ func_verbose "filter symbol list for \`$libname.la' to tag DATA exports"
+ # FIXME: $output_objdir/$libname.filter potentially contains lots of
+ # 's' commands which not all seds can handle. GNU sed should be fine
+ # though. Also, the filter scales superlinearly with the number of
+ # global variables. join(1) would be nice here, but unfortunately
+ # isn't a blessed tool.
+ $opt_dry_run || $SED -e '/[ ,]DATA/!d;s,\(.*\)\([ \,].*\),s|^\1$|\1\2|,' < $export_symbols > $output_objdir/$libname.filter
+ delfiles="$delfiles $export_symbols $output_objdir/$libname.filter"
+ export_symbols=$output_objdir/$libname.def
+ $opt_dry_run || $SED -f $output_objdir/$libname.filter < $orig_export_symbols > $export_symbols
+ fi
+ fi
+
+ libobjs=$output
+ # Restore the value of output.
+ output=$save_output
+
+ if test -n "$convenience" && test -n "$whole_archive_flag_spec"; then
+ eval libobjs=\"\$libobjs $whole_archive_flag_spec\"
+ test "X$libobjs" = "X " && libobjs=
+ fi
+ # Expand the library linking commands again to reset the
+ # value of $libobjs for piecewise linking.
+
+ # Do each of the archive commands.
+ if test "$module" = yes && test -n "$module_cmds" ; then
+ if test -n "$export_symbols" && test -n "$module_expsym_cmds"; then
+ cmds=$module_expsym_cmds
+ else
+ cmds=$module_cmds
+ fi
+ else
+ if test -n "$export_symbols" && test -n "$archive_expsym_cmds"; then
+ cmds=$archive_expsym_cmds
+ else
+ cmds=$archive_cmds
+ fi
+ fi
+ fi
+
+ if test -n "$delfiles"; then
+ # Append the command to remove temporary files to $cmds.
+ eval cmds=\"\$cmds~\$RM $delfiles\"
+ fi
+
+ # Add any objects from preloaded convenience libraries
+ if test -n "$dlprefiles"; then
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $dlprefiles
+ libobjs="$libobjs $func_extract_archives_result"
+ test "X$libobjs" = "X " && libobjs=
+ fi
+
+ save_ifs="$IFS"; IFS='~'
+ for cmd in $cmds; do
+ IFS="$save_ifs"
+ eval cmd=\"$cmd\"
+ $opt_silent || {
+ func_quote_for_expand "$cmd"
+ eval "func_echo $func_quote_for_expand_result"
+ }
+ $opt_dry_run || eval "$cmd" || {
+ lt_exit=$?
+
+ # Restore the uninstalled library and exit
+ if test "$mode" = relink; then
+ ( cd "$output_objdir" && \
+ $RM "${realname}T" && \
+ $MV "${realname}U" "$realname" )
+ fi
+
+ exit $lt_exit
+ }
+ done
+ IFS="$save_ifs"
+
+ # Restore the uninstalled library and exit
+ if test "$mode" = relink; then
+ $opt_dry_run || eval '(cd $output_objdir && $RM ${realname}T && $MV $realname ${realname}T && $MV ${realname}U $realname)' || exit $?
+
+ if test -n "$convenience"; then
+ if test -z "$whole_archive_flag_spec"; then
+ func_show_eval '${RM}r "$gentop"'
+ fi
+ fi
+
+ exit $EXIT_SUCCESS
+ fi
+
+ # Create links to the real library.
+ for linkname in $linknames; do
+ if test "$realname" != "$linkname"; then
+ func_show_eval '(cd "$output_objdir" && $RM "$linkname" && $LN_S "$realname" "$linkname")' 'exit $?'
+ fi
+ done
+
+ # If -module or -export-dynamic was specified, set the dlname.
+ if test "$module" = yes || test "$export_dynamic" = yes; then
+ # On all known operating systems, these are identical.
+ dlname="$soname"
+ fi
+ fi
+ ;;
+
+ obj)
+ if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
+ func_warning "\`-dlopen' is ignored for objects"
+ fi
+
+ case " $deplibs" in
+ *\ -l* | *\ -L*)
+ func_warning "\`-l' and \`-L' are ignored for objects" ;;
+ esac
+
+ test -n "$rpath" && \
+ func_warning "\`-rpath' is ignored for objects"
+
+ test -n "$xrpath" && \
+ func_warning "\`-R' is ignored for objects"
+
+ test -n "$vinfo" && \
+ func_warning "\`-version-info' is ignored for objects"
+
+ test -n "$release" && \
+ func_warning "\`-release' is ignored for objects"
+
+ case $output in
+ *.lo)
+ test -n "$objs$old_deplibs" && \
+ func_fatal_error "cannot build library object \`$output' from non-libtool objects"
+
+ libobj=$output
+ func_lo2o "$libobj"
+ obj=$func_lo2o_result
+ ;;
+ *)
+ libobj=
+ obj="$output"
+ ;;
+ esac
+
+ # Delete the old objects.
+ $opt_dry_run || $RM $obj $libobj
+
+ # Objects from convenience libraries. This assumes
+ # single-version convenience libraries. Whenever we create
+ # different ones for PIC/non-PIC, this we'll have to duplicate
+ # the extraction.
+ reload_conv_objs=
+ gentop=
+ # reload_cmds runs $LD directly, so let us get rid of
+ # -Wl from whole_archive_flag_spec and hope we can get by with
+ # turning comma into space..
+ wl=
+
+ if test -n "$convenience"; then
+ if test -n "$whole_archive_flag_spec"; then
+ eval tmp_whole_archive_flags=\"$whole_archive_flag_spec\"
+ reload_conv_objs=$reload_objs\ `$ECHO "X$tmp_whole_archive_flags" | $Xsed -e 's|,| |g'`
+ else
+ gentop="$output_objdir/${obj}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $convenience
+ reload_conv_objs="$reload_objs $func_extract_archives_result"
+ fi
+ fi
+
+ # Create the old-style object.
+ reload_objs="$objs$old_deplibs "`$ECHO "X$libobjs" | $SP2NL | $Xsed -e '/\.'${libext}$'/d' -e '/\.lib$/d' -e "$lo2o" | $NL2SP`" $reload_conv_objs" ### testsuite: skip nested quoting test
+
+ output="$obj"
+ func_execute_cmds "$reload_cmds" 'exit $?'
+
+ # Exit if we aren't doing a library object file.
+ if test -z "$libobj"; then
+ if test -n "$gentop"; then
+ func_show_eval '${RM}r "$gentop"'
+ fi
+
+ exit $EXIT_SUCCESS
+ fi
+
+ if test "$build_libtool_libs" != yes; then
+ if test -n "$gentop"; then
+ func_show_eval '${RM}r "$gentop"'
+ fi
+
+ # Create an invalid libtool object if no PIC, so that we don't
+ # accidentally link it into a program.
+ # $show "echo timestamp > $libobj"
+ # $opt_dry_run || eval "echo timestamp > $libobj" || exit $?
+ exit $EXIT_SUCCESS
+ fi
+
+ if test -n "$pic_flag" || test "$pic_mode" != default; then
+ # Only do commands if we really have different PIC objects.
+ reload_objs="$libobjs $reload_conv_objs"
+ output="$libobj"
+ func_execute_cmds "$reload_cmds" 'exit $?'
+ fi
+
+ if test -n "$gentop"; then
+ func_show_eval '${RM}r "$gentop"'
+ fi
+
+ exit $EXIT_SUCCESS
+ ;;
+
+ prog)
+ case $host in
+ *cygwin*) func_stripname '' '.exe' "$output"
+ output=$func_stripname_result.exe;;
+ esac
+ test -n "$vinfo" && \
+ func_warning "\`-version-info' is ignored for programs"
+
+ test -n "$release" && \
+ func_warning "\`-release' is ignored for programs"
+
+ test "$preload" = yes \
+ && test "$dlopen_support" = unknown \
+ && test "$dlopen_self" = unknown \
+ && test "$dlopen_self_static" = unknown && \
+ func_warning "\`LT_INIT([dlopen])' not used. Assuming no dlopen support."
+
+ case $host in
+ *-*-rhapsody* | *-*-darwin1.[012])
+ # On Rhapsody replace the C library is the System framework
+ compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'`
+ finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's/ -lc / System.ltframework /'`
+ ;;
+ esac
+
+ case $host in
+ *-*-darwin*)
+ # Don't allow lazy linking, it breaks C++ global constructors
+ # But is supposedly fixed on 10.4 or later (yay!).
+ if test "$tagname" = CXX ; then
+ case ${MACOSX_DEPLOYMENT_TARGET-10.0} in
+ 10.[0123])
+ compile_command="$compile_command ${wl}-bind_at_load"
+ finalize_command="$finalize_command ${wl}-bind_at_load"
+ ;;
+ esac
+ fi
+ # Time to change all our "foo.ltframework" stuff back to "-framework foo"
+ compile_deplibs=`$ECHO "X $compile_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ finalize_deplibs=`$ECHO "X $finalize_deplibs" | $Xsed -e 's% \([^ $]*\).ltframework% -framework \1%g'`
+ ;;
+ esac
+
+
+ # move library search paths that coincide with paths to not yet
+ # installed libraries to the beginning of the library search list
+ new_libs=
+ for path in $notinst_path; do
+ case " $new_libs " in
+ *" -L$path/$objdir "*) ;;
+ *)
+ case " $compile_deplibs " in
+ *" -L$path/$objdir "*)
+ new_libs="$new_libs -L$path/$objdir" ;;
+ esac
+ ;;
+ esac
+ done
+ for deplib in $compile_deplibs; do
+ case $deplib in
+ -L*)
+ case " $new_libs " in
+ *" $deplib "*) ;;
+ *) new_libs="$new_libs $deplib" ;;
+ esac
+ ;;
+ *) new_libs="$new_libs $deplib" ;;
+ esac
+ done
+ compile_deplibs="$new_libs"
+
+
+ compile_command="$compile_command $compile_deplibs"
+ finalize_command="$finalize_command $finalize_deplibs"
+
+ if test -n "$rpath$xrpath"; then
+ # If the user specified any rpath flags, then add them.
+ for libdir in $rpath $xrpath; do
+ # This is the magic to use -rpath.
+ case "$finalize_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_rpath="$finalize_rpath $libdir" ;;
+ esac
+ done
+ fi
+
+ # Now hardcode the library paths
+ rpath=
+ hardcode_libdirs=
+ for libdir in $compile_rpath $finalize_rpath; do
+ if test -n "$hardcode_libdir_flag_spec"; then
+ if test -n "$hardcode_libdir_separator"; then
+ if test -z "$hardcode_libdirs"; then
+ hardcode_libdirs="$libdir"
+ else
+ # Just accumulate the unique libdirs.
+ case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in
+ *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*)
+ ;;
+ *)
+ hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir"
+ ;;
+ esac
+ fi
+ else
+ eval flag=\"$hardcode_libdir_flag_spec\"
+ rpath="$rpath $flag"
+ fi
+ elif test -n "$runpath_var"; then
+ case "$perm_rpath " in
+ *" $libdir "*) ;;
+ *) perm_rpath="$perm_rpath $libdir" ;;
+ esac
+ fi
+ case $host in
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-cegcc*)
+ testbindir=`${ECHO} "$libdir" | ${SED} -e 's*/lib$*/bin*'`
+ case :$dllsearchpath: in
+ *":$libdir:"*) ;;
+ ::) dllsearchpath=$libdir;;
+ *) dllsearchpath="$dllsearchpath:$libdir";;
+ esac
+ case :$dllsearchpath: in
+ *":$testbindir:"*) ;;
+ ::) dllsearchpath=$testbindir;;
+ *) dllsearchpath="$dllsearchpath:$testbindir";;
+ esac
+ ;;
+ esac
+ done
+ # Substitute the hardcoded libdirs into the rpath.
+ if test -n "$hardcode_libdir_separator" &&
+ test -n "$hardcode_libdirs"; then
+ libdir="$hardcode_libdirs"
+ eval rpath=\" $hardcode_libdir_flag_spec\"
+ fi
+ compile_rpath="$rpath"
+
+ rpath=
+ hardcode_libdirs=
+ for libdir in $finalize_rpath; do
+ if test -n "$hardcode_libdir_flag_spec"; then
+ if test -n "$hardcode_libdir_separator"; then
+ if test -z "$hardcode_libdirs"; then
+ hardcode_libdirs="$libdir"
+ else
+ # Just accumulate the unique libdirs.
+ case $hardcode_libdir_separator$hardcode_libdirs$hardcode_libdir_separator in
+ *"$hardcode_libdir_separator$libdir$hardcode_libdir_separator"*)
+ ;;
+ *)
+ hardcode_libdirs="$hardcode_libdirs$hardcode_libdir_separator$libdir"
+ ;;
+ esac
+ fi
+ else
+ eval flag=\"$hardcode_libdir_flag_spec\"
+ rpath="$rpath $flag"
+ fi
+ elif test -n "$runpath_var"; then
+ case "$finalize_perm_rpath " in
+ *" $libdir "*) ;;
+ *) finalize_perm_rpath="$finalize_perm_rpath $libdir" ;;
+ esac
+ fi
+ done
+ # Substitute the hardcoded libdirs into the rpath.
+ if test -n "$hardcode_libdir_separator" &&
+ test -n "$hardcode_libdirs"; then
+ libdir="$hardcode_libdirs"
+ eval rpath=\" $hardcode_libdir_flag_spec\"
+ fi
+ finalize_rpath="$rpath"
+
+ if test -n "$libobjs" && test "$build_old_libs" = yes; then
+ # Transform all the library objects into standard objects.
+ compile_command=`$ECHO "X$compile_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+ finalize_command=`$ECHO "X$finalize_command" | $SP2NL | $Xsed -e "$lo2o" | $NL2SP`
+ fi
+
+ func_generate_dlsyms "$outputname" "@PROGRAM@" "no"
+
+ # template prelinking step
+ if test -n "$prelink_cmds"; then
+ func_execute_cmds "$prelink_cmds" 'exit $?'
+ fi
+
+ wrappers_required=yes
+ case $host in
+ *cygwin* | *mingw* )
+ if test "$build_libtool_libs" != yes; then
+ wrappers_required=no
+ fi
+ ;;
+ *cegcc)
+ # Disable wrappers for cegcc, we are cross compiling anyway.
+ wrappers_required=no
+ ;;
+ *)
+ if test "$need_relink" = no || test "$build_libtool_libs" != yes; then
+ wrappers_required=no
+ fi
+ ;;
+ esac
+ if test "$wrappers_required" = no; then
+ # Replace the output file specification.
+ compile_command=`$ECHO "X$compile_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'`
+ link_command="$compile_command$compile_rpath"
+
+ # We have no uninstalled library dependencies, so finalize right now.
+ exit_status=0
+ func_show_eval "$link_command" 'exit_status=$?'
+
+ # Delete the generated files.
+ if test -f "$output_objdir/${outputname}S.${objext}"; then
+ func_show_eval '$RM "$output_objdir/${outputname}S.${objext}"'
+ fi
+
+ exit $exit_status
+ fi
+
+ if test -n "$compile_shlibpath$finalize_shlibpath"; then
+ compile_command="$shlibpath_var=\"$compile_shlibpath$finalize_shlibpath\$$shlibpath_var\" $compile_command"
+ fi
+ if test -n "$finalize_shlibpath"; then
+ finalize_command="$shlibpath_var=\"$finalize_shlibpath\$$shlibpath_var\" $finalize_command"
+ fi
+
+ compile_var=
+ finalize_var=
+ if test -n "$runpath_var"; then
+ if test -n "$perm_rpath"; then
+ # We should set the runpath_var.
+ rpath=
+ for dir in $perm_rpath; do
+ rpath="$rpath$dir:"
+ done
+ compile_var="$runpath_var=\"$rpath\$$runpath_var\" "
+ fi
+ if test -n "$finalize_perm_rpath"; then
+ # We should set the runpath_var.
+ rpath=
+ for dir in $finalize_perm_rpath; do
+ rpath="$rpath$dir:"
+ done
+ finalize_var="$runpath_var=\"$rpath\$$runpath_var\" "
+ fi
+ fi
+
+ if test "$no_install" = yes; then
+ # We don't need to create a wrapper script.
+ link_command="$compile_var$compile_command$compile_rpath"
+ # Replace the output file specification.
+ link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'`
+ # Delete the old output file.
+ $opt_dry_run || $RM $output
+ # Link the executable and exit
+ func_show_eval "$link_command" 'exit $?'
+ exit $EXIT_SUCCESS
+ fi
+
+ if test "$hardcode_action" = relink; then
+ # Fast installation is not supported
+ link_command="$compile_var$compile_command$compile_rpath"
+ relink_command="$finalize_var$finalize_command$finalize_rpath"
+
+ func_warning "this platform does not like uninstalled shared libraries"
+ func_warning "\`$output' will be relinked during installation"
+ else
+ if test "$fast_install" != no; then
+ link_command="$finalize_var$compile_command$finalize_rpath"
+ if test "$fast_install" = yes; then
+ relink_command=`$ECHO "X$compile_var$compile_command$compile_rpath" | $Xsed -e 's%@OUTPUT@%\$progdir/\$file%g'`
+ else
+ # fast_install is set to needless
+ relink_command=
+ fi
+ else
+ link_command="$compile_var$compile_command$compile_rpath"
+ relink_command="$finalize_var$finalize_command$finalize_rpath"
+ fi
+ fi
+
+ # Replace the output file specification.
+ link_command=`$ECHO "X$link_command" | $Xsed -e 's%@OUTPUT@%'"$output_objdir/$outputname"'%g'`
+
+ # Delete the old output files.
+ $opt_dry_run || $RM $output $output_objdir/$outputname $output_objdir/lt-$outputname
+
+ func_show_eval "$link_command" 'exit $?'
+
+ # Now create the wrapper script.
+ func_verbose "creating $output"
+
+ # Quote the relink command for shipping.
+ if test -n "$relink_command"; then
+ # Preserve any variables that may affect compiler behavior
+ for var in $variables_saved_for_relink; do
+ if eval test -z \"\${$var+set}\"; then
+ relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command"
+ elif eval var_value=\$$var; test -z "$var_value"; then
+ relink_command="$var=; export $var; $relink_command"
+ else
+ func_quote_for_eval "$var_value"
+ relink_command="$var=$func_quote_for_eval_result; export $var; $relink_command"
+ fi
+ done
+ relink_command="(cd `pwd`; $relink_command)"
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e "$sed_quote_subst"`
+ fi
+
+ # Quote $ECHO for shipping.
+ if test "X$ECHO" = "X$SHELL $progpath --fallback-echo"; then
+ case $progpath in
+ [\\/]* | [A-Za-z]:[\\/]*) qecho="$SHELL $progpath --fallback-echo";;
+ *) qecho="$SHELL `pwd`/$progpath --fallback-echo";;
+ esac
+ qecho=`$ECHO "X$qecho" | $Xsed -e "$sed_quote_subst"`
+ else
+ qecho=`$ECHO "X$ECHO" | $Xsed -e "$sed_quote_subst"`
+ fi
+
+ # Only actually do things if not in dry run mode.
+ $opt_dry_run || {
+ # win32 will think the script is a binary if it has
+ # a .exe suffix, so we strip it off here.
+ case $output in
+ *.exe) func_stripname '' '.exe' "$output"
+ output=$func_stripname_result ;;
+ esac
+ # test for cygwin because mv fails w/o .exe extensions
+ case $host in
+ *cygwin*)
+ exeext=.exe
+ func_stripname '' '.exe' "$outputname"
+ outputname=$func_stripname_result ;;
+ *) exeext= ;;
+ esac
+ case $host in
+ *cygwin* | *mingw* )
+ func_dirname_and_basename "$output" "" "."
+ output_name=$func_basename_result
+ output_path=$func_dirname_result
+ cwrappersource="$output_path/$objdir/lt-$output_name.c"
+ cwrapper="$output_path/$output_name.exe"
+ $RM $cwrappersource $cwrapper
+ trap "$RM $cwrappersource $cwrapper; exit $EXIT_FAILURE" 1 2 15
+
+ func_emit_cwrapperexe_src > $cwrappersource
+
+ # The wrapper executable is built using the $host compiler,
+ # because it contains $host paths and files. If cross-
+ # compiling, it, like the target executable, must be
+ # executed on the $host or under an emulation environment.
+ $opt_dry_run || {
+ $LTCC $LTCFLAGS -o $cwrapper $cwrappersource
+ $STRIP $cwrapper
+ }
+
+ # Now, create the wrapper script for func_source use:
+ func_ltwrapper_scriptname $cwrapper
+ $RM $func_ltwrapper_scriptname_result
+ trap "$RM $func_ltwrapper_scriptname_result; exit $EXIT_FAILURE" 1 2 15
+ $opt_dry_run || {
+ # note: this script will not be executed, so do not chmod.
+ if test "x$build" = "x$host" ; then
+ $cwrapper --lt-dump-script > $func_ltwrapper_scriptname_result
+ else
+ func_emit_wrapper no > $func_ltwrapper_scriptname_result
+ fi
+ }
+ ;;
+ * )
+ $RM $output
+ trap "$RM $output; exit $EXIT_FAILURE" 1 2 15
+
+ func_emit_wrapper no > $output
+ chmod +x $output
+ ;;
+ esac
+ }
+ exit $EXIT_SUCCESS
+ ;;
+ esac
+
+ # See if we need to build an old-fashioned archive.
+ for oldlib in $oldlibs; do
+
+ if test "$build_libtool_libs" = convenience; then
+ oldobjs="$libobjs_save $symfileobj"
+ addlibs="$convenience"
+ build_libtool_libs=no
+ else
+ if test "$build_libtool_libs" = module; then
+ oldobjs="$libobjs_save"
+ build_libtool_libs=no
+ else
+ oldobjs="$old_deplibs $non_pic_objects"
+ if test "$preload" = yes && test -f "$symfileobj"; then
+ oldobjs="$oldobjs $symfileobj"
+ fi
+ fi
+ addlibs="$old_convenience"
+ fi
+
+ if test -n "$addlibs"; then
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $addlibs
+ oldobjs="$oldobjs $func_extract_archives_result"
+ fi
+
+ # Do each command in the archive commands.
+ if test -n "$old_archive_from_new_cmds" && test "$build_libtool_libs" = yes; then
+ cmds=$old_archive_from_new_cmds
+ else
+
+ # Add any objects from preloaded convenience libraries
+ if test -n "$dlprefiles"; then
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+
+ func_extract_archives $gentop $dlprefiles
+ oldobjs="$oldobjs $func_extract_archives_result"
+ fi
+
+ # POSIX demands no paths to be encoded in archives. We have
+ # to avoid creating archives with duplicate basenames if we
+ # might have to extract them afterwards, e.g., when creating a
+ # static archive out of a convenience library, or when linking
+ # the entirety of a libtool archive into another (currently
+ # not supported by libtool).
+ if (for obj in $oldobjs
+ do
+ func_basename "$obj"
+ $ECHO "$func_basename_result"
+ done | sort | sort -uc >/dev/null 2>&1); then
+ :
+ else
+ $ECHO "copying selected object files to avoid basename conflicts..."
+ gentop="$output_objdir/${outputname}x"
+ generated="$generated $gentop"
+ func_mkdir_p "$gentop"
+ save_oldobjs=$oldobjs
+ oldobjs=
+ counter=1
+ for obj in $save_oldobjs
+ do
+ func_basename "$obj"
+ objbase="$func_basename_result"
+ case " $oldobjs " in
+ " ") oldobjs=$obj ;;
+ *[\ /]"$objbase "*)
+ while :; do
+ # Make sure we don't pick an alternate name that also
+ # overlaps.
+ newobj=lt$counter-$objbase
+ func_arith $counter + 1
+ counter=$func_arith_result
+ case " $oldobjs " in
+ *[\ /]"$newobj "*) ;;
+ *) if test ! -f "$gentop/$newobj"; then break; fi ;;
+ esac
+ done
+ func_show_eval "ln $obj $gentop/$newobj || cp $obj $gentop/$newobj"
+ oldobjs="$oldobjs $gentop/$newobj"
+ ;;
+ *) oldobjs="$oldobjs $obj" ;;
+ esac
+ done
+ fi
+ eval cmds=\"$old_archive_cmds\"
+
+ func_len " $cmds"
+ len=$func_len_result
+ if test "$len" -lt "$max_cmd_len" || test "$max_cmd_len" -le -1; then
+ cmds=$old_archive_cmds
+ else
+ # the command line is too long to link in one step, link in parts
+ func_verbose "using piecewise archive linking..."
+ save_RANLIB=$RANLIB
+ RANLIB=:
+ objlist=
+ concat_cmds=
+ save_oldobjs=$oldobjs
+ oldobjs=
+ # Is there a better way of finding the last object in the list?
+ for obj in $save_oldobjs
+ do
+ last_oldobj=$obj
+ done
+ eval test_cmds=\"$old_archive_cmds\"
+ func_len " $test_cmds"
+ len0=$func_len_result
+ len=$len0
+ for obj in $save_oldobjs
+ do
+ func_len " $obj"
+ func_arith $len + $func_len_result
+ len=$func_arith_result
+ func_append objlist " $obj"
+ if test "$len" -lt "$max_cmd_len"; then
+ :
+ else
+ # the above command should be used before it gets too long
+ oldobjs=$objlist
+ if test "$obj" = "$last_oldobj" ; then
+ RANLIB=$save_RANLIB
+ fi
+ test -z "$concat_cmds" || concat_cmds=$concat_cmds~
+ eval concat_cmds=\"\${concat_cmds}$old_archive_cmds\"
+ objlist=
+ len=$len0
+ fi
+ done
+ RANLIB=$save_RANLIB
+ oldobjs=$objlist
+ if test "X$oldobjs" = "X" ; then
+ eval cmds=\"\$concat_cmds\"
+ else
+ eval cmds=\"\$concat_cmds~\$old_archive_cmds\"
+ fi
+ fi
+ fi
+ func_execute_cmds "$cmds" 'exit $?'
+ done
+
+ test -n "$generated" && \
+ func_show_eval "${RM}r$generated"
+
+ # Now create the libtool archive.
+ case $output in
+ *.la)
+ old_library=
+ test "$build_old_libs" = yes && old_library="$libname.$libext"
+ func_verbose "creating $output"
+
+ # Preserve any variables that may affect compiler behavior
+ for var in $variables_saved_for_relink; do
+ if eval test -z \"\${$var+set}\"; then
+ relink_command="{ test -z \"\${$var+set}\" || $lt_unset $var || { $var=; export $var; }; }; $relink_command"
+ elif eval var_value=\$$var; test -z "$var_value"; then
+ relink_command="$var=; export $var; $relink_command"
+ else
+ func_quote_for_eval "$var_value"
+ relink_command="$var=$func_quote_for_eval_result; export $var; $relink_command"
+ fi
+ done
+ # Quote the link command for shipping.
+ relink_command="(cd `pwd`; $SHELL $progpath $preserve_args --mode=relink $libtool_args @inst_prefix_dir@)"
+ relink_command=`$ECHO "X$relink_command" | $Xsed -e "$sed_quote_subst"`
+ if test "$hardcode_automatic" = yes ; then
+ relink_command=
+ fi
+
+ # Only create the output if not a dry run.
+ $opt_dry_run || {
+ for installed in no yes; do
+ if test "$installed" = yes; then
+ if test -z "$install_libdir"; then
+ break
+ fi
+ output="$output_objdir/$outputname"i
+ # Replace all uninstalled libtool libraries with the installed ones
+ newdependency_libs=
+ for deplib in $dependency_libs; do
+ case $deplib in
+ *.la)
+ func_basename "$deplib"
+ name="$func_basename_result"
+ eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib`
+ test -z "$libdir" && \
+ func_fatal_error "\`$deplib' is not a valid libtool archive"
+ newdependency_libs="$newdependency_libs $libdir/$name"
+ ;;
+ *) newdependency_libs="$newdependency_libs $deplib" ;;
+ esac
+ done
+ dependency_libs="$newdependency_libs"
+ newdlfiles=
+
+ for lib in $dlfiles; do
+ case $lib in
+ *.la)
+ func_basename "$lib"
+ name="$func_basename_result"
+ eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib`
+ test -z "$libdir" && \
+ func_fatal_error "\`$lib' is not a valid libtool archive"
+ newdlfiles="$newdlfiles $libdir/$name"
+ ;;
+ *) newdlfiles="$newdlfiles $lib" ;;
+ esac
+ done
+ dlfiles="$newdlfiles"
+ newdlprefiles=
+ for lib in $dlprefiles; do
+ case $lib in
+ *.la)
+ # Only pass preopened files to the pseudo-archive (for
+ # eventual linking with the app. that links it) if we
+ # didn't already link the preopened objects directly into
+ # the library:
+ func_basename "$lib"
+ name="$func_basename_result"
+ eval libdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $lib`
+ test -z "$libdir" && \
+ func_fatal_error "\`$lib' is not a valid libtool archive"
+ newdlprefiles="$newdlprefiles $libdir/$name"
+ ;;
+ esac
+ done
+ dlprefiles="$newdlprefiles"
+ else
+ newdlfiles=
+ for lib in $dlfiles; do
+ case $lib in
+ [\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;;
+ *) abs=`pwd`"/$lib" ;;
+ esac
+ newdlfiles="$newdlfiles $abs"
+ done
+ dlfiles="$newdlfiles"
+ newdlprefiles=
+ for lib in $dlprefiles; do
+ case $lib in
+ [\\/]* | [A-Za-z]:[\\/]*) abs="$lib" ;;
+ *) abs=`pwd`"/$lib" ;;
+ esac
+ newdlprefiles="$newdlprefiles $abs"
+ done
+ dlprefiles="$newdlprefiles"
+ fi
+ $RM $output
+ # place dlname in correct position for cygwin
+ tdlname=$dlname
+ case $host,$output,$installed,$module,$dlname in
+ *cygwin*,*lai,yes,no,*.dll | *mingw*,*lai,yes,no,*.dll | *cegcc*,*lai,yes,no,*.dll) tdlname=../bin/$dlname ;;
+ esac
+ $ECHO > $output "\
+# $outputname - a libtool library file
+# Generated by $PROGRAM (GNU $PACKAGE$TIMESTAMP) $VERSION
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# The name that we can dlopen(3).
+dlname='$tdlname'
+
+# Names of this library.
+library_names='$library_names'
+
+# The name of the static archive.
+old_library='$old_library'
+
+# Linker flags that can not go in dependency_libs.
+inherited_linker_flags='$new_inherited_linker_flags'
+
+# Libraries that this one depends upon.
+dependency_libs='$dependency_libs'
+
+# Names of additional weak libraries provided by this library
+weak_library_names='$weak_libs'
+
+# Version information for $libname.
+current=$current
+age=$age
+revision=$revision
+
+# Is this an already installed library?
+installed=$installed
+
+# Should we warn about portability when linking against -modules?
+shouldnotlink=$module
+
+# Files to dlopen/dlpreopen
+dlopen='$dlfiles'
+dlpreopen='$dlprefiles'
+
+# Directory that this library needs to be installed in:
+libdir='$install_libdir'"
+ if test "$installed" = no && test "$need_relink" = yes; then
+ $ECHO >> $output "\
+relink_command=\"$relink_command\""
+ fi
+ done
+ }
+
+ # Do a symbolic link so that the libtool archive can be found in
+ # LD_LIBRARY_PATH before the program is installed.
+ func_show_eval '( cd "$output_objdir" && $RM "$outputname" && $LN_S "../$outputname" "$outputname" )' 'exit $?'
+ ;;
+ esac
+ exit $EXIT_SUCCESS
+}
+
+{ test "$mode" = link || test "$mode" = relink; } &&
+ func_mode_link ${1+"$@"}
+
+
+# func_mode_uninstall arg...
+func_mode_uninstall ()
+{
+ $opt_debug
+ RM="$nonopt"
+ files=
+ rmforce=
+ exit_status=0
+
+ # This variable tells wrapper scripts just to set variables rather
+ # than running their programs.
+ libtool_install_magic="$magic"
+
+ for arg
+ do
+ case $arg in
+ -f) RM="$RM $arg"; rmforce=yes ;;
+ -*) RM="$RM $arg" ;;
+ *) files="$files $arg" ;;
+ esac
+ done
+
+ test -z "$RM" && \
+ func_fatal_help "you must specify an RM program"
+
+ rmdirs=
+
+ origobjdir="$objdir"
+ for file in $files; do
+ func_dirname "$file" "" "."
+ dir="$func_dirname_result"
+ if test "X$dir" = X.; then
+ objdir="$origobjdir"
+ else
+ objdir="$dir/$origobjdir"
+ fi
+ func_basename "$file"
+ name="$func_basename_result"
+ test "$mode" = uninstall && objdir="$dir"
+
+ # Remember objdir for removal later, being careful to avoid duplicates
+ if test "$mode" = clean; then
+ case " $rmdirs " in
+ *" $objdir "*) ;;
+ *) rmdirs="$rmdirs $objdir" ;;
+ esac
+ fi
+
+ # Don't error if the file doesn't exist and rm -f was used.
+ if { test -L "$file"; } >/dev/null 2>&1 ||
+ { test -h "$file"; } >/dev/null 2>&1 ||
+ test -f "$file"; then
+ :
+ elif test -d "$file"; then
+ exit_status=1
+ continue
+ elif test "$rmforce" = yes; then
+ continue
+ fi
+
+ rmfiles="$file"
+
+ case $name in
+ *.la)
+ # Possibly a libtool archive, so verify it.
+ if func_lalib_p "$file"; then
+ func_source $dir/$name
+
+ # Delete the libtool libraries and symlinks.
+ for n in $library_names; do
+ rmfiles="$rmfiles $objdir/$n"
+ done
+ test -n "$old_library" && rmfiles="$rmfiles $objdir/$old_library"
+
+ case "$mode" in
+ clean)
+ case " $library_names " in
+ # " " in the beginning catches empty $dlname
+ *" $dlname "*) ;;
+ *) rmfiles="$rmfiles $objdir/$dlname" ;;
+ esac
+ test -n "$libdir" && rmfiles="$rmfiles $objdir/$name $objdir/${name}i"
+ ;;
+ uninstall)
+ if test -n "$library_names"; then
+ # Do each command in the postuninstall commands.
+ func_execute_cmds "$postuninstall_cmds" 'test "$rmforce" = yes || exit_status=1'
+ fi
+
+ if test -n "$old_library"; then
+ # Do each command in the old_postuninstall commands.
+ func_execute_cmds "$old_postuninstall_cmds" 'test "$rmforce" = yes || exit_status=1'
+ fi
+ # FIXME: should reinstall the best remaining shared library.
+ ;;
+ esac
+ fi
+ ;;
+
+ *.lo)
+ # Possibly a libtool object, so verify it.
+ if func_lalib_p "$file"; then
+
+ # Read the .lo file
+ func_source $dir/$name
+
+ # Add PIC object to the list of files to remove.
+ if test -n "$pic_object" &&
+ test "$pic_object" != none; then
+ rmfiles="$rmfiles $dir/$pic_object"
+ fi
+
+ # Add non-PIC object to the list of files to remove.
+ if test -n "$non_pic_object" &&
+ test "$non_pic_object" != none; then
+ rmfiles="$rmfiles $dir/$non_pic_object"
+ fi
+ fi
+ ;;
+
+ *)
+ if test "$mode" = clean ; then
+ noexename=$name
+ case $file in
+ *.exe)
+ func_stripname '' '.exe' "$file"
+ file=$func_stripname_result
+ func_stripname '' '.exe' "$name"
+ noexename=$func_stripname_result
+ # $file with .exe has already been added to rmfiles,
+ # add $file without .exe
+ rmfiles="$rmfiles $file"
+ ;;
+ esac
+ # Do a test to see if this is a libtool program.
+ if func_ltwrapper_p "$file"; then
+ if func_ltwrapper_executable_p "$file"; then
+ func_ltwrapper_scriptname "$file"
+ relink_command=
+ func_source $func_ltwrapper_scriptname_result
+ rmfiles="$rmfiles $func_ltwrapper_scriptname_result"
+ else
+ relink_command=
+ func_source $dir/$noexename
+ fi
+
+ # note $name still contains .exe if it was in $file originally
+ # as does the version of $file that was added into $rmfiles
+ rmfiles="$rmfiles $objdir/$name $objdir/${name}S.${objext}"
+ if test "$fast_install" = yes && test -n "$relink_command"; then
+ rmfiles="$rmfiles $objdir/lt-$name"
+ fi
+ if test "X$noexename" != "X$name" ; then
+ rmfiles="$rmfiles $objdir/lt-${noexename}.c"
+ fi
+ fi
+ fi
+ ;;
+ esac
+ func_show_eval "$RM $rmfiles" 'exit_status=1'
+ done
+ objdir="$origobjdir"
+
+ # Try to remove the ${objdir}s in the directories where we deleted files
+ for dir in $rmdirs; do
+ if test -d "$dir"; then
+ func_show_eval "rmdir $dir >/dev/null 2>&1"
+ fi
+ done
+
+ exit $exit_status
+}
+
+{ test "$mode" = uninstall || test "$mode" = clean; } &&
+ func_mode_uninstall ${1+"$@"}
+
+test -z "$mode" && {
+ help="$generic_help"
+ func_fatal_help "you must specify a MODE"
+}
+
+test -z "$exec_cmd" && \
+ func_fatal_help "invalid operation mode \`$mode'"
+
+if test -n "$exec_cmd"; then
+ eval exec "$exec_cmd"
+ exit $EXIT_FAILURE
+fi
+
+exit $exit_status
+
+
+# The TAGs below are defined such that we never get into a situation
+# in which we disable both kinds of libraries. Given conflicting
+# choices, we go for a static library, that is the most portable,
+# since we can't tell whether shared libraries were disabled because
+# the user asked for that or because the platform doesn't support
+# them. This is particularly important on AIX, because we don't
+# support having both static and shared libraries enabled at the same
+# time on that platform, so we default to a shared-only configuration.
+# If a disable-shared tag is given, we'll fallback to a static-only
+# configuration. But we'll never go from static-only to shared-only.
+
+# ### BEGIN LIBTOOL TAG CONFIG: disable-shared
+build_libtool_libs=no
+build_old_libs=yes
+# ### END LIBTOOL TAG CONFIG: disable-shared
+
+# ### BEGIN LIBTOOL TAG CONFIG: disable-static
+build_old_libs=`case $build_libtool_libs in yes) echo no;; *) echo yes;; esac`
+# ### END LIBTOOL TAG CONFIG: disable-static
+
+# Local Variables:
+# mode:shell-script
+# sh-indentation:2
+# End:
+# vi:sw=2
+
--- /dev/null
+# ===========================================================================
+# http://www.gnu.org/software/autoconf-archive/ax_openmp.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+# AX_OPENMP([ACTION-IF-FOUND[, ACTION-IF-NOT-FOUND]])
+#
+# DESCRIPTION
+#
+# This macro tries to find out how to compile programs that use OpenMP a
+# standard API and set of compiler directives for parallel programming
+# (see http://www-unix.mcs/)
+#
+# On success, it sets the OPENMP_CFLAGS/OPENMP_CXXFLAGS/OPENMP_F77FLAGS
+# output variable to the flag (e.g. -omp) used both to compile *and* link
+# OpenMP programs in the current language.
+#
+# NOTE: You are assumed to not only compile your program with these flags,
+# but also link it with them as well.
+#
+# If you want to compile everything with OpenMP, you should set:
+#
+# CFLAGS="$CFLAGS $OPENMP_CFLAGS"
+# #OR# CXXFLAGS="$CXXFLAGS $OPENMP_CXXFLAGS"
+# #OR# FFLAGS="$FFLAGS $OPENMP_FFLAGS"
+#
+# (depending on the selected language).
+#
+# The user can override the default choice by setting the corresponding
+# environment variable (e.g. OPENMP_CFLAGS).
+#
+# ACTION-IF-FOUND is a list of shell commands to run if an OpenMP flag is
+# found, and ACTION-IF-NOT-FOUND is a list of commands to run it if it is
+# not found. If ACTION-IF-FOUND is not specified, the default action will
+# define HAVE_OPENMP.
+#
+# LICENSE
+#
+# Copyright (c) 2008 Steven G. Johnson <stevenj@alum.mit.edu>
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
+# Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program. If not, see <http://www.gnu.org/licenses/>.
+#
+# As a special exception, the respective Autoconf Macro's copyright owner
+# gives unlimited permission to copy, distribute and modify the configure
+# scripts that are the output of Autoconf when processing the Macro. You
+# need not follow the terms of the GNU General Public License when using
+# or distributing such scripts, even though portions of the text of the
+# Macro appear in them. The GNU General Public License (GPL) does govern
+# all other use of the material that constitutes the Autoconf Macro.
+#
+# This special exception to the GPL applies to versions of the Autoconf
+# Macro released by the Autoconf Archive. When you make and distribute a
+# modified version of the Autoconf Macro, you may extend this special
+# exception to the GPL to apply to your modified version as well.
+
+#serial 8
+
+AC_DEFUN([AX_OPENMP], [
+AC_PREREQ(2.59) dnl for _AC_LANG_PREFIX
+
+AC_CACHE_CHECK([for OpenMP flag of _AC_LANG compiler], ax_cv_[]_AC_LANG_ABBREV[]_openmp, [save[]_AC_LANG_PREFIX[]FLAGS=$[]_AC_LANG_PREFIX[]FLAGS
+ax_cv_[]_AC_LANG_ABBREV[]_openmp=unknown
+# Flags to try: -fopenmp (gcc), -openmp (icc), -mp (SGI & PGI),
+# -xopenmp (Sun), -omp (Tru64), -qsmp=omp (AIX), none
+ax_openmp_flags="-fopenmp -openmp -mp -xopenmp -omp -qsmp=omp none"
+if test "x$OPENMP_[]_AC_LANG_PREFIX[]FLAGS" != x; then
+ ax_openmp_flags="$OPENMP_[]_AC_LANG_PREFIX[]FLAGS $ax_openmp_flags"
+fi
+for ax_openmp_flag in $ax_openmp_flags; do
+ case $ax_openmp_flag in
+ none) []_AC_LANG_PREFIX[]FLAGS=$save[]_AC_LANG_PREFIX[] ;;
+ *) []_AC_LANG_PREFIX[]FLAGS="$save[]_AC_LANG_PREFIX[]FLAGS $ax_openmp_flag" ;;
+ esac
+ AC_TRY_LINK_FUNC(omp_set_num_threads,
+ [ax_cv_[]_AC_LANG_ABBREV[]_openmp=$ax_openmp_flag; break])
+done
+[]_AC_LANG_PREFIX[]FLAGS=$save[]_AC_LANG_PREFIX[]FLAGS
+])
+if test "x$ax_cv_[]_AC_LANG_ABBREV[]_openmp" = "xunknown"; then
+ m4_default([$2],:)
+else
+ if test "x$ax_cv_[]_AC_LANG_ABBREV[]_openmp" != "xnone"; then
+ OPENMP_[]_AC_LANG_PREFIX[]FLAGS=$ax_cv_[]_AC_LANG_ABBREV[]_openmp
+ fi
+ m4_default([$1], [AC_DEFINE(HAVE_OPENMP,1,[Define if OpenMP is enabled])])
+fi
+])dnl AX_OPENMP
--- /dev/null
+# ===========================================================================
+# http://www.gnu.org/software/autoconf-archive/ax_prefix_config_h.html
+# ===========================================================================
+#
+# SYNOPSIS
+#
+# AX_PREFIX_CONFIG_H [(OUTPUT-HEADER [,PREFIX [,ORIG-HEADER]])]
+#
+# DESCRIPTION
+#
+# This is a new variant from ac_prefix_config_ this one will use a
+# lowercase-prefix if the config-define was starting with a
+# lowercase-char, e.g. "#define const", "#define restrict", or "#define
+# off_t", (and this one can live in another directory, e.g.
+# testpkg/config.h therefore I decided to move the output-header to be the
+# first arg)
+#
+# takes the usual config.h generated header file; looks for each of the
+# generated "#define SOMEDEF" lines, and prefixes the defined name (ie.
+# makes it "#define PREFIX_SOMEDEF". The result is written to the output
+# config.header file. The PREFIX is converted to uppercase for the
+# conversions.
+#
+# Defaults:
+#
+# OUTPUT-HEADER = $PACKAGE-config.h
+# PREFIX = $PACKAGE
+# ORIG-HEADER, from AM_CONFIG_HEADER(config.h)
+#
+# Your configure.ac script should contain both macros in this order, and
+# unlike the earlier variations of this prefix-macro it is okay to place
+# the AX_PREFIX_CONFIG_H call before the AC_OUTPUT invokation.
+#
+# Example:
+#
+# AC_INIT(config.h.in) # config.h.in as created by "autoheader"
+# AM_INIT_AUTOMAKE(testpkg, 0.1.1) # makes #undef VERSION and PACKAGE
+# AM_CONFIG_HEADER(config.h) # prep config.h from config.h.in
+# AX_PREFIX_CONFIG_H(mylib/_config.h) # prep mylib/_config.h from it..
+# AC_MEMORY_H # makes "#undef NEED_MEMORY_H"
+# AC_C_CONST_H # makes "#undef const"
+# AC_OUTPUT(Makefile) # creates the "config.h" now
+# # and also mylib/_config.h
+#
+# if the argument to AX_PREFIX_CONFIG_H would have been omitted then the
+# default outputfile would have been called simply "testpkg-config.h", but
+# even under the name "mylib/_config.h" it contains prefix-defines like
+#
+# #ifndef TESTPKG_VERSION
+# #define TESTPKG_VERSION "0.1.1"
+# #endif
+# #ifndef TESTPKG_NEED_MEMORY_H
+# #define TESTPKG_NEED_MEMORY_H 1
+# #endif
+# #ifndef _testpkg_const
+# #define _testpkg_const _const
+# #endif
+#
+# and this "mylib/_config.h" can be installed along with other
+# header-files, which is most convenient when creating a shared library
+# (that has some headers) where some functionality is dependent on the
+# OS-features detected at compile-time. No need to invent some
+# "mylib-confdefs.h.in" manually. :-)
+#
+# Note that some AC_DEFINEs that end up in the config.h file are actually
+# self-referential - e.g. AC_C_INLINE, AC_C_CONST, and the AC_TYPE_OFF_T
+# say that they "will define inline|const|off_t if the system does not do
+# it by itself". You might want to clean up about these - consider an
+# extra mylib/conf.h that reads something like:
+#
+# #include <mylib/_config.h>
+# #ifndef _testpkg_const
+# #define _testpkg_const const
+# #endif
+#
+# and then start using _testpkg_const in the header files. That is also a
+# good thing to differentiate whether some library-user has starting to
+# take up with a different compiler, so perhaps it could read something
+# like this:
+#
+# #ifdef _MSC_VER
+# #include <mylib/_msvc.h>
+# #else
+# #include <mylib/_config.h>
+# #endif
+# #ifndef _testpkg_const
+# #define _testpkg_const const
+# #endif
+#
+# LICENSE
+#
+# Copyright (c) 2008 Guido U. Draheim <guidod@gmx.de>
+# Copyright (c) 2008 Marten Svantesson
+# Copyright (c) 2008 Gerald Point <Gerald.Point@labri.fr>
+#
+# This program is free software; you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the
+# Free Software Foundation; either version 3 of the License, or (at your
+# option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
+# Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program. If not, see <http://www.gnu.org/licenses/>.
+#
+# As a special exception, the respective Autoconf Macro's copyright owner
+# gives unlimited permission to copy, distribute and modify the configure
+# scripts that are the output of Autoconf when processing the Macro. You
+# need not follow the terms of the GNU General Public License when using
+# or distributing such scripts, even though portions of the text of the
+# Macro appear in them. The GNU General Public License (GPL) does govern
+# all other use of the material that constitutes the Autoconf Macro.
+#
+# This special exception to the GPL applies to versions of the Autoconf
+# Macro released by the Autoconf Archive. When you make and distribute a
+# modified version of the Autoconf Macro, you may extend this special
+# exception to the GPL to apply to your modified version as well.
+
+#serial 11
+
+AC_DEFUN([AX_PREFIX_CONFIG_H],[dnl
+AC_PREREQ([2.62])
+AC_BEFORE([AC_CONFIG_HEADERS],[$0])dnl
+AC_CONFIG_COMMANDS([ifelse($1,,$PACKAGE-config.h,$1)],[dnl
+AS_VAR_PUSHDEF([_OUT],[ac_prefix_conf_OUT])dnl
+AS_VAR_PUSHDEF([_DEF],[ac_prefix_conf_DEF])dnl
+AS_VAR_PUSHDEF([_PKG],[ac_prefix_conf_PKG])dnl
+AS_VAR_PUSHDEF([_LOW],[ac_prefix_conf_LOW])dnl
+AS_VAR_PUSHDEF([_UPP],[ac_prefix_conf_UPP])dnl
+AS_VAR_PUSHDEF([_INP],[ac_prefix_conf_INP])dnl
+m4_pushdef([_script],[conftest.prefix])dnl
+m4_pushdef([_symbol],[m4_cr_Letters[]m4_cr_digits[]_])dnl
+_OUT=`echo ifelse($1, , $PACKAGE-config.h, $1)`
+_DEF=`echo _$_OUT | sed -e "y:m4_cr_letters:m4_cr_LETTERS[]:" -e "s/@<:@^m4_cr_Letters@:>@/_/g"`
+_PKG=`echo ifelse($2, , $PACKAGE, $2)`
+_LOW=`echo _$_PKG | sed -e "y:m4_cr_LETTERS-:m4_cr_letters[]_:"`
+_UPP=`echo $_PKG | sed -e "y:m4_cr_letters-:m4_cr_LETTERS[]_:" -e "/^@<:@m4_cr_digits@:>@/s/^/_/"`
+_INP=`echo "ifelse($3,,,$3)" | sed -e 's/ *//'`
+if test ".$_INP" = "."; then
+ for ac_file in : $CONFIG_HEADERS; do test "_$ac_file" = _: && continue
+ case "$ac_file" in
+ *.h) _INP=$ac_file ;;
+ *)
+ esac
+ test ".$_INP" != "." && break
+ done
+fi
+if test ".$_INP" = "."; then
+ case "$_OUT" in
+ */*) _INP=`basename "$_OUT"`
+ ;;
+ *-*) _INP=`echo "$_OUT" | sed -e "s/@<:@_symbol@:>@*-//"`
+ ;;
+ *) _INP=config.h
+ ;;
+ esac
+fi
+if test -z "$_PKG" ; then
+ AC_MSG_ERROR([no prefix for _PREFIX_PKG_CONFIG_H])
+else
+ if test ! -f "$_INP" ; then if test -f "$srcdir/$_INP" ; then
+ _INP="$srcdir/$_INP"
+ fi fi
+ AC_MSG_NOTICE(creating $_OUT - prefix $_UPP for $_INP defines)
+ if test -f $_INP ; then
+ AS_ECHO(["s/^@%:@undef *\\(@<:@m4_cr_LETTERS[]_@:>@\\)/@%:@undef $_UPP""_\\1/"]) > _script
+ AS_ECHO(["s/^@%:@undef *\\(@<:@m4_cr_letters@:>@\\)/@%:@undef $_LOW""_\\1/"]) >> _script
+ AS_ECHO(["s/^@%:@def[]ine *\\(@<:@m4_cr_LETTERS[]_@:>@@<:@_symbol@:>@*\\)\\(.*\\)/@%:@ifndef $_UPP""_\\1\\"]) >> _script
+ AS_ECHO(["@%:@def[]ine $_UPP""_\\1\\2\\"]) >> _script
+ AS_ECHO(["@%:@endif/"]) >> _script
+ AS_ECHO(["s/^@%:@def[]ine *\\(@<:@m4_cr_letters@:>@@<:@_symbol@:>@*\\)\\(.*\\)/@%:@ifndef $_LOW""_\\1\\"]) >> _script
+ AS_ECHO(["@%:@define $_LOW""_\\1\\2\\"]) >> _script
+ AS_ECHO(["@%:@endif/"]) >> _script
+ # now executing _script on _DEF input to create _OUT output file
+ echo "@%:@ifndef $_DEF" >$tmp/pconfig.h
+ echo "@%:@def[]ine $_DEF 1" >>$tmp/pconfig.h
+ echo ' ' >>$tmp/pconfig.h
+ echo /'*' $_OUT. Generated automatically at end of configure. '*'/ >>$tmp/pconfig.h
+
+ sed -f _script $_INP >>$tmp/pconfig.h
+ echo ' ' >>$tmp/pconfig.h
+ echo '/* once:' $_DEF '*/' >>$tmp/pconfig.h
+ echo "@%:@endif" >>$tmp/pconfig.h
+ if cmp -s $_OUT $tmp/pconfig.h 2>/dev/null; then
+ AC_MSG_NOTICE([$_OUT is unchanged])
+ else
+ ac_dir=`AS_DIRNAME(["$_OUT"])`
+ AS_MKDIR_P(["$ac_dir"])
+ rm -f "$_OUT"
+ mv $tmp/pconfig.h "$_OUT"
+ fi
+ cp _script _configs.sed
+ else
+ AC_MSG_ERROR([input file $_INP does not exist - skip generating $_OUT])
+ fi
+ rm -f conftest.*
+fi
+m4_popdef([_symbol])dnl
+m4_popdef([_script])dnl
+AS_VAR_POPDEF([_INP])dnl
+AS_VAR_POPDEF([_UPP])dnl
+AS_VAR_POPDEF([_LOW])dnl
+AS_VAR_POPDEF([_PKG])dnl
+AS_VAR_POPDEF([_DEF])dnl
+AS_VAR_POPDEF([_OUT])dnl
+],[PACKAGE="$PACKAGE"])])
--- /dev/null
+# libtool.m4 - Configure libtool for the host system. -*-Autoconf-*-
+#
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005,
+# 2006, 2007, 2008 Free Software Foundation, Inc.
+# Written by Gordon Matzigkeit, 1996
+#
+# This file is free software; the Free Software Foundation gives
+# unlimited permission to copy and/or distribute it, with or without
+# modifications, as long as this notice is preserved.
+
+m4_define([_LT_COPYING], [dnl
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005,
+# 2006, 2007, 2008 Free Software Foundation, Inc.
+# Written by Gordon Matzigkeit, 1996
+#
+# This file is part of GNU Libtool.
+#
+# GNU Libtool is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License as
+# published by the Free Software Foundation; either version 2 of
+# the License, or (at your option) any later version.
+#
+# As a special exception to the GNU General Public License,
+# if you distribute this file as part of a program or library that
+# is built using GNU Libtool, you may include this file under the
+# same distribution terms that you use for the rest of that program.
+#
+# GNU Libtool is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GNU Libtool; see the file COPYING. If not, a copy
+# can be downloaded from http://www.gnu.org/licenses/gpl.html, or
+# obtained by writing to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+])
+
+# serial 56 LT_INIT
+
+
+# LT_PREREQ(VERSION)
+# ------------------
+# Complain and exit if this libtool version is less that VERSION.
+m4_defun([LT_PREREQ],
+[m4_if(m4_version_compare(m4_defn([LT_PACKAGE_VERSION]), [$1]), -1,
+ [m4_default([$3],
+ [m4_fatal([Libtool version $1 or higher is required],
+ 63)])],
+ [$2])])
+
+
+# _LT_CHECK_BUILDDIR
+# ------------------
+# Complain if the absolute build directory name contains unusual characters
+m4_defun([_LT_CHECK_BUILDDIR],
+[case `pwd` in
+ *\ * | *\ *)
+ AC_MSG_WARN([Libtool does not cope well with whitespace in `pwd`]) ;;
+esac
+])
+
+
+# LT_INIT([OPTIONS])
+# ------------------
+AC_DEFUN([LT_INIT],
+[AC_PREREQ([2.58])dnl We use AC_INCLUDES_DEFAULT
+AC_BEFORE([$0], [LT_LANG])dnl
+AC_BEFORE([$0], [LT_OUTPUT])dnl
+AC_BEFORE([$0], [LTDL_INIT])dnl
+m4_require([_LT_CHECK_BUILDDIR])dnl
+
+dnl Autoconf doesn't catch unexpanded LT_ macros by default:
+m4_pattern_forbid([^_?LT_[A-Z_]+$])dnl
+m4_pattern_allow([^(_LT_EOF|LT_DLGLOBAL|LT_DLLAZY_OR_NOW|LT_MULTI_MODULE)$])dnl
+dnl aclocal doesn't pull ltoptions.m4, ltsugar.m4, or ltversion.m4
+dnl unless we require an AC_DEFUNed macro:
+AC_REQUIRE([LTOPTIONS_VERSION])dnl
+AC_REQUIRE([LTSUGAR_VERSION])dnl
+AC_REQUIRE([LTVERSION_VERSION])dnl
+AC_REQUIRE([LTOBSOLETE_VERSION])dnl
+m4_require([_LT_PROG_LTMAIN])dnl
+
+dnl Parse OPTIONS
+_LT_SET_OPTIONS([$0], [$1])
+
+# This can be used to rebuild libtool when needed
+LIBTOOL_DEPS="$ltmain"
+
+# Always use our own libtool.
+LIBTOOL='$(SHELL) $(top_builddir)/libtool'
+AC_SUBST(LIBTOOL)dnl
+
+_LT_SETUP
+
+# Only expand once:
+m4_define([LT_INIT])
+])# LT_INIT
+
+# Old names:
+AU_ALIAS([AC_PROG_LIBTOOL], [LT_INIT])
+AU_ALIAS([AM_PROG_LIBTOOL], [LT_INIT])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_PROG_LIBTOOL], [])
+dnl AC_DEFUN([AM_PROG_LIBTOOL], [])
+
+
+# _LT_CC_BASENAME(CC)
+# -------------------
+# Calculate cc_basename. Skip known compiler wrappers and cross-prefix.
+m4_defun([_LT_CC_BASENAME],
+[for cc_temp in $1""; do
+ case $cc_temp in
+ compile | *[[\\/]]compile | ccache | *[[\\/]]ccache ) ;;
+ distcc | *[[\\/]]distcc | purify | *[[\\/]]purify ) ;;
+ \-*) ;;
+ *) break;;
+ esac
+done
+cc_basename=`$ECHO "X$cc_temp" | $Xsed -e 's%.*/%%' -e "s%^$host_alias-%%"`
+])
+
+
+# _LT_FILEUTILS_DEFAULTS
+# ----------------------
+# It is okay to use these file commands and assume they have been set
+# sensibly after `m4_require([_LT_FILEUTILS_DEFAULTS])'.
+m4_defun([_LT_FILEUTILS_DEFAULTS],
+[: ${CP="cp -f"}
+: ${MV="mv -f"}
+: ${RM="rm -f"}
+])# _LT_FILEUTILS_DEFAULTS
+
+
+# _LT_SETUP
+# ---------
+m4_defun([_LT_SETUP],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+AC_REQUIRE([AC_CANONICAL_BUILD])dnl
+_LT_DECL([], [host_alias], [0], [The host system])dnl
+_LT_DECL([], [host], [0])dnl
+_LT_DECL([], [host_os], [0])dnl
+dnl
+_LT_DECL([], [build_alias], [0], [The build system])dnl
+_LT_DECL([], [build], [0])dnl
+_LT_DECL([], [build_os], [0])dnl
+dnl
+AC_REQUIRE([AC_PROG_CC])dnl
+AC_REQUIRE([LT_PATH_LD])dnl
+AC_REQUIRE([LT_PATH_NM])dnl
+dnl
+AC_REQUIRE([AC_PROG_LN_S])dnl
+test -z "$LN_S" && LN_S="ln -s"
+_LT_DECL([], [LN_S], [1], [Whether we need soft or hard links])dnl
+dnl
+AC_REQUIRE([LT_CMD_MAX_LEN])dnl
+_LT_DECL([objext], [ac_objext], [0], [Object file suffix (normally "o")])dnl
+_LT_DECL([], [exeext], [0], [Executable file suffix (normally "")])dnl
+dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_CHECK_SHELL_FEATURES])dnl
+m4_require([_LT_CMD_RELOAD])dnl
+m4_require([_LT_CHECK_MAGIC_METHOD])dnl
+m4_require([_LT_CMD_OLD_ARCHIVE])dnl
+m4_require([_LT_CMD_GLOBAL_SYMBOLS])dnl
+
+_LT_CONFIG_LIBTOOL_INIT([
+# See if we are running on zsh, and set the options which allow our
+# commands through without removal of \ escapes INIT.
+if test -n "\${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+fi
+])
+if test -n "${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+fi
+
+_LT_CHECK_OBJDIR
+
+m4_require([_LT_TAG_COMPILER])dnl
+_LT_PROG_ECHO_BACKSLASH
+
+case $host_os in
+aix3*)
+ # AIX sometimes has problems with the GCC collect2 program. For some
+ # reason, if we set the COLLECT_NAMES environment variable, the problems
+ # vanish in a puff of smoke.
+ if test "X${COLLECT_NAMES+set}" != Xset; then
+ COLLECT_NAMES=
+ export COLLECT_NAMES
+ fi
+ ;;
+esac
+
+# Sed substitution that helps us do robust quoting. It backslashifies
+# metacharacters that are still active within double-quoted strings.
+sed_quote_subst='s/\([["`$\\]]\)/\\\1/g'
+
+# Same as above, but do not quote variable references.
+double_quote_subst='s/\([["`\\]]\)/\\\1/g'
+
+# Sed substitution to delay expansion of an escaped shell variable in a
+# double_quote_subst'ed string.
+delay_variable_subst='s/\\\\\\\\\\\$/\\\\\\$/g'
+
+# Sed substitution to delay expansion of an escaped single quote.
+delay_single_quote_subst='s/'\''/'\'\\\\\\\'\''/g'
+
+# Sed substitution to avoid accidental globbing in evaled expressions
+no_glob_subst='s/\*/\\\*/g'
+
+# Global variables:
+ofile=libtool
+can_build_shared=yes
+
+# All known linkers require a `.a' archive for static linking (except MSVC,
+# which needs '.lib').
+libext=a
+
+with_gnu_ld="$lt_cv_prog_gnu_ld"
+
+old_CC="$CC"
+old_CFLAGS="$CFLAGS"
+
+# Set sane defaults for various variables
+test -z "$CC" && CC=cc
+test -z "$LTCC" && LTCC=$CC
+test -z "$LTCFLAGS" && LTCFLAGS=$CFLAGS
+test -z "$LD" && LD=ld
+test -z "$ac_objext" && ac_objext=o
+
+_LT_CC_BASENAME([$compiler])
+
+# Only perform the check for file, if the check method requires it
+test -z "$MAGIC_CMD" && MAGIC_CMD=file
+case $deplibs_check_method in
+file_magic*)
+ if test "$file_magic_cmd" = '$MAGIC_CMD'; then
+ _LT_PATH_MAGIC
+ fi
+ ;;
+esac
+
+# Use C for the default configuration in the libtool script
+LT_SUPPORTED_TAG([CC])
+_LT_LANG_C_CONFIG
+_LT_LANG_DEFAULT_CONFIG
+_LT_CONFIG_COMMANDS
+])# _LT_SETUP
+
+
+# _LT_PROG_LTMAIN
+# ---------------
+# Note that this code is called both from `configure', and `config.status'
+# now that we use AC_CONFIG_COMMANDS to generate libtool. Notably,
+# `config.status' has no value for ac_aux_dir unless we are using Automake,
+# so we pass a copy along to make sure it has a sensible value anyway.
+m4_defun([_LT_PROG_LTMAIN],
+[m4_ifdef([AC_REQUIRE_AUX_FILE], [AC_REQUIRE_AUX_FILE([ltmain.sh])])dnl
+_LT_CONFIG_LIBTOOL_INIT([ac_aux_dir='$ac_aux_dir'])
+ltmain="$ac_aux_dir/ltmain.sh"
+])# _LT_PROG_LTMAIN
+
+
+## ------------------------------------- ##
+## Accumulate code for creating libtool. ##
+## ------------------------------------- ##
+
+# So that we can recreate a full libtool script including additional
+# tags, we accumulate the chunks of code to send to AC_CONFIG_COMMANDS
+# in macros and then make a single call at the end using the `libtool'
+# label.
+
+
+# _LT_CONFIG_LIBTOOL_INIT([INIT-COMMANDS])
+# ----------------------------------------
+# Register INIT-COMMANDS to be passed to AC_CONFIG_COMMANDS later.
+m4_define([_LT_CONFIG_LIBTOOL_INIT],
+[m4_ifval([$1],
+ [m4_append([_LT_OUTPUT_LIBTOOL_INIT],
+ [$1
+])])])
+
+# Initialize.
+m4_define([_LT_OUTPUT_LIBTOOL_INIT])
+
+
+# _LT_CONFIG_LIBTOOL([COMMANDS])
+# ------------------------------
+# Register COMMANDS to be passed to AC_CONFIG_COMMANDS later.
+m4_define([_LT_CONFIG_LIBTOOL],
+[m4_ifval([$1],
+ [m4_append([_LT_OUTPUT_LIBTOOL_COMMANDS],
+ [$1
+])])])
+
+# Initialize.
+m4_define([_LT_OUTPUT_LIBTOOL_COMMANDS])
+
+
+# _LT_CONFIG_SAVE_COMMANDS([COMMANDS], [INIT_COMMANDS])
+# -----------------------------------------------------
+m4_defun([_LT_CONFIG_SAVE_COMMANDS],
+[_LT_CONFIG_LIBTOOL([$1])
+_LT_CONFIG_LIBTOOL_INIT([$2])
+])
+
+
+# _LT_FORMAT_COMMENT([COMMENT])
+# -----------------------------
+# Add leading comment marks to the start of each line, and a trailing
+# full-stop to the whole comment if one is not present already.
+m4_define([_LT_FORMAT_COMMENT],
+[m4_ifval([$1], [
+m4_bpatsubst([m4_bpatsubst([$1], [^ *], [# ])],
+ [['`$\]], [\\\&])]m4_bmatch([$1], [[!?.]$], [], [.])
+)])
+
+
+
+## ------------------------ ##
+## FIXME: Eliminate VARNAME ##
+## ------------------------ ##
+
+
+# _LT_DECL([CONFIGNAME], VARNAME, VALUE, [DESCRIPTION], [IS-TAGGED?])
+# -------------------------------------------------------------------
+# CONFIGNAME is the name given to the value in the libtool script.
+# VARNAME is the (base) name used in the configure script.
+# VALUE may be 0, 1 or 2 for a computed quote escaped value based on
+# VARNAME. Any other value will be used directly.
+m4_define([_LT_DECL],
+[lt_if_append_uniq([lt_decl_varnames], [$2], [, ],
+ [lt_dict_add_subkey([lt_decl_dict], [$2], [libtool_name],
+ [m4_ifval([$1], [$1], [$2])])
+ lt_dict_add_subkey([lt_decl_dict], [$2], [value], [$3])
+ m4_ifval([$4],
+ [lt_dict_add_subkey([lt_decl_dict], [$2], [description], [$4])])
+ lt_dict_add_subkey([lt_decl_dict], [$2],
+ [tagged?], [m4_ifval([$5], [yes], [no])])])
+])
+
+
+# _LT_TAGDECL([CONFIGNAME], VARNAME, VALUE, [DESCRIPTION])
+# --------------------------------------------------------
+m4_define([_LT_TAGDECL], [_LT_DECL([$1], [$2], [$3], [$4], [yes])])
+
+
+# lt_decl_tag_varnames([SEPARATOR], [VARNAME1...])
+# ------------------------------------------------
+m4_define([lt_decl_tag_varnames],
+[_lt_decl_filter([tagged?], [yes], $@)])
+
+
+# _lt_decl_filter(SUBKEY, VALUE, [SEPARATOR], [VARNAME1..])
+# ---------------------------------------------------------
+m4_define([_lt_decl_filter],
+[m4_case([$#],
+ [0], [m4_fatal([$0: too few arguments: $#])],
+ [1], [m4_fatal([$0: too few arguments: $#: $1])],
+ [2], [lt_dict_filter([lt_decl_dict], [$1], [$2], [], lt_decl_varnames)],
+ [3], [lt_dict_filter([lt_decl_dict], [$1], [$2], [$3], lt_decl_varnames)],
+ [lt_dict_filter([lt_decl_dict], $@)])[]dnl
+])
+
+
+# lt_decl_quote_varnames([SEPARATOR], [VARNAME1...])
+# --------------------------------------------------
+m4_define([lt_decl_quote_varnames],
+[_lt_decl_filter([value], [1], $@)])
+
+
+# lt_decl_dquote_varnames([SEPARATOR], [VARNAME1...])
+# ---------------------------------------------------
+m4_define([lt_decl_dquote_varnames],
+[_lt_decl_filter([value], [2], $@)])
+
+
+# lt_decl_varnames_tagged([SEPARATOR], [VARNAME1...])
+# ---------------------------------------------------
+m4_define([lt_decl_varnames_tagged],
+[m4_assert([$# <= 2])dnl
+_$0(m4_quote(m4_default([$1], [[, ]])),
+ m4_ifval([$2], [[$2]], [m4_dquote(lt_decl_tag_varnames)]),
+ m4_split(m4_normalize(m4_quote(_LT_TAGS)), [ ]))])
+m4_define([_lt_decl_varnames_tagged],
+[m4_ifval([$3], [lt_combine([$1], [$2], [_], $3)])])
+
+
+# lt_decl_all_varnames([SEPARATOR], [VARNAME1...])
+# ------------------------------------------------
+m4_define([lt_decl_all_varnames],
+[_$0(m4_quote(m4_default([$1], [[, ]])),
+ m4_if([$2], [],
+ m4_quote(lt_decl_varnames),
+ m4_quote(m4_shift($@))))[]dnl
+])
+m4_define([_lt_decl_all_varnames],
+[lt_join($@, lt_decl_varnames_tagged([$1],
+ lt_decl_tag_varnames([[, ]], m4_shift($@))))dnl
+])
+
+
+# _LT_CONFIG_STATUS_DECLARE([VARNAME])
+# ------------------------------------
+# Quote a variable value, and forward it to `config.status' so that its
+# declaration there will have the same value as in `configure'. VARNAME
+# must have a single quote delimited value for this to work.
+m4_define([_LT_CONFIG_STATUS_DECLARE],
+[$1='`$ECHO "X$][$1" | $Xsed -e "$delay_single_quote_subst"`'])
+
+
+# _LT_CONFIG_STATUS_DECLARATIONS
+# ------------------------------
+# We delimit libtool config variables with single quotes, so when
+# we write them to config.status, we have to be sure to quote all
+# embedded single quotes properly. In configure, this macro expands
+# each variable declared with _LT_DECL (and _LT_TAGDECL) into:
+#
+# <var>='`$ECHO "X$<var>" | $Xsed -e "$delay_single_quote_subst"`'
+m4_defun([_LT_CONFIG_STATUS_DECLARATIONS],
+[m4_foreach([_lt_var], m4_quote(lt_decl_all_varnames),
+ [m4_n([_LT_CONFIG_STATUS_DECLARE(_lt_var)])])])
+
+
+# _LT_LIBTOOL_TAGS
+# ----------------
+# Output comment and list of tags supported by the script
+m4_defun([_LT_LIBTOOL_TAGS],
+[_LT_FORMAT_COMMENT([The names of the tagged configurations supported by this script])dnl
+available_tags="_LT_TAGS"dnl
+])
+
+
+# _LT_LIBTOOL_DECLARE(VARNAME, [TAG])
+# -----------------------------------
+# Extract the dictionary values for VARNAME (optionally with TAG) and
+# expand to a commented shell variable setting:
+#
+# # Some comment about what VAR is for.
+# visible_name=$lt_internal_name
+m4_define([_LT_LIBTOOL_DECLARE],
+[_LT_FORMAT_COMMENT(m4_quote(lt_dict_fetch([lt_decl_dict], [$1],
+ [description])))[]dnl
+m4_pushdef([_libtool_name],
+ m4_quote(lt_dict_fetch([lt_decl_dict], [$1], [libtool_name])))[]dnl
+m4_case(m4_quote(lt_dict_fetch([lt_decl_dict], [$1], [value])),
+ [0], [_libtool_name=[$]$1],
+ [1], [_libtool_name=$lt_[]$1],
+ [2], [_libtool_name=$lt_[]$1],
+ [_libtool_name=lt_dict_fetch([lt_decl_dict], [$1], [value])])[]dnl
+m4_ifval([$2], [_$2])[]m4_popdef([_libtool_name])[]dnl
+])
+
+
+# _LT_LIBTOOL_CONFIG_VARS
+# -----------------------
+# Produce commented declarations of non-tagged libtool config variables
+# suitable for insertion in the LIBTOOL CONFIG section of the `libtool'
+# script. Tagged libtool config variables (even for the LIBTOOL CONFIG
+# section) are produced by _LT_LIBTOOL_TAG_VARS.
+m4_defun([_LT_LIBTOOL_CONFIG_VARS],
+[m4_foreach([_lt_var],
+ m4_quote(_lt_decl_filter([tagged?], [no], [], lt_decl_varnames)),
+ [m4_n([_LT_LIBTOOL_DECLARE(_lt_var)])])])
+
+
+# _LT_LIBTOOL_TAG_VARS(TAG)
+# -------------------------
+m4_define([_LT_LIBTOOL_TAG_VARS],
+[m4_foreach([_lt_var], m4_quote(lt_decl_tag_varnames),
+ [m4_n([_LT_LIBTOOL_DECLARE(_lt_var, [$1])])])])
+
+
+# _LT_TAGVAR(VARNAME, [TAGNAME])
+# ------------------------------
+m4_define([_LT_TAGVAR], [m4_ifval([$2], [$1_$2], [$1])])
+
+
+# _LT_CONFIG_COMMANDS
+# -------------------
+# Send accumulated output to $CONFIG_STATUS. Thanks to the lists of
+# variables for single and double quote escaping we saved from calls
+# to _LT_DECL, we can put quote escaped variables declarations
+# into `config.status', and then the shell code to quote escape them in
+# for loops in `config.status'. Finally, any additional code accumulated
+# from calls to _LT_CONFIG_LIBTOOL_INIT is expanded.
+m4_defun([_LT_CONFIG_COMMANDS],
+[AC_PROVIDE_IFELSE([LT_OUTPUT],
+ dnl If the libtool generation code has been placed in $CONFIG_LT,
+ dnl instead of duplicating it all over again into config.status,
+ dnl then we will have config.status run $CONFIG_LT later, so it
+ dnl needs to know what name is stored there:
+ [AC_CONFIG_COMMANDS([libtool],
+ [$SHELL $CONFIG_LT || AS_EXIT(1)], [CONFIG_LT='$CONFIG_LT'])],
+ dnl If the libtool generation code is destined for config.status,
+ dnl expand the accumulated commands and init code now:
+ [AC_CONFIG_COMMANDS([libtool],
+ [_LT_OUTPUT_LIBTOOL_COMMANDS], [_LT_OUTPUT_LIBTOOL_COMMANDS_INIT])])
+])#_LT_CONFIG_COMMANDS
+
+
+# Initialize.
+m4_define([_LT_OUTPUT_LIBTOOL_COMMANDS_INIT],
+[
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+sed_quote_subst='$sed_quote_subst'
+double_quote_subst='$double_quote_subst'
+delay_variable_subst='$delay_variable_subst'
+_LT_CONFIG_STATUS_DECLARATIONS
+LTCC='$LTCC'
+LTCFLAGS='$LTCFLAGS'
+compiler='$compiler_DEFAULT'
+
+# Quote evaled strings.
+for var in lt_decl_all_varnames([[ \
+]], lt_decl_quote_varnames); do
+ case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in
+ *[[\\\\\\\`\\"\\\$]]*)
+ eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$sed_quote_subst\\"\\\`\\\\\\""
+ ;;
+ *)
+ eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\""
+ ;;
+ esac
+done
+
+# Double-quote double-evaled strings.
+for var in lt_decl_all_varnames([[ \
+]], lt_decl_dquote_varnames); do
+ case \`eval \\\\\$ECHO "X\\\\\$\$var"\` in
+ *[[\\\\\\\`\\"\\\$]]*)
+ eval "lt_\$var=\\\\\\"\\\`\\\$ECHO \\"X\\\$\$var\\" | \\\$Xsed -e \\"\\\$double_quote_subst\\" -e \\"\\\$sed_quote_subst\\" -e \\"\\\$delay_variable_subst\\"\\\`\\\\\\""
+ ;;
+ *)
+ eval "lt_\$var=\\\\\\"\\\$\$var\\\\\\""
+ ;;
+ esac
+done
+
+# Fix-up fallback echo if it was mangled by the above quoting rules.
+case \$lt_ECHO in
+*'\\\[$]0 --fallback-echo"')dnl "
+ lt_ECHO=\`\$ECHO "X\$lt_ECHO" | \$Xsed -e 's/\\\\\\\\\\\\\\\[$]0 --fallback-echo"\[$]/\[$]0 --fallback-echo"/'\`
+ ;;
+esac
+
+_LT_OUTPUT_LIBTOOL_INIT
+])
+
+
+# LT_OUTPUT
+# ---------
+# This macro allows early generation of the libtool script (before
+# AC_OUTPUT is called), incase it is used in configure for compilation
+# tests.
+AC_DEFUN([LT_OUTPUT],
+[: ${CONFIG_LT=./config.lt}
+AC_MSG_NOTICE([creating $CONFIG_LT])
+cat >"$CONFIG_LT" <<_LTEOF
+#! $SHELL
+# Generated by $as_me.
+# Run this file to recreate a libtool stub with the current configuration.
+
+lt_cl_silent=false
+SHELL=\${CONFIG_SHELL-$SHELL}
+_LTEOF
+
+cat >>"$CONFIG_LT" <<\_LTEOF
+AS_SHELL_SANITIZE
+_AS_PREPARE
+
+exec AS_MESSAGE_FD>&1
+exec AS_MESSAGE_LOG_FD>>config.log
+{
+ echo
+ AS_BOX([Running $as_me.])
+} >&AS_MESSAGE_LOG_FD
+
+lt_cl_help="\
+\`$as_me' creates a local libtool stub from the current configuration,
+for use in further configure time tests before the real libtool is
+generated.
+
+Usage: $[0] [[OPTIONS]]
+
+ -h, --help print this help, then exit
+ -V, --version print version number, then exit
+ -q, --quiet do not print progress messages
+ -d, --debug don't remove temporary files
+
+Report bugs to <bug-libtool@gnu.org>."
+
+lt_cl_version="\
+m4_ifset([AC_PACKAGE_NAME], [AC_PACKAGE_NAME ])config.lt[]dnl
+m4_ifset([AC_PACKAGE_VERSION], [ AC_PACKAGE_VERSION])
+configured by $[0], generated by m4_PACKAGE_STRING.
+
+Copyright (C) 2008 Free Software Foundation, Inc.
+This config.lt script is free software; the Free Software Foundation
+gives unlimited permision to copy, distribute and modify it."
+
+while test $[#] != 0
+do
+ case $[1] in
+ --version | --v* | -V )
+ echo "$lt_cl_version"; exit 0 ;;
+ --help | --h* | -h )
+ echo "$lt_cl_help"; exit 0 ;;
+ --debug | --d* | -d )
+ debug=: ;;
+ --quiet | --q* | --silent | --s* | -q )
+ lt_cl_silent=: ;;
+
+ -*) AC_MSG_ERROR([unrecognized option: $[1]
+Try \`$[0] --help' for more information.]) ;;
+
+ *) AC_MSG_ERROR([unrecognized argument: $[1]
+Try \`$[0] --help' for more information.]) ;;
+ esac
+ shift
+done
+
+if $lt_cl_silent; then
+ exec AS_MESSAGE_FD>/dev/null
+fi
+_LTEOF
+
+cat >>"$CONFIG_LT" <<_LTEOF
+_LT_OUTPUT_LIBTOOL_COMMANDS_INIT
+_LTEOF
+
+cat >>"$CONFIG_LT" <<\_LTEOF
+AC_MSG_NOTICE([creating $ofile])
+_LT_OUTPUT_LIBTOOL_COMMANDS
+AS_EXIT(0)
+_LTEOF
+chmod +x "$CONFIG_LT"
+
+# configure is writing to config.log, but config.lt does its own redirection,
+# appending to config.log, which fails on DOS, as config.log is still kept
+# open by configure. Here we exec the FD to /dev/null, effectively closing
+# config.log, so it can be properly (re)opened and appended to by config.lt.
+if test "$no_create" != yes; then
+ lt_cl_success=:
+ test "$silent" = yes &&
+ lt_config_lt_args="$lt_config_lt_args --quiet"
+ exec AS_MESSAGE_LOG_FD>/dev/null
+ $SHELL "$CONFIG_LT" $lt_config_lt_args || lt_cl_success=false
+ exec AS_MESSAGE_LOG_FD>>config.log
+ $lt_cl_success || AS_EXIT(1)
+fi
+])# LT_OUTPUT
+
+
+# _LT_CONFIG(TAG)
+# ---------------
+# If TAG is the built-in tag, create an initial libtool script with a
+# default configuration from the untagged config vars. Otherwise add code
+# to config.status for appending the configuration named by TAG from the
+# matching tagged config vars.
+m4_defun([_LT_CONFIG],
+[m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+_LT_CONFIG_SAVE_COMMANDS([
+ m4_define([_LT_TAG], m4_if([$1], [], [C], [$1]))dnl
+ m4_if(_LT_TAG, [C], [
+ # See if we are running on zsh, and set the options which allow our
+ # commands through without removal of \ escapes.
+ if test -n "${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+ fi
+
+ cfgfile="${ofile}T"
+ trap "$RM \"$cfgfile\"; exit 1" 1 2 15
+ $RM "$cfgfile"
+
+ cat <<_LT_EOF >> "$cfgfile"
+#! $SHELL
+
+# `$ECHO "$ofile" | sed 's%^.*/%%'` - Provide generalized library-building support services.
+# Generated automatically by $as_me ($PACKAGE$TIMESTAMP) $VERSION
+# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
+# NOTE: Changes made to this file will be lost: look at ltmain.sh.
+#
+_LT_COPYING
+_LT_LIBTOOL_TAGS
+
+# ### BEGIN LIBTOOL CONFIG
+_LT_LIBTOOL_CONFIG_VARS
+_LT_LIBTOOL_TAG_VARS
+# ### END LIBTOOL CONFIG
+
+_LT_EOF
+
+ case $host_os in
+ aix3*)
+ cat <<\_LT_EOF >> "$cfgfile"
+# AIX sometimes has problems with the GCC collect2 program. For some
+# reason, if we set the COLLECT_NAMES environment variable, the problems
+# vanish in a puff of smoke.
+if test "X${COLLECT_NAMES+set}" != Xset; then
+ COLLECT_NAMES=
+ export COLLECT_NAMES
+fi
+_LT_EOF
+ ;;
+ esac
+
+ _LT_PROG_LTMAIN
+
+ # We use sed instead of cat because bash on DJGPP gets confused if
+ # if finds mixed CR/LF and LF-only lines. Since sed operates in
+ # text mode, it properly converts lines to CR/LF. This bash problem
+ # is reportedly fixed, but why not run on old versions too?
+ sed '/^# Generated shell functions inserted here/q' "$ltmain" >> "$cfgfile" \
+ || (rm -f "$cfgfile"; exit 1)
+
+ _LT_PROG_XSI_SHELLFNS
+
+ sed -n '/^# Generated shell functions inserted here/,$p' "$ltmain" >> "$cfgfile" \
+ || (rm -f "$cfgfile"; exit 1)
+
+ mv -f "$cfgfile" "$ofile" ||
+ (rm -f "$ofile" && cp "$cfgfile" "$ofile" && rm -f "$cfgfile")
+ chmod +x "$ofile"
+],
+[cat <<_LT_EOF >> "$ofile"
+
+dnl Unfortunately we have to use $1 here, since _LT_TAG is not expanded
+dnl in a comment (ie after a #).
+# ### BEGIN LIBTOOL TAG CONFIG: $1
+_LT_LIBTOOL_TAG_VARS(_LT_TAG)
+# ### END LIBTOOL TAG CONFIG: $1
+_LT_EOF
+])dnl /m4_if
+],
+[m4_if([$1], [], [
+ PACKAGE='$PACKAGE'
+ VERSION='$VERSION'
+ TIMESTAMP='$TIMESTAMP'
+ RM='$RM'
+ ofile='$ofile'], [])
+])dnl /_LT_CONFIG_SAVE_COMMANDS
+])# _LT_CONFIG
+
+
+# LT_SUPPORTED_TAG(TAG)
+# ---------------------
+# Trace this macro to discover what tags are supported by the libtool
+# --tag option, using:
+# autoconf --trace 'LT_SUPPORTED_TAG:$1'
+AC_DEFUN([LT_SUPPORTED_TAG], [])
+
+
+# C support is built-in for now
+m4_define([_LT_LANG_C_enabled], [])
+m4_define([_LT_TAGS], [])
+
+
+# LT_LANG(LANG)
+# -------------
+# Enable libtool support for the given language if not already enabled.
+AC_DEFUN([LT_LANG],
+[AC_BEFORE([$0], [LT_OUTPUT])dnl
+m4_case([$1],
+ [C], [_LT_LANG(C)],
+ [C++], [_LT_LANG(CXX)],
+ [Java], [_LT_LANG(GCJ)],
+ [Fortran 77], [_LT_LANG(F77)],
+ [Fortran], [_LT_LANG(FC)],
+ [Windows Resource], [_LT_LANG(RC)],
+ [m4_ifdef([_LT_LANG_]$1[_CONFIG],
+ [_LT_LANG($1)],
+ [m4_fatal([$0: unsupported language: "$1"])])])dnl
+])# LT_LANG
+
+
+# _LT_LANG(LANGNAME)
+# ------------------
+m4_defun([_LT_LANG],
+[m4_ifdef([_LT_LANG_]$1[_enabled], [],
+ [LT_SUPPORTED_TAG([$1])dnl
+ m4_append([_LT_TAGS], [$1 ])dnl
+ m4_define([_LT_LANG_]$1[_enabled], [])dnl
+ _LT_LANG_$1_CONFIG($1)])dnl
+])# _LT_LANG
+
+
+# _LT_LANG_DEFAULT_CONFIG
+# -----------------------
+m4_defun([_LT_LANG_DEFAULT_CONFIG],
+[AC_PROVIDE_IFELSE([AC_PROG_CXX],
+ [LT_LANG(CXX)],
+ [m4_define([AC_PROG_CXX], defn([AC_PROG_CXX])[LT_LANG(CXX)])])
+
+AC_PROVIDE_IFELSE([AC_PROG_F77],
+ [LT_LANG(F77)],
+ [m4_define([AC_PROG_F77], defn([AC_PROG_F77])[LT_LANG(F77)])])
+
+AC_PROVIDE_IFELSE([AC_PROG_FC],
+ [LT_LANG(FC)],
+ [m4_define([AC_PROG_FC], defn([AC_PROG_FC])[LT_LANG(FC)])])
+
+dnl The call to [A][M_PROG_GCJ] is quoted like that to stop aclocal
+dnl pulling things in needlessly.
+AC_PROVIDE_IFELSE([AC_PROG_GCJ],
+ [LT_LANG(GCJ)],
+ [AC_PROVIDE_IFELSE([A][M_PROG_GCJ],
+ [LT_LANG(GCJ)],
+ [AC_PROVIDE_IFELSE([LT_PROG_GCJ],
+ [LT_LANG(GCJ)],
+ [m4_ifdef([AC_PROG_GCJ],
+ [m4_define([AC_PROG_GCJ], defn([AC_PROG_GCJ])[LT_LANG(GCJ)])])
+ m4_ifdef([A][M_PROG_GCJ],
+ [m4_define([A][M_PROG_GCJ], defn([A][M_PROG_GCJ])[LT_LANG(GCJ)])])
+ m4_ifdef([LT_PROG_GCJ],
+ [m4_define([LT_PROG_GCJ], defn([LT_PROG_GCJ])[LT_LANG(GCJ)])])])])])
+
+AC_PROVIDE_IFELSE([LT_PROG_RC],
+ [LT_LANG(RC)],
+ [m4_define([LT_PROG_RC], defn([LT_PROG_RC])[LT_LANG(RC)])])
+])# _LT_LANG_DEFAULT_CONFIG
+
+# Obsolete macros:
+AU_DEFUN([AC_LIBTOOL_CXX], [LT_LANG(C++)])
+AU_DEFUN([AC_LIBTOOL_F77], [LT_LANG(Fortran 77)])
+AU_DEFUN([AC_LIBTOOL_FC], [LT_LANG(Fortran)])
+AU_DEFUN([AC_LIBTOOL_GCJ], [LT_LANG(Java)])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_CXX], [])
+dnl AC_DEFUN([AC_LIBTOOL_F77], [])
+dnl AC_DEFUN([AC_LIBTOOL_FC], [])
+dnl AC_DEFUN([AC_LIBTOOL_GCJ], [])
+
+
+# _LT_TAG_COMPILER
+# ----------------
+m4_defun([_LT_TAG_COMPILER],
+[AC_REQUIRE([AC_PROG_CC])dnl
+
+_LT_DECL([LTCC], [CC], [1], [A C compiler])dnl
+_LT_DECL([LTCFLAGS], [CFLAGS], [1], [LTCC compiler flags])dnl
+_LT_TAGDECL([CC], [compiler], [1], [A language specific compiler])dnl
+_LT_TAGDECL([with_gcc], [GCC], [0], [Is the compiler the GNU compiler?])dnl
+
+# If no C compiler was specified, use CC.
+LTCC=${LTCC-"$CC"}
+
+# If no C compiler flags were specified, use CFLAGS.
+LTCFLAGS=${LTCFLAGS-"$CFLAGS"}
+
+# Allow CC to be a program name with arguments.
+compiler=$CC
+])# _LT_TAG_COMPILER
+
+
+# _LT_COMPILER_BOILERPLATE
+# ------------------------
+# Check for compiler boilerplate output or warnings with
+# the simple compiler test code.
+m4_defun([_LT_COMPILER_BOILERPLATE],
+[m4_require([_LT_DECL_SED])dnl
+ac_outfile=conftest.$ac_objext
+echo "$lt_simple_compile_test_code" >conftest.$ac_ext
+eval "$ac_compile" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_compiler_boilerplate=`cat conftest.err`
+$RM conftest*
+])# _LT_COMPILER_BOILERPLATE
+
+
+# _LT_LINKER_BOILERPLATE
+# ----------------------
+# Check for linker boilerplate output or warnings with
+# the simple link test code.
+m4_defun([_LT_LINKER_BOILERPLATE],
+[m4_require([_LT_DECL_SED])dnl
+ac_outfile=conftest.$ac_objext
+echo "$lt_simple_link_test_code" >conftest.$ac_ext
+eval "$ac_link" 2>&1 >/dev/null | $SED '/^$/d; /^ *+/d' >conftest.err
+_lt_linker_boilerplate=`cat conftest.err`
+$RM -r conftest*
+])# _LT_LINKER_BOILERPLATE
+
+# _LT_REQUIRED_DARWIN_CHECKS
+# -------------------------
+m4_defun_once([_LT_REQUIRED_DARWIN_CHECKS],[
+ case $host_os in
+ rhapsody* | darwin*)
+ AC_CHECK_TOOL([DSYMUTIL], [dsymutil], [:])
+ AC_CHECK_TOOL([NMEDIT], [nmedit], [:])
+ AC_CHECK_TOOL([LIPO], [lipo], [:])
+ AC_CHECK_TOOL([OTOOL], [otool], [:])
+ AC_CHECK_TOOL([OTOOL64], [otool64], [:])
+ _LT_DECL([], [DSYMUTIL], [1],
+ [Tool to manipulate archived DWARF debug symbol files on Mac OS X])
+ _LT_DECL([], [NMEDIT], [1],
+ [Tool to change global to local symbols on Mac OS X])
+ _LT_DECL([], [LIPO], [1],
+ [Tool to manipulate fat objects and archives on Mac OS X])
+ _LT_DECL([], [OTOOL], [1],
+ [ldd/readelf like tool for Mach-O binaries on Mac OS X])
+ _LT_DECL([], [OTOOL64], [1],
+ [ldd/readelf like tool for 64 bit Mach-O binaries on Mac OS X 10.4])
+
+ AC_CACHE_CHECK([for -single_module linker flag],[lt_cv_apple_cc_single_mod],
+ [lt_cv_apple_cc_single_mod=no
+ if test -z "${LT_MULTI_MODULE}"; then
+ # By default we will add the -single_module flag. You can override
+ # by either setting the environment variable LT_MULTI_MODULE
+ # non-empty at configure time, or by adding -multi_module to the
+ # link flags.
+ rm -rf libconftest.dylib*
+ echo "int foo(void){return 1;}" > conftest.c
+ echo "$LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
+-dynamiclib -Wl,-single_module conftest.c" >&AS_MESSAGE_LOG_FD
+ $LTCC $LTCFLAGS $LDFLAGS -o libconftest.dylib \
+ -dynamiclib -Wl,-single_module conftest.c 2>conftest.err
+ _lt_result=$?
+ if test -f libconftest.dylib && test ! -s conftest.err && test $_lt_result = 0; then
+ lt_cv_apple_cc_single_mod=yes
+ else
+ cat conftest.err >&AS_MESSAGE_LOG_FD
+ fi
+ rm -rf libconftest.dylib*
+ rm -f conftest.*
+ fi])
+ AC_CACHE_CHECK([for -exported_symbols_list linker flag],
+ [lt_cv_ld_exported_symbols_list],
+ [lt_cv_ld_exported_symbols_list=no
+ save_LDFLAGS=$LDFLAGS
+ echo "_main" > conftest.sym
+ LDFLAGS="$LDFLAGS -Wl,-exported_symbols_list,conftest.sym"
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([],[])],
+ [lt_cv_ld_exported_symbols_list=yes],
+ [lt_cv_ld_exported_symbols_list=no])
+ LDFLAGS="$save_LDFLAGS"
+ ])
+ case $host_os in
+ rhapsody* | darwin1.[[012]])
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}suppress' ;;
+ darwin1.*)
+ _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;
+ darwin*) # darwin 5.x on
+ # if running on 10.5 or later, the deployment target defaults
+ # to the OS version, if on x86, and 10.4, the deployment
+ # target defaults to 10.4. Don't you love it?
+ case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in
+ 10.0,*86*-darwin8*|10.0,*-darwin[[91]]*)
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;
+ 10.[[012]]*)
+ _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;
+ 10.*)
+ _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;
+ esac
+ ;;
+ esac
+ if test "$lt_cv_apple_cc_single_mod" = "yes"; then
+ _lt_dar_single_mod='$single_module'
+ fi
+ if test "$lt_cv_ld_exported_symbols_list" = "yes"; then
+ _lt_dar_export_syms=' ${wl}-exported_symbols_list,$output_objdir/${libname}-symbols.expsym'
+ else
+ _lt_dar_export_syms='~$NMEDIT -s $output_objdir/${libname}-symbols.expsym ${lib}'
+ fi
+ if test "$DSYMUTIL" != ":"; then
+ _lt_dsymutil='~$DSYMUTIL $lib || :'
+ else
+ _lt_dsymutil=
+ fi
+ ;;
+ esac
+])
+
+
+# _LT_DARWIN_LINKER_FEATURES
+# --------------------------
+# Checks for linker and compiler features on darwin
+m4_defun([_LT_DARWIN_LINKER_FEATURES],
+[
+ m4_require([_LT_REQUIRED_DARWIN_CHECKS])
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_automatic, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=''
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(allow_undefined_flag, $1)="$_lt_dar_allow_undefined"
+ case $cc_basename in
+ ifort*) _lt_dar_can_shared=yes ;;
+ *) _lt_dar_can_shared=$GCC ;;
+ esac
+ if test "$_lt_dar_can_shared" = "yes"; then
+ output_verbose_link_cmd=echo
+ _LT_TAGVAR(archive_cmds, $1)="\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring $_lt_dar_single_mod${_lt_dsymutil}"
+ _LT_TAGVAR(module_cmds, $1)="\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dsymutil}"
+ _LT_TAGVAR(archive_expsym_cmds, $1)="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \$libobjs \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring ${_lt_dar_single_mod}${_lt_dar_export_syms}${_lt_dsymutil}"
+ _LT_TAGVAR(module_expsym_cmds, $1)="sed -e 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC \$allow_undefined_flag -o \$lib -bundle \$libobjs \$deplibs \$compiler_flags${_lt_dar_export_syms}${_lt_dsymutil}"
+ m4_if([$1], [CXX],
+[ if test "$lt_cv_apple_cc_single_mod" != "yes"; then
+ _LT_TAGVAR(archive_cmds, $1)="\$CC -r -keep_private_externs -nostdlib -o \${lib}-master.o \$libobjs~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \${lib}-master.o \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring${_lt_dsymutil}"
+ _LT_TAGVAR(archive_expsym_cmds, $1)="sed 's,^,_,' < \$export_symbols > \$output_objdir/\${libname}-symbols.expsym~\$CC -r -keep_private_externs -nostdlib -o \${lib}-master.o \$libobjs~\$CC -dynamiclib \$allow_undefined_flag -o \$lib \${lib}-master.o \$deplibs \$compiler_flags -install_name \$rpath/\$soname \$verstring${_lt_dar_export_syms}${_lt_dsymutil}"
+ fi
+],[])
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+])
+
+# _LT_SYS_MODULE_PATH_AIX
+# -----------------------
+# Links a minimal program and checks the executable
+# for the system default hardcoded library path. In most cases,
+# this is /usr/lib:/lib, but when the MPI compilers are used
+# the location of the communication and MPI libs are included too.
+# If we don't find anything, use the default library path according
+# to the aix ld manual.
+m4_defun([_LT_SYS_MODULE_PATH_AIX],
+[m4_require([_LT_DECL_SED])dnl
+AC_LINK_IFELSE(AC_LANG_PROGRAM,[
+lt_aix_libpath_sed='
+ /Import File Strings/,/^$/ {
+ /^0/ {
+ s/^0 *\(.*\)$/\1/
+ p
+ }
+ }'
+aix_libpath=`dump -H conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+# Check for a 64-bit object if we didn't find anything.
+if test -z "$aix_libpath"; then
+ aix_libpath=`dump -HX64 conftest$ac_exeext 2>/dev/null | $SED -n -e "$lt_aix_libpath_sed"`
+fi],[])
+if test -z "$aix_libpath"; then aix_libpath="/usr/lib:/lib"; fi
+])# _LT_SYS_MODULE_PATH_AIX
+
+
+# _LT_SHELL_INIT(ARG)
+# -------------------
+m4_define([_LT_SHELL_INIT],
+[ifdef([AC_DIVERSION_NOTICE],
+ [AC_DIVERT_PUSH(AC_DIVERSION_NOTICE)],
+ [AC_DIVERT_PUSH(NOTICE)])
+$1
+AC_DIVERT_POP
+])# _LT_SHELL_INIT
+
+
+# _LT_PROG_ECHO_BACKSLASH
+# -----------------------
+# Add some code to the start of the generated configure script which
+# will find an echo command which doesn't interpret backslashes.
+m4_defun([_LT_PROG_ECHO_BACKSLASH],
+[_LT_SHELL_INIT([
+# Check that we are running under the correct shell.
+SHELL=${CONFIG_SHELL-/bin/sh}
+
+case X$lt_ECHO in
+X*--fallback-echo)
+ # Remove one level of quotation (which was required for Make).
+ ECHO=`echo "$lt_ECHO" | sed 's,\\\\\[$]\\[$]0,'[$]0','`
+ ;;
+esac
+
+ECHO=${lt_ECHO-echo}
+if test "X[$]1" = X--no-reexec; then
+ # Discard the --no-reexec flag, and continue.
+ shift
+elif test "X[$]1" = X--fallback-echo; then
+ # Avoid inline document here, it may be left over
+ :
+elif test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' ; then
+ # Yippee, $ECHO works!
+ :
+else
+ # Restart under the correct shell.
+ exec $SHELL "[$]0" --no-reexec ${1+"[$]@"}
+fi
+
+if test "X[$]1" = X--fallback-echo; then
+ # used as fallback echo
+ shift
+ cat <<_LT_EOF
+[$]*
+_LT_EOF
+ exit 0
+fi
+
+# The HP-UX ksh and POSIX shell print the target directory to stdout
+# if CDPATH is set.
+(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
+
+if test -z "$lt_ECHO"; then
+ if test "X${echo_test_string+set}" != Xset; then
+ # find a string as large as possible, as long as the shell can cope with it
+ for cmd in 'sed 50q "[$]0"' 'sed 20q "[$]0"' 'sed 10q "[$]0"' 'sed 2q "[$]0"' 'echo test'; do
+ # expected sizes: less than 2Kb, 1Kb, 512 bytes, 16 bytes, ...
+ if { echo_test_string=`eval $cmd`; } 2>/dev/null &&
+ { test "X$echo_test_string" = "X$echo_test_string"; } 2>/dev/null
+ then
+ break
+ fi
+ done
+ fi
+
+ if test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ $ECHO "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ :
+ else
+ # The Solaris, AIX, and Digital Unix default echo programs unquote
+ # backslashes. This makes it impossible to quote backslashes using
+ # echo "$something" | sed 's/\\/\\\\/g'
+ #
+ # So, first we look for a working echo in the user's PATH.
+
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for dir in $PATH /usr/ucb; do
+ IFS="$lt_save_ifs"
+ if (test -f $dir/echo || test -f $dir/echo$ac_exeext) &&
+ test "X`($dir/echo '\t') 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`($dir/echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ ECHO="$dir/echo"
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+
+ if test "X$ECHO" = Xecho; then
+ # We didn't find a better echo, so look for alternatives.
+ if test "X`{ print -r '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ print -r "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ # This shell has a builtin print -r that does the trick.
+ ECHO='print -r'
+ elif { test -f /bin/ksh || test -f /bin/ksh$ac_exeext; } &&
+ test "X$CONFIG_SHELL" != X/bin/ksh; then
+ # If we have ksh, try running configure again with it.
+ ORIGINAL_CONFIG_SHELL=${CONFIG_SHELL-/bin/sh}
+ export ORIGINAL_CONFIG_SHELL
+ CONFIG_SHELL=/bin/ksh
+ export CONFIG_SHELL
+ exec $CONFIG_SHELL "[$]0" --no-reexec ${1+"[$]@"}
+ else
+ # Try using printf.
+ ECHO='printf %s\n'
+ if test "X`{ $ECHO '\t'; } 2>/dev/null`" = 'X\t' &&
+ echo_testing_string=`{ $ECHO "$echo_test_string"; } 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ # Cool, printf works
+ :
+ elif echo_testing_string=`($ORIGINAL_CONFIG_SHELL "[$]0" --fallback-echo '\t') 2>/dev/null` &&
+ test "X$echo_testing_string" = 'X\t' &&
+ echo_testing_string=`($ORIGINAL_CONFIG_SHELL "[$]0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ CONFIG_SHELL=$ORIGINAL_CONFIG_SHELL
+ export CONFIG_SHELL
+ SHELL="$CONFIG_SHELL"
+ export SHELL
+ ECHO="$CONFIG_SHELL [$]0 --fallback-echo"
+ elif echo_testing_string=`($CONFIG_SHELL "[$]0" --fallback-echo '\t') 2>/dev/null` &&
+ test "X$echo_testing_string" = 'X\t' &&
+ echo_testing_string=`($CONFIG_SHELL "[$]0" --fallback-echo "$echo_test_string") 2>/dev/null` &&
+ test "X$echo_testing_string" = "X$echo_test_string"; then
+ ECHO="$CONFIG_SHELL [$]0 --fallback-echo"
+ else
+ # maybe with a smaller string...
+ prev=:
+
+ for cmd in 'echo test' 'sed 2q "[$]0"' 'sed 10q "[$]0"' 'sed 20q "[$]0"' 'sed 50q "[$]0"'; do
+ if { test "X$echo_test_string" = "X`eval $cmd`"; } 2>/dev/null
+ then
+ break
+ fi
+ prev="$cmd"
+ done
+
+ if test "$prev" != 'sed 50q "[$]0"'; then
+ echo_test_string=`eval $prev`
+ export echo_test_string
+ exec ${ORIGINAL_CONFIG_SHELL-${CONFIG_SHELL-/bin/sh}} "[$]0" ${1+"[$]@"}
+ else
+ # Oops. We lost completely, so just stick with echo.
+ ECHO=echo
+ fi
+ fi
+ fi
+ fi
+ fi
+fi
+
+# Copy echo and quote the copy suitably for passing to libtool from
+# the Makefile, instead of quoting the original, which is used later.
+lt_ECHO=$ECHO
+if test "X$lt_ECHO" = "X$CONFIG_SHELL [$]0 --fallback-echo"; then
+ lt_ECHO="$CONFIG_SHELL \\\$\[$]0 --fallback-echo"
+fi
+
+AC_SUBST(lt_ECHO)
+])
+_LT_DECL([], [SHELL], [1], [Shell to use when invoking shell scripts])
+_LT_DECL([], [ECHO], [1],
+ [An echo program that does not interpret backslashes])
+])# _LT_PROG_ECHO_BACKSLASH
+
+
+# _LT_ENABLE_LOCK
+# ---------------
+m4_defun([_LT_ENABLE_LOCK],
+[AC_ARG_ENABLE([libtool-lock],
+ [AS_HELP_STRING([--disable-libtool-lock],
+ [avoid locking (might break parallel builds)])])
+test "x$enable_libtool_lock" != xno && enable_libtool_lock=yes
+
+# Some flags need to be propagated to the compiler or linker for good
+# libtool support.
+case $host in
+ia64-*-hpux*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if AC_TRY_EVAL(ac_compile); then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *ELF-32*)
+ HPUX_IA64_MODE="32"
+ ;;
+ *ELF-64*)
+ HPUX_IA64_MODE="64"
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+*-*-irix6*)
+ # Find out which ABI we are using.
+ echo '[#]line __oline__ "configure"' > conftest.$ac_ext
+ if AC_TRY_EVAL(ac_compile); then
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ case `/usr/bin/file conftest.$ac_objext` in
+ *32-bit*)
+ LD="${LD-ld} -melf32bsmip"
+ ;;
+ *N32*)
+ LD="${LD-ld} -melf32bmipn32"
+ ;;
+ *64-bit*)
+ LD="${LD-ld} -melf64bmip"
+ ;;
+ esac
+ else
+ case `/usr/bin/file conftest.$ac_objext` in
+ *32-bit*)
+ LD="${LD-ld} -32"
+ ;;
+ *N32*)
+ LD="${LD-ld} -n32"
+ ;;
+ *64-bit*)
+ LD="${LD-ld} -64"
+ ;;
+ esac
+ fi
+ fi
+ rm -rf conftest*
+ ;;
+
+x86_64-*kfreebsd*-gnu|x86_64-*linux*|ppc*-*linux*|powerpc*-*linux*| \
+s390*-*linux*|s390*-*tpf*|sparc*-*linux*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if AC_TRY_EVAL(ac_compile); then
+ case `/usr/bin/file conftest.o` in
+ *32-bit*)
+ case $host in
+ x86_64-*kfreebsd*-gnu)
+ LD="${LD-ld} -m elf_i386_fbsd"
+ ;;
+ x86_64-*linux*)
+ LD="${LD-ld} -m elf_i386"
+ ;;
+ ppc64-*linux*|powerpc64-*linux*)
+ LD="${LD-ld} -m elf32ppclinux"
+ ;;
+ s390x-*linux*)
+ LD="${LD-ld} -m elf_s390"
+ ;;
+ sparc64-*linux*)
+ LD="${LD-ld} -m elf32_sparc"
+ ;;
+ esac
+ ;;
+ *64-bit*)
+ case $host in
+ x86_64-*kfreebsd*-gnu)
+ LD="${LD-ld} -m elf_x86_64_fbsd"
+ ;;
+ x86_64-*linux*)
+ LD="${LD-ld} -m elf_x86_64"
+ ;;
+ ppc*-*linux*|powerpc*-*linux*)
+ LD="${LD-ld} -m elf64ppc"
+ ;;
+ s390*-*linux*|s390*-*tpf*)
+ LD="${LD-ld} -m elf64_s390"
+ ;;
+ sparc*-*linux*)
+ LD="${LD-ld} -m elf64_sparc"
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+
+*-*-sco3.2v5*)
+ # On SCO OpenServer 5, we need -belf to get full-featured binaries.
+ SAVE_CFLAGS="$CFLAGS"
+ CFLAGS="$CFLAGS -belf"
+ AC_CACHE_CHECK([whether the C compiler needs -belf], lt_cv_cc_needs_belf,
+ [AC_LANG_PUSH(C)
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([[]],[[]])],[lt_cv_cc_needs_belf=yes],[lt_cv_cc_needs_belf=no])
+ AC_LANG_POP])
+ if test x"$lt_cv_cc_needs_belf" != x"yes"; then
+ # this is probably gcc 2.8.0, egcs 1.0 or newer; no need for -belf
+ CFLAGS="$SAVE_CFLAGS"
+ fi
+ ;;
+sparc*-*solaris*)
+ # Find out which ABI we are using.
+ echo 'int i;' > conftest.$ac_ext
+ if AC_TRY_EVAL(ac_compile); then
+ case `/usr/bin/file conftest.o` in
+ *64-bit*)
+ case $lt_cv_prog_gnu_ld in
+ yes*) LD="${LD-ld} -m elf64_sparc" ;;
+ *)
+ if ${LD-ld} -64 -r -o conftest2.o conftest.o >/dev/null 2>&1; then
+ LD="${LD-ld} -64"
+ fi
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ rm -rf conftest*
+ ;;
+esac
+
+need_locks="$enable_libtool_lock"
+])# _LT_ENABLE_LOCK
+
+
+# _LT_CMD_OLD_ARCHIVE
+# -------------------
+m4_defun([_LT_CMD_OLD_ARCHIVE],
+[AC_CHECK_TOOL(AR, ar, false)
+test -z "$AR" && AR=ar
+test -z "$AR_FLAGS" && AR_FLAGS=cru
+_LT_DECL([], [AR], [1], [The archiver])
+_LT_DECL([], [AR_FLAGS], [1])
+
+AC_CHECK_TOOL(STRIP, strip, :)
+test -z "$STRIP" && STRIP=:
+_LT_DECL([], [STRIP], [1], [A symbol stripping program])
+
+AC_CHECK_TOOL(RANLIB, ranlib, :)
+test -z "$RANLIB" && RANLIB=:
+_LT_DECL([], [RANLIB], [1],
+ [Commands used to install an old-style archive])
+
+# Determine commands to create old-style static archives.
+old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs'
+old_postinstall_cmds='chmod 644 $oldlib'
+old_postuninstall_cmds=
+
+if test -n "$RANLIB"; then
+ case $host_os in
+ openbsd*)
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB -t \$oldlib"
+ ;;
+ *)
+ old_postinstall_cmds="$old_postinstall_cmds~\$RANLIB \$oldlib"
+ ;;
+ esac
+ old_archive_cmds="$old_archive_cmds~\$RANLIB \$oldlib"
+fi
+_LT_DECL([], [old_postinstall_cmds], [2])
+_LT_DECL([], [old_postuninstall_cmds], [2])
+_LT_TAGDECL([], [old_archive_cmds], [2],
+ [Commands used to build an old-style archive])
+])# _LT_CMD_OLD_ARCHIVE
+
+
+# _LT_COMPILER_OPTION(MESSAGE, VARIABLE-NAME, FLAGS,
+# [OUTPUT-FILE], [ACTION-SUCCESS], [ACTION-FAILURE])
+# ----------------------------------------------------------------
+# Check whether the given compiler option works
+AC_DEFUN([_LT_COMPILER_OPTION],
+[m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_SED])dnl
+AC_CACHE_CHECK([$1], [$2],
+ [$2=no
+ m4_if([$4], , [ac_outfile=conftest.$ac_objext], [ac_outfile=$4])
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+ lt_compiler_flag="$3"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ # The option is referenced via a variable to avoid confusing sed.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [[^ ]]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:__oline__: $lt_compile\"" >&AS_MESSAGE_LOG_FD)
+ (eval "$lt_compile" 2>conftest.err)
+ ac_status=$?
+ cat conftest.err >&AS_MESSAGE_LOG_FD
+ echo "$as_me:__oline__: \$? = $ac_status" >&AS_MESSAGE_LOG_FD
+ if (exit $ac_status) && test -s "$ac_outfile"; then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings other than the usual output.
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' >conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if test ! -s conftest.er2 || diff conftest.exp conftest.er2 >/dev/null; then
+ $2=yes
+ fi
+ fi
+ $RM conftest*
+])
+
+if test x"[$]$2" = xyes; then
+ m4_if([$5], , :, [$5])
+else
+ m4_if([$6], , :, [$6])
+fi
+])# _LT_COMPILER_OPTION
+
+# Old name:
+AU_ALIAS([AC_LIBTOOL_COMPILER_OPTION], [_LT_COMPILER_OPTION])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_COMPILER_OPTION], [])
+
+
+# _LT_LINKER_OPTION(MESSAGE, VARIABLE-NAME, FLAGS,
+# [ACTION-SUCCESS], [ACTION-FAILURE])
+# ----------------------------------------------------
+# Check whether the given linker option works
+AC_DEFUN([_LT_LINKER_OPTION],
+[m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_SED])dnl
+AC_CACHE_CHECK([$1], [$2],
+ [$2=no
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS $3"
+ echo "$lt_simple_link_test_code" > conftest.$ac_ext
+ if (eval $ac_link 2>conftest.err) && test -s conftest$ac_exeext; then
+ # The linker can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ if test -s conftest.err; then
+ # Append any errors to the config.log.
+ cat conftest.err 1>&AS_MESSAGE_LOG_FD
+ $ECHO "X$_lt_linker_boilerplate" | $Xsed -e '/^$/d' > conftest.exp
+ $SED '/^$/d; /^ *+/d' conftest.err >conftest.er2
+ if diff conftest.exp conftest.er2 >/dev/null; then
+ $2=yes
+ fi
+ else
+ $2=yes
+ fi
+ fi
+ $RM -r conftest*
+ LDFLAGS="$save_LDFLAGS"
+])
+
+if test x"[$]$2" = xyes; then
+ m4_if([$4], , :, [$4])
+else
+ m4_if([$5], , :, [$5])
+fi
+])# _LT_LINKER_OPTION
+
+# Old name:
+AU_ALIAS([AC_LIBTOOL_LINKER_OPTION], [_LT_LINKER_OPTION])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_LINKER_OPTION], [])
+
+
+# LT_CMD_MAX_LEN
+#---------------
+AC_DEFUN([LT_CMD_MAX_LEN],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+# find the maximum length of command line arguments
+AC_MSG_CHECKING([the maximum length of command line arguments])
+AC_CACHE_VAL([lt_cv_sys_max_cmd_len], [dnl
+ i=0
+ teststring="ABCD"
+
+ case $build_os in
+ msdosdjgpp*)
+ # On DJGPP, this test can blow up pretty badly due to problems in libc
+ # (any single argument exceeding 2000 bytes causes a buffer overrun
+ # during glob expansion). Even if it were fixed, the result of this
+ # check would be larger than it should be.
+ lt_cv_sys_max_cmd_len=12288; # 12K is about right
+ ;;
+
+ gnu*)
+ # Under GNU Hurd, this test is not required because there is
+ # no limit to the length of command line arguments.
+ # Libtool will interpret -1 as no limit whatsoever
+ lt_cv_sys_max_cmd_len=-1;
+ ;;
+
+ cygwin* | mingw* | cegcc*)
+ # On Win9x/ME, this test blows up -- it succeeds, but takes
+ # about 5 minutes as the teststring grows exponentially.
+ # Worse, since 9x/ME are not pre-emptively multitasking,
+ # you end up with a "frozen" computer, even though with patience
+ # the test eventually succeeds (with a max line length of 256k).
+ # Instead, let's just punt: use the minimum linelength reported by
+ # all of the supported platforms: 8192 (on NT/2K/XP).
+ lt_cv_sys_max_cmd_len=8192;
+ ;;
+
+ amigaos*)
+ # On AmigaOS with pdksh, this test takes hours, literally.
+ # So we just punt and use a minimum line length of 8192.
+ lt_cv_sys_max_cmd_len=8192;
+ ;;
+
+ netbsd* | freebsd* | openbsd* | darwin* | dragonfly*)
+ # This has been around since 386BSD, at least. Likely further.
+ if test -x /sbin/sysctl; then
+ lt_cv_sys_max_cmd_len=`/sbin/sysctl -n kern.argmax`
+ elif test -x /usr/sbin/sysctl; then
+ lt_cv_sys_max_cmd_len=`/usr/sbin/sysctl -n kern.argmax`
+ else
+ lt_cv_sys_max_cmd_len=65536 # usable default for all BSDs
+ fi
+ # And add a safety zone
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+ ;;
+
+ interix*)
+ # We know the value 262144 and hardcode it with a safety zone (like BSD)
+ lt_cv_sys_max_cmd_len=196608
+ ;;
+
+ osf*)
+ # Dr. Hans Ekkehard Plesser reports seeing a kernel panic running configure
+ # due to this test when exec_disable_arg_limit is 1 on Tru64. It is not
+ # nice to cause kernel panics so lets avoid the loop below.
+ # First set a reasonable default.
+ lt_cv_sys_max_cmd_len=16384
+ #
+ if test -x /sbin/sysconfig; then
+ case `/sbin/sysconfig -q proc exec_disable_arg_limit` in
+ *1*) lt_cv_sys_max_cmd_len=-1 ;;
+ esac
+ fi
+ ;;
+ sco3.2v5*)
+ lt_cv_sys_max_cmd_len=102400
+ ;;
+ sysv5* | sco5v6* | sysv4.2uw2*)
+ kargmax=`grep ARG_MAX /etc/conf/cf.d/stune 2>/dev/null`
+ if test -n "$kargmax"; then
+ lt_cv_sys_max_cmd_len=`echo $kargmax | sed 's/.*[[ ]]//'`
+ else
+ lt_cv_sys_max_cmd_len=32768
+ fi
+ ;;
+ *)
+ lt_cv_sys_max_cmd_len=`(getconf ARG_MAX) 2> /dev/null`
+ if test -n "$lt_cv_sys_max_cmd_len"; then
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 4`
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \* 3`
+ else
+ # Make teststring a little bigger before we do anything with it.
+ # a 1K string should be a reasonable start.
+ for i in 1 2 3 4 5 6 7 8 ; do
+ teststring=$teststring$teststring
+ done
+ SHELL=${SHELL-${CONFIG_SHELL-/bin/sh}}
+ # If test is not a shell built-in, we'll probably end up computing a
+ # maximum length that is only half of the actual maximum length, but
+ # we can't tell.
+ while { test "X"`$SHELL [$]0 --fallback-echo "X$teststring$teststring" 2>/dev/null` \
+ = "XX$teststring$teststring"; } >/dev/null 2>&1 &&
+ test $i != 17 # 1/2 MB should be enough
+ do
+ i=`expr $i + 1`
+ teststring=$teststring$teststring
+ done
+ # Only check the string length outside the loop.
+ lt_cv_sys_max_cmd_len=`expr "X$teststring" : ".*" 2>&1`
+ teststring=
+ # Add a significant safety factor because C++ compilers can tack on
+ # massive amounts of additional arguments before passing them to the
+ # linker. It appears as though 1/2 is a usable value.
+ lt_cv_sys_max_cmd_len=`expr $lt_cv_sys_max_cmd_len \/ 2`
+ fi
+ ;;
+ esac
+])
+if test -n $lt_cv_sys_max_cmd_len ; then
+ AC_MSG_RESULT($lt_cv_sys_max_cmd_len)
+else
+ AC_MSG_RESULT(none)
+fi
+max_cmd_len=$lt_cv_sys_max_cmd_len
+_LT_DECL([], [max_cmd_len], [0],
+ [What is the maximum length of a command?])
+])# LT_CMD_MAX_LEN
+
+# Old name:
+AU_ALIAS([AC_LIBTOOL_SYS_MAX_CMD_LEN], [LT_CMD_MAX_LEN])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_SYS_MAX_CMD_LEN], [])
+
+
+# _LT_HEADER_DLFCN
+# ----------------
+m4_defun([_LT_HEADER_DLFCN],
+[AC_CHECK_HEADERS([dlfcn.h], [], [], [AC_INCLUDES_DEFAULT])dnl
+])# _LT_HEADER_DLFCN
+
+
+# _LT_TRY_DLOPEN_SELF (ACTION-IF-TRUE, ACTION-IF-TRUE-W-USCORE,
+# ACTION-IF-FALSE, ACTION-IF-CROSS-COMPILING)
+# ----------------------------------------------------------------
+m4_defun([_LT_TRY_DLOPEN_SELF],
+[m4_require([_LT_HEADER_DLFCN])dnl
+if test "$cross_compiling" = yes; then :
+ [$4]
+else
+ lt_dlunknown=0; lt_dlno_uscore=1; lt_dlneed_uscore=2
+ lt_status=$lt_dlunknown
+ cat > conftest.$ac_ext <<_LT_EOF
+[#line __oline__ "configure"
+#include "confdefs.h"
+
+#if HAVE_DLFCN_H
+#include <dlfcn.h>
+#endif
+
+#include <stdio.h>
+
+#ifdef RTLD_GLOBAL
+# define LT_DLGLOBAL RTLD_GLOBAL
+#else
+# ifdef DL_GLOBAL
+# define LT_DLGLOBAL DL_GLOBAL
+# else
+# define LT_DLGLOBAL 0
+# endif
+#endif
+
+/* We may have to define LT_DLLAZY_OR_NOW in the command line if we
+ find out it does not work in some platform. */
+#ifndef LT_DLLAZY_OR_NOW
+# ifdef RTLD_LAZY
+# define LT_DLLAZY_OR_NOW RTLD_LAZY
+# else
+# ifdef DL_LAZY
+# define LT_DLLAZY_OR_NOW DL_LAZY
+# else
+# ifdef RTLD_NOW
+# define LT_DLLAZY_OR_NOW RTLD_NOW
+# else
+# ifdef DL_NOW
+# define LT_DLLAZY_OR_NOW DL_NOW
+# else
+# define LT_DLLAZY_OR_NOW 0
+# endif
+# endif
+# endif
+# endif
+#endif
+
+void fnord() { int i=42;}
+int main ()
+{
+ void *self = dlopen (0, LT_DLGLOBAL|LT_DLLAZY_OR_NOW);
+ int status = $lt_dlunknown;
+
+ if (self)
+ {
+ if (dlsym (self,"fnord")) status = $lt_dlno_uscore;
+ else if (dlsym( self,"_fnord")) status = $lt_dlneed_uscore;
+ /* dlclose (self); */
+ }
+ else
+ puts (dlerror ());
+
+ return status;
+}]
+_LT_EOF
+ if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext} 2>/dev/null; then
+ (./conftest; exit; ) >&AS_MESSAGE_LOG_FD 2>/dev/null
+ lt_status=$?
+ case x$lt_status in
+ x$lt_dlno_uscore) $1 ;;
+ x$lt_dlneed_uscore) $2 ;;
+ x$lt_dlunknown|x*) $3 ;;
+ esac
+ else :
+ # compilation failed
+ $3
+ fi
+fi
+rm -fr conftest*
+])# _LT_TRY_DLOPEN_SELF
+
+
+# LT_SYS_DLOPEN_SELF
+# ------------------
+AC_DEFUN([LT_SYS_DLOPEN_SELF],
+[m4_require([_LT_HEADER_DLFCN])dnl
+if test "x$enable_dlopen" != xyes; then
+ enable_dlopen=unknown
+ enable_dlopen_self=unknown
+ enable_dlopen_self_static=unknown
+else
+ lt_cv_dlopen=no
+ lt_cv_dlopen_libs=
+
+ case $host_os in
+ beos*)
+ lt_cv_dlopen="load_add_on"
+ lt_cv_dlopen_libs=
+ lt_cv_dlopen_self=yes
+ ;;
+
+ mingw* | pw32* | cegcc*)
+ lt_cv_dlopen="LoadLibrary"
+ lt_cv_dlopen_libs=
+ ;;
+
+ cygwin*)
+ lt_cv_dlopen="dlopen"
+ lt_cv_dlopen_libs=
+ ;;
+
+ darwin*)
+ # if libdl is installed we need to link against it
+ AC_CHECK_LIB([dl], [dlopen],
+ [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"],[
+ lt_cv_dlopen="dyld"
+ lt_cv_dlopen_libs=
+ lt_cv_dlopen_self=yes
+ ])
+ ;;
+
+ *)
+ AC_CHECK_FUNC([shl_load],
+ [lt_cv_dlopen="shl_load"],
+ [AC_CHECK_LIB([dld], [shl_load],
+ [lt_cv_dlopen="shl_load" lt_cv_dlopen_libs="-ldld"],
+ [AC_CHECK_FUNC([dlopen],
+ [lt_cv_dlopen="dlopen"],
+ [AC_CHECK_LIB([dl], [dlopen],
+ [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-ldl"],
+ [AC_CHECK_LIB([svld], [dlopen],
+ [lt_cv_dlopen="dlopen" lt_cv_dlopen_libs="-lsvld"],
+ [AC_CHECK_LIB([dld], [dld_link],
+ [lt_cv_dlopen="dld_link" lt_cv_dlopen_libs="-ldld"])
+ ])
+ ])
+ ])
+ ])
+ ])
+ ;;
+ esac
+
+ if test "x$lt_cv_dlopen" != xno; then
+ enable_dlopen=yes
+ else
+ enable_dlopen=no
+ fi
+
+ case $lt_cv_dlopen in
+ dlopen)
+ save_CPPFLAGS="$CPPFLAGS"
+ test "x$ac_cv_header_dlfcn_h" = xyes && CPPFLAGS="$CPPFLAGS -DHAVE_DLFCN_H"
+
+ save_LDFLAGS="$LDFLAGS"
+ wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $export_dynamic_flag_spec\"
+
+ save_LIBS="$LIBS"
+ LIBS="$lt_cv_dlopen_libs $LIBS"
+
+ AC_CACHE_CHECK([whether a program can dlopen itself],
+ lt_cv_dlopen_self, [dnl
+ _LT_TRY_DLOPEN_SELF(
+ lt_cv_dlopen_self=yes, lt_cv_dlopen_self=yes,
+ lt_cv_dlopen_self=no, lt_cv_dlopen_self=cross)
+ ])
+
+ if test "x$lt_cv_dlopen_self" = xyes; then
+ wl=$lt_prog_compiler_wl eval LDFLAGS=\"\$LDFLAGS $lt_prog_compiler_static\"
+ AC_CACHE_CHECK([whether a statically linked program can dlopen itself],
+ lt_cv_dlopen_self_static, [dnl
+ _LT_TRY_DLOPEN_SELF(
+ lt_cv_dlopen_self_static=yes, lt_cv_dlopen_self_static=yes,
+ lt_cv_dlopen_self_static=no, lt_cv_dlopen_self_static=cross)
+ ])
+ fi
+
+ CPPFLAGS="$save_CPPFLAGS"
+ LDFLAGS="$save_LDFLAGS"
+ LIBS="$save_LIBS"
+ ;;
+ esac
+
+ case $lt_cv_dlopen_self in
+ yes|no) enable_dlopen_self=$lt_cv_dlopen_self ;;
+ *) enable_dlopen_self=unknown ;;
+ esac
+
+ case $lt_cv_dlopen_self_static in
+ yes|no) enable_dlopen_self_static=$lt_cv_dlopen_self_static ;;
+ *) enable_dlopen_self_static=unknown ;;
+ esac
+fi
+_LT_DECL([dlopen_support], [enable_dlopen], [0],
+ [Whether dlopen is supported])
+_LT_DECL([dlopen_self], [enable_dlopen_self], [0],
+ [Whether dlopen of programs is supported])
+_LT_DECL([dlopen_self_static], [enable_dlopen_self_static], [0],
+ [Whether dlopen of statically linked programs is supported])
+])# LT_SYS_DLOPEN_SELF
+
+# Old name:
+AU_ALIAS([AC_LIBTOOL_DLOPEN_SELF], [LT_SYS_DLOPEN_SELF])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_DLOPEN_SELF], [])
+
+
+# _LT_COMPILER_C_O([TAGNAME])
+# ---------------------------
+# Check to see if options -c and -o are simultaneously supported by compiler.
+# This macro does not hard code the compiler like AC_PROG_CC_C_O.
+m4_defun([_LT_COMPILER_C_O],
+[m4_require([_LT_DECL_SED])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_TAG_COMPILER])dnl
+AC_CACHE_CHECK([if $compiler supports -c -o file.$ac_objext],
+ [_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)],
+ [_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)=no
+ $RM -r conftest 2>/dev/null
+ mkdir conftest
+ cd conftest
+ mkdir out
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ lt_compiler_flag="-o out/conftest2.$ac_objext"
+ # Insert the option either (1) after the last *FLAGS variable, or
+ # (2) before a word containing "conftest.", or (3) at the end.
+ # Note that $ac_compile itself does not contain backslashes and begins
+ # with a dollar sign (not a hyphen), so the echo should work correctly.
+ lt_compile=`echo "$ac_compile" | $SED \
+ -e 's:.*FLAGS}\{0,1\} :&$lt_compiler_flag :; t' \
+ -e 's: [[^ ]]*conftest\.: $lt_compiler_flag&:; t' \
+ -e 's:$: $lt_compiler_flag:'`
+ (eval echo "\"\$as_me:__oline__: $lt_compile\"" >&AS_MESSAGE_LOG_FD)
+ (eval "$lt_compile" 2>out/conftest.err)
+ ac_status=$?
+ cat out/conftest.err >&AS_MESSAGE_LOG_FD
+ echo "$as_me:__oline__: \$? = $ac_status" >&AS_MESSAGE_LOG_FD
+ if (exit $ac_status) && test -s out/conftest2.$ac_objext
+ then
+ # The compiler can only warn and ignore the option if not recognized
+ # So say no if there are warnings
+ $ECHO "X$_lt_compiler_boilerplate" | $Xsed -e '/^$/d' > out/conftest.exp
+ $SED '/^$/d; /^ *+/d' out/conftest.err >out/conftest.er2
+ if test ! -s out/conftest.er2 || diff out/conftest.exp out/conftest.er2 >/dev/null; then
+ _LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)=yes
+ fi
+ fi
+ chmod u+w . 2>&AS_MESSAGE_LOG_FD
+ $RM conftest*
+ # SGI C++ compiler will create directory out/ii_files/ for
+ # template instantiation
+ test -d out/ii_files && $RM out/ii_files/* && rmdir out/ii_files
+ $RM out/* && rmdir out
+ cd ..
+ $RM -r conftest
+ $RM conftest*
+])
+_LT_TAGDECL([compiler_c_o], [lt_cv_prog_compiler_c_o], [1],
+ [Does compiler simultaneously support -c and -o options?])
+])# _LT_COMPILER_C_O
+
+
+# _LT_COMPILER_FILE_LOCKS([TAGNAME])
+# ----------------------------------
+# Check to see if we can do hard links to lock some files if needed
+m4_defun([_LT_COMPILER_FILE_LOCKS],
+[m4_require([_LT_ENABLE_LOCK])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+_LT_COMPILER_C_O([$1])
+
+hard_links="nottested"
+if test "$_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)" = no && test "$need_locks" != no; then
+ # do not overwrite the value of need_locks provided by the user
+ AC_MSG_CHECKING([if we can lock with hard links])
+ hard_links=yes
+ $RM conftest*
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ touch conftest.a
+ ln conftest.a conftest.b 2>&5 || hard_links=no
+ ln conftest.a conftest.b 2>/dev/null && hard_links=no
+ AC_MSG_RESULT([$hard_links])
+ if test "$hard_links" = no; then
+ AC_MSG_WARN([`$CC' does not support `-c -o', so `make -j' may be unsafe])
+ need_locks=warn
+ fi
+else
+ need_locks=no
+fi
+_LT_DECL([], [need_locks], [1], [Must we lock files when doing compilation?])
+])# _LT_COMPILER_FILE_LOCKS
+
+
+# _LT_CHECK_OBJDIR
+# ----------------
+m4_defun([_LT_CHECK_OBJDIR],
+[AC_CACHE_CHECK([for objdir], [lt_cv_objdir],
+[rm -f .libs 2>/dev/null
+mkdir .libs 2>/dev/null
+if test -d .libs; then
+ lt_cv_objdir=.libs
+else
+ # MS-DOS does not allow filenames that begin with a dot.
+ lt_cv_objdir=_libs
+fi
+rmdir .libs 2>/dev/null])
+objdir=$lt_cv_objdir
+_LT_DECL([], [objdir], [0],
+ [The name of the directory that contains temporary libtool files])dnl
+m4_pattern_allow([LT_OBJDIR])dnl
+AC_DEFINE_UNQUOTED(LT_OBJDIR, "$lt_cv_objdir/",
+ [Define to the sub-directory in which libtool stores uninstalled libraries.])
+])# _LT_CHECK_OBJDIR
+
+
+# _LT_LINKER_HARDCODE_LIBPATH([TAGNAME])
+# --------------------------------------
+# Check hardcoding attributes.
+m4_defun([_LT_LINKER_HARDCODE_LIBPATH],
+[AC_MSG_CHECKING([how to hardcode library paths into programs])
+_LT_TAGVAR(hardcode_action, $1)=
+if test -n "$_LT_TAGVAR(hardcode_libdir_flag_spec, $1)" ||
+ test -n "$_LT_TAGVAR(runpath_var, $1)" ||
+ test "X$_LT_TAGVAR(hardcode_automatic, $1)" = "Xyes" ; then
+
+ # We can hardcode non-existent directories.
+ if test "$_LT_TAGVAR(hardcode_direct, $1)" != no &&
+ # If the only mechanism to avoid hardcoding is shlibpath_var, we
+ # have to relink, otherwise we might link with an installed library
+ # when we should be linking with a yet-to-be-installed one
+ ## test "$_LT_TAGVAR(hardcode_shlibpath_var, $1)" != no &&
+ test "$_LT_TAGVAR(hardcode_minus_L, $1)" != no; then
+ # Linking always hardcodes the temporary library directory.
+ _LT_TAGVAR(hardcode_action, $1)=relink
+ else
+ # We can link without hardcoding, and we can hardcode nonexisting dirs.
+ _LT_TAGVAR(hardcode_action, $1)=immediate
+ fi
+else
+ # We cannot hardcode anything, or else we can only hardcode existing
+ # directories.
+ _LT_TAGVAR(hardcode_action, $1)=unsupported
+fi
+AC_MSG_RESULT([$_LT_TAGVAR(hardcode_action, $1)])
+
+if test "$_LT_TAGVAR(hardcode_action, $1)" = relink ||
+ test "$_LT_TAGVAR(inherit_rpath, $1)" = yes; then
+ # Fast installation is not supported
+ enable_fast_install=no
+elif test "$shlibpath_overrides_runpath" = yes ||
+ test "$enable_shared" = no; then
+ # Fast installation is not necessary
+ enable_fast_install=needless
+fi
+_LT_TAGDECL([], [hardcode_action], [0],
+ [How to hardcode a shared library path into an executable])
+])# _LT_LINKER_HARDCODE_LIBPATH
+
+
+# _LT_CMD_STRIPLIB
+# ----------------
+m4_defun([_LT_CMD_STRIPLIB],
+[m4_require([_LT_DECL_EGREP])
+striplib=
+old_striplib=
+AC_MSG_CHECKING([whether stripping libraries is possible])
+if test -n "$STRIP" && $STRIP -V 2>&1 | $GREP "GNU strip" >/dev/null; then
+ test -z "$old_striplib" && old_striplib="$STRIP --strip-debug"
+ test -z "$striplib" && striplib="$STRIP --strip-unneeded"
+ AC_MSG_RESULT([yes])
+else
+# FIXME - insert some real tests, host_os isn't really good enough
+ case $host_os in
+ darwin*)
+ if test -n "$STRIP" ; then
+ striplib="$STRIP -x"
+ old_striplib="$STRIP -S"
+ AC_MSG_RESULT([yes])
+ else
+ AC_MSG_RESULT([no])
+ fi
+ ;;
+ *)
+ AC_MSG_RESULT([no])
+ ;;
+ esac
+fi
+_LT_DECL([], [old_striplib], [1], [Commands to strip libraries])
+_LT_DECL([], [striplib], [1])
+])# _LT_CMD_STRIPLIB
+
+
+# _LT_SYS_DYNAMIC_LINKER([TAG])
+# -----------------------------
+# PORTME Fill in your ld.so characteristics
+m4_defun([_LT_SYS_DYNAMIC_LINKER],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+m4_require([_LT_DECL_EGREP])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_OBJDUMP])dnl
+m4_require([_LT_DECL_SED])dnl
+AC_MSG_CHECKING([dynamic linker characteristics])
+m4_if([$1],
+ [], [
+if test "$GCC" = yes; then
+ case $host_os in
+ darwin*) lt_awk_arg="/^libraries:/,/LR/" ;;
+ *) lt_awk_arg="/^libraries:/" ;;
+ esac
+ lt_search_path_spec=`$CC -print-search-dirs | awk $lt_awk_arg | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$lt_search_path_spec" | $GREP ';' >/dev/null ; then
+ # if the path contains ";" then we assume it to be the separator
+ # otherwise default to the standard path separator (i.e. ":") - it is
+ # assumed that no part of a normal pathname contains ";" but that should
+ # okay in the real world where ";" in dirpaths is itself problematic.
+ lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ lt_search_path_spec=`$ECHO "$lt_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ # Ok, now we have the path, separated by spaces, we can step through it
+ # and add multilib dir if necessary.
+ lt_tmp_lt_search_path_spec=
+ lt_multi_os_dir=`$CC $CPPFLAGS $CFLAGS $LDFLAGS -print-multi-os-directory 2>/dev/null`
+ for lt_sys_path in $lt_search_path_spec; do
+ if test -d "$lt_sys_path/$lt_multi_os_dir"; then
+ lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path/$lt_multi_os_dir"
+ else
+ test -d "$lt_sys_path" && \
+ lt_tmp_lt_search_path_spec="$lt_tmp_lt_search_path_spec $lt_sys_path"
+ fi
+ done
+ lt_search_path_spec=`$ECHO $lt_tmp_lt_search_path_spec | awk '
+BEGIN {RS=" "; FS="/|\n";} {
+ lt_foo="";
+ lt_count=0;
+ for (lt_i = NF; lt_i > 0; lt_i--) {
+ if ($lt_i != "" && $lt_i != ".") {
+ if ($lt_i == "..") {
+ lt_count++;
+ } else {
+ if (lt_count == 0) {
+ lt_foo="/" $lt_i lt_foo;
+ } else {
+ lt_count--;
+ }
+ }
+ }
+ }
+ if (lt_foo != "") { lt_freq[[lt_foo]]++; }
+ if (lt_freq[[lt_foo]] == 1) { print lt_foo; }
+}'`
+ sys_lib_search_path_spec=`$ECHO $lt_search_path_spec`
+else
+ sys_lib_search_path_spec="/lib /usr/lib /usr/local/lib"
+fi])
+library_names_spec=
+libname_spec='lib$name'
+soname_spec=
+shrext_cmds=".so"
+postinstall_cmds=
+postuninstall_cmds=
+finish_cmds=
+finish_eval=
+shlibpath_var=
+shlibpath_overrides_runpath=unknown
+version_type=none
+dynamic_linker="$host_os ld.so"
+sys_lib_dlsearch_path_spec="/lib /usr/lib"
+need_lib_prefix=unknown
+hardcode_into_libs=no
+
+# when you set need_version to no, make sure it does not cause -set_version
+# flags to be left without arguments
+need_version=unknown
+
+case $host_os in
+aix3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname.a'
+ shlibpath_var=LIBPATH
+
+ # AIX 3 has no versioning support, so we append a major version to the name.
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+
+aix[[4-9]]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ hardcode_into_libs=yes
+ if test "$host_cpu" = ia64; then
+ # AIX 5 supports IA64
+ library_names_spec='${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext}$versuffix $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ else
+ # With GCC up to 2.95.x, collect2 would create an import file
+ # for dependence libraries. The import file would start with
+ # the line `#! .'. This would cause the generated library to
+ # depend on `.', always an invalid library. This was fixed in
+ # development snapshots of GCC prior to 3.0.
+ case $host_os in
+ aix4 | aix4.[[01]] | aix4.[[01]].*)
+ if { echo '#if __GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ >= 97)'
+ echo ' yes '
+ echo '#endif'; } | ${CC} -E - | $GREP yes > /dev/null; then
+ :
+ else
+ can_build_shared=no
+ fi
+ ;;
+ esac
+ # AIX (on Power*) has no versioning support, so currently we can not hardcode correct
+ # soname into executable. Probably we can add versioning support to
+ # collect2, so additional links can be useful in future.
+ if test "$aix_use_runtimelinking" = yes; then
+ # If using run time linking (on AIX 4.2 or later) use lib<name>.so
+ # instead of lib<name>.a to let people know that these are not
+ # typical AIX shared libraries.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ else
+ # We preserve .a as extension for shared libraries through AIX4.2
+ # and later when we are not doing run time linking.
+ library_names_spec='${libname}${release}.a $libname.a'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ fi
+ shlibpath_var=LIBPATH
+ fi
+ ;;
+
+amigaos*)
+ case $host_cpu in
+ powerpc)
+ # Since July 2007 AmigaOS4 officially supports .so libraries.
+ # When compiling the executable, add -use-dynld -Lsobjs: to the compileline.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ ;;
+ m68k)
+ library_names_spec='$libname.ixlibrary $libname.a'
+ # Create ${libname}_ixlibrary.a entries in /sys/libs.
+ finish_eval='for lib in `ls $libdir/*.ixlibrary 2>/dev/null`; do libname=`$ECHO "X$lib" | $Xsed -e '\''s%^.*/\([[^/]]*\)\.ixlibrary$%\1%'\''`; test $RM /sys/libs/${libname}_ixlibrary.a; $show "cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a"; cd /sys/libs && $LN_S $lib ${libname}_ixlibrary.a || exit 1; done'
+ ;;
+ esac
+ ;;
+
+beos*)
+ library_names_spec='${libname}${shared_ext}'
+ dynamic_linker="$host_os ld.so"
+ shlibpath_var=LIBRARY_PATH
+ ;;
+
+bsdi[[45]]*)
+ version_type=linux
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/shlib /usr/lib /usr/X11/lib /usr/contrib/lib /lib /usr/local/lib"
+ sys_lib_dlsearch_path_spec="/shlib /usr/lib /usr/local/lib"
+ # the default ld.so.conf also contains /usr/contrib/lib and
+ # /usr/X11R6/lib (/usr/X11 is a link to /usr/X11R6), but let us allow
+ # libtool to hard-code these into programs
+ ;;
+
+cygwin* | mingw* | pw32* | cegcc*)
+ version_type=windows
+ shrext_cmds=".dll"
+ need_version=no
+ need_lib_prefix=no
+
+ case $GCC,$host_os in
+ yes,cygwin* | yes,mingw* | yes,pw32* | yes,cegcc*)
+ library_names_spec='$libname.dll.a'
+ # DLL is installed to $(libdir)/../bin by postinstall_cmds
+ postinstall_cmds='base_file=`basename \${file}`~
+ dlpath=`$SHELL 2>&1 -c '\''. $dir/'\''\${base_file}'\''i; echo \$dlname'\''`~
+ dldir=$destdir/`dirname \$dlpath`~
+ test -d \$dldir || mkdir -p \$dldir~
+ $install_prog $dir/$dlname \$dldir/$dlname~
+ chmod a+x \$dldir/$dlname~
+ if test -n '\''$stripme'\'' && test -n '\''$striplib'\''; then
+ eval '\''$striplib \$dldir/$dlname'\'' || exit \$?;
+ fi'
+ postuninstall_cmds='dldll=`$SHELL 2>&1 -c '\''. $file; echo \$dlname'\''`~
+ dlpath=$dir/\$dldll~
+ $RM \$dlpath'
+ shlibpath_overrides_runpath=yes
+
+ case $host_os in
+ cygwin*)
+ # Cygwin DLLs use 'cyg' prefix rather than 'lib'
+ soname_spec='`echo ${libname} | sed -e 's/^lib/cyg/'``echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec="/usr/lib /lib/w32api /lib /usr/local/lib"
+ ;;
+ mingw* | cegcc*)
+ # MinGW DLLs use traditional 'lib' prefix
+ soname_spec='${libname}`echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}'
+ sys_lib_search_path_spec=`$CC -print-search-dirs | $GREP "^libraries:" | $SED -e "s/^libraries://" -e "s,=/,/,g"`
+ if $ECHO "$sys_lib_search_path_spec" | [$GREP ';[c-zC-Z]:/' >/dev/null]; then
+ # It is most probably a Windows format PATH printed by
+ # mingw gcc, but we are running on Cygwin. Gcc prints its search
+ # path with ; separators, and with drive letters. We can handle the
+ # drive letters (cygwin fileutils understands them), so leave them,
+ # especially as we might pass files found there to a mingw objdump,
+ # which wouldn't understand a cygwinified path. Ahh.
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e 's/;/ /g'`
+ else
+ sys_lib_search_path_spec=`$ECHO "$sys_lib_search_path_spec" | $SED -e "s/$PATH_SEPARATOR/ /g"`
+ fi
+ ;;
+ pw32*)
+ # pw32 DLLs use 'pw' prefix rather than 'lib'
+ library_names_spec='`echo ${libname} | sed -e 's/^lib/pw/'``echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext}'
+ ;;
+ esac
+ ;;
+
+ *)
+ library_names_spec='${libname}`echo ${release} | $SED -e 's/[[.]]/-/g'`${versuffix}${shared_ext} $libname.lib'
+ ;;
+ esac
+ dynamic_linker='Win32 ld.exe'
+ # FIXME: first we should search . and the directory the executable is in
+ shlibpath_var=PATH
+ ;;
+
+darwin* | rhapsody*)
+ dynamic_linker="$host_os dyld"
+ version_type=darwin
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${major}$shared_ext ${libname}$shared_ext'
+ soname_spec='${libname}${release}${major}$shared_ext'
+ shlibpath_overrides_runpath=yes
+ shlibpath_var=DYLD_LIBRARY_PATH
+ shrext_cmds='`test .$module = .yes && echo .so || echo .dylib`'
+m4_if([$1], [],[
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /usr/local/lib"])
+ sys_lib_dlsearch_path_spec='/usr/local/lib /lib /usr/lib'
+ ;;
+
+dgux*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname$shared_ext'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+freebsd1*)
+ dynamic_linker=no
+ ;;
+
+freebsd* | dragonfly*)
+ # DragonFly does not have aout. When/if they implement a new
+ # versioning mechanism, adjust this.
+ if test -x /usr/bin/objformat; then
+ objformat=`/usr/bin/objformat`
+ else
+ case $host_os in
+ freebsd[[123]]*) objformat=aout ;;
+ *) objformat=elf ;;
+ esac
+ fi
+ version_type=freebsd-$objformat
+ case $version_type in
+ freebsd-elf*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ need_version=no
+ need_lib_prefix=no
+ ;;
+ freebsd-*)
+ library_names_spec='${libname}${release}${shared_ext}$versuffix $libname${shared_ext}$versuffix'
+ need_version=yes
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_os in
+ freebsd2*)
+ shlibpath_overrides_runpath=yes
+ ;;
+ freebsd3.[[01]]* | freebsdelf3.[[01]]*)
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ freebsd3.[[2-9]]* | freebsdelf3.[[2-9]]* | \
+ freebsd4.[[0-5]] | freebsdelf4.[[0-5]] | freebsd4.1.1 | freebsdelf4.1.1)
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+ *) # from 4.6 on, and DragonFly
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+ esac
+ ;;
+
+gnu*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}${major} ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ hardcode_into_libs=yes
+ ;;
+
+hpux9* | hpux10* | hpux11*)
+ # Give a soname corresponding to the major version so that dld.sl refuses to
+ # link against other versions.
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ case $host_cpu in
+ ia64*)
+ shrext_cmds='.so'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.so"
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ if test "X$HPUX_IA64_MODE" = X32; then
+ sys_lib_search_path_spec="/usr/lib/hpux32 /usr/local/lib/hpux32 /usr/local/lib"
+ else
+ sys_lib_search_path_spec="/usr/lib/hpux64 /usr/local/lib/hpux64"
+ fi
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ hppa*64*)
+ shrext_cmds='.sl'
+ hardcode_into_libs=yes
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=LD_LIBRARY_PATH # How should we handle SHLIB_PATH
+ shlibpath_overrides_runpath=yes # Unless +noenvvar is specified.
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ sys_lib_search_path_spec="/usr/lib/pa20_64 /usr/ccs/lib/pa20_64"
+ sys_lib_dlsearch_path_spec=$sys_lib_search_path_spec
+ ;;
+ *)
+ shrext_cmds='.sl'
+ dynamic_linker="$host_os dld.sl"
+ shlibpath_var=SHLIB_PATH
+ shlibpath_overrides_runpath=no # +s is required to enable SHLIB_PATH
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ ;;
+ esac
+ # HP-UX runs *really* slowly unless shared libraries are mode 555.
+ postinstall_cmds='chmod 555 $lib'
+ ;;
+
+interix[[3-9]]*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='Interix 3.x ld.so.1 (PE, like ELF)'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $host_os in
+ nonstopux*) version_type=nonstopux ;;
+ *)
+ if test "$lt_cv_prog_gnu_ld" = yes; then
+ version_type=linux
+ else
+ version_type=irix
+ fi ;;
+ esac
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${release}${shared_ext} $libname${shared_ext}'
+ case $host_os in
+ irix5* | nonstopux*)
+ libsuff= shlibsuff=
+ ;;
+ *)
+ case $LD in # libtool.m4 will add one of these switches to LD
+ *-32|*"-32 "|*-melf32bsmip|*"-melf32bsmip ")
+ libsuff= shlibsuff= libmagic=32-bit;;
+ *-n32|*"-n32 "|*-melf32bmipn32|*"-melf32bmipn32 ")
+ libsuff=32 shlibsuff=N32 libmagic=N32;;
+ *-64|*"-64 "|*-melf64bmip|*"-melf64bmip ")
+ libsuff=64 shlibsuff=64 libmagic=64-bit;;
+ *) libsuff= shlibsuff= libmagic=never-match;;
+ esac
+ ;;
+ esac
+ shlibpath_var=LD_LIBRARY${shlibsuff}_PATH
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec="/usr/lib${libsuff} /lib${libsuff} /usr/local/lib${libsuff}"
+ sys_lib_dlsearch_path_spec="/usr/lib${libsuff} /lib${libsuff}"
+ hardcode_into_libs=yes
+ ;;
+
+# No shared lib support for Linux oldld, aout, or coff.
+linux*oldld* | linux*aout* | linux*coff*)
+ dynamic_linker=no
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ # Some binutils ld are patched to set DT_RUNPATH
+ save_LDFLAGS=$LDFLAGS
+ save_libdir=$libdir
+ eval "libdir=/foo; wl=\"$_LT_TAGVAR(lt_prog_compiler_wl, $1)\"; \
+ LDFLAGS=\"\$LDFLAGS $_LT_TAGVAR(hardcode_libdir_flag_spec, $1)\""
+ AC_LINK_IFELSE([AC_LANG_PROGRAM([],[])],
+ [AS_IF([ ($OBJDUMP -p conftest$ac_exeext) 2>/dev/null | grep "RUNPATH.*$libdir" >/dev/null],
+ [shlibpath_overrides_runpath=yes])])
+ LDFLAGS=$save_LDFLAGS
+ libdir=$save_libdir
+
+ # This implies no fast_install, which is unacceptable.
+ # Some rework will be needed to allow for fast_install
+ # before this can be enabled.
+ hardcode_into_libs=yes
+
+ # Append ld.so.conf contents to the search path
+ if test -f /etc/ld.so.conf; then
+ lt_ld_extra=`awk '/^include / { system(sprintf("cd /etc; cat %s 2>/dev/null", \[$]2)); skip = 1; } { if (!skip) print \[$]0; skip = 0; }' < /etc/ld.so.conf | $SED -e 's/#.*//;/^[ ]*hwcap[ ]/d;s/[:, ]/ /g;s/=[^=]*$//;s/=[^= ]* / /g;/^$/d' | tr '\n' ' '`
+ sys_lib_dlsearch_path_spec="/lib /usr/lib $lt_ld_extra"
+ fi
+
+ # We used to test for /lib/ld.so.1 and disable shared libraries on
+ # powerpc, because MkLinux only supported shared libraries with the
+ # GNU dynamic linker. Since this was broken with cross compilers,
+ # most powerpc-linux boxes support dynamic linking these days and
+ # people can always --disable-shared, the test was removed, and we
+ # assume the GNU/Linux dynamic linker is in use.
+ dynamic_linker='GNU/Linux ld.so'
+ ;;
+
+netbsdelf*-gnu)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='NetBSD ld.elf_so'
+ ;;
+
+netbsd*)
+ version_type=sunos
+ need_lib_prefix=no
+ need_version=no
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ dynamic_linker='NetBSD (a.out) ld.so'
+ else
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major ${libname}${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ dynamic_linker='NetBSD ld.elf_so'
+ fi
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ ;;
+
+newsos6)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ ;;
+
+*nto* | *qnx*)
+ version_type=qnx
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ dynamic_linker='ldqnx.so'
+ ;;
+
+openbsd*)
+ version_type=sunos
+ sys_lib_dlsearch_path_spec="/usr/lib"
+ need_lib_prefix=no
+ # Some older versions of OpenBSD (3.3 at least) *do* need versioned libs.
+ case $host_os in
+ openbsd3.3 | openbsd3.3.*) need_version=yes ;;
+ *) need_version=no ;;
+ esac
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/sbin" ldconfig -m $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ case $host_os in
+ openbsd2.[[89]] | openbsd2.[[89]].*)
+ shlibpath_overrides_runpath=no
+ ;;
+ *)
+ shlibpath_overrides_runpath=yes
+ ;;
+ esac
+ else
+ shlibpath_overrides_runpath=yes
+ fi
+ ;;
+
+os2*)
+ libname_spec='$name'
+ shrext_cmds=".dll"
+ need_lib_prefix=no
+ library_names_spec='$libname${shared_ext} $libname.a'
+ dynamic_linker='OS/2 ld.exe'
+ shlibpath_var=LIBPATH
+ ;;
+
+osf3* | osf4* | osf5*)
+ version_type=osf
+ need_lib_prefix=no
+ need_version=no
+ soname_spec='${libname}${release}${shared_ext}$major'
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ sys_lib_search_path_spec="/usr/shlib /usr/ccs/lib /usr/lib/cmplrs/cc /usr/lib /usr/local/lib /var/shlib"
+ sys_lib_dlsearch_path_spec="$sys_lib_search_path_spec"
+ ;;
+
+rdos*)
+ dynamic_linker=no
+ ;;
+
+solaris*)
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ # ldd complains unless libraries are executable
+ postinstall_cmds='chmod +x $lib'
+ ;;
+
+sunos4*)
+ version_type=sunos
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${shared_ext}$versuffix'
+ finish_cmds='PATH="\$PATH:/usr/etc" ldconfig $libdir'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ if test "$with_gnu_ld" = yes; then
+ need_lib_prefix=no
+ fi
+ need_version=yes
+ ;;
+
+sysv4 | sysv4.3*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ case $host_vendor in
+ sni)
+ shlibpath_overrides_runpath=no
+ need_lib_prefix=no
+ runpath_var=LD_RUN_PATH
+ ;;
+ siemens)
+ need_lib_prefix=no
+ ;;
+ motorola)
+ need_lib_prefix=no
+ need_version=no
+ shlibpath_overrides_runpath=no
+ sys_lib_search_path_spec='/lib /usr/lib /usr/ccs/lib'
+ ;;
+ esac
+ ;;
+
+sysv4*MP*)
+ if test -d /usr/nec ;then
+ version_type=linux
+ library_names_spec='$libname${shared_ext}.$versuffix $libname${shared_ext}.$major $libname${shared_ext}'
+ soname_spec='$libname${shared_ext}.$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ fi
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ version_type=freebsd-elf
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext} $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=yes
+ hardcode_into_libs=yes
+ if test "$with_gnu_ld" = yes; then
+ sys_lib_search_path_spec='/usr/local/lib /usr/gnu/lib /usr/ccs/lib /usr/lib /lib'
+ else
+ sys_lib_search_path_spec='/usr/ccs/lib /usr/lib'
+ case $host_os in
+ sco3.2v5*)
+ sys_lib_search_path_spec="$sys_lib_search_path_spec /lib"
+ ;;
+ esac
+ fi
+ sys_lib_dlsearch_path_spec='/usr/lib'
+ ;;
+
+tpf*)
+ # TPF is a cross-target only. Preferred cross-host = GNU/Linux.
+ version_type=linux
+ need_lib_prefix=no
+ need_version=no
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ shlibpath_var=LD_LIBRARY_PATH
+ shlibpath_overrides_runpath=no
+ hardcode_into_libs=yes
+ ;;
+
+uts4*)
+ version_type=linux
+ library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+ soname_spec='${libname}${release}${shared_ext}$major'
+ shlibpath_var=LD_LIBRARY_PATH
+ ;;
+
+*)
+ dynamic_linker=no
+ ;;
+esac
+AC_MSG_RESULT([$dynamic_linker])
+test "$dynamic_linker" = no && can_build_shared=no
+
+variables_saved_for_relink="PATH $shlibpath_var $runpath_var"
+if test "$GCC" = yes; then
+ variables_saved_for_relink="$variables_saved_for_relink GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+fi
+
+if test "${lt_cv_sys_lib_search_path_spec+set}" = set; then
+ sys_lib_search_path_spec="$lt_cv_sys_lib_search_path_spec"
+fi
+if test "${lt_cv_sys_lib_dlsearch_path_spec+set}" = set; then
+ sys_lib_dlsearch_path_spec="$lt_cv_sys_lib_dlsearch_path_spec"
+fi
+
+_LT_DECL([], [variables_saved_for_relink], [1],
+ [Variables whose values should be saved in libtool wrapper scripts and
+ restored at link time])
+_LT_DECL([], [need_lib_prefix], [0],
+ [Do we need the "lib" prefix for modules?])
+_LT_DECL([], [need_version], [0], [Do we need a version for libraries?])
+_LT_DECL([], [version_type], [0], [Library versioning type])
+_LT_DECL([], [runpath_var], [0], [Shared library runtime path variable])
+_LT_DECL([], [shlibpath_var], [0],[Shared library path variable])
+_LT_DECL([], [shlibpath_overrides_runpath], [0],
+ [Is shlibpath searched before the hard-coded library search path?])
+_LT_DECL([], [libname_spec], [1], [Format of library name prefix])
+_LT_DECL([], [library_names_spec], [1],
+ [[List of archive names. First name is the real one, the rest are links.
+ The last name is the one that the linker finds with -lNAME]])
+_LT_DECL([], [soname_spec], [1],
+ [[The coded name of the library, if different from the real name]])
+_LT_DECL([], [postinstall_cmds], [2],
+ [Command to use after installation of a shared archive])
+_LT_DECL([], [postuninstall_cmds], [2],
+ [Command to use after uninstallation of a shared archive])
+_LT_DECL([], [finish_cmds], [2],
+ [Commands used to finish a libtool library installation in a directory])
+_LT_DECL([], [finish_eval], [1],
+ [[As "finish_cmds", except a single script fragment to be evaled but
+ not shown]])
+_LT_DECL([], [hardcode_into_libs], [0],
+ [Whether we should hardcode library paths into libraries])
+_LT_DECL([], [sys_lib_search_path_spec], [2],
+ [Compile-time system search path for libraries])
+_LT_DECL([], [sys_lib_dlsearch_path_spec], [2],
+ [Run-time system search path for libraries])
+])# _LT_SYS_DYNAMIC_LINKER
+
+
+# _LT_PATH_TOOL_PREFIX(TOOL)
+# --------------------------
+# find a file program which can recognize shared library
+AC_DEFUN([_LT_PATH_TOOL_PREFIX],
+[m4_require([_LT_DECL_EGREP])dnl
+AC_MSG_CHECKING([for $1])
+AC_CACHE_VAL(lt_cv_path_MAGIC_CMD,
+[case $MAGIC_CMD in
+[[\\/*] | ?:[\\/]*])
+ lt_cv_path_MAGIC_CMD="$MAGIC_CMD" # Let the user override the test with a path.
+ ;;
+*)
+ lt_save_MAGIC_CMD="$MAGIC_CMD"
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+dnl $ac_dummy forces splitting on constant user-supplied paths.
+dnl POSIX.2 word splitting is done only on the output of word expansions,
+dnl not every word. This closes a longstanding sh security hole.
+ ac_dummy="m4_if([$2], , $PATH, [$2])"
+ for ac_dir in $ac_dummy; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f $ac_dir/$1; then
+ lt_cv_path_MAGIC_CMD="$ac_dir/$1"
+ if test -n "$file_magic_test_file"; then
+ case $deplibs_check_method in
+ "file_magic "*)
+ file_magic_regex=`expr "$deplibs_check_method" : "file_magic \(.*\)"`
+ MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+ if eval $file_magic_cmd \$file_magic_test_file 2> /dev/null |
+ $EGREP "$file_magic_regex" > /dev/null; then
+ :
+ else
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the command libtool uses to detect shared libraries,
+*** $file_magic_cmd, produces output that libtool cannot recognize.
+*** The result is that libtool may fail to recognize shared libraries
+*** as such. This will affect the creation of libtool libraries that
+*** depend on shared libraries, but programs linked with such libtool
+*** libraries will work regardless of this problem. Nevertheless, you
+*** may want to report the problem to your system manager and/or to
+*** bug-libtool@gnu.org
+
+_LT_EOF
+ fi ;;
+ esac
+ fi
+ break
+ fi
+ done
+ IFS="$lt_save_ifs"
+ MAGIC_CMD="$lt_save_MAGIC_CMD"
+ ;;
+esac])
+MAGIC_CMD="$lt_cv_path_MAGIC_CMD"
+if test -n "$MAGIC_CMD"; then
+ AC_MSG_RESULT($MAGIC_CMD)
+else
+ AC_MSG_RESULT(no)
+fi
+_LT_DECL([], [MAGIC_CMD], [0],
+ [Used to examine libraries when file_magic_cmd begins with "file"])dnl
+])# _LT_PATH_TOOL_PREFIX
+
+# Old name:
+AU_ALIAS([AC_PATH_TOOL_PREFIX], [_LT_PATH_TOOL_PREFIX])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_PATH_TOOL_PREFIX], [])
+
+
+# _LT_PATH_MAGIC
+# --------------
+# find a file program which can recognize a shared library
+m4_defun([_LT_PATH_MAGIC],
+[_LT_PATH_TOOL_PREFIX(${ac_tool_prefix}file, /usr/bin$PATH_SEPARATOR$PATH)
+if test -z "$lt_cv_path_MAGIC_CMD"; then
+ if test -n "$ac_tool_prefix"; then
+ _LT_PATH_TOOL_PREFIX(file, /usr/bin$PATH_SEPARATOR$PATH)
+ else
+ MAGIC_CMD=:
+ fi
+fi
+])# _LT_PATH_MAGIC
+
+
+# LT_PATH_LD
+# ----------
+# find the pathname to the GNU or non-GNU linker
+AC_DEFUN([LT_PATH_LD],
+[AC_REQUIRE([AC_PROG_CC])dnl
+AC_REQUIRE([AC_CANONICAL_HOST])dnl
+AC_REQUIRE([AC_CANONICAL_BUILD])dnl
+m4_require([_LT_DECL_SED])dnl
+m4_require([_LT_DECL_EGREP])dnl
+
+AC_ARG_WITH([gnu-ld],
+ [AS_HELP_STRING([--with-gnu-ld],
+ [assume the C compiler uses GNU ld @<:@default=no@:>@])],
+ [test "$withval" = no || with_gnu_ld=yes],
+ [with_gnu_ld=no])dnl
+
+ac_prog=ld
+if test "$GCC" = yes; then
+ # Check if gcc -print-prog-name=ld gives a path.
+ AC_MSG_CHECKING([for ld used by $CC])
+ case $host in
+ *-*-mingw*)
+ # gcc leaves a trailing carriage return which upsets mingw
+ ac_prog=`($CC -print-prog-name=ld) 2>&5 | tr -d '\015'` ;;
+ *)
+ ac_prog=`($CC -print-prog-name=ld) 2>&5` ;;
+ esac
+ case $ac_prog in
+ # Accept absolute paths.
+ [[\\/]]* | ?:[[\\/]]*)
+ re_direlt='/[[^/]][[^/]]*/\.\./'
+ # Canonicalize the pathname of ld
+ ac_prog=`$ECHO "$ac_prog"| $SED 's%\\\\%/%g'`
+ while $ECHO "$ac_prog" | $GREP "$re_direlt" > /dev/null 2>&1; do
+ ac_prog=`$ECHO $ac_prog| $SED "s%$re_direlt%/%"`
+ done
+ test -z "$LD" && LD="$ac_prog"
+ ;;
+ "")
+ # If it fails, then pretend we aren't using GCC.
+ ac_prog=ld
+ ;;
+ *)
+ # If it is relative, then search for the first ld in PATH.
+ with_gnu_ld=unknown
+ ;;
+ esac
+elif test "$with_gnu_ld" = yes; then
+ AC_MSG_CHECKING([for GNU ld])
+else
+ AC_MSG_CHECKING([for non-GNU ld])
+fi
+AC_CACHE_VAL(lt_cv_path_LD,
+[if test -z "$LD"; then
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ if test -f "$ac_dir/$ac_prog" || test -f "$ac_dir/$ac_prog$ac_exeext"; then
+ lt_cv_path_LD="$ac_dir/$ac_prog"
+ # Check to see if the program is GNU ld. I'd rather use --version,
+ # but apparently some variants of GNU ld only accept -v.
+ # Break only if it was the GNU/non-GNU ld that we prefer.
+ case `"$lt_cv_path_LD" -v 2>&1 </dev/null` in
+ *GNU* | *'with BFD'*)
+ test "$with_gnu_ld" != no && break
+ ;;
+ *)
+ test "$with_gnu_ld" != yes && break
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+else
+ lt_cv_path_LD="$LD" # Let the user override the test with a path.
+fi])
+LD="$lt_cv_path_LD"
+if test -n "$LD"; then
+ AC_MSG_RESULT($LD)
+else
+ AC_MSG_RESULT(no)
+fi
+test -z "$LD" && AC_MSG_ERROR([no acceptable ld found in \$PATH])
+_LT_PATH_LD_GNU
+AC_SUBST([LD])
+
+_LT_TAGDECL([], [LD], [1], [The linker used to build libraries])
+])# LT_PATH_LD
+
+# Old names:
+AU_ALIAS([AM_PROG_LD], [LT_PATH_LD])
+AU_ALIAS([AC_PROG_LD], [LT_PATH_LD])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AM_PROG_LD], [])
+dnl AC_DEFUN([AC_PROG_LD], [])
+
+
+# _LT_PATH_LD_GNU
+#- --------------
+m4_defun([_LT_PATH_LD_GNU],
+[AC_CACHE_CHECK([if the linker ($LD) is GNU ld], lt_cv_prog_gnu_ld,
+[# I'd rather use --version here, but apparently some GNU lds only accept -v.
+case `$LD -v 2>&1 </dev/null` in
+*GNU* | *'with BFD'*)
+ lt_cv_prog_gnu_ld=yes
+ ;;
+*)
+ lt_cv_prog_gnu_ld=no
+ ;;
+esac])
+with_gnu_ld=$lt_cv_prog_gnu_ld
+])# _LT_PATH_LD_GNU
+
+
+# _LT_CMD_RELOAD
+# --------------
+# find reload flag for linker
+# -- PORTME Some linkers may need a different reload flag.
+m4_defun([_LT_CMD_RELOAD],
+[AC_CACHE_CHECK([for $LD option to reload object files],
+ lt_cv_ld_reload_flag,
+ [lt_cv_ld_reload_flag='-r'])
+reload_flag=$lt_cv_ld_reload_flag
+case $reload_flag in
+"" | " "*) ;;
+*) reload_flag=" $reload_flag" ;;
+esac
+reload_cmds='$LD$reload_flag -o $output$reload_objs'
+case $host_os in
+ darwin*)
+ if test "$GCC" = yes; then
+ reload_cmds='$LTCC $LTCFLAGS -nostdlib ${wl}-r -o $output$reload_objs'
+ else
+ reload_cmds='$LD$reload_flag -o $output$reload_objs'
+ fi
+ ;;
+esac
+_LT_DECL([], [reload_flag], [1], [How to create reloadable object files])dnl
+_LT_DECL([], [reload_cmds], [2])dnl
+])# _LT_CMD_RELOAD
+
+
+# _LT_CHECK_MAGIC_METHOD
+# ----------------------
+# how to check for library dependencies
+# -- PORTME fill in with the dynamic library characteristics
+m4_defun([_LT_CHECK_MAGIC_METHOD],
+[m4_require([_LT_DECL_EGREP])
+m4_require([_LT_DECL_OBJDUMP])
+AC_CACHE_CHECK([how to recognize dependent libraries],
+lt_cv_deplibs_check_method,
+[lt_cv_file_magic_cmd='$MAGIC_CMD'
+lt_cv_file_magic_test_file=
+lt_cv_deplibs_check_method='unknown'
+# Need to set the preceding variable on all platforms that support
+# interlibrary dependencies.
+# 'none' -- dependencies not supported.
+# `unknown' -- same as none, but documents that we really don't know.
+# 'pass_all' -- all dependencies passed with no checks.
+# 'test_compile' -- check by making test program.
+# 'file_magic [[regex]]' -- check by looking for files in library path
+# which responds to the $file_magic_cmd with a given extended regex.
+# If you have `file' or equivalent on your system and you're not sure
+# whether `pass_all' will *always* work, you probably want this one.
+
+case $host_os in
+aix[[4-9]]*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+beos*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+bsdi[[45]]*)
+ lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (shared object|dynamic lib)'
+ lt_cv_file_magic_cmd='/usr/bin/file -L'
+ lt_cv_file_magic_test_file=/shlib/libc.so
+ ;;
+
+cygwin*)
+ # func_win32_libid is a shell function defined in ltmain.sh
+ lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL'
+ lt_cv_file_magic_cmd='func_win32_libid'
+ ;;
+
+mingw* | pw32*)
+ # Base MSYS/MinGW do not provide the 'file' command needed by
+ # func_win32_libid shell function, so use a weaker test based on 'objdump',
+ # unless we find 'file', for example because we are cross-compiling.
+ if ( file / ) >/dev/null 2>&1; then
+ lt_cv_deplibs_check_method='file_magic ^x86 archive import|^x86 DLL'
+ lt_cv_file_magic_cmd='func_win32_libid'
+ else
+ lt_cv_deplibs_check_method='file_magic file format pei*-i386(.*architecture: i386)?'
+ lt_cv_file_magic_cmd='$OBJDUMP -f'
+ fi
+ ;;
+
+cegcc)
+ # use the weaker test based on 'objdump'. See mingw*.
+ lt_cv_deplibs_check_method='file_magic file format pe-arm-.*little(.*architecture: arm)?'
+ lt_cv_file_magic_cmd='$OBJDUMP -f'
+ ;;
+
+darwin* | rhapsody*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+freebsd* | dragonfly*)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
+ case $host_cpu in
+ i*86 )
+ # Not sure whether the presence of OpenBSD here was a mistake.
+ # Let's accept both of them until this is cleared up.
+ lt_cv_deplibs_check_method='file_magic (FreeBSD|OpenBSD|DragonFly)/i[[3-9]]86 (compact )?demand paged shared library'
+ lt_cv_file_magic_cmd=/usr/bin/file
+ lt_cv_file_magic_test_file=`echo /usr/lib/libc.so.*`
+ ;;
+ esac
+ else
+ lt_cv_deplibs_check_method=pass_all
+ fi
+ ;;
+
+gnu*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+hpux10.20* | hpux11*)
+ lt_cv_file_magic_cmd=/usr/bin/file
+ case $host_cpu in
+ ia64*)
+ lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|ELF-[[0-9]][[0-9]]) shared object file - IA64'
+ lt_cv_file_magic_test_file=/usr/lib/hpux32/libc.so
+ ;;
+ hppa*64*)
+ [lt_cv_deplibs_check_method='file_magic (s[0-9][0-9][0-9]|ELF-[0-9][0-9]) shared object file - PA-RISC [0-9].[0-9]']
+ lt_cv_file_magic_test_file=/usr/lib/pa20_64/libc.sl
+ ;;
+ *)
+ lt_cv_deplibs_check_method='file_magic (s[[0-9]][[0-9]][[0-9]]|PA-RISC[[0-9]].[[0-9]]) shared library'
+ lt_cv_file_magic_test_file=/usr/lib/libc.sl
+ ;;
+ esac
+ ;;
+
+interix[[3-9]]*)
+ # PIC code is broken on Interix 3.x, that's why |\.a not |_pic\.a here
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|\.a)$'
+ ;;
+
+irix5* | irix6* | nonstopux*)
+ case $LD in
+ *-32|*"-32 ") libmagic=32-bit;;
+ *-n32|*"-n32 ") libmagic=N32;;
+ *-64|*"-64 ") libmagic=64-bit;;
+ *) libmagic=never-match;;
+ esac
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+# This must be Linux ELF.
+linux* | k*bsd*-gnu)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ > /dev/null; then
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$'
+ else
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so|_pic\.a)$'
+ fi
+ ;;
+
+newos6*)
+ lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (executable|dynamic lib)'
+ lt_cv_file_magic_cmd=/usr/bin/file
+ lt_cv_file_magic_test_file=/usr/lib/libnls.so
+ ;;
+
+*nto* | *qnx*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+openbsd*)
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|\.so|_pic\.a)$'
+ else
+ lt_cv_deplibs_check_method='match_pattern /lib[[^/]]+(\.so\.[[0-9]]+\.[[0-9]]+|_pic\.a)$'
+ fi
+ ;;
+
+osf3* | osf4* | osf5*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+rdos*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+solaris*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX* | sysv4*uw2*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+
+sysv4 | sysv4.3*)
+ case $host_vendor in
+ motorola)
+ lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[ML]]SB (shared object|dynamic lib) M[[0-9]][[0-9]]* Version [[0-9]]'
+ lt_cv_file_magic_test_file=`echo /usr/lib/libc.so*`
+ ;;
+ ncr)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ sequent)
+ lt_cv_file_magic_cmd='/bin/file'
+ lt_cv_deplibs_check_method='file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB (shared object|dynamic lib )'
+ ;;
+ sni)
+ lt_cv_file_magic_cmd='/bin/file'
+ lt_cv_deplibs_check_method="file_magic ELF [[0-9]][[0-9]]*-bit [[LM]]SB dynamic lib"
+ lt_cv_file_magic_test_file=/lib/libc.so
+ ;;
+ siemens)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ pc)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+ esac
+ ;;
+
+tpf*)
+ lt_cv_deplibs_check_method=pass_all
+ ;;
+esac
+])
+file_magic_cmd=$lt_cv_file_magic_cmd
+deplibs_check_method=$lt_cv_deplibs_check_method
+test -z "$deplibs_check_method" && deplibs_check_method=unknown
+
+_LT_DECL([], [deplibs_check_method], [1],
+ [Method to check whether dependent libraries are shared objects])
+_LT_DECL([], [file_magic_cmd], [1],
+ [Command to use when deplibs_check_method == "file_magic"])
+])# _LT_CHECK_MAGIC_METHOD
+
+
+# LT_PATH_NM
+# ----------
+# find the pathname to a BSD- or MS-compatible name lister
+AC_DEFUN([LT_PATH_NM],
+[AC_REQUIRE([AC_PROG_CC])dnl
+AC_CACHE_CHECK([for BSD- or MS-compatible name lister (nm)], lt_cv_path_NM,
+[if test -n "$NM"; then
+ # Let the user override the test.
+ lt_cv_path_NM="$NM"
+else
+ lt_nm_to_check="${ac_tool_prefix}nm"
+ if test -n "$ac_tool_prefix" && test "$build" = "$host"; then
+ lt_nm_to_check="$lt_nm_to_check nm"
+ fi
+ for lt_tmp_nm in $lt_nm_to_check; do
+ lt_save_ifs="$IFS"; IFS=$PATH_SEPARATOR
+ for ac_dir in $PATH /usr/ccs/bin/elf /usr/ccs/bin /usr/ucb /bin; do
+ IFS="$lt_save_ifs"
+ test -z "$ac_dir" && ac_dir=.
+ tmp_nm="$ac_dir/$lt_tmp_nm"
+ if test -f "$tmp_nm" || test -f "$tmp_nm$ac_exeext" ; then
+ # Check to see if the nm accepts a BSD-compat flag.
+ # Adding the `sed 1q' prevents false positives on HP-UX, which says:
+ # nm: unknown option "B" ignored
+ # Tru64's nm complains that /dev/null is an invalid object file
+ case `"$tmp_nm" -B /dev/null 2>&1 | sed '1q'` in
+ */dev/null* | *'Invalid file or object type'*)
+ lt_cv_path_NM="$tmp_nm -B"
+ break
+ ;;
+ *)
+ case `"$tmp_nm" -p /dev/null 2>&1 | sed '1q'` in
+ */dev/null*)
+ lt_cv_path_NM="$tmp_nm -p"
+ break
+ ;;
+ *)
+ lt_cv_path_NM=${lt_cv_path_NM="$tmp_nm"} # keep the first match, but
+ continue # so that we can try to find one that supports BSD flags
+ ;;
+ esac
+ ;;
+ esac
+ fi
+ done
+ IFS="$lt_save_ifs"
+ done
+ : ${lt_cv_path_NM=no}
+fi])
+if test "$lt_cv_path_NM" != "no"; then
+ NM="$lt_cv_path_NM"
+else
+ # Didn't find any BSD compatible name lister, look for dumpbin.
+ AC_CHECK_TOOLS(DUMPBIN, ["dumpbin -symbols" "link -dump -symbols"], :)
+ AC_SUBST([DUMPBIN])
+ if test "$DUMPBIN" != ":"; then
+ NM="$DUMPBIN"
+ fi
+fi
+test -z "$NM" && NM=nm
+AC_SUBST([NM])
+_LT_DECL([], [NM], [1], [A BSD- or MS-compatible name lister])dnl
+
+AC_CACHE_CHECK([the name lister ($NM) interface], [lt_cv_nm_interface],
+ [lt_cv_nm_interface="BSD nm"
+ echo "int some_variable = 0;" > conftest.$ac_ext
+ (eval echo "\"\$as_me:__oline__: $ac_compile\"" >&AS_MESSAGE_LOG_FD)
+ (eval "$ac_compile" 2>conftest.err)
+ cat conftest.err >&AS_MESSAGE_LOG_FD
+ (eval echo "\"\$as_me:__oline__: $NM \\\"conftest.$ac_objext\\\"\"" >&AS_MESSAGE_LOG_FD)
+ (eval "$NM \"conftest.$ac_objext\"" 2>conftest.err > conftest.out)
+ cat conftest.err >&AS_MESSAGE_LOG_FD
+ (eval echo "\"\$as_me:__oline__: output\"" >&AS_MESSAGE_LOG_FD)
+ cat conftest.out >&AS_MESSAGE_LOG_FD
+ if $GREP 'External.*some_variable' conftest.out > /dev/null; then
+ lt_cv_nm_interface="MS dumpbin"
+ fi
+ rm -f conftest*])
+])# LT_PATH_NM
+
+# Old names:
+AU_ALIAS([AM_PROG_NM], [LT_PATH_NM])
+AU_ALIAS([AC_PROG_NM], [LT_PATH_NM])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AM_PROG_NM], [])
+dnl AC_DEFUN([AC_PROG_NM], [])
+
+
+# LT_LIB_M
+# --------
+# check for math library
+AC_DEFUN([LT_LIB_M],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+LIBM=
+case $host in
+*-*-beos* | *-*-cygwin* | *-*-pw32* | *-*-darwin*)
+ # These system don't have libm, or don't need it
+ ;;
+*-ncr-sysv4.3*)
+ AC_CHECK_LIB(mw, _mwvalidcheckl, LIBM="-lmw")
+ AC_CHECK_LIB(m, cos, LIBM="$LIBM -lm")
+ ;;
+*)
+ AC_CHECK_LIB(m, cos, LIBM="-lm")
+ ;;
+esac
+AC_SUBST([LIBM])
+])# LT_LIB_M
+
+# Old name:
+AU_ALIAS([AC_CHECK_LIBM], [LT_LIB_M])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_CHECK_LIBM], [])
+
+
+# _LT_COMPILER_NO_RTTI([TAGNAME])
+# -------------------------------
+m4_defun([_LT_COMPILER_NO_RTTI],
+[m4_require([_LT_TAG_COMPILER])dnl
+
+_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=
+
+if test "$GCC" = yes; then
+ _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -fno-builtin'
+
+ _LT_COMPILER_OPTION([if $compiler supports -fno-rtti -fno-exceptions],
+ lt_cv_prog_compiler_rtti_exceptions,
+ [-fno-rtti -fno-exceptions], [],
+ [_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)="$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1) -fno-rtti -fno-exceptions"])
+fi
+_LT_TAGDECL([no_builtin_flag], [lt_prog_compiler_no_builtin_flag], [1],
+ [Compiler flag to turn off builtin functions])
+])# _LT_COMPILER_NO_RTTI
+
+
+# _LT_CMD_GLOBAL_SYMBOLS
+# ----------------------
+m4_defun([_LT_CMD_GLOBAL_SYMBOLS],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+AC_REQUIRE([AC_PROG_CC])dnl
+AC_REQUIRE([LT_PATH_NM])dnl
+AC_REQUIRE([LT_PATH_LD])dnl
+m4_require([_LT_DECL_SED])dnl
+m4_require([_LT_DECL_EGREP])dnl
+m4_require([_LT_TAG_COMPILER])dnl
+
+# Check for command to grab the raw symbol name followed by C symbol from nm.
+AC_MSG_CHECKING([command to parse $NM output from $compiler object])
+AC_CACHE_VAL([lt_cv_sys_global_symbol_pipe],
+[
+# These are sane defaults that work on at least a few old systems.
+# [They come from Ultrix. What could be older than Ultrix?!! ;)]
+
+# Character class describing NM global symbol codes.
+symcode='[[BCDEGRST]]'
+
+# Regexp to match symbols that can be accessed directly from C.
+sympat='\([[_A-Za-z]][[_A-Za-z0-9]]*\)'
+
+# Define system-specific variables.
+case $host_os in
+aix*)
+ symcode='[[BCDT]]'
+ ;;
+cygwin* | mingw* | pw32* | cegcc*)
+ symcode='[[ABCDGISTW]]'
+ ;;
+hpux*)
+ if test "$host_cpu" = ia64; then
+ symcode='[[ABCDEGRST]]'
+ fi
+ ;;
+irix* | nonstopux*)
+ symcode='[[BCDEGRST]]'
+ ;;
+osf*)
+ symcode='[[BCDEGQRST]]'
+ ;;
+solaris*)
+ symcode='[[BDRT]]'
+ ;;
+sco3.2v5*)
+ symcode='[[DT]]'
+ ;;
+sysv4.2uw2*)
+ symcode='[[DT]]'
+ ;;
+sysv5* | sco5v6* | unixware* | OpenUNIX*)
+ symcode='[[ABDT]]'
+ ;;
+sysv4)
+ symcode='[[DFNSTU]]'
+ ;;
+esac
+
+# If we're using GNU nm, then use its standard symbol codes.
+case `$NM -V 2>&1` in
+*GNU* | *'with BFD'*)
+ symcode='[[ABCDGIRSTW]]' ;;
+esac
+
+# Transform an extracted symbol line into a proper C declaration.
+# Some systems (esp. on ia64) link data and code symbols differently,
+# so use this general approach.
+lt_cv_sys_global_symbol_to_cdecl="sed -n -e 's/^T .* \(.*\)$/extern int \1();/p' -e 's/^$symcode* .* \(.*\)$/extern char \1;/p'"
+
+# Transform an extracted symbol line into symbol name and symbol address
+lt_cv_sys_global_symbol_to_c_name_address="sed -n -e 's/^: \([[^ ]]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p'"
+lt_cv_sys_global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \([[^ ]]*\) $/ {\\\"\1\\\", (void *) 0},/p' -e 's/^$symcode* \([[^ ]]*\) \(lib[[^ ]]*\)$/ {\"\2\", (void *) \&\2},/p' -e 's/^$symcode* \([[^ ]]*\) \([[^ ]]*\)$/ {\"lib\2\", (void *) \&\2},/p'"
+
+# Handle CRLF in mingw tool chain
+opt_cr=
+case $build_os in
+mingw*)
+ opt_cr=`$ECHO 'x\{0,1\}' | tr x '\015'` # option cr in regexp
+ ;;
+esac
+
+# Try without a prefix underscore, then with it.
+for ac_symprfx in "" "_"; do
+
+ # Transform symcode, sympat, and symprfx into a raw symbol and a C symbol.
+ symxfrm="\\1 $ac_symprfx\\2 \\2"
+
+ # Write the raw and C identifiers.
+ if test "$lt_cv_nm_interface" = "MS dumpbin"; then
+ # Fake it for dumpbin and say T for any non-static function
+ # and D for any global variable.
+ # Also find C++ and __fastcall symbols from MSVC++,
+ # which start with @ or ?.
+ lt_cv_sys_global_symbol_pipe="$AWK ['"\
+" {last_section=section; section=\$ 3};"\
+" /Section length .*#relocs.*(pick any)/{hide[last_section]=1};"\
+" \$ 0!~/External *\|/{next};"\
+" / 0+ UNDEF /{next}; / UNDEF \([^|]\)*()/{next};"\
+" {if(hide[section]) next};"\
+" {f=0}; \$ 0~/\(\).*\|/{f=1}; {printf f ? \"T \" : \"D \"};"\
+" {split(\$ 0, a, /\||\r/); split(a[2], s)};"\
+" s[1]~/^[@?]/{print s[1], s[1]; next};"\
+" s[1]~prfx {split(s[1],t,\"@\"); print t[1], substr(t[1],length(prfx))}"\
+" ' prfx=^$ac_symprfx]"
+ else
+ lt_cv_sys_global_symbol_pipe="sed -n -e 's/^.*[[ ]]\($symcode$symcode*\)[[ ]][[ ]]*$ac_symprfx$sympat$opt_cr$/$symxfrm/p'"
+ fi
+
+ # Check to see that the pipe works correctly.
+ pipe_works=no
+
+ rm -f conftest*
+ cat > conftest.$ac_ext <<_LT_EOF
+#ifdef __cplusplus
+extern "C" {
+#endif
+char nm_test_var;
+void nm_test_func(void);
+void nm_test_func(void){}
+#ifdef __cplusplus
+}
+#endif
+int main(){nm_test_var='a';nm_test_func();return(0);}
+_LT_EOF
+
+ if AC_TRY_EVAL(ac_compile); then
+ # Now try to grab the symbols.
+ nlist=conftest.nm
+ if AC_TRY_EVAL(NM conftest.$ac_objext \| $lt_cv_sys_global_symbol_pipe \> $nlist) && test -s "$nlist"; then
+ # Try sorting and uniquifying the output.
+ if sort "$nlist" | uniq > "$nlist"T; then
+ mv -f "$nlist"T "$nlist"
+ else
+ rm -f "$nlist"T
+ fi
+
+ # Make sure that we snagged all the symbols we need.
+ if $GREP ' nm_test_var$' "$nlist" >/dev/null; then
+ if $GREP ' nm_test_func$' "$nlist" >/dev/null; then
+ cat <<_LT_EOF > conftest.$ac_ext
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+_LT_EOF
+ # Now generate the symbol file.
+ eval "$lt_cv_sys_global_symbol_to_cdecl"' < "$nlist" | $GREP -v main >> conftest.$ac_ext'
+
+ cat <<_LT_EOF >> conftest.$ac_ext
+
+/* The mapping between symbol names and symbols. */
+const struct {
+ const char *name;
+ void *address;
+}
+lt__PROGRAM__LTX_preloaded_symbols[[]] =
+{
+ { "@PROGRAM@", (void *) 0 },
+_LT_EOF
+ $SED "s/^$symcode$symcode* \(.*\) \(.*\)$/ {\"\2\", (void *) \&\2},/" < "$nlist" | $GREP -v main >> conftest.$ac_ext
+ cat <<\_LT_EOF >> conftest.$ac_ext
+ {0, (void *) 0}
+};
+
+/* This works around a problem in FreeBSD linker */
+#ifdef FREEBSD_WORKAROUND
+static const void *lt_preloaded_setup() {
+ return lt__PROGRAM__LTX_preloaded_symbols;
+}
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+_LT_EOF
+ # Now try linking the two files.
+ mv conftest.$ac_objext conftstm.$ac_objext
+ lt_save_LIBS="$LIBS"
+ lt_save_CFLAGS="$CFLAGS"
+ LIBS="conftstm.$ac_objext"
+ CFLAGS="$CFLAGS$_LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)"
+ if AC_TRY_EVAL(ac_link) && test -s conftest${ac_exeext}; then
+ pipe_works=yes
+ fi
+ LIBS="$lt_save_LIBS"
+ CFLAGS="$lt_save_CFLAGS"
+ else
+ echo "cannot find nm_test_func in $nlist" >&AS_MESSAGE_LOG_FD
+ fi
+ else
+ echo "cannot find nm_test_var in $nlist" >&AS_MESSAGE_LOG_FD
+ fi
+ else
+ echo "cannot run $lt_cv_sys_global_symbol_pipe" >&AS_MESSAGE_LOG_FD
+ fi
+ else
+ echo "$progname: failed program was:" >&AS_MESSAGE_LOG_FD
+ cat conftest.$ac_ext >&5
+ fi
+ rm -rf conftest* conftst*
+
+ # Do not use the global_symbol_pipe unless it works.
+ if test "$pipe_works" = yes; then
+ break
+ else
+ lt_cv_sys_global_symbol_pipe=
+ fi
+done
+])
+if test -z "$lt_cv_sys_global_symbol_pipe"; then
+ lt_cv_sys_global_symbol_to_cdecl=
+fi
+if test -z "$lt_cv_sys_global_symbol_pipe$lt_cv_sys_global_symbol_to_cdecl"; then
+ AC_MSG_RESULT(failed)
+else
+ AC_MSG_RESULT(ok)
+fi
+
+_LT_DECL([global_symbol_pipe], [lt_cv_sys_global_symbol_pipe], [1],
+ [Take the output of nm and produce a listing of raw symbols and C names])
+_LT_DECL([global_symbol_to_cdecl], [lt_cv_sys_global_symbol_to_cdecl], [1],
+ [Transform the output of nm in a proper C declaration])
+_LT_DECL([global_symbol_to_c_name_address],
+ [lt_cv_sys_global_symbol_to_c_name_address], [1],
+ [Transform the output of nm in a C name address pair])
+_LT_DECL([global_symbol_to_c_name_address_lib_prefix],
+ [lt_cv_sys_global_symbol_to_c_name_address_lib_prefix], [1],
+ [Transform the output of nm in a C name address pair when lib prefix is needed])
+]) # _LT_CMD_GLOBAL_SYMBOLS
+
+
+# _LT_COMPILER_PIC([TAGNAME])
+# ---------------------------
+m4_defun([_LT_COMPILER_PIC],
+[m4_require([_LT_TAG_COMPILER])dnl
+_LT_TAGVAR(lt_prog_compiler_wl, $1)=
+_LT_TAGVAR(lt_prog_compiler_pic, $1)=
+_LT_TAGVAR(lt_prog_compiler_static, $1)=
+
+AC_MSG_CHECKING([for $compiler option to produce PIC])
+m4_if([$1], [CXX], [
+ # C++ specific cases for pic, static, wl, etc.
+ if test "$GXX" = yes; then
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+
+ case $host_os in
+ aix*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ m68k)
+ # FIXME: we need at least 68020 code to build shared libraries, but
+ # adding the `-m68020' flag to GCC prevents building anything better,
+ # like `-m68040'.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4'
+ ;;
+ esac
+ ;;
+
+ beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+ # PIC is the default for these OSes.
+ ;;
+ mingw* | cygwin* | os2* | pw32* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ # Although the cygwin gcc ignores -fPIC, still need this for old-style
+ # (--disable-auto-import) libraries
+ m4_if([$1], [GCJ], [],
+ [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT'])
+ ;;
+ darwin* | rhapsody*)
+ # PIC is the default on this platform
+ # Common symbols not allowed in MH_DYLIB files
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common'
+ ;;
+ *djgpp*)
+ # DJGPP does not support shared libraries at all
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ ;;
+ interix[[3-9]]*)
+ # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+ # Instead, we relocate shared libraries at runtime.
+ ;;
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic
+ fi
+ ;;
+ hpux*)
+ # PIC is the default for 64-bit PA HP-UX, but not for 32-bit
+ # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag
+ # sets the default TLS model and affects inlining.
+ case $host_cpu in
+ hppa*64*)
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ esac
+ ;;
+ *qnx* | *nto*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared'
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ esac
+ else
+ case $host_os in
+ aix[[4-9]]*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ else
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp'
+ fi
+ ;;
+ chorus*)
+ case $cc_basename in
+ cxch68*)
+ # Green Hills C++ Compiler
+ # _LT_TAGVAR(lt_prog_compiler_static, $1)="--no_auto_instantiation -u __main -u __premain -u _abort -r $COOL_DIR/lib/libOrb.a $MVME_DIR/lib/CC/libC.a $MVME_DIR/lib/classix/libcx.s.a"
+ ;;
+ esac
+ ;;
+ dgux*)
+ case $cc_basename in
+ ec++*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ ;;
+ ghcx*)
+ # Green Hills C++ Compiler
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ freebsd* | dragonfly*)
+ # FreeBSD uses GNU C++
+ ;;
+ hpux9* | hpux10* | hpux11*)
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive'
+ if test "$host_cpu" != ia64; then
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z'
+ fi
+ ;;
+ aCC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive'
+ case $host_cpu in
+ hppa*64*|ia64*)
+ # +Z the default
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z'
+ ;;
+ esac
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ interix*)
+ # This is c89, which is MS Visual C++ (no shared libs)
+ # Anyone wants to do a port?
+ ;;
+ irix5* | irix6* | nonstopux*)
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ # CC pic flag -KPIC is the default.
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ linux* | k*bsd*-gnu)
+ case $cc_basename in
+ KCC*)
+ # KAI C++ Compiler
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ ecpc* )
+ # old Intel C++ for x86_64 which still supported -KPIC.
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+ ;;
+ icpc* )
+ # Intel C++, used to be incompatible with GCC.
+ # ICC 10 doesn't accept -KPIC any more.
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+ ;;
+ pgCC* | pgcpp*)
+ # Portland Group C++ compiler
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+ cxx*)
+ # Compaq C++
+ # Make sure the PIC flag is empty. It appears that all Alpha
+ # Linux and Compaq Tru64 Unix objects are PIC.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+ xlc* | xlC*)
+ # IBM XL 8.0 on PPC
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink'
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld '
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+ lynxos*)
+ ;;
+ m88k*)
+ ;;
+ mvs*)
+ case $cc_basename in
+ cxx*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-W c,exportall'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ netbsd* | netbsdelf*-gnu)
+ ;;
+ *qnx* | *nto*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared'
+ ;;
+ osf3* | osf4* | osf5*)
+ case $cc_basename in
+ KCC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='--backend -Wl,'
+ ;;
+ RCC*)
+ # Rational C++ 2.4.1
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ ;;
+ cxx*)
+ # Digital/Compaq C++
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # Make sure the PIC flag is empty. It appears that all Alpha
+ # Linux and Compaq Tru64 Unix objects are PIC.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ psos*)
+ ;;
+ solaris*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.2, 5.x and Centerline C++
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld '
+ ;;
+ gcx*)
+ # Green Hills C++ Compiler
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ sunos4*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.x
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+ lcc*)
+ # Lucid
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+ esac
+ ;;
+ tandem*)
+ case $cc_basename in
+ NCC*)
+ # NonStop-UX NCC 3.20
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ ;;
+ *)
+ ;;
+ esac
+ ;;
+ vxworks*)
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+ ;;
+ esac
+ fi
+],
+[
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+
+ case $host_os in
+ aix*)
+ # All AIX code is PIC.
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ m68k)
+ # FIXME: we need at least 68020 code to build shared libraries, but
+ # adding the `-m68020' flag to GCC prevents building anything better,
+ # like `-m68040'.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-m68020 -resident32 -malways-restore-a4'
+ ;;
+ esac
+ ;;
+
+ beos* | irix5* | irix6* | nonstopux* | osf3* | osf4* | osf5*)
+ # PIC is the default for these OSes.
+ ;;
+
+ mingw* | cygwin* | pw32* | os2* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ # Although the cygwin gcc ignores -fPIC, still need this for old-style
+ # (--disable-auto-import) libraries
+ m4_if([$1], [GCJ], [],
+ [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT'])
+ ;;
+
+ darwin* | rhapsody*)
+ # PIC is the default on this platform
+ # Common symbols not allowed in MH_DYLIB files
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fno-common'
+ ;;
+
+ hpux*)
+ # PIC is the default for 64-bit PA HP-UX, but not for 32-bit
+ # PA HP-UX. On IA64 HP-UX, PIC is the default but the pic flag
+ # sets the default TLS model and affects inlining.
+ case $host_cpu in
+ hppa*64*)
+ # +Z the default
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ esac
+ ;;
+
+ interix[[3-9]]*)
+ # Interix 3.x gcc -fpic/-fPIC options generate broken code.
+ # Instead, we relocate shared libraries at runtime.
+ ;;
+
+ msdosdjgpp*)
+ # Just because we use GCC doesn't mean we suddenly get shared libraries
+ # on systems that don't support them.
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+ enable_shared=no
+ ;;
+
+ *nto* | *qnx*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=-Kconform_pic
+ fi
+ ;;
+
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ ;;
+ esac
+ else
+ # PORTME Check for flag to pass linker flags through the system compiler.
+ case $host_os in
+ aix*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ if test "$host_cpu" = ia64; then
+ # AIX 5 now supports IA64 processor
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ else
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-bnso -bI:/lib/syscalls.exp'
+ fi
+ ;;
+
+ mingw* | cygwin* | pw32* | os2* | cegcc*)
+ # This hack is so that the source file can tell whether it is being
+ # built for inclusion in a dll (and should export symbols for example).
+ m4_if([$1], [GCJ], [],
+ [_LT_TAGVAR(lt_prog_compiler_pic, $1)='-DDLL_EXPORT'])
+ ;;
+
+ hpux9* | hpux10* | hpux11*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # PIC is the default for IA64 HP-UX and 64-bit HP-UX, but
+ # not for PA HP-UX.
+ case $host_cpu in
+ hppa*64*|ia64*)
+ # +Z the default
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='+Z'
+ ;;
+ esac
+ # Is there a better lt_prog_compiler_static that works with the bundled CC?
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='${wl}-a ${wl}archive'
+ ;;
+
+ irix5* | irix6* | nonstopux*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # PIC (with -KPIC) is the default.
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+
+ linux* | k*bsd*-gnu)
+ case $cc_basename in
+ # old Intel for x86_64 which still supported -KPIC.
+ ecc*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+ ;;
+ # icc used to be incompatible with GCC.
+ # ICC 10 doesn't accept -KPIC any more.
+ icc* | ifort*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-static'
+ ;;
+ # Lahey Fortran 8.1.
+ lf95*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='--shared'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='--static'
+ ;;
+ pgcc* | pgf77* | pgf90* | pgf95*)
+ # Portland Group compilers (*not* the Pentium gcc compiler,
+ # which looks to be a dead project)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fpic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+ ccc*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # All Alpha code is PIC.
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+ xl*)
+ # IBM XL C 8.0/Fortran 10.1 on PPC
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-qpic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-qstaticlink'
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C 5.9
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ ;;
+ *Sun\ F*)
+ # Sun Fortran 8.3 passes all unrecognized flags to the linker
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)=''
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+
+ newsos6)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ *nto* | *qnx*)
+ # QNX uses GNU C++, but need to define -shared option too, otherwise
+ # it will coredump.
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-fPIC -shared'
+ ;;
+
+ osf3* | osf4* | osf5*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ # All OSF/1 code is PIC.
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+
+ rdos*)
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-non_shared'
+ ;;
+
+ solaris*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ case $cc_basename in
+ f77* | f90* | f95*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld ';;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,';;
+ esac
+ ;;
+
+ sunos4*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Qoption ld '
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-PIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ sysv4 | sysv4.2uw2* | sysv4.3*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec ;then
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-Kconform_pic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ fi
+ ;;
+
+ sysv5* | unixware* | sco3.2v5* | sco5v6* | OpenUNIX*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-KPIC'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ unicos*)
+ _LT_TAGVAR(lt_prog_compiler_wl, $1)='-Wl,'
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+ ;;
+
+ uts4*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)='-pic'
+ _LT_TAGVAR(lt_prog_compiler_static, $1)='-Bstatic'
+ ;;
+
+ *)
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no
+ ;;
+ esac
+ fi
+])
+case $host_os in
+ # For platforms which do not support PIC, -DPIC is meaningless:
+ *djgpp*)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ ;;
+ *)
+ _LT_TAGVAR(lt_prog_compiler_pic, $1)="$_LT_TAGVAR(lt_prog_compiler_pic, $1)@&t@m4_if([$1],[],[ -DPIC],[m4_if([$1],[CXX],[ -DPIC],[])])"
+ ;;
+esac
+AC_MSG_RESULT([$_LT_TAGVAR(lt_prog_compiler_pic, $1)])
+_LT_TAGDECL([wl], [lt_prog_compiler_wl], [1],
+ [How to pass a linker flag through the compiler])
+
+#
+# Check to make sure the PIC flag actually works.
+#
+if test -n "$_LT_TAGVAR(lt_prog_compiler_pic, $1)"; then
+ _LT_COMPILER_OPTION([if $compiler PIC flag $_LT_TAGVAR(lt_prog_compiler_pic, $1) works],
+ [_LT_TAGVAR(lt_cv_prog_compiler_pic_works, $1)],
+ [$_LT_TAGVAR(lt_prog_compiler_pic, $1)@&t@m4_if([$1],[],[ -DPIC],[m4_if([$1],[CXX],[ -DPIC],[])])], [],
+ [case $_LT_TAGVAR(lt_prog_compiler_pic, $1) in
+ "" | " "*) ;;
+ *) _LT_TAGVAR(lt_prog_compiler_pic, $1)=" $_LT_TAGVAR(lt_prog_compiler_pic, $1)" ;;
+ esac],
+ [_LT_TAGVAR(lt_prog_compiler_pic, $1)=
+ _LT_TAGVAR(lt_prog_compiler_can_build_shared, $1)=no])
+fi
+_LT_TAGDECL([pic_flag], [lt_prog_compiler_pic], [1],
+ [Additional compiler flags for building library objects])
+
+#
+# Check to make sure the static flag actually works.
+#
+wl=$_LT_TAGVAR(lt_prog_compiler_wl, $1) eval lt_tmp_static_flag=\"$_LT_TAGVAR(lt_prog_compiler_static, $1)\"
+_LT_LINKER_OPTION([if $compiler static flag $lt_tmp_static_flag works],
+ _LT_TAGVAR(lt_cv_prog_compiler_static_works, $1),
+ $lt_tmp_static_flag,
+ [],
+ [_LT_TAGVAR(lt_prog_compiler_static, $1)=])
+_LT_TAGDECL([link_static_flag], [lt_prog_compiler_static], [1],
+ [Compiler flag to prevent dynamic linking])
+])# _LT_COMPILER_PIC
+
+
+# _LT_LINKER_SHLIBS([TAGNAME])
+# ----------------------------
+# See if the linker supports building shared libraries.
+m4_defun([_LT_LINKER_SHLIBS],
+[AC_REQUIRE([LT_PATH_LD])dnl
+AC_REQUIRE([LT_PATH_NM])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_EGREP])dnl
+m4_require([_LT_DECL_SED])dnl
+m4_require([_LT_CMD_GLOBAL_SYMBOLS])dnl
+m4_require([_LT_TAG_COMPILER])dnl
+AC_MSG_CHECKING([whether the $compiler linker ($LD) supports shared libraries])
+m4_if([$1], [CXX], [
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ case $host_os in
+ aix[[4-9]]*)
+ # If we're using GNU nm, then we don't want the "-C" option.
+ # -C means demangle to AIX nm, but means don't demangle with GNU nm
+ if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ else
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ fi
+ ;;
+ pw32*)
+ _LT_TAGVAR(export_symbols_cmds, $1)="$ltdll_cmds"
+ ;;
+ cygwin* | mingw* | cegcc*)
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[[BCDGRS]][[ ]]/s/.*[[ ]]\([[^ ]]*\)/\1 DATA/;/^.*[[ ]]__nm__/s/^.*[[ ]]__nm__\([[^ ]]*\)[[ ]][[^ ]]*/\1 DATA/;/^I[[ ]]/d;/^[[AITW]][[ ]]/s/.* //'\'' | sort | uniq > $export_symbols'
+ ;;
+ linux* | k*bsd*-gnu)
+ _LT_TAGVAR(link_all_deplibs, $1)=no
+ ;;
+ *)
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ ;;
+ esac
+ _LT_TAGVAR(exclude_expsyms, $1)=['_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*']
+], [
+ runpath_var=
+ _LT_TAGVAR(allow_undefined_flag, $1)=
+ _LT_TAGVAR(always_export_symbols, $1)=no
+ _LT_TAGVAR(archive_cmds, $1)=
+ _LT_TAGVAR(archive_expsym_cmds, $1)=
+ _LT_TAGVAR(compiler_needs_object, $1)=no
+ _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)=
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+ _LT_TAGVAR(hardcode_automatic, $1)=no
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+ _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=
+ _LT_TAGVAR(hardcode_minus_L, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
+ _LT_TAGVAR(inherit_rpath, $1)=no
+ _LT_TAGVAR(link_all_deplibs, $1)=unknown
+ _LT_TAGVAR(module_cmds, $1)=
+ _LT_TAGVAR(module_expsym_cmds, $1)=
+ _LT_TAGVAR(old_archive_from_new_cmds, $1)=
+ _LT_TAGVAR(old_archive_from_expsyms_cmds, $1)=
+ _LT_TAGVAR(thread_safe_flag_spec, $1)=
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ # include_expsyms should be a list of space-separated symbols to be *always*
+ # included in the symbol list
+ _LT_TAGVAR(include_expsyms, $1)=
+ # exclude_expsyms can be an extended regexp of symbols to exclude
+ # it will be wrapped by ` (' and `)$', so one must not match beginning or
+ # end of line. Example: `a|bc|.*d.*' will exclude the symbols `a' and `bc',
+ # as well as any symbol that contains `d'.
+ _LT_TAGVAR(exclude_expsyms, $1)=['_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*']
+ # Although _GLOBAL_OFFSET_TABLE_ is a valid symbol C name, most a.out
+ # platforms (ab)use it in PIC code, but their linkers get confused if
+ # the symbol is explicitly referenced. Since portable code cannot
+ # rely on this symbol name, it's probably fine to never include it in
+ # preloaded symbol tables.
+ # Exclude shared library initialization/finalization symbols.
+dnl Note also adjust exclude_expsyms for C++ above.
+ extract_expsyms_cmds=
+
+ case $host_os in
+ cygwin* | mingw* | pw32* | cegcc*)
+ # FIXME: the MSVC++ port hasn't been tested in a loooong time
+ # When not using gcc, we currently assume that we are using
+ # Microsoft Visual C++.
+ if test "$GCC" != yes; then
+ with_gnu_ld=no
+ fi
+ ;;
+ interix*)
+ # we just hope/assume this is gcc and not c89 (= MSVC++)
+ with_gnu_ld=yes
+ ;;
+ openbsd*)
+ with_gnu_ld=no
+ ;;
+ esac
+
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ if test "$with_gnu_ld" = yes; then
+ # If archive_cmds runs LD, not CC, wlarc should be empty
+ wlarc='${wl}'
+
+ # Set some defaults for GNU ld with shared library support. These
+ # are reset later if shared libraries are not supported. Putting them
+ # here allows them to be overridden if necessary.
+ runpath_var=LD_RUN_PATH
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+ # ancient GNU ld didn't support --whole-archive et. al.
+ if $LD --help 2>&1 | $GREP 'no-whole-archive' > /dev/null; then
+ _LT_TAGVAR(whole_archive_flag_spec, $1)="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ else
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ fi
+ supports_anon_versioning=no
+ case `$LD -v 2>&1` in
+ *\ [[01]].* | *\ 2.[[0-9]].* | *\ 2.10.*) ;; # catch versions < 2.11
+ *\ 2.11.93.0.2\ *) supports_anon_versioning=yes ;; # RH7.3 ...
+ *\ 2.11.92.0.12\ *) supports_anon_versioning=yes ;; # Mandrake 8.2 ...
+ *\ 2.11.*) ;; # other 2.11 versions
+ *) supports_anon_versioning=yes ;;
+ esac
+
+ # See if GNU ld supports shared libraries.
+ case $host_os in
+ aix[[3-9]]*)
+ # On AIX/PPC, the GNU linker is very broken
+ if test "$host_cpu" != ia64; then
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: the GNU linker, at least up to release 2.9.1, is reported
+*** to be unable to reliably create shared libraries on AIX.
+*** Therefore, libtool is disabling shared libraries support. If you
+*** really care for shared libraries, you may want to modify your PATH
+*** so that a non-GNU linker is found, and then restart.
+
+_LT_EOF
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)=''
+ ;;
+ m68k)
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ ;;
+ esac
+ ;;
+
+ beos*)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ # Joseph Beckenbach <jrb3@best.com> says some releases of gcc
+ # support --undefined. This deserves some investigation. FIXME
+ _LT_TAGVAR(archive_cmds, $1)='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # _LT_TAGVAR(hardcode_libdir_flag_spec, $1) is actually meaningless,
+ # as there is no search path for DLLs.
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ _LT_TAGVAR(always_export_symbols, $1)=no
+ _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM $libobjs $convenience | $global_symbol_pipe | $SED -e '\''/^[[BCDGRS]][[ ]]/s/.*[[ ]]\([[^ ]]*\)/\1 DATA/'\'' | $SED -e '\''/^[[AITW]][[ ]]/s/.*[[ ]]//'\'' | sort | uniq > $export_symbols'
+
+ if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ # If the export-symbols file already is a .def file (1st line
+ # is EXPORTS), use it as is; otherwise, prepend...
+ _LT_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+ cp $export_symbols $output_objdir/$soname.def;
+ else
+ echo EXPORTS > $output_objdir/$soname.def;
+ cat $export_symbols >> $output_objdir/$soname.def;
+ fi~
+ $CC -shared $output_objdir/$soname.def $libobjs $deplibs $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ interix[[3-9]]*)
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+ # Instead, shared libraries are loaded at an image base (0x10000000 by
+ # default) and relocated if they conflict, which is a slow very memory
+ # consuming and fragmenting process. To avoid this, we pick a random,
+ # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+ # time. Moving up from 0x10000000 also allows more sbrk(2) space.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ ;;
+
+ gnu* | linux* | tpf* | k*bsd*-gnu)
+ tmp_diet=no
+ if test "$host_os" = linux-dietlibc; then
+ case $cc_basename in
+ diet\ *) tmp_diet=yes;; # linux-dietlibc with static linking (!diet-dyn)
+ esac
+ fi
+ if $LD --help 2>&1 | $EGREP ': supported targets:.* elf' > /dev/null \
+ && test "$tmp_diet" = no
+ then
+ tmp_addflag=
+ tmp_sharedflag='-shared'
+ case $cc_basename,$host_cpu in
+ pgcc*) # Portland Group C compiler
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ tmp_addflag=' $pic_flag'
+ ;;
+ pgf77* | pgf90* | pgf95*) # Portland Group f77 and f90 compilers
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ tmp_addflag=' $pic_flag -Mnomain' ;;
+ ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64
+ tmp_addflag=' -i_dynamic' ;;
+ efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64
+ tmp_addflag=' -i_dynamic -nofor_main' ;;
+ ifc* | ifort*) # Intel Fortran compiler
+ tmp_addflag=' -nofor_main' ;;
+ lf95*) # Lahey Fortran 8.1
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ tmp_sharedflag='--shared' ;;
+ xl[[cC]]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ tmp_sharedflag='-qmkshrobj'
+ tmp_addflag= ;;
+ esac
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*) # Sun C 5.9
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ _LT_TAGVAR(compiler_needs_object, $1)=yes
+ tmp_sharedflag='-G' ;;
+ *Sun\ F*) # Sun Fortran 8.3
+ tmp_sharedflag='-G' ;;
+ esac
+ _LT_TAGVAR(archive_cmds, $1)='$CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+
+ if test "x$supports_anon_versioning" = xyes; then
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $CC '"$tmp_sharedflag""$tmp_addflag"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+ fi
+
+ case $cc_basename in
+ xlf*)
+ # IBM XL Fortran 10.1 on PPC cannot create shared libs itself
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='--whole-archive$convenience --no-whole-archive'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+ _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)='-rpath $libdir'
+ _LT_TAGVAR(archive_cmds, $1)='$LD -shared $libobjs $deplibs $compiler_flags -soname $soname -o $lib'
+ if test "x$supports_anon_versioning" = xyes; then
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $LD -shared $libobjs $deplibs $compiler_flags -soname $soname -version-script $output_objdir/$libname.ver -o $lib'
+ fi
+ ;;
+ esac
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable $libobjs $deplibs $linker_flags -o $lib'
+ wlarc=
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ fi
+ ;;
+
+ solaris*)
+ if $LD -v 2>&1 | $GREP 'BFD 2\.8' > /dev/null; then
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: The releases 2.8.* of the GNU linker cannot reliably
+*** create shared libraries on Solaris systems. Therefore, libtool
+*** is disabling shared libraries support. We urge you to upgrade GNU
+*** binutils to release 2.9.1 or newer. Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+ elif $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6* | unixware* | OpenUNIX*)
+ case `$LD -v 2>&1` in
+ *\ [[01]].* | *\ 2.[[0-9]].* | *\ 2.1[[0-5]].*)
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ cat <<_LT_EOF 1>&2
+
+*** Warning: Releases of the GNU linker prior to 2.16.91.0.3 can not
+*** reliably create shared libraries on SCO systems. Therefore, libtool
+*** is disabling shared libraries support. We urge you to upgrade GNU
+*** binutils to release 2.16.91.0.3 or newer. Another option is to modify
+*** your PATH or compiler configuration so that the native linker is
+*** used, and then restart.
+
+_LT_EOF
+ ;;
+ *)
+ # For security reasons, it is highly recommended that you always
+ # use absolute paths for naming shared libraries, and exclude the
+ # DT_RUNPATH tag from executables and libraries. But doing so
+ # requires that you compile everything twice, which is a pain.
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+ ;;
+
+ sunos4*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -assert pure-text -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ wlarc=
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ *)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+
+ if test "$_LT_TAGVAR(ld_shlibs, $1)" = no; then
+ runpath_var=
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)=
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ fi
+ else
+ # PORTME fill in a description of your system's linker (not GNU ld)
+ case $host_os in
+ aix3*)
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ _LT_TAGVAR(always_export_symbols, $1)=yes
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$LD -o $output_objdir/$soname $libobjs $deplibs $linker_flags -bE:$export_symbols -T512 -H512 -bM:SRE~$AR $AR_FLAGS $lib $output_objdir/$soname'
+ # Note: this linker hardcodes the directories in LIBPATH if there
+ # are no directories specified by -L.
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ if test "$GCC" = yes && test -z "$lt_prog_compiler_static"; then
+ # Neither direct hardcoding nor static linking is supported with a
+ # broken collect2.
+ _LT_TAGVAR(hardcode_direct, $1)=unsupported
+ fi
+ ;;
+
+ aix[[4-9]]*)
+ if test "$host_cpu" = ia64; then
+ # On IA64, the linker does run time linking by default, so we don't
+ # have to do anything special.
+ aix_use_runtimelinking=no
+ exp_sym_flag='-Bexport'
+ no_entry_flag=""
+ else
+ # If we're using GNU nm, then we don't want the "-C" option.
+ # -C means demangle to AIX nm, but means don't demangle with GNU nm
+ if $NM -V 2>&1 | $GREP 'GNU' > /dev/null; then
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM -Bpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ else
+ _LT_TAGVAR(export_symbols_cmds, $1)='$NM -BCpg $libobjs $convenience | awk '\''{ if (((\$ 2 == "T") || (\$ 2 == "D") || (\$ 2 == "B")) && ([substr](\$ 3,1,1) != ".")) { print \$ 3 } }'\'' | sort -u > $export_symbols'
+ fi
+ aix_use_runtimelinking=no
+
+ # Test if we are trying to use run time linking or normal
+ # AIX style linking. If -brtl is somewhere in LDFLAGS, we
+ # need to do runtime linking.
+ case $host_os in aix4.[[23]]|aix4.[[23]].*|aix[[5-9]]*)
+ for ld_flag in $LDFLAGS; do
+ if (test $ld_flag = "-brtl" || test $ld_flag = "-Wl,-brtl"); then
+ aix_use_runtimelinking=yes
+ break
+ fi
+ done
+ ;;
+ esac
+
+ exp_sym_flag='-bexport'
+ no_entry_flag='-bnoentry'
+ fi
+
+ # When large executables or shared objects are built, AIX ld can
+ # have problems creating the table of contents. If linking a library
+ # or program results in "error TOC overflow" add -mminimal-toc to
+ # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not
+ # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+ _LT_TAGVAR(archive_cmds, $1)=''
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=':'
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(file_list_spec, $1)='${wl}-f,'
+
+ if test "$GCC" = yes; then
+ case $host_os in aix4.[[012]]|aix4.[[012]].*)
+ # We only want to do this on AIX 4.2 and lower, the check
+ # below for broken collect2 doesn't work under 4.3+
+ collect2name=`${CC} -print-prog-name=collect2`
+ if test -f "$collect2name" &&
+ strings "$collect2name" | $GREP resolve_lib_name >/dev/null
+ then
+ # We have reworked collect2
+ :
+ else
+ # We have old collect2
+ _LT_TAGVAR(hardcode_direct, $1)=unsupported
+ # It fails to find uninstalled libraries when the uninstalled
+ # path is not listed in the libpath. Setting hardcode_minus_L
+ # to unsupported forces relinking
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=
+ fi
+ ;;
+ esac
+ shared_flag='-shared'
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag="$shared_flag "'${wl}-G'
+ fi
+ _LT_TAGVAR(link_all_deplibs, $1)=no
+ else
+ # not using gcc
+ if test "$host_cpu" = ia64; then
+ # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+ # chokes on -Wl,-G. The following line is correct:
+ shared_flag='-G'
+ else
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag='${wl}-G'
+ else
+ shared_flag='${wl}-bM:SRE'
+ fi
+ fi
+ fi
+
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-bexpall'
+ # It seems that -bexpall does not export symbols beginning with
+ # underscore (_), so it is better to generate a list of symbols to export.
+ _LT_TAGVAR(always_export_symbols, $1)=yes
+ if test "$aix_use_runtimelinking" = yes; then
+ # Warning - without using the other runtime loading flags (-brtl),
+ # -berok will link without error, but may produce a broken library.
+ _LT_TAGVAR(allow_undefined_flag, $1)='-berok'
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ _LT_SYS_MODULE_PATH_AIX
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+ else
+ if test "$host_cpu" = ia64; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $libdir:/usr/lib:/lib'
+ _LT_TAGVAR(allow_undefined_flag, $1)="-z nodefs"
+ _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+ else
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ _LT_SYS_MODULE_PATH_AIX
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+ # Warning - without using the other run time loading flags,
+ # -berok will link without error, but may produce a broken library.
+ _LT_TAGVAR(no_undefined_flag, $1)=' ${wl}-bernotok'
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-berok'
+ # Exported symbols can be pulled into shared objects from archives
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='$convenience'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=yes
+ # This is similar to how AIX traditionally builds its shared libraries.
+ _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+ fi
+ fi
+ ;;
+
+ amigaos*)
+ case $host_cpu in
+ powerpc)
+ # see comment about AmigaOS4 .so support
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)=''
+ ;;
+ m68k)
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/a2ixlibrary.data~$ECHO "#define NAME $libname" > $output_objdir/a2ixlibrary.data~$ECHO "#define LIBRARY_ID 1" >> $output_objdir/a2ixlibrary.data~$ECHO "#define VERSION $major" >> $output_objdir/a2ixlibrary.data~$ECHO "#define REVISION $revision" >> $output_objdir/a2ixlibrary.data~$AR $AR_FLAGS $lib $libobjs~$RANLIB $lib~(cd $output_objdir && a2ixlibrary -32)'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ ;;
+ esac
+ ;;
+
+ bsdi[[45]]*)
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)=-rdynamic
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # When not using gcc, we currently assume that we are using
+ # Microsoft Visual C++.
+ # hardcode_libdir_flag_spec is actually meaningless, as there is
+ # no search path for DLLs.
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)=' '
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ # Tell ltmain to make .lib files, not .a files.
+ libext=lib
+ # Tell ltmain to make .dll files, not .so files.
+ shrext_cmds=".dll"
+ # FIXME: Setting linknames here is a bad hack.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -o $lib $libobjs $compiler_flags `$ECHO "X$deplibs" | $Xsed -e '\''s/ -lc$//'\''` -link -dll~linknames='
+ # The linker will automatically build a .lib file if we build a DLL.
+ _LT_TAGVAR(old_archive_from_new_cmds, $1)='true'
+ # FIXME: Should let the user specify the lib program.
+ _LT_TAGVAR(old_archive_cmds, $1)='lib -OUT:$oldlib$oldobjs$old_deplibs'
+ _LT_TAGVAR(fix_srcfile_path, $1)='`cygpath -w "$srcfile"`'
+ _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes
+ ;;
+
+ darwin* | rhapsody*)
+ _LT_DARWIN_LINKER_FEATURES($1)
+ ;;
+
+ dgux*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ freebsd1*)
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ # FreeBSD 2.2.[012] allows us to include c++rt0.o to get C++ constructor
+ # support. Future versions do this automatically, but an explicit c++rt0.o
+ # does not break anything, and helps significantly (at the cost of a little
+ # extra space).
+ freebsd2.2*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags /usr/lib/c++rt0.o'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ # Unfortunately, older versions of FreeBSD 2 do not have this feature.
+ freebsd2*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ # FreeBSD 3 and greater uses gcc -shared to do shared libraries.
+ freebsd* | dragonfly*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ hpux9*)
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$CC -shared -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $libobjs $deplibs $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$LD -b +b $install_libdir -o $output_objdir/$soname $libobjs $deplibs $linker_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ fi
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ ;;
+
+ hpux10*)
+ if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$LD -b +h $soname +b $install_libdir -o $lib $libobjs $deplibs $linker_flags'
+ fi
+ if test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)='+b $libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ fi
+ ;;
+
+ hpux11*)
+ if test "$GCC" = yes -a "$with_gnu_ld" = no; then
+ case $host_cpu in
+ hppa*64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ ia64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ else
+ case $host_cpu in
+ hppa*64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ ia64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ fi
+ if test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ case $host_cpu in
+ hppa*64*|ia64*)
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+ *)
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+
+ # hardcode_minus_L: Not really in the search PATH,
+ # but as the default location of the library.
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ ;;
+ esac
+ fi
+ ;;
+
+ irix5* | irix6* | nonstopux*)
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ # Try to use the -exported_symbol ld option, if it does not
+ # work, assume that -exports_file does not work either and
+ # implicitly export all symbols.
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS -shared ${wl}-exported_symbol ${wl}foo ${wl}-update_registry ${wl}/dev/null"
+ AC_LINK_IFELSE(int foo(void) {},
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations ${wl}-exports_file ${wl}$export_symbols -o $lib'
+ )
+ LDFLAGS="$save_LDFLAGS"
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -exports_file $export_symbols -o $lib'
+ fi
+ _LT_TAGVAR(archive_cmds_need_lc, $1)='no'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(inherit_rpath, $1)=yes
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ ;;
+
+ netbsd* | netbsdelf*-gnu)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags' # a.out
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$LD -shared -o $lib $libobjs $deplibs $linker_flags' # ELF
+ fi
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ newsos6)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ *nto* | *qnx*)
+ ;;
+
+ openbsd*)
+ if test -f /usr/libexec/ld.so; then
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ if test -z "`echo __ELF__ | $CC -E - | $GREP __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags ${wl}-retain-symbols-file,$export_symbols'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ else
+ case $host_os in
+ openbsd[[01]].* | openbsd2.[[0-7]] | openbsd2.[[0-7]].*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ ;;
+ esac
+ fi
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ os2*)
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ _LT_TAGVAR(archive_cmds, $1)='$ECHO "LIBRARY $libname INITINSTANCE" > $output_objdir/$libname.def~$ECHO "DESCRIPTION \"$libname\"" >> $output_objdir/$libname.def~$ECHO DATA >> $output_objdir/$libname.def~$ECHO " SINGLE NONSHARED" >> $output_objdir/$libname.def~$ECHO EXPORTS >> $output_objdir/$libname.def~emxexp $libobjs >> $output_objdir/$libname.def~$CC -Zdll -Zcrtdll -o $lib $libobjs $deplibs $compiler_flags $output_objdir/$libname.def'
+ _LT_TAGVAR(old_archive_from_new_cmds, $1)='emximp -o $output_objdir/$libname.a $output_objdir/$libname.def'
+ ;;
+
+ osf3*)
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ else
+ _LT_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ fi
+ _LT_TAGVAR(archive_cmds_need_lc, $1)='no'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ ;;
+
+ osf4* | osf5*) # as osf3* with the addition of -msym flag
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ else
+ _LT_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $libobjs $deplibs $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done; printf "%s\\n" "-hidden">> $lib.exp~
+ $CC -shared${allow_undefined_flag} ${wl}-input ${wl}$lib.exp $compiler_flags $libobjs $deplibs -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~$RM $lib.exp'
+
+ # Both c and cxx compiler support -rpath directly
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir'
+ fi
+ _LT_TAGVAR(archive_cmds_need_lc, $1)='no'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ ;;
+
+ solaris*)
+ _LT_TAGVAR(no_undefined_flag, $1)=' -z defs'
+ if test "$GCC" = yes; then
+ wlarc='${wl}'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-z ${wl}text ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -shared ${wl}-z ${wl}text ${wl}-M ${wl}$lib.exp ${wl}-h ${wl}$soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp'
+ else
+ case `$CC -V 2>&1` in
+ *"Compilers 5.0"*)
+ wlarc=''
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $LD -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $linker_flags~$RM $lib.exp'
+ ;;
+ *)
+ wlarc='${wl}'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G${allow_undefined_flag} -h $soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G${allow_undefined_flag} -M $lib.exp -h $soname -o $lib $libobjs $deplibs $compiler_flags~$RM $lib.exp'
+ ;;
+ esac
+ fi
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ case $host_os in
+ solaris2.[[0-5]] | solaris2.[[0-5]].*) ;;
+ *)
+ # The compiler driver will combine and reorder linker options,
+ # but understands `-z linker_flag'. GCC discards it without `$wl',
+ # but is careful enough not to reorder.
+ # Supported since Solaris 2.6 (maybe 2.5.1?)
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract'
+ else
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='-z allextract$convenience -z defaultextract'
+ fi
+ ;;
+ esac
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ ;;
+
+ sunos4*)
+ if test "x$host_vendor" = xsequent; then
+ # Use $CC to link under sequent, because it throws in some extra .o
+ # files that make .init and .fini sections work.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h $soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$LD -assert pure-text -Bstatic -o $lib $libobjs $deplibs $linker_flags'
+ fi
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ sysv4)
+ case $host_vendor in
+ sni)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_direct, $1)=yes # is this really true???
+ ;;
+ siemens)
+ ## LD is ld it makes a PLAMLIB
+ ## CC just makes a GrossModule.
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(reload_cmds, $1)='$CC -r -o $output$reload_objs'
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ ;;
+ motorola)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_direct, $1)=no #Motorola manual says yes, but my tests say they lie
+ ;;
+ esac
+ runpath_var='LD_RUN_PATH'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ sysv4.3*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='-Bexport'
+ ;;
+
+ sysv4*MP*)
+ if test -d /usr/nec; then
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ runpath_var=LD_RUN_PATH
+ hardcode_runpath_var=yes
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ fi
+ ;;
+
+ sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[[01]].[[10]]* | unixware7* | sco3.2v5.0.[[024]]*)
+ _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ runpath_var='LD_RUN_PATH'
+
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ fi
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6*)
+ # Note: We can NOT use -z defs as we might desire, because we do not
+ # link with -lc, and that would cause any symbols used from libc to
+ # always be unresolved, which means just about no library would
+ # ever link correctly. If we're not using GNU ld we use -z text
+ # though, which does catch some bad symbols but isn't as heavy-handed
+ # as -z defs.
+ _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+ _LT_TAGVAR(allow_undefined_flag, $1)='${wl}-z,nodefs'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R,$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=':'
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-Bexport'
+ runpath_var='LD_RUN_PATH'
+
+ if test "$GCC" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ fi
+ ;;
+
+ uts4*)
+ _LT_TAGVAR(archive_cmds, $1)='$LD -G -h $soname -o $lib $libobjs $deplibs $linker_flags'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+
+ *)
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+
+ if test x$host_vendor = xsni; then
+ case $host in
+ sysv4 | sysv4.2uw2* | sysv4.3* | sysv5*)
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-Blargedynsym'
+ ;;
+ esac
+ fi
+ fi
+])
+AC_MSG_RESULT([$_LT_TAGVAR(ld_shlibs, $1)])
+test "$_LT_TAGVAR(ld_shlibs, $1)" = no && can_build_shared=no
+
+_LT_TAGVAR(with_gnu_ld, $1)=$with_gnu_ld
+
+_LT_DECL([], [libext], [0], [Old archive suffix (normally "a")])dnl
+_LT_DECL([], [shrext_cmds], [1], [Shared library suffix (normally ".so")])dnl
+_LT_DECL([], [extract_expsyms_cmds], [2],
+ [The commands to extract the exported symbol list from a shared archive])
+
+#
+# Do we need to explicitly link libc?
+#
+case "x$_LT_TAGVAR(archive_cmds_need_lc, $1)" in
+x|xyes)
+ # Assume -lc should be added
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=yes
+
+ if test "$enable_shared" = yes && test "$GCC" = yes; then
+ case $_LT_TAGVAR(archive_cmds, $1) in
+ *'~'*)
+ # FIXME: we may have to deal with multi-command sequences.
+ ;;
+ '$CC '*)
+ # Test whether the compiler implicitly links with -lc since on some
+ # systems, -lgcc has to come before -lc. If gcc already passes -lc
+ # to ld, don't add -lc before -lgcc.
+ AC_MSG_CHECKING([whether -lc should be explicitly linked in])
+ $RM conftest*
+ echo "$lt_simple_compile_test_code" > conftest.$ac_ext
+
+ if AC_TRY_EVAL(ac_compile) 2>conftest.err; then
+ soname=conftest
+ lib=conftest
+ libobjs=conftest.$ac_objext
+ deplibs=
+ wl=$_LT_TAGVAR(lt_prog_compiler_wl, $1)
+ pic_flag=$_LT_TAGVAR(lt_prog_compiler_pic, $1)
+ compiler_flags=-v
+ linker_flags=-v
+ verstring=
+ output_objdir=.
+ libname=conftest
+ lt_save_allow_undefined_flag=$_LT_TAGVAR(allow_undefined_flag, $1)
+ _LT_TAGVAR(allow_undefined_flag, $1)=
+ if AC_TRY_EVAL(_LT_TAGVAR(archive_cmds, $1) 2\>\&1 \| $GREP \" -lc \" \>/dev/null 2\>\&1)
+ then
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ else
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=yes
+ fi
+ _LT_TAGVAR(allow_undefined_flag, $1)=$lt_save_allow_undefined_flag
+ else
+ cat conftest.err 1>&5
+ fi
+ $RM conftest*
+ AC_MSG_RESULT([$_LT_TAGVAR(archive_cmds_need_lc, $1)])
+ ;;
+ esac
+ fi
+ ;;
+esac
+
+_LT_TAGDECL([build_libtool_need_lc], [archive_cmds_need_lc], [0],
+ [Whether or not to add -lc for building shared libraries])
+_LT_TAGDECL([allow_libtool_libs_with_static_runtimes],
+ [enable_shared_with_static_runtimes], [0],
+ [Whether or not to disallow shared libs when runtime libs are static])
+_LT_TAGDECL([], [export_dynamic_flag_spec], [1],
+ [Compiler flag to allow reflexive dlopens])
+_LT_TAGDECL([], [whole_archive_flag_spec], [1],
+ [Compiler flag to generate shared objects directly from archives])
+_LT_TAGDECL([], [compiler_needs_object], [1],
+ [Whether the compiler copes with passing no objects directly])
+_LT_TAGDECL([], [old_archive_from_new_cmds], [2],
+ [Create an old-style archive from a shared archive])
+_LT_TAGDECL([], [old_archive_from_expsyms_cmds], [2],
+ [Create a temporary old-style archive to link instead of a shared archive])
+_LT_TAGDECL([], [archive_cmds], [2], [Commands used to build a shared archive])
+_LT_TAGDECL([], [archive_expsym_cmds], [2])
+_LT_TAGDECL([], [module_cmds], [2],
+ [Commands used to build a loadable module if different from building
+ a shared archive.])
+_LT_TAGDECL([], [module_expsym_cmds], [2])
+_LT_TAGDECL([], [with_gnu_ld], [1],
+ [Whether we are building with GNU ld or not])
+_LT_TAGDECL([], [allow_undefined_flag], [1],
+ [Flag that allows shared libraries with undefined symbols to be built])
+_LT_TAGDECL([], [no_undefined_flag], [1],
+ [Flag that enforces no undefined symbols])
+_LT_TAGDECL([], [hardcode_libdir_flag_spec], [1],
+ [Flag to hardcode $libdir into a binary during linking.
+ This must work even if $libdir does not exist])
+_LT_TAGDECL([], [hardcode_libdir_flag_spec_ld], [1],
+ [[If ld is used when linking, flag to hardcode $libdir into a binary
+ during linking. This must work even if $libdir does not exist]])
+_LT_TAGDECL([], [hardcode_libdir_separator], [1],
+ [Whether we need a single "-rpath" flag with a separated argument])
+_LT_TAGDECL([], [hardcode_direct], [0],
+ [Set to "yes" if using DIR/libNAME${shared_ext} during linking hardcodes
+ DIR into the resulting binary])
+_LT_TAGDECL([], [hardcode_direct_absolute], [0],
+ [Set to "yes" if using DIR/libNAME${shared_ext} during linking hardcodes
+ DIR into the resulting binary and the resulting library dependency is
+ "absolute", i.e impossible to change by setting ${shlibpath_var} if the
+ library is relocated])
+_LT_TAGDECL([], [hardcode_minus_L], [0],
+ [Set to "yes" if using the -LDIR flag during linking hardcodes DIR
+ into the resulting binary])
+_LT_TAGDECL([], [hardcode_shlibpath_var], [0],
+ [Set to "yes" if using SHLIBPATH_VAR=DIR during linking hardcodes DIR
+ into the resulting binary])
+_LT_TAGDECL([], [hardcode_automatic], [0],
+ [Set to "yes" if building a shared library automatically hardcodes DIR
+ into the library and all subsequent libraries and executables linked
+ against it])
+_LT_TAGDECL([], [inherit_rpath], [0],
+ [Set to yes if linker adds runtime paths of dependent libraries
+ to runtime path list])
+_LT_TAGDECL([], [link_all_deplibs], [0],
+ [Whether libtool must link a program against all its dependency libraries])
+_LT_TAGDECL([], [fix_srcfile_path], [1],
+ [Fix the shell variable $srcfile for the compiler])
+_LT_TAGDECL([], [always_export_symbols], [0],
+ [Set to "yes" if exported symbols are required])
+_LT_TAGDECL([], [export_symbols_cmds], [2],
+ [The commands to list exported symbols])
+_LT_TAGDECL([], [exclude_expsyms], [1],
+ [Symbols that should not be listed in the preloaded symbols])
+_LT_TAGDECL([], [include_expsyms], [1],
+ [Symbols that must always be exported])
+_LT_TAGDECL([], [prelink_cmds], [2],
+ [Commands necessary for linking programs (against libraries) with templates])
+_LT_TAGDECL([], [file_list_spec], [1],
+ [Specify filename containing input files])
+dnl FIXME: Not yet implemented
+dnl _LT_TAGDECL([], [thread_safe_flag_spec], [1],
+dnl [Compiler flag to generate thread safe objects])
+])# _LT_LINKER_SHLIBS
+
+
+# _LT_LANG_C_CONFIG([TAG])
+# ------------------------
+# Ensure that the configuration variables for a C compiler are suitably
+# defined. These variables are subsequently used by _LT_CONFIG to write
+# the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_C_CONFIG],
+[m4_require([_LT_DECL_EGREP])dnl
+lt_save_CC="$CC"
+AC_LANG_PUSH(C)
+
+# Source file extension for C test sources.
+ac_ext=c
+
+# Object file extension for compiled C test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="int some_variable = 0;"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='int main(){return(0);}'
+
+_LT_TAG_COMPILER
+# Save the default compiler, since it gets overwritten when the other
+# tags are being tested, and _LT_TAGVAR(compiler, []) is a NOP.
+compiler_DEFAULT=$CC
+
+# save warnings/boilerplate of simple test code
+_LT_COMPILER_BOILERPLATE
+_LT_LINKER_BOILERPLATE
+
+## CAVEAT EMPTOR:
+## There is no encapsulation within the following macros, do not change
+## the running order or otherwise move them around unless you know exactly
+## what you are doing...
+if test -n "$compiler"; then
+ _LT_COMPILER_NO_RTTI($1)
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_SYS_DYNAMIC_LINKER($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+ LT_SYS_DLOPEN_SELF
+ _LT_CMD_STRIPLIB
+
+ # Report which library types will actually be built
+ AC_MSG_CHECKING([if libtool supports shared libraries])
+ AC_MSG_RESULT([$can_build_shared])
+
+ AC_MSG_CHECKING([whether to build shared libraries])
+ test "$can_build_shared" = "no" && enable_shared=no
+
+ # On AIX, shared libraries and static libraries use the same namespace, and
+ # are all built from PIC.
+ case $host_os in
+ aix3*)
+ test "$enable_shared" = yes && enable_static=no
+ if test -n "$RANLIB"; then
+ archive_cmds="$archive_cmds~\$RANLIB \$lib"
+ postinstall_cmds='$RANLIB $lib'
+ fi
+ ;;
+
+ aix[[4-9]]*)
+ if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+ test "$enable_shared" = yes && enable_static=no
+ fi
+ ;;
+ esac
+ AC_MSG_RESULT([$enable_shared])
+
+ AC_MSG_CHECKING([whether to build static libraries])
+ # Make sure either enable_shared or enable_static is yes.
+ test "$enable_shared" = yes || enable_static=yes
+ AC_MSG_RESULT([$enable_static])
+
+ _LT_CONFIG($1)
+fi
+AC_LANG_POP
+CC="$lt_save_CC"
+])# _LT_LANG_C_CONFIG
+
+
+# _LT_PROG_CXX
+# ------------
+# Since AC_PROG_CXX is broken, in that it returns g++ if there is no c++
+# compiler, we have our own version here.
+m4_defun([_LT_PROG_CXX],
+[
+pushdef([AC_MSG_ERROR], [_lt_caught_CXX_error=yes])
+AC_PROG_CXX
+if test -n "$CXX" && ( test "X$CXX" != "Xno" &&
+ ( (test "X$CXX" = "Xg++" && `g++ -v >/dev/null 2>&1` ) ||
+ (test "X$CXX" != "Xg++"))) ; then
+ AC_PROG_CXXCPP
+else
+ _lt_caught_CXX_error=yes
+fi
+popdef([AC_MSG_ERROR])
+])# _LT_PROG_CXX
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([_LT_PROG_CXX], [])
+
+
+# _LT_LANG_CXX_CONFIG([TAG])
+# --------------------------
+# Ensure that the configuration variables for a C++ compiler are suitably
+# defined. These variables are subsequently used by _LT_CONFIG to write
+# the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_CXX_CONFIG],
+[AC_REQUIRE([_LT_PROG_CXX])dnl
+m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+m4_require([_LT_DECL_EGREP])dnl
+
+AC_LANG_PUSH(C++)
+_LT_TAGVAR(archive_cmds_need_lc, $1)=no
+_LT_TAGVAR(allow_undefined_flag, $1)=
+_LT_TAGVAR(always_export_symbols, $1)=no
+_LT_TAGVAR(archive_expsym_cmds, $1)=
+_LT_TAGVAR(compiler_needs_object, $1)=no
+_LT_TAGVAR(export_dynamic_flag_spec, $1)=
+_LT_TAGVAR(hardcode_direct, $1)=no
+_LT_TAGVAR(hardcode_direct_absolute, $1)=no
+_LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
+_LT_TAGVAR(hardcode_libdir_separator, $1)=
+_LT_TAGVAR(hardcode_minus_L, $1)=no
+_LT_TAGVAR(hardcode_shlibpath_var, $1)=unsupported
+_LT_TAGVAR(hardcode_automatic, $1)=no
+_LT_TAGVAR(inherit_rpath, $1)=no
+_LT_TAGVAR(module_cmds, $1)=
+_LT_TAGVAR(module_expsym_cmds, $1)=
+_LT_TAGVAR(link_all_deplibs, $1)=unknown
+_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+_LT_TAGVAR(no_undefined_flag, $1)=
+_LT_TAGVAR(whole_archive_flag_spec, $1)=
+_LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no
+
+# Source file extension for C++ test sources.
+ac_ext=cpp
+
+# Object file extension for compiled C++ test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# No sense in running all these tests if we already determined that
+# the CXX compiler isn't working. Some variables (like enable_shared)
+# are currently assumed to apply to all compilers on this platform,
+# and will be corrupted by setting them based on a non-working compiler.
+if test "$_lt_caught_CXX_error" != yes; then
+ # Code to be used in simple compile tests
+ lt_simple_compile_test_code="int some_variable = 0;"
+
+ # Code to be used in simple link tests
+ lt_simple_link_test_code='int main(int, char *[[]]) { return(0); }'
+
+ # ltmain only uses $CC for tagged configurations so make sure $CC is set.
+ _LT_TAG_COMPILER
+
+ # save warnings/boilerplate of simple test code
+ _LT_COMPILER_BOILERPLATE
+ _LT_LINKER_BOILERPLATE
+
+ # Allow CC to be a program name with arguments.
+ lt_save_CC=$CC
+ lt_save_LD=$LD
+ lt_save_GCC=$GCC
+ GCC=$GXX
+ lt_save_with_gnu_ld=$with_gnu_ld
+ lt_save_path_LD=$lt_cv_path_LD
+ if test -n "${lt_cv_prog_gnu_ldcxx+set}"; then
+ lt_cv_prog_gnu_ld=$lt_cv_prog_gnu_ldcxx
+ else
+ $as_unset lt_cv_prog_gnu_ld
+ fi
+ if test -n "${lt_cv_path_LDCXX+set}"; then
+ lt_cv_path_LD=$lt_cv_path_LDCXX
+ else
+ $as_unset lt_cv_path_LD
+ fi
+ test -z "${LDCXX+set}" || LD=$LDCXX
+ CC=${CXX-"c++"}
+ compiler=$CC
+ _LT_TAGVAR(compiler, $1)=$CC
+ _LT_CC_BASENAME([$compiler])
+
+ if test -n "$compiler"; then
+ # We don't want -fno-exception when compiling C++ code, so set the
+ # no_builtin_flag separately
+ if test "$GXX" = yes; then
+ _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=' -fno-builtin'
+ else
+ _LT_TAGVAR(lt_prog_compiler_no_builtin_flag, $1)=
+ fi
+
+ if test "$GXX" = yes; then
+ # Set up default GNU C++ configuration
+
+ LT_PATH_LD
+
+ # Check if GNU C++ uses GNU ld as the underlying linker, since the
+ # archiving commands below assume that GNU ld is being used.
+ if test "$with_gnu_ld" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+
+ # If archive_cmds runs LD, not CC, wlarc should be empty
+ # XXX I think wlarc can be eliminated in ltcf-cxx, but I need to
+ # investigate it a little bit more. (MM)
+ wlarc='${wl}'
+
+ # ancient GNU ld didn't support --whole-archive et. al.
+ if eval "`$CC -print-prog-name=ld` --help 2>&1" |
+ $GREP 'no-whole-archive' > /dev/null; then
+ _LT_TAGVAR(whole_archive_flag_spec, $1)="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ else
+ _LT_TAGVAR(whole_archive_flag_spec, $1)=
+ fi
+ else
+ with_gnu_ld=no
+ wlarc=
+
+ # A generic and very simple default shared library creation
+ # command for GNU C++ for the case where it uses the native
+ # linker, instead of GNU ld. If possible, this setting should
+ # overridden to take advantage of the native linker features on
+ # the platform it is being used on.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+ fi
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+
+ else
+ GXX=no
+ with_gnu_ld=no
+ wlarc=
+ fi
+
+ # PORTME: fill in a description of your system's C++ link characteristics
+ AC_MSG_CHECKING([whether the $compiler linker ($LD) supports shared libraries])
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ case $host_os in
+ aix3*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ aix[[4-9]]*)
+ if test "$host_cpu" = ia64; then
+ # On IA64, the linker does run time linking by default, so we don't
+ # have to do anything special.
+ aix_use_runtimelinking=no
+ exp_sym_flag='-Bexport'
+ no_entry_flag=""
+ else
+ aix_use_runtimelinking=no
+
+ # Test if we are trying to use run time linking or normal
+ # AIX style linking. If -brtl is somewhere in LDFLAGS, we
+ # need to do runtime linking.
+ case $host_os in aix4.[[23]]|aix4.[[23]].*|aix[[5-9]]*)
+ for ld_flag in $LDFLAGS; do
+ case $ld_flag in
+ *-brtl*)
+ aix_use_runtimelinking=yes
+ break
+ ;;
+ esac
+ done
+ ;;
+ esac
+
+ exp_sym_flag='-bexport'
+ no_entry_flag='-bnoentry'
+ fi
+
+ # When large executables or shared objects are built, AIX ld can
+ # have problems creating the table of contents. If linking a library
+ # or program results in "error TOC overflow" add -mminimal-toc to
+ # CXXFLAGS/CFLAGS for g++/gcc. In the cases where that is not
+ # enough to fix the problem, add -Wl,-bbigtoc to LDFLAGS.
+
+ _LT_TAGVAR(archive_cmds, $1)=''
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=':'
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(file_list_spec, $1)='${wl}-f,'
+
+ if test "$GXX" = yes; then
+ case $host_os in aix4.[[012]]|aix4.[[012]].*)
+ # We only want to do this on AIX 4.2 and lower, the check
+ # below for broken collect2 doesn't work under 4.3+
+ collect2name=`${CC} -print-prog-name=collect2`
+ if test -f "$collect2name" &&
+ strings "$collect2name" | $GREP resolve_lib_name >/dev/null
+ then
+ # We have reworked collect2
+ :
+ else
+ # We have old collect2
+ _LT_TAGVAR(hardcode_direct, $1)=unsupported
+ # It fails to find uninstalled libraries when the uninstalled
+ # path is not listed in the libpath. Setting hardcode_minus_L
+ # to unsupported forces relinking
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=
+ fi
+ esac
+ shared_flag='-shared'
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag="$shared_flag "'${wl}-G'
+ fi
+ else
+ # not using gcc
+ if test "$host_cpu" = ia64; then
+ # VisualAge C++, Version 5.5 for AIX 5L for IA-64, Beta 3 Release
+ # chokes on -Wl,-G. The following line is correct:
+ shared_flag='-G'
+ else
+ if test "$aix_use_runtimelinking" = yes; then
+ shared_flag='${wl}-G'
+ else
+ shared_flag='${wl}-bM:SRE'
+ fi
+ fi
+ fi
+
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-bexpall'
+ # It seems that -bexpall does not export symbols beginning with
+ # underscore (_), so it is better to generate a list of symbols to
+ # export.
+ _LT_TAGVAR(always_export_symbols, $1)=yes
+ if test "$aix_use_runtimelinking" = yes; then
+ # Warning - without using the other runtime loading flags (-brtl),
+ # -berok will link without error, but may produce a broken library.
+ _LT_TAGVAR(allow_undefined_flag, $1)='-berok'
+ # Determine the default libpath from the value encoded in an empty
+ # executable.
+ _LT_SYS_MODULE_PATH_AIX
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags `if test "x${allow_undefined_flag}" != "x"; then $ECHO "X${wl}${allow_undefined_flag}" | $Xsed; else :; fi` '"\${wl}$exp_sym_flag:\$export_symbols $shared_flag"
+ else
+ if test "$host_cpu" = ia64; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $libdir:/usr/lib:/lib'
+ _LT_TAGVAR(allow_undefined_flag, $1)="-z nodefs"
+ _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs '"\${wl}$no_entry_flag"' $compiler_flags ${wl}${allow_undefined_flag} '"\${wl}$exp_sym_flag:\$export_symbols"
+ else
+ # Determine the default libpath from the value encoded in an
+ # empty executable.
+ _LT_SYS_MODULE_PATH_AIX
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-blibpath:$libdir:'"$aix_libpath"
+ # Warning - without using the other run time loading flags,
+ # -berok will link without error, but may produce a broken library.
+ _LT_TAGVAR(no_undefined_flag, $1)=' ${wl}-bernotok'
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-berok'
+ # Exported symbols can be pulled into shared objects from archives
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='$convenience'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=yes
+ # This is similar to how AIX traditionally builds its shared
+ # libraries.
+ _LT_TAGVAR(archive_expsym_cmds, $1)="\$CC $shared_flag"' -o $output_objdir/$soname $libobjs $deplibs ${wl}-bnoentry $compiler_flags ${wl}-bE:$export_symbols${allow_undefined_flag}~$AR $AR_FLAGS $output_objdir/$libname$release.a $output_objdir/$soname'
+ fi
+ fi
+ ;;
+
+ beos*)
+ if $LD --help 2>&1 | $GREP ': supported targets:.* elf' > /dev/null; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ # Joseph Beckenbach <jrb3@best.com> says some releases of gcc
+ # support --undefined. This deserves some investigation. FIXME
+ _LT_TAGVAR(archive_cmds, $1)='$CC -nostart $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ chorus*)
+ case $cc_basename in
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ cygwin* | mingw* | pw32* | cegcc*)
+ # _LT_TAGVAR(hardcode_libdir_flag_spec, $1) is actually meaningless,
+ # as there is no search path for DLLs.
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-L$libdir'
+ _LT_TAGVAR(allow_undefined_flag, $1)=unsupported
+ _LT_TAGVAR(always_export_symbols, $1)=no
+ _LT_TAGVAR(enable_shared_with_static_runtimes, $1)=yes
+
+ if $LD --help 2>&1 | $GREP 'auto-import' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ # If the export-symbols file already is a .def file (1st line
+ # is EXPORTS), use it as is; otherwise, prepend...
+ _LT_TAGVAR(archive_expsym_cmds, $1)='if test "x`$SED 1q $export_symbols`" = xEXPORTS; then
+ cp $export_symbols $output_objdir/$soname.def;
+ else
+ echo EXPORTS > $output_objdir/$soname.def;
+ cat $export_symbols >> $output_objdir/$soname.def;
+ fi~
+ $CC -shared -nostdlib $output_objdir/$soname.def $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $output_objdir/$soname ${wl}--enable-auto-image-base -Xlinker --out-implib -Xlinker $lib'
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ darwin* | rhapsody*)
+ _LT_DARWIN_LINKER_FEATURES($1)
+ ;;
+
+ dgux*)
+ case $cc_basename in
+ ec++*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ ghcx*)
+ # Green Hills C++ Compiler
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ freebsd[[12]]*)
+ # C++ shared libraries reported to be fairly broken before
+ # switch to ELF
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ freebsd-elf*)
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ ;;
+
+ freebsd* | dragonfly*)
+ # FreeBSD 3 and later use GNU C++ and GNU ld with standard ELF
+ # conventions
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ ;;
+
+ gnu*)
+ ;;
+
+ hpux9*)
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes # Not in the search PATH,
+ # but as the default
+ # location of the library.
+
+ case $cc_basename in
+ CC*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ aCC*)
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$CC -b ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | $EGREP "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ _LT_TAGVAR(archive_cmds, $1)='$RM $output_objdir/$soname~$CC -shared -nostdlib -fPIC ${wl}+b ${wl}$install_libdir -o $output_objdir/$soname $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~test $output_objdir/$soname = $lib || mv $output_objdir/$soname $lib'
+ else
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+ ;;
+
+ hpux10*|hpux11*)
+ if test $with_gnu_ld = no; then
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}+b ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ case $host_cpu in
+ hppa*64*|ia64*)
+ ;;
+ *)
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ ;;
+ esac
+ fi
+ case $host_cpu in
+ hppa*64*|ia64*)
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ ;;
+ *)
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(hardcode_minus_L, $1)=yes # Not in the search PATH,
+ # but as the default
+ # location of the library.
+ ;;
+ esac
+
+ case $cc_basename in
+ CC*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ aCC*)
+ case $host_cpu in
+ hppa*64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ ia64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -b ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ esac
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`($CC -b $CFLAGS -v conftest.$objext 2>&1) | $GREP "\-L"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ if test $with_gnu_ld = no; then
+ case $host_cpu in
+ hppa*64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ ia64*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+nodefaultrpath -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib -fPIC ${wl}+h ${wl}$soname ${wl}+b ${wl}$install_libdir -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ ;;
+ esac
+ fi
+ else
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+ ;;
+
+ interix[[3-9]]*)
+ _LT_TAGVAR(hardcode_direct, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ # Hack: On Interix 3.x, we cannot compile PIC because of a broken gcc.
+ # Instead, shared libraries are loaded at an image base (0x10000000 by
+ # default) and relocated if they conflict, which is a slow very memory
+ # consuming and fragmenting process. To avoid this, we pick a random,
+ # 256 KiB-aligned image base between 0x50000000 and 0x6FFC0000 at link
+ # time. Moving up from 0x10000000 also allows more sbrk(2) space.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='sed "s,^,_," $export_symbols >$output_objdir/$soname.expsym~$CC -shared $pic_flag $libobjs $deplibs $compiler_flags ${wl}-h,$soname ${wl}--retain-symbols-file,$output_objdir/$soname.expsym ${wl}--image-base,`expr ${RANDOM-$$} % 4096 / 2 \* 262144 + 1342177280` -o $lib'
+ ;;
+ irix5* | irix6*)
+ case $cc_basename in
+ CC*)
+ # SGI C++
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -all -multigot $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+
+ # Archives containing C++ object files must be created using
+ # "CC -ar", where "CC" is the IRIX C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC -ar -WR,-u -o $oldlib $oldobjs'
+ ;;
+ *)
+ if test "$GXX" = yes; then
+ if test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ else
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` -o $lib'
+ fi
+ fi
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ ;;
+ esac
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+ _LT_TAGVAR(inherit_rpath, $1)=yes
+ ;;
+
+ linux* | k*bsd*-gnu)
+ case $cc_basename in
+ KCC*)
+ # Kuck and Associates, Inc. (KAI) C++ Compiler
+
+ # KCC will only create a shared library if the output file
+ # ends with ".so" (or ".sl" for HP-UX), so rename the library
+ # to its proper name (with version) after linking.
+ _LT_TAGVAR(archive_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo $lib | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib ${wl}-retain-symbols-file,$export_symbols; mv \$templib $lib'
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1 | $GREP "ld"`; rm -f libconftest$shared_ext; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+
+ # Archives containing C++ object files must be created using
+ # "CC -Bstatic", where "CC" is the KAI C++ compiler.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC -Bstatic -o $oldlib $oldobjs'
+ ;;
+ icpc* | ecpc* )
+ # Intel C++
+ with_gnu_ld=yes
+ # version 8.0 and above of icpc choke on multiply defined symbols
+ # if we add $predep_objects and $postdep_objects, however 7.1 and
+ # earlier do not add the objects themselves.
+ case `$CC -V 2>&1` in
+ *"Version 7."*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ ;;
+ *) # Version 8.0 or newer
+ tmp_idyn=
+ case $host_cpu in
+ ia64*) tmp_idyn=' -i_dynamic';;
+ esac
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared'"$tmp_idyn"' $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-retain-symbols-file $wl$export_symbols -o $lib'
+ ;;
+ esac
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive$convenience ${wl}--no-whole-archive'
+ ;;
+ pgCC* | pgcpp*)
+ # Portland Group C++ compiler
+ case `$CC -V` in
+ *pgCC\ [[1-5]]* | *pgcpp\ [[1-5]]*)
+ _LT_TAGVAR(prelink_cmds, $1)='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $objs $libobjs $compile_deplibs~
+ compile_command="$compile_command `find $tpldir -name \*.o | $NL2SP`"'
+ _LT_TAGVAR(old_archive_cmds, $1)='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $oldobjs$old_deplibs~
+ $AR $AR_FLAGS $oldlib$oldobjs$old_deplibs `find $tpldir -name \*.o | $NL2SP`~
+ $RANLIB $oldlib'
+ _LT_TAGVAR(archive_cmds, $1)='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $predep_objects $libobjs $deplibs $convenience $postdep_objects~
+ $CC -shared $pic_flag $predep_objects $libobjs $deplibs `find $tpldir -name \*.o | $NL2SP` $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='tpldir=Template.dir~
+ rm -rf $tpldir~
+ $CC --prelink_objects --instantiation_dir $tpldir $predep_objects $libobjs $deplibs $convenience $postdep_objects~
+ $CC -shared $pic_flag $predep_objects $libobjs $deplibs `find $tpldir -name \*.o | $NL2SP` $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib'
+ ;;
+ *) # Version 6 will use weak symbols
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname ${wl}-retain-symbols-file ${wl}$export_symbols -o $lib'
+ ;;
+ esac
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}--rpath ${wl}$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ ;;
+ cxx*)
+ # Compaq C++
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $wl$soname -o $lib ${wl}-retain-symbols-file $wl$export_symbols'
+
+ runpath_var=LD_RUN_PATH
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld .*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ xl*)
+ # IBM XL 8.0 on PPC, with GNU ld
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}--export-dynamic'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+ if test "x$supports_anon_versioning" = xyes; then
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $output_objdir/$libname.ver~
+ cat $export_symbols | sed -e "s/\(.*\)/\1;/" >> $output_objdir/$libname.ver~
+ echo "local: *; };" >> $output_objdir/$libname.ver~
+ $CC -qmkshrobj $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+ fi
+ ;;
+ *)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+ _LT_TAGVAR(no_undefined_flag, $1)=' -zdefs'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file ${wl}$export_symbols'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}--whole-archive`new_convenience=; for conv in $convenience\"\"; do test -z \"$conv\" || new_convenience=\"$new_convenience,$conv\"; done; $ECHO \"$new_convenience\"` ${wl}--no-whole-archive'
+ _LT_TAGVAR(compiler_needs_object, $1)=yes
+
+ # Not sure whether something based on
+ # $CC $CFLAGS -v conftest.$objext -o libconftest$shared_ext 2>&1
+ # would be better.
+ output_verbose_link_cmd='echo'
+
+ # Archives containing C++ object files must be created using
+ # "CC -xar", where "CC" is the Sun C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC -xar -o $oldlib $oldobjs'
+ ;;
+ esac
+ ;;
+ esac
+ ;;
+
+ lynxos*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ m88k*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ mvs*)
+ case $cc_basename in
+ cxx*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ netbsd*)
+ if echo __ELF__ | $CC -E - | $GREP __ELF__ >/dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$LD -Bshareable -o $lib $predep_objects $libobjs $deplibs $postdep_objects $linker_flags'
+ wlarc=
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ fi
+ # Workaround some broken pre-1.5 toolchains
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP conftest.$objext | $SED -e "s:-lgcc -lc -lgcc::"'
+ ;;
+
+ *nto* | *qnx*)
+ _LT_TAGVAR(ld_shlibs, $1)=yes
+ ;;
+
+ openbsd2*)
+ # C++ shared libraries are fairly broken
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ openbsd*)
+ if test -f /usr/libexec/ld.so; then
+ _LT_TAGVAR(hardcode_direct, $1)=yes
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_direct_absolute, $1)=yes
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -o $lib'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared $pic_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-retain-symbols-file,$export_symbols -o $lib'
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-E'
+ _LT_TAGVAR(whole_archive_flag_spec, $1)="$wlarc"'--whole-archive$convenience '"$wlarc"'--no-whole-archive'
+ fi
+ output_verbose_link_cmd=echo
+ else
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+
+ osf3* | osf4* | osf5*)
+ case $cc_basename in
+ KCC*)
+ # Kuck and Associates, Inc. (KAI) C++ Compiler
+
+ # KCC will only create a shared library if the output file
+ # ends with ".so" (or ".sl" for HP-UX), so rename the library
+ # to its proper name (with version) after linking.
+ _LT_TAGVAR(archive_cmds, $1)='tempext=`echo $shared_ext | $SED -e '\''s/\([[^()0-9A-Za-z{}]]\)/\\\\\1/g'\''`; templib=`echo "$lib" | $SED -e "s/\${tempext}\..*/.so/"`; $CC $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags --soname $soname -o \$templib; mv \$templib $lib'
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath,$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ # Archives containing C++ object files must be created using
+ # the KAI C++ compiler.
+ case $host in
+ osf3*) _LT_TAGVAR(old_archive_cmds, $1)='$CC -Bstatic -o $oldlib $oldobjs' ;;
+ *) _LT_TAGVAR(old_archive_cmds, $1)='$CC -o $oldlib $oldobjs' ;;
+ esac
+ ;;
+ RCC*)
+ # Rational C++ 2.4.1
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ cxx*)
+ case $host in
+ osf3*)
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname $soname `test -n "$verstring" && $ECHO "X${wl}-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ ;;
+ *)
+ _LT_TAGVAR(allow_undefined_flag, $1)=' -expect_unresolved \*'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='for i in `cat $export_symbols`; do printf "%s %s\\n" -exported_symbol "\$i" >> $lib.exp; done~
+ echo "-hidden">> $lib.exp~
+ $CC -shared$allow_undefined_flag $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags -msym -soname $soname ${wl}-input ${wl}$lib.exp `test -n "$verstring" && $ECHO "X-set_version $verstring" | $Xsed` -update_registry ${output_objdir}/so_locations -o $lib~
+ $RM $lib.exp'
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-rpath $libdir'
+ ;;
+ esac
+
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ #
+ # There doesn't appear to be a way to prevent this compiler from
+ # explicitly linking system object files so we need to strip them
+ # from the output so that they don't get included in the library
+ # dependencies.
+ output_verbose_link_cmd='templist=`$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "ld" | $GREP -v "ld:"`; templist=`$ECHO "X$templist" | $Xsed -e "s/\(^.*ld.*\)\( .*ld.*$\)/\1/"`; list=""; for z in $templist; do case $z in conftest.$objext) list="$list $z";; *.$objext);; *) list="$list $z";;esac; done; $ECHO "X$list" | $Xsed'
+ ;;
+ *)
+ if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(allow_undefined_flag, $1)=' ${wl}-expect_unresolved ${wl}\*'
+ case $host in
+ osf3*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "X${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib ${allow_undefined_flag} $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-msym ${wl}-soname ${wl}$soname `test -n "$verstring" && $ECHO "${wl}-set_version ${wl}$verstring" | $Xsed` ${wl}-update_registry ${wl}${output_objdir}/so_locations -o $lib'
+ ;;
+ esac
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-rpath ${wl}$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=:
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+
+ else
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ fi
+ ;;
+ esac
+ ;;
+
+ psos*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ sunos4*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.x
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ lcc*)
+ # Lucid
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ solaris*)
+ case $cc_basename in
+ CC*)
+ # Sun C++ 4.2, 5.x and Centerline C++
+ _LT_TAGVAR(archive_cmds_need_lc,$1)=yes
+ _LT_TAGVAR(no_undefined_flag, $1)=' -zdefs'
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G${allow_undefined_flag} -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G${allow_undefined_flag} ${wl}-M ${wl}$lib.exp -h$soname -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='-R$libdir'
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ case $host_os in
+ solaris2.[[0-5]] | solaris2.[[0-5]].*) ;;
+ *)
+ # The compiler driver will combine and reorder linker options,
+ # but understands `-z linker_flag'.
+ # Supported since Solaris 2.6 (maybe 2.5.1?)
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='-z allextract$convenience -z defaultextract'
+ ;;
+ esac
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+
+ output_verbose_link_cmd='echo'
+
+ # Archives containing C++ object files must be created using
+ # "CC -xar", where "CC" is the Sun C++ compiler. This is
+ # necessary to make sure instantiated templates are included
+ # in the archive.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC -xar -o $oldlib $oldobjs'
+ ;;
+ gcx*)
+ # Green Hills C++ Compiler
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+
+ # The C++ compiler must be used to create the archive.
+ _LT_TAGVAR(old_archive_cmds, $1)='$CC $LDFLAGS -archive -o $oldlib $oldobjs'
+ ;;
+ *)
+ # GNU C++ compiler with Solaris linker
+ if test "$GXX" = yes && test "$with_gnu_ld" = no; then
+ _LT_TAGVAR(no_undefined_flag, $1)=' ${wl}-z ${wl}defs'
+ if $CC --version | $GREP -v '^2\.7' > /dev/null; then
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -shared -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -shared $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+ else
+ # g++ 2.7 appears to require `-G' NOT `-shared' on this
+ # platform.
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G -nostdlib $LDFLAGS $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags ${wl}-h $wl$soname -o $lib'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='echo "{ global:" > $lib.exp~cat $export_symbols | $SED -e "s/\(.*\)/\1;/" >> $lib.exp~echo "local: *; };" >> $lib.exp~
+ $CC -G -nostdlib ${wl}-M $wl$lib.exp -o $lib $predep_objects $libobjs $deplibs $postdep_objects $compiler_flags~$RM $lib.exp'
+
+ # Commands to make compiler produce verbose output that lists
+ # what "hidden" libraries, object files and flags are used when
+ # linking a shared library.
+ output_verbose_link_cmd='$CC -G $CFLAGS -v conftest.$objext 2>&1 | $GREP "\-L"'
+ fi
+
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R $wl$libdir'
+ case $host_os in
+ solaris2.[[0-5]] | solaris2.[[0-5]].*) ;;
+ *)
+ _LT_TAGVAR(whole_archive_flag_spec, $1)='${wl}-z ${wl}allextract$convenience ${wl}-z ${wl}defaultextract'
+ ;;
+ esac
+ fi
+ ;;
+ esac
+ ;;
+
+ sysv4*uw2* | sysv5OpenUNIX* | sysv5UnixWare7.[[01]].[[10]]* | unixware7* | sco3.2v5.0.[[024]]*)
+ _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ runpath_var='LD_RUN_PATH'
+
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ ;;
+
+ sysv5* | sco3.2v5* | sco5v6*)
+ # Note: We can NOT use -z defs as we might desire, because we do not
+ # link with -lc, and that would cause any symbols used from libc to
+ # always be unresolved, which means just about no library would
+ # ever link correctly. If we're not using GNU ld we use -z text
+ # though, which does catch some bad symbols but isn't as heavy-handed
+ # as -z defs.
+ _LT_TAGVAR(no_undefined_flag, $1)='${wl}-z,text'
+ _LT_TAGVAR(allow_undefined_flag, $1)='${wl}-z,nodefs'
+ _LT_TAGVAR(archive_cmds_need_lc, $1)=no
+ _LT_TAGVAR(hardcode_shlibpath_var, $1)=no
+ _LT_TAGVAR(hardcode_libdir_flag_spec, $1)='${wl}-R,$libdir'
+ _LT_TAGVAR(hardcode_libdir_separator, $1)=':'
+ _LT_TAGVAR(link_all_deplibs, $1)=yes
+ _LT_TAGVAR(export_dynamic_flag_spec, $1)='${wl}-Bexport'
+ runpath_var='LD_RUN_PATH'
+
+ case $cc_basename in
+ CC*)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -G ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -G ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ *)
+ _LT_TAGVAR(archive_cmds, $1)='$CC -shared ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ _LT_TAGVAR(archive_expsym_cmds, $1)='$CC -shared ${wl}-Bexport:$export_symbols ${wl}-h,$soname -o $lib $libobjs $deplibs $compiler_flags'
+ ;;
+ esac
+ ;;
+
+ tandem*)
+ case $cc_basename in
+ NCC*)
+ # NonStop-UX NCC 3.20
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+ ;;
+
+ vxworks*)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+
+ *)
+ # FIXME: insert proper C++ library support
+ _LT_TAGVAR(ld_shlibs, $1)=no
+ ;;
+ esac
+
+ AC_MSG_RESULT([$_LT_TAGVAR(ld_shlibs, $1)])
+ test "$_LT_TAGVAR(ld_shlibs, $1)" = no && can_build_shared=no
+
+ _LT_TAGVAR(GCC, $1)="$GXX"
+ _LT_TAGVAR(LD, $1)="$LD"
+
+ ## CAVEAT EMPTOR:
+ ## There is no encapsulation within the following macros, do not change
+ ## the running order or otherwise move them around unless you know exactly
+ ## what you are doing...
+ _LT_SYS_HIDDEN_LIBDEPS($1)
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_SYS_DYNAMIC_LINKER($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+
+ _LT_CONFIG($1)
+ fi # test -n "$compiler"
+
+ CC=$lt_save_CC
+ LDCXX=$LD
+ LD=$lt_save_LD
+ GCC=$lt_save_GCC
+ with_gnu_ld=$lt_save_with_gnu_ld
+ lt_cv_path_LDCXX=$lt_cv_path_LD
+ lt_cv_path_LD=$lt_save_path_LD
+ lt_cv_prog_gnu_ldcxx=$lt_cv_prog_gnu_ld
+ lt_cv_prog_gnu_ld=$lt_save_with_gnu_ld
+fi # test "$_lt_caught_CXX_error" != yes
+
+AC_LANG_POP
+])# _LT_LANG_CXX_CONFIG
+
+
+# _LT_SYS_HIDDEN_LIBDEPS([TAGNAME])
+# ---------------------------------
+# Figure out "hidden" library dependencies from verbose
+# compiler output when linking a shared library.
+# Parse the compiler output and extract the necessary
+# objects, libraries and library flags.
+m4_defun([_LT_SYS_HIDDEN_LIBDEPS],
+[m4_require([_LT_FILEUTILS_DEFAULTS])dnl
+# Dependencies to place before and after the object being linked:
+_LT_TAGVAR(predep_objects, $1)=
+_LT_TAGVAR(postdep_objects, $1)=
+_LT_TAGVAR(predeps, $1)=
+_LT_TAGVAR(postdeps, $1)=
+_LT_TAGVAR(compiler_lib_search_path, $1)=
+
+dnl we can't use the lt_simple_compile_test_code here,
+dnl because it contains code intended for an executable,
+dnl not a library. It's possible we should let each
+dnl tag define a new lt_????_link_test_code variable,
+dnl but it's only used here...
+m4_if([$1], [], [cat > conftest.$ac_ext <<_LT_EOF
+int a;
+void foo (void) { a = 0; }
+_LT_EOF
+], [$1], [CXX], [cat > conftest.$ac_ext <<_LT_EOF
+class Foo
+{
+public:
+ Foo (void) { a = 0; }
+private:
+ int a;
+};
+_LT_EOF
+], [$1], [F77], [cat > conftest.$ac_ext <<_LT_EOF
+ subroutine foo
+ implicit none
+ integer*4 a
+ a=0
+ return
+ end
+_LT_EOF
+], [$1], [FC], [cat > conftest.$ac_ext <<_LT_EOF
+ subroutine foo
+ implicit none
+ integer a
+ a=0
+ return
+ end
+_LT_EOF
+], [$1], [GCJ], [cat > conftest.$ac_ext <<_LT_EOF
+public class foo {
+ private int a;
+ public void bar (void) {
+ a = 0;
+ }
+};
+_LT_EOF
+])
+dnl Parse the compiler output and extract the necessary
+dnl objects, libraries and library flags.
+if AC_TRY_EVAL(ac_compile); then
+ # Parse the compiler output and extract the necessary
+ # objects, libraries and library flags.
+
+ # Sentinel used to keep track of whether or not we are before
+ # the conftest object file.
+ pre_test_object_deps_done=no
+
+ for p in `eval "$output_verbose_link_cmd"`; do
+ case $p in
+
+ -L* | -R* | -l*)
+ # Some compilers place space between "-{L,R}" and the path.
+ # Remove the space.
+ if test $p = "-L" ||
+ test $p = "-R"; then
+ prev=$p
+ continue
+ else
+ prev=
+ fi
+
+ if test "$pre_test_object_deps_done" = no; then
+ case $p in
+ -L* | -R*)
+ # Internal compiler library paths should come after those
+ # provided the user. The postdeps already come after the
+ # user supplied libs so there is no need to process them.
+ if test -z "$_LT_TAGVAR(compiler_lib_search_path, $1)"; then
+ _LT_TAGVAR(compiler_lib_search_path, $1)="${prev}${p}"
+ else
+ _LT_TAGVAR(compiler_lib_search_path, $1)="${_LT_TAGVAR(compiler_lib_search_path, $1)} ${prev}${p}"
+ fi
+ ;;
+ # The "-l" case would never come before the object being
+ # linked, so don't bother handling this case.
+ esac
+ else
+ if test -z "$_LT_TAGVAR(postdeps, $1)"; then
+ _LT_TAGVAR(postdeps, $1)="${prev}${p}"
+ else
+ _LT_TAGVAR(postdeps, $1)="${_LT_TAGVAR(postdeps, $1)} ${prev}${p}"
+ fi
+ fi
+ ;;
+
+ *.$objext)
+ # This assumes that the test object file only shows up
+ # once in the compiler output.
+ if test "$p" = "conftest.$objext"; then
+ pre_test_object_deps_done=yes
+ continue
+ fi
+
+ if test "$pre_test_object_deps_done" = no; then
+ if test -z "$_LT_TAGVAR(predep_objects, $1)"; then
+ _LT_TAGVAR(predep_objects, $1)="$p"
+ else
+ _LT_TAGVAR(predep_objects, $1)="$_LT_TAGVAR(predep_objects, $1) $p"
+ fi
+ else
+ if test -z "$_LT_TAGVAR(postdep_objects, $1)"; then
+ _LT_TAGVAR(postdep_objects, $1)="$p"
+ else
+ _LT_TAGVAR(postdep_objects, $1)="$_LT_TAGVAR(postdep_objects, $1) $p"
+ fi
+ fi
+ ;;
+
+ *) ;; # Ignore the rest.
+
+ esac
+ done
+
+ # Clean up.
+ rm -f a.out a.exe
+else
+ echo "libtool.m4: error: problem compiling $1 test program"
+fi
+
+$RM -f confest.$objext
+
+# PORTME: override above test on systems where it is broken
+m4_if([$1], [CXX],
+[case $host_os in
+interix[[3-9]]*)
+ # Interix 3.5 installs completely hosed .la files for C++, so rather than
+ # hack all around it, let's just trust "g++" to DTRT.
+ _LT_TAGVAR(predep_objects,$1)=
+ _LT_TAGVAR(postdep_objects,$1)=
+ _LT_TAGVAR(postdeps,$1)=
+ ;;
+
+linux*)
+ case `$CC -V 2>&1 | sed 5q` in
+ *Sun\ C*)
+ # Sun C++ 5.9
+
+ # The more standards-conforming stlport4 library is
+ # incompatible with the Cstd library. Avoid specifying
+ # it if it's in CXXFLAGS. Ignore libCrun as
+ # -library=stlport4 depends on it.
+ case " $CXX $CXXFLAGS " in
+ *" -library=stlport4 "*)
+ solaris_use_stlport4=yes
+ ;;
+ esac
+
+ if test "$solaris_use_stlport4" != yes; then
+ _LT_TAGVAR(postdeps,$1)='-library=Cstd -library=Crun'
+ fi
+ ;;
+ esac
+ ;;
+
+solaris*)
+ case $cc_basename in
+ CC*)
+ # The more standards-conforming stlport4 library is
+ # incompatible with the Cstd library. Avoid specifying
+ # it if it's in CXXFLAGS. Ignore libCrun as
+ # -library=stlport4 depends on it.
+ case " $CXX $CXXFLAGS " in
+ *" -library=stlport4 "*)
+ solaris_use_stlport4=yes
+ ;;
+ esac
+
+ # Adding this requires a known-good setup of shared libraries for
+ # Sun compiler versions before 5.6, else PIC objects from an old
+ # archive will be linked into the output, leading to subtle bugs.
+ if test "$solaris_use_stlport4" != yes; then
+ _LT_TAGVAR(postdeps,$1)='-library=Cstd -library=Crun'
+ fi
+ ;;
+ esac
+ ;;
+esac
+])
+
+case " $_LT_TAGVAR(postdeps, $1) " in
+*" -lc "*) _LT_TAGVAR(archive_cmds_need_lc, $1)=no ;;
+esac
+ _LT_TAGVAR(compiler_lib_search_dirs, $1)=
+if test -n "${_LT_TAGVAR(compiler_lib_search_path, $1)}"; then
+ _LT_TAGVAR(compiler_lib_search_dirs, $1)=`echo " ${_LT_TAGVAR(compiler_lib_search_path, $1)}" | ${SED} -e 's! -L! !g' -e 's!^ !!'`
+fi
+_LT_TAGDECL([], [compiler_lib_search_dirs], [1],
+ [The directories searched by this compiler when creating a shared library])
+_LT_TAGDECL([], [predep_objects], [1],
+ [Dependencies to place before and after the objects being linked to
+ create a shared library])
+_LT_TAGDECL([], [postdep_objects], [1])
+_LT_TAGDECL([], [predeps], [1])
+_LT_TAGDECL([], [postdeps], [1])
+_LT_TAGDECL([], [compiler_lib_search_path], [1],
+ [The library search path used internally by the compiler when linking
+ a shared library])
+])# _LT_SYS_HIDDEN_LIBDEPS
+
+
+# _LT_PROG_F77
+# ------------
+# Since AC_PROG_F77 is broken, in that it returns the empty string
+# if there is no fortran compiler, we have our own version here.
+m4_defun([_LT_PROG_F77],
+[
+pushdef([AC_MSG_ERROR], [_lt_disable_F77=yes])
+AC_PROG_F77
+if test -z "$F77" || test "X$F77" = "Xno"; then
+ _lt_disable_F77=yes
+fi
+popdef([AC_MSG_ERROR])
+])# _LT_PROG_F77
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([_LT_PROG_F77], [])
+
+
+# _LT_LANG_F77_CONFIG([TAG])
+# --------------------------
+# Ensure that the configuration variables for a Fortran 77 compiler are
+# suitably defined. These variables are subsequently used by _LT_CONFIG
+# to write the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_F77_CONFIG],
+[AC_REQUIRE([_LT_PROG_F77])dnl
+AC_LANG_PUSH(Fortran 77)
+
+_LT_TAGVAR(archive_cmds_need_lc, $1)=no
+_LT_TAGVAR(allow_undefined_flag, $1)=
+_LT_TAGVAR(always_export_symbols, $1)=no
+_LT_TAGVAR(archive_expsym_cmds, $1)=
+_LT_TAGVAR(export_dynamic_flag_spec, $1)=
+_LT_TAGVAR(hardcode_direct, $1)=no
+_LT_TAGVAR(hardcode_direct_absolute, $1)=no
+_LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
+_LT_TAGVAR(hardcode_libdir_separator, $1)=
+_LT_TAGVAR(hardcode_minus_L, $1)=no
+_LT_TAGVAR(hardcode_automatic, $1)=no
+_LT_TAGVAR(inherit_rpath, $1)=no
+_LT_TAGVAR(module_cmds, $1)=
+_LT_TAGVAR(module_expsym_cmds, $1)=
+_LT_TAGVAR(link_all_deplibs, $1)=unknown
+_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+_LT_TAGVAR(no_undefined_flag, $1)=
+_LT_TAGVAR(whole_archive_flag_spec, $1)=
+_LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no
+
+# Source file extension for f77 test sources.
+ac_ext=f
+
+# Object file extension for compiled f77 test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# No sense in running all these tests if we already determined that
+# the F77 compiler isn't working. Some variables (like enable_shared)
+# are currently assumed to apply to all compilers on this platform,
+# and will be corrupted by setting them based on a non-working compiler.
+if test "$_lt_disable_F77" != yes; then
+ # Code to be used in simple compile tests
+ lt_simple_compile_test_code="\
+ subroutine t
+ return
+ end
+"
+
+ # Code to be used in simple link tests
+ lt_simple_link_test_code="\
+ program t
+ end
+"
+
+ # ltmain only uses $CC for tagged configurations so make sure $CC is set.
+ _LT_TAG_COMPILER
+
+ # save warnings/boilerplate of simple test code
+ _LT_COMPILER_BOILERPLATE
+ _LT_LINKER_BOILERPLATE
+
+ # Allow CC to be a program name with arguments.
+ lt_save_CC="$CC"
+ lt_save_GCC=$GCC
+ CC=${F77-"f77"}
+ compiler=$CC
+ _LT_TAGVAR(compiler, $1)=$CC
+ _LT_CC_BASENAME([$compiler])
+ GCC=$G77
+ if test -n "$compiler"; then
+ AC_MSG_CHECKING([if libtool supports shared libraries])
+ AC_MSG_RESULT([$can_build_shared])
+
+ AC_MSG_CHECKING([whether to build shared libraries])
+ test "$can_build_shared" = "no" && enable_shared=no
+
+ # On AIX, shared libraries and static libraries use the same namespace, and
+ # are all built from PIC.
+ case $host_os in
+ aix3*)
+ test "$enable_shared" = yes && enable_static=no
+ if test -n "$RANLIB"; then
+ archive_cmds="$archive_cmds~\$RANLIB \$lib"
+ postinstall_cmds='$RANLIB $lib'
+ fi
+ ;;
+ aix[[4-9]]*)
+ if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+ test "$enable_shared" = yes && enable_static=no
+ fi
+ ;;
+ esac
+ AC_MSG_RESULT([$enable_shared])
+
+ AC_MSG_CHECKING([whether to build static libraries])
+ # Make sure either enable_shared or enable_static is yes.
+ test "$enable_shared" = yes || enable_static=yes
+ AC_MSG_RESULT([$enable_static])
+
+ _LT_TAGVAR(GCC, $1)="$G77"
+ _LT_TAGVAR(LD, $1)="$LD"
+
+ ## CAVEAT EMPTOR:
+ ## There is no encapsulation within the following macros, do not change
+ ## the running order or otherwise move them around unless you know exactly
+ ## what you are doing...
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_SYS_DYNAMIC_LINKER($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+
+ _LT_CONFIG($1)
+ fi # test -n "$compiler"
+
+ GCC=$lt_save_GCC
+ CC="$lt_save_CC"
+fi # test "$_lt_disable_F77" != yes
+
+AC_LANG_POP
+])# _LT_LANG_F77_CONFIG
+
+
+# _LT_PROG_FC
+# -----------
+# Since AC_PROG_FC is broken, in that it returns the empty string
+# if there is no fortran compiler, we have our own version here.
+m4_defun([_LT_PROG_FC],
+[
+pushdef([AC_MSG_ERROR], [_lt_disable_FC=yes])
+AC_PROG_FC
+if test -z "$FC" || test "X$FC" = "Xno"; then
+ _lt_disable_FC=yes
+fi
+popdef([AC_MSG_ERROR])
+])# _LT_PROG_FC
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([_LT_PROG_FC], [])
+
+
+# _LT_LANG_FC_CONFIG([TAG])
+# -------------------------
+# Ensure that the configuration variables for a Fortran compiler are
+# suitably defined. These variables are subsequently used by _LT_CONFIG
+# to write the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_FC_CONFIG],
+[AC_REQUIRE([_LT_PROG_FC])dnl
+AC_LANG_PUSH(Fortran)
+
+_LT_TAGVAR(archive_cmds_need_lc, $1)=no
+_LT_TAGVAR(allow_undefined_flag, $1)=
+_LT_TAGVAR(always_export_symbols, $1)=no
+_LT_TAGVAR(archive_expsym_cmds, $1)=
+_LT_TAGVAR(export_dynamic_flag_spec, $1)=
+_LT_TAGVAR(hardcode_direct, $1)=no
+_LT_TAGVAR(hardcode_direct_absolute, $1)=no
+_LT_TAGVAR(hardcode_libdir_flag_spec, $1)=
+_LT_TAGVAR(hardcode_libdir_flag_spec_ld, $1)=
+_LT_TAGVAR(hardcode_libdir_separator, $1)=
+_LT_TAGVAR(hardcode_minus_L, $1)=no
+_LT_TAGVAR(hardcode_automatic, $1)=no
+_LT_TAGVAR(inherit_rpath, $1)=no
+_LT_TAGVAR(module_cmds, $1)=
+_LT_TAGVAR(module_expsym_cmds, $1)=
+_LT_TAGVAR(link_all_deplibs, $1)=unknown
+_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+_LT_TAGVAR(no_undefined_flag, $1)=
+_LT_TAGVAR(whole_archive_flag_spec, $1)=
+_LT_TAGVAR(enable_shared_with_static_runtimes, $1)=no
+
+# Source file extension for fc test sources.
+ac_ext=${ac_fc_srcext-f}
+
+# Object file extension for compiled fc test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# No sense in running all these tests if we already determined that
+# the FC compiler isn't working. Some variables (like enable_shared)
+# are currently assumed to apply to all compilers on this platform,
+# and will be corrupted by setting them based on a non-working compiler.
+if test "$_lt_disable_FC" != yes; then
+ # Code to be used in simple compile tests
+ lt_simple_compile_test_code="\
+ subroutine t
+ return
+ end
+"
+
+ # Code to be used in simple link tests
+ lt_simple_link_test_code="\
+ program t
+ end
+"
+
+ # ltmain only uses $CC for tagged configurations so make sure $CC is set.
+ _LT_TAG_COMPILER
+
+ # save warnings/boilerplate of simple test code
+ _LT_COMPILER_BOILERPLATE
+ _LT_LINKER_BOILERPLATE
+
+ # Allow CC to be a program name with arguments.
+ lt_save_CC="$CC"
+ lt_save_GCC=$GCC
+ CC=${FC-"f95"}
+ compiler=$CC
+ GCC=$ac_cv_fc_compiler_gnu
+
+ _LT_TAGVAR(compiler, $1)=$CC
+ _LT_CC_BASENAME([$compiler])
+
+ if test -n "$compiler"; then
+ AC_MSG_CHECKING([if libtool supports shared libraries])
+ AC_MSG_RESULT([$can_build_shared])
+
+ AC_MSG_CHECKING([whether to build shared libraries])
+ test "$can_build_shared" = "no" && enable_shared=no
+
+ # On AIX, shared libraries and static libraries use the same namespace, and
+ # are all built from PIC.
+ case $host_os in
+ aix3*)
+ test "$enable_shared" = yes && enable_static=no
+ if test -n "$RANLIB"; then
+ archive_cmds="$archive_cmds~\$RANLIB \$lib"
+ postinstall_cmds='$RANLIB $lib'
+ fi
+ ;;
+ aix[[4-9]]*)
+ if test "$host_cpu" != ia64 && test "$aix_use_runtimelinking" = no ; then
+ test "$enable_shared" = yes && enable_static=no
+ fi
+ ;;
+ esac
+ AC_MSG_RESULT([$enable_shared])
+
+ AC_MSG_CHECKING([whether to build static libraries])
+ # Make sure either enable_shared or enable_static is yes.
+ test "$enable_shared" = yes || enable_static=yes
+ AC_MSG_RESULT([$enable_static])
+
+ _LT_TAGVAR(GCC, $1)="$ac_cv_fc_compiler_gnu"
+ _LT_TAGVAR(LD, $1)="$LD"
+
+ ## CAVEAT EMPTOR:
+ ## There is no encapsulation within the following macros, do not change
+ ## the running order or otherwise move them around unless you know exactly
+ ## what you are doing...
+ _LT_SYS_HIDDEN_LIBDEPS($1)
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_SYS_DYNAMIC_LINKER($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+
+ _LT_CONFIG($1)
+ fi # test -n "$compiler"
+
+ GCC=$lt_save_GCC
+ CC="$lt_save_CC"
+fi # test "$_lt_disable_FC" != yes
+
+AC_LANG_POP
+])# _LT_LANG_FC_CONFIG
+
+
+# _LT_LANG_GCJ_CONFIG([TAG])
+# --------------------------
+# Ensure that the configuration variables for the GNU Java Compiler compiler
+# are suitably defined. These variables are subsequently used by _LT_CONFIG
+# to write the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_GCJ_CONFIG],
+[AC_REQUIRE([LT_PROG_GCJ])dnl
+AC_LANG_SAVE
+
+# Source file extension for Java test sources.
+ac_ext=java
+
+# Object file extension for compiled Java test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code="class foo {}"
+
+# Code to be used in simple link tests
+lt_simple_link_test_code='public class conftest { public static void main(String[[]] argv) {}; }'
+
+# ltmain only uses $CC for tagged configurations so make sure $CC is set.
+_LT_TAG_COMPILER
+
+# save warnings/boilerplate of simple test code
+_LT_COMPILER_BOILERPLATE
+_LT_LINKER_BOILERPLATE
+
+# Allow CC to be a program name with arguments.
+lt_save_CC="$CC"
+lt_save_GCC=$GCC
+GCC=yes
+CC=${GCJ-"gcj"}
+compiler=$CC
+_LT_TAGVAR(compiler, $1)=$CC
+_LT_TAGVAR(LD, $1)="$LD"
+_LT_CC_BASENAME([$compiler])
+
+# GCJ did not exist at the time GCC didn't implicitly link libc in.
+_LT_TAGVAR(archive_cmds_need_lc, $1)=no
+
+_LT_TAGVAR(old_archive_cmds, $1)=$old_archive_cmds
+
+## CAVEAT EMPTOR:
+## There is no encapsulation within the following macros, do not change
+## the running order or otherwise move them around unless you know exactly
+## what you are doing...
+if test -n "$compiler"; then
+ _LT_COMPILER_NO_RTTI($1)
+ _LT_COMPILER_PIC($1)
+ _LT_COMPILER_C_O($1)
+ _LT_COMPILER_FILE_LOCKS($1)
+ _LT_LINKER_SHLIBS($1)
+ _LT_LINKER_HARDCODE_LIBPATH($1)
+
+ _LT_CONFIG($1)
+fi
+
+AC_LANG_RESTORE
+
+GCC=$lt_save_GCC
+CC="$lt_save_CC"
+])# _LT_LANG_GCJ_CONFIG
+
+
+# _LT_LANG_RC_CONFIG([TAG])
+# -------------------------
+# Ensure that the configuration variables for the Windows resource compiler
+# are suitably defined. These variables are subsequently used by _LT_CONFIG
+# to write the compiler configuration to `libtool'.
+m4_defun([_LT_LANG_RC_CONFIG],
+[AC_REQUIRE([LT_PROG_RC])dnl
+AC_LANG_SAVE
+
+# Source file extension for RC test sources.
+ac_ext=rc
+
+# Object file extension for compiled RC test sources.
+objext=o
+_LT_TAGVAR(objext, $1)=$objext
+
+# Code to be used in simple compile tests
+lt_simple_compile_test_code='sample MENU { MENUITEM "&Soup", 100, CHECKED }'
+
+# Code to be used in simple link tests
+lt_simple_link_test_code="$lt_simple_compile_test_code"
+
+# ltmain only uses $CC for tagged configurations so make sure $CC is set.
+_LT_TAG_COMPILER
+
+# save warnings/boilerplate of simple test code
+_LT_COMPILER_BOILERPLATE
+_LT_LINKER_BOILERPLATE
+
+# Allow CC to be a program name with arguments.
+lt_save_CC="$CC"
+lt_save_GCC=$GCC
+GCC=
+CC=${RC-"windres"}
+compiler=$CC
+_LT_TAGVAR(compiler, $1)=$CC
+_LT_CC_BASENAME([$compiler])
+_LT_TAGVAR(lt_cv_prog_compiler_c_o, $1)=yes
+
+if test -n "$compiler"; then
+ :
+ _LT_CONFIG($1)
+fi
+
+GCC=$lt_save_GCC
+AC_LANG_RESTORE
+CC="$lt_save_CC"
+])# _LT_LANG_RC_CONFIG
+
+
+# LT_PROG_GCJ
+# -----------
+AC_DEFUN([LT_PROG_GCJ],
+[m4_ifdef([AC_PROG_GCJ], [AC_PROG_GCJ],
+ [m4_ifdef([A][M_PROG_GCJ], [A][M_PROG_GCJ],
+ [AC_CHECK_TOOL(GCJ, gcj,)
+ test "x${GCJFLAGS+set}" = xset || GCJFLAGS="-g -O2"
+ AC_SUBST(GCJFLAGS)])])[]dnl
+])
+
+# Old name:
+AU_ALIAS([LT_AC_PROG_GCJ], [LT_PROG_GCJ])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([LT_AC_PROG_GCJ], [])
+
+
+# LT_PROG_RC
+# ----------
+AC_DEFUN([LT_PROG_RC],
+[AC_CHECK_TOOL(RC, windres,)
+])
+
+# Old name:
+AU_ALIAS([LT_AC_PROG_RC], [LT_PROG_RC])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([LT_AC_PROG_RC], [])
+
+
+# _LT_DECL_EGREP
+# --------------
+# If we don't have a new enough Autoconf to choose the best grep
+# available, choose the one first in the user's PATH.
+m4_defun([_LT_DECL_EGREP],
+[AC_REQUIRE([AC_PROG_EGREP])dnl
+AC_REQUIRE([AC_PROG_FGREP])dnl
+test -z "$GREP" && GREP=grep
+_LT_DECL([], [GREP], [1], [A grep program that handles long lines])
+_LT_DECL([], [EGREP], [1], [An ERE matcher])
+_LT_DECL([], [FGREP], [1], [A literal string matcher])
+dnl Non-bleeding-edge autoconf doesn't subst GREP, so do it here too
+AC_SUBST([GREP])
+])
+
+
+# _LT_DECL_OBJDUMP
+# --------------
+# If we don't have a new enough Autoconf to choose the best objdump
+# available, choose the one first in the user's PATH.
+m4_defun([_LT_DECL_OBJDUMP],
+[AC_CHECK_TOOL(OBJDUMP, objdump, false)
+test -z "$OBJDUMP" && OBJDUMP=objdump
+_LT_DECL([], [OBJDUMP], [1], [An object symbol dumper])
+AC_SUBST([OBJDUMP])
+])
+
+
+# _LT_DECL_SED
+# ------------
+# Check for a fully-functional sed program, that truncates
+# as few characters as possible. Prefer GNU sed if found.
+m4_defun([_LT_DECL_SED],
+[AC_PROG_SED
+test -z "$SED" && SED=sed
+Xsed="$SED -e 1s/^X//"
+_LT_DECL([], [SED], [1], [A sed program that does not truncate output])
+_LT_DECL([], [Xsed], ["\$SED -e 1s/^X//"],
+ [Sed that helps us avoid accidentally triggering echo(1) options like -n])
+])# _LT_DECL_SED
+
+m4_ifndef([AC_PROG_SED], [
+############################################################
+# NOTE: This macro has been submitted for inclusion into #
+# GNU Autoconf as AC_PROG_SED. When it is available in #
+# a released version of Autoconf we should remove this #
+# macro and use it instead. #
+############################################################
+
+m4_defun([AC_PROG_SED],
+[AC_MSG_CHECKING([for a sed that does not truncate output])
+AC_CACHE_VAL(lt_cv_path_SED,
+[# Loop through the user's path and test for sed and gsed.
+# Then use that list of sed's as ones to test for truncation.
+as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+ IFS=$as_save_IFS
+ test -z "$as_dir" && as_dir=.
+ for lt_ac_prog in sed gsed; do
+ for ac_exec_ext in '' $ac_executable_extensions; do
+ if $as_executable_p "$as_dir/$lt_ac_prog$ac_exec_ext"; then
+ lt_ac_sed_list="$lt_ac_sed_list $as_dir/$lt_ac_prog$ac_exec_ext"
+ fi
+ done
+ done
+done
+IFS=$as_save_IFS
+lt_ac_max=0
+lt_ac_count=0
+# Add /usr/xpg4/bin/sed as it is typically found on Solaris
+# along with /bin/sed that truncates output.
+for lt_ac_sed in $lt_ac_sed_list /usr/xpg4/bin/sed; do
+ test ! -f $lt_ac_sed && continue
+ cat /dev/null > conftest.in
+ lt_ac_count=0
+ echo $ECHO_N "0123456789$ECHO_C" >conftest.in
+ # Check for GNU sed and select it if it is found.
+ if "$lt_ac_sed" --version 2>&1 < /dev/null | grep 'GNU' > /dev/null; then
+ lt_cv_path_SED=$lt_ac_sed
+ break
+ fi
+ while true; do
+ cat conftest.in conftest.in >conftest.tmp
+ mv conftest.tmp conftest.in
+ cp conftest.in conftest.nl
+ echo >>conftest.nl
+ $lt_ac_sed -e 's/a$//' < conftest.nl >conftest.out || break
+ cmp -s conftest.out conftest.nl || break
+ # 10000 chars as input seems more than enough
+ test $lt_ac_count -gt 10 && break
+ lt_ac_count=`expr $lt_ac_count + 1`
+ if test $lt_ac_count -gt $lt_ac_max; then
+ lt_ac_max=$lt_ac_count
+ lt_cv_path_SED=$lt_ac_sed
+ fi
+ done
+done
+])
+SED=$lt_cv_path_SED
+AC_SUBST([SED])
+AC_MSG_RESULT([$SED])
+])#AC_PROG_SED
+])#m4_ifndef
+
+# Old name:
+AU_ALIAS([LT_AC_PROG_SED], [AC_PROG_SED])
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([LT_AC_PROG_SED], [])
+
+
+# _LT_CHECK_SHELL_FEATURES
+# ------------------------
+# Find out whether the shell is Bourne or XSI compatible,
+# or has some other useful features.
+m4_defun([_LT_CHECK_SHELL_FEATURES],
+[AC_MSG_CHECKING([whether the shell understands some XSI constructs])
+# Try some XSI features
+xsi_shell=no
+( _lt_dummy="a/b/c"
+ test "${_lt_dummy##*/},${_lt_dummy%/*},"${_lt_dummy%"$_lt_dummy"}, \
+ = c,a/b,, \
+ && eval 'test $(( 1 + 1 )) -eq 2 \
+ && test "${#_lt_dummy}" -eq 5' ) >/dev/null 2>&1 \
+ && xsi_shell=yes
+AC_MSG_RESULT([$xsi_shell])
+_LT_CONFIG_LIBTOOL_INIT([xsi_shell='$xsi_shell'])
+
+AC_MSG_CHECKING([whether the shell understands "+="])
+lt_shell_append=no
+( foo=bar; set foo baz; eval "$[1]+=\$[2]" && test "$foo" = barbaz ) \
+ >/dev/null 2>&1 \
+ && lt_shell_append=yes
+AC_MSG_RESULT([$lt_shell_append])
+_LT_CONFIG_LIBTOOL_INIT([lt_shell_append='$lt_shell_append'])
+
+if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then
+ lt_unset=unset
+else
+ lt_unset=false
+fi
+_LT_DECL([], [lt_unset], [0], [whether the shell understands "unset"])dnl
+
+# test EBCDIC or ASCII
+case `echo X|tr X '\101'` in
+ A) # ASCII based system
+ # \n is not interpreted correctly by Solaris 8 /usr/ucb/tr
+ lt_SP2NL='tr \040 \012'
+ lt_NL2SP='tr \015\012 \040\040'
+ ;;
+ *) # EBCDIC based system
+ lt_SP2NL='tr \100 \n'
+ lt_NL2SP='tr \r\n \100\100'
+ ;;
+esac
+_LT_DECL([SP2NL], [lt_SP2NL], [1], [turn spaces into newlines])dnl
+_LT_DECL([NL2SP], [lt_NL2SP], [1], [turn newlines into spaces])dnl
+])# _LT_CHECK_SHELL_FEATURES
+
+
+# _LT_PROG_XSI_SHELLFNS
+# ---------------------
+# Bourne and XSI compatible variants of some useful shell functions.
+m4_defun([_LT_PROG_XSI_SHELLFNS],
+[case $xsi_shell in
+ yes)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_dirname file append nondir_replacement
+# Compute the dirname of FILE. If nonempty, add APPEND to the result,
+# otherwise set result to NONDIR_REPLACEMENT.
+func_dirname ()
+{
+ case ${1} in
+ */*) func_dirname_result="${1%/*}${2}" ;;
+ * ) func_dirname_result="${3}" ;;
+ esac
+}
+
+# func_basename file
+func_basename ()
+{
+ func_basename_result="${1##*/}"
+}
+
+# func_dirname_and_basename file append nondir_replacement
+# perform func_basename and func_dirname in a single function
+# call:
+# dirname: Compute the dirname of FILE. If nonempty,
+# add APPEND to the result, otherwise set result
+# to NONDIR_REPLACEMENT.
+# value returned in "$func_dirname_result"
+# basename: Compute filename of FILE.
+# value retuned in "$func_basename_result"
+# Implementation must be kept synchronized with func_dirname
+# and func_basename. For efficiency, we do not delegate to
+# those functions but instead duplicate the functionality here.
+func_dirname_and_basename ()
+{
+ case ${1} in
+ */*) func_dirname_result="${1%/*}${2}" ;;
+ * ) func_dirname_result="${3}" ;;
+ esac
+ func_basename_result="${1##*/}"
+}
+
+# func_stripname prefix suffix name
+# strip PREFIX and SUFFIX off of NAME.
+# PREFIX and SUFFIX must not contain globbing or regex special
+# characters, hashes, percent signs, but SUFFIX may contain a leading
+# dot (in which case that matches only a dot).
+func_stripname ()
+{
+ # pdksh 5.2.14 does not do ${X%$Y} correctly if both X and Y are
+ # positional parameters, so assign one to ordinary parameter first.
+ func_stripname_result=${3}
+ func_stripname_result=${func_stripname_result#"${1}"}
+ func_stripname_result=${func_stripname_result%"${2}"}
+}
+
+# func_opt_split
+func_opt_split ()
+{
+ func_opt_split_opt=${1%%=*}
+ func_opt_split_arg=${1#*=}
+}
+
+# func_lo2o object
+func_lo2o ()
+{
+ case ${1} in
+ *.lo) func_lo2o_result=${1%.lo}.${objext} ;;
+ *) func_lo2o_result=${1} ;;
+ esac
+}
+
+# func_xform libobj-or-source
+func_xform ()
+{
+ func_xform_result=${1%.*}.lo
+}
+
+# func_arith arithmetic-term...
+func_arith ()
+{
+ func_arith_result=$(( $[*] ))
+}
+
+# func_len string
+# STRING may not start with a hyphen.
+func_len ()
+{
+ func_len_result=${#1}
+}
+
+_LT_EOF
+ ;;
+ *) # Bourne compatible functions.
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_dirname file append nondir_replacement
+# Compute the dirname of FILE. If nonempty, add APPEND to the result,
+# otherwise set result to NONDIR_REPLACEMENT.
+func_dirname ()
+{
+ # Extract subdirectory from the argument.
+ func_dirname_result=`$ECHO "X${1}" | $Xsed -e "$dirname"`
+ if test "X$func_dirname_result" = "X${1}"; then
+ func_dirname_result="${3}"
+ else
+ func_dirname_result="$func_dirname_result${2}"
+ fi
+}
+
+# func_basename file
+func_basename ()
+{
+ func_basename_result=`$ECHO "X${1}" | $Xsed -e "$basename"`
+}
+
+dnl func_dirname_and_basename
+dnl A portable version of this function is already defined in general.m4sh
+dnl so there is no need for it here.
+
+# func_stripname prefix suffix name
+# strip PREFIX and SUFFIX off of NAME.
+# PREFIX and SUFFIX must not contain globbing or regex special
+# characters, hashes, percent signs, but SUFFIX may contain a leading
+# dot (in which case that matches only a dot).
+# func_strip_suffix prefix name
+func_stripname ()
+{
+ case ${2} in
+ .*) func_stripname_result=`$ECHO "X${3}" \
+ | $Xsed -e "s%^${1}%%" -e "s%\\\\${2}\$%%"`;;
+ *) func_stripname_result=`$ECHO "X${3}" \
+ | $Xsed -e "s%^${1}%%" -e "s%${2}\$%%"`;;
+ esac
+}
+
+# sed scripts:
+my_sed_long_opt='1s/^\(-[[^=]]*\)=.*/\1/;q'
+my_sed_long_arg='1s/^-[[^=]]*=//'
+
+# func_opt_split
+func_opt_split ()
+{
+ func_opt_split_opt=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_opt"`
+ func_opt_split_arg=`$ECHO "X${1}" | $Xsed -e "$my_sed_long_arg"`
+}
+
+# func_lo2o object
+func_lo2o ()
+{
+ func_lo2o_result=`$ECHO "X${1}" | $Xsed -e "$lo2o"`
+}
+
+# func_xform libobj-or-source
+func_xform ()
+{
+ func_xform_result=`$ECHO "X${1}" | $Xsed -e 's/\.[[^.]]*$/.lo/'`
+}
+
+# func_arith arithmetic-term...
+func_arith ()
+{
+ func_arith_result=`expr "$[@]"`
+}
+
+# func_len string
+# STRING may not start with a hyphen.
+func_len ()
+{
+ func_len_result=`expr "$[1]" : ".*" 2>/dev/null || echo $max_cmd_len`
+}
+
+_LT_EOF
+esac
+
+case $lt_shell_append in
+ yes)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_append var value
+# Append VALUE to the end of shell variable VAR.
+func_append ()
+{
+ eval "$[1]+=\$[2]"
+}
+_LT_EOF
+ ;;
+ *)
+ cat << \_LT_EOF >> "$cfgfile"
+
+# func_append var value
+# Append VALUE to the end of shell variable VAR.
+func_append ()
+{
+ eval "$[1]=\$$[1]\$[2]"
+}
+
+_LT_EOF
+ ;;
+ esac
+])
--- /dev/null
+# Helper functions for option handling. -*- Autoconf -*-
+#
+# Copyright (C) 2004, 2005, 2007, 2008 Free Software Foundation, Inc.
+# Written by Gary V. Vaughan, 2004
+#
+# This file is free software; the Free Software Foundation gives
+# unlimited permission to copy and/or distribute it, with or without
+# modifications, as long as this notice is preserved.
+
+# serial 6 ltoptions.m4
+
+# This is to help aclocal find these macros, as it can't see m4_define.
+AC_DEFUN([LTOPTIONS_VERSION], [m4_if([1])])
+
+
+# _LT_MANGLE_OPTION(MACRO-NAME, OPTION-NAME)
+# ------------------------------------------
+m4_define([_LT_MANGLE_OPTION],
+[[_LT_OPTION_]m4_bpatsubst($1__$2, [[^a-zA-Z0-9_]], [_])])
+
+
+# _LT_SET_OPTION(MACRO-NAME, OPTION-NAME)
+# ---------------------------------------
+# Set option OPTION-NAME for macro MACRO-NAME, and if there is a
+# matching handler defined, dispatch to it. Other OPTION-NAMEs are
+# saved as a flag.
+m4_define([_LT_SET_OPTION],
+[m4_define(_LT_MANGLE_OPTION([$1], [$2]))dnl
+m4_ifdef(_LT_MANGLE_DEFUN([$1], [$2]),
+ _LT_MANGLE_DEFUN([$1], [$2]),
+ [m4_warning([Unknown $1 option `$2'])])[]dnl
+])
+
+
+# _LT_IF_OPTION(MACRO-NAME, OPTION-NAME, IF-SET, [IF-NOT-SET])
+# ------------------------------------------------------------
+# Execute IF-SET if OPTION is set, IF-NOT-SET otherwise.
+m4_define([_LT_IF_OPTION],
+[m4_ifdef(_LT_MANGLE_OPTION([$1], [$2]), [$3], [$4])])
+
+
+# _LT_UNLESS_OPTIONS(MACRO-NAME, OPTION-LIST, IF-NOT-SET)
+# -------------------------------------------------------
+# Execute IF-NOT-SET unless all options in OPTION-LIST for MACRO-NAME
+# are set.
+m4_define([_LT_UNLESS_OPTIONS],
+[m4_foreach([_LT_Option], m4_split(m4_normalize([$2])),
+ [m4_ifdef(_LT_MANGLE_OPTION([$1], _LT_Option),
+ [m4_define([$0_found])])])[]dnl
+m4_ifdef([$0_found], [m4_undefine([$0_found])], [$3
+])[]dnl
+])
+
+
+# _LT_SET_OPTIONS(MACRO-NAME, OPTION-LIST)
+# ----------------------------------------
+# OPTION-LIST is a space-separated list of Libtool options associated
+# with MACRO-NAME. If any OPTION has a matching handler declared with
+# LT_OPTION_DEFINE, dispatch to that macro; otherwise complain about
+# the unknown option and exit.
+m4_defun([_LT_SET_OPTIONS],
+[# Set options
+m4_foreach([_LT_Option], m4_split(m4_normalize([$2])),
+ [_LT_SET_OPTION([$1], _LT_Option)])
+
+m4_if([$1],[LT_INIT],[
+ dnl
+ dnl Simply set some default values (i.e off) if boolean options were not
+ dnl specified:
+ _LT_UNLESS_OPTIONS([LT_INIT], [dlopen], [enable_dlopen=no
+ ])
+ _LT_UNLESS_OPTIONS([LT_INIT], [win32-dll], [enable_win32_dll=no
+ ])
+ dnl
+ dnl If no reference was made to various pairs of opposing options, then
+ dnl we run the default mode handler for the pair. For example, if neither
+ dnl `shared' nor `disable-shared' was passed, we enable building of shared
+ dnl archives by default:
+ _LT_UNLESS_OPTIONS([LT_INIT], [shared disable-shared], [_LT_ENABLE_SHARED])
+ _LT_UNLESS_OPTIONS([LT_INIT], [static disable-static], [_LT_ENABLE_STATIC])
+ _LT_UNLESS_OPTIONS([LT_INIT], [pic-only no-pic], [_LT_WITH_PIC])
+ _LT_UNLESS_OPTIONS([LT_INIT], [fast-install disable-fast-install],
+ [_LT_ENABLE_FAST_INSTALL])
+ ])
+])# _LT_SET_OPTIONS
+
+
+## --------------------------------- ##
+## Macros to handle LT_INIT options. ##
+## --------------------------------- ##
+
+# _LT_MANGLE_DEFUN(MACRO-NAME, OPTION-NAME)
+# -----------------------------------------
+m4_define([_LT_MANGLE_DEFUN],
+[[_LT_OPTION_DEFUN_]m4_bpatsubst(m4_toupper([$1__$2]), [[^A-Z0-9_]], [_])])
+
+
+# LT_OPTION_DEFINE(MACRO-NAME, OPTION-NAME, CODE)
+# -----------------------------------------------
+m4_define([LT_OPTION_DEFINE],
+[m4_define(_LT_MANGLE_DEFUN([$1], [$2]), [$3])[]dnl
+])# LT_OPTION_DEFINE
+
+
+# dlopen
+# ------
+LT_OPTION_DEFINE([LT_INIT], [dlopen], [enable_dlopen=yes
+])
+
+AU_DEFUN([AC_LIBTOOL_DLOPEN],
+[_LT_SET_OPTION([LT_INIT], [dlopen])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you
+put the `dlopen' option into LT_INIT's first parameter.])
+])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_DLOPEN], [])
+
+
+# win32-dll
+# ---------
+# Declare package support for building win32 dll's.
+LT_OPTION_DEFINE([LT_INIT], [win32-dll],
+[enable_win32_dll=yes
+
+case $host in
+*-*-cygwin* | *-*-mingw* | *-*-pw32* | *-cegcc*)
+ AC_CHECK_TOOL(AS, as, false)
+ AC_CHECK_TOOL(DLLTOOL, dlltool, false)
+ AC_CHECK_TOOL(OBJDUMP, objdump, false)
+ ;;
+esac
+
+test -z "$AS" && AS=as
+_LT_DECL([], [AS], [0], [Assembler program])dnl
+
+test -z "$DLLTOOL" && DLLTOOL=dlltool
+_LT_DECL([], [DLLTOOL], [0], [DLL creation program])dnl
+
+test -z "$OBJDUMP" && OBJDUMP=objdump
+_LT_DECL([], [OBJDUMP], [0], [Object dumper program])dnl
+])# win32-dll
+
+AU_DEFUN([AC_LIBTOOL_WIN32_DLL],
+[AC_REQUIRE([AC_CANONICAL_HOST])dnl
+_LT_SET_OPTION([LT_INIT], [win32-dll])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you
+put the `win32-dll' option into LT_INIT's first parameter.])
+])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_WIN32_DLL], [])
+
+
+# _LT_ENABLE_SHARED([DEFAULT])
+# ----------------------------
+# implement the --enable-shared flag, and supports the `shared' and
+# `disable-shared' LT_INIT options.
+# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'.
+m4_define([_LT_ENABLE_SHARED],
+[m4_define([_LT_ENABLE_SHARED_DEFAULT], [m4_if($1, no, no, yes)])dnl
+AC_ARG_ENABLE([shared],
+ [AS_HELP_STRING([--enable-shared@<:@=PKGS@:>@],
+ [build shared libraries @<:@default=]_LT_ENABLE_SHARED_DEFAULT[@:>@])],
+ [p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_shared=yes ;;
+ no) enable_shared=no ;;
+ *)
+ enable_shared=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_shared=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac],
+ [enable_shared=]_LT_ENABLE_SHARED_DEFAULT)
+
+ _LT_DECL([build_libtool_libs], [enable_shared], [0],
+ [Whether or not to build shared libraries])
+])# _LT_ENABLE_SHARED
+
+LT_OPTION_DEFINE([LT_INIT], [shared], [_LT_ENABLE_SHARED([yes])])
+LT_OPTION_DEFINE([LT_INIT], [disable-shared], [_LT_ENABLE_SHARED([no])])
+
+# Old names:
+AC_DEFUN([AC_ENABLE_SHARED],
+[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[shared])
+])
+
+AC_DEFUN([AC_DISABLE_SHARED],
+[_LT_SET_OPTION([LT_INIT], [disable-shared])
+])
+
+AU_DEFUN([AM_ENABLE_SHARED], [AC_ENABLE_SHARED($@)])
+AU_DEFUN([AM_DISABLE_SHARED], [AC_DISABLE_SHARED($@)])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AM_ENABLE_SHARED], [])
+dnl AC_DEFUN([AM_DISABLE_SHARED], [])
+
+
+
+# _LT_ENABLE_STATIC([DEFAULT])
+# ----------------------------
+# implement the --enable-static flag, and support the `static' and
+# `disable-static' LT_INIT options.
+# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'.
+m4_define([_LT_ENABLE_STATIC],
+[m4_define([_LT_ENABLE_STATIC_DEFAULT], [m4_if($1, no, no, yes)])dnl
+AC_ARG_ENABLE([static],
+ [AS_HELP_STRING([--enable-static@<:@=PKGS@:>@],
+ [build static libraries @<:@default=]_LT_ENABLE_STATIC_DEFAULT[@:>@])],
+ [p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_static=yes ;;
+ no) enable_static=no ;;
+ *)
+ enable_static=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_static=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac],
+ [enable_static=]_LT_ENABLE_STATIC_DEFAULT)
+
+ _LT_DECL([build_old_libs], [enable_static], [0],
+ [Whether or not to build static libraries])
+])# _LT_ENABLE_STATIC
+
+LT_OPTION_DEFINE([LT_INIT], [static], [_LT_ENABLE_STATIC([yes])])
+LT_OPTION_DEFINE([LT_INIT], [disable-static], [_LT_ENABLE_STATIC([no])])
+
+# Old names:
+AC_DEFUN([AC_ENABLE_STATIC],
+[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[static])
+])
+
+AC_DEFUN([AC_DISABLE_STATIC],
+[_LT_SET_OPTION([LT_INIT], [disable-static])
+])
+
+AU_DEFUN([AM_ENABLE_STATIC], [AC_ENABLE_STATIC($@)])
+AU_DEFUN([AM_DISABLE_STATIC], [AC_DISABLE_STATIC($@)])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AM_ENABLE_STATIC], [])
+dnl AC_DEFUN([AM_DISABLE_STATIC], [])
+
+
+
+# _LT_ENABLE_FAST_INSTALL([DEFAULT])
+# ----------------------------------
+# implement the --enable-fast-install flag, and support the `fast-install'
+# and `disable-fast-install' LT_INIT options.
+# DEFAULT is either `yes' or `no'. If omitted, it defaults to `yes'.
+m4_define([_LT_ENABLE_FAST_INSTALL],
+[m4_define([_LT_ENABLE_FAST_INSTALL_DEFAULT], [m4_if($1, no, no, yes)])dnl
+AC_ARG_ENABLE([fast-install],
+ [AS_HELP_STRING([--enable-fast-install@<:@=PKGS@:>@],
+ [optimize for fast installation @<:@default=]_LT_ENABLE_FAST_INSTALL_DEFAULT[@:>@])],
+ [p=${PACKAGE-default}
+ case $enableval in
+ yes) enable_fast_install=yes ;;
+ no) enable_fast_install=no ;;
+ *)
+ enable_fast_install=no
+ # Look at the argument we got. We use all the common list separators.
+ lt_save_ifs="$IFS"; IFS="${IFS}$PATH_SEPARATOR,"
+ for pkg in $enableval; do
+ IFS="$lt_save_ifs"
+ if test "X$pkg" = "X$p"; then
+ enable_fast_install=yes
+ fi
+ done
+ IFS="$lt_save_ifs"
+ ;;
+ esac],
+ [enable_fast_install=]_LT_ENABLE_FAST_INSTALL_DEFAULT)
+
+_LT_DECL([fast_install], [enable_fast_install], [0],
+ [Whether or not to optimize for fast installation])dnl
+])# _LT_ENABLE_FAST_INSTALL
+
+LT_OPTION_DEFINE([LT_INIT], [fast-install], [_LT_ENABLE_FAST_INSTALL([yes])])
+LT_OPTION_DEFINE([LT_INIT], [disable-fast-install], [_LT_ENABLE_FAST_INSTALL([no])])
+
+# Old names:
+AU_DEFUN([AC_ENABLE_FAST_INSTALL],
+[_LT_SET_OPTION([LT_INIT], m4_if([$1], [no], [disable-])[fast-install])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you put
+the `fast-install' option into LT_INIT's first parameter.])
+])
+
+AU_DEFUN([AC_DISABLE_FAST_INSTALL],
+[_LT_SET_OPTION([LT_INIT], [disable-fast-install])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you put
+the `disable-fast-install' option into LT_INIT's first parameter.])
+])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_ENABLE_FAST_INSTALL], [])
+dnl AC_DEFUN([AM_DISABLE_FAST_INSTALL], [])
+
+
+# _LT_WITH_PIC([MODE])
+# --------------------
+# implement the --with-pic flag, and support the `pic-only' and `no-pic'
+# LT_INIT options.
+# MODE is either `yes' or `no'. If omitted, it defaults to `both'.
+m4_define([_LT_WITH_PIC],
+[AC_ARG_WITH([pic],
+ [AS_HELP_STRING([--with-pic],
+ [try to use only PIC/non-PIC objects @<:@default=use both@:>@])],
+ [pic_mode="$withval"],
+ [pic_mode=default])
+
+test -z "$pic_mode" && pic_mode=m4_default([$1], [default])
+
+_LT_DECL([], [pic_mode], [0], [What type of objects to build])dnl
+])# _LT_WITH_PIC
+
+LT_OPTION_DEFINE([LT_INIT], [pic-only], [_LT_WITH_PIC([yes])])
+LT_OPTION_DEFINE([LT_INIT], [no-pic], [_LT_WITH_PIC([no])])
+
+# Old name:
+AU_DEFUN([AC_LIBTOOL_PICMODE],
+[_LT_SET_OPTION([LT_INIT], [pic-only])
+AC_DIAGNOSE([obsolete],
+[$0: Remove this warning and the call to _LT_SET_OPTION when you
+put the `pic-only' option into LT_INIT's first parameter.])
+])
+
+dnl aclocal-1.4 backwards compatibility:
+dnl AC_DEFUN([AC_LIBTOOL_PICMODE], [])
+
+## ----------------- ##
+## LTDL_INIT Options ##
+## ----------------- ##
+
+m4_define([_LTDL_MODE], [])
+LT_OPTION_DEFINE([LTDL_INIT], [nonrecursive],
+ [m4_define([_LTDL_MODE], [nonrecursive])])
+LT_OPTION_DEFINE([LTDL_INIT], [recursive],
+ [m4_define([_LTDL_MODE], [recursive])])
+LT_OPTION_DEFINE([LTDL_INIT], [subproject],
+ [m4_define([_LTDL_MODE], [subproject])])
+
+m4_define([_LTDL_TYPE], [])
+LT_OPTION_DEFINE([LTDL_INIT], [installable],
+ [m4_define([_LTDL_TYPE], [installable])])
+LT_OPTION_DEFINE([LTDL_INIT], [convenience],
+ [m4_define([_LTDL_TYPE], [convenience])])
--- /dev/null
+# ltsugar.m4 -- libtool m4 base layer. -*-Autoconf-*-
+#
+# Copyright (C) 2004, 2005, 2007, 2008 Free Software Foundation, Inc.
+# Written by Gary V. Vaughan, 2004
+#
+# This file is free software; the Free Software Foundation gives
+# unlimited permission to copy and/or distribute it, with or without
+# modifications, as long as this notice is preserved.
+
+# serial 6 ltsugar.m4
+
+# This is to help aclocal find these macros, as it can't see m4_define.
+AC_DEFUN([LTSUGAR_VERSION], [m4_if([0.1])])
+
+
+# lt_join(SEP, ARG1, [ARG2...])
+# -----------------------------
+# Produce ARG1SEPARG2...SEPARGn, omitting [] arguments and their
+# associated separator.
+# Needed until we can rely on m4_join from Autoconf 2.62, since all earlier
+# versions in m4sugar had bugs.
+m4_define([lt_join],
+[m4_if([$#], [1], [],
+ [$#], [2], [[$2]],
+ [m4_if([$2], [], [], [[$2]_])$0([$1], m4_shift(m4_shift($@)))])])
+m4_define([_lt_join],
+[m4_if([$#$2], [2], [],
+ [m4_if([$2], [], [], [[$1$2]])$0([$1], m4_shift(m4_shift($@)))])])
+
+
+# lt_car(LIST)
+# lt_cdr(LIST)
+# ------------
+# Manipulate m4 lists.
+# These macros are necessary as long as will still need to support
+# Autoconf-2.59 which quotes differently.
+m4_define([lt_car], [[$1]])
+m4_define([lt_cdr],
+[m4_if([$#], 0, [m4_fatal([$0: cannot be called without arguments])],
+ [$#], 1, [],
+ [m4_dquote(m4_shift($@))])])
+m4_define([lt_unquote], $1)
+
+
+# lt_append(MACRO-NAME, STRING, [SEPARATOR])
+# ------------------------------------------
+# Redefine MACRO-NAME to hold its former content plus `SEPARATOR'`STRING'.
+# Note that neither SEPARATOR nor STRING are expanded; they are appended
+# to MACRO-NAME as is (leaving the expansion for when MACRO-NAME is invoked).
+# No SEPARATOR is output if MACRO-NAME was previously undefined (different
+# than defined and empty).
+#
+# This macro is needed until we can rely on Autoconf 2.62, since earlier
+# versions of m4sugar mistakenly expanded SEPARATOR but not STRING.
+m4_define([lt_append],
+[m4_define([$1],
+ m4_ifdef([$1], [m4_defn([$1])[$3]])[$2])])
+
+
+
+# lt_combine(SEP, PREFIX-LIST, INFIX, SUFFIX1, [SUFFIX2...])
+# ----------------------------------------------------------
+# Produce a SEP delimited list of all paired combinations of elements of
+# PREFIX-LIST with SUFFIX1 through SUFFIXn. Each element of the list
+# has the form PREFIXmINFIXSUFFIXn.
+# Needed until we can rely on m4_combine added in Autoconf 2.62.
+m4_define([lt_combine],
+[m4_if(m4_eval([$# > 3]), [1],
+ [m4_pushdef([_Lt_sep], [m4_define([_Lt_sep], m4_defn([lt_car]))])]]dnl
+[[m4_foreach([_Lt_prefix], [$2],
+ [m4_foreach([_Lt_suffix],
+ ]m4_dquote(m4_dquote(m4_shift(m4_shift(m4_shift($@)))))[,
+ [_Lt_sep([$1])[]m4_defn([_Lt_prefix])[$3]m4_defn([_Lt_suffix])])])])])
+
+
+# lt_if_append_uniq(MACRO-NAME, VARNAME, [SEPARATOR], [UNIQ], [NOT-UNIQ])
+# -----------------------------------------------------------------------
+# Iff MACRO-NAME does not yet contain VARNAME, then append it (delimited
+# by SEPARATOR if supplied) and expand UNIQ, else NOT-UNIQ.
+m4_define([lt_if_append_uniq],
+[m4_ifdef([$1],
+ [m4_if(m4_index([$3]m4_defn([$1])[$3], [$3$2$3]), [-1],
+ [lt_append([$1], [$2], [$3])$4],
+ [$5])],
+ [lt_append([$1], [$2], [$3])$4])])
+
+
+# lt_dict_add(DICT, KEY, VALUE)
+# -----------------------------
+m4_define([lt_dict_add],
+[m4_define([$1($2)], [$3])])
+
+
+# lt_dict_add_subkey(DICT, KEY, SUBKEY, VALUE)
+# --------------------------------------------
+m4_define([lt_dict_add_subkey],
+[m4_define([$1($2:$3)], [$4])])
+
+
+# lt_dict_fetch(DICT, KEY, [SUBKEY])
+# ----------------------------------
+m4_define([lt_dict_fetch],
+[m4_ifval([$3],
+ m4_ifdef([$1($2:$3)], [m4_defn([$1($2:$3)])]),
+ m4_ifdef([$1($2)], [m4_defn([$1($2)])]))])
+
+
+# lt_if_dict_fetch(DICT, KEY, [SUBKEY], VALUE, IF-TRUE, [IF-FALSE])
+# -----------------------------------------------------------------
+m4_define([lt_if_dict_fetch],
+[m4_if(lt_dict_fetch([$1], [$2], [$3]), [$4],
+ [$5],
+ [$6])])
+
+
+# lt_dict_filter(DICT, [SUBKEY], VALUE, [SEPARATOR], KEY, [...])
+# --------------------------------------------------------------
+m4_define([lt_dict_filter],
+[m4_if([$5], [], [],
+ [lt_join(m4_quote(m4_default([$4], [[, ]])),
+ lt_unquote(m4_split(m4_normalize(m4_foreach(_Lt_key, lt_car([m4_shiftn(4, $@)]),
+ [lt_if_dict_fetch([$1], _Lt_key, [$2], [$3], [_Lt_key ])])))))])[]dnl
+])
--- /dev/null
+# ltversion.m4 -- version numbers -*- Autoconf -*-
+#
+# Copyright (C) 2004 Free Software Foundation, Inc.
+# Written by Scott James Remnant, 2004
+#
+# This file is free software; the Free Software Foundation gives
+# unlimited permission to copy and/or distribute it, with or without
+# modifications, as long as this notice is preserved.
+
+# Generated from ltversion.in.
+
+# serial 3012 ltversion.m4
+# This file is part of GNU Libtool
+
+m4_define([LT_PACKAGE_VERSION], [2.2.6])
+m4_define([LT_PACKAGE_REVISION], [1.3012])
+
+AC_DEFUN([LTVERSION_VERSION],
+[macro_version='2.2.6'
+macro_revision='1.3012'
+_LT_DECL(, macro_version, 0, [Which release of libtool.m4 was used?])
+_LT_DECL(, macro_revision, 0)
+])
--- /dev/null
+# lt~obsolete.m4 -- aclocal satisfying obsolete definitions. -*-Autoconf-*-
+#
+# Copyright (C) 2004, 2005, 2007 Free Software Foundation, Inc.
+# Written by Scott James Remnant, 2004.
+#
+# This file is free software; the Free Software Foundation gives
+# unlimited permission to copy and/or distribute it, with or without
+# modifications, as long as this notice is preserved.
+
+# serial 4 lt~obsolete.m4
+
+# These exist entirely to fool aclocal when bootstrapping libtool.
+#
+# In the past libtool.m4 has provided macros via AC_DEFUN (or AU_DEFUN)
+# which have later been changed to m4_define as they aren't part of the
+# exported API, or moved to Autoconf or Automake where they belong.
+#
+# The trouble is, aclocal is a bit thick. It'll see the old AC_DEFUN
+# in /usr/share/aclocal/libtool.m4 and remember it, then when it sees us
+# using a macro with the same name in our local m4/libtool.m4 it'll
+# pull the old libtool.m4 in (it doesn't see our shiny new m4_define
+# and doesn't know about Autoconf macros at all.)
+#
+# So we provide this file, which has a silly filename so it's always
+# included after everything else. This provides aclocal with the
+# AC_DEFUNs it wants, but when m4 processes it, it doesn't do anything
+# because those macros already exist, or will be overwritten later.
+# We use AC_DEFUN over AU_DEFUN for compatibility with aclocal-1.6.
+#
+# Anytime we withdraw an AC_DEFUN or AU_DEFUN, remember to add it here.
+# Yes, that means every name once taken will need to remain here until
+# we give up compatibility with versions before 1.7, at which point
+# we need to keep only those names which we still refer to.
+
+# This is to help aclocal find these macros, as it can't see m4_define.
+AC_DEFUN([LTOBSOLETE_VERSION], [m4_if([1])])
+
+m4_ifndef([AC_LIBTOOL_LINKER_OPTION], [AC_DEFUN([AC_LIBTOOL_LINKER_OPTION])])
+m4_ifndef([AC_PROG_EGREP], [AC_DEFUN([AC_PROG_EGREP])])
+m4_ifndef([_LT_AC_PROG_ECHO_BACKSLASH], [AC_DEFUN([_LT_AC_PROG_ECHO_BACKSLASH])])
+m4_ifndef([_LT_AC_SHELL_INIT], [AC_DEFUN([_LT_AC_SHELL_INIT])])
+m4_ifndef([_LT_AC_SYS_LIBPATH_AIX], [AC_DEFUN([_LT_AC_SYS_LIBPATH_AIX])])
+m4_ifndef([_LT_PROG_LTMAIN], [AC_DEFUN([_LT_PROG_LTMAIN])])
+m4_ifndef([_LT_AC_TAGVAR], [AC_DEFUN([_LT_AC_TAGVAR])])
+m4_ifndef([AC_LTDL_ENABLE_INSTALL], [AC_DEFUN([AC_LTDL_ENABLE_INSTALL])])
+m4_ifndef([AC_LTDL_PREOPEN], [AC_DEFUN([AC_LTDL_PREOPEN])])
+m4_ifndef([_LT_AC_SYS_COMPILER], [AC_DEFUN([_LT_AC_SYS_COMPILER])])
+m4_ifndef([_LT_AC_LOCK], [AC_DEFUN([_LT_AC_LOCK])])
+m4_ifndef([AC_LIBTOOL_SYS_OLD_ARCHIVE], [AC_DEFUN([AC_LIBTOOL_SYS_OLD_ARCHIVE])])
+m4_ifndef([_LT_AC_TRY_DLOPEN_SELF], [AC_DEFUN([_LT_AC_TRY_DLOPEN_SELF])])
+m4_ifndef([AC_LIBTOOL_PROG_CC_C_O], [AC_DEFUN([AC_LIBTOOL_PROG_CC_C_O])])
+m4_ifndef([AC_LIBTOOL_SYS_HARD_LINK_LOCKS], [AC_DEFUN([AC_LIBTOOL_SYS_HARD_LINK_LOCKS])])
+m4_ifndef([AC_LIBTOOL_OBJDIR], [AC_DEFUN([AC_LIBTOOL_OBJDIR])])
+m4_ifndef([AC_LTDL_OBJDIR], [AC_DEFUN([AC_LTDL_OBJDIR])])
+m4_ifndef([AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH], [AC_DEFUN([AC_LIBTOOL_PROG_LD_HARDCODE_LIBPATH])])
+m4_ifndef([AC_LIBTOOL_SYS_LIB_STRIP], [AC_DEFUN([AC_LIBTOOL_SYS_LIB_STRIP])])
+m4_ifndef([AC_PATH_MAGIC], [AC_DEFUN([AC_PATH_MAGIC])])
+m4_ifndef([AC_PROG_LD_GNU], [AC_DEFUN([AC_PROG_LD_GNU])])
+m4_ifndef([AC_PROG_LD_RELOAD_FLAG], [AC_DEFUN([AC_PROG_LD_RELOAD_FLAG])])
+m4_ifndef([AC_DEPLIBS_CHECK_METHOD], [AC_DEFUN([AC_DEPLIBS_CHECK_METHOD])])
+m4_ifndef([AC_LIBTOOL_PROG_COMPILER_NO_RTTI], [AC_DEFUN([AC_LIBTOOL_PROG_COMPILER_NO_RTTI])])
+m4_ifndef([AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE], [AC_DEFUN([AC_LIBTOOL_SYS_GLOBAL_SYMBOL_PIPE])])
+m4_ifndef([AC_LIBTOOL_PROG_COMPILER_PIC], [AC_DEFUN([AC_LIBTOOL_PROG_COMPILER_PIC])])
+m4_ifndef([AC_LIBTOOL_PROG_LD_SHLIBS], [AC_DEFUN([AC_LIBTOOL_PROG_LD_SHLIBS])])
+m4_ifndef([AC_LIBTOOL_POSTDEP_PREDEP], [AC_DEFUN([AC_LIBTOOL_POSTDEP_PREDEP])])
+m4_ifndef([LT_AC_PROG_EGREP], [AC_DEFUN([LT_AC_PROG_EGREP])])
+m4_ifndef([LT_AC_PROG_SED], [AC_DEFUN([LT_AC_PROG_SED])])
+m4_ifndef([_LT_CC_BASENAME], [AC_DEFUN([_LT_CC_BASENAME])])
+m4_ifndef([_LT_COMPILER_BOILERPLATE], [AC_DEFUN([_LT_COMPILER_BOILERPLATE])])
+m4_ifndef([_LT_LINKER_BOILERPLATE], [AC_DEFUN([_LT_LINKER_BOILERPLATE])])
+m4_ifndef([_AC_PROG_LIBTOOL], [AC_DEFUN([_AC_PROG_LIBTOOL])])
+m4_ifndef([AC_LIBTOOL_SETUP], [AC_DEFUN([AC_LIBTOOL_SETUP])])
+m4_ifndef([_LT_AC_CHECK_DLFCN], [AC_DEFUN([_LT_AC_CHECK_DLFCN])])
+m4_ifndef([AC_LIBTOOL_SYS_DYNAMIC_LINKER], [AC_DEFUN([AC_LIBTOOL_SYS_DYNAMIC_LINKER])])
+m4_ifndef([_LT_AC_TAGCONFIG], [AC_DEFUN([_LT_AC_TAGCONFIG])])
+m4_ifndef([AC_DISABLE_FAST_INSTALL], [AC_DEFUN([AC_DISABLE_FAST_INSTALL])])
+m4_ifndef([_LT_AC_LANG_CXX], [AC_DEFUN([_LT_AC_LANG_CXX])])
+m4_ifndef([_LT_AC_LANG_F77], [AC_DEFUN([_LT_AC_LANG_F77])])
+m4_ifndef([_LT_AC_LANG_GCJ], [AC_DEFUN([_LT_AC_LANG_GCJ])])
+m4_ifndef([AC_LIBTOOL_RC], [AC_DEFUN([AC_LIBTOOL_RC])])
+m4_ifndef([AC_LIBTOOL_LANG_C_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_C_CONFIG])])
+m4_ifndef([_LT_AC_LANG_C_CONFIG], [AC_DEFUN([_LT_AC_LANG_C_CONFIG])])
+m4_ifndef([AC_LIBTOOL_LANG_CXX_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_CXX_CONFIG])])
+m4_ifndef([_LT_AC_LANG_CXX_CONFIG], [AC_DEFUN([_LT_AC_LANG_CXX_CONFIG])])
+m4_ifndef([AC_LIBTOOL_LANG_F77_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_F77_CONFIG])])
+m4_ifndef([_LT_AC_LANG_F77_CONFIG], [AC_DEFUN([_LT_AC_LANG_F77_CONFIG])])
+m4_ifndef([AC_LIBTOOL_LANG_GCJ_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_GCJ_CONFIG])])
+m4_ifndef([_LT_AC_LANG_GCJ_CONFIG], [AC_DEFUN([_LT_AC_LANG_GCJ_CONFIG])])
+m4_ifndef([AC_LIBTOOL_LANG_RC_CONFIG], [AC_DEFUN([AC_LIBTOOL_LANG_RC_CONFIG])])
+m4_ifndef([_LT_AC_LANG_RC_CONFIG], [AC_DEFUN([_LT_AC_LANG_RC_CONFIG])])
+m4_ifndef([AC_LIBTOOL_CONFIG], [AC_DEFUN([AC_LIBTOOL_CONFIG])])
+m4_ifndef([_LT_AC_FILE_LTDLL_C], [AC_DEFUN([_LT_AC_FILE_LTDLL_C])])
--- /dev/null
+#! /bin/sh
+# Common stub for a few missing GNU programs while installing.
+
+scriptversion=2009-04-28.21; # UTC
+
+# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006,
+# 2008, 2009 Free Software Foundation, Inc.
+# Originally by Fran,cois Pinard <pinard@iro.umontreal.ca>, 1996.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+if test $# -eq 0; then
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+fi
+
+run=:
+sed_output='s/.* --output[ =]\([^ ]*\).*/\1/p'
+sed_minuso='s/.* -o \([^ ]*\).*/\1/p'
+
+# In the cases where this matters, `missing' is being run in the
+# srcdir already.
+if test -f configure.ac; then
+ configure_ac=configure.ac
+else
+ configure_ac=configure.in
+fi
+
+msg="missing on your system"
+
+case $1 in
+--run)
+ # Try to run requested program, and just exit if it succeeds.
+ run=
+ shift
+ "$@" && exit 0
+ # Exit code 63 means version mismatch. This often happens
+ # when the user try to use an ancient version of a tool on
+ # a file that requires a minimum version. In this case we
+ # we should proceed has if the program had been absent, or
+ # if --run hadn't been passed.
+ if test $? = 63; then
+ run=:
+ msg="probably too old"
+ fi
+ ;;
+
+ -h|--h|--he|--hel|--help)
+ echo "\
+$0 [OPTION]... PROGRAM [ARGUMENT]...
+
+Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
+error status if there is no known handling for PROGRAM.
+
+Options:
+ -h, --help display this help and exit
+ -v, --version output version information and exit
+ --run try to run the given command, and emulate it if it fails
+
+Supported PROGRAM values:
+ aclocal touch file \`aclocal.m4'
+ autoconf touch file \`configure'
+ autoheader touch file \`config.h.in'
+ autom4te touch the output file, or create a stub one
+ automake touch all \`Makefile.in' files
+ bison create \`y.tab.[ch]', if possible, from existing .[ch]
+ flex create \`lex.yy.c', if possible, from existing .c
+ help2man touch the output file
+ lex create \`lex.yy.c', if possible, from existing .c
+ makeinfo touch the output file
+ tar try tar, gnutar, gtar, then tar without non-portable flags
+ yacc create \`y.tab.[ch]', if possible, from existing .[ch]
+
+Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
+\`g' are ignored when checking the name.
+
+Send bug reports to <bug-automake@gnu.org>."
+ exit $?
+ ;;
+
+ -v|--v|--ve|--ver|--vers|--versi|--versio|--version)
+ echo "missing $scriptversion (GNU Automake)"
+ exit $?
+ ;;
+
+ -*)
+ echo 1>&2 "$0: Unknown \`$1' option"
+ echo 1>&2 "Try \`$0 --help' for more information"
+ exit 1
+ ;;
+
+esac
+
+# normalize program name to check for.
+program=`echo "$1" | sed '
+ s/^gnu-//; t
+ s/^gnu//; t
+ s/^g//; t'`
+
+# Now exit if we have it, but it failed. Also exit now if we
+# don't have it and --version was passed (most likely to detect
+# the program). This is about non-GNU programs, so use $1 not
+# $program.
+case $1 in
+ lex*|yacc*)
+ # Not GNU programs, they don't have --version.
+ ;;
+
+ tar*)
+ if test -n "$run"; then
+ echo 1>&2 "ERROR: \`tar' requires --run"
+ exit 1
+ elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+ exit 1
+ fi
+ ;;
+
+ *)
+ if test -z "$run" && ($1 --version) > /dev/null 2>&1; then
+ # We have it, but it failed.
+ exit 1
+ elif test "x$2" = "x--version" || test "x$2" = "x--help"; then
+ # Could not run --version or --help. This is probably someone
+ # running `$TOOL --version' or `$TOOL --help' to check whether
+ # $TOOL exists and not knowing $TOOL uses missing.
+ exit 1
+ fi
+ ;;
+esac
+
+# If it does not exist, or fails to run (possibly an outdated version),
+# try to emulate it.
+case $program in
+ aclocal*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acinclude.m4' or \`${configure_ac}'. You might want
+ to install the \`Automake' and \`Perl' packages. Grab them from
+ any GNU archive site."
+ touch aclocal.m4
+ ;;
+
+ autoconf*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`${configure_ac}'. You might want to install the
+ \`Autoconf' and \`GNU m4' packages. Grab them from any GNU
+ archive site."
+ touch configure
+ ;;
+
+ autoheader*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`acconfig.h' or \`${configure_ac}'. You might want
+ to install the \`Autoconf' and \`GNU m4' packages. Grab them
+ from any GNU archive site."
+ files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' ${configure_ac}`
+ test -z "$files" && files="config.h"
+ touch_files=
+ for f in $files; do
+ case $f in
+ *:*) touch_files="$touch_files "`echo "$f" |
+ sed -e 's/^[^:]*://' -e 's/:.*//'`;;
+ *) touch_files="$touch_files $f.in";;
+ esac
+ done
+ touch $touch_files
+ ;;
+
+ automake*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified \`Makefile.am', \`acinclude.m4' or \`${configure_ac}'.
+ You might want to install the \`Automake' and \`Perl' packages.
+ Grab them from any GNU archive site."
+ find . -type f -name Makefile.am -print |
+ sed 's/\.am$/.in/' |
+ while read f; do touch "$f"; done
+ ;;
+
+ autom4te*)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, but is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them.
+ You can get \`$1' as part of \`Autoconf' from any GNU
+ archive site."
+
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -f "$file"; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo "#! /bin/sh"
+ echo "# Created by GNU Automake missing as a replacement of"
+ echo "# $ $@"
+ echo "exit 0"
+ chmod +x $file
+ exit 1
+ fi
+ ;;
+
+ bison*|yacc*)
+ echo 1>&2 "\
+WARNING: \`$1' $msg. You should only need it if
+ you modified a \`.y' file. You may need the \`Bison' package
+ in order for those modifications to take effect. You can get
+ \`Bison' from any GNU archive site."
+ rm -f y.tab.c y.tab.h
+ if test $# -ne 1; then
+ eval LASTARG="\${$#}"
+ case $LASTARG in
+ *.y)
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" y.tab.c
+ fi
+ SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" y.tab.h
+ fi
+ ;;
+ esac
+ fi
+ if test ! -f y.tab.h; then
+ echo >y.tab.h
+ fi
+ if test ! -f y.tab.c; then
+ echo 'main() { return 0; }' >y.tab.c
+ fi
+ ;;
+
+ lex*|flex*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.l' file. You may need the \`Flex' package
+ in order for those modifications to take effect. You can get
+ \`Flex' from any GNU archive site."
+ rm -f lex.yy.c
+ if test $# -ne 1; then
+ eval LASTARG="\${$#}"
+ case $LASTARG in
+ *.l)
+ SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
+ if test -f "$SRCFILE"; then
+ cp "$SRCFILE" lex.yy.c
+ fi
+ ;;
+ esac
+ fi
+ if test ! -f lex.yy.c; then
+ echo 'main() { return 0; }' >lex.yy.c
+ fi
+ ;;
+
+ help2man*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a dependency of a manual page. You may need the
+ \`Help2man' package in order for those modifications to take
+ effect. You can get \`Help2man' from any GNU archive site."
+
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -f "$file"; then
+ touch $file
+ else
+ test -z "$file" || exec >$file
+ echo ".ab help2man is required to generate this page"
+ exit $?
+ fi
+ ;;
+
+ makeinfo*)
+ echo 1>&2 "\
+WARNING: \`$1' is $msg. You should only need it if
+ you modified a \`.texi' or \`.texinfo' file, or any other file
+ indirectly affecting the aspect of the manual. The spurious
+ call might also be the consequence of using a buggy \`make' (AIX,
+ DU, IRIX). You might want to install the \`Texinfo' package or
+ the \`GNU make' package. Grab either from any GNU archive site."
+ # The file to touch is that specified with -o ...
+ file=`echo "$*" | sed -n "$sed_output"`
+ test -z "$file" && file=`echo "$*" | sed -n "$sed_minuso"`
+ if test -z "$file"; then
+ # ... or it is the one specified with @setfilename ...
+ infile=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
+ file=`sed -n '
+ /^@setfilename/{
+ s/.* \([^ ]*\) *$/\1/
+ p
+ q
+ }' $infile`
+ # ... or it is derived from the source name (dir/f.texi becomes f.info)
+ test -z "$file" && file=`echo "$infile" | sed 's,.*/,,;s,.[^.]*$,,'`.info
+ fi
+ # If the file does not exist, the user really needs makeinfo;
+ # let's fail without touching anything.
+ test -f $file || exit 1
+ touch $file
+ ;;
+
+ tar*)
+ shift
+
+ # We have already tried tar in the generic part.
+ # Look for gnutar/gtar before invocation to avoid ugly error
+ # messages.
+ if (gnutar --version > /dev/null 2>&1); then
+ gnutar "$@" && exit 0
+ fi
+ if (gtar --version > /dev/null 2>&1); then
+ gtar "$@" && exit 0
+ fi
+ firstarg="$1"
+ if shift; then
+ case $firstarg in
+ *o*)
+ firstarg=`echo "$firstarg" | sed s/o//`
+ tar "$firstarg" "$@" && exit 0
+ ;;
+ esac
+ case $firstarg in
+ *h*)
+ firstarg=`echo "$firstarg" | sed s/h//`
+ tar "$firstarg" "$@" && exit 0
+ ;;
+ esac
+ fi
+
+ echo 1>&2 "\
+WARNING: I can't seem to be able to run \`tar' with the given arguments.
+ You may want to install GNU tar or Free paxutils, or check the
+ command line arguments."
+ exit 1
+ ;;
+
+ *)
+ echo 1>&2 "\
+WARNING: \`$1' is needed, and is $msg.
+ You might have modified some files without having the
+ proper tools for further handling them. Check the \`README' file,
+ it often tells you about the needed prerequisites for installing
+ this package. You may also peek at any GNU archive site, in case
+ some other package would contain this missing \`$1' program."
+ exit 1
+ ;;
+esac
+
+exit 0
+
+# Local variables:
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:
--- /dev/null
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+
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+
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+
+
+# the following is the clustalo convenience library which wraps all
+# the other noinst libraries
+
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+
+libclustalo_la_SOURCES = clustal-omega.c
+libclustalo_la_LIBADD = clustal/libclustal.la \
+ hhalign/libhhalign.la \
+ squid/libsquid.la \
+ kmpp/libkmpp.la
+libclustalo_la_LDFLAGS = -static
+library_includedir=$(includedir)/clustalo/
+library_include_HEADERS = clustal-omega-config.h clustal-omega.h
+
+
+
+bin_PROGRAMS = clustalo
+
+clustalo_SOURCES = main.cpp \
+ mymain.c mymain.h
+
+clustalo_LDADD = libclustalo.la
--- /dev/null
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+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
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+
+@SET_MAKE@
+
+
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+ hhalign/libhhalign.la squid/libsquid.la kmpp/libkmpp.la
+am_libclustalo_la_OBJECTS = clustal-omega.lo
+libclustalo_la_OBJECTS = $(am_libclustalo_la_OBJECTS)
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+ $(LDFLAGS) -o $@
+CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
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+ install-dvi-recursive install-exec-recursive \
+ install-html-recursive install-info-recursive \
+ install-pdf-recursive install-ps-recursive install-recursive \
+ installcheck-recursive installdirs-recursive pdf-recursive \
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+HEADERS = $(library_include_HEADERS)
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+top_srcdir = @top_srcdir@
+EXTRA_DIST = clustalo-api-test.c
+SUBDIRS = hhalign squid kmpp clustal
+
+# the following is the clustalo convenience library which wraps all
+# the other noinst libraries
+lib_LTLIBRARIES = libclustalo.la
+libclustalo_la_SOURCES = clustal-omega.c
+libclustalo_la_LIBADD = clustal/libclustal.la \
+ hhalign/libhhalign.la \
+ squid/libsquid.la \
+ kmpp/libkmpp.la
+
+libclustalo_la_LDFLAGS = -static
+library_includedir = $(includedir)/clustalo/
+library_include_HEADERS = clustal-omega-config.h clustal-omega.h
+clustalo_SOURCES = main.cpp \
+ mymain.c mymain.h
+
+clustalo_LDADD = libclustalo.la
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+ $(MAKE) $(AM_MAKEFLAGS) all-recursive
+
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+ @for dep in $?; do \
+ case '$(am__configure_deps)' in \
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+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
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+
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+
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+ rm -f "$(DESTDIR)$(bindir)/$$f"; \
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+
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+ f=`echo $$p|sed 's/$(EXEEXT)$$//'`; \
+ echo " rm -f $$p $$f"; \
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+ done
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+ @rm -f clustalo$(EXEEXT)
+ $(CXXLINK) $(clustalo_OBJECTS) $(clustalo_LDADD) $(LIBS)
+
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+
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+
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+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
--- /dev/null
+#ifndef _SRC_CLUSTAL_OMEGA_CONFIG_H
+#define _SRC_CLUSTAL_OMEGA_CONFIG_H 1
+
+/* src/clustal-omega-config.h. Generated automatically at end of configure. */
+/* src/config.h. Generated from config.h.in by configure. */
+/* src/config.h.in. Generated from configure.ac by autoheader. */
+
+/* Define if building universal (internal helper macro) */
+/* #undef AC_APPLE_UNIVERSAL_BUILD */
+
+/* Let all files know they are being used inside Clustal Omega */
+#ifndef CLUSTAL_OMEGA_CLUSTALO
+#define CLUSTAL_OMEGA_CLUSTALO 1
+#endif
+
+/* This is a CYGWIN system */
+/* #undef CYGWIN */
+
+/* This is a Darwin system */
+/* #undef DARWIN */
+
+/* Define to 1 if you have the <argtable2.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_ARGTABLE2_H
+#define CLUSTAL_OMEGA_HAVE_ARGTABLE2_H 1
+#endif
+
+/* Define to 1 if you have the <assert.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_ASSERT_H
+#define CLUSTAL_OMEGA_HAVE_ASSERT_H 1
+#endif
+
+/* Define to 1 if you have the <ctype.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_CTYPE_H
+#define CLUSTAL_OMEGA_HAVE_CTYPE_H 1
+#endif
+
+/* Define to 1 if you have the <dlfcn.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_DLFCN_H
+#define CLUSTAL_OMEGA_HAVE_DLFCN_H 1
+#endif
+
+/* Define to 1 if you have the <float.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_FLOAT_H
+#define CLUSTAL_OMEGA_HAVE_FLOAT_H 1
+#endif
+
+/* Define to 1 if you have the `fseek64' function. */
+/* #undef HAVE_FSEEK64 */
+
+/* Define to 1 if you have the `fseeko' function. */
+#ifndef CLUSTAL_OMEGA_HAVE_FSEEKO
+#define CLUSTAL_OMEGA_HAVE_FSEEKO 1
+#endif
+
+/* Define to 1 if you have the `fseeko64' function. */
+#ifndef CLUSTAL_OMEGA_HAVE_FSEEKO64
+#define CLUSTAL_OMEGA_HAVE_FSEEKO64 1
+#endif
+
+/* Define to 1 if you have the `ftell64' function. */
+/* #undef HAVE_FTELL64 */
+
+/* Define to 1 if you have the `ftello' function. */
+#ifndef CLUSTAL_OMEGA_HAVE_FTELLO
+#define CLUSTAL_OMEGA_HAVE_FTELLO 1
+#endif
+
+/* Define to 1 if you have the `ftello64' function. */
+#ifndef CLUSTAL_OMEGA_HAVE_FTELLO64
+#define CLUSTAL_OMEGA_HAVE_FTELLO64 1
+#endif
+
+/* Define to 1 if you have the <inttypes.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_INTTYPES_H
+#define CLUSTAL_OMEGA_HAVE_INTTYPES_H 1
+#endif
+
+/* Define to 1 if you have the `argtable2' library (-largtable2). */
+#ifndef CLUSTAL_OMEGA_HAVE_LIBARGTABLE2
+#define CLUSTAL_OMEGA_HAVE_LIBARGTABLE2 1
+#endif
+
+/* Define to 1 if you have the `m' library (-lm). */
+#ifndef CLUSTAL_OMEGA_HAVE_LIBM
+#define CLUSTAL_OMEGA_HAVE_LIBM 1
+#endif
+
+/* Define to 1 if you have the <limits.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_LIMITS_H
+#define CLUSTAL_OMEGA_HAVE_LIMITS_H 1
+#endif
+
+/* Has log2() */
+#ifndef CLUSTAL_OMEGA_HAVE_LOG2
+#define CLUSTAL_OMEGA_HAVE_LOG2 1
+#endif
+
+/* Define to 1 if you have the <math.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_MATH_H
+#define CLUSTAL_OMEGA_HAVE_MATH_H 1
+#endif
+
+/* Define to 1 if you have the <memory.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_MEMORY_H
+#define CLUSTAL_OMEGA_HAVE_MEMORY_H 1
+#endif
+
+/* Define to 1 if you have the `ntohl' function. */
+#ifndef CLUSTAL_OMEGA_HAVE_NTOHL
+#define CLUSTAL_OMEGA_HAVE_NTOHL 1
+#endif
+
+/* Define to 1 if you have the `ntohs' function. */
+#ifndef CLUSTAL_OMEGA_HAVE_NTOHS
+#define CLUSTAL_OMEGA_HAVE_NTOHS 1
+#endif
+
+/* Define to 1 if you have the `ntonl' function. */
+/* #undef HAVE_NTONL */
+
+/* Define to 1 if you have the `ntons' function. */
+/* #undef HAVE_NTONS */
+
+/* Defined if OpenMP should and can be used */
+#ifndef CLUSTAL_OMEGA_HAVE_OPENMP
+#define CLUSTAL_OMEGA_HAVE_OPENMP 1
+#endif
+
+/* Define to 1 if you have the <stdarg.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_STDARG_H
+#define CLUSTAL_OMEGA_HAVE_STDARG_H 1
+#endif
+
+/* Define to 1 if you have the <stdint.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_STDINT_H
+#define CLUSTAL_OMEGA_HAVE_STDINT_H 1
+#endif
+
+/* Define to 1 if you have the <stdio.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_STDIO_H
+#define CLUSTAL_OMEGA_HAVE_STDIO_H 1
+#endif
+
+/* Define to 1 if you have the <stdlib.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_STDLIB_H
+#define CLUSTAL_OMEGA_HAVE_STDLIB_H 1
+#endif
+
+/* Define to 1 if you have the <strings.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_STRINGS_H
+#define CLUSTAL_OMEGA_HAVE_STRINGS_H 1
+#endif
+
+/* Define to 1 if you have the <string.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_STRING_H
+#define CLUSTAL_OMEGA_HAVE_STRING_H 1
+#endif
+
+/* Define to 1 if you have the `stroul' function. */
+/* #undef HAVE_STROUL */
+
+/* Define to 1 if you have the `strtoull' function. */
+#ifndef CLUSTAL_OMEGA_HAVE_STRTOULL
+#define CLUSTAL_OMEGA_HAVE_STRTOULL 1
+#endif
+
+/* Define to 1 if you have the <sys/stat.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_SYS_STAT_H
+#define CLUSTAL_OMEGA_HAVE_SYS_STAT_H 1
+#endif
+
+/* Define to 1 if you have the <sys/types.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_SYS_TYPES_H
+#define CLUSTAL_OMEGA_HAVE_SYS_TYPES_H 1
+#endif
+
+/* Define to 1 if you have the <time.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_TIME_H
+#define CLUSTAL_OMEGA_HAVE_TIME_H 1
+#endif
+
+/* Define to 1 if you have the <unistd.h> header file. */
+#ifndef CLUSTAL_OMEGA_HAVE_UNISTD_H
+#define CLUSTAL_OMEGA_HAVE_UNISTD_H 1
+#endif
+
+/* This is a LINUX system */
+#ifndef CLUSTAL_OMEGA_LINUX
+#define CLUSTAL_OMEGA_LINUX 1
+#endif
+
+/* Define to the sub-directory in which libtool stores uninstalled libraries.
+ */
+#ifndef CLUSTAL_OMEGA_LT_OBJDIR
+#define CLUSTAL_OMEGA_LT_OBJDIR ".libs/"
+#endif
+
+/* This is a MinGW system */
+/* #undef MINGW */
+
+/* No-debug Mode */
+#ifndef CLUSTAL_OMEGA_NDEBUG
+#define CLUSTAL_OMEGA_NDEBUG /**/
+#endif
+
+/* Some strange OS */
+/* #undef OTHEROS */
+
+/* Name of package */
+#ifndef CLUSTAL_OMEGA_PACKAGE
+#define CLUSTAL_OMEGA_PACKAGE "clustal-omega"
+#endif
+
+/* Define to the address where bug reports for this package should be sent. */
+#ifndef CLUSTAL_OMEGA_PACKAGE_BUGREPORT
+#define CLUSTAL_OMEGA_PACKAGE_BUGREPORT "clustalw@ucd.ie"
+#endif
+
+/* The package code name */
+#ifndef CLUSTAL_OMEGA_PACKAGE_CODENAME
+#define CLUSTAL_OMEGA_PACKAGE_CODENAME "DeshilHollesEamus"
+#endif
+
+/* Define to the full name of this package. */
+#ifndef CLUSTAL_OMEGA_PACKAGE_NAME
+#define CLUSTAL_OMEGA_PACKAGE_NAME "Clustal Omega"
+#endif
+
+/* Define to the full name and version of this package. */
+#ifndef CLUSTAL_OMEGA_PACKAGE_STRING
+#define CLUSTAL_OMEGA_PACKAGE_STRING "Clustal Omega 1.0.2"
+#endif
+
+/* Define to the one symbol short name of this package. */
+#ifndef CLUSTAL_OMEGA_PACKAGE_TARNAME
+#define CLUSTAL_OMEGA_PACKAGE_TARNAME "clustal-omega"
+#endif
+
+/* Define to the version of this package. */
+#ifndef CLUSTAL_OMEGA_PACKAGE_VERSION
+#define CLUSTAL_OMEGA_PACKAGE_VERSION "1.0.2"
+#endif
+
+/* The size of `fpos_t', as computed by sizeof. */
+#ifndef CLUSTAL_OMEGA_SIZEOF_FPOS_T
+#define CLUSTAL_OMEGA_SIZEOF_FPOS_T 16
+#endif
+
+/* The size of `unsigned int', as computed by sizeof. */
+#ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_INT
+#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_INT 4
+#endif
+
+/* The size of `unsigned long', as computed by sizeof. */
+#ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG
+#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG 8
+#endif
+
+/* The size of `unsigned long long', as computed by sizeof. */
+#ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG_LONG
+#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_LONG_LONG 8
+#endif
+
+/* The size of `unsigned short', as computed by sizeof. */
+#ifndef CLUSTAL_OMEGA_SIZEOF_UNSIGNED_SHORT
+#define CLUSTAL_OMEGA_SIZEOF_UNSIGNED_SHORT 2
+#endif
+
+/* This is a Solaris system */
+/* #undef SOLARIS */
+
+/* This is a BSD system */
+/* #undef SOMEBSD */
+
+/* Define to 1 if you have the ANSI C header files. */
+#ifndef CLUSTAL_OMEGA_STDC_HEADERS
+#define CLUSTAL_OMEGA_STDC_HEADERS 1
+#endif
+
+/* Enable extensions on AIX 3, Interix. */
+#ifndef _ALL_SOURCE
+# define _ALL_SOURCE 1
+#endif
+/* Enable GNU extensions on systems that have them. */
+#ifndef _GNU_SOURCE
+# define _GNU_SOURCE 1
+#endif
+/* Enable threading extensions on Solaris. */
+#ifndef _POSIX_PTHREAD_SEMANTICS
+# define _POSIX_PTHREAD_SEMANTICS 1
+#endif
+/* Enable extensions on HP NonStop. */
+#ifndef _TANDEM_SOURCE
+# define _TANDEM_SOURCE 1
+#endif
+/* Enable general extensions on Solaris. */
+#ifndef __EXTENSIONS__
+# define __EXTENSIONS__ 1
+#endif
+
+
+/* Version number of package */
+#ifndef CLUSTAL_OMEGA_VERSION
+#define CLUSTAL_OMEGA_VERSION "1.0.2"
+#endif
+
+/* Define if using the dmalloc debugging malloc package */
+/* #undef WITH_DMALLOC */
+
+/* Define WORDS_BIGENDIAN to 1 if your processor stores words with the most
+ significant byte first (like Motorola and SPARC, unlike Intel). */
+#if defined AC_APPLE_UNIVERSAL_BUILD
+# if defined __BIG_ENDIAN__
+# define WORDS_BIGENDIAN 1
+# endif
+#else
+# ifndef WORDS_BIGENDIAN
+/* # undef WORDS_BIGENDIAN */
+# endif
+#endif
+
+/* Define to 1 if on MINIX. */
+/* #undef _MINIX */
+
+/* Define to 2 if the system does not provide POSIX.1 features except with
+ this defined. */
+/* #undef _POSIX_1_SOURCE */
+
+/* Define to 1 if you need to in order for `stat' and other things to work. */
+/* #undef _POSIX_SOURCE */
+
+/* Define to empty if `const' does not conform to ANSI C. */
+/* #undef const */
+
+/* Define to `__inline__' or `__inline' if that's what the C compiler
+ calls it, or to nothing if 'inline' is not supported under any name. */
+#ifndef __cplusplus
+/* #undef inline */
+#endif
+
+/* Define to `long int' if <sys/types.h> does not define. */
+/* #undef off_t */
+
+/* Define to `unsigned int' if <sys/types.h> does not define. */
+/* #undef size_t */
+
+/* once: _SRC_CLUSTAL_OMEGA_CONFIG_H */
+#endif
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: clustal-omega.c 254 2011-06-21 13:07:50Z andreas $
+ */
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <assert.h>
+
+#include "clustal-omega.h"
+#include "hhalign/general.h"
+
+/* The following comment block contains the frontpage/mainpage of the doxygen
+ * documentation. Please add some more info. FIXME add more
+ */
+
+/**
+ *
+ * @mainpage Clustal-Omega Documentation
+ *
+ * @section intro_sec Introduction
+ *
+ * For more information see http://www.clustal.org/
+ *
+ * @section api_section API
+ *
+ * @subsection example_prog_subsection An Example Program
+ *
+ * To use libclustalo you will have to include the clustal-omega.h header and
+ * link against libclustalo. For linking against libclustalo you will have to
+ * use a C++ compiler, no matter if your program was written in C or C++.
+ *
+ * First compile (no linking) your source (for an example see section "\ref
+ * example_src_subsubsec"):
+ *
+ * @code
+ * $ gcc -c -ansi -Wall clustalo-api-test.c
+ * @endcode
+ *
+ * Then link against libclustalo (we recommend the use of pkg-config as
+ * explained in \ref pkgconfig_subsubsec). Assuming Clustal Omega was installed
+ * in system-wide default directory (e.g. /usr) just type:
+ *
+ * @code
+ * $ g++ -ansi -Wall -o clustalo-api-test clustalo-api-test.o -lclustalo
+ * @endcode
+ *
+ * Voila! Now you have your own alignment program which can be run with
+ *
+ * @code
+ * $ ./clustalo-api-test <your-sequence-input>
+ * @endcode
+ *
+ * It's best to use the same compiler that you used for compiling libclustal.
+ * If libclustal was compiled with OpenMP support, you will have to use OpenMP
+ * flags for you program as well.
+ *
+ *
+ * @subsubsection pkgconfig_subsubsec Using pkg-config / Figuring out compiler flags
+ *
+ * Clustal Omega comes with support for <a
+ * href="http://pkg-config.freedesktop.org">pkg-config</a>, which means you
+ * can run
+ *
+ * @code
+ * $ pkg-config --cflags --libs clustalo
+ * @endcode
+ *
+ * to figure out cflags and library flags needed to compile and link against
+ * libclustalo. This is especially handy if Clustal Omega was installed to a
+ * non-standard directory.
+ *
+ * You might have to change PKG_CONFIG_PATH. For example, if you used the prefix $HOME/local/ for
+ * installation then you will first need to set PKG_CONFIG_PATH:
+ *
+ * @code
+ * $ export PKG_CONFIG_PATH=$HOME/local/lib/pkgconfig
+ * $ pkg-config --cflags --libs clustalo
+ * @endcode
+ *
+ *
+ * To compile your source use:
+ *
+ * @code
+ * $ export PKG_CONFIG_PATH=$HOME/local/lib/pkgconfig
+ * $ gcc -c -ansi -Wall clustalo-api-test.c $(pkg-config --cflags clustalo)
+ * $ g++ -ansi -Wall -o clustalo-api-test clustalo-api-test.o $(pkg-config --libs clustalo)
+ * @endcode
+ *
+ *
+ * @subsubsection example_src_subsubsec Example Source Code
+ *
+ * @include "clustalo-api-test.c"
+ *
+ *
+ */
+
+
+
+
+/* FIXME: doc */
+/* the following are temporary flags while the code is still under construction;
+ had problems internalising hhmake, so as temporary crutch
+ write alignment to file and get external hmmer/hhmake via system call
+ to read alignment and convert into HMM
+ All this will go, once hhmake is properly internalised */
+#define INDIRECT_HMM 0 /* temp flag: (1) write aln to file, use system(hmmer/hhmake), (0) internal hhmake */
+#define USEHMMER 1 /* temp flag: use system(hmmer) to build HMM */
+#define USEHHMAKE (!USEHMMER) /* temp flag: use system(hhmake) to build HMM */
+
+
+/* shuffle order of input sequences */
+#define SHUFFLE_INPUT_SEQ_ORDER 0
+
+/* sort input sequences by length */
+#define SORT_INPUT_SEQS 0
+
+
+int iNumberOfThreads;
+
+/* broken, unused and lonely */
+static const int ITERATION_SCORE_IMPROVEMENT_THRESHOLD = 0.01;
+
+
+/**
+ * @brief Print Long version information to pre-allocated char.
+ *
+ * @note short version
+ * information is equivalent to PACKAGE_VERSION
+ *
+ * @param[out] pcStr
+ * char pointer to write to preallocated to hold iSize chars.
+ * @param[in] iSize
+ * size of pcStr
+ */
+void
+PrintLongVersion(char *pcStr, int iSize)
+{
+ snprintf(pcStr, iSize, "version %s; code-name '%s'; build date %s",
+ PACKAGE_VERSION, PACKAGE_CODENAME, __DATE__);
+}
+/* end of PrintLongVersion() */
+
+
+
+/**
+ * @brief free aln opts members
+ *
+ */
+void
+FreeAlnOpts(opts_t *prAlnOpts) {
+ if (NULL != prAlnOpts->pcGuidetreeInfile) {
+ CKFREE(prAlnOpts->pcGuidetreeInfile);
+ }
+ if (NULL != prAlnOpts->pcGuidetreeOutfile) {
+ CKFREE(prAlnOpts->pcGuidetreeOutfile);
+ }
+ if (NULL != prAlnOpts->pcDistmatOutfile) {
+ CKFREE(prAlnOpts->pcDistmatOutfile);
+ }
+ if (NULL != prAlnOpts->pcDistmatInfile) {
+ CKFREE(prAlnOpts->pcDistmatInfile);
+ }
+}
+/* end of FreeAlnOpts() */
+
+
+
+/**
+ * @brief Sets members of given user opts struct to default values
+ *
+ * @param[out] prOpts
+ * User opt struct to initialise
+ *
+ */
+void
+SetDefaultAlnOpts(opts_t *prOpts) {
+ prOpts->bAutoOptions = FALSE;
+
+ prOpts->pcDistmatInfile = NULL;
+ prOpts->pcDistmatOutfile = NULL;
+
+ prOpts->iClusteringType = CLUSTERING_UPGMA;
+ prOpts->iPairDistType = PAIRDIST_KTUPLE;
+ prOpts->bUseMbed = TRUE; /* FS, r250 -> */
+ prOpts->bUseMbedForIteration = TRUE; /* FS, r250 -> */
+ prOpts->pcGuidetreeOutfile = NULL;
+ prOpts->pcGuidetreeInfile = NULL;
+
+ prOpts->ppcHMMInput = NULL;
+ prOpts->iHMMInputFiles = 0;
+
+ prOpts->iNumIterations = 0;
+ prOpts->bIterationsAuto = FALSE;
+ prOpts->iMaxGuidetreeIterations = INT_MAX;
+ prOpts->iMaxHMMIterations = INT_MAX;
+ prOpts->iMacRam = 2048; /* give 2GB to MAC algorithm. FS, r240 -> r241 */
+ }
+/* end of SetDefaultAlnOpts() */
+
+
+
+/**
+ * @brief Check logic of parsed user options. Will exit (call Log(&rLog, LOG_FATAL, ))
+ * on Fatal logic error
+ *
+ * @param[in] prOpts
+ * Already parsed user options
+ *
+ */
+void
+AlnOptsLogicCheck(opts_t *prOpts)
+{
+ /* guide-tree & distmat
+ *
+ */
+ if (prOpts->pcDistmatInfile && prOpts->pcGuidetreeInfile) {
+ Log(&rLog, LOG_FATAL, "Read distances *and* guide-tree from file doesn't make sense.");
+ }
+
+ if (prOpts->pcDistmatOutfile && prOpts->pcGuidetreeInfile) {
+ Log(&rLog, LOG_FATAL, "Won't be able to save distances to file, because I got a guide-tree as input.");
+ }
+
+ /* combination of options that don't make sense when not iterating
+ */
+ if (prOpts->iNumIterations==0 && prOpts->bIterationsAuto != TRUE) {
+
+ if (prOpts->pcGuidetreeInfile && prOpts->pcGuidetreeOutfile) {
+ Log(&rLog, LOG_FATAL, "Got a guide-tree as input and output which doesn't make sense when not iterating.");
+ }
+ /*
+ if (prOpts->pcGuidetreeInfile && prOpts->bUseMbed > 0) {
+ Log(&rLog, LOG_FATAL, "Got a guide-tree as input and was requested to cluster with mBed, which doesn't make sense when not iterating.");
+ }
+ */
+ /*
+ AW: bUseMbedForIteration default since at least R252
+ if (prOpts->bUseMbedForIteration > 0) {
+ Log(&rLog, LOG_FATAL, "No iteration requested, but mbed for iteration was set. Paranoia exit.");
+ }
+ */
+ }
+
+ if (prOpts->iMacRam < 512) {
+
+ Log(&rLog, LOG_INFO, "Memory for MAC Algorithm quite low, Viterbi Algorithm may be triggered.");
+
+ if (prOpts->iMacRam < 1) {
+
+ Log(&rLog, LOG_WARN, "Viterbi Algorithm always turned on, increase MAC-RAM to turn on MAC.");
+ }
+ }
+
+ return;
+}
+/* end of AlnOptsLogicCheck() */
+
+
+/**
+ * @brief FIXME doc
+ */
+void
+PrintAlnOpts(FILE *prFile, opts_t *prOpts)
+{
+ int iAux;
+
+
+ /* keep in same order as struct */
+ fprintf(prFile, "option: auto-options = %d\n", prOpts->bAutoOptions);
+ fprintf(prFile, "option: distmat-infile = %s\n",
+ NULL != prOpts->pcDistmatInfile? prOpts->pcDistmatInfile: "(null)");
+ fprintf(prFile, "option: distmat-outfile = %s\n",
+ NULL != prOpts->pcDistmatOutfile? prOpts->pcDistmatOutfile: "(null)");
+ fprintf(prFile, "option: clustering-type = %d\n", prOpts->iClusteringType);
+ fprintf(prFile, "option: pair-dist-type = %d\n", prOpts->iPairDistType);
+ fprintf(prFile, "option: use-mbed = %d\n", prOpts->bUseMbed);
+ fprintf(prFile, "option: use-mbed-for-iteration = %d\n", prOpts->bUseMbedForIteration);
+ fprintf(prFile, "option: guidetree-outfile = %s\n",
+ NULL != prOpts->pcGuidetreeOutfile? prOpts->pcGuidetreeOutfile: "(null)");
+ fprintf(prFile, "option: guidetree-infile = %s\n",
+ NULL != prOpts->pcGuidetreeInfile? prOpts->pcGuidetreeInfile: "(null)");
+ for (iAux=0; iAux<prOpts->iHMMInputFiles; iAux++) {
+ fprintf(prFile, "option: hmm-input no %d = %s\n", iAux, prOpts->ppcHMMInput[iAux]);
+ }
+ fprintf(prFile, "option: hmm-input-files = %d\n", prOpts->iHMMInputFiles);
+ fprintf(prFile, "option: num-iterations = %d\n", prOpts->iNumIterations);
+ fprintf(prFile, "option: iterations-auto = %d\n", prOpts->bIterationsAuto);
+ fprintf(prFile, "option: max-hmm-iterations = %d\n", prOpts->iMaxHMMIterations);
+ fprintf(prFile, "option: max-guidetree-iterations = %d\n", prOpts->iMaxGuidetreeIterations);
+}
+/* end of PrintAlnOpts() */
+
+
+
+/**
+ * @brief Returns major version of HMMER. Whichever hmmbuild version
+ * is found first in your PATH will be used
+ *
+ * @return -1 on error, major hmmer version otherwise
+ *
+ */
+int
+HmmerVersion()
+{
+ char zcHmmerTestCall[] = "hmmbuild -h";
+ FILE *fp = NULL;
+ int iMajorVersion = 0;
+ char zcLine[16384];
+
+ if (NULL == (fp = popen(zcHmmerTestCall, "r"))) {
+ Log(&rLog, LOG_ERROR, "Couldn't exec %s", zcHmmerTestCall);
+ return -1;
+ }
+ while (fgets(zcLine, sizeof(zcLine), fp)) {
+ char *pcLocate;
+ if ((pcLocate = strstr(zcLine, "HMMER "))) {
+ iMajorVersion = atoi(&pcLocate[6]);
+ break;
+ }
+ }
+ pclose(fp);
+
+ return iMajorVersion;
+}
+/* end of HmmerVersion() */
+
+
+
+/**
+ * @brief Create a HHM file from aligned sequences
+ *
+ * @warning Should be eliminated in the future
+ * as building routine should not create intermediate files
+ *
+ * @param[in] prMSeq
+ * Aligned mseq_t
+ * @param[in] pcHMMOut
+ * HMM output file name
+ *
+ * @return Non-zero on error
+ *
+ */
+int
+AlnToHHMFile(mseq_t *prMSeq, char *pcHMMOut)
+{
+ char *tmp_aln = NULL;
+ int retcode = OK;
+
+ assert(NULL!=prMSeq);
+ assert(NULL!=pcHMMOut);
+
+ if (FALSE == prMSeq->aligned) {
+ Log(&rLog, LOG_ERROR, "Sequences need to be aligned to create an HMM");
+ return FAILURE;
+ }
+
+ /* Convert alignment to a2m, and call hhmake
+ *
+ * can't be static templates, or mktemp fails (at least on os x
+ * (with a bus error))
+ *
+ * gcc says we should use mkstemp to avoid race conditions,
+ * but that returns a file descriptor, which is of no use to
+ * us
+ */
+ /* NOTE: the following won't work on windows: missing /tmp/ */
+ tmp_aln = CkStrdup("/tmp/clustalo_tmpaln_XXXXXX");
+ if (NULL == mktemp(tmp_aln)) {
+ Log(&rLog, LOG_ERROR, "Could not create temporary alignment filename");
+ retcode = FAILURE;
+ goto cleanup_and_return;
+ }
+ if (WriteAlignment(prMSeq, tmp_aln, MSAFILE_A2M)) {
+ Log(&rLog, LOG_ERROR, "Could not save alignment to %s", tmp_aln);
+ retcode = FAILURE;
+ goto cleanup_and_return;
+ }
+
+ if (HHMake_Wrapper(tmp_aln, pcHMMOut)){
+ Log(&rLog, LOG_ERROR, "Could not convert alignment %s into HHM", tmp_aln);
+ retcode = FAILURE;
+ goto cleanup_and_return;
+ }
+
+
+ cleanup_and_return:
+
+ if (NULL != tmp_aln) {
+ if (FileExists(tmp_aln)) {
+ if (remove(tmp_aln)) {
+ Log(&rLog, LOG_WARN, "Removing %s failed. Continuing anyway", tmp_aln);
+ }
+ }
+ CKFREE(tmp_aln);
+ }
+
+ return retcode;
+
+} /* end of AlnToHHMFile() */
+
+
+
+/**
+ * @brief Create a HMM file from aligned sequences
+ *
+ * @warning Should be replaced in the future by some internal HMM
+ * building routine that does not call external programs
+ *
+ * @param[in] prMSeq
+ * Aligned mseq_t
+ * @param[in] pcHMMOut
+ * HMM output file name
+ *
+ * @return Non-zero on error
+ *
+
+ */
+int
+AlnToHMMFile(mseq_t *prMSeq, const char *pcHMMOut)
+{
+ char *tmp_aln = NULL;
+ char *tmp_hmm = NULL; /* only needed for hmmer3 to hmmer2 conversion */
+ char cmdbuf[16384];
+ int iHmmerVersion = 0;
+ int retcode = OK;
+
+ assert(NULL!=prMSeq);
+ assert(NULL!=pcHMMOut);
+
+ if (FALSE == prMSeq->aligned) {
+ Log(&rLog, LOG_ERROR, "Sequences need to be aligned to create an HMM");
+ return FAILURE;
+ }
+
+ iHmmerVersion = HmmerVersion();
+ if (2 != iHmmerVersion && 3 != iHmmerVersion) {
+ Log(&rLog, LOG_ERROR, "Could not find suitable HMMER binaries");
+ return FAILURE;
+ }
+
+ /* Convert alignment to stockholm, call hmmbuild and then
+ * either hmmconvert (hmmer3) or hmmcalibrate (hmmer2)
+ *
+ * can't be static templates, or mktemp fails (at least on os x
+ * (with a bus error))
+ *
+ * gcc says we should use mkstemp to avoid race conditions,
+ * but that returns a file descriptor, which is of no use to
+ * us
+ */
+ /* NOTE: the following won't work on windows: missing /tmp/ */
+ tmp_aln = CkStrdup("/tmp/clustalo_tmpaln_XXXXXX");
+ if (NULL == mktemp(tmp_aln)) {
+ Log(&rLog, LOG_ERROR, "Could not create temporary alignment filename");
+ retcode = FAILURE;
+ goto cleanup_and_return;
+ }
+ if (WriteAlignment(prMSeq, tmp_aln, MSAFILE_STOCKHOLM)) {
+ Log(&rLog, LOG_ERROR, "Could not save alignment to %s", tmp_aln);
+ retcode = FAILURE;
+ goto cleanup_and_return;
+ }
+
+ if (2 == iHmmerVersion) {
+ sprintf(cmdbuf, "hmmbuild %s %s >/dev/null && hmmcalibrate %s >/dev/null",
+ pcHMMOut, tmp_aln, pcHMMOut);
+ if (system(cmdbuf)) {
+ Log(&rLog, LOG_ERROR, "Command '%s' failed", cmdbuf);
+ retcode = FAILURE;
+ goto cleanup_and_return;
+ }
+ } else if (3 == iHmmerVersion) {
+ /* NOTE: the following won't work on windows: missing /tmp/ */
+ tmp_hmm = CkStrdup("/tmp/clustalo_tmphmm2_XXXXXX");
+ if (NULL == mktemp(tmp_hmm)) {
+ Log(&rLog, LOG_ERROR, "Could not create temporary hmm filename");
+ retcode = FAILURE;
+ goto cleanup_and_return;
+ }
+ sprintf(cmdbuf, "hmmbuild %s %s >/dev/null && hmmconvert -2 %s > %s",
+ tmp_hmm, tmp_aln, tmp_hmm, pcHMMOut);
+ if (system(cmdbuf)) {
+ Log(&rLog, LOG_ERROR, "Command '%s' failed", cmdbuf);
+ retcode = FAILURE;
+ goto cleanup_and_return;
+ }
+ } else {
+ CKFREE(tmp_aln);
+ Log(&rLog, LOG_FATAL, "Internal error: Unknown Hmmer version %d", iHmmerVersion);
+ }
+
+
+ cleanup_and_return:
+
+ if (NULL != tmp_aln) {
+ if (FileExists(tmp_aln)) {
+ if (remove(tmp_aln)) {
+ Log(&rLog, LOG_WARN, "Removing %s failed. Continuing anyway", tmp_aln);
+ }
+ }
+ CKFREE(tmp_aln);
+ }
+ if (NULL != tmp_hmm) {
+ if (FileExists(tmp_hmm)) {
+ if (remove(tmp_hmm)) {
+ Log(&rLog, LOG_WARN, "Removing %s failed. Continuing anyway", tmp_hmm);
+ }
+ }
+ CKFREE(tmp_hmm);
+ }
+
+ return retcode;
+}
+/* end of AlnToHMMFile() */
+
+
+
+/**
+ * @brief Convert a multiple sequence structure into a HMM
+ *
+ * @param[out] prHMM
+ * Pointer to preallocted HMM which will be set here
+ * @param[in] prMSeq
+ * Pointer to an alignment
+ *
+ * @return 0 on error, non-0 otherwise
+ *
+ * @see AlnToHMMFile()
+ *
+ */
+int
+AlnToHMM(hmm_light *prHMM, mseq_t *prMSeq)
+{
+ char *pcHMM; /* temp hmm file */
+
+ Log(&rLog, LOG_INFO,
+ "Using HMMER version %d to calculate a new HMM.",
+ HmmerVersion());
+ /* FIXME replace all this with internal HMM computation (HHmake) */
+
+ /**
+ * @warning the following probably won't work on windows: missing
+ * /tmp/. Should be ok on Cygwin though
+ */
+ pcHMM = CkStrdup("/tmp/clustalo-hmm-iter_XXXXXX");
+ if (NULL == mktemp(pcHMM)) {
+ Log(&rLog, LOG_ERROR, "Could not create temporary hmm filename");
+ CKFREE(pcHMM);
+ return FAILURE;
+ }
+
+ /* Create a HMM representing the current alignment
+ */
+#if USEHMMER
+ if (AlnToHMMFile(prMSeq, pcHMM)) {
+ Log(&rLog, LOG_ERROR, "AlnToHMMFile() on %s failed.", pcHMM);
+ CKFREE(pcHMM);
+ return FAILURE;
+ }
+#elif USEHHMAKE
+ if (AlnToHHMFile(prMSeq, pcHMM)) {
+ Log(&rLog, LOG_ERROR, "AlnToHHMFile() on %s failed.", pcHMM);
+ CKFREE(pcHMM);
+ return FAILURE;
+ }
+ /* Log(&rLog, LOG_FATAL, "Method to create HHM (HMM using hhmake) not installed yet"); */
+#else
+ Log(&rLog, LOG_FATAL, "Unknown method to create temporary HMM");
+#endif
+
+ /* Read HMM information
+ */
+ if (OK != readHMMWrapper(prHMM, pcHMM)){
+ Log(&rLog, LOG_ERROR, "Processing of HMM file %s failed", pcHMM);
+ CKFREE(pcHMM);
+ return FAILURE;
+ }
+
+ if (remove(pcHMM)) {
+ Log(&rLog, LOG_WARN, "Removing %s failed. Continuing anyway", pcHMM);
+ }
+ CKFREE(pcHMM);
+
+ return OK;
+}
+/* end of AlnToHMM() */
+
+
+
+/**
+ * @brief FIXME
+ *
+ */
+void
+InitClustalOmega(int iNumThreadsRequested)
+{
+
+#ifdef HAVE_OPENMP
+ iNumberOfThreads = iNumThreadsRequested;
+ omp_set_num_threads(iNumberOfThreads);
+#else
+ if (iNumThreadsRequested>1) {
+ Log(&rLog, LOG_FATAL, "Cannot change number of threads to %d. %s was build without OpenMP support.",
+ iNumThreadsRequested, PACKAGE_NAME);
+ }
+ iNumberOfThreads = 1; /* need to set this, even if build without support */
+#endif
+
+ Log(&rLog, LOG_INFO, "Using %d threads",
+ iNumberOfThreads);
+
+}
+/* end of InitClustalOmega() */
+
+
+
+/**
+ * @brief Defines an alignment order, which adds sequences
+ * sequentially, i.e. one at a time starting with seq 1 & 2
+ *
+ * @param[out] piOrderLR_p
+ * order in which nodes/profiles are to be merged/aligned
+ * @param[in] iNumSeq
+ * Number of sequences
+ *
+ * @see TraverseTree()
+ *
+ */
+void
+SequentialAlignmentOrder(int **piOrderLR_p, int iNumSeq)
+{
+ unsigned int uNodes = iNumSeq*2-1;
+ unsigned int uNodeCounter = 0;
+ unsigned int uSeqCounter = 0;
+
+ Log(&rLog, LOG_FATAL, "FIXME: Untested...");
+
+ (*piOrderLR_p) = (int *)CKCALLOC(DIFF_NODE * uNodes, sizeof(int));
+ /* loop over merge nodes, which have per definition even indices
+ * and set up children which have odd indices
+ */
+ uSeqCounter = 0;
+ for (uNodeCounter=iNumSeq; uNodeCounter<uNodes; uNodeCounter+=1) {
+ unsigned int uLeftChildNodeIndex = uNodeCounter-1;
+ unsigned int uRightChildNodeIndex = uNodeCounter-iNumSeq+1;
+ unsigned int uParentNodeIndex = uNodeCounter+1;
+
+ /* merge node setup */
+ (*piOrderLR_p)[DIFF_NODE*uNodeCounter+LEFT_NODE] = uLeftChildNodeIndex;
+ (*piOrderLR_p)[DIFF_NODE*uNodeCounter+RGHT_NODE] = uRightChildNodeIndex;
+ (*piOrderLR_p)[DIFF_NODE*uNodeCounter+PRNT_NODE] = uParentNodeIndex;
+ /* only setup left child if at first merge node, all other left childs
+ * should be merge nodes that are already set up. also correct
+ * left node number here.
+ */
+ if (uNodeCounter==iNumSeq) {
+ (*piOrderLR_p)[DIFF_NODE*uNodeCounter+LEFT_NODE] = 0;
+
+ (*piOrderLR_p)[0+LEFT_NODE] = 0;
+ (*piOrderLR_p)[0+RGHT_NODE] = 0;
+ (*piOrderLR_p)[0+PRNT_NODE] = uNodeCounter;
+ uSeqCounter++;
+
+ Log(&rLog, LOG_FORCED_DEBUG, "Set up first leaf with node counter %d: left=%d right=%d parent=%d",
+ 0,
+ (*piOrderLR_p)[DIFF_NODE*uLeftChildNodeIndex+LEFT_NODE],
+ (*piOrderLR_p)[DIFF_NODE*uLeftChildNodeIndex+RGHT_NODE],
+ (*piOrderLR_p)[DIFF_NODE*uLeftChildNodeIndex+PRNT_NODE]);
+ }
+ Log(&rLog, LOG_FORCED_DEBUG, "Set up merge node with node counter %d: left=%d right=%d parent=%d",
+ uNodeCounter, (*piOrderLR_p)[DIFF_NODE*uNodeCounter+LEFT_NODE],
+ (*piOrderLR_p)[DIFF_NODE*uNodeCounter+RGHT_NODE],
+ (*piOrderLR_p)[DIFF_NODE*uNodeCounter+PRNT_NODE]);
+
+ /* right child */
+ (*piOrderLR_p)[DIFF_NODE*uRightChildNodeIndex+LEFT_NODE] = uSeqCounter;
+ (*piOrderLR_p)[DIFF_NODE*uRightChildNodeIndex+RGHT_NODE] = uSeqCounter;
+ (*piOrderLR_p)[DIFF_NODE*uRightChildNodeIndex+PRNT_NODE] = uNodeCounter;
+ uSeqCounter++;
+
+ Log(&rLog, LOG_FORCED_DEBUG, "Set up leaf with node counter %d: left=%d right=%d parent=%d",
+ uRightChildNodeIndex, (*piOrderLR_p)[DIFF_NODE*uRightChildNodeIndex+LEFT_NODE],
+ (*piOrderLR_p)[DIFF_NODE*uRightChildNodeIndex+RGHT_NODE],
+ (*piOrderLR_p)[DIFF_NODE*uRightChildNodeIndex+PRNT_NODE]);
+ }
+}
+/* end of SequentialAlignmentOrder() */
+
+
+
+/**
+ * @brief Defines the alignment order by calculating a guide tree. In
+ * a first-step pairwise distances will be calculated (or read from a
+ * file). In a second step those distances will be clustered and a
+ * guide-tree created. Steps 1 and 2 will be skipped if a guide-tree
+ * file was given, in which case the guide-tree will be just read from
+ * the file.
+ *
+ * @param[out] piOrderLR_p
+ * order in which nodes/profiles are to be merged/aligned
+ * @param[out] pdSeqWeights_p
+ * Sequence weights
+ * @param[out] pdSeqWeights_p
+ * Sequence weights
+ * @param[in] prMSeq
+ * The sequences from which the alignment order is to be calculated
+ * @param[in] iPairDistType
+ * Method of pairwise distance comparison
+ * @param[in] pcDistmatInfile
+ * If not NULL distances will be read from this file instead of being
+ * calculated
+ * @param[in] pcDistmatOutfile
+ * If not NULL computed pairwise distances will be written to this file
+ * @param[in] iClusteringType
+ * Clustering method to be used to cluster the pairwise distances
+ * @param[in] pcGuidetreeInfile
+ * If not NULL guidetree will be read from this file. Skips pairwise
+ * distance and guidetree computation
+ * @param[in] pcGuidetreeOutfile
+ * If not NULL computed guidetree will be written to this file
+ * @param[in] bUseMbed
+ * If TRUE, fast mBed guidetree computation will be employed
+ *
+ * @return Non-zero on error
+ *
+ */
+int
+AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq,
+ int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile,
+ int iClusteringType, char *pcGuidetreeInfile, char *pcGuidetreeOutfile,
+ bool bUseMbed)
+{
+ /* pairwise distance matrix (tmat in 1.83) */
+ symmatrix_t *distmat = NULL;
+ /* guide tree */
+ tree_t *prTree = NULL;
+ int i = 0;
+
+
+ /* Shortcut for only two sequences: Do not compute k-tuple
+ * distances. Use the same logic as in TraverseTree() to setup
+ * piOrderLR_p. Changes there will have to be reflected here as
+ * well. */
+ if (2==prMSeq->nseqs) {
+ Log(&rLog, LOG_VERBOSE,
+ "Have only two sequences: No need to compute pairwise score and compute a tree.");
+
+ (*piOrderLR_p) = (int*) CKMALLOC(DIFF_NODE * 3 * sizeof(int));
+ (*piOrderLR_p)[DIFF_NODE*0+LEFT_NODE] = 0;
+ (*piOrderLR_p)[DIFF_NODE*0+RGHT_NODE] = 0;
+ (*piOrderLR_p)[DIFF_NODE*0+PRNT_NODE] = 0;
+
+ (*piOrderLR_p)[DIFF_NODE*1+LEFT_NODE] = 1;
+ (*piOrderLR_p)[DIFF_NODE*1+RGHT_NODE] = 1;
+ (*piOrderLR_p)[DIFF_NODE*1+PRNT_NODE] = 1;
+
+ /* root */
+ (*piOrderLR_p)[DIFF_NODE*2+LEFT_NODE] = 0;
+ (*piOrderLR_p)[DIFF_NODE*2+RGHT_NODE] = 1;
+ (*piOrderLR_p)[DIFF_NODE*2+PRNT_NODE] = 2;
+
+ /* Same logic as CalcClustalWeights(). Changes there will
+ have to be reflected here as well. */
+#if USE_WEIGHTS
+ (*pdWeights_p) = (double *) CKMALLOC(uNodeCount * sizeof(double));
+ (*pdWeights_p)[0] = 0.5;
+ (*pdWeights_p)[1] = 0.5;
+#endif
+
+ return OK;
+ }
+
+
+ /* compute distance & guide tree, alternatively read distances or
+ * guide tree from file
+ *
+ */
+ if (NULL != pcGuidetreeInfile) {
+ Log(&rLog, LOG_INFO, "Reading guide-tree from %s", pcGuidetreeInfile);
+ if (GuideTreeFromFile(&prTree, prMSeq, pcGuidetreeInfile)) {
+ Log(&rLog, LOG_ERROR, "Reading of guide tree %s failed.", pcGuidetreeInfile);
+ return FAILURE;
+ }
+
+ } else {
+
+ if (bUseMbed) {
+ if (Mbed(&prTree, prMSeq, iPairDistType, pcGuidetreeOutfile)) {
+ Log(&rLog, LOG_ERROR, "mbed execution failed.");
+ return FAILURE;
+ }
+ Log(&rLog, LOG_INFO, "Guide-tree computation (mBed) done.");
+ if (NULL != pcDistmatOutfile) {
+ Log(&rLog, LOG_INFO,
+ "Ignoring request to write distance matrix (am in mBed mode)");
+ }
+ } else {
+
+ if (PairDistances(&distmat, prMSeq, iPairDistType,
+ 0, prMSeq->nseqs, 0, prMSeq->nseqs,
+ pcDistmatInfile, pcDistmatOutfile)) {
+ Log(&rLog, LOG_ERROR, "Couldn't compute pair distances");
+ return FAILURE;
+ }
+
+ /* clustering of distances to get guide tree
+ */
+ if (CLUSTERING_UPGMA == iClusteringType) {
+ char **labels;
+ labels = (char**) CKMALLOC(prMSeq->nseqs * sizeof(char*));
+ for (i=0; i<prMSeq->nseqs; i++) {
+ labels[i] = prMSeq->sqinfo[i].name;
+ }
+
+ GuideTreeUpgma(&prTree, labels, distmat, pcGuidetreeOutfile);
+ Log(&rLog, LOG_INFO, "Guide-tree computation done.");
+
+ CKFREE(labels);
+ } else {
+ Log(&rLog, LOG_FATAL, "INTERNAL ERROR %s",
+ "clustering method should have been checked before");
+ }
+ }
+ }
+
+#if USE_WEIGHTS
+ /* derive sequence weights from tree
+ *
+ */
+ Log(&rLog, LOG_INFO, "Calculating sequence weights");
+ CalcClustalWeights(pdSeqWeights_p, prTree);
+ for (i = 0; i < GetLeafCount(prTree); i++) {
+ Log(&rLog, LOG_VERBOSE,
+ "Weight for seq no %d: %s = %f",
+ i, prMSeq->sqinfo[i].name, (*pdSeqWeights_p)[i]);
+ }
+#else
+ Log(&rLog, LOG_DEBUG, "Not using weights");
+#endif
+
+
+ /* define traversing order of tree
+ *
+ */
+ TraverseTree(piOrderLR_p, prTree, prMSeq);
+ if (rLog.iLogLevelEnabled <= LOG_DEBUG) {
+ /* FIXME: debug only, FS */
+ uint uNodeIndex;
+ FILE *fp = LogGetFP(&rLog, LOG_INFO);
+ Log(&rLog, LOG_DEBUG, "left/right order after tree traversal");
+ for (uNodeIndex = 0; uNodeIndex < GetNodeCount(prTree); uNodeIndex++) {
+ fprintf(fp, "%3d:\t%2d/%2d -> %d\n", i,
+ (*piOrderLR_p)[DIFF_NODE*uNodeIndex+LEFT_NODE],
+ (*piOrderLR_p)[DIFF_NODE*uNodeIndex+RGHT_NODE],
+ (*piOrderLR_p)[DIFF_NODE*uNodeIndex+PRNT_NODE]);
+ }
+ }
+
+ FreeMuscleTree(prTree);
+ FreeSymMatrix(&distmat);
+
+#if 0
+ Log(&rLog, LOG_FATAL, "DEBUG EXIT before leaving %s", __FUNCTION__);
+#endif
+ return OK;
+}
+/* end of AlignmentOrder() */
+
+
+
+/**
+ * @brief Set some options automatically based on number of sequences. Might
+ * overwrite some user-set options.
+ *
+ * @param[out] prOpts
+ * Pointer to alignment options structure
+ * @param[in] iNumSeq
+ * Number of sequences to align
+ */
+void
+SetAutoOptions(opts_t *prOpts, int iNumSeq) {
+
+ Log(&rLog, LOG_INFO,
+ "Setting options automatically based on input sequence characteristics (might overwrite some of your options).");
+
+ /* AW: new version of mbed is always good (uses subclusters) */
+ if (FALSE == prOpts->bUseMbed) {
+ Log(&rLog, LOG_INFO, "Auto settings: Enabling mBed.");
+ prOpts->bUseMbed = TRUE;
+ }
+
+ if (iNumSeq >= 1000) {
+ if (0 != prOpts->iNumIterations) {
+ Log(&rLog, LOG_INFO, "Auto settings: Disabling iterations.");
+ prOpts->iNumIterations = 0;
+ }
+
+ } else if (iNumSeq < 1000) {
+ if (1 != prOpts->iNumIterations) {
+ Log(&rLog, LOG_INFO, "Auto settings: Setting iteration to 1.");
+ prOpts->iNumIterations = 1;
+ }
+ }
+}
+/* end of */
+
+
+
+/**
+ * @brief The main alignment function which wraps everything else.
+ *
+ * @param[out] prMSeq
+ * *the* multiple sequences structure
+ * @param[in] prMSeqProfile
+ * optional profile to align against
+ * @param[in] prOpts
+ * alignmemnt options to use
+ *
+ * @return 0 on success, -1 on failure
+ *
+ */
+int
+Align(mseq_t *prMSeq,
+ mseq_t *prMSeqProfile,
+ opts_t *prOpts,
+ hhalign_para rHhalignPara) {
+
+ /* HMM
+ */
+ /* structs with pseudocounts etc; one for each HMM infile, i.e.
+ * index range: 0..iHMMInputFiles */
+ hmm_light *prHMMs = NULL;
+
+ /* MSA order in which nodes/profiles are to be merged/aligned
+ (order of nodes in guide tree (left/right)*/
+ int *piOrderLR = NULL;
+
+ /* weights per sequence */
+ double *pdSeqWeights = NULL;
+
+ /* Iteration
+ */
+ int iIterationCounter = 0;
+ double dAlnScore;
+ /* last dAlnScore for iteration */
+ double dLastAlnScore = -666.666;
+
+ int i, j; /* aux */
+
+ assert(NULL != prMSeq);
+ if (NULL != prMSeqProfile) {
+ assert(TRUE == prMSeqProfile->aligned);
+ }
+
+
+ /* automatic setting of options
+ *
+ */
+ if (prOpts->bAutoOptions) {
+ SetAutoOptions(prOpts, prMSeq->nseqs);
+ }
+
+
+#if SHUFFLE_INPUT_SEQ_ORDER
+ /*
+ * shuffle input: only useful for testing/debugging
+ */
+ Log(&rLog, LOG_WARN, "Shuffling input sequences! (Will also change output order)");
+ ShuffleMSeq(prMSeq);
+#endif
+
+
+#if SORT_INPUT_SEQS
+ /*
+ * sort input:
+ *
+ * would ensure we *always* (unless we get into the mbed k-means stage)
+ * get the same answer. usually you don't, because most pairwise alignment
+ * scores are in theory not symmetric, therefore sequence ordering might
+ * have an effect on the guide-tree. Sorting by length should get rid of
+ * this (and takes no time even for 100k seqs). Benchmark results on
+ * Balibase show almost no difference after sorting.
+ */
+ Log(&rLog, LOG_WARN, "Sorting input seq by length! This will also change the output order");
+ SortMSeqByLength(prMSeq, 'd');
+
+#endif
+
+
+ /* Read backgrounds HMMs and store in prHMMs
+ *
+ */
+ if (0 < prOpts->iHMMInputFiles) {
+ int iHMMInfileIndex;
+
+ /**
+ * @warning old structure used to be initialised like this:
+ * hmm_light rHMM = {0};
+ */
+ prHMMs = (hmm_light *) CKMALLOC(prOpts->iHMMInputFiles * sizeof(hmm_light));
+
+ for (iHMMInfileIndex=0; iHMMInfileIndex<prOpts->iHMMInputFiles; iHMMInfileIndex++) {
+ char *pcHMMInput = prOpts->ppcHMMInput[iHMMInfileIndex];
+ if (OK != readHMMWrapper(&prHMMs[iHMMInfileIndex], pcHMMInput)){
+ Log(&rLog, LOG_ERROR, "Processing of HMM file %s failed", pcHMMInput);
+ return -1;
+ }
+
+#if 0
+ Log(&rLog, LOG_FORCED_DEBUG, "HMM length is %d", prHMMs[iHMMInfileIndex].L);
+ Log(&rLog, LOG_FORCED_DEBUG, "n-display is %d", prHMMs[iHMMInfileIndex].n_display);
+ for (i = 0; NULL != prHMMs[prOpts->iHMMInputFiles].seq[i]; i++){
+ printf("seq[%d]: %s\n", i, prHMMs[iHMMInfileIndex].seq[i]);
+ }
+ Log(&rLog, LOG_FORCED_DEBUG, "Neff_HMM is %f", prHMMs[iHMMInfileIndex].Neff_HMM);
+#endif
+ if (rLog.iLogLevelEnabled <= LOG_DEBUG){
+ Log(&rLog, LOG_DEBUG, "print frequencies");
+ for (i = 0; i < prHMMs[iHMMInfileIndex].L; i++){
+#define PRINT_TAIL 5
+ if ( (PRINT_TAIL+1 == i) && (prHMMs[iHMMInfileIndex].L-PRINT_TAIL != i) ){
+ printf("....\n");
+ }
+ if ( (i > PRINT_TAIL) && (i < prHMMs[iHMMInfileIndex].L-PRINT_TAIL) ){
+ continue;
+ }
+ printf("%3d:", i);
+ for (j = 0; j < 20; j++){
+ printf("\t%1.3f", prHMMs[iHMMInfileIndex].f[i][j]);
+ }
+ printf("\n");
+ }
+ } /* debug print block */
+
+ CKFREE(prOpts->ppcHMMInput[iHMMInfileIndex]);
+ } /* for each background HMM file */
+ CKFREE(prOpts->ppcHMMInput);
+ } /* there were background HMM files */
+
+
+
+ /* If the input ("non-profile") sequences are aligned, then turn
+ * the alignment into a HMM and add to the list of background HMMs
+ *
+ */
+ if (TRUE == prMSeq->aligned) {
+ /* FIXME: gcc warns about missing initialiser here (-Wall -Wextra -pedantic) */
+ hmm_light rHMMLocal = {0};
+
+ Log(&rLog, LOG_INFO,
+ "Input sequences are aligned. Will turn alignment into HMM and add it to the user provided background HMMs.");
+ if (OK !=
+#if INDIRECT_HMM
+ AlnToHMM(&rHMMLocal, prMSeq)
+#else
+ AlnToHMM2(&rHMMLocal, prMSeq->seq, prMSeq->nseqs)
+#endif
+ ) {
+ Log(&rLog, LOG_ERROR, "Couldn't convert aligned input sequences to HMM. Will try to continue");
+ } else {
+ prHMMs = (hmm_light *) CKREALLOC(prHMMs, ((prOpts->iHMMInputFiles+1) * sizeof(hmm_light)));
+ memcpy(&(prHMMs[prOpts->iHMMInputFiles]), &rHMMLocal, sizeof(hmm_light));
+ prOpts->iHMMInputFiles++;
+ }
+ }
+
+
+ /* If we have a profile turn it into a HMM and add to
+ * the list of background HMMs.
+ *
+ */
+ if (NULL != prMSeqProfile) {
+ /* FIXME: gcc warns about missing initialiser here (-Wall -Wextra -pedantic) */
+ hmm_light rHMMLocal = {0};
+ Log(&rLog, LOG_INFO,
+ "Turning profile1 into HMM and will use it during progressive alignment.");
+ if (OK !=
+#if INDIRECT_HMM
+ AlnToHMM(&rHMMLocal, prMSeqProfile)
+#else
+ AlnToHMM2(&rHMMLocal, prMSeqProfile->seq, prMSeqProfile->nseqs)
+#endif
+ ) {
+ Log(&rLog, LOG_ERROR, "Couldn't convert profile1 to HMM. Will try to continue");
+ } else {
+ prHMMs = (hmm_light *) CKREALLOC(prHMMs, ((prOpts->iHMMInputFiles+1) * sizeof(hmm_light)));
+ memcpy(&(prHMMs[prOpts->iHMMInputFiles]), &rHMMLocal, sizeof(hmm_light));
+ prOpts->iHMMInputFiles++;
+ }
+ }
+
+
+ /* Now do a first alignment of the input sequences (prMSeq) adding
+ * all collected background HMMs
+ *
+ */
+ /* Determine progressive alignment order
+ */
+ if (TRUE == prMSeq->aligned) {
+ Log(&rLog, LOG_INFO, "%s %s",
+ "Input sequences are aligned.",
+ "Will use Kimura distances of aligned sequences.");
+ prOpts->iPairDistType = PAIRDIST_SQUIDID_KIMURA;
+ }
+
+#if 0
+ Log(&rLog, LOG_WARN, "Using a sequential alignment order.");
+ SequentialAlignmentOrder(&piOrderLR, prMSeq->nseqs);
+#else
+ if (OK != AlignmentOrder(&piOrderLR, &pdSeqWeights, prMSeq,
+ prOpts->iPairDistType,
+ prOpts->pcDistmatInfile, prOpts->pcDistmatOutfile,
+ prOpts->iClusteringType,
+ prOpts->pcGuidetreeInfile, prOpts->pcGuidetreeOutfile,
+ prOpts->bUseMbed)) {
+ Log(&rLog, LOG_ERROR, "AlignmentOrder() failed. Cannot continue");
+ return -1;
+ }
+#endif
+
+ /* Progressive alignment of input sequences. Order defined by
+ * branching of guide tree (piOrderLR). Use optional
+ * background HMM information (prHMMs[0..prOpts->iHMMInputFiles-1])
+ *
+ */
+ dAlnScore = HHalignWrapper(prMSeq, piOrderLR, pdSeqWeights,
+ 2*prMSeq->nseqs -1/* nodes */,
+ prHMMs, prOpts->iHMMInputFiles, -1, rHhalignPara);
+ dLastAlnScore = dAlnScore;
+ Log(&rLog, LOG_VERBOSE,
+ "Alignment score for first alignment = %f", dAlnScore);
+
+
+
+
+ /* ------------------------------------------------------------
+ *
+ * prMSeq is aligned now. Now start iterations if requested and save the
+ * alignment at the very end.
+ *
+ * @note We discard the background HMM information at this point,
+ * because it was already used. Could consider to make this choice
+ * optional. FIXME
+ *
+ * ------------------------------------------------------------ */
+
+
+ /* iteration after first alignment was computed (if not profile-profile
+ * alignment)
+ *
+ */
+ for (iIterationCounter=0;
+ (iIterationCounter < prOpts->iNumIterations || prOpts->bIterationsAuto);
+ iIterationCounter++) {
+
+ hmm_light rHMMLocal = {0};
+ /* FIXME Keep copy of old alignment in case new one sucks? */
+
+
+ if (iIterationCounter >= prOpts->iMaxHMMIterations
+ &&
+ iIterationCounter >= prOpts->iMaxGuidetreeIterations) {
+ Log(&rLog, LOG_VERBOSE, "Reached maximum number of HMM and guide-tree iterations");
+ break;
+ }
+
+ if (! prOpts->bIterationsAuto) {
+ Log(&rLog, LOG_INFO, "Iteration step %d out of %d",
+ iIterationCounter+1, prOpts->iNumIterations);
+ } else {
+ Log(&rLog, LOG_INFO, "Iteration step %d out of <auto>",
+ iIterationCounter+1);
+ }
+#if 0
+ if (rLog.iLogLevelEnabled <= LOG_VERBOSE) {
+ char zcIntermediate[1000] = {0};
+ char *pcFormat = "fasta";
+ sprintf(zcIntermediate, "clustalo-aln-iter~%d~", iIterationCounter);
+ if (WriteAlignment(prMSeq, zcIntermediate, MSAFILE_A2M)) {
+ Log(&rLog, LOG_ERROR, "Could not save alignment to %s", zcIntermediate);
+ return -1;
+ }
+ }
+#endif
+
+
+ /* new guide-tree
+ *
+ */
+ if (iIterationCounter < prOpts->iMaxGuidetreeIterations) {
+ /* determine progressive alignment order
+ *
+ * few things are different now when calling AlignmentOrder:
+ * - we have to ignore prOpts->pcDistmatInfile and pcGuidetreeInfile
+ * as they were used before
+ * - the corresponding outfiles are still valid though
+ */
+ /* Free stuff that has already been allocated by or further
+ * downstream of AlignmentOrder()
+ */
+ if (NULL != piOrderLR)
+ CKFREE(piOrderLR);
+ if (NULL != pdSeqWeights)
+ CKFREE(pdSeqWeights);
+ if (AlignmentOrder(&piOrderLR, &pdSeqWeights, prMSeq,
+ PAIRDIST_SQUIDID_KIMURA /* override */, NULL, prOpts->pcDistmatOutfile,
+ prOpts->iClusteringType, NULL, prOpts->pcGuidetreeOutfile,
+ prOpts->bUseMbedForIteration)) {
+ Log(&rLog, LOG_ERROR, "AlignmentOrder() failed. Cannot continue");
+ return -1;
+ }
+ } else {
+ Log(&rLog, LOG_INFO, "Skipping guide-tree iteration at iteration step %d (reached maximum)",
+ iIterationCounter);
+ }
+
+
+ /* new local hmm iteration
+ *
+ */
+ if (iIterationCounter < prOpts->iMaxHMMIterations) {
+ if (OK !=
+#if INDIRECT_HMM
+ AlnToHMM(&rHMMLocal, prMSeq)
+#else
+ AlnToHMM2(&rHMMLocal, prMSeq->seq, prMSeq->nseqs)
+#endif
+ ) {
+ Log(&rLog, LOG_ERROR, "Couldn't convert alignment to HMM. Will stop iterating now...");
+ break;
+ }
+ } else {
+ Log(&rLog, LOG_INFO, "Skipping HMM iteration at iteration step %d (reached maximum)",
+ iIterationCounter);
+ }
+
+
+ /* align the sequences (again)
+ */
+ dAlnScore = HHalignWrapper(prMSeq, piOrderLR, pdSeqWeights,
+ 2*prMSeq->nseqs -1/* nodes */, &rHMMLocal, 1, -1, rHhalignPara);
+ Log(&rLog, LOG_VERBOSE,
+ "Alignment score for alignmnent in hmm-iteration no %d = %f (last score = %f)",
+ iIterationCounter+1, dAlnScore, dLastAlnScore);
+
+
+ FreeHMMstruct(&rHMMLocal);
+
+#if 0
+ /* FIXME: need a better score for automatic iteration */
+ if (prOpts->bIterationsAuto) {
+ /* automatic iteration: break if score improvement was not
+ * big enough
+ */
+ double dScoreImprovement = (dAlnScore-dLastAlnScore)/dLastAlnScore;
+ if (dScoreImprovement < ITERATION_SCORE_IMPROVEMENT_THRESHOLD) {
+ Log(&rLog, LOG_INFO,
+ "Stopping after %d guide-tree iterations. No further alignment score improvement achieved.",
+ iIterationCounter+1);
+ /* use previous alignment */
+ FreeMSeq(&prMSeq);
+ Log(&rLog, LOG_FORCED_DEBUG, "FIXME: %s", "CopyMSeq breaks things in this context");
+ CopyMSeq(&prMSeq, prMSeqCopy);
+ /* FIXME: prOpts->pcDistmatOutfile and pcGuidetreeOutfile
+ * might have been updated, but then discarded here?
+ */
+ break;
+ } else {
+ Log(&rLog, LOG_INFO,
+ "Got a %d%% better score in iteration step %d",
+ (int)dScoreImprovement*100, iIterationCounter+1);
+ FreeMSeq(&prMSeqCopy);
+ }
+ }
+ dLastAlnScore = dAlnScore;
+#endif
+
+ }
+ /* end of iterations */
+
+
+
+ /* Last step: if a profile was also provided then align now-aligned mseq
+ * with this profile
+ *
+ * Don't use the backgrounds HMMs anymore and don't iterate.
+ * (which was done before).
+ *
+ */
+ if (NULL != prMSeqProfile) {
+ if (AlignProfiles(prMSeq, prMSeqProfile, rHhalignPara)) {
+ Log(&rLog, LOG_ERROR, "An error occured during the profile/profile alignment");
+ return -1;
+ }
+ }
+
+
+ if (NULL != piOrderLR) {
+ CKFREE(piOrderLR);
+ }
+ if (NULL != pdSeqWeights) {
+ CKFREE(pdSeqWeights);
+ }
+ if (0 < prOpts->iHMMInputFiles) {
+ for (i=0; i<prOpts->iHMMInputFiles; i++) {
+ FreeHMMstruct(&prHMMs[i]);
+ }
+ CKFREE(prHMMs);
+ }
+
+ return 0;
+}
+/* end of Align() */
+
+
+
+
+/**
+ * @brief Align two profiles, ie two sets of prealigned sequences. Already
+ * aligned columns won't be changed.
+ *
+ * @param[out] prMSeqProfile1
+ * First profile/aligned set of sequences. Merged alignment will be found in
+ * here.
+ * @param[in] prMSeqProfile2
+ * First profile/aligned set of sequences
+ *
+ * @return 0 on success, -1 on failure
+ *
+ */
+int
+AlignProfiles(mseq_t *prMSeqProfile1,
+ mseq_t *prMSeqProfile2, hhalign_para rHhalignPara) {
+
+ double dAlnScore;
+
+ /* number of seqs in first half of joined profile */
+ int iProfProfSeparator = prMSeqProfile1->nseqs;
+
+ assert(TRUE == prMSeqProfile1->aligned);
+ assert(TRUE == prMSeqProfile2->aligned);
+
+ Log(&rLog, LOG_INFO, "Performing profile/profile alignment");
+
+ /* Combine the available mseqs into prMSeq
+ * which will be aligned afterwards.
+ */
+ JoinMSeqs(&prMSeqProfile1, prMSeqProfile2);
+
+
+ /* set alignment flag explicitly to FALSE */
+ prMSeqProfile1->aligned = FALSE;
+
+ dAlnScore = HHalignWrapper(prMSeqProfile1,
+ NULL, /* no order */
+ NULL, /* no weights */
+ 3, /* nodes: root+2profiles */
+ NULL, 0 /* no bg-hmms */,
+ iProfProfSeparator, rHhalignPara);
+
+ Log(&rLog, LOG_VERBOSE, "Alignment score is = %f", dAlnScore);
+
+ return 0;
+}
+/* end of AlignProfiles() */
+
+
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: clustal-omega.h 212 2011-03-10 15:09:46Z andreas $
+ */
+
+#ifndef CLUSTALO_H
+#define CLUSTALO_H
+
+
+
+#ifdef HAVE_OPENMP
+#include <omp.h>
+#endif
+
+#include "clustal-omega-config.h"
+
+/* the following needs to be kept in sync with library_include_HEADERS of all
+ * subdir Makefile.am's
+ */
+
+/* hhalign */
+#include "hhalign/general.h"
+#include "hhalign/hhfunc.h"
+
+
+/* clustal */
+#include "clustal/log.h"
+#include "clustal/util.h"
+#include "clustal/symmatrix.h"
+#include "clustal/tree.h"
+#include "clustal/seq.h"
+#include "clustal/mbed.h"
+#include "clustal/weights.h"
+#include "clustal/pair_dist.h"
+#include "clustal/hhalign_wrapper.h"
+
+
+
+#define CLUSTERING_UNKNOWN 0
+#define CLUSTERING_UPGMA 1
+
+/* weights will be computed if 1. but are not really used for now and they
+ * might slow things down. also, mbed's screws up branch lengths which will
+ * have a negative effect on weights
+*/
+#define USE_WEIGHTS 0
+
+extern int iNumberOfThreads;
+
+
+/** user/commandline options
+ *
+ * changes here will have to be reflected in ParseCommandLine()
+ * and during setup of the default opts
+ *
+ */
+typedef struct {
+ /* auto: Clustal (know what) is good for you
+ */
+ bool bAutoOptions;
+
+ /* Distance matrix
+ */
+ /** distance matrix input file */
+ char *pcDistmatInfile;
+ /** distance matrix output file */
+ char *pcDistmatOutfile;
+
+ /* Clustering / guide-tree
+ */
+ /** clustering type (from cmdline arg) */
+ int iClusteringType;
+ /** pairwise distance method */
+ int iPairDistType;
+ /** use mbed-like clustering */
+ bool bUseMbed;
+ /** use mbed-like clustering also during iteration */
+ bool bUseMbedForIteration;
+ /** guidetree output file */
+ char *pcGuidetreeOutfile;
+ /** guidetree input file */
+ char *pcGuidetreeInfile;
+
+ /* HMMs
+ */
+ /** HMM input files. index range: 0..iHMMInputFiles */
+ char **ppcHMMInput;
+ /** number of provided HMM input files. not really a user
+ option but need for ppcHMMInput */
+ int iHMMInputFiles;
+
+ /* Iteration
+ */
+ /** number of iterations */
+ int iNumIterations;
+ /** determine number of iterations automatically */
+ bool bIterationsAuto;
+ /** maximum number of hmm iterations */
+ int iMaxHMMIterations;
+ /** max number of guidetree iterations */
+ int iMaxGuidetreeIterations;
+
+ /** max MAC RAM (maximum amount of RAM set aside for MAC algorithm) */
+ int iMacRam; /* FS, r240 -> */
+
+ /* changes here will have to be reflected in FreeAlnOpts(),
+ * SetDefaultAlnOpts(), AlnOptsLogicCheck() etc
+ */
+} opts_t;
+
+
+
+
+
+extern void
+PrintLongVersion(char *pcStr, int iSize);
+
+extern void
+SetDefaultAlnOpts(opts_t *opts);
+
+extern void
+FreeAlnOpts(opts_t *aln_opts);
+
+extern void
+AlnOptsLogicCheck(opts_t *opts);
+
+extern void
+PrintAlnOpts(FILE *prFile, opts_t *opts);
+
+extern void
+InitClustalOmega(int iNumThreadsToUse);
+
+extern void
+SequentialAlignmentOrder(int **piOrderLR_p, int iNumSeq);
+
+extern int
+AlignmentOrder(int **piOrderLR_p, double **pdSeqWeights_p, mseq_t *prMSeq,
+ int iPairDistType, char *pcDistmatInfile, char *pcDistmatOutfile,
+ int iClusteringType, char *pcGuidetreeInfile, char *pcGuidetreeOutfile,
+ bool bUseMBed);
+
+extern int
+Align(mseq_t *prMSeq,
+ mseq_t *prMSeqProfile,
+ opts_t *prOpts,
+ hhalign_para rHhalignPara);
+
+extern int
+AlignProfiles(mseq_t *prMSeqProfile1,
+ mseq_t *prMSeqProfile2, hhalign_para rHhalignPara);
+
+#endif
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+ test -n "$$unique" || unique=$$empty_fix; \
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+ fi
+ctags: CTAGS
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+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
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+ test -f $(distdir)/$$file \
+ || cp -p $$d/$$file $(distdir)/$$file \
+ || exit 1; \
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+ done
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+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
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+
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+
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+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
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+ distclean-compile distclean-generic distclean-libtool \
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+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhalign_wrapper.c 256 2011-06-23 13:57:28Z fabian $
+ */
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include <ctype.h>
+
+#include "seq.h"
+#include "tree.h"
+#include "progress.h"
+#include "hhalign/general.h"
+#include "hhalign/hhfunc.h"
+#include "hhalign/hhalign.h"
+
+/* up to this level (from leaf) will background HMM info be applied */
+#define APPLY_BG_HMM_UP_TO_TREE_DEPTH 10
+
+#define TIMING 0
+
+#define TRACE 0
+
+/**
+ * @brief get rid of unknown residues
+ *
+ * @note HHalignWrapper can be entered in 2 different ways: (i) all
+ * sequences are un-aligned (ii) there are 2 (aligned) profiles. in
+ * the un-aligned case (i) the sequences come straight from Squid,
+ * that is, they have been sanitised, all non-alphabetic residues
+ * have been rendered as X's. In profile mode (ii) one profile may
+ * have been produced internally. In that case residues may have
+ * been translated back into their 'native' form, that is, they may
+ * contain un-sanitised residues. These will cause trouble during
+ * alignment
+ * FS, r213->214
+ */
+void
+SanitiseUnknown(mseq_t *mseq)
+{
+
+ int iS; /* iterator for sequence */
+ int iR; /* iterator for residue */
+ int iLen; /* length of sequence */
+ char *pcRes = NULL;
+
+
+ for (iS = 0; iS < mseq->nseqs; iS++){
+
+ for (pcRes = mseq->seq[iS]; '\0' != *pcRes; pcRes++){
+
+ if (isgap(*pcRes)){
+ continue;
+ }
+
+ if (mseq->seqtype==SEQTYPE_PROTEIN) {
+ if (NULL == strchr(AMINO_ALPHABET, toupper(*pcRes))) {
+ *pcRes = AMINOACID_ANY;
+ }
+ } else if (mseq->seqtype==SEQTYPE_DNA) {
+ if (NULL == strchr(DNA_ALPHABET, toupper(*pcRes))) {
+ *pcRes = NUCLEOTIDE_ANY;
+ }
+ } else if (mseq->seqtype==SEQTYPE_RNA) {
+ if (NULL == strchr(RNA_ALPHABET, toupper(*pcRes))) {
+ *pcRes = NUCLEOTIDE_ANY;
+ }
+ }
+
+ } /* !EO String */
+
+ } /* 0 <= iS < mseq->nseqs */
+
+ return;
+
+} /*** end: SanitiseUnknown() ***/
+
+/**
+ * @brief translate unknown residues back to ambiguity codes;
+ * hhalign translates ambiguity codes (B,Z) into unknown residue (X).
+ * we still have the original (un-aligned) residue information,
+ * by iterating along the original and aligned sequences we can
+ * reconstruct where codes have been changed and restore them
+ * to their original value
+ *
+ * @param[in,out] mseq
+ * sequence/profile data, mseq->seq [in,out] is changed to conform
+ * with mseq->orig_seq [in]
+ *
+ */
+void
+TranslateUnknown2Ambiguity(mseq_t *mseq)
+{
+
+ int iS; /* iterator for sequence */
+ int iR, iRo; /* iterator for residue (original) */
+ int iChange, iCase, iAmbi; /* counts how many replacements */
+ static int siOffset = 'a' - 'A';
+
+ for (iS = 0; iS < mseq->nseqs; iS++){
+
+ iR = iRo = 0;
+ iChange = iCase = iAmbi = 0;
+
+ while(('\0' != mseq->seq[iS][iR]) &&
+ ('\0' != mseq->orig_seq[iS][iRo])) {
+
+ /* skip gaps in aligned sequences */
+ while(isgap(mseq->seq[iS][iR])) {
+ iR++;
+ } /* was gap in unaligned seq
+ * this should probably not happen */
+ while(isgap(mseq->orig_seq[iS][iRo])) {
+ iRo++;
+ } /* was gap in aligned seq */
+
+ /* check if we reached the end of the sequence after
+ * skipping the gaps */
+ if ( ('\0' == mseq->seq[iS][iR]) ||
+ ('\0' == mseq->orig_seq[iS][iRo]) ){
+ break;
+ }
+
+
+ if (mseq->seq[iS][iR] != mseq->orig_seq[iS][iRo]){
+ /* FIXME: count replacements, discard case changes */
+ iChange++;
+ if ( (mseq->seq[iS][iR] == mseq->orig_seq[iS][iRo]+siOffset) ||
+ (mseq->seq[iS][iR] == mseq->orig_seq[iS][iRo]-siOffset) ){
+ iCase++;
+ }
+ else {
+ iAmbi++;
+ }
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "seq=%d, pos=(%d:%d), (%c:%c)",
+ iS, iR, iRo,
+ mseq->seq[iS][iR], mseq->orig_seq[iS][iRo]);
+#endif
+ mseq->seq[iS][iR] = mseq->orig_seq[iS][iRo];
+ }
+
+ iR++;
+ iRo++;
+
+ } /* !EO seq */
+
+ Log(&rLog, LOG_DEBUG,
+ "in seq %d re-translated %d residue codes (%d true, %d case)",
+ iS, iChange, iAmbi, iCase);
+
+ /* assert that both sequences (un/aligned) have terminated */
+ /* skip gaps in aligned sequences */
+ while(isgap(mseq->seq[iS][iR])) {
+ iR++;
+ } /* was gap in unaligned seq
+ * this should probably not happen */
+ while(isgap(mseq->orig_seq[iS][iRo])) {
+ iRo++;
+ } /* was gap in aligned seq */
+
+
+ if ( ('\0' != mseq->seq[iS][iR]) ||
+ ('\0' != mseq->orig_seq[iS][iRo]) ){
+
+ Log(&rLog, LOG_FATAL, "inconsistency in un/aligned sequence %d\n>%s\n>%s\n",
+ iS, mseq->seq[iS], mseq->orig_seq[iS]);
+ }
+
+ } /* 0 <= iS < mseq->nseqs */
+
+} /*** end: TranslateUnknown2Ambiguity() ***/
+
+
+/**
+ * @brief re-attach leading and trailing gaps to alignment
+ *
+ * @param[in,out] prMSeq,
+ * alignment structure (at this stage there should be no un-aligned sequences)
+ * @param[in] iProfProfSeparator
+ * gives sizes of input profiles, -1 if no input-profiles but un-aligned sequences
+ *
+ * @note leading and tailing profile columns
+ * that only contain gaps have no effect on the alignment
+ * and are removed during the alignment. if they are
+ * encountered a warning message is printed to screen.
+ * some users like to preserve these gap columns
+ * FS, r213->214
+ */
+void
+ReAttachLeadingGaps(mseq_t *prMSeq, int iProfProfSeparator)
+{
+
+ int i, j;
+ int iSize1 = 0; /* #seqs in 1st profile */
+ int iSize2 = 0; /* #seqs in 2nd profile */
+ int iPPS = iProfProfSeparator;
+ int iLeadO1 = 0; /* leading gaps in 1st seq of 1st profile */
+ int iLeadO2 = 0; /* leading gaps in 1st seq of 2nd profile */
+ int iLeadA1 = 0; /* leading gaps in 1st seq of final alignment */
+ int iLeadA2 = 0; /* leading gaps in PPS seq of final alignment */
+ int iTrailO1 = 0; /* trailing gaps in 1st seq of 1st profile */
+ int iTrailO2 = 0; /* trailing gaps in 1st seq of 2nd profile */
+ int iTrailA1 = 0; /* trailing gaps in 1st seq of final alignment */
+ int iTrailA2 = 0; /* trailing gaps in PPS seq of final alignment */
+ int iLen = 0; /* length of final alignment */
+ int iLen1 = 0; /* length of 1st profile */
+ int iLen2 = 0; /* length of 2nd profile */
+ int iCutHead = 0; /* make up truncation at head */
+ int iCutTail = 0; /* make up truncation at tail */
+ char *pcIter = NULL;
+
+ if (-1 == iProfProfSeparator){
+ return;
+ }
+ else {
+ assert(prMSeq->aligned);
+ assert(prMSeq->nseqs > iProfProfSeparator);
+ }
+ iSize1 = iProfProfSeparator;
+ iSize2 = prMSeq->nseqs - iProfProfSeparator;
+ iLen = strlen(prMSeq->seq[0]);
+ iLen1 = strlen(prMSeq->orig_seq[0]);
+ iLen2 = strlen(prMSeq->orig_seq[iPPS]);
+
+ /* count leading/trailing gaps in 1st sequence of 1st/2nd profile and final alignmant */
+ for (iLeadO1 = 0, pcIter = prMSeq->orig_seq[0]; isgap(*pcIter); pcIter++, iLeadO1++);
+ for (iLeadO2 = 0, pcIter = prMSeq->orig_seq[iPPS]; isgap(*pcIter); pcIter++, iLeadO2++);
+ for (iLeadA1 = 0, pcIter = prMSeq->seq[0]; isgap(*pcIter); pcIter++, iLeadA1++);
+ for (iLeadA2 = 0, pcIter = prMSeq->seq[iPPS]; isgap(*pcIter); pcIter++, iLeadA2++);
+ for (iTrailO1 = 0, pcIter = &prMSeq->orig_seq[0][iLen1-1]; isgap(*pcIter); pcIter--, iTrailO1++);
+ for (iTrailO2 = 0, pcIter = &prMSeq->orig_seq[iPPS][iLen2-1]; isgap(*pcIter); pcIter--, iTrailO2++);
+ for (iTrailA1 = 0, pcIter = &prMSeq->seq[0][iLen-1]; isgap(*pcIter); pcIter--, iTrailA1++);
+ for (iTrailA2 = 0, pcIter = &prMSeq->seq[iPPS][iLen-1]; isgap(*pcIter); pcIter--, iTrailA2++);
+
+
+ /* turn leading/trailing gaps into truncation */
+ iLeadO1 = iLeadO1 > iLeadA1 ? iLeadO1-iLeadA1 : 0;
+ iLeadO2 = iLeadO2 > iLeadA2 ? iLeadO2-iLeadA2 : 0;
+ iTrailO1 = iTrailO1 > iTrailA1 ? iTrailO1-iTrailA1 : 0;
+ iTrailO2 = iTrailO2 > iTrailA2 ? iTrailO2-iTrailA2 : 0;
+ iCutHead = iLeadO1 > iLeadO2 ? iLeadO1 : iLeadO2;
+ iCutTail = iTrailO1 > iTrailO2 ? iTrailO1 : iTrailO2;
+
+ /* re-allocate and shift memory */
+ if ( (iCutHead > 0) || (iCutTail > 0) ){ /* skip if no re-attachment, FS, r244 -> r245 */
+ for (i = 0; i < prMSeq->nseqs; i++){
+
+ CKREALLOC(prMSeq->seq[i], iLen+iCutHead+iCutTail+2);
+ if (iCutHead > 0){ /* skip if no re-attachment, FS, r244 -> r245 */
+ memmove(prMSeq->seq[i]+iCutHead, prMSeq->seq[i], iLen);
+ }
+ for (j = 0; j < iCutHead; j++){
+ prMSeq->seq[i][j] = '-';
+ }
+ for (j = iLen+iCutHead; j < iLen+iCutHead+iCutTail; j++){
+ prMSeq->seq[i][j] = '-';
+ }
+ prMSeq->seq[i][j] = '\0';
+ }
+ } /* (iCutHead > 0) || (iCutTail > 0) */
+
+} /*** end: ReAttachLeadingGaps() ***/
+
+/**
+ * @brief reallocate enough memory for alignment and
+ * attach sequence pointers to profiles
+ *
+ * @param[in,out] mseq
+ * sequence/profile data, increase memory for sequences in profiles
+ * @param[out] ppcProfile1
+ * pointers to sequencese in 1st profile
+ * @param[out] ppcProfile2
+ * pointers to sequencese in 2nd profile
+ * @param[out] pdWeightsL
+ * weights (normalised to 1.0) for sequences in left profile
+ * @param[out] pdWeightsR
+ * weights (normalised to 1.0) for sequences in right profile
+ * @param[in] pdSeqWeights
+ * weights for _all_ sequences in alignment
+ * @param[in] iLeafCountL
+ * number of sequences in 1st profile
+ * @param[in] piLeafListL
+ * array of integer IDs of sequences in 1st profile
+ * @param[in] iLeafCountR
+ * number of sequences in 2nd profile
+ * @param[in] piLeafListR
+ * array of integer IDs of sequences in 2nd profile
+ *
+ */
+void
+PrepareAlignment(mseq_t *mseq, char **ppcProfile1, char **ppcProfile2,
+ double *pdWeightsL, double *pdWeightsR, double *pdSeqWeights,
+ int iLeafCountL, int *piLeafListL,
+ int iLeafCountR, int *piLeafListR)
+{
+
+ int iLenL = 0; /* length of 1st profile */
+ int iLenR = 0; /* length of 2nd profile */
+ int iMaxLen = 0; /* maximum possible length of alignment */
+ int i; /* aux */
+ double dWeight = 0.00;
+ double dWeightInv = 0.00;
+
+ assert(NULL!=mseq);
+ assert(NULL!=ppcProfile1);
+ assert(NULL!=ppcProfile2);
+ assert(NULL!=piLeafListL);
+ assert(NULL!=piLeafListR);
+
+ /* get length of profiles,
+ * in a profile all sequences should have same length so only look at 1st
+ */
+ iLenL = strlen(mseq->seq[piLeafListL[0]]);
+ iLenR = strlen(mseq->seq[piLeafListR[0]]);
+ iMaxLen = iLenL + iLenR + 1;
+
+ /* reallocate enough memory for sequences in alignment (for adding
+ * gaps)
+ */
+ for (i = 0; i < iLeafCountL; i++){
+ mseq->seq[piLeafListL[i]] =
+ CKREALLOC(mseq->seq[piLeafListL[i]], iMaxLen);
+ }
+ for (i = 0; i < iLeafCountR; i++){
+ mseq->seq[piLeafListR[i]] =
+ CKREALLOC(mseq->seq[piLeafListR[i]], iMaxLen);
+ }
+
+ /* attach sequences to profiles
+ */
+ for (i = 0; i < iLeafCountL; i++){
+ ppcProfile1[i] = mseq->seq[piLeafListL[i]];
+ }
+ ppcProfile1[i] = NULL;
+
+ for (i = 0; i < iLeafCountR; i++){
+ ppcProfile2[i] = mseq->seq[piLeafListR[i]];
+ }
+ ppcProfile2[i] = NULL;
+
+
+ /* remove terminal 'X' for single sequences:
+ * it is a quirk of hhalign() to delete 2 individual sequences
+ * if 2 terminal X's meet during alignment,
+ * just replace (one of) them.
+ * this can be undone at the end.
+ * profiles -consisting of more than 1 sequence-
+ * appear to be all-right.
+ * there seems to be no problem with B's and Z's
+ */
+ if ( (1 == iLeafCountL) && (1 == iLeafCountR) ){
+
+ if ( ('X' == ppcProfile1[0][0]) && ('X' == ppcProfile2[0][0]) ){
+#define NOTX 'N'
+ ppcProfile1[0][0] = NOTX; /* FIXME: arbitrary assignment */
+ ppcProfile2[0][0] = NOTX; /* FIXME: arbitrary assignment */
+ }
+ if ( ('X' == ppcProfile1[0][iLenL-1]) && ('X' == ppcProfile2[0][iLenR-1]) ){
+ ppcProfile1[0][iLenL-1] = NOTX; /* FIXME: arbitrary assignment */
+ ppcProfile2[0][iLenR-1] = NOTX; /* FIXME: arbitrary assignment */
+ }
+ }
+
+ /* obtain sequence weights
+ */
+ if (NULL != pdSeqWeights){
+
+ dWeight = 0.00;
+ for (i = 0; i < iLeafCountL; i++){
+ register double dAux = pdSeqWeights[piLeafListL[i]];
+#ifndef NDEBUG
+ if (dAux <= 0.00){
+ Log(&rLog, LOG_DEBUG, "seq-weight %d = %f", piLeafListL[i], dAux);
+ }
+#endif
+ pdWeightsL[i] = dAux;
+ dWeight += dAux;
+ } /* 0 <= i < iLeafCountL */
+ dWeightInv = 1.00 / dWeight;
+ for (i = 0; i < iLeafCountL; i++){
+ pdWeightsL[i] *= dWeightInv;
+ }
+
+ dWeight = 0.00;
+ for (i = 0; i < iLeafCountR; i++){
+ register double dAux = pdSeqWeights[piLeafListR[i]];
+#ifndef NDEBUG
+ if (dAux <= 0.00){
+ Log(&rLog, LOG_DEBUG, "seq-weight %d = %f", piLeafListR[i], dAux);
+ }
+#endif
+ pdWeightsR[i] = dAux;
+ dWeight += dAux;
+ } /* 0 <= i < iLeafCountL */
+ dWeightInv = 1.00 / dWeight;
+ for (i = 0; i < iLeafCountR; i++){
+ pdWeightsR[i] *= dWeightInv;
+ }
+ } /* (NULL != pdSeqWeights) */
+ else {
+ pdWeightsL[0] = pdWeightsR[0] = -1.00;
+ }
+
+#if TRACE
+ for (i = 0; i < iLeafCountL; i++){
+ Log(&rLog, LOG_FORCED_DEBUG, "ppcProfile1[%d/%d] pointing to mseq %d = %s",
+ i, iLeafCountR, piLeafListL[i], ppcProfile1[i]);
+ }
+ for (i = 0; i < iLeafCountR; i++){
+ Log(&rLog, LOG_FORCED_DEBUG, "ppcProfile2[%d/%d] pointing to mseq %d = %s",
+ i, iLeafCountR, piLeafListR[i], ppcProfile2[i]);
+ }
+#endif
+
+ return;
+
+} /*** end: PrepareAlignment() ***/
+
+
+/**
+ * @brief wrapper for hhalign. This is a frontend function to
+ * the ported hhalign code.
+ *
+ * @param[in,out] prMSeq
+ * holds the unaligned sequences [in] and the final alignment [out]
+ * @param[in] piOrderLR
+ * holds order in which sequences/profiles are to be aligned,
+ * even elements specify left nodes, odd elements right nodes,
+ * if even and odd are same then it is a leaf
+ * @param[in] pdSeqWeights
+ * Weight per sequence. No weights used if NULL
+ * @param[in] iNodeCount
+ * number of nodes in tree, piOrderLR has 2*iNodeCount elements
+ * @param[in] prHMMList
+ * List of background HMMs (transition/emission probabilities)
+ * @param[in] iHMMCount
+ * Number of input background HMMs
+ * @param[in] iProfProfSeparator
+ * Gives the number of sequences in the first profile, if in
+ * profile/profile alignment mode (iNodeCount==3). That assumes mseqs
+ * holds the sequences of profile 1 and profile 2.
+ * @param[in] rHhalignPara
+ * various parameters read from commandline
+ *
+ * @return score of the alignment FIXME what is this?
+ *
+ * @note complex function. could use some simplification, more and
+ * documentation and a struct'uring of piOrderLR
+ *
+ * @note HHalignWrapper can be entered in 2 different ways:
+ * (i) all sequences are un-aligned (ii) there are 2 (aligned) profiles.
+ * in the un-aligned case (i) the sequences come straight from Squid,
+ * that is, they have been sanitised, all non-alphabetic residues
+ * have been rendered as X's. In profile mode (ii) one profile may
+ * have been produced internally. In that case residues may have
+ * been translated back into their 'native' form, that is, they
+ * may contain un-sanitised residues. These will cause trouble
+ * during alignment
+ *
+ * @note: introduced argument hhalign_para rHhalignPara; FS, r240 -> r241
+ * @note: if hhalign() fails then try with Viterbi by setting MAC-RAM=0; FS, r241 -> r243
+ */
+
+double
+HHalignWrapper(mseq_t *prMSeq, int *piOrderLR,
+ double *pdSeqWeights, int iNodeCount,
+ hmm_light *prHMMList, int iHMMCount,
+ int iProfProfSeparator, hhalign_para rHhalignPara)
+{
+ int iN; /* node iterator */
+ int *piLeafCount = NULL; /* number of leaves beneath a certain node */
+ int **ppiLeafList = NULL; /* list of leaves beneath a certain node */
+ char **ppcProfile1 = NULL; /* pointer to sequences in profile */
+ char **ppcProfile2 = NULL; /* pointer to sequences in profile */
+ char *pcReprsnt1 = NULL; /* representative of HMM aligned to left */
+ char *pcReprsnt2 = NULL; /* representative of HMM aligned to right */
+ char **ppcReprsnt1 = &pcReprsnt1; /* representative of HMM aligned to L */
+ char **ppcReprsnt2 = &pcReprsnt2; /* representative of HMM aligned to R */
+ char *pcConsens1 = NULL; /* copy of left sequence */
+ char *pcConsens2 = NULL; /* copy of right sequence */
+ char **ppcCopy1 = /*&pcCopy1*/NULL; /* copy of left sequences */
+ char **ppcCopy2 = /*&pcCopy2*/NULL; /* copy of right sequences */
+ double *pdScores = NULL; /* alignment scores (seq/HMM) */
+ double dScore = 0.0; /* alignment score (seq/HMM) */
+ int iAux_FS = 0;
+ char zcAux[10000] = {0};
+ char zcError[10000] = {0};
+ int i; /* aux */
+ progress_t *prProgress;
+ int iAlnLen; /* alignment length */
+ double *pdWeightsL = NULL; /* sequence weights of left profile */
+ double *pdWeightsR = NULL; /* sequence weights of right profile */
+ int iMergeNodeCounter = 0;
+ hmm_light *prHMM = NULL;
+ bool bPrintCR = (rLog.iLogLevelEnabled<=LOG_VERBOSE) ? FALSE : TRUE;
+#if TIMING
+ char zcStopwatchMsg[1024];
+ Stopwatch_t *stopwatch = StopwatchCreate();
+ StopwatchZero(stopwatch);
+ StopwatchStart(stopwatch);
+#endif
+
+
+ if (NULL != prHMMList) {
+ if (iHMMCount>1) {
+ Log(&rLog, LOG_WARN, "FIXME: Using only first of %u HMMs (needs implementation)", iHMMCount);
+ }
+ prHMM = &(prHMMList[0]);
+ } else {
+ /* FIXME: prHMM not allowed to be NULL and therefore pseudo allocated here */
+ prHMM = (hmm_light *) CKCALLOC(1, sizeof(hmm_light));
+ }
+
+ assert(NULL!=prMSeq);
+
+ if (NULL==piOrderLR) {
+ assert(3==iNodeCount);
+ }
+ SanitiseUnknown(prMSeq);
+
+ /* hhalign was not made for DNA/RNA. So warn if sequences are not
+ * protein
+ */
+ if (SEQTYPE_PROTEIN != prMSeq->seqtype) {
+ Log(&rLog, LOG_WARN, "Sequence type is %s. HHalign has only been tested on protein.",
+ SeqTypeToStr(prMSeq->seqtype));
+ }
+
+ /* hhalign produces funny results if sequences contain gaps, so
+ * dealign. Only way to use alignment info is to use it as a
+ * background HMM
+ */
+ if (TRUE == prMSeq->aligned) {
+ Log(&rLog, LOG_DEBUG, "Dealigning aligned sequences (inside %s)", __FUNCTION__);
+ DealignMSeq(prMSeq);
+ }
+
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "iNodeCount = %d", iNodeCount);
+#endif
+
+
+ /* allocate top-level memory for leaf tracking arrays and profiles,
+ * and sequence weights*/
+ piLeafCount = CKCALLOC(iNodeCount, sizeof(int));
+ ppiLeafList = CKCALLOC(iNodeCount, sizeof(int *));
+ ppcProfile1 = CKCALLOC(prMSeq->nseqs*2-1, sizeof(char *));
+ ppcProfile2 = CKCALLOC(prMSeq->nseqs*2-1, sizeof(char *));
+ pdScores = CKCALLOC(iNodeCount, sizeof(double));
+ pdWeightsL = CKCALLOC(iNodeCount, sizeof(double));
+ pdWeightsR = CKCALLOC(iNodeCount, sizeof(double));
+
+ NewProgress(&prProgress, LogGetFP(&rLog, LOG_INFO),
+ "Progressive alignment progress", bPrintCR);
+
+
+ /* Profile-profile alignment? Then setup piLeafCount and
+ * piLeafList here. FIXME this is just an awful haaaack
+ */
+ if (iNodeCount==3 && NULL==piOrderLR) {
+ int iSizeProf1 = iProfProfSeparator;
+ int iSizeProf2 = prMSeq->nseqs - iProfProfSeparator;
+
+ piLeafCount[0] = iSizeProf1;
+ ppiLeafList[0] = (int *)CKMALLOC(iSizeProf1 * sizeof(int));
+ for (i=0;i<iSizeProf1;i++) {
+ ppiLeafList[0][i] = i;
+ }
+ piLeafCount[1] = iSizeProf2;
+ ppiLeafList[1] = (int *)CKMALLOC(iSizeProf2 * sizeof(int));
+ for (i=0;i<iSizeProf2;i++) {
+ ppiLeafList[1][i] = i+iSizeProf1;
+ }
+
+ /* awful hack inside an awful hack: we had to setup piLeafCount
+ * and piLeafList outside the node iteration. this which is
+ * normally done at leaf level inside the node iteration. to
+ * avoid overwriting the already setup vars set...
+ */
+ iNodeCount=1;
+
+ piOrderLR = (int *)CKCALLOC(DIFF_NODE, sizeof(int));
+ piOrderLR[LEFT_NODE] = 0;
+ piOrderLR[RGHT_NODE] = 1;
+ piOrderLR[PRNT_NODE] = 2;
+ }
+
+
+
+ iMergeNodeCounter = 0;
+ for (iN = 0; iN < iNodeCount; iN++){
+
+ register int riAux = DIFF_NODE * iN;
+
+ /*LOG_DEBUG("node %d ", iN);*/
+
+ if (piOrderLR[riAux+LEFT_NODE] == piOrderLR[riAux+RGHT_NODE]){
+
+ register int riLeaf = piOrderLR[riAux+LEFT_NODE];
+#if TRACE
+ if (NULL == pdSeqWeights) {
+ Log(&rLog, LOG_FORCED_DEBUG, "node %d is a leaf with entry %d (seq %s)",
+ iN, riLeaf, prMSeq->sqinfo[riLeaf].name);
+ } else {
+ Log(&rLog, LOG_FORCED_DEBUG, "node %d is a leaf with entry %d (seq %s) and weight %f",
+ iN, riLeaf, prMSeq->sqinfo[riLeaf].name, pdSeqWeights[riLeaf]);
+ }
+#endif
+ /* left/right entry same, this is a leaf */
+ piLeafCount[piOrderLR[riAux+PRNT_NODE]] = 1; /* number of leaves is '1' */
+ ppiLeafList[piOrderLR[riAux+PRNT_NODE]] = (int *)CKMALLOC(1 * sizeof(int));
+ ppiLeafList[piOrderLR[riAux+PRNT_NODE]][0] = riLeaf;
+
+ } /* was a leaf */
+ else {
+ int iL, iR, iP; /* ID of left/right nodes, parent */
+ int i, j; /* aux */
+
+ Log(&rLog, LOG_DEBUG,
+ "merge profiles at node %d", iN, piOrderLR[riAux]);
+
+ /* iNodeCount - prMSeq->nseqs = total # of merge-nodes
+ * unless in profile/profile alignment mode
+ */
+ if (1 == iNodeCount) {
+ ProgressLog(prProgress, ++iMergeNodeCounter,
+ 1, FALSE);
+ } else {
+ ProgressLog(prProgress, ++iMergeNodeCounter,
+ iNodeCount - prMSeq->nseqs, FALSE);
+ }
+
+ /* left/right entry are not same, this is a merge node */
+ iL = piOrderLR[riAux+LEFT_NODE];
+ iR = piOrderLR[riAux+RGHT_NODE];
+ iP = piOrderLR[riAux+PRNT_NODE];
+ piLeafCount[iP] = piLeafCount[iL] + piLeafCount[iR];
+ ppiLeafList[iP] = (int *)CKMALLOC(piLeafCount[iP] * sizeof(int));
+
+ for (i = j = 0; i < piLeafCount[iL]; i++, j++){
+ ppiLeafList[iP][j] = ppiLeafList[iL][i];
+ }
+ for (i = 0; i < piLeafCount[iR]; i++, j++){
+ ppiLeafList[iP][j] = ppiLeafList[iR][i];
+ }
+
+ /* prepare simulation arena:
+ * - make sure enough memory in sequences
+ * - attach sequence pointers to profiles
+ */
+ /* idea: switch template and query according to nseq? */
+
+ PrepareAlignment(prMSeq, ppcProfile1, ppcProfile2,
+ pdWeightsL, pdWeightsR, pdSeqWeights,
+ piLeafCount[iL], ppiLeafList[iL],
+ piLeafCount[iR], ppiLeafList[iR]);
+ if (rLog.iLogLevelEnabled <= LOG_DEBUG){
+ int i;
+ FILE *fp = LogGetFP(&rLog, LOG_DEBUG);
+ Log(&rLog, LOG_DEBUG, "merging profiles %d & %d", iL, iR);
+ for (i = 0; i < piLeafCount[iL]; i++){
+ fprintf(fp, "L/#=%3d (ID=%3d, w=%f): %s\n",
+ i, ppiLeafList[iL][i], pdWeightsL[i], ppcProfile1[i]);
+ }
+ for (i = 0; i < piLeafCount[iR]; i++){
+ fprintf(fp, "R/#=%3d (ID=%3d, w=%f): %s\n",
+ i, ppiLeafList[iR][i], pdWeightsR[i], ppcProfile2[i]);
+ }
+ }
+
+
+
+ /* align individual sequences to HMM;
+ * - use representative sequence to get gapping
+ * - create copies of both, individual/representative sequences
+ * as we don't want to introduce gaps into original
+ *
+ * FIXME: representative sequence is crutch, should use
+ * full HMM but that does not seem to work at all
+ * -- try harder! Fail better!
+ */
+ if ( (piLeafCount[iL] <= APPLY_BG_HMM_UP_TO_TREE_DEPTH) && (0 != prHMM->L) ){
+ int i, j;
+ pcReprsnt1 = CKCALLOC(prHMM->L+strlen(ppcProfile1[0])+1, sizeof(char));
+ for (i = 0; i < prHMM->L; i++){
+ pcReprsnt1[i] = prHMM->seq[prHMM->ncons][i+1];
+ }
+ ppcCopy1 = CKCALLOC(piLeafCount[iL], sizeof(char *));
+ for (j = 0; j < piLeafCount[iL]; j++){
+ ppcCopy1[j] = CKCALLOC(prHMM->L+strlen(ppcProfile1[0])+1, sizeof(char));
+ for (i = 0; i < (int) strlen(ppcProfile1[0]); i++){
+ ppcCopy1[j][i] = ppcProfile1[j][i];
+ }
+ }
+
+ {
+ /* the size of the elements in the forward/backward matrices
+ depends very much on the lengths of the profiles _and_
+ in which position (1st/2nd) the longer/shorter profile/HMM is.
+ the matrix elements can easily exceed the size of a (long?) double
+ if the longer profile/HMM is associated with the query (q) and the
+ shorter with the target (t).
+ FIXME: however, pseudo-count adding may also depend on position,
+ this is only really tested for the HMM being in the 1st position (q)
+ MUST TEST THIS MORE THOROUGHLY
+
+ this switch appears to be most easily (although unelegantly)
+ effected here. Don't want to do it (upstairs) in PrepareAlignment()
+ because it might jumble up the nodes. Don't want to do it in hhalign()
+ either because ppcProfile1/2 and q/t may be used independently.
+ FS, r236 -> r237
+ */
+ int iLenA = strlen(ppcCopy1[0]);
+ int iLenH = prHMM->L;
+ int iHHret = 0;
+
+ if (iLenH < iLenA){
+ iHHret = hhalign(ppcReprsnt1, 0/* only one representative seq*/, NULL,
+ ppcCopy1, piLeafCount[iL], pdWeightsL,
+ &dScore, prHMM,
+ NULL, NULL, NULL, NULL,
+ rHhalignPara,
+ iAux_FS++, /* DEBUG ARGUMENT */
+ zcAux, zcError);
+ }
+ else {
+ iHHret = hhalign(ppcCopy1, piLeafCount[iL], pdWeightsL,
+ ppcReprsnt1, 0/* only one representative seq*/, NULL,
+ &dScore, prHMM,
+ NULL, NULL, NULL, NULL,
+ rHhalignPara,
+ iAux_FS++, /* DEBUG ARGUMENT */
+ zcAux, zcError);
+ }
+ if (0 != iHHret){ /* FS, r255 -> */
+ fprintf(stderr, "%s:%s:%d: (not essential) HMM pre-alignment failed, error %d, \n"
+ "\t#=%d (len=%d), lead-seq=%s, len(HMM)=%d\tCARRY ON REGARDLESS\n",
+ __FUNCTION__, __FILE__, __LINE__, iHHret,
+ piLeafCount[iL], (int)strlen(ppcCopy1[0]), prMSeq->sqinfo[ppiLeafList[iL][0]].name, (int)strlen(ppcReprsnt1[0]));
+ }
+ }
+ pdScores[ppiLeafList[iL][0]] = dScore;
+#if 0
+ printf("score: %f\nL: %s\nH: %s\n",
+ dScore, ppcCopy1[0], ppcReprsnt1[0]);
+#endif
+ /* assemble 'consensus';
+ * this is not a real consensus, it is more a gap indicator,
+ * for each position it consists of residues/gaps in the 1st sequences,
+ * or a residue (if any) of the other sequences.
+ * it only contains a gap if all sequences of the profile
+ * have a gap at this position
+ */
+ pcConsens1 = CKCALLOC(prHMM->L+strlen(ppcProfile1[0])+1, sizeof(char));
+ for (i = 0; i < prHMM->L; i++){
+ for (j = 0, pcConsens1[i] = '-'; (j < piLeafCount[iL]) && ('-' == pcConsens1[i]); j++){
+ pcConsens1[i] = ppcCopy1[j][i];
+ }
+ }
+#if 0
+ for (j = 0; (j < piLeafCount[iL]); j++){
+ printf("L%d:%s\n", j, ppcCopy1[j]);
+ }
+ printf("LC:%s\n", pcConsens1);
+#endif
+ } /* ( (1 == piLeafCount[iL]) && (0 != prHMM->L) ) */
+
+ if ( (piLeafCount[iR] <= APPLY_BG_HMM_UP_TO_TREE_DEPTH) && (0 != prHMM->L) ){
+ int i, j;
+
+ pcReprsnt2 = CKCALLOC(prHMM->L+strlen(ppcProfile2[0])+1, sizeof(char));
+ for (i = 0; i < prHMM->L; i++){
+ pcReprsnt2[i] = prHMM->seq[prHMM->ncons][i+1];
+ }
+ ppcCopy2 = CKCALLOC(piLeafCount[iR], sizeof(char *));
+ for (j = 0; j < piLeafCount[iR]; j++){
+ ppcCopy2[j] = CKCALLOC(prHMM->L+strlen(ppcProfile2[0])+1, sizeof(char));
+ for (i = 0; i < (int) strlen(ppcProfile2[0]); i++){
+ ppcCopy2[j][i] = ppcProfile2[j][i];
+ }
+ }
+
+ {
+ /* the size of the elements in the forward/backward matrices
+ depends very much on the lengths of the profiles _and_
+ in which position (1st/2nd) the longer/shorter profile/HMM is.
+ the matrix elements can easily exceed the size of a (long?) double
+ if the longer profile/HMM is associated with the query (q) and the
+ shorter with the target (t).
+ FIXME: however, pseudo-count adding may also depend on position,
+ this is only really tested for the HMM being in the 1st position (q)
+ MUST TEST THIS MORE THOROUGHLY
+
+ this switch appears to be most easily (although unelegantly)
+ effected here. Don't want to do it (upstairs) in PrepareAlignment()
+ because it might jumble up the nodes. Don't want to do it in hhalign()
+ either because ppcProfile1/2 and q/t may be used independently.
+ FS, r236 -> r237
+ */
+ int iLenA = strlen(ppcCopy2[0]);
+ int iLenH = prHMM->L;
+ int iHHret = 0;
+
+ if (iLenH < iLenA){
+ iHHret = hhalign(ppcReprsnt2, 0/* only one representative seq */, NULL,
+ ppcCopy2, piLeafCount[iR], pdWeightsR,
+ &dScore, prHMM,
+ NULL, NULL, NULL, NULL,
+ rHhalignPara,
+ iAux_FS++, /* DEBUG ARGUMENT */
+ zcAux, zcError);
+ }
+ else {
+ iHHret = hhalign(ppcCopy2, piLeafCount[iR], pdWeightsR,
+ ppcReprsnt2, 0/* only one representative seq */, NULL,
+ &dScore, prHMM,
+ NULL, NULL, NULL, NULL,
+ rHhalignPara,
+ iAux_FS++, /* DEBUG ARGUMENT */
+ zcAux, zcError);
+ }
+ if (0 != iHHret){ /* FS, r255 -> */
+ fprintf(stderr, "%s:%s:%d: (not essential) HMM pre-alignment failed, error %d, \n"
+ "\t#=%d (len=%d), lead-seq=%s, len(HMM)=%d\tCARRY ON REGARDLESS\n",
+ __FUNCTION__, __FILE__, __LINE__, iHHret,
+ piLeafCount[iR], (int)strlen(ppcCopy2[0]), prMSeq->sqinfo[ppiLeafList[iR][0]].name, (int)strlen(ppcReprsnt2[0]));
+ }
+ }
+ pdScores[ppiLeafList[iR][0]] = dScore;
+#if 0
+ printf("H: %s\nR: %s\nscore: %f\n",
+ ppcReprsnt2[0], ppcCopy2[0], dScore);
+#endif
+ /* assemble 'consensus';
+ * this is not a real consensus, it is more a gap indicator,
+ * for each position it consists of residues/gaps in the 1st sequences,
+ * or a residue (if any) of the other sequences.
+ * it only contains a gap if all sequences of the profile
+ * have a gap at this position
+ */
+ pcConsens2 = CKCALLOC(prHMM->L+strlen(ppcProfile2[0])+1, sizeof(char));
+ for (i = 0; i < prHMM->L; i++){
+ for (j = 0, pcConsens2[i] = '-'; (j < piLeafCount[iR]) && ('-' == pcConsens2[i]); j++){
+ pcConsens2[i] = ppcCopy2[j][i];
+ }
+ }
+#if 0
+ for (j = 0; (j < piLeafCount[iR]); j++){
+ printf("R%d:%s\n", j, ppcCopy2[j]);
+ }
+ printf("RC:%s\n", pcConsens2);
+#endif
+ } /* ( (1 == piLeafCount[iR]) && (0 != prHMM->L) ) */
+
+
+
+ /* do alignment here (before free)
+ */
+ {
+ /* the size of the elements in the forward/backward matrices
+ depends very much on the lengths of the profiles _and_
+ in which position (1st/2nd) the longer/shorter profile is.
+ the matrix elements can easily exceed the size of a (long?) double
+ if the longer profile is associated with the query (q) and the
+ shorter with the target (t).
+ this switch appears to be most easily (although unelegantly)
+ effected here. Don't want to do it (upstairs) in PrepareAlignment()
+ because it might jumble up the nodes. Don't want to do it in hhalign()
+ either because ppcProfile1/2 and q/t may be used independently.
+ FS, r228 -> 229
+ */
+ int iLen1 = strlen(ppcProfile1[0]);
+ int iLen2 = strlen(ppcProfile2[0]);
+ /* potential problem with empty profiles, FS, r249 -> r250 */
+ if ( (0 == iLen1) || (0 == iLen2) ){
+ Log(&rLog, LOG_FATAL, "strlen(prof1)=%d, strlen(prof2)=%d -- nothing to align\n",
+ iLen1, iLen2);
+ }
+
+
+ if (iLen1 < iLen2){
+ int iHHret = 0;
+ int iOldMacRam = rHhalignPara.iMacRamMB;
+ iHHret = hhalign(ppcProfile1, piLeafCount[iL], pdWeightsL,
+ ppcProfile2, piLeafCount[iR], pdWeightsR,
+ &dScore, prHMM,
+ pcConsens1, pcReprsnt1,
+ pcConsens2, pcReprsnt2,
+ rHhalignPara,
+ iAux_FS++, /* DEBUG ARGUMENT */
+ zcAux, zcError);
+
+ if (RETURN_OK != iHHret){ /* FS, r241 -> */
+ fprintf(stderr,
+ "%s:%s:%d: problem in alignment (profile sizes: %d + %d) (%s + %s), forcing Viterbi\n"
+ "\thh-error-code=%d (mac-ram=%d)\n",
+ __FUNCTION__, __FILE__, __LINE__, piLeafCount[iL], piLeafCount[iR],
+ prMSeq->sqinfo[ppiLeafList[iL][0]].name, prMSeq->sqinfo[ppiLeafList[iR][0]].name,
+ iHHret, rHhalignPara.iMacRamMB);
+ /* at this stage hhalign() has failed,
+ the only thing we can do (easily) is to re-run it in Viterbi mode,
+ for this set MAC-RAM=0, set it back to its original value after 2nd try.
+ FS, r241 -> r243 */
+ if (RETURN_FROM_MAC == iHHret){
+ /* Note: the default way to run hhalign() is to initially select MAC
+ by giving it all the memory it needs. MAC may fail due to overflow (repeats?).
+ alternatively, the problem may be (genuinely) too big for MAC.
+ in thses cases it is legitimate to switch to Viterbi.
+ However, selecting Viterbi from the outset is an abuse (abomination!),
+ should this 1st invocation of Viterbi fail, then we (FS) will overrule
+ the user and hammer the system with a massive memory request.
+ (Jos 2:19) If anyone goes outside your house into the street,
+ his blood will be on his own head; we will not be responsible. FS, r246 -> r247 */
+ rHhalignPara.iMacRamMB = 0;
+ }
+ else {
+ rHhalignPara.iMacRamMB = REALLY_BIG_MEMORY_MB;
+ }
+
+ iHHret = hhalign(ppcProfile1, piLeafCount[iL], pdWeightsL,
+ ppcProfile2, piLeafCount[iR], pdWeightsR,
+ &dScore, prHMM,
+ pcConsens1, pcReprsnt1,
+ pcConsens2, pcReprsnt2,
+ rHhalignPara,
+ iAux_FS++, /* DEBUG ARGUMENT */
+ zcAux, zcError);
+ if (RETURN_OK != iHHret){ /* at this stage hhalign() has failed twice,
+ 1st time MAC, 2nd time Viterbi, don't know what to do else. FS, r241 -> r243 */
+ fprintf(stderr, "%s:%s:%d: problem in alignment, even Viterbi did not work\n"
+ "\thh-error-code=%d (mac-ram=%d)\n",
+ __FUNCTION__, __FILE__, __LINE__, iHHret, rHhalignPara.iMacRamMB);
+ Log(&rLog, LOG_FATAL, "could not perform alignment -- bailing out\n");
+ }
+ else {
+ fprintf(stderr, "%s:%s:%d: 2nd attempt worked", __FUNCTION__, __FILE__, __LINE__);
+ }
+ rHhalignPara.iMacRamMB = iOldMacRam;
+ } /* 1st invocation failed */
+
+ } /* 1st profile was shorter than 2nd */
+ else {
+ int iHHret = 0;
+ int iOldMacRam = rHhalignPara.iMacRamMB;
+ iHHret = hhalign(ppcProfile2, piLeafCount[iR], pdWeightsR,
+ ppcProfile1, piLeafCount[iL], pdWeightsL,
+ &dScore, prHMM,
+ pcConsens2, pcReprsnt2,
+ pcConsens1, pcReprsnt1,
+ rHhalignPara,
+ iAux_FS++, /* DEBUG ARGUMENT */
+ zcAux, zcError);
+
+ if (RETURN_OK != iHHret){ /* FS, r241 -> r243 */
+ fprintf(stderr,
+ "%s:%s:%d: problem in alignment (profile sizes: %d + %d) (%s + %s), forcing Viterbi\n"
+ "\thh-error-code=%d (mac-ram=%d)\n",
+ __FUNCTION__, __FILE__, __LINE__, piLeafCount[iL], piLeafCount[iR],
+ prMSeq->sqinfo[ppiLeafList[iL][0]].name, prMSeq->sqinfo[ppiLeafList[iR][0]].name,
+ iHHret, rHhalignPara.iMacRamMB);
+ /* at this stage hhalign() has failed,
+ the only thing we can do (easily) is to re-run it in Viterbi mode,
+ for this set MAC-RAM=0, set it back to its original value after 2nd try.
+ FS, r241 -> r243 */
+ if (RETURN_FROM_MAC == iHHret){
+ /* see above */
+ rHhalignPara.iMacRamMB = 0;
+ }
+ else {
+ rHhalignPara.iMacRamMB = REALLY_BIG_MEMORY_MB;
+ }
+
+ iHHret = hhalign(ppcProfile2, piLeafCount[iR], pdWeightsR,
+ ppcProfile1, piLeafCount[iL], pdWeightsL,
+ &dScore, prHMM,
+ pcConsens2, pcReprsnt2,
+ pcConsens1, pcReprsnt1,
+ rHhalignPara,
+ iAux_FS++, /* DEBUG ARGUMENT */
+ zcAux, zcError);
+ if (RETURN_OK != iHHret){ /* at this stage hhalign() has failed twice,
+ 1st time MAC, 2nd time Viterbi, don't know what to do else. FS, r241 -> r243 */
+ fprintf(stderr, "%s:%s:%d: problem in alignment, even Viterbi did not work\n"
+ "\thh-error-code=%d (mac-ram=%d)\n",
+ __FUNCTION__, __FILE__, __LINE__, iHHret, rHhalignPara.iMacRamMB);
+ Log(&rLog, LOG_FATAL, "could not perform alignment -- bailing out\n");
+ }
+ else {
+ fprintf(stderr, "%s:%s:%d: 2nd attempt worked", __FUNCTION__, __FILE__, __LINE__);
+ }
+ rHhalignPara.iMacRamMB = iOldMacRam;
+ } /* 1st invocation failed */
+
+ } /* 2nd profile was shorter than 1st */
+
+ }
+ /* free left/right node lists,
+ * after alignment left/right profiles no longer needed
+ */
+ if (NULL != ppcCopy1){
+ int i;
+ for (i = 0; i < piLeafCount[iL]; i++){
+ CKFREE(ppcCopy1[i]);
+ }
+ CKFREE(ppcCopy1);
+ CKFREE(pcReprsnt1);
+ CKFREE(pcConsens1);
+ }
+ if (NULL != ppcCopy2){
+ int i;
+ for (i = 0; i < piLeafCount[iR]; i++){
+ CKFREE(ppcCopy2[i]);
+ }
+ CKFREE(ppcCopy2);
+ CKFREE(pcReprsnt2);
+ CKFREE(pcConsens2);
+ }
+ ppiLeafList[iL] = CKFREE(ppiLeafList[iL]);
+ ppiLeafList[iR] = CKFREE(ppiLeafList[iR]);
+ piLeafCount[iL] = piLeafCount[iR] = 0;
+
+ } /* was a merge node */
+
+ if (rLog.iLogLevelEnabled <= LOG_DEBUG){
+ int i, j;
+ FILE *fp = LogGetFP(&rLog, LOG_DEBUG);
+ for (i = 0; i < iNodeCount; i++){
+ if (0 == piLeafCount[i]){
+ continue;
+ }
+ fprintf(fp, "node %3d, #leaves=%d:\t", i, piLeafCount[i]);
+ for (j = 0; ppiLeafList && (j < piLeafCount[i]); j++){
+ fprintf(fp, "%d,", ppiLeafList[i][j]);
+ }
+ fprintf(fp, "\n");
+ }
+ }
+
+
+ } /* 0 <= iN < iNodeCount */
+ ProgressDone(prProgress);
+
+
+ /* check length and set length info
+ */
+ iAlnLen = strlen(prMSeq->seq[0]);
+ for (i=0; i<prMSeq->nseqs; i++) {
+#if 0
+ Log(&rLog, LOG_FORCED_DEBUG, "seq no %d: name %s; len %d; %s",
+ i, prMSeq->sqinfo[i].name, strlen(prMSeq->seq[i]), prMSeq->seq[i]);
+#endif
+
+#ifndef NDEBUG
+ assert(iAlnLen == strlen(prMSeq->seq[i]));
+#endif
+ prMSeq->sqinfo[i].len = iAlnLen;
+ }
+ prMSeq->aligned = TRUE;
+
+
+ if (rLog.iLogLevelEnabled <= LOG_DEBUG){
+ if (0 != prHMM->L){
+ int i;
+ Log(&rLog, LOG_DEBUG, "Alignment scores with HMM:");
+ for (i = 0; /*pdScores[i] > 0.0*/i < prMSeq->nseqs; i++){
+ Log(&rLog, LOG_DEBUG, "%2d:\t%f\n", i, pdScores[i]);
+ }
+ }
+ }
+
+
+ /** translate back ambiguity residues
+ * hhalign translates ambiguity codes (B,Z) into unknown residues (X).
+ * as we still have the original input we can substitute them back
+ */
+ TranslateUnknown2Ambiguity(prMSeq);
+ ReAttachLeadingGaps(prMSeq, iProfProfSeparator);
+
+ if (NULL == prHMMList){
+ CKFREE(prHMM);
+ }
+ CKFREE(ppcProfile2);
+ CKFREE(ppcProfile1);
+ CKFREE(ppiLeafList[piOrderLR[DIFF_NODE*(iNodeCount-1)+PRNT_NODE]]);
+ CKFREE(ppiLeafList);
+ CKFREE(piLeafCount);
+ CKFREE(pdScores);
+ FreeProgress(&prProgress);
+ CKFREE(pdWeightsL);
+ CKFREE(pdWeightsR);
+
+#if TIMING
+ StopwatchStop(stopwatch);
+ StopwatchDisplay(stdout, "Total time for HHalignWrapper():" , stopwatch);
+ StopwatchFree(stopwatch);
+#endif
+
+ return dScore; /* FIXME alternative: return averaged pdScores */
+
+}
+/*** end: HHalignWrapper() ***/
--- /dev/null
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhalign_wrapper.h 241 2011-05-04 14:37:17Z fabian $
+ */
+
+
+extern double
+HHalignWrapper(mseq_t *mseq, int *piOrderLR,
+ double *pdSeqWeights, int iNodeCount,
+ hmm_light *prHMMList, int iHMMCount,
+ int iProfProfSeparator, hhalign_para rHhalignPara);
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: ktuple_pair.c 230 2011-04-09 15:37:50Z andreas $
+ *
+ *
+ * K-Tuple code for pairwise alignment (Wilbur and Lipman, 1983; PMID
+ * 6572363). Most code taken from showpair.c (Clustal 1.83)
+ * DD: some functions now have lots of parameters as static variables
+ * were removed to make code OpenMP-friendly
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+
+#include <stdio.h>
+#include <string.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <math.h>
+#include <assert.h>
+
+#ifdef HAVE_OPENMP
+#include <omp.h>
+#endif
+
+#include "squid/squid.h"
+#include "util.h"
+#include "symmatrix.h"
+#include "ktuple_pair.h"
+#include "log.h"
+#include "progress.h"
+
+#define END_MARK -3 /* see interface.c in 1.83 */
+#define NUMRES 32 /* max size of comparison matrix */
+
+/* see notes below */
+#undef SORT_LAST_ELEMENT_AS_WELL
+
+/* gap_pos1 = NUMRES-2; /@ code for gaps inserted by clustalw @/ */
+static const int GAP_POS2 = NUMRES-1; /* code for gaps already in alignment */
+static bool DNAFLAG = FALSE;
+
+static const char *AMINO_ACID_CODES = "ABCDEFGHIKLMNPQRSTUVWXYZ-";
+static const char *NUCLEIC_ACID_CODES = "ACGTUN-";
+/* As far as I understand the gap symbol should not be necessary here,
+ * because we use isgap for testing later anyway. But changing this,
+ * will affect max_res_code and max_nuc as well. So I leave it for now
+ * as it is. AW
+ */
+
+static bool percent = TRUE;
+
+static void make_ptrs(int *tptr, int *pl, const int naseq, const int l, const int ktup, const int max_res_code, char **seq_array);
+static void put_frag(const int fs, const int v1, const int v2, const int flen, const int curr_frag, int *next, int *maxsf, int **accum);
+static bool frag_rel_pos(int a1, int b1, int a2, int b2, int ktup);
+static void des_quick_sort(int *array1, int *array2, const int array_size);
+static void pair_align(int seq_no, int l1, int l2, int max_res_code, ktuple_param_t *aln_param,
+ char **seq_array, int *maxsf, int **accum, int max_aln_length,
+ int *zza, int *zzb, int *zzc, int *zzd);
+static void encode(char *seq, char *naseq, int l, const char *res_codes);
+static int res_index(const char *lookup, char c);
+
+
+typedef struct {
+ int i1;
+ int i2;
+} two_ints_t;
+
+
+
+/* default ktuple pairwise alignment parameters
+ *
+ */
+/* protein
+ */
+/* designated initializer */
+const ktuple_param_t default_protein_param = {
+ .ktup = 1,
+ .wind_gap = 3,
+ .signif = 5,
+ .window = 5,
+};
+/* dna
+ */
+/* designated initializer */
+const ktuple_param_t default_dna_param = {
+ .ktup = 2,
+ .wind_gap = 5,
+ .signif = 4,
+ .window = 4,
+};
+
+
+/**
+ * note: naseq should be unit-offset
+ */
+static void
+encode(char *seq, char *naseq, int l, const char *res_codes)
+{
+ /* code seq as ints .. use GAP_POS2 for gap */
+ register int i;
+ bool seq_contains_unknown_char = FALSE;
+ /*LOG_DEBUG("seq=%s naseq=%p l=%d", &(seq[1]), naseq, l); */
+
+
+ for (i=1; i<=l; i++) {
+ char res = toupper(seq[i]);
+ if (isgap(res)) {
+ naseq[i] = GAP_POS2; /* gap in input */
+ } else {
+ naseq[i] = res_index(res_codes, res);
+ }
+
+ /*LOG_DEBUG("Character '%c' at pos %d", res, i);*/
+ if (-1 == naseq[i]) {
+ seq_contains_unknown_char = TRUE;
+ /*LOG_DEBUG("Unknown character '%c' at pos %d", res, i);*/
+ }
+ /*LOG_DEBUG("na_seq[%d]=%d", i, naseq[i]);*/
+ }
+
+ if (TRUE == seq_contains_unknown_char)
+ Log(&rLog, LOG_WARN, "Unknown character in seq '%s'", &(seq[1]));
+
+ naseq[i] = END_MARK;
+
+ return;
+}
+/* end of encode */
+
+
+/**
+ *
+ */
+static int
+res_index(const char *t, char c)
+{
+ register int i;
+ for (i=0; t[i] && t[i] != c; i++)
+ ;
+ if (t[i]) {
+ return (i);
+ } else {
+ return -1;
+ }
+}
+/* end of res_index */
+
+
+/**
+ *
+ */
+static void
+make_ptrs(int *tptr, int *pl, const int naseq, const int l, const int ktup, const int max_res_code, char **seq_array)
+{
+ /* FIXME make 10 a constant and give it a nice name */
+ static int a[10];
+ int i, j, code, flag;
+ char residue;
+ const int limit = (int) pow((double)(max_res_code+1),(double)ktup);
+
+ for (i=1;i<=ktup;i++)
+ a[i] = (int) pow((double)(max_res_code+1),(double)(i-1));
+
+ for (i=1; i<=limit; ++i)
+ pl[i]=0;
+ for (i=1; i<=l; ++i)
+ tptr[i]=0;
+
+ for (i=1; i<=(l-ktup+1); ++i) {
+ code=0;
+ flag=FALSE;
+ for (j=1; j<=ktup; ++j) {
+ /* Log(&rLog, LOG_FORCED_DEBUG, "naseq=%d i=%d j=%d seq_array[naseq]=%p",
+ * naseq, i, j, seq_array[naseq]);
+ */
+ residue = seq_array[naseq][i+j-1];
+ /* Log(&rLog, LOG_FORCED_DEBUG, "residue = %d", residue); */
+ if ((residue<0) || (residue > max_res_code)){
+ flag=TRUE;
+ break;
+ }
+ code += ((residue) * a[j]);
+ }
+ if (flag)
+ continue;
+ ++code;
+ if (0 != pl[code])
+ tptr[i] =pl[code];
+ pl[code] = i;
+ }
+
+ return;
+}
+/* end of make_ptrs */
+
+
+/**
+ *
+ * FIXME Why hardcoding of 5?
+ */
+static void
+put_frag(const int fs, const int v1, const int v2, const int flen, const int curr_frag, int *next, int *maxsf, int **accum)
+{
+ int end;
+ accum[0][curr_frag]=fs;
+ accum[1][curr_frag]=v1;
+ accum[2][curr_frag]=v2;
+ accum[3][curr_frag]=flen;
+
+ if (!*maxsf) {
+ *maxsf=1;
+ accum[4][curr_frag]=0;
+ return;
+ }
+
+ if (fs >= accum[0][*maxsf]) {
+ accum[4][curr_frag]=*maxsf;
+ *maxsf=curr_frag;
+ return;
+ } else {
+ *next=*maxsf;
+ while (TRUE) {
+ end=*next;
+ *next=accum[4][*next];
+ if (fs>=accum[0][*next])
+ break;
+ }
+ accum[4][curr_frag]=*next;
+ accum[4][end]=curr_frag;
+ }
+
+ return;
+}
+/* end of put_frag */
+
+
+/**
+ *
+ */
+static bool
+frag_rel_pos(int a1, int b1, int a2, int b2, int ktup)
+{
+ if (a1-b1 == a2-b2) {
+ if (a2<a1) {
+ return TRUE;
+ }
+ } else {
+ if (a2+ktup-1<a1 && b2+ktup-1<b1) {
+ return TRUE;
+ }
+ }
+ return FALSE;
+}
+/* end of frag_rel_pos */
+
+
+
+
+/**
+ *
+ * @note: This is together with des_quick_sort most time consuming
+ * routine according to gprof on r110. Tried to replace it with qsort
+ * and/or QSortAndTrackIndex(), which is always slower! So we keep the
+ * original.
+ *
+ * Original doc: Quicksort routine, adapted from chapter 4, page 115
+ * of software tools by Kernighan and Plauger, (1986). Sort the
+ * elements of array1 and sort the elements of array2 accordingly
+ *
+ * There might be a bug here. The original function apparently never
+ * touches the last element and keeps it as is. Tried to fix this (see
+ * SORT_LAST_ELEMENT_AS_WELL) which gives slightly worse performance
+ * (-0.5% on BB). My fix might not be working or it's not a bug at
+ * all...
+ *
+ *
+ *
+ */
+static void
+des_quick_sort(int *array1, int *array2, const int array_size)
+{
+ int temp1, temp2;
+ int p, pivlin;
+ int i, j;
+ int lst[50], ust[50]; /* the maximum no. of elements must be*/
+ /* < log(base2) of 50 */
+
+#if 0
+ for (i=1; i<=array_size; i++) {
+ Log(&rLog, LOG_FORCED_DEBUG, "b4 sort array1[%d]=%d array2[%d]=%d", i, array1[i], i, array2[i]);
+ }
+#endif
+ lst[1] = 1;
+
+#ifdef SORT_LAST_ELEMENT_AS_WELL
+ ust[1] = array_size;
+#else
+ /* original */
+ ust[1] = array_size-1;
+#endif
+ p = 1;
+
+
+ while (p > 0) {
+ if (lst[p] >= ust[p]) {
+ p--;
+ } else {
+ i = lst[p] - 1;
+ j = ust[p];
+ pivlin = array1[j];
+ while (i < j) {
+ for (i=i+1; array1[i] < pivlin; i++)
+ ;
+ for (j=j-1; j > i; j--)
+ if (array1[j] <= pivlin) break;
+ if (i < j) {
+ temp1 = array1[i];
+ array1[i] = array1[j];
+ array1[j] = temp1;
+
+ temp2 = array2[i];
+ array2[i] = array2[j];
+ array2[j] = temp2;
+ }
+ }
+
+ j = ust[p];
+
+ temp1 = array1[i];
+ array1[i] = array1[j];
+ array1[j] = temp1;
+
+ temp2 = array2[i];
+ array2[i] = array2[j];
+ array2[j] = temp2;
+
+ if (i-lst[p] < ust[p] - i) {
+ lst[p+1] = lst[p];
+ ust[p+1] = i - 1;
+ lst[p] = i + 1;
+
+ } else {
+ lst[p+1] = i + 1;
+ ust[p+1] = ust[p];
+ ust[p] = i - 1;
+ }
+ p = p + 1;
+ }
+ }
+
+#if 0
+ for (i=1; i<=array_size; i++) {
+ Log(&rLog, LOG_FORCED_DEBUG, "after sort array1[%d]=%d array2[%d]=%d", i, array1[i], i, array2[i]);
+ }
+#endif
+
+ return;
+}
+/* end of des_quick_sort */
+
+
+
+/**
+ *
+ * FIXME together with des_quick_sort most time consuming routine
+ * according to gprof on r110
+ *
+ */
+static void
+pair_align(int seq_no, int l1, int l2, int max_res_code, ktuple_param_t *aln_param,
+ char **seq_array, int *maxsf, int **accum, int max_aln_length,
+ int *zza, int *zzb, int *zzc, int *zzd)
+{
+ int next; /* forrmerly static */
+ int pot[8],i, j, l, m, flag, limit, pos, vn1, vn2, flen, osptr, fs;
+ int tv1, tv2, encrypt, subt1, subt2, rmndr;
+ char residue;
+ int *diag_index;
+ int *displ;
+ char *slopes;
+ int curr_frag;
+ const int tl1 = (l1+l2)-1;
+
+ assert(NULL!=aln_param);
+
+ /*
+ Log(&rLog, LOG_FORCED_DEBUG, "DNAFLAG=%d seq_no=%d l1=%d l2=%d window=%d ktup=%d signif=%d wind_gap=%d",
+ DNAFLAG, seq_no, l1, l2, window, ktup, signif,
+ wind_gap);
+ */
+
+ slopes = (char *) CKCALLOC(tl1+1, sizeof(char));
+ displ = (int *) CKCALLOC(tl1+1, sizeof(int));
+ diag_index = (int *) CKMALLOC((tl1+1) * sizeof(int));
+
+ for (i=1; i<=tl1; ++i) {
+ /* unnecessary, because we calloced: slopes[i] = displ[i] = 0; */
+ diag_index[i] = i;
+ }
+
+ for (i=1;i<=aln_param->ktup;i++)
+ pot[i] = (int) pow((double)(max_res_code+1),(double)(i-1));
+ limit = (int) pow((double)(max_res_code+1),(double)aln_param->ktup);
+
+
+
+ /* increment diagonal score for each k_tuple match */
+
+ for (i=1; i<=limit; ++i) {
+ vn1=zzc[i];
+ while (TRUE) {
+ if (!vn1) break;
+ vn2 = zzd[i];
+ while (0 != vn2) {
+ osptr = vn1-vn2+l2;
+ ++displ[osptr];
+ vn2 = zzb[vn2];
+ }
+ vn1=zza[vn1];
+ }
+ }
+
+
+ /* choose the top SIGNIF diagonals
+ */
+
+#ifdef QSORT_REPLACEMENT
+ /* This was an attempt to replace des_quick_sort with qsort(),
+ * which turns out to be much slower, so don't use this
+ */
+
+ /* FIXME: if we use this branch, we don't need to init diag_index
+ * before, because that is done in QSortAndTrackIndex()
+ * automatically.
+ */
+#if 0
+ for (i=1; i<=tl1; i++) {
+ Log(&rLog, LOG_FORCED_DEBUG, "b4 sort disp[%d]=%d diag_index[%d]=%d", i, diag_index[i], i, displ[i]);
+ }
+#endif
+
+ QSortAndTrackIndex(&(diag_index[1]), &(displ[1]), tl1, 'a', TRUE);
+
+#if 0
+ for (i=1; i<=tl1; i++) {
+ Log(&rLog, LOG_FORCED_DEBUG, "after sort disp[%d]=%d diag_index[%d]=%d", i, diag_index[i], i, displ[i]);
+ }
+#endif
+
+#else
+
+ des_quick_sort(displ, diag_index, tl1);
+
+#endif
+
+ j = tl1 - aln_param->signif + 1;
+
+ if (j < 1) {
+ j = 1;
+ }
+
+ /* flag all diagonals within WINDOW of a top diagonal */
+
+ for (i=tl1; i>=j; i--) {
+ if (displ[i] > 0) {
+ pos = diag_index[i];
+ l = (1 > pos - aln_param->window) ?
+ 1 : pos - aln_param->window;
+ m = (tl1 < pos + aln_param->window) ?
+ tl1 : pos + aln_param->window;
+ for (; l <= m; l++)
+ slopes[l] = 1;
+ }
+ }
+
+ for (i=1; i<=tl1; i++) {
+ displ[i] = 0;
+ }
+
+ curr_frag=*maxsf=0;
+
+ for (i=1; i<=(l1-aln_param->ktup+1); ++i) {
+ encrypt=flag=0;
+ for (j=1; j<=aln_param->ktup; ++j) {
+ residue = seq_array[seq_no][i+j-1];
+ if ((residue<0) || (residue>max_res_code)) {
+ flag=TRUE;
+ break;
+ }
+ encrypt += ((residue)*pot[j]);
+ }
+ if (flag) {
+ continue;
+ }
+ ++encrypt;
+
+ vn2=zzd[encrypt];
+
+ flag=FALSE;
+ while (TRUE) {
+ if (!vn2) {
+ flag=TRUE;
+ break;
+ }
+ osptr=i-vn2+l2;
+ if (1 != slopes[osptr]) {
+ vn2=zzb[vn2];
+ continue;
+ }
+ flen=0;
+ fs=aln_param->ktup;
+ next=*maxsf;
+
+ /*
+ * A-loop
+ */
+
+ while (TRUE) {
+ if (!next) {
+ ++curr_frag;
+ if (curr_frag >= 2*max_aln_length) {
+ Log(&rLog, LOG_VERBOSE, "(Partial alignment)");
+ goto free_and_exit; /* Yesss! Always wanted to
+ * use a goto (AW) */
+ }
+ displ[osptr]=curr_frag;
+ put_frag(fs, i, vn2, flen, curr_frag, &next, maxsf, accum);
+
+ } else {
+ tv1=accum[1][next];
+ tv2=accum[2][next];
+
+ if (frag_rel_pos(i, vn2, tv1, tv2, aln_param->ktup)) {
+ if (i-vn2 == accum[1][next]-accum[2][next]) {
+ if (i > accum[1][next]+(aln_param->ktup-1)) {
+ fs = accum[0][next]+aln_param->ktup;
+ } else {
+ rmndr = i-accum[1][next];
+ fs = accum[0][next]+rmndr;
+ }
+ flen=next;
+ next=0;
+ continue;
+
+ } else {
+ if (0 == displ[osptr]) {
+ subt1=aln_param->ktup;
+ } else {
+ if (i > accum[1][displ[osptr]]+(aln_param->ktup-1)) {
+ subt1=accum[0][displ[osptr]]+aln_param->ktup;
+ } else {
+ rmndr=i-accum[1][displ[osptr]];
+ subt1=accum[0][displ[osptr]]+rmndr;
+ }
+ }
+ subt2=accum[0][next] - aln_param->wind_gap + aln_param->ktup;
+ if (subt2>subt1) {
+ flen=next;
+ fs=subt2;
+ } else {
+ flen=displ[osptr];
+ fs=subt1;
+ }
+ next=0;
+ continue;
+ }
+ } else {
+ next=accum[4][next];
+ continue;
+ }
+ }
+ break;
+ }
+ /*
+ * End of Aloop
+ */
+
+ vn2=zzb[vn2];
+ }
+ }
+
+free_and_exit:
+ CKFREE(displ);
+ CKFREE(slopes);
+ CKFREE(diag_index);
+
+ return;
+}
+/* end of pair_align */
+
+
+
+/**
+ *
+ * Will compute ktuple scores and store in tmat
+ * Following values will be set: tmat[i][j], where
+ * istart <= i <iend
+ * and
+ * jstart <= j < jend
+ * i.e. zero-offset
+ * tmat data members have to be preallocated
+ *
+ * if ktuple_param_t *aln_param == NULL defaults will be used
+ */
+void
+KTuplePairDist(symmatrix_t *tmat, mseq_t *mseq,
+ int istart, int iend,
+ int jstart, int jend,
+ ktuple_param_t *param_override,
+ progress_t *prProgress,
+ unsigned long int *ulStepNo, unsigned long int ulTotalStepNo)
+{
+ /* this first group of variables were previously static
+ and hence un-parallelisable */
+ char **seq_array;
+ int maxsf;
+ int **accum;
+ int max_aln_length;
+ /* divide score with length of smallest sequence */
+ int *zza, *zzb, *zzc, *zzd;
+ int private_step_no = 0;
+
+ int i, j, dsr;
+ double calc_score;
+ int max_res_code = -1;
+
+ int max_seq_len;
+ int *seqlen_array;
+ /* progress_t *prProgress; */
+ /* int uStepNo, uTotalStepNo; */
+ ktuple_param_t aln_param = default_protein_param;
+ bool bPrintCR = (rLog.iLogLevelEnabled<=LOG_VERBOSE) ? FALSE : TRUE;
+
+
+ if(prProgress == NULL) {
+ NewProgress(&prProgress, LogGetFP(&rLog, LOG_INFO),
+ "Ktuple-distance calculation progress", bPrintCR);
+ }
+
+ /* conversion to old style data types follows
+ *
+ */
+
+ seqlen_array = (int*) CKMALLOC((mseq->nseqs+1) * sizeof(int));
+ for (i=0; i<mseq->nseqs; i++) {
+ seqlen_array[i+1] = mseq->sqinfo[i].len;
+ }
+
+ /* setup alignment parameters
+ */
+ if (SEQTYPE_PROTEIN == mseq->seqtype) {
+ DNAFLAG = FALSE;
+ max_res_code = strlen(AMINO_ACID_CODES)-2;
+ aln_param = default_protein_param;
+
+ } else if (SEQTYPE_RNA == mseq->seqtype || SEQTYPE_DNA == mseq->seqtype) {
+ DNAFLAG = TRUE;
+ max_res_code = strlen(NUCLEIC_ACID_CODES)-2;
+ aln_param = default_dna_param;
+
+ } else {
+ Log(&rLog, LOG_FATAL, "Internal error in %s: Unknown sequence type.", __FUNCTION__);
+ }
+
+ if (NULL!=param_override) {
+ aln_param.ktup = param_override->ktup;
+ aln_param.wind_gap = param_override->wind_gap;
+ aln_param.signif = param_override->signif;
+ aln_param.window = param_override->window;
+ }
+
+ /*LOG_DEBUG("DNAFLAG = %d max_res_code = %d", DNAFLAG, max_res_code);*/
+
+ /* convert mseq to clustal's old-style int encoded sequences (unit-offset)
+ */
+ max_aln_length = 0;
+ max_seq_len = 0;
+ seq_array = (char **) CKMALLOC((mseq->nseqs+1) * sizeof(char *));
+ seq_array[0] = NULL;
+ /* FIXME check that non of the seqs is smaller than ktup (?).
+ * Otherwise segfault occurs
+ */
+ for (i=0; i<mseq->nseqs; i++) {
+ seq_array[i+1] = (char *) CKMALLOC((seqlen_array[i+1]+2) * sizeof (char));;
+ }
+ for (i=0; i<mseq->nseqs; i++) {
+ /*LOG_DEBUG("calling encode with seq_array[%d+1] len=%d and seq=%s",
+ i, seqlen_array[i+1], mseq->seq[i]);*/
+ if (TRUE == DNAFLAG) {
+ encode(&(mseq->seq[i][-1]), seq_array[i+1],
+ seqlen_array[i+1], NUCLEIC_ACID_CODES);
+ } else {
+ encode(&(mseq->seq[i][-1]), seq_array[i+1],
+ seqlen_array[i+1], AMINO_ACID_CODES);
+ }
+
+ if (seqlen_array[i+1]>max_seq_len) {
+ max_seq_len = seqlen_array[i+1];
+ }
+ }
+ max_aln_length = max_seq_len * 2;
+ /* see sequence.c in old source */
+
+ /* FIXME: short sequences can cause seg-fault
+ * because max_aln_length can get shorter
+ * than (max_res_code+1)^k
+ * FS, r222->r223 */
+ max_aln_length = max_aln_length > pow((max_res_code+1), aln_param.ktup)+1 ?
+ max_aln_length : pow((max_res_code+1), aln_param.ktup)+1;
+
+ /*
+ *
+ * conversion to old style clustal done (in no time) */
+
+
+ accum = (int **) CKCALLOC(5, sizeof (int *));
+ for (i=0;i<5;i++) {
+ accum[i] = (int *) CKCALLOC((2*max_aln_length+1), sizeof(int));
+ }
+ zza = (int *) CKCALLOC( (max_aln_length+1), sizeof(int));
+ zzb = (int *) CKCALLOC( (max_aln_length+1), sizeof(int));
+ zzc = (int *) CKCALLOC( (max_aln_length+1), sizeof(int));
+ zzd = (int *) CKCALLOC( (max_aln_length+1), sizeof(int));
+
+ /* estimation of total number of steps (if istart and jstart are
+ * both 0) (now handled in the calling routine)
+ */
+ /* uTotalStepNo = iend*jend - iend*iend/2 + iend/2;
+ uStepNo = 0; */
+ /*LOG_DEBUG("istart=%d iend=%d jstart=%d jend=%d", istart, iend, jstart, jend);*/
+
+ for (i=istart+1; i<=iend; ++i) {
+ /* by definition a sequence compared to itself should give
+ a score of 0. AW */
+ SymMatrixSetValue(tmat, i-1, i-1, 0.0);
+ make_ptrs(zza, zzc, i, seqlen_array[i], aln_param.ktup, max_res_code, seq_array);
+
+#ifdef HAVE_OPENMP
+ #pragma omp critical(ktuple)
+#endif
+ {
+ ProgressLog(prProgress, *ulStepNo, ulTotalStepNo, FALSE);
+ }
+
+ for (j=MAX(i+1, jstart+1); j<=jend; ++j) {
+ (*ulStepNo)++;
+ private_step_no++;
+ /*LOG_DEBUG("comparing pair %d:%d", i, j);*/
+
+ make_ptrs(zzb, zzd, j, seqlen_array[j], aln_param.ktup, max_res_code, seq_array);
+ pair_align(i, seqlen_array[i], seqlen_array[j], max_res_code, &aln_param,
+ seq_array, &maxsf, accum, max_aln_length, zza, zzb, zzc, zzd);
+
+ if (!maxsf) {
+ calc_score=0.0;
+ } else {
+ calc_score=(double)accum[0][maxsf];
+ if (percent) {
+ dsr=(seqlen_array[i]<seqlen_array[j]) ?
+ seqlen_array[i] : seqlen_array[j];
+ calc_score = (calc_score/(double)dsr) * 100.0;
+ }
+ }
+
+ /* printf("%d %d %d\n", i-1, j-1, (100.0 - calc_score)/100.0); */
+ SymMatrixSetValue(tmat, i-1, j-1, (100.0 - calc_score)/100.0);
+
+ /* the function allows you not to compute the full matrix.
+ * here we explicitely make the resulting matrix a
+ * rectangle, i.e. we always set full rows. in other
+ * words, if we don't complete the full matrix then we
+ * don't have a full symmetry. so only use the defined
+ * symmetric part. AW
+ */
+ /*LOG_DEBUG("setting %d : %d = %f", j, i, tmat[i][j]);*/
+ /* not needed anymore since we use symmatrix_t
+ if (j<=iend) {
+ tmat[j][i] = tmat[i][j];
+ }
+ */
+#ifdef HAVE_OPENMP
+ #pragma omp critical(ktuple)
+#endif
+ {
+ Log(&rLog, LOG_DEBUG, "K-tuple distance for sequence pair %d:%d = %lg",
+ i, j, SymMatrixGetValue(tmat, i-1, j-1));
+ }
+ }
+ }
+ /*
+ Log(&rLog, LOG_FORCED_DEBUG, "uTotalStepNo=%d for istart=%d iend=%d jstart=%d jend=%d", uStepNo, istart, iend, jstart, jend);
+ Log(&rLog, LOG_FORCED_DEBUG, "Fabian = %d", iend*jend - iend*iend/2 + iend/2);
+ */
+
+/* printf("\n\n%d\t%d\t%d\t%d\n\n", omp_get_thread_num(), uStepNo, istart, iend); */
+
+ for (i=0;i<5;i++) {
+ CKFREE(accum[i]);
+ }
+ CKFREE(accum);
+
+#ifdef HAVE_OPENMP
+ #pragma omp critical(ktuple)
+#if 0
+ {
+ printf("steps: %d\n", private_step_no);
+ }
+#endif
+#endif
+
+ CKFREE(zza);
+ CKFREE(zzb);
+ CKFREE(zzc);
+ CKFREE(zzd);
+
+ free(seqlen_array);
+
+ for (i=1; i<=mseq->nseqs; i++) {
+ CKFREE(seq_array[i]);
+ }
+ CKFREE(seq_array);
+}
+/* end of KTuplePairDist */
--- /dev/null
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: ktuple_pair.h 193 2011-02-07 15:45:21Z andreas $
+ */
+
+/* K-Tuple code for pairwise alignment (Wilbur and Lipman (1983)
+ * Most code taken from showpair (Clustal 1.83)
+ */
+
+
+#ifndef CLUSTALO_KTUPLE_PAIR_H
+#define CLUSTALO_KTUPLE_PAIR_H
+
+#include "seq.h"
+#include "symmatrix.h"
+#include "progress.h"
+
+typedef struct {
+ int ktup;
+ int window;
+ int wind_gap;
+ int signif;
+} ktuple_param_t;
+
+
+extern void
+KTuplePairDist(symmatrix_t *tmat, mseq_t *mseq,
+ int istart, int iend,
+ int jstart, int jend,
+ ktuple_param_t *aln_param,
+ progress_t *prProgress,
+ unsigned long int *ulStepNo, unsigned long int ulTotalStepNo);
+
+#endif
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: list.c 156 2010-11-18 10:52:40Z andreas $
+ *
+ * Single linked list and FIFO/Queue
+ *
+ * Based on Kyle Loudon's Mastering Algorithms with C
+ * http://oreilly.com/catalog/9781565924536
+ *
+ * Allows generic data types by using void* pointers, which works fine
+ * as long as your data is just pointers.
+ *
+ */
+
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <assert.h>
+#include <string.h> /* for memset */
+
+#include "list.h"
+
+#ifdef LIST_TEST
+#include <stdio.h>
+#include "queue.h"
+#include "time.h"
+#endif
+
+/**
+ * @brief Initialise data members of a list
+ *
+ * @param[in] prList
+ * List to initialise
+ * @param[in] destroy
+ * A function to be called with pointer to data when destroying the
+ * list. NULL if in doubt, free in most other cases.
+ * Note: doxygen will always fail to parse this...
+ */
+void
+ListInit(list_t *prList, void (*destroy)(void *data)) {
+ prList->size = 0;
+ prList->destroy = destroy;
+ prList->head = NULL;
+ prList->tail = NULL;
+
+ return;
+}
+/* end of ListInit() */
+
+
+
+/**
+ * @brief Calls user defined function to free data in list and resets
+ * the list to NULL. Call even if your destroy function is NULL.
+ *
+ * @param[in] prList
+ * The list to destroy
+ *
+ */
+void
+ListDestroy(list_t *prList) {
+ void *pvData;
+
+ while (LIST_SIZE(prList) > 0) {
+ if (0 == ListRemoveNext(prList, NULL, (void **)&pvData)
+ &&
+ NULL != prList->destroy) {
+ prList->destroy(pvData);
+ }
+ }
+ /* precaution */
+ memset(prList, 0, sizeof(list_t));
+
+ return;
+}
+/* end of ListDestroy() */
+
+
+
+/**
+ *
+ * @brief Insert data next to given element
+ *
+ * @param[in] prList
+ * List into which to insert
+ * @param[in] prElement
+ * Current position/element. Element after which to insert. If NULL
+ * head is used.
+ * @param[in] pvData
+ * Pointer to data to store
+ *
+ * @return Non-zero on failure
+ */
+int
+ListInsertNext(list_t *prList, list_elem_t *prElement, const void *pvData)
+{
+ list_elem_t *prNewElement;
+
+ if (NULL == (prNewElement = (list_elem_t *) malloc(sizeof(list_elem_t))))
+ return -1;
+
+ prNewElement->data = (void *)pvData;
+
+ if (NULL == prElement) {
+ /* insertion at head */
+ if (LIST_SIZE(prList) == 0)
+ prList->tail = prNewElement;
+ prNewElement->next = prList->head;
+ prList->head = prNewElement;
+
+ } else {
+ /* insert somewhere other than at head */
+ if (NULL == prElement->next)
+ prList->tail = prNewElement;
+ prNewElement->next = prElement->next;
+ prElement->next = prNewElement;
+ }
+
+ prList->size++;
+
+ return 0;
+}
+/* end of ListInsertNext() */
+
+
+
+/**
+ * @brief Remove next element from current element/position.
+ *
+ * @param[in] prList
+ * List from which an element is to be removed.
+ * @param[in] prElement
+ * Current element/position. Next item will be removed. If NULL head
+ * is used.
+ * @param[out] pvData_p
+ * Will be pointed to removed elements data.
+ *
+ * @return Non-zero on failure
+ */
+int
+ListRemoveNext(list_t *prList, list_elem_t *prElement, void **pvData_p)
+{
+ list_elem_t *prOldElement;
+
+ if (0 == LIST_SIZE(prList))
+ return -1;
+
+ if (NULL == prElement) {
+ /* handle removal from the head of the list */
+ *pvData_p = prList->head->data;
+ prOldElement = prList->head;
+ prList->head = prList->head->next;
+ if (1 == LIST_SIZE(prList))
+ prList->tail = NULL;
+
+ } else {
+ /* handle removal from somewhere other than the head */
+ if (NULL == prElement->next)
+ return -1;
+
+ *pvData_p = prElement->next->data;
+ prOldElement = prElement->next;
+ prElement->next = prElement->next->next;
+
+ if (NULL == prElement->next)
+ prList->tail = prElement;
+ }
+
+ free(prOldElement);
+
+ prList->size--;
+
+ return 0;
+}
+/* end of ListRemoveNext() */
+
+
+
+/**
+ * @brief Insert int next to given element
+ *
+ * @param[in] prList
+ * List into which to insert
+ * @param[in] prElement
+ * Current position/element. Element after which to insert. If NULL
+ * head is used.
+ * @param[in] data
+ * int to store
+ *
+ * @return Non-zero on failure
+ *
+ */
+int
+IntListInsertNext(list_t *prList, list_elem_t *prElement, const int data)
+{
+ int *piInt;
+
+ if (NULL == (piInt = malloc(sizeof(int)))) {
+ return -1;
+ }
+ *piInt = data;
+
+ return ListInsertNext(prList, prElement, piInt);
+ }
+/* end if IntListInsertNext() */
+
+
+/**
+ * @brief Remove next element from current element/position.
+ *
+ * @param[in] prList
+ * List from which an element is to be removed.
+ * @param[in] prElement
+ * Current element/position. Next item will be removed. If NULL head
+ * is used.
+ * @param[out] iData_p
+ * Will be pointed to removed elements data.
+ *
+ * @return Non-zero on failure
+ *
+ */
+int
+IntListRemoveNext(list_t *prList, list_elem_t *prElement, int *iData_p)
+{
+ int *piData;
+ int res;
+ res = ListRemoveNext(prList, prElement, (void **)&piData);
+ *iData_p = *piData;
+ prList->destroy(piData);
+ return res;
+}
+/* end of IntListRemoveNext */
+
+
+
+
+#ifdef LIST_TEST
+/* gcc list.c -o list_test -ansi -Wall -DLIST_TEST */
+
+int main(int argc, char **argv)
+{
+
+ int i;
+ list_t *mylist;
+ int_list_t *myintlist;
+ queue_t *myqueue;
+ int_queue_t *myintqueue;
+ int res;
+
+ int iSeed = (int)time(NULL);
+ srand((unsigned int)iSeed);
+
+ printf("%s", "list test! also delete #include!\n");
+
+
+ mylist = malloc(sizeof(list_t));
+ ListInit(mylist, NULL);
+
+ printf("LIST test\n");
+
+ for (i=0; i<argc; i++) {
+ res = LIST_APPEND(mylist, argv[i]);
+ printf("LIST Result for appending '%s' was %d\n", argv[i], res);
+ }
+
+ while (LIST_SIZE(mylist)) {
+ char *argv_ptr;
+ if (ListRemoveNext(mylist, NULL, (void **)&argv_ptr))
+ perror("ListRemoveNext() failed");
+ printf("LIST Popped %s\n", argv_ptr);
+ }
+ printf("LIST %s", "No more elements to pop");
+
+ /* could become list_free */
+ ListDestroy(mylist);
+ free(mylist);
+
+
+
+
+ myintlist = malloc(sizeof(list_t));
+ INT_LIST_INIT(myintlist);
+
+ printf("\n");
+ printf("%s", "INT_LIST test");
+
+ for (i=0; i<argc; i++) {
+ int data = 666-i;
+ res = INT_LIST_APPEND(myintlist, data);
+ printf("INT_LIST Result for appending '%d' was %d\n", data, res);
+ }
+
+ while (INT_LIST_SIZE(myintlist)) {
+ int data;
+ if (IntListRemoveNext(myintlist, NULL, &data))
+ perror("ListRemoveNext() failed\n");
+ printf("INT_LIST Popped %d\n", data);
+ }
+ printf("INT_LIST %s\n", "No more elements to pop");
+
+ /* could become list_free */
+ INT_LIST_DESTROY(myintlist);
+ free(myintlist);
+
+
+
+
+
+ myqueue = malloc(sizeof(queue_t));
+ QUEUE_INIT(myqueue, NULL);
+
+ printf("\n");
+ printf("%s", "QUEUE test\n");
+
+ for (i=0; i<argc; i++) {
+ res = QUEUE_PUSH(myqueue, argv[i]);
+ printf("QUEUE Result for pushing '%s' was %d\n", argv[i], res);
+ }
+
+ while (! QUEUE_EMPTY(myqueue)) {
+ char *argv_ptr;
+ if (QUEUE_POP(myqueue, (void **)&argv_ptr))
+ perror("QUEUE_POP() failed\n");
+ printf("QUEUE Popped %s\n", argv_ptr);
+ }
+ printf("QUEUE %s\n", "QUEUE No more elements to pop");
+
+ /* could become list_free */
+ QUEUE_DESTROY(myqueue);
+ free(myqueue);
+
+
+
+
+ myintqueue = malloc(sizeof(queue_t));
+ INT_QUEUE_INIT(myintqueue);
+
+ printf("\n");
+ printf("%s\n", "INT_QUEUE test");
+
+ for (i=0; i<argc; i++) {
+ res = INT_QUEUE_PUSH(myintqueue, i);
+ printf("INT_QUEUE Result for appending '%d' was %d\n", i, res);
+ }
+
+ while (! INT_QUEUE_EMPTY(myintqueue)) {
+ int data;
+ int rand_data;
+ if (INT_QUEUE_POP(myintqueue, &data))
+ perror("INT_QUEUE_POP() failed\n");
+ printf("INT_QUEUE Popped %d\n", data);
+
+ rand_data = (int)( 10.0 * rand() / ( RAND_MAX+1.0));
+ if (! (rand_data%3)) {
+ res = INT_QUEUE_PUSH(myintqueue, rand_data);
+ printf("INT_QUEUE Result for pushing random number '%d' was %d\n", rand_data, res);
+ }
+ }
+ printf("INT_QUEUE %s\n", "INT_QUEUE No more elements to pop");
+
+ /* could become list_free */
+ INT_QUEUE_DESTROY(myintqueue);
+ free(myintqueue);
+
+
+ exit(0);
+}
+
+#endif
+
+
+
--- /dev/null
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: list.h 193 2011-02-07 15:45:21Z andreas $
+ *
+ * Generic single linked list storing pointers to data
+ *
+ */
+
+#ifndef CLUSTALO_LIST_H
+#define CLUSTALO_LIST_H
+
+#include <stdlib.h>
+
+typedef struct list_elem_s {
+ void *data;
+ struct list_elem_s *next;
+} list_elem_t;
+
+typedef struct {
+ /* size of list */
+ int size;
+ /* user defined function for freeing data */
+ void (*destroy)(void *data);
+ list_elem_t *head;
+ list_elem_t *tail;
+} list_t;
+
+void ListInit(list_t *prList, void (*destroy)(void *data));
+
+void ListDestroy(list_t *prList);
+
+int ListInsertNext(list_t *prList, list_elem_t *prElement, const void *data);
+
+#define LIST_APPEND(prList, data) ListInsertNext((prList), LIST_TAIL(prList), (data))
+
+#define LIST_PREPEND(prList, data) ListInsertNext((prList), CLUSTALO_LIST_HEAD(prList), (data))
+
+int ListRemoveNext(list_t *prList, list_elem_t *prElement, void **data);
+
+#define LIST_SIZE(prList) ((prList)->size)
+
+#define CLUSTALO_LIST_HEAD(prList) ((prList)->head)
+
+#define LIST_TAIL(prList) ((prList)->tail)
+
+#define LIST_IS_HEAD(prList, prElement) ((prElement) == (prList)->head ? 1 : 0)
+
+#define LIST_IS_TAIL(prElement) ((prElement)->next == NULL ? 1 : 0)
+
+#define LIST_DATA(prElement) ((prElement)->data)
+
+#define LIST_NEXT(prElement) ((prElement)->next)
+
+
+
+
+
+/* special int list: stores ints by copying them (instead of storing
+ * pointers as generic list)
+ *
+ */
+
+typedef list_t int_list_t;
+
+#define INT_LIST_INIT(prList) ListInit((prList), free)
+
+#define INT_LIST_DESTROY(prList) ListDestroy((prList));
+
+int IntListInsertNext(list_t *prList, list_elem_t *prElement, const int data);
+
+#define INT_LIST_APPEND(prList, data) IntListInsertNext((prList), LIST_TAIL(prList), (data))
+
+#define INT_LIST_PREPEND(prList, data) IntListInsertNext((prList), CLUSTALO_LIST_HEAD(prList), (data))
+
+int IntListRemoveNext(list_t *prList, list_elem_t *prElement, int *data);
+
+#define INT_LIST_SIZE(prList) LIST_SIZE(prList)
+
+#define INT_CLUSTALO_LIST_HEAD(prList) CLUSTALO_LIST_HEAD_INT((prList))
+
+#define INT_LIST_TAIL(prList) LIST_TAIL_INT((prList) )
+
+#define INT_LIST_IS_HEAD(prList, prElement) LIST_IS_HEAD(prList, prElement)
+
+#define INT_LIST_IS_TAIL(prElement) LIST_IS_TAIL((prElement))
+
+#define INT_LIST_DATA(prElement) LIST_DATA((prElement))
+
+#define INT_LIST_NEXT(prElement) LIST_NEXT((prElement))
+
+
+#endif
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id$
+ */
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdarg.h>
+#include <assert.h>
+
+#include "log.h"
+
+/* a default standard logger */
+log_t rLog;
+
+
+
+void
+LogVfprintf(FILE *prFP, char *pcFmt, va_list rVArgList);
+void
+LogWarn(FILE *prFP, char *pcFmt, va_list rVArgList);
+void
+LogError(FILE *prFP, char *pcFmt, va_list rVArgList);
+void
+LogCritical(FILE *prFP, char *pcFmt, va_list rVArgList);
+void
+LogFatal(FILE *prFP, char *pcFmt, va_list rVArgList);
+void
+LogForcedDebug(FILE *prFP, char *pcFmt, va_list rVArgList);
+
+
+
+
+/**
+ * @brief Plain, default print function
+ *
+ * Newline character is automatically appended to message.
+ *
+ */
+void
+LogVfprintf(FILE *prFP, char *pcFmt, va_list rVArgList)
+{
+ /* print prefix */
+ vfprintf(prFP, pcFmt, rVArgList);
+ fprintf(prFP,"\n");
+
+#ifndef NDEBUG
+ fflush(prFP);
+#endif
+}
+/* end of LogVfprintf() */
+
+
+
+/**
+ * @brief
+ *
+ */
+void
+LogWarn(FILE *prFP, char *pcFmt, va_list rVArgList)
+{
+ fprintf(prFP, "WARNING: ");
+ LogVfprintf(prFP, pcFmt, rVArgList);
+}
+/* end of LogWarn() */
+
+
+
+/**
+ * @brief
+ *
+ */
+void
+LogError(FILE *prFP, char *pcFmt, va_list rVArgList)
+{
+ fprintf(prFP, "ERROR: ");
+ LogVfprintf(prFP, pcFmt, rVArgList);
+}
+/* end of LogError() */
+
+
+
+/**
+ * @brief
+ *
+ */
+void
+LogCritical(FILE *prFP, char *pcFmt, va_list rVArgList)
+{
+ fprintf(prFP, "CRITICAL ERROR: ");
+ LogVfprintf(prFP, pcFmt, rVArgList);
+}
+/* end of LogCritical() */
+
+
+
+/**
+ * @brief Will also exit!
+ */
+void
+LogFatal(FILE *prFP, char *pcFmt, va_list rVArgList)
+{
+ fprintf(prFP, "FATAL: ");
+ LogVfprintf(prFP, pcFmt, rVArgList);
+
+ exit(EXIT_FAILURE);
+}
+/* end of LogFatal() */
+
+
+
+/**
+ * @brief
+ *
+ */
+void
+LogForcedDebug(FILE *prFP, char *pcFmt, va_list rVArgList)
+{
+ fprintf(prFP, "FORCED DEBUG: ");
+ LogVfprintf(prFP, pcFmt, rVArgList);
+}
+/* end of LogForcedDebug() */
+
+
+
+/**
+ *
+ * @brief Sets up default function pointers
+ *
+ */
+void
+LogDefaultSetup(log_t *log)
+{
+ log->iLogLevelEnabled = LOG_WARN;
+
+ log->prFP[LOG_DEBUG] = stdout;
+ log->prFP[LOG_INFO] = stdout;
+ log->prFP[LOG_WARN] = stderr;
+ log->prFP[LOG_ERROR] = stderr;
+ log->prFP[LOG_CRITICAL] = stderr;
+ log->prFP[LOG_FATAL] = stderr;
+ log->prFP[LOG_FORCED_DEBUG] = stderr;
+
+ log->prFunc[LOG_DEBUG] = &LogVfprintf;
+ log->prFunc[LOG_INFO] = &LogVfprintf;
+ log->prFunc[LOG_WARN] = &LogWarn;
+ log->prFunc[LOG_ERROR] = &LogError;
+ log->prFunc[LOG_CRITICAL] = &LogCritical;
+ log->prFunc[LOG_FATAL] = &LogFatal;
+ log->prFunc[LOG_FORCED_DEBUG] = &LogForcedDebug;
+}
+/* end of LogDefaultSetup() */
+
+
+
+/**
+ * @brief Log to certain level
+ *
+ * See also comp.lang.c FAQ list · Question 15.12
+ * http://c-faq.com/varargs/handoff.html How can I write a function which
+ * takes a variable number of arguments and passes them to some other function
+ * (which takes a variable number of arguments)?
+ *
+ */
+void
+Log(log_t *prLog, int iLevel, char *pcFmt, ...)
+{
+ va_list rVArgList;
+ void (*prFunc) (FILE *prFP, char *pcFormat, va_list rVArgList);
+ FILE *prFP;
+
+ assert(iLevel>=0 && iLevel<=LOG_NUM_LEVELS);
+
+ /* fprintf(stderr, "DEBUG: iLevel=%d and iLogLevelEnabled=%d\n", iLevel, prLog->iLogLevelEnabled); */
+
+ /* return if below current loglevel */
+ if (iLevel < prLog->iLogLevelEnabled) {
+ return;
+ }
+
+ prFunc = prLog->prFunc[iLevel];
+ prFP = prLog->prFP[iLevel];
+
+ /* return if muted */
+ if (NULL == prFunc) {
+ return;
+ }
+
+ va_start(rVArgList, pcFmt);
+ prFunc(prFP, pcFmt, rVArgList);
+ va_end(rVArgList);
+}
+/* end of Log() */
+
+
+
+/**
+ *
+ * @brief Change file pointer for certain level
+ *
+ */
+void
+LogSetFP(log_t *prLog, int iLevel, FILE *prFP)
+{
+ assert(iLevel>=0 && iLevel<=LOG_NUM_LEVELS);
+
+ prLog->prFP[iLevel] = prFP;
+}
+/* end of LogSetFP() */
+
+
+
+/**
+ *
+ * @brief Return file pointer for certain level
+ *
+ */
+FILE *
+LogGetFP(log_t *prLog, int iLevel)
+{
+ assert(iLevel>=0 && iLevel<=LOG_NUM_LEVELS);
+
+ return prLog->prFP[iLevel];
+}
+/* end of LogGetFP() */
+
+
+
+
+
+/**
+ *
+ * @brief Change file pointer for all levels
+ *
+ */
+void
+LogSetFPForAll(log_t *prLog, FILE *prFP)
+{
+ int iAux;
+
+ for (iAux=0; iAux<LOG_NUM_LEVELS; iAux++) {
+ prLog->prFP[iAux] = prFP;
+ }
+}
+/* end of LogSetFP() */
+
+
+
+/**
+ *
+ * @brief Mute certain level (i.e set the corresponding function to NULL)
+ *
+ */
+void
+LogMute(log_t *prLog, int iLevel)
+{
+ assert(iLevel>=0 && iLevel<=LOG_NUM_LEVELS);
+
+ prLog->prFunc[iLevel] = NULL;
+}
+/* end of LogMute() */
+
+
+/**
+ *
+ * @brief Mute all channels
+ *
+ */
+void
+LogMuteAll(log_t *prLog)
+{
+ int iAux;
+
+ for (iAux=0; iAux<LOG_NUM_LEVELS; iAux++) {
+ LogMute(prLog, iAux);
+ }
+}
+/* end of LogMuteAll() */
+
+
+
+/**
+ * @brief
+ *
+ */
+void
+LogFuncOverwrite(log_t *prLog, int iLevel,
+ void (*Func) (FILE *prFP, char *pcFormat, va_list rVArgList))
+{
+ assert(iLevel>=0 && iLevel<=LOG_NUM_LEVELS);
+
+ prLog->prFunc[iLevel] = Func;
+
+}
+/* end of LogFuncOverwrite() */
+
+
+
+#ifdef LOG_TEST
+
+
+#define TEXT "Lorem ipsum dolor sit amet"
+
+void
+PrintSomeTextToAll(log_t *prLog) {
+ int iAux;
+ for (iAux=0; iAux<LOG_NUM_LEVELS; iAux++) {
+ Log(prLog, iAux, TEXT);
+ }
+}
+
+
+int
+main(int argc, char**argv) {
+ log_t prLog;
+ log_t pr2ndLog;
+ FILE *prFP;
+ char *pcTmpFileName = "schmock.txt";
+
+ prFP = fopen(pcTmpFileName, "w");
+
+
+ LogDefaultSetup(&prLog);
+ LogDefaultSetup(&pr2ndLog);
+
+ printf("Printing to log:\n");
+ PrintSomeTextToAll(&prLog);
+ printf("---\n");
+
+ printf("Printing to pr2ndLog:\n");
+ PrintSomeTextToAll(&prLog);
+ printf("---\n");
+
+
+
+ printf("Changing second log's FP to write to '%s'\n", pcTmpFileName);
+ LogSetFPForAll(&pr2ndLog, prFP);
+
+ printf("Printing to pr2ndLog:\n");
+ PrintSomeTextToAll(&pr2ndLog);
+ printf("---\n");
+
+
+ printf("Changing Info() to new function (Fatal()) in log:\n");
+ LogFuncOverwrite(&prLog, LOG_INFO, &LogFatal);
+
+ printf("Printing to log:\n");
+ PrintSomeTextToAll(&prLog);
+ printf("---\n");
+
+
+
+ fclose(prFP);
+
+ return 0;
+}
+
+
+#endif
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id$
+ */
+
+
+#include <stdio.h>
+#include <stdarg.h>
+
+#ifndef LOG_H
+#define LOG_H
+
+
+#define LOG_DEBUG 0
+#define LOG_VERBOSE 1
+#define LOG_INFO 2
+#define LOG_WARN 3
+#define LOG_FORCED_DEBUG 4
+#define LOG_ERROR 5
+#define LOG_CRITICAL 6
+#define LOG_FATAL 7
+
+#define LOG_NUM_LEVELS 8
+
+
+typedef struct {
+ /* the higher the level, the more priority it has. numbers must be
+ * sequential
+ */
+
+ /* array of function pointers */
+ void (*prFunc[LOG_NUM_LEVELS]) (FILE *prFP, char *pcFormat, va_list rVArgList);
+ FILE *prFP[LOG_NUM_LEVELS];
+ char *prPrefix[LOG_NUM_LEVELS];
+
+ /* everything above this level will be printed */
+ int iLogLevelEnabled;
+} log_t;
+
+
+
+/* a standard logger */
+extern log_t rLog;
+
+
+
+void
+LogDefaultSetup(log_t *log);
+void
+Log(log_t *prLog, int iLevel, char *pcFmt, ...);
+void
+LogSetFP(log_t *log, int level, FILE *fp);
+void
+LogSetFPForAll(log_t *log, FILE *fp);
+FILE *
+LogGetFP(log_t *prLog, int iLevel);
+void
+LogMute(log_t *log, int level);
+void
+LogMuteAll(log_t *log);
+void
+LogFuncOverwrite(log_t *prLog, int iLevel,
+ void (*Func) (FILE *prFP, char *pcFormat, va_list rVArgList));
+
+
+#endif
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: mbed.c 254 2011-06-21 13:07:50Z andreas $
+ *
+ *
+ * Reimplementation from scratch of mBed:
+ * Blackshields et al. (2010); PMID 20470396
+ *
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <assert.h>
+#include <float.h>
+
+#include "mbed.h"
+#include "pair_dist.h"
+#include "symmatrix.h"
+#include "ktuple_pair.h"
+#include "tree.h"
+#include "util.h"
+#include "progress.h"
+#include "queue.h"
+
+#include "log.h"
+#include "kmpp/KMeans.h"
+#include "mbed.h"
+
+#define TIMING 0
+#if TIMING
+#include "squid/stopwatch.h"
+#endif
+
+
+/* If FULL_WITHIN_CLUSTER_DISTANCES is not 0, distances within each
+ * bisecting kmeans subcluster are not estimated using the vectors,
+ * but calculated normally (using ktuple or kimura). Surprisingly this
+ * results in 3% loss on a Homfam p24-h2010-08-09 subset (100-5000
+ * seqs in test, at least 5 ref seqs; MAX_SEQ 100 vs 10000; NUM_SEEDS
+ * log2 instead of log2^2). And of course it slows things down.
+ */
+#define FULL_WITHIN_CLUSTER_DISTANCES 1
+
+#define COMPUTE_WITHIN_SUBCLUSTER_AVERAGE 0
+
+/* Cluster size limits. Maximum is a soft limit, which might be
+ * exceeded if a K-Means split was unsuccesful, where unsuccesful
+ * might also mean that the minimum required number seqs. was not
+ * reached */
+#if FULL_WITHIN_CLUSTER_DISTANCES
+static const int MAX_ALLOWED_SEQ_PER_PRECLUSTER = 100;
+static const int MIN_REQUIRED_SEQ_PER_PRECLUSTER = 1;
+#else
+static const int MAX_ALLOWED_SEQ_PER_PRECLUSTER = 10000;
+static const int MIN_REQUIRED_SEQ_PER_PRECLUSTER = 100;
+#endif
+
+/* How many restarts per bisecting kmeans split. 10 give 0.5% increase
+ * in quality on original HOMFAM over just 1. It also increases kmeans
+ * time by a factor of ~3, but overall time is insignificant
+ * compared to pairdist/progressive alignment part.
+ */
+static const int RESTARTS_PER_SPLIT = 10;
+
+
+/* Use standard kmeans (lloyds) or kmeans++. Both are almost
+ * indistinguishable here, although kmeans++ is slightly ahead the
+ * fewer seeds you pick (and it should be better in theory)
+ */
+#define USE_KMEANS_LLOYDS 0
+
+
+#ifndef HAVE_LOG2
+#define log2(x) (log(x) / 0.69314718055994530942)
+#endif
+#define NUMBER_OF_SEEDS(n) pow(log2(((double)n)), 2)
+
+
+/* Seed selection method: SAMPLE_SEEDS_BY_LENGTH is the original mBed
+ * approach: Sample iSeeds sequence with constant stride from length-sorted X.
+ * It might be better to pick the seeds randomly, because length sorting might
+ * be more prone to including outliers (e.g. very long and very short seqs).
+ * However, we could never observer such a thing. So just stick to the
+ * original version as this also removes the random element.
+ */
+enum SEED_SELECTION_TYPE {
+ SELECT_SEEDS_RANDOMLY,
+ SELECT_SEEDS_BY_LENGTH
+};
+#define SEED_SELECTION SELECT_SEEDS_BY_LENGTH
+
+
+/* Tests on BAliBase (RV11,12,20,30,40,50; 10 runs each) show there is
+ * no difference between mbed-trees created from cosine or euclidean
+ * distances (simple version, just using disparities).
+ */
+#define USE_EUCLIDEAN_DISTANCE 1
+
+
+/* print some mbed pre-cluster usage to screen */
+#define PRINT_CLUSTER_DISTRIBUTION 0
+
+
+#define TRACE 0
+
+
+typedef struct {
+ /* Number of final clusters
+ */
+ int iNClusters;
+
+ /* Coordinates (columns) for each cluster (rows)
+ * valid indices: [0...iNClusters][0...dim-1]
+ */
+ double **ppdClusterCenters;
+
+ /* Dimensionality of input data and cluster center coordinates
+ */
+ int iDim;
+
+ /* Number of objects per cluster
+ */
+ int *piNObjsPerCluster;
+
+ /* Objects (indices) for each cluster. [i][j] will point to (index
+ * of) object j in cluster i
+ */
+ int **ppiObjIndicesPerCluster;
+} bisecting_kmeans_result_t;
+
+
+
+/**
+ * @brief Free KMeans result structure.
+ *
+ * @param[out] prResult_p
+ * K-Means result to free
+ *
+ * @see NewKMeansResult()
+ */
+void
+FreeKMeansResult(bisecting_kmeans_result_t **prResult_p)
+{
+ int iAux;
+ CKFREE((*prResult_p)->piNObjsPerCluster);
+ for (iAux=0; iAux<(*prResult_p)->iNClusters; iAux++) {
+ CKFREE((*prResult_p)->ppiObjIndicesPerCluster[iAux]);
+ CKFREE((*prResult_p)->ppdClusterCenters[iAux]);
+ }
+ CKFREE((*prResult_p)->ppiObjIndicesPerCluster);
+ CKFREE((*prResult_p)->ppdClusterCenters);
+ (*prResult_p)->iNClusters = 0;
+ (*prResult_p)->iDim = 0;
+ CKFREE(*prResult_p);
+}
+/*** end: FreeKMeansResult() ***/
+
+
+
+/**
+ * @brief Allocate new KMeans result
+ *
+ * @param[out] prKMeansResult_p
+ * K-Means result to free
+ *
+ * @see NewKMeansResult()
+ */
+void
+NewKMeansResult(bisecting_kmeans_result_t **prKMeansResult_p)
+{
+ (*prKMeansResult_p) = (bisecting_kmeans_result_t *)
+ CKCALLOC(1, sizeof(bisecting_kmeans_result_t));
+ (*prKMeansResult_p)->iNClusters = 0;
+ (*prKMeansResult_p)->iDim = 0;
+ (*prKMeansResult_p)->ppdClusterCenters = NULL;
+ (*prKMeansResult_p)->piNObjsPerCluster = NULL;
+ (*prKMeansResult_p)->ppiObjIndicesPerCluster = NULL;
+
+}
+/*** end: NewKMeansResult() ***/
+
+
+
+/**
+ * @brief Calculate the euclidean distance between two vectors
+ *
+ * @param[in] v1
+ * First vector with dim dimensions
+ * @param[in] v2
+ * Second vector with dim dimensions
+ * @param[in] dim
+ * Dimensionality of v1 and v2
+ *
+ * @return euclidean distance as double
+ *
+ * @note Could probably be inlined. Also perfect for SSE
+ */
+double
+EuclDist(const double *v1, const double *v2, const int dim)
+{
+ int i; /* aux */
+ double dist; /* returned distance */
+
+ assert(v1!=NULL);
+ assert(v2!=NULL);
+
+ dist = 0.0;
+ for (i=0; i<dim; i++) {
+ dist += pow(v1[i]-v2[i], 2.0);
+ }
+
+ return sqrt(dist);
+}
+/*** end: EuclDist() ***/
+
+
+
+/**
+ * @brief Calculate the cosine distance between two vectors
+ *
+ * @param[in] v1
+ * First vector with dim dimensions
+ * @param[in] v2
+ * Second vector with dim dimensions
+ * @param[in] dim
+ * Dimensionality of v1 and v2
+ *
+ * @return cosine distance as double
+ *
+ * @note Could probably be inlined. Also perfect for SSE
+ */
+double
+CosDist(const double *v1, const double *v2, const int dim)
+{
+ int i; /* aux */
+ double dist; /* returned distance */
+ double s, sq1, sq2;
+
+ assert(v1!=NULL);
+ assert(v2!=NULL);
+
+ s = 0.0;
+ sq1 = 0.0;
+ sq2 = 0.0;
+ for (i=0; i<dim; i++) {
+ s += (v1[i]*v2[i]);
+ sq1 += pow(v1[i], 2.0);
+ sq2 += pow(v2[i], 2.0);
+ }
+ sq1 = sqrt(sq1);
+ sq2 = sqrt(sq2);
+
+ if ((sq1 * sq2) < DBL_EPSILON) {
+ dist = 1 - s / (sq1 * sq2);
+ } else {
+ /* if the denominator gets small, the fraction gets big, hence dist
+ gets small: */
+ dist = 0.0;
+ }
+ return dist;
+}
+/*** end: CosDist() ***/
+
+
+
+/**
+ * @brief convert sequences into mbed-like (distance) vector
+ * representation. Seeds (prMSeq sequence indices) have to be picked before
+ *
+ * @param[out] ppdSeqVec
+ * Pointer to preallocated matrix of size nseqs x iSeeds
+ * @param[in] prMSeq
+ * Sequences which are to be converted
+ * @param[in] piSeeds
+ * Array of sequences in prMSeq which are to be used as seeds.
+ * @param[in] iNumSeeds
+ * Number of seeds/elements in piSeeds
+ * @param[in] iPairDistType
+ * Type of pairwise distance comparison
+ *
+ */
+int
+SeqToVec(double **ppdSeqVec, mseq_t *prMSeq,
+ int *piSeeds, const int iNumSeeds,
+ const int iPairDistType)
+{
+ symmatrix_t *prDistmat = NULL;
+ int iSeqIndex;
+ int iSeedIndex;
+ /* indices for restoring order */
+ int *restore;
+ /* sorted copy of piSeeds */
+ int *piSortedSeeds;
+
+#if TIMING
+ Stopwatch_t *stopwatch = StopwatchCreate();
+ StopwatchZero(stopwatch);
+ StopwatchStart(stopwatch);
+#endif
+
+ assert(NULL != ppdSeqVec);
+ assert(iNumSeeds>0 && iNumSeeds<=prMSeq->nseqs);
+
+ piSortedSeeds = CKMALLOC(iNumSeeds * sizeof(int));
+ memcpy(piSortedSeeds, piSeeds, iNumSeeds*sizeof(int));
+
+ /* need them sorted, otherwise the swapping approach below might
+ * break
+ */
+ qsort(piSortedSeeds, iNumSeeds, sizeof(int), IntCmp);
+
+
+ /* rearrange mseq order so that we can use ktuple_pairdist code as
+ * is. That is, swap seeds and non-seeds such that the seeds end
+ * up in front of mseq. This way we can use the KTuplePairDist()
+ * code, without making a copy of mseq. Also, keep an array of
+ * indices which serves to restore the original sequence order
+ * after putting the seeds in front
+ *
+ */
+ restore = (int *) CKMALLOC(prMSeq->nseqs * sizeof(int));
+ for (iSeqIndex=0; iSeqIndex<prMSeq->nseqs; iSeqIndex++) {
+ restore[iSeqIndex] = iSeqIndex;
+ }
+ for (iSeedIndex=0; iSeedIndex<iNumSeeds; iSeedIndex++) {
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "Swapping seqs %d and %u", piSortedSeeds[iSeedIndex], iSeedIndex);
+#endif
+ if (piSortedSeeds[iSeedIndex]!=iSeedIndex) {
+ int swap;
+ SeqSwap(prMSeq, piSortedSeeds[iSeedIndex], iSeedIndex);
+
+ swap = restore[iSeedIndex];
+ restore[iSeedIndex] = restore[piSortedSeeds[iSeedIndex]];
+ restore[piSortedSeeds[iSeedIndex]] = swap;
+ }
+ }
+#if TRACE
+ printf("DEBUG(%s|%s():%d): restore indices =",
+ __FILE__, __FUNCTION__, __LINE__);
+ for (iSeqIndex=0; iSeqIndex<prMSeq->nseqs; iSeqIndex++) {
+ printf(" %u:%u", iSeqIndex, restore[iSeqIndex]);
+ }
+ printf("\n");
+
+ for (iSeqIndex=0; iSeqIndex<prMSeq->nseqs; iSeqIndex++) {
+ Log(&rLog, LOG_FORCED_DEBUG, "swapped seq no %d now: seq = %s",
+ iSeqIndex, prMSeq->sqinfo[iSeqIndex].name);
+ }
+#endif
+
+
+ /* convert sequences into vectors of distances by calling pairwise
+ * distance function for each seq/seed pair
+ *
+ */
+ if (0 != PairDistances(&prDistmat, prMSeq, iPairDistType,
+ 0, iNumSeeds, 0, prMSeq->nseqs,
+ NULL, NULL)) {
+ Log(&rLog, LOG_ERROR, "Could not compute pairwise distances for mbed.");
+ FreeSymMatrix(&prDistmat);
+ CKFREE(piSortedSeeds);
+ CKFREE(restore);
+ return -1;
+ }
+#if TRACE
+ {
+ char **labels;
+ labels = (char **) CKMALLOC(prMSeq->nseqs * sizeof(char *));
+ for (iSeqIndex=0; iSeqIndex<prMSeq->nseqs; iSeqIndex++) {
+ labels[iSeqIndex] = prMSeq->sqinfo[iSeqIndex].name;
+ }
+ SymMatrixPrint(prDistmat, labels, NULL);
+ CKFREE(labels);
+ }
+#endif
+
+
+ /* update ppdSeqVec according to prDistmat. keep in mind that we
+ * changed mseq order
+ *
+ */
+ for (iSeqIndex=0; iSeqIndex<prMSeq->nseqs; iSeqIndex++) {
+ for (iSeedIndex=0; iSeedIndex<iNumSeeds; iSeedIndex++) {
+ ppdSeqVec[restore[iSeqIndex]][iSeedIndex] =
+ SymMatrixGetValue(prDistmat, iSeqIndex, iSeedIndex);
+ }
+ }
+
+
+ /* restore mseq order by reverse swapping
+ *
+ * need reverse order now, so start from top index
+ */
+ iSeedIndex=iNumSeeds-1;
+ do {
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "Swapping seqs %d and %d", piSortedSeeds[iSeedIndex], iSeedIndex);
+#endif
+ if (piSortedSeeds[iSeedIndex]!=iSeedIndex) {
+ int swap;
+
+ SeqSwap(prMSeq, piSortedSeeds[iSeedIndex], iSeedIndex);
+
+ swap = restore[iSeedIndex];
+ restore[iSeedIndex] = restore[piSortedSeeds[iSeedIndex]];
+ restore[piSortedSeeds[iSeedIndex]] = swap;
+ }
+ } while (0 != iSeedIndex--);
+#if TRACE
+ for (iSeqIndex=0; iSeqIndex<prMSeq->nseqs; iSeqIndex++) {
+ Log(&rLog, LOG_FORCED_DEBUG, "restored seq no %d: seq = %s %s",
+ iSeqIndex, prMSeq->sqinfo[iSeqIndex].name, prMSeq->seq[iSeqIndex]);
+ }
+#endif
+
+#if TRACE
+ for (iSeqIndex=0; iSeqIndex<prMSeq->nseqs; iSeqIndex++) {
+ printf("DEBUG: seq %-4u as distance vector =", iSeqIndex);
+ for (iSeedIndex=0; iSeedIndex<iNumSeeds; iSeedIndex++) {
+ printf(" %f", ppdSeqVec[iSeqIndex][iSeedIndex]);
+ }
+ printf("\n");
+ }
+#endif
+
+
+ FreeSymMatrix(&prDistmat);
+ CKFREE(restore);
+#if TIMING
+ StopwatchStop(stopwatch);
+ StopwatchDisplay(stdout, "Total time for SeqToVec(): ", stopwatch);
+ StopwatchFree(stopwatch);
+#endif
+
+
+ return 0;
+}
+/*** end: SeqToVec() ***/
+
+
+
+/**
+ * @brief Select seeds to be used from an prMSeq
+ *
+ * @param[out] piSeeds
+ * Will store the indices of prMSeqs seqs used to be as seeds here. Must be preallocated.
+ * @param[in] iNumSeeds
+ * Number of seeds to be picked
+ * @param[in] iSelectionMethod
+ * Seed selection method to be used
+ * @param[in] prMSeq
+ * The prMSeq structure to pick sequences from
+ *
+ * @return: Non-zero on failure
+ *
+ */
+int
+SeedSelection(int *piSeeds, int iNumSeeds, int iSelectionMethod, mseq_t *prMSeq)
+{
+ /* seed iterator */
+ int iSeedIndex;
+ /* sequence iterator */
+ int iSeqIndex;
+
+ if (SELECT_SEEDS_RANDOMLY == iSelectionMethod) {
+ int *piPermArray;
+
+ Log(&rLog, LOG_INFO,
+ "Using %d seeds (randomly chosen) for mBed (from a total of %d sequences)",
+ iNumSeeds, prMSeq->nseqs);
+
+ PermutationArray(&piPermArray, iNumSeeds);
+ /* copy to piSeeds */
+ for (iSeedIndex=0; iSeedIndex<iNumSeeds; iSeedIndex++) {
+ piSeeds[iSeedIndex] = piPermArray[iSeedIndex];
+ }
+ CKFREE(piPermArray);
+
+ } else if (SELECT_SEEDS_BY_LENGTH == iSelectionMethod) {
+
+ /* step size for picking with constant stride */
+ int iStep;
+ int *piSeqLen = CKMALLOC(prMSeq->nseqs * sizeof(int));
+ int *piOrder = CKMALLOC(prMSeq->nseqs * sizeof(int));
+
+ Log(&rLog, LOG_INFO,
+ "Using %d seeds (chosen with constant stride from length sorted seqs) for mBed (from a total of %d sequences)",
+ iNumSeeds, prMSeq->nseqs);
+
+ iStep = prMSeq->nseqs / iNumSeeds; /* iStep will never get too big
+ * due to rounding */
+ /* first get an array of seq indices order according to
+ corresponding sequence length: piOrder */
+ for (iSeqIndex=0; iSeqIndex<prMSeq->nseqs; iSeqIndex++) {
+ piSeqLen[iSeqIndex] = prMSeq->sqinfo[iSeqIndex].len;
+ }
+ QSortAndTrackIndex(piOrder, piSeqLen, prMSeq->nseqs, 'd', FALSE);
+#if 0
+ for (iSeqIndex=0; iSeqIndex<prMSeq->nseqs; iSeqIndex++) {
+ Log(&rLog, LOG_FORCED_DEBUG, "Descending order (no %d): seq %d has len %d)",
+ iSeqIndex, piOrder[iSeqIndex], piSeqLen[piOrder[iSeqIndex]]);
+ }
+#endif
+ CKFREE(piSeqLen);
+ iSeedIndex = 0;
+ for (iSeqIndex=0; iSeedIndex<iNumSeeds; iSeqIndex+=iStep) {
+ piSeeds[iSeedIndex++] = piOrder[iSeqIndex];
+ }
+ CKFREE(piOrder);
+
+ } else {
+
+ Log(&rLog, LOG_ERROR, "Internal error: unknown seed selection type");
+ return -1;
+ }
+
+
+#ifdef PICK_SEEDS_FROM_KMEANS_CLUSTERS
+ /* do initial mbedding and kmeans. then pick seeds from each cluster and
+ do full mbed with these seeds. idea is that those seeds represent the
+ sequence space better than random seeds. however, this reduces the
+ quality slightly. random is almost always better.
+ */
+
+ if (1) {
+ /* seqs represented as distance vectors */
+ double **ppdSeqVec;
+ double dCost = -1.0;
+ /* assignments for each seq to the K newly created clusters */
+ int *piKMeansClusterAssignments = CKMALLOC(prMSeq->nseqs * sizeof(int));
+ double *pdKMeansClusterCenters = CKCALLOC(iNumSeeds * iNumSeeds, sizeof(double));
+ /* create a copy of ppdSeqVec suitable for KMeans */
+ double *pdKMeansVectors = CKMALLOC(prMSeq->nseqs * iNumSeeds * sizeof(double));
+ bool *pbClusterUsed = CKCALLOC(iNumSeeds, sizeof(bool));
+
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "FIXME Experimental feature: K-means on first round embedding to get better seeds");
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "FIXME Reuse seeds from clusters");
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "FIXME Could try log(n) instead of log(n)^2 in first round");
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "FIXME hardcoded iPairDistType PAIRDIST_KTUPLE");
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "FIXME Show that this is fast *and* good");
+
+ /*
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "Overriding iNumSeeds");
+ iNumSeeds = (int) pow(log2((double)prMSeq->nseqs), 2);
+ */
+
+ ppdSeqVec = (double **) CKMALLOC(prMSeq->nseqs * sizeof(double *));
+ for (iSeqIndex=0; iSeqIndex<prMSeq->nseqs; iSeqIndex++) {
+ ppdSeqVec[iSeqIndex] = (double *) CKMALLOC(iNumSeeds * sizeof(double));
+ }
+ if (0 != SeqToVec(ppdSeqVec, prMSeq, piSeeds, iNumSeeds, PAIRDIST_KTUPLE)) {
+ Log(&rLog, LOG_ERROR, "Could not convert sequences into vectors for mbed");
+ return -1;
+ }
+
+ for (iSeqIndex=0; iSeqIndex<prMSeq->nseqs; iSeqIndex++) {
+ int iDim;
+ for (iDim=0; iDim<iNumSeeds; ++iDim) {
+ pdKMeansVectors[iDim*iSeqIndex + iDim] = ppdSeqVec[iSeqIndex][iDim];
+ }
+ }
+
+
+ Log(&rLog, LOG_FORCED_DEBUG, "%s\n", "FIXME hardcoded RESTARTS_PER_SPLIT");
+ dCost = KMeans(prMSeq->nseqs, iNumSeeds, iNumSeeds,
+ pdKMeansVectors,
+ RESTARTS_PER_SPLIT, USE_KMEANS_LLOYDS,
+ pdKMeansClusterCenters, piKMeansClusterAssignments);
+ Log(&rLog, LOG_FORCED_DEBUG, "Best split cost = %f", dCost);
+
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "FIXME Check for Nan in cluster centers");
+
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "K-Means output:");
+ for (iSeqIndex=0; iSeqIndex<prMSeq->nseqs; iSeqIndex++) {
+ Log(&rLog, LOG_FORCED_DEBUG, " Raw assignment: Seq %u (%s) to cluster %d",
+ iSeqIndex, prMSeq->sqinfo[iSeqIndex].name,
+ piKMeansClusterAssignments[iSeqIndex]);
+ }
+#endif
+
+ Log(&rLog, LOG_FORCED_DEBUG, "FIXME %s", "proof of concept implementation: Pick first sequences from each clusters instead of reusing seeds");
+ iSeedIndex = 0;
+ for (iSeqIndex=0; iSeqIndex<prMSeq->nseqs; iSeqIndex++) {
+ int iAssignedCluster = piKMeansClusterAssignments[iSeqIndex];
+ if (pbClusterUsed[iAssignedCluster]) {
+ continue;
+ } else {
+ /*LOG_DEBUG("Picked seed %d from cluster %d", iSeqIndex,iAssignedCluster);*/
+ piSeeds[iSeedIndex++] = iSeqIndex;
+ pbClusterUsed[iAssignedCluster] = TRUE;
+ }
+ }
+ CKFREE(pbClusterUsed);
+
+ CKFREE(pdKMeansVectors);
+ CKFREE(pdKMeansClusterCenters);
+ CKFREE(piKMeansClusterAssignments);
+
+ }
+ /* if (1) */
+#endif
+
+
+ if (LOG_DEBUG <= rLog.iLogLevelEnabled) {
+ for (iSeedIndex=0; iSeedIndex<iNumSeeds; iSeedIndex++) {
+ Log(&rLog, LOG_DEBUG, "Picked sequence %d (%s) as seed no %d",
+ piSeeds[iSeedIndex], prMSeq->sqinfo[piSeeds[iSeedIndex]].name, iSeedIndex);
+ }
+ }
+
+ return 0;
+}
+/* end of SeedSelection() */
+
+
+
+
+/**
+ * @brief Bisecting K-Means clustering. Repeatedly calls K-Means with
+ * a K of 2 until no cluster has more than iMaxAllowedObjsPerCluster.
+ *
+ * @param[out] prKMeansResult_p
+ * Result of Bisecting KMeans. Will be allocated here.
+ * Caller has to free. See @see FreeKMeansResult()
+ * @param[in] iNObjs
+ * Number of objects/sequences to cluster
+ * @param[in] iDim
+ * Dimensionality of input data
+ * @param[in] ppdVectors
+ * each row holds iDim points for this object's coordinates
+ * @param[in] iMinRequiredObjsPerCluster
+ * Minimum number of objects per Cluster (inclusive)/
+ * @param[in] iMaxAllowedObjsPerCluster
+ * Maximum number of objects per Cluster (inclusive). Function returns once no
+ * cluster contains more then this number of objects. Soft limit!
+ *
+ * @note Convoluted code. Could use some restructuring. My apologies.
+ * AW
+ *
+ */
+void
+BisectingKmeans(bisecting_kmeans_result_t **prKMeansResult_p,
+ const int iNObjs, const int iDim, double **ppdVectors,
+ const int iMinRequiredObjsPerCluster,
+ const int iMaxAllowedObjsPerCluster)
+{
+ int iN, iD;
+ /* cluster centers for each cluster created at each split */
+ double *pdKClusterCenters;
+ /* keep track of updated object indices per newly created
+ * cluster */
+ int *piCurObjToUpdate;
+ /* number of times we called 2-means */
+ int iNRounds;
+ /* flag for unsuccessful cluster split */
+ bool bNaNDetected = FALSE;
+ /* flag for detected small cluster after split */
+ bool bSmallClusterDetected;
+ /* queue of clusters which are to be split */
+ int_queue_t rClusterSplitQueue;
+
+#if TIMING
+ Stopwatch_t *stopwatch = StopwatchCreate();
+#endif
+
+
+ piCurObjToUpdate = (int *) CKMALLOC(2 * sizeof(int));
+
+ NewKMeansResult(prKMeansResult_p);
+
+ /* new cluster centers created at each split/KMeans run
+ */
+ pdKClusterCenters = (double *) CKCALLOC(2 * iDim, sizeof(double));
+
+ /* init results by setting a first cluster that contains all objects
+ */
+ (*prKMeansResult_p)->iNClusters = 1;
+ (*prKMeansResult_p)->iDim = iDim;
+ /* fake center coordinates of first cluster */
+ (*prKMeansResult_p)->ppdClusterCenters =
+ (double **) CKMALLOC(1 * sizeof(double *));
+ (*prKMeansResult_p)->ppdClusterCenters[0] =
+ (double *) CKMALLOC(iDim * sizeof(double));
+ /* objects per cluster */
+ (*prKMeansResult_p)->piNObjsPerCluster =
+ (int *) CKMALLOC(1 * sizeof(int));
+ (*prKMeansResult_p)->piNObjsPerCluster[0] = iNObjs;
+ /* object indices per cluster */
+ (*prKMeansResult_p)->ppiObjIndicesPerCluster =
+ (int **) CKMALLOC(1 * sizeof(int *));
+ (*prKMeansResult_p)->ppiObjIndicesPerCluster[0] = (int *)
+ CKMALLOC(iNObjs * sizeof(int));
+ for (iN=0; iN<iNObjs; iN++) {
+ (*prKMeansResult_p)->ppiObjIndicesPerCluster[0][iN] = iN;
+ }
+
+
+
+ /* Starting with the first cluster that now contains all the
+ * sequences keep splitting until no cluster contains more than
+ * iMaxAllowedObjsPerCluster
+ *
+ * Keep a queue of clusters (rClusterSplitQueue) to split
+ *
+ * At each split values/memory of the just split cluster will be
+ * reused and exactly one new only allocated.
+ *
+ * Example:
+ * Given the following cluster assignments
+ * 0 0 0 0 1 1 2 2 2 3 3 3 3 3 3 3 4 4
+ * and a K-Means split in cluster 3 at |:
+ * 0 0 0 0 1 1 2 2 2 3 3 3 | 3 3 3 3 4 4
+ * The result should be this:
+ * 0 0 0 0 1 1 2 2 2 3 3 3 | 5 5 5 5 4 4
+ *
+ *
+ */
+ INT_QUEUE_INIT(&rClusterSplitQueue);
+ if (iNObjs>iMaxAllowedObjsPerCluster) {
+ /* pish fake first cluster index */
+ INT_QUEUE_PUSH(&rClusterSplitQueue, 0);
+ }
+ iNRounds = 0;
+ while (! INT_QUEUE_EMPTY(&rClusterSplitQueue)) {
+ /* assignments for each seq to the K newly created clusters */
+ int *piKClusterAssignments;
+ /* number of objects in cluster that is to be split */
+ int iNObjsInClusterToSplit;
+ /* coordinates of points in cluster that is to be split
+ * array of size n*d where [d*i + j] gives coordinate j of point i
+ */
+ double *pdVectorsInClusterToSplit;
+ /* copy of object indices in split cluster */
+ int *piObjIndicesOfSplitCluster;
+ /* best cost of kmeans rounds */
+ double dCost = -1.0;
+
+ /* indices for the two created clusters
+ */
+ /* index of cluster to split */
+ int iClusterToSplot;
+ /* index of newly created cluster at each round. data for the
+ other created cluster goes to the one just split,
+ i.e. (*piClusterToSplot) */
+ int iNewClusterIdx;
+
+#if TIMING
+ StopwatchZero(stopwatch);
+ StopwatchStart(stopwatch);
+#endif
+
+ INT_QUEUE_POP(&rClusterSplitQueue, &iClusterToSplot);
+
+ iNObjsInClusterToSplit = (*prKMeansResult_p)->piNObjsPerCluster[iClusterToSplot];
+ piKClusterAssignments = (int *)
+ CKMALLOC(iNObjsInClusterToSplit * sizeof(int));
+
+ pdVectorsInClusterToSplit = (double *)
+ CKMALLOC(iNObjsInClusterToSplit * iDim * sizeof(double));
+ for (iN=0; iN<iNObjsInClusterToSplit; iN++) {
+ for (iD=0; iD<iDim; ++iD) {
+ int iThisObjIdx =
+ (*prKMeansResult_p)->ppiObjIndicesPerCluster[iClusterToSplot][iN];
+ pdVectorsInClusterToSplit[iDim*iN + iD] = ppdVectors[iThisObjIdx][iD];
+ }
+ }
+
+#if TRACE
+ Log(&rLog, LOG_FOCRED_DEBUG, "Round %d: Will split cluster %d which has %d objects",
+ iNRounds, iClusterToSplot, iNObjsInClusterToSplit);
+ fprintf(stderr, "DEBUG(%s|%s():%d): Object indices in cluster to split are:",
+ __FILE__, __FUNCTION__, __LINE__);
+ for (iN=0; iN<iNObjsInClusterToSplit; iN++) {
+ fprintf(stderr, " %u",
+ (*prKMeansResult_p)->ppiObjIndicesPerCluster[iClusterToSplot][iN]);
+ }
+ fprintf(stderr, "\n");
+ (void) fflush(stderr);
+#endif
+
+#if TRACE
+ for (iN=0; iN<iNObjsInClusterToSplit; iN++) {
+ fprintf(stderr,
+ "DEBUG(%s|%s():%d): Coordinate of object %u (real index %u) in cluster to split:",
+ __FILE__, __FUNCTION__, __LINE__, iN,
+ (*prKMeansResult_p)->ppiObjIndicesPerCluster[iClusterToSplot][iN]);
+ for (iD=0; iD<iDim; iD++) {
+ fprintf(stderr, " %f", pdVectorsInClusterToSplit[iDim*iN + iD]);
+ }
+ fprintf(stderr, "\n");
+ (void) fflush(stderr);
+ }
+#endif
+
+ /* KMeans(1 "The number of points in the data set",
+ * 2 "The number of clusters to look for",
+ * 3 "The number of dimensions that the data set lives in",
+ * 4 "points: An array of size n*d where points[d*i + j] gives coordinate j of point i",
+ * 5 "attempts: The number of times to independently run k-means",
+ * 6 "use_lloyds_method: uses kmpp if false, otherwise lloyds method",
+ * 7 "centers: This can either be null or an array of size k*d.
+ * In the latter case, centers[d*i + j] will give coordinate j of center i.
+ * If the cluster is unused, it will contain NaN instead.",
+ * 8 "assignments: This can either be null or an array of size n.
+ * In the latter case, it will be filled with the cluster that each point is assigned to
+ * (an integer between 0 and k-1 inclusive).");
+ */
+ dCost = KMeans(iNObjsInClusterToSplit, 2, iDim,
+ pdVectorsInClusterToSplit,
+ RESTARTS_PER_SPLIT, USE_KMEANS_LLOYDS,
+ pdKClusterCenters, piKClusterAssignments);
+
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "Raw K-Means output:");
+ for (iN=0; iN<2; iN++) {
+ fprintf(stderr, "DEBUG(%s|%s():%d): Cluster Center %u =",
+ __FILE__, __FUNCTION__, __LINE__, iN);
+ for (iD=0; iD<iDim; iD++) {
+ fprintf(stderr, " %f", pdKClusterCenters[iN*iDim+iD]);
+ }
+ fprintf(stderr, "\n");
+ (void) fflush(stderr);
+ }
+ for (iN=0; iN<iNObjsInClusterToSplit; iN++) {
+ Log(&rLog, LOG_FORCED_DEBUG, " Raw assignment: Seq %u to cluster %d (of #%u)",
+ iN, piKClusterAssignments[iN], 2);
+ }
+#endif
+
+ /* real index of one of the newly created clusters. the other
+ * one is iClusterToSplot */
+ iNewClusterIdx = (*prKMeansResult_p)->iNClusters;
+
+
+ /* We don't want Clusters which are too small. Check here if a
+ * split created a small cluster and if yes, discard the
+ * solution. Because the cluster has already been removed from
+ * the queue, we can just continue.
+ */
+ bSmallClusterDetected = FALSE;
+ if (iMinRequiredObjsPerCluster>1) {
+ int iNObjsCluster[2];
+ iNObjsCluster[0] = 0; /* first cluster */
+ iNObjsCluster[1] = 0; /* second cluster */
+ for (iN=0; iN<iNObjsInClusterToSplit; iN++) {
+ iNObjsCluster[piKClusterAssignments[iN]]+=1;
+ }
+
+ if (iNObjsCluster[0]<iMinRequiredObjsPerCluster
+ ||
+ iNObjsCluster[1]<iMinRequiredObjsPerCluster) {
+ bSmallClusterDetected = TRUE;
+ Log(&rLog, LOG_FORCED_DEBUG, "Skipping this split because objs in 1st/2nd cluster = %d/%d < %d",
+ iNObjsCluster[0], iNObjsCluster[1], iMinRequiredObjsPerCluster);
+ }
+ }
+
+ /* Same logic as for small clusters applies if KMeans couldn't
+ * split the cluster. In this case one of its center
+ * coordinates will be NaN, which we check for in the
+ * following.
+ */
+ if (! bSmallClusterDetected) {
+ for (iN=0; iN<2; iN++) {
+ bNaNDetected = FALSE;
+ for (iD=0; iD<iDim; iD++) {
+ if (0 != isnan(pdKClusterCenters[iN*iDim+iN])) {
+ /* Got NaN as coordinate after splitting */
+ Log(&rLog, LOG_WARN, "%s(): Can't split cluster no. %d which has %d objects any further. %s",
+ __FUNCTION__,
+ iClusterToSplot, iNObjsInClusterToSplit,
+ "Hope it's not too big and doesn't slow things down."
+ );
+ bNaNDetected = TRUE;
+ break;
+ }
+ }
+ if (bNaNDetected) {
+ break;
+ }
+ }
+ }
+
+ /* Discarding split of this cluster. It has been removed from the
+ * queue already. so just continue
+ */
+ if (bNaNDetected || bSmallClusterDetected) {
+ CKFREE(piKClusterAssignments);
+ CKFREE(pdVectorsInClusterToSplit);
+ continue;
+ }
+
+
+ /* update cluster centers: pdClusterCenters
+ *
+ */
+ /* reuse memory of existing/old/split cluster
+ */
+ for (iN=0; iN<iDim; iN++) {
+ double dCoord = pdKClusterCenters[0*iDim+iN];
+ (*prKMeansResult_p)->ppdClusterCenters[iClusterToSplot][iN] = dCoord;
+ }
+ /* realloc and set new one
+ */
+ (*prKMeansResult_p)->ppdClusterCenters = (double **)
+ CKREALLOC((*prKMeansResult_p)->ppdClusterCenters,
+ ((*prKMeansResult_p)->iNClusters+1) * sizeof(double *));
+ (*prKMeansResult_p)->ppdClusterCenters[iNewClusterIdx] = (double *)
+ CKMALLOC(iDim * sizeof(double));
+ for (iD=0; iD<iDim; iD++) {
+ double dCoord = pdKClusterCenters[1*iDim+iD];
+ (*prKMeansResult_p)->ppdClusterCenters[iNewClusterIdx][iD] = dCoord;
+ }
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "* Update of cluster centers done. Cluster centers so far:");
+ for (iN=0; iN<(*prKMeansResult_p)->iNClusters+1; iN++) {
+ fprintf(stderr, "DEBUG(%s|%s():%d): Center %u =",
+ __FILE__, __FUNCTION__, __LINE__, iN);
+ for (iD=0; iD<iDim; iD++) {
+ fprintf(stderr, " %f", (*prKMeansResult_p)->ppdClusterCenters[iN][iD]);
+ }
+ fprintf(stderr, "\n");
+ (void) fflush(stderr);
+ }
+#endif
+
+
+ /* update #seqs per cluster: piNObjsPerCluster
+ *
+ */
+ (*prKMeansResult_p)->piNObjsPerCluster = (int *)
+ CKREALLOC((*prKMeansResult_p)->piNObjsPerCluster,
+ ((*prKMeansResult_p)->iNClusters+1) * sizeof(int));
+ /* init new and old one to zero */
+ (*prKMeansResult_p)->piNObjsPerCluster[iClusterToSplot] = 0;
+ (*prKMeansResult_p)->piNObjsPerCluster[iNewClusterIdx] = 0;
+ /* now update values */
+ for (iN=0; iN<iNObjsInClusterToSplit; iN++) {
+ if (0 == piKClusterAssignments[iN]) {
+ (*prKMeansResult_p)->piNObjsPerCluster[iClusterToSplot] += 1;
+ } else if (1 == piKClusterAssignments[iN]) {
+ (*prKMeansResult_p)->piNObjsPerCluster[iNewClusterIdx] += 1;
+ } else {
+ /* there used to be code for iK>=2 in r101 */
+ Log(&rLog, LOG_FATAL, "Internal error: split into more than two clusters (got assignment %d)",
+ piKClusterAssignments[iN]);
+ }
+ }
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "* Update of NObjs per cluster done:");
+ for (iN=0; iN<(*prKMeansResult_p)->iNClusters+1; iN++) {
+ Log(&rLog, LOG_FORCED_DEBUG, "Cluster %d contains %d sequences",
+ iN, (*prKMeansResult_p)->piNObjsPerCluster[iN]);
+ }
+#endif
+ /* queue clusters if still they are still too big
+ */
+ if ((*prKMeansResult_p)->piNObjsPerCluster[iClusterToSplot] > iMaxAllowedObjsPerCluster) {
+ INT_QUEUE_PUSH(&rClusterSplitQueue, iClusterToSplot);
+ }
+ if ((*prKMeansResult_p)->piNObjsPerCluster[iNewClusterIdx] > iMaxAllowedObjsPerCluster) {
+ INT_QUEUE_PUSH(&rClusterSplitQueue, iNewClusterIdx);
+ }
+
+
+
+ /* update which objects belong to which cluster:
+ *
+ * note: piNObjsPerCluster needs to be already updated
+ *
+ */
+ /* create a copy of the object indices in the split cluster
+ * (original will be overwritten)
+ */
+ piObjIndicesOfSplitCluster = (int *) CKMALLOC(iNObjsInClusterToSplit * sizeof(int));
+ memcpy(piObjIndicesOfSplitCluster,
+ (*prKMeansResult_p)->ppiObjIndicesPerCluster[iClusterToSplot],
+ iNObjsInClusterToSplit * sizeof(int));
+
+ (*prKMeansResult_p)->ppiObjIndicesPerCluster = (int **)
+ CKREALLOC((*prKMeansResult_p)->ppiObjIndicesPerCluster,
+ ((*prKMeansResult_p)->iNClusters+1) * sizeof(int *));
+
+
+ (*prKMeansResult_p)->ppiObjIndicesPerCluster[iClusterToSplot] =
+ (int *) CKREALLOC((*prKMeansResult_p)->ppiObjIndicesPerCluster[iClusterToSplot],
+ (*prKMeansResult_p)->piNObjsPerCluster[iClusterToSplot] * sizeof(int));
+
+ (*prKMeansResult_p)->ppiObjIndicesPerCluster[iNewClusterIdx] =
+ (int *) CKMALLOC((*prKMeansResult_p)->piNObjsPerCluster[iNewClusterIdx] * sizeof(int));
+
+
+ /* now reassign the object indices to the assigned cluster
+ */
+ piCurObjToUpdate[0] = 0;
+ piCurObjToUpdate[1] = 0;
+ for (iN=0; iN<iNObjsInClusterToSplit; iN++) {
+ int iThisObjIdx = piObjIndicesOfSplitCluster[iN];
+ int iThisClusterAssignment = piKClusterAssignments[iN];
+ int iThisOffset = piCurObjToUpdate[iThisClusterAssignment];
+ int iThisClusterIndex = 0;
+
+ if (0 == iThisClusterAssignment) {
+ iThisClusterIndex = iClusterToSplot;
+ } else if (1 == iThisClusterAssignment) {
+ iThisClusterIndex = iNewClusterIdx;
+ } else {
+ /* there used to be code for iK>=2 in r101 */
+ Log(&rLog, LOG_FATAL, "Internal error: split into more than two clusters (got assignment %d)",
+ piKClusterAssignments[iN]);
+ }
+#if 0
+ Log(&rLog, LOG_FORCED_DEBUG, "Setting (*prKMeansResult_p)->ppiObjIndicesPerCluster[%d][%d] = %d",
+ iThisClusterIndex, iThisOffset, iThisObjIdx);
+#endif
+ (*prKMeansResult_p)->ppiObjIndicesPerCluster[iThisClusterIndex][iThisOffset] = iThisObjIdx;
+ piCurObjToUpdate[iThisClusterAssignment]+=1;
+ }
+ CKFREE(piObjIndicesOfSplitCluster);
+#if TRACE
+ for (iN=0; iN<(*prKMeansResult_p)->iNClusters+1; iN++) {
+ int iObj;
+ fprintf(stderr, "DEBUG(%s|%s():%d): Objects in cluster %u: ",
+ __FILE__, __FUNCTION__, __LINE__, iN);
+ for (iObj=0; iObj<(*prKMeansResult_p)->piNObjsPerCluster[iN]; iObj++) {
+ fprintf(stderr, " %u", (*prKMeansResult_p)->ppiObjIndicesPerCluster[iN][iObj]);
+ }
+ fprintf(stderr, "\n");
+ (void) fflush(stderr);
+ }
+#endif
+
+
+#if TIMING
+ StopwatchStop(stopwatch);
+ StopwatchDisplay(stdout, "Total time after next round in Bisecting-KMeans: ", stopwatch);
+#endif
+
+
+ /* finally: increase number of clusters
+ */
+ (*prKMeansResult_p)->iNClusters += 1;
+ iNRounds += 1;
+ CKFREE(piKClusterAssignments);
+ CKFREE(pdVectorsInClusterToSplit);
+
+ } /* while */
+ INT_QUEUE_DESTROY(&rClusterSplitQueue);
+
+
+ Log(&rLog, LOG_DEBUG,
+ "Bisecting K-means finished after %d rounds (no more clusters to split)",
+ iNRounds);
+
+#if TIMING
+ StopwatchFree(stopwatch);
+#endif
+
+ /* @note could use progress/timer */
+
+ CKFREE(pdKClusterCenters);
+ CKFREE(piCurObjToUpdate);
+
+ return;
+}
+/*** end: BisectingKmeans() ***/
+
+
+
+/**
+ *
+ * @brief From scratch reimplementation of mBed: Blackshields et al.
+ * (2010); PMID 20470396.
+ *
+ * Idea is a follows:
+ * - convert sequences into vectors of distances
+ * - cluster the vectors using k-means
+ * - cluster each of the k clusters using upgma (used cached distances
+ * from above?)
+ * - join the sub-clusters to create on tree (use UPGMA on k-means
+ * medoids)
+ *
+ *
+ * @param[out] prMbedTree_p
+ * Created upgma tree. will be allocated here. use FreeMuscleTree()
+ * to free
+ * @param[in] prMSeq
+ * Multiple sequences
+ * @param[in] iPairDistType
+ * Distance measure for pairwise alignments
+ * @param[in] pcGuidetreeOut
+ * Passed down to GuideTreeUpgma()
+ *
+ * @return Zero on success, non-zero on error
+ *
+ */
+int
+Mbed(tree_t **prMbedTree_p, mseq_t *prMSeq, const int iPairDistType,
+ const char *pcGuidetreeOut)
+{
+ /* number of seeds */
+ int iNumSeeds;
+ /* seed indices matching prMSeq */
+ int *piSeeds;
+ /* seqs represented as distance vectors */
+ double **ppdSeqVec;
+ /* kmeans result */
+ bisecting_kmeans_result_t *prKMeansResult = NULL;
+ /* distance matrix of kmeans (pre-)cluster centers */
+ symmatrix_t *prPreClusterDistmat = NULL;
+ /* auxiliary for symmetric matrix output; tree routines etc */
+ char **ppcLabels;
+ int iNodeIndex;
+ /* mapping of cluster-center tree node indices to corresponding
+ cluster */
+ int *piClusterToTreeNode;
+ int iClusterIndex;
+ int iI, iJ;
+ FILE *pfOut;
+ progress_t *prSubClusterDistanceProgress;
+ bool bPrintCR = (rLog.iLogLevelEnabled<=LOG_VERBOSE) ? FALSE : TRUE;
+
+#if FULL_WITHIN_CLUSTER_DISTANCES
+ Log(&rLog, LOG_DEBUG, "Computing real distances within subclusters for mBed.");
+#else
+ Log(&rLog, LOG_DEBUG, "Computing vector distances within subclusters for mBed.");
+#endif
+
+#if MBED_TIMING
+ Stopwatch_t *stopwatch = StopwatchCreate();
+#endif
+
+ assert(NULL != prMbedTree_p);
+ assert(NULL != prMSeq);
+
+
+ iNumSeeds = (int) NUMBER_OF_SEEDS(prMSeq->nseqs);
+ if (iNumSeeds >= prMSeq->nseqs) {
+ /* -1 is condition for RandomUniqueIntArray */
+ iNumSeeds = prMSeq->nseqs-1;
+ Log(&rLog, LOG_DEBUG,
+ "Automatically determined number of seeds is bigger (or equal) the number of sequences. Will set it to %d",
+ iNumSeeds);
+ }
+
+
+ /* Turn sequences into vectors of distances to the seeds
+ *
+ */
+ piSeeds = (int *) CKMALLOC(iNumSeeds * sizeof(int));
+ if (0 != SeedSelection(piSeeds, iNumSeeds, SEED_SELECTION, prMSeq)) {
+ Log(&rLog, LOG_ERROR, "Something went wrong during seed selection for mbed");
+ return -1;
+ }
+ ppdSeqVec = (double **) CKMALLOC(prMSeq->nseqs * sizeof(double *));
+ for (iI=0; iI<prMSeq->nseqs; iI++) {
+ ppdSeqVec[iI] = (double *) CKMALLOC(iNumSeeds * sizeof(double));
+ }
+ if (0 != SeqToVec(ppdSeqVec, prMSeq, piSeeds, iNumSeeds, iPairDistType)) {
+ Log(&rLog, LOG_ERROR, "Could not convert sequences into vectors for mbed");
+ return -1;
+ }
+ CKFREE(piSeeds);
+
+
+ /* Calculate (pre-)clusters of sequence vectors by applying
+ * bisecting kmeans
+ *
+ */
+#if MBED_TIMING
+ /* start clock only here, to make sure we don't include pairwise
+ * distance computation */
+ StopwatchZero(stopwatch);
+ StopwatchStart(stopwatch);
+#endif
+
+ BisectingKmeans(&prKMeansResult, prMSeq->nseqs, iNumSeeds, ppdSeqVec,
+ MIN_REQUIRED_SEQ_PER_PRECLUSTER,
+ MAX_ALLOWED_SEQ_PER_PRECLUSTER);
+ Log(&rLog, LOG_INFO,
+ "mBed created %u cluster/s (with a minimum of %d and a soft maximum of %d sequences each)",
+ prKMeansResult->iNClusters,
+ MIN_REQUIRED_SEQ_PER_PRECLUSTER,
+ MAX_ALLOWED_SEQ_PER_PRECLUSTER);
+
+
+#if PRINT_CLUSTER_DISTRIBUTION
+ Log(&rLog, LOG_FORCED_DEBUG, "Bisecting Kmeans returned %d clusters", prKMeansResult->iNClusters);
+ for (iI=0; iI<prKMeansResult->iNClusters; iI++) {
+#if TRACE
+ int iD;
+ Log(&rLog, LOG_FORCED_DEBUG, "Diagnostic output for cluster %d follows:", iI);
+ fprintf(stderr, "DEBUG(%s|%s():%d): center coordinates =",
+ __FILE__, __FUNCTION__, __LINE__);
+ for (iD=0; iD<iNumSeeds; iD++) {
+ fprintf(stderr, " %f", prKMeansResult->ppdClusterCenters[iI][iD]);
+ }
+ fprintf(stderr, "\n");
+ fflush(stderr);
+#endif
+ Log(&rLog, LOG_FORCED_DEBUG, "Cluster %d has %d objects assigned",
+ iI, prKMeansResult->piNObjsPerCluster[iI]);
+#if TRACE
+ for (iJ=0; iJ<prKMeansResult->piNObjsPerCluster[iI]; iJ++) {
+ int iRealIndex = prKMeansResult->ppiObjIndicesPerCluster[iI][iJ];
+
+ Log(&rLog, LOG_FORCED_DEBUG, "Cluster %u: object %u has index %u (= seq %s)",
+ iI, iJ, iRealIndex, prMSeq->sqinfo[iRealIndex].name);
+ }
+#endif
+ }
+#endif
+
+
+ /* Cluster pre-clusters produced by k-means.
+ *
+ * Do this by calculating the vector distances of the cluster
+ * centers and applying UPGMA.
+ *
+ * @note could try to force-balance the tree here
+ *
+ */
+ if (0 != NewSymMatrix(&prPreClusterDistmat,
+ prKMeansResult->iNClusters, prKMeansResult->iNClusters)) {
+ Log(&rLog, LOG_FATAL, "%s", "Memory allocation for pre-cluster distance-matrix failed");
+ }
+ for (iI=0; iI<prKMeansResult->iNClusters; iI++) {
+ for (iJ=iI+1; iJ<prKMeansResult->iNClusters; iJ++) {
+ double dDist;
+ dDist = EuclDist(prKMeansResult->ppdClusterCenters[iI],
+ prKMeansResult->ppdClusterCenters[iJ],
+ iNumSeeds);
+ SymMatrixSetValue(prPreClusterDistmat, iI, iJ, dDist);
+ /* Log(&rLog, LOG_FORCED_DEBUG, "Euclidean distance between clusters %d and %d = %f",
+ iI, iJ, dDist); */
+ }
+ }
+
+
+ /* labels needed for the guide tree building routine only */
+ ppcLabels = (char **) CKMALLOC(prKMeansResult->iNClusters * sizeof(char*));
+ for (iI=0; iI<prKMeansResult->iNClusters; iI++) {
+ ppcLabels[iI] = (char *) CKMALLOC(32 * sizeof(char));
+ (void) snprintf(ppcLabels[iI], 32, "Subcluster-%u", iI);
+ }
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "Distance matrix for pre-cluster centers:");
+ SymMatrixPrint(prPreClusterDistmat, ppcLabels, NULL);
+#endif
+
+ GuideTreeUpgma(prMbedTree_p,
+ ppcLabels, prPreClusterDistmat, NULL);
+
+ for (iI=0; iI<prKMeansResult->iNClusters; iI++) {
+ CKFREE(ppcLabels[iI]);
+ }
+ CKFREE(ppcLabels);
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "Cluster-center guide-tree:");
+ LogTree(*prMbedTree_p);
+#endif
+
+
+
+ /* Now replace each leaf in the pre-cluster-center tree
+ * appropriately, i.e. with the corresponding sub-cluster.
+ *
+ * For each leaf/sub-cluster, create a distance matrix for the
+ * corresponding sequences. Use distances between vectors as
+ * approximated distances between sequences. Then create a
+ * guide-tree by applying UPGMA.
+ *
+ */
+
+ /* Get a mapping of (pre)cluster number and leaf-node indices in
+ * the cluster-center tree. We can add trees to prMbedTree_p
+ * because AppendTrees() guarantees that no other than the node to
+ * append to changes.
+ */
+ piClusterToTreeNode = (int*)
+ CKMALLOC(prKMeansResult->iNClusters * sizeof(int));
+ iNodeIndex = FirstDepthFirstNode(*prMbedTree_p);
+ do {
+ if (IsLeaf(iNodeIndex, *prMbedTree_p)) {
+ int iLeafId = GetLeafId(iNodeIndex, *prMbedTree_p);
+ piClusterToTreeNode[iLeafId] = iNodeIndex;
+ }
+ iNodeIndex = NextDepthFirstNode(iNodeIndex, *prMbedTree_p);
+ } while (NULL_NEIGHBOR != iNodeIndex);
+
+
+
+
+ /* Now step through all the leafs and replace them with the
+ * corresponding sub-trees
+ */
+ NewProgress(&prSubClusterDistanceProgress, LogGetFP(&rLog, LOG_INFO),
+ "Distance calculation within sub-clusters", bPrintCR);
+ /* for each cluster */
+ for (iClusterIndex=0;
+ iClusterIndex < prKMeansResult->iNClusters; iClusterIndex++) {
+ /* distance matrix for the sub-cluster */
+ symmatrix_t *prWithinClusterDistances = NULL;
+ int iNSeqInCluster;
+ tree_t *prSubClusterTree = NULL;
+
+ ProgressLog(prSubClusterDistanceProgress,
+ iClusterIndex, prKMeansResult->iNClusters, FALSE);
+
+#if FULL_WITHIN_CLUSTER_DISTANCES
+ mseq_t *prSubClusterMSeq;
+ int iPairDistType;
+ int iSeqIndex;
+ int iOldLogLevel;
+
+ Log(&rLog, LOG_DEBUG,
+ "%s\n", "Calling new Mbed use makes only sense if nseq>MAX_ALLOWED_SEQ_PER_PRECLUSTER");
+
+ if (TRUE == prMSeq->aligned) {
+ iPairDistType = PAIRDIST_SQUIDID_KIMURA;
+ } else {
+ iPairDistType = PAIRDIST_KTUPLE;
+ }
+#endif
+
+ iNSeqInCluster = prKMeansResult->piNObjsPerCluster[iClusterIndex];
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "#seqs in subcluster no %d = %d",
+ iClusterIndex, iNSeqInCluster);
+#endif
+
+#if FULL_WITHIN_CLUSTER_DISTANCES
+ /* create an mseq structure for sequences in this cluster
+ * don't need most of the members (e.g. orig_seq) but copy
+ * them anyway for the sake of completeness
+ */
+ NewMSeq(&prSubClusterMSeq);
+
+ prSubClusterMSeq->nseqs = iNSeqInCluster;
+ prSubClusterMSeq->seqtype = prMSeq->seqtype;
+ if (NULL!=prMSeq->filename) {
+ prSubClusterMSeq->filename = CkStrdup(prMSeq->filename);
+ }
+ prSubClusterMSeq->aligned = prMSeq->aligned; /* FS, r252 */
+ prSubClusterMSeq->seq = (char **)
+ CKMALLOC(prSubClusterMSeq->nseqs * sizeof(char *));
+ prSubClusterMSeq->orig_seq = (char **)
+ CKMALLOC(prSubClusterMSeq->nseqs * sizeof(char *));
+ prSubClusterMSeq->sqinfo = (SQINFO *)
+ CKMALLOC(prSubClusterMSeq->nseqs * sizeof(SQINFO));
+
+ for (iSeqIndex=0; iSeqIndex<iNSeqInCluster; iSeqIndex++) {
+ int iRealSeqIndex = prKMeansResult->ppiObjIndicesPerCluster[iClusterIndex][iSeqIndex];
+ prSubClusterMSeq->seq[iSeqIndex] = CkStrdup(prMSeq->seq[iRealSeqIndex]);
+ prSubClusterMSeq->orig_seq[iSeqIndex] = CkStrdup(prMSeq->orig_seq[iRealSeqIndex]);
+ SeqinfoCopy(&prSubClusterMSeq->sqinfo[iSeqIndex], &prMSeq->sqinfo[iRealSeqIndex]);
+#if TRACE
+ Log(&rLog, LOG_DEBUG, "seq no %d in cluster %d is %s (real index = %d)",
+ iSeqIndex, iClusterIndex, prSubClusterMSeq->sqinfo[iSeqIndex].name,
+ iRealSeqIndex);
+#endif
+ }
+#endif
+
+
+ /* Create a distance matrix for this sub-cluster
+ * (prWithinClusterDistances) by using the vector distances or
+ * ktuple distances.
+ *
+ * Then apply UPGMA to get a subcluster tree
+ * (prSubClusterTree) and append created tree to the
+ * pre-cluster-tree (prMbedTree_p)
+ *
+ */
+#if FULL_WITHIN_CLUSTER_DISTANCES
+
+ iOldLogLevel = rLog.iLogLevelEnabled;
+ rLog.iLogLevelEnabled = LOG_WARN;
+ /* compute distances, but be quiet */
+ if (PairDistances(&prWithinClusterDistances, prSubClusterMSeq, iPairDistType,
+ 0, prSubClusterMSeq->nseqs, 0, prSubClusterMSeq->nseqs,
+ NULL, NULL)) {
+ Log(&rLog, LOG_ERROR, "Couldn't compute pair distances");
+ return -1;
+ }
+ rLog.iLogLevelEnabled = iOldLogLevel;
+
+#if COMPUTE_WITHIN_SUBCLUSTER_AVERAGE
+ {
+ double dSum = 0.0;
+ for (iI=0; iI<prSubClusterMSeq->nseqs; iI++) {
+ for (iJ=iI+1; iJ<prSubClusterMSeq->nseqs; iJ++) {
+ dSum += SymMatrixGetValue(prWithinClusterDistances, iI, iJ);
+ }
+ }
+ Log(&rLog, LOG_FORCED_DEBUG,
+ "mean pair-wise distance within subcluster %d of %d = %f",
+ iClusterIndex, prKMeansResult->iNClusters, dSum/prSubClusterMSeq->nseqs);
+ }
+#endif
+
+#else
+ if (NewSymMatrix(&prWithinClusterDistances, iNSeqInCluster, iNSeqInCluster)!=0) {
+ Log(&rLog, LOG_FATAL, "%s", "Memory allocation for disparity matrix failed");
+ }
+ for (iI=0; iI<iNSeqInCluster; iI++) {
+ int iRealIndexI = prKMeansResult->ppiObjIndicesPerCluster[iClusterIndex][iI];
+
+ for (iJ=iI+1; iJ<iNSeqInCluster; iJ++) {
+ int iRealIndexJ = prKMeansResult->ppiObjIndicesPerCluster[iClusterIndex][iJ];
+ double dist;
+
+ /* Log(&rLog, LOG_FORCED_DEBUG, "Cluster %d: compute distance between %d:%s and %d:%s",
+ iClusterIndex, i, prMSeq->sqinfo[iRealIndexI].name,
+ iJ, prMSeq->sqinfo[iRealIndexJ].name); */
+
+ if (1 == USE_EUCLIDEAN_DISTANCE) {
+ dist = EuclDist(ppdSeqVec[iRealIndexI],
+ ppdSeqVec[iRealIndexJ], iNumSeeds);
+ } else {
+ dist = CosDist(ppdSeqVec[iRealIndexI],
+ ppdSeqVec[iRealIndexJ], iNumSeeds);
+ }
+ SymMatrixSetValue(prWithinClusterDistances, iI, iJ, dist);
+ }
+ }
+#endif
+
+ /* labels needed for the guide tree building routine only */
+ ppcLabels = (char**) CKMALLOC(iNSeqInCluster * sizeof(char*));
+ for (iI=0; iI<iNSeqInCluster; iI++) {
+#if FULL_WITHIN_CLUSTER_DISTANCES
+ ppcLabels[iI] = prSubClusterMSeq->sqinfo[iI].name;
+#else
+ int iRealIndex = prKMeansResult->ppiObjIndicesPerCluster[iClusterIndex][iI];
+ ppcLabels[iI] = prMSeq->sqinfo[iRealIndex].name;
+#endif
+ }
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "Distance matrix for seqs within sub cluster %d/%d",
+ iClusterIndex, prKMeansResult->iNClusters);
+ SymMatrixPrint(prWithinClusterDistances, ppcLabels, NULL);
+#endif
+
+
+ GuideTreeUpgma(&prSubClusterTree, ppcLabels,
+ prWithinClusterDistances, NULL);
+
+ CKFREE(ppcLabels); /* don't free members, they just point */
+#if 0
+ Log(&rLog, LOG_FORCED_DEBUG, "Cluster %d guide-tree:", iClusterIndex);
+ LogTree(prSubClusterTree);
+#endif
+
+
+ /* The guide tree id's (that point to the sequences) now start
+ * from 0, i.e. the association with the prMSeq numbering is
+ * broken and fixed in the following
+ */
+ for (iNodeIndex = 0; iNodeIndex < (int)GetNodeCount(prSubClusterTree); iNodeIndex++) {
+ if (IsLeaf(iNodeIndex, prSubClusterTree)) {
+ int iLeafId = GetLeafId(iNodeIndex, prSubClusterTree);
+ int iRealId = prKMeansResult->ppiObjIndicesPerCluster[iClusterIndex][iLeafId];
+#if 0
+ Log(&rLog, LOG_FORCED_DEBUG, "Correcting leaf node %d which has (wrong) id %d and name %s to id %d (prMSeq name %s)",
+ iNodeIndex, iLeafId,
+ GetLeafName(iNodeIndex, prSubClusterTree),
+ iRealId, prMSeq->sqinfo[iRealId].name);
+#endif
+ SetLeafId(prSubClusterTree, iNodeIndex, iRealId);
+ }
+ }
+
+
+ /* Append the newly created tree (prSubClusterTree) to the
+ * corresponding node index of prMbedTree_p.
+ */
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "Will join trees at leaf node %d = %s",
+ piClusterToTreeNode[iClusterIndex],
+ GetLeafName(piClusterToTreeNode[iClusterIndex], *prMbedTree_p));
+#endif
+
+ AppendTree(*prMbedTree_p,
+ piClusterToTreeNode[iClusterIndex],
+ prSubClusterTree);
+ /* Note: piClusterToTreeNode is still valid, because
+ * AppendTrees() guarantees that no other than the node to
+ * append to changes. */
+
+#if 0
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "prMbedTree_p after cluster %d has appended:", iClusterIndex);
+ LogTree(*prMbedTree_p);
+
+ if (0) {
+ char fname[] = "mbed-joined-tree.dnd";
+ FILE *pfOut;
+ if (NULL == (pfOut = fopen(fname, "w"))) {
+ Log(&rLog, LOG_FATAL, "Couldn't open %s for writing", fname);
+ }
+ MuscleTreeToFile(pfOut, *prMbedTree_p);
+ Log(&rLog, LOG_FORCED_DEBUG, "Joined tree written to %s", fname);
+ fclose(pfOut);
+ Log(&rLog, LOG_FATAL, "DEBUG EXIT");
+ }
+#endif
+
+ /* cleanup
+ */
+ FreeMuscleTree(prSubClusterTree);
+ FreeSymMatrix(&prWithinClusterDistances);
+#if FULL_WITHIN_CLUSTER_DISTANCES
+ FreeMSeq(&prSubClusterMSeq);
+#endif
+ } /* end for each cluster */
+ ProgressDone(prSubClusterDistanceProgress);
+ FreeProgress(&prSubClusterDistanceProgress);
+
+
+ if (NULL != pcGuidetreeOut) {
+ if (NULL == (pfOut = fopen(pcGuidetreeOut, "w"))) {
+ Log(&rLog, LOG_ERROR, "Couldn't open %s for writing", pcGuidetreeOut);
+ } else {
+ MuscleTreeToFile(pfOut, *prMbedTree_p);
+ Log(&rLog, LOG_INFO, "Guide tree written to %s", pcGuidetreeOut);
+ (void) fclose(pfOut);
+ }
+ }
+
+
+ /* cleanup
+ *
+ */
+#if MBED_TIMING
+ StopwatchStop(stopwatch);
+ StopwatchDisplay(stdout, "mBed time (without pairwise distance computation): ", stopwatch);
+ StopwatchFree(stopwatch);
+#endif
+
+ FreeKMeansResult(&prKMeansResult);
+ FreeSymMatrix(&prPreClusterDistmat);
+ for (iI=0; iI<prMSeq->nseqs; iI++) {
+ CKFREE(ppdSeqVec[iI]);
+ }
+ CKFREE(ppdSeqVec);
+ CKFREE(piClusterToTreeNode);
+
+#ifndef NDEBUG
+ TreeValidate(*prMbedTree_p);
+#endif
+
+ return 0;
+}
+/*** end: Mbed() ***/
--- /dev/null
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: mbed.h 193 2011-02-07 15:45:21Z andreas $
+ */
+
+#ifndef CLUSTALO_MBED_H
+#define CLUSTALO_MBED_H
+
+#include "muscle_tree.h"
+#include "seq.h"
+
+
+extern int
+Mbed(tree_t **tree, mseq_t *prMSeq,
+ const int iPairDistType, const char *pcGuidetreeOutfile);
+
+#endif
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/* This a mix of tree functions and data-structures from
+ * Bob Edgar's Muscle (version 3.7) ported to pure C, topped up with
+ * some of our own stuff.
+ *
+ * Used files: phy.cpp, tree.h, phytofile.cpp and phyfromclust.cpp
+ *
+ * Muscle's code is public domain and so is this code here.
+
+ * From http://www.drive5.com/muscle/license.htm:
+ * """
+ * MUSCLE is public domain software
+ *
+ * The MUSCLE software, including object and source code and
+ * documentation, is hereby donated to the public domain.
+ *
+ * Disclaimer of warranty
+ * THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND,
+ * EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * """
+ *
+ */
+
+/*
+ * RCS $Id: muscle_tree.c 230 2011-04-09 15:37:50Z andreas $
+ */
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <limits.h>
+#include <assert.h>
+#include <ctype.h>
+
+#include "util.h"
+#include "log.h"
+#include "muscle_tree.h"
+
+
+static const double VERY_NEGATIVE_DOUBLE = -9e29;
+/*const double dInsane = VERY_NEGATIVE_DOUBLE;*/
+static const double dInsane = -9e29;
+static const unsigned uInsane = 8888888;
+
+typedef enum
+{
+ NTT_Unknown,
+
+ /* Returned from Tree::GetToken: */
+ NTT_Lparen,
+ NTT_Rparen,
+ NTT_Colon,
+ NTT_Comma,
+ NTT_Semicolon,
+ NTT_String,
+
+ /* Following are never returned from Tree::GetToken: */
+ NTT_SingleQuotedString,
+ NTT_DoubleQuotedString,
+ NTT_Comment
+} NEWICK_TOKEN_TYPE;
+
+
+static void
+InitCache(uint uCacheCount, tree_t *tree);
+static void
+TreeZero(tree_t *tree);
+static uint
+GetNeighborCount(unsigned uNodeIndex, tree_t *tree);
+static bool
+IsEdge(unsigned uNodeIndex1, unsigned uNodeIndex2, tree_t *tree);
+static bool
+HasEdgeLength(uint uNodeIndex1, uint uNodeIndex2, tree_t *tree);
+static void
+TreeToFileNodeRooted(tree_t *tree, uint m_uRootNodeIndex, FILE *fp);
+static void
+ValidateNode(uint uNodeIndex, tree_t *tree);
+static void
+AssertAreNeighbors(unsigned uNodeIndex1, unsigned uNodeIndex2, tree_t *tree);
+static void
+ExpandCache(tree_t *tree);
+static void
+TreeCreateRooted(tree_t *tree);
+static bool
+GetGroupFromFile(FILE *fp, uint uNodeIndex, double *ptrdEdgeLength, tree_t *tree);
+static NEWICK_TOKEN_TYPE
+GetToken(FILE *fp, char szToken[], uint uBytes);
+/* stuff from textfile.cpp */
+static void
+FileSkipWhite(FILE *fp);
+static bool
+FileSkipWhiteX(FILE *fp);
+static void
+SetLeafName(uint uNodeIndex, const char *ptrName, tree_t *tree);
+uint
+AppendBranch(tree_t *tree, uint uExistingLeafIndex);
+static void
+SetEdgeLength(uint uNodeIndex1, uint uNodeIndex2,
+ double dLength, tree_t *tree);
+static uint
+UnrootFromFile(tree_t *tree);
+uint
+GetNeighbor(uint uNodeIndex, uint uNeighborSubscript, tree_t *tree);
+static void
+InitNode(tree_t *prTree, uint uNodeIndex);
+
+
+/**
+ * @param[in] uNodeIndex
+ * node to examine
+ * @param[in] tree
+ * tree to examine
+ * @return id of left node
+ * @note called GetRight in Muscle3.7
+ */
+uint
+GetLeft(uint uNodeIndex, tree_t *tree)
+{
+ assert(NULL != tree);
+ assert(tree->m_bRooted && uNodeIndex < tree->m_uNodeCount);
+ return tree->m_uNeighbor2[uNodeIndex];
+}
+/*** end: GetLeft ***/
+
+
+
+/**
+ * @param[in] uNodeIndex
+ * node to examine
+ * @param[in] tree
+ * tree to examine
+ * @return id of right node
+ * @note called GetRight in Muscle3.7
+ */
+uint
+GetRight(uint uNodeIndex, tree_t *tree)
+{
+ assert(NULL != tree);
+ assert(tree->m_bRooted && uNodeIndex < tree->m_uNodeCount);
+ return tree->m_uNeighbor3[uNodeIndex];
+}
+/*** end: GetRight ***/
+
+
+
+/**
+ * @param[in] uNodeIndex
+ * node to examine
+ * @param[in] tree
+ * tree to examine
+ * @return leaf id of current node
+ */
+uint
+GetLeafId(uint uNodeIndex, tree_t *tree)
+{
+ assert(NULL != tree);
+ assert(uNodeIndex < tree->m_uNodeCount);
+ assert(IsLeaf(uNodeIndex, tree));
+
+ return tree->m_Ids[uNodeIndex];
+}
+/*** end: GetLeafId ***/
+
+
+
+/**
+ * @note originally called GetLeafName
+ *
+ */
+char *
+GetLeafName(unsigned uNodeIndex, tree_t *tree)
+{
+ assert(NULL != tree);
+ assert(uNodeIndex < tree->m_uNodeCount);
+ assert(IsLeaf(uNodeIndex, tree));
+ return tree->m_ptrName[uNodeIndex];
+}
+/*** end: GetLeafName ***/
+
+
+
+/**
+ * @brief returns first leaf node for a depth-first traversal of tree
+ *
+ * @param[in] tree
+ * tree to traverse
+ *
+ * @return node index of first leaf node for depth-first traversal
+ *
+ * @note called FirstDepthFirstNode in Muscle3.7
+ *
+ */
+uint
+FirstDepthFirstNode(tree_t *tree)
+{
+ uint uNodeIndex;
+
+ assert(NULL != tree);
+ assert(IsRooted(tree));
+
+ /* Descend via left branches until we hit a leaf */
+ uNodeIndex = tree->m_uRootNodeIndex;
+ while (!IsLeaf(uNodeIndex, tree))
+ uNodeIndex = GetLeft(uNodeIndex, tree);
+ return uNodeIndex;
+}
+/*** end: FirstDepthFirstNode ***/
+
+
+/**
+ * @brief returns next leaf node index for depth-first traversal of
+ * tree
+ *
+ * @param[in] tree
+ * tree to traverse
+ * @param[in] uNodeIndex
+ * Current node index
+ *
+ * @return node index of next leaf node during depth-first traversal
+ *
+ * @note called NextDepthFirstNode in Muscle3.7
+ */
+uint
+NextDepthFirstNode(uint uNodeIndex, tree_t *tree)
+{
+ uint uParent;
+
+ assert(NULL != tree);
+ assert(IsRooted(tree));
+ assert(uNodeIndex < tree->m_uNodeCount);
+
+ if (IsRoot(uNodeIndex, tree))
+ {
+ /* Node uNodeIndex is root, end of traversal */
+ return NULL_NEIGHBOR;
+ }
+
+ uParent = GetParent(uNodeIndex, tree);
+ if (GetRight(uParent, tree) == uNodeIndex) {
+ /* Is right branch, return parent=uParent */
+ return uParent;
+ }
+
+ uNodeIndex = GetRight(uParent, tree);
+ /* Descend left from right sibling uNodeIndex */
+ while (!IsLeaf(uNodeIndex, tree)) {
+ uNodeIndex = GetLeft(uNodeIndex, tree);
+ }
+
+ /* bottom out at leaf uNodeIndex */
+ return uNodeIndex;
+}
+/*** end: NextDepthFirstNode ***/
+
+
+
+/**
+ * @brief check if tree is a rooted tree
+ * @param[in] tree
+ * tree to check
+ * @return TRUE if given tree is rooted, FALSE otherwise
+ *
+ */
+bool
+IsRooted(tree_t *tree)
+{
+ assert(NULL != tree);
+ return tree->m_bRooted;
+}
+/*** end: IsRooted ***/
+
+
+/**
+ *
+ */
+void
+FreeMuscleTree(tree_t *tree)
+{
+ uint i;
+
+ assert(tree!=NULL);
+
+
+ /* FIXME use GetLeafNodeIndex? or
+ for (unsigned uNodeIndex = 0; uNodeIndex < m_uNodeCount; ++uNodeIndex)
+ {
+ if (tree.IsLeaf(uNodeIndex))
+ {
+ const char *ptrName =
+ tree.GetLeafName(uNodeIndex);
+ */
+ /* IsLeaf needs m_uNodeCount and all m_uNeighbor's
+ * so free first
+ */
+ for (i=0; i<tree->m_uNodeCount; i++) {
+ /* IsLeaf needs neighbour count, so free those guys later */
+ if (IsLeaf(i, tree)) {
+ CKFREE(tree->m_ptrName[i]);
+ }
+ }
+ CKFREE(tree->m_ptrName);
+
+ CKFREE(tree->m_uNeighbor1);
+ CKFREE(tree->m_uNeighbor2);
+ CKFREE(tree->m_uNeighbor3);
+
+ CKFREE(tree->m_Ids);
+
+ CKFREE(tree->m_dEdgeLength1);
+ CKFREE(tree->m_dEdgeLength2);
+ CKFREE(tree->m_dEdgeLength3);
+#if USE_HEIGHT
+ CKFREE(tree->m_dHeight);
+ CKFREE(tree->m_bHasHeight);
+#endif
+ CKFREE(tree->m_bHasEdgeLength1);
+ CKFREE(tree->m_bHasEdgeLength2);
+ CKFREE(tree->m_bHasEdgeLength3);
+
+ TreeZero(tree);
+
+ free(tree);
+}
+/*** end: FreeMuscleTree ***/
+
+
+
+/**
+ * @brief create a muscle tree
+ *
+ * @note Original comment in Muscle code: "Create rooted tree from a
+ * vector description. Node indexes are 0..N-1 for leaves, N..2N-2 for
+ * internal nodes. Vector subscripts are i-N and have values for
+ * internal nodes only, but those values are node indexes 0..2N-2. So
+ * e.g. if N=6 and Left[2]=1, this means that the third internal node
+ * (node index 8) has the second leaf (node index 1) as its left
+ * child. uRoot gives the vector subscript of the root, so add N to
+ * get the node index."
+ *
+ * @param[out] tree
+ * newly created tree
+ * @param[in] uLeafCount
+ * number of leaf nodes
+ * @param[in] uRoot
+ * Internal node index of root node
+ * @param[in] Left
+ * Node index of left sibling of an internal node.
+ * Index range: 0--uLeafCount-1
+ * @param[in] Right
+ * Node index of right sibling of an internal node.
+ * Index range: 0--uLeafCount-1
+ * @param[in] LeftLength
+ * Branch length of left branch of an internal node.
+ * Index range: 0--uLeafCount-1
+ * @param[in] RightLength
+ * Branch length of right branch of an internal node.
+ * Index range: 0--uLeafCount-1
+ * @param[in] LeafIds
+ * Leaf id. Index range: 0--uLeafCount
+ * @param[in] LeafNames
+ * Leaf label. Index range: 0--uLeafCount
+ *
+ */
+void
+MuscleTreeCreate(tree_t *tree,
+ uint uLeafCount, uint uRoot,
+ const uint *Left, const uint *Right,
+ const float *LeftLength, const float* RightLength,
+ const uint *LeafIds, char **LeafNames)
+{
+ uint uNodeIndex;
+
+ TreeZero(tree);
+ tree->m_uNodeCount = 2*uLeafCount - 1;
+ InitCache(tree->m_uNodeCount, tree);
+
+ for (uNodeIndex = 0; uNodeIndex < uLeafCount; ++uNodeIndex) {
+ tree->m_Ids[uNodeIndex] = LeafIds[uNodeIndex];
+ tree->m_ptrName[uNodeIndex] = CkStrdup(LeafNames[uNodeIndex]);
+ }
+
+ for (uNodeIndex = uLeafCount; uNodeIndex < tree->m_uNodeCount; ++uNodeIndex) {
+ uint v = uNodeIndex - uLeafCount;
+ uint uLeft = Left[v];
+ uint uRight = Right[v];
+ float fLeft = LeftLength[v];
+ float fRight = RightLength[v];
+
+ tree->m_uNeighbor2[uNodeIndex] = uLeft;
+ tree->m_uNeighbor3[uNodeIndex] = uRight;
+
+ tree->m_bHasEdgeLength2[uNodeIndex] = TRUE;
+ tree->m_bHasEdgeLength3[uNodeIndex] = TRUE;
+
+ tree->m_dEdgeLength2[uNodeIndex] = fLeft;
+ tree->m_dEdgeLength3[uNodeIndex] = fRight;
+
+ tree->m_uNeighbor1[uLeft] = uNodeIndex;
+ tree->m_uNeighbor1[uRight] = uNodeIndex;
+
+ tree->m_dEdgeLength1[uLeft] = fLeft;
+ tree->m_dEdgeLength1[uRight] = fRight;
+
+ tree->m_bHasEdgeLength1[uLeft] = TRUE;
+ tree->m_bHasEdgeLength1[uRight] = TRUE;
+ }
+
+ tree->m_bRooted = TRUE;
+ tree->m_uRootNodeIndex = uRoot + uLeafCount;
+#ifndef NDEBUG
+ TreeValidate(tree);
+#endif
+}
+/*** end: MuscleTreeCreate ***/
+
+
+
+/**
+ * @param[in] tree
+ * tree to write
+ * @param[out] fp
+ * filepointer to write to2
+ *
+ * @brief write a muscle tree to a file in newick format (distances
+ * and all names)
+ *
+ *
+ */
+void
+MuscleTreeToFile(FILE *fp, tree_t *tree)
+{
+ assert(NULL != tree);
+ if (IsRooted(tree)) {
+ TreeToFileNodeRooted(tree, tree->m_uRootNodeIndex, fp);
+ fprintf(fp, ";\n");
+ return;
+ } else {
+ Log(&rLog, LOG_FATAL, "FIXME: output of unrooted muscle trees not implemented");
+ }
+}
+/*** end: MuscleTreeToFile ***/
+
+
+
+/**
+ * @brief check if given node is a leaf node
+ *
+ * @param[in] uNodeIndex
+ * the node index
+ * @param tree
+ * the tree
+ *
+ * @return TRUE if given node is a leaf, FALSE otherwise
+ *
+ * @note called IsLeaf in Muscle3.7. See tree.h in original code
+ */
+bool
+IsLeaf(uint uNodeIndex, tree_t *tree)
+{
+ assert(NULL != tree);
+ assert(uNodeIndex < tree->m_uNodeCount);
+ if (1 == tree->m_uNodeCount)
+ return TRUE;
+ return 1 == GetNeighborCount(uNodeIndex, tree);
+}
+/*** end: IsLeaf ***/
+
+
+
+/**
+ */
+bool
+IsRoot(uint uNodeIndex, tree_t *tree)
+{
+ assert(NULL != tree);
+ return IsRooted(tree) && tree->m_uRootNodeIndex == uNodeIndex;
+}
+/*** end: IsRoot ***/
+
+
+
+/**
+ */
+uint
+GetNeighborCount(uint uNodeIndex, tree_t *tree)
+{
+ uint n1, n2, n3;
+ assert(uNodeIndex < tree->m_uNodeCount);
+ assert(NULL != tree);
+ assert(NULL != tree->m_uNeighbor1);
+ assert(NULL != tree->m_uNeighbor2);
+ assert(NULL != tree->m_uNeighbor3);
+ n1 = tree->m_uNeighbor1[uNodeIndex];
+ n2 = tree->m_uNeighbor2[uNodeIndex];
+ n3 = tree->m_uNeighbor3[uNodeIndex];
+ return (NULL_NEIGHBOR != n1) + (NULL_NEIGHBOR != n2) + (NULL_NEIGHBOR != n3);
+}
+/*** end: GetNeighborCount ***/
+
+
+/**
+ */
+uint
+GetParent(unsigned uNodeIndex, tree_t *tree)
+{
+ assert(NULL != tree);
+ assert(tree->m_bRooted && uNodeIndex < tree->m_uNodeCount);
+ return tree->m_uNeighbor1[uNodeIndex];
+}
+/*** end: GetParent ***/
+
+
+
+/**
+ */
+bool
+IsEdge(unsigned uNodeIndex1, unsigned uNodeIndex2, tree_t *tree)
+{
+ assert(uNodeIndex1 < tree->m_uNodeCount && uNodeIndex2 < tree->m_uNodeCount);
+ assert(NULL != tree);
+
+ return tree->m_uNeighbor1[uNodeIndex1] == uNodeIndex2 ||
+ tree->m_uNeighbor2[uNodeIndex1] == uNodeIndex2 ||
+ tree->m_uNeighbor3[uNodeIndex1] == uNodeIndex2;
+}
+/*** end: IsEdge ***/
+
+
+
+/**
+ */
+bool
+HasEdgeLength(uint uNodeIndex1, uint uNodeIndex2, tree_t *tree)
+{
+ assert(NULL != tree);
+ assert(uNodeIndex1 < tree->m_uNodeCount);
+ assert(uNodeIndex2 < tree->m_uNodeCount);
+ assert(IsEdge(uNodeIndex1, uNodeIndex2, tree));
+
+ if (tree->m_uNeighbor1[uNodeIndex1] == uNodeIndex2)
+ return tree->m_bHasEdgeLength1[uNodeIndex1];
+ else if (tree->m_uNeighbor2[uNodeIndex1] == uNodeIndex2)
+ return tree->m_bHasEdgeLength2[uNodeIndex1];
+ assert(tree->m_uNeighbor3[uNodeIndex1] == uNodeIndex2);
+ return tree->m_bHasEdgeLength3[uNodeIndex1];
+}
+/*** end: ***/
+
+
+/**
+ */
+double
+GetEdgeLength(uint uNodeIndex1, uint uNodeIndex2, tree_t *tree)
+{
+ assert(NULL != tree);
+ assert(uNodeIndex1 < tree->m_uNodeCount && uNodeIndex2 < tree->m_uNodeCount);
+ if (!HasEdgeLength(uNodeIndex1, uNodeIndex2, tree))
+ {
+ Log(&rLog, LOG_FATAL, "Missing edge length in tree %u-%u", uNodeIndex1, uNodeIndex2);
+ }
+
+ if (tree->m_uNeighbor1[uNodeIndex1] == uNodeIndex2)
+ return tree->m_dEdgeLength1[uNodeIndex1];
+ else if (tree->m_uNeighbor2[uNodeIndex1] == uNodeIndex2)
+ return tree->m_dEdgeLength2[uNodeIndex1];
+ assert(tree->m_uNeighbor3[uNodeIndex1] == uNodeIndex2);
+ return tree->m_dEdgeLength3[uNodeIndex1];
+}
+/*** end: GetEdgeLength ***/
+
+
+/**
+ *
+ */
+void
+InitNode(tree_t *prTree, uint uNodeIndex)
+{
+ prTree->m_uNeighbor1[uNodeIndex] = NULL_NEIGHBOR;
+ prTree->m_uNeighbor2[uNodeIndex] = NULL_NEIGHBOR;
+ prTree->m_uNeighbor3[uNodeIndex] = NULL_NEIGHBOR;
+ prTree->m_bHasEdgeLength1[uNodeIndex] = FALSE;
+ prTree->m_bHasEdgeLength2[uNodeIndex] = FALSE;
+ prTree->m_bHasEdgeLength3[uNodeIndex] = FALSE;
+#if USE_HEIGHT
+ prTree->m_bHasHeight[uNodeIndex] = FALSE;
+ prTree->m_dHeight[uNodeIndex] = dInsane;
+#endif
+ prTree->m_dEdgeLength1[uNodeIndex] = dInsane;
+ prTree->m_dEdgeLength2[uNodeIndex] = dInsane;
+ prTree->m_dEdgeLength3[uNodeIndex] = dInsane;
+
+ prTree->m_ptrName[uNodeIndex] = NULL;
+ prTree->m_Ids[uNodeIndex] = uInsane;
+}
+/*** end: InitNode ***/
+
+
+/**
+ *
+ */
+void
+InitCache(uint uCacheCount, tree_t *tree)
+{
+ uint uNodeIndex;
+
+ tree->m_uCacheCount = uCacheCount;
+
+ tree->m_uNeighbor1 = (uint *) CKMALLOC(sizeof(uint) * tree->m_uCacheCount);
+ tree->m_uNeighbor2 = (uint *) CKMALLOC(sizeof(uint) * tree->m_uCacheCount);
+ tree->m_uNeighbor3 = (uint *) CKMALLOC(sizeof(uint) * tree->m_uCacheCount);
+
+ tree->m_Ids = (uint *) CKMALLOC(sizeof(uint) * tree->m_uCacheCount);
+
+ tree->m_dEdgeLength1 = (double *) CKMALLOC(sizeof(double) * tree->m_uCacheCount);
+ tree->m_dEdgeLength2 = (double *) CKMALLOC(sizeof(double) * tree->m_uCacheCount);
+ tree->m_dEdgeLength3 = (double *) CKMALLOC(sizeof(double) * tree->m_uCacheCount);
+#if USE_HEIGHT
+ tree->m_dHeight = (double *) CKMALLOC(sizeof(double) * tree->m_uCacheCount);
+ tree->m_bHasHeight = (bool *) CKMALLOC(sizeof(bool) * tree->m_uCacheCount);
+#endif
+ tree->m_bHasEdgeLength1 = (bool *) CKMALLOC(sizeof(bool) * tree->m_uCacheCount);
+ tree->m_bHasEdgeLength2 = (bool *) CKMALLOC(sizeof(bool) * tree->m_uCacheCount);
+ tree->m_bHasEdgeLength3 = (bool *) CKMALLOC(sizeof(bool) * tree->m_uCacheCount);
+
+ tree->m_ptrName = (char **) CKMALLOC(sizeof(char *) * tree->m_uCacheCount);
+
+ for (uNodeIndex = 0; uNodeIndex < tree->m_uNodeCount; ++uNodeIndex) {
+ InitNode(tree, uNodeIndex);
+ }
+}
+/*** end: InitCache ***/
+
+
+
+
+/**
+ *
+ * @note Replacing Tree::Clear but no freeing of memory! Just setting
+ * everything to 0/NULL
+ */
+void
+TreeZero(tree_t *tree)
+{
+ assert(NULL != tree);
+ tree->m_uNodeCount = 0;
+ tree->m_uCacheCount = 0;
+
+ tree->m_uNeighbor1 = NULL;
+ tree->m_uNeighbor2 = NULL;
+ tree->m_uNeighbor3 = NULL;
+
+ tree->m_dEdgeLength1 = NULL;
+ tree->m_dEdgeLength2 = NULL;
+ tree->m_dEdgeLength3 = NULL;
+
+#if USE_HEIGHT
+ tree->m_dHeight = NULL;
+ tree->m_bHasHeight = NULL;
+#endif
+ tree->m_bHasEdgeLength1 = NULL;
+ tree->m_bHasEdgeLength2 = NULL;
+ tree->m_bHasEdgeLength3 = NULL;
+
+ tree->m_ptrName = NULL;
+ tree->m_Ids = NULL;
+
+ tree->m_bRooted = FALSE;
+ tree->m_uRootNodeIndex = 0;
+}
+/* end: TreeZero */
+
+
+
+/**
+ *
+ */
+void
+TreeToFileNodeRooted(tree_t *tree, uint uNodeIndex, FILE *fp)
+{
+ bool bGroup;
+
+ assert(IsRooted(tree));
+ assert(NULL != tree);
+ bGroup = !IsLeaf(uNodeIndex, tree) || IsRoot(uNodeIndex, tree);
+
+ if (bGroup)
+ fprintf(fp, "(\n");
+
+
+ if (IsLeaf(uNodeIndex, tree)) {
+ /* File.PutString(GetName(uNodeIndex)); */
+ fprintf(fp, "%s", tree->m_ptrName[uNodeIndex]);
+ } else {
+ TreeToFileNodeRooted(tree, GetLeft(uNodeIndex, tree), fp);
+ fprintf(fp, ",\n");
+ TreeToFileNodeRooted(tree, GetRight(uNodeIndex, tree), fp);
+ }
+
+ if (bGroup)
+ fprintf(fp, ")");
+
+ if (!IsRoot(uNodeIndex, tree)) {
+ uint uParent = GetParent(uNodeIndex, tree);
+ if (HasEdgeLength(uNodeIndex, uParent, tree))
+ fprintf(fp, ":%g", GetEdgeLength(uNodeIndex, uParent, tree));
+ }
+ fprintf(fp, "\n");
+}
+/*** end: TreeToFileNodeRooted ***/
+
+
+/**
+ *
+ *
+ */
+void
+TreeValidate(tree_t *tree)
+{
+ uint uNodeIndex;
+ assert(NULL != tree);
+ for (uNodeIndex = 0; uNodeIndex < tree->m_uNodeCount; ++uNodeIndex) {
+ ValidateNode(uNodeIndex, tree);
+ }
+ /* FIXME: maybe set negative length to zero? What impact would
+ * that have? */
+}
+/*** end TreeValidate ***/
+
+
+
+/**
+ *
+ *
+ */
+void
+ValidateNode(uint uNodeIndex, tree_t *tree)
+{
+ uint uNeighborCount;
+ uint n1, n2, n3;
+ assert(NULL != tree);
+
+ if (uNodeIndex >= tree->m_uNodeCount)
+ Log(&rLog, LOG_FATAL, "ValidateNode(%u), %u nodes", uNodeIndex, tree->m_uNodeCount);
+
+ uNeighborCount = GetNeighborCount(uNodeIndex, tree);
+
+
+ if (2 == uNeighborCount) {
+ if (!tree->m_bRooted) {
+ Log(&rLog, LOG_FATAL, "Tree::ValidateNode: Node %u has two neighbors, tree is not rooted",
+ uNodeIndex);
+ }
+ if (uNodeIndex != tree->m_uRootNodeIndex) {
+ Log(&rLog, LOG_FATAL, "Tree::ValidateNode: Node %u has two neighbors, but not root node=%u",
+ uNodeIndex, tree->m_uRootNodeIndex);
+ }
+ }
+
+ n1 = tree->m_uNeighbor1[uNodeIndex];
+ n2 = tree->m_uNeighbor2[uNodeIndex];
+ n3 = tree->m_uNeighbor3[uNodeIndex];
+
+ if (NULL_NEIGHBOR == n2 && NULL_NEIGHBOR != n3) {
+ Log(&rLog, LOG_FATAL, "Tree::ValidateNode, n2=null, n3!=null", uNodeIndex);
+ }
+ if (NULL_NEIGHBOR == n3 && NULL_NEIGHBOR != n2) {
+ Log(&rLog, LOG_FATAL, "Tree::ValidateNode, n3=null, n2!=null", uNodeIndex);
+ }
+
+ if (n1 != NULL_NEIGHBOR)
+ AssertAreNeighbors(uNodeIndex, n1, tree);
+ if (n2 != NULL_NEIGHBOR)
+ AssertAreNeighbors(uNodeIndex, n2, tree);
+ if (n3 != NULL_NEIGHBOR)
+ AssertAreNeighbors(uNodeIndex, n3, tree);
+
+
+
+ if (n1 != NULL_NEIGHBOR && (n1 == n2 || n1 == n3)) {
+ Log(&rLog, LOG_FATAL, "Tree::ValidateNode, duplicate neighbors in node %u", uNodeIndex);
+ }
+ if (n2 != NULL_NEIGHBOR && (n2 == n1 || n2 == n3)) {
+ Log(&rLog, LOG_FATAL, "Tree::ValidateNode, duplicate neighbors in node %u", uNodeIndex);
+ }
+ if (n3 != NULL_NEIGHBOR && (n3 == n1 || n3 == n2)) {
+ Log(&rLog, LOG_FATAL, "Tree::ValidateNode, duplicate neighbors in node %u", uNodeIndex);
+ }
+
+
+ if (IsRooted(tree)) {
+ if (NULL_NEIGHBOR == GetParent(uNodeIndex, tree)) {
+ if (uNodeIndex != tree->m_uRootNodeIndex) {
+ Log(&rLog, LOG_FATAL, "Tree::ValiateNode(%u), no parent", uNodeIndex);
+ }
+ } else if (GetLeft(GetParent(uNodeIndex, tree), tree) != uNodeIndex &&
+ GetRight(GetParent(uNodeIndex, tree), tree) != uNodeIndex) {
+ Log(&rLog, LOG_FATAL, "Tree::ValidateNode(%u), parent / child mismatch", uNodeIndex);
+ }
+ }
+}
+/*** end: ValidateNode ***/
+
+
+/**
+ *
+ *
+ */
+void
+AssertAreNeighbors(unsigned uNodeIndex1, unsigned uNodeIndex2, tree_t *tree)
+{
+ bool Has12, Has21;
+ assert(NULL != tree);
+
+ if (uNodeIndex1 >= tree->m_uNodeCount || uNodeIndex2 >= tree->m_uNodeCount)
+ Log(&rLog, LOG_FATAL, "AssertAreNeighbors(%u,%u), are %u nodes",
+ uNodeIndex1, uNodeIndex2, tree->m_uNodeCount);
+
+ if (tree->m_uNeighbor1[uNodeIndex1] != uNodeIndex2 &&
+ tree->m_uNeighbor2[uNodeIndex1] != uNodeIndex2 &&
+ tree->m_uNeighbor3[uNodeIndex1] != uNodeIndex2) {
+ Log(&rLog, LOG_FATAL, "AssertAreNeighbors(%u,%u) failed", uNodeIndex1, uNodeIndex2);
+ }
+
+
+ if (tree->m_uNeighbor1[uNodeIndex2] != uNodeIndex1 &&
+ tree->m_uNeighbor2[uNodeIndex2] != uNodeIndex1 &&
+ tree->m_uNeighbor3[uNodeIndex2] != uNodeIndex1) {
+ Log(&rLog, LOG_FATAL, "AssertAreNeighbors(%u,%u) failed", uNodeIndex1, uNodeIndex2);
+ }
+
+
+ Has12 = HasEdgeLength(uNodeIndex1, uNodeIndex2, tree);
+ Has21 = HasEdgeLength(uNodeIndex2, uNodeIndex1, tree);
+ if (Has12 != Has21) {
+ HasEdgeLength(uNodeIndex1, uNodeIndex2, tree);
+ HasEdgeLength(uNodeIndex2, uNodeIndex1, tree);
+ Log(&rLog, LOG_ERROR, "HasEdgeLength(%u, %u)=%c HasEdgeLength(%u, %u)=%c\n",
+ uNodeIndex1,
+ uNodeIndex2,
+ Has12 ? 'T' : 'F',
+ uNodeIndex2,
+ uNodeIndex1,
+ Has21 ? 'T' : 'F');
+ Log(&rLog, LOG_FATAL, "Tree::AssertAreNeighbors, HasEdgeLength not symmetric");
+ }
+
+
+ if (Has12) {
+ double d12 = GetEdgeLength(uNodeIndex1, uNodeIndex2, tree);
+ double d21 = GetEdgeLength(uNodeIndex2, uNodeIndex1, tree);
+ if (d12 != d21) {
+ Log(&rLog, LOG_FATAL, "Tree::AssertAreNeighbors, Edge length disagrees %u-%u=%.3g, %u-%u=%.3g",
+ uNodeIndex1, uNodeIndex2, d12,
+ uNodeIndex2, uNodeIndex1, d21);
+ }
+ }
+}
+/*** end: AssertAreNeighbors ***/
+
+
+
+/**
+ *
+ * @note see phyfromfile.cpp in Muscle3.7. Tree has to be a pointer to
+ * an already allocated tree structure.
+ *
+ * return non-Zero on failure
+ *
+ * leafids will not be set here (FIXME:CHECK if true)
+ */
+int
+MuscleTreeFromFile(tree_t *tree, char *ftree)
+{
+ double dEdgeLength;
+ bool bEdgeLength;
+ char szToken[16];
+ NEWICK_TOKEN_TYPE NTT;
+ unsigned uThirdNode;
+ FILE *fp = NULL;
+
+ assert(tree!=NULL);
+ assert(ftree!=NULL);
+
+ if (NULL == (fp=fopen(ftree, "r"))) {
+ Log(&rLog, LOG_ERROR, "Couldn't open tree-file '%s' for reading. Skipping", ftree);
+ return -1;
+ }
+
+ /* Assume rooted.
+ * If we discover that it is unrooted, will convert on the fly.
+ */
+ TreeCreateRooted(tree);
+
+ bEdgeLength = GetGroupFromFile(fp, 0, &dEdgeLength, tree);
+
+
+ /* Next token should be either ';' for rooted tree or ',' for
+ * unrooted.
+ */
+ NTT = GetToken(fp, szToken, sizeof(szToken));
+
+ /* If rooted, all done. */
+ if (NTT_Semicolon == NTT) {
+ if (bEdgeLength)
+ Log(&rLog, LOG_WARN, " *** Warning *** edge length on root group in Newick file %s\n", ftree);
+ TreeValidate(tree);
+ fclose(fp);
+ return 0;
+ }
+
+ if (NTT_Comma != NTT)
+ Log(&rLog, LOG_FATAL, "Tree::FromFile, expected ';' or ',', got '%s'", szToken);
+
+ uThirdNode = UnrootFromFile(tree);
+ bEdgeLength = GetGroupFromFile(fp, uThirdNode, &dEdgeLength, tree);
+ if (bEdgeLength)
+ SetEdgeLength(0, uThirdNode, dEdgeLength, tree);
+ TreeValidate(tree);
+
+ fclose(fp);
+ return 0;
+}
+/*** end MuscleTreeFromFile ***/
+
+
+
+/**
+ *
+ */
+void
+ExpandCache(tree_t *tree)
+{
+ const uint uNodeCount = 100;
+ uint uNewCacheCount;
+ uint *uNewNeighbor1, *uNewNeighbor2, *uNewNeighbor3;
+ uint *uNewIds;
+ double *dNewEdgeLength1, *dNewEdgeLength2, *dNewEdgeLength3;
+#if USE_HEIGHT
+ double *dNewHeight;
+ bool *bNewHasHeight;
+#endif
+ bool *bNewHasEdgeLength1, *bNewHasEdgeLength2, *bNewHasEdgeLength3;
+ char **ptrNewName;
+
+ assert(NULL != tree);
+ uNewCacheCount = tree->m_uCacheCount + uNodeCount;
+ uNewNeighbor1 = (uint *) CKMALLOC(
+ uNewCacheCount * sizeof(uint));
+ uNewNeighbor2 = (uint *) CKMALLOC(
+ uNewCacheCount * sizeof(uint));
+ uNewNeighbor3 = (uint *) CKMALLOC(
+ uNewCacheCount * sizeof(uint));
+
+ uNewIds = (uint *) CKCALLOC(
+ uNewCacheCount, sizeof(uint));
+
+ dNewEdgeLength1 = (double *) CKMALLOC(
+ uNewCacheCount * sizeof(double));
+ dNewEdgeLength2 = (double *) CKMALLOC(
+ uNewCacheCount * sizeof(double));
+ dNewEdgeLength3 = (double *) CKMALLOC(
+ uNewCacheCount * sizeof(double));
+#if USE_HEIGHT
+ dNewHeight = (double *) CKMALLOC(
+ uNewCacheCount * sizeof(double));
+ bNewHasHeight = (bool *) CKMALLOC(
+ uNewCacheCount * sizeof(bool));
+#endif
+
+ bNewHasEdgeLength1 = (bool *) CKMALLOC(
+ uNewCacheCount * sizeof(bool));
+ bNewHasEdgeLength2 = (bool *) CKMALLOC(
+ uNewCacheCount * sizeof(bool));
+ bNewHasEdgeLength3 = (bool *) CKMALLOC(
+ uNewCacheCount * sizeof(bool));
+ ptrNewName = (char **) CKCALLOC(uNewCacheCount, sizeof(char*));
+
+ if (tree->m_uCacheCount > 0) {
+ uint uUnsignedBytes, uEdgeBytes;
+ uint uBoolBytes, uNameBytes;
+
+ uUnsignedBytes = tree->m_uCacheCount*sizeof(uint);
+
+ memcpy(uNewNeighbor1, tree->m_uNeighbor1, uUnsignedBytes);
+ memcpy(uNewNeighbor2, tree->m_uNeighbor2, uUnsignedBytes);
+ memcpy(uNewNeighbor3, tree->m_uNeighbor3, uUnsignedBytes);
+
+ memcpy(uNewIds, tree->m_Ids, uUnsignedBytes);
+
+ uEdgeBytes = tree->m_uCacheCount*sizeof(double);
+ memcpy(dNewEdgeLength1, tree->m_dEdgeLength1, uEdgeBytes);
+ memcpy(dNewEdgeLength2, tree->m_dEdgeLength2, uEdgeBytes);
+ memcpy(dNewEdgeLength3, tree->m_dEdgeLength3, uEdgeBytes);
+#if USE_HEIGHT
+ memcpy(dNewHeight, tree->m_dHeight, uEdgeBytes);
+#endif
+
+ uBoolBytes = tree->m_uCacheCount*sizeof(bool);
+ memcpy(bNewHasEdgeLength1, tree->m_bHasEdgeLength1, uBoolBytes);
+ memcpy(bNewHasEdgeLength2, tree->m_bHasEdgeLength2, uBoolBytes);
+ memcpy(bNewHasEdgeLength3, tree->m_bHasEdgeLength3, uBoolBytes);
+#if USE_HEIGHT
+ memcpy(bNewHasHeight, tree->m_bHasHeight, uBoolBytes);
+#endif
+ uNameBytes = tree->m_uCacheCount*sizeof(char *);
+ memcpy(ptrNewName, tree->m_ptrName, uNameBytes);
+
+ /* similiar to FreeMuscleTree
+ */
+
+ /* IsLeaf needs m_uNodeCount and all m_uNeighbor's
+ * so free first
+ */
+#if 0
+ for (i=0; i<tree->m_uNodeCount; i++) {
+ if (IsLeaf(i, tree)) {
+#ifndef NDEBUG
+ if (NULL==tree->m_ptrName[i]) {
+ Log(&rLog, LOG_WARN, "FIXME tree->m_ptrName[%d] is already NULL", i);
+ }
+#endif
+ CKFREE(tree->m_ptrName[i]);
+ }
+ }
+#endif
+ CKFREE(tree->m_ptrName);
+
+ CKFREE(tree->m_uNeighbor1);
+ CKFREE(tree->m_uNeighbor2);
+ CKFREE(tree->m_uNeighbor3);
+
+ CKFREE(tree->m_Ids);
+
+ CKFREE(tree->m_dEdgeLength1);
+ CKFREE(tree->m_dEdgeLength2);
+ CKFREE(tree->m_dEdgeLength3);
+
+ CKFREE(tree->m_bHasEdgeLength1);
+ CKFREE(tree->m_bHasEdgeLength2);
+ CKFREE(tree->m_bHasEdgeLength3);
+#if USE_HEIGHT
+ CKFREE(tree->m_bHasHeight);
+ CKFREE(tree->m_dHeight);
+#endif
+ }
+
+ tree->m_uCacheCount = uNewCacheCount;
+ tree->m_uNeighbor1 = uNewNeighbor1;
+ tree->m_uNeighbor2 = uNewNeighbor2;
+ tree->m_uNeighbor3 = uNewNeighbor3;
+ tree->m_Ids = uNewIds;
+ tree->m_dEdgeLength1 = dNewEdgeLength1;
+ tree->m_dEdgeLength2 = dNewEdgeLength2;
+ tree->m_dEdgeLength3 = dNewEdgeLength3;
+
+#ifdef USE_HEIGHT
+ tree->m_dHeight = dNewHeight;
+ tree->m_bHasHeight = bNewHasHeight;
+#endif
+ tree->m_bHasEdgeLength1 = bNewHasEdgeLength1;
+ tree->m_bHasEdgeLength2 = bNewHasEdgeLength2;
+ tree->m_bHasEdgeLength3 = bNewHasEdgeLength3;
+
+ tree->m_ptrName = ptrNewName;
+
+}
+/*** end: ExpandCache ***/
+
+
+
+/**
+ *
+ * Tree must be pointer to an already allocated tree structure
+ *
+ */
+void
+TreeCreateRooted(tree_t *tree)
+{
+ TreeZero(tree);
+ ExpandCache(tree);
+ tree->m_uNodeCount = 1;
+
+ tree->m_uNeighbor1[0] = NULL_NEIGHBOR;
+ tree->m_uNeighbor2[0] = NULL_NEIGHBOR;
+ tree->m_uNeighbor3[0] = NULL_NEIGHBOR;
+
+ tree->m_bHasEdgeLength1[0] = FALSE;
+ tree->m_bHasEdgeLength2[0] = FALSE;
+ tree->m_bHasEdgeLength3[0] = FALSE;
+#if USE_HEIGHT
+ tree->m_bHasHeight[0] = FALSE;
+#endif
+
+ tree->m_uRootNodeIndex = 0;
+ tree->m_bRooted = TRUE;
+
+#ifndef NDEBUG
+ TreeValidate(tree);
+#endif
+}
+/*** end: TreeCreateRooted ***/
+
+
+/**
+ *
+ */
+uint
+UnrootFromFile(tree_t *tree)
+{
+ uint uThirdNode;
+#if TRACE
+ Log("Before unroot:\n");
+ LogMe();
+#endif
+
+ if (!tree->m_bRooted)
+ Log(&rLog, LOG_FATAL, "Tree::Unroot, not rooted");
+
+ /* Convention: root node is always node zero */
+ assert(IsRoot(0, tree));
+ assert(NULL_NEIGHBOR == tree->m_uNeighbor1[0]);
+
+ uThirdNode = tree->m_uNodeCount++;
+
+ tree->m_uNeighbor1[0] = uThirdNode;
+ tree->m_uNeighbor1[uThirdNode] = 0;
+
+ tree->m_uNeighbor2[uThirdNode] = NULL_NEIGHBOR;
+ tree->m_uNeighbor3[uThirdNode] = NULL_NEIGHBOR;
+
+ tree->m_dEdgeLength1[0] = 0;
+ tree->m_dEdgeLength1[uThirdNode] = 0;
+ tree->m_bHasEdgeLength1[uThirdNode] = TRUE;
+
+ tree->m_bRooted = FALSE;
+
+#if TRACE
+ Log("After unroot:\n");
+ LogMe();
+#endif
+
+ return uThirdNode;
+}
+/*** end: UnrootFromFile ***/
+
+
+
+/**
+ *
+ *
+ */
+bool
+GetGroupFromFile(FILE *fp, uint uNodeIndex, double *ptrdEdgeLength, tree_t *tree)
+{
+ char szToken[1024];
+ NEWICK_TOKEN_TYPE NTT = GetToken(fp, szToken, sizeof(szToken));
+ bool bRightLength;
+ bool bEof;
+ char c;
+
+ /* Group is either leaf name or (left, right). */
+ if (NTT_String == NTT) {
+ SetLeafName(uNodeIndex, szToken, tree);
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "Group is leaf '%s'", szToken);
+#endif
+ } else if (NTT_Lparen == NTT) {
+ const unsigned uLeft = AppendBranch(tree, uNodeIndex);
+ const unsigned uRight = uLeft + 1;
+ double dEdgeLength;
+ bool bLeftLength = GetGroupFromFile(fp, uLeft, &dEdgeLength, tree);
+
+ /* Left sub-group...
+ */
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "Got '(', group is compound, expect left sub-group");
+
+ if (bLeftLength) {
+ Log(&rLog, LOG_FORCED_DEBUG, "Edge length for left sub-group: %.3g", dEdgeLength);
+ } else {
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "No edge length for left sub-group");
+ }
+#endif
+ if (bLeftLength)
+ SetEdgeLength(uNodeIndex, uLeft, dEdgeLength, tree);
+
+ /* ... then comma ...
+ */
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "Expect comma");
+#endif
+ NTT = GetToken(fp, szToken, sizeof(szToken));
+ if (NTT_Comma != NTT)
+ Log(&rLog, LOG_FATAL, "Tree::GetGroupFromFile, expected ',', got '%s'", szToken);
+
+ /* ...then right sub-group...
+ */
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "Expect right sub-group");
+#endif
+ bRightLength = GetGroupFromFile(fp, uRight, &dEdgeLength, tree);
+ if (bRightLength)
+ SetEdgeLength(uNodeIndex, uRight, dEdgeLength, tree);
+
+#if TRACE
+ if (bRightLength)
+ Log(&rLog, LOG_FORCED_DEBUG, "Edge length for right sub-group: %.3g", dEdgeLength);
+ else
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "No edge length for right sub-group");
+#endif
+
+ /* ... then closing parenthesis.
+ */
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "Expect closing parenthesis (or comma if > 2-ary)");
+#endif
+ NTT = GetToken(fp, szToken, sizeof(szToken));
+ if (NTT_Rparen == NTT)
+ ;
+ else if (NTT_Comma == NTT) {
+ if (ungetc(',', fp)==EOF)
+ Log(&rLog, LOG_FATAL, "%s" "ungetc failed");
+ return FALSE;
+ } else
+ Log(&rLog, LOG_FATAL, "Tree::GetGroupFromFile, expected ')' or ',', got '%s'", szToken);
+ } else {
+ Log(&rLog, LOG_FATAL, "Tree::GetGroupFromFile, expected '(' or leaf name, got '%s'",
+ szToken);
+ }
+
+ /* Group may optionally be followed by edge length.
+ */
+ bEof = FileSkipWhiteX(fp);
+ if (bEof)
+ return FALSE;
+ if ((c = fgetc(fp))==EOF) /* GetCharX */
+ Log(&rLog, LOG_FATAL, "%s", "fgetc reached end of file");
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "Character following group, could be colon, is '%c'", c);
+#endif
+ if (':' == c) {
+ NTT = GetToken(fp, szToken, sizeof(szToken));
+ if (NTT_String != NTT)
+ Log(&rLog, LOG_FATAL, "Tree::GetGroupFromFile, expected edge length, got '%s'", szToken);
+ *ptrdEdgeLength = atof(szToken);
+ return TRUE;
+ }
+ if (ungetc(c, fp)==EOF)
+ Log(&rLog, LOG_FATAL, "%s" "ungetc failed");
+
+ return FALSE;
+}
+/*** end: GetGroupFromFile ***/
+
+
+
+
+/**
+ *
+ */
+void
+FileSkipWhite(FILE *fp)
+{
+ bool bEof = FileSkipWhiteX(fp);
+ if (bEof)
+ Log(&rLog, LOG_FATAL, "%s", "End-of-file skipping white space");
+}
+/*** end: FileSkipWhite ***/
+
+
+
+
+/**
+ *
+ */
+bool
+FileSkipWhiteX(FILE *fp)
+{
+ for (;;) {
+ int c;
+ bool bEof;
+
+ /* GetChar */
+ if ((c = fgetc(fp))==EOF) {
+ bEof = TRUE;
+ } else {
+ bEof = FALSE;
+ }
+
+ if (bEof)
+ return TRUE;
+ if (!isspace(c)) {
+ if (ungetc(c, fp)==EOF)
+ Log(&rLog, LOG_FATAL, "%s" "ungetc failed");
+ break;
+ }
+ }
+ return FALSE;
+}
+/*** end: FileSkipWhiteX ***/
+
+
+
+
+/**
+ *
+ */
+NEWICK_TOKEN_TYPE
+GetToken(FILE *fp, char szToken[], uint uBytes)
+{
+ char c;
+ unsigned uBytesCopied = 0;
+ NEWICK_TOKEN_TYPE TT;
+
+ /* Skip leading white space */
+ FileSkipWhite(fp);
+
+ if ((c = fgetc(fp))==EOF) /* GetCharX */
+ Log(&rLog, LOG_FATAL, "%s", "fgetc reached end of file");
+
+ /* In case a single-character token */
+ szToken[0] = c;
+ szToken[1] = 0;
+
+ switch (c) {
+
+ case '(':
+ return NTT_Lparen;
+
+ case ')':
+ return NTT_Rparen;
+
+ case ':':
+ return NTT_Colon;
+
+ case ';':
+ return NTT_Semicolon;
+
+ case ',':
+ return NTT_Comma;
+
+ case '\'':
+ TT = NTT_SingleQuotedString;
+ if ((c = fgetc(fp))==EOF) /* GetCharX */
+ Log(&rLog, LOG_FATAL, "%s", "fgetc reached end of file");
+ break;
+
+ case '"':
+ TT = NTT_DoubleQuotedString;
+ if ((c = fgetc(fp))==EOF) /* GetCharX */
+ Log(&rLog, LOG_FATAL, "%s", "fgetc reached end of file");
+ break;
+
+ case '[':
+ TT = NTT_Comment;
+ break;
+
+ default:
+ TT = NTT_String;
+ break;
+ }
+
+ for (;;)
+ {
+ bool bEof;
+ if (TT != NTT_Comment) {
+ if (uBytesCopied < uBytes - 2) {
+ szToken[uBytesCopied++] = c;
+ szToken[uBytesCopied] = 0;
+ } else {
+ Log(&rLog, LOG_FATAL, "Tree::GetToken: input buffer too small, token so far='%s'", szToken);
+ }
+ }
+ c = fgetc(fp); /* GetChar */
+ bEof = (c==EOF ? TRUE : FALSE);
+ if (bEof)
+ return TT;
+
+ switch (TT) {
+
+ case NTT_String:
+ if (0 != strchr("():;,", c)) {
+ if (ungetc(c, fp)==EOF)
+ Log(&rLog, LOG_FATAL, "%s" "ungetc failed");
+ return NTT_String;
+ }
+ if (isspace(c))
+ return NTT_String;
+ break;
+
+ case NTT_SingleQuotedString:
+ if ('\'' == c)
+ return NTT_String;
+ break;
+
+ case NTT_DoubleQuotedString:
+ if ('"' == c)
+ return NTT_String;
+ break;
+
+ case NTT_Comment:
+ if (']' == c)
+ return GetToken(fp, szToken, uBytes);
+ break;
+
+ default:
+ Log(&rLog, LOG_FATAL, "Tree::GetToken, invalid TT=%u", TT);
+ }
+ }
+}
+/*** end: GetToken ***/
+
+
+
+/*** SetLeafName
+ *
+ */
+void
+SetLeafName(unsigned uNodeIndex, const char *ptrName, tree_t *tree)
+{
+ assert(uNodeIndex < tree->m_uNodeCount);
+ assert(IsLeaf(uNodeIndex, tree));
+ free(tree->m_ptrName[uNodeIndex]);
+ /*LOG_DEBUG("Setting tree->m_ptrName[uNodeIndex=%d] to %s", uNodeIndex, ptrName);*/
+ tree->m_ptrName[uNodeIndex] = CkStrdup(ptrName);
+}
+/*** end: SetLeafName ***/
+
+
+
+
+/**
+ *
+ * Append a new branch. This adds two new nodes and joins them to an
+ * existing leaf node. Return value is k, new nodes have indexes k and
+ * k+1 respectively.
+ *
+ */
+uint
+AppendBranch(tree_t *tree, uint uExistingLeafIndex)
+{
+ uint uNewLeaf1;
+ uint uNewLeaf2;
+
+ assert(tree!=NULL);
+ if (0 == tree->m_uNodeCount) {
+ Log(&rLog, LOG_FATAL, "%s(): %s", __FUNCTION__, "tree has not been created");
+ }
+ assert(NULL_NEIGHBOR == tree->m_uNeighbor2[uExistingLeafIndex]);
+ assert(NULL_NEIGHBOR == tree->m_uNeighbor3[uExistingLeafIndex]);
+ assert(uExistingLeafIndex < tree->m_uNodeCount);
+#ifndef NDEBUG
+ if (!IsLeaf(uExistingLeafIndex, tree)) {
+ Log(&rLog, LOG_FATAL, "AppendBranch(%u): not leaf", uExistingLeafIndex);
+ }
+#endif
+
+ if (tree->m_uNodeCount >= tree->m_uCacheCount - 2) {
+ ExpandCache(tree);
+ }
+ uNewLeaf1 = tree->m_uNodeCount;
+ uNewLeaf2 = tree->m_uNodeCount + 1;
+
+ tree->m_uNodeCount += 2;
+
+ tree->m_uNeighbor2[uExistingLeafIndex] = uNewLeaf1;
+ tree->m_uNeighbor3[uExistingLeafIndex] = uNewLeaf2;
+
+ tree->m_uNeighbor1[uNewLeaf1] = uExistingLeafIndex;
+ tree->m_uNeighbor1[uNewLeaf2] = uExistingLeafIndex;
+
+ tree->m_uNeighbor2[uNewLeaf1] = NULL_NEIGHBOR;
+ tree->m_uNeighbor2[uNewLeaf2] = NULL_NEIGHBOR;
+
+ tree->m_uNeighbor3[uNewLeaf1] = NULL_NEIGHBOR;
+ tree->m_uNeighbor3[uNewLeaf2] = NULL_NEIGHBOR;
+
+ tree->m_dEdgeLength2[uExistingLeafIndex] = 0;
+ tree->m_dEdgeLength3[uExistingLeafIndex] = 0;
+
+ tree->m_dEdgeLength1[uNewLeaf1] = 0;
+ tree->m_dEdgeLength2[uNewLeaf1] = 0;
+ tree->m_dEdgeLength3[uNewLeaf1] = 0;
+
+ tree->m_dEdgeLength1[uNewLeaf2] = 0;
+ tree->m_dEdgeLength2[uNewLeaf2] = 0;
+ tree->m_dEdgeLength3[uNewLeaf2] = 0;
+
+ tree->m_bHasEdgeLength1[uNewLeaf1] = FALSE;
+ tree->m_bHasEdgeLength2[uNewLeaf1] = FALSE;
+ tree->m_bHasEdgeLength3[uNewLeaf1] = FALSE;
+
+ tree->m_bHasEdgeLength1[uNewLeaf2] = FALSE;
+ tree->m_bHasEdgeLength2[uNewLeaf2] = FALSE;
+ tree->m_bHasEdgeLength3[uNewLeaf2] = FALSE;
+
+#if USE_HEIGHT
+ tree->m_bHasHeight[uNewLeaf1] = FALSE;
+ tree->m_bHasHeight[uNewLeaf2] = FALSE;
+#endif
+ tree->m_Ids[uNewLeaf1] = uInsane;
+ tree->m_Ids[uNewLeaf2] = uInsane;
+
+ return uNewLeaf1;
+}
+/*** end: AppendBranch ***/
+
+
+/**
+ *
+ *
+ */
+void
+SetEdgeLength(uint uNodeIndex1, uint uNodeIndex2,
+ double dLength, tree_t *tree)
+{
+ assert(uNodeIndex1 < tree->m_uNodeCount && uNodeIndex2 < tree->m_uNodeCount);
+ assert(IsEdge(uNodeIndex1, uNodeIndex2, tree));
+
+ if (tree->m_uNeighbor1[uNodeIndex1] == uNodeIndex2) {
+ tree->m_dEdgeLength1[uNodeIndex1] = dLength;
+ tree->m_bHasEdgeLength1[uNodeIndex1] = TRUE;
+ } else if (tree->m_uNeighbor2[uNodeIndex1] == uNodeIndex2) {
+ tree->m_dEdgeLength2[uNodeIndex1] = dLength;
+ tree->m_bHasEdgeLength2[uNodeIndex1] = TRUE;
+
+ } else {
+ assert(tree->m_uNeighbor3[uNodeIndex1] == uNodeIndex2);
+ tree->m_dEdgeLength3[uNodeIndex1] = dLength;
+ tree->m_bHasEdgeLength3[uNodeIndex1] = TRUE;
+ }
+
+ if (tree->m_uNeighbor1[uNodeIndex2] == uNodeIndex1) {
+ tree->m_dEdgeLength1[uNodeIndex2] = dLength;
+ tree->m_bHasEdgeLength1[uNodeIndex2] = TRUE;
+ } else if (tree->m_uNeighbor2[uNodeIndex2] == uNodeIndex1) {
+ tree->m_dEdgeLength2[uNodeIndex2] = dLength;
+ tree->m_bHasEdgeLength2[uNodeIndex2] = TRUE;
+ } else {
+ assert(tree->m_uNeighbor3[uNodeIndex2] == uNodeIndex1);
+ tree->m_dEdgeLength3[uNodeIndex2] = dLength;
+ tree->m_bHasEdgeLength3[uNodeIndex2] = TRUE;
+ }
+}
+/*** end: SetEdgeLength ***/
+
+
+
+/**
+ *
+ * Debug output
+ *
+ * LogMe in phy.cpp
+ *
+ */
+void
+LogTree(tree_t *tree, FILE *fp)
+{
+ uint uNodeIndex;
+ uint n1, n2, n3;
+ char *ptrName;
+
+ fprintf(fp, "This is a tree with %u nodes, which is ", tree->m_uNodeCount);
+
+ if (IsRooted(tree)) {
+ fprintf(fp, "rooted:\n");
+ fprintf(fp, "Index Parnt LengthP Left LengthL Right LengthR Id Name\n");
+ fprintf(fp, "----- ----- ------- ---- ------- ----- ------- ----- ----\n");
+
+ } else {
+ fprintf(fp, "unrooted;\n");
+ fprintf(fp, "Index Nbr_1 Length1 Nbr_2 Length2 Nbr_3 Length3 Id Name\n");
+ fprintf(fp, "----- ----- ------- ----- ------- ----- ------- ----- ----\n");
+ }
+
+ for (uNodeIndex = 0; uNodeIndex < tree->m_uNodeCount; ++uNodeIndex) {
+ fprintf(fp, "%5u ", uNodeIndex);
+ n1 = tree->m_uNeighbor1[uNodeIndex];
+ n2 = tree->m_uNeighbor2[uNodeIndex];
+ n3 = tree->m_uNeighbor3[uNodeIndex];
+
+ if (NULL_NEIGHBOR != n1) {
+ fprintf(fp, "%5u ", n1);
+ if (tree->m_bHasEdgeLength1[uNodeIndex])
+ fprintf(fp, "%7.3g ", tree->m_dEdgeLength1[uNodeIndex]);
+ else
+ fprintf(fp, " * ");
+ } else {
+ fprintf(fp, " ");
+ }
+
+ if (NULL_NEIGHBOR != n2) {
+ fprintf(fp, "%5u ", n2);
+ if (tree->m_bHasEdgeLength2[uNodeIndex])
+ fprintf(fp, "%7.3g ", tree->m_dEdgeLength2[uNodeIndex]);
+ else
+ fprintf(fp, " * ");
+ } else {
+ fprintf(fp, " ");
+ }
+
+ if (NULL_NEIGHBOR != n3) {
+ fprintf(fp, "%5u ", n3);
+ if (tree->m_bHasEdgeLength3[uNodeIndex])
+ fprintf(fp, "%7.3g ", tree->m_dEdgeLength3[uNodeIndex]);
+ else
+ fprintf(fp, " * ");
+ } else {
+ fprintf(fp, " ");
+ }
+
+ if (tree->m_Ids != 0 && IsLeaf(uNodeIndex, tree)) {
+ unsigned uId = tree->m_Ids[uNodeIndex];
+ if (uId == uInsane)
+ fprintf(fp, " *");
+ else
+ fprintf(fp, "%5u", uId);
+ } else {
+ fprintf(fp, " ");
+ }
+
+ if (tree->m_bRooted && uNodeIndex == tree->m_uRootNodeIndex)
+ fprintf(fp, " [ROOT] ");
+ ptrName = tree->m_ptrName[uNodeIndex];
+ if (ptrName != 0)
+ fprintf(fp, " %s", ptrName);
+
+ fprintf(fp, "\n");
+ }
+}
+/*** end: LogTree ***/
+
+
+
+/**
+ *
+ * replaces m_uLeafCount
+ */
+uint
+GetLeafCount(tree_t *tree)
+{
+ assert(tree!=NULL);
+
+ return (tree->m_uNodeCount+1)/2;
+}
+/*** GetLeafCount ***/
+
+
+
+/**
+ *
+ */
+uint
+GetNodeCount(tree_t *tree)
+{
+ assert(tree!=NULL);
+
+ return 2*(GetLeafCount(tree)) - 1;
+}
+/*** end: GetNodeCount ***/
+
+
+/**
+ *
+ */
+uint
+GetNeighbor(uint uNodeIndex, uint uNeighborSubscript, tree_t *prTree)
+{
+ assert(uNodeIndex < prTree->m_uNodeCount);
+ switch (uNeighborSubscript)
+ {
+ case 0:
+ return prTree->m_uNeighbor1[uNodeIndex];
+ case 1:
+ return prTree->m_uNeighbor2[uNodeIndex];
+ case 2:
+ return prTree->m_uNeighbor3[uNodeIndex];
+ }
+ Log(&rLog, LOG_FATAL, "Internal error in %s: sub=%u", __FUNCTION__, uNeighborSubscript);
+ return NULL_NEIGHBOR;
+}
+/*** end: GetNeighbor ***/
+
+
+
+
+
+/**
+ *
+ */
+void
+SetLeafId(tree_t *tree, uint uNodeIndex, uint uId)
+{
+ assert(uNodeIndex < tree->m_uNodeCount);
+ assert(IsLeaf(uNodeIndex, tree));
+ tree->m_Ids[uNodeIndex] = uId;
+}
+/*** end: SetLeafId ***/
+
+
+/**
+ *
+ */
+uint
+GetRootNodeIndex(tree_t *tree)
+{
+ assert(NULL!=tree);
+ return tree->m_uRootNodeIndex;
+}
+/*** end: GetRootNodeIndex ***/
+
+
+
+/**
+ * @note avoid usage if you want to iterate over all indices, because
+ * this will be slow
+ *
+ */
+uint
+LeafIndexToNodeIndex(uint uLeafIndex, tree_t *prTree) {
+ uint uLeafCount = 0;
+ unsigned uNodeCount = GetNodeCount(prTree);
+ uint uNodeIndex;
+
+ for (uNodeIndex = 0; uNodeIndex < uNodeCount; uNodeIndex++) {
+ if (IsLeaf(uNodeIndex, prTree)) {
+ if (uLeafCount == uLeafIndex) {
+ return uNodeIndex;
+ } else {
+ uLeafCount++;
+ }
+ }
+ }
+ Log(&rLog, LOG_FATAL, "Internal error: node index out of range");
+ return 0;
+}
+/*** end: LeafIndexToNodeIndex ***/
+
+
+
+
+/**
+ * @brief Append a (source) tree to a (dest) tree to a given node
+ * which will be replaced. All other nodes in that tree will stay the
+ * same.
+ *
+ * @param[out] prDstTree
+ * The tree to append to
+ * @param[in] uDstTreeReplaceNodeIndex
+ * Dest tree node to which source tree will be appended
+ * @param[in] prSrcTree
+ * The tree to append
+ *
+ * @note No nodes inside prDstTree will change except
+ * uDstTreeReplaceNodeIndex
+ *
+ *
+ * @warning: Function won't check or touch the m_Ids/leaf-indices!
+ * That means if you want to join two trees with leaf indices 1-10 and
+ * 1-10 your m_Ids/leaf-indices won't be unique anymore and the
+ * association between your sequences and the tree are broken. Make
+ * sure m_Ids are unique before calling me.
+ *
+ * The easiest would have been to do this by recursively calling
+ * AppendBranch() (after adding uSrcTreeNodeIndex as extra argument to
+ * this function). But recursion is evil. Yet another version would be
+ * to setup all the data and call MuscleTreeCreate() to create a third
+ * tree, which seems complicated and wasteful. The approach taken here
+ * is the following: increase dest tree memory, copy over each src
+ * tree node data and update the indices and counters. This is tricky
+ * and has a lot of potential for bugs if tree interface is changed
+ * (and even if it isn't).
+ *
+ */
+void
+AppendTree(tree_t *prDstTree, uint uDstTreeReplaceNodeIndex, tree_t *prSrcTree)
+{
+ uint uSrcTreeNodeIndex;
+ uint uOrgDstTreeNodeCount;
+
+ assert(NULL!=prDstTree);
+ assert(NULL!=prSrcTree);
+ assert(uDstTreeReplaceNodeIndex < prDstTree->m_uNodeCount);
+ assert(IsLeaf(uDstTreeReplaceNodeIndex, prDstTree));
+ assert(IsRooted(prDstTree) && IsRooted(prSrcTree));
+
+
+ uOrgDstTreeNodeCount = prDstTree->m_uNodeCount;
+
+
+ /* increase dest tree memory
+ */
+ while (prDstTree->m_uCacheCount
+ <
+ (GetNodeCount(prDstTree) + GetNodeCount(prSrcTree))) {
+ ExpandCache(prDstTree);
+ }
+
+
+ /* copy all src tree nodes
+ *
+ */
+ for (uSrcTreeNodeIndex=0;
+ uSrcTreeNodeIndex<GetNodeCount(prSrcTree); uSrcTreeNodeIndex++) {
+ uint uNewDstNodeIndex = prDstTree->m_uNodeCount;
+
+ /* distinguish 4 cases for src nodes to copy:
+ *
+ * 1. src node is the only node, i.e. root & leaf
+ *
+ * 2. src node is root: set only left & right, but not parent
+ * and just replace the given dest index
+ *
+ * 3. src node is leaf: set only parent
+ *
+ * 4. src node is internal node: update all three neighbours
+ *
+ * FIXME: this is messy. Is there a cleaner way to do this by
+ * merging all cases?
+ *
+ */
+ if (IsRoot(uSrcTreeNodeIndex, prSrcTree) && IsLeaf(uSrcTreeNodeIndex, prSrcTree)) {
+ /* special case: if this is the only member in
+ * tree, i.e. it's root and leaf. Copy leaf name and leaf
+ * id. No neighbours to update
+ */
+
+ /* free dst node name if set */
+ if (NULL != prDstTree->m_ptrName[uDstTreeReplaceNodeIndex]) {
+ CKFREE(prDstTree->m_ptrName[uDstTreeReplaceNodeIndex]);
+ }
+
+ prDstTree->m_ptrName[uDstTreeReplaceNodeIndex] =
+ CkStrdup(GetLeafName(uSrcTreeNodeIndex, prSrcTree));
+
+ prDstTree->m_Ids[uDstTreeReplaceNodeIndex] =
+ prSrcTree->m_Ids[uSrcTreeNodeIndex];
+
+ /* no updated of uNodeCount, because we used the replace node */
+
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "Updated dst rpl node %d with the only src leaf node: parent=%d (%f)",
+ uDstTreeReplaceNodeIndex,
+ prDstTree->m_uNeighbor1[uDstTreeReplaceNodeIndex], prDstTree->m_dEdgeLength1[uDstTreeReplaceNodeIndex]);
+#endif
+
+ } else if (IsRoot(uSrcTreeNodeIndex, prSrcTree)) {
+ /* src node is root: replace uDstTreeReplaceNodeIndex
+ * (not uNewDstNodeIndex) with src root, i.e. the
+ * uDstTreeReplaceNodeIndex becomes an internal node now.
+ *
+ * We only have two neighbours 2 & 3 (no parent). Keep old
+ * parent info (neighbor 1).
+ */
+
+ /* free dst node name if set */
+ if (NULL != prDstTree->m_ptrName[uDstTreeReplaceNodeIndex]) {
+ CKFREE(prDstTree->m_ptrName[uDstTreeReplaceNodeIndex]);
+ }
+
+ prDstTree->m_uNeighbor2[uDstTreeReplaceNodeIndex] =
+ prSrcTree->m_uNeighbor2[uSrcTreeNodeIndex] + uOrgDstTreeNodeCount;
+ prDstTree->m_uNeighbor3[uDstTreeReplaceNodeIndex] =
+ prSrcTree->m_uNeighbor3[uSrcTreeNodeIndex] + uOrgDstTreeNodeCount;
+
+ prDstTree->m_bHasEdgeLength2[uDstTreeReplaceNodeIndex] =
+ prSrcTree->m_bHasEdgeLength2[uSrcTreeNodeIndex];
+ prDstTree->m_bHasEdgeLength3[uDstTreeReplaceNodeIndex] =
+ prSrcTree->m_bHasEdgeLength3[uSrcTreeNodeIndex];
+
+ prDstTree->m_dEdgeLength2[uDstTreeReplaceNodeIndex] =
+ prSrcTree->m_dEdgeLength2[uSrcTreeNodeIndex];
+ prDstTree->m_dEdgeLength3[uDstTreeReplaceNodeIndex] =
+ prSrcTree->m_dEdgeLength3[uSrcTreeNodeIndex];
+
+ /* make Id invalid */
+ prDstTree->m_Ids[uDstTreeReplaceNodeIndex] = uInsane;
+
+ /* no updated of uNodeCount, because we used the replace node */
+
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "Updated dst rpl node %d with the src root node: (untouched) parent=%d (%f) left=%d (%f) right=%d (%f)",
+ uDstTreeReplaceNodeIndex,
+ prDstTree->m_uNeighbor1[uDstTreeReplaceNodeIndex], prDstTree->m_dEdgeLength1[uDstTreeReplaceNodeIndex],
+ prDstTree->m_uNeighbor2[uDstTreeReplaceNodeIndex], prDstTree->m_dEdgeLength2[uDstTreeReplaceNodeIndex],
+ prDstTree->m_uNeighbor3[uDstTreeReplaceNodeIndex], prDstTree->m_dEdgeLength3[uDstTreeReplaceNodeIndex]);
+#endif
+
+ } else if (IsLeaf(uSrcTreeNodeIndex, prSrcTree)) {
+ /* src node is a leaf, which means we only have one
+ * neighbour, and that is its parent, i.e. n1
+ *
+ */
+
+ /* initialise/zero new node to default values
+ */
+ InitNode(prDstTree, uNewDstNodeIndex);
+
+
+ /* update m_ptrName/leaf name
+ */
+ prDstTree->m_ptrName[uNewDstNodeIndex] =
+ CkStrdup(GetLeafName(uSrcTreeNodeIndex, prSrcTree));
+
+ /* update parent node (beware of special case: parent was
+ src tree root */
+ if (IsRoot(prSrcTree->m_uNeighbor1[uSrcTreeNodeIndex], prSrcTree)) {
+ prDstTree->m_uNeighbor1[uNewDstNodeIndex] =
+ uDstTreeReplaceNodeIndex;
+ } else {
+ prDstTree->m_uNeighbor1[uNewDstNodeIndex] =
+ prSrcTree->m_uNeighbor1[uSrcTreeNodeIndex] + uOrgDstTreeNodeCount;
+ }
+
+ /* update edge length info to parent
+ */
+ prDstTree->m_bHasEdgeLength1[uNewDstNodeIndex] =
+ prSrcTree->m_bHasEdgeLength1[uSrcTreeNodeIndex];
+ prDstTree->m_dEdgeLength1[uNewDstNodeIndex] =
+ prSrcTree->m_dEdgeLength1[uSrcTreeNodeIndex];
+
+ /* update sequence/object id
+ */
+ prDstTree->m_Ids[uNewDstNodeIndex] =
+ prSrcTree->m_Ids[uSrcTreeNodeIndex];
+
+ /* we used a new node so increase their count */
+ prDstTree->m_uNodeCount += 1;
+
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "Updated dst node %d with a src leaf node: parent=%d (%f)",
+ uNewDstNodeIndex,
+ prDstTree->m_uNeighbor1[uNewDstNodeIndex], prDstTree->m_dEdgeLength1[uNewDstNodeIndex]);
+#endif
+
+ } else {
+ /* src node is not root neither leaf, means we have an
+ * internal node. Update all neighbour info
+ *
+ */
+
+ /* initialise/zero node values to default values
+ */
+ InitNode(prDstTree, uNewDstNodeIndex);
+
+ /* update neigbours
+ */
+ /* parent: special case if parent was src tree root */
+ if (IsRoot(prSrcTree->m_uNeighbor1[uSrcTreeNodeIndex], prSrcTree)) {
+ prDstTree->m_uNeighbor1[uNewDstNodeIndex] =
+ uDstTreeReplaceNodeIndex;
+ } else {
+ prDstTree->m_uNeighbor1[uNewDstNodeIndex] =
+ prSrcTree->m_uNeighbor1[uSrcTreeNodeIndex] + uOrgDstTreeNodeCount;
+ }
+ /* left */
+ prDstTree->m_uNeighbor2[uNewDstNodeIndex] =
+ prSrcTree->m_uNeighbor2[uSrcTreeNodeIndex] + uOrgDstTreeNodeCount;
+ /* right */
+ prDstTree->m_uNeighbor3[uNewDstNodeIndex] =
+ prSrcTree->m_uNeighbor3[uSrcTreeNodeIndex] + uOrgDstTreeNodeCount;
+
+ /* update edge length info
+ */
+ /* parent */
+ prDstTree->m_bHasEdgeLength1[uNewDstNodeIndex] =
+ prSrcTree->m_bHasEdgeLength1[uSrcTreeNodeIndex];
+ prDstTree->m_dEdgeLength1[uNewDstNodeIndex] =
+ prSrcTree->m_dEdgeLength1[uSrcTreeNodeIndex];
+ /* left */
+ prDstTree->m_bHasEdgeLength2[uNewDstNodeIndex] =
+ prSrcTree->m_bHasEdgeLength2[uSrcTreeNodeIndex];
+ prDstTree->m_dEdgeLength2[uNewDstNodeIndex] =
+ prSrcTree->m_dEdgeLength2[uSrcTreeNodeIndex];
+ /* right */
+ prDstTree->m_bHasEdgeLength3[uNewDstNodeIndex] =
+ prSrcTree->m_bHasEdgeLength3[uSrcTreeNodeIndex];
+ prDstTree->m_dEdgeLength3[uNewDstNodeIndex] =
+ prSrcTree->m_dEdgeLength3[uSrcTreeNodeIndex];
+
+ /* we used a new node so increase their count */
+ prDstTree->m_uNodeCount += 1;
+
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "Updated dst node %d with an internal src node: parent=%d (%f) left=%d (%f) right=%d (%f)",
+ uNewDstNodeIndex,
+ prDstTree->m_uNeighbor1[uNewDstNodeIndex], prDstTree->m_dEdgeLength1[uNewDstNodeIndex],
+ prDstTree->m_uNeighbor2[uNewDstNodeIndex], prDstTree->m_dEdgeLength2[uNewDstNodeIndex],
+ prDstTree->m_uNeighbor3[uNewDstNodeIndex], prDstTree->m_dEdgeLength3[uNewDstNodeIndex]);
+#endif
+ }
+
+ }
+ /* end for each src tree node */
+
+
+ /*
+ * m_uRootNodeIndex stays the same.
+ *
+ * No need to touch m_uCacheCount.
+ *
+ */
+#if USE_HEIGHT
+ Log(&rLog, LOG_FATAL, "Internal error: Height usage not implemented in %s", __FUNCTION__);
+#endif
+
+
+#ifndef NDEBUG
+ TreeValidate(prDstTree);
+#endif
+
+ return;
+}
+/*** end: AppendTree() ***/
+
--- /dev/null
+/* This a mix of tree functions and data-structures from
+ * Bob Edgar's Muscle (version 3.7) ported to pure C.
+ *
+ * Used files: phy.cpp, tree.h, phytofile.cpp and phyfromclust.cpp
+ *
+ * Muscle's code is public domain and so is this code here.
+
+ * From http://www.drive5.com/muscle/license.htm:
+ * """
+ * MUSCLE is public domain software
+ *
+ * The MUSCLE software, including object and source code and
+ * documentation, is hereby donated to the public domain.
+ *
+ * Disclaimer of warranty
+ * THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND,
+ * EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * """
+ *
+ */
+
+/*
+ * RCS $Id: muscle_tree.h 230 2011-04-09 15:37:50Z andreas $
+ */
+
+
+#ifndef CLUSTALO_MUSCLE_CLUSTALO_TREE_H
+#define CLUSTALO_MUSCLE_CLUSTALO_TREE_H
+
+#include <stdio.h>
+#include "util.h"
+
+#ifndef uint
+/* limit use of uint (see coding_style_guideline.txt) */
+typedef unsigned int uint;
+#endif
+
+static const uint NULL_NEIGHBOR = UINT_MAX;
+
+/**
+ * @brief guide-tree structure
+ *
+ * @note We kept the original variable names here, to make it easy to
+ * search through Muscle's source code.
+ * From phy.cpp:
+ * Node has 0 to 3 neighbors:
+ * 0 neighbors: singleton root
+ * 1 neighbor: leaf, neighbor is parent
+ * 2 neigbors: non-singleton root
+ * 3 neighbors: internal node (other than root)
+ *
+ * Minimal rooted tree is single node.
+ * Minimal unrooted tree is single edge.
+ * Leaf node always has nulls in neighbors 2 and 3, neighbor 1 is parent.
+ * When tree is rooted, neighbor 1=parent, 2=left, 3=right.
+ *
+ */
+typedef struct {
+ uint m_uNodeCount;/**< number of nodes */
+ uint m_uCacheCount;/**< reserved memory */
+
+ uint *m_uNeighbor1;/**< parent node */
+ uint *m_uNeighbor2;/**< left node */
+ uint *m_uNeighbor3;/**< right node */
+
+ /* do we have edge lengths info stored (m_dEdgeLength[123]) */
+ bool *m_bHasEdgeLength1;
+ bool *m_bHasEdgeLength2;
+ bool *m_bHasEdgeLength3;
+
+ double *m_dEdgeLength1;
+ double *m_dEdgeLength2;
+ double *m_dEdgeLength3;
+
+#if USE_HEIGHT
+ /* unused in our version of the code. we might need it at some
+ * stage so keep it in here, but disable via USE_HEIGHT throughout
+ * the code */
+ double *m_dHeight;
+ bool *m_bHasHeight;
+#endif
+
+ /**
+ * leaf labels.
+ * index range: 0 -- (m_uNodeCount+1)/2
+ */
+ char **m_ptrName;
+
+ /**
+ * node id.
+ * index range: 0 -- m_uNodeCount
+ */
+ uint *m_Ids;
+
+ bool m_bRooted; /**< tree is rooted */
+ uint m_uRootNodeIndex;
+} tree_t;
+
+
+extern void
+MuscleTreeCreate(tree_t *tree, uint uLeafCount, uint uRoot, const uint *Left,
+ const uint *Right, const float *LeftLength, const float* RightLength,
+ const uint *LeafIds, char **LeafNames);
+
+extern void
+MuscleTreeToFile(FILE *fp, tree_t *tree);
+
+extern int
+MuscleTreeFromFile(tree_t *tree, char *ftree);
+
+extern void
+FreeMuscleTree(tree_t *tree);
+
+extern void
+LogTree(tree_t *tree, FILE *fp);
+
+extern bool
+IsRooted(tree_t *tree);
+
+extern uint
+GetNodeCount(tree_t *tree);
+
+extern uint
+GetLeafCount(tree_t *tree);
+
+extern uint
+FirstDepthFirstNode(tree_t *tree);
+
+extern uint
+NextDepthFirstNode(uint nodeindex, tree_t *tree);
+
+extern bool
+IsLeaf(uint nodeindex, tree_t *tree);
+
+extern void
+SetLeafId(tree_t *tree, uint uNodeIndex, uint uId);
+
+extern uint
+GetLeafId(uint nodeindex, tree_t *tree);
+
+extern char *
+GetLeafName(unsigned uNodeIndex, tree_t *tree);
+
+extern uint
+GetLeft(uint nodeindex, tree_t *tree);
+
+extern uint
+GetRight(uint nodeindex, tree_t *tree);
+
+extern uint
+GetRootNodeIndex(tree_t *tree);
+
+extern bool
+IsRoot(uint uNodeIndex, tree_t *tree);
+
+extern uint
+GetParent(unsigned uNodeIndex, tree_t *tree);
+
+extern double
+GetEdgeLength(uint uNodeIndex1, uint uNodeIndex2, tree_t *tree);
+
+extern uint
+LeafIndexToNodeIndex(uint uLeafIndex, tree_t *prTree);
+
+extern void
+AppendTree(tree_t *prDstTree,
+ uint uDstTreeNodeIndex, tree_t *prSrcTree);
+
+extern void
+TreeValidate(tree_t *tree);
+
+#endif
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/* This the fast UPGMA algorithm (O(N^2)) as implemented in Bob Edgar's
+ * Muscle (UPGMA2.cpp; version 3.7) ported to pure C.
+ *
+ * Muscle's code is public domain and so is this code here.
+ *
+ * From http://www.drive5.com/muscle/license.htm:
+ * """
+ * MUSCLE is public domain software
+ *
+ * The MUSCLE software, including object and source code and
+ * documentation, is hereby donated to the public domain.
+ *
+ * Disclaimer of warranty
+ * THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND,
+ * EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * """
+ *
+ */
+
+/*
+ * RCS $Id: muscle_upgma.c 230 2011-04-09 15:37:50Z andreas $
+ *
+ *
+ * Notes:
+ * ------
+ * LINKAGE become linkage_t here
+ *
+ * Replaced the the following member functions for DistCalc DC:
+ * DC.GetId = sequence id as int
+ * DC.GetName = sequence name
+ * DC.GetCount = matrix dim
+ * DC.DistRange = vector / matrix row for object i with index j<i
+ *
+ * Log() has been replaced with Clustal's Info(), Quiet() with Log(&rLog, LOG_FATAL)
+ *
+ * Made TriangleSubscript() and g_ulTriangleSize ulong to prevent overflow for many sequences
+ */
+
+#ifndef ulint
+/* limit use of unsigned vars (see coding_style_guideline.txt) */
+typedef unsigned long int ulong;
+#endif
+
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <assert.h>
+
+#include "util.h"
+#include "log.h"
+#include "symmatrix.h"
+
+#include "muscle_tree.h"
+#include "muscle_upgma.h"
+
+/* from distcalc.h */
+typedef float dist_t;
+static const dist_t BIG_DIST = (dist_t) 1e29;
+/* from muscle.h */
+static const unsigned uInsane = 8888888;
+
+
+
+
+/*static inline*/
+ulong TriangleSubscript(uint uIndex1, uint uIndex2);
+
+
+
+
+#define TRACE 0
+
+#ifndef MIN
+#define MIN(x, y) ((x) < (y) ? (x) : (y))
+#endif
+#ifndef MIN
+#define MAX(x, y) ((x) > (y) ? (x) : (y))
+#endif
+#define AVG(x, y) (((x) + (y))/2)
+
+static uint g_uLeafCount;
+static ulong g_ulTriangleSize;
+static uint g_uInternalNodeCount;
+static uint g_uInternalNodeIndex;
+
+/* Triangular distance matrix is g_Dist, which is allocated
+ * as a one-dimensional vector of length g_ulTriangleSize.
+ * TriangleSubscript(i,j) maps row,column=i,j to the subscript
+ * into this vector.
+ * Row / column coordinates are a bit messy.
+ * Initially they are leaf indexes 0..N-1.
+ * But each time we create a new node (=new cluster, new subtree),
+ * we re-use one of the two rows that become available (the children
+ * of the new node). This saves memory.
+ * We keep track of this through the g_uNodeIndex vector.
+ */
+static dist_t *g_Dist;
+
+/* Distance to nearest neighbor in row i of distance matrix.
+ * Subscript is distance matrix row.
+ */
+static dist_t *g_MinDist;
+
+/* Nearest neighbor to row i of distance matrix.
+ * Subscript is distance matrix row.
+ */
+static uint *g_uNearestNeighbor;
+
+/* Node index of row i in distance matrix.
+ * Node indexes are 0..N-1 for leaves, N..2N-2 for internal nodes.
+ * Subscript is distance matrix row.
+ */
+static uint *g_uNodeIndex;
+
+/* The following vectors are defined on internal nodes,
+ * subscripts are internal node index 0..N-2.
+ * For g_uLeft/Right, value is the node index 0 .. 2N-2
+ * because a child can be internal or leaf.
+ */
+static uint *g_uLeft;
+static uint *g_uRight;
+static dist_t *g_Height;
+static dist_t *g_LeftLength;
+static dist_t *g_RightLength;
+
+
+/*** CalcDistRange
+ *
+ * Imitation of DistCalc.DistRange
+ *
+ * Sets values of row (vector / matrix row) to distances for object i with index j<i
+ *
+ * row must be preallocated
+ */
+void CalcDistRange(symmatrix_t *distmat, uint i, dist_t *row)
+{
+ uint j;
+ for (j = 0; j < i; ++j) {
+ row[j] = SymMatrixGetValue(distmat, i, j);
+ }
+}
+/* end of CalcDistRange */
+
+
+
+/*static inline*/
+ulong
+TriangleSubscript(uint uIndex1, uint uIndex2)
+{
+ ulong v;
+#ifndef NDEBUG
+ if (uIndex1 >= g_uLeafCount || uIndex2 >= g_uLeafCount)
+ Log(&rLog, LOG_FATAL, "TriangleSubscript(%u,%u) %u", uIndex1, uIndex2, g_uLeafCount);
+#endif
+ if (uIndex1 >= uIndex2)
+ v = uIndex2 + (uIndex1*(uIndex1 - 1))/2;
+ else
+ v = uIndex1 + (uIndex2*(uIndex2 - 1))/2;
+ assert(v < (g_uLeafCount*(g_uLeafCount - 1))/2);
+ return v;
+}
+
+#ifdef UNUSED
+static void ListState()
+{
+ uint i, j;
+ Info("Dist matrix\n");
+ Info(" ");
+ for (i = 0; i < g_uLeafCount; ++i)
+ {
+ if (uInsane == g_uNodeIndex[i])
+ continue;
+ Info(" %5u", g_uNodeIndex[i]);
+ }
+ Info("\n");
+
+ for (i = 0; i < g_uLeafCount; ++i)
+ {
+ if (uInsane == g_uNodeIndex[i])
+ continue;
+ Info("%5u ", g_uNodeIndex[i]);
+ for (j = 0; j < g_uLeafCount; ++j)
+ {
+ if (uInsane == g_uNodeIndex[j])
+ continue;
+ if (i == j)
+ Info(" ");
+ else
+ {
+ ulong v = TriangleSubscript(i, j);
+ Info("%5.2g ", g_Dist[v]);
+ }
+ }
+ Info("\n");
+ }
+
+ Info("\n");
+ Info(" i Node NrNb Dist\n");
+ Info("----- ----- ----- --------\n");
+ for (i = 0; i < g_uLeafCount; ++i)
+ {
+ if (uInsane == g_uNodeIndex[i])
+ continue;
+ Info("%5u %5u %5u %8.3f\n",
+ i,
+ g_uNodeIndex[i],
+ g_uNearestNeighbor[i],
+ g_MinDist[i]);
+ }
+
+ Info("\n");
+ Info(" Node L R Height LLength RLength\n");
+ Info("----- ----- ----- ------ ------- -------\n");
+ for (i = 0; i <= g_uInternalNodeIndex; ++i)
+ Info("%5u %5u %5u %6.2g %6.2g %6.2g\n",
+ i,
+ g_uLeft[i],
+ g_uRight[i],
+ g_Height[i],
+ g_LeftLength[i],
+ g_RightLength[i]);
+}
+#endif
+/* ifdef UNUSED */
+
+/**
+ * @brief Creates a UPGMA in O(N^2) tree from given distmat
+ *
+ * @param[out] tree
+ * newly created rooted UPGMA tree
+ * @param[in] distmat
+ * distance matrix to be clustered
+ * @param[in] linkage
+ * linkage type
+ * @param[in] names
+ * leaf names, will be copied
+ *
+ * @note called UPGMA2() in Muscle3.7.
+ * caller has to free with FreeMuscleTree()
+ *
+ * @see FreeMuscleTree()
+ */
+void
+MuscleUpgma2(tree_t *tree, symmatrix_t *distmat, linkage_t linkage, char **names)
+{
+ int i, j;
+ uint *Ids;
+
+ /* only works on full symmetric matrices */
+ assert (distmat->nrows==distmat->ncols);
+
+ g_uLeafCount = distmat->ncols;
+ g_ulTriangleSize = (g_uLeafCount*(g_uLeafCount - 1))/2;
+ g_uInternalNodeCount = g_uLeafCount - 1;
+
+ g_Dist = (dist_t *) CKMALLOC(g_ulTriangleSize * sizeof(dist_t));
+
+ g_uNodeIndex = (uint*) CKMALLOC(sizeof(uint) * g_uLeafCount);
+ g_uNearestNeighbor = (uint*) CKMALLOC(sizeof(uint) * g_uLeafCount);
+ g_MinDist = (dist_t *) CKMALLOC(sizeof(dist_t) * g_uLeafCount);
+ Ids = (uint*) CKMALLOC(sizeof(uint) * g_uLeafCount);
+ /* NOTE: we replaced Names with argument names */
+
+ /**
+ * left and right node indices, as well as left and right
+ * branch-length and height for for internal nodes
+ */
+ g_uLeft = (uint*) CKMALLOC(sizeof(uint) * g_uInternalNodeCount);
+ g_uRight = (uint*) CKMALLOC(sizeof(uint) * g_uInternalNodeCount);
+ g_Height = (dist_t*) CKMALLOC(sizeof(dist_t) * g_uInternalNodeCount);
+ g_LeftLength = (dist_t*) CKMALLOC(sizeof(dist_t) * g_uInternalNodeCount);
+ g_RightLength = (dist_t*) CKMALLOC(sizeof(dist_t) * g_uInternalNodeCount);
+
+ for (i = 0; i < g_uLeafCount; ++i) {
+ g_MinDist[i] = BIG_DIST;
+ g_uNodeIndex[i] = i;
+ g_uNearestNeighbor[i] = uInsane;
+ Ids[i] = i;
+ }
+
+ for (i = 0; i < g_uInternalNodeCount; ++i) {
+ g_uLeft[i] = uInsane;
+ g_uRight[i] = uInsane;
+ g_LeftLength[i] = BIG_DIST;
+ g_RightLength[i] = BIG_DIST;
+ g_Height[i] = BIG_DIST;
+ }
+
+/* Compute initial NxN triangular distance matrix.
+ * Store minimum distance for each full (not triangular) row.
+ * Loop from 1, not 0, because "row" is 0, 1 ... i-1,
+ * so nothing to do when i=0.
+ */
+ for (i = 1; i < g_uLeafCount; ++i) {
+ dist_t *Row = g_Dist + TriangleSubscript(i, 0);
+ CalcDistRange(distmat, i, Row);
+ for (j = 0; j < i; ++j) {
+ const dist_t d = Row[j];
+ if (d < g_MinDist[i]) {
+ g_MinDist[i] = d;
+ g_uNearestNeighbor[i] = j;
+ }
+ if (d < g_MinDist[j]) {
+ g_MinDist[j] = d;
+ g_uNearestNeighbor[j] = i;
+ }
+ }
+ }
+
+#if TRACE
+ Info("Initial state:\n");
+ ListState();
+#endif
+
+ for (g_uInternalNodeIndex = 0;
+ g_uInternalNodeIndex < g_uLeafCount - 1;
+ ++g_uInternalNodeIndex) {
+
+ dist_t dtNewMinDist = BIG_DIST;
+ uint uNewNearestNeighbor = uInsane;
+
+#if TRACE
+ Info("\n");
+ Info("Internal node index %5u\n", g_uInternalNodeIndex);
+ Info("-------------------------\n");
+#endif
+
+ /* Find nearest neighbors */
+ uint Lmin = uInsane;
+ uint Rmin = uInsane;
+ dist_t dtMinDist = BIG_DIST;
+ for (j = 0; j < g_uLeafCount; ++j) {
+ dist_t d;
+ if (uInsane == g_uNodeIndex[j])
+ continue;
+
+ d = g_MinDist[j];
+ if (d < dtMinDist) {
+ dtMinDist = d;
+ Lmin = j;
+ Rmin = g_uNearestNeighbor[j];
+ assert(uInsane != Rmin);
+ assert(uInsane != g_uNodeIndex[Rmin]);
+ }
+ }
+
+ assert(Lmin != uInsane);
+ assert(Rmin != uInsane);
+ assert(dtMinDist != BIG_DIST);
+
+#if TRACE
+ Info("Nearest neighbors Lmin %u[=%u] Rmin %u[=%u] dist %.3g\n",
+ Lmin,
+ g_uNodeIndex[Lmin],
+ Rmin,
+ g_uNodeIndex[Rmin],
+ dtMinDist);
+#endif
+
+ /* Compute distances to new node
+ * New node overwrites row currently assigned to Lmin
+ */
+ for ( j = 0; j < g_uLeafCount; ++j) {
+ ulong vL, vR;
+ dist_t dL, dR;
+ dist_t dtNewDist;
+
+ if (j == Lmin || j == Rmin)
+ continue;
+ if (uInsane == g_uNodeIndex[j])
+ continue;
+
+ vL = TriangleSubscript(Lmin, j);
+ vR = TriangleSubscript(Rmin, j);
+ dL = g_Dist[vL];
+ dR = g_Dist[vR];
+ dtNewDist = 0.0;
+
+ switch (linkage) {
+ case LINKAGE_AVG:
+ dtNewDist = AVG(dL, dR);
+ break;
+
+ case LINKAGE_MIN:
+ dtNewDist = MIN(dL, dR);
+ break;
+
+ case LINKAGE_MAX:
+ dtNewDist = MAX(dL, dR);
+ break;
+/* couldn't be arsed to figure out proper usage of g_dSUEFF */
+#if 0
+ case LINKAGE_BIASED:
+ dtNewDist = g_dSUEFF*AVG(dL, dR) + (1 - g_dSUEFF)*MIN(dL, dR);
+ break;
+#endif
+ default:
+ Log(&rLog, LOG_FATAL, "UPGMA2: Invalid LINKAGE_%u", linkage);
+ }
+
+ /* Nasty special case.
+ * If nearest neighbor of j is Lmin or Rmin, then make the new
+ * node (which overwrites the row currently occupied by Lmin)
+ * the nearest neighbor. This situation can occur when there are
+ * equal distances in the matrix. If we don't make this fix,
+ * the nearest neighbor pointer for j would become invalid.
+ * (We don't need to test for == Lmin, because in that case
+ * the net change needed is zero due to the change in row
+ * numbering).
+ */
+ if (g_uNearestNeighbor[j] == Rmin)
+ g_uNearestNeighbor[j] = Lmin;
+
+#if TRACE
+ Info("New dist to %u = (%u/%.3g + %u/%.3g)/2 = %.3g\n",
+ j, Lmin, dL, Rmin, dR, dtNewDist);
+#endif
+ g_Dist[vL] = dtNewDist;
+ if (dtNewDist < dtNewMinDist) {
+ dtNewMinDist = dtNewDist;
+ uNewNearestNeighbor = j;
+ }
+ }
+
+ assert(g_uInternalNodeIndex < g_uLeafCount - 1 || BIG_DIST != dtNewMinDist);
+ assert(g_uInternalNodeIndex < g_uLeafCount - 1 || uInsane != uNewNearestNeighbor);
+
+ const ulong v = TriangleSubscript(Lmin, Rmin);
+ const dist_t dLR = g_Dist[v];
+ const dist_t dHeightNew = dLR/2;
+ const uint uLeft = g_uNodeIndex[Lmin];
+ const uint uRight = g_uNodeIndex[Rmin];
+ const dist_t HeightLeft =
+ uLeft < g_uLeafCount ? 0 : g_Height[uLeft - g_uLeafCount];
+ const dist_t HeightRight =
+ uRight < g_uLeafCount ? 0 : g_Height[uRight - g_uLeafCount];
+
+ g_uLeft[g_uInternalNodeIndex] = uLeft;
+ g_uRight[g_uInternalNodeIndex] = uRight;
+ g_LeftLength[g_uInternalNodeIndex] = dHeightNew - HeightLeft;
+ g_RightLength[g_uInternalNodeIndex] = dHeightNew - HeightRight;
+ g_Height[g_uInternalNodeIndex] = dHeightNew;
+
+ /* Row for left child overwritten by row for new node */
+ g_uNodeIndex[Lmin] = g_uLeafCount + g_uInternalNodeIndex;
+ g_uNearestNeighbor[Lmin] = uNewNearestNeighbor;
+ g_MinDist[Lmin] = dtNewMinDist;
+
+ /* Delete row for right child */
+ g_uNodeIndex[Rmin] = uInsane;
+
+#if TRACE
+ Info("\nInternalNodeIndex=%u Lmin=%u Rmin=%u\n",
+ g_uInternalNodeIndex, Lmin, Rmin);
+ ListState();
+#endif
+ }
+
+ uint uRoot = g_uLeafCount - 2;
+
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "uRoot=%d g_uLeafCount=%d g_uInternalNodeCount=%d", uRoot, g_uLeafCount, g_uInternalNodeCount);
+ for (i=0; i<g_uInternalNodeCount; i++) {
+ Log(&rLog, LOG_FORCED_DEBUG, "internal node=%d: g_uLeft=%d g_uRight=%d g_LeftLength=%f g_RightLength=%f g_Height=%f",
+ i, g_uLeft[i], g_uRight[i],
+ g_LeftLength[i], g_RightLength[i],
+ g_Height[i]);
+ }
+ for (i=0; i<g_uLeafCount; i++) {
+ Log(&rLog, LOG_FORCED_DEBUG, "leaf node=%d: Ids=%d names=%s",
+ i, Ids[i], names[i]);
+ }
+#endif
+
+ MuscleTreeCreate(tree, g_uLeafCount, uRoot,
+ g_uLeft, g_uRight,
+ g_LeftLength, g_RightLength,
+ Ids, names);
+#if TRACE
+ tree.LogMe();
+#endif
+
+ free(g_Dist);
+
+ free(g_uNodeIndex);
+ free(g_uNearestNeighbor);
+ free(g_MinDist);
+ free(g_Height);
+
+ free(g_uLeft);
+ free(g_uRight);
+ free(g_LeftLength);
+ free(g_RightLength);
+
+ /* NOTE: Muscle's "Names" variable is here the argument "names" */
+ free(Ids);
+}
+/*** end of UPGMA2 ***/
--- /dev/null
+/* This the fast UPGMA algorithm (O(N^2)) as implemented in Bob Edgar's
+ * Muscle (UPGMA2.cpp; version 3.7) ported to pure C.
+ *
+ * Muscle's code is public domain and so is this code here.
+ *
+ * From http://www.drive5.com/muscle/license.htm:
+ * """
+ * MUSCLE is public domain software
+ *
+ * The MUSCLE software, including object and source code and
+ * documentation, is hereby donated to the public domain.
+ *
+ * Disclaimer of warranty
+ * THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND,
+ * EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * """
+ *
+ */
+
+/*
+ * RCS $Id: muscle_upgma.h 193 2011-02-07 15:45:21Z andreas $
+ */
+
+#ifndef CLUSTALO_UPGMA_H
+#define CLUSTALO_UPGMA_H
+
+#include "symmatrix.h"
+#include "muscle_tree.h"
+
+enum linkage_e {
+ LINKAGE_MIN,
+ LINKAGE_AVG,
+ LINKAGE_MAX,
+ LINKAGE_NEIGHBORJOINING,
+ LINKAGE_BIASED
+};
+typedef enum linkage_e linkage_t;
+
+void MuscleUpgma2(tree_t *tree, symmatrix_t *distmat,
+ linkage_t linkage, char **names);
+
+#endif
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: pair_dist.c 242 2011-05-27 14:04:21Z andreas $
+ */
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdlib.h>
+#include <ctype.h>
+#include <assert.h>
+#include <time.h>
+
+/* only neededfor iNumberOfThreads */
+#include "clustal-omega.h"
+
+#include "ktuple_pair.h"
+#include "pair_dist.h"
+#include "progress.h"
+#include "util.h"
+
+
+/* Up to rev 173 we had a USE_SYM_KTUPLE switch implemented here. When active
+ * ktuple distances were computed twice for each pair and averaged. Idea was
+ * to avoid assymmetries in the pairwise scores (score(a, b) is often not the
+ * same as score(b, a)). Results on BAliBASE indicate that this is overkill:
+ *
+ * r92_default core columns: avg-sp=0.800656 avg-tc=0.47711 (of total 218)
+ * r93-mod--norm-ktuple/ core columns: avg-sp=0.800656 avg-tc=0.47711 (of total 218)
+ * r93-mod--sym-ktuple/ core columns: avg-sp=0.801083 avg-tc=0.476544 (of total 217)
+ * r93-mod--rand-ktuple-1 core columns: avg-sp=0.799289 avg-tc=0.468028 (of total 218)
+ * r93-mod--rand-ktuple-2 core columns: avg-sp=0.801654 avg-tc=0.47659 (of total 217)
+ * r93-mod--rand-ktuple-3 core columns: avg-sp=0.800234 avg-tc=0.474908 (of total 218)
+ * r93-mod--rand-ktuple-4 core columns: avg-sp=0.800573 avg-tc=0.476514 (of total 218)
+ * r93-mod--rand-ktuple-5 core columns: avg-sp=0.799679 avg-tc=0.468716 (of total 218)
+ *
+ */
+
+static double
+KimuraCorrection(double frac_id);
+
+static int
+SquidIdPairDist(symmatrix_t *tmat, mseq_t *mseq,
+ int istart, int iend,
+ int jstart, int jend,
+ bool use_KimuraCorrection, progress_t *prProgress,
+ unsigned long int *ulStepNo, unsigned long int ulTotalStepNo);
+
+/* Taken from Muscle's msadistkimura.cpp */
+static int DAYHOFF_PAMS[]={
+ 195, /* 75.0% observed d; 195 PAMs estimated = 195% estimated d */
+ 196, /* 75.1% observed d; 196 PAMs estimated */
+ 197, 198, 199, 200, 200, 201, 202, 203,
+ 204, 205, 206, 207, 208, 209, 209, 210, 211, 212,
+ 213, 214, 215, 216, 217, 218, 219, 220, 221, 222,
+ 223, 224, 226, 227, 228, 229, 230, 231, 232, 233,
+ 234, 236, 237, 238, 239, 240, 241, 243, 244, 245,
+ 246, 248, 249, 250, /* 250 PAMs = 80.3% observed d */
+ 252, 253, 254, 255, 257, 258,
+ 260, 261, 262, 264, 265, 267, 268, 270, 271, 273,
+ 274, 276, 277, 279, 281, 282, 284, 285, 287, 289,
+ 291, 292, 294, 296, 298, 299, 301, 303, 305, 307,
+ 309, 311, 313, 315, 317, 319, 321, 323, 325, 328,
+ 330, 332, 335, 337, 339, 342, 344, 347, 349, 352,
+ 354, 357, 360, 362, 365, 368, 371, 374, 377, 380,
+ 383, 386, 389, 393, 396, 399, 403, 407, 410, 414,
+ 418, 422, 426, 430, 434, 438, 442, 447, 451, 456,
+ 461, 466, 471, 476, 482, 487, 493, 498, 504, 511,
+ 517, 524, 531, 538, 545, 553, 560, 569, 577, 586,
+ 595, 605, 615, 626, 637, 649, 661, 675, 688, 703,
+ 719, 736, 754, 775, 796, 819, 845, 874, 907, 945,
+ /* 92.9% observed; 945 PAMs */
+ 988 /* 93.0% observed; 988 PAMs */
+};
+static int DAYHOFF_TABLE_ENTRIES = sizeof(DAYHOFF_PAMS)/sizeof(DAYHOFF_PAMS[0]);
+
+
+
+/**
+ *
+ * @brief Compute Kimura corrected distance.
+ *
+ * Original Muscle documentation following:
+ * """
+ * This is defined to be:
+ * log_e(1 - p - p*p/5)
+ * where p is the fraction of residues that differ, i.e.:
+ * p = (1 - fractional_conservation)
+ * This measure is infinite for p = 0.8541 and is considered
+ * unreliable for p >= 0.75 (according to the ClustalW docs).
+ * ClustalW uses a table lookup for values > 0.75. The following table
+ * was copied from the ClustalW file dayhoff.h.
+ * """
+ *
+ * @note copied from Muscle's msadistkimura.cpp:KimuraDist()
+ *
+ * @warning For protein only (uses Dayhoff substitution parameters)
+ *
+ * @param[in] p
+ * distance, e.g. 1.0 - fractional/relative identity
+ *
+ * @return The Kimura corrected distance
+ *
+ */
+double
+KimuraCorrection(double p)
+{
+ int table_index;
+
+ /* Typical case: use Kimura's empirical formula */
+ if (p < 0.75)
+ return -log(1 - p - (p*p)/5);
+
+ /* Per ClustalW, return 10.0 for anything over 93% */
+ if (p > 0.93)
+ return 10.0;
+
+ /* If 0.75 >= p <= 0.93, use table lookup */
+ table_index = (int) ((p - 0.75)*1000 + 0.5);
+ if (table_index < 0 || table_index >= DAYHOFF_TABLE_ENTRIES)
+ Log(&rLog, LOG_FATAL, "Internal error in %s:%s", __FILE__, __FUNCTION__);
+
+ return DAYHOFF_PAMS[table_index] / 100.0;
+}
+/*** end: KimuraCorrection() ***/
+
+
+
+
+/**
+ * @brief Compute distances between all aligned sequence pairs using
+ * squid's PairwiseIdentity, which is: idents / MIN(len1, len2)
+ *
+ * @param[out] tmat
+ * Where to store the computed distances
+ * @param[in] mseq
+ * The aligned sequences
+ * @param[in] istart
+ * For distances [i][j] i>=istart, i<j
+ * @param[in] iend
+ * For distances [i][j] i<iend, i<j
+ * @param[in] jstart
+ * For distances [i][j] j>=jstart, i<j
+ * @param[in] jend
+ * For distances [i][j] i<j<jend, i<j
+ * @param[in] use_kimura
+ * Use Kimura corrected values (Proteins only)
+ *
+ * @return Non-zero on error
+ *
+ */
+int
+SquidIdPairDist(symmatrix_t *tmat, mseq_t *mseq,
+ int istart, int iend,
+ int jstart, int jend,
+ bool use_kimura, progress_t *prProgress,
+ unsigned long int *ulStepNo, unsigned long int ulTotalStepNo)
+{
+ int i, j; /* aux */
+ /* progress_t *prProgress; */
+ bool bPrintCR = (rLog.iLogLevelEnabled<=LOG_VERBOSE) ? FALSE : TRUE;
+ /* unsigned long int ulStepNo;
+ unsigned long ulTotalStepNo; */
+
+ assert(NULL != tmat);
+ assert(NULL != mseq);
+
+ if (TRUE != mseq->aligned) {
+ Log(&rLog, LOG_ERROR, "Sequences need to be aligned (%s)", __FUNCTION__);
+ return -1;
+ }
+ if (SEQTYPE_PROTEIN != mseq->seqtype && TRUE == use_kimura) {
+ Log(&rLog, LOG_WARN, "Using Kimura distance corretion which includes Dayhoff substitution table lookup for non-protein sequences");
+ }
+
+ NewProgress(&prProgress, LogGetFP(&rLog, LOG_INFO),
+ "Pairwise distance calculation progress", bPrintCR);
+ /* estimation of total number of steps (if istart and jstart are
+ * both 0)
+ */
+ /* ulTotalStepNo = iend*jend - iend*iend/2 + iend/2;
+ ulStepNo = 0; */
+ /*LOG_DEBUG("istart=%d iend=%d jstart=%d jend=%d", istart, iend, jstart, jend);*/
+ for (i=istart; i<iend; ++i) {
+ /* by definition a sequence compared to itself should give a
+ score of 0 */
+ SymMatrixSetValue(tmat, i, i, 0.0);
+#ifdef HAVE_OPENMP
+ #pragma omp critical(squidid)
+#endif
+ {
+ ProgressLog(prProgress, *ulStepNo, ulTotalStepNo, FALSE);
+ }
+
+ for (j=MAX(i+1, jstart); j<jend; ++j) {
+ float dist;
+ dist = 1.0 - PairwiseIdentity(mseq->seq[i], mseq->seq[j]);
+
+
+#ifdef HAVE_OPENMP
+ #pragma omp atomic
+#endif
+ (*ulStepNo)++;
+ /*LOG_DEBUG("%d:%d raw dist = %f", i, j, dist);*/
+ if (use_kimura) {
+ dist = KimuraCorrection(dist);
+ /*LOG_DEBUG("cor dist = %f", dist);*/
+ }
+ SymMatrixSetValue(tmat, i, j, dist);
+#ifdef HAVE_OPENMP
+ #pragma omp critical(squidid)
+#endif
+ {
+ Log(&rLog, LOG_DEBUG, "Aligned distance for sequence pair %d:%d= %lg",
+ i+1, j+1, dist);
+ }
+ }
+ }
+
+ return 0;
+}
+/*** end: SquidIdPairDist() ***/
+
+
+
+
+/**
+ * @brief compute or read precomputed distances for given sequences
+ *
+ * @param[out] distmat
+ * Distances will be written to this matrix. will be allocated here as
+ * well. Caller must free with FreeSymMatrix()
+ * @param[in] mseq
+ * Distances will be computed for these sequences
+ * @param[in] pairdist_type
+ * Type of pairwise distance comparison
+ * @param[in] fdist_in
+ * If not NULL, sequences will be written from this file instead of
+ * computing them
+ * @param[in] istart
+ * Compute distances for sequences i:j, i>=istart, i<j.
+ * Usually 0.
+ * @param[in] iend
+ * Compute distances for sequences i:j, i<iend, i<j
+ * Usually mseq->nseqs.
+ * @param[in] jstart
+ * Compute distances for sequences i:j, j>=jstart, i<j
+ * Usually 0.
+ * @param[in] jend
+ * Compute distances for sequences i:j, j<iend, i<j
+ * Usually mseq->nseqs.
+ * @param[in] fdist_out
+ * If not NULL, distances will be written to this files
+ *
+ *
+ */
+int
+PairDistances(symmatrix_t **distmat, mseq_t *mseq, int pairdist_type,
+ int istart, int iend,
+ int jstart, int jend,
+ char *fdist_in, char *fdist_out)
+{
+ int uSeqIndex;
+ unsigned long int ulStepNo = 0, ulTotalStepNo; /* DD: moved from SquidIdPairDist so progress bar works multithreaded */
+ int iChunk, iChunkStart, iChunkEnd;
+ int iChunkStarts[iNumberOfThreads];
+ int iChunkEnds[iNumberOfThreads];
+ progress_t *prProgress = NULL;
+ int iSquidSuccess = 0;
+ bool bPrintCR = (rLog.iLogLevelEnabled<=LOG_VERBOSE) ? FALSE : TRUE;
+
+ assert(NULL!=distmat);
+ assert(NULL!=mseq);
+ assert(istart<iend);
+ assert(jstart<jend);
+
+ if (NewSymMatrix(distmat, iend, jend)!=0) {
+ Log(&rLog, LOG_FATAL, "%s", "Memory allocation for distance matrix failed");
+ }
+
+
+ /* compute pairwise distances or read from file
+ *
+ */
+#if 0
+#include "random-dist.h"
+#else
+ if (NULL != fdist_in) {
+ Log(&rLog, LOG_FATAL, "FIXME: reading of distance matrix from file not implemented");
+
+ } else {
+
+ /* break into chunks, one for each thread
+ matrix is a triangle, not a square
+ hence making even chunk sizes is slightly fiddlier
+ */
+ ulTotalStepNo = iend*jend - iend*iend/2 + iend/2;
+
+ /* FIXME: can get rid of iChunkStart, iChunkEnd now that we're using the arrays */
+ iChunkStart = iend;
+ for(iChunk = 0; iChunk <= iNumberOfThreads; iChunk++)
+ {
+ iChunkEnd = iChunkStart;
+ if(iChunk == iNumberOfThreads - 1)
+ iChunkStart = 0;
+ else
+ iChunkStart = iend - ((double)(iend - istart) * sqrt(((double)iChunk + 1.0)/(double)iNumberOfThreads));
+ iChunkStarts[iChunk] = iChunkStart;
+ iChunkEnds[iChunk] = iChunkEnd;
+ }
+
+ if (PAIRDIST_KTUPLE == pairdist_type) {
+
+ Log(&rLog, LOG_INFO, "Calculating pairwise ktuple-distances...");
+
+ NewProgress(&prProgress, LogGetFP(&rLog, LOG_INFO),
+ "Ktuple-distance calculation progress", bPrintCR);
+#ifdef HAVE_OPENMP
+ #pragma omp parallel for private(iChunk) schedule(dynamic)
+#endif
+ for(iChunk = 0; iChunk < iNumberOfThreads; iChunk++)
+ {
+ KTuplePairDist((*distmat), mseq, iChunkStarts[iChunk],
+ iChunkEnds[iChunk], jstart, jend, NULL, prProgress,
+ &ulStepNo, ulTotalStepNo);
+ }
+
+#if 0
+ printf("total ops %d\n", ulStepNo);
+#endif
+ /* old format:
+ KTuplePairDist((*distmat), mseq,
+ istart, iend,
+ jstart, jend, NULL); */
+
+ } else if (PAIRDIST_SQUIDID == pairdist_type) {
+ Log(&rLog, LOG_INFO, "Calculating pairwise aligned identity distances...");
+
+ NewProgress(&prProgress, LogGetFP(&rLog, LOG_INFO),
+ "Pairwise identity calculation progress", bPrintCR);
+#ifdef HAVE_OPENMP
+ #pragma omp parallel for private(iChunk) schedule(dynamic)
+#endif
+ for(iChunk = 0; iChunk < iNumberOfThreads; iChunk++)
+ {
+ iSquidSuccess = SquidIdPairDist((*distmat), mseq,
+ iChunkStarts[iChunk], iChunkEnds[iChunk],
+ jstart, jend, FALSE, prProgress,
+ &ulStepNo, ulTotalStepNo);
+ }
+ if(iSquidSuccess != 0)
+ return -1;
+
+ } else if (PAIRDIST_SQUIDID_KIMURA == pairdist_type) {
+ Log(&rLog, LOG_INFO, "Calculating Kimura-corrected pairwise aligned identity distances...");
+ NewProgress(&prProgress, LogGetFP(&rLog, LOG_INFO),
+ "Pairwise identity calculation progress", bPrintCR);
+#ifdef HAVE_OPENMP
+ #pragma omp parallel for private(iChunk) schedule(dynamic)
+#endif
+ for(iChunk = 0; iChunk < iNumberOfThreads; iChunk++)
+ {
+ iSquidSuccess = SquidIdPairDist((*distmat), mseq,
+ iChunkStarts[iChunk], iChunkEnds[iChunk],
+ jstart, jend, TRUE, prProgress,
+ &ulStepNo, ulTotalStepNo);
+ }
+ if(iSquidSuccess != 0)
+ return -1;
+ } else {
+ Log(&rLog, LOG_FATAL, "INTERNAL ERROR: don't know about pairdist_type %d",
+ pairdist_type);
+ }
+ }
+#endif /* random/proper distance calculation */
+
+
+ /* optional printing of matrix to file
+ */
+ if (NULL != fdist_out) {
+ /* need a copy of sequence names for printing */
+ char **names;
+ names = (char **)CKMALLOC(mseq->nseqs * sizeof(char*));
+ for (uSeqIndex=0; uSeqIndex<mseq->nseqs; uSeqIndex++) {
+ names[uSeqIndex] = mseq->sqinfo[uSeqIndex].name;
+ }
+
+ SymMatrixPrint((*distmat), names, fdist_out);
+
+ Log(&rLog, LOG_INFO, "Pairwise distance matrix written to %s",
+ fdist_out);
+ CKFREE(names);
+ }
+
+#if 0
+#include "distance-distrib.h"
+#endif
+
+ if (NULL != prProgress) {
+ ProgressDone(prProgress);
+ FreeProgress(&prProgress);
+ }
+
+ return 0;
+}
+/*** end: PairDistances() ***/
+
+
+
--- /dev/null
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: pair_dist.h 193 2011-02-07 15:45:21Z andreas $
+ */
+
+
+#ifndef CLUSTALO_PAIR_DIST_H
+#define CLUSTALO_PAIR_DIST_H
+
+#define PAIRDIST_UNKNOWN 0
+/* k-tuple distances: Wilbur and Lipman (1983) */
+#define PAIRDIST_KTUPLE 1
+/* fractional identity between aligned sequences. denominator is
+ * minimum seq len (see squid:aligneval.c) */
+#define PAIRDIST_SQUIDID 2
+/* SQUIDID + Kimura correction */
+#define PAIRDIST_SQUIDID_KIMURA 3
+
+#include "seq.h"
+#include "symmatrix.h"
+
+extern int
+PairDistances(symmatrix_t **distmat, mseq_t *mseq, const int pairdist_type,
+ const int istart, const int iend,
+ const int jstart, const int jend,
+ char *fdist_in, char *fdist_out);
+
+#endif
+
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: progress.c 230 2011-04-09 15:37:50Z andreas $
+ */
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <assert.h>
+
+#include "util.h"
+#include "log.h"
+#include "progress.h"
+
+#define LOGLEVEL_THRESHOLD LOG_INFO
+
+/**
+ * @brief Allocates a new progress structure and initialises its members.
+ * Free with FreeProgress()
+ *
+ * @note Starts the internal stopwatch immediatly!
+ *
+ * @see FreeProgress()
+ *
+ * @param[out] pprProgress
+ * Pointer pointer to progress structure. Progress structure will be
+ * allocated here.
+ * @param[in] prFile
+ * Where to log messages to
+ * @param[in] pcPrefix
+ * What prefix to use for messages
+ * @param[in] bPrintCR
+ * If TRUE carriage return instead of newline will be printed between log messages
+ */
+void
+NewProgress(progress_t **pprProgress, FILE *prFile,
+ char *pcPrefix, bool bPrintCR)
+{
+ assert(NULL!=pprProgress);
+ assert(NULL!=prFile);
+ assert(NULL!=pcPrefix);
+
+ (*pprProgress) = (progress_t *) CKMALLOC(1*sizeof(progress_t));
+ (*pprProgress)->prFile = prFile;
+ (*pprProgress)->bPrintCR = bPrintCR;
+ (*pprProgress)->pcPrefix = CkStrdup(pcPrefix);
+ strcpy((*pprProgress)->pcLastLogMsg, "\0");
+ (*pprProgress)->prStopwatch = StopwatchCreate();
+ StopwatchZero((*pprProgress)->prStopwatch);
+ StopwatchStart((*pprProgress)->prStopwatch);
+
+ return;
+}
+/*** end: NewProgress() ***/
+
+
+
+/**
+ * @brief Frees progress structure and its members
+ *
+ * @param[out] pprProgress
+ * Pointer pointer to progress structure
+ *
+ * @see NewProgress()
+ *
+ */
+void
+FreeProgress(progress_t **pprProgress)
+{
+ (*pprProgress)->prFile = NULL;
+ CKFREE((*pprProgress)->pcPrefix);
+ StopwatchFree((*pprProgress)->prStopwatch);
+
+ CKFREE(*pprProgress);
+ return;
+}
+/*** end: FreeProgress() ***/
+
+
+
+
+/**
+ * @brief Prints a progress update (and a carriage return)
+ *
+ * @param[in] prProgress
+ * Pointer to the progress structure
+ * @param[in] iStep
+ * Current step number
+ * @param[in] iTotalSteps
+ * Total step number
+ * @param[in] bForceOutput
+ * If percentage hasn't changed output is normally supressed
+ * normally. Output can be forced with this flag.
+ *
+ */
+void
+ProgressLog(progress_t *prProgress,
+ unsigned long int iStep, unsigned long int iTotalSteps,
+ bool bForceOutput)
+{
+ char pcLogMsg[1024];
+ assert(0!=iTotalSteps);
+
+ if (rLog.iLogLevelEnabled>LOGLEVEL_THRESHOLD) {
+ return;
+ }
+
+ (void) snprintf(pcLogMsg, sizeof(pcLogMsg), "%s: %lu %%",
+ prProgress->pcPrefix, (unsigned long int)(iStep/(float)iTotalSteps*100.0));
+
+ if (! bForceOutput) {
+ /* Skip logging, if we've just logged the same message */
+ if (STR_EQ(pcLogMsg, prProgress->pcLastLogMsg)) {
+ return;
+ }
+ }
+
+ strncpy(prProgress->pcLastLogMsg, pcLogMsg,
+ sizeof(prProgress->pcLastLogMsg));
+
+ fprintf(prProgress->prFile, "%s (%lu out of %lu)", pcLogMsg, iStep, iTotalSteps);
+ if (prProgress->bPrintCR) {
+ fprintf(prProgress->prFile, "\r");
+ } else {
+ fprintf(prProgress->prFile, "\n");
+
+ }
+ (void) fflush(prProgress->prFile);
+
+ return;
+}
+/*** end: ProgressLog() ***/
+
+
+/**
+ * @brief Finishes progress output by printing the elapsed time
+ *
+ * @param[in] prProgress
+ * Pointer to the progress structure
+ *
+ */
+void
+ProgressDone(progress_t *prProgress)
+{
+ char pcBuf[1024];
+
+ if (rLog.iLogLevelEnabled>LOGLEVEL_THRESHOLD) {
+ return;
+ }
+
+ (void) snprintf(pcBuf, sizeof(pcBuf), "%s done. CPU time: ",
+ prProgress->pcPrefix);
+ StopwatchStop(prProgress->prStopwatch);
+ StopwatchDisplay(prProgress->prFile, pcBuf, prProgress->prStopwatch);
+ (void) fflush(prProgress->prFile);
+
+ return;
+}
+/*** end: ProgressDone() ***/
--- /dev/null
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: progress.h 193 2011-02-07 15:45:21Z andreas $
+ */
+
+
+#ifndef CLUSTALO_PROGRESS_H
+#define CLUSTALO_PROGRESS_H
+
+#include "squid/stopwatch.h"
+
+typedef struct {
+ /* where to write to */
+ FILE *prFile;
+ /* prefix printed before each step */
+ char *pcPrefix;
+ bool bPrintCR;
+ char pcLastLogMsg[1024];
+ Stopwatch_t *prStopwatch;
+} progress_t;
+
+
+extern void
+NewProgress(progress_t **pprProgress, FILE *prFile, char *pcPrefix, bool bPrintCR);
+
+extern void
+FreeProgress(progress_t **pprProgress);
+
+extern void
+ProgressLog(progress_t *prProgress,
+ unsigned long int iStep, unsigned long int iTotalSteps,
+ bool bForceOutput);
+
+extern void
+ProgressDone(progress_t *pprProgress);
+
+#endif
--- /dev/null
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: queue.h 193 2011-02-07 15:45:21Z andreas $
+ *
+ * Functions/Macros for FIFOs/Queues
+ *
+ */
+
+#ifndef CLUSTALO_QUEUE_H
+#define CLUSTALO_QUEUE_H
+
+#include "list.h"
+
+
+
+/* FIFO/Queue as list_t, storing data pointers
+ *
+ */
+
+typedef list_t queue_t;
+
+/* setup queue */
+#define QUEUE_INIT(prQueue, destroy_func) ListInit((prQueue), (destroy_func))
+
+/* free all elements from queue */
+#define QUEUE_DESTROY(prQueue) ListDestroy((prQueue))
+
+/* enqueue */
+#define QUEUE_PUSH(prQueue, data) LIST_APPEND((prQueue), (data))
+
+/* dequeue */
+#define QUEUE_POP(prQueue, data) ListRemoveNext((prQueue), NULL, (data))
+
+/* is queue empty ? */
+#define QUEUE_EMPTY(prQueue) (0==LIST_SIZE((prQueue)))
+
+
+
+/* Special int FIF/Queue, storing ints by copying them instead of
+ * keeping pointers only
+ */
+
+typedef queue_t int_queue_t;
+
+/* setup queue */
+#define INT_QUEUE_INIT(prQueue) INT_LIST_INIT((prQueue))
+
+/* free all elements from queue */
+#define INT_QUEUE_DESTROY(prQueue) INT_LIST_DESTROY((prQueue))
+
+/* enqueue */
+#define INT_QUEUE_PUSH(prQueue, data) INT_LIST_APPEND((prQueue), (data))
+
+/* dequeue */
+#define INT_QUEUE_POP(prQueue, data) IntListRemoveNext((prQueue), NULL, (data))
+
+/* is queue empty ? */
+#define INT_QUEUE_EMPTY(prQueue) (0==INT_LIST_SIZE((prQueue)))
+
+
+
+#endif
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: seq.c 245 2011-06-15 12:38:53Z fabian $
+ *
+ *
+ * Module for sequence/alignment IO and misc.
+ *
+ * This depends heavily on Sean Eddy's squid library, which is obsoleted by
+ * HMMER3's Easel. However, easel doesn't support that many non-aligned input
+ * formats.
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <assert.h>
+#include "squid/squid.h"
+#include <ctype.h>
+
+#include "util.h"
+#include "log.h"
+#include "seq.h"
+
+
+#define ALLOW_ONLY_PROTEIN 0 /* requested by Hamish, FS, r244 -> r245 */
+
+
+
+
+/**
+ * @brief Stripped down version of squid's alistat
+ *
+ *
+ * @param[in] prMSeq
+ * The alignment to analyse
+ * @param[in] bSampling
+ * For many sequences: samples from pool
+ * @param[in] bReportAll
+ * Report identities for all sequence pairs
+ *
+ * Don't have to worry about sequence case because our version of PairwiseIdentity is case insensitive
+ */
+void
+AliStat(mseq_t *prMSeq, bool bSampling, bool bReportAll) {
+
+ /*
+ * bSampling = squid's do_fast
+ * bReportAll = squid's allreport
+ */
+ float **ppdIdentMx; /* identity matrix (squid: imx) */
+ const int iNumSample = 1000; /* sample size (squid: nsample) */
+ int iAux;
+
+ MSA *msa; /* squid's alignment structure */
+ int small, large;
+ int bestj, worstj;
+ float sum;
+ float worst_worst, worst_best, best_best;
+ float avgid;
+ int i, j;
+ int nres; /* number of residues */
+
+ if (bSampling && bReportAll) {
+ Log(&rLog, LOG_WARN,
+ "Cannot report all and sample at the same time. Skipping %s()", __FUNCTION__);
+ return;
+ }
+ if (FALSE == prMSeq->aligned) {
+ Log(&rLog, LOG_WARN,
+ "Sequences are not aligned. Skipping %s()", __FUNCTION__);
+ return;
+ }
+
+ /* silence gcc warnings about uninitialized variables
+ */
+ worst_worst = worst_best = best_best = 0.0;
+ bestj = worstj = -1;
+
+
+ /** mseq to squid msa
+ *
+ * FIXME code overlap with WriteAlignment. Make it a function and take
+ * code there (contains more comments) as template
+ *
+ */
+ msa = MSAAlloc(prMSeq->nseqs,
+ /* derive alignment length from first seq */
+ strlen(prMSeq->seq[0]));
+ for (i=0; i<prMSeq->nseqs; i++) {
+ int key; /* MSA struct internal index for sequence */
+ char *this_name = prMSeq->sqinfo[i].name; /* prMSeq sequence name */
+ char *this_seq = prMSeq->seq[i]; /* prMSeq sequence */
+ SQINFO *this_sqinfo = &prMSeq->sqinfo[i]; /* prMSeq sequence name */
+
+ key = GKIStoreKey(msa->index, this_name);
+ msa->sqname[key] = sre_strdup(this_name, strlen(this_name));
+ /* setting msa->sqlen[idx] and msa->aseq[idx] */
+ msa->sqlen[key] = sre_strcat(&(msa->aseq[key]), msa->sqlen[key],
+ this_seq, strlen(this_seq));
+ if (this_sqinfo->flags & SQINFO_DESC) {
+ MSASetSeqDescription(msa, key, this_sqinfo->desc);
+ }
+ msa->nseq++;
+ }
+
+
+
+ nres = 0;
+ small = large = -1;
+ for (i = 0; i < msa->nseq; i++) {
+ int rlen; /* raw sequence length */
+ rlen = DealignedLength(msa->aseq[i]);
+ nres += rlen;
+ if (small == -1 || rlen < small) small = rlen;
+ if (large == -1 || rlen > large) large = rlen;
+ }
+
+
+ if (bSampling) {
+ avgid = AlignmentIdentityBySampling(msa->aseq, msa->alen,
+ msa->nseq, iNumSample);
+
+ } else {
+ float best, worst;
+
+ /* this might be slow...could use openmp inside squid */
+ MakeIdentityMx(msa->aseq, msa->nseq, &ppdIdentMx);
+ if (bReportAll) {
+ printf(" %-15s %5s %7s %-15s %7s %-15s\n",
+ "NAME", "LEN", "HIGH ID", "(TO)", "LOW ID", "(TO)");
+ printf(" --------------- ----- ------- --------------- ------- ---------------\n");
+ }
+
+ sum = 0.0;
+ worst_best = 1.0;
+ best_best = 0.0;
+ worst_worst = 1.0;
+ for (i = 0; i < msa->nseq; i++) {
+ worst = 1.0;
+ best = 0.0;
+ for (j = 0; j < msa->nseq; j++) {
+ /* closest seq to this one = best */
+ if (i != j && ppdIdentMx[i][j] > best) {
+ best = ppdIdentMx[i][j]; bestj = j;
+ }
+ if (ppdIdentMx[i][j] < worst) {
+ worst = ppdIdentMx[i][j]; worstj = j;
+ }
+ }
+
+ if (bReportAll) {
+ printf("* %-15s %5d %7.1f %-15s %7.1f %-15s\n",
+ msa->sqname[i], DealignedLength(msa->aseq[i]),
+ best * 100., msa->sqname[bestj],
+ worst * 100., msa->sqname[worstj]);
+ }
+ if (best > best_best) best_best = best;
+ if (best < worst_best) worst_best = best;
+ if (worst < worst_worst) worst_worst = worst;
+ for (j = 0; j < i; j++)
+ sum += ppdIdentMx[i][j];
+ }
+ avgid = sum / (float) (msa->nseq * (msa->nseq-1)/2.0);
+ if (bReportAll)
+ puts("");
+ FMX2Free(ppdIdentMx);
+ } /* else bSampling */
+
+
+
+ /* Print output
+ */
+ if (msa->name != NULL)
+ printf("Alignment name: %s\n", msa->name);
+ /*printf("Format: %s\n", SeqfileFormat2String(afp->format));*/
+ printf("Number of sequences: %d\n", msa->nseq);
+ printf("Total # residues: %d\n", nres);
+ printf("Smallest: %d\n", small);
+ printf("Largest: %d\n", large);
+ printf("Average length: %.1f\n", (float) nres / (float) msa->nseq);
+ printf("Alignment length: %d\n", msa->alen);
+ printf("Average identity: %.2f%%\n", 100.*avgid);
+
+ if (! bSampling) {
+ printf("Most related pair: %.2f%%\n", 100.*best_best);
+ printf("Most unrelated pair: %.2f%%\n", 100.*worst_worst);
+ printf("Most distant seq: %.2f%%\n", 100.*worst_best);
+ }
+
+ /*
+ char *cs;
+ cs = MajorityRuleConsensus(msa->aseq, msa->nseq, msa->alen);
+ printf cs;
+ */
+
+ MSAFree(msa);
+}
+/* end of AliStat() */
+
+
+
+
+
+/**
+ * @brief Shuffle mseq order
+ *
+ * @param[out] mseq
+ * mseq structure to shuffle
+ *
+ */
+void
+ShuffleMSeq(mseq_t *mseq)
+{
+ int iSeqIndex;
+ int *piPermArray;
+
+
+ /* quick and dirty: create an array with permuted indices and
+ * swap accordingly (which amounts to shuffling twice)
+ */
+
+ PermutationArray(&piPermArray, mseq->nseqs);
+
+ for (iSeqIndex=0; iSeqIndex<mseq->nseqs; iSeqIndex++) {
+ SeqSwap(mseq, piPermArray[iSeqIndex], iSeqIndex);
+ }
+
+ CKFREE(piPermArray);
+}
+/*** end: ShuffleMSeq() ***/
+
+
+/**
+ * @brief Swap two sequences in an mseq_t structure.
+ *
+ * @param[out] prMSeq
+ * Multiple sequence struct
+ * @param[in] i
+ * Index of first sequence
+ * @param[in] j
+ * Index of seconds sequence
+ *
+ *
+ */
+void
+SeqSwap(mseq_t *prMSeq, int i, int j)
+{
+ char *pcTmp;
+ SQINFO rSqinfoTmp;
+
+ assert(NULL!=prMSeq);
+ assert(i<prMSeq->nseqs && j<prMSeq->nseqs);
+
+ if (i==j) {
+ return;
+ }
+
+ pcTmp = prMSeq->seq[i];
+ prMSeq->seq[i] = prMSeq->seq[j];
+ prMSeq->seq[j] = pcTmp;
+
+ pcTmp = prMSeq->orig_seq[i];
+ prMSeq->orig_seq[i] = prMSeq->orig_seq[j];
+ prMSeq->orig_seq[j] = pcTmp;
+
+ rSqinfoTmp = prMSeq->sqinfo[i];
+ prMSeq->sqinfo[i] = prMSeq->sqinfo[j];
+ prMSeq->sqinfo[j] = rSqinfoTmp;
+
+ return;
+}
+/*** end: SeqSwap() ***/
+
+
+
+
+/**
+ * @brief Dealigns all sequences in mseq structure, updates the
+ * sequence length info and sets aligned to FALSE
+ *
+ * @param[out] mseq
+ * The mseq structure to dealign
+ *
+ */
+void
+DealignMSeq(mseq_t *mseq)
+{
+ int i; /* aux */
+ for (i=0; i<mseq->nseqs; i++) {
+ DealignSeq(mseq->seq[i]);
+ mseq->sqinfo[i].len = strlen(mseq->seq[i]);
+ }
+ mseq->aligned = FALSE;
+
+ return;
+}
+/*** end: DealinMSeq() ***/
+
+
+
+/**
+ * @brief debug output of sqinfo struct
+ *
+ * @param[in] sqinfo
+ * Squid's SQINFO struct for a certain seqeuence
+ *
+ * @note useful for debugging only
+ *
+ */
+void
+LogSqInfo(SQINFO *sqinfo)
+{
+
+ /*LOG_DEBUG("sqinfo->flags = %d", sqinfo->flags);*/
+ if (sqinfo->flags & SQINFO_NAME)
+ Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->name = %s", sqinfo->name);
+
+ if (sqinfo->flags & SQINFO_ID)
+ Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->id = %s", sqinfo->id);
+
+ if (sqinfo->flags & SQINFO_ACC)
+ Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->acc = %s", sqinfo->acc);
+
+ if (sqinfo->flags & SQINFO_DESC)
+ Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->desc = %s", sqinfo->desc);
+
+ if (sqinfo->flags & SQINFO_LEN)
+ Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->len = %d", sqinfo->len);
+
+ if (sqinfo->flags & SQINFO_START)
+ Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->start = %d", sqinfo->start);
+
+ if (sqinfo->flags & SQINFO_STOP)
+ Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->stop = %d", sqinfo->stop);
+
+ if (sqinfo->flags & SQINFO_OLEN)
+ Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->olen = %d", sqinfo->olen);
+
+ if (sqinfo->flags & SQINFO_TYPE)
+ Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->type = %d", sqinfo->type);
+
+ if (sqinfo->flags & SQINFO_SS)
+ Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->ss = %s", sqinfo->ss);
+
+ if (sqinfo->flags & SQINFO_SA)
+ Log(&rLog, LOG_FORCED_DEBUG, "sqinfo->sa = %s", sqinfo->sa);
+}
+/*** end: log_sqinfo ***/
+
+
+/**
+ * @brief convert int-encoded seqtype to string
+ *
+ * @param[in] seqtype int-encoded sequence type
+ *
+ * @return character pointer describing the sequence type
+ *
+ */
+const char*
+SeqTypeToStr(int seqtype)
+{
+ switch (seqtype) {
+ case SEQTYPE_DNA:
+ return "DNA";
+ case SEQTYPE_RNA:
+ return "RNA";
+ case SEQTYPE_PROTEIN:
+ return "Protein";
+ case SEQTYPE_UNKNOWN:
+ return "UNKNOWN";
+ default:
+ Log(&rLog, LOG_FATAL, "Internal error in %s", __FUNCTION__);
+ }
+ return "Will never get here";
+}
+/*** end: seqtype_to_str ***/
+
+
+
+/**
+ * @brief reads sequences from file
+ *
+ * @param[out] prMSeq
+ * Multiple sequence struct. Must be preallocated.
+ * FIXME: would make more sense to allocate it here.
+ * @param[in] seqfile
+ * Sequence file name. If '-' sequence will be read from stdin.
+ * @param[in] seqtype
+ * int-encoded sequence type. Set to
+ * SEQTYPE_UNKNOWN for autodetect (guessed from first sequence)
+ * @param[in] iMaxNumSeq
+ * Return an error, if more than iMaxNumSeq have been read
+ * @param[in] iMaxSeqLen
+ * Return an error, if a seq longer than iMaxSeqLen has been read
+ *
+ * @return 0 on success, -1 on error
+ *
+ * @note
+ * - Depends heavily on squid
+ * - Sequence file format will be guessed
+ * - If supported by squid, gzipped files can be read as well.
+ */
+int
+ReadSequences(mseq_t *prMSeq, char *seqfile, int seqtype,
+ int iMaxNumSeq, int iMaxSeqLen)
+{
+ int fmt = SQFILE_UNKNOWN; /* file format: auto detect if unknown */
+ SQFILE *dbfp; /* sequence file descriptor */
+ char *cur_seq;
+ SQINFO cur_sqinfo;
+ int iSeqIdx; /* sequence counter */
+ int iSeqPos; /* sequence string position counter */
+
+ assert(NULL!=seqfile);
+
+
+ /* Try to work around inability to autodetect from a pipe or .gz:
+ * assume FASTA format
+ */
+ if (SQFILE_UNKNOWN == fmt &&
+ (Strparse("^.*\\.gz$", seqfile, 0) || strcmp(seqfile, "-") == 0)) {
+ fmt = SQFILE_FASTA;
+ }
+
+ /* Using squid routines to read input. taken from seqstat_main.c. we don't
+ * know if input is aligned, so we use SeqfileOpen instead of MSAFileOpen
+ * etc. NOTE this also means we discard some information, e.g. when
+ * reading from and writing to a stockholm file, all extra MSA
+ * info/annotation will be lost.
+ *
+ */
+
+ if (NULL == (dbfp = SeqfileOpen(seqfile, fmt, NULL))) {
+ Log(&rLog, LOG_ERROR, "Failed to open sequence file %s for reading", seqfile);
+ return -1;
+ }
+
+
+ /* FIXME squid's ReadSeq() will exit with fatal error if format is
+ * unknown. This will be a problem for a GUI. Same is true for many squid
+ * other functions.
+ *
+ * The original squid:ReadSeq() dealigns sequences on input. We
+ * use a patched version.
+ *
+ */
+ while (ReadSeq(dbfp, dbfp->format,
+ &cur_seq,
+ &cur_sqinfo)) {
+
+ if (prMSeq->nseqs+1>iMaxNumSeq) {
+ Log(&rLog, LOG_ERROR, "Maximum number of sequences (=%d) exceeded after reading sequence '%s' from '%s'",
+ iMaxNumSeq, cur_sqinfo.name, seqfile);
+ return -1;
+ }
+ if ((int)strlen(cur_seq)>iMaxSeqLen) {
+ Log(&rLog, LOG_ERROR, "Sequence '%s' has %d residues and is therefore longer than allowed (max. sequence length is %d)",
+ cur_sqinfo.name, strlen(cur_seq), iMaxSeqLen);
+ return -1;
+ }
+
+ /* FIXME: use modified version of AddSeq() that allows handing down SqInfo
+ */
+
+ prMSeq->seq = (char **)
+ CKREALLOC(prMSeq->seq, (prMSeq->nseqs+1) * sizeof(char *));
+ prMSeq->seq[prMSeq->nseqs] = CkStrdup(cur_seq);
+
+
+ prMSeq->sqinfo = (SQINFO *)
+ CKREALLOC(prMSeq->sqinfo, (prMSeq->nseqs+1) * sizeof(SQINFO));
+ SeqinfoCopy(&prMSeq->sqinfo[prMSeq->nseqs], &cur_sqinfo);
+
+#ifdef TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "seq no %d: seq = %s", prMSeq->nseqs, prMSeq->seq[prMSeq->nseqs]);
+ LogSqInfo(&prMSeq->sqinfo[prMSeq->nseqs]);
+#endif
+ /* always guess type from first seq. use squid function and
+ * convert value
+ */
+ if (0 == prMSeq->nseqs) {
+ int type = Seqtype(prMSeq->seq[prMSeq->nseqs]);
+ switch (type) {
+ case kDNA:
+ prMSeq->seqtype = SEQTYPE_DNA;
+ break;
+ case kRNA:
+ prMSeq->seqtype = SEQTYPE_RNA;
+ break;
+ case kAmino:
+ prMSeq->seqtype = SEQTYPE_PROTEIN;
+ break;
+ case kOtherSeq:
+ prMSeq->seqtype = SEQTYPE_UNKNOWN;
+ break;
+ default:
+ Log(&rLog, LOG_FATAL, "Internal error in %s", __FUNCTION__);
+ }
+
+ /* override with given sequence type but check with
+ * automatically detected type and warn if necessary
+ */
+ if (SEQTYPE_UNKNOWN != seqtype) {
+ if (prMSeq->seqtype != seqtype) {
+ Log(&rLog, LOG_WARN, "Overriding automatically determined seq-type %s to %s as requested",
+ SeqTypeToStr(prMSeq->seqtype), SeqTypeToStr(seqtype));
+ prMSeq->seqtype = seqtype;
+ }
+ }
+ /* if type could not be determined and was not set return error */
+ if (SEQTYPE_UNKNOWN == seqtype && SEQTYPE_UNKNOWN == prMSeq->seqtype) {
+ Log(&rLog, LOG_ERROR, "Couldn't guess sequence type from first sequence");
+ FreeSequence(cur_seq, &cur_sqinfo);
+ SeqfileClose(dbfp);
+ return -1;
+ }
+ }
+
+ Log(&rLog, LOG_DEBUG, "seq-no %d: type=%s name=%s len=%d seq=%s",
+ prMSeq->nseqs, SeqTypeToStr(prMSeq->seqtype),
+ prMSeq->sqinfo[prMSeq->nseqs].name, prMSeq->sqinfo[prMSeq->nseqs].len,
+ prMSeq->seq[prMSeq->nseqs]);
+
+ /* FIXME IPUAC and/or case conversion? If yes see
+ * corresponding squid functions. Special treatment of
+ * Stockholm tilde-gaps for ktuple code?
+ */
+
+ prMSeq->nseqs++;
+
+ FreeSequence(cur_seq, &cur_sqinfo);
+ }
+ SeqfileClose(dbfp);
+
+#if ALLOW_ONLY_PROTEIN
+ if (SEQTYPE_PROTEIN != prMSeq->seqtype) {
+ Log(&rLog, LOG_FATAL, "Sequence type is %s. %s only works on protein.",
+ SeqTypeToStr(prMSeq->seqtype), PACKAGE_NAME);
+ }
+#endif
+
+ /* Check if sequences are aligned */
+ prMSeq->aligned = SeqsAreAligned(prMSeq);
+
+
+ /* keep original sequence as copy and convert "working" sequence
+ *
+ */
+ prMSeq->orig_seq = (char**) CKMALLOC(prMSeq->nseqs * sizeof(char *));
+ for (iSeqIdx=0; iSeqIdx<prMSeq->nseqs; iSeqIdx++) {
+
+ prMSeq->orig_seq[iSeqIdx] = CkStrdup(prMSeq->seq[iSeqIdx]);
+
+
+ /* convert unknown characters according to set seqtype
+ * be conservative, i.e. don't allow any fancy ambiguity
+ * characters to make sure that ktuple code etc. works.
+ */
+
+ /* first on the fly conversion between DNA and RNA
+ */
+ if (prMSeq->seqtype==SEQTYPE_DNA)
+ ToDNA(prMSeq->seq[iSeqIdx]);
+ if (prMSeq->seqtype==SEQTYPE_RNA)
+ ToRNA(prMSeq->seq[iSeqIdx]);
+
+ /* then check of each character
+ */
+ for (iSeqPos=0; iSeqPos<(int)strlen(prMSeq->seq[iSeqIdx]); iSeqPos++) {
+ char *res = &(prMSeq->seq[iSeqIdx][iSeqPos]);
+ if (isgap(*res))
+ continue;
+
+ if (prMSeq->seqtype==SEQTYPE_PROTEIN) {
+ if (NULL == strchr(AMINO_ALPHABET, toupper(*res))) {
+ *res = AMINOACID_ANY;
+ }
+ } else if (prMSeq->seqtype==SEQTYPE_DNA) {
+ if (NULL == strchr(DNA_ALPHABET, toupper(*res))) {
+ *res = NUCLEOTIDE_ANY;
+ }
+ } else if (prMSeq->seqtype==SEQTYPE_RNA) {
+ if (NULL == strchr(RNA_ALPHABET, toupper(*res))) {
+ *res = NUCLEOTIDE_ANY;
+ }
+ }
+ }
+ }
+
+
+ prMSeq->filename = CkStrdup(seqfile);
+ Log(&rLog, LOG_INFO, "Read %d sequences (type: %s) from %s",
+ prMSeq->nseqs, SeqTypeToStr(prMSeq->seqtype), prMSeq->filename);
+
+ return 0;
+}
+/*** end: ReadSequences ***/
+
+
+/**
+ * @brief allocate and initialise new mseq_t
+ *
+ * @param[out] prMSeq
+ * newly allocated and initialised mseq_t
+ *
+ * @note caller has to free by calling FreeMSeq()
+ *
+ * @see FreeMSeq
+ *
+ */
+void
+NewMSeq(mseq_t **prMSeq)
+{
+ *prMSeq = (mseq_t *) CKMALLOC(1 * sizeof(mseq_t));
+
+ (*prMSeq)->nseqs = 0;
+ (*prMSeq)->seq = NULL;
+ (*prMSeq)->orig_seq = NULL;
+ (*prMSeq)->seqtype = SEQTYPE_UNKNOWN;
+ (*prMSeq)->sqinfo = NULL;
+ (*prMSeq)->filename = NULL;
+}
+/*** end: NewMSeq ***/
+
+
+
+/**
+ * @brief copies an mseq structure
+ *
+ * @param[out] prMSeqDest_p
+ * Copy of mseq structure
+ * @param[in] prMSeqSrc
+ * Source mseq structure to copy
+ *
+ * @note caller has to free copy by calling FreeMSeq()
+ *
+ */
+void
+CopyMSeq(mseq_t **prMSeqDest_p, mseq_t *prMSeqSrc)
+{
+ int i;
+ assert(prMSeqSrc != NULL && prMSeqDest_p != NULL);
+
+ NewMSeq(prMSeqDest_p);
+
+ (*prMSeqDest_p)->nseqs = prMSeqSrc->nseqs;
+ (*prMSeqDest_p)->seqtype = prMSeqSrc->seqtype;
+ if (prMSeqSrc->filename!=NULL) {
+ (*prMSeqDest_p)->filename = CkStrdup(prMSeqSrc->filename);
+ }
+
+ (*prMSeqDest_p)->seq = (char **)
+ CKMALLOC((*prMSeqDest_p)->nseqs * sizeof(char *));
+ (*prMSeqDest_p)->orig_seq = (char **)
+ CKMALLOC((*prMSeqDest_p)->nseqs * sizeof(char *));
+ (*prMSeqDest_p)->sqinfo = (SQINFO *)
+ CKMALLOC((*prMSeqDest_p)->nseqs * sizeof(SQINFO));
+
+
+
+ for (i=0; i<(*prMSeqDest_p)->nseqs; i++) {
+ (*prMSeqDest_p)->seq[i] = CkStrdup(prMSeqSrc->seq[i]);
+ (*prMSeqDest_p)->orig_seq[i] = CkStrdup(prMSeqSrc->orig_seq[i]);
+ SeqinfoCopy(&(*prMSeqDest_p)->sqinfo[i], &prMSeqSrc->sqinfo[i]);
+ }
+}
+/*** end: CopyMSeq ***/
+
+
+
+/**
+ * @brief
+ *
+ * @param[in] seqname
+ * The sequence name to search for
+ * @param[in] mseq
+ * The multiple sequence structure to search in
+ *
+ * @return -1 on failure, sequence index of matching name otherwise
+ *
+ * @warning If sequence name happens to be used twice, only the first
+ * one will be reported back
+ *
+ */
+int
+FindSeqName(char *seqname, mseq_t *mseq)
+{
+ int i; /* aux */
+
+ assert(NULL!=mseq);
+
+ for (i=0; i<mseq->nseqs; i++) {
+ if (STR_EQ(mseq->sqinfo[i].name, seqname)) {
+ return i;
+ }
+ }
+
+ return -1;
+}
+/*** end: FindSeqName() ***/
+
+
+/**
+ * @brief Frees an mseq_t and it's members and zeros all members
+ *
+ * @param[in] mseq mseq_to to free
+ *
+ * @note use in conjunction with NewMSeq()
+ * @see new_mseq
+ */
+void
+FreeMSeq(mseq_t **mseq)
+{
+ int i;
+
+ if (NULL==(*mseq)) {
+ return;
+ }
+
+ if ((*mseq)->filename) {
+ (*mseq)->filename = CKFREE((*mseq)->filename);
+ }
+
+ for (i=0; i<(*mseq)->nseqs; i++) {
+ FreeSequence((*mseq)->seq[i], &(*mseq)->sqinfo[i]);
+ CKFREE((*mseq)->orig_seq[i]);
+ }
+ if ((*mseq)->seq) {
+ CKFREE((*mseq)->seq);
+ }
+ if ((*mseq)->orig_seq) { /* FIXME (FS): only ptr to ptr freed, actual sequences NOT freed*/
+ CKFREE((*mseq)->orig_seq);
+ }
+ if ((*mseq)->sqinfo) {
+ CKFREE((*mseq)->sqinfo);
+ }
+
+ (*mseq)->seqtype = SEQTYPE_UNKNOWN;
+ (*mseq)->nseqs = 0;
+
+ CKFREE((*mseq));
+}
+/*** end: FreeMSeq ***/
+
+
+/**
+ * @brief Write alignment to file.
+ *
+ * @param[in] mseq
+ * The mseq_t struct containing the aligned sequences
+ * @param[in] pcAlnOutfile
+ * The name of the output file
+ * @param[in] outfmt
+ * The alignment output format (defined in squid.h)
+ *
+ * @return Non-zero on error
+ *
+ * @note We create a temporary squid MSA struct in here because we never
+ * use it within clustal. We might be better of using the old clustal
+ * output routines instead.
+ *
+ */
+int
+WriteAlignment(mseq_t *mseq, const char *pcAlnOutfile, int outfmt)
+{
+ int i; /* aux */
+ MSA *msa; /* squid's alignment structure */
+ FILE *pfOut = NULL;
+ int key; /* MSA struct internal index for sequence */
+ int alen; /* alignment length */
+ bool use_stdout;
+
+ assert(mseq!=NULL);
+
+ if (MSAFILE_UNKNOWN == outfmt) {
+ Log(&rLog, LOG_ERROR, "Unknown output format chosen");
+ return -1;
+ }
+
+ if (NULL == pcAlnOutfile) {
+ pfOut = stdout;
+ use_stdout = TRUE;
+ } else {
+ use_stdout = FALSE;
+ if (NULL == (pfOut = fopen(pcAlnOutfile, "w"))) {
+ Log(&rLog, LOG_ERROR, "Could not open file %s for writing", pcAlnOutfile);
+ return -1;
+ }
+ }
+
+
+ /* derive alignment length from first seq */
+ alen = strlen(mseq->seq[0]);
+
+ msa = MSAAlloc(mseq->nseqs, alen);
+
+ /* basic structure borrowed code from squid-1.9g/a2m.c:ReadA2M()
+ * we actually create a copy of mseq. keeping the pointers becomes
+ * messy when calling MSAFree()
+ */
+ for (i=0; i<mseq->nseqs; i++) {
+ char *this_name = mseq->sqinfo[i].name; /* mseq sequence name */
+ char *this_seq = mseq->seq[i]; /* mseq sequence */
+ SQINFO *this_sqinfo = &mseq->sqinfo[i]; /* mseq sequence name */
+
+ key = GKIStoreKey(msa->index, this_name);
+ msa->sqname[key] = sre_strdup(this_name, strlen(this_name));
+
+ /* setting msa->sqlen[idx] and msa->aseq[idx] */
+ msa->sqlen[key] = sre_strcat(&(msa->aseq[key]), msa->sqlen[key],
+ this_seq, strlen(this_seq));
+
+ if (this_sqinfo->flags & SQINFO_DESC) {
+ /* FIXME never get here ... */
+ MSASetSeqDescription(msa, key, this_sqinfo->desc);
+ }
+ /* FIXME extend this by copying more stuff according to flags.
+ * See MSAFileRead() in msa.c and used functions there
+ *
+ * Problem is that we never parse MSA information as we use squid'sSeqFile
+ */
+
+ msa->nseq++;
+ }
+
+
+ /* FIXME Would like to, but can't use MSAVerifyParse(msa) here, as it
+ * will die on error. Need to implement our own version
+ */
+#if 0
+ MSAVerifyParse(msa);
+#endif
+
+ /* The below is copy of MSAFileWrite() which originally only writes to stdout.
+ */
+
+ /* Be sloppy and make a2m and fasta the same. same for vienna (which is
+ the same). same same. can can. boleh boleh */
+ if (outfmt==SQFILE_FASTA)
+ outfmt = MSAFILE_A2M;
+ if (outfmt==SQFILE_VIENNA)
+ outfmt = MSAFILE_VIENNA;
+
+ switch (outfmt) {
+ case MSAFILE_A2M:
+ WriteA2M(pfOut, msa, 0);
+ break;
+ case MSAFILE_VIENNA:
+ WriteA2M(pfOut, msa, 1);
+ break;
+ case MSAFILE_CLUSTAL:
+ WriteClustal(pfOut, msa);
+ break;
+ case MSAFILE_MSF:
+ WriteMSF(pfOut, msa);
+ break;
+ case MSAFILE_PHYLIP:
+ WritePhylip(pfOut, msa);
+ break;
+ case MSAFILE_SELEX:
+ WriteSELEX(pfOut, msa);
+ break;
+ case MSAFILE_STOCKHOLM:
+ WriteStockholm(pfOut, msa);
+ break;
+ default:
+ Log(&rLog, LOG_FATAL, "internal error: %s",
+ "invalid output format should have been detected before");
+ }
+
+ if (use_stdout == FALSE) {
+ (void) fclose(pfOut);
+ Log(&rLog, LOG_INFO,
+ "Alignment written to %s", pcAlnOutfile);
+ }
+ MSAFree(msa);
+
+ return 0;
+}
+/*** end of WriteAlignment() ***/
+
+
+/**
+ * @brief Removes all gap-characters from a sequence.
+ *
+ * @param[out] seq
+ * Sequence to dealign
+ *
+ * @note seq will not be reallocated
+ */
+void
+DealignSeq(char *seq)
+{
+ int aln_pos;
+ int dealn_pos;
+
+ assert(seq!=NULL);
+
+ dealn_pos=0;
+ for (aln_pos=0; aln_pos<(int)strlen(seq); aln_pos++) {
+ if (! isgap(seq[aln_pos])) {
+ seq[dealn_pos++] = seq[aln_pos];
+ }
+ }
+ seq[dealn_pos] = '\0';
+
+ return;
+}
+/*** end: DealignSeq() ***/
+
+
+
+/**
+ * @brief Sort sequences by length
+ *
+ * @param[out] prMSeq
+ * mseq to sort by length
+ * @param[out] cOrder
+ * Sorting order. 'd' for descending, 'a' for ascending.
+ *
+ *
+ */
+void
+SortMSeqByLength(mseq_t *prMSeq, const char cOrder)
+{
+ int *piSeqLen;
+ int *piOrder;
+ int iSeqIndex;
+ mseq_t *prMSeqCopy = NULL;
+
+ assert('a'==cOrder || 'd'==cOrder);
+
+ Log(&rLog, LOG_WARN,
+ "FIXME: This modifies sequence ordering. Might not be what user wants. Will change output order as well");
+
+ piSeqLen = (int *) CKMALLOC(prMSeq->nseqs * sizeof(int));
+ piOrder = (int *) CKMALLOC(prMSeq->nseqs * sizeof(int));
+ for (iSeqIndex=0; iSeqIndex<prMSeq->nseqs; iSeqIndex++) {
+ piSeqLen[iSeqIndex] = prMSeq->sqinfo[iSeqIndex].len;
+ }
+ QSortAndTrackIndex(piOrder, piSeqLen, prMSeq->nseqs, cOrder, FALSE);
+
+ CopyMSeq(&prMSeqCopy, prMSeq);
+ for (iSeqIndex=0; iSeqIndex<prMSeq->nseqs; iSeqIndex++) {
+ /* copy mseq entry
+ */
+ CKFREE(prMSeq->seq[iSeqIndex]);
+ prMSeq->seq[iSeqIndex] = CkStrdup(prMSeqCopy->seq[piOrder[iSeqIndex]]);
+
+ CKFREE(prMSeq->orig_seq[iSeqIndex]);
+ prMSeq->orig_seq[iSeqIndex] = CkStrdup(prMSeqCopy->orig_seq[piOrder[iSeqIndex]]);
+
+ SeqinfoCopy(&prMSeq->sqinfo[iSeqIndex], &prMSeqCopy->sqinfo[piOrder[iSeqIndex]]);
+ }
+
+ CKFREE(piSeqLen);
+ CKFREE(piOrder);
+ FreeMSeq(&prMSeqCopy);
+
+ return;
+}
+/*** end: SortMSeqByLength() ***/
+
+
+
+/**
+ * @brief Checks if sequences in given mseq structure are aligned. By
+ * definition this is only true, if sequences are of the same length
+ * and at least one gap was found
+ *
+ * @param[in] prMSeq
+ * Sequences to check
+ *
+ * @return TRUE if sequences are aligned, FALSE if not
+ *
+ *
+ */
+bool
+SeqsAreAligned(mseq_t *prMSeq)
+{
+ bool bGapFound, bSameLength;
+ int iSeqIdx; /* sequence counter */
+ int iSeqPos; /* sequence string position counter */
+
+ /* Special case of just one sequence:
+ * it is arguable that a single sequence qualifies as a profile,
+ * however, this is what we do at the first stage of MSA anyway.
+ * So, if there is only 1 sequence it is a 1-profile
+ * and it is (defined to be) aligned (with itself). FS, r240 -> 241
+ */
+ if (1 == prMSeq->nseqs) {
+ return TRUE;
+ }
+
+
+ /* Check if sequences are aligned. For being aligned, the
+ * sequences have to be of same length (bSameLength) and at least
+ * one of them has to contain at least one gap (bGapFound)
+ */
+ bGapFound = FALSE;
+ bSameLength = TRUE;
+ for (iSeqIdx=0; iSeqIdx<prMSeq->nseqs; iSeqIdx++) {
+ if (FALSE == bGapFound) {
+ for (iSeqPos=0;
+ iSeqPos<prMSeq->sqinfo[iSeqIdx].len && false==bGapFound;
+ iSeqPos++) {
+ if (isgap(prMSeq->seq[iSeqIdx][iSeqPos])) {
+ bGapFound = TRUE;
+ /* skip rest of sequence */
+ break;
+ }
+ }
+ }
+
+ if (iSeqIdx>0) {
+ if (prMSeq->sqinfo[iSeqIdx].len != prMSeq->sqinfo[iSeqIdx-1].len) {
+ bSameLength = FALSE;
+ /* no need to continue search, bSameLength==FALSE is
+ * sufficient condition */
+ break;
+ }
+ }
+ }
+#if 0
+ Log(&rLog, LOG_FORCED_DEBUG, "bSameLength=%d bGapFound=%d", bSameLength, bGapFound);
+#endif
+ if (TRUE == bSameLength && TRUE == bGapFound) {
+ return TRUE;
+ } else {
+ return FALSE;
+ }
+
+}
+/*** end: SeqsAreAligned() ***/
+
+
+
+/**
+ * @brief Creates a new sequence entry and appends it to an existing mseq
+ * structure.
+ *
+ * @param[out] prMSeqDest_p
+ * Already existing and initialised mseq structure
+ * @param[in] pcSeqName
+ * sequence name of the sequence to add
+ * @param[in] pcSeqRes
+ * the actual sequence (residues) to add
+ *
+ * @note Don't forget to update the align and type flag if necessary!
+ *
+ * FIXME allow adding of more features
+ *
+ */
+void
+AddSeq(mseq_t **prMSeqDest_p, char *pcSeqName, char *pcSeqRes)
+{
+ int iSeqIdx = 0;
+ SQINFO sqinfo;
+
+ assert(NULL != prMSeqDest_p);
+ assert(NULL != pcSeqName);
+ assert(NULL != pcSeqRes);
+
+ iSeqIdx = (*prMSeqDest_p)->nseqs;
+
+ (*prMSeqDest_p)->seq = (char **)
+ CKREALLOC((*prMSeqDest_p)->seq, (iSeqIdx+1) * sizeof(char *));
+ (*prMSeqDest_p)->orig_seq = (char **)
+ CKREALLOC((*prMSeqDest_p)->orig_seq, (iSeqIdx+1) * sizeof(char *));
+ (*prMSeqDest_p)->sqinfo = (SQINFO *)
+ CKREALLOC((*prMSeqDest_p)->sqinfo, (iSeqIdx+1) * sizeof(SQINFO));
+
+
+ (*prMSeqDest_p)->seq[iSeqIdx] = CkStrdup(pcSeqRes);
+ (*prMSeqDest_p)->orig_seq[iSeqIdx] = CkStrdup(pcSeqRes);
+
+ /* should probably get ri of SqInfo altogether in the long run and just
+ transfer the intersting members into our own struct
+ */
+ sqinfo.flags = 0; /* init */
+
+ sqinfo.len = strlen(pcSeqRes);
+ sqinfo.flags |= SQINFO_LEN;
+
+ /* name is an array of SQINFO_NAMELEN length */
+ strncpy(sqinfo.name, pcSeqName, SQINFO_NAMELEN-1);
+ sqinfo.name[SQINFO_NAMELEN-1] = '\0';
+ sqinfo.flags |= SQINFO_NAME;
+
+ SeqinfoCopy(&(*prMSeqDest_p)->sqinfo[iSeqIdx],
+ & sqinfo);
+
+ (*prMSeqDest_p)->nseqs++;
+
+ return;
+}
+/* end of AddSeq() */
+
+
+
+
+/**
+ * @brief Appends an mseq structure to an already existing one.
+ * filename will be left untouched.
+ *
+ * @param[in] prMSeqDest_p
+ * MSeq structure to which to append to
+ * @param[out] prMSeqToAdd
+ * MSeq structure which is to append
+ *
+ *
+ */
+void
+JoinMSeqs(mseq_t **prMSeqDest_p, mseq_t *prMSeqToAdd)
+{
+ int iSrcSeqIndex;
+ int iNewNSeq;
+
+ assert(NULL != prMSeqDest_p && NULL != (*prMSeqDest_p));
+ assert(NULL != prMSeqToAdd);
+
+ if (0 == prMSeqToAdd->nseqs) {
+ Log(&rLog, LOG_WARN, "Was asked to add 0 sequences");
+ return;
+ }
+
+ /* warn on seqtype mismatch and keep original seqtype */
+ if ((*prMSeqDest_p)->seqtype != prMSeqToAdd->seqtype) {
+ Log(&rLog, LOG_WARN, "Joining sequences of different type");
+ }
+
+ /* leave filename as it is */
+
+ /*
+ * copy new seq/s, orig_seq/s, sqinfo/s
+ */
+ iNewNSeq = (*prMSeqDest_p)->nseqs + prMSeqToAdd->nseqs;
+
+ (*prMSeqDest_p)->seq = (char **)
+ CKREALLOC((*prMSeqDest_p)->seq, iNewNSeq * sizeof(char *));
+
+ (*prMSeqDest_p)->orig_seq = (char **)
+ CKREALLOC((*prMSeqDest_p)->orig_seq, iNewNSeq * sizeof(char *));
+
+ (*prMSeqDest_p)->sqinfo = (SQINFO *)
+ CKREALLOC((*prMSeqDest_p)->sqinfo, iNewNSeq * sizeof(SQINFO));
+
+
+ for (iSrcSeqIndex=0; iSrcSeqIndex < prMSeqToAdd->nseqs; iSrcSeqIndex++) {
+ int iDstSeqIndex = (*prMSeqDest_p)->nseqs++;
+
+ (*prMSeqDest_p)->seq[iDstSeqIndex] =
+ CkStrdup(prMSeqToAdd->seq[iSrcSeqIndex]);
+
+ (*prMSeqDest_p)->orig_seq[iDstSeqIndex] =
+ CkStrdup(prMSeqToAdd->orig_seq[iSrcSeqIndex]);
+
+ SeqinfoCopy(&(*prMSeqDest_p)->sqinfo[iDstSeqIndex],
+ & prMSeqToAdd->sqinfo[iSrcSeqIndex]);
+ }
+
+ (*prMSeqDest_p)->nseqs = iNewNSeq;
+
+ (*prMSeqDest_p)->aligned = SeqsAreAligned(*prMSeqDest_p);
+
+ return;
+}
+/*** end: JoinMSeqs() ***/
--- /dev/null
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: seq.h 234 2011-04-13 05:26:16Z andreas $
+ */
+
+#ifndef CLUSTALO_SEQ_H
+#define CLUSTALO_SEQ_H
+
+#include "squid/squid.h"
+
+#include "util.h"
+
+
+/**
+ * int-encoded sequence types.
+ * these are in sync with squid's seqtypes and only used for
+ * convenience here
+ */
+#define SEQTYPE_UNKNOWN kOtherSeq
+#define SEQTYPE_DNA kDNA
+#define SEQTYPE_RNA kRNA
+#define SEQTYPE_PROTEIN kAmino
+
+/* Alphabets are defined in squid.h: AMINO_ALPHABET, DNA_ALPHABET,
+ * RNA_ALPHABET (all uppercase)
+ */
+#define AMINOACID_ANY 'X'
+#define NUCLEOTIDE_ANY 'N'
+
+/**
+ * @brief structure for storing multiple sequences
+ *
+ */
+typedef struct {
+ int nseqs; /**< number of sequences */
+ int seqtype; /**< sequence type */
+ char *filename; /**< input file / source of sequences */
+ bool aligned; /**< true if all seqs are same length **/
+
+ /** (working) sequence residues as char pointer.
+ * range for first index: 0--nseq-1.
+ * changes during alignment.
+ */
+ char **seq;
+
+ /** original sequence residues as char pointer.
+ * range for first index: 0--nseq-1.
+ * only set during input
+ */
+ char **orig_seq;
+
+ /**
+ * @brief Squid's sequence info structure.
+ * Index range: 0--nseq-1.
+ *
+ * extra data are available:
+ * int flags;
+ *
+ * name:
+ * char name[SQINFO_NAMELEN];
+ *
+ * database identifier:
+ * char id[SQINFO_NAMELEN];
+ *
+ * database accession no:
+ * char acc[SQINFO_NAMELEN];
+ *
+ * description:
+ * char desc[SQINFO_DESCLEN];
+ *
+ * length of this seq, incl gaps in our case!:
+ * int len;
+ *
+ * start position on source seq (valid range: 1..len):
+ * int start;
+ *
+ * end position on source seq (valid range: 1..len):
+ * int stop;
+ *
+ * original length of source seq:
+ * int olen;
+ *
+ * kRNA, kDNA, kAmino, or kOther:
+ * int type;
+ *
+ * secondary structure string (index range: 0..len-1):
+ * char *ss;
+ *
+ * percent side chain surface access (index range: 0..len-1):
+ * char *sa;
+ *
+ * @see squid.h
+ * @see LogSqInfo()
+ *
+ */
+ SQINFO *sqinfo;
+} mseq_t;
+
+extern void
+AliStat(mseq_t *prMSeq, bool bSampling, bool bReportAll);
+
+extern void
+AddSeq(mseq_t **prMSeqDest_p, char *pcSeqName, char *pcSeqRes);
+
+extern void
+SeqSwap(mseq_t *mseq, int i, int j);
+
+extern void
+DealignMSeq(mseq_t *mseq);
+
+extern const char *
+SeqTypeToStr(int seqtype);
+
+extern int
+ReadSequences(mseq_t *prMSeq_p, char *pcSeqFile, int iSeqType,
+ int iMaxNumSeq, int iMaxSeqLen);
+
+extern void
+NewMSeq(mseq_t **mseq);
+
+extern void
+FreeMSeq(mseq_t **mseq);
+
+extern void
+CopyMSeq(mseq_t **prMSeqDest_p, mseq_t *prMSeqSrc);
+
+extern void
+LogSqInfo(SQINFO *sqinfo);
+
+extern int
+FindSeqName(char *seqname, mseq_t *mseq);
+
+extern int
+WriteAlignment(mseq_t *mseq, const char *aln_outfile, int msafile_format);
+
+extern void
+DealignSeq(char *seq);
+
+extern void
+ShuffleMSeq(mseq_t *prMSeq);
+
+extern void
+SortMSeqByLength(mseq_t *prMSeq, const char cOrder);
+
+void
+JoinMSeqs(mseq_t **prMSeqDest_p, mseq_t *prMSeqToAdd);
+
+bool
+SeqsAreAligned(mseq_t *prMSeq);
+
+#endif
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: symmatrix.c 230 2011-04-09 15:37:50Z andreas $
+ *
+ *
+ * Functions for symmetric (square) matrices including diagonal.
+ * supports the notion of non-square sub-matrices of a symmetric
+ * matrix, i.e. where |rows|<|cols|.
+ *
+ * FIXME Allocating one big chunk of memory is probably
+ * much faster and also easier to maintain.
+ */
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <ctype.h>
+#include <string.h>
+#include <assert.h>
+#include "symmatrix.h"
+
+
+#if 0
+#define DEBUG
+#endif
+
+#define MAX_BUF_SIZE 65536
+
+/**
+ * @brief Allocates symmat and its members and initialises them. Data
+ * will be calloced, i.e. initialised with zeros.
+ *
+ * @param[out] symmat
+ * newly allocated and initialised symmatrix instance
+ * @param[in] nrows
+ * number of rows
+ * @param[in]
+ * ncols number of columns
+ *
+ * @return: non-zero on error
+ *
+ * @see FreeSymMatrix()
+ *
+ * @note: symmat data will be of fake shape nrows x ncols
+ *
+ */
+int
+NewSymMatrix(symmatrix_t **symmat, int nrows, int ncols)
+{
+ int i; /* aux */
+
+ assert(nrows>0 && ncols>0 && ncols>=nrows);
+ assert(ncols>0 && ncols>=nrows);
+
+ (*symmat) = (symmatrix_t *) malloc(1*sizeof(symmatrix_t));
+ if (NULL == (*symmat)) {
+ fprintf(stderr, "Couldn't allocate memory (%s|%s)\n",
+ __FILE__, __FUNCTION__);
+ return -1;
+ }
+
+ (*symmat)->data = (double **) malloc(nrows * sizeof(double *));
+ if (NULL == (*symmat)->data) {
+ fprintf(stderr, "Couldn't allocate memory (%s|%s)\n",
+ __FILE__, __FUNCTION__);
+ free(*symmat);
+ *symmat = NULL;
+ return -1;
+ }
+ for (i=0; i<nrows; i++) {
+ (*symmat)->data[i] = (double *) calloc((ncols-i), sizeof(double));
+ if (NULL == (*symmat)->data[i]) {
+ fprintf(stderr, "Couldn't allocate memory (%s|%s)\n",
+ __FILE__, __FUNCTION__);
+ while (0!=--i) {
+ free((*symmat)->data[i]);
+ }
+ free((*symmat)->data);
+ free(*symmat);
+ *symmat = NULL;
+ return -1;
+ }
+#ifdef TRACE
+ fprintf(stderr, "DEBUG(%s|%s():%d) initialising symmat with the number of the beast\n",
+ __FILE__, __FUNCTION__, __LINE__);
+ {
+ int j;
+ for (j=0; j<ncols-i; j++) {
+ (*symmat)->data[i][j] = -666.0;
+ }
+
+ }
+#endif
+ }
+
+ (*symmat)->nrows = nrows;
+ (*symmat)->ncols = ncols;
+
+ return 0;
+}
+/*** end: new_symmatrix ***/
+
+
+/**
+ * @brief Sets symmat data of given index to given value
+ *
+ * @param[in] symmat
+ * symmatrix_t whose data is to be set
+ * @param[in] i
+ * first index
+ * @param[in] j
+ * second index
+ * @param[in] value
+ * value used to set data point
+ *
+ * @see SymMatrixGetValue()
+ *
+ * @note This is a convenience function that checks index order.
+ *
+ */
+void
+SymMatrixSetValue(symmatrix_t *symmat, const int i, const int j, const double value)
+{
+ assert(NULL != symmat);
+
+ if (i<=j) {
+ assert(i < symmat->nrows && j < symmat->ncols);
+ symmat->data[i][j-i] = value;
+ } else {
+ assert(j < symmat->nrows && i < symmat->ncols);
+ symmat->data[j][i-j] = value;
+ }
+}
+/*** end: symmatrix_setvalue ***/
+
+
+
+/**
+ * @brief Returns element of symmat corresponding to given indices
+ *
+ * @param[in] symmat
+ * symmatrix_t of question
+ * @param[in] i
+ * index i
+ * @param[in] j
+ * index j
+ *
+ * @return requested value
+ *
+ * @see SymMatrixSetValue()
+ *
+ * @note This is a convenience function that checks index order.
+ */
+double
+SymMatrixGetValue(symmatrix_t *symmat, const int i, const int j)
+{
+ assert(NULL != symmat);
+
+ if (i<=j) {
+ assert(i < symmat->nrows && j < symmat->ncols);
+ return symmat->data[i][j-i];
+ } else {
+ assert(j < symmat->nrows && i < symmat->ncols);
+ return symmat->data[j][i-j];
+ }
+}
+/*** end: symmatrix_getvalue ***/
+
+
+
+
+
+/**
+ * @brief Returns a pointer to an element of symmat corresponding to
+ * given indices
+ *
+ * @param[out] val
+ * Value to be set
+ * @param[in] symmat
+ * symmatrix_t of question
+ * @param[in] i
+ * index i
+ * @param[in] j
+ * index j
+ *
+ * @return pointer to value
+ *
+ * @see SymMatrixGetValue()
+ *
+ * @note This is a convenience function that checks index order.
+ *
+ */
+void
+SymMatrixGetValueP(double **val, symmatrix_t *symmat,
+ const int i, const int j)
+{
+ assert(NULL != symmat);
+
+ if (i<=j) {
+ assert(i < symmat->nrows && j < symmat->ncols);
+ *val = &(symmat->data[i][j-i]);
+ } else {
+ assert(j < symmat->nrows && i < symmat->ncols);
+ *val = &(symmat->data[j][i-j]);
+ }
+}
+/*** end: symmatrix_getvaluep ***/
+
+
+/**
+ * @brief Frees memory allocated by data members of symmat and symmat
+ * itself.
+ *
+ * @param[in] symmat
+ * symmatrix_t to be freed
+ *
+ * @note Use in conjunction with NewSymMatrix()
+ *
+ * @see NewSymMatrix()
+ *
+ */
+void
+FreeSymMatrix(symmatrix_t **symmat)
+{
+ int i;
+ if (NULL != (*symmat)) {
+ if (NULL != (*symmat)->data) {
+ for (i=0; i<(*symmat)->nrows; i++) {
+ free((*symmat)->data[i]);
+ }
+ free((*symmat)->data);
+ }
+ }
+ free(*symmat);
+ *symmat = NULL;
+}
+/*** end: free_symmatrix ***/
+
+
+
+/**
+ * @brief Print out a symmat in phylip style. Distances are printed on
+ * one line per sequence/object. Since we also support matrices with
+ * rows\<cols, the first line can also be nrows by ncolumns instead
+ * of just nrows
+ *
+ * @param[in] symmat
+ * the symmatrix_t to print
+ * @param[in] labels
+ * sequence/objects labels/names. must be at least of length symmat nrows
+ * @param[in] path
+ * filename or NULL. If NULL stdout will be used.
+ *
+ */
+void
+SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path)
+{
+ FILE *fp = NULL;
+ int i, j; /* aux */
+ int max_label_len = 0;
+
+ if (NULL==symmat || NULL==labels) {
+ fprintf(stderr,
+ "One of the provided arguments is empty or NULL (print_matrix)\n");
+ return;
+ }
+ if (NULL==path) {
+ fp = stdout;
+ } else {
+ if (NULL==(fp=fopen(path, "w"))) {
+ fprintf(stderr, "Couldn't open %s for writing.", path);
+ return;
+ }
+ }
+
+ /* find maximum label length for pretty printing
+ */
+ for (i=0; i<symmat->nrows; i++) {
+ int this_len;
+ assert(NULL != labels[i]);
+ this_len = strlen(labels[i]);
+ if (this_len>max_label_len)
+ max_label_len = this_len;
+ }
+
+ if (symmat->ncols==symmat->nrows) {
+ fprintf(fp, "%u\n", symmat->ncols);
+ } else {
+ /* this is not standard phylip, but necessary to indicate
+ seed matrices */
+ fprintf(fp, "%u x %u\n", symmat->nrows, symmat->ncols);
+ }
+ for (i=0; i<symmat->nrows; i++) {
+ /* phylip restriction is 10 characters. we don't care here
+ */
+ fprintf(fp, "%-*s", max_label_len, labels[i]);
+ /* we are lazy and do it like fastdist: write all distances
+ * for one seq to one line
+ */
+ for (j=0; j<symmat->ncols; j++) {
+ fprintf(fp, " %f", SymMatrixGetValue(symmat, i, j));
+ }
+ fprintf(fp, "%s", "\n");
+ }
+ if (NULL != path) {
+ (void) fclose(fp);
+ } else {
+ (void) fflush(fp);
+ }
+}
+/*** end: SymMatrixPrint ***/
+
+
+
+/**
+ *
+ * @brief Read a distance matrix in phylip format
+ *
+ * @param[in] pcFileIn
+ * distance matrix filename
+ * @param[out] prSymMat_p
+ * the symmatrix_t. will be allocated here.
+ * @return:
+ * non-zero on error
+ *
+ * @note:
+ * FIXME untested code
+ */
+int
+SymMatrixRead(char *pcFileIn, symmatrix_t **prSymMat_p)
+{
+ FILE *prFilePointer;
+ char *buf;
+ /* number of parsed sequences */
+ int iNParsedSeq = 0;
+ /* number of parsed distances per sequence */
+ int iNParsedDists = 0;
+ /* total number of sequences/objects */
+ int iTotalNSeq = 0;
+ int iRetCode = 0;
+
+ assert(NULL!=pcFileIn);
+
+ /* FIXME: test correctness and implement label checking */
+ fprintf(stderr, "WARNING: Reading of distance matrix from file not thoroughly tested!\n");
+ fprintf(stderr, "WARNING: Assuming same order of sequences in sequence file and distance matrix file (matching of labels not implemented)\n");
+
+ if (NULL == (buf = (char *) malloc(MAX_BUF_SIZE * sizeof(char)))) {
+ fprintf(stderr, "ERROR: couldn't allocate memory at %s:%s:%d\n",
+ __FILE__, __FUNCTION__, __LINE__);
+ return -1;
+ }
+
+ if (NULL == (prFilePointer = fopen(pcFileIn, "r"))) {
+ fprintf(stderr, "ERROR: Couldn't open %s for reading\n", pcFileIn);
+ free(buf);
+ return -1;
+ }
+
+ /* get number of sequences from first line and allocate memory for
+ * distance matrix
+ *
+ */
+ if (NULL == fgets(buf, MAX_BUF_SIZE, prFilePointer) ) {
+ fprintf(stderr, "Couldn't read first line from %s\n", pcFileIn);
+ iRetCode = -1;
+ goto closefile_and_freebuf;
+ }
+ if (strlen(buf)==MAX_BUF_SIZE-1) {
+ fprintf(stderr, "%s\n", "Looks like I couldn't read complete line. Wrong format (or too small MAX_BUF_SIZE)");
+ iRetCode = -1;
+ goto closefile_and_freebuf;
+ }
+ if (sscanf(buf, "%d", &iTotalNSeq)!=1) {
+ fprintf(stderr, "ERROR: couldn't parse number of sequences from first line of %s\n", pcFileIn);
+ iRetCode = -1;
+ goto closefile_and_freebuf;
+ }
+
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "iTotalNSeq parsed from %s is %d\n", pcFileIn, iTotalNSeq);
+#endif
+
+ if (NewSymMatrix(prSymMat_p, iTotalNSeq, iTotalNSeq)) {
+ fprintf(stderr, "FATAL %s", "Memory allocation for distance matrix failed");
+ iRetCode = -1;
+ goto closefile_and_freebuf;
+ }
+
+
+ /* parse file line by line
+ *
+ */
+ while (NULL != fgets(buf, MAX_BUF_SIZE, prFilePointer)) {
+ char *szToken;
+ int is_newseq;
+
+ if (MAX_BUF_SIZE-1 == strlen(buf)) {
+ fprintf(stderr, "%s\n", "Looks like I couldn't read complete line. Wrong format (or too small MAX_BUF_SIZE)");
+ iRetCode = -1;
+ goto closefile_and_freebuf;
+ }
+
+#ifdef DEBUG
+ Log(&rLog, LOG_FORCED_DEBUG, "Got line: %s\n", buf);
+#endif
+
+ /* new sequence label at beginning of line?
+ */
+ if (isblank(buf[0])) {
+ is_newseq = 0;
+ } else {
+ is_newseq = 1;
+ }
+
+ /* tokenise line and treat new sequence specially
+ */
+ szToken = strtok(buf, " \t");
+ if (is_newseq==1) {
+ iNParsedSeq++;
+ iNParsedDists=0;
+
+ /* if format is lower dimensional matrix then first
+ * sequence has no distances but might have newline
+ * character at it's end.
+ */
+ while (isspace(szToken[strlen(szToken)-1])) {
+ szToken[strlen(szToken)-1]='\0';
+ }
+ /* FIXME save label? */
+ szToken = strtok(NULL, " \t");
+ }
+ /* from here on it's only parsing of distances */
+ while (szToken != NULL) {
+ double dist;
+ iNParsedDists++;
+
+ /* only parse what's needed */
+ if (iNParsedDists!=iNParsedSeq) {
+ /* parse and store distance
+ */
+ if (sscanf(szToken, "%lf", &dist)!=1) {
+ fprintf(stderr, "Couldn't parse float from entry '%s'\n", szToken);
+ iRetCode = -1;
+ goto closefile_and_freebuf;
+ }
+#if TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "Parsed distance %d for seq %d = %f\n", iNParsedDists-1, iNParsedSeq-1, dist);
+#endif
+ SymMatrixSetValue(*prSymMat_p, iNParsedSeq-1, iNParsedDists-1, dist);
+ SymMatrixSetValue(*prSymMat_p, iNParsedDists-1, iNParsedSeq-1, dist);
+ }
+ szToken = strtok(NULL, " \t");
+ }
+ }
+
+ if (iTotalNSeq!=iNParsedSeq) {
+ fprintf(stderr, "expected %d seqs, but only parsed %d\n", iTotalNSeq, iNParsedSeq);
+ iRetCode = -1;
+ goto closefile_and_freebuf;
+ }
+#if TRACE
+ for (i=0; i<iNParsedSeq; i++) {
+ int j;
+ for (j=0; j<iNParsedSeq; j++) {
+ Log(&rLog, LOG_FORCED_DEBUG, "prSymMat_p[%d][%d]=%f\n", i, j, (*prSymMat_p)[i][j]);
+ }
+ }
+#endif
+
+closefile_and_freebuf:
+ fclose(prFilePointer);
+ free(buf);
+
+ return iRetCode;
+}
+/*** end: SymMatrixRead ***/
+
--- /dev/null
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: symmatrix.h 216 2011-03-19 10:11:53Z andreas $
+ */
+
+/**
+ * Functions for symmetric (square) matrices including diagonal.
+ *
+ * Supports the notion of non-square sub-matrices of a symmetric
+ * matrix, i.e. where |rows|<|cols| and the corresponding full matrix
+ * would be |cols|x|cols|
+ *
+ * Instead of making this one big chunk of memory we keep pointers to
+ * pointers, so that we can easily realloc (the project where this file
+ * originated from needed this for growing a "seed" matrix).
+ *
+ * FIXME Allocating one big chunk of memory is probably
+ * much faster and also easier to maintain.
+ *
+ *
+ */
+
+#ifndef CLUSTALO_SYMMATRIX_H
+#define CLUSTALO_SYMMATRIX_H
+
+
+/**
+ * @brief symmetric matrix structure
+ */
+typedef struct {
+ int nrows; /**< number of rows */
+ int ncols; /**< number of columns */
+ /**
+ * stored data
+ *
+ * @note indices range: [i][j-i] i<=j. use getvalue() and
+ * setvalue() instead of accessing directly
+ *
+ * @see SymMatrixGetValue(), SymMatrixSetValue()
+ */
+ double **data;
+} symmatrix_t;
+
+
+
+extern int
+NewSymMatrix(symmatrix_t **symmat, const int nrows, const int ncols);
+
+extern void
+SymMatrixSetValue(symmatrix_t *symmat, const int i, const int j, const double value);
+
+extern double
+SymMatrixGetValue(symmatrix_t *symmat, const int i, const int j);
+
+extern void
+SymMatrixGetValueP(double **value, symmatrix_t *symmat, const int i, const int j);
+
+extern void
+FreeSymMatrix(symmatrix_t **symmat);
+
+extern void
+SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path);
+
+extern int
+SymMatrixRead(char *pcFileIn, symmatrix_t **prSymMat_p);
+
+#endif
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: tree.c 230 2011-04-09 15:37:50Z andreas $
+ */
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+
+#include "util.h"
+#include "log.h"
+#include "muscle_upgma.h"
+#include "tree.h"
+
+/**
+ *
+ * @brief Creates a UPGMA guide tree. This is a frontend function to
+ * the ported Muscle UPGMA code ().
+ *
+ * @param[out] tree
+ * created upgma tree. will be allocated here. use FreeMuscleTree()
+ * to free
+ * @param[in] labels
+ * pointer to nseq sequence names
+ * @param[in] distmat
+ * distance matrix
+ * @param[in] ftree
+ * optional: if non-NULL, tree will be written to this files
+ *
+ * @see FreeMuscleTree()
+ * @see MuscleUpgma2()
+ *
+ */
+void
+GuideTreeUpgma(tree_t **tree, char **labels,
+ symmatrix_t *distmat, char *ftree)
+{
+ linkage_t linkage = LINKAGE_AVG;
+ FILE *fp = NULL;
+
+ if (NULL != ftree) {
+ if (NULL == (fp=fopen(ftree, "w"))) {
+ Log(&rLog, LOG_ERROR, "Couldn't open tree-file '%s' for writing. Skipping", ftree);
+ }
+ /* fp NULL is handled later */
+ }
+
+ (*tree) = (tree_t *) CKMALLOC(1 * sizeof(tree_t));
+ MuscleUpgma2((*tree), distmat, linkage, labels);
+
+ if (rLog.iLogLevelEnabled <= LOG_DEBUG) {
+ Log(&rLog, LOG_DEBUG, "tree logging...");
+ LogTree((*tree), LogGetFP(&rLog, LOG_DEBUG));
+ }
+
+ if (NULL != fp) {
+ MuscleTreeToFile(fp, (*tree));
+ Log(&rLog, LOG_INFO, "Guide tree written to %s", ftree);
+ fclose(fp);
+ }
+}
+/*** end: guidetree_upgma ***/
+
+
+
+/**
+ *
+ * @brief
+ *
+ * @param[out] tree
+ * created upgma tree. will be allocated here. use FreeMuscleTree()
+ * to free
+ * @param[in] mseq
+ * @param[in] ftree
+ *
+ * @return non-zero on error
+ *
+ */
+int
+GuideTreeFromFile(tree_t **tree, mseq_t *mseq, char *ftree)
+{
+ int iNodeCount;
+ int iNodeIndex;
+
+ (*tree) = (tree_t *) CKMALLOC(1 * sizeof(tree_t));
+ if (MuscleTreeFromFile((*tree), ftree)!=0) {
+ Log(&rLog, LOG_ERROR, "%s", "MuscleTreeFromFile failed");
+ return -1;
+ }
+
+ /* Make sure tree is rooted */
+ if (!IsRooted((*tree))) {
+ Log(&rLog, LOG_ERROR, "User tree must be rooted");
+ return -1;
+ }
+
+ if ((int)GetLeafCount((*tree)) != mseq->nseqs) {
+ Log(&rLog, LOG_ERROR, "User tree does not match input sequences");
+ return -1;
+ }
+
+ /* compare tree labels and sequence names and set leaf-ids */
+ iNodeCount = GetNodeCount((*tree));
+ for (iNodeIndex = 0; iNodeIndex < iNodeCount; ++iNodeIndex) {
+ char *LeafName;
+ int iSeqIndex;
+
+ if (!IsLeaf(iNodeIndex, (*tree)))
+ continue;
+ LeafName = GetLeafName(iNodeIndex, (*tree));
+
+ if ((iSeqIndex=FindSeqName(LeafName, mseq))==-1) {
+ Log(&rLog, LOG_ERROR, "Label '%s' in tree could not be found in sequence names", LeafName);
+ return -1;
+ }
+
+ SetLeafId((*tree), iNodeIndex, iSeqIndex);
+ }
+
+ if (rLog.iLogLevelEnabled <= LOG_DEBUG) {
+ Log(&rLog, LOG_DEBUG, "tree logging...");
+ LogTree((*tree), LogGetFP(&rLog, LOG_DEBUG));
+ }
+
+ return 0;
+}
+/*** end: GuideTreeFromFile() ***/
+
+
+
+/**
+ *
+ * @brief Depth first traversal of tree, i.e. leaf nodes (sequences)
+ * will be visited first. Order can be used to guide progressive
+ * alignment order.
+ *
+ * @param[out] piOrderLR_p
+ * order in which left/right nodes (profiles) are to be aligned.
+ * allocated here; caller must free.
+ * @param[in] tree
+ * The tree to traverse; has to be rooted
+ * @param[in] mseq
+ * corresponding multiple sequence structure
+ *
+ */
+void
+TraverseTree(int **piOrderLR_p,
+ tree_t *tree, mseq_t *mseq)
+{
+ int tree_nodeindex = 0;
+ int order_index = 0;
+
+ assert(NULL!=tree);
+ assert(NULL!=mseq);
+ assert(IsRooted(tree));
+
+ /* allocate memory for node/profile alignment order;
+ * for every node allocate DIFF_NODE (3) int (1 left, 1 right, 1 parent)
+ */
+ *piOrderLR_p = (int *)CKCALLOC(DIFF_NODE * GetNodeCount(tree), sizeof(int));
+
+ /* Log(&rLog, LOG_FORCED_DEBUG, "print tree->m_iNodeCount=%d", tree->m_iNodeCount); */
+
+
+ tree_nodeindex = FirstDepthFirstNode(tree);
+ /*LOG_DEBUG("Starting with treenodeindex = %d", tree_nodeindex);*/
+
+ order_index = 0;
+
+ do {
+ if (IsLeaf(tree_nodeindex, tree)) {
+ int leafid = GetLeafId(tree_nodeindex, tree);
+ if (leafid >= mseq->nseqs)
+ Log(&rLog, LOG_FATAL, "Sequence index out of range during tree traversal (leafid=%d nseqs=%d)",
+ leafid, mseq->nseqs);
+
+ /* this is a leaf node,
+ * indicate this by registering same leafid for left/right
+ */
+
+ (*piOrderLR_p)[DIFF_NODE*order_index+LEFT_NODE] = leafid;
+ (*piOrderLR_p)[DIFF_NODE*order_index+RGHT_NODE] = leafid;
+ (*piOrderLR_p)[DIFF_NODE*order_index+PRNT_NODE] = tree_nodeindex;
+
+ Log(&rLog, LOG_DEBUG, "Tree traversal: Visited leaf-node %d (leaf-id %d = Seq '%s')",
+ tree_nodeindex, leafid, mseq->sqinfo[leafid].name);
+
+ } else {
+ int merge_nodeindex;
+ int left;
+ int right;
+
+ merge_nodeindex = tree_nodeindex;
+ left = GetLeft(tree_nodeindex, tree);
+ right = GetRight(tree_nodeindex, tree);
+
+ /* this is not a leaf node but a merge node,
+ * register left node (even) and right node (odd)
+ */
+ (*piOrderLR_p)[DIFF_NODE*order_index+LEFT_NODE] = left;
+ (*piOrderLR_p)[DIFF_NODE*order_index+RGHT_NODE] = right;
+ (*piOrderLR_p)[DIFF_NODE*order_index+PRNT_NODE] = merge_nodeindex;
+
+ Log(&rLog, LOG_DEBUG, "Tree traversal: Visited non-leaf node %d with siblings %d (L) and %d (R)",
+ merge_nodeindex, left, right);
+ }
+ tree_nodeindex = NextDepthFirstNode(tree_nodeindex, tree);
+
+ order_index++;
+
+ } while (NULL_NEIGHBOR != tree_nodeindex);
+
+ return;
+}
+/*** end: TraverseTree ***/
--- /dev/null
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: tree.h 193 2011-02-07 15:45:21Z andreas $
+ */
+
+#ifndef CLUSTALO_TREE_H
+#define CLUSTALO_TREE_H
+
+#include "symmatrix.h"
+#include "muscle_tree.h"
+#include "seq.h"
+
+enum {LEFT_NODE = 0, RGHT_NODE, PRNT_NODE, DIFF_NODE};
+
+extern void
+GuideTreeUpgma(tree_t **tree,
+ char **labels, symmatrix_t *tmat, char *ftree);
+
+extern int
+GuideTreeFromFile(tree_t **tree,
+ mseq_t *mseq, char *ftree);
+
+extern void
+TraverseTree(int **piOrderLR_p,
+ tree_t *tree, mseq_t *mseq);
+
+#endif
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: util.c 235 2011-04-13 14:13:19Z andreas $
+ */
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include <time.h>
+
+#include "log.h"
+#include "util.h"
+
+
+
+
+/* struct for QSortAndTrackIndex and SortAndTrackIndexCmp[Asc|Desc] */
+typedef struct {
+ int piIndex;
+ int piValue;
+} sortwithindex_t;
+
+
+
+
+/**
+ * @brief Copy of squid's FileExists(). Copied here to make squid independent.
+ */
+int
+CheckIfFileExists(char *pcFilename)
+{
+ FILE *prFile;
+ if ((prFile = fopen(pcFilename, "r"))) {
+ fclose(prFile);
+ return TRUE;
+ }
+ return FALSE;
+}
+/* end of CheckIfFileExists */
+
+
+/**
+ * @brief Allocates memory (malloc)
+ *
+ * @param[in] bytes
+ * bytes to allocated
+ * @param[in] function
+ * calling function name
+ * @param[in] line
+ * calling function line
+ *
+ * @return void pointer to the newly allocated memory
+ *
+ * @note use provided macro CKMALLOC() which automatically adds
+ * function name and line number
+ *
+ */
+void *
+CkMalloc(size_t bytes, const char *function, const int line)
+{
+ void *ret;
+
+ if(NULL == (ret = malloc(bytes * sizeof(char)))) {
+ Log(&rLog, LOG_FATAL, "Out of memory (requested from %s:%d)\n", function, line);
+ }
+
+ return ret;
+}
+/*** end: ckmalloc ***/
+
+
+
+/**
+ * @brief Allocates memory (calloc). Memory will be
+ * set to zero.
+ *
+ * @param[in] count
+ * Allocate space for count objects
+ * @param[in] size
+ * Objects are of this size
+ * @param[in] function
+ * calling function name
+ * @param[in] line
+ * calling function line
+ *
+ * @return void pointer to the newly allocated and zeroed memory (calloc).
+ *
+ * @note use provided macro CKCALLOC() which automatically adds
+ * function name and line number
+ *
+ *
+ */
+void *
+CkCalloc(size_t count, size_t size, const char *function, const int line)
+{
+ void *ret;
+
+ if(NULL == (ret = calloc(count, size))) {
+ Log(&rLog, LOG_FATAL, "Out of memory (requested from %s:%d)\n",
+ function, line);
+ exit(EXIT_FAILURE);
+ }
+
+ return ret;
+}
+/*** end: CkCalloc ***/
+
+
+/**
+* @brief Reallocates memory
+ *
+ * @param[in] ptr
+ * Pointer to memory to be reallocated
+ * @param[in] bytes
+ * bytes to allocated
+ * @param[in] function
+ * calling function name
+ * @param[in] line
+ * calling function line
+ *
+ * @return void pointer to the newly allocated memory
+ *
+ * @note use provided macro CKREALLOC() which automatically adds
+ * function name and line number
+ *
+ */
+void *
+CkRealloc(void *ptr, size_t bytes, const char *function, const int line)
+{
+ void *ret=NULL;
+
+ if(NULL == (ret = realloc(ptr, bytes))) {
+ Log(&rLog, LOG_FATAL, "FATAL: Out of memory (requested from %s:%d)\n",
+ function, line);
+ }
+
+ return ret;
+}
+/*** end: ckrealloc ***/
+
+
+
+/**
+ *
+ * @brief Frees memory
+ *
+ * @param[in] ptr
+ * Pointer to memory to be freed
+ * @param[in] function
+ * calling function name
+ * @param[in] line
+ * calling function line
+ *
+ * @return void pointer to the now zeroed memory
+ *
+ * @note use provided macro CKFREE()
+ *
+ */
+void *
+CkFree(void *ptr, const char *function, const int line)
+{
+ if (ptr == NULL) {
+ Log(&rLog, LOG_WARN, "Bad call to CkFree from %s:%d (pointer was NULL)\n", function, line);
+ } else {
+ free(ptr);
+ ptr = NULL;
+ }
+ return ptr;
+}
+/*** end: CkFree ***/
+
+
+
+
+/**
+ * @brief safe version of strdup
+ *
+ * @param[in] src
+ * String to copy from
+ *
+ * @return copy of string
+ *
+ * @note src is not allowed to be NULL.
+ *
+ */
+char *
+CkStrdup(const char *src)
+{
+ char *cp;
+ assert(NULL!=src);
+
+ /*cp = strdup(src); always makes trouble... */
+ cp = (char *) CKMALLOC(strlen(src) +1);
+ strcpy(cp, src);
+
+ return cp;
+}
+/*** end: CkStrdup ***/
+
+
+
+
+/**
+ * @brief Creates an int array of size len with len-1 random but unique
+ * integers with values 0--len-1. This is "a modified version of
+ * Fisher-Yates known as Durstenfeld-Fisher-Yates or
+ * Knuth-Fisher-Yates". See
+ * http://stackoverflow.com/questions/196017/unique-random-numbers-in-o1
+ *
+ * @param[in] perm
+ * The permutation array. Has to be preallocated
+ * @param[out] len
+ * Length of the permutation array
+ *
+ */
+void
+PermutationArray(int **perm, const int len)
+{
+ int max, i;
+
+ assert(len>0);
+
+ srand((unsigned int) time(0));
+ (*perm) = (int *) CKMALLOC(len * sizeof(int));
+ max = len-1;
+ for (i=0; i<len; i++) {
+ (*perm)[i] = i;
+ }
+
+ while (max>=0) {
+ int tmp, randno;
+ /* randno = addrand((unsigned long) len); / returns 0--n-1 */
+ randno = (rand()%len);
+
+ /* swap */
+ tmp = (*perm)[randno];
+ (*perm)[randno] = (*perm)[max];
+ (*perm)[max] = tmp;
+
+ max--;
+ }
+ return;
+}
+/*** end: PermutationArray() ***/
+
+
+
+/**
+ * @brief Creates an array filled with random, but unique ints of
+ * given range. Implementation of the Floyd algorithm. See
+ * http://stackoverflow.com/questions/1608181/unique-random-numbers-in-an-integer-array-in-the-c-programming-language
+ * Assuming M is the length of the desired array and N is the numeric
+ * range: "This approach has the complexity of about O(M) (depends on
+ * the search structure used), so it is better suitable when M << N.
+ * This approach keeps track of already generated random numbers, so
+ * it requires extra memory. However, the beauty of it is that it does
+ * not make any of those horrendous "trial and error" iterations,
+ * trying to find an unused random number. This algorithm is
+ * guaranteed to generate one unique random number after each single
+ * call to the random number generator."
+ *
+ * @warning This won't work if max_value<=array_len. Only use for
+ * cases where array_len<<max_value
+ *
+ * @param[in] array
+ * Preallocated int array whose values will be set
+ * @param[in] array_len
+ * Size of array
+ * @param[in] max_value
+ *
+ */
+void
+RandomUniqueIntArray(int *array, const int array_len, const int max_value)
+{
+ bool *is_used;
+ int in, im;
+
+ assert(array_len<max_value);
+ srand((unsigned int) time(0));
+ is_used = (bool *) CKCALLOC(max_value, sizeof(bool));
+
+ im = 0;
+
+ for (in = max_value - array_len; in < max_value && im < array_len; ++in) {
+ int r = rand() % (in + 1);
+ if (is_used[r]==TRUE) {
+ r = in; /* use 'in' instead of generated number */
+ }
+ assert(! is_used[r]);
+ array[im++] = r;
+ is_used[r] = TRUE;
+ }
+
+ assert(im == array_len);
+
+ free(is_used);
+
+ return;
+}
+/*** end: RandomUniqueIntArray() ***/
+
+
+
+/**
+ * @brief int comparison function for qsort
+ *
+ */
+int
+IntCmp(const void *a, const void *b)
+{
+ const int *ia = (const int *)a;
+ const int *ib = (const int *)b;
+ return *ia - *ib;
+}
+/*** end: IntCmp() ***/
+
+
+
+
+
+/**
+ * @brief Compare two sortwithindex_t pointers and return the
+ * difference between the int value of the 1st sortwithindex_t and the
+ * 2nd. Used for ascending sort order in QSortWithIndexes()/
+ *
+ * @see SortAndTrackIndexCmpDesc() and QSortAndTrackIndex()
+ */
+int
+SortAndTrackIndexCmpAsc(const void *a, const void *b)
+{
+ const sortwithindex_t *a_t = (const sortwithindex_t *)a;
+ const sortwithindex_t *b_t = (const sortwithindex_t *)b;
+
+ const int ia = (const int) a_t->piValue;
+ const int ib = (const int) b_t->piValue;
+ return ia - ib;
+}
+/*** end: SortAndTrackIndexCmpAsc ***/
+
+
+
+
+/**
+ * @brief Compare two sortwithindex_t pointers and return the
+ * difference between the int value of the 2nd sortwithindex_t and the
+ * 1st. Used for descending sort order in QSortWithIndexes()
+ *
+ * @see SortAndTrackIndexCmpDesc() and QSortAndTrackIndex()
+ */
+int
+SortAndTrackIndexCmpDesc(const void *a, const void *b)
+{
+ const sortwithindex_t *a_t = (const sortwithindex_t *)a;
+ const sortwithindex_t *b_t = (const sortwithindex_t *)b;
+
+ const int ia = (const int) a_t->piValue;
+ const int ib = (const int) b_t->piValue;
+ return ib - ia;
+}
+/*** end: SortAndTrackIndexCmpDesc ***/
+
+
+
+
+/**
+ * @brief Sort a given int array in ascending or descending order,
+ * while keeping track of the element order.
+ *
+ * @param[out] piSortedIndices
+ * Will contain the indices of the sorted elements. Has to be preallocated.
+ * @param[out] piArrayToSort
+ * Array with values to sort. Will only be overwritten if
+ * bOverwriteArrayToSort it true.
+ * @param[in] iArrayLen
+ * Number of elements in piArrayToSort.
+ * @param[in] cOrder
+ * Sort order. 'a' for ascending, 'd' for descending.
+ * @param[in] bOverwriteArrayToSort
+ * If false do not overwrite the array to sort.
+ *
+ */
+void
+QSortAndTrackIndex(int *piSortedIndices, int *piArrayToSort,
+ const int iArrayLen, const char cOrder,
+ const bool bOverwriteArrayToSort)
+{
+ int iCtr; /**< aux */
+
+ sortwithindex_t *prSort;
+
+
+ assert(NULL!=piSortedIndices);
+ assert(iArrayLen>0);
+ assert(NULL!=piArrayToSort);
+ assert('a'==cOrder || 'd'==cOrder);
+
+ prSort = (sortwithindex_t *) CKMALLOC(iArrayLen * sizeof(sortwithindex_t));
+
+ for (iCtr=0; iCtr<iArrayLen; iCtr++) {
+ prSort[iCtr].piIndex = iCtr;
+ prSort[iCtr].piValue = piArrayToSort[iCtr];
+#if 0
+ LOG_DEBUG("b4 sort: prSort idx %d = val %d",
+ prSort[iCtr].piIndex, prSort[iCtr].piValue);
+#endif
+ }
+
+ if ('a'==cOrder) {
+ qsort(prSort, iArrayLen, sizeof(sortwithindex_t), SortAndTrackIndexCmpAsc);
+ } else if ('d'==cOrder) {
+ qsort(prSort, iArrayLen, sizeof(sortwithindex_t), SortAndTrackIndexCmpDesc);
+ } else {
+ Log(&rLog, LOG_FATAL, "Internal error: unknown order %c", cOrder);
+ }
+
+ for (iCtr=0; iCtr<iArrayLen; iCtr++) {
+ piSortedIndices[iCtr] = prSort[iCtr].piIndex;
+
+ if (bOverwriteArrayToSort) {
+ piArrayToSort[iCtr] = prSort[iCtr].piValue;
+ }
+#if 0
+ LOG_DEBUG("after sort: prSort idx %d = val %d",
+ prSort[iCtr].piIndex, prSort[iCtr].piValue);
+#endif
+ }
+ free(prSort);
+
+ return;
+}
+/*** end: QSortWithIndexes() ***/
+
+
+
+
+/**
+ * @brief Test if file is writable. File may or may not exist.
+ *
+ * @param[in] pcFileName
+ * Filename to check
+ *
+ * @return True if file is writable at the time of calling
+ *
+ */
+bool
+FileIsWritable(char *pcFileName)
+{
+ bool bFileAlreadyExisted;
+ FILE *prFilePointer;
+ bool bIsWritable;
+
+ if (0 != CheckIfFileExists(pcFileName)) {
+ bFileAlreadyExisted = TRUE;
+ } else {
+ bFileAlreadyExisted = FALSE;
+ }
+
+ if (NULL == (prFilePointer=fopen(pcFileName, "a"))) {
+ bIsWritable = FALSE;
+ } else {
+ bIsWritable = TRUE;
+ if (0 != fclose(prFilePointer)) {
+ Log(&rLog, LOG_ERROR, "Couldn't close temporily created file %s. Expect trouble...");
+ }
+ }
+
+#if 0
+ LOG_DEBUG("%s existed?=%d writable=%d", pcFileName,
+ (TRUE==bFileAlreadyExisted? 1 : 0),
+ (TRUE==bIsWritable? 1:0));
+#endif
+
+ /* delete if file didn't exist before and was created here
+ * temporarily
+ */
+ if (FALSE==bFileAlreadyExisted && TRUE==bIsWritable) {
+ if (0 != remove(pcFileName)) {
+ Log(&rLog, LOG_ERROR, "Removing of temporarily created file %s failed. Expect trouble...");
+ }
+ }
+ return bIsWritable;
+}
+/*** end: FileIsWritable() ***/
+
+
--- /dev/null
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: util.h 230 2011-04-09 15:37:50Z andreas $
+ */
+
+#include <limits.h>
+#include <string.h>
+#include <strings.h>
+#include <stdarg.h>
+#include <stdbool.h>
+
+#ifndef CLUSTALO_UTIL_H
+#define CLUSTALO_UTIL_H
+
+
+#define CKMALLOC(b) CkMalloc((b), __FUNCTION__, __LINE__)
+#define CKCALLOC(c, s) CkCalloc((c), (s), __FUNCTION__, __LINE__)
+#define CKREALLOC(p, b) CkRealloc((p), (b), __FUNCTION__, __LINE__)
+#define CKFREE(b) ((b)=CkFree((b), __FUNCTION__, __LINE__))
+
+#ifndef MAX
+#define MAX(a,b) ((a)>(b)?(a):(b))
+#endif
+#ifndef MIN
+#define MIN(a,b) ((a)<(b)?(a):(b))
+#endif
+
+/* STR_EQ: strings are equal, case sensitive */
+#define STR_EQ(a,b) (strcmp((a),(b)) == 0)
+/* STR_NC_EQ: strings are equal, ignoring case */
+#define STR_NC_EQ(a,b) (strcasecmp((a),(b)) == 0)
+
+
+/* type boolean and false and true defined in stdbool.h */
+#ifndef TRUE
+#define TRUE true
+#endif
+#ifndef FALSE
+#define FALSE false
+#endif
+
+/* clashes with hhalign
+#define FAIL -1
+#define OK 0
+*/
+
+
+
+/* don't use the following directly; use macros provided above instead
+ */
+void *CkMalloc(size_t size, const char *function, const int line);
+void *CkCalloc(size_t count, size_t size, const char *function, const int line);
+void *CkRealloc(void *ptr, size_t bytes, const char *function, const int line);
+void *CkFree(void *ptr, const char *function, const int line);
+char *CkStrdup(const char *s);
+void PermutationArray(int **array, const int len);
+void RandomUniqueIntArray(int *array, const int array_len, const int max_value);
+int IntCmp(const void *a, const void *b);
+bool FileIsWritable(char *pcFileName);
+void QSortAndTrackIndex(int *piSortedIndices, int *piArrayToSort,
+ const int uArrayLen, const char cOrder, const bool bOverwriteArrayToSort);
+
+#endif
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/* Module for deriving sequence weights from a tree. Largely based on
+ * Bob Edgar's Muscle (mainly clwwt.cpp; version 3.7). Ported to pure
+ * C. Most functions where apparently based on Clustal 1.8 anyway.
+ *
+ * Muscle's code is public domain and so is this code here.
+ *
+ * From http://www.drive5.com/muscle/license.htm:
+ * """
+ * MUSCLE is public domain software
+ *
+ * The MUSCLE software, including object and source code and
+ * documentation, is hereby donated to the public domain.
+ *
+ * Disclaimer of warranty
+ * THIS SOFTWARE IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND,
+ * EITHER EXPRESS OR IMPLIED, INCLUDING WITHOUT LIMITATION IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * """
+ *
+ */
+
+/*
+ * RCS $Id: weights.c 231 2011-04-09 17:13:06Z andreas $
+ */
+
+/*
+ * Documentation from Muscle
+ *
+ * """
+ * Compute weights by the CLUSTALW method.
+ * Thompson, Higgins and Gibson (1994), CABIOS (10) 19-29;
+ * see also CLUSTALW paper.
+ *
+ * Weights are computed from the edge lengths of a rooted tree.
+ *
+ * Define the strength of an edge to be its length divided by the number
+ * of leaves under that edge. The weight of a sequence is then the sum
+ * of edge strengths on the path from the root to the leaf.
+ *
+ * Example.
+ *
+ * 0.2
+ * -----A 0.1
+ * -x ------- B 0.7
+ * --------y ----------- C
+ * 0.3 ----------z
+ * 0.4 -------------- D
+ * 0.8
+ *
+ * Edge Length Leaves Strength
+ * ---- ----- ------ --------
+ * xy 0.3 3 0.1
+ * xA 0.2 1 0.2
+ * yz 0.4 2 0.2
+ * yB 0.1 1 0.1
+ * zC 0.7 1 0.7
+ * zD 0.8 1 0.8
+ *
+ * Leaf Path Strengths Weight
+ * ---- ---- --------- ------
+ * A xA 0.2 0.2
+ * B xy-yB 0.1 + 0.1 0.2
+ * C xy-yz-zC 0.1 + 0.2 + 0.7 1.0
+ * D xy-yz-zD 0.1 + 0.2 + 0.8 1.1
+ * """
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <assert.h>
+#include "log.h"
+#include "muscle_tree.h"
+#include "weights.h"
+
+
+/*
+ #undef DEBUG
+*/
+
+
+/**
+ * @brief FIXME
+ *
+ * @param[out] puLeavesUnderNode
+ * FIXME
+ * @param[in] prTree
+ * FIXME
+ * @param[in] uNodeIndex
+ * FIXME
+ *
+ * @return The return value
+ *
+ * @note see Muscle3.7:clwwt.cpp
+ *
+ */
+uint
+CountLeaves(uint *puLeavesUnderNode, tree_t *prTree, uint uNodeIndex)
+{
+ uint uLeft;
+ uint uRight;
+ uint uRightCount;
+ uint uLeftCount;
+ uint uCount;
+
+
+ if (IsLeaf(uNodeIndex, prTree)) {
+ puLeavesUnderNode[uNodeIndex] = 1;
+ return 1;
+ }
+
+ uLeft = GetLeft(uNodeIndex, prTree);
+ uRight = GetRight(uNodeIndex, prTree);
+ uRightCount = CountLeaves(puLeavesUnderNode, prTree, uRight);
+ uLeftCount = CountLeaves(puLeavesUnderNode, prTree, uLeft);
+ uCount = uRightCount + uLeftCount;
+
+ puLeavesUnderNode[uNodeIndex] = uCount;
+
+ return uCount;
+}
+/*** end: CountLeaves() ***/
+
+
+
+
+/**
+ * @brief Normalise values in a double array to values between 0 and 1.
+ *
+ * @param[out] p
+ * double array with n elements
+ * @param[in] n
+ * number of elements in p
+ *
+ * @note From Muscle3.7: intmath.cpp:Normalize()
+ *
+ */
+void
+Normalise(double *p, uint n) {
+ unsigned i;
+ double dSum = 0.0;
+ for (i = 0; i < n; ++i) {
+ dSum += p[i];
+ }
+ if (0.0 == dSum) {
+ Log(&rLog, LOG_FATAL, "Normalise, sum=0");
+ }
+ for (i = 0; i < n; ++i) {
+ p[i] /= dSum;
+ }
+}
+/*** end: Normalise() ***/
+
+
+
+/**
+ * @brief Calculate "Clustal" weights from a tree.
+ *
+ * FIXME see doc in muscle:clwwt.cpp
+ *
+ * @param[out] pdWeights_p
+ * Will contain a weight for each leaf/sequence. Allocated here. User
+ * has to free
+ * @param[in] prTree
+ * Tree to derive weights from
+ *
+ * @return 0 on success, non-zero otherwise
+ *
+ * @note Largely copied from Muscle3.7: clwwt.cpp:CalcClustalWWeights()
+ *
+ * @warning FIXME Not sure if Muscle routines are most efficient here.
+ * Couldn't we do all this while traversing the tree and thereby safe
+ * time?
+ *
+ */
+int
+CalcClustalWeights(double **pdWeights_p, tree_t *prTree)
+{
+ int i; /* aux */
+ uint uLeafCount;
+ uint uNodeCount;
+ uint *puLeavesUnderNode;
+ uint uLeavesUnderRoot;
+ uint uRootNodeIndex;
+ double *pdStrengths;
+ uint uNodeIndex;
+ bool bLogWeights = FALSE; /* verbose output of weights */
+
+
+ assert(NULL != pdWeights_p);
+ assert(NULL != prTree);
+
+ if (rLog.iLogLevelEnabled <= LOG_DEBUG) {
+ bLogWeights = TRUE;
+ }
+
+ uLeafCount = GetLeafCount(prTree);
+ uNodeCount = GetNodeCount(prTree);
+
+
+ (*pdWeights_p) = (double *) CKMALLOC(uNodeCount * sizeof(double));
+
+ if (0 == uLeafCount) {
+ return 0;
+ } else if (1 == uLeafCount) {
+ (*pdWeights_p)[0] = 1.0;
+ return 0;
+ } else if (2 == uLeafCount) {
+ (*pdWeights_p)[0] = 0.5;
+ (*pdWeights_p)[1] = 0.5;
+ return 0;
+ }
+
+ if (!IsRooted(prTree)) {
+ Log(&rLog, LOG_ERROR, "Tree must be rooted to get weights");
+ CKFREE(pdWeights_p);
+ return -1;
+ }
+
+
+#ifdef TRACE
+ Log(&rLog, LOG_FORCED_DEBUG, "%s", "Weights follow");
+ fprintf(stderr, "Node Leaves Length Strength\n");
+ fprintf(stderr, "---- ------ -------- --------\n");
+ /* 1234 123456 12345678 12345678 */
+#endif
+
+ uRootNodeIndex = GetRootNodeIndex(prTree);
+ puLeavesUnderNode = (uint *) CKCALLOC(uNodeCount, sizeof(uint));
+
+ uLeavesUnderRoot = CountLeaves(puLeavesUnderNode, prTree, uRootNodeIndex);
+ if (uLeavesUnderRoot != uLeafCount) {
+ Log(&rLog, LOG_FATAL, "Internal error, root count %u %u",
+ uLeavesUnderRoot, uLeafCount);
+ }
+#if 0
+ for (uNodeIndex=0; uNodeIndex<uNodeCount; uNodeIndex++) {
+ Log(&rLog, LOG_FORCED_DEBUG, "LeavesUnderNode[%d]=%d", uNodeIndex, puLeavesUnderNode[uNodeIndex]);
+ }
+#endif
+
+ pdStrengths = (double *) CKMALLOC(uNodeCount * sizeof(double));
+
+ for (uNodeIndex=0; uNodeIndex < uNodeCount; uNodeIndex++) {
+ uint uParent;
+ double dLength;
+ uint uLeaves;
+ double dStrength;
+
+ if (IsRoot(uNodeIndex, prTree)) {
+ pdStrengths[uNodeIndex] = 0.0;
+ continue;
+ }
+
+ uParent = GetParent(uNodeIndex, prTree);
+ dLength = GetEdgeLength(uNodeIndex, uParent, prTree);
+ uLeaves = puLeavesUnderNode[uNodeIndex];
+ dStrength = dLength / (double) uLeaves;
+ pdStrengths[uNodeIndex] = dStrength;
+
+#ifdef TRACE
+ fprintf(stderr, "%4u %6u %8g %8g\n", uNodeIndex, uLeaves, dLength, dStrength);
+#endif
+ }
+
+
+
+
+
+ if (bLogWeights){
+ fprintf(stderr, "\n");
+ fprintf(stderr, " Seq Path..Weight\n");
+ fprintf(stderr, "-------------------- ------------\n");
+ }
+ for (i=0; i<uLeafCount; i++) {
+ double dWeight = 0.0;
+ unsigned uLeafNodeIndex;
+ unsigned uNode;
+
+ uLeafNodeIndex = LeafIndexToNodeIndex(i, prTree);
+ uNode = uLeafNodeIndex;
+
+ if (bLogWeights){
+ fprintf(stderr, "%20.20s %4u ", GetLeafName(uLeafNodeIndex, prTree), uLeafNodeIndex);
+ }
+ if (! IsLeaf(uLeafNodeIndex, prTree)) {
+ Log(&rLog, LOG_FATAL,
+ "Internal error: non-leaf-node %d", uLeafNodeIndex);
+ }
+
+ /*LOG_DEBUG("dWeight = %f", dWeight);*/
+ while (! IsRoot(uNode, prTree)) {
+ dWeight += pdStrengths[uNode];
+ /*LOG_DEBUG("dWeight +== %f", pdStrengths[uNode]);*/
+ uNode = GetParent(uNode, prTree);
+ if (bLogWeights){
+ fprintf(stderr, "->%u(%g)", uNode, pdStrengths[uNode]);
+ }
+ }
+ /* AW: no idea what this is, but it's done like this in Muscle */
+ if (dWeight < 0.0001) {
+#ifdef TRACE
+ fprintf(stderr, "zero->one");
+#endif
+ dWeight = 1.0;
+ }
+
+ /* @note: the only difference to the muscle code is here: we
+ * use the input index for storing weights, instead of the
+ * tree leaf index
+ */
+ (*pdWeights_p)[GetLeafId(uLeafNodeIndex, prTree)] = dWeight;
+ if (bLogWeights){
+ fprintf(stderr, " = %g\n", dWeight);
+ }
+ }
+
+#if 0
+ for (i=0; i<uLeafCount; i++) {
+ Log(&rLog, LOG_FORCED_DEBUG, "Weights before normalisation: pdWeights_p[%d]=%f", i, (*pdWeights_p)[i]);
+ /*LOG_DEBUG("Should be %d", GetLeafId(LeafIndexToNodeIndex(i, prTree), prTree));*/
+ }
+#endif
+
+ Normalise((*pdWeights_p), uLeafCount);
+
+
+ CKFREE(puLeavesUnderNode);
+ CKFREE(pdStrengths);
+
+ return 0;
+}
+/*** end: CalcWeights() ***/
--- /dev/null
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: weights.h 193 2011-02-07 15:45:21Z andreas $
+ */
+
+#ifndef CLUSTALO_WEIGHTS_H
+#define CLUSTALO_WEIGHTS_H
+
+extern int
+CalcClustalWeights(double **pdWeights_p, tree_t *prTree);
+
+
+#endif
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: clustalo-api-test.c 213 2011-03-11 16:10:15Z andreas $
+ */
+
+
+#include <stdio.h>
+
+/* Include clustal-omega's header. That's all you need
+ *
+ * If you developing in C++, use the following instead:
+ * extern "C" {
+ * #include "clustal-omega.h"
+ * }
+ */
+#include "clustal-omega.h"
+
+
+int
+main(int argc, char **argv)
+{
+ /* the multiple sequence structure */
+ mseq_t *prMSeq = NULL;
+ /* for openmp: number of threads to use */
+ int iThreads = 1;
+ /* alignment options to use */
+ opts_t rAlnOpts;
+ /* an input file */
+ char *pcSeqInfile;
+ int iAux;
+
+ /* use LOGLEVEL_QUIET to make Clustal shut up */
+ iVerbosityLevel = LOGLEVEL_INFO;
+
+ SetDefaultAlnOpts(&rAlnOpts);
+
+ InitClustalOmega(iThreads);
+
+ /* Get sequence input file name from command line
+ */
+ if (argc!=2) {
+ Fatal("Need sequence file as argument");
+ }
+ pcSeqInfile = argv[1];
+
+ /* Read sequence file
+ */
+ NewMSeq(&prMSeq);
+ if (ReadSequences(prMSeq, pcSeqInfile,
+ SEQTYPE_UNKNOWN,
+ INT_MAX, INT_MAX)) {
+ Fatal("Reading sequence file '%s' failed", pcSeqInfile);
+ }
+
+ /* Dump some info about the sequences
+ */
+ for (iAux=0; iAux<prMSeq->nseqs; iAux++) {
+ Info(LOGLEVEL_INFO,
+ "Sequence no %d has the following name: %s",
+ iAux, prMSeq->sqinfo[iAux].name);
+ Info(LOGLEVEL_INFO,
+ "Sequence no %d has the following residues: %s",
+ iAux, prMSeq->seq[iAux]);
+ /* more info can be found in prMSeq->sqinfo[iAux] */
+ }
+
+
+ /* Align the sequences without a profile (NULL)
+ */
+ if (Align(prMSeq, NULL, & rAlnOpts)) {
+ Fatal("A fatal error happended during the alignment process");
+ }
+
+
+ /* Output of final alignment to stdout (NULL) as aligned fasta/a2m
+ */
+ if (WriteAlignment(prMSeq, NULL, MSAFILE_A2M)) {
+ Fatal("Could not save alignment");
+ }
+
+ FreeMSeq(&prMSeq);
+
+ Info(LOGLEVEL_INFO, "Successfull program exit");
+
+ return EXIT_SUCCESS;
+}
+/*** end of main() ***/
--- /dev/null
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+distdir: $(DISTFILES)
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+ -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
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+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: general.h 247 2011-06-16 11:41:15Z fabian $
+ */
+
+
+#ifndef GENERAL_H
+#define GENERAL_H
+
+
+#include "../clustal/log.h"
+
+/*
+***** Omega definitions************************************
+ FS, 2010-02-19
+*/
+enum {NO = 0, YES};
+enum {BASE10 = 10};
+enum {AMINOACIDS = 20, STATE_TRANSITIONS = 7};
+enum {MAXWORD = 100, MAXLEN = 10000};
+enum {OVER_ALLOCATE = 2};
+enum {FAILURE = -1, OK};
+enum {RETURN_OK = 0, RETURN_FROM_MAC, RETURN_FROM_VITERBI, RETURN_FROM_PRINT_ALI, RETURN_FROM_RNP, RETURN_UNKNOWN};
+enum {REALLY_BIG_MEMORY_MB = 64000};
+enum {F_OFFSET = 1};
+enum {INTERN_ALN_2_HMM = 0, READ_ALN_2_HMM, READ_HMM_2_HMM, INTERN_HMM_2_HMM};
+#define UNITY 1.00
+
+/*#define MIN(a,b) ((a)<(b)?(a):(b))*/
+
+
+/* parameters passed from Clustal-Omega to hhalign; FS, r240 -> */
+typedef struct {
+
+ int iMacRamMB; /* dedicated amount of RAM for Maximum Accuracy (in MB) */
+
+} hhalign_para;
+
+typedef struct {
+ /***public***/
+ int n_display;
+ char **sname;
+ char **seq;
+ int ncons;
+ int nfirst;
+ int nss_dssp;
+ int nsa_dssp;
+ int nss_pred;
+ int nss_conf;
+ int L;
+ int N_in;
+ int N_filtered;
+ float *Neff_M;
+ float *Neff_I;
+ float *Neff_D;
+ float Neff_HMM;
+ char *longname;
+ char name[511];
+ char file[511];
+ char fam[511];
+ char sfam[511];
+ char fold[511];
+ char cl[511];
+ float lamda;
+ float mu;
+ /***private***/
+ float **f;
+ float **g;
+ float **p;
+ float **tr;
+ float **linTr;
+ char trans_lin;
+ char *ss_dssp;
+ char *sa_dssp;
+ char *ss_pred;
+ char *ss_conf;
+ char *Xcons;
+ float pav[20];
+ float pnul[20];
+ int *l;
+
+} hmm_light;
+
+
+#endif
+
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hash-C.h 143 2010-10-14 13:11:14Z andreas $
+ */
+
+// hash.C
+// Class for Hash data structure
+// * works in the same way as a hash in Perl
+// * keys are strings of type char*
+// * data elements are of type Typ
+// * objects have to be declared with maximal size, e.g. Hash hash1(10000) (num_slots should not be a power of 2)
+// * works also if maximal size is exceeded, but gets slower by a factor ~num_keys/num_slots
+
+/*
+ * RCS $Id: hash-C.h 143 2010-10-14 13:11:14Z andreas $
+ */
+
+#ifndef HASH
+#define HASH
+
+#ifndef MAIN
+#include <iostream> // cin, cout, cerr
+#include <cstdio> // printf
+#include <stdlib.h> // exit
+#include <string> // strcmp, strstr
+#include <math.h> // sqrt, pow
+#include <limits.h> // INT_MIN
+#include <float.h> // FLT_MIN
+#include <ctype.h> // islower, isdigit etc
+#include <time.h> // clock
+#include <errno.h> // perror()
+using std::cout;
+using std::cerr;
+using std::endl;
+using std::ios;
+using std::ifstream;
+using std::ofstream;
+#endif
+
+#ifndef JLIST
+#define JLIST
+#include "list.h" // List<Typ>
+#include "list-C.h" ////////////////////////////////// DEBUG
+#endif
+
+#include "hash.h"
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+////////////////////// Methods of class Hash /////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+
+//////////////////////////////////////////////////////////////////////////////
+// Private Methods
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Constructor and Destructor of Hash
+//////////////////////////////////////////////////////////////////////////////
+// Constructor of class Hash
+//////////////////////////////////////////////////////////////////////////////
+template<class Typ>
+Hash<Typ>::Hash()
+{
+ num_keys=0; max_len=0; prev=curr=num_slots = 0; slot=NULL;
+}
+
+template<class Typ>
+Hash<Typ>::Hash(int nslots)
+{
+ num_keys=0; max_len=0; prev=curr=num_slots = nslots;
+ slot = new Slot<Typ>*[num_slots]; //Create array of num_slots slots
+ for (int i=0; i<num_slots; i++) slot[i]=NULL; //set pointers to NULL
+ fail = static_cast<Typ>(0);
+}
+
+template<class Typ>
+Hash<Typ>::Hash(int nslots, Typ f)
+{
+ num_keys=0; max_len=0; prev=curr=num_slots = nslots;
+ slot = new Slot<Typ>*[num_slots]; //Create array of num_slots slots
+ for (int i=0; i<num_slots; i++) slot[i]=NULL; //set pointers to NULL
+ fail=f;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////////////////
+// Destructor of class Hash
+////////////////////////////////////////////////////////////////////////////////////////////
+template<class Typ>
+Hash<Typ>::~Hash()
+{
+ RemoveAll();
+ delete[] slot; slot = NULL;
+}
+
+
+////////////////////////////////////////////////////////////////////////////////////////////
+// Hash function
+////////////////////////////////////////////////////////////////////////////////////////////
+template<class Typ>
+inline unsigned int Hash<Typ>::HashValue(char* key) //returns the hash value for key
+ {
+ // Calculate a hash value by the division method:
+ // Transform key into a natural number k = sum ( key[i]*128^(L-i) ) and calculate i= k % num_slots.
+ // Since calculating k would lead to an overflow, i is calculated iteratively
+ // and at each iteration the part divisible by num_slots is subtracted, i.e. (% num_slots is taken).
+ if (key==NULL) {printf("Warning from hash.C: key=NULL\n"); return 0;}
+ unsigned int i=0; // Start of iteration: k is zero
+ char* c = key;
+ while(*c) i = ((i<<7) + *(c++)) % num_slots;
+ key_len = c - key;
+ // cerr<<" Hash value for \'"<<key<<"\' is "<<i<<"\n";
+ return i;
+ }
+
+////////////////////////////////////////////////////////////////////////////////////////////
+// Create new hash (and delete any data present)
+////////////////////////////////////////////////////////////////////////////////////////////
+template<class Typ>
+void Hash<Typ>::New(int nslots, Typ f)
+{
+ fail=f;
+ RemoveAll();
+ delete[] slot; slot = NULL;
+ num_keys=0; max_len=0; prev=curr=num_slots = nslots;
+ slot = new Slot<Typ>*[num_slots]; //Create array of num_slots slots
+ for (int i=0; i<num_slots; i++) slot[i]=NULL; //set pointers to NULL
+}
+
+
+
+////////////////////////////////////////////////////////////////////////////////////////////
+// Methods that work with a key supplied as an argument
+
+////////////////////////////////////////////////////////////////////////////////////////////
+// Return data element for key. Returns 'fail' if key does not exist
+////////////////////////////////////////////////////////////////////////////////////////////
+template<class Typ>
+Typ Hash<Typ>::Show(char* key)
+{
+ Slot<Typ>* pslot;
+ int i = HashValue(key);
+
+ pslot = slot[i];
+ if (!pslot) return fail;
+ pslot->Reset();
+ do{
+ if(!strcmp(pslot->ReadNext().key,key)) return pslot->ReadCurrent().data;
+ } while(!pslot->End());
+ return fail;
+}
+
+////////////////////////////////////////////////////////////////////////////////////////////
+// Add/replace key/data pair to hash and return address of data element
+////////////////////////////////////////////////////////////////////////////////////////////
+template<class Typ>
+Typ* Hash<Typ>::Add(char* key, Typ data)
+{
+ Pair<Typ>* pairp;
+ Slot<Typ>* pslot;
+ int i = HashValue(key);
+
+ pslot = slot[i];
+ if (!pslot) { num_keys++; KeyLen(); slot[i]=new(Slot<Typ>); return slot[i]->Push(key_len,key,data);}
+ pslot->Reset();
+ do
+ {
+ pairp = pslot->ReadNextAddress();
+ if(!strcmp(pairp->key,key))
+ {
+ pairp->data=data;
+ pslot->Overwrite(*pairp);
+ return &(pairp->data);
+ }
+ } while(!pslot->End());
+ num_keys++;
+ KeyLen();
+ return pslot->Push(key_len,key,data);
+}
+
+
+
+////////////////////////////////////////////////////////////////////////////////////////////
+// Add key to hash and return address of data element.
+// If key exists leave data element unchanged, else set it to 'fail'.
+////////////////////////////////////////////////////////////////////////////////////////////
+template<class Typ>
+Typ* Hash<Typ>::Add(char* key)
+{
+ Slot<Typ>* pslot;
+ int i = HashValue(key);
+
+ pslot = slot[i];
+ if (!pslot) { num_keys++; KeyLen(); slot[i]=new(Slot<Typ>); return slot[i]->Push(key_len,key,fail);}
+ pslot->Reset();
+ do
+ {
+ if(!strcmp(pslot->ReadNext().key,key))
+ {
+ return &((pslot->ReadCurrentAddress())->data);
+ }
+ } while(!pslot->End());
+ num_keys++;
+ KeyLen();
+ return pslot->Push(key_len,key,fail);
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////////////
+// Remove key from hash and return data element for key ('fail' if key does not exist)
+/////////////////////////////////////////////////////////////////////////////////////////////
+template<class Typ>
+Typ Hash<Typ>::Remove(char* key)
+{
+ Slot<Typ>* pslot;
+ int i = HashValue(key);
+
+ pslot = slot[i];
+ if (!pslot) return fail;
+ pslot->Reset();
+ do
+ {
+ if(!strcmp(pslot->ReadNext().key,key))
+ {
+ num_keys--;
+ pslot->Delete();
+ // if key was the only element in pslot then delete whole list
+ if (pslot->Size()==0) {delete pslot; pslot = NULL;slot[i]=0;}
+ return pslot->ReadCurrent().data;
+ }
+ } while(!pslot->End());
+ return fail;
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Remove all keys from hash;
+//////////////////////////////////////////////////////////////////////////////
+template<class Typ>
+void Hash<Typ>::RemoveAll()
+{
+ for(int i=0; i<num_slots; i++)
+ if(slot[i]) {delete slot[i]; slot[i]=NULL;}
+ num_keys=0;
+ max_len=0;
+ curr=prev=num_slots;
+}
+
+
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Methods that work with an internal "current key":
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Return data of next key. Return 'fail' data and empty key if at end
+//////////////////////////////////////////////////////////////////////////////
+template<class Typ>
+Typ Hash<Typ>::ReadNext()
+{
+ Pair<Typ>* pairp;
+ Slot<Typ>* pslot;
+
+ if (curr>=num_slots) {return fail;}
+ pslot = slot[curr]; // current list is never empty, except when current=num_slots
+ pairp = pslot->ReadNextAddress();
+ if (pslot->End()) {
+ prev=curr;
+ do // move on to next non-empty list
+ {
+ if (++curr>=num_slots) return pairp->data;
+ pslot = slot[curr];
+ } while (!pslot);
+ pslot->Reset();
+ }
+ return pairp->data;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// Write next key into variable key and return data. Return 'fail' data and empty key if at end
+// Attention: 'key' must have memory of at least char[MaxLen()+1] allocated!
+//////////////////////////////////////////////////////////////////////////////
+template<class Typ>
+Typ Hash<Typ>::ReadNext(char* key)
+{
+ Pair<Typ>* pairp;
+ Slot<Typ>* pslot;
+
+ if (curr>=num_slots) {*key='\0'; return fail;}
+ pslot = slot[curr]; // current list is never empty, except when current=num_slots
+ pairp = pslot->ReadNextAddress();
+ strcpy(key,pairp->key);
+ if (pslot->End()) {
+ prev=curr;
+ do // move on to next non-empty list
+ {
+ if (++curr>=num_slots) return pairp->data;
+ pslot = slot[curr];
+ } while (!pslot);
+ pslot->Reset();
+ }
+ return pairp->data;
+}
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Return data of current key
+//////////////////////////////////////////////////////////////////////////////
+template<class Typ>
+Typ Hash<Typ>::ReadCurrent()
+{
+ Pair<Typ>* pairp;
+ Slot<Typ>* pslot;
+
+ curr=prev;
+ if (curr>=num_slots) {return fail;}
+ pslot = slot[curr]; // current list is never empty, except when current=num_slots
+ pairp = &(pslot->ReadCurrent());
+ if (pslot->End()) {
+ do // move on to next non-empty list
+ {
+ if (++curr>=num_slots) return pairp->data;
+ pslot = slot[curr];
+ } while (!pslot);
+ pslot->Reset();
+ }
+ return pairp->data;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// Write key last read into variable key and return data
+// Attention: 'key' must have memory of at least char[MaxLen()+1] allocated!
+//////////////////////////////////////////////////////////////////////////////
+template<class Typ>
+Typ Hash<Typ>::ReadCurrent(char* key)
+{
+ Pair<Typ>* pairp;
+ Slot<Typ>* pslot;
+
+ curr=prev;
+ if (curr>=num_slots) {*key='\0'; return fail;}
+ pslot = slot[curr]; // current list is never empty, except when current=num_slots
+ pairp = &(pslot->ReadCurrent());
+ strcpy(key,pairp->key);
+ if (pslot->End()) {
+ do // move on to next non-empty list
+ {
+ if (++curr>=num_slots) return pairp->data;
+ pslot = slot[curr];
+ } while (!pslot);
+ pslot->Reset();
+ }
+ return pairp->data;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// Remove current key, return data, and advance to next key (after Reset() remove first element)
+//////////////////////////////////////////////////////////////////////////////
+template<class Typ>
+Typ Hash<Typ>::RemoveCurrent()
+{
+ Pair<Typ>* pairp;
+ Slot<Typ>* pslot;
+ curr=prev;
+
+ if (curr>=num_slots) {return fail;}
+ pslot = slot[curr]; // current list is never empty, except when current=num_slots
+ pairp = &(pslot->Delete());
+ num_keys--;
+ // if key was the only element in pslot then delete whole list
+ if (pslot->Size()==0) {delete pslot; pslot = NULL; slot[curr]=0;}
+ if (!pslot || pslot->End()) {
+ do // move on to next non-empty list
+ {
+ if (++curr>=num_slots) {prev=curr; return pairp->data;}
+ pslot = slot[curr];
+ } while (!pslot);
+ pslot->Reset();
+ }
+ prev=curr;
+ return pairp->data;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// Remove current key, return data, copy current key into key, and advance to next key
+// (After Reset() remove first element)
+// Attention: 'key' must have memory of at least char[MaxLen()+1] allocated!
+//////////////////////////////////////////////////////////////////////////////
+template<class Typ>
+Typ Hash<Typ>::RemoveCurrent(char* key)
+{
+ Pair<Typ>* pairp;
+ Slot<Typ>* pslot;
+
+ curr=prev;
+ if (curr>=num_slots) {*key='\0'; return fail;}
+ pslot = slot[curr]; // current list is never empty, except when current=num_slots
+ pairp = &(pslot->Delete());
+ strcpy(key,pairp->key);
+ num_keys--;
+ // if key was the only element in pslot then delete whole list
+ if (pslot->Size()==0) {delete pslot; pslot = NULL; slot[curr]=0;}
+ if (!pslot || pslot->End()) {
+ do // move on to next non-empty list
+ {
+ if (++curr>=num_slots) {prev=curr; return pairp->data;}
+ pslot = slot[curr];
+ } while (!pslot);
+ pslot->Reset();
+ }
+ prev=curr;
+ return pairp->data;
+}
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Reset current position to beginning of hash
+//////////////////////////////////////////////////////////////////////////////
+template<class Typ>
+void Hash<Typ>::Reset()
+ {
+ curr=-1;
+ Slot<Typ>* pslot;
+ do
+ {
+ curr++;
+ if (curr>=num_slots) {prev=curr; return;}
+ pslot = slot[curr];
+ } while (!pslot);
+ pslot->Reset();
+ prev=curr;
+ return;
+ }
+
+
+/////////////////////////////////////////////////////////////////////////////////////////////
+// Methods that return usefull information about the data stored in Hash:
+
+
+////////////////////////////////////////////////////////////////////////////////////////////
+// Returns 1 if the hash contains key, 0 otherwise
+////////////////////////////////////////////////////////////////////////////////////////////
+template<class Typ>
+int Hash<Typ>::Contains(char* key)
+{
+ Slot<Typ>* pslot;
+ int i = HashValue(key);
+
+ pslot = slot[i];
+ if (!pslot) return 0;
+ pslot->Reset();
+ do{
+ if(!strcmp(pslot->ReadNext().key,key)) return 1;
+ } while(!pslot->End());
+ return 0;
+}
+
+/////////////////////////////////////////////////////////////////////////////////////////////
+//print out list of keys and data
+/////////////////////////////////////////////////////////////////////////////////////////////
+template<class Typ>
+void Hash<Typ>::Print()
+{
+ char key[MaxLen()+1];
+
+ cout<<"\nPrint hash:\n";
+ Reset();
+ while(!End())
+ cout<<key<<"->"<<ReadNext(key)<<"\n";
+}
+
+/////////////////////////////////////////////////////////////////////////////////////////////
+//Print out hash with internal representation as array
+/////////////////////////////////////////////////////////////////////////////////////////////
+template<class Typ>
+void Hash<Typ>::DebugPrint()
+{
+ Pair<Typ>* pairp;
+ Slot<Typ>* pslot;
+
+ cout<<"\n";
+ cout<<"Debug-print hash:";
+ for(int i=0; i<num_slots; i++)
+ {
+ pslot = slot[i];
+ if (pslot)
+ {
+ cout<<"\nhash value "<<i;
+ pslot->Reset();
+ while(!pslot->End())
+ {
+ pairp = pslot->ReadNextAddress();
+ cout<<" "<<pairp->key<<"->"<<pairp->data;
+ }
+ }
+ }
+ cout<<"\n\n";
+ return;
+}
+
+
+
+#endif /* HASH */
+
+
+
+////////////////////////////////////////////////////////////////////////////////
+// Main program: test class Hash
+////////////////////////////////////////////////////////////////////////////////
+// int main()
+// {
+// Hash<int> ihash(5);
+// char* key=new char[128];
+// int data;
+
+// ihash.Fail(1000);
+// ihash.Add("So many monsters",36);
+// ihash.Add("So many chickens",25);
+
+// // cerr<<"Address of ihash(\"So many monsters\") is "<<ihash("So many monsters")<<"\n";
+// // cerr<<"Address of ihash(\"So many monsters\") is "<<ihash("So many monsters")<<"\n";
+// // *ihash("So many monsters")=2;
+// // (*ihash("So many monsters"))++;
+// // (*ihash("So many monsters"))++;
+// cout<<"Size of hash="<<ihash.Size()<<"\n";
+// ihash.DebugPrint();
+// ihash.Print();
+
+// strcpy(key,"Some more monsters");
+// ihash.Add(key,3);
+// strcpy(key,"Even more monsters");
+// ihash.Add(key,7);
+// cout<<"Size of hash="<<ihash.Size()<<"\n";
+// cout<<"Maximum key length = "<<ihash.MaxLen()<<"\n";
+// ihash.Print();
+
+// cout<<"ihash.Remove(\"Even more monsters\") returns "<<ihash.Remove("Even more monsters")<<"\n";
+// ihash.Print();
+
+
+// cout<<"ihash.Remove(\"More monsters\") returns "<<ihash.Remove("More monsters")<<"\n";
+// ihash.Add("So many chickens",999);
+// ihash.Add("So many monster",1);
+// ihash.Print();
+
+// cout<<"So many chickens:"<<ihash.Show("So many chickens")<<"\n";
+// cout<<"Size of hash="<<ihash.Size()<<"\n";
+
+
+
+// ihash.Reset();
+// while (!ihash.End())
+// {
+// data = ihash.ReadNext(key);
+// cout<<" "<<key<<"->"<<data<<endl;
+// data = ihash.ReadCurrent(key);
+// cout<<" "<<key<<"->"<<data<<endl;
+// }
+// cout<<"Removing all keys..."<<endl;
+// cout<<"Size of hash="<<ihash.Size()<<"\n";
+// ihash.Reset();
+// while (ihash.Size())
+// {
+// data = ihash.RemoveCurrent(key);
+// cout<<" "<<key<<"->"<<data<<"\n";
+// cout<<"Size of hash="<<ihash.Size()<<"\n";
+// }
+
+// ihash.ReadCurrent(key);
+
+// ihash.Print();
+// return 0;
+// }
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hash.h 143 2010-10-14 13:11:14Z andreas $
+ */
+
+// Class for Hash data structure
+// * works in the same way as a hash in Perl
+// * keys are strings of type char*
+// * data elements are of type Typ
+// * objects have to be declared with maximal size, e.g. Hash hash1(10000) (num_slots should not be a power of 2)
+// * works also if maximal size is exceeded, but gets slower by a factor ~num_keys/num_slots
+//
+// Applications
+// * fast storage and retrieval of data by a key
+// * fast check if a string occurs in a list of strings (data field not used)
+//
+// Time complexity: (L is the length of the key string)
+// * Show(key), Add(key), Remove(key): O(L) for calculating hash value & compare keys in slot list
+// * ReadNext, ReadCurrent, RemoveCurrent: O(L) for copying key into returned string
+// * Contains: O(L) for calculating hash value
+// * Size, MaxLen, Reset: O(1)
+// * RemoveAll(), Hash() and ~Hash(): O(num_slots)
+//
+// Memory complexity: ~3*num_keys*(datasize+12bytes) + num_slots*4bytes + total added length of keys (including \0)
+//
+// Implementation:
+// Hash is an array of pointers to lists of size num_slots. The lists, called slots, contain key/data pairs.
+// When a key/data pair is added (e.g. with Add()) the array index i for the key (0<=i<num_slots)
+// is calculated with the HashValue() function.
+// When data is to be retrieved for key (e.g. with Show()) the hash value for key is calculated and
+// the corresponding list (=slot) is searched for the occurence of the key.
+// Array elements of hash values that have no keys associated yet contain the null pointer
+// for faster rejection of undefined keys.
+//
+
+////////////////////////////////////////////////////////////////////////////////////////////
+// Declaration of Pair, consisting of a key string and a data element of type Typ
+////////////////////////////////////////////////////////////////////////////////////////////
+
+template<class Typ>
+class Pair
+{
+public:
+ char* key; //hash key
+ Typ data; //data for key
+ Pair() {}
+ Pair(char* k, Typ& d) {key = new char[strlen(k)+1]; strcpy(key,k); data=d;}
+ Pair(int& l, char* k, Typ& d) {key = new char[l+1]; strcpy(key,k); data=d;}
+};
+
+
+////////////////////////////////////////////////////////////////////////////////////////////
+// Declaration of Slot, a list of key/data pairs
+////////////////////////////////////////////////////////////////////////////////////////////
+
+template<class Typ>
+class Slot : public List< Pair<Typ> >
+{
+public:
+ //Destructor of Slot deletes whole list TOGETHER WITH THE KEY STRINGS
+ ~Slot() {this->Reset(); while (!this->End()) delete[] this->Pop().key; }
+
+ // Push key/data pair onto slot list and return address of data element
+ // Attention: l must be at least length of key
+ inline Typ* Push(int& l, char* key, Typ& data)
+ {
+ Pair<Typ> pair(l,key,data); //create a pair with key/data
+ return &(List<Pair<Typ> >::Push(pair)->data);
+ }
+};
+
+
+////////////////////////////////////////////////////////////////////////////////////////////
+// Declaration of Hash, an array of slots, i.e. pointers to lists of key/data
+////////////////////////////////////////////////////////////////////////////////////////////
+
+template<class Typ>
+class Hash
+{
+private:
+ int num_slots; //number of slots in slot[]. num_slots is set with the constructor
+ int curr; //index of current slot
+ int prev; //index of slot from previous ReadNext()
+ int num_keys; //total number of keys in hash
+ int max_len; //length of longest key in hash
+ int key_len; //length of key in argument
+ Typ fail;
+
+ Slot<Typ>** slot; //each slot[i] (i<num_slots) points to a list of key/data pairs for this slot
+
+ inline unsigned int HashValue(char* key); //returns the hash value for key
+
+public:
+ Hash();
+ Hash(int nslots);
+ Hash(int nslots, Typ n);
+ ~Hash();
+
+ // Set Fail element to be returned when the current key or supplied key are not defined
+ inline void Null(Typ f) {fail=f;}
+ inline void Fail(Typ f) {fail=f;}
+
+ // Set 'fail' element to be returned when the current key or supplied key are not defined (default: 0)
+ void New(int nslots, Typ n=static_cast<Typ>(0));
+
+ // Update maximum key length and caculate key_len;
+ inline void KeyLen() {if(key_len>max_len) max_len=key_len; return;}
+
+
+////////////////////////////////////////////////////////////////////////////////////////////
+// Methods that work with a key supplied as an argument
+
+ // Return data element for key. Returns 'fail' if key does not exist
+ Typ Show(char* key);
+ inline Typ operator[](char* key) {return Show(key);}
+
+ // Add/replace key/data pair to hash and return address of data element for key
+ Typ* Add(char* key, Typ data);
+
+ // Add key to hash and return address of data element. If key exists leave data element unchanged, else set it to 'fail'.
+ Typ* Add(char* key);
+ inline Typ* operator()(char* key) {return Add(key);}
+
+ // Remove key from hash and return data element for key ('fail' if key does not exist)
+ Typ Remove(char* key);
+
+ // Remove all keys from hash
+ void RemoveAll();
+
+
+///////////////////////////////////////////////////////////////////////////////////////////
+// Methods that work with an internal "current key":
+// It is set to the first key by Reset() and moves to the next key with ReadNext or RemoveCurrent
+// Note:the methods above (e.g. Store, Show, [], Add, (), etc. DO NOT CHANGE the current key
+
+ // Return data of next key. Return 'fail' data and empty key if at end
+ Typ ReadNext();
+
+ // Write next key into variable key and return data. Return 'fail' data and empty key if at end
+ // Attention: 'key' must have memory of at least char[MaxLen()+1] allocated!
+ Typ ReadNext(char* key);
+
+ // Return data of current key
+ Typ ReadCurrent();
+
+ // Write key last read into variable key and return data
+ // Attention: 'key' must have memory of at least char[MaxLen()+1] allocated!
+ Typ ReadCurrent(char* key);
+
+ // Remove current key, return data and advance to next key
+ Typ RemoveCurrent();
+
+ // Remove current key, return data, copy current key into key, and advance to next key
+ // (After Reset() remove first element)
+ // Attention: 'key' must have memory of at least char[MaxLen()+1] allocated!
+ Typ RemoveCurrent(char* key);
+
+ // Reset readout of keys to beginning of hash
+ void Reset();
+
+ // Returns 1 if the current key has arrived at the end, 0 otherwise
+ int End() {return (curr>=num_slots);}
+
+
+
+///////////////////////////////////////////////////////////////////////////////////////////
+// Methods that return usefull information about the data stored in Hash:
+
+ // Returns 1 if the hash contains key, 0 otherwise
+ int Contains(char* key);
+
+ // Return number of slots
+ int Size() {return num_keys;}
+
+ // Return length of longest key INCLUDING DELETED KEYS (excluding \0)
+ int MaxLen() {return max_len;}
+
+ //print out list of keys and data
+ void Print();
+
+ //Print out hash with internal representation as array
+ void DebugPrint();
+};
+
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhalign.cpp 250 2011-06-17 13:06:20Z fabian $
+ */
+
+/* hhalign.C:
+ * Align a multiple alignment to an alignment or HMM
+ * Print out aligned input sequences in a3m format
+ * Compile: g++ hhalign.C -o hhalign -I/usr/include/ -L/usr/lib -lpng -lz -O3 -fno-strict-aliasing
+ * Compile with efence: g++ hhalign.C -o hhalign -I/usr/include/ -lefence -L/usr/lib -lpng -lz -O -g
+ *
+ * Error codes: 0: ok 1: file format error 2: file access error
+ * 3: memory error 4: internal numeric error
+ * 5: command line error
+ */
+#undef PNG /* include options for making png files?
+ (will need the png library) */
+#define MAIN
+#include <iostream> // cin, cout, cerr
+#include <fstream> // ofstream, ifstream
+#include <string.h> // strcmp, strstr
+#include <stdio.h> // printf
+#include <stdlib.h> // exit
+#include <math.h> // sqrt, pow
+#include <limits.h> // INT_MIN
+#include <float.h> // FLT_MIN
+#include <time.h> // clock
+#include <ctype.h> // islower, isdigit etc
+
+using std::cout;
+using std::cerr;
+using std::endl;
+using std::ios;
+using std::ifstream;
+using std::ofstream;
+
+int iAux_GLOBAL;
+
+#include "general.h"
+#include "util-C.h" /* imax, fmax, iround, iceil, ifloor, strint, strscn,
+ strcut, substr, uprstr, uprchr, Basename etc. */
+#include "list-C.h" // list data structure
+#include "hash-C.h" // hash data structure
+
+#include "hhdecl-C.h" // Constants, global variables, struct Parameters
+#include "hhutil-C.h" /* MatchChr, InsertChr, aa2i, i2aa, log2,
+ fast_log2, WriteToScreen, */
+#include "hhmatrices-C.h" // BLOSUM50, GONNET, HSDM
+#include "hhhmm.h" // class HMM
+#include "hhhit.h" // class Hit
+#include "hhalignment.h" // class Alignment
+#include "hhhalfalignment.h" // class HalfAlignment
+#include "hhfullalignment.h" // class FullAlignment
+#include "hhhitlist.h" // class Hit
+#include "hhhmm-C.h" // class HMM
+#include "hhalignment-C.h" // class Alignment
+#include "hhhit-C.h" // class Hit
+#include "hhhalfalignment-C.h" // class HalfAlignment
+#include "hhfullalignment-C.h" // class FullAlignment
+#include "hhhitlist-C.h" // class HitList
+#include "hhfunc-C.h" // some functions common to hh programs
+
+#ifdef PNG
+#include "pngwriter.h" //PNGWriter (http://pngwriter.sourceforge.net/)
+#include "pngwriter.cc" //PNGWriter (http://pngwriter.sourceforge.net/)
+#endif
+
+////////////////////////////////////////////////////////////////////////
+// Global variables
+////////////////////////////////////////////////////////////////////////
+HMM *q; // Create query HMM with maximum of MAXRES match states
+HMM *t; /* Create template HMM with maximum of MAXRES
+ match states */
+Alignment *qali; /* (query alignment might be needed outside of hhfunc.C
+ for -a option) */
+Hit hit; // Ceate new hit object pointed at by hit
+HitList hitlist; /* list of hits with one Hit object for each
+ pairwise comparison done */
+char aliindices[256]; /* hash containing indices of all alignments
+ which to show in dot plot */
+char* dmapfile=NULL; /* where to write the coordinates for the HTML map file
+ (to click the alignments) */
+char* alitabfile=NULL; // where to write pairs of aligned residues
+char* strucfile=NULL; // where to read structure scores
+char* pngfile=NULL; // pointer to pngfile
+char* tcfile=NULL; // TCoffee output file name
+float probmin_tc=0.05; /* 5% minimum posterior probability for printing
+ pairs of residues for TCoffee */
+
+int dotW=10; // average score of dot plot over window [i-W..i+W]
+float dotthr=0.5; // score threshold for dot plot
+int dotscale=600; // size scale of dotplot
+char dotali=0; // show no alignments in dotplot
+float dotsat=0.3; // saturation of grid and alignments in dot plot
+float pself=0.001; // maximum p-value of 2nd and following self-alignments
+int Nstochali=0; // # of stochastically traced alignments in dot plot
+float** Pstruc=NULL; /* structure matrix which can be multiplied to prob
+ ratios from aa column comparisons in Forward() */
+float** Sstruc=NULL; /* structure matrix which can be added to log odds
+ from aa column comparisons in Forward() */
+
+
+
+
+
+////////////////////////////////////////////////////////////////////////////
+// Help functions
+////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief general help function, not accessible in Clustal-Omega
+ */
+#if 0
+void
+help()
+{
+ printf("\n");
+ printf("HHalign %s\n",VERSION_AND_DATE);
+ printf("Align a query alignment/HMM to a template alignment/HMM by HMM-HMM alignment\n");
+ printf("If only one alignment/HMM is given it is compared to itself and the best\n");
+ printf("off-diagonal alignment plus all further non-overlapping alignments above \n");
+ printf("significance threshold are shown.\n");
+ printf("%s",REFERENCE);
+ printf("%s",COPYRIGHT);
+ printf("\n");
+ printf("Usage: %s -i query [-t template] [options] \n",program_name);
+ printf(" -i <file> input query alignment (fasta/a2m/a3m) or HMM file (.hhm)\n");
+ printf(" -t <file> input template alignment (fasta/a2m/a3m) or HMM file (.hhm)\n");
+#ifdef PNG
+ printf(" -png <file> write dotplot into PNG-file (default=none) \n");
+#endif
+ printf("\n");
+ printf("Output options: \n");
+ printf(" -o <file> write output alignment to file\n");
+ printf(" -ofas <file> write alignments in FASTA, A2M (-oa2m) or A3M (-oa3m) format \n");
+ printf(" -a <file> write query alignment in a3m format to file (default=none)\n");
+ printf(" -aa <file> append query alignment in a3m format to file (default=none)\n");
+ printf(" -atab <file> write alignment as a table (with posteriors) to file (default=none)\n");
+ printf(" -v <int> verbose mode: 0:no screen output 1:only warings 2: verbose\n");
+ printf(" -seq [1,inf[ max. number of query/template sequences displayed (def=%i) \n",par.nseqdis);
+ printf(" -nocons don't show consensus sequence in alignments (default=show) \n");
+ printf(" -nopred don't show predicted 2ndary structure in alignments (default=show) \n");
+ printf(" -nodssp don't show DSSP 2ndary structure in alignments (default=show) \n");
+ printf(" -aliw int number of columns per line in alignment list (def=%i)\n",par.aliwidth);
+ printf(" -P <float> for self-comparison: max p-value of alignments (def=%.2g\n",pself);
+ printf(" -p <float> minimum probability in summary and alignment list (def=%G) \n",par.p);
+ printf(" -E <float> maximum E-value in summary and alignment list (def=%G) \n",par.E);
+ printf(" -Z <int> maximum number of lines in summary hit list (def=%i) \n",par.Z);
+ printf(" -z <int> minimum number of lines in summary hit list (def=%i) \n",par.z);
+ printf(" -B <int> maximum number of alignments in alignment list (def=%i) \n",par.B);
+ printf(" -b <int> minimum number of alignments in alignment list (def=%i) \n",par.b);
+ printf(" -rank int specify rank of alignment to write with -a or -aa option (default=1)\n");
+ printf("\n");
+#ifdef PNG
+ printf("Dotplot options:\n");
+ printf(" -dwin <int> average score in dotplot over window [i-W..i+W] (def=%i) \n",dotW);
+ printf(" -dthr <float> score threshold for dotplot (default=%.2f) \n",dotthr);
+ printf(" -dsca <int> if value <= 20: size of dot plot unit box in pixels \n");
+ printf(" if value > 20: maximum dot plot size in pixels (default=%i) \n",dotscale);
+ printf(" -dali <list> show alignments with indices in <list> in dot plot \n");
+ printf(" <list> = <index1> ... <indexN> or <list> = all \n");
+ printf("\n");
+#endif
+ printf("Filter input alignment (options can be combined): \n");
+ printf(" -id [0,100] maximum pairwise sequence identity (%%) (def=%i) \n",par.max_seqid);
+ printf(" -diff [0,inf[ filter most diverse set of sequences, keeping at least this \n");
+ printf(" many sequences in each block of >50 columns (def=%i)\n",par.Ndiff);
+ printf(" -cov [0,100] minimum coverage with query (%%) (def=%i) \n",par.coverage);
+ printf(" -qid [0,100] minimum sequence identity with query (%%) (def=%i) \n",par.qid);
+ printf(" -qsc [0,100] minimum score per column with query (def=%.1f)\n",par.qsc);
+// printf(" -csc [0,100] minimum score per column with core alignment (def=%-.2f)\n",par.coresc);
+// printf(" -qscc [0,100] minimum score per column of core sequence with query (def=%-.2f)\n",par.qsc_core);
+ printf("\n");
+ printf("Input alignment format: \n");
+ printf(" -M a2m use A2M/A3M (default): upper case = Match; lower case = Insert;\n");
+ printf(" '-' = Delete; '.' = gaps aligned to inserts (may be omitted) \n");
+ printf(" -M first use FASTA: columns with residue in 1st sequence are match states\n");
+ printf(" -M [0,100] use FASTA: columns with fewer than X%% gaps are match states \n");
+ printf("\n");
+ printf("HMM-HMM alignment options: \n");
+ printf(" -glob/-loc global or local alignment mode (def=local) \n");
+ printf(" -alt <int> show up to this number of alternative alignments (def=%i) \n",par.altali);
+ printf(" -vit use Viterbi algorithm for alignment instead of MAC algorithm \n");
+ printf(" -mac use Maximum Accuracy (MAC) alignment (default) \n");
+ printf(" -mact [0,1[ posterior probability threshold for MAC alignment (def=%.3f) \n",par.mact);
+ printf(" A threshold value of 0.0 yields global alignments.\n");
+ printf(" -sto <int> use global stochastic sampling algorithm to sample this many alignments\n");
+ printf(" -excl <range> exclude query positions from the alignment, e.g. '1-33,97-168'\n");
+ printf(" -shift [-1,1] score offset (def=%-.3f) \n",par.shift);
+ printf(" -corr [0,1] weight of term for pair correlations (def=%.2f) \n",par.corr);
+ printf(" -ssm 0-4 0:no ss scoring [default=%i] \n",par.ssm);
+ printf(" 1:ss scoring after alignment \n");
+ printf(" 2:ss scoring during alignment \n");
+ printf(" -ssw [0,1] weight of ss score (def=%-.2f) \n",par.ssw);
+ printf("\n");
+ printf(" -def read default options from ./.hhdefaults or <home>/.hhdefault. \n");
+ printf("\n");
+ printf("Example: %s -i T0187.a3m -t d1hz4a_.hhm -png T0187pdb.png \n",program_name);
+ cout<<endl;
+// printf("More help: \n");
+// printf(" -h out output options \n");
+// printf(" -h hmm options for building HMM from multiple alignment \n");
+// printf(" -h gap options for setting gap penalties \n");
+// printf(" -h ali options for HMM-HMM alignment \n");
+// printf(" -h all all options \n");
+}
+#endif
+
+/**
+ * @brief helpt for output, not accessible in Clustal-Omega
+ */
+#if 0
+void
+help_out()
+{
+ printf("\n");
+ printf("Output options: \n");
+ printf(" -v verbose mode (default: show only warnings) \n");
+ printf(" -v 0 suppress all screen output \n");
+ printf(" -nocons don't show consensus sequence in alignments (default=show) \n");
+ printf(" -nopred don't show predicted 2ndary structure in alignments (default=show) \n");
+ printf(" -nodssp don't show DSSP SS 2ndary structure in alignments (default=show) \n");
+ printf(" -seq [1,inf[ max. number of query/template sequences displayed (def=%i) \n",par.nseqdis);
+ printf(" -aliw [40,..[ number of columns per line in alignment list (def=%i)\n",par.aliwidth);
+ printf(" -P <float> for self-comparison: max p-value of alignments (def=%.2g\n",pself);
+ printf(" -p <float> minimum probability in summary and alignment list (def=%G) \n",par.p);
+ printf(" -E <float> maximum E-value in summary and alignment list (def=%G) \n",par.E);
+ printf(" -Z <int> maximum number of lines in summary hit list (def=%i) \n",par.Z);
+ printf(" -z <int> minimum number of lines in summary hit list (def=%i) \n",par.z);
+ printf(" -B <int> maximum number of alignments in alignment list (def=%i) \n",par.B);
+ printf(" -b <int> minimum number of alignments in alignment list (def=%i) \n",par.b);
+ printf(" -rank int specify rank of alignment to write with -a or -aa option (def=1)\n");
+ printf(" -tc <file> write a TCoffee library file for the pairwise comparison \n");
+ printf(" -tct [0,100] min. probobability of residue pairs for TCoffee (def=%i%%)\n",iround(100*probmin_tc));
+ printf("\n");
+#ifdef PNG
+ printf("Dotplot options:\n");
+ printf(" -dwin int average score in dotplot over window [i-W..i+W] (def=%i) \n",dotW);
+ printf(" -dthr float score threshold for dotplot (default=%.2f) \n",dotthr);
+ printf(" -dsca int size of dot plot box in pixels (default=%i) \n",dotscale);
+ printf(" -dali <list> show alignments with indices in <list> in dot plot\n");
+ printf(" <list> = <index1> ... <indexN> or <list> = all \n");
+ printf(" -dmap <file> print list of coordinates in png plot \n");
+#endif
+}
+#endif
+
+/**
+ * @brief help hit HMM options, not accessible in Clustal-Omega
+ */
+#if 0
+void
+help_hmm()
+{
+ printf("\n");
+ printf("Options to filter input alignment (options can be combined): \n");
+ printf(" -id [0,100] maximum pairwise sequence identity (%%) (def=%i) \n",par.max_seqid);
+ printf(" -diff [0,inf[ filter most diverse set of sequences, keeping at least this \n");
+ printf(" many sequences in each block of >50 columns (def=%i)\n",par.Ndiff);
+ printf(" -cov [0,100] minimum coverage with query (%%) (def=%i) \n",par.coverage);
+ printf(" -qid [0,100] minimum sequence identity with query (%%) (def=%i) \n",par.qid);
+ printf(" -qsc [0,100] minimum score per column with query (def=%.1f)\n",par.qsc);
+// printf(" -csc [0,100] minimum score per column with core alignment (def=%-.2f)\n",par.coresc);
+// printf(" -qscc [0,100] minimum score per column of core sequence with query (def=%-.2f)\n",par.qsc_core);
+ printf(" \n");
+ printf("HMM-building options: \n");
+ printf(" -M a2m use A2M/A3M (default): upper case = Match; lower case = Insert;\n");
+ printf(" '-' = Delete; '.' = gaps aligned to inserts (may be omitted) \n");
+ printf(" -M first use FASTA: columns with residue in 1st sequence are match states\n");
+ printf(" -M [0,100] use FASTA: columns with fewer than X%% gaps are match states \n");
+ printf(" -tags do NOT neutralize His-, C-myc-, FLAG-tags, and \n");
+ printf(" trypsin recognition sequence to background distribution \n");
+ printf(" \n");
+ printf("Pseudocount options: \n");
+ printf(" -Gonnet use the Gonnet substitution matrix (default) \n");
+ printf(" -Blosum50 use the Blosum50 substitution matrix \n");
+ printf(" -Blosum62 use the Blosum62 substitution matrix \n");
+ printf(" -HSDM use the structure-derived HSDM substitution matrix \n");
+ printf(" -pcm 0-3 Pseudocount mode (default=%-i) \n",par.pcm);
+ printf(" tau = substitution matrix pseudocount admixture \n");
+ printf(" 0: no pseudo counts: tau = 0 \n");
+ printf(" 1: constant tau = a \n");
+ printf(" 2: divergence-dependent: tau = a/(1 + ((Neff-1)/b)^c) \n");
+ printf(" Neff=( (Neff_q^d+Neff_t^d)/2 )^(1/d) \n");
+ printf(" Neff_q = av number of different AAs per column in query \n");
+ printf(" 3: column-specific: tau = \'2\' * (Neff(i)/Neff)^(w*Neff/20)\n");
+ printf(" -pca [0,1] set a (overall admixture) (def=%-.1f) \n",par.pca);
+ printf(" -pcb [1,inf[ set b (threshold for Neff) (def=%-.1f) \n",par.pcb);
+ printf(" -pcc [0,3] set c (extinction exponent for tau(Neff)) (def=%-.1f) \n",par.pcc);
+ printf(" -pcw [0,3] set w (weight of pos-specificity for pcs) (def=%-.1f) \n",par.pcw);
+}
+#endif
+
+/**
+ * @brief help with gap handling, not accessible in Clustal-Omega
+ */
+#if 0
+void
+help_gap()
+{
+ printf("\n");
+ printf("Gap cost options: \n");
+ printf(" -gapb [0,inf[ transition pseudocount admixture (def=%-.2f) \n",par.gapb);
+ printf(" -gapd [0,inf[ Transition pseudocount admixture for opening gap (default=%-.2f)\n",par.gapd);
+ printf(" -gape [0,1.5] Transition pseudocount admixture for extending gap (def=%-.1f)\n",par.gape);
+ printf(" -gapf ]0,inf] factor for increasing/reducing the gap open penalty for deletes (def=%-.2f)\n",par.gapf);
+ printf(" -gapg ]0,inf] factor for increasing/reducing the gap open penalty for deletes (def=%-.2f)\n",par.gapg);
+ printf(" -gaph ]0,inf] factor for increasing/reducing the gap extension penalty for deletes(def=%-.2f)\n",par.gaph);
+ printf(" -gapi ]0,inf] factor for increasing/reducing the gap extension penalty for inserts(def=%-.2f)\n",par.gapi);
+ printf(" -egq [0,inf[ penalty (bits) for end gaps aligned to query residues (def=%-.2f)\n",par.egq);
+ printf(" -egt [0,inf[ penalty (bits) for end gaps aligned to template residues (def=%-.2f)\n",par.egt);
+}
+#endif
+
+/**
+ * @brief help with alignment options, not accessible in Clustal-Omega
+ */
+#if 0
+void
+help_ali()
+{
+ printf("\n");
+ printf("Alignment options: \n");
+ printf(" -glob/-loc global or local alignment mode (def=global) \n");
+ printf(" -mac use Maximum Accuracy (MAC) alignment instead of Viterbi\n");
+ printf(" -mact [0,1] posterior prob threshold for MAC alignment (def=%.3f) \n",par.mact);
+ printf(" -sto <int> use global stochastic sampling algorithm to sample this many alignments\n");
+ printf(" -sc <int> amino acid score (tja: template HMM at column j) (def=%i)\n",par.columnscore);
+ printf(" 0 = log2 Sum(tja*qia/pa) (pa: aa background frequencies) \n");
+ printf(" 1 = log2 Sum(tja*qia/pqa) (pqa = 1/2*(pa+ta) ) \n");
+ printf(" 2 = log2 Sum(tja*qia/ta) (ta: av. aa freqs in template) \n");
+ printf(" 3 = log2 Sum(tja*qia/qa) (qa: av. aa freqs in query) \n");
+ printf(" -corr [0,1] weight of term for pair correlations (def=%.2f) \n",par.corr);
+ printf(" -shift [-1,1] score offset (def=%-.3f) \n",par.shift);
+ printf(" -r repeat identification: multiple hits not treated as independent\n");
+ printf(" -ssm 0-2 0:no ss scoring [default=%i] \n",par.ssm);
+ printf(" 1:ss scoring after alignment \n");
+ printf(" 2:ss scoring during alignment \n");
+ printf(" -ssw [0,1] weight of ss score compared to column score (def=%-.2f) \n",par.ssw);
+ printf(" -ssa [0,1] ss confusion matrix = (1-ssa)*I + ssa*psipred-confusion-matrix [def=%-.2f)\n",par.ssa);
+}
+#endif
+
+/**
+ * @brief general help menu, not accessible in Clustal-Omega
+ */
+#if 0
+void
+help_all()
+{
+ help();
+ help_out();
+ help_hmm();
+ help_gap();
+ help_ali();
+ printf("\n");
+ printf("Default options can be specified in './.hhdefaults' or '~/.hhdefaults'\n");
+}
+#endif
+
+/////////////////////////////////////////////////////////////////////////////
+//// Processing input options from command line and .hhdefaults file
+/////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief process arguments from commandline, not accessible from Clustal-Omega
+ */
+#if 0
+void
+ProcessArguments(int argc, char** argv)
+{
+ //Processing command line input
+ for (int i=1; i<argc; i++)
+ {
+ if (v>=4) cout<<i<<" "<<argv[i]<<endl; //PRINT
+ if (!strcmp(argv[i],"-i"))
+ {
+ if (++i>=argc || argv[i][0]=='-')
+ {help(); cerr<<endl<<"Error in "<<program_name<<": no query file following -i\n"; exit(4);}
+ else strcpy(par.infile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-t"))
+ {
+ if (++i>=argc || argv[i][0]=='-')
+ {help(); cerr<<endl<<"Error in "<<program_name<<": no template file following -d\n"; exit(4);}
+ else strcpy(par.tfile,argv[i]); /* FS, ProcessArguments */
+ }
+ else if (!strcmp(argv[i],"-o"))
+ {
+ if (++i>=argc)
+ {help(); cerr<<endl<<"Error in "<<program_name<<": no filename following -o\n"; exit(4);}
+ else strcpy(par.outfile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-ofas"))
+ {
+ par.outformat=1;
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -o\n"; exit(4);}
+ else strcpy(par.pairwisealisfile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-oa2m"))
+ {
+ par.outformat=2;
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -o\n"; exit(4);}
+ else strcpy(par.pairwisealisfile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-oa3m"))
+ {
+ par.outformat=3;
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -o\n"; exit(4);}
+ else strcpy(par.pairwisealisfile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-rank") && (i<argc-1)) par.hitrank=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-Oa3m"))
+ {
+ par.append=0;
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -Oa3m\n"; exit(4);}
+ else strcpy(par.alnfile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-Aa3m"))
+ {
+ par.append=1;
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -Aa3m\n"; exit(4);}
+ else strcpy(par.alnfile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-Ohhm"))
+ {
+ par.append=0;
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -Ohhm\n"; exit(4);}
+ else strcpy(par.hhmfile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-Ahhm"))
+ {
+ par.append=1;
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -Ahhm\n"; exit(4);}
+ else strcpy(par.hhmfile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-Opsi"))
+ {
+ par.append=0;
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -Opsi\n"; exit(4);}
+ else strcpy(par.psifile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-Apsi"))
+ {
+ par.append=1;
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -Apsi\n"; exit(4);}
+ else strcpy(par.psifile,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-png"))
+ {
+ if (++i>=argc)
+ {help(); cerr<<endl<<"Error in "<<program_name<<": no filename following -png\n"; exit(4);}
+ else
+ {
+ pngfile = new(char[strlen(argv[i])+1]);
+ strcpy(pngfile,argv[i]);
+ }
+ }
+ else if (!strcmp(argv[i],"-Struc"))
+ {
+ if (++i>=argc || argv[i][0]=='-')
+ {help(); cerr<<endl<<"Error in "<<program_name<<": no query file following -Struc\n"; exit(4);}
+ else
+ {
+ strucfile = new(char[strlen(argv[i])+1]);
+ strcpy(strucfile,argv[i]);
+ }
+ }
+ else if (!strcmp(argv[i],"-atab") || !strcmp(argv[i],"-Aliout"))
+ {
+ if (++i>=argc || argv[i][0]=='-')
+ {help(); cerr<<endl<<"Error in "<<program_name<<": no query file following -Struc\n"; exit(4);}
+ else
+ {
+ alitabfile = new(char[strlen(argv[i])+1]);
+ strcpy(alitabfile,argv[i]);
+ }
+ }
+ else if (!strcmp(argv[i],"-tc"))
+ {
+ if (++i>=argc || argv[i][0]=='-')
+ {help() ; cerr<<endl<<"Error in "<<program_name<<": no output file following -Opsi\n"; exit(4);}
+ else
+ {
+ tcfile = new(char[strlen(argv[i])+1]);
+ strcpy(tcfile,argv[i]);
+ }
+ }
+ else if (!strcmp(argv[i],"-h")|| !strcmp(argv[i],"--help"))
+ {
+ if (++i>=argc) {help(); exit(0);}
+ if (!strcmp(argv[i],"out")) {help_out(); exit(0);}
+ if (!strcmp(argv[i],"hmm")) {help_hmm(); exit(0);}
+ if (!strcmp(argv[i],"gap")) {help_gap(); exit(0);}
+ if (!strcmp(argv[i],"ali")) {help_ali(); exit(0);}
+ if (!strcmp(argv[i],"all")) {help_all(); exit(0);}
+ else {help(); exit(0);}
+ }
+ else if (!strcmp(argv[i],"-excl"))
+ {
+ if (++i>=argc) {help(); exit(4);}
+ par.exclstr = new(char[strlen(argv[i])+1]);
+ strcpy(par.exclstr,argv[i]);
+ }
+ else if (!strcmp(argv[i],"-v") && (i<argc-1) && argv[i+1][0]!='-' ) v=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-v")) v=2;
+ else if (!strcmp(argv[i],"-v0")) v=0;
+ else if (!strcmp(argv[i],"-v1")) v=1;
+ else if (!strcmp(argv[i],"-v2")) v=2;
+ else if (!strcmp(argv[i],"-v3")) v=3;
+ else if (!strcmp(argv[i],"-v4")) v=4;
+ else if (!strcmp(argv[i],"-v5")) v=5;
+ else if (!strcmp(argv[i],"-P") && (i<argc-1)) pself=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-p") && (i<argc-1)) par.p = atof(argv[++i]);
+ else if (!strcmp(argv[i],"-e") && (i<argc-1)) par.E = atof(argv[++i]);
+ else if (!strcmp(argv[i],"-E") && (i<argc-1)) par.E = atof(argv[++i]);
+ else if (!strcmp(argv[i],"-b") && (i<argc-1)) par.b = atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-B") && (i<argc-1)) par.B = atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-z") && (i<argc-1)) par.z = atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-Z") && (i<argc-1)) par.Z = atoi(argv[++i]);
+ else if (!strncmp(argv[i],"-nocons",7)) par.showcons=0;
+ else if (!strncmp(argv[i],"-nopred",7)) par.showpred=0;
+ else if (!strncmp(argv[i],"-nodssp",7)) par.showdssp=0;
+ else if (!strncmp(argv[i],"-mark",7)) par.mark=1;
+ else if (!strcmp(argv[i],"-seq") && (i<argc-1)) par.nseqdis=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-aliw") && (i<argc-1)) par.aliwidth=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-id") && (i<argc-1)) par.max_seqid=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-tct") && (i<argc-1)) probmin_tc=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-dwin") && (i<argc-1)) dotW=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-dsca") && (i<argc-1)) dotscale=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-dthr") && (i<argc-1)) dotthr=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-dali") && (i<argc-1))
+ {
+ dotali=1;
+ for (int index=0; index<256; index++) aliindices[index]=0;
+ while (i+1<argc && argv[i+1][0]!='-') // adds index to hash aliindices
+ {
+ i++;
+ if (strcmp(argv[i],"all")) aliindices[atoi(argv[i])]=1;
+ else dotali=2;
+ }
+ }
+ else if (!strcmp(argv[i],"-dmap"))
+ {
+ if (++i>=argc)
+ {help(); cerr<<endl<<"Error in "<<program_name<<": no filename following -o\n"; exit(4);}
+ else
+ {
+ dmapfile = new(char[strlen(argv[i])+1]);
+ strcpy(dmapfile,argv[i]);
+ }
+ }
+ else if (!strcmp(argv[i],"-dsat") && (i<argc-1)) dotsat=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-qid") && (i<argc-1)) par.qid=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-qsc") && (i<argc-1)) par.qsc=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-cov") && (i<argc-1)) par.coverage=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-diff") && (i<argc-1)) par.Ndiff=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-qscc") && (i<argc-1)) par.qsc_core=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-csc") && (i<argc-1)) par.coresc=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-Gonnet")) par.matrix=0;
+ else if (!strcmp(argv[i],"-HSDM")) par.matrix=1;
+ else if (!strcmp(argv[i],"-BLOSUM50")) par.matrix=2;
+ else if (!strcmp(argv[i],"-Blosum50")) par.matrix=2;
+ else if (!strcmp(argv[i],"-B50")) par.matrix=2;
+ else if (!strcmp(argv[i],"-BLOSUM62")) par.matrix=3;
+ else if (!strcmp(argv[i],"-Blosum62")) par.matrix=3;
+ else if (!strcmp(argv[i],"-B62")) par.matrix=3;
+ else if (!strcmp(argv[i],"-pcm") && (i<argc-1)) par.pcm=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-pca") && (i<argc-1)) par.pca=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-pcb") && (i<argc-1)) par.pcb=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-pcc") && (i<argc-1)) par.pcc=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-pcw") && (i<argc-1)) par.pcw=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-gapb") && (i<argc-1)) { par.gapb=atof(argv[++i]); if (par.gapb<=0.01) par.gapb=0.01;}
+ else if (!strcmp(argv[i],"-gapd") && (i<argc-1)) par.gapd=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-gape") && (i<argc-1)) par.gape=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-gapf") && (i<argc-1)) par.gapf=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-gapg") && (i<argc-1)) par.gapg=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-gaph") && (i<argc-1)) par.gaph=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-gapi") && (i<argc-1)) par.gapi=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-egq") && (i<argc-1)) par.egq=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-egt") && (i<argc-1)) par.egt=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-ssgap")) par.ssgap=1;
+ else if (!strcmp(argv[i],"-ssgapd") && (i<argc-1)) par.ssgapd=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-ssgape") && (i<argc-1)) par.ssgape=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-ssgapi") && (i<argc-1)) par.ssgapi=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-ssm") && (i<argc-1)) par.ssm=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-ssw") && (i<argc-1)) par.ssw=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-ssa") && (i<argc-1)) par.ssa=atof(argv[++i]);
+ else if (!strncmp(argv[i],"-glo",3)) {par.loc=0; if (par.mact>0.3 && par.mact<0.301) {par.mact=0;} }
+ else if (!strncmp(argv[i],"-loc",3)) par.loc=1;
+ else if (!strncmp(argv[i],"-alt",4) && (i<argc-1)) par.altali=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-map") || !strcmp(argv[i],"-MAP")) par.forward=2;
+ else if (!strcmp(argv[i],"-mac") || !strcmp(argv[i],"-MAC")) par.forward=2;
+ else if (!strcmp(argv[i],"-vit")) par.forward=0;
+ else if (!strcmp(argv[i],"-sto") && (i<argc-1)) {Nstochali=atoi(argv[++i]); par.forward=1;}
+ else if (!strcmp(argv[i],"-r")) par.repmode=1;
+ else if (!strcmp(argv[i],"-M") && (i<argc-1))
+ if (!strcmp(argv[++i],"a2m") || !strcmp(argv[i],"a3m")) par.M=1;
+ else if(!strcmp(argv[i],"first")) par.M=3;
+ else if (argv[i][0]>='0' && argv[i][0]<='9') {par.Mgaps=atoi(argv[i]); par.M=2;}
+ else cerr<<endl<<"WARNING: Ignoring unknown argument: -M "<<argv[i]<<"\n";
+ else if (!strcmp(argv[i],"-shift") && (i<argc-1)) par.shift=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-mact") && (i<argc-1)) {par.mact=atof(argv[++i]); par.forward=2;}
+ else if (!strcmp(argv[i],"-wstruc") && (i<argc-1)) par.wstruc=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-opt") && (i<argc-1)) par.opt=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-sc") && (i<argc-1)) par.columnscore=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-corr") && (i<argc-1)) par.corr=atof(argv[++i]);
+ else if (!strcmp(argv[i],"-def")) par.readdefaultsfile=1;
+ else if (!strcmp(argv[i],"-ovlp") && (i<argc-1)) par.min_overlap=atoi(argv[++i]);
+ else if (!strcmp(argv[i],"-tags")) par.notags=0;
+ else if (!strcmp(argv[i],"-notags")) par.notags=1;
+ else cerr<<endl<<"WARNING: Ignoring unknown option "<<argv[i]<<" ...\n";
+ if (v>=4) cout<<i<<" "<<argv[i]<<endl; //PRINT
+ } // end of for-loop for command line input
+}
+#endif
+
+
+
+
+/////////////////////////////////////////////////////////////////////////////
+//// MAIN PROGRAM
+/////////////////////////////////////////////////////////////////////////////
+/**
+ *
+ * hhalign()
+ *
+ * @param[in,out] ppcFirstProf
+ * first profile to be aligned
+ * @param[in] iFirstCnt
+ * number of sequences in 1st profile
+ * @param[in,out] ppcSecndProf
+ * second profile to be aligned
+ * @param[in] iSecndCnt
+ * number of sequences in 2nd profile
+ * @param[out] dScore_p
+ * score of alignment
+ * @param[in] prHMM
+ * HMM info of external HMM (background)
+ * @param[in] pcPrealigned1
+ * (gapped) 1st sequence aligned to background HMM
+ * @param[in] pcRepresent1
+ * (gapped) sequence representing background HMM aligned to 1st sequence
+ * @param[in] pcPrealigned2
+ * (gapped) 2nd sequence aligned to background HMM
+ * @param[in] pcRepresent2
+ * (gapped) sequence representing background HMM aligned to 2nd sequence
+ * @param[in] rHhalignPara,
+ * various parameters passed down from commandline
+ * e.g., iMaxRamMB
+ *
+ * iFlag,zcAux,zcError are debugging arguments
+ *
+ * @return Non-zero on error
+ */
+extern "C" int
+hhalign(char **ppcFirstProf, int iFirstCnt, double *pdWeightsL,
+ char **ppcSecndProf, int iSecndCnt, double *pdWeightsR,
+ double *dScore_p, hmm_light *prHMM,
+ char *pcPrealigned1, char *pcRepresent1,
+ char *pcPrealigned2, char *pcRepresent2,
+ hhalign_para rHhalignPara,
+ int iFlag,
+ char zcAux[], char zcError[]) {
+
+
+#ifdef CLUSTALO
+ int iRetVal = RETURN_OK;
+ iAux_GLOBAL = iFlag;
+#ifndef CLUSTALO_NOFILE
+ int argc = 0;
+ char **argv = NULL;
+ argv = (char **)malloc(argc*sizeof(char *));
+ for (int i = 0; i < argc; i++){
+ argv[i] = (char *)malloc(100);
+ }
+ strcpy(argv[0], "./hhalign");
+ strcpy(argv[1], "-t");
+ strcpy(argv[2], "hhalign.C");
+ strcpy(argv[3], "-i");
+ strcpy(argv[4], "hhalign.C");
+ strcpy(argv[5], "-ofas");
+ strcpy(argv[6], "out");
+#endif
+#endif
+ /*char* argv_conf[MAXOPT];*/ /* Input arguments from .hhdefaults file
+ (first=1: argv_conf[0] is not used) */
+ /*int argc_conf;*/ // Number of arguments in argv_conf
+ /*char inext[IDLEN]="";*/ // Extension of query input file (hhm or a3m)
+ /*char text[IDLEN]="";*/ // Extension of template input file (hhm or a3m)
+ /*int** ali=NULL;*/ // ali[i][j]=1 if (i,j) is part of an alignment
+ /*int** alisto=NULL;*/ // ali[i][j]=1 if (i,j) is part of an alignment
+ int Nali; /* number of normally backtraced alignments
+ in dot plot */
+
+ SetDefaults();
+ strcpy(par.tfile,""); /* FS, Initialise Argument */
+ strcpy(par.alnfile,"");
+ par.p=0.0 ; /* minimum threshold for inclusion in hit list
+ and alignment listing */
+ par.E=1e6; /* maximum threshold for inclusion in hit list
+ and alignment listing */
+ par.b=1; // min number of alignments
+ par.B=100; // max number of alignments
+ par.z=1; // min number of lines in hit list
+ par.Z=100; // max number of lines in hit list
+ par.append=0; /* append alignment to output file
+ with -a option */
+ par.altali=1; /* find only ONE (possibly overlapping)
+ subalignment */
+ par.hitrank=0; /* rank of hit to be printed as a3m alignment
+ (default=0) */
+ par.outformat=3; // default output format for alignment is a3m
+ hit.self=0; // no self-alignment
+ par.forward=2; /* 0: Viterbi algorithm;
+ 1: Viterbi+stochastic sampling;
+ 2:Maximum Accuracy (MAC) algorithm */
+
+ // Make command line input globally available
+#ifndef CLUSTALO_NOFILE
+ par.argv=argv;
+ par.argc=argc;
+ RemovePathAndExtension(program_name,argv[0]);
+#endif
+
+#ifndef CLUSTALO_NOFILE
+ /* Enable changing verbose mode before defaults file
+ and command line are processed */
+ for (int i=1; i<argc; i++)
+ {
+ if (!strcmp(argv[i],"-def")) par.readdefaultsfile=1;
+ else if (argc>1 && !strcmp(argv[i],"-v0")) v=0;
+ else if (argc>1 && !strcmp(argv[i],"-v1")) v=1;
+ else if (argc>2 && !strcmp(argv[i],"-v")) v=atoi(argv[i+1]);
+ }
+
+ // Read .hhdefaults file?
+ if (par.readdefaultsfile)
+ {
+ // Process default otpions from .hhconfig file
+ ReadDefaultsFile(argc_conf,argv_conf);
+ ProcessArguments(argc_conf,argv_conf);
+ }
+#endif
+ /* Process command line options
+ (they override defaults from .hhdefaults file) */
+#ifndef CLUSTALO_NOFILE
+ ProcessArguments(argc,argv);
+#endif
+
+
+#ifdef CLUSTALO
+ int iAuxLen1 = strlen(ppcFirstProf[0]);
+ int iAuxLen2 = strlen(ppcSecndProf[0]);
+ if ( (0 == iAuxLen1) || (0 == iAuxLen2) ){ /* problem with empty profiles, FS, r249 -> r250 */
+ sprintf(zcError, "%s:%s:%d: strlen(prof1)=%d, strlen(prof2)=%d -- Nothing to align!\n",
+ __FUNCTION__, __FILE__, __LINE__, iAuxLen1, iAuxLen2);
+ iRetVal = RETURN_UNKNOWN;
+ /* Note: at this stage cannot do 'goto this_is_the_end;'
+ because would cross initialisation of several variables */
+ return iRetVal;
+ }
+ par.maxResLen = iAuxLen1 > iAuxLen2 ? iAuxLen1 : iAuxLen2;
+ const int ciGoodMeasureSeq = 10;
+ par.maxResLen += ciGoodMeasureSeq;
+ par.maxColCnt = iAuxLen1 + iAuxLen2 + ciGoodMeasureSeq;
+ //par.max_seqid=iFirstCnt+iSecndCnt+3; /* -id */
+ par.max_seqid=DEFAULT_FILTER; /* -id */
+ par.loc=0; par.mact=0; /* -glob */
+ par.nseqdis=iFirstCnt+iSecndCnt; /* -seq */
+ par.showcons=0; /* -nocons */
+ par.showdssp=0; /* -nodssp */
+ par.Mgaps=100; /* -M */
+ par.M=2; /* -M */
+ par.pdWg1=pdWeightsL; /* tree wg */
+ par.pdWg2=pdWeightsR; /* tree wg */
+ v = 0; /* -v0 */
+ /* NOTE: *qali declared globally but only created here,
+ pass in number of sequences to get rid of statically
+ defined MAXSEQ (FS)
+ */
+ Alignment qali(iFirstCnt+iSecndCnt);
+ HMM q(iFirstCnt+iSecndCnt);
+ HMM t(iFirstCnt+iSecndCnt);
+#endif
+
+
+#ifndef CLUSTALO_NOFILE
+ // Check command line input and default values
+ if (!*par.infile)
+ {help(); cerr<<endl<<"Error in "<<program_name<<": no query alignment file given (-i file)\n"; exit(4);}
+ if (par.forward==2 && par.loc==0)
+ {
+ if (par.mact<0.301 || par.mact>0.300)
+ if (v>=1) fprintf(stderr,"REMARK: in -mac -global mode -mact is forced to 0\n");
+ par.mact=0;
+ // par.loc=1; // global forward-backward algorithm seems to work fine! use it in place of local version.
+ }
+
+ // Get rootname (no directory path, no extension) and extension of infile
+ RemoveExtension(q.file,par.infile);
+ RemoveExtension(t.file,par.tfile); /* FS, NOFILE2 (commented out) */
+ Extension(inext,par.infile);
+ Extension(text,par.tfile); /*FS, NOFILE2 (commented out) */
+
+ // Check option compatibilities
+ if (par.nseqdis>MAXSEQDIS-3-par.showcons) par.nseqdis=MAXSEQDIS-3-par.showcons; //3 reserved for secondary structure
+ if (par.aliwidth<20) par.aliwidth=20;
+ if (par.pca<0.001) par.pca=0.001; // to avoid log(0)
+ if (par.b>par.B) par.B=par.b;
+ if (par.z>par.Z) par.Z=par.z;
+ if (par.hitrank>0) par.altali=0;
+
+ // Input parameters
+ if (v>=3)
+ {
+ cout<<"query file : "<<par.infile<<"\n";
+ cout<<"template file: "<<par.tfile<<"\n";/*FS, NOFILE2 (commented out) */
+ cout<<"Output file: "<<par.outfile<<"\n";
+ cout<<"Alignment file: "<<par.alnfile<<"\n";
+ }
+#endif /* NOFILE2 */
+
+
+ // Set (global variable) substitution matrix and derived matrices
+ SetSubstitutionMatrix();
+
+
+ // Set secondary structure substitution matrix
+ SetSecStrucSubstitutionMatrix();
+
+
+ /* moved Viterbi switch from after RnP() to here,
+ switch after RnP() ineffectual as RnP decides log/lin of transition,
+ however log/lin of transitions depends on MAC/Viterbi,
+ FS, r228 -> r229 */
+ int qL, tL;
+ if (iFirstCnt > 0) {
+ qL = strlen(ppcFirstProf[0]);
+ }
+ else {
+ qL = prHMM->L;
+ }
+ if (iSecndCnt > 0) {
+ tL = strlen(ppcSecndProf[0]);
+ }
+ else {
+ tL = prHMM->L;
+ }
+
+
+ // const float MEMSPACE_DYNPROG = 512*1024*1024;
+ /* determine amount of memory available for MAC on command-line; FS, r240 -> r241 */
+ const float MEMSPACE_DYNPROG = (double)1024*1024*rHhalignPara.iMacRamMB;
+ // longest allowable length of database HMM
+ int Lmaxmem=(int)((float)MEMSPACE_DYNPROG/qL/6/8);
+ if (par.forward==2 && tL+2>=Lmaxmem) {
+ if (v>=1)
+ cerr<<"WARNING: Not sufficient memory to realign with MAC algorithm. Using Viterbi algorithm."<<endl;
+ par.forward=0;
+
+ /* use different 'fudge' parameters for Viterbi, FS, r228 -> r229 */
+ par.pca = par.pcaV;
+ par.pcb = par.pcbV;
+ par.pcc = par.pccV;
+ par.pcw = par.pcwV;
+
+ par.gapb = par.gapbV;
+ par.gapd = par.gapdV;
+ par.gape = par.gapeV;
+ par.gapf = par.gapfV;
+ par.gapg = par.gapgV;
+ par.gaph = par.gaphV;
+ par.gapi = par.gapiV;
+
+ }
+
+
+ // Read input file (HMM, HHM, or alignment format), and add pseudocounts etc.
+ q.cQT = 'q';
+ if (OK != ReadAndPrepare(INTERN_ALN_2_HMM,
+ ppcFirstProf, iFirstCnt, prHMM,
+ pcPrealigned1, pcRepresent1, pdWeightsL,
+ (char*)(""), q, &qali)) {
+ sprintf(zcError, "%s:%s:%d: Problem Reading/Preparing q-profile (len=%d)\n",
+ __FUNCTION__, __FILE__, __LINE__, qL);
+ iRetVal = RETURN_FROM_RNP;
+ goto this_is_the_end;
+ }
+ // Set query columns in His-tags etc to Null model distribution
+ if (par.notags) q.NeutralizeTags();
+
+ // Do self-comparison?
+ if (0 /* !*par.tfile // FS, 2010-03-10 */)
+ {
+ // Deep-copy q into t
+ t = q;
+
+ // Find overlapping alternative alignments
+ hit.self=1;
+ }
+ // Read template alignment/HMM t and add pseudocounts
+ else
+ {
+ char infile[] = "";
+ /* Read input file (HMM, HHM, or alignment format),
+ and add pseudocounts etc. */
+ t.cQT = 't';
+ if (OK != ReadAndPrepare(INTERN_ALN_2_HMM,
+ ppcSecndProf, iSecndCnt, prHMM,
+ pcPrealigned2, pcRepresent2, pdWeightsR,
+ infile, t)) {
+ sprintf(zcError, "%s:%s:%d: Problem Reading/Preparing t-profile (len=%d)\n",
+ __FUNCTION__, __FILE__, __LINE__, tL);
+ iRetVal = RETURN_FROM_RNP;
+ goto this_is_the_end;
+ }
+ }
+
+ // Factor Null model into HMM t
+ t.IncludeNullModelInHMM(q,t);
+
+ /* switch at this stage is ineffectual as log/lin already decided in RnP().
+ FS, r228 -> r229 */
+ /*const float MEMSPACE_DYNPROG = 512*1024*1024;
+ // longest allowable length of database HMM
+ int Lmaxmem=(int)((float)MEMSPACE_DYNPROG/q.L/6/8);
+ if (par.forward==2 && t.L+2>=Lmaxmem)
+ {
+ if (v>=1)
+ cerr<<"WARNING: Not sufficient memory to realign with MAC algorithm. Using Viterbi algorithm."<<endl;
+ par.forward=0;
+ }*/
+
+ // Allocate memory for dynamic programming matrix
+ hit.AllocateBacktraceMatrix(q.L+2,t.L+2); // ...with a separate dynamic programming matrix (memory!!)
+ if (par.forward>=1 || Nstochali)
+ hit.AllocateForwardMatrix(q.L+2,t.L+2);
+ if (par.forward==2)
+ hit.AllocateBackwardMatrix(q.L+2,t.L+2);
+
+#ifndef CLUSTALO_NOFILE
+ // Read structure file for Forward() function?
+ if (strucfile && par.wstruc>0)
+ {
+ float PMIN=1E-20;
+ Pstruc = new(float*[q.L+2]);
+ for (int i=0; i<q.L+2; i++) Pstruc[i] = new(float[t.L+2]);
+ Sstruc = new(float*[q.L+2]);
+ for (int i=0; i<q.L+2; i++) Sstruc[i] = new(float[t.L+2]);
+ FILE* strucf=NULL;
+ if (strcmp(strucfile,"stdin"))
+ {
+ strucf = fopen(strucfile, "r");
+ if (!strucf) OpenFileError(strucfile);
+ }
+ else
+ {
+ strucf = stdin;
+ if (v>=2) printf("Reading structure matrix from standard input ... (for UNIX use ^D for 'end-of-file')\n");
+ }
+ for (int i=1; i<=q.L; i++)
+ {
+ for (int j=1; j<=t.L; j++)
+ {
+ float f;
+ if (fscanf(strucf,"%f",&f) <=0 )
+ {
+ fprintf(stderr,"Error: too few numbers in file %s while reading line %i, column %i\n",strucfile,i,j);
+ exit(1);
+ }
+ if (par.wstruc==1)
+ Pstruc[i][j]=fmax(f,PMIN);
+ else
+ Pstruc[i][j]=fmax(pow(f,par.wstruc),PMIN);
+// printf("%10.2E ",f);
+ Sstruc[i][j] = par.wstruc * log2(f);
+ }
+// printf("\n");
+ }
+ fclose(strucf);
+ } /* (strucfile && par.wstruc>0) */
+#endif
+
+ /* Do (self-)comparison, store results if score>SMIN,
+ and try next best alignment */
+ /* FIXME very ambigous and possibly faulty if-else */
+ if (v>=2) {
+ if (par.forward==2) {
+ printf("Using maximum accuracy (MAC) alignment algorithm ...\n");
+ }
+ else if (par.forward==0) {
+ printf("Using Viterbi algorithm ...\n");
+ }
+ else if (par.forward==1) {
+ printf("Using stochastic sampling algorithm ...\n");
+ }
+ else {
+ printf("\nWhat alignment algorithm are we using??\n");
+ }
+ }
+
+
+ for (hit.irep=1; hit.irep<=imax(par.hitrank,par.altali); hit.irep++)
+ {
+ if (par.forward==0)
+ {
+ // generate Viterbi alignment
+ hit.Viterbi(q,t,Sstruc);
+ hit.Backtrace(q,t);
+ }
+ else if (par.forward==1)
+ {
+ // generate a single stochastically sampled alignment
+ hit.Forward(q,t,Pstruc);
+ srand( time(NULL) ); // initialize random generator
+ hit.StochasticBacktrace(q,t);
+ hitlist.Push(hit); /* insert hit at beginning of list
+ (last repeats first!) */
+ (hit.irep)++;
+ break;
+ }
+ else if (par.forward==2)
+ {
+ // generate forward alignment
+ if (OK != hit.Forward(q,t,Pstruc)){
+ fprintf(stderr, "%s:%s:%d: cannot complete hit.Forward\n",
+ __FUNCTION__, __FILE__, __LINE__);
+ iRetVal = RETURN_FROM_MAC; /* spot double overflow in Forward(). FS, r241 -> r243 */
+ goto this_is_the_end;
+ }
+ if (OK != hit.Backward(q,t)){
+ fprintf(stderr, "%s:%s:%d: cannot complete hit.backward\n",
+ __FUNCTION__, __FILE__, __LINE__);
+ iRetVal = RETURN_FROM_MAC; /* spot double overflow in hit.Backward(). FS, r241 -> r243 */
+ goto this_is_the_end;
+ }
+ hit.MACAlignment(q,t);
+ if ((isnan(hit.score)) || (isnan(hit.Pforward))){
+ printf("nan after MAC\n");
+ }
+ hit.BacktraceMAC(q,t);
+ if ((isnan(hit.score)) || (isnan(hit.Pforward))){
+ printf("nan after backtrace\n");
+ }
+ } /* use MAC algorithm */
+ // printf ("%-12.12s %-12.12s irep=%-2i score=%6.2f hit.Pvalt=%.2g\n",hit.name,hit.fam,hit.irep,hit.score,hit.Pvalt);
+ *dScore_p = hit.score;
+
+ if (hit.irep<=par.hitrank || hit.score>SMIN || (hit.Pvalt<pself && hit.score>0 ))
+ hitlist.Push(hit); // insert hit at beginning of list (last repeats first!) and do next alignment
+ else
+ {
+ if (hit.irep==1) hitlist.Push(hit); // first hit will be inserted into hitlist anyway, even if not significant
+ hit = hitlist.ReadLast(); // last alignment was not significant => read last (significant) hit from list
+ break;
+ /* FIXME: memory leak during normal alignment: both push'es above are not freed:
+ * valgrind --leak-check=full --show-reachable=yes ./src/clustalo -i ~/void/protein.fa -o /dev/null -v
+ ==9506== 1,456 bytes in 1 blocks are still reachable in loss record 4 of 5
+ ==9506== at 0x4C2726C: operator new(unsigned long) (vg_replace_malloc.c:230)
+ ==9506== by 0x4618C5: List<Hit>::Push(Hit) (list-C.h:134)
+ ==9506== by 0x45E87A: hhalign (hhalign.cpp:914)
+ ==9506== by 0x413F8C: HhalignWrapper (hhalign_wrapper.c:405)
+ ==9506== by 0x41A7B5: MyMain (mymain.c:676)
+ ==9506== by 0x4031A6: main (main.cpp:37)
+ ==9506==
+ ==9506==
+ ==9506== 4,442 (4,368 direct, 74 indirect) bytes in 3 blocks are definitely lost in loss record 5 of 5
+ ==9506== at 0x4C2726C: operator new(unsigned long) (vg_replace_malloc.c:230)
+ ==9506== by 0x4618C5: List<Hit>::Push(Hit) (list-C.h:134)
+ ==9506== by 0x45E7C0: hhalign (hhalign.cpp:911)
+ ==9506== by 0x413F8C: HhalignWrapper (hhalign_wrapper.c:405)
+ ==9506== by 0x41A7B5: MyMain (mymain.c:676)
+ ==9506== by 0x4031A6: main (main.cpp:37)
+ */
+ }
+ } /* 1 <= hit.irep <= imax(par.hitrank,par.altali) */
+ Nali = hit.irep;
+
+
+#ifndef CLUSTALO_NOFILE
+ // Write posterior probability matrix as TCoffee library file
+ if (tcfile)
+ {
+ if (v>=2) printf("Writing TCoffee library file to %s\n",tcfile);
+ int i,j;
+ FILE* tcf=NULL;
+ if (strcmp(tcfile,"stdout")) tcf = fopen(tcfile, "w"); else tcf = stdout;
+ if (!tcf) OpenFileError(tcfile);
+ fprintf(tcf,"! TC_LIB_FORMAT_01\n");
+ fprintf(tcf,"%i\n",2); // two sequences in library file
+ fprintf(tcf,"%s %i %s\n",q.name,q.L,q.seq[q.nfirst]+1);
+ fprintf(tcf,"%s %i %s\n",hit.name,hit.L,hit.seq[hit.nfirst]+1);
+ fprintf(tcf,"#1 2\n");
+ for (i=1; i<=q.L; i++) // print all pairs (i,j) with probability above PROBTCMIN
+ for (j=1; j<=t.L; j++)
+ if (hit.B_MM[i][j]>probmin_tc)
+ fprintf(tcf,"%5i %5i %5i\n",i,j,iround(100.0*hit.B_MM[i][j]));
+ for (int step=hit.nsteps; step>=1; step--) // print all pairs on MAC alignment which were not yet printed
+ {
+ i=hit.i[step]; j=hit.j[step];
+ // printf("%5i %5i %5i %i\n",i,j,iround(100.0*hit.B_MM[i][j]),hit.states[step]);
+ if (hit.states[step]>=MM && hit.B_MM[i][j]<=probmin_tc)
+ fprintf(tcf,"%5i %5i %5i\n",i,j,iround(100.0*hit.B_MM[i][j]));
+ }
+
+
+ fprintf(tcf,"! SEQ_1_TO_N\n");
+ fclose(tcf);
+ // for (i=1; i<=q.L; i++)
+ // {
+ // double sum=0.0;
+ // for (j=1; j<=t.L; j++) sum+=hit.B_MM[i][j];
+ // printf("i=%-3i sum=%7.4f\n",i,sum);
+ // }
+ // printf("\n");
+ } /* if (tcfile) */
+
+ // Write last alignment into alitabfile
+ if (alitabfile)
+ {
+ FILE* alitabf=NULL;
+ if (strcmp(alitabfile,"stdout")) alitabf = fopen(alitabfile, "w"); else alitabf = stdout;
+ if (!alitabf) OpenFileError(alitabfile);
+ if (par.forward==2)
+ {
+ fprintf(alitabf," i j score SS probab\n");
+ for (int step=hit.nsteps; step>=1; step--)
+ if (hit.states[step]>=MM)
+ fprintf(alitabf,"%5i %5i %6.2f %6.2f %7.4f\n",hit.i[step],hit.j[step],hit.S[step],hit.S_ss[step],hit.P_posterior[step]);
+ }
+ else
+ {
+ fprintf(alitabf," i j score SS\n");
+ for (int step=hit.nsteps; step>=1; step--)
+ if (hit.states[step]>=MM)
+ fprintf(alitabf,"%5i %5i %6.2f %6.2f\n",hit.i[step],hit.j[step],hit.S[step],hit.S_ss[step]);
+ }
+ fclose(alitabf);
+ } /* if (alitabfile) */
+#endif
+
+ // Do Stochastic backtracing?
+ if (par.forward==1)
+ for (int i=1; i<Nstochali; i++)
+ {
+ hit.StochasticBacktrace(q,t);
+ hitlist.Push(hit); //insert hit at beginning of list (last repeats first!)
+ (hit.irep)++;
+ }
+ else // Set P-value, E-value and probability
+ {
+ if (q.mu) hitlist.GetPvalsFromCalibration(q);
+ else if (t.mu) hitlist.GetPvalsFromCalibration(t);
+ }
+
+ // Print FASTA or A2M alignments?
+#ifndef CLUSTALO_NOFILE
+ if (*par.pairwisealisfile)
+#endif
+ {
+ if (v>=2) {
+ cout<<"Printing alignments in " <<
+ (par.outformat==1? "FASTA" : par.outformat==2?"A2M" :"A3M") <<
+ " format to "<<par.pairwisealisfile<<"\n";
+ }
+ int iPrAliRtn = hitlist.PrintAlignments(
+#ifdef CLUSTALO
+ ppcFirstProf, ppcSecndProf,
+#endif
+ q, par.pairwisealisfile, par.outformat);
+ if (OK != iPrAliRtn){
+ fprintf(stderr, "%s:%s:%d: Could not print alignments\n",
+ __FUNCTION__, __FILE__, __LINE__);
+ iRetVal = RETURN_FROM_PRINT_ALI; /* this is where mis-alignment was originally spotted,
+ hope to trap it now earlier. FS, r241 -> r243 */
+ goto this_is_the_end;
+ }
+ } /* if (*par.pairwisealisfile) */
+
+#ifndef CLUSTALO_NOFILE
+ // Print hit list and alignments
+ if (*par.outfile)
+ {
+ hitlist.PrintHitList(q, par.outfile);
+ hitlist.PrintAlignments(
+#ifdef CLUSTALO
+ ppcFirstProf, ppcSecndProf,
+#endif
+ q, par.outfile);
+ if (v>=2) {
+ WriteToScreen(par.outfile,1000); //write only hit list to screen
+ }
+ }
+#endif
+
+
+ ///////////////////////////////////////////////////////////////////////
+#ifndef CLUSTALO_NOFILE
+ // Show results for hit with rank par.hitrank
+ if (par.hitrank==0) hit=hitlist.Read(1); else hit=hitlist.Read(par.hitrank);
+
+ // Generate output alignment or HMM file?
+ if (*par.alnfile || *par.psifile || *par.hhmfile)
+ {
+ if (par.append==0)
+ {
+ if (v>=2 && *par.alnfile) printf("Merging template to query alignment and writing resulting alignment in A3M format to %s...\n",par.alnfile);
+ if (v>=2 && *par.psifile) printf("Merging template to query alignment and writing resulting alignment in PSI format to %s...\n",par.psifile);
+ }
+ else
+ {
+ if (v>=2 && *par.alnfile) printf("Merging template to query alignment and appending template alignment in A3M format to %s...\n",par.alnfile);
+ if (v>=2 && *par.psifile) printf("Merging template to query alignment and appending template alignment in PSI format to %s...\n",par.psifile);
+ }
+
+ // Read query alignment into Qali
+ Alignment Qali; // output A3M generated by merging A3M alignments for significant hits to the query alignment
+ char qa3mfile[NAMELEN];
+ RemoveExtension(qa3mfile,par.infile); // directory??
+ strcat(qa3mfile,".a3m");
+ FILE* qa3mf=fopen(qa3mfile,"r");
+ if (!qa3mf) OpenFileError(qa3mfile);
+ Qali.Read(qa3mf,qa3mfile);
+ fclose(qa3mf);
+
+ // Align query with template in master-slave mode
+ Qali.MergeMasterSlave(hit,par.tfile); /*FS, NOFILE2 (commented out) */
+
+ // Write output A3M alignment?
+ if (*par.alnfile) {
+ Qali.WriteToFile(par.alnfile,"a3m");
+ }
+
+ if (*par.psifile)
+ {
+ /* Convert ASCII to int (0-20),throw out all insert states,
+ record their number in I[k][i] */
+ Qali.Compress("merged A3M file");
+
+ // Write output PSI-BLAST-formatted alignment?
+ Qali.WriteToFile(par.psifile,"psi");
+ }
+ } /* if (*par.alnfile || *par.psifile || *par.hhmfile) */
+#endif /* NOFILE2 */
+ //////////////////////////////////////////////////////////////////////////
+
+
+
+
+ // double log2Pvalue;
+ // if (par.ssm && (par.ssm1 || par.ssm2))
+ // {
+ // log2Pvalue=hit.logPval/0.693147181+0.45*(4.0*par.ssw/0.15-hit.score_ss);
+ // if (v>=2)
+ // printf("Aligned %s with %s:\nApproximate P-value INCLUDING SS SCORE = %7.2g\n",q.name,t.name,pow(2.0,log2Pvalue));
+ // } else {
+ // if (v>=2)
+ // printf("Aligned %s with %s:\nApproximate P-value (without SS score) = %7.2g\n",q.name,t.name,hit.Pval);
+ // }
+
+ if (v>=2)
+ {
+ if (par.hitrank==0)
+ printf("Aligned %s with %s: Score = %-7.2f P-value = %-7.2g\n",
+ q.name,t.name,hit.score,hit.Pval);
+ else
+ printf("Aligned %s with %s (rank %i): Score = %-7.2f P-value = %-7.2g\n",
+ q.name,t.name,par.hitrank,hit.score,hit.Pval);
+ }
+
+
+ this_is_the_end:
+
+ // Delete memory for dynamic programming matrix
+ hit.DeleteBacktraceMatrix(q.L+2);
+ if (par.forward>=1 || Nstochali)
+ hit.DeleteForwardMatrix(q.L+2);
+ if (par.forward==2)
+ hit.DeleteBackwardMatrix(q.L+2);
+ /* if (Pstruc) {
+ for (int i=0; i<q.L+2; i++) delete[](Pstruc[i]); delete[](Pstruc);}
+ */
+
+ // Delete content of hits in hitlist
+ hitlist.Reset();
+ while (!hitlist.End())
+ hitlist.ReadNext().Delete(); // Delete content of hit object
+
+ if (strucfile && par.wstruc>0)
+ {
+ for (int i=0; i<q.L+2; i++){
+ delete[] Pstruc[i]; Pstruc[i] = NULL;
+ }
+ delete[] Pstruc; Pstruc = NULL;
+ for (int i=0; i<q.L+2; i++){
+ delete[] Sstruc[i]; Sstruc[i] = NULL;
+ }
+ delete[] Sstruc; Sstruc = NULL;
+ delete[] strucfile; strucfile = NULL;
+ }
+
+ if (pngfile){
+ delete[] pngfile; pngfile = NULL;
+ }
+ if (alitabfile){
+ delete[] alitabfile; alitabfile = NULL;
+ }
+ if (tcfile){
+ delete[] tcfile; tcfile = NULL;
+ }
+ if (par.exclstr){
+ delete[] par.exclstr; par.exclstr = NULL;
+ }
+
+#ifndef CLUSTALO_NOFILE
+ // Print 'Done!'
+ FILE* outf=NULL;
+ if (!strcmp(par.outfile,"stdout")) printf("Done!\n");
+ else
+ {
+ if (*par.outfile)
+ {
+ outf=fopen(par.outfile,"a"); //open for append
+ fprintf(outf,"Done!\n");
+ fclose(outf);
+ }
+ if (v>=2) printf("Done\n");
+ }
+#endif
+
+ //qali.ClobberGlobal();
+ hit.ClobberGlobal();
+ if (iFirstCnt > 0){
+ q.ClobberGlobal();
+ }
+ if (iSecndCnt > 0){
+ t.ClobberGlobal();
+ }
+ hitlist.ClobberGlobal();
+
+ return iRetVal;
+
+} /* this is the end of hhalign() //end main */
+
+//////////////////////////////////////////////////////////////////////////////
+// END OF MAIN
+//////////////////////////////////////////////////////////////////////////////
+
+/*
+ * EOF hhalign.C
+ */
+
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhalign.h 241 2011-05-04 14:37:17Z fabian $
+ */
+
+
+extern int
+hhalign(char **ppcFirstProf, int iFirstCnt, double *pdWeightsL,
+ char **ppcSecndProf, int iSecndCnt, double *pdWeightsR,
+ double *dScore_p, hmm_light *prHMM,
+ char *pcPrealigned1, char *pcRepresent1,
+ char *pcPrealigned2, char *pcRepresent2,
+ hhalign_para rHhalignPara,
+ int iFlag,
+ char zcAux[], char zcError[]);
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhalignment-C.h 236 2011-04-14 11:30:04Z fabian $
+ */
+
+
+/*
+ * Changelog: Michael Remmert made changes to hhalign stand-alone code
+ * FS implemented some of the changes on 2010-10-28 -> MR1
+ *
+ * Note: MR seems to have changed all [aijk]++ to ++[aijk],
+ * FS did not do that on 2010-10-28
+ */
+
+// hhalignment.C
+
+//////////////////////////////////////////////////////////////////////////////
+//// Class Alignment
+//////////////////////////////////////////////////////////////////////////////
+
+// hhalignment.C
+
+#ifndef MAIN
+#define MAIN
+#include <iostream> // cin, cout, cerr
+#include <fstream> // ofstream, ifstream
+#include <stdio.h> // printf
+using std::cout;
+using std::cerr;
+using std::endl;
+using std::ios;
+using std::ifstream;
+using std::ofstream;
+#include <stdlib.h> // exit
+#include <string> // strcmp, strstr
+#include <math.h> // sqrt, pow
+#include <limits.h> // INT_MIN
+#include <float.h> // FLT_MIN
+#include <time.h> // clock
+#include <ctype.h> // islower, isdigit etc
+#include "util-C.h" // imax, fmax, iround, iceil, ifloor, strint, strscn, strcut, substr, uprstr, uprchr, Basename etc.
+#include "list.h" // list data structure
+#include "hash.h" // hash data structure
+#include "hhdecl-C.h"
+#include "hhutil-C.h" // imax, fmax, iround, iceil, ifloor, strint, strscn, strcut, substr, uprstr, uprchr, Basename etc.
+#include "hhhmm.h"
+#endif
+
+
+enum {KEEP_NOT = 0, KEEP_CONDITIONALLY, KEEP_ALWAYS};
+
+//////////////////////////////////////////////////////////////////////////////
+// Class Alignment
+//////////////////////////////////////////////////////////////////////////////
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Object constructor
+//////////////////////////////////////////////////////////////////////////////
+Alignment::Alignment(int maxseq, int maxres)
+{
+
+ //printf(">>>>>>>>%s:%s:%d: maxseq=%d, maxres=%d\n", __FUNCTION__, __FILE__, __LINE__, maxseq, maxres); /* (FS) */
+ longname = new(char[DESCLEN]);
+ sname = new(char*[maxseq+2]); /* MR1 */
+ seq = new(char*[maxseq+2]); /* MR1 */
+ l = new(int[maxres]);
+ X = new(char*[maxseq+2]); /* MR1 */
+ I = new(short unsigned int*[maxseq+2]); /* MR1 */
+ keep = new(char[maxseq+2]); /* MR1 */
+ display = new(char[maxseq+2]); /* MR1 */
+ wg = new(float[maxseq+2]); /* MR1 */
+ nseqs = new(int[maxres+2]); /* MR1 */
+ N_in=L=0;
+ nres=NULL; // number of residues per sequence k
+ first=NULL; // first residue in sequence k
+ last=NULL; // last residue in sequence k
+ ksort=NULL; // sequence indices sorted by descending nres[k]
+ name[0]='\0'; // no name defined yet
+ longname[0]='\0'; // no name defined yet
+ fam[0]='\0'; // no name defined yet
+ file[0]='\0'; // no name defined yet
+ readCommentLine = '0'; /* MR1 */
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// Object destructor
+//////////////////////////////////////////////////////////////////////////////
+Alignment::~Alignment()
+{
+ delete[] longname; longname = NULL;
+ for(int k=0; k<N_in; k++)
+ {
+ delete[] sname[k]; sname[k] = NULL;
+ delete[] seq[k]; seq[k] = NULL;
+ delete[] X[k]; X[k] = NULL;
+ delete[] I[k]; I[k] = NULL;
+ }
+ delete[] sname; sname = NULL;
+ delete[] seq; seq = NULL;
+ delete[] X; X = NULL;
+ delete[] I; I = NULL;
+ delete[] l; l = NULL;
+ delete[] keep; keep = NULL;
+ delete[] display; display = NULL;
+ delete[] wg; wg = NULL;
+ delete[] nseqs; nseqs = NULL;
+ delete[] nres; nres = NULL;
+ delete[] first; first = NULL;
+ delete[] last; last = NULL;
+ delete[] ksort; ksort = NULL;
+}
+
+
+/**
+ * @brief Reads in an alignment from file into matrix seq[k][l] as ASCII
+ */
+void
+Alignment::Read(FILE* inf, char infile[], char* firstline)
+{
+ int l; // Postion in alignment incl. gaps (first=1)
+ int h; // Position in input line (first=0)
+ int k; // Index of sequence being read currently (first=0)
+ char line[LINELEN]=""; // input line
+ //char cur_seq[MAXCOL]; // Sequence currently read in
+ char *cur_seq=new(char[par.maxColCnt]);
+ char* cur_name; // Sequence currently read in
+ int linenr=0; // current line number in input file
+ char skip_sequence=0;
+ RemoveExtension(file,infile); //copy rootname (w/o path) of infile into file variable of class object
+
+ kss_dssp=ksa_dssp=kss_pred=kss_conf=kfirst=-1;
+ n_display=0;
+ N_in=0;
+ N_filtered=0;
+ N_ss=0;
+ cur_seq[0]=' '; // overwrite '\0' character at beginning to be able to do strcpy(*,cur_seq)
+ l=1; k=-1;
+
+ // Does firstline already contain first line of file?
+ if (firstline!= NULL) strcpy(line,firstline);
+
+ /////////////////////////////////////////////////////////////////////////
+ // Read infile line by line
+ /* FIXME: not safe to use MAXSEQ, however, don't think we ever get here (FS) */
+ while(firstline || (fgetline(line,LINELEN,inf) && (k<MAXSEQ))) /* FIXME: FS introduced () around &&, precedence! MR1 */
+ {
+ linenr++;
+ firstline=NULL;
+ if (line[0]=='>') //line contains sequence name
+ {
+ if (k>=MAXSEQ-1)
+ {
+ if (v>=1 && k>=MAXSEQ)
+ cerr<<endl<<"WARNING: maximum number "<<MAXSEQ<<" of sequences exceded in file "<<infile<<"\n";
+ break;
+ }
+ cur_name=line+1; //beginning of current sequence name
+ if (k>=0) //if this is at least the second name line
+ {
+ if (strlen(cur_seq)==0)
+ {
+ cerr<<endl<<"Error: sequence "<<sname[k]<<" contains no residues."<<endl;
+ exit(1);
+ }
+
+ // Create space for residues and paste new sequence in
+ seq[k]=new(char[strlen(cur_seq)+2]);
+ if (!seq[k]) MemoryError("array for input sequences");
+ X[k]=new(char[strlen(cur_seq)+2]);
+ if (!X[k]) MemoryError("array for input sequences");
+ I[k]=new(short unsigned int[strlen(cur_seq)+2]);
+ if (!I[k]) MemoryError("array for input sequences");
+ strcpy(seq[k],cur_seq);
+ }
+ skip_sequence=0;
+
+ k++;
+ l=1; //position in current sequence (first=1)
+
+ // display[k]= 0: do not show in Q-T alignments 1: show if not filtered out later 2: show in any case (do not filter out)
+ // keep[k] = 0: do not include in profile 1: include if not filtered out later 2: include in any case (do not filter out)
+ /* {KEEP_NOT=0, KEEP_CONDITIONALLY=1, KEEP_ALWAYS=2} */
+ if (line[1]=='@') cur_name++; //skip @-character in name
+ if (!strncmp(line,">ss_dssp",8)) {
+ if (kss_dssp<0) {display[k]=2; n_display++; keep[k]=KEEP_NOT; kss_dssp=k; N_ss++;} else {skip_sequence=1; k--; continue;}
+ }
+ else if (!strncmp(line,">sa_dssp",8)) {
+ if (ksa_dssp<0) {display[k]=KEEP_ALWAYS; n_display++; keep[k]=KEEP_NOT; ksa_dssp=k; N_ss++;} else {skip_sequence=1; k--; continue;}
+ }
+ else if (!strncmp(line,">ss_pred",8)) {
+ if (kss_pred<0) {display[k]=KEEP_ALWAYS; n_display++; keep[k]=KEEP_NOT; kss_pred=k; N_ss++;} else {skip_sequence=1; k--; continue;}
+ }
+ else if (!strncmp(line,">ss_conf",8)) {
+ if (kss_conf<0) {display[k]=KEEP_ALWAYS; n_display++; keep[k]=KEEP_NOT; kss_conf=k; N_ss++;} else {skip_sequence=1; k--; continue;}
+ }
+ else if (!strncmp(line,">ss_",4) || !strncmp(line,">sa_",4)) {
+ display[k]=KEEP_ALWAYS; n_display++; keep[k]=KEEP_NOT; N_ss++;
+ }
+ else if (!strncmp(line,">aa_",4)) { // ignore sequences beginning with ">aa_"
+ skip_sequence=1; k--; continue;
+ }
+ //store first real seq
+ else if (kfirst<0)
+ {
+ char word[NAMELEN];
+ strwrd(word,line); // Copies first word in ptr to str
+ if (strstr(word,"_consensus"))
+ {display[k]=2; keep[k]=0; n_display++; kfirst=k;} /* MR1 */
+ else
+ {display[k]=keep[k]=KEEP_ALWAYS; n_display++; kfirst=k;}
+ }
+ //store all sequences
+ else if (par.mark==0) {display[k]=keep[k]=KEEP_CONDITIONALLY; n_display++;}
+ //store sequences up to nseqdis
+ else if (line[1]=='@'&& n_display-N_ss<par.nseqdis) {display[k]=keep[k]=KEEP_ALWAYS; n_display++;}
+ else {display[k]=KEEP_NOT; keep[k]=KEEP_CONDITIONALLY;}
+
+ // store sequence name
+ if (v>=4) printf("Reading seq %-16.16s k=%3i n_displ=%3i display[k]=%i keep[k]=%i\n",cur_name,k,n_display,display[k],keep[k]);
+ sname[k] = new(char[strlen(cur_name)+1]);
+ if (!sname[k]) {MemoryError("array for sequence names");}
+ strcpy(sname[k],cur_name);
+ } // end if(line contains sequence name)
+
+ else if (line[0]=='#') // Commentary line?
+ {
+ // #PF01367.9 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; PDB 1taq, 1bgx (T:271-174), 1taq (271-174)
+ if (name[0]) continue; // if already name defined: skip commentary line
+ char *ptr1, *ptr2;
+ ptr1=strscn_(line+1); // set ptr1 to first non-whitespace character after '#' -> AC number
+ strncpy(longname,ptr1,DESCLEN-1); // copy whole commentary line after '# ' into longname
+ longname[DESCLEN-1]='\0';
+ strtr(longname,""," ");
+ ptr2=strcut_(ptr1); // cut after AC number and set ptr2 to first non-whitespace character after AC number
+ // strcpy(fam,ptr1); // copy AC number to fam
+ // if (!strncmp(fam,"PF",2)) strcut_(fam,'.'); // if PFAM identifier contains '.' cut it off
+ // strcut_(ptr2); // cut after first word ...
+ strcpy(name,ptr1); // ... and copy first word into name
+ readCommentLine = '1'; /* MR1 */
+ }
+
+ //line contains sequence residues or SS information and does not belong to a >aa_ sequence
+ else if (!skip_sequence)
+ {
+ if (v>=4) cout<<line<<"\n"; //DEBUG
+ if (k==-1 && v)
+ {
+ cerr<<endl<<"WARNING: No sequence name preceding following line in "<<infile<<":\n\'"<<line<<"\'\n";
+ continue;
+ }
+
+ h=0; //counts characters in current line
+
+ // Check whether all characters are correct; store into cur_seq
+ if (keep[k] || (k == kfirst) ) // normal line containing residues /* MR1 */
+ {
+ while (h<LINELEN && line[h]>'\0' && l</*MAXCOL*/par.maxColCnt-1)
+ {
+ if (aa2i(line[h])>=0) // ignore white-space characters ' ', \t and \n (aa2i()==-1)
+ {cur_seq[l]=line[h]; l++;}
+ else if (aa2i(line[h])==-2 && v)
+ cerr<<endl<<"WARNING: invalid symbol \'"<<line[h]<<"\' at pos. "<<h<<" in line "<<linenr<<" of "<<infile<<"\n";
+ h++;
+ }
+ }
+ else if (k==kss_dssp) // lines with dssp secondary structure states (. - H E C S T G B)
+ {
+ while (h<LINELEN && line[h]>'\0' && l</*MAXCOL*/par.maxColCnt-1)
+ {
+ if (ss2i(line[h])>=0 && ss2i(line[h])<=7)
+ {cur_seq[l]=ss2ss(line[h]); l++;}
+ else if (v)
+ cerr<<endl<<"WARNING: invalid symbol \'"<<line[h]<<"\' at pos. "<<h<<" in line "<<linenr<<" of "<<infile<<"\n";
+ h++;
+ }
+ }
+ else if (k==ksa_dssp) // lines with dssp solvent accessibility states (. - ???)
+ {
+ while (h<LINELEN && line[h]>'\0' && l</*MAXCOL*/par.maxColCnt-1)
+ {
+ if (sa2i(line[h])>=0)
+ cur_seq[l++]=line[h];
+ else if (v)
+ cerr<<endl<<"WARNING: invalid symbol \'"<<line[h]<<"\' at pos. "<<h<<" in line "<<linenr<<" of "<<infile<<"\n";
+ h++;
+ }
+ }
+ else if (k==kss_pred) // lines with predicted secondary structure (. - H E C)
+ {
+ while (h<LINELEN && line[h]>'\0' && l</*MAXCOL*/par.maxColCnt-1)
+ {
+ if (ss2i(line[h])>=0 && ss2i(line[h])<=3)
+ {cur_seq[l]=ss2ss(line[h]); l++;}
+ else if (v)
+ cerr<<endl<<"WARNING: invalid symbol \'"<<line[h]<<"\' at pos. "<<h<<" in line "<<linenr<<" of "<<infile<<"\n";
+ h++;
+ }
+ }
+ else if (k==kss_conf) // lines with confidence values should contain only 0-9, '-', or '.'
+ {
+ while (h<LINELEN && line[h]>'\0' && l</*MAXCOL*/par.maxColCnt-1)
+ {
+ if (line[h]=='-' || line[h]=='.' || (line[h]>='0' && line[h]<='9'))
+ {cur_seq[l]=line[h]; l++;}
+ else if (v)
+ cerr<<endl<<"WARNING: invalid symbol \'"<<line[h]<<"\' at pos. "<<l<<" in line "<<linenr<<" of "<<infile<<"\n";
+ h++;
+ }
+ }
+ else if (display[k]) // other lines such as >sa_pred etc
+ {
+ while (h<LINELEN && line[h]>'\0' && l</*MAXCOL*/par.maxColCnt-1)
+ {
+ if (line[h]=='-' || line[h]=='.' || (line[h]>='0' && line[h]<='9') || (line[h]>='A' && line[h]<='B'))
+ {cur_seq[l]=line[h]; l++;}
+ else if (v)
+ cerr<<endl<<"WARNING: invalid symbol \'"<<line[h]<<"\' at pos. "<<l<<" in line "<<linenr<<" of "<<infile<<"\n";
+ h++;
+ }
+ }
+ if (v && l>=/*MAXCOL*/par.maxColCnt-1)
+ {
+ cerr<<endl<<"WARNING: maximum number of residues "<</*MAXCOL*/par.maxColCnt-2<<" exceded in sequence "<<sname[k]<<"\n";
+ skip_sequence=1;
+ }
+ cur_seq[l]='\0'; //Ensure that cur_seq ends with a '\0' character
+ } //end else
+
+ }
+ /////////////////////////////////////////////////////////////////////////
+
+
+ if (k>=0) //if at least one sequence was read in
+ {
+ seq[k]=new(char[strlen(cur_seq)+2]);
+ if (!seq[k]) MemoryError("array for input sequences");
+ X[k]=new(char[strlen(cur_seq)+2]);
+ if (!X[k]) MemoryError("array for input sequences");
+ I[k]=new(short unsigned int[strlen(cur_seq)+2]);
+ if (!I[k]) MemoryError("array for input sequences");
+ strcpy(seq[k],cur_seq);
+ }
+ else
+ {cerr<<endl<<"Error: no sequences found in file "<<infile<<"\n"; exit(1);}
+
+ N_in = k+1;
+
+ // Set name, longname, fam
+ if (!*name) // longname, name and family were not set by '#...' line yet -> extract from first sequence
+ {
+ char* ptr;
+ // strtr(sname[kfirst],"~"," "); // 'transpose': replaces the tilde with a blanc everywhere in sname[kfirst]
+ strncpy(longname,sname[kfirst],DESCLEN-1); // longname is name of first sequence
+ longname[DESCLEN-1]='\0';
+ strncpy(name,sname[kfirst],NAMELEN-1); // Shortname is first word of longname...
+ name[NAMELEN-1]='\0';
+ ptr = strcut(name); // ...until first white-space character
+ if (ptr && islower(ptr[0]) && ptr[1]=='.' && isdigit(ptr[2])) //Scop family code present as second word?
+ {
+ lwrstr(name); // Transform upper case to lower case
+ strcut(ptr); // Non-white-space characters until next white-space character..
+ strcpy(fam,ptr); // ...are the SCOP familiy code
+ }
+ else if (name[0]=='P' && name[1]=='F' && isdigit(name[2]) && isdigit(name[3]) ) //Pfam code
+ {
+ strcpy(fam,name); // set family name = Pfam code
+ }
+ }
+
+
+
+ delete[] cur_seq; cur_seq = NULL;
+
+ // Checking for warning messages
+ if (v==0) return;
+ if (v>=2) cout<<"Read "<<infile<<" with "<<N_in<<" sequences\n";
+ if (v>=3) cout<<"Query sequence for alignment has number "<<kfirst<<" (0 is first)\n";
+ return;
+}
+
+/*
+ * At this point GetSeqsFromHMM() slots in, however,
+ * only needed in hhbliys.C, so will skip it for moment, MR1
+ */
+
+
+/////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Convert ASCII in seq[k][l] to int (0-20) in X[k][i],
+ * throw out all insert states, record their number in I[k][i]
+ * and store sequences to be displayed in seq[k] */
+/////////////////////////////////////////////////////////////////////////////
+void
+Alignment::Compress(const char infile[])
+{
+ int i; // Index for match state (first=1)
+ int l; // Postion in alignment incl. gaps (first=1)
+ int k; // Index for sequences (first=0)
+ int a; // amino acid index
+ char c;
+ int unequal_lengths=0; /* k: seq k doesn't have same number
+ of match states as seq 0 => WARNING */
+ /* points to next character in seq[k] to be written */
+ /*static short unsigned int h[MAXSEQ];*/
+ /*short*/ unsigned int *h = NULL; /* short may lead to overflow for long alignments, FS, r235 -> r236 */
+
+ h = new(/*short*/ unsigned int[N_in+2]); /* short -> overflow, FS, r235 -> r236 */
+ float *percent_gaps = NULL; /* FS, 2010-Nov */
+ char *match_state = NULL; /* FS, 2010-Nov */
+
+
+ // Initialize
+ for (k=0;k<N_in; k++)
+ {I[k][0]=0;}
+
+ if (v>=3)
+ {
+ if (par.M==1)
+ cout<<"Using match state assignment by capital letters (a2m format)\n";
+ else if (par.M==2) cout<<"Using percentage-rule match state assignment\n";
+ else if (par.M==3) cout<<"Using residues of first sequence as match states\n";
+ }
+
+ // Create matrices X and I with amino acids represented by integer numbers
+ switch(par.M)
+ {
+
+ /////////////////////////////////////////////////////////////////////////
+ /* a2m/a3m format: match states capital case,
+ inserts lower case, delete states '-', inserted gaps '.'
+ The confidence values for ss prediction are interpreted as follows:
+ 0-9:match states(!) '-' :match state '.':insert */
+ case 1:
+ default:
+
+ // Warn if alignment is ment to be -M first or -M NN instead of A2M/A3M
+ if (v>=2 && strchr(seq[kfirst],'-') ) // Seed/query sequence contains a gap ...
+ {
+ for (k=1; k<N_in; k++)
+ if (strpbrk(seq[k],"abcdefghiklmnpqrstuvwxyz.")) break;
+ if (k==N_in) // ... but alignment contains no lower case residue
+ printf("WARNING: input alignment %s looks like aligned FASTA instead of A2M/A3M format. Consider using '-M first' or '-M 50'\n",infile);
+ }
+
+ // Remove '.' characters from seq[k]
+ for(k=0; k<N_in; k++)
+ {
+ char* ptrS=seq[k]; // pointer to source: character in seq[k]
+ char* ptrD=seq[k]; // pointer to destination: seq[k]
+ while(1) // omit '.' symbols
+ {
+ if (*ptrS!='.') {*ptrD=*ptrS; ptrD++;} //leave out '.' symbols
+ if (!*ptrS) break;
+ ptrS++;
+ }
+ }
+ L=/*MAXRES*/par.maxResLen-2; // needed because L=imin(L,i)
+ for (k=0; k<N_in; k++)
+ {
+ i=1; l=1; // start at i=1, not i=0!
+ if (keep[k]) //skip >ss_dssp, >ss_pred, >ss_conf, >aa_... sequences
+ {
+ while((c=seq[k][l++])) // assign residue to c at same time
+ {
+ if (c>='a' && c<='z') I[k][i-1]++;//insert state = lower case character
+ else if (c!='.') //match state = upper case character
+ {
+ X[k][i]=aa2i(c);
+ I[k][i]=0;
+ i++;
+ }
+ }
+ }
+ else if (k==kss_dssp || k==kss_pred) // does alignment contain sequence of secondary structure states?
+ {
+ while((c=seq[k][l++])) // assign residue to c at same time
+ if (c!='.' && !(c>='a' && c<='z')) X[k][i++]=ss2i(c); //match state = upper case character
+ }
+ else if (k==ksa_dssp) // does alignment contain sequence of prediction confidence values?
+ {
+ while((c=seq[k][l++])) // assign residue to c at same time
+ if (c!='.' && !(c>='a' && c<='z')) X[k][i++]=sa2i(c); //match state = upper case character
+ }
+ else if (k==kss_conf) // does alignment contain sequence of prediction confidence values?
+ {
+ while((c=seq[k][l++])) // assign residue to c at same time
+ if (c!='.') X[k][i++]=cf2i(c); //match state = 0-9 or '-'
+ }
+ else if (k==kfirst) // does alignment contain sequence of prediction confidence values?
+ {
+ while((c=seq[k][l++])) // assign residue to c at same time
+ if (c!='.')
+ {
+ X[k][i]=aa2i(c);
+ I[k][i]=0;
+ ++i;
+ }
+ }
+ else continue;
+ i--;
+ if (L!=i && L!=/*MAXRES*/par.maxResLen-2 && !unequal_lengths) unequal_lengths=k; //sequences have different lengths
+ L=imin(L,i);
+ }
+ if (unequal_lengths) break;
+
+ //Replace GAP with ENDGAP for all end gaps /* MR1 */
+ for (k=0; k<N_in; ++k)
+ {
+ if (!keep[k]) continue;
+ for (i=1; i<=L && X[k][i]==GAP; i++) X[k][i]=ENDGAP; /* MR1: NOTE i++ <- ++i */
+ for (i=L; i>=1 && X[k][i]==GAP; i--) X[k][i]=ENDGAP; /* MR1 */
+ }
+
+ for (i=1; i<=L; i++) this->l[i]=i; //assign column indices to match states
+ if (L<=0)
+ {
+ cout<<"\nError: Alignment in "<<infile<<" contains no match states. Consider using -M first or -M <int> option"<<endl;
+ exit(1);
+ }
+
+ if (L==/*MAXRES*/par.maxResLen-2 && v>=2)
+ {
+ printf("WARNING: Number of match columns too large. Only first %i match columns will be kept!\n",L);
+ break;
+ }
+ if (v>=2) cout<<"Alignment in "<<infile<<" contains "<<L<<" match states\n";
+ break;
+
+ /////////////////////////////////////////////////////////////////////////
+ // gap-rule assignment of match states
+ case 2:
+ int nl[NAA+2]; //nl[a] = number of seq's with amino acid a at position l
+ /* Note: allocating statically is fine most of the time
+ but when the sequences/profiles get really long
+ we might run out of memory, so must really do it dynamically.
+ had to move declaration of float *percent_gaps out of switch()
+ */
+ //float percent_gaps[MAXCOL]; //percentage of gaps in column k (with weighted sequences)
+ percent_gaps = new(float[par.maxColCnt]);
+
+ //determine number of columns L in alignment
+ L=strlen(seq[kfirst])-1;
+
+ // Conversion to integer representation, checking for unequal lengths and initialization
+ if (nres==NULL) nres=new(int[N_in]);
+ for (k=0; k<N_in; k++)
+ {
+ if (!keep[k]) continue;
+ int nr=0;
+ wg[k]=0; nres[k]=0;
+ for (l=1; l<=L; l++)
+ {
+ X[k][l]=aa2i(seq[k][l]);
+ if (X[k][l]<NAA) nr++;
+ }
+ nres[k]=nr;
+ if (seq[k][L+1]!='\0' && !unequal_lengths) unequal_lengths=k;
+ }
+ if (unequal_lengths) break;
+
+ // Quick and dirty calculation of the weight per sequence wg[k]
+ for (l=1; l<=L; l++) // for all positions l in alignment
+ {
+ int naa=0; //number of different amino acids
+ for (a=0; a<20; a++) nl[a]=0;
+ for (k=0; k<N_in; k++) if (keep[k]) nl[ (int)X[k][l]]++;
+ for (a=0; a<20; a++) if(nl[a]) naa++;
+ if (!naa) naa=1; //naa=0 when column consists of only gaps and Xs (=ANY)
+ for (k=0; k<N_in; k++)
+ if (keep[k] && (X[k][l]<20) )
+ {
+ //wg[k]+=1.0/float(nl[ (int)X[k][l]]*naa*nres[k]+30.0); /* original version */
+ wg[k] += 1.0/float(nl[ (int)X[k][l]]*naa*(nres[k]+30.0)); /* MR1 */
+ // wg[k] += 1.0/float(nl[ (int)X[k][l]]*(nres[k]+30.0)); /* MR1 commented out */
+ // wg[k] += (naa-1.0)/float(nl[ (int)X[k][l]]*(nres[k]+30.0)); /* MR1 commented out */
+ }
+ } /* 1=l<=L*/
+
+ //Replace GAP with ENDGAP for all end gaps
+ for (k=0; k<N_in; ++k)
+ {
+ if (!keep[k]) continue;
+ for (i=1; i<=L && X[k][i]==GAP; i++) X[k][i]=ENDGAP; /* MR1: NOTE i++ <- ++i */
+ for (i=L; i>=1 && X[k][i]==GAP; i--) X[k][i]=ENDGAP; /* MR1 */
+ }
+
+ // Add up percentage of gaps
+ for (l=1; l<=L; l++)
+ {
+ float res=0;
+ float gap=0;
+ for (k=0; k< N_in; k++){
+ if (keep[k]){
+ if ( X[k][l]<GAP) res+=wg[k]; /* MR1, AA or ANY, changed from <ANY */
+ else if ( X[k][l] != ENDGAP) gap+=wg[k]; /* MR1, else: GAP. ENDGAPs are ignored for counting percentage */
+ }
+ }
+ percent_gaps[l]=100.*gap/(res+gap);
+ if (v>=4) cout<<"percent gaps["<<l<<"]="<<percent_gaps[l]<<" first seq:"<<seq[0][l]<<"\n";
+ }
+
+ /* Insert states 'bloat' the HMM,
+ throwing them out 'slims' down the HMM.
+ A slimmer HMM takes less time to construct.
+ However, the marriage of Clustal and Hhalign
+ is particularly sensitive to residues
+ at the very end of the profile; these I call
+ 'telomeres'. Telomeres must not be shed when
+ throwing out insert states, for the telomeres
+ we set the match threshold to 100%.
+ */
+#define MGAP_LOGIC 0
+#define TELOMERE_LOGIC 1
+#define TELOMERE_DYNAMIC 0
+
+#define ALWAYS_ACCEPT 101.0 /* do NOT change this parameter, must be >=100,
+ make slightly bigger than 100% -- to be sure to be sure */
+#define DEFAULT_MGAPS 100.0 /* Soeding's default is 50, omega default prior to telomere logic was 100
+ FIXME: this used to be par.Mgaps,
+ in a later version re-introduce par.Mgaps to keep this value flexible */
+#define TELOMER_LENGTH 10 /* this parameter must be > 0 (unless DEFAULT_MGAPS=100),
+ if it is too big (L/2) then telomere logic has no effect,
+ don't think it should be changed (much) */
+#define TELOMER_FRACTION 0.10
+ //#define HMM_MIN_LENGTH 0.923
+#define HMM_MIN_LENGTH 0.950
+#define FORTRAN_OFFSET 1
+ double dDefaultMgaps;
+ dDefaultMgaps = DEFAULT_MGAPS;
+
+#if TELOMERE_LOGIC /* turn telomere logic on (1) or off (0) */
+ int iTelomereLength;
+
+#if TELOMERE_DYNAMIC /* keep telomere length 'dynamic' */
+ iTelomereLength = TELOMER_LENGTH > (int)(L*TELOMER_FRACTION) ? TELOMER_LENGTH : (int)(L*TELOMER_FRACTION);
+#else
+ iTelomereLength = TELOMER_LENGTH;
+#endif /* this was dynamic telomere */
+#endif /* this was telomere logic */
+
+ /* if HMMs get too small (much smaller than profile length L)
+ then one is liable to get a back-tracking error.
+ So we should ensure that the DEFAULT_MGAPS parameter does NOT
+ shrink the HMM too much.
+ take percentage-gap vector, sort it, and fix dDefaultMgaps,
+ such that at least (HMM_MIN_LENGTH)*(L) are left
+ */
+#if MGAP_LOGIC /* try to adapt Mgaps to size of final HMM */
+ {
+ float *pfPercentGaps = NULL;
+ if (NULL == (pfPercentGaps = (float *)malloc((L+1)*sizeof(float)))){
+ printf("%s:%s:%d: could not malloc %d float for sorted percent-gaps\n",
+ __FUNCTION__, __FILE__, __LINE__, L+1);
+ dDefaultMgaps = DEFAULT_MGAPS;
+ }
+ else {
+ for (l = 0; l < L; l++) {
+ pfPercentGaps[l] = percent_gaps[l+FORTRAN_OFFSET];
+ }
+ qsort(pfPercentGaps, L, sizeof(float), CompFltAsc);
+
+ dDefaultMgaps = pfPercentGaps[(int)(HMM_MIN_LENGTH*L)];
+ if (dDefaultMgaps < DEFAULT_MGAPS){
+ //printf("Mgaps = %f <- %f\n", DEFAULT_MGAPS, dDefaultMgaps);
+ dDefaultMgaps = DEFAULT_MGAPS;
+ }
+ else {
+ //printf("Mgaps = %f\n", dDefaultMgaps);
+ }
+
+ free(pfPercentGaps); pfPercentGaps = NULL;
+ }
+ }
+#endif /* tried to adapt Mgaps to size of final HMM */
+
+ // Throw out insert states and keep only match states
+ i=0;
+ for (k=0; k<N_in; k++) {h[k]=1; seq[k][0]='-';}
+ for (l=1; l<=L; l++)
+ {
+#if TELOMERE_LOGIC
+ float fMgaps = ALWAYS_ACCEPT;
+ if ( (l < iTelomereLength) || (L-l < iTelomereLength) ){
+ /* residue is in telomere, always retain this position */
+ fMgaps = ALWAYS_ACCEPT;
+ }
+ else if (0){
+ /* FIXME: would like to put a transition phase in here,
+ where the Mgap value gradually goes down from 100 to DEFAULT_MGAPS,
+ however, may not be necessary and will make code more clunky */
+ }
+ else {
+ /* position is in centre of sequence,
+ retain position if less than DEFAULT_MGAPS% gaps at this position,
+ for example, if DEFAULT_MGAPS=30 throw out if more than 30% gap.
+ conversely, if DEFAULT_MGAPS=100 throw out if more than 100% gaps,
+ which can never happen, so always retain */
+ fMgaps = dDefaultMgaps;
+ }
+ if (percent_gaps[l] <= fMgaps)
+#else /* this was telomere logic */
+ if (percent_gaps[l]<=float(par.Mgaps))
+#endif /* this was Soeding default */
+ {
+ if (i>=/*MAXRES*/par.maxResLen-2) {
+ if (v>=1)
+ printf("WARNING: Number of match columns too large. Only first %i match columns will be kept!\n",i);
+ break;
+ }
+ i++;
+ this->l[i]=l;
+ for (k=0; k<N_in; k++)
+ {
+ if (keep[k])
+ {
+ seq[k][h[k]++]=MatchChr(seq[k][l]);
+ X[k][i]=X[k][l];
+ I[k][i]=0;
+ }
+ else if (k==kss_dssp || k==kss_pred)
+ {
+ seq[k][h[k]++]=MatchChr(seq[k][l]);
+ X[k][i]=ss2i(seq[k][l]);
+ }
+ else if (k==ksa_dssp)
+ {
+ seq[k][h[k]++]=MatchChr(seq[k][l]);
+ X[k][i]=sa2i(seq[k][l]);
+ }
+ else if (k==kss_conf)
+ {
+ seq[k][h[k]++]=seq[k][l];
+ X[k][i]=cf2i(seq[k][l]);
+ }
+ }
+ }
+ else
+ {
+ for (k=0; k<N_in; k++)
+ if (keep[k] && X[k][l]<GAP)
+ {
+ I[k][i]++;
+ seq[k][h[k]++]=InsertChr(seq[k][l]);
+ }
+ }
+ }
+ for (k=0; k<N_in; k++) seq[k][h[k]]='\0';
+
+ //printf("%d\t%d\t%d\tN/L/M\n", N_in, L, i); /* -------- FIXME */
+
+ if (v>=2) cout<<"Alignment in "<<infile<<" contains "<<L<<" columns and "<<i<<" match states\n";
+ L = i; //Number of match states
+
+ delete[] percent_gaps; percent_gaps = NULL;
+ break;
+
+
+ ////////////////////////////////////////////////////////////////////////
+ // Using residues of first sequence as match states
+ case 3:
+ /* Note: allocating statically is fine most of the time
+ but when the sequences/profiles get really long
+ we might run out of memory, so must really do it dynamically.
+ had to move declaration of float *percent_gaps out of switch()
+ */
+ //char match_state[MAXCOL]; //1: column assigned to match state 0: insert state
+ match_state = new(char[par.maxColCnt]);
+
+ // Determine number of columns L in alignment
+ L=strlen(seq[0]+1);
+ if (v>=3) printf("Length of first seq = %i\n",L);
+ // Check for sequences with unequal lengths
+ for (k=1; k<N_in; k++)
+ if (int(strlen(seq[k]+1))!=L) {unequal_lengths=k; break;}
+ if (unequal_lengths) break;
+
+ // Determine match states: seq kfirst has residue at pos l -> match state
+ for (l=1; l<=L; l++)
+ if (isalpha(seq[kfirst][l])) match_state[l]=1; else match_state[l]=0;
+ // Throw out insert states and keep only match states
+ for (k=0; k<N_in; k++) {h[k]=1; seq[k][0]='-';}
+ i=0;
+ for (l=1; l<=L; l++)
+ {
+ if (match_state[l]) // does sequence 0 have residue at position l?
+ {
+ if (i>=/*MAXRES*/par.maxResLen-2) {
+ if (v>=1)
+ printf("WARNING: Number of match columns too large. Only first %i match columns will be kept!\n",i);
+ break;
+ }
+ i++;
+ this->l[i]=l;
+ for (k=0; k<N_in; k++)
+ {
+ if (keep[k])
+ {
+ seq[k][h[k]++]=MatchChr(seq[k][l]);
+ X[k][i]=aa2i(seq[k][l]);
+ I[k][i]=0;
+ }
+ else if (k==kss_dssp || k==kss_pred)
+ {
+ seq[k][h[k]++]=MatchChr(seq[k][l]);
+ X[k][i]=ss2i(seq[k][l]);
+ }
+ else if (k==ksa_dssp)
+ {
+ seq[k][h[k]++]=MatchChr(seq[k][l]);
+ X[k][i]=sa2i(seq[k][l]);
+ }
+ else if (k==kss_conf)
+ {
+ seq[k][h[k]++]=seq[k][l];
+ X[k][i]=cf2i(seq[k][l]);
+ }
+ }
+ }
+ else
+ {
+ for (k=0; k<N_in; k++)
+ if (keep[k] && aa2i(seq[k][l])<GAP)
+ {
+ I[k][i]++;
+ seq[k][h[k]++]=InsertChr(seq[k][l]);
+ }
+ }
+ }
+ for (k=0; k<N_in; k++) seq[k][h[k]]='\0';
+
+ //Replace GAP with ENDGAP for all end gaps /* MR1 */
+ for (k=0; k<N_in; ++k)
+ {
+ if (!keep[k]) continue;
+ for (i=1; i<=L && X[k][i]==GAP; i++) X[k][i]=ENDGAP; /* MR1, note i++ <- ++i */
+ for (i=L; i>=1 && X[k][i]==GAP; i--) X[k][i]=ENDGAP; /* MR1 */
+ }
+
+ if (v>=2) cout<<"Alignment in "<<infile<<" contains "<<L<<" columns and "<<i<<" match states\n";
+ L = i; //Number of match states
+
+ delete[] match_state; match_state = NULL;
+ break;
+
+ } //end switch()
+ ///////////////////////////////////////////////////////////////////////////
+
+
+ // Error
+ if (unequal_lengths)
+ {
+ strcut(sname[unequal_lengths]);
+ cerr<<endl<<"Error: sequences in "<<infile<<" do not all have the same number of columns, \ne.g. first sequence and sequence "<<sname[unequal_lengths]<<".\n";
+ if(par.M==1) cerr<<".\nCheck input format for '-M a2m' option and consider using '-M first' or '-M 50'\n";
+ exit(1);
+ }
+
+ // Avert user about -cons option?
+ if (v>=2 && !par.cons)
+ {
+ for (i=1; i<=L; i++)
+ if (X[kfirst][i]==GAP)
+ {
+ printf("NOTE: Use the '-cons' option to calculate a consensus sequence as first sequence of the alignment.\n");
+ break;
+ }
+ }
+ /* MR1
+ //Replace GAP with ENDGAP for all end gaps
+ for (k=0; k<N_in; k++)
+ {
+ if (!keep[k]) continue;
+ for (i=1; i<=L && X[k][i]==GAP; i++) X[k][i]=ENDGAP;
+ for (i=L; i>=1 && X[k][i]==GAP; i--) X[k][i]=ENDGAP;
+ }*/
+
+ // DEBUG
+ if (v>=4)
+ for (k=0; k<N_in; k++)
+ {
+ if (!display[k]) continue;
+ cout<<">"<<sname[k]<<"\n";
+ if (k==kss_dssp || k==kss_pred) {for (i=1; i<=L; i++) cout<<char(i2ss(X[k][i]));}
+ else if (k==kss_conf) {for (i=1; i<=L; i++) cout<<char(i2cf(X[k][i]));}
+ else if (k==ksa_dssp) {for (i=1; i<=L; i++) cout<<char(i2sa(X[k][i]));}
+ else
+ {
+ for (i=1; i<=L; i++) cout<<char(i2aa(X[k][i]));
+ cout<<"\n";
+ for (i=1; i<=L; i++)
+ if (I[k][i]==0) cout<<"-"; else if (I[k][i]>9) cout<<"X"; else cout<<I[k][i];
+ }
+ cout<<"\n";
+ }
+
+ delete[](h); h = NULL;
+}
+
+
+/**
+ * @brief Remove sequences with seq. identity larger than seqid percent
+ *(remove the shorter of two) or coverage<cov_thr
+ *
+ * FIXME: originally max_seqid is a variable that is the cutoff
+ * above which sequences are thrown out. We want to throw out sequences
+ * when building the HMM but not for display, there we want to keep all.
+ * This should be really easy, but there is some hidden stuff going on
+ * in this function, so I did a minimal-invasive change and just stuck
+ * (effectively) a hard-wired 100 instead of the variable.
+ * At a later stage we should get rid of this function alltogether
+ * as it does gobble up some time (and is quadratic in noof sequences, I think)
+ * FS, 2010-10-04
+ */
+////////////////////////////////////////////////////////////////////////////
+/*
+ */
+inline int
+Alignment::FilterForDisplay(int max_seqid, int coverage, int qid, float qsc, int N)
+{
+
+ /* FIXME
+ * by just returning n_display and not doing anything
+ * I think we display everything and not do any work for it
+ */
+ return n_display; /* FS, 2010-10-04*/
+
+
+ if (par.mark) return n_display;
+ char *dummy = new(char[N_in+1]);
+ int vtmp=v, seqid;
+ v=0;
+ n_display=0;
+ if (kss_dssp>=0) display[kss_dssp]=KEEP_NOT;
+ if (ksa_dssp>=0) display[ksa_dssp]=KEEP_NOT;
+ if (kss_pred>=0) display[kss_pred]=KEEP_NOT;
+ if (kss_conf>=0) display[kss_conf]=KEEP_NOT;
+ for (seqid=imin(10,max_seqid); n_display<N && seqid<=max_seqid; seqid++)
+ {
+ for (int k=0; k<N_in; k++) dummy[k]=display[k];
+ n_display = Filter2(dummy,coverage,qid,qsc,20,seqid,0);
+ // printf("Seqid=%3i n_display=%4i\n",seqid,n_display);
+ }
+ if (n_display>N)
+ {
+ for (int k=0; k<N_in; k++) dummy[k]=display[k];
+ n_display = Filter2(dummy,coverage,qid,qsc,20,--(--seqid),0);
+ }
+ v=vtmp;
+ for (int k=0; k<N_in; k++) display[k]=dummy[k];
+ if (kss_dssp>=0) {display[kss_dssp]=KEEP_CONDITIONALLY; n_display++;}
+ if (ksa_dssp>=0) {display[ksa_dssp]=KEEP_CONDITIONALLY; n_display++;}
+ if (kss_pred>=0) {display[kss_pred]=KEEP_CONDITIONALLY; n_display++;}
+ if (kss_conf>=0) {display[kss_conf]=KEEP_CONDITIONALLY; n_display++;}
+ delete[] dummy; dummy = NULL;
+ return n_display;
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+// Remove sequences with seq. identity larger than seqid percent (remove the shorter of two) or coverage<cov_thr
+/////////////////////////////////////////////////////////////////////////////////////
+inline int Alignment::Filter(int max_seqid, int coverage, int qid, float qsc, int N)
+{
+ return Filter2(keep,coverage,qid,qsc,20,max_seqid,N);
+}
+
+/////////////////////////////////////////////////////////////////////////////
+/*
+ * @brief Select set of representative sequences in the multiple sequence alignment
+ *
+ * Filter criteria:
+ * Remove sequences with coverage of query less than "coverage" percent
+ * Remove sequences with sequence identity to query of less than "qid" percent
+ * If Ndiff==0, remove sequences with seq. identity larger than seqid2(=max_seqid) percent
+ * If Ndiff>0, remove sequences with minimum-sequence-identity filter of between seqid1
+ * and seqid2 (%), where the minimum seqid threshold is determined such that,
+ * in all column blocks of at least WMIN=25 residues, at least Ndiff sequences are left.
+ * This ensures that in multi-domain proteins sequences covering one domain are not
+ * removed completely because sequences covering other domains are more diverse.
+ *
+ * Allways the shorter of two compared sequences is removed (=> sort sequences by length first).
+ * Please note: sequence identity of sequence x with y when filtering x is calculated as
+ * number of residues in sequence x that are identical to an aligned residue in y / number of residues in x
+ * Example: two sequences x and y are 100% identical in their overlapping region but one overlaps by 10% of its
+ * length on the left and the other by 20% on the right. Then x has 10% seq.id with y and y has 20% seq.id. with x.
+ */
+//////////////////////////////////////////////////////////////////////////////
+int
+Alignment::Filter2(char keep[], int coverage, int qid, float qsc, int seqid1, int seqid2, int Ndiff)
+{
+ // In the beginnning, keep[k] is 1 for all regular amino acid sequences and 0 for all others (ss_conf, ss_pred,...)
+ // In the end, keep[k] will be 1 for all regular representative sequences kept in the alignment, 0 for all others
+ char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid
+ char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0;
+ int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering /* MR1, used to be called idmax*/
+ int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL]
+ int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid)
+ int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i
+ const int WFIL=25; // see previous line
+
+ int diffNmax=Ndiff; // current maximum difference of Nmax[i] and Ndiff /* MR1 */
+ int diffNmax_prev=0; // previous maximum difference of Nmax[i] and Ndiff /* MR1 */
+
+ int seqid; // current maximum value for the position-dependent maximum-sequence-identity thresholds in idmax[]
+ int seqid_step=0; // previous increment of seqid /* MR1 */
+
+ float diff_min_frac; // minimum fraction of differing positions between sequence j and k needed to accept sequence k
+ float qdiff_max_frac=0.9999-0.01*qid; // maximum allowable number of residues different from query sequence
+ int diff; // number of differing positions between sequences j and k (counted so far)
+ int diff_suff; // number of differing positions between sequences j and k that would be sufficient
+ int qdiff_max; // maximum number of residues required to be different from query
+ int cov_kj; // upper limit of number of positions where both sequence k and j have a residue
+ int first_kj; // first non-gap position in sequence j AND k
+ int last_kj; // last non-gap position in sequence j AND k
+ int kk, jj; // indices for sequence from 1 to N_in
+ int k, j; // kk=ksort[k], jj=ksort[j]
+ int i; // counts residues
+ int n; // number of sequences accepted so far
+
+
+ // Initialize in[k]
+ for (n=k=0; k<N_in; k++) if (keep[k]==KEEP_ALWAYS) {in[k]=2/*KEEP_ALWAYS??*/; n++;} else in[k]=0;
+
+ // Determine first[k], last[k]?
+ if (first==NULL)
+ {
+ first=new(int[N_in]);// first non-gap position in sequence k
+ last =new(int[N_in]);// last non-gap position in sequence k
+ for (k=0; k<N_in; k++) // do this for ALL sequences, not only those with in[k]==1 (since in[k] may be display[k])
+ {
+ for (i=1; i<=L; i++) if (X[k][i]<NAA) break;
+ first[k]=i;
+ for (i=L; i>=1; i--) if (X[k][i]<NAA) break;
+ last[k]=i;
+ }
+ }
+
+ // Determine number of residues nres[k]?
+ if ( (nres==NULL) || (sizeof(nres)<N_in*sizeof(int)) )
+ {
+ nres=new(int[N_in]);
+ for (k=0; k<N_in; k++) // do this for ALL sequences, not only those with in[k]==1 (since in[k] may be display[k])
+ {
+ int nr=0;
+ for (i=first[k]; i<=last[k]; i++)
+ if (X[k][i]<NAA) nr++;
+ nres[k]=nr;
+ // printf("%20.20s nres=%3i first=%3i last=%3i\n",sname[k],nr,first[k],last[k]);
+ }
+ }
+
+ // Sort sequences according to length; afterwards, nres[ksort[kk]] is sorted by size
+ if (ksort==NULL)
+ {
+ ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences
+ for (k=0; k<N_in; k++) ksort[k]=k;
+ QSortInt(nres,ksort,kfirst+1,N_in-1,-1); //Sort sequences after kfirst (query) in descending order
+ }
+ for (kk=0; kk<N_in; kk++) inkk[kk]=in[ksort[kk]];
+
+ // Initialize N[i], idmax[i], idprev[i]
+ for (i=1; i<first[kfirst]; i++) N[i]=0;
+ for (i=first[kfirst]; i<=last[kfirst]; i++) N[i]=1;
+ for (i=last[kfirst]+1; i<=L; i++) N[i]=0;
+ //for (i=1; i<=L; i++) {idmax[i]=seqid1; idmaxwin[i]=-1;}
+ for (i=1; i<=L; ++i) {Nmax[i]=0; idmaxwin[i]=-1;} /* MR1 */
+ for (k=0; k<N_in; k++) seqid_prev[k]=-1;
+ if (Ndiff<=0 || Ndiff>=N_in) {seqid1=seqid2; Ndiff=N_in; diffNmax=Ndiff;}
+
+ // Check coverage and sim-to-query criteria for each sequence k
+ for (k=0; k<N_in; k++)
+ {
+ if (keep[k]==KEEP_NOT || keep[k]==KEEP_ALWAYS) continue; // seq k not regular sequence OR is marked sequence
+ if (100*nres[k]<coverage*L) {keep[k]=KEEP_NOT; continue;} // coverage too low? => reject once and for all
+
+ float qsc_sum=0.0;
+
+ // Check if score-per-column with query is at least qsc
+ if (qsc>-10)
+ {
+ float qsc_min = qsc*nres[k]; // minimum total score of seq k with query
+
+ int gapq=0, gapk=0; // number of consecutive gaps in query or k'th sequence at position i
+ for (int i=first[k]; i<=last[k]; i++)
+ {
+ if (X[k][i]<20)
+ {
+ gapk=0;
+ if (X[kfirst][i]<20)
+ {
+ gapq=0;
+ qsc_sum += S[(int)X[kfirst][i]][(int)X[k][i]];
+ }
+ else if (gapq++) qsc_sum-=PLTY_GAPEXTD; else qsc_sum-=PLTY_GAPOPEN;
+ }
+ else if (X[kfirst][i]<20)
+ {
+ gapq=0;
+ if (gapk++) qsc_sum-=PLTY_GAPEXTD; else qsc_sum-=PLTY_GAPOPEN;
+ }
+ }
+ // printf("k=%3i qsc=%6.2f\n",k,qsc_sum);
+ if (qsc_sum<qsc_min) {keep[k]=KEEP_NOT; continue;} // too different from query? => reject once and for all
+ }
+
+ //Check if sequence similarity with query at least qid?
+ if (qdiff_max_frac<0.999)
+ {
+ qdiff_max=int(qdiff_max_frac*nres[k]+0.9999);
+ // printf("k=%-4i nres=%-4i qdiff_max=%-4i first=%-4i last=%-4i",k,nres[k],qdiff_max,first[k],last[k]);
+ diff=0;
+ for (int i=first[k]; i<=last[k]; i++)
+ // enough different residues to reject based on minimum qid with query? => break
+ if (X[k][i]<20 && X[k][i]!=X[kfirst][i] && ++diff>=qdiff_max) break;
+ // printf(" diff=%4i\n",diff);
+ if (diff>=qdiff_max) {keep[k]=KEEP_NOT; continue;} // too different from query? => reject once and for all
+ }
+ // printf(" qsc=%6.2f qid=%6.2f \n",qsc_sum/nres[k],100.0*(1.0-(float)(diff)/nres[k]));
+ }
+
+ if (seqid1>seqid2)
+ {
+ for (n=k=0; k<N_in; k++) if (keep[k]>KEEP_NOT) n++;
+ return n;
+ }
+
+ // Successively increment idmax[i] at positons where N[i]<Ndiff
+ //for (seqid=seqid1; seqid<=seqid2; seqid+=1+(seqid>=50)) /* MR1 */
+ seqid=seqid1;
+ while (seqid<=seqid2)
+ {
+ /*
+ // Update idmax[i]
+ for (i=1; i<=L; i++) if (N[i]<Ndiff) idmax[i]=seqid;
+
+ // Update idmaxwin[i] as minimum of idmax[i-WFIL,i+WFIL]. If idmaxwin[] has not changed then stop
+ char stop=1;
+ for (i=1; i<=L; i++)
+ {
+ int idmax_min=seqid2;
+ for (j=imax(1,imin(L-2*WFIL+1,i-WFIL)); j<=imin(L,imax(2*WFIL,i+WFIL)); j++)
+ if (idmax[j]<idmax_min) idmax_min=idmax[j];
+ if (idmax_min>idmaxwin[i]) stop=0; // idmaxwin[i] has changed => do not stop
+ idmaxwin[i]=idmax_min;
+ }
+ */
+ char stop=1;
+ // Update Nmax[i]
+ diffNmax_prev = diffNmax;
+ diffNmax = 0;
+ for (i=1; i<=L; ++i)
+ {
+ int max=0;
+ for (j=imax(1,imin(L-2*WFIL+1,i-WFIL)); j<=imin(L,imax(2*WFIL,i+WFIL)); ++j)
+ if (N[j]>max) max=N[j];
+ if (Nmax[i]<max) Nmax[i]=max;
+ if (Nmax[i]<Ndiff)
+ {
+ stop=0;
+ idmaxwin[i]=seqid;
+ if (diffNmax<Ndiff-Nmax[i]) diffNmax=Ndiff-Nmax[i];
+ }
+
+ }
+
+ //printf("seqid=%3i diffNmax_prev= %-4i diffNmax= %-4i n=%-5i N_in-N_ss=%-5i\n",seqid,diffNmax_prev,diffNmax,n,N_in-N_ss);
+
+ if (stop) break;
+
+ // // DEBUG
+ // printf("idmax ");
+ // for (i=1; i<=L; i++) printf("%2i ",idmax[i]);
+ // printf("\n");
+ // printf("idmaxwin ");
+ // for (i=1; i<=L; i++) printf("%2i ",idmaxwin[i]);
+ // printf("\n");
+ // printf("N[i] ");
+ // for (i=1; i<=L; i++) printf("%2i ",N[i]);
+ // printf("\n");
+
+ // Loop over all candidate sequences kk (-> k)
+ for (kk=0; kk<N_in; kk++)
+ {
+ if (inkk[kk]) continue; // seq k already accepted
+ k=ksort[kk];
+ if (!keep[k]) continue; // seq k is not regular aa sequence or already suppressed by coverage or qid criterion
+ if (keep[k]==KEEP_ALWAYS) {inkk[kk]=2; continue;} // accept all marked sequences (no n++, since this has been done already)
+
+ // Calculate max-seq-id threshold seqidk for sequence k (as maximum over idmaxwin[i])
+ if (seqid>=100) {in[k]=inkk[kk]=1; n++; continue;}
+ float seqidk=seqid1;
+ for (i=first[k]; i<=last[k]; i++)
+ if (idmaxwin[i]>seqidk) seqidk=idmaxwin[i];
+ if (seqid==seqid_prev[k]) continue; // sequence has already been rejected at this seqid threshold => reject this time
+ seqid_prev[k]=seqid;
+ diff_min_frac =0.9999-0.01*seqidk; // min fraction of differing positions between sequence j and k needed to accept sequence k
+
+ // Loop over already accepted sequences
+ for (jj=0; jj<kk; jj++)
+ {
+ if (!inkk[jj]) continue;
+ j=ksort[jj];
+ first_kj=imax(first[k],first[j]);
+ last_kj =imin(last[k],last[j]);
+ cov_kj = last_kj-first_kj+1;
+ diff_suff=int(diff_min_frac*imin(nres[k],cov_kj)+0.999); // nres[j]>nres[k] anyway because of sorting /* MR1 0.999 */
+ diff=0;
+ for (int i=first_kj; i<=last_kj; i++)
+ {
+ // enough different residues to accept? => break
+ if (X[k][i]>=NAA || X[j][i]>=NAA)
+ cov_kj--;
+ else
+ if (X[k][i]!=X[j][i] && ++diff>=diff_suff) break; // accept (k,j)
+ }
+ // // DEBUG
+ // printf("%20.20s with %20.20s: diff=%i diff_min_frac*cov_kj=%f diff_suff=%i nres=%i cov_kj=%i\n",sname[k],sname[j],diff,diff_min_frac*cov_kj,diff_suff,nres[k],cov_kj);
+ // printf("%s\n%s\n\n",seq[k],seq[j]);
+
+ //if (float(diff)<fmin(diff_min_frac*cov_kj,diff_suff)) break; //similarity > acceptace threshold? Reject! /* MR1 */
+ if (diff<diff_suff && float(diff)<=diff_min_frac*cov_kj) break; //dissimilarity < acceptace threshold? Reject! /* MR1 */
+
+
+ }
+ if (jj>=kk) // did loop reach end? => accept k. Otherwise reject k (the shorter of the two)
+ {
+ in[k]=inkk[kk]=1;
+ n++;
+ for (i=first[k]; i<=last[k]; i++) N[i]++; // update number of sequences at position i
+ // printf("%i %20.20s accepted\n",k,sname[k]);
+ }
+ // else
+ // {
+ // printf("%20.20s rejected: too similar with seq %20.20s diff=%i diff_min_frac*cov_kj=%f diff_suff=%i nres=%i cov_kj=%i\n",sname[k],sname[j],diff,diff_min_frac*cov_kj,diff_suff,nres[k],cov_kj);
+ // printf("%s\n%s\n\n",seq[k],seq[j]);
+ // }
+
+ } // End Loop over all candidate sequences kk
+
+ // // DEBUG
+ // printf("\n");
+ // printf("seqid_prev[k]= \n");
+ // for (k=0; k<N_in; k++) printf("%2i ",seqid_prev[k]);
+ // printf("\n");
+
+ // Increment seqid /* MR1 */
+ seqid_step = imax(1,imin(5,diffNmax/(diffNmax_prev-diffNmax+1)*seqid_step/2));
+ seqid += seqid_step;
+
+ } // End Loop over seqid
+
+ if (v>=2)
+ {
+ printf("%i out of %i sequences passed filter (",n,N_in-N_ss);
+ if (par.coverage)
+ printf("%i%% min coverage, ",coverage);
+ if (qid)
+ printf("%i%% min sequence identity to query, ",qid);
+ if (qsc>-10)
+ printf("%.2f bits min score per column to query, ",qsc);
+ if (Ndiff<N_in && Ndiff>0)
+ printf("up to %i%% position-dependent max pairwise sequence identity)\n",seqid);
+ else
+ printf("%i%% max pairwise sequence identity)\n",seqid1);
+ }
+
+ for (k=0; k<N_in; k++) keep[k]=in[k];
+ delete[] in; in = NULL;
+ delete[] inkk; inkk = NULL;
+ //delete[] idmax; idmax = NULL;
+ delete[] Nmax; /* MR1 */
+ delete[] idmaxwin; idmaxwin = NULL;
+ delete[] seqid_prev; seqid_prev = NULL;
+ delete[] N; N = NULL;
+#if 0
+ printf("%s:%s:%d: sequences accepted = %d/%d\n", __FUNCTION__, __FILE__, __LINE__, n, N_in-N_ss);
+#endif
+ return n;
+}
+
+
+
+/* MR1: the Alignment::HomologyFilter is no longer needed in hhalign-stand-alone */
+/////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Filter for min score per column coresc with core query profile,
+ * defined by coverage_core and qsc_core
+ */
+/////////////////////////////////////////////////////////////////////////////
+int
+Alignment::HomologyFilter(int coverage_core, float qsc_core, float coresc)
+{
+ const int seqid_core=90; //maximum sequence identity in core alignment
+ const int qid_core=0;
+ const int Ndiff_core=0;
+ int n;
+ HMM qcore;
+ char* coreseq=new(char[N_in]); // coreseq[k]=1 if sequence belongs to core of alignment (i.e. it is very similar to query)
+ for (int k=0; k<N_in; k++) coreseq[k]=keep[k]; // Copy keep[] into coreseq[]
+
+ // Remove sequences with seq. identity larger than seqid percent (remove the shorter of two)
+ int v1=v; v=1;
+ n = Filter2(coreseq,coverage_core,qid_core,qsc_core,seqid_core,seqid_core,Ndiff_core);
+ v=v1;
+ if (v>=2)
+ {
+ printf("%i out of %i core alignment sequences passed filter (",n,N_in-N_ss);
+ if (par.coverage_core)
+ printf("%i%% min coverage, ",coverage_core);
+ if (qid_core)
+ printf("%i%% min sequence identity to query, ",qid_core);
+ if (qsc_core>-10)
+ printf("%.2f bits min score per column to query, ",qsc_core);
+ printf("%i%% max pairwise sequence identity)\n",seqid_core);
+ }
+
+ // Calculate bare AA frequencies and transition probabilities -> qcore.f[i][a], qcore.tr[i][a]
+ FrequenciesAndTransitions(qcore,coreseq);
+
+ // Add transition pseudocounts to query -> q.p[i][a] (gapd=1.0, gape=0.333, gapf=gapg=1.0, gaph=gapi=1.0, gapb=1.0
+ qcore.AddTransitionPseudocounts(1.0,0.333,1.0,1.0,1.0,1.0,1.0);
+
+ // Generate an amino acid frequency matrix from f[i][a] with full pseudocount admixture (tau=1) -> g[i][a]
+ qcore.PreparePseudocounts();
+
+ // Add amino acid pseudocounts to query: qcore.p[i][a] = (1-tau)*f[i][a] + tau*g[i][a]
+ qcore.AddAminoAcidPseudocounts(2,1.5,2.0,1.0); // pcm=2, pca=1.0, pcb=2.5, pcc=1.0
+
+ // Filter out all sequences below min score per column with qcore
+ n=FilterWithCoreHMM(keep, coresc, qcore);
+
+ if (v>=2) cout<<n<<" out of "<<N_in-N_ss<<" sequences filtered by minimum score-per-column threshold of "<<qsc_core<<"\n";
+ delete[] coreseq; coreseq = NULL;
+ return n;
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Filter out all sequences below a minimum score per column with profile qcore
+ */
+int
+Alignment::FilterWithCoreHMM(char in[], float coresc, HMM& qcore)
+{
+ int k; // count sequences in alignment
+ int i; // column in query alignment
+ int a; // amino acid (0..19)
+ int n=1; // number of sequences that passed filter
+ float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore
+ char gap; // 1: previous state in seq k was a gap 0: previous state in seq k was an amino acid
+ float score; // score of sequence k aligned with qcore
+
+ for (i=1; i<=L; i++) logodds[i]=new(float[21]);
+
+ // Determine first[k], last[k]?
+ if (first==NULL)
+ {
+ first=new(int[N_in]);// first non-gap position in sequence k
+ last =new(int[N_in]);// last non-gap position in sequence k
+ for (k=0; k<N_in; k++) // do this for ALL sequences, not only those with in[k]==1 (since in[k] may be display[k])
+ {
+ for (i=1; i<=L; i++) if (X[k][i]<NAA) break;
+ first[k]=i;
+ for (i=L; i>=1; i--) if (X[k][i]<NAA) break;
+ last[k]=i;
+ }
+ }
+
+ // Determine number of residues nres[k]?
+ if (nres==NULL)
+ {
+ nres=new(int[N_in]);
+ for (k=0; k<N_in; k++) // do this for ALL sequences, not only those with in[k]==1 (since in[k] may be display[k])
+ {
+ int nr=0;
+ for (i=first[k]; i<=last[k]; i++)
+ if (X[k][i]<NAA) nr++;
+ nres[k]=nr;
+ // printf("%20.20s nres=%3i first=%3i last=%3i\n",sname[k],nr,f,l);
+ }
+ }
+
+ // Precalculate the log-odds for qcore
+ for (i=1; i<=L; i++)
+ {
+ for (a=0; a<NAA; a++)
+ logodds[i][a]=fast_log2(qcore.p[i][a]/pb[a]);
+ logodds[i][ANY]=-0.5; // half a bit penalty for X
+
+ // printf(" A R N D C Q E G H I L K M F P S T W Y V\n");
+ // printf("%6i ",i);
+ // for (a=0; a<20; ++a) fprintf(stdout,"%5.1f ",100*qcore.f[i][a]);
+ // printf("\n");
+ // printf(" ");
+ // for (a=0; a<20; ++a) fprintf(stdout,"%5.1f ",100*qcore.g[i][a]);
+ // printf("\n");
+ // printf(" ");
+ // for (a=0; a<20; ++a) fprintf(stdout,"%5.1f ",100*qcore.p[i][a]);
+ // printf("\n");
+ // printf(" ");
+ // for (a=0; a<20; ++a) fprintf(stdout,"%5.1f ",100*pb[a]);
+ // printf("\n");
+ // printf(" ");
+ // for (a=0; a<20; ++a) fprintf(stdout,"%5.2f ",fast_log2(qcore.p[i][a]/pb[a]));
+ // printf("\n");
+ }
+
+ // Main loop: test all sequences k
+ for (k=kfirst+1; k<N_in; k++)
+ {
+ if (!in[k]) continue; // if in[k]==0 sequence k will be suppressed directly
+
+ float score_M=0.0;
+ float score_prev=0.0;
+
+ // Calculate score of sequence k with core HMM
+ score=0; gap=0;
+ for (i=first[k]; i<=last[k]; i++)
+ {
+ score_M=0.0;
+ if (X[k][i]<=ANY) // current state is Match
+ {
+ score_M=logodds[i][ (int)X[k][i]];
+ score+=logodds[i][ (int)X[k][i]];
+ if (gap) score+=qcore.tr[i][D2M]; else score+=qcore.tr[i][M2M];
+ gap=0;
+ }
+ else if (X[k][i]==GAP) // current state is Delete (ignore ENDGAPs)
+ {
+ if (gap) score+=qcore.tr[i][D2D]; else score+=qcore.tr[i][M2D];
+ gap=1;
+ }
+ if (I[k][i]) score+=qcore.tr[i][M2I]+(I[k][i]-1)*qcore.tr[i][I2I]+qcore.tr[i][I2M];
+ // if (k==2) printf("i=%3i %c:%c score_M=%6.2f score=%6.2f score_sum=%6.2f \n",i,i2aa(X[kfirst][i]),i2aa(X[k][i]),score_M,score-score_prev,score);
+ score_prev=score;
+ }
+
+ printf("k=%3i score=%6.2f\n",k,score);
+ if (score<nres[k]*coresc) in[k]=0; else n++;// reject sequence k?
+ }
+ for (i=1; i<=L; i++){
+ delete[] logodds[i]; logodds[i] = NULL;
+ }
+ delete[] logodds; logodds = NULL;
+ return n;
+}
+
+
+/* MR1 */
+#if 0
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Filter alignment to given diversity/Neff
+ */
+bool
+Alignment::FilterNeff()
+{
+ int v1=v;
+ v=v1-1;
+ const float TOLX=0.001;
+ const float TOLY=0.02;
+ char dummy[N_in+1];
+ for (int k=0; k<N_in; ++k) dummy[k]=keep[k];
+ float x=0.0,y=0.0;
+ float x0=-1.0;
+ float x1=+2.0;
+ float y0=filter_by_qsc(x0,dummy);
+ float y1=filter_by_qsc(x1,dummy);
+ int i=2;
+ while (y0-par.Neff>0 && par.Neff-y1>0)
+ {
+ x = x0 + (par.Neff-y0)*(x1-x0)/(y1-y0); // linear interpolation between (x0,y0) and (x1,y1)
+ y = filter_by_qsc(x,dummy);
+ if (v>=2) printf(" %3i x0=%6.3f -> %6.3f x=%6.3f -> %6.3f x1=%6.3f -> %6.3f \n",++i,x0,y0,x,y,x1,y1);
+ if (y>par.Neff) {x0=x; y0=y;} else {x1=x; y1=y;}
+ if (fabs(par.Neff-y)<TOLY || x1-x0<TOLX) break;
+ }
+ v=v1;
+
+ if (y0>=par.Neff && y1<=par.Neff)
+ {
+ // Write filtered alignment WITH insert states (lower case) to alignment file
+ if (v>=2) printf("Found Neff=%6.3f at filter threshold qsc=%6.3f\n",y,x);
+ return true;
+ }
+ else if (v>=1)
+ printf("Diversity of unfiltered alignment %.2f is below target diversity %.2f. No alignment written\n",y0,par.Neff);
+
+ return false;
+}
+
+float Alignment::filter_by_qsc(float qsc, char* dummy)
+{
+ HMM q;
+ for (int k=0; k<N_in; ++k) keep[k]=dummy[k];
+ Filter2(keep,par.coverage,0,qsc,par.max_seqid+1,par.max_seqid,0);
+ FrequenciesAndTransitions(q);
+ // printf("qsc=%4.1f N_filtered=%-3i Neff=%6.3f\n",qsc,n,q.Neff_HMM);
+ return q.Neff_HMM;
+}
+#endif
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Calculate AA frequencies q.p[i][a] and transition probabilities q.tr[i][a] from alignment
+ */
+void
+Alignment::FrequenciesAndTransitions(HMM& q, char* in)
+{
+ int k; // index of sequence
+ int i; // position in alignment
+ int a; // amino acid (0..19)
+ int ni[NAA+3]; // number of times amino acid a occurs at position i
+ int naa; // number of different amino acids
+
+ if (v>=3)
+ cout<<"Calculating position-dependent weights on subalignments\n";
+
+ if (in==NULL) in=keep; // what's this good for?
+
+ if (N_filtered>1)
+ {
+ for (k=0; k<N_in; k++) wg[k]=0.0; // initialized wg[k]
+ // Calculate global weights
+ for (i=1; i<=L; i++) // for all positions i in alignment
+ {
+ for (a=0; a<20; a++) ni[a]=0;
+ for (k=0; k<N_in; k++) if (in[k]) ni[ (int)X[k][i]]++;
+ naa=0; for (a=0; a<20; a++) if(ni[a]) naa++;
+ if (!naa) naa=1; //naa=0 when column consists of only gaps and Xs (=ANY)
+ for (k=0; k<N_in; k++)
+ if (in[k] && X[k][i]<20)
+ wg[k] += 1.0/float(ni[ (int)X[k][i]]*naa*(nres[k]+30));
+ // ensure that each residue of a short sequence contributes as much as a residue of a long sequence:
+ // contribution is proportional to one over sequence length nres[k] plus 30.
+ }
+ NormalizeTo1(wg,N_in);
+
+
+ // Do pos-specific sequence weighting and calculate amino acid frequencies and transitions
+ for (k=0; k<N_in; k++) X[k][0]=ENDGAP; // make sure that sequences ENTER subalignment j for j=1
+ for (k=0; k<N_in; k++) X[k][L+1]=ENDGAP; // does it have an influence?
+
+#ifdef HAVE_OPENMP
+ if(par.wg != 1)
+ {
+ #pragma omp parallel sections
+ {
+ #pragma omp section
+ Amino_acid_frequencies_and_transitions_from_M_state(q,in); // use subalignments of seqs with residue in i
+ #pragma omp section
+ Transitions_from_I_state(q,in); // use subalignments of seqs with insert in i
+ #pragma omp section
+ Transitions_from_D_state(q,in); // use subalignments of seqs with delete in i. Must be last of these three calls if par.wg==1!
+ }
+ }
+ else
+ {
+ #pragma omp parallel sections
+ {
+ #pragma omp section
+ Amino_acid_frequencies_and_transitions_from_M_state(q,in); // use subalignments of seqs with residue in i
+ #pragma omp section
+ Transitions_from_I_state(q,in); // use subalignments of seqs with insert in i
+ }
+ Transitions_from_D_state(q,in); // use subalignments of seqs with delete in i. Must be last of these three calls if par.wg==1!
+ }
+#else
+ Amino_acid_frequencies_and_transitions_from_M_state(q,in);
+ Transitions_from_I_state(q,in);
+ Transitions_from_D_state(q,in);
+#endif
+ }
+ else // N_filtered==1
+ {
+ X[kfirst][0]=X[kfirst][L+1]=ANY; // (to avoid anallowed access within loop)
+ q.Neff_HMM=1.0f;
+ for (i=0; i<=L+1; i++) // for all positions i in alignment
+ {
+ q.Neff_M[i]=1.0f;
+ q.Neff_I[i]=q.Neff_D[i]=0.0f;
+ for (a=0; a<20; a++) q.f[i][a]=0.0;
+ /* this is the crucial change that makes terminal-X work */
+ //q.f[i][ (int)(X[kfirst][i]) ] = 1.0; /* MR1 */
+ if (X[kfirst][i] < ANY) /* MR1 */
+ q.f[i][(unsigned int) X[kfirst][i] ] = 1.0;
+ else
+ for (a=0; a<20; ++a) q.f[i][a]=pb[a];
+ q.tr[i][M2M]=0;
+ q.tr[i][M2I]=-100000.0;
+ q.tr[i][M2D]=-100000.0;
+ q.tr[i][I2M]=-100000.0;
+ q.tr[i][I2I]=-100000.0;
+ q.tr[i][D2M]=-100000.0;
+ q.tr[i][D2D]=-100000.0;
+ }
+ q.tr[0][I2M]=0;
+ q.tr[L][I2M]=0;
+ q.tr[0][D2M]=0;
+ q.Neff_M[0]=q.Neff_I[0]=q.Neff_D[0]=99.999; // Neff_av[0] is used for calculation of transition pseudocounts for the start state
+ }
+
+ if (v>=3)
+ {
+ printf("\nMatches:\n");
+ printf("col Neff nseqs\n");
+ for (i=1; i<=imin(L,100); i++)
+ printf("%3i %5.2f %3i\n",i,q.Neff_M[i],nseqs[i]);
+
+ printf("\nInserts:\n");
+ printf("col Neff nseqs\n");
+ for (i=1; i<=imin(L,100); i++)
+ printf("%3i %5.2f %3i\n",i,q.Neff_I[i],nseqs[i]);
+
+ printf("\nDeletes:\n");
+ printf("col Neff nseqs\n");
+ for (i=1; i<=imin(L,100); i++)
+ printf("%3i %5.2f %3i\n",i,q.Neff_D[i],nseqs[i]);
+ }
+
+ // Copy column information into HMM q
+ q.L=L;
+ q.N_in=N_in;
+ q.N_filtered=N_filtered;
+ for (i=1; i<=L; i++) q.l[i]=l[i];
+
+ // Set names in HMM q
+ if (strlen(q.name)==0) strcpy(q.name,name);
+ if (strlen(q.longname)==0) strcpy(q.longname,longname);
+ if (strlen(q.fam)==0) strcpy(q.fam,fam);
+ ScopID(q.cl,q.fold,q.sfam,q.fam); // derive superfamily, fold and class code from family name
+ strcpy(q.file,file); // Store basename of alignment file name in q.file
+
+ // Copy sequences to be displayed into HMM
+ q.nss_dssp=q.nsa_dssp=q.nss_pred=q.nss_conf=q.nfirst=-1;
+ int n=0;
+ if (kss_dssp>=0) q.nss_dssp=n++; // copy dssp sequence?
+ if (ksa_dssp>=0) q.nsa_dssp=n++; // copy dssp sequence?
+ if (kss_pred>=0) q.nss_pred=n++; // copy psipred sequence?
+ if (kss_conf>=0) q.nss_conf=n++; // copy confidence value sequence?
+
+ // Calculate consensus sequence?
+ if (par.showcons || par.cons)
+ {
+ float maxw;
+ int maxa;
+ if (par.showcons)
+ {
+ // Reserve space for consensus/conservation sequence as Q-T alignment mark-up
+ q.ncons=n++;
+ q.sname[q.ncons]=new(char[10]);
+ if (!q.sname[q.ncons]) {MemoryError("array of names for displayed sequences");}
+ strcpy(q.sname[q.ncons],"Consensus");
+ q.seq[q.ncons]=new(char[L+2]);
+ if (!q.seq[q.ncons]) {MemoryError("array of names for displayed sequences");}
+ }
+ if (par.cons)
+ {
+ // Reserve space for consensus sequence as first sequence in alignment
+ q.nfirst=n++; kfirst=-1;
+ q.sname[q.nfirst]=new(char[strlen(name)+11]);
+ if (!q.sname[q.nfirst]) {MemoryError("array of names for displayed sequences");}
+ strcpy(q.sname[q.nfirst],name);
+ strcat(q.sname[q.nfirst],"_consensus");
+ q.seq[q.nfirst]=new(char[L+2]);
+ if (!q.seq[q.nfirst]) {MemoryError("array of names for displayed sequences");}
+ }
+ // Calculate consensus amino acids using similarity matrix
+ for (i=1; i<=L; i++)
+ {
+ maxw=0.0; maxa=0;
+ for (a=0; a<20; a++)
+ if (q.f[i][a]-pb[a]>maxw) {maxw = q.f[i][a]-pb[a]; maxa = a;}
+
+ if (par.showcons)
+ {
+ maxw =0.0;
+ for (int b=0; b<20; b++) maxw += q.f[i][b]*Sim[maxa][b]*Sim[maxa][b];
+ maxw *= q.Neff_M[i]/(q.Neff_HMM+1); // columns with many gaps don't get consensus symbol
+ if (maxw>0.6) q.seq[q.ncons][i] = uprchr(i2aa(maxa));
+ else if (maxw>0.4) q.seq[q.ncons][i] = lwrchr(i2aa(maxa));
+ else q.seq[q.ncons][i] = 'x';
+ }
+ if (par.cons) q.seq[q.nfirst][i] = uprchr(i2aa(maxa));
+ }
+ if (par.showcons)
+ {
+ q.seq[q.ncons][0]='-';
+ q.seq[q.ncons][L+1]='\0';
+ }
+ if (par.cons)
+ {
+ q.seq[q.nfirst][0]='-';
+ q.seq[q.nfirst][L+1]='\0';
+ }
+ }
+
+ // Copy sequences to be displayed from alignment to HMM
+ for (k=0; k<N_in; k++)
+ {
+ int nn;
+ if (display[k])
+ {
+ if (0 && (n>=MAXSEQDIS)) {
+ /* FIXME: the test was if(n>=MAXSEQDIS),
+ this test was necessary because alignment memory was static,
+ now it should be dynamic, and should always have the right size,
+ there are at least number-of-sequences plus a 'bit' more
+ however, I do not know what that 'bit' is likely to be (in the future).
+ at the moment it is 1 for the consnseus and 1 for structure,
+ but this might change (FS)
+ */
+ if (par.mark) cerr<<"WARNING: maximum number "<<MAXSEQDIS<<" of sequences for display of alignment exceeded\n";
+ break;
+ }
+ if (k==kss_dssp) nn=q.nss_dssp; // copy dssp sequence to nss_dssp
+ else if (k==ksa_dssp) nn=q.nsa_dssp;
+ else if (k==kss_pred) nn=q.nss_pred;
+ else if (k==kss_conf) nn=q.nss_conf;
+ else if (k==kfirst) nn=q.nfirst=n++;
+ else nn=n++;
+ // strcut(sname[k]," "); // delete rest of name line beginning with two spaces " " // Why this?? Problem for pdb seqs without chain
+ q.sname[nn]=new(char[strlen(sname[k])+1]);
+ if (!q.sname[nn]) {MemoryError("array of names for displayed sequences");}
+ strcpy(q.sname[nn],sname[k]);
+ q.seq[nn]=new(char[strlen(seq[k])+1]);
+ if (!q.seq[nn]) {MemoryError("array of names for displayed sequences");}
+ strcpy(q.seq[nn],seq[k]);
+ }
+ }
+ q.n_display=n; // how many sequences to be displayed in alignments?
+
+ // Copy secondary structure information into HMM
+ if (kss_dssp>=0)
+ for (i=1; i<=L; i++) q.ss_dssp[i]=X[kss_dssp][i];
+ if (ksa_dssp>=0)
+ for (i=1; i<=L; i++) q.sa_dssp[i]=X[ksa_dssp][i];
+ if (kss_pred>=0)
+ {
+ for (i=1; i<=L; i++) q.ss_pred[i]=X[kss_pred][i];
+ if (kss_conf>=0)
+ for (i=1; i<=L; i++) q.ss_conf[i]=X[kss_conf][i];
+ else
+ for (i=1; i<=L; i++) q.ss_conf[i]=5;
+ }
+
+ q.lamda=0.0;
+ q.mu=0.0;
+
+ // Debug: print occurence of amino acids for each position i
+ if (v>=2) printf("Effective number of sequences exp(entropy) = %-4.1f\n",q.Neff_HMM); //PRINT
+ if (v>=3)
+ {
+ cout<<"\nMatr: ";
+ for (a=0; a<20; a++) printf("%4.1f ",100*pb[a]);
+ cout<<"\nAmino acid frequencies without pseudocounts:\n";
+ cout<<" A R N D C Q E G H I L K M F P S T W Y V\n";
+ for (i=1; i<=L; i++)
+ {
+ printf("%3i: ",i);
+ for (a=0; a<20; a++) printf("%4.0f ",100*q.f[i][a]);
+ cout<<endl;
+ }
+ cout<<"\n";
+
+ printf("\nListing transition probabilities without pseudocounts:\n");
+ printf(" i M->M M->I M->D I->M I->I D->M D->D Neff_M Neff_I Neff_D\n");
+ for (i=0; i<=L; i++)
+ {
+ printf("%4i %6.3f %6.3f %6.3f ",i,pow(2.0,q.tr[i][M2M]),pow(2.0,q.tr[i][M2I]),pow(2.0,q.tr[i][M2D]));
+ printf("%6.3f %6.3f ",pow(2.0,q.tr[i][I2M]),pow(2.0,q.tr[i][I2I]));
+ printf("%6.3f %6.3f ",pow(2.0,q.tr[i][D2M]),pow(2.0,q.tr[i][D2D]));
+ printf("%6.3f %6.3f %6.3f\n",q.Neff_M[i],q.Neff_I[i],q.Neff_D[i]);
+ }
+ }
+ q.trans_lin=0;
+ q.has_pseudocounts=false; /* MR1 */
+
+ return;
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/*
+ * FIXME: one of the most time consuming routines (according to gprof on r112)
+ */
+/**
+ * @brief Calculate freqs q.f[i][a] and transitions q.tr[i][a] (a=MM,MI,MD) with pos-specific subalignments
+ * Pos-specific weights are calculated like in "GetPositionSpecificWeights()"
+ */
+void
+Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM& q, char* in)
+{
+ // Calculate position-dependent weights wi[k] for each i.
+ // For calculation of weights in column i use sub-alignment
+ // over sequences which have a *residue* in column i (no gap, no end gap)
+ // and over columns where none of these sequences has an end gap.
+ // This is done by updating the arrays n[j][a] at each step i-1->i while letting i run from 1 to L.
+ // n[j][a] = number of occurences of amino acid a at column j of the subalignment,
+ // => only columns with n[j][ENDGAP]=0 are contained in the subalignment!
+ // If no sequences enter or leave the subalignment at the step i-1 -> i (i.e. change=0)
+ // then the old values wi[k], Neff[i-1], and ncol are used for the new position i.
+ // Index a can be an amino acid (0-19), ANY=20, GAP=21, or ENDGAP=22
+
+ int k; // index of sequence
+ int i,j; // position in alignment
+ int a; // amino acid (0..19)
+ int naa; // number of different amino acids
+ int** n; // n[j][a] = number of seq's with some residue at column i AND a at position j
+ //float wi[MAXSEQ]; // weight of sequence k in column i, calculated from subalignment i
+ float *wi=NULL; // weight of sequence k in column i, calculated from subalignment i
+ //float Neff[MAXRES]; // diversity of subalignment i
+ float *Neff = new(float[par.maxResLen]); // diversity of subalignment i
+ int nseqi=0; // number of sequences in subalignment i
+ int ncol=0; // number of columns j that contribute to Neff[i]
+ char change; // has the set of sequences in subalignment changed? 0:no 1:yes
+ float fj[NAA+3]; // to calculate entropy
+ float sum;
+
+ wi = new(float[N_in+2]);
+
+ // Global weights?
+ if (par.wg==1)
+ for (k=0; k<N_in; k++) wi[k]=wg[k];
+
+ // Initialization
+ q.Neff_HMM=0.0f;
+ Neff[0]=0.0; // if the first column has no residues (i.e. change==0), Neff[i]=Neff[i-1]=Neff[0]
+ n = new(int*[L+2]);
+ for (j=1; j<=L; j++) n[j]=new(int[NAA+3]);
+ for (j=1; j<=L; j++)
+ for (a=0; a<NAA+3; a++) n[j][a]=0;
+
+
+ //////////////////////////////////////////////////////////////////////////////////////////////
+ // Main loop through alignment columns
+ for (i=1; i<=L; i++) // Calculate wi[k] at position i as well as Neff[i]
+ {
+
+ if (par.wg==0)
+ {
+
+ change=0;
+ // Check all sequences k and update n[j][a] and ri[j] if necessary
+ for (k=0; k<N_in; k++)
+ {
+ if (!in[k]) continue;
+ if (X[k][i-1]>=ANY && X[k][i]<ANY)
+ { // ... if sequence k was NOT included in i-1 and has to be included for column i
+ change=1;
+ nseqi++;
+ for (int j=1; j<=L; j++) n[j][ (int)X[k][j]]++;
+ }
+ else if (X[k][i-1]<ANY && X[k][i]>=ANY)
+ { // ... if sequence k WAS included in i-1 and has to be thrown out for column i
+ change=1;
+ nseqi--;
+ for (int j=1; j<=L; j++) n[j][ (int)X[k][j]]--;
+ }
+ } //end for (k)
+ nseqs[i]=nseqi;
+
+ // If subalignment changed: update weights wi[k] and Neff[i]
+ if (change)
+ {
+ // Initialize weights and numbers of residues for subalignment i
+ ncol=0;
+ for (k=0; k<N_in; k++) wi[k]=1E-8; // for pathological alignments all wi[k] can get 0; /* MR1 */
+
+ // sum wi[k] over all columns j and sequences k of subalignment
+ for (j=1; j<=L; j++)
+ {
+ // do at least a fraction MAXENDGAPFRAC of sequences in subalignment contain an end gap in j?
+ if (n[j][ENDGAP]>MAXENDGAPFRAC*nseqi) continue;
+ naa=0; for (a=0; a<20; a++) if(n[j][a]) naa++;
+ if (naa==0) continue;
+ ncol++;
+ for (k=0; k<N_in; k++)
+ {
+ if (in[k] && X[k][i]<ANY && X[k][j]<ANY)
+ {
+ // if (!n[j][ (int)X[k][j]]) {fprintf(stderr,"Error: Mi=%i: n[%i][X[%i]]=0! (X[%i]=%i)\n",i,j,k,k,X[k][j]);}
+ wi[k]+=1.0/float(n[j][ (int)X[k][j] ]*naa);
+ }
+ }
+ }
+
+ // Check whether number of columns in subalignment is sufficient
+ if (ncol<NCOLMIN)
+ // Take global weights
+ for (k=0; k<N_in; k++)
+ if(in[k] && X[k][i]<ANY) wi[k]=wg[k]; else wi[k]=0.0;
+
+ // Calculate Neff[i]
+ Neff[i]=0.0;
+ for (j=1; j<=L; j++)
+ {
+ // do at least a fraction MAXENDGAPFRA of sequences in subalignment contain an end gap in j?
+ if (n[j][ENDGAP]>MAXENDGAPFRAC*nseqi) continue;
+ for (a=0; a<20; a++) fj[a]=0;
+ for (k=0; k<N_in; k++)
+ if (in[k] && X[k][i]<ANY && X[k][j]<ANY)
+ fj[ (int)X[k][j] ]+=wi[k];
+ NormalizeTo1(fj,NAA);
+ for (a=0; a<20; a++)
+ if (fj[a]>1E-10) Neff[i]-=fj[a]*fast_log2(fj[a]);
+ }
+ if (ncol>0) Neff[i]=pow(2.0,Neff[i]/ncol); else Neff[i]=1.0;
+
+ }
+
+ else //no update was necessary; copy values for i-1
+ {
+ Neff[i]=Neff[i-1];
+ }
+ }
+
+
+ // Calculate amino acid frequencies q.f[i][a] from weights wi[k]
+ for (a=0; a<20; a++) q.f[i][a]=0;
+ for (k=0; k<N_in; k++) if (in[k]) q.f[i][ (int)X[k][i] ]+=wi[k];
+ NormalizeTo1(q.f[i],NAA,pb);
+
+ // Calculate transition probabilities from M state
+ q.tr[i][M2M]=q.tr[i][M2D]=q.tr[i][M2I]=0.0;
+ for (k=0; k<N_in; k++) //for all sequences
+ {
+ if (!in[k]) continue;
+ //if input alignment is local ignore transitions from and to end gaps
+ if (X[k][i]<ANY) //current state is M
+ {
+ if (I[k][i]) //next state is I
+ q.tr[i][M2I]+=wi[k];
+ else if (X[k][i+1]<=ANY) //next state is M
+ q.tr[i][M2M]+=wi[k];
+ else if (X[k][i+1]==GAP) //next state is D
+ q.tr[i][M2D]+=wi[k];
+ }
+ } // end for(k)
+ // Normalize and take log
+ sum = q.tr[i][M2M]+q.tr[i][M2I]+q.tr[i][M2D]+FLT_MIN;
+ q.tr[i][M2M]=log2(q.tr[i][M2M]/sum);
+ q.tr[i][M2I]=log2(q.tr[i][M2I]/sum);
+ q.tr[i][M2D]=log2(q.tr[i][M2D]/sum);
+
+ // for (k=0; k<N_in; k++) if (in[k]) w[k][i]=wi[k];
+ }
+ // DD TODO:fill in all the missing Neff values
+
+
+ // end loop through alignment columns i
+ //////////////////////////////////////////////////////////////////////////////////////////////
+
+ delete[](wi); wi=NULL;
+ // delete n[][]
+ for (j=1; j<=L; j++){
+ delete[](n[j]); (n[j]) = NULL;
+ }
+ delete[](n); (n) = NULL;
+
+ q.tr[0][M2M]=0;
+ q.tr[0][M2I]=-100000;
+ q.tr[0][M2D]=-100000;
+ q.tr[L][M2M]=0;
+ q.tr[L][M2I]=-100000;
+ q.tr[L][M2D]=-100000;
+ q.Neff_M[0]=99.999; // Neff_av[0] is used for calculation of transition pseudocounts for the start state
+
+ // Set emission probabilities of zero'th (begin) state and L+1st (end) state to background probabilities
+ for (a=0; a<20; a++) q.f[0][a]=q.f[L+1][a]=pb[a];
+
+ // Assign Neff_M[i] and calculate average over alignment, Neff_M[0]
+ if (par.wg==1)
+ {
+ for (i=1; i<=L; i++)
+ {
+ float sum=0.0f;
+ for (a=0; a<20; a++)
+ if (q.f[i][a]>1E-10) sum -= q.f[i][a]*fast_log2(q.f[i][a]);
+ q.Neff_HMM+=pow(2.0,sum);
+ }
+ q.Neff_HMM/=L;
+ float Nlim=fmax(10.0,q.Neff_HMM+1.0); // limiting Neff
+ float scale=log2((Nlim-q.Neff_HMM)/(Nlim-1.0)); // for calculating Neff for those seqs with inserts at specific pos
+ for (i=1; i<=L; i++)
+ {
+ float w_M=-1.0/N_filtered;
+ for (k=0; k<N_in; k++)
+ if (in[k] && X[k][i]<=ANY) w_M+=wg[k];
+ if (w_M<0) q.Neff_M[i]=1.0;
+ else q.Neff_M[i] = Nlim - (Nlim-1.0)*fpow2(scale*w_M);
+ // fprintf(stderr,"M i=%3i ncol=--- Neff_M=%5.2f Nlim=%5.2f w_M=%5.3f Neff_M=%5.2f\n",i,q.Neff_HMM,Nlim,w_M,q.Neff_M[i]);
+ }
+ }
+ else
+ {
+ for (i=1; i<=L; i++)
+ {
+ q.Neff_HMM+=Neff[i];
+ q.Neff_M[i]=Neff[i];
+ if (q.Neff_M[i] == 0) { q.Neff_M[i] = 1; } /* MR1 */
+ }
+ q.Neff_HMM/=L;
+ }
+
+ delete[] Neff; Neff = NULL;
+
+ return;
+
+} /* this is the end of Alignment::Amino_acid_frequencies_and_transitions_from_M_state() */
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Calculate transitions q.tr[i][a] (a=DM,DD) with pos-specific subalignments
+ */
+void
+Alignment::Transitions_from_I_state(HMM& q, char* in)
+{
+ // Calculate position-dependent weights wi[k] for each i.
+ // For calculation of weights in column i use sub-alignment
+ // over sequences which have a INSERT in column i
+ // and over columns where none of these sequences has an end gap.
+ // This is done by calculating the arrays n[j][a] and rj[j] at each step i-1->i while letting i run from 1 to L.
+ // n[j][a] = number of occurences of amino acid a at column j of the subalignment,
+ // => only columns with n[j][ENDGAP]=0 are contained in the subalignment!
+ // If no sequences enter or leave the subalignment at the step i-1 -> i (i.e. change=0)
+ // then the old values wi[k], Neff[i-1], and ncol are used for the new position i.
+ // Index a can be an amino acid (0-19), ANY=20, GAP=21, or ENDGAP=22
+
+ int k; // index of sequence
+ int i,j; // position in alignment
+ int a; // amino acid (0..19)
+ int naa; // number of different amino acids
+ int** n; // n[j][a] = number of seq's with some residue at column i AND a at position j
+ //float wi[MAXSEQ]; // weight of sequence k in column i, calculated from subalignment i
+ float *wi = NULL; // weight of sequence k in column i, calculated from subalignment i
+ //float Neff[MAXRES]; // diversity of subalignment i
+ float *Neff = new(float[par.maxResLen]); // diversity of subalignment i
+ int nseqi; // number of sequences in subalignment i
+ int ncol; // number of columns j that contribute to Neff[i]
+ float fj[NAA+3]; // to calculate entropy
+ float sum;
+ float Nlim=0.0; // only for global weights
+ float scale=0.0; // only for global weights
+
+ wi = new(float[N_in+2]);
+
+ // Global weights?
+ if (par.wg==1)
+ {
+ for (k=0; k<N_in; k++) wi[k]=wg[k];
+ Nlim=fmax(10.0,q.Neff_HMM+1.0); // limiting Neff
+ scale=log2((Nlim-q.Neff_HMM)/(Nlim-1.0)); // for calculating Neff for those seqs with inserts at specific pos
+ }
+
+ // Initialization
+ n = new(int*[L+2]);
+ for (j=1; j<=L; j++) n[j]=new(int[NAA+3]);
+
+ //////////////////////////////////////////////////////////////////////////////////////////////
+ // Main loop through alignment columns
+ for (i=1; i<=L; i++) // Calculate wi[k] at position i as well as Neff[i]
+ {
+ if (par.wg==0) // local weights?
+ {
+
+ // Calculate n[j][a] and ri[j]
+ nseqi=0;
+ for (k=0; k<N_in; k++)
+ {
+ if (in[k] && I[k][i]>0)
+ {
+ if (nseqi==0) // Initialize only if inserts present! Otherwise O(L*L) even for single sequences!
+ {
+ // Initialization of n[j][a]
+ for (j=1; j<=L; j++)
+ for (a=0; a<NAA+3; a++) n[j][a]=0;
+ }
+ nseqi++;
+ for (int j=1; j<=L; j++) n[j][ (int)X[k][j]]++;
+ }
+ } //end for (k)
+ nseqs[i]=nseqi;
+
+ // If there is no sequence in subalignment j ...
+ if (nseqi==0)
+ {
+ ncol=0;
+ Neff[i]=0.0; // effective number of sequence = 0!
+ q.tr[i][I2M]=-100000;
+ q.tr[i][I2I]=-100000;
+ continue;
+ }
+
+ // update weights wi[k] and Neff[i]
+ // if (1)
+ {
+ // Initialize weights and numbers of residues for subalignment i
+ ncol=0;
+ for (k=0; k<N_in; k++) wi[k]=0.0;
+
+ // sum wi[k] over all columns j and sequences k of subalignment
+ for (j=1; j<=L; j++)
+ {
+ if (n[j][ENDGAP]>MAXENDGAPFRAC*nseqi) continue;
+ naa=0; for (a=0; a<20; a++) if(n[j][a]) naa++;
+ if (naa==0) continue;
+ ncol++;
+ for (k=0; k<N_in; k++)
+ {
+ if (in[k] && I[k][i]>0 && X[k][j]<ANY)
+ {
+ if (!n[j][ (int)X[k][j]]) {fprintf(stderr,"Error: Ii=%i: n[%i][X[%i]]=0! (X[%i]=%i)\n",i,j,k,k,X[k][j]);}
+ wi[k]+=1.0/float(n[j][ (int)X[k][j] ]*naa);
+ }
+ }
+ }
+
+ // Check whether number of columns in subalignment is sufficient
+ if (ncol>=NCOLMIN)
+ // Take global weights
+ for (k=0; k<N_in; k++)
+ if(in[k] && I[k][i]>0) wi[k]=wg[k]; else wi[k]=0.0;
+
+ // Calculate Neff[i]
+ Neff[i]=0.0;
+ for (j=1; j<=L; j++)
+ {
+ if (n[j][ENDGAP]>MAXENDGAPFRAC*nseqi) continue;
+ for (a=0; a<20; a++) fj[a]=0;
+ for (k=0; k<N_in; k++)
+ if (in[k] && I[k][i]>0 && X[k][j]<ANY)
+ fj[ (int)X[k][j] ]+=wi[k];
+ NormalizeTo1(fj,NAA);
+ for (a=0; a<20; a++)
+ if (fj[a]>1E-10) Neff[i]-=fj[a]*fast_log2(fj[a]);
+ }
+ if (ncol>0) Neff[i]=pow(2.0,Neff[i]/ncol); else Neff[i]=1.0;
+
+ }
+ // Calculate transition probabilities from I state
+ q.tr[i][I2M]=q.tr[i][I2I]=0.0;
+ for (k=0; k<N_in; k++) //for all sequences
+ {
+ if (in[k] && I[k][i]>0) //current state is I
+ {
+ q.tr[i][I2M]+=wi[k];
+ q.tr[i][I2I]+=wi[k]*(I[k][i]-1);
+ }
+ } // end for(k)
+ }
+
+ else // fast global weights?
+ {
+ float w_I=-1.0/N_filtered;
+ ncol=0;
+ q.tr[i][I2M]=q.tr[i][I2I]=0.0;
+ // Calculate amino acid frequencies fj[a] from weights wg[k]
+ for (k=0; k<N_in; k++)
+ if (in[k] && I[k][i]>0)
+ {
+ ncol++;
+ w_I+=wg[k];
+ q.tr[i][I2M]+=wi[k];
+ q.tr[i][I2I]+=wi[k]*(I[k][i]-1);
+ }
+ if (ncol>0)
+ {
+ if (w_I<0) Neff[i]=1.0;
+ else Neff[i] = Nlim - (Nlim-1.0)*fpow2(scale*w_I);
+ // fprintf(stderr,"I i=%3i ncol=%3i Neff_M=%5.2f Nlim=%5.2f w_I=%5.3f Neff_I=%5.2f\n",i,ncol,q.Neff_HMM,Nlim,w_I,Neff[i]);
+ }
+ else
+ {
+ Neff[i]=0.0;
+ q.tr[i][I2M]=-100000;
+ q.tr[i][I2I]=-100000;
+ continue;
+ }
+ }
+
+ // Normalize and take log
+ sum = q.tr[i][I2M]+q.tr[i][I2I];
+ q.tr[i][I2M]=log2(q.tr[i][I2M]/sum);
+ q.tr[i][I2I]=log2(q.tr[i][I2I]/sum);
+
+ }
+ // end loop through alignment columns i
+ //////////////////////////////////////////////////////////////////////////////////////////////
+
+ delete[](wi); wi = NULL;
+ // delete n[][]
+ for (j=1; j<=L; j++){
+ delete[](n[j]); (n[j]) = NULL;
+ }
+ delete[](n); (n) = NULL;
+
+ q.tr[0][I2M]=0;
+ q.tr[0][I2I]=-100000;
+ q.tr[L][I2M]=0;
+ q.tr[L][I2I]=-100000;
+ q.Neff_I[0]=99.999;
+
+ // Assign Neff_I[i]
+ for (i=1; i<=L; i++) // Calculate wi[k] at position i as well as Neff[i] and Neff[i]
+ q.Neff_I[i]=Neff[i];
+
+ delete[] Neff; Neff = NULL;
+ return;
+
+} /* this is the end of Alignment::Transitions_from_I_state() */
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Calculate transitions q.tr[i][a] (a=DM,DD) with pos-specific subalignments
+ */
+void
+Alignment::Transitions_from_D_state(HMM& q, char* in)
+{
+ // Calculate position-dependent weights wi[k] for each i.
+ // For calculation of weights in column i use sub-alignment
+ // over sequences which have a DELETE in column i
+ // and over columns where none of these sequences has an end gap.
+ // This is done by updating the arrays n[j][a] and rj[j] at each step i-1->i while letting i run from 1 to L.
+ // n[j][a] = number of occurences of index a at column j of the subalignment,
+ // => only columns with n[j][ENDGAP]=0 are contained in the subalignment!
+ // If no sequences enter or leave the subalignment at the step i-1 -> i (i.e. change=0)
+ // then the old values wi[k], Neff[i-1], and ncol are used for the new position i.
+ // Index a can be an amino acid (0-19), ANY=20, GAP=21, or ENDGAP=22
+
+ int k; // index of sequence
+ int i,j; // position in alignment
+ int a; // amino acid (0..19)
+ int naa; // number of different amino acids
+ int** n; // n[j][a] = number of seq's with some residue at column i AND a at position j
+ //float wi[MAXSEQ]; // weight of sequence k in column i, calculated from subalignment i
+ float *wi=NULL; // weight of sequence k in column i, calculated from subalignment i
+ //float Neff[MAXRES]; // diversity of subalignment i
+ float *Neff = new(float[par.maxResLen]); // diversity of subalignment i
+ int nseqi=0; // number of sequences in subalignment i (for DEBUGGING)
+ int ncol=0; // number of columns j that contribute to Neff[i]
+ char change; // has the set of sequences in subalignment changed? 0:no 1:yes
+ float fj[NAA+3]; // to calculate entropy
+ float sum;
+ float Nlim=0.0; // only for global weights
+ float scale=0.0; // only for global weights
+
+ wi = new(float[N_in+2]); /* FIXME: FS */
+ // Global weights?
+ if (par.wg==1)
+ {
+ for (k=0; k<N_in; k++) wi[k]=wg[k];
+ Nlim=fmax(10.0,q.Neff_HMM+1.0); // limiting Neff
+ scale=log2((Nlim-q.Neff_HMM)/(Nlim-1.0)); // for calculating Neff for those seqs with dels at specific pos
+ }
+
+ // Initialization
+ n = new(int*[L+2]);
+ for (j=1; j<=L; j++) n[j]=new(int[NAA+3]);
+ for (j=1; j<=L; j++)
+ for (a=0; a<NAA+3; a++) n[j][a]=0;
+
+
+
+ //////////////////////////////////////////////////////////////////////////////////////////////
+ // Main loop through alignment columns
+ for (i=1; i<=L; i++) // Calculate wi[k] at position i as well as Neff[i]
+ {
+ if (par.wg==0) // if local weights
+ {
+ change=0;
+ // Check all sequences k and update n[j][a] and ri[j] if necessary
+ for (k=0; k<N_in; k++)
+ {
+ if (!in[k]) continue;
+ if (X[k][i-1]!=GAP && X[k][i]==GAP)
+ { // ... if sequence k was NOT included in i-1 and has to be included for column i
+ change=1;
+ nseqi++;
+ for (int j=1; j<=L; j++) n[j][ (int)X[k][j]]++;
+ }
+ else if (X[k][i-1]==GAP && X[k][i]!=GAP)
+ { // ... if sequence k WAS included in i-1 and has to be thrown out for column i
+ change=1;
+ nseqi--;
+ for (int j=1; j<=L; j++) n[j][ (int)X[k][j]]--;
+ }
+ } //end for (k)
+ nseqs[i]=nseqi;
+
+ // If there is no sequence in subalignment j ...
+ if (nseqi==0)
+ {
+ ncol=0;
+ Neff[i]=0.0; // effective number of sequences = 0!
+ q.tr[i][D2M]=-100000;
+ q.tr[i][D2D]=-100000;
+ continue;
+ }
+
+ // If subalignment changed: update weights wi[k] and Neff[i]
+ if (change)
+ {
+ // Initialize weights and numbers of residues for subalignment i
+ ncol=0;
+ for (k=0; k<N_in; k++) wi[k]=0.0;
+
+ // sum wg[k][i] over all columns j and sequences k of subalignment
+ for (j=1; j<=L; j++)
+ {
+ if (n[j][ENDGAP]>MAXENDGAPFRAC*nseqi) continue;
+ naa=0; for (a=0; a<20; a++) if(n[j][a]) naa++;
+ if (naa==0) continue;
+ ncol++;
+ for (k=0; k<N_in; k++)
+ {
+ if (in[k] && X[k][i]==GAP && X[k][j]<ANY)
+ {
+ if (!n[j][ (int)X[k][j]]) {fprintf(stderr,"Error: Di=%i: n[%i][X[%i]]=0! (X[%i]=%i)\n",i,j,k,k,X[k][j]);}
+ wi[k]+=1.0/float(n[j][ (int)X[k][j] ]*naa);
+ }
+ }
+ }
+
+ // Check whether number of columns in subalignment is sufficient
+ if (ncol<NCOLMIN)
+ // Take global weights
+ for (k=0; k<N_in; k++)
+ if(in[k] && X[k][i]==GAP) wi[k]=wg[k]; else wi[k]=0.0;
+
+ // Calculate Neff[i]
+ Neff[i]=0.0;
+ for (j=1; j<=L; j++)
+ {
+ if (n[j][ENDGAP]>MAXENDGAPFRAC*nseqi) continue;
+ for (a=0; a<20; a++) fj[a]=0;
+ for (k=0; k<N_in; k++)
+ if (in[k] && X[k][i]==GAP && X[k][j]<ANY)
+ fj[ (int)X[k][j] ]+=wi[k];
+ NormalizeTo1(fj,NAA);
+ for (a=0; a<20; a++)
+ if (fj[a]>1E-10) Neff[i]-=fj[a]*fast_log2(fj[a]);
+ }
+ if (ncol>0) Neff[i]=pow(2.0,Neff[i]/ncol); else Neff[i]=1.0;
+
+ }
+
+ else //no update was necessary; copy values for i-1
+ {
+ Neff[i]=Neff[i-1];
+ }
+
+ // Calculate transition probabilities from D state
+ q.tr[i][D2M]=q.tr[i][D2D]=0.0;
+ for (k=0; k<N_in; k++) //for all sequences
+ {
+ if (in[k] && X[k][i]==GAP) //current state is D
+ {
+ if (X[k][i+1]==GAP) //next state is D
+ q.tr[i][D2D]+=wi[k];
+ else if (X[k][i+1]<=ANY) //next state is M
+ q.tr[i][D2M]+=wi[k];
+ }
+ } // end for(k)
+ }
+
+ else // fast global weights?
+ {
+ float w_D=-1.0/N_filtered;
+ ncol=0;
+ q.tr[i][D2M]=q.tr[i][D2D]=0.0;
+ // Calculate amino acid frequencies fj[a] from weights wg[k]
+ for (k=0; k<N_in; k++) //for all sequences
+ if (in[k] && X[k][i]==GAP) //current state is D
+ {
+ ncol++;
+ w_D+=wg[k];
+ if (X[k][i+1]==GAP) //next state is D
+ q.tr[i][D2D]+=wi[k];
+ else if (X[k][i+1]<=ANY) //next state is M
+ q.tr[i][D2M]+=wi[k];
+ }
+ if (ncol>0)
+ {
+ if (w_D<0) Neff[i]=1.0;
+ else Neff[i] = Nlim - (Nlim-1.0)*fpow2(scale*w_D);
+ // fprintf(stderr,"D i=%3i ncol=%3i Neff_M=%5.2f Nlim=%5.2f w_D=%5.3f Neff_D=%5.2f\n",i,ncol,q.Neff_HMM,Nlim,w_D,Neff[i]);
+ }
+ else
+ {
+ Neff[i]=0.0; // effective number of sequences = 0!
+ q.tr[i][D2M]=-100000;
+ q.tr[i][D2D]=-100000;
+ continue;
+ }
+ }
+
+ // Normalize and take log
+ sum = q.tr[i][D2M]+q.tr[i][D2D];
+ q.tr[i][D2M]=log2(q.tr[i][D2M]/sum);
+ q.tr[i][D2D]=log2(q.tr[i][D2D]/sum);
+
+ }
+ // end loop through alignment columns i
+ //////////////////////////////////////////////////////////////////////////////////////////////
+
+ q.tr[0][D2M]=0;
+ q.tr[0][D2D]=-100000;
+ q.Neff_D[0]=99.999;
+
+ // Assign Neff_D[i]
+ for (i=1; i<=L; i++)
+ q.Neff_D[i]=Neff[i];
+
+ delete[](wi); wi = NULL;/* FIXME: FS */
+ // delete n[][]
+ for (j=1; j<=L; j++){
+ delete[](n[j]); (n[j]) = NULL;
+ }
+ delete[](n); (n) = NULL;
+
+ delete[] Neff; Neff = NULL;
+ return;
+
+} /* this is the end of Alignment::Transitions_from_D_state() */
+
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Write alignment without insert states (lower case) to alignment file?
+ */
+void
+Alignment::WriteWithoutInsertsToFile(char* alnfile)
+{
+ if (v>=2) cout<<"Writing alignment to "<<alnfile<<"\n";
+ FILE* alnf;
+ if (!par.append) alnf = fopen(alnfile,"w"); else alnf = fopen(alnfile,"a");
+ if (!alnf) OpenFileError(alnfile);
+ // If alignment name is different from that of query: write name into commentary line
+ if (strncmp(longname,sname[kfirst],DESCLEN-1)) fprintf(alnf,"#%s\n",longname);
+ if (v>=2) cout<<"Writing alignment to "<<alnfile<<"\n";
+ for (int k=0; k<N_in; k++)
+ if (keep[k] || display[k]==KEEP_ALWAYS) // print if either in profile (keep[k]>0) or display is obligatory (display[k]==2)
+ {
+ fprintf(alnf,">%s\n",sname[k]);
+ for (int i=1; i<=L; i++) fprintf(alnf,"%c",i2aa(X[k][i]));
+ fprintf(alnf,"\n");
+ }
+ fclose(alnf);
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+// Write stored,filtered sequences WITH insert states (lower case) to alignment file?
+/////////////////////////////////////////////////////////////////////////////////////
+void Alignment::WriteToFile(char* alnfile, const char format[])
+{
+ FILE* alnf;
+ if (!par.append) alnf = fopen(alnfile,"w"); else alnf = fopen(alnfile,"a");
+ if (!alnf) OpenFileError(alnfile);
+ // If alignment name is different from that of query: write name into commentary line
+ if (strncmp(longname,sname[kfirst],DESCLEN-1)) fprintf(alnf,"#%s\n",longname);
+ if (!format || !strcmp(format,"a3m"))
+ {
+ if (v>=2) cout<<"Writing A3M alignment to "<<alnfile<<"\n";
+ for (int k=0; k<N_in; k++)
+ if (keep[k] || display[k]==KEEP_ALWAYS) // print if either in profile (keep[k]>0) or display obligatory (display[k]==2)
+ fprintf(alnf,">%s\n%s\n",sname[k],seq[k]+1);
+ }
+ else // PSI-BLAST format
+ {
+ if (v>=2) cout<<"Writing PSI-BLAST-formatted alignment to "<<alnfile<<"\n";
+ for (int k=kfirst; k<N_in; k++) // skip sequences before kfirst!!
+ if (keep[k] || display[k]==KEEP_ALWAYS) // print if either in profile (keep[k]>0) or display obligatory (display[k]==2)
+ {
+ strcut(sname[k]);
+ fprintf(alnf,"%-20.20s ",sname[k]);
+ // for (int i=1; i<=L; i++) fprintf(alnf,"%c",i2aa(X[k][i]));
+ // fprintf(alnf,"\n");
+ char* ptr=seq[k];
+ for (; *ptr!='\0'; ptr++)
+ if (*ptr==45 || (*ptr>=65 && *ptr<=90)) fprintf(alnf,"%c",*ptr);
+ fprintf(alnf,"\n");
+ }
+ }
+
+ fclose(alnf);
+}
+
+
+
+/*
+ * FIXME: this function contains a reference to MAXSEQ & MAXCOL
+ * however, this may not be accessed (FS)
+ */
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Read a3m slave alignment of hit from file and merge into (query) master alignment
+ */
+void
+Alignment::MergeMasterSlave(Hit& hit, char ta3mfile[])
+{
+ Alignment Tali;
+ char* cur_seq = new(char[MAXCOL]); // Sequence currently read in
+ int maxcol=MAXCOL;
+ int l,ll; // position in unaligned template (T) sequence Tali.seq[l]
+ int i; // counts match states in query (Q) HMM
+ int j; // counts match states in T sequence Tali.seq[l]
+ int h; // position in aligned T sequence cur_seq[h]
+ int k; // sequence index
+ char c; //
+ printf("****************%s:%s:%d: did get into MergeMasterSlave\n", __FUNCTION__, __FILE__, __LINE__);
+ if (v>=3) printf("Merging %s to query alignment\n",ta3mfile);
+
+ // If par.append==1 do not print query alignment
+ if (par.append) for (k=0; k<N_in; k++) keep[k]=display[k]=KEEP_NOT;
+
+ // Read template alignment into Tali
+ FILE* ta3mf=fopen(ta3mfile,"r");
+ if (!ta3mf) OpenFileError(ta3mfile);
+ Tali.Read(ta3mf,ta3mfile);
+ fclose(ta3mf);
+
+ // Filter Tali alignment
+ Tali.Compress(ta3mfile);
+ N_filtered = Tali.Filter(par.max_seqid,par.coverage,par.qid,par.qsc,par.Ndiff);
+
+ // Record imatch[j]
+ int* imatch=new(int[hit.j2+1]);
+ int step = hit.nsteps;
+ for (j=hit.j1; j<=hit.j2; j++)
+ {
+ // Advance to position of next T match state j
+ while (hit.j[step]<j) step--;
+ imatch[j] = hit.i[step];
+// printf("step=%-3i i=%-3i j=%-3i\n",step,imatch[j],j);
+ }
+
+ // Determine number of match states of Qali
+ for (L=0,l=1; seq[kfirst][l]>'\0'; l++)
+ if ((seq[kfirst][l]>='A' && seq[kfirst][l]<='Z') || seq[kfirst][l]=='-') L++;
+
+ // For each sequence in T alignment: align to Qali
+ for (k=0; k<Tali.N_in; k++)
+ {
+ if (!Tali.keep[k]) continue;
+ if (N_in>=MAXSEQ)
+ {
+ fprintf(stderr,"WARNING in %s: maximum number of %i sequences exceeded while reading %s. Skipping all following sequences\n",program_name,MAXSEQ,ta3mfile);
+ break;
+ }
+ cur_seq[0]=' '; // 0'th position not used
+
+ // Add the hit.i1-1 left end gaps to aligned sequence
+ for (h=1; h<hit.i1; h++) cur_seq[h]='-';
+
+ // Advance to match state hit.j1 of Tali.seq[k]
+ for (j=0, l=1; (c=Tali.seq[k][l])>'\0'; l++)
+ if ((c>='A' && c<='Z') || c=='-') // match state at position l?
+ if ((++j)==hit.j1) break; // yes: increment j. Reached hit,j1? yes: break
+
+ if (j<hit.j1)
+ {printf("Error: did not find %i match states in sequence %i of %s. Sequence:\n%s\n",hit.j1,k,Tali.name,Tali.seq[k]); exit(1);}
+
+ // Write first match state to cur_seq
+ int iprev=hit.i1; // index of previous query match state
+ int lprev=l; // previous T match state in Tali.seq[k][l]
+ cur_seq[h++] = Tali.seq[k][l]; // first column of alignment is Match-Match state
+
+ // For each further match state j in alignment
+ step = hit.nsteps;
+ for (j=hit.j1+1; j<=hit.j2; j++)
+ {
+ // Advance to position of next T match state j
+ i=imatch[j];
+
+ // Advance to position of next T match state j
+ while ((c=Tali.seq[k][++l])>'\0' && ((c>='a' && c<='z') || c=='.')) ;
+
+ int di=i-iprev; // number of Match states in Q between T match state j-1 and j
+ int dl=l-lprev; // 1 + number of inserted residues in T sequence between T match state j-1 and j
+ if (di==1)
+ {
+ // One Q match state for one T match state (treated as special case for speed reasons)
+ // i: i-1 i di=1
+ // Q: XXXXXX.....XXXXXX
+ // T: YYYYYYyyyyyYYYYYY
+ // j: j-1 j
+ // l: lprev l dl=6
+
+ // Inserts in lower case
+ for (ll=lprev+1; ll<l; ll++)
+ if (Tali.seq[k][ll]!='-' && Tali.seq[k][ll]!='.') cur_seq[h++] = lwrchr(Tali.seq[k][ll]);
+
+ // Template Match state -> upper case
+ cur_seq[h++] = Tali.seq[k][ll];
+ }
+ else if (di==0)
+ {
+ // Gap in query: no Q match state for on T match state (special case for speed reasons)
+ // i: i-1 i-1 di=0
+ // Q: XXXXXX.....~~~XXX
+ // T: YYYYYYyyyyyYYYYYY
+ // j: j-1 j
+ // l: lprev l dl=6
+
+ // All T residues (including T match state) in lower case
+ for (ll=lprev+1; ll<=l; ll++)
+ if (Tali.seq[k][ll]!='-' && Tali.seq[k][ll]!='.') cur_seq[h++] = lwrchr(Tali.seq[k][ll]);
+ }
+ else if (di>=dl)
+ {
+ // More Match states in Q than Inserts in the T sequence
+ // => half T inserts y left, half right-aligned in uc, gaps to fill up
+ // Number of T insert residues to be left-aligned: (int)(dl/2)
+ // i: iprev i di=7
+ // Q: XXXXXXXXXXXXXXXXXX
+ // T: YYYYYYYyyy-yyYYYYY
+ // j: j-1 j
+ // l: lprev l dl=6
+
+ // Add left-bounded template residues
+ for (ll=lprev+1; ll<=lprev+(int)(dl/2); ll++)
+ cur_seq[h++]=uprchr(Tali.seq[k][ll]);
+
+ // Add central gaps
+ for (int gap=1; gap<=di-dl; gap++) cur_seq[h++]='-';
+
+ // Add right-bounded residues
+ for (; ll<=l; ll++)
+ cur_seq[h++]=uprchr(Tali.seq[k][ll]);
+ }
+ else if (di<dl)
+ {
+ // Fewer Match states in Q than inserts in T sequence
+ // => half of available space di for left- half for right-aligned T inserts, rest in lc
+ // number of T inserts to be left-aligned in uc: (int)(di/2),
+ // i: iprev i di=5
+ // Q: XXXXXXXXX.XXXXXXX
+ // T: YYYYYYYyyyyyYYYYY
+ // j: j-1 j
+ // l: lprev l dl=6
+
+ // Add left-bounded template residues
+ for (ll=lprev+1; ll<=lprev+(int)(di/2); ll++)
+ cur_seq[h++]=uprchr(Tali.seq[k][ll]);
+
+ // Add central inserts
+ for (int ins=1; ins<=dl-di; ins++,ll++)
+ if (Tali.seq[k][ll]!='-' && Tali.seq[k][ll]!='.') cur_seq[h++] = lwrchr(Tali.seq[k][ll]);
+
+ // Add right-bounded residues
+ for (; ll<=l; ll++)
+ cur_seq[h++]=uprchr(Tali.seq[k][ll]);
+ }
+// printf("i=%-3i j=%-3i l=%-3i cur_seq=%s\n",i,j,l,cur_seq);
+
+ iprev=i; lprev=l;
+ if (h>=maxcol-1000) // too few columns? Reserve double space
+ {
+ char* new_seq=new(char[2*maxcol]);
+ strncpy(new_seq,cur_seq,maxcol); //////// check: maxcol-1 ????
+ delete[](cur_seq); (cur_seq) = NULL;
+ cur_seq=new_seq;
+ maxcol*=2;
+ }
+ }
+
+ // Add the remaining gaps '-' to the end of the template sequence
+ for (i=hit.i2+1; i<=L; i++) cur_seq[h++]='-';
+ cur_seq[h++]='\0';
+
+ keep[N_in] = display[N_in] = KEEP_CONDITIONALLY;
+ seq[N_in]=new(char[h]);
+ if (!seq[N_in]) MemoryError("array for input sequences");
+ strcpy(seq[N_in],cur_seq);
+ X[N_in]=new(char[h]);
+ if (!X[N_in]) MemoryError("array for input sequences");
+ I[N_in]=new(short unsigned int[h]);
+ if (!I[N_in]) MemoryError("array for input sequences");
+ sname[N_in]=new(char[strlen(Tali.sname[k])+1]);
+ if (!sname[N_in]) MemoryError("array for input sequences");
+ strcpy(sname[N_in],Tali.sname[k]);
+ N_in++;
+
+// printf("k=%-3i %s\n",k,Tali.seq[k]);
+// printf("Query %s\n",seq[kfirst]);
+// printf("k=%-3i %s\n\n",k,cur_seq);
+
+ } // end for (k)
+
+// printf("N_in=%-5i HMM=%s with %i sequences\n",N_in,ta3mfile,N_filtered);
+
+ delete[] cur_seq; cur_seq = NULL;
+ delete[] imatch; imatch = NULL;
+ delete[] ksort; ksort=NULL; // if ksort already existed it will be to short for merged alignment
+ delete[] first; first=NULL; // if first already existed it will be to short for merged alignment
+ delete[] last; last=NULL; // if last already existed it will be to short for merged alignment
+
+} /* this is the end of Alignment::MergeMasterSlave() */
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Add a sequence to Qali
+ */
+void
+Alignment::AddSequence(char Xk[], int Ik[])
+{
+ int i; // position in query and target
+ if (L<=0) InternalError("L is not set in AddSequence()");
+ X[N_in]=new(char[L+2]);
+ for (i=0; i<=L+1; i++) X[N_in][i]=Xk[i];
+ if (Ik==NULL)
+ for (i=0; i<=L+1; i++) I[N_in][i]=0;
+ else
+ for (i=0; i<=L+1; i++) I[N_in][i]=Ik[i];
+ N_in++;
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Determine matrix of position-specific weights w[k][i] for multiple alignment
+ * Pos-specific weights are calculated like in "Amino_acid_frequencies_and_transitions_from_M_state()"
+ */
+void
+Alignment::GetPositionSpecificWeights(float* w[])
+{
+ // Calculate position-dependent weights wi[k] for each i.
+ // For calculation of weights in column i use sub-alignment
+ // over sequences which have a *residue* in column i (no gap, no end gap)
+ // and over columns where none of these sequences has an end gap.
+ // This is done by updating the arrays n[j][a] at each step i-1->i while letting i run from 1 to L.
+ // n[j][a] = number of occurences of amino acid a at column j of the subalignment,
+ // => only columns with n[j][ENDGAP]=0 are contained in the subalignment!
+ // If no sequences enter or leave the subalignment at the step i-1 -> i (i.e. change=0)
+ // then the old values w[k][i] and ncol are used for the new position i.
+ // Index a can be an amino acid (0-19), ANY=20, GAP=21, or ENDGAP=22
+
+ char* in=keep; // to keep the code similar to Amino_acid_frequencies_and_transitions_from_M_state()
+ int k; // index of sequence
+ int i,j; // position in alignment
+ int a; // amino acid (0..19)
+ int naa; // number of different amino acids
+ int** n; // n[j][a] = number of seq's with some residue at column i AND a at position j
+ int nseqi=0; // number of sequences in subalignment i
+ int ncol=0; // number of columns j that contribute to Neff[i]
+ char change; // has the set of sequences in subalignment changed? 0:no 1:yes
+
+
+ // Global weights?
+ if (par.wg==1)
+ {
+ for (k=0; k<N_in; k++)
+ for (i=1; i<=L; i++) w[k][i]=wg[k];
+ }
+ else
+ {
+
+ // Initialization
+ n = new(int*[L+2]);
+ for (j=1; j<=L; j++) n[j]=new(int[NAA+3]);
+ for (j=1; j<=L; j++)
+ for (a=0; a<NAA+3; a++) n[j][a]=0;
+
+ //////////////////////////////////////////////////////////////////////////////////////////////
+ // Main loop through alignment columns
+ for (i=1; i<=L; i++) // Calculate w[k][i]
+ {
+ change=0;
+ // Check all sequences k and update n[j][a] and ri[j] if necessary
+ for (k=0; k<N_in; k++)
+ {
+ if (!in[k]) continue;
+ if (X[k][i-1]>=ANY && X[k][i]<ANY)
+ { // ... if sequence k was NOT included in i-1 and has to be included for column i
+ change=1;
+ nseqi++;
+ for (int j=1; j<=L; j++) n[j][ (int)X[k][j]]++;
+ }
+ else if (X[k][i-1]<ANY && X[k][i]>=ANY)
+ { // ... if sequence k WAS included in i-1 and has to be thrown out for column i
+ change=1;
+ nseqi--;
+ for (int j=1; j<=L; j++) n[j][ (int)X[k][j]]--;
+ }
+ } //end for (k)
+ nseqs[i]=nseqi;
+
+ // If subalignment changed: update weights w[k][i] and Neff[i]
+ if (change)
+ {
+ // Initialize weights and numbers of residues for subalignment i
+ ncol=0;
+ for (k=0; k<N_in; k++) w[k][i]=0.0;
+
+ // sum wi[k] over all columns j and sequences k of subalignment
+ for (j=1; j<=L; j++)
+ {
+ // do at least a fraction MAXENDGAPFRAC of sequences in subalignment contain an end gap in j?
+ if (n[j][ENDGAP]>MAXENDGAPFRAC*nseqi) continue;
+ naa=0; for (a=0; a<20; a++) if(n[j][a]) naa++;
+ if (naa==0) continue;
+ ncol++;
+ for (k=0; k<N_in; k++)
+ {
+ if (in[k] && X[k][i]<ANY && X[k][j]<ANY)
+ {
+// if (!n[j][ (int)X[k][j]]) {fprintf(stderr,"Error: Mi=%i: n[%i][X[%i]]=0! (X[%i]=%i)\n",i,j,k,k,X[k][j]);}
+ w[k][i]+=1.0/float(n[j][ (int)X[k][j] ]*naa);
+ }
+ }
+ }
+
+ // Check whether number of columns in subalignment is sufficient
+ if (ncol<NCOLMIN)
+ // Take global weights
+ for (k=0; k<N_in; k++)
+ if(in[k]) {if(X[k][i]<ANY) w[k][i]=wg[k]; else w[k][i]=0.0;}
+ }
+ }
+ // end loop through alignment columns i
+ ///////////////////////////////////////////////////////////////////////
+
+ // delete n[][]
+ for (j=1; j<=L; j++){
+ delete[](n[j]); (n[j]) = NULL;
+ }
+ delete[](n); (n) = NULL;
+
+ }
+ return;
+}
+
+#ifdef CLUSTALO
+/* @* Transfer
+ *
+ * take sequence data from Clustal and transfer it into
+ * hhalign accessible information (structure/class)
+ *
+ * Note that hhalign does not see all sequences/profiles
+ * but only sequences that are elements of the 2 profiles
+ * to be aligned.
+ *
+ * References to the required sequences are passed into hhalign
+ * through auxilliary pointers that are shallow copies of the
+ * sequence/profile data available to Clustal.
+ *
+ * Re-allocating memory for these auxilliary pointers
+ * would be desaterous, as it might detach the memory
+ * seen by Clustal.
+ */
+void
+Alignment::Transfer(char **ppcProf, int iCnt){
+
+ /* @<variables local to Transfer@> */
+ int iLen; /* length of profile */
+ int k; /* generic iterator */
+
+ /* @<initialisation@> */
+ N_in = iCnt;
+ N_filtered = N_ss = 0;
+ kss_dssp = ksa_dssp = kss_pred = kss_conf = -1;
+ kfirst = 0;
+ strcpy(longname, "unknown_long_seq_name");
+ strcpy(name, "unknown_seq_name");
+ strcpy(file, "unknown_file_name");
+ n_display = iCnt;
+
+ /* @<determine length of profile@>
+ all sequences in profile should have same length,
+ so only do it for 1st */
+ for (iLen = 0; '\0' != ppcProf[0][iLen]; iLen++);
+
+ /* @<allocate memory for sequences etc@> */
+ for (k = 0; k < iCnt; k++){
+#define GOOD_MEASURE 1000 /* Temporary -- can be removed once rest in place */
+ I[k] = new(short unsigned int[iLen+2+GOOD_MEASURE]);
+ X[k] = new(char[iLen+2+GOOD_MEASURE]);
+ seq[k] = new(char[iLen+2+GOOD_MEASURE]);
+ seq[k][0] = ' ';
+ seq[k][1] = '\0';
+ if (NULL == ppcProf[k]){
+ printf("%s:%d: Arena[%d]=NULL, cnt=%d\n", __FILE__, __LINE__, k, iCnt);
+ exit(-1);
+ }
+ strcat(seq[k], ppcProf[k]);
+ keep[k] = KEEP_CONDITIONALLY;
+ display[k] = KEEP_CONDITIONALLY;
+ sname[k] = new(char[GOOD_MEASURE]);
+ strcpy(sname[k], "unknown_sname");
+ } /* (0 <= k < iCnt) */
+ /* FIXME: Soeding always makes 1st sequence permanent */
+ /*keep[0] = KEEP_ALWAYS;
+ display[k] = KEEP_ALWAYS;*/
+#if 1
+ /* Believe that the first and last positions are
+ most important in stability of this algorithm.
+ Must make sure that at least 2 sequences with
+ residues in these positions are kept.
+ Think any sequence will do, but better to keep
+ the one with the longest 'contig'
+ */
+ int iSeq; /* sequence iterator */
+ int iHeadLen = 0, iHeadID = -1; /* length & ID of longest head contig */
+ int iTailLen = 0, iTailID = -1; /* length & ID of longest head contig */
+ int iCont = -1;
+ char *pcFind = NULL;
+
+#if 0
+ printf("%s:%s:%d: NEW PROFILE (%d seq) ================\n",
+ __FUNCTION__, __FILE__, __LINE__, iCnt);
+#endif
+ for (iSeq = 0; iSeq < iCnt; iSeq++){
+#if 0
+ printf("%s:%s:%d: consider seq %d ------------------\n",
+ __FUNCTION__, __FILE__, __LINE__, iSeq);
+#endif
+ pcFind = strchr(&seq[iSeq][1], '-');
+ if (NULL == pcFind){
+ /* no gap at all in this sequences, spans entire profile */
+ iHeadID = iTailID = iSeq;
+ iHeadLen = iTailLen = iLen;
+ break;
+ }
+ iCont = (int)(pcFind - &seq[iSeq][1]);
+ if (iCont > iHeadLen){
+ iHeadLen = iCont;
+ iHeadID = iSeq;
+ }
+ pcFind = strrchr(seq[iSeq], '-');
+ iCont = iLen - (int)(pcFind - seq[iSeq]);
+ if (iCont > iTailLen){
+ iTailLen = iCont;
+ iTailID = iSeq;
+ }
+
+#if 0
+ printf("%s:%s:%d: seq %3d: len = %d(%d) %s\n",
+ __FUNCTION__, __FILE__, __LINE__, iSeq, iCont, iLen, seq[iSeq]);
+#endif
+ } /* 0 <= iSeq < iCnt */
+#if 0
+ printf("%s:%s:%d: seq %d is winner with head contig of %d, seq %d tail contig of %d\n"
+ , __FUNCTION__, __FILE__, __LINE__, iHeadID, iHeadLen, iTailID, iTailLen);
+#endif
+ if ( (-1 == iHeadID) || (-1 == iTailID) ){
+ printf("%s:%s:%d: profile has no leading and/or trailing residues (h=%d:t=%d:#=%d)\n",
+ __FUNCTION__, __FILE__, __LINE__, iHeadID, iTailID, iCnt);
+ }
+ else{
+ keep[iHeadID] = KEEP_ALWAYS;
+ keep[iTailID] = KEEP_ALWAYS;
+ }
+#endif
+ /* @= */
+ return;
+
+} /* this is the end of Transfer() */
+#endif
+
+#ifdef CLUSTALO
+/* @* Alignment::ClobberGlobal (eg: qali)
+ *
+ * Note: originally hhalign() was stand-alone code,
+ * there are a couple of GLOBAL (!) variables,
+ * which would have been destroyed on exit.
+ * However, now there is no 'exit' from hhalign(),
+ * and on re-entry the global variable must be clean again.
+ */
+void
+Alignment::ClobberGlobal(void){
+
+ /* @<essentials@>
+ these are essential to re-set (as some of them are used as flags) */
+ for(int k=0; k<N_in; k++)
+ {
+ delete[] sname[k]; sname[k] = NULL;
+ delete[] seq[k]; seq[k] = NULL;
+ delete[] X[k]; X[k] = NULL;
+ delete[] I[k]; I[k] = NULL;
+ }
+ delete[] nres; nres = NULL;
+ delete[] first; first = NULL;
+ delete[] last; last = NULL;
+ delete[] ksort; ksort = NULL;
+ N_in = N_filtered = n_display = 0;
+ L = 0;
+ kss_dssp = ksa_dssp = kss_pred = kss_conf = kfirst = -1;
+
+ /* @<re-set but keep memory@>
+ do not free the memory but re-set content */
+ longname[0] = '\0'; //delete[] longname; longname = NULL;
+ keep[0] = '\0'; //delete[] keep; keep = NULL;
+ display[0] = '\0'; //delete[] display; display = NULL;
+ wg[0] = 0; //delete[] wg; wg = NULL;
+ nseqs[0] = 0; //delete[] nseqs; nseqs = NULL;
+ name[0]='\0';
+ fam[0]='\0';
+ file[0]='\0';
+ //delete[] sname; sname = NULL;
+ //delete[] seq; seq = NULL;
+ //delete[] X; X = NULL;
+ //delete[] I; I = NULL;
+ //delete[] l; l = NULL;
+
+ /* @= */
+ return;
+}
+#endif
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhalignment.h 154 2010-11-09 18:29:05Z fabian $
+ */
+
+// hhalignment.h
+
+class Alignment
+{
+public:
+ int L; // number of match states of alignment
+ int N_in; // total number of sequences in alignment
+ int N_filtered; /* number of sequences after sequence identity
+ filtering */
+ int N_ss; // number of >ss_ or >sa sequences
+
+ int kss_dssp; /* index of sequence with secondary structure
+ by dssp -1:no >ss_dssp line found */
+ int ksa_dssp; /* index of sequence with solvent accessibility
+ by dssp -1:no >sa_dssp line found */
+ int kss_pred; /* index of sequence with predicted secondary
+ structure -1:no >ss_pred line found */
+ int kss_conf; /* index of sequence with confidence values of
+ prediction -1:no >ss_conf line found */
+ int kfirst; // index of first real sequence
+
+ char* longname; /* Full name of first sequence of original alignment
+ (NAME field) */
+ char name[NAMELEN]; // HMM name = first word in longname in lower case
+ char fam[NAMELEN]; // family ID (derived from name) (FAM field)
+ char file[NAMELEN]; /* Rootname (w/o path, with extension) of alignment
+ file that is used to construct the HMM */
+
+ int n_display; /* number of sequences to be displayed
+ (INCLUDING >ss_pred, >ss_conf, >ss_dssp sequences) */
+ char** sname; // names of display sequences (first seq=0, first char=0)
+ char** seq; // residues of display sequences (first char=1)
+ int* l; // l[i] = position of i'th match state in alignment
+
+ char* keep; /* keep[k]=1 if sequence is included in amino acid
+ frequencies; 0 otherwise (first=0) */
+
+ double *pdExWeight; /* external sequence weight as given by tree FIXME (FS) */
+
+ Alignment(int maxseq=MAXSEQ, int maxres=/*MAXRES*/par.maxResLen);
+ ~Alignment();
+
+ // Read alignment into X (uncompressed) in ASCII characters
+ void Read(FILE* inf, char infile[NAMELEN], char* line=NULL);
+#ifdef CLUSTALO
+ void Transfer(char **ppcProf, int iCnt);
+ void ClobberGlobal();
+#endif
+
+ /* Convert ASCII to numbers between 0 and 20, throw out all insert states,
+ record their number in I[k][i] and store sequences to be displayed
+ in sname[k] and seq[k] */
+ void Compress(const char infile[NAMELEN]);
+
+ // Apply sequence identity filter
+ inline int FilterForDisplay(int max_seqid, int coverage=0, int qid=0, float qsc=0, int N=0);
+ inline int Filter(int max_seqid, int coverage=0, int qid=0, float qsc=0, int N=0);
+ int Filter2(char keep[], int coverage, int qid, float qsc, int seqid1, int seqid2, int Ndiff);
+
+ bool FilterNeff(); /* MR1 */
+ float filter_by_qsc(float qsc, char* dummy); /* MR1 */
+
+ // Filter alignment for min score per column with core query profile, defined by min_coverage_core and min_seqid_core
+ int HomologyFilter(int coverage_core, float qsc_core, float coresc);
+
+ // Calculate AA frequencies q.p[i][a] and transition probabilities q.tr[i][a] from alignment
+ void FrequenciesAndTransitions(HMM& q, char* in=NULL);
+
+ // Calculate freqs q.f[i][a] and transitions q.tr[i][a] (a=MM,MI,MD) with pos-specific subalignments
+ void Amino_acid_frequencies_and_transitions_from_M_state(HMM& q, char* in);
+
+ // Calculate transitions q.tr[i][a] (a=DM,DD) with pos-specific subalignments
+ void Transitions_from_D_state(HMM& q, char* in);
+
+ // Calculate transitions q.tr[i][a] (a=DM,DD) with pos-specific subalignments
+ void Transitions_from_I_state(HMM& q, char* in);
+
+ // Write alignment without insert states to alignment file
+ void WriteWithoutInsertsToFile(char* alnfile);
+
+ // Write alignment to alignment file
+ void WriteToFile(char* alnfile, const char format[]=NULL);
+
+ // Read a3m slave alignment of hit from ta3mfile and merge into (query) master alignment
+ void MergeMasterSlave(Hit& hit, char ta3mfile[]);
+
+ // Read a3m alignment of hit from ta3mfile and merge-combine with query alignment
+ void Merge(Hit& hit, char ta3mfile[]);
+
+ // Add a sequence to Qali
+ void AddSequence(char Xk[], int Ik[]=NULL);
+
+ // Determine matrix of position-specific weights w[k][i] for multiple alignment
+ void GetPositionSpecificWeights(float* w[]);
+
+ char readCommentLine; // Set to 1, if a comment line with '#' is read /* MR1 */
+
+private:
+ char** X; // X[k][i] contains column i of sequence k in alignment (first seq=0, first char=1) (0-3: ARND ..., 20:X, 21:GAP)
+ short unsigned int** I; // I[k][i] contains the number of inserts AFTER match state i (first=0)
+ char* display; // display[k]=1 if sequence will be displayed in output alignments; 0 otherwise (first=0)
+ float* wg; // w[k] = global weight of sequence k
+ int* nseqs; // number of sequences in subalignment i (only for DEBUGGING)
+ int* nres; // number of residues in sequence k
+ int* first; // first residue in sequence k
+ int* last; // last residue in sequence k
+ int* ksort; // index for sorting sequences: X[ksort[k]]
+ int FilterWithCoreHMM(char in[], float coresc, HMM& qcore);
+};
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhdecl-C.h 227 2011-03-28 17:03:09Z fabian $
+ */
+
+/////////////////////////////////////////////////////////////////////////////////////
+//// Constants
+/////////////////////////////////////////////////////////////////////////////////////
+
+const char VERSION_AND_DATE[]="version 1.5.1.3 (November 2008)";
+const char REFERENCE[]="Soding, J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005, 21, 951-960.\n";
+const char COPYRIGHT[]="(C) Johannes Soeding (see LICENSE file)\n";
+const int MAXSEQ=65535; //max number of sequences in input alignment (must be <~30000 on cluster nodes)
+#if 0
+const int MAXCOL=32765; //max number of residues in input files; must be <= LINELEN and >= MAXRES
+const int MAXRES=15002; //max number of columns in HMM; must be <= LINELEN
+#else
+const int MAXCOL=2/*131072*/; //max number of residues in input files; must be <= LINELEN and >= MAXRES
+const int MAXRES=1/*65536*/; //max number of columns in HMM; must be <= LINELEN
+#endif
+const int LINELEN=262144; //max length of line read in from input files; must be >= MAXCOL
+const int MAXSEQDIS=3; //10238;//max number of sequences stored in 'hit' objects and displayed in output alignment
+const int IDLEN=255; //max length of scop hierarchy id and pdb-id
+const int DESCLEN=32765;//max length of sequence description (longname)
+const int NAMELEN=511; //max length of file names etc.
+const int MAXOPT=127; //Maximum number of options to be read in from .hhconfig or command line
+const int NAA=20; //number of amino acids (0-19)
+const int NTRANS=10; //number of transitions recorded in HMM (M2M,M2I,M2D,I2M,I2I,D2M,D2D,M2M_GAPOPEN,GAPOPEN,GAPEXTD)
+const int NCOLMIN=10; //min number of cols in subalignment for calculating pos-specific weights w[k][i]
+const int ANY=20; //number representing an X (any amino acid) internally
+const int GAP=21; //number representing a gap internally
+const int ENDGAP=22; //Important to distinguish because end gaps do not contribute to tansition counts
+const int HMMSCALE=1000;//Scaling number for log2-values in HMMs
+const int NFAMMAX=5119; //Size of hash for counting number of HMMs in each family
+const int MAXPROF=32766;//Maximum number of HMM scores for fitting EVD
+const float MAXENDGAPFRAC=0.1; //For weighting: include only columns into subalignment i that have a max fraction of seqs with endgap
+const float SMIN= 20.; //Minimum score of hit needed to search for another repeat of same profile: p=exp(-(4-mu)/lamda)=0.01
+const float LAMDA=0.388; //lamda in score EVD used for -local mode in length correction: S = S-log(Lq*Lt)/LAMDA)
+const float LAMDA_GLOB=0.42; //lamda in score EVD used for -global mode
+const float PMAX=1E-2; //Maximum single-repeat p-value that can contribute to whole-protein p-value
+const float MINEVALEXCL=0.5; //above this E-value from first ML fit hits are not used for final ML fit of EVD
+const int SELFEXCL=3; // exclude self-alignments with j-i<SELFEXCL
+const float PLTY_GAPOPEN=6.0f; // for -qsc option (filter for min similarity to query): 6 bits to open gap
+const float PLTY_GAPEXTD=1.0f; // for -qsc option (filter for min similarity to query): 1 bit to extend gap
+const int MINCOLS_REALIGN=6; // hits with MAC alignments with fewer matched columns will be deleted in hhsearch hitlist
+
+enum transitions {M2M,M2I,M2D,I2M,I2I,D2M,D2D,M2M_GAPOPEN,GAPOPEN,GAPEXTD}; // index for transitions within a HMM
+enum pair_states {STOP=0,SAME=1,GD=2,IM=3,DG=4,MI=5,MS=6,ML=7,SM=8,LM=9,MM=10};
+
+// const char aa[]="ARNDCQEGHILKMFPSTWYVX-";
+//Amino acids Sorted by alphabet -> internal numbers a
+// 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
+// A C D E F G H I K L M N P Q R S T V W Y X
+const int s2a[]={ 0, 4, 3, 6,13, 7, 8, 9,11,10,12, 2,14, 5, 1,15,16,19,17,18,20};
+//Internal numbers a for amino acids -> amino acids Sorted by alphabet:
+// 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
+// A R N D C Q E G H I L K M F P S T W Y V X
+const int a2s[]={ 0,14,11, 2, 1,13, 3, 5, 6, 7, 9, 8,10, 4,12,15,16,18,19,17,20};
+
+// Secondary structure
+const int NDSSP=8; //number of different ss states determined by dssp: 0-7 (0: no state available)
+const int NSSPRED=4; //number of different ss states predicted by psipred: 0-3 (0: no prediction availabe)
+const int MAXCF=11; //number of different confidence values: 0-10 (0: no prediction availabe)
+const int NSA=7; //number of classes relative solvent accesiblity (0:no coord, 1:<2%, 2:<14%, 3:<33%, 4:<55%, 5:>55%, 6:S-S bridge)
+
+/////////////////////////////////////////////////////////////////////////////////////
+/////////////////////////////////////////////////////////////////////////////////////
+
+// Input parameters
+class Parameters // Parameters for gap penalties and pseudocounts
+{
+public:
+ char** argv; //command line parameters
+ char argc; //dimension of argv
+
+ char infile[NAMELEN]; // input filename
+ char outfile[NAMELEN]; // output filename
+ char pairwisealisfile[NAMELEN]; // output filename with pairwise alignments
+ char alnfile[NAMELEN]; // name of output alignment file in A3M format (for iterative search)
+ char hhmfile[NAMELEN]; // name of output HHM file for (iterative search)
+ char psifile[NAMELEN]; // name of output alignmen file in PSI-BLAST format (iterative search)
+ char scorefile[NAMELEN];// table of scores etc for all HMMs in searched database
+ char tfile[NAMELEN]; // template filename (in hhalign)
+ char buffer[NAMELEN]; // buffer to write results for other programs into
+ char pngfile[NAMELEN]; // png image file for dotplot
+ char wfile[NAMELEN]; // weights file generated with hhformat
+ char* blafile; // output of 'blastpgp -m 8' with PSI-BLAST E-values for HHblast
+ char* dbfiles; // database filenames, separated by colons
+ char* exclstr; // optional string containing list of excluded residues, e.g. '1-33,97-168'
+ int aliwidth; // number of characters per line in output alignments for HMM search
+ char append; // append to output file? (hhmake)
+ float p; // minimum probability for inclusion in hit list and alignments
+ float E; // maximum E-value for inclusion in hit list and alignment list
+ float e; // maximum E-value for inclusion in output alignment, output HMM, and PSI-BLAST checkpoint model
+ int Z; // max number of lines in hit list
+ int z; // min number of lines in hit list
+ int B; // max number of lines in alignment list
+ int b; // min number of lines in alignment list
+ int showcons; // 0: don't show consensus sequence in alignments 1:show
+ int showdssp; // 0: don't show consensus sequence in alignments 1:show
+ int showpred; // 0: don't show consensus sequence in alignments 1:show
+ int nseqdis; // maximum number of query or template sequences in output alignments
+ char cons; // if set to 1, include consensus as first representative sequence of HMM
+ char mark; // which sequences to mark for display in output alignments? 0: auto; 1:all
+ char outformat; // 0: hhr 1: FASTA 2:A2M 3:A3M
+ char mode; //
+ //0:MAC alignment, master-slave 1:MAC blending, master-slave 2:MAC alignment, combining
+
+ int max_seqid; // Maximum sequence identity with all other sequences in alignment
+ int qid; // Minimum sequence identity with query sequence (sequence 0)
+ float qsc; // Minimum score per column with query sequence (sequence 0)
+ int coverage; // Minimum coverage threshold
+ int Ndiff; // Pick Ndiff most different sequences that passed the other filter thresholds
+ int coverage_core; // Minimum coverage for sequences in core alignment
+ float qsc_core; // Minimum sequence identity with query for sequences in core alignment
+ float coresc; // Minimum score per column with core alignment (HMM)
+
+ int maxResLen; /* length of longest sequence/profile, FS 2010-11-05 */
+ int maxColCnt; /* maximum number of columns in HMM, FS 2010-11-05 */
+
+ int Mgaps; // Maximum percentage of gaps for match states
+ int M; // Match state assignment by 1:upper/lower case 2:percentage rule 3:marked sequence
+ char matrix; // Subst.matrix 0: Gonnet, 1: HSDM, 2: BLOSUM50
+
+ char wg; // 0: use local sequence weights 1: use local ones
+ double *pdWg1; /* seq weights 1st profile, derived from tree */
+ double *pdWg2; /* seq weights 2nd profile, derived from tree */
+
+ char pcm; // 0:no pseudocounts, 1:pos-specific pcs, 2:PSIBLAST pcs
+ /* pseudo-count parameters for MAC*/
+ float pca; // Pseudocount matrix = (1-tau(i))*I + tau(i)*S
+ float pcb; // tau(i) = pca/(1 + ((Neff-1)/pcb)^pcc
+ float pcc; //
+ float pcw; // Decrease pseudocounts for conserved columns
+
+ /* gap parameters for MAC*/
+ float gapb; // Diversity threshold for adding pseudocounts to transitions from M state
+ float gapd; // Gap open penalty factor for deletions
+ float gape; // Gap extend penalty: factor to multiply hmmer values (def=1)
+ float gapf; // factor for increasing/reducing the gap opening penalty for deletes
+ float gapg; // factor for increasing/reducing the gap opening penalty for inserts
+ float gaph; // factor for increasing/reducing the gap extension penalty for deletes
+ float gapi; // factor for increasing/reducing the gap extension penalty for inserts
+
+ /* pseudo-count parameters for Viterbi, FS, r226->r227 */
+ float pcaV; // Pseudocount matrix = (1-tau(i))*I + tau(i)*S
+ float pcbV; // tau(i) = pca/(1 + ((Neff-1)/pcb)^pcc
+ float pccV; //
+ float pcwV; // Decrease pseudocounts for conserved columns
+
+ /* gap parameters for Viterbi, FS, r226->r227 */
+ float gapbV; // Diversity threshold for adding pseudocounts to transitions from M state
+ float gapdV; // Gap open penalty factor for deletions
+ float gapeV; // Gap extend penalty: factor to multiply hmmer values (def=1)
+ float gapfV; // factor for increasing/reducing the gap opening penalty for deletes
+ float gapgV; // factor for increasing/reducing the gap opening penalty for inserts
+ float gaphV; // factor for increasing/reducing the gap extension penalty for deletes
+ float gapiV; // factor for increasing/reducing the gap extension penalty for inserts
+
+ float egq; // penalty for end gaps when query not fully covered
+ float egt; // penalty for end gaps when template not fully covered
+
+ float neffa; // Coefficients to estimate Neff-dependent weights for HMM merging procedure
+ float neffb; // Coefficients to estimate Neff-dependent weights for HMM merging procedure
+
+ char ssgap; // 1: add secondary structure-dependent gap penalties 0:off
+ float ssgapd; // secondary structure-dependent gap-opening penalty (per residue)
+ float ssgape; // secondary structure-dependent gap-extension penalty (per residue)
+ char ssgapi; // max. number of inside-integer(ii); gap-open-penalty= -ii*ssgapd
+
+ char ssm; // SS comparison mode: 0:no ss scoring 1:ss scoring AFTER alignment 2:ss score in column score
+ float ssw; // SS weight as compared to column score
+ float ssa; // SS state evolution matrix M1 = (1-ssa)*I + ssa*M0
+
+ char loc; // 0: local alignment (wrt. query), 1: global alignement
+ char forward; // 0:Viterbi algorithm 1:Forward algorithm 2: MAC
+ char realign; // realign database hits to be displayed with MAC algorithm
+ char altali; // find up to this many possibly overlapping alignments
+ int columnscore; // 0: no aa comp corr 1: 1/2(qav+tav) 2: template av freqs 3: query av freqs 4:...
+ float corr; // Weight of correlations between scores with |i-j|<=4
+ float shift; // Score offset for match-match states
+ float mact; // Score threshold (negative offset) in MAC alignment
+
+ char calibrate; // calibration of query HMM? 0:no, 1:yes (write lamda,mu into query profile)
+ char calm; // derive P-values from: 0:query calibration 1:template calibration 2:both
+ int opt; // for optimization: compare only every opt'th negative; 0: mode off
+ int readdefaultsfile ; // read defaults file ./.hhdefaults or HOME/.hhdefaults?
+ int min_overlap; // all cells of dyn. programming matrix with L_T-j+i or L_Q-i+j < min_overlap will be ignored
+ int hitrank; // rank of hit to be printed as a3m alignment
+ char notags; // neutralize His-tags, FLAG tags, C-myc tags?
+ unsigned int maxdbstrlen; // maximum length of database string to be printed in 'Command' line of hhr file
+
+ char trans; // 0: normal pairwise scoring; 1:transitive scoring
+ float Emax_trans; // max E-value for intermediate HMMs in transitive scoring (i.e. l is intermediate HMM if E_lq, E_lk <Emax_trans)
+ float wtrans; // Ztot[k] = Zq[k] + wtrans * (Zforward[k]+Zreverse[k])
+
+
+ // SCRAP THE FOLLOWING VARIABLES?
+
+ float wstruc; // weight of structure scores
+ char repmode; // 1:repeat identification: multiple hits not treated as independent 0: repeat mode off
+
+ int idummy;
+ int jdummy;
+ float fdummy;
+};
+
+/////////////////////////////////////////////////////////////////////////////////////
+//// Global variable declarations
+/////////////////////////////////////////////////////////////////////////////////////
+
+char v=1; // 1: show only warnings 2:verbose mode
+Parameters par;
+char program_name[NAMELEN]; //name of program executed (e.g. hhmake of hhsearch)
+
+// substitution matrix flavours
+float P[21][21]; // P[a][b] = combined probability for a aligned to b
+float R[21][21]; // R[a][b]=P[a][b]/p[b]=P(a|b); precalculated for pseudocounts
+float Sim[21][21]; // Similarity matrix Sim[a][b]: how similar are a and b?
+float S[21][21]; // Substitution score matrix S[a][b] = log2(Pab/pa/pb)
+float pb[21]; // pb[a] = background amino acid probabilities for chosen substitution matrix
+float qav[21]; // qav[a] = background amino acid probabilities for query HMM (needed for rate matrix rescaling)
+
+// secondary structure matrices
+float S73[NDSSP][NSSPRED][MAXCF]; // P[A][B][cf] = log2 P(A,B,cf)/P(A)/P(B,cf)
+float S33[NSSPRED][MAXCF][NSSPRED][MAXCF]; // P[B][cf][B'][cf'] = log2 sum_B' P(A,B',cf)/P(A)/P(B,cf) * P_b(B'|B)
+// float S77[NDSSP][DSSP]; // P[A][B] = log2 P(A,B)/P(A)/P(B)
+
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhfullalignment-C.h 243 2011-05-31 13:49:19Z fabian $
+ */
+
+// hhfullalignment.C
+
+#ifndef MAIN
+#define MAIN
+#include <iostream> // cin, cout, cerr
+#include <fstream> // ofstream, ifstream
+#include <stdio.h> // printf
+#include <stdlib.h> // exit
+#include <string> // strcmp, strstr
+#include <math.h> // sqrt, pow
+#include <limits.h> // INT_MIN
+#include <float.h> // FLT_MIN
+#include <time.h> // clock
+#include <ctype.h> // islower, isdigit etc
+using std::ios;
+using std::ifstream;
+using std::ofstream;
+using std::cout;
+using std::cerr;
+using std::endl;
+#include "util-C.h" // imax, fmax, iround, iceil, ifloor, strint, strscn, strcut, substr, uprstr, uprchr, Basename etc.
+#include "list.h" // list data structure
+#include "hash.h" // hash data structure
+#include "hhdecl-C.h" // constants, class
+#include "hhutil-C.h" // imax, fmax, iround, iceil, ifloor, strint, strscn, strcut, substr, uprstr, uprchr, Basename etc.
+#include "hhhmm.h" // class HMM
+#include "hhalignment.h" // class Alignment
+#include "hhhit.h"
+#include "hhhalfalignment.h"
+#endif
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+// Methods of class FullAlignment
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Output Results: use classes HalfAlignment and FullAlignment
+//
+// Example:
+// Each column list contains at least a match state
+// Insert states between the match states are omitted
+//
+// step 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1
+// i 0 0 1 2 3 4 5 6 7 8 9 9 9 9 10 11 12 13 14
+//
+// Q ~ ~ X X X X X X X X X ~ ~ ~ X X X X X
+// T Y Y Y Y Y Y Y Y ~ Y Y Y Y Y Y Y Y ~ ~
+//
+// j 7 8 9 10 11 12 13 14 14 15 16 17 18 19 20 21 22 22 22
+// state IM IM MM MM MM MM MM MM DG MM MM GD GD GD MM MM MM MI MI
+//
+// nsteps=19
+//
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Constructor
+FullAlignment::FullAlignment(int maxseqdis)
+{
+ qa = new HalfAlignment(maxseqdis);
+ ta = new HalfAlignment(maxseqdis);
+ for (int h=0; h<LINELEN-1; h++) symbol[h]=' ';
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// Destructor
+FullAlignment::~FullAlignment()
+{
+ delete qa; qa = NULL;
+ delete ta; ta = NULL;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// Free memory of arrays s[][], l[][], and m[][] in HalfAlignment
+void FullAlignment::FreeMemory()
+{
+ qa->Unset();
+ ta->Unset();
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Add columns for match (and delete) states.
+ */
+void
+FullAlignment::AddColumns(int i, int j, char prev_state, char state, float S)
+{
+ switch(state)
+ {
+ case MM: //MM pair state (both query and template in Match state)
+ AddGaps(); //fill up gaps until query and template parts have same length
+ symbol[qa->pos] =ScoreChr(S);
+ qa->AddColumn(i);
+ ta->AddColumn(j);
+ qa->AddInsertsAndFillUpGaps(i);
+ ta->AddInsertsAndFillUpGaps(j);
+ break;
+
+ case GD: //-D state
+ if (prev_state==DG) AddGaps();
+ symbol[ta->pos]='Q';
+ ta->AddColumn(j); //query has gap -> add nothing
+ ta->AddInsertsAndFillUpGaps(j);
+ break;
+ case IM: //IM state
+ if (prev_state==MI) AddGaps();
+ symbol[ta->pos]='Q';
+ ta->AddColumn(j); //query has gap -> add nothing
+ ta->AddInsertsAndFillUpGaps(j);
+ break;
+
+ case DG: //D- state
+ if (prev_state==GD) AddGaps();
+ symbol[qa->pos]='T';
+ qa->AddColumn(i);//template has gap -> add nothing
+ qa->AddInsertsAndFillUpGaps(i);
+ break;
+ case MI: //MI state
+ if (prev_state==IM) AddGaps();
+ symbol[qa->pos]='T';
+ qa->AddColumn(i);//template has gap -> add nothing
+ qa->AddInsertsAndFillUpGaps(i);
+ break;
+ }
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Fill up gaps until query and template parts have same length
+ */
+void
+FullAlignment::AddGaps()
+{
+ while (qa->pos<ta->pos) qa->AddChar('.');
+ while (ta->pos<qa->pos) ta->AddChar('.');
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Build full alignment -> qa->s[k][h] and ta->s[k][h]
+ */
+int
+FullAlignment::Build(HMM& q, Hit& hit)
+{
+ int step;
+ char prev_state=MM, state=MM;
+ int n;
+ int hh;
+ int k;
+ identities=0; // number of identical residues in query and template sequence
+ score_sim=0.0f;// substitution matrix similarity score between query and template
+
+ ClearSymbols();
+
+ // Set up half-alignments
+ // n is the sequence index up to which sequences are prepared for display
+ n = imin( q.n_display,par.nseqdis+( q.nss_dssp>=0)+( q.nsa_dssp>=0)+( q.nss_pred>=0)+( q.nss_conf>=0)+( q.ncons>=0));
+ qa->Set( q.name, q.seq, q.sname, n, q.L, q.nss_dssp , q.nss_pred , q.nss_conf, q.nsa_dssp, q.ncons, hit.L/*<--FS*/);
+ n = imin(hit.n_display,par.nseqdis+(hit.nss_dssp>=0)+(hit.nsa_dssp>=0)+(hit.nss_pred>=0)+(hit.nss_conf>=0)+(hit.ncons>=0));
+ ta->Set(hit.name,hit.seq,hit.sname, n,hit.L,hit.nss_dssp,hit.nss_pred,hit.nss_conf,hit.nsa_dssp, hit.ncons, q.L/*<--FS*/);
+
+
+// printf("HMM: %s\nstep nst i j state hq ht\n",hit.name);
+
+#ifdef CLUSTALO
+ if ((1 == hit.i1) && (1 == hit.j1)){
+ /* do nothing */
+ }
+ else if ((1 == hit.i1) && (1 != hit.j1)){
+ for (int j = 1; j < hit.j1; j++){
+ AddColumns(0, j, MM, IM, 0.0);
+ }
+ if (rLog.iLogLevelEnabled <= LOG_DEBUG){
+ int iK, iL;
+ printf("%d: j1=%d -> temp has leading gaps\n", __LINE__, hit.j1);
+ for (iK = 0; iK < ta->n; iK++){
+ //printf("T%d: %s\n", iK, ta->s[iK]);
+ for (iL = 0; iL < hit.j1; iL++){
+ ta->s[iK][iL] = tolower(ta->s[iK][iL]);
+ }
+ }
+ }
+ }
+ else if ((1 != hit.i1) && (1 == hit.j1)){
+ for (int i = 1; i < hit.i1; i++){
+ AddColumns(i, 0, MM, MI, 0.0);
+ }
+ if (rLog.iLogLevelEnabled <= LOG_DEBUG){
+ FILE *fp = rLog.prFP[LOG_DEBUG];
+
+ fprintf(fp, "%d: i1=%d -> query has leading gaps\n", __LINE__, hit.i1);
+ int iK, iL;
+ for (iK = 0; iK < qa->n; iK++){
+ //printf("Q%d: %s\n", iK, qa->s[iK]);
+ for (iL = 0; iL < hit.i1; iL++){
+ qa->s[iK][iL] = tolower(qa->s[iK][iL]);
+ }
+ }
+ }
+ }
+ else {
+ fprintf(stderr,
+ "+-------------------------------+\n"
+ "| both sequences truncated left |\n"
+ "+-------------------------------+\n"
+ "i1 = %d, j1 = %d\n", hit.i1, hit.j1);
+ return FAILURE; /* FS, r241 -> r243 */
+ }
+#endif
+
+ for (step=hit.nsteps; step>=1; step--)
+ {
+ prev_state = state;
+ state = hit.states[step];
+
+ // Add column to alignment and compute identities and sequence-sequence similarity score
+ AddColumns(hit.i[step],hit.j[step],prev_state,state,hit.S[step]);
+ if (state==MM)
+ {
+ char qc=qa->seq[ q.nfirst][ qa->m[ q.nfirst][hit.i[step]] ];
+ char tc=ta->seq[hit.nfirst][ ta->m[hit.nfirst][hit.j[step]] ];
+ if (qc==tc) identities++; // count identical amino acids
+ score_sim += S[(int)aa2i(qc)][(int)aa2i(tc)];
+ // fprintf(stderr,"%3i %3i %3i %3i %3i %1c %1c %6.2f %6.2f %6.2f %6.2f \n",step,hit.nsteps,hit.i[step],hit.j[step],int(state),qc,tc,S[(int)aa2i(qc)][(int)aa2i(tc)],score_sim,hit.P_posterior[step],hit.sum_of_probs); //DEBUG
+ }
+ }
+
+#ifdef CLUSTALO
+ if ((qa->L == hit.i2) && (ta->L == hit.j2)){
+ /* do nothing */
+ }
+ else if ((qa->L == hit.i2) && (ta->L != hit.j2)){
+ for (int j = hit.j2+1; j <= ta->L; j++){
+ AddColumns(0, j, MM, IM, 0.0);
+ }
+ if (rLog.iLogLevelEnabled <= LOG_DEBUG){
+ int iK;
+ unsigned int uiL;
+ FILE *fp = rLog.prFP[LOG_DEBUG];
+
+ fprintf(fp, "%d: j2=%d (%d) -> temp has trailing gaps\n", __LINE__, hit.j2, ta->L);
+ for (iK = 0; iK < ta->n; iK++){
+ //printf("T%d: %s\n", iK, ta->s[iK]+strlen(ta->s[iK])-(ta->L-hit.j2));
+ for (uiL = strlen(ta->s[iK])-(ta->L-hit.j2); uiL < strlen(ta->s[iK]); uiL++){
+ ta->s[iK][uiL] = tolower(ta->s[iK][uiL]);
+ }
+ }
+ }
+ }
+ else if ((qa->L != hit.i2) && (ta->L == hit.j2)){
+ for (int i = hit.i2+1; i <= qa->L; i++){
+ AddColumns(i, 0, MM, MI, 0.0);
+ }
+ if (rLog.iLogLevelEnabled <= LOG_DEBUG){
+ int iK;
+ unsigned int uiL;
+ printf("%d: i2=%d (%d)-> query has trailing gaps\n", __LINE__, hit.i2, qa->L);
+ for (iK = 0; iK < qa->n; iK++){
+ //printf("Q%d: %s\n", iK, qa->s[iK]+strlen(qa->s[iK])-(qa->L-hit.i2));
+ for (uiL = strlen(qa->s[iK])-(qa->L-hit.i2); uiL < strlen(qa->s[iK]); uiL++){
+ qa->s[iK][uiL] = tolower(qa->s[iK][uiL]);
+ }
+ }
+ }
+ }
+ else{
+ fprintf(stderr,
+ "+--------------------------------+\n"
+ "| both sequences truncated right |\n"
+ "+--------------------------------+\n"
+ "i2 = %d != %d = qa->L, j2 = %d != %d = ta->L\n",
+ hit.i2, qa->L, hit.j2, ta->L);
+ return FAILURE; /* FS, r241 -> r243 */
+ }
+
+#endif
+
+ AddGaps(); //fill up gaps until query and template parts have same length
+ qa->AddChar('\0');
+ ta->AddChar('\0');
+
+ // Change gap symbol '.' (gap aligned to insert) to '~' if one HMM has gap with respect to other HMM
+ for (hh=1; hh<qa->pos; hh++)
+ {
+ if (symbol[hh]=='Q')
+ {
+ // Gap in query (IM or GD state)
+ symbol[hh]=' ';
+ for (k=0; k<qa->n; k++) if (qa->s[k][hh]=='.') qa->s[k][hh]='-';
+ }
+ else if (symbol[hh]=='T')
+ {
+ // Gap in target (MI or DG state)
+ symbol[hh]=' ';
+ for (k=0; k<ta->n; k++) if (ta->s[k][hh]=='.') ta->s[k][hh]='-';
+ }
+ }
+ return OK;
+} /* this is the end of FullAlignment::Build() */
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Print out header before full alignment
+ */
+void
+FullAlignment::PrintHeader(FILE* outf, HMM& q, Hit& hit)
+{
+ fprintf(outf,">%s\n",hit.longname);
+ fprintf(outf,"Probab=%-.2f E-value=%-.2g Score=%-.2f Aligned_cols=%i Identities=%i%% Similarity=%-.3f Sum_probs=%.1f\n\n",
+ hit.Probab,hit.Eval,hit.score,hit.matched_cols,iround(100.0*identities/hit.matched_cols),score_sim/hit.matched_cols,hit.sum_of_probs);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Print out full alignment in HHR format
+ */
+void
+FullAlignment::PrintHHR(FILE* outf, Hit& hit)
+{
+ const int NLEN=14; //Length of name field in front of multiple alignment
+ int h=0; //counts position (column) in alignment
+ int hh=0; //points to column at start of present output block of alignment
+ int k; //counts sequences in query and template
+ //short unsigned int lq[MAXSEQ]; // lq[k] counts index of residue from query sequence k to be printed next;
+ short unsigned int *lq = NULL; // lq[k] counts index of residue from query sequence k to be printed next;
+ //short unsigned int lt[MAXSEQ]; // lt[k] counts index of residue from template sequence k to be printed next;
+ short unsigned int *lt = NULL; // lt[k] counts index of residue from template sequence k to be printed next;
+ char namestr[NAMELEN]; //name of sequence
+ int iq=hit.i1; // match state counter for query HMM (displayed in consensus line)
+ int jt=hit.j1; // match state counter for template HMM (displayed in consensus line)
+
+ lq = new(short unsigned int[qa->n+2]);
+ lt = new(short unsigned int[ta->n+2]);
+
+ for (k=0; k<qa->n; k++) lq[k]=qa->l[k][hit.i1];
+ for (k=0; k<ta->n; k++) lt[k]=ta->l[k][hit.j1];
+
+ while (hh<ta->pos-1) // print alignment block
+ {
+ // Print query secondary structure sequences
+ for (k=0; k<qa->n; k++)
+ {
+ if (k==qa->nsa_dssp) continue;
+ if (!(k==qa->nss_dssp || k==qa->nsa_dssp || k==qa->nss_pred || k==qa->nss_conf)) continue;
+ if (k==qa->nss_dssp && !par.showdssp) continue;
+ if ((k==qa->nss_pred || k==qa->nss_conf) && !par.showpred) continue;
+ strncpy(namestr,qa->sname[k],NAMELEN-2);
+ namestr[NAMELEN-1]='\0';
+ strcut(namestr);
+ fprintf(outf,"Q %-*.*s ",NLEN,NLEN,namestr);
+ for (h=hh; h<imin(hh+par.aliwidth,qa->pos-1); h++) fprintf(outf,"%1c",qa->s[k][h]);
+ fprintf(outf,"\n");
+ }
+
+ // Print query sequences
+ for (k=0; k<qa->n; k++)
+ {
+ if (k==qa->nss_dssp || k==qa->nsa_dssp || k==qa->nss_pred || k==qa->nss_conf || k==qa->ncons) continue;
+ strncpy(namestr,qa->sname[k],NAMELEN-2);
+ namestr[NAMELEN-1]='\0';
+ strcut(namestr);
+ fprintf(outf,"Q %-*.*s %4i ",NLEN,NLEN,namestr,lq[k]);
+ for (h=hh; h<imin(hh+par.aliwidth,qa->pos-1); h++)
+ {fprintf(outf,"%1c",qa->s[k][h]); lq[k]+=WordChr(qa->s[k][h]);} //WordChr() returns 1 if a-z or A-Z; 0 otherwise
+ fprintf(outf," %4i (%i)\n",lq[k]-1,qa->l[k][qa->L+1]);
+ }
+
+ // Print query consensus sequence
+ if (par.showcons && qa->ncons>=0)
+ {
+ k=qa->ncons;
+ strncpy(namestr,qa->sname[k],NAMELEN-2);
+ namestr[NAMELEN-1]='\0';
+ strcut(namestr);
+ fprintf(outf,"Q %-*.*s %4i ",NLEN,NLEN,namestr,iq);
+ for (h=hh; h<imin(hh+par.aliwidth,qa->pos-1); h++)
+ {
+ if (qa->s[k][h]=='x') qa->s[k][h]='~';
+ if (qa->s[k][h]!='-' && qa->s[k][h]!='.') iq++;
+ fprintf(outf,"%1c",qa->s[k][h]);
+ }
+ fprintf(outf," %4i (%i)\n",iq-1,qa->L);
+ }
+
+
+ // Print symbols representing the score
+ fprintf(outf," %*.*s ",NLEN,NLEN," ");
+ for (h=hh; h<imin(hh+par.aliwidth,qa->pos-1); h++) fprintf(outf,"%1c",symbol[h]);
+ fprintf(outf,"\n");
+
+ // Print template consensus sequence
+ if (par.showcons && ta->ncons>=0)
+ {
+ k=ta->ncons;
+ strncpy(namestr,ta->sname[k],NAMELEN-2);
+ namestr[NAMELEN-1]='\0';
+ strcut(namestr);
+ fprintf(outf,"T %-*.*s %4i ",NLEN,NLEN,namestr,jt);
+ for (h=hh; h<imin(hh+par.aliwidth,ta->pos-1); h++)
+ {
+ if (ta->s[k][h]=='x') ta->s[k][h]='~';
+ if (ta->s[k][h]!='-' && ta->s[k][h]!='.') jt++;
+ fprintf(outf,"%1c",ta->s[k][h]);
+ }
+ fprintf(outf," %4i (%i)\n",jt-1,ta->L);
+ }
+ // Print template sequences
+ for (k=0; k<ta->n; k++)
+ {
+ if (k==ta->nss_dssp || k==ta->nsa_dssp || k==ta->nss_pred || k==ta->nss_conf || k==ta->ncons) continue;
+ strncpy(namestr,ta->sname[k],NAMELEN-2);
+ namestr[NAMELEN-1]='\0';
+ strcut(namestr);
+ fprintf(outf,"T %-*.*s %4i ",NLEN,NLEN,namestr,lt[k]);
+ for (h=hh; h<imin(hh+par.aliwidth,ta->pos-1); h++)
+ {fprintf(outf,"%1c",ta->s[k][h]); lt[k]+=WordChr(ta->s[k][h]);} //WordChr() returns 1 if a-z or A-Z; 0 otherwise
+ fprintf(outf," %4i (%i)\n",lt[k]-1,ta->l[k][ta->L+1]);
+ }
+
+ // Print template secondary structure sequences
+ for (k=0; k<ta->n; k++)
+ {
+ if (k==ta->nsa_dssp) continue;
+ if (!(k==ta->nss_dssp || k==ta->nss_pred || k==ta->nss_conf)) continue;
+ if (k==ta->nss_dssp && !par.showdssp) continue;
+ if ((k==ta->nss_pred || k==ta->nss_conf)&& !par.showpred) continue;
+ strncpy(namestr,ta->sname[k],NAMELEN-2);
+ namestr[NAMELEN-1]='\0';
+ strcut(namestr);
+ fprintf(outf,"T %-*.*s ",NLEN,NLEN,namestr);
+ for (h=hh; h<imin(hh+par.aliwidth,ta->pos-1); h++) fprintf(outf,"%1c",ta->s[k][h]);
+ fprintf(outf,"\n");
+ }
+
+ hh=h;
+ fprintf(outf,"\n\n");
+ }
+
+ delete[](lq); lq = NULL;
+ delete[](lt); lt = NULL;
+
+} /* this is the rnd of PrintHHR() */
+
+//////////////////////////////////////////////////////////////////////////////
+// Print out full alignment in A2M format
+//////////////////////////////////////////////////////////////////////////////
+#define TELOMER_PRINT 0
+void FullAlignment::PrintA2M(FILE* outf, Hit& hit)
+{
+ int k; //counts sequences in query and template
+ int h,hh;
+#if TELOMER_PRINT
+ int iTelomerLeft = hit.i1 - hit.j1;
+ int iTelomerRght = (qa->L - hit.i2) - (ta->L - hit.j2);
+#endif
+
+ // Print query sequences
+ for (k=0; k<qa->n; k++)
+ {
+ if (k==qa->nsa_dssp) continue;
+ if (k==qa->nss_dssp && !par.showdssp) continue;
+ if ((k==qa->nss_pred || k==qa->nss_conf) && !par.showpred) continue;
+ if (k==qa->ncons && !par.showcons) continue;
+ fprintf(outf,">%s\n",qa->sname[k]);
+#if TELOMER_PRINT
+ /* @<print left cut-off@> */
+ if (iTelomerLeft > 0){
+ for (int iI = 1; iI <= iTelomerLeft; iI++){
+ fprintf(outf, "%1c", qa->seq[k][iI]);
+ }
+ /* this may be unnecessary */
+ for (int iI = iTelomerLeft+1; iI < hit.i1; iI++){
+ fprintf(outf, "%1c", qa->seq[k][iI]);
+ }
+ }
+ else {
+ for (int iI = iTelomerLeft; iI < 0; iI++){
+ fprintf(outf, "%1c", '-');
+ }
+ /* this may be unnecessary */
+ /* think about it */
+ }
+ /* @<print consensus@> */
+ for (h = 0; qa->s[k][h] > 0; h++){
+ fprintf(outf, "%1c", qa->s[k][h]);
+ }
+ /* @<print out rght cut-off@> */
+ for (int iI = hit.i2+1; iI <= qa->L; iI++){
+ fprintf(outf, "%1c", qa->seq[k][iI]);
+ }
+ for (int iI = 0; iI > iTelomerRght; iI--){
+ fprintf(outf, "%1c", '-');
+ }
+#else
+ for (h=0,hh=-par.aliwidth; qa->s[k][h]>0; h++,hh++)
+ {
+ if (!hh) {fprintf(outf,"\n"); hh-=par.aliwidth;}
+ fprintf(outf,"%1c",qa->s[k][h]);
+ }
+#endif
+ fprintf(outf,"\n");
+ }
+
+ // Print template sequences
+ for (k=0; k<ta->n; k++)
+ {
+ if (k==ta->nsa_dssp) continue;
+ if (k==ta->nss_dssp && !par.showdssp) continue;
+ if ((k==ta->nss_pred || k==ta->nss_conf) && !par.showpred) continue;
+ if (k==ta->ncons && !par.showcons) continue;
+ fprintf(outf,">%s\n",ta->sname[k]);
+#if TELOMER_PRINT
+ /* @<print left cut-off@> */
+ if (iTelomerLeft > 0){
+ for (int iI = 1; iI <= iTelomerLeft; iI++){
+ fprintf(outf, "%1c", '-');
+ }
+ /* this may be unnecessary */
+ for (int iI = iTelomerLeft+1; iI < hit.j1; iI++){
+ fprintf(outf, "%1c", ta->seq[k][iI]);
+ }
+ }
+ else{
+ for (int iI = 1; iI <= -iTelomerLeft; iI++){
+ fprintf(outf, "%1c", ta->seq[k][iI]);
+ }
+ /* this may be unnecessary */
+ /* think about it */
+ }
+ /* @<print consensus@> */
+ for (h = 0; ta->s[k][h] > 0; h++){
+ fprintf(outf, "%1c", ta->s[k][h]);
+ }
+
+ /* @<print out rght cut-off@> */
+ for (int iI = hit.j2+1; iI <= ta->L; iI++){
+ fprintf(outf, "%1c", ta->seq[k][iI]);
+ }
+ for (int iI = 0; iI < iTelomerRght; iI++){
+ fprintf(outf, "%1c", '-');
+ }
+
+#else
+ for (h=0,hh=-par.aliwidth; ta->s[k][h]>0; h++,hh++)
+ {
+ if (!hh) {fprintf(outf,"\n"); hh-=par.aliwidth;}
+ fprintf(outf,"%1c",ta->s[k][h]);
+ }
+#endif
+ fprintf(outf,"\n");
+ }
+ fprintf(outf,"\n");
+
+} /* this is the end of PrintA2M() */
+
+////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Print out full alignment in A2M format
+ */
+void
+FullAlignment::PrintFASTA(FILE* outf, Hit& hit)
+{
+ // Transform sequences to uppercase and '.' to '-'
+ qa->ToFASTA();
+ ta->ToFASTA();
+ PrintA2M(outf,hit);
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Print out full alignment in A2M format
+ */
+void
+FullAlignment::PrintA3M(FILE* outf, Hit& hit)
+{
+ // Remove all '.' from sequences
+ qa->RemoveChars('.');
+ ta->RemoveChars('.');
+ PrintA2M(outf,hit);
+}
+
+
+/*
+ * @* OverWriteSeqs()
+ */
+void
+FullAlignment::OverWriteSeqs(char **ppcFirstProf, char **ppcSecndProf){
+
+ int iS, iR;
+ char cRes;
+
+ for (iS = 0; iS < qa->n; iS++){
+ for (iR = 0; iR < qa->pos; iR++){
+ cRes = qa->s[iS][iR];
+ ppcFirstProf[iS][iR] = ('.' == cRes) ? '-' : cRes;
+
+ } /* 0 <= iR < qa.L */
+ ppcFirstProf[iS][iR] = '\0';
+ } /* 0 <= iS < qa.n */
+
+ for (iS = 0; iS < ta->n; iS++){
+ for (iR = 0; iR < ta->pos; iR++){
+ cRes = ta->s[iS][iR];
+ ppcSecndProf[iS][iR] = ('.' == cRes) ? '-' : cRes;
+
+ } /* 0 <= iR < ta.L */
+ ppcSecndProf[iS][iR] = '\0';
+ } /* 0 <= iS < ta.n */
+
+} /* this is the end of OverWriteSeqs() */
+
+
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhfullalignment.h 243 2011-05-31 13:49:19Z fabian $
+ */
+
+//////////////////////////////////////////////////////////////////////////////
+// Class for output alignment of query against template sequences
+//////////////////////////////////////////////////////////////////////////////
+
+class FullAlignment
+{
+public:
+ FullAlignment(int maxseqdis=MAXSEQDIS);
+ ~FullAlignment();
+ void FreeMemory();
+ int Build(HMM& q, Hit& hit);
+ void PrintHeader(FILE* outf, HMM& q, Hit& hit);
+ void PrintHHR(FILE* outf, Hit& hit);
+ void PrintA2M(FILE* outf, Hit& hit);
+ void PrintFASTA(FILE* outf, Hit& hit);
+ void PrintA3M(FILE* outf, Hit& hit);
+ void OverWriteSeqs(char **ppcFirstProf, char **ppcSecndProf);
+ int identities; // number of identical residues in query and template sequence
+ float score_sim; // substitution matrix similarity score between query and template
+
+private:
+ HalfAlignment* qa; //query and template parts of the alignment
+ HalfAlignment* ta; //query and template parts of the alignment
+ char symbol[LINELEN]; //symbol[h] = symbol (= - . + |) indicating match score for col h of alignment
+ void ClearSymbols() {for (int h=0; h<LINELEN-1; h++) symbol[h]=' ';}
+ void AddColumns(int i, int j, char prev_state, char state, float S);
+ void AddGaps();
+ int ScoreChr(float S) {return (S<-1.5?'=':(S<-0.5?'-':(S<0.5?'.':(S<1.5?'+':'|'))));}
+};
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhfunc-C.h 256 2011-06-23 13:57:28Z fabian $
+ */
+
+/*
+ * Changelog: Michael Remmert made changes to hhalign stand-alone code
+ * FS implemented some of the changes on 2010-11-11 -> MR1
+ *
+ * did not incorporate SS prediction PSIpred (yet); functions are:
+ * CalculateSS(3),
+ */
+
+
+// hhfunc.C
+
+
+/**
+ * AddBackgroundFrequencies()
+ *
+ * @brief add background frequencies (derived from HMM) to
+ * sequence/profile
+ *
+ * @param[in,out] ppfFreq,
+ * [in] residue frequencies of sequence/profile,
+ * [out] overlayed with HMM background frequencies
+ * @param[in,out] ppfPseudoF,
+ * [in] residue frequencies+pseudocounts of sequence/profile,
+ * [out] overlayed with HMM background frequencies+pseudocounts
+ * @param[in] iSeqLen,
+ * length of sequence/profile (not aligned to HMM)
+ * @pram[in] prHMM,
+ * background HMM
+ * @param[in] ppcSeq,
+ * sequences/profile to be 'softened'
+ * @param[in] pcPrealigned,
+ * sequence aligned to HMM, this is not quite a consensus,
+ * it is identical to 1st sequence but over-writes gap information,
+ * if other sequences in profile have (non-gap) residues
+ * @param[in] iPreCnt
+ * number of sequences pre-aligned (pcPrealigned is 'consensus' of these sequences)
+ * @param[in] pcRepresent
+ * sequence representative of HMM, aligned to pcSeq0
+ */
+void
+AddBackgroundFrequencies(float **ppfFreq, float **ppfPseudoF, float **ppfPseudoTr,
+ int iSeqLen, hmm_light *prHMM,
+ char **ppcSeq, char *pcPrealigned, int iPreCnt, char *pcRepresent)
+{
+
+ char *pcS = pcPrealigned; /* current residue in pre-aligned sequence */
+ char *pcH = pcRepresent; /* current residue in pre-aligned HMM */
+ int iS = 0; /* position in un-aligned sequence (corresponds to pcS) */
+ int iH = 0; /* position in un-aligned HMM (corresponds to pcH) */
+ int iA; /* residue iterator */
+ int iT; /* transition state iterator */
+ float fFWeight = 0.50 / sqrt((float)(iPreCnt)); /* weight of backgroud frequencies */ /* FIXME: tune value, 0.50 default */
+ //float fFWeight = 0.75;
+ float fFThgiew = UNITY - fFWeight; /* weight of 'true' frequencies */
+ float fGWeight = 0.50 / sqrt((float)(iPreCnt)); /* weight of backgroud transitions */ /* FIXME: tune value, 0.50 default */
+ //float fGWeight = 0.50 /*/ (float)(iPreCnt)*/; /* weight of backgroud transitions */ /* FIXME: tune value, 0.50 default */
+ float fGThgiew = UNITY - fGWeight; /* weight of 'true' transitions */
+ float fAux;
+ /* zf1SeqTrans[] are the (phenomenological) transition probabilities (+ pseudo-counts)
+ for a single sequence. It is almost certain (0.99) to stay in a match state, and very
+ unlikely (0.05) to go from match to insertion/deletion */
+ float zf1SeqTrans[] = {0.98, 0.01, 0.01, 0.25, 0.75, 0.25, 0.75};
+ float zf1SeqInit[] = {0.98, 0.01, 0.01, 0.99, 0.01, 0.99, 0.01};
+ float zf1SeqDel[] = {0.24, 0.01, 0.75, 0.01, 0.01, 0.01, 0.01};
+ float zf1SeqRevrt[] = {0.98, 0.01, 0.01, 0.01, 0.01, 0.99, 0.01};
+
+ if ( (NULL == pcPrealigned) || (NULL == pcRepresent) ){
+ /*printf("%s/%s:%d: WARNING HMM=NULL -- didn't think I would get here (carry on, no danger)\n",
+ __FUNCTION__, __FILE__, __LINE__);*/
+ return;
+ }
+
+ if (NULL == prHMM->p){
+ printf("%s:%s:%d: WARNING -- Background Pseudocounts point to NULL\n"
+ "\tthis is not intended - don't add background but CONTINUE\n",
+ __FUNCTION__, __FILE__, __LINE__);
+ return;
+
+ }
+
+ /* FIXME: should be 0 (FS thinks) but -1 gives better results */
+ iH = iS = 0/*-1*//*+1*/;
+ while ( ('\0' != *pcS) && ('\0' != *pcH) ){
+
+ if ( ('-' != *pcH) && ('-' != *pcS) ){
+ iH++;
+ iS++;
+
+#if 0
+ /* match state
+ * - HMM had a gap in previous position (now closed)
+ * FIXME: this does not really work */
+ if ((iH > 0) && ('-' == *(pcH-1))){
+
+ for (iT = 0; iT < STATE_TRANSITIONS; iT++){
+ ppfPseudoTr[iS-1][iT] = log2f(zf1SeqRevrt[iT]);
+ }
+ }
+#endif
+
+#if 1
+ /* do frequencies -- this is not really useful;
+ frequencies are derived from HMM
+ and contain already pseudocounts (PCs),
+ adding frequencies and then PCs will add PCs _twice_
+ results are better than not to add them,
+ but not as good as PCs */
+ for (iA = 0; iA < AMINOACIDS; iA++){
+ fAux = fFThgiew * ppfFreq[iS][iA] + fFWeight * prHMM->f[iH][iA];
+ ppfFreq[iS][iA] = fAux;
+ }
+#endif
+ /* do pseudo-counts */
+ for (iA = 0; iA < AMINOACIDS; iA++){
+ fAux =
+ fFThgiew * ppfPseudoF[iS][iA] + fFWeight * prHMM->p[iH][iA];
+ ppfPseudoF[iS][iA] = fAux;
+ }
+#if 0 /* do state transitions */
+ for (iT = 0; iT < STATE_TRANSITIONS; iT++){
+#if 1
+ /* this is a very crude method,
+ which averages the logarithms of the transitions,
+ effectively performing a geometric mean -
+ this presumably violates normalisation.
+ however, results are surprisingly good */
+ fAux =
+ fGThgiew * ppfPseudoTr[iS][iT] +
+ fGWeight * prHMM->tr[iH][iT];
+ ppfPseudoTr[iS][iT] = fAux;
+#else /* crude averaging */
+ /* There are 2 things to consider:
+ (1) one should really blend the probabilities of
+ the transitions, however, by default we have
+ the logarithms thereof.
+ So must exponentiate, blend, and then take log again.
+ This is expensive, and does not seem to lead to better
+ results than blending the logarithms
+ (and violating normalisation)
+ (2) transition probabilities for a single sequence
+ are really easy, there are no insert/delete transitions.
+ However, there is a begin state that is different
+ from the main body.
+ But again, this does not seem to make a blind bit
+ of difference
+ */
+ if (iS > 0){
+ fAux =
+ fGThgiew * zf1SeqTrans[iT] +
+ fGWeight * prHMM->linTr[iH][iT];
+ ppfPseudoTr[iS][iT] = log2f(fAux);
+ }
+ else {
+ fAux =
+ fGThgiew * zf1SeqInit[iT] +
+ fGWeight * prHMM->linTr[iH][iT];
+ ppfPseudoTr[iS][iT] = log2f(fAux);
+ }
+#endif /* mixing of linear/log */
+ } /* 0 <= iT < STATE_TRANSITIONS */
+#endif /* did state transitions */
+ } /* was Match -- neither HMM nor sequence have gap */
+
+ else if ('-' == *pcH){
+ /* sequence opened up gap in HMM */
+#if 0
+ if ((iH > 0) && ('-' != *(pcH-1)) && (iS > 0)){
+ /* this is the first gap in HMM
+ * FIXME: this does not really work */
+ for (iT = 0; iT < STATE_TRANSITIONS; iT++){
+ ppfPseudoTr[iS-1][iT] = log2f(zf1SeqDel[iT]);
+ }
+ }
+ else {
+ /* do nothing, keep single sequence values exactly as they are*/
+ }
+#endif
+ iS++;
+ }
+ else if ('-' == *pcS){
+ /* here the single sequence has a gap,
+ and the HMM (as a whole) does not. There may be individual gaps
+ in the HMM at this stage. By ignoring this we say that the HMM
+ dominates the overall behaviour - as in the M2M state as well
+ */
+ iH++;
+ }
+
+ pcH++;
+ pcS++;
+
+ } /* !EO[seq/hmm] */
+
+ return;
+
+} /* this is the end of AddBackgroundFrequencies() */
+
+
+
+/**
+ * ReadAndPrepare()
+ *
+ * @brief Read HMM input file or transfer alignment
+ * and add pseudocounts etc.
+ *
+ * @param[in] iRnPtype
+ * type of read/prepare
+ * enum {INTERN_ALN_2_HMM = 0, READ_ALN_2_HMM, READ_HMM_2_HMM};
+ * @param[in] ppcProf
+ * alignment
+ * @param[in] iCnt
+ * number of seqs in alignment
+ * @param[in,out] prHMM,
+ * [in] if sequences read/prepared, [out] if HMM from file
+ * @param[in] pcPrealigned,
+ * (single) sequence aligned to background HMM
+ * @param[in] pcRepresent,
+ * sequence representing HMM aligned to individual sequence
+ * param[in] pdExWeights
+ * (external) sequence weights, derived from tree
+ * @param[in] infile
+ * name of file with HMM info (formerly also alignment)
+ * @param[out] q
+ * HMM structure with transition probabilities, residue frequencies etc
+ * @param[???] qali
+ * FIXME: what is qali?
+ *
+ * @return FAILURE on error, OK otherwise
+ */
+int
+ReadAndPrepare(int iRnPtype,
+ char **ppcProf, int iCnt, hmm_light *prHMM,
+ char *pcPrealigned, char *pcRepresent, double *pdExWeights,
+ char* infile, HMM& q, Alignment* qali=NULL) {
+
+ //#ifndef CLUSTALO_NOFILE
+ char path[NAMELEN];
+
+ /* NOTE: there are different scenarios:
+
+ (i) ("" != infile) - read HMM from file,
+ transfer frequency/transition/pseudo-count (f/t/p) info into prHMM
+
+ (ii) ('\0' != ppcProf[0]) - transfer sequence/alignment into q/qali,
+ don't save f/t/p into prHMM,
+ on the contrary, if prior f/t/p available then add it to q/qali,
+ this is only done if (1==iCnt)
+
+ (iii) ('\0' == ppcProf[0]) - re-cycle old HMM information
+ recreate a HMM from previous data
+ */
+
+ /********************************/
+ /*** (o) Recycle internal HMM ***/
+ /********************************/
+ if ( (INTERN_ALN_2_HMM == iRnPtype) && (iCnt <= 0) ){
+
+ /* NOTE: here we are writing into a HMM structure/class;
+ memory has been allocated for this in hhalign.cpp;
+ however, as iCnt<=0, there may not be memory for
+ prHMM->n_display sequences/names.
+ But then, there doesn't have to be.
+ At this stage we are just copying one HMM into another HMM,
+ sequences are irrelevant. The only sequence of (marginal)
+ interest is the consensus sequence */
+ /* FIXME: check that prHMM is valid -- how? */
+
+ const int ciCons = 0;
+ const int ciNoof = ciCons+1;
+ const int ciInvalid = -1;
+ q.n_display = ciNoof; /* only consensus */
+ q.sname = NULL;
+ q.ncons = ciCons;
+ q.nfirst = ciCons;//prHMM->nfirst;
+ q.nss_dssp = ciInvalid;//prHMM->nss_dssp;
+ q.nsa_dssp = ciInvalid;//prHMM->nsa_dssp;
+ q.nss_pred = ciInvalid;//prHMM->nss_pred;
+ q.nss_conf = ciInvalid;//prHMM->nss_conf;
+ q.L = prHMM->L;
+ q.N_in = prHMM->N_in;
+ q.N_filtered = prHMM->N_filtered;
+ /* NOTE: I (FS) think that only ever 1 sequence will be transferred here,
+ that is, the consensus sequence. However, we might want to allow
+ (in the future) to transfer more sequences,
+ hence the awkward for() loop */
+#if 0
+ for (int i = prHMM->ncons+0; i < prHMM->ncons+q.n_display; i++){
+ /* NOTE: In the original hhalign code the first position
+ is kept open ('\0'). This makes it difficult to use
+ string functions like strlen/strdup etc.
+ Insert a temporary gap (.) to facilitate string operations */
+ char cHead = prHMM->seq[i][0];
+ prHMM->seq[i][0] = '.';
+ q.seq[i] = strdup(prHMM->seq[i]);
+ prHMM->seq[i][0] = q.seq[i][0] = cHead;
+ }
+#else
+ {
+ char cHead = prHMM->seq[prHMM->ncons][0];
+ prHMM->seq[prHMM->ncons][0] = '.';
+ q.seq[q.ncons] = strdup(prHMM->seq[prHMM->ncons]);
+ prHMM->seq[prHMM->ncons][0] = q.seq[q.ncons][0] = cHead;
+ }
+#endif
+ const int NEFF_SCORE = 10; /* FIXME: Magic Number */
+ for (int i = 0; i < prHMM->L+1; i++){
+ q.Neff_M[i] = prHMM->Neff_M[i];
+ q.Neff_I[i] = prHMM->Neff_I[i];
+ q.Neff_D[i] = prHMM->Neff_D[i];
+ }
+ q.Neff_HMM = prHMM->Neff_HMM;
+ /* skip longname,name,file,fam,sfam,fold,cl */
+ q.lamda = prHMM->lamda;
+ q.mu = prHMM->mu;
+
+ HMMshadow rShadow = {0}; /* friend of HMM to access private members */
+ rShadow.copyShadowToHMM(q, *prHMM);
+
+ /* skip trans_lin,ss_dssp,sa_dssp,ss_pred,ss_conf,Xcons */
+ /* pav already done in copyShadowToHMM */
+ /* skip pnul */
+
+ return OK;
+
+
+ } /* INTERN_ALN_2_HMM && iCnt<=0 */
+
+ /******************************/
+ /*** (i) Read HMM from file ***/
+ /******************************/
+ char line[LINELEN] = {0}; // input line
+ FILE *inf = NULL;
+ //if ( (0 != strcmp(infile,"")) /*&& (iCnt > 0)*/ )
+ if ( (READ_HMM_2_HMM == iRnPtype) || (READ_ALN_2_HMM == iRnPtype)) {
+
+ if (0 == strcmp(infile,"")){
+ printf("%s:%s:%d:\n"
+ "\texpected to re %s from file but no file specified\n"
+ ""
+ , __FUNCTION__, __FILE__, __LINE__
+ , (READ_HMM_2_HMM==iRnPtype?"HMM":"alignment"));
+ return FAILURE;
+ }
+ inf = fopen(infile, "r");
+ if (!inf) OpenFileError(infile);
+ Pathname(path,infile);
+
+ //}
+ //else {
+ //inf = stdin;
+ //if (v>=2) printf("Reading HMM / multiple alignment from standard input ...\n(To get a help list instead, quit and type %s -h.)\n",program_name);
+ //*path='\0';
+ //}
+
+ fgetline(line,LINELEN-1,inf);
+ }
+
+ //if ( (0 != strcmp(infile,"")) && (iCnt > 0) )
+ if ( (READ_HMM_2_HMM == iRnPtype) ){
+
+ if (0 == strcmp(infile,"")){
+ printf("%s:%s:%d: expected to read HMM from file but no file-name\n",
+ __FUNCTION__, __FILE__, __LINE__);
+ }
+
+ // Is infile a HMMER3 file? /* MR1 */
+ if (!strncmp(line,"HMMER3",6))
+ {
+ if (v>=2) {
+ cout<<"Query file is in HMMER3 format\n";
+ cout<<"WARNING! Use of HMMER3 format as input results in dramatically loss of sensitivity!\n";
+ }
+
+ // Read 'query HMMER file
+ rewind(inf);
+ q.ReadHMMer3(inf,path);
+
+ // Don't add transition pseudocounts to query!!
+
+ // Generate an amino acid frequency matrix from f[i][a] with full pseudocount admixture (tau=1) -> g[i][a]
+ q.PreparePseudocounts();
+
+ // DON'T ADD amino acid pseudocounts to query: pcm=0! q.p[i][a] = f[i][a]
+ q.AddAminoAcidPseudocounts(0, par.pca, par.pcb, par.pcc);
+
+ /* further down there is a q.Log2LinTransitionProbs
+ but only if (iCnt>0), however, we still need it it here (i think),
+ there is no danger of doing this twice, as trans_lin is checked
+ FIXME (FS, 2011-01-12) */
+ /* further down there is a q.Log2LinTransitionProbs
+ but only if (iCnt>0), however, we still need it it here (i think),
+ there is no danger of doing this twice, as trans_lin is checked
+ FIXME (FS, 2011-01-12) */
+ //if (par.forward >= 1)
+ {
+ q.Log2LinTransitionProbs(1.0);
+ }
+
+ }
+ // ... or Is infile an old HMMER file?
+ else if (!strncmp(line,"HMMER",5)) {
+ if (v>=2) {
+ cout<<"Query file is in HMMER format\n";
+ cout<<"WARNING! Use of HMMER format as input results in dramatically loss of sensitivity!\n";
+ }
+
+ // Read 'query HMMER file
+ q.ReadHMMer(inf,path);
+ if (v>=2 && q.Neff_HMM>11.0)
+ fprintf(stderr,"WARNING: HMM %s looks too diverse (Neff=%.1f>11). Better check the underlying alignment... \n",q.name,q.Neff_HMM);
+
+ // Don't add transition pseudocounts to query!!
+
+ // Generate an amino acid frequency matrix from f[i][a] with full pseudocount admixture (tau=1) -> g[i][a]
+ q.PreparePseudocounts();
+
+ // DON'T ADD amino acid pseudocounts to query: pcm=0! q.p[i][a] = f[i][a]
+ q.AddAminoAcidPseudocounts(0, par.pca, par.pcb, par.pcc);
+
+ /* further down there is a q.Log2LinTransitionProbs
+ but only if (iCnt>0), however, we still need it it here (i think),
+ there is no danger of doing this twice, as trans_lin is checked
+ FIXME (FS, 2011-01-12) */
+ //if (par.forward >= 1)
+ {
+ q.Log2LinTransitionProbs(1.0);
+ }
+
+ } /* it was a HMMer file */
+
+ // ... or is it an hhm file?
+ else if (!strncmp(line,"NAME",4) || !strncmp(line,"HH",2)) {
+
+ if (v>=2) cout<<"Query file is in HHM format\n";
+
+ // Rewind to beginning of line and read query hhm file
+ rewind(inf);
+ q.Read(inf,path);
+ if (v>=2 && q.Neff_HMM>11.0)
+ fprintf(stderr,"WARNING: HMM %s looks too diverse (Neff=%.1f>11). Better check the underlying alignment... \n",q.name,q.Neff_HMM);
+
+ // Add transition pseudocounts to query -> q.p[i][a]
+ q.AddTransitionPseudocounts();
+
+ // Generate an amino acid frequency matrix from f[i][a] with full pseudocount admixture (tau=1) -> g[i][a]
+ q.PreparePseudocounts();
+
+ // Add amino acid pseudocounts to query: q.p[i][a] = (1-tau)*f[i][a] + tau*g[i][a]
+ q.AddAminoAcidPseudocounts();
+
+ } /* it was a HHM file */
+ else {
+ fprintf(stderr, "%s:%s:%d: Unknown HMM format in infile\n"
+ "infile=%s, #seq=%d\n"
+ , __FUNCTION__, __FILE__, __LINE__
+ , infile, iCnt);
+ return FAILURE;
+ }
+
+ /*fclose(inf);*/
+
+ /*** transfer class info to struct */
+ prHMM->n_display = q.n_display;
+ /* ignore sname*/
+ prHMM->seq = (char **)calloc((q.n_display+1), sizeof(char *));
+ /* FIXME valgrind says bytes get lost in the above calloc during
+ * hmm-iteration
+ */
+ for (int i = 0; i < q.n_display; i++){
+ /* NOTE: In the original hhalign code the first position
+ is kept open ('\0'). This makes it difficult to use
+ string functions like strlen/strdup etc.
+ Insert a temporary gap (.) to facilitate string operations */
+ char cHead = q.seq[i][0];
+ q.seq[i][0] = '.';
+ prHMM->seq[i] = strdup(q.seq[i]);
+ q.seq[i][0] = prHMM->seq[i][0] = cHead;
+ }
+ prHMM->ncons = q.ncons;
+ prHMM->nfirst = q.nfirst;
+ prHMM->nss_dssp = q.nss_dssp;
+ prHMM->nsa_dssp = q.nsa_dssp;
+ prHMM->nss_pred = q.nss_pred;
+ prHMM->nss_conf = q.nss_conf;
+ prHMM->L = q.L;
+ prHMM->N_in = q.N_in;
+ prHMM->N_filtered = q.N_filtered;
+ const int NEFF_SCORE = 10; /* FIXME: Magic Number */
+ prHMM->Neff_M = (float *)calloc(prHMM->L+1, sizeof(float));
+ prHMM->Neff_I = (float *)calloc(prHMM->L+1, sizeof(float));
+ prHMM->Neff_D = (float *)calloc(prHMM->L+1, sizeof(float));
+ /*for (int i = 0; i < prHMM->L+1; i++){
+ prHMM->Neff_M[i] = prHMM->Neff_I[i] = prHMM->Neff_D[i] = NEFF_SCORE;
+ }*/
+ prHMM->Neff_HMM = q.Neff_HMM;
+ /* skip longname,name,file,fam,sfam,fold,cl */
+ prHMM->lamda = q.lamda;
+ prHMM->mu = q.mu;
+
+ HMMshadow rShadow = {0}; /* friend of HMM to access private members */
+ rShadow.copyHMMtoShadow(q);
+
+ prHMM->f = (float **)calloc(prHMM->L+1, sizeof(float *));
+ prHMM->g = (float **)calloc(prHMM->L+1, sizeof(float *));
+ prHMM->p = (float **)calloc(prHMM->L+1, sizeof(float *));
+ prHMM->tr = (float **)calloc(prHMM->L+1, sizeof(float *));
+ prHMM->linTr = (float **)calloc(prHMM->L+1, sizeof(float *));
+ for (int i = 0; i < prHMM->L+1; i++){
+ prHMM->f[i] = (float *)calloc(AMINOACIDS, sizeof(float));
+ prHMM->g[i] = (float *)calloc(AMINOACIDS, sizeof(float));
+ prHMM->p[i] = (float *)calloc(AMINOACIDS, sizeof(float));
+ for (int j = 0; j < AMINOACIDS; j++){
+ prHMM->f[i][j] = (float)rShadow.f[i][j];
+ prHMM->g[i][j] = (float)rShadow.g[i][j];
+ prHMM->p[i][j] = (float)rShadow.p[i][j];
+ }
+ prHMM->tr[i] = (float *)calloc(STATE_TRANSITIONS, sizeof(float));
+ prHMM->linTr[i] = (float *)calloc(STATE_TRANSITIONS, sizeof(float));
+ for (int j = 0; j< STATE_TRANSITIONS; j++){
+ prHMM->tr[i][j] = (float)rShadow.tr[i][j];
+ prHMM->linTr[i][j] = fpow2(rShadow.tr[i][j]);
+ }
+ } /*0 <= i < prHMM->L+1 */
+ /* skip trans_lin,ss_dssp,sa_dssp,ss_pred,ss_conf,Xcons */
+ for (int j = 0; j < AMINOACIDS; j++){
+ prHMM->pav[j] = (float)rShadow.pav[j];
+ }
+ /* skip pnul */
+
+ } /* have read HHM from file */
+ /*else if ( ((NULL != ppcProf) && (iCnt > 0) && ('\0' != ppcProf[0][0])) ||
+ ( (0 != strcmp(infile,"") && (0 == iCnt) )) )*/
+ else if ( (INTERN_ALN_2_HMM == iRnPtype) || (READ_ALN_2_HMM == iRnPtype) ) {
+
+ if ( (INTERN_ALN_2_HMM == iRnPtype) &&
+ ( (NULL == ppcProf) || (iCnt <= 0) || ('\0' == ppcProf[0][0]) ) ){
+ printf("%s:%s:%d: was expecting internal alignment but\n"
+ "\tppcProf=%p, #seq=%d, ppcProf[0][0]=%c\n"
+ , __FUNCTION__, __FILE__, __LINE__
+ , ppcProf, iCnt, ppcProf[0][0]);
+ return FAILURE;
+ }
+ else if ( (READ_ALN_2_HMM == iRnPtype) &&
+ (0 == strcmp(infile,"")) ){
+ printf("%s:%s:%d: was expecting to read alignment from file but no filename\n"
+ , __FUNCTION__, __FILE__, __LINE__);
+ return FAILURE;
+ }
+
+ /*******************************/
+ /*** (ii) it is an alignment ***/
+ /*******************************/
+ /* transfer alignment information from clustal character array
+ into pali/q/t classes */
+ /*
+ * NOTE that emissions in HMMer file format contain pseudo-counts.
+ * HHM file format does not contain emission pseudo-counts.
+ * the structure that stores background HMM information does contain pseudo-counts
+ */
+ Alignment* pali;
+ if (qali==NULL){
+ pali=new Alignment(iCnt); /* FIXME: pass in iCnt to get rid of MAXSEQ */
+ }
+ else{
+ pali=qali;
+ }
+
+ if (par.calibrate) {
+ printf("\nError in %s: only HHM files can be calibrated.\n",program_name);
+ printf("Build an HHM file from your alignment with 'hhmake -i %s' and rerun hhsearch with the hhm file\n\n",infile);
+ exit(1);
+ }
+
+ if (v>=2 && strcmp(infile,"stdin")) cout<<infile<<" is in A2M, A3M or FASTA format\n";
+
+ /* Read alignment from infile into matrix X[k][l] as ASCII
+ (and supply first line as extra argument) */
+ //if (iCnt > 0)
+ if (INTERN_ALN_2_HMM == iRnPtype){
+ pali->Transfer(ppcProf, iCnt);
+ }
+ //else if (0 == iCnt)
+ else if (READ_ALN_2_HMM == iRnPtype){
+ pali->Read(inf, infile, line);
+ }
+ else {
+ printf("%s:%s:%d: FATAL problem\n"
+ "infile = (%s), #seq = %d\n"
+ , __FUNCTION__, __FILE__, __LINE__
+ , infile, iCnt);
+ return FAILURE;
+ }
+
+ /* Convert ASCII to int (0-20), throw out all insert states,
+ record their number in I[k][i]
+ and store marked sequences in name[k] and seq[k] */
+ pali->Compress(infile);
+
+ /* Sort out the nseqdis most dissimilar sequences for display
+ in the output alignments */
+ pali->FilterForDisplay(par.max_seqid, par.coverage, par.qid,
+ par.qsc,par.nseqdis);
+
+ // Filter alignment for min score per column with core query profile, defined by coverage_core and qsc_core
+ //if (par.coresc>-10) pali->HomologyFilter(par.coverage_core, par.qsc_core, par.coresc);
+
+ /* Remove sequences with seq. identity larger than seqid percent
+ (remove the shorter of two) */
+ pali->N_filtered = pali->Filter(par.max_seqid, par.coverage,
+ par.qid, par.qsc, par.Ndiff);
+
+ /* Calculate pos-specific weights,
+ AA frequencies and transitions -> f[i][a], tr[i][a] */
+ pali->FrequenciesAndTransitions(q);
+ if (v>=2 && q.Neff_HMM>11.0)
+ fprintf(stderr,"WARNING: alignment %s looks too diverse (Neff=%.1f>11). Better check it with an alignment viewer... \n",q.name,q.Neff_HMM);
+
+ /*printf("%d %d %f %d (N,Nf,Neff,L) %s:%s:%d\n"
+ , q.N_in, q.N_filtered, q.Neff_HMM, q.L, __FUNCTION__, __FILE__, __LINE__);*/
+
+ // Add transition pseudocounts to query -> p[i][a]
+ q.AddTransitionPseudocounts();
+
+ /* Generate an amino acid frequency matrix from f[i][a]
+ with full pseudocount admixture (tau=1) -> g[i][a] */
+ q.PreparePseudocounts();
+
+ /* Add amino acid pseudocounts to query:
+ p[i][a] = (1-tau)*f[i][a] + tau*g[i][a] */
+ q.AddAminoAcidPseudocounts();
+
+ /* ****** add aligned background pseudocounts ***** */
+ HMMshadow rShadowQ = {0};
+ rShadowQ.copyHMMtoShadow(q);
+
+ AddBackgroundFrequencies(rShadowQ.f, rShadowQ.p, rShadowQ.tr,
+ q.L, prHMM,
+ q.seq, pcPrealigned, iCnt, pcRepresent);
+
+
+ if (qali==NULL){
+ delete(pali); pali = NULL;
+ }
+
+ } /* else if (NULL != ppcProf) // not hmmer/hhalign but alignment */
+
+ //else if ((prHMM->L > 0) && ('\0' == ppcProf[0][0]))
+ else if (INTERN_HMM_2_HMM == iRnPtype){
+
+ /******************************************/
+ /*** (iii) re-cycle old HMM information ***/
+ /******************************************/
+
+ if (prHMM->L <= 0){
+ printf("%s:%s:%d: was expecting to copy HMM structure but L=%d\n"
+ , __FUNCTION__, __FILE__, __LINE__, prHMM->L);
+ }
+
+ printf("%s:%s:%d: RE-CYCLING HMM\n", __FUNCTION__, __FILE__, __LINE__);
+
+#if 0
+ q.n_display = prHMM->n_display;
+ /* ignore sname*/
+ for (int i = 0; i < q.n_display; i++){
+ /* NOTE: In the original hhalign code the first position
+ is kept open ('\0'). This makes it difficult to use
+ string functions like strlen/strdup etc.
+ Insert a temporary gap (.) to facilitate string operations */
+ char cHead = prHMM->seq[i][0];
+ prHMM->seq[i][0] = '.';
+ q.seq[i] = strdup(prHMM->seq[i]);
+ q.seq[i][0] = prHMM->seq[i][0] = cHead;
+ }
+ q.nfirst = prHMM->nfirst;
+#else
+ q.n_display = 1;
+ q.nfirst = 0;
+ char cHead = prHMM->seq[prHMM->nfirst][0];
+ prHMM->seq[prHMM->nfirst][0] = '.';
+ q.seq[0] = strdup(prHMM->seq[prHMM->nfirst]);
+ q.seq[q.n_display-1][0] = prHMM->seq[prHMM->nfirst][0] = cHead;
+#endif
+ q.ncons = prHMM->ncons;
+ q.nss_dssp = prHMM->nss_dssp;
+ q.nsa_dssp = prHMM->nsa_dssp;
+ q.nss_pred = prHMM->nss_pred;
+ q.nss_conf = prHMM->nss_conf;
+ q.L = prHMM->L;
+ q.N_in = prHMM->N_in;
+ q.N_filtered = prHMM->N_filtered;
+#define NEFF_SCORE 10 /* FIXME: Magic Number */
+ /*for (int i; i < prHMM->L+1; i++){
+ q.Neff_M[i] = q.Neff_I[i] = q.Neff_D[i] = NEFF_SCORE;
+ }*/
+ q.Neff_HMM = prHMM->Neff_HMM;
+ /* skip longname,name,file,fam,sfam,fold,cl */
+ q.lamda = prHMM->lamda;
+ q.mu = prHMM->mu;
+
+ HMMshadow rShadow = {0}; /* friend of HMM to access private members */
+ rShadow.copyShadowToHMM(q, *prHMM);
+
+ }
+
+ if (iCnt > 0){
+ if (par.forward>=1) q.Log2LinTransitionProbs(1.0);
+ }
+
+ if (NULL != inf){
+ fclose(inf);
+ }
+
+ return OK;
+
+} /*** end: ReadAndPrepare() ***/
+
+/**
+ * FreeHMMstruct()
+ *
+ * @brief FIXME
+ *
+ * @param[in,out]
+ */
+extern "C" void
+FreeHMMstruct(hmm_light *prHMM)
+{
+ int i;
+
+ if (NULL != prHMM->f){
+ for (i = 0; i < prHMM->L+1; i++){
+ if (NULL != prHMM->f[i]){
+ free(prHMM->f[i]); prHMM->f[i] = NULL;
+ }
+ } /* 0 <= i < prHMM->L+1 */
+ free(prHMM->f); prHMM->f = NULL;
+ }
+ if (NULL != prHMM->g){
+ for (i = 0; i < prHMM->L+1; i++){
+ if (NULL != prHMM->g[i]){
+ free(prHMM->g[i]); prHMM->g[i] = NULL;
+ }
+ } /* 0 <= i < prHMM->L+1 */
+ free(prHMM->g); prHMM->g = NULL;
+ }
+ if (NULL != prHMM->p){
+ for (i = 0; i < prHMM->L+1; i++){
+ if (NULL != prHMM->p[i]){
+ free(prHMM->p[i]); prHMM->p[i] = NULL;
+ }
+ } /* 0 <= i < prHMM->L+1 */
+ free(prHMM->p); prHMM->p = NULL;
+ }
+ if (NULL != prHMM->tr){
+ for (i = 0; i < prHMM->L+1; i++){
+ if (NULL != prHMM->tr[i]){
+ free(prHMM->tr[i]); prHMM->tr[i] = NULL;
+ }
+ } /* 0 <= i < prHMM->L+1 */
+ free(prHMM->tr); prHMM->tr = NULL;
+ }
+ if (NULL != prHMM->linTr){
+ for (i = 0; i < prHMM->L+1; i++){
+ if (NULL != prHMM->linTr[i]){
+ free(prHMM->linTr[i]); prHMM->linTr[i] = NULL;
+ }
+ } /* 0 <= i < prHMM->L+1 */
+ free(prHMM->linTr); prHMM->linTr = NULL;
+ }
+
+ if (NULL != prHMM->Neff_M){
+ free(prHMM->Neff_M); prHMM->Neff_M = NULL;
+ }
+ if (NULL != prHMM->Neff_I){
+ free(prHMM->Neff_I); prHMM->Neff_I = NULL;
+ }
+ if (NULL != prHMM->Neff_D){
+ free(prHMM->Neff_D); prHMM->Neff_D = NULL;
+ }
+
+ if (NULL != prHMM->seq){
+ for (i = 0; i < prHMM->n_display; i++){
+ if (NULL != prHMM->seq[i]){
+ free(prHMM->seq[i]); prHMM->seq[i] = NULL;
+ }
+ }
+ free(prHMM->seq); prHMM->seq = NULL;
+ }
+
+ memset(prHMM, 0, sizeof(hmm_light));
+
+} /*** end: FreeHMMstruct() ***/
+
+
+/**
+ * @brief comparisin function for ascending qsort() of doubles
+ */
+int
+CompDblAsc(const void *pv1, const void *pv2){
+
+ double d1 = *(double *)pv1;
+ double d2 = *(double *)pv2;
+
+ if (d1 > d2) { return +1; }
+ else if (d1 < d2) { return -1; }
+ else { return 0; }
+
+} /*** end: CompDblAsc() ***/
+
+
+/**
+ * AlnToHMM2()
+ *
+ * @brief convert alignment into HMM (hhmake)
+ *
+ * @param[out] prHMM
+ * structure with pseudocounts etc
+ * @param[in] pcHMM_input
+ * name of file with HMM
+ *
+ */
+extern "C" int
+AlnToHMM2(hmm_light *rHMM_p,
+ char **ppcSeq, int iN){
+
+ if (0 == par.M){
+ SetDefaults();
+ SetSubstitutionMatrix();
+ par.cons = 1;
+ par.M = 2;
+ par.forward=2;
+ par.Mgaps=100;
+ const int ciGoodMeasureSeq = 10;
+ int iAuxLen = strlen(ppcSeq[0]);
+ par.maxResLen = iAuxLen;
+ par.maxResLen += ciGoodMeasureSeq;
+ par.maxColCnt = iAuxLen + ciGoodMeasureSeq;
+ par.max_seqid=DEFAULT_FILTER;
+ par.loc=0; par.mact=0;
+ /* some minor parameters, affecting alignment (i think) */
+ par.p = 0.0; /* minimum threshold for inclusion in hit list */
+ par.Z = 100; /* minimum threshold for inclusion in hit list and alignment listing */
+ par.z = 1; /* min number of lines in hit list */
+ par.B = 100; /* max number of alignments */
+ par.b = 1; /* min number of alignments */
+ par.E = 1e6; /* maximum threshold for inclusion in hit list and alignment listing */
+ par.altali=1;par.hitrank=0;par.showcons=1; par.showdssp=1;par.showpred=1;par.nseqdis=iN;par.cons=1;
+ }
+
+ const int ciGoodMeasure = 10;
+ int iLen = strlen(ppcSeq[0]) + ciGoodMeasure;
+ if (iLen > par.maxResLen){
+ par.maxResLen = par.maxColCnt = iLen;
+ }
+ HMM rTemp(iN+2, iLen); /* temporary template */
+ Alignment rTempAli(iN+2, iLen); /* temporary alignment */
+ int iParCons = par.cons;
+
+ /*printf(">>>>>>>>>>> %s:%s:%d: there are %d sequences\n", __FUNCTION__, __FILE__, __LINE__, iN);*/
+
+ par.cons = 1;
+ if (OK != ReadAndPrepare(INTERN_ALN_2_HMM,
+ ppcSeq, iN, rHMM_p,
+ NULL/*prealigned*/, NULL/*representative*/, NULL/*weights*/, //YES/*transfer*/,
+ (char*)("")/*in-file*/, rTemp, &rTempAli)) {
+ return FAILURE;
+ }
+ par.cons = iParCons;
+
+ /******/
+ /*** transfer class info to struct */
+ rHMM_p->n_display = rTemp.n_display;
+ rHMM_p->sname = NULL;
+ rHMM_p->seq = (char **)calloc((rTemp.n_display+1), sizeof(char *));
+
+ for (int i = 0; i < rTemp.n_display; i++){
+ /* NOTE: In the original hhalign code the first position
+ is kept open ('\0'). This makes it difficult to use
+ string functions like strlen/strdup etc.
+ Insert a temporary gap (.) to facilitate string operations */
+ char cHead = rTemp.seq[i][0];
+ rTemp.seq[i][0] = '.';
+ rHMM_p->seq[i] = strdup(rTemp.seq[i]);
+ rTemp.seq[i][0] = rHMM_p->seq[i][0] = cHead;
+ }
+ rHMM_p->ncons = rTemp.ncons;
+ rHMM_p->nfirst = rTemp.nfirst;
+ if (-1 == rHMM_p->ncons){
+ /* ncons needed later for alignment of
+ representative sequence and copy of profile.
+ ncons not always set (-1 default),
+ this will cause segmentation fault.
+ nfirst (probably) right index -
+ no problem if not */
+ rHMM_p->ncons = rTemp.nfirst;
+ }
+ rHMM_p->nss_dssp = rTemp.nss_dssp;
+ rHMM_p->nsa_dssp = rTemp.nsa_dssp;
+ rHMM_p->nss_pred = rTemp.nss_pred;
+ rHMM_p->nss_conf = rTemp.nss_conf;
+ rHMM_p->L = rTemp.L;
+ rHMM_p->N_in = rTemp.N_in;
+ rHMM_p->N_filtered = rTemp.N_filtered;
+#define NEFF_SCORE 10 /* FIXME: Magic Number */ //// get rid of that, FS, 2010-12-22
+ rHMM_p->Neff_M = (float *)calloc(rHMM_p->L+1, sizeof(float));
+ rHMM_p->Neff_I = (float *)calloc(rHMM_p->L+1, sizeof(float));
+ rHMM_p->Neff_D = (float *)calloc(rHMM_p->L+1, sizeof(float));
+ for (int i = 0; i < rHMM_p->L+1; i++){
+ rHMM_p->Neff_M[i] = rHMM_p->Neff_I[i] = rHMM_p->Neff_D[i] = NEFF_SCORE; //// get rid of that, FS, 2010-12-22
+ }
+ rHMM_p->Neff_HMM = rTemp.Neff_HMM;
+ /* skip longname,name,file,fam,sfam,fold,cl */
+ rHMM_p->lamda = rTemp.lamda;
+ rHMM_p->mu = rTemp.mu;
+
+ HMMshadow rShadow = {0}; /* friend of HMM to access private members */
+ rShadow.copyHMMtoShadow(rTemp);
+
+ rHMM_p->Neff_M = (float *)calloc(rHMM_p->L+1, sizeof(float));
+ rHMM_p->Neff_I = (float *)calloc(rHMM_p->L+1, sizeof(float));
+ rHMM_p->Neff_D = (float *)calloc(rHMM_p->L+1, sizeof(float));
+ rHMM_p->f = (float **)calloc(rHMM_p->L+1, sizeof(float *));
+ rHMM_p->g = (float **)calloc(rHMM_p->L+1, sizeof(float *));
+ rHMM_p->p = (float **)calloc(rHMM_p->L+1, sizeof(float *));
+ rHMM_p->tr = (float **)calloc(rHMM_p->L+1, sizeof(float *));
+ rHMM_p->linTr = (float **)calloc(rHMM_p->L+1, sizeof(float *));
+
+ for (int i = 0; i < rHMM_p->L+1; i++){
+ rHMM_p->Neff_M[i] = (float)rShadow.Neff_M[i];
+ rHMM_p->Neff_I[i] = (float)rShadow.Neff_I[i];
+ rHMM_p->Neff_D[i] = (float)rShadow.Neff_D[i];
+ rHMM_p->f[i] = (float *)calloc(AMINOACIDS, sizeof(float));
+ rHMM_p->g[i] = (float *)calloc(AMINOACIDS, sizeof(float));
+ rHMM_p->p[i] = (float *)calloc(AMINOACIDS, sizeof(float));
+ for (int j = 0; j < AMINOACIDS; j++){
+ rHMM_p->f[i][j] = (float)rShadow.f[i][j];
+ rHMM_p->g[i][j] = (float)rShadow.g[i][j];
+ rHMM_p->p[i][j] = (float)rShadow.p[i][j];
+ }
+ rHMM_p->tr[i] = (float *)calloc(STATE_TRANSITIONS, sizeof(float));
+ rHMM_p->linTr[i] = (float *)calloc(STATE_TRANSITIONS, sizeof(float));
+ for (int j = 0; j< STATE_TRANSITIONS; j++){
+ rHMM_p->tr[i][j] = (float)rShadow.tr[i][j];
+ rHMM_p->linTr[i][j] = fpow2(rShadow.tr[i][j]);
+ }
+ } /*0 <= i < prHMM->L+1 */
+ /* skip trans_lin,ss_dssp,sa_dssp,ss_pred,ss_conf,Xcons */
+ for (int j = 0; j < AMINOACIDS; j++){
+ rHMM_p->pav[j] = (float)rShadow.pav[j];
+ }
+ /* skip pnul */
+
+
+ /******/
+
+
+ rTemp.ClobberGlobal();
+ rTempAli.ClobberGlobal();
+
+ return OK;
+
+} /*** end of AlnToHMM2() ***/
+
+
+/**
+ * HHMake_Wrapper()
+ *
+ * @brief turn alignment (from file) into HHM (HMM) on file
+ *
+ * @param[out] hmm_out
+ * name of file with HMM info corresponding to tmp_aln
+ * @param[in] tmp_aln
+ * name of file with alignment, to be turned into HMM (HHM)
+ *
+ */
+extern "C" int
+HHMake_Wrapper(char *tmp_aln, char *hmm_out)
+{
+
+ HMM rTemp; /* temporary template */
+ Alignment rTempAli; /* temporary alignment */
+ hmm_light *rHMM_p = NULL;
+
+ /** Note:
+ this is a wrapper for a stand-alone program hhmake.
+ hhmake uses a different set of parameters than hhalign.
+ However, all parameters are GLOBAL.
+ So at this point we register the hhalign settings,
+ reset them to hhmake settings and set them back
+ at the end of the function
+ */
+
+ /* save settings from hhalign */
+ int iParShowcons=par.showcons;
+ int iParAppend=par.append;
+ int iParNseqdis=par.nseqdis;
+ int iParMark=par.mark;
+ int iParMaxSeqid=par.max_seqid;
+ int iParQid=par.qid;
+ double dParQsc=par.qsc;
+ int iParCoverage=par.coverage;
+ int iParNdiff=par.Ndiff;
+ int iParCoverageCore=par.coverage_core;
+ double dParQscCore=par.qsc_core;
+ double dParCoresc=par.coresc;
+ int iParM=par.M;
+ int iParMgaps=par.Mgaps;
+ int iParMatrix=par.matrix;
+ int iParPcm=par.pcm;
+ double dParPcw=par.pcw;
+ double dParGapb=par.gapb;
+ int iParWg=par.wg;
+
+ /* these are settings suitable for hhmake */
+ par.showcons=1; // write consensus sequence into hhm file
+ par.append=0; // overwrite output file
+ par.nseqdis=10; // maximum number of query or template sequences to be recoreded in HMM and diplayed in output alignments
+ par.mark=0; // 1: only marked sequences (or first) get displayed; 0: most divergent ones get displayed
+ par.max_seqid=90; // default for maximum sequence identity threshold
+ par.qid=0; // default for maximum sequence identity threshold
+ par.qsc=-20.0f; // default for minimum score per column with query
+ par.coverage=0; // default for minimum coverage threshold
+ par.Ndiff=100; // pick Ndiff most different sequences from alignment
+ par.coverage_core=30; // Minimum coverage for sequences in core alignment
+ par.qsc_core=0.3f; // Minimum score per column with core alignment (HMM)
+ par.coresc=-20.0f; // Minimum score per column with core alignment (HMM)
+ par.M=1; // match state assignment is by A2M/A3M
+ par.Mgaps=50; // above this percentage of gaps, columns are assigned to insert states
+ par.matrix=0; // Subst.matrix 0: Gonnet, 1: HSDM, 2: BLOSUM50 3: BLOSUM62
+ par.pcm=0; // no amino acid and transition pseudocounts added
+ par.pcw=0; // wc>0 weighs columns according to their intra-clomun similarity
+ par.gapb=0.0; // default values for transition pseudocounts; 0.0: add no transition pseudocounts!
+ par.wg=0; // 0: use local sequence weights 1: use local ones
+
+
+ if (OK != ReadAndPrepare(READ_ALN_2_HMM,
+ NULL, 0, rHMM_p, NULL, NULL, NULL,
+ tmp_aln, rTemp, &rTempAli)) {
+ return FAILURE;
+ }
+
+ rTemp.WriteToFile(hmm_out);
+
+
+
+ /* restore settings from hhalign */
+ par.showcons=iParShowcons;
+ par.append=iParAppend;
+ par.nseqdis=iParNseqdis;
+ par.mark=iParMark;
+ par.max_seqid=iParMaxSeqid;
+ par.qid=iParQid;
+ par.qsc=dParQsc;
+ par.coverage=iParCoverage;
+ par.Ndiff=iParNdiff;
+ par.coverage_core=iParCoverageCore;
+ par.qsc_core=dParQscCore;
+ par.coresc=dParCoresc;
+ par.M=iParM;
+ par.Mgaps=iParMgaps;
+ par.matrix=iParMatrix;
+ par.pcm=iParPcm;
+ par.pcw=dParPcw;
+ par.gapb=dParGapb;
+ par.wg=iParWg;
+
+
+ /* prepare exit */
+ rTemp.ClobberGlobal();
+ rTempAli.ClobberGlobal();
+
+ return OK;
+}
+
+/**
+ * readHMMWrapper()
+ *
+ * @brief read HMM from file, copy (relevant) info into struct
+ *
+ * @param[out] prHMM
+ * structure with pseudocounts etc, probably uninitialised on entry
+ * @param[in] pcHMM_input
+ * name of file with HMM
+ *
+ */
+extern "C" int
+readHMMWrapper(hmm_light *rHMM_p,
+ char *pcHMM_input)
+{
+ par.maxResLen = 15002;
+ HMM rTemp(1000,par.maxResLen); /* temporary template */
+ Alignment rTempAli; /* temporary alignment */
+ /* AW changed init from {0} to 0 because it failed to compile with
+ * gcc 4.3.3 with the following error:
+ * error: braces around initializer for non-aggregate type
+ */
+ /* FS taken out initialiser alltogether */
+
+ /* 0th arg of RnP is the type of RnP, ie,
+ enum {INTERN_ALN_2_HMM = 0, READ_ALN_2_HMM, READ_HMM_2_HMM};*/
+ /* 1st arg of ReadAndPrepare() is ppcSeqs, 2nd is #seq */
+ /* FIXME: at this stage the 3rd arg, rHMM_p, only acts as a dummy.
+ this is rather silly, as it is the actual struct that will
+ carry the HMM info at the end.
+ If we write it already in ReadAndPrepare() then we could
+ dispense with all this friend-class nonsense */
+ if (OK != ReadAndPrepare(READ_HMM_2_HMM,
+ NULL, 0, rHMM_p, NULL, NULL, NULL,
+ pcHMM_input, rTemp, &rTempAli)) {
+ return FAILURE;
+ }
+
+ /* an important piece of information I want to get out of here
+ is the consenssus sequence. there are however certain
+ Pfam HMMs that don't trigger consensus calculation.
+ at the moment I (FS) don't understand why this is
+ (or rather why this is not). The proper place to do this
+ should be inside ReadAndPrepare():ReadHMMer(), but
+ I have not quite penetrated the logic there.
+ Therefore I try to catch this condition at this point (here)
+ and rectify it.
+ */
+ if (-1 == rHMM_p->ncons){
+ int i, iA;
+ rHMM_p->ncons = rHMM_p->nfirst;
+
+ for (i = 0; i < rHMM_p->L; i++){
+ double dPmax = 0.00;
+ int iAmax = -1;
+ for (iA = 0; iA < AMINOACIDS; iA++){
+ if (rHMM_p->f[i][iA] > dPmax){
+ iAmax = iA;
+ dPmax = rHMM_p->f[i][iA];
+ }
+ } /* (0 <= iA < AMINOACIDS) */
+ rHMM_p->seq[rHMM_p->ncons][i] = i2aa(iAmax);
+ } /* (0 <= i < rHMM_p->L) */
+
+ } /* ncons not set */
+
+
+ rTemp.ClobberGlobal();
+ rTempAli.ClobberGlobal();
+
+ return OK;
+
+} /*** end: readHMMWrapper() ***/
+
+
+
+
+
+
+/////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Do precalculations for q and t to prepare comparison
+ */
+void
+PrepareTemplate(HMM& q, HMM& t, int format)
+{
+ if (format==0) // HHM format
+ {
+ // Add transition pseudocounts to template
+ t.AddTransitionPseudocounts();
+
+ // Generate an amino acid frequency matrix from t.f[i][a] with max pseudocounts (tau=1) -> t.g[i][a]
+ t.PreparePseudocounts();
+
+ // Add amino acid pseudocounts to template: t.p[i][a] = (1-tau)*f[i][a] + tau*g[i][a]
+ t.AddAminoAcidPseudocounts();
+ }
+ else // HHMER format
+ {
+ // Don't add transition pseudocounts to template
+ // t.AddTransitionPseudocounts(par.gapd, par.gape, par.gapf, par.gapg, par.gaph, par.gapi, 0.0);
+
+ // Generate an amino acid frequency matrix from f[i][a] with full pseudocount admixture (tau=1) -> g[i][a]
+ t.PreparePseudocounts();
+
+ // DON'T ADD amino acid pseudocounts to temlate: pcm=0! t.p[i][a] = t.f[i][a]
+ t.AddAminoAcidPseudocounts(0, par.pca, par.pcb, par.pcc);
+ }
+
+ // Modify transition probabilities to include SS-dependent penalties
+ if (par.ssgap) t.UseSecStrucDependentGapPenalties();
+
+ if (par.forward>=1) t.Log2LinTransitionProbs(1.0);
+
+ // Factor Null model into HMM t
+ // ATTENTION! t.p[i][a] is divided by pnul[a] (for reasons of efficiency) => do not reuse t.p
+ t.IncludeNullModelInHMM(q,t); // Can go BEFORE the loop if not dependent on template
+
+ return;
+}
+
+
+/*** end of hhfunc-C.h ***/
--- /dev/null
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhfunc.h 143 2010-10-14 13:11:14Z andreas $
+ */
+
+
+int readHMMWrapper(hmm_light *rHMM_p,
+ char *pcHMM_input);
+void FreeHMMstruct(hmm_light *prHMM);
+int AlnToHMM2(hmm_light *rHMM_p,
+ char **ppcSeq, int iN);
+int HHMake_Wrapper(char *tmp_aln, char *hmm_out);
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhhalfalignment-C.h 227 2011-03-28 17:03:09Z fabian $
+ */
+
+// hhfullalignment.C
+
+#ifndef MAIN
+#define MAIN
+#include <iostream> // cin, cout, cerr
+#include <fstream> // ofstream, ifstream
+#include <stdio.h> // printf
+#include <stdlib.h> // exit
+#include <string> // strcmp, strstr
+#include <math.h> // sqrt, pow
+#include <limits.h> // INT_MIN
+#include <float.h> // FLT_MIN
+#include <time.h> // clock
+#include <ctype.h> // islower, isdigit etc
+using std::ios;
+using std::ifstream;
+using std::ofstream;
+using std::cout;
+using std::cerr;
+using std::endl;
+#include "util-C.h" // imax, fmax, iround, iceil, ifloor, strint, strscn, strcut, substr, uprstr, uprchr, Basename etc.
+#include "list.h" // list data structure
+#include "hash.h" // hash data structure
+#include "hhdecl-C.h" // constants, class
+#include "hhutil-C.h" // imax, fmax, iround, iceil, ifloor, strint, strscn, strcut, substr, uprstr, uprchr, Basename etc.
+#include "hhhmm.h" // class HMM
+#include "hhalignment.h" // class Alignment
+#include "hhhit.h"
+#endif
+
+/////////////////////////////////////////////////////////////////////////////
+/////////////////////////////////////////////////////////////////////////////
+// Methods of class HalfAlignment
+/////////////////////////////////////////////////////////////////////////////
+/////////////////////////////////////////////////////////////////////////////
+
+
+
+/////////////////////////////////////////////////////////////////////////////
+// Constructor
+HalfAlignment::HalfAlignment(int maxseqdis)
+{
+ n=0;
+ sname=seq=NULL;
+ nss_dssp = nss_pred = nss_conf = nsa_dssp = ncons= -1;
+ h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written
+ s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment
+ l = new(int*[maxseqdis]); //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k
+ m = new(int*[maxseqdis]); //counts positions: m[k][i] = position of match state i in string seq[k]
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+// Destructor
+HalfAlignment::~HalfAlignment()
+{
+ Unset();
+ delete[] h; h = NULL;
+ delete[] s; s = NULL;
+ delete[] l; l = NULL;
+ delete[] m; m = NULL;
+}
+
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Free memory in HalfAlignment arrays s[][], l[][], and m[][]
+ */
+void
+HalfAlignment::Unset()
+{
+ // Free memory for alignment characters and residue counts
+ for (int k=0; k<n; k++)
+ {
+ delete[] s[k]; s[k] = NULL;
+ delete[] l[k]; l[k] = NULL;
+ delete[] m[k]; m[k] = NULL;
+ }
+ n=0;
+ sname=seq=NULL;
+ nss_dssp = nss_pred = nss_conf = nsa_dssp = ncons= -1;
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Prepare a2m/a3m alignment:
+ * Calculate l[k][i] (residue indices) and m[k][i] (position in seq[k])
+*/
+void
+HalfAlignment::Set(char* name, char** seq_in, char** sname_in, int n_in, int L_in, int n1, int n2, int n3, int n4, int nc, int L_in2/*<--FS*/)
+{
+ int i; /* counts match states in seq[k] */
+ int ll; /* counts residues LEFT from or at current position in seq[k] */
+ int mm; /* counts postions in string seq[k] */
+ int k; /* counts sequences */
+ char c;
+ char warned=0;
+
+ nss_dssp=n1; nss_pred=n2; nss_conf=n3; nsa_dssp=n4; ncons=nc;
+ seq=seq_in; /* flat copy of sequences */
+ sname=sname_in; /* flat copy of sequence names */
+ n=n_in;
+ L=L_in;
+ pos=0;
+
+ /* Allocate memory for alignment characters and residue counts */
+ for (k=0; k<n; k++) {
+ s[k]=new char[LINELEN];
+ l[k]=new int[L+10+L_in2/*<--FS*/];
+ m[k]=new int[L+10+L_in2/*<--FS*/];
+ if (!s[k] || !l[k] || !m[k]) MemoryError("space for formatting HMM-HMM alignment");
+ h[k]=0; //starting positions in alignment = 0
+ } /* k <= 0 < n (= n_in) */
+
+ for (k=0; k<n; k++) {
+ m[k][0]=0; // 0'th match state (virtual) is begin state at 0
+ //if k is consensus sequence
+ if (k==nc) {
+ for (i=1; i<=L; i++) m[k][i]=l[k][i]=i;
+ m[k][L+1]=l[k][L+1]=L;
+ continue;
+ }
+ i=1; mm=1; ll=1;
+ while ((c=seq[k][mm]))
+ {
+ if (MatchChr(c)==c) //count match/delete states
+ {
+ l[k][i]=ll;
+ m[k][i]=mm;
+ i++;
+ }
+ if (WordChr(c)) ll++; //index of next residue
+ mm++;
+ }
+ l[k][i]=ll-1; //set l[k][L+1] eq number of residues in seq k (-1 since there is no residue at L+1st match state)
+ m[k][i]=mm; //set m[k][L+1]
+
+ if ((i-1)!=L && !warned)
+ {
+ cerr<<"Warning: sequence "<<sname[k]<<" in HMM "<<name<<" has "<<i<<" match states but should have "<<L<<"\n";
+ warned=1;
+ }
+ } /* k <= 0 < n (= n_in) */
+ //DEBUG
+ if (v>=5)
+ {
+ printf(" i chr m l\n");
+ for(i=0;i<=L+1;i++) printf("%3i %1c %3i %3i\n",i,seq[0][m[0][i]],m[0][i],l[0][i]);
+ printf("\n");
+ }
+
+} /*** end HalfAlignment::Set() ***/
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Fill in insert states following match state i (without inserting '.' to fill up)
+ */
+void
+HalfAlignment::AddInserts(int i)
+{
+ for (int k=0; k<n; k++) // for all sequences...
+ for (int mm=m[k][i]+1; mm<m[k][i+1]; mm++) // for all inserts between match state i and i+1...
+ s[k][h[k]++]=seq[k][mm]; // fill inserts into output alignment s[k]
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Fill up alignment with gaps '.' to generate flush end (all h[k] equal)
+ */
+void
+HalfAlignment::FillUpGaps()
+{
+ int k; //counts sequences
+ pos=0;
+
+ // Determine max position h[k]
+ for (k=0; k<n; k++) pos = imax(h[k],pos);
+
+ // Fill in gaps up to pos
+ for (k=0; k<n; k++)
+ {
+ for (int hh=h[k]; hh<pos; hh++) s[k][hh]='.';
+ h[k]=pos;
+ }
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Fill in insert states following match state i and fill up gaps with '.'
+ */
+void
+HalfAlignment::AddInsertsAndFillUpGaps(int i)
+{
+ AddInserts(i);
+ FillUpGaps();
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Add gap column '.'
+ */
+void
+HalfAlignment::AddChar(char c)
+{
+ for (int k=0; k<n; k++) s[k][h[k]++]=c;
+ pos++;
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Add match state column i as is
+ */
+void
+HalfAlignment::AddColumn(int i)
+{
+ for (int k=0; k<n; k++) s[k][h[k]++]=seq[k][m[k][i]];
+ pos++;
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Add match state column i as insert state
+ */
+void
+HalfAlignment::AddColumnAsInsert(int i)
+{
+ char c;
+ for (int k=0; k<n; k++)
+ if ((c=seq[k][m[k][i]])!='-' && (c<'0' || c>'9'))
+ s[k][h[k]++]=InsertChr(c);
+ pos++;
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Remove all characters c from template sequences
+ */
+void
+HalfAlignment::RemoveChars(char c)
+{
+ int k,h,hh;
+ for (k=0; k<n; k++)
+ {
+ for (h=hh=0; h<pos; h++)
+ if (s[k][h]!=c) s[k][hh++]=s[k][h];
+ s[k][++hh]='\0';
+ }
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Transform alignment sequences from A3M to A2M (insert ".")
+ */
+void
+HalfAlignment::BuildFASTA()
+{
+ AddInserts(0);
+ FillUpGaps();
+ for (int i=1; i<=L; i++)
+ {
+ AddColumn(i);
+ AddInserts(i);
+ FillUpGaps();
+ }
+ ToFASTA();
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Transform alignment sequences from A3M to A2M (insert ".")
+ */
+void
+HalfAlignment::BuildA2M()
+{
+ AddInserts(0);
+ FillUpGaps();
+ for (int i=1; i<=L; i++)
+ {
+ AddColumn(i);
+ AddInserts(i);
+ FillUpGaps();
+ }
+ AddChar('\0');
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Transform alignment sequences from A3M to A2M (insert ".")
+ */
+void
+HalfAlignment::BuildA3M()
+{
+ AddInserts(0);
+ for (int i=1; i<=L; i++)
+ {
+ AddColumn(i);
+ AddInserts(i);
+ }
+ AddChar('\0');
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Transform alignment sequences from A2M to FASTA ( lowercase to uppercase and '.' to '-')
+ */
+void
+HalfAlignment::ToFASTA()
+{
+ for (int k=0; k<n; k++)
+ {
+ uprstr(s[k]);
+ strtr(s[k],".","-");
+ }
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Align query (HalfAlignment) to template (i.e. hit) match state structure
+ */
+void
+HalfAlignment::AlignToTemplate(Hit& hit)
+{
+ int i,j;
+ int step; // column of the HMM-HMM alignment (first:nstep, last:1)
+ char state;
+
+ if(0) { //par.loc==0) { //////////////////////////////////////////// STILL NEEDED??
+ // If in global mode: Add part of alignment before first MM state
+ AddInserts(0); // Fill in insert states before first match state
+ for (i=1; i<hit.i[hit.nsteps]; i++)
+ {
+ AddColumnAsInsert(i);
+ AddInserts(i);
+ if (par.outformat<=2) FillUpGaps();
+ }
+ }
+
+ // Add endgaps (First state must be an MM state!!)
+ for (j=1; j<hit.j[hit.nsteps]; j++)
+ {
+ AddChar('-');
+ }
+
+ // Add alignment between first and last MM state
+ for (step=hit.nsteps; step>=1; step--)
+ {
+ state = hit.states[step];
+ i = hit.i[step];
+
+ switch(state)
+ {
+ case MM: //MM pair state (both query and template in Match state)
+ AddColumn(i);
+ AddInserts(i);
+ break;
+ case DG: //D- state
+ case MI: //MI state
+ AddColumnAsInsert(i);
+ AddInserts(i);
+ break;
+ case GD: //-D state
+ case IM: //IM state
+ AddChar('-');
+ break;
+ }
+ if (par.outformat<=2) FillUpGaps();
+
+ }
+
+ if(0) { //par.loc==0) { //////////////////////////////////////////// STILL NEEDED??
+
+ // If in global mode: Add part of alignment after last MM state
+ for (i=hit.i[1]+1; i<=L; i++)
+ {
+ AddColumnAsInsert(i);
+ AddInserts(i);
+ if (par.outformat==2) FillUpGaps();
+ }
+ }
+
+ // Add endgaps
+ for (j=hit.j[1]+1; j<=hit.L; j++)
+ {
+ AddChar('-');
+ }
+
+ // Add end-of-string character
+ AddChar('\0');
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Write the a2m/a3m alignment into alnfile
+ */
+void
+HalfAlignment::Print(char* alnfile)
+{
+ int k; //counts sequences
+ int omitted=0; // counts number of sequences with no residues in match states
+ FILE *outf;
+ if (strcmp(alnfile,"stdout"))
+ {
+ if (par.append) outf=fopen(alnfile,"a"); else outf=fopen(alnfile,"w");
+ if (!outf) OpenFileError(alnfile);
+ }
+ else
+ outf = stdout;
+ if (v>=3) cout<<"Writing alignment to "<<alnfile<<"\n";
+
+ for (k=0; k<n; k++)
+ {
+ // Print sequence only if it contains at least one residue in a match state
+ if (1) //strpbrk(s[k],"ABCDEFGHIKLMNPQRSTUVWXYZ1234567890"))
+ {
+ fprintf(outf,">%s\n",sname[k]);
+ fprintf(outf,"%s\n",s[k]);
+ } else {
+ omitted++;
+ if (v>=3) printf("%-14.14s contains no residue in match state. Omitting sequence\n",sname[k]);
+ }
+ }
+ if (v>=2 && omitted) printf("Omitted %i sequences in %s which contained no residue in match state\n",omitted,alnfile);
+ fclose(outf);
+}
+
+
+/** EOF hhhalfalignment-C.h **/
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhhalfalignment.h 143 2010-10-14 13:11:14Z andreas $
+ */
+
+/////////////////////////////////////////////////////////////////////////////////////
+// Class representing a2m/a3m-formatted alignment corresponding to one HMM
+/////////////////////////////////////////////////////////////////////////////////////
+
+
+class HalfAlignment
+{
+public:
+ HalfAlignment(int maxseqdis=MAXSEQDIS);
+ ~HalfAlignment();
+
+ // Initialize HalfAlignment; create index arrays s [],l[], m[]
+ void Set(char* name, char** seq_in, char** sname_in, int n_in, int L_in, int n1, int n2, int n3, int n4, int nc, int L_in2/*<--FS*/);
+
+ // Free memory in HalfAlignment arrays s[][], l[][], and m[][]
+ void Unset();
+
+ // Align query (HalfAlignment) to template (i.e. hit) match state structure
+ void AlignToTemplate(Hit& hit);
+
+ // Write the a2m/a3m query alignment into alnfile
+ void Print(char* outfile);
+
+ // Fill in insert states following match state i
+ void AddInserts(int i);
+
+ // Fill up alignment with gaps '.' to generate flush end (all h[k] equal)
+ void FillUpGaps();
+
+ // Fill in insert states following match state i and fill up gaps with '.'
+ void AddInsertsAndFillUpGaps(int i);
+
+ // Add gap column '.' or character column
+ void AddChar(char c);
+
+ // Add match state column i as is
+ void AddColumn(int i);
+
+ // Add match state column i as insert state
+ void AddColumnAsInsert(int i);
+
+ // Build alignment in FASTA format
+ void BuildFASTA();
+
+ // Build alignment in A2M format
+ void BuildA2M();
+
+ // Build alignment in A3M format
+ void BuildA3M();
+
+ // Transform alignment sequences from A2M to FASTA ( lowercase to uppercase and '.' to '-')
+ void ToFASTA();
+
+ // Remove all characters c from template sequences
+ void RemoveChars(char c);
+
+private:
+ friend class FullAlignment;
+
+ int n; //number of sequences in half-alignment
+ char** seq; //sequences (in ASCII) in alignment
+ char** sname; //names of sequences in alignment
+ int nss_dssp; //index of sequence with dssp sec structure states
+ int nsa_dssp; //index of sequence with dssp solvent accessiblity states
+ int nss_pred; //index of sequence with predicted sec structure states
+ int nss_conf; //index of sequence with prediction confidence values
+ int ncons; //index of consensus sequence
+
+ int pos; //After FillUpGaps() all h[k] have value pos
+ int L; //number of match states in corresponding profile
+ int* h; //h[k] = next position of sequence k to be written
+ char** s; //s[k][h] = column h, sequence k of output alignment
+ int** l; //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k
+ int** m; //counts positions: m[k][i] = position of match state i in string seq[k]
+/* int h[MAXSEQ]; //h[k] = next position of sequence k to be written */
+/* char* s[MAXSEQ]; //s[k][h] = column h, sequence k of output alignment */
+/* int* l[MAXSEQ]; //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k */
+/* int* m[MAXSEQ]; //counts positions: m[k][i] = position of match state i in string seq[k] */
+};
+
+
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhhit-C.h 245 2011-06-15 12:38:53Z fabian $
+ */
+
+// hhhit.C
+
+#ifndef MAIN
+#define MAIN
+#include <iostream> // cin, cout, cerr
+#include <fstream> // ofstream, ifstream
+#include <stdio.h> // printf
+using std::cout;
+using std::cerr;
+using std::endl;
+using std::ios;
+using std::ifstream;
+using std::ofstream;
+#include <stdlib.h> // exit
+#include <string> // strcmp, strstr
+#include <math.h> // sqrt, pow
+#include <limits.h> // INT_MIN
+#include <float.h> // FLT_MIN
+#include <time.h> // clock
+#include <ctype.h> // islower, isdigit etc
+#include "util-C.h" // imax, fmax, iround, iceil, ifloor, strint, strscn, strcut, substr, uprstr, uprchr, Basename etc.
+#include "list.h" // list data structure
+#include "hash.h" // hash data structure
+#include "hhdecl-C.h" // constants, class
+#include "hhutil-C.h" // imax, fmax, iround, iceil, ifloor, strint, strscn, strcut, substr, uprstr, uprchr, Basename etc.
+#include "hhhmm.h" // class HMM
+#include "hhalignment.h" // class Alignment
+#include "hhhitlist.h" // class HitList
+#endif
+
+#define CALCULATE_MAX6(max, var1, var2, var3, var4, var5, var6, varb) \
+if (var1>var2) { max=var1; varb=STOP;} \
+else { max=var2; varb=MM;}; \
+if (var3>max) { max=var3; varb=GD;}; \
+if (var4>max) { max=var4; varb=IM;}; \
+if (var5>max) { max=var5; varb=DG;}; \
+if (var6>max) { max=var6; varb=MI;};
+
+#define CALCULATE_SUM6(sum, var1, var2, var3, var4, var5, var6, varb) \
+if (var1>var2) { sum=var1; varb=STOP;} \
+else { sum=var2; varb=MM;}; \
+if (var3>sum) { sum=var3; varb=GD;}; \
+if (var4>sum) { sum=var4; varb=IM;}; \
+if (var5>sum) { sum=var5; varb=DG;}; \
+if (var6>sum) { sum=var6; varb=MI;}; \
+sum = var1 + var2 + var3 + var4 + var5 + var6;
+
+#define CALCULATE_MAX4(max, var1, var2, var3, var4, varb) \
+if (var1>var2) { max=var1; varb=STOP;} \
+else { max=var2; varb=MM;}; \
+if (var3>max) { max=var3; varb=MI;}; \
+if (var4>max) { max=var4; varb=IM;};
+
+// Generate random number in [0,1[
+#define frand() ((float) rand()/(RAND_MAX+1.0))
+
+
+// Function declarations
+inline float Score(float* qi, float* tj);
+inline float ProbFwd(float* qi, float* tj);
+inline float max2(const float& xMM, const float& xX, char& b);
+inline int pickprob2(const double& xMM, const double& xX, const int& state);
+inline int pickprob3_GD(const double& xMM, const double& xDG, const double& xGD);
+inline int pickprob3_IM(const double& xMM, const double& xMI, const double& xIM);
+inline int pickprob6(const double& x0, const double& xMM, const double& xGD, const double& xIM, const double& xDG, const double& xMI);
+inline int pickmax2(const double& xMM, const double& xX, const int& state);
+inline int pickmax3_GD(const double& xMM, const double& xDG, const double& xGD);
+inline int pickmax3_IM(const double& xMM, const double& xMI, const double& xIM);
+inline int pickmax6(const double& x0, const double& xMM, const double& xGD, const double& xIM, const double& xDG, const double& xMI);
+inline double Pvalue(double x, double a[]);
+inline double Pvalue(float x, float lamda, float mu);
+inline double logPvalue(float x, float lamda, float mu);
+inline double logPvalue(float x, double a[]);
+inline double Probab(Hit& hit);
+
+//////////////////////////////////////////////////////////////////////////////
+//// Constructor
+//////////////////////////////////////////////////////////////////////////////
+Hit::Hit()
+{
+ longname = name = file = dbfile = NULL;
+ sname = NULL;
+ seq = NULL;
+ bMM = bGD = bDG = bIM = bMI = NULL;
+ self = 0;
+ i = j = NULL;
+ states = NULL;
+ S = S_ss = P_posterior = NULL;
+ Xcons = NULL;
+ B_MM=B_MI=B_IM=B_DG=B_GD=NULL;
+ F_MM=F_MI=F_IM=F_DG=F_GD=NULL;
+ cell_off = NULL;
+ scale = NULL;
+ sum_of_probs=0.0;
+ Neff_HMM=0.0;
+ score_ss = Pval = logPval = Eval = Probab = Pforward = 0.0;
+ nss_conf = nfirst = i1 = i2 = j1 = j2 = matched_cols = ssm1 = ssm2 = 0;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Free all allocated memory (to delete list of hits)
+ */
+void
+Hit::Delete()
+{
+ if (i){
+ delete[] i; i = NULL;
+ }
+ if (j){
+ delete[] j; j = NULL;
+ }
+ if (states){
+ delete[] states; states = NULL;
+ }
+ if (S){
+ delete[] S; S = NULL;
+ }
+ if (S_ss){
+ delete[] S_ss; S_ss = NULL;
+ }
+ if (P_posterior){
+ delete[] P_posterior; P_posterior = NULL;
+ }
+ if (Xcons){
+ delete[] Xcons; Xcons = NULL;
+ }
+ // delete[] l; l = NULL;
+ i = j = NULL;
+ states = NULL;
+ S = S_ss = P_posterior = NULL;
+ Xcons = NULL;
+ if (irep==1) // if irep>1 then longname etc point to the same memory locations as the first repeat.
+ { // but these have already been deleted.
+ // printf("Delete name = %s\n",name);//////////////////
+ delete[] longname; longname = NULL;
+ delete[] name; name = NULL;
+ delete[] file; file = NULL;
+ delete[] dbfile; dbfile = NULL;
+ for (int k=0; k<n_display; k++)
+ {
+ //delete[] sname[k]; sname[k] = NULL;
+ delete[] seq[k]; seq[k] = NULL;
+ }
+ //delete[] sname; sname = NULL;
+ delete[] seq; seq = NULL;
+ }
+}
+
+
+///////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Allocate/delete memory for dynamic programming matrix
+ */
+void
+Hit::AllocateBacktraceMatrix(int Nq, int Nt)
+{
+ int i;
+ bMM=new(char*[Nq]);
+ bMI=new(char*[Nq]);
+ bIM=new(char*[Nq]);
+ bDG=new(char*[Nq]);
+ bGD=new(char*[Nq]);
+ cell_off=new(char*[Nq]);
+ for (i=0; i<Nq; i++)
+ {
+ bMM[i]=new(char[Nt]);
+ bMI[i]=new(char[Nt]);
+ bIM[i]=new(char[Nt]);
+ bGD[i]=new(char[Nt]);
+ bDG[i]=new(char[Nt]);
+ cell_off[i]=new(char[Nt]);
+ if (!bMM[i] || !bMI[i] || !bIM[i] || !bGD[i] || !bDG[i] || !cell_off[i])
+ {
+ fprintf(stderr,"Error: out of memory while allocating row %i (out of %i) for dynamic programming matrices \n",i+1,Nq);
+ fprintf(stderr,"Suggestions:\n");
+ fprintf(stderr,"1. Cut query sequence into shorter segments\n");
+ fprintf(stderr,"2. Check stack size limit (Linux: ulimit -a)\n");
+ fprintf(stderr,"3. Run on a computer with bigger memory\n");
+ exit(3);
+ }
+ }
+}
+
+/**
+ * @brief
+ */
+void
+Hit::DeleteBacktraceMatrix(int Nq)
+{
+ int i;
+ for (i=0; i<Nq; i++)
+ {
+ delete[] bMM[i]; bMM[i] = NULL;
+ delete[] bMI[i]; bMI[i] = NULL;
+ delete[] bIM[i]; bIM[i] = NULL;
+ delete[] bGD[i]; bGD[i] = NULL;
+ delete[] bDG[i]; bDG[i] = NULL;
+ delete[] cell_off[i]; cell_off[i] = NULL;
+ }
+ delete[] bMM; bMM = NULL;
+ delete[] bMI; bMI = NULL;
+ delete[] bIM; bIM = NULL;
+ delete[] bDG; bDG = NULL;
+ delete[] bGD; bGD = NULL;
+ delete[] cell_off; cell_off = NULL;
+}
+
+
+///////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Allocate/delete memory for Forward dynamic programming matrix
+ */
+void
+Hit::AllocateForwardMatrix(int Nq, int Nt)
+{
+ F_MM=new(double*[Nq]);
+ F_MI=new(double*[Nq]);
+ F_DG=new(double*[Nq]);
+ F_IM=new(double*[Nq]);
+ F_GD=new(double*[Nq]);
+ scale=new(double[Nq+1]); // need Nq+3?
+ for (int i=0; i<Nq; i++)
+ {
+ F_MM[i] = new(double[Nt]);
+ F_MI[i] = new(double[Nt]);
+ F_DG[i] = new(double[Nt]);
+ F_IM[i] = new(double[Nt]);
+ F_GD[i] = new(double[Nt]);
+ if (!F_MM[i] || !F_MI[i] || !F_IM[i] || !F_GD[i] || !F_DG[i])
+ {
+ fprintf(stderr,"Error: out of memory while allocating row %i (out of %i) for dynamic programming matrices \n",i+1,Nq);
+ fprintf(stderr,"Suggestions:\n");
+ fprintf(stderr,"1. Cut query sequence into shorter segments\n");
+ fprintf(stderr,"2. Check stack size limit (Linux: ulimit -a)\n");
+ fprintf(stderr,"3. Run on a computer with bigger memory\n");
+ exit(3);
+ }
+
+ }
+}
+
+/**
+ * @brief
+ */
+void
+Hit::DeleteForwardMatrix(int Nq)
+{
+ for (int i=0; i<Nq; i++)
+ {
+ delete[] F_MM[i]; F_MM[i] = NULL;
+ delete[] F_MI[i]; F_MI[i] = NULL;
+ delete[] F_IM[i]; F_IM[i] = NULL;
+ delete[] F_GD[i]; F_GD[i] = NULL;
+ delete[] F_DG[i]; F_DG[i] = NULL;
+ }
+ delete[] F_MM; F_MM = NULL;
+ delete[] F_MI; F_MI = NULL;
+ delete[] F_IM; F_IM = NULL;
+ delete[] F_DG; F_DG = NULL;
+ delete[] F_GD; F_GD = NULL;
+ delete[] scale; scale = NULL;
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Allocate/delete memory for Backward dynamic programming matrix (DO ONLY AFTER FORWARD MATRIX HAS BEEN ALLOCATED)
+ */
+void
+Hit::AllocateBackwardMatrix(int Nq, int Nt)
+{
+ B_MM=new(double*[Nq]);
+ B_MI=F_MI;
+ B_DG=F_DG;
+ B_IM=F_IM;
+ B_GD=F_GD;
+ for (int i=0; i<Nq; i++)
+ {
+ B_MM[i] = new(double[Nt]);
+ if (!B_MM[i])
+ {
+ fprintf(stderr,"Error: out of memory while allocating row %i (out of %i) for dynamic programming matrices \n",i+1,Nq);
+ fprintf(stderr,"Suggestions:\n");
+ fprintf(stderr,"1. Cut query sequence into shorter segments\n");
+ fprintf(stderr,"2. Check stack size limit (Linux: ulimit -a)\n");
+ fprintf(stderr,"3. Run on a computer with bigger memory\n");
+ exit(3);
+ }
+ }
+}
+
+void Hit::DeleteBackwardMatrix(int Nq)
+{
+ for (int i=0; i<Nq; i++)
+ {
+ delete[] B_MM[i]; B_MM[i] = NULL; /* is this all? FS */
+ }
+ delete[] B_MM; B_MM = NULL;
+ B_MM=B_MI=B_IM=B_DG=B_GD=NULL;
+}
+
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Compare HMMs with one another and look for sub-optimal alignments that share no pair with previous ones
+ * The function is called with q and t
+ * If q and t are equal (self==1), only the upper right part of the matrix is calculated: j>=i+3
+ */
+void
+Hit::Viterbi(HMM& q, HMM& t, float** Sstruc)
+{
+
+ // Linear topology of query (and template) HMM:
+ // 1. The HMM HMM has L+2 columns. Columns 1 to L contain
+ // a match state, a delete state and an insert state each.
+ // 2. The Start state is M0, the virtual match state in column i=0 (j=0). (Therefore X[k][0]=ANY)
+ // This column has only a match state and it has only a transitions to the next match state.
+ // 3. The End state is M(L+1), the virtual match state in column i=L+1.(j=L+1) (Therefore X[k][L+1]=ANY)
+ // Column L has no transitions to the delete state: tr[L][M2D]=tr[L][D2D]=0.
+ // 4. Transitions I->D and D->I are ignored, since they do not appear in PsiBlast alignments
+ // (as long as the gap opening penalty d is higher than the best match score S(a,b)).
+
+ // Pairwise alignment of two HMMs:
+ // 1. Pair-states for the alignment of two HMMs are
+ // MM (Q:Match T:Match) , GD (Q:Gap T:Delete), IM (Q:Insert T:Match), DG (Q:Delelte, T:Match) , MI (Q:Match T:Insert)
+ // 2. Transitions are allowed only between the MM-state and each of the four other states.
+
+ // Saving space:
+ // The best score ending in pair state XY sXY[i][j] is calculated from left to right (j=1->t.L)
+ // and top to bottom (i=1->q.L). To save space, only the last row of scores calculated is kept in memory.
+ // (The backtracing matrices are kept entirely in memory [O(t.L*q.L)]).
+ // When the calculation has proceeded up to the point where the scores for cell (i,j) are caculated,
+ // sXY[i-1][j'] = sXY[j'] for j'>=j (A below)
+ // sXY[i][j'] = sXY[j'] for j'<j (B below)
+ // sXY[i-1][j-1]= sXY_i_1_j_1 (C below)
+ // sXY[i][j] = sXY_i_j (D below)
+ // j-1
+ // j
+ // i-1: CAAAAAAAAAAAAAAAAAA
+ // i : BBBBBBBBBBBBBD
+
+
+ // Variable declarations
+ //float sMM[MAXRES]; // sMM[i][j] = score of best alignment up to indices (i,j) ending in (Match,Match)
+ //float sGD[MAXRES]; // sGD[i][j] = score of best alignment up to indices (i,j) ending in (Gap,Delete)
+ //float sDG[MAXRES]; // sDG[i][j] = score of best alignment up to indices (i,j) ending in (Delete,Gap)
+ //float sIM[MAXRES]; // sIM[i][j] = score of best alignment up to indices (i,j) ending in (Ins,Match)
+ //float sMI[MAXRES]; // sMI[i][j] = score of best alignment up to indices (i,j) ending in (Match,Ins)
+ float *sMM = new(float[par.maxResLen]); // sMM[i][j] = score of best alignment up to indices (i,j) ending in (Match,Match)
+ float *sGD = new(float[par.maxResLen]); // sGD[i][j] = score of best alignment up to indices (i,j) ending in (Gap,Delete)
+ float *sDG = new(float[par.maxResLen]); // sDG[i][j] = score of best alignment up to indices (i,j) ending in (Delete,Gap)
+ float *sIM = new(float[par.maxResLen]); // sIM[i][j] = score of best alignment up to indices (i,j) ending in (Ins,Match)
+ float *sMI = new(float[par.maxResLen]); // sMI[i][j] = score of best alignment up to indices (i,j) ending in (Match,Ins)
+ float smin=(par.loc? 0:-FLT_MAX); //used to distinguish between SW and NW algorithms in maximization
+ int i,j; //query and template match state indices
+ float sMM_i_j=0,sMI_i_j,sIM_i_j,sGD_i_j,sDG_i_j;
+ float sMM_i_1_j_1,sMI_i_1_j_1,sIM_i_1_j_1,sGD_i_1_j_1,sDG_i_1_j_1;
+ int jmin,jmax;
+
+ // Reset crossed out cells?
+ if(irep==1) InitializeForAlignment(q,t);
+
+ // Initialization of top row, i.e. cells (0,j)
+ for (j=0; j<=t.L; j++)
+ {
+ sMM[j] = (self? 0 : -j*par.egt);
+ sIM[j] = sMI[j] = sDG[j] = sGD[j] = -FLT_MAX;
+ }
+ score=-INT_MAX; i2=j2=0; bMM[0][0]=STOP;
+
+ // Viterbi algorithm
+ for (i=1; i<=q.L; i++) // Loop through query positions i
+ {
+// if (v>=5) printf("\n");
+
+
+ if (self)
+ {
+ // If q is compared to itself, ignore cells below diagonal+SELFEXCL
+ jmin = i+SELFEXCL;
+ jmax = t.L;
+ if (jmin>jmax) continue;
+ }
+ else
+ {
+ // If q is compared to t, exclude regions where overlap of q with t < min_overlap residues
+ jmin=imax( 1, i+min_overlap-q.L); // Lq-i+j>=Ovlap => j>=i+Ovlap-Lq => jmin=max{1, i+Ovlap-Lq}
+ jmax=imin(t.L,i-min_overlap+t.L); // Lt-j+i>=Ovlap => j<=i-Ovlap+Lt => jmax=min{Lt,i-Ovlap+Lt}
+ }
+
+ // Initialize cells
+ if (jmin==1)
+ {
+ sMM_i_1_j_1 = -(i-1)*par.egq; // initialize at (i-1,0)
+ sMM[0] = -i*par.egq; // initialize at (i,0)
+ sIM_i_1_j_1 = sMI_i_1_j_1 = sDG_i_1_j_1 = sGD_i_1_j_1 = -FLT_MAX; // initialize at (i-1,jmin-1)
+ }
+ else
+ {
+ // Initialize at (i-1,jmin-1) if lower left triagonal is excluded due to min overlap
+ sMM_i_1_j_1 = sMM[jmin-1]; // initialize at (i-1,jmin-1)
+ sIM_i_1_j_1 = sIM[jmin-1]; // initialize at (i-1,jmin-1)
+ sMI_i_1_j_1 = sMI[jmin-1]; // initialize at (i-1,jmin-1)
+ sDG_i_1_j_1 = sDG[jmin-1]; // initialize at (i-1,jmin-1)
+ sGD_i_1_j_1 = sGD[jmin-1]; // initialize at (i-1,jmin-1)
+ sMM[jmin-1] = -FLT_MAX; // initialize at (i,jmin-1)
+ }
+ if (jmax<t.L) // initialize at (i-1,jmmax) if upper right triagonal is excluded due to min overlap
+ sMM[jmax] = sIM[jmax] = sMI[jmax] = sDG[jmax] = sGD[jmax] = -FLT_MAX;
+ sIM[jmin-1] = sMI[jmin-1] = sDG[jmin-1] = sGD[jmin-1] = -FLT_MAX; // initialize at (i,jmin-1)
+
+ for (j=jmin; j<=jmax; j++) // Loop through template positions j
+ {
+
+ if (cell_off[i][j])
+ {
+ sMM_i_1_j_1 = sMM[j]; // sMM_i_1_j_1 (for j->j+1) = sMM(i-1,(j+1)-1) = sMM[j]
+ sGD_i_1_j_1 = sGD[j];
+ sIM_i_1_j_1 = sIM[j];
+ sDG_i_1_j_1 = sDG[j];
+ sMI_i_1_j_1 = sMI[j];
+ sMM[j]=sMI[j]=sIM[j]=sDG[j]=sGD[j]=-FLT_MAX; // sMM[j] = sMM(i,j) is cell_off
+ }
+ else
+ {
+ // Recursion relations
+// printf("S[%i][%i]=%4.1f ",i,j,Score(q.p[i],t.p[j])); // DEBUG!!
+
+ CALCULATE_MAX6( sMM_i_j,
+ smin,
+ sMM_i_1_j_1 + q.tr[i-1][M2M] + t.tr[j-1][M2M],
+ sGD_i_1_j_1 + q.tr[i-1][M2M] + t.tr[j-1][D2M],
+ sIM_i_1_j_1 + q.tr[i-1][I2M] + t.tr[j-1][M2M],
+ sDG_i_1_j_1 + q.tr[i-1][D2M] + t.tr[j-1][M2M],
+ sMI_i_1_j_1 + q.tr[i-1][M2M] + t.tr[j-1][I2M],
+ bMM[i][j]
+ );
+ sMM_i_j += Score(q.p[i],t.p[j]) + ScoreSS(q,t,i,j) + par.shift
+ + (Sstruc==NULL? 0: Sstruc[i][j]);
+
+
+ sGD_i_j = max2
+ (
+ sMM[j-1] + t.tr[j-1][M2D], // MM->GD gap opening in query
+ sGD[j-1] + t.tr[j-1][D2D], // GD->GD gap extension in query
+ bGD[i][j]
+ );
+ sIM_i_j = max2
+ (
+// sMM[j-1] + q.tr[i][M2I] + t.tr[j-1][M2M] ,
+ sMM[j-1] + q.tr[i][M2I] + t.tr[j-1][M2M_GAPOPEN], // MM->IM gap opening in query
+ sIM[j-1] + q.tr[i][I2I] + t.tr[j-1][M2M], // IM->IM gap extension in query
+ bIM[i][j]
+ );
+ sDG_i_j = max2
+ (
+// sMM[j] + q.tr[i-1][M2D],
+// sDG[j] + q.tr[i-1][D2D], //gap extension (DD) in query
+ sMM[j] + q.tr[i-1][M2D] + t.tr[j][GAPOPEN], // MM->DG gap opening in template
+ sDG[j] + q.tr[i-1][D2D] + t.tr[j][GAPEXTD], // DG->DG gap extension in template
+ bDG[i][j]
+ );
+ sMI_i_j = max2
+ (
+ sMM[j] + q.tr[i-1][M2M] + t.tr[j][M2I], // MM->MI gap opening M2I in template
+ sMI[j] + q.tr[i-1][M2M] + t.tr[j][I2I], // MI->MI gap extension I2I in template
+ bMI[i][j]
+ );
+
+ sMM_i_1_j_1 = sMM[j];
+ sGD_i_1_j_1 = sGD[j];
+ sIM_i_1_j_1 = sIM[j];
+ sDG_i_1_j_1 = sDG[j];
+ sMI_i_1_j_1 = sMI[j];
+ sMM[j] = sMM_i_j;
+ sGD[j] = sGD_i_j;
+ sIM[j] = sIM_i_j;
+ sDG[j] = sDG_i_j;
+ sMI[j] = sMI_i_j;
+
+ //if (isnan(sMM_i_j)||isinf(sMM_i_j)){
+ // printf("."); /* <DEBUG> FS*/
+ //}
+ // Find maximum score; global alignment: maxize only over last row and last column
+ if(sMM_i_j>score && (par.loc || i==q.L)) { i2=i; j2=j; score=sMM_i_j; }
+
+ } // end if
+ //printf("i= %d\tj= %d\ti2= %d\tj2= %d\tsMM= %f\tscore= %f\n", i, j, i2, j2, sMM_i_j, score);
+ } //end for j
+
+ // if global alignment: look for best cell in last column
+ if (!par.loc && sMM_i_j>score) { i2=i; j2=jmax; score=sMM_i_j; }
+
+ } // end for i
+
+ state=MM; // state with maximum score is MM state
+
+ // If local alignment do length correction: -log(length)
+ if (par.loc)
+ {
+ if (self)
+ score=score-log(0.5*t.L*q.L/200.0/200.0)/LAMDA - 11.2; // offset of -11.2 to get approx same mean as for -global
+ else
+ if (par.idummy==0 && q.lamda>0) //////////////////////////////////////////////
+ score=score-log(t.L*q.L/200.0/200.0)/q.lamda - 11.2; // offset of -11.2 to get approx same mean as for -global
+ else if (par.idummy<=1) //////////////////////////////////////////////
+ score=score-log(t.L*q.L/200.0/200.0)/LAMDA - 11.2; // offset of -11.2 to get approx same mean as for -global
+ }
+// printf("Template=%-12.12s i=%-4i j=%-4i score=%6.3f\n",t.name,i2,j2,score);
+
+ delete[] sMM; sMM = NULL;
+ delete[] sGD; sGD = NULL;
+ delete[] sDG; sDG = NULL;
+ delete[] sIM; sIM = NULL;
+ delete[] sMI; sMI = NULL;
+
+ return;
+
+} /* this is the end of Hit::Viterbi() */
+
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Compare two HMMs with Forward Algorithm in lin-space (~ 2x faster than in log-space)
+ */
+int
+Hit::Forward(HMM& q, HMM& t, float** Pstruc)
+{
+
+ // Variable declarations
+ int i,j; // query and template match state indices
+ double pmin=(par.loc? 1.0: 0.0); // used to distinguish between SW and NW algorithms in maximization
+ double Cshift = pow(2.0,par.shift); // score offset transformed into factor in lin-space
+ double Pmax_i; // maximum of F_MM in row i
+ double scale_prod=1.0; // Prod_i=1^i (scale[i])
+ int jmin;
+
+ // First alignment of this pair of HMMs?
+ if(irep==1)
+ {
+ q.tr[0][M2D] = q.tr[0][M2I] = 0.0;
+ q.tr[0][I2M] = q.tr[0][I2I] = 0.0;
+ q.tr[0][D2M] = q.tr[0][D2D] = 0.0;
+ t.tr[0][M2M] = 1.0;
+ t.tr[0][M2D] = t.tr[0][M2I] = 0.0;
+ t.tr[0][I2M] = t.tr[0][I2I] = 0.0;
+ t.tr[0][D2M] = t.tr[0][D2D] = 0.0;
+ q.tr[q.L][M2M] = 1.0;
+ q.tr[q.L][M2D] = q.tr[q.L][M2I] = 0.0;
+ q.tr[q.L][I2M] = q.tr[q.L][I2I] = 0.0;
+ q.tr[q.L][D2M] = 1.0;
+ q.tr[q.L][D2D] = 0.0;
+ t.tr[t.L][M2M] = 1.0;
+ t.tr[t.L][M2D] = t.tr[t.L][M2I] = 0.0;
+ t.tr[t.L][I2M] = t.tr[t.L][I2I] = 0.0;
+ t.tr[t.L][D2M] = 1.0;
+ t.tr[t.L][D2D] = 0.0;
+ InitializeForAlignment(q,t);
+ }
+
+
+ // Initialization of top row, i.e. cells (0,j)
+ F_MM[1][0] = F_IM[1][0] = F_GD[1][0] = F_MM[0][1] = F_MI[0][1] = F_DG[0][1] = 0.0;
+ for (j=1; j<=t.L; j++)
+ {
+ if (cell_off[1][j])
+ F_MM[1][j] = F_MI[1][j] = F_DG[1][j] = F_IM[1][j] = F_GD[1][j] = 0.0;
+ else
+ {
+ F_MM[1][j] = ProbFwd(q.p[1],t.p[j]) * fpow2(ScoreSS(q,t,1,j)) * Cshift * (Pstruc==NULL? 1: Pstruc[1][j]) ;
+ F_MI[1][j] = F_DG[1][j] = 0.0;
+ F_IM[1][j] = F_MM[1][j-1] * q.tr[1][M2I] * t.tr[j-1][M2M] + F_IM[1][j-1] * q.tr[1][I2I] * t.tr[j-1][M2M];
+ F_GD[1][j] = F_MM[1][j-1] * t.tr[j-1][M2D] + F_GD[1][j-1] * t.tr[j-1][D2D];
+ }
+ }
+ scale[0]=scale[1]=scale[2]=1.0;
+
+ // Forward algorithm
+ for (i=2; i<=q.L; i++) // Loop through query positions i
+ {
+ // if (v>=5) printf("\n");
+
+ if (self) jmin = imin(i+SELFEXCL+1,t.L); else jmin=1;
+
+ if (scale_prod<DBL_MIN*100) scale_prod = 0.0; else scale_prod *= scale[i];
+
+ // Initialize cells at (i,0)
+ if (cell_off[i][jmin])
+ F_MM[i][jmin] = F_MI[i][jmin] = F_DG[i][jmin] = F_IM[i][jmin] = F_GD[i][jmin] = 0.0;
+ else
+ {
+ F_MM[i][jmin] = scale_prod * ProbFwd(q.p[i],t.p[jmin]) * fpow2(ScoreSS(q,t,i,jmin)) * Cshift * (Pstruc==NULL? 1: Pstruc[i][jmin]);
+ F_IM[i][jmin] = F_GD[i][jmin] = 0.0;
+ F_MI[i][jmin] = scale[i] * (F_MM[i-1][jmin] * q.tr[i-1][M2M] * t.tr[jmin][M2I] + F_MI[i-1][jmin] * q.tr[i-1][M2M] * t.tr[jmin][I2I]);
+ F_DG[i][jmin] = scale[i] * (F_MM[i-1][jmin] * q.tr[i-1][M2D] + F_DG[i-1][jmin] * q.tr[i-1][D2D]);
+ }
+ Pmax_i=0;
+
+ for (j=jmin+1; j<=t.L; j++) // Loop through template positions j
+ {
+ // Recursion relations
+ // printf("S[%i][%i]=%4.1f ",i,j,Score(q.p[i],t.p[j]));
+
+ if (cell_off[i][j])
+ F_MM[i][j] = F_MI[i][j] = F_DG[i][j] = F_IM[i][j] = F_GD[i][j] = 0.0;
+ else
+ {
+ F_MM[i][j] = ProbFwd(q.p[i],t.p[j]) * fpow2(ScoreSS(q,t,i,j)) * Cshift * (Pstruc==NULL? 1: Pstruc[i][j]) * scale[i] *
+ ( pmin
+ + F_MM[i-1][j-1] * q.tr[i-1][M2M] * t.tr[j-1][M2M] // BB -> MM (BB = Begin/Begin, for local alignment)
+ + F_GD[i-1][j-1] * q.tr[i-1][M2M] * t.tr[j-1][D2M] // GD -> MM
+ + F_IM[i-1][j-1] * q.tr[i-1][I2M] * t.tr[j-1][M2M] // IM -> MM
+ + F_DG[i-1][j-1] * q.tr[i-1][D2M] * t.tr[j-1][M2M] // DG -> MM
+ + F_MI[i-1][j-1] * q.tr[i-1][M2M] * t.tr[j-1][I2M] // MI -> MM
+ );
+ F_GD[i][j] =
+ ( F_MM[i][j-1] * t.tr[j-1][M2D] // GD -> MM
+ + F_GD[i][j-1] * t.tr[j-1][D2D] // GD -> GD
+ + (Pstruc==NULL? 0 : F_DG[i][j-1] * t.tr[j-1][M2D] * q.tr[i][D2M] ) // DG -> GD (only when structure scores given)
+ );
+ F_IM[i][j] =
+ ( F_MM[i][j-1] * q.tr[i][M2I] * t.tr[j-1][M2M] // MM -> IM
+ + F_IM[i][j-1] * q.tr[i][I2I] * t.tr[j-1][M2M] // IM -> IM
+ + (Pstruc==NULL? 0 : F_MI[i][j-1] * q.tr[i][M2I] * t.tr[j-1][I2M] ) // MI -> IM (only when structure scores given)
+ );
+ F_DG[i][j] = scale[i] *
+ ( F_MM[i-1][j] * q.tr[i-1][M2D] // DG -> MM
+ + F_DG[i-1][j] * q.tr[i-1][D2D] // DG -> DG
+ ) ;
+ F_MI[i][j] = scale[i] *
+ ( F_MM[i-1][j] * q.tr[i-1][M2M] * t.tr[j][M2I] // MI -> MM
+ + F_MI[i-1][j] * q.tr[i-1][M2M] * t.tr[j][I2I] // MI -> MI
+ );
+
+ if(F_MM[i][j]>Pmax_i) Pmax_i=F_MM[i][j];
+
+ } // end else
+
+ } //end for j
+
+ pmin *= scale[i];
+ scale[i+1] = 1.0/(Pmax_i+1.0);
+ // scale[i+1] = 1.0;
+
+ } // end for i
+
+ // Calculate P_forward * Product_{i=1}^{Lq+1}(scale[i])
+ if (par.loc)
+ {
+ Pforward = 1.0; // alignment contains no residues (see Mueckstein, Stadler et al.)
+ for (i=1; i<=q.L; i++) // Loop through query positions i
+ {
+ for (j=1; j<=t.L; j++) // Loop through template positions j
+ Pforward += F_MM[i][j];
+ Pforward *= scale[i+1];
+ }
+ }
+ else // global alignment
+ {
+ Pforward = 0.0;
+ for (i=1; i<q.L; i++) {
+ Pforward = (Pforward + F_MM[i][t.L]) * scale[i+1];
+ }
+ for (j=1; j<=t.L; j++) {
+ Pforward += F_MM[q.L][j];
+ }
+ Pforward *= scale[q.L+1];
+ }
+
+ // Calculate log2(P_forward)
+ score = log2(Pforward)-10.0f;
+ for (i=1; i<=q.L+1; i++) score -= log2(scale[i]);
+ // state = MM;
+
+ if (par.loc)
+ {
+ if (self)
+ score=score-log(0.5*t.L*q.L)/LAMDA+14.; // +14.0 to get approx same mean as for -global
+ else
+ score=score-log(t.L*q.L)/LAMDA+14.; // +14.0 to get approx same mean as for -global
+ }
+
+ // Debugging output
+ if (v>=6)
+ {
+ const int i0=0, i1=q.L;
+ const int j0=0, j1=t.L;
+ scale_prod=1;
+ printf("\nFwd scale ");
+ for (j=j0; j<=j1; j++) printf("%3i ",j);
+ printf("\n");
+ for (i=i0; i<=i1; i++)
+ {
+ scale_prod *= scale[i];
+ printf("%3i: %9.3G ",i,1/scale_prod);
+ for (j=j0; j<=j1; j++)
+ printf("%7.4f ",(F_MM[i][j]+F_MI[i][j]+F_IM[i][j]+F_DG[i][j]+F_GD[i][j]));
+ printf("\n");
+ // printf(" MM %9.5f ",1/scale[i]);
+ // for (j=j0; j<=j1; j++)
+ // printf("%7.4f ",F_MM[i][j]);
+ // printf("\n");
+ }
+ }
+ // printf("Template=%-12.12s score=%6.3f i2=%i j2=%i \n",t.name,score,i2,j2);
+
+ /* check for NaN and or infinities, FS, r241 -> r243 */
+ if (isnan(score) || isinf(score) || isnan(Pforward) || isinf(Pforward) ){
+ fprintf(stderr, "%s:%s:%d: Forward score is %g, Pforward is %g\n",
+ __FUNCTION__, __FILE__, __LINE__, score, Pforward);
+ return FAILURE;
+ }
+ i = q.L-1; j = t.L-1; /* FS, r241 -> r243 */
+ if (isinf(F_MM[i][j]+F_MI[i][j]+F_IM[i][j]+F_DG[i][j]+F_GD[i][j])){
+ fprintf(stderr, "%s:%s:%d: F_MM[i][j]=%g, F_IM[i][j]=%g, F_MI[i][j]=%g, F_DG[i][j]=%g, F_GD[i][j]=%g (i=%d,j=%d)\n",
+ __FUNCTION__, __FILE__, __LINE__, F_MM[i][j], F_MI[i][j], F_IM[i][j], F_DG[i][j], F_GD[i][j], i, j);
+ return FAILURE;
+ }
+ return OK;
+
+} /* this is the end of Hit::Forward() */
+
+
+
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Compare two HMMs with Backward Algorithm (in lin-space, 2x faster), for use in MAC alignment
+ */
+int
+Hit::Backward(HMM& q, HMM& t)
+{
+
+ // Variable declarations
+ int i,j; // query and template match state indices
+ double pmin=(par.loc? 1.0: 0.0); // used to distinguish between SW and NW algorithms in maximization
+ double Cshift = pow(2.0,par.shift); // score offset transformed into factor in lin-space
+ double scale_prod=scale[q.L+1];
+ int jmin;
+ //double dMaxB = -1.0;
+
+ // Initialization of top row, i.e. cells (0,j)
+ for (j=t.L; j>=1; j--)
+ {
+ if (cell_off[q.L][j])
+ B_MM[q.L][j] = 0.0;
+ else
+ B_MM[q.L][j] = scale[q.L+1];
+ //dMaxB = dMaxB>B_MM[q.L][j]?dMaxB:B_MM[q.L][j];
+ B_IM[q.L][j] = B_MI[q.L][j] = B_DG[q.L][j] = B_GD[q.L][j] = 0.0;
+ }
+ if (par.loc) pmin = scale[q.L+1]; // transform pmin (for local alignment) to scale of present (i'th) row
+
+ // Backward algorithm
+ for (i=q.L-1; i>=1; i--) // Loop through query positions i
+ {
+ // if (v>=5) printf("\n");
+
+ if (self) jmin = imin(i+SELFEXCL,t.L); else jmin=1; // jmin = i+SELFEXCL and not (i+SELFEXCL+1) to set matrix element at boundary to zero
+
+ // Initialize cells at (i,t.L+1)
+ scale_prod *= scale[i+1];
+ if (cell_off[i][t.L])
+ B_MM[i][t.L] = 0.0;
+ else
+ B_MM[i][t.L] = scale_prod;
+ //if (isnan(B_MM[i][t.L])||isinf(B_MM[i][t.L])){
+ // printf("."); /* <DEBUG> FS*/
+ //}
+ //dMaxB = dMaxB>B_MM[i][t.L]?dMaxB:B_MM[i][t.L];
+ B_IM[i][t.L] = B_MI[i][t.L] = B_DG[i][t.L] = B_GD[i][t.L] = 0.0;
+ pmin *= scale[i+1]; // transform pmin (for local alignment) to scale of present (i'th) row
+
+ for (j=t.L-1; j>=jmin; j--) // Loop through template positions j
+ {
+ // Recursion relations
+ // printf("S[%i][%i]=%4.1f ",i,j,Score(q.p[i],t.p[j]));
+ if (cell_off[i][j])
+ B_MM[i][j] = B_GD[i][j] = B_IM[i][j] = B_DG[i][j] = B_MI[i][j] = 0.0;
+ else
+ {
+ double pmatch = B_MM[i+1][j+1] * ProbFwd(q.p[i+1],t.p[j+1]) * fpow2(ScoreSS(q,t,i+1,j+1)) * Cshift * scale[i+1];
+ //if (isnan(pmatch)||isinf(pmatch)){
+ // printf("."); /* <DEBUG> FS*/
+ //}
+ B_MM[i][j] =
+ (
+ + pmin // MM -> EE (End/End, for local alignment)
+ + pmatch * q.tr[i][M2M] * t.tr[j][M2M] // MM -> MM
+ + B_GD[i][j+1] * t.tr[j][M2D] // MM -> GD (q.tr[i][M2M] is already contained in GD->MM)
+ + B_IM[i][j+1] * q.tr[i][M2I] * t.tr[j][M2M] // MM -> IM
+ + B_DG[i+1][j] * q.tr[i][M2D] * scale[i+1] // MM -> DG (t.tr[j][M2M] is already contained in DG->MM)
+ + B_MI[i+1][j] * q.tr[i][M2M] * t.tr[j][M2I] * scale[i+1] // MM -> MI
+ );
+ //if (isnan(B_MM[i][j])||isinf(B_MM[i][j])){
+ // printf("."); /* <DEBUG> FS*/
+ //}
+ //dMaxB = dMaxB>B_MM[i][j]?dMaxB:B_MM[i][j];
+
+ B_GD[i][j] =
+ (
+ + pmatch * q.tr[i][M2M] * t.tr[j][D2M] // GD -> MM
+ + B_GD[i][j+1] * t.tr[j][D2D] // DG -> DG
+ );
+ B_IM[i][j] =
+ (
+ + pmatch * q.tr[i][I2M] * t.tr[j][M2M] // IM -> MM
+ + B_IM[i][j+1] * q.tr[i][I2I] * t.tr[j][M2M] // IM -> IM
+ );
+ B_DG[i][j] =
+ (
+ + pmatch * q.tr[i][D2M] * t.tr[j][M2M] // DG -> MM
+ + B_DG[i+1][j] * q.tr[i][D2D] * scale[i+1] // DG -> DG
+ // + B_GD[i][j+1] * q.tr[i][D2M] * t.tr[j][M2D] // DG -> GD
+ );
+ B_MI[i][j] =
+ (
+ + pmatch * q.tr[i][M2M] * t.tr[j][I2M] // MI -> MM
+ + B_MI[i+1][j] * q.tr[i][M2M] * t.tr[j][I2I] * scale[i+1] // MI -> MI
+ // + B_IM[i][j+1] * q.tr[i][M2I] * t.tr[j][I2M] // MI -> IM
+ );
+
+ } // end else
+
+ } //end for j
+
+ } // end for i
+
+ // Debugging output
+ if (v>=6)
+ {
+ const int i0=0, i1=q.L;
+ const int j0=0, j1=t.L;
+ double scale_prod[q.L+2];
+ scale_prod[q.L] = scale[q.L+1];
+ for (i=q.L-1; i>=1; i--) scale_prod[i] = scale_prod[i+1] * scale[i+1];
+
+ printf("\nBwd scale ");
+ for (j=j0; j<=j1; j++) printf("%3i ",j);
+ printf("\n");
+ for (i=i0; i<=i1; i++)
+ {
+ printf("%3i: %9.3G ",i,1/scale_prod[i]);
+ for (j=j0; j<=j1; j++)
+ printf("%7.4f ",(B_MM[i][j]+B_MI[i][j]+B_IM[i][j]+B_DG[i][j]+B_GD[i][j]) * (ProbFwd(q.p[i],t.p[j])*fpow2(ScoreSS(q,t,i,j)) * Cshift));
+ printf("\n");
+
+ // printf("MM %9.5f ",1/scale[i]);
+ // for (j=j0; j<=j1; j++)
+ // printf("%7.4f ",B_MM[i][j] * (ProbFwd(q.p[i],t.p[j])*fpow2(ScoreSS(q,t,i,j)) * Cshift));
+ // printf("\n");
+ }
+ printf("\nPost scale ");
+ for (j=j0; j<=j1; j++) printf("%3i ",j);
+ printf("\n");
+ for (i=i0; i<=i1; i++)
+ {
+ printf("%3i: %9.3G ",i,1/scale_prod[i]);
+ for (j=j0; j<=j1; j++)
+ printf("%7.4f ",B_MM[i][j]*F_MM[i][j]/Pforward);
+ printf("\n");
+ }
+ printf("\n");
+ }
+
+ if (v>=4) printf("\nForward total probability ratio: %8.3G\n",Pforward);
+
+ // Calculate Posterior matrix and overwrite Backward matrix with it
+ for (i=1; i<=q.L; i++) {
+ for (j=1; j<=t.L; j++) {
+ B_MM[i][j] *= F_MM[i][j]/Pforward;
+ //if (isnan(B_MM[i][j]) || isinf(B_MM[i][j])){
+ // printf("."); /* <DEBUG> FS*/
+ //}
+ //dMaxB = dMaxB>B_MM[i][j]?dMaxB:B_MM[i][j];
+ }
+ }
+
+ //printf("Max-B_MM = %f\n", dMaxB);
+
+ /* check for NaN and or infinities, FS, r241 -> r243 */
+ if (isnan(score) || isinf(score)){
+ fprintf(stderr, "%s:%s:%d: Backward score is %g\n",
+ __FUNCTION__, __FILE__, __LINE__, score);
+ return FAILURE;
+ }
+ i = j = 1;
+ if (isinf(B_MM[i][j]+B_MI[i][j]+B_IM[i][j]+B_DG[i][j]+B_GD[i][j])){
+ fprintf(stderr, "%s:%s:%d: B_MM[1][1]=%g, B_IM[1][1]=%g, B_MI[1][1]=%g, B_DG[1][1]=%g, B_GD[1][1]=%g\n",
+ __FUNCTION__, __FILE__, __LINE__, B_MM[i][j], B_MI[i][j], B_IM[i][j], B_DG[i][j], B_GD[i][j]);
+ for (i = 1; (i < q.L) && isinf(B_MM[i][1]); i++);
+ i--;
+ for (j = 1; (j < t.L) && isinf(B_MM[i][j]); j++);
+ j--;
+ fprintf(stderr, "%s:%s:%d: B_MM[%d][%d]=%g, B_MM[%d][%d]=%g, B_MM[%d][%d]=%g\n",
+ __FUNCTION__, __FILE__, __LINE__,
+ i, j, B_MM[i][j], i+1, 1, B_MM[i+1][1], i, j+1, B_MM[i][j+1]);
+ return FAILURE;
+ }
+ return OK;
+
+} /* this is the end of Hit::Backward() */
+
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Maximum Accuracy alignment
+ */
+void
+Hit::MACAlignment(HMM& q, HMM& t)
+{
+ // Use Forward and Backward matrices to find that alignment which
+ // maximizes the expected number of correctly aligned pairs of residues (mact=0)
+ // or, more generally, which maximizes the expectation value of the number of
+ // correctly aligned pairs minus (mact x number of aligned pairs)
+ // "Correctly aligned" can be based on posterior probabilities calculated with
+ // a local or a global version of the Forward-Backward algorithm.
+
+ int i,j; // query and template match state indices
+ int jmin,jmax; // range of dynamic programming for j
+ double** S=F_MI; // define alias for new score matrix
+ double score_MAC; // score of the best MAC alignment
+
+ // Initialization of top row, i.e. cells (0,j)
+ for (j=0; j<=t.L; j++) S[0][j] = 0.0;
+ score_MAC=-INT_MAX; i2=j2=0; bMM[0][0]=STOP;
+
+ // Dynamic programming
+ for (i=1; i<=q.L; i++) // Loop through query positions i
+ {
+
+ if (self)
+ {
+ // If q is compared to itself, ignore cells below diagonal+SELFEXCL
+ jmin = i+SELFEXCL;
+ jmax = t.L;
+ if (jmin>jmax) continue;
+ }
+ else
+ {
+ // If q is compared to t, exclude regions where overlap of q with t < min_overlap residues
+ jmin=imax( 1, i+min_overlap-q.L); // Lq-i+j>=Ovlap => j>=i+Ovlap-Lq => jmin=max{1, i+Ovlap-Lq}
+ jmax=imin(t.L,i-min_overlap+t.L); // Lt-j+i>=Ovlap => j<=i-Ovlap+Lt => jmax=min{Lt,i-Ovlap+Lt}
+ }
+
+ // Initialize cells
+ S[i][jmin-1] = 0.0;
+ if (jmax<t.L) S[i-1][jmax] = 0.0; // initialize at (i-1,jmax) if upper right triagonal is excluded due to min overlap
+
+ for (j=jmin; j<=jmax; j++) // Loop through template positions j
+ {
+
+ if (cell_off[i][j])
+ S[i][j] = -FLT_MIN;
+ else
+ {
+ // Recursion
+
+ // NOT the state before the first MM state)
+ CALCULATE_MAX4(
+ S[i][j],
+ B_MM[i][j] - par.mact, // STOP signifies the first MM state, NOT the state before the first MM state (as in Viterbi)
+ S[i-1][j-1] + B_MM[i][j] - par.mact, // B_MM[i][j] contains posterior probability
+ S[i-1][j] - 0.5*par.mact, // gap penalty prevents alignments such as this: XX--xxXX
+ S[i][j-1] - 0.5*par.mact, // YYyy--YY
+ bMM[i][j] // backtracing matrix
+ );
+
+// if (i==6 && j==8)
+// printf("i=%i j=%i S[i][j]=%8.3f MM:%7.3f MI:%7.3f IM:%7.3f b:%i\n",i,j,S[i][j],S[i-1][j-1]+B_MM[i][j]-par.mact,S[i-1][j],S[i][j-1],bMM[i][j]);
+
+ // Find maximum score; global alignment: maximize only over last row and last column
+ if(S[i][j]>score_MAC && (par.loc || i==q.L)) { i2=i; j2=j; score_MAC=S[i][j]; }
+
+ } // end if
+
+ } //end for j
+
+ // if global alignment: look for best cell in last column
+ if (!par.loc && S[i][jmax]>score_MAC) { i2=i; j2=jmax; score_MAC=S[i][jmax]; }
+
+ } // end for i
+
+ // DEBUG
+ if (v>=5)
+ {
+ printf("\nScore ");
+ for (j=0; j<=t.L; j++) printf("%3i ",j);
+ printf("\n");
+ for (i=0; i<=q.L; i++)
+ {
+ printf("%2i: ",i);
+ for (j=0; j<=t.L; j++)
+ printf("%5.2f ",S[i][j]);
+ printf("\n");
+ }
+ printf("\n");
+ printf("Template=%-12.12s i=%-4i j=%-4i score=%6.3f\n",t.name,i2,j2,score);
+ }
+
+ return;
+
+} /* this is the end of Hit::MACAlignment() */
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Trace back alignment of two profiles based on matrices bXX[][]
+ */
+void
+Hit::Backtrace(HMM& q, HMM& t)
+{
+ // Trace back trough the matrices bXY[i][j] until first match state is found (STOP-state)
+
+ int step; // counts steps in path through 5-layered dynamic programming matrix
+ int i,j; // query and template match state indices
+
+ InitializeBacktrace(q,t);
+
+ // Make sure that backtracing stops when t:M1 or q:M1 is reached (Start state), e.g. sMM[i][1], or sIM[i][1] (M:MM, B:IM)
+ for (i=0; i<=q.L; i++) bMM[i][1]=bGD[i][1]=bIM[i][1] = STOP;
+ for (j=1; j<=t.L; j++) bMM[1][j]=bDG[1][j]=bMI[1][j] = STOP;
+
+
+ // Back-tracing loop
+ matched_cols=0; // for each MACTH (or STOP) state matched_col is incremented by 1
+ step=0; // steps through the matrix correspond to alignment columns (from 1 to nsteps)
+ // state=MM; // state with maximum score must be MM state // already set at the end of Viterbi()
+ i=i2; j=j2; // last aligned pair is (i2,j2)
+ while (state) // while (state!=STOP) because STOP=0
+ {
+ step++;
+ states[step] = state;
+ this->i[step] = i;
+ this->j[step] = j;
+ // Exclude cells in direct neighbourhood from all further alignments
+ for (int ii=imax(i-2,1); ii<=imin(i+2,q.L); ii++)
+ cell_off[ii][j]=1;
+ for (int jj=imax(j-2,1); jj<=imin(j+2,t.L); jj++)
+ cell_off[i][jj]=1;
+
+ switch (state)
+ {
+ case MM: // current state is MM, previous state is bMM[i][j]
+ matched_cols++;
+ state = bMM[i--][j--];
+ break;
+ case GD: // current state is GD
+ switch (bGD[i][j--])
+ {
+ case STOP: state = STOP; break; // current state does not have predecessor
+ case MM: state = MM; break; // previous state is Match state
+ } // default: previous state is same state (GD)
+ break;
+ case IM:
+ switch (bIM[i][j--])
+ {
+ case STOP: state = STOP; break; // current state does not have predecessor
+ case MM: state = MM; break; // previous state is Match state
+ } // default: previous state is same state (IM)
+ break;
+ case DG:
+ switch (bDG[i--][j])
+ {
+ case STOP: state = STOP; break; // current state does not have predecessor
+ case MM: state = MM; break; // previous state is Match state
+ } // default: previous state is same state (DG)
+ break;
+ case MI:
+ switch (bMI[i--][j])
+ {
+ case STOP: state = STOP; break; // current state does not have predecessor
+ case MM: state = MM; break; // previous state is Match state
+ } // default: previous state is same state (MI)
+ break;
+ default:
+ fprintf(stderr,"Error: unallowed state value %i occurred during backtracing at step %i, (i,j)=(%i,%i)\n",state,step,i,j);
+ state=0;
+ v=4;
+ break;
+ } //end switch (state)
+ } //end while (state)
+
+ i1 = this->i[step];
+ j1 = this->j[step];
+ states[step] = MM; // first state (STOP state) is set to MM state
+ nsteps=step;
+
+ // Allocate new space for alignment scores
+ if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query
+ S = new( float[nsteps+1]);
+ S_ss = new( float[nsteps+1]);
+ if (!S_ss) MemoryError("space for HMM-HMM alignments");
+
+ // Add contribution from secondary structure score, record score along alignment,
+ // and record template consensus sequence in master-slave-alignment to query sequence
+ score_ss=0.0f;
+ int ssm=ssm1+ssm2;
+ for (step=1; step<=nsteps; step++)
+ {
+ switch(states[step])
+ {
+ case MM:
+ i = this->i[step];
+ j = this->j[step];
+ S[step] = Score(q.p[i],t.p[j]);
+ S_ss[step] = ScoreSS(q,t,i,j,ssm);
+ score_ss += S_ss[step];
+ if (Xcons) Xcons[i]=t.Xcons[j]; //record database consensus sequence
+ break;
+ case MI: //if gap in template
+ case DG:
+ if (Xcons) Xcons[this->i[step]]=GAP; //(no break hereafter)
+ default: //if gap in T or Q
+ S[step]=S_ss[step]=0.0f;
+ break;
+ }
+ }
+ if (ssm2>=1) score-=score_ss; // subtract SS score added during alignment!!!!
+ if (Xcons)
+ {
+ for (i=0; i<i1; i++) Xcons[i]=ENDGAP; // set end gap code at beginning and end of template consensus sequence
+ for (i=i2+1; i<=q.L+1; i++) Xcons[i]=ENDGAP;
+ }
+
+ // Add contribution from correlation of neighboring columns to score
+ float Scorr=0;
+ if (nsteps)
+ {
+ for (step=2; step<=nsteps; step++) Scorr+=S[step]*S[step-1];
+ for (step=3; step<=nsteps; step++) Scorr+=S[step]*S[step-2];
+ for (step=4; step<=nsteps; step++) Scorr+=S[step]*S[step-3];
+ for (step=5; step<=nsteps; step++) Scorr+=S[step]*S[step-4];
+ score+=par.corr*Scorr;
+ }
+
+ // Set score, P-value etc.
+ score_sort = score_aass = -score;
+ logPval=0; Pval=1;
+ if (t.mu)
+ {
+ logPvalt=logPvalue(score,t.lamda,t.mu);
+ Pvalt=Pvalue(score,t.lamda,t.mu);
+ }
+ else { logPvalt=0; Pvalt=1;}
+ // printf("%-10.10s lamda=%-9f score=%-9f logPval=%-9g\n",name,t.lamda,score,logPvalt);
+
+
+ //DEBUG: Print out Viterbi path
+ if (v>=4)
+ {
+ printf("NAME=%7.7s score=%7.3f score_ss=%7.3f\n",name,score,score_ss);
+ printf("step Q T i j state score T Q cf ss-score\n");
+ for (step=nsteps; step>=1; step--)
+ {
+ switch(states[step])
+ {
+ case MM:
+ printf("%4i %1c %1c ",step,q.seq[q.nfirst][this->i[step]],seq[nfirst][this->j[step]]);
+ break;
+ case GD:
+ case IM:
+ printf("%4i - %1c ",step,seq[nfirst][this->j[step]]);
+ break;
+ case DG:
+ case MI:
+ printf("%4i %1c - ",step,q.seq[q.nfirst][this->i[step]]);
+ break;
+ }
+ printf("%4i %4i %2i %7.2f ",this->i[step],this->j[step],(int)states[step],S[step]);
+ printf("%c %c %1i %7.2f\n",i2ss(t.ss_dssp[this->j[step]]),i2ss(q.ss_pred[this->i[step]]),q.ss_conf[this->i[step]]-1,S_ss[step]);
+ }
+ }
+
+ return;
+
+} /* this is the end of Hit::Backtrace() */
+
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief GLOBAL stochastic trace back through the forward matrix of probability ratios
+ */
+void
+Hit::StochasticBacktrace(HMM& q, HMM& t, char maximize)
+{
+ int step; // counts steps in path through 5-layered dynamic programming matrix
+ int i,j; // query and template match state indices
+// float pmin=(par.loc? 1.0: 0.0); // used to distinguish between SW and NW algorithms in maximization
+ const float pmin=0;
+ double* scale_cum = new(double[q.L+2]);
+
+
+ scale_cum[0]=1;
+ for (i=1; i<=q.L+1; i++) scale_cum[i] = scale_cum[i-1]*scale[i];
+
+ // Select start cell for GLOBAL alignment
+ // (Implementing this in a local version would make this method work for local backtracing as well)
+ if (maximize)
+ {
+ double F_max=0;
+ for (i=q.L-1; i>=1; i--)
+ if (F_MM[i][t.L]/scale_cum[i]>F_max) {i2=i; j2=t.L; F_max=F_MM[i][t.L]/scale_cum[i];}
+ for (j=t.L; j>=1; j--)
+ if (F_MM[q.L][j]/scale_cum[q.L]>F_max) {i2=q.L; j2=j; F_max=F_MM[q.L][j]/scale_cum[q.L];}
+ }
+ else
+ {
+// float sumF[q.L+t.L];
+ double* sumF=new(double[q.L+t.L]);
+ sumF[0]=0.0;
+ for (j=1; j<=t.L; j++) sumF[j] = sumF[j-1] + F_MM[q.L][j]/scale_cum[q.L];;
+ for (j=t.L+1; j<t.L+q.L; j++) sumF[j] = sumF[j-1] + F_MM[j-t.L][t.L]/scale_cum[j-t.L];;
+ float x = sumF[t.L+q.L-1]*frand(); // generate random number between 0 and sumF[t.L+q.L-1]
+ for (j=1; j<t.L+q.L; j++)
+ if (x<sumF[j]) break;
+ if (j<=t.L) {i2=q.L; j2=j;} else {i2=j-t.L; j2=t.L;}
+ delete[] sumF; sumF = NULL;
+ }
+
+ InitializeBacktrace(q,t);
+
+ int (*pick2)(const double&, const double&, const int&);
+ int (*pick3_GD)(const double&, const double&, const double&);
+ int (*pick3_IM)(const double&, const double&, const double&);
+ int (*pick6)(const double&, const double&, const double&, const double&, const double&, const double&);
+ if (maximize)
+ {
+ pick2 = &pickmax2;
+ pick3_GD = &pickmax3_GD;
+ pick3_IM = &pickmax3_IM;
+ pick6 = &pickmax6;
+ }
+ else
+ {
+ pick2 = &pickprob2;
+ pick3_GD = &pickprob3_GD;
+ pick3_IM = &pickprob3_IM;
+ pick6 = &pickprob6;
+ }
+
+ // Back-tracing loop
+ matched_cols=0; // for each MACTH (or STOP) state matched_col is incremented by 1
+ step=0; // steps through the matrix correspond to alignment columns (from 1 to nsteps)
+ state = MM;
+ i=i2; j=j2; // start at end of query and template
+ while (state) // while not reached STOP state or upper or left border
+ {
+ step++;
+ states[step] = state;
+ this->i[step] = i;
+ this->j[step] = j;
+
+ switch (state)
+ {
+
+ case MM: // current state is MM, previous state is state
+// fprintf(stderr,"%4i %1c %1c %4i %4i MM %7.2f\n",step,q.seq[q.nfirst][i],seq[nfirst][j],i,j,Score(q.p[i],t.p[j]));
+// printf("0:%7.3f MM:%7.3f GD:%7.3f IM:%7.3f DG:%7.3f MI:%7.3f \n",
+// pmin*scale_cum[i-1],
+// F_MM[i-1][j-1] * q.tr[i-1][M2M] * t.tr[j-1][M2M],
+// F_GD[i-1][j-1] * q.tr[i-1][M2M] * t.tr[j-1][D2M],
+// F_IM[i-1][j-1] * q.tr[i-1][I2M] * t.tr[j-1][M2M],
+// F_DG[i-1][j-1] * q.tr[i-1][D2M] * t.tr[j-1][M2M],
+// F_MI[i-1][j-1] * q.tr[i-1][M2M] * t.tr[j-1][I2M]);
+ matched_cols++;
+ if (j>1 && i>1)
+ state = (*pick6)(
+ pmin*scale_cum[i-1],
+ F_MM[i-1][j-1] * q.tr[i-1][M2M] * t.tr[j-1][M2M],
+ F_GD[i-1][j-1] * q.tr[i-1][M2M] * t.tr[j-1][D2M],
+ F_IM[i-1][j-1] * q.tr[i-1][I2M] * t.tr[j-1][M2M],
+ F_DG[i-1][j-1] * q.tr[i-1][D2M] * t.tr[j-1][M2M],
+ F_MI[i-1][j-1] * q.tr[i-1][M2M] * t.tr[j-1][I2M]
+ );
+ else state=0;
+ i--; j--;
+ break;
+ case GD: // current state is GD
+// fprintf(stderr,"%4i - %1c %4i %4i GD %7.2f\n",step,q.seq[q.nfirst][j],i,j,Score(q.p[i],t.p[j]));
+ if (j>1)
+ state = (*pick3_GD)(
+ F_MM[i][j-1] * t.tr[j-1][M2D],
+ F_DG[i][j-1] * t.tr[j-1][M2D] * q.tr[i][D2M], // DG -> GD
+ F_GD[i][j-1] * t.tr[j-1][D2D] // gap extension (DD) in template
+ );
+ else state=0;
+ j--;
+ break;
+ case IM:
+// fprintf(stderr,"%4i - %1c %4i %4i IM %7.2f\n",step,q.seq[q.nfirst][j],i,j,Score(q.p[i],t.p[j]));
+ if (j>1)
+ state = (*pick3_IM)(
+ F_MM[i][j-1] * q.tr[i][M2I] * t.tr[j-1][M2M_GAPOPEN],
+ F_MI[i][j-1] * q.tr[i][M2I] * t.tr[j-1][I2M], // MI -> IM
+ F_IM[i][j-1] * q.tr[i][I2I] * t.tr[j-1][M2M] // gap extension (II) in query
+ );
+ else state=0;
+ j--;
+ break;
+ case DG:
+// fprintf(stderr,"%4i %1c - %4i %4i DG %7.2f\n",step,q.seq[q.nfirst][i],i,j,Score(q.p[i],t.p[j]));
+ if (i>1)
+ state = (*pick2)(
+ F_MM[i-1][j] * q.tr[i-1][M2D] * t.tr[j][GAPOPEN],
+ F_DG[i-1][j] * q.tr[i-1][D2D] * t.tr[j][GAPEXTD], //gap extension (DD) in query
+ DG
+ );
+ else state=0;
+ i--;
+ break;
+ case MI:
+// fprintf(stderr,"%4i %1c - %4i %4i MI %7.2f\n",step,q.seq[q.nfirst][i],i,j,Score(q.p[i],t.p[j]));
+ if (i>1)
+ state = (*pick2)(
+ F_MM[i-1][j] * q.tr[i-1][M2M] * t.tr[j][M2I],
+ F_MI[i-1][j] * q.tr[i-1][M2M] * t.tr[j][I2I], //gap extension (II) in template
+ MI
+ );
+ else state=0;
+ i--;
+ break;
+
+ } //end switch (state)
+
+ } //end while (state)
+
+ i1 = this->i[step];
+ j1 = this->j[step];
+ states[step] = MM; // first state (STOP state) is set to MM state
+ nsteps=step;
+
+ // Allocate new space for alignment scores
+ if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query
+ S = new( float[nsteps+1]);
+ S_ss = new( float[nsteps+1]);
+ if (!S_ss) MemoryError("space for HMM-HMM alignments");
+
+ // Add contribution from secondary structure score, record score along alignment,
+ // and record template consensus sequence in master-slave-alignment to query sequence
+ score_ss=0.0f;
+ int ssm=ssm1+ssm2;
+ for (step=1; step<=nsteps; step++)
+ {
+ switch(states[step])
+ {
+ case MM:
+ i = this->i[step];
+ j = this->j[step];
+ S[step] = Score(q.p[i],t.p[j]);
+ S_ss[step] = ScoreSS(q,t,i,j,ssm);
+ score_ss += S_ss[step];
+ if (Xcons) Xcons[i]=t.Xcons[j]; //record database consensus sequence
+ break;
+ case MI: //if gap in template
+ case DG:
+ if (Xcons) Xcons[this->i[step]]=GAP; //(no break hereafter)
+ default: //if gap in T or Q
+ S[step]=S_ss[step]=0.0f;
+ break;
+ }
+ }
+ if (ssm2>=1) score-=score_ss; // subtract SS score added during alignment!!!!
+ if (Xcons)
+ {
+ for (i=0; i<i1; i++) Xcons[i]=ENDGAP; // set end gap code at beginning and end of template consensus sequence
+ for (i=i2+1; i<=q.L+1; i++) Xcons[i]=ENDGAP;
+ }
+
+ delete[] scale_cum; scale_cum = NULL;
+
+ return;
+}
+
+
+
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Trace back alignment of two profiles based on matrices bXX[][]
+ */
+void
+Hit::BacktraceMAC(HMM& q, HMM& t)
+{
+ // Trace back trough the matrix b[i][j] until STOP state is found
+
+ char** b=bMM; // define alias for backtracing matrix
+ int step; // counts steps in path through 5-layered dynamic programming matrix
+ int i,j; // query and template match state indices
+
+ InitializeBacktrace(q,t);
+
+ // Make sure that backtracing stops when t:M1 or q:M1 is reached (Start state), e.g. sMM[i][1], or sIM[i][1] (M:MM, B:IM)
+ for (i=0; i<=q.L; i++) b[i][1] = STOP;
+ for (j=1; j<=t.L; j++) b[1][j] = STOP;
+
+
+ // Back-tracing loop
+ // In contrast to the Viterbi-Backtracing, STOP signifies the first Match-Match state, NOT the state before the first MM state
+ matched_cols=1; // for each MACTH (or STOP) state matched_col is incremented by 1
+ state=MM; // lowest state with maximum score must be match-match state
+ step=0; // steps through the matrix correspond to alignment columns (from 1 to nsteps)
+ i=i2; j=j2; // last aligned pair is (i2,j2)
+ while (state!=STOP)
+ {
+ step++;
+ states[step] = state = b[i][j];
+ this->i[step] = i;
+ this->j[step] = j;
+ // Exclude cells in direct neighbourhood from all further alignments
+ for (int ii=imax(i-2,1); ii<=imin(i+2,q.L); ii++)
+ cell_off[ii][j]=1;
+ for (int jj=imax(j-2,1); jj<=imin(j+2,t.L); jj++)
+ cell_off[i][jj]=1;
+ if (state==MM) matched_cols++;
+
+ switch (state)
+ {
+ case MM: i--; j--; break;
+ case IM: j--; break;
+ case MI: i--; break;
+ case STOP: break;
+ default:
+ fprintf(stderr,"Error: unallowed state value %i occurred during backtracing at step %i, (i,j)=(%i,%i)\n",state,step,i,j);
+ state=0;
+ v=4;
+ break;
+ } //end switch (state)
+ } //end while (state)
+
+ i1 = this->i[step];
+ j1 = this->j[step];
+ states[step] = MM; // first state (STOP state) is set to MM state
+ nsteps=step;
+
+ // Allocate new space for alignment scores
+ if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query
+ S = new( float[nsteps+1]);
+ S_ss = new( float[nsteps+1]);
+ P_posterior = new( float[nsteps+1]);
+ if (!P_posterior) MemoryError("space for HMM-HMM alignments");
+
+ // Add contribution from secondary structure score, record score along alignment,
+ // and record template consensus sequence in master-slave-alignment to query sequence
+ score_ss=0.0f;
+ sum_of_probs=0.0; // number of identical residues in query and template sequence
+ int ssm=ssm1+ssm2;
+// printf("Hit=%s\n",name); /////////////////////////////////////////////////////////////
+ for (step=1; step<=nsteps; step++)
+ {
+ switch(states[step])
+ {
+ case MM:
+ i = this->i[step];
+ j = this->j[step];
+ S[step] = Score(q.p[i],t.p[j]);
+ S_ss[step] = ScoreSS(q,t,i,j,ssm);
+ score_ss += S_ss[step];
+ P_posterior[step] = B_MM[this->i[step]][this->j[step]];
+ // Add probability to sum of probs if no dssp states given or dssp states exist and state is resolved in 3D structure
+ if (t.nss_dssp<0 || t.ss_dssp[j]>0) sum_of_probs += P_posterior[step];
+// printf("j=%-3i dssp=%1i P=%4.2f sum=%6.2f\n",j,t.ss_dssp[j],P_posterior[step],sum_of_probs); //////////////////////////
+ if (Xcons) Xcons[i]=t.Xcons[j]; //record database consensus sequence
+ break;
+ case MI: //if gap in template
+ case DG:
+ if (Xcons) Xcons[this->i[step]]=GAP; //(no break hereafter)
+ default: //if gap in T or Q
+ S[step] = S_ss[step] = P_posterior[step] = 0.0;
+ break;
+ }
+ }
+// printf("\n"); /////////////////////////////////////////////////////////////
+ if (ssm2>=1) score-=score_ss; // subtract SS score added during alignment!!!!
+ if (Xcons)
+ {
+ for (i=0; i<i1; i++) Xcons[i]=ENDGAP; // set end gap code at beginning and end of template consensus sequence
+ for (i=i2+1; i<=q.L+1; i++) Xcons[i]=ENDGAP;
+ }
+
+ // Add contribution from correlation of neighboring columns to score
+ float Scorr=0;
+ if (nsteps)
+ {
+ for (step=1; step<=nsteps-1; step++) Scorr+=S[step]*S[step+1];
+ for (step=1; step<=nsteps-2; step++) Scorr+=S[step]*S[step+2];
+ for (step=1; step<=nsteps-3; step++) Scorr+=S[step]*S[step+3];
+ for (step=1; step<=nsteps-4; step++) Scorr+=S[step]*S[step+4];
+ score+=par.corr*Scorr;
+ }
+
+ // Set score, P-value etc.
+ score_sort = score_aass = -score;
+ logPval=0; Pval=1;
+ if (t.mu)
+ {
+ logPvalt=logPvalue(score,t.lamda,t.mu);
+ Pvalt=Pvalue(score,t.lamda,t.mu);
+ }
+ else { logPvalt=0; Pvalt=1;}
+// printf("%-10.10s lamda=%-9f score=%-9f logPval=%-9g\n",name,t.lamda,score,logPvalt);
+
+
+ //DEBUG: Print out MAC alignment path
+ if (v>=4)
+ {
+ float sum_post=0.0;
+ printf("NAME=%7.7s score=%7.3f score_ss=%7.3f\n",name,score,score_ss);
+ printf("step Q T i j state score T Q cf ss-score P_post Sum_post\n");
+ for (step=nsteps; step>=1; step--)
+ {
+ switch(states[step])
+ {
+ case MM:
+ sum_post+=P_posterior[step];
+ printf("%4i %1c %1c ",step,q.seq[q.nfirst][this->i[step]],seq[nfirst][this->j[step]]);
+ break;
+ case IM:
+ printf("%4i - %1c ",step,seq[nfirst][this->j[step]]);
+ break;
+ case MI:
+ printf("%4i %1c - ",step,q.seq[q.nfirst][this->i[step]]);
+ break;
+ }
+ printf("%4i %4i %2i %7.1f ",this->i[step],this->j[step],(int)states[step],S[step]);
+ printf("%c %c %1i %7.1f ",i2ss(t.ss_dssp[this->j[step]]),i2ss(q.ss_pred[this->i[step]]),q.ss_conf[this->i[step]]-1,S_ss[step]);
+ printf("%7.5f %7.2f\n",P_posterior[step],sum_post);
+ }
+ }
+
+ return;
+}
+
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Functions that calculate probabilities
+ */
+void
+Hit::InitializeForAlignment(HMM& q, HMM& t)
+{
+ int i,j;
+
+ // SS scoring during (ssm2>0) or after (ssm1>0) alignment? Query SS known or Template SS known?
+ switch (par.ssm)
+ {
+ case 0:
+ ssm1=0;
+ ssm2=0;
+ break;
+ case 1:
+ ssm2=0; // SS scoring after alignment
+ if (t.nss_dssp>=0 && q.nss_pred>=0) ssm1=1;
+ else if (q.nss_dssp>=0 && t.nss_pred>=0) ssm1=2;
+ else if (q.nss_pred>=0 && t.nss_pred>=0) ssm1=3;
+ else ssm1=0;
+ break;
+ case 2:
+ ssm1=0; // SS scoring during alignment
+ if (t.nss_dssp>=0 && q.nss_pred>=0) ssm2=1;
+ else if (q.nss_dssp>=0 && t.nss_pred>=0) ssm2=2;
+ else if (q.nss_pred>=0 && t.nss_pred>=0) ssm2=3;
+ else ssm2=0;
+ break;
+ case 3:
+ ssm2=0; // SS scoring after alignment
+ if (q.nss_pred>=0 && t.nss_pred>=0) ssm1=3; else ssm1=0;
+ break;
+ case 4:
+ ssm1=0; // SS scoring during alignment
+ if (q.nss_pred>=0 && t.nss_pred>=0) ssm2=3; else ssm2=0;
+ break;
+ // case 5:
+ // ssm2=0; // SS scoring after alignment
+ // if (q.nss_dssp>=0 && t.nss_dssp>=0) ssm1=4; else ssm1=0;
+ // break;
+ // case 6:
+ // ssm1=0; // SS scoring during alignment
+ // if (q.nss_dssp>=0 && t.nss_dssp>=0) ssm2=4; else ssm2=0;
+ // break;
+ }
+
+ if (self)
+ {
+ // Cross out cells in lower diagonal for self-comparison?
+ for (i=1; i<=q.L; i++)
+ {
+ int jmax = imin(i+SELFEXCL,t.L);
+ for (j=1; j<=jmax; j++)
+ cell_off[i][j]=1; // cross out cell near diagonal
+ for (j=jmax+1; j<=t.L+1; j++)
+ cell_off[i][j]=0; // no other cells crossed out yet
+ }
+ }
+ else
+ // Compare two different HMMs Q and T
+ {
+ // Activate all cells in dynamic programming matrix
+ for (i=1; i<=q.L; i++)
+ for (j=1; j<=t.L; j++)
+ cell_off[i][j]=0; // no other cells crossed out yet
+
+ // Cross out cells that are excluded by the minimum-overlap criterion
+ if (par.min_overlap==0)
+ min_overlap = imin(60, (int)(0.333f*imin(q.L,t.L))+1); // automatic minimum overlap
+ else
+ min_overlap = imin(par.min_overlap, (int)(0.8f*imin(q.L,t.L)));
+
+ for (i=0; i<min_overlap; i++)
+ for (j=i-min_overlap+t.L+1; j<=t.L; j++) // Lt-j+i>=Ovlap => j<=i-Ovlap+Lt => jmax=min{Lt,i-Ovlap+Lt}
+ cell_off[i][j]=1;
+ for (i=q.L-min_overlap+1; i<=q.L; i++)
+ for (j=1; j<i+min_overlap-q.L; j++) // Lq-i+j>=Ovlap => j>=i+Ovlap-Lq => jmin=max{1, i+Ovlap-Lq}
+ cell_off[i][j]=1;
+ }
+
+ // Cross out rows which are contained in range given by exclstr ("3-57,238-314")
+ if (par.exclstr)
+ {
+ char* ptr=par.exclstr;
+ int i0, i1;
+ while (1)
+ {
+ i0 = abs(strint(ptr));
+ i1 = abs(strint(ptr));
+ if (!ptr) break;
+ for (i=i0; i<=imin(i1,q.L); i++)
+ for (j=1; j<=t.L; j++)
+ cell_off[i][j]=1;
+ }
+ }
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Allocate memory for data of new alignment (sequence names, alignment, scores,...)
+ */
+void
+Hit::InitializeBacktrace(HMM& q, HMM& t)
+{
+ if (irep==1) //if this is the first single repeat repeat hit with this template
+ {
+ //Copy information about template profile to hit and reset template pointers to avoid destruction
+ longname=new(char[strlen(t.longname)+1]);
+ name =new(char[strlen(t.name)+1]);
+ file =new(char[strlen(t.file)+1]);
+ if (!file) MemoryError("space for alignments with database HMMs. \nNote that all alignments have to be kept in memory");
+ strcpy(longname,t.longname);
+ strcpy(name,t.name);
+ strcpy(fam ,t.fam);
+ strcpy(sfam ,t.sfam);
+ strcpy(fold ,t.fold);
+ strcpy(cl ,t.cl);
+ strcpy(file,t.file);
+ sname=new(char*[t.n_display]); // Call Compare only once with irep=1
+ seq =new(char*[t.n_display]); // Call Compare only once with irep=1
+ if (!sname || !seq)
+ MemoryError("space for alignments with database HMMs.\nNote that all sequences for display have to be kept in memory");
+
+ for (int k=0; k<t.n_display; k++) {
+ if (NULL != t.sname){
+ sname[k]=t.sname[k]; t.sname[k]=NULL;
+ }
+ else {
+ sname[k]=NULL;
+ }
+ seq[k] =t.seq[k]; t.seq[k]=NULL;
+ }
+
+ n_display=t.n_display; t.n_display=0;
+ ncons = t.ncons;
+ nfirst = t.nfirst;
+ nss_dssp = t.nss_dssp;
+ nsa_dssp = t.nsa_dssp;
+ nss_pred = t.nss_pred;
+ nss_conf = t.nss_conf;
+ L = t.L;
+ Neff_HMM = t.Neff_HMM;
+ Eval = 1.0;
+ Pval = 1.0;
+ Pvalt = 1.0;
+ logPval = 0.0;
+ logPvalt= 0.0;
+ Probab = 1.0;
+ }
+
+ // Allocate new space
+ this->i = new( int[i2+j2+2]);
+ this->j = new( int[i2+j2+2]);
+ states = new( char[i2+j2+2]);
+ S = S_ss = P_posterior = NULL; // set to NULL to avoid deleting data from irep=1 when hit with irep=2 is removed
+ Xcons = NULL;
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+// Some score functions
+/////////////////////////////////////////////////////////////////////////////////////
+
+
+/**
+ * @brief Calculate score between columns i and j of two HMMs (query and template)
+ */
+inline float
+Score(float* qi, float* tj)
+{
+// if (par.columnscore==9)
+// return (tj[0] *qi[0] +tj[1] *qi[1] +tj[2] *qi[2] +tj[3] *qi[3] +tj[4]*qi[4]
+// +tj[5] *qi[5] +tj[6] *qi[6] +tj[7] *qi[7] +tj[8] *qi[8] +tj[9]*qi[9]
+// +tj[10]*qi[10]+tj[11]*qi[11]+tj[12]*qi[12]+tj[13]*qi[13]+tj[14]*qi[14]
+// +tj[15]*qi[15]+tj[16]*qi[16]+tj[17]*qi[17]+tj[18]*qi[18]+tj[19]*qi[19]);
+// else
+ return fast_log2(
+ tj[0] *qi[0] +tj[1] *qi[1] +tj[2] *qi[2] +tj[3] *qi[3] +tj[4] *qi[4]
+ +tj[5] *qi[5] +tj[6] *qi[6] +tj[7] *qi[7] +tj[8] *qi[8] +tj[9] *qi[9]
+ +tj[10]*qi[10]+tj[11]*qi[11]+tj[12]*qi[12]+tj[13]*qi[13]+tj[14]*qi[14]
+ +tj[15]*qi[15]+tj[16]*qi[16]+tj[17]*qi[17]+tj[18]*qi[18]+tj[19]*qi[19]
+ );
+}
+
+/**
+ * @brief Calculate score between columns i and j of two HMMs (query and template)
+ */
+inline float
+ProbFwd(float* qi, float* tj)
+{
+ return tj[0] *qi[0] +tj[1] *qi[1] +tj[2] *qi[2] +tj[3] *qi[3] +tj[4] *qi[4]
+ +tj[5] *qi[5] +tj[6] *qi[6] +tj[7] *qi[7] +tj[8] *qi[8] +tj[9] *qi[9]
+ +tj[10]*qi[10]+tj[11]*qi[11]+tj[12]*qi[12]+tj[13]*qi[13]+tj[14]*qi[14]
+ +tj[15]*qi[15]+tj[16]*qi[16]+tj[17]*qi[17]+tj[18]*qi[18]+tj[19]*qi[19];
+}
+
+
+/**
+ * @brief Calculate secondary structure score between columns i and j of two HMMs (query and template)
+ */
+inline float
+Hit::ScoreSS(HMM& q, HMM& t, int i, int j, int ssm)
+{
+ switch (ssm) //SS scoring during alignment
+ {
+ case 0: // no SS scoring during alignment
+ return 0.0;
+ case 1: // t has dssp information, q has psipred information
+ return par.ssw * S73[ (int)t.ss_dssp[j]][ (int)q.ss_pred[i]][ (int)q.ss_conf[i]];
+ case 2: // q has dssp information, t has psipred information
+ return par.ssw * S73[ (int)q.ss_dssp[i]][ (int)t.ss_pred[j]][ (int)t.ss_conf[j]];
+ case 3: // q has dssp information, t has psipred information
+ return par.ssw * S33[ (int)q.ss_pred[i]][ (int)q.ss_conf[i]][ (int)t.ss_pred[j]][ (int)t.ss_conf[j]];
+// case 4: // q has dssp information, t has dssp information
+// return par.ssw*S77[ (int)t.ss_dssp[j]][ (int)t.ss_conf[j]];
+ }
+ return 0.0;
+}
+
+/**
+ * @brief Calculate secondary structure score between columns i and j of two HMMs (query and template)
+ */
+inline float
+Hit::ScoreSS(HMM& q, HMM& t, int i, int j)
+{
+ return ScoreSS(q,t,i,j,ssm2);
+}
+
+
+/**
+ * @brief Calculate score between columns i and j of two HMMs (query and template)
+ */
+inline float
+Hit::ScoreTot(HMM& q, HMM& t, int i, int j)
+{
+ return Score(q.p[i],t.p[j]) + ScoreSS(q,t,i,j) + par.shift;
+}
+
+/*
+ * Calculate score between columns i and j of two HMMs (query and template)
+ */
+inline float
+Hit::ScoreAA(HMM& q, HMM& t, int i, int j)
+{
+ return Score(q.p[i],t.p[j]);
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/*
+ * Function for Viterbi()
+ */
+inline float
+max2(const float& xMM, const float& xX, char& b)
+{
+ if (xMM>xX) { b=MM; return xMM;} else { b=SAME; return xX;}
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/*
+ * Functions for StochasticBacktrace()
+ */
+
+inline int
+pickprob2(const double& xMM, const double& xX, const int& state)
+{
+ if ( (xMM+xX)*frand() < xMM) return MM; else return state;
+}
+
+inline int
+pickprob3_GD(const double& xMM, const double& xDG, const double& xGD)
+{
+ double x = (xMM+xDG+xGD)*frand();
+ if ( x<xMM) return MM;
+ else if ( x<xMM+xDG) return DG;
+ else return GD;
+}
+
+inline int
+pickprob3_IM(const double& xMM, const double& xMI, const double& xIM)
+{
+ double x = (xMM+xMI+xIM)*frand();
+ if ( x<xMM) return MM;
+ else if ( x<xMM+xMI) return MI;
+ else return IM;
+}
+
+inline int
+pickprob6(const double& x0, const double& xMM, const double& xGD, const double& xIM, const double& xDG, const double& xMI)
+{
+ double x = (x0+xMM+xGD+xIM+xDG+xMI)*frand();
+ x-=xMM; if (x<0) return MM;
+ x-=x0; if (x<0) return STOP;
+ x-=xGD; if (x<0) return GD;
+ x-=xIM; if (x<0) return IM;
+ if (x < xDG) return DG; else return MI;
+}
+
+inline int
+pickmax2(const double& xMM, const double& xX, const int& state)
+{
+ if (xMM > xX) return MM; else return state;
+}
+
+inline int
+pickmax3_GD(const double& xMM, const double& xDG, const double& xGD)
+{
+ char state;
+ double x;
+ if ( xMM>xDG) {state=MM; x=xMM;}
+ else {state=DG; x=xDG;}
+ if ( xGD>x) {state=GD; x=xGD;}
+ return state;
+}
+
+inline int
+pickmax3_IM(const double& xMM, const double& xMI, const double& xIM)
+{
+ char state;
+ double x;
+ if ( xMM>xMI) {state=MM; x=xMM;}
+ else {state=MI; x=xMI;}
+ if ( xIM>x) {state=IM; x=xIM;}
+ return state;
+}
+
+inline int
+pickmax6(const double& x0, const double& xMM, const double& xGD, const double& xIM, const double& xDG, const double& xMI)
+{
+ char state;
+ double x;
+ if ( x0 >xMM) {state=STOP; x=x0;}
+ else {state=MM; x=xMM;}
+ if ( xGD>x) {state=GD; x=xGD;}
+ if ( xIM>x) {state=IM; x=xIM;}
+ if ( xDG>x) {state=DG; x=xDG;}
+ if ( xMI>x) {state=MI; x=xMI;}
+ return state;
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+//// Functions that calculate P-values and probabilities
+/////////////////////////////////////////////////////////////////////////////////////
+
+
+//// Evaluate the CUMULATIVE extreme value distribution at point x
+//// p(s)ds = lamda * exp{ -exp[-lamda*(s-mu)] - lamda*(s-mu) } ds = exp( -exp(-x) - x) dx = p(x) dx
+//// => P(s>S) = integral_-inf^inf {p(x) dx} = 1 - exp{ -exp[-lamda*(S-mu)] }
+inline double
+Pvalue(double x, double a[])
+{
+ //a[0]=lamda, a[1]=mu
+ double h = a[0]*(x-a[1]);
+ return (h>10)? exp(-h) : double(1.0)-exp( -exp(-h));
+}
+
+inline double
+Pvalue(float x, float lamda, float mu)
+{
+ double h = lamda*(x-mu);
+ return (h>10)? exp(-h) : (double(1.0)-exp( -exp(-h)));
+}
+
+inline double
+logPvalue(float x, float lamda, float mu)
+{
+ double h = lamda*(x-mu);
+ return (h>10)? -h : (h<-2.5)? -exp(-exp(-h)): log( ( double(1.0) - exp(-exp(-h)) ) );
+}
+
+inline double
+logPvalue(float x, double a[])
+{
+ double h = a[0]*(x-a[1]);
+ return (h>10)? -h : (h<-2.5)? -exp(-exp(-h)): log( ( double(1.0) - exp(-exp(-h)) ) );
+}
+
+// Calculate probability of true positive : p_TP(score)/( p_TP(score)+p_FP(score) )
+// TP: same superfamily OR MAXSUB score >=0.1
+inline double
+Probab(Hit& hit)
+{
+ double s=-hit.score_aass;
+ double t;
+ if (s>200) return 100.0;
+ if (par.loc)
+ {
+ if (par.ssm && (hit.ssm1 || hit.ssm2) && par.ssw>0)
+ {
+ // local with SS
+ const double a=sqrt(6000.0);
+ const double b=2.0*2.5;
+ const double c=sqrt(0.12);
+ const double d=2.0*32.0;
+ t = a*exp(-s/b) + c*exp(-s/d);
+ }
+ else
+ {
+ // local no SS
+ const double a=sqrt(4000.0);
+ const double b=2.0*2.5;
+ const double c=sqrt(0.15);
+ const double d=2.0*34.0;
+ t = a*exp(-s/b) + c*exp(-s/d);
+ }
+ }
+ else
+ {
+ if ( (par.ssm>0) && (par.ssw>0) ) /* FIXME: was '&', should be '&&' (or not?) */
+ {
+ // global with SS
+ const double a=sqrt(4000.0);
+ const double b=2.0*3.0;
+ const double c=sqrt(0.13);
+ const double d=2.0*34.0;
+ t = a*exp(-s/b) + c*exp(-s/d);
+ }
+ else
+ {
+ // global no SS
+ const double a=sqrt(6000.0);
+ const double b=2.0*2.5;
+ const double c=sqrt(0.10);
+ const double d=2.0*37.0;
+ t = a*exp(-s/b) + c*exp(-s/d);
+ }
+
+ }
+
+ return 100.0/(1.0+t*t);
+}
+
+// #define Weff(Neff) (1.0+par.neffa*(Neff-1.0)+(par.neffb-4.0*par.neffa)/16.0*(Neff-1.0)*(Neff-1.0))
+
+// /////////////////////////////////////////////////////////////////////////////////////
+// // Merge HMM with next aligned HMM
+// /////////////////////////////////////////////////////////////////////////////////////
+// void Hit::MergeHMM(HMM& Q, HMM& t, float wk[])
+// {
+// int i,j; // position in query and target
+// int a; // amino acid
+// int step; // alignment position (step=1 is end)
+// float Weff_M, Weff_D, Weff_I;
+// for (step=nsteps; step>=2; step--) // iterate only to one before last alignment column
+// {
+// i = this->i[step];
+// j = this->j[step];
+// switch(states[step])
+// {
+// case MM:
+// Weff_M = Weff(t.Neff_M[j]-1.0);
+// Weff_D = Weff(t.Neff_D[j]-1.0);
+// Weff_I = Weff(t.Neff_I[j]-1.0);
+// for (a=0; a<20; a++) Q.f[i][a] += t.f[j][a]*wk[j]*Weff_M;
+// switch(states[step-1])
+// {
+// case MM: // MM->MM
+// Q.tr_lin[i][M2M]+= t.tr_lin[j][M2M]*wk[j]*Weff_M;
+// Q.tr_lin[i][M2D]+= t.tr_lin[j][M2D]*wk[j]*Weff_M;
+// Q.tr_lin[i][M2I]+= t.tr_lin[j][M2I]*wk[j]*Weff_M;
+// Q.tr_lin[i][D2M]+= t.tr_lin[j][D2M]*wk[j]*Weff_D;
+// Q.tr_lin[i][D2D]+= t.tr_lin[j][D2D]*wk[j]*Weff_D;
+// Q.tr_lin[i][I2M]+= t.tr_lin[j][I2M]*wk[j]*Weff_I;
+// Q.tr_lin[i][I2I]+= t.tr_lin[j][I2I]*wk[j]*Weff_I;
+// break;
+// case MI: // MM->MI
+// Q.tr_lin[i][M2D]+= t.tr_lin[j][M2M]*wk[j]*Weff_M;
+// Q.tr_lin[i][M2D]+= t.tr_lin[j][M2D]*wk[j]*Weff_M;
+// Q.tr_lin[i][M2M]+= t.tr_lin[j][M2I]*wk[j]*Weff_M;
+// Q.tr_lin[i][D2D]+= t.tr_lin[j][D2M]*wk[j]*Weff_D;
+// Q.tr_lin[i][D2D]+= t.tr_lin[j][D2D]*wk[j]*Weff_D;
+// Q.tr_lin[i][I2M]+= t.tr_lin[j][I2M]*wk[j]*Weff_I;
+// Q.tr_lin[i][I2I]+= t.tr_lin[j][I2I]*wk[j]*Weff_I;
+// break;
+// case DG: // MM->DG
+// Q.tr_lin[i][M2D]+= t.tr_lin[j][M2M]*wk[j]*Weff_M;
+// Q.tr_lin[i][M2D]+= t.tr_lin[j][M2D]*wk[j]*Weff_M;
+// Q.tr_lin[i][M2M]+= t.tr_lin[j][M2I]*wk[j]*Weff_M;
+// Q.tr_lin[i][D2D]+= t.tr_lin[j][D2M]*wk[j]*Weff_D;
+// Q.tr_lin[i][D2D]+= t.tr_lin[j][D2D]*wk[j]*Weff_D;
+// Q.tr_lin[i][I2M]+= t.tr_lin[j][I2M]*wk[j]*Weff_I;
+// Q.tr_lin[i][I2I]+= t.tr_lin[j][I2I]*wk[j]*Weff_I;
+// break;
+// case IM: // MM->IM
+// Q.tr_lin[i][M2I]+= t.tr_lin[j][M2M]*wk[j]*Weff_M;
+// Q.tr_lin[i][M2M]+= t.tr_lin[j][M2D]*wk[j]*Weff_M;
+// Q.tr_lin[i][M2I]+= t.tr_lin[j][M2I]*wk[j]*Weff_M;
+// Q.tr_lin[i][D2M]+= t.tr_lin[j][D2M]*wk[j]*Weff_D;
+// Q.tr_lin[i][D2D]+= t.tr_lin[j][D2D]*wk[j]*Weff_D;
+// Q.tr_lin[i][I2M]+= t.tr_lin[j][I2M]*wk[j]*Weff_I;
+// Q.tr_lin[i][I2I]+= t.tr_lin[j][I2I]*wk[j]*Weff_I;
+// break;
+// case GD: // MM->GD
+// Q.tr_lin[i][M2I]+= t.tr_lin[j][M2M]*wk[j]*Weff_M;
+// Q.tr_lin[i][M2M]+= t.tr_lin[j][M2D]*wk[j]*Weff_M;
+// Q.tr_lin[i][M2I]+= t.tr_lin[j][M2I]*wk[j]*Weff_M;
+// Q.tr_lin[i][D2M]+= t.tr_lin[j][D2M]*wk[j]*Weff_D;
+// Q.tr_lin[i][D2D]+= t.tr_lin[j][D2D]*wk[j]*Weff_D;
+// Q.tr_lin[i][I2M]+= t.tr_lin[j][I2M]*wk[j]*Weff_I;
+// Q.tr_lin[i][I2I]+= t.tr_lin[j][I2I]*wk[j]*Weff_I;
+// break;
+// }
+// break;
+
+// case MI: // if gap in template
+// Weff_I = Weff(t.Neff_I[j]-1.0);
+// switch(states[step-1])
+// {
+// case MI: // MI->MI
+// Q.tr_lin[i][M2M]+= t.tr_lin[j][I2I]*wk[j]*Weff_I;
+// break;
+// case MM: // MI->MM
+// Q.tr_lin[i][M2M]+= t.tr_lin[j][I2M]*wk[j]*Weff_I;
+// break;
+// }
+// break;
+
+// case DG:
+// Weff_M = Weff(t.Neff_M[j]-1.0);
+// Weff_D = Weff(t.Neff_D[j]-1.0);
+// Weff_I = Weff(t.Neff_I[j]-1.0);
+// switch(states[step-1])
+// {
+// case DG: // DG->DG
+// Q.tr_lin[i][D2D]+= t.tr_lin[j][M2M]*wk[j]*Weff_M;
+// Q.tr_lin[i][D2D]+= t.tr_lin[j][D2M]*wk[j]*Weff_D;
+// Q.tr_lin[i][D2D]+= t.tr_lin[j][D2D]*wk[j]*Weff_D;
+// Q.tr_lin[i][M2M]+= t.tr_lin[j][I2I]*wk[j]*Weff_I;
+// Q.tr_lin[i][M2D]+= t.tr_lin[j][I2M]*wk[j]*Weff_I;
+// break;
+// case MM: // DG->MM
+// Q.tr_lin[i][D2M]+= t.tr_lin[j][M2M]*wk[j]*Weff_M;
+// Q.tr_lin[i][D2D]+= t.tr_lin[j][M2D]*wk[j]*Weff_M;
+// Q.tr_lin[i][D2M]+= t.tr_lin[j][D2M]*wk[j]*Weff_D;
+// Q.tr_lin[i][D2D]+= t.tr_lin[j][D2D]*wk[j]*Weff_D;
+// Q.tr_lin[i][I2I]+= t.tr_lin[j][I2I]*wk[j]*Weff_I;
+// Q.tr_lin[i][M2M]+= t.tr_lin[j][I2M]*wk[j]*Weff_I;
+// break;
+// }
+// break;
+
+// case IM: // if gap in query
+// Weff_M = Weff(t.Neff_M[j]-1.0);
+// switch(states[step-1])
+// {
+// case IM: // IM->IM
+// Q.tr_lin[i][I2I]+= t.tr_lin[j][M2M]*wk[j]*Weff_M;
+// Q.tr_lin[i][I2M]+= t.tr_lin[j][M2D]*wk[j]*Weff_M;
+// Q.tr_lin[i][I2I]+= t.tr_lin[j][M2I]*wk[j]*Weff_M;
+// break;
+// case MM: // IM->MM
+// Weff_D = Weff(t.Neff_D[j]-1.0);
+// Weff_I = Weff(t.Neff_I[j]-1.0);
+// Q.tr_lin[i][I2M]+= t.tr_lin[j][M2M]*wk[j]*Weff_M;
+// Q.tr_lin[i][I2M]+= t.tr_lin[j][M2D]*wk[j]*Weff_M;
+// Q.tr_lin[i][I2I]+= t.tr_lin[j][M2I]*wk[j]*Weff_M;
+// Q.tr_lin[i][I2M]+= t.tr_lin[j][D2M]*wk[j]*Weff_D;
+// Q.tr_lin[i][D2D]+= t.tr_lin[j][D2D]*wk[j]*Weff_D;
+// Q.tr_lin[i][I2M]+= t.tr_lin[j][I2M]*wk[j]*Weff_I;
+// Q.tr_lin[i][I2I]+= t.tr_lin[j][I2I]*wk[j]*Weff_I;
+// break;
+// }
+// break;
+
+// case GD:
+// Weff_M = Weff(t.Neff_M[j]-1.0);
+// switch(states[step-1])
+// {
+// case GD: // GD->GD
+// Weff_I = Weff(t.Neff_I[j]-1.0);
+// Q.tr_lin[i][I2I]+= t.tr_lin[j][M2M]*wk[j]*Weff_M;
+// Q.tr_lin[i][I2M]+= t.tr_lin[j][M2D]*wk[j]*Weff_M;
+// Q.tr_lin[i][I2I]+= t.tr_lin[j][M2I]*wk[j]*Weff_M;
+// Q.tr_lin[i][I2I]+= t.tr_lin[j][I2M]*wk[j]*Weff_I;
+// Q.tr_lin[i][I2I]+= t.tr_lin[j][I2I]*wk[j]*Weff_I;
+// break;
+// case MM: // GD->MM
+// Weff_D = Weff(t.Neff_D[j]-1.0);
+// Weff_I = Weff(t.Neff_I[j]-1.0);
+// Q.tr_lin[i][I2M]+= t.tr_lin[j][M2M]*wk[j]*Weff_M;
+// Q.tr_lin[i][I2M]+= t.tr_lin[j][M2D]*wk[j]*Weff_M;
+// Q.tr_lin[i][I2I]+= t.tr_lin[j][M2I]*wk[j]*Weff_M;
+// Q.tr_lin[i][D2D]+= t.tr_lin[j][D2D]*wk[j]*Weff_D;
+// Q.tr_lin[i][I2M]+= t.tr_lin[j][I2M]*wk[j]*Weff_I;
+// Q.tr_lin[i][I2I]+= t.tr_lin[j][I2I]*wk[j]*Weff_I;
+// break;
+// }
+// break;
+
+// }
+// }
+// i = this->i[step];
+// j = this->j[step];
+// Weff_M = Weff(t.Neff_M[j]-1.0);
+// for (a=0; a<20; a++) Q.f[i][a] += t.f[j][a]*wk[j]*Weff_M;
+// }
+
+
+#ifdef CLUSTALO
+/* @* Hit::ClobberGlobal (eg, hit)
+ *
+ */
+void
+Hit::ClobberGlobal(void){
+
+ if (i){
+ //delete[] i;
+ i = NULL;
+ }
+ if (j){
+ //delete[] j;
+ j = NULL;
+ }
+ if (states){
+ //delete[] states;
+ states = NULL;
+ }
+ if (S){
+ //delete[] S;
+ S = NULL;
+ }
+ if (S_ss){
+ //delete[] S_ss;
+ S_ss = NULL;
+ }
+ if (P_posterior){
+ //delete[] P_posterior;
+ P_posterior = NULL;
+ }
+ if (Xcons){
+ //delete[] Xcons;
+ Xcons = NULL;
+ }
+ // delete[] l; l = NULL;
+ i = j = NULL;
+ states = NULL;
+ S = S_ss = P_posterior = NULL;
+ Xcons = NULL;
+ if (irep==1) // if irep>1 then longname etc point to the same memory locations as the first repeat.
+ { // but these have already been deleted.
+ // printf("Delete name = %s\n",name);//////////////////////////
+ //delete[] longname;
+ longname = NULL;
+ //delete[] name;
+ name = NULL;
+ //delete[] file;
+ file = NULL;
+ //delete[] dbfile;
+ dbfile = NULL;
+ /*for (int k=0; k<n_display; k++)
+ {
+ delete[] sname[k]; sname[k] = NULL;
+ delete[] seq[k]; seq[k] = NULL;
+ }*/
+ //delete[] sname;
+ sname = NULL;
+ //delete[] seq;
+ seq = NULL;
+ }
+
+ score = score_sort = score_aass = 0.0;
+ Pval = Pvalt = Eval = Probab = 0;
+ Pforward = sum_of_probs = 0.00;
+ L = irep = nrep = n_display = nsteps = 0;
+ i1 = i2 = j1 = j2 = matched_cols = min_overlap = 0;
+}
+#endif
+
+
+/*
+ * EOF hhhit-C.h
+ */
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhhit.h 243 2011-05-31 13:49:19Z fabian $
+ */
+
+// hhhit.h
+
+//////////////////////////////////////////////////////////////////////////////
+/* Describes an alignment of two profiles.
+ Used as list element in Hits : List<Hit> */
+//////////////////////////////////////////////////////////////////////////////
+class Hit
+{
+ public:
+ char* longname; // Name of HMM
+ char* name; // One-word name of HMM
+ char* file; // Basename (with path, without extension) of alignment file that was used to construct the HMM
+ // (path from db-file is prepended to FILE record in HMM file!)
+ char fam[IDLEN]; // family ID (derived from name) (FAM field)
+ char sfam[IDLEN]; // superfamily ID (derived from name)
+ char fold[IDLEN]; // fold ID (derived from name)
+ char cl[IDLEN]; // class ID (derived from name)
+ int index; // index of HMM in order of reading in (first=0)
+ char* dbfile; // full database file name from which HMM was read
+ long ftellpos; // start position of HMM in database file
+
+ float score; // Score of alignment (i.e. of Viterbi path)
+ float score_sort; // score to sort hits in output list (negative means first/best!)
+ float score_aass; // first: just hit.score, then hit.logPval-SSSCORE2NATLOG*hit.score_ss;(negative means best!)
+ float score_ss; // Part of score due to secondary structure
+ float Pval; // P-value for whole protein based on score distribution of query
+ float Pvalt; // P-value for whole protein based on score distribution of template
+ float logPval; // natural logarithm of Pval
+ float logPvalt; // natural logarithm of Pvalt
+ float Eval; // E-value for whole protein
+ float Probab; // probability in % for a positive (depends only on score)
+ float weight; // weight of hit for P-value calculation (= 1/#HMMs-in-family/#families-in-superfamily)
+ double Pforward; // scaled total forward probability : Pforward * Product_{i=1}^{Lq+1}(scale[i])
+
+/* float score_comp; // compositional similarity score */
+/* float logPcomp; // natural logarithm of Pvalue for compositional similarity score */
+/* float Prep; // P-value for single-repeat hit */
+/* float Erep; // E-value for single-repeat hit */
+/* float logPrep; // natural logarithm of P-value for single-repeat hit */
+ float E1val; // E-value for whole protein from transitive scoring
+ float logP1val; // natural logarithm of P1val, the transitive P-value
+
+ int L; // Number of match states in template
+ int irep; // Index of single-repeat hit (1: highest scoring repeat hit)
+ int nrep; // Number of single-repeat hits with one template
+
+ int n_display; // number of sequences stored for display of alignment
+ char** sname; // names of stored sequences
+ char** seq; // residues of stored sequences (first at pos 1)
+ int nss_dssp; // index of dssp secondary structure sequence in seq[]
+ int nsa_dssp; // index of of dssp solvent accessibility in seq[]
+ int nss_pred; // index of dssp secondary structure sequence in seq[]
+ int nss_conf; // index of dssp secondary structure sequence in seq[]
+ int nfirst; // index of query sequence in seq[]
+ int ncons; // index of consensus sequence
+
+ int nsteps; // index for last step in Viterbi path; (first=1)
+ int* i; // i[step] = query match state at step of Viterbi path
+ int* j; // j[step] = template match state at step of Viterbi path
+ char* states; // state at step of Viterbi path 0: Start 1: M(MM) 2: A(-D) 3: B(IM) 4: C(D-) 5 D(MI)
+ float* S; // S[step] = match-match score contribution at alignment step
+ float* S_ss; // S_ss[step] = secondary structure score contribution
+ float* P_posterior; // P_posterior[step] = posterior prob for MM states (otherwise zero)
+ char* Xcons; // consensus sequence for aligned states in internal representation (A=0 R=1 N=2 D=3 ...)
+ int i1; // First aligned residue in query
+ int i2; // Last aligned residue in query
+ int j1; // First aligned residue in template
+ int j2; // Last aligned residue in template
+ int matched_cols; // number of matched columns in alignment against query
+ int ssm1; // SS scoring AFTER alignment? 0:no 1:yes; t->dssp q->psipred 2:yes; q->dssp t->psipred
+ int ssm2; // SS scoring DURING alignment? 0:no 1:yes; t->dssp q->psipred 2:yes; q->dssp t->psipred
+ char self; // 0: align two different HMMs 1: align HMM with itself
+ int min_overlap; // Minimum overlap between query and template
+ float sum_of_probs; // sum of probabilities for Maximum ACcuracy alignment (if dssp states defined, only aligned pairs with defined dssp state contribute to sum)
+ float Neff_HMM; // Diversity of underlying alignment
+
+ // Constructor (only set pointers to NULL)
+ Hit();
+ ~Hit(){};
+
+ // Free all allocated memory (to delete list of hits)
+ void Delete();
+
+ // Allocate/delete memory for dynamic programming matrix
+ void AllocateBacktraceMatrix(int Nq, int Nt);
+ void DeleteBacktraceMatrix(int Nq);
+ void AllocateForwardMatrix(int Nq, int Nt);
+ void DeleteForwardMatrix(int Nq);
+ void AllocateBackwardMatrix(int Nq, int Nt);
+ void DeleteBackwardMatrix(int Nq);
+
+ // Compare an HMM with overlapping subalignments
+ void Viterbi(HMM& q, HMM& t, float** Sstruc=NULL);
+
+ // Compare two HMMs with each other in lin space
+ int Forward(HMM& q, HMM& t, float** Pstruc=NULL);
+
+ // Compare two HMMs with each other in lin space
+ int Backward(HMM& q, HMM& t);
+
+ // Find maximum accuracy alignment (after running Forward and Backward algorithms)
+ void MACAlignment(HMM& q, HMM& t);
+
+ // Trace back alignment of two profiles based on matrices bXX[][]
+ void Backtrace(HMM& q, HMM& t);
+
+ // Trace back alignment of two profiles based on matrices bXX[][]
+ void StochasticBacktrace(HMM& q, HMM& t, char maximize=0);
+
+ // Trace back MAC alignment of two profiles based on matrix bMM[][]
+ void BacktraceMAC(HMM& q, HMM& t);
+
+ // Calculate secondary structure score between columns i and j of two HMMs (query and template)
+ inline float ScoreSS(HMM& q, HMM& t, int i, int j, int ssm);
+
+ // Calculate secondary structure score between columns i and j of two HMMs (query and template)
+ inline float ScoreSS(HMM& q, HMM& t, int i, int j);
+
+ // Calculate total score (including secondary structure score and compositional bias correction
+ inline float ScoreTot(HMM& q, HMM& t, int i, int j);
+
+ // Calculate score (excluding secondary structure score and compositional bias correction
+ inline float ScoreAA(HMM& q, HMM& t, int i, int j);
+
+ // Comparison (used to sort list of hits)
+ int operator<(const Hit& hit2) {return score_sort<hit2.score_sort;}
+
+ // Merge HMM with next aligned HMM
+ void MergeHMM(HMM& Q, HMM& t, float wk[]);
+
+#ifdef CLUSTALO
+ void ClobberGlobal(void);
+#endif
+
+
+ double** B_MM; // Backward matrices
+
+private:
+ char state; // 0: Start/STOP state 1: MM state 2: GD state (-D) 3: IM state 4: DG state (D-) 5 MI state
+ char** bMM; // (backtracing) bMM[i][j] = STOP:start of alignment MM:prev was MM GD:prev was GD etc
+ char** bGD; // (backtracing) bMM[i][j] = STOP:start of alignment MM:prev was MM SAME:prev was GD
+ char** bDG; // (backtracing)
+ char** bIM; // (backtracing)
+ char** bMI; // (backtracing)
+ char** cell_off; // cell_off[i][j]=1 means this cell will get score -infinity
+
+ double** F_MM; // Forward matrices
+ double** F_GD; // F_XY[i][j] * Prod_1^i(scale[i])
+ double** F_DG; // = Sum_x1..xl{ P(HMMs aligned up to Xi||Yj co-emmitted x1..xl ) / (Prod_k=1^l f(x_k)) }
+ double** F_IM; // end gaps are not penalized!
+ double** F_MI; //
+ double* scale; //
+
+ double** B_GD; // B_XY[i][j] * Prod_i+1^(L+1) (scale[i])
+ double** B_DG; // = Sum_x2..xl{ P(HMMs aligned from Xi||Yj to end co-emmitted x2..xl ) / (Prod_k=2^l f(x_k)) }
+ double** B_IM; // end gaps are not penalized!
+ double** B_MI; //
+
+ void InitializeBacktrace(HMM& q, HMM& t);
+ void InitializeForAlignment(HMM& q, HMM& t);
+};
+
+
+double Pvalue(double x, double a[]);
+double Pvalue(float x, float lamda, float mu);
+double logPvalue(float x, float lamda, float mu);
+double logPvalue(float x, double a[]);
+double Probab(Hit& hit);
+
+
+
+
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhhitlist-C.h 243 2011-05-31 13:49:19Z fabian $
+ */
+
+// hhhitlist.C
+
+#ifndef MAIN
+#define MAIN
+#include <iostream> // cin, cout, cerr
+#include <fstream> // ofstream, ifstream
+#include <stdio.h> // printf
+#include <stdlib.h> // exit
+#include <string> // strcmp, strstr
+#include <math.h> // sqrt, pow
+#include <limits.h> // INT_MIN
+#include <float.h> // FLT_MIN
+#include <time.h> // clock
+#include <ctype.h> // islower, isdigit etc
+using std::ios;
+using std::ifstream;
+using std::ofstream;
+using std::cout;
+using std::cerr;
+using std::endl;
+#include "util-C.h" // imax, fmax, iround, iceil, ifloor, strint, strscn, strcut, substr, uprstr, uprchr, Basename etc.
+#include "list.h" // list data structure
+#include "hash.h" // hash data structure
+#include "hhdecl-C.h" // constants, class
+#include "hhutil-C.h" // imax, fmax, iround, iceil, ifloor, strint, strscn, strcut, substr, uprstr, uprchr, Basename etc.
+#include "hhhmm.h" // class HMM
+#include "hhalignment.h" // class Alignment
+#include "hhhit.h"
+#include "hhhalfalignment.h"
+#include "hhfullalignment.h"
+#endif
+
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+//// Methods of class HitList
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Print summary listing of hits
+ */
+void
+HitList::PrintHitList(HMM& q, char* outfile)
+{
+ Hit hit;
+ int nhits=0;
+ char str[NAMELEN]="";
+
+ FILE* outf=NULL;
+ if (strcmp(outfile,"stdout"))
+ {
+ outf=fopen(outfile,"w");
+ if (!outf) OpenFileError(outfile);
+ }
+ else
+ outf = stdout;
+
+
+ fprintf(outf,"Query %s\n",q.longname);
+// fprintf(outf,"Family %s\n",q.fam);
+ fprintf(outf,"Match_columns %i\n",q.L);
+ fprintf(outf,"No_of_seqs %i out of %i\n",q.N_filtered,q.N_in);
+ fprintf(outf,"Neff %-4.1f\n",q.Neff_HMM);
+ fprintf(outf,"Searched_HMMs %i\n",N_searched);
+
+ // Print date stamp
+ time_t* tp=new(time_t);
+ *tp=time(NULL);
+ fprintf(outf,"Date %s",ctime(tp));
+ delete (tp); (tp) = NULL;
+
+ // Print command line
+ fprintf(outf,"Command ");
+ for (int i=0; i<par.argc; i++)
+ if (strlen(par.argv[i])<=par.maxdbstrlen)
+ fprintf(outf,"%s ",par.argv[i]);
+ else
+ fprintf(outf,"<%i characters> ",(int)strlen(par.argv[i]));
+ fprintf(outf,"\n\n");
+
+#ifdef WINDOWS
+ if (par.trans)
+ fprintf(outf," No Hit Prob E-trans E-value Score SS Cols Query HMM Template HMM\n");
+ else
+ fprintf(outf," No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM\n");
+#else
+ if (par.trans)
+ fprintf(outf," No Hit Prob E-trans E-value Score SS Cols Query HMM Template HMM\n");
+ else
+ fprintf(outf," No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM\n");
+#endif
+
+ Reset();
+ while (!End()) // print hit list
+ {
+ hit = ReadNext();
+ if (nhits>=par.Z) break; //max number of lines reached?
+ if (nhits>=par.z && hit.Probab < par.p) break;
+ if (nhits>=par.z && hit.Eval > par.E) continue;
+// if (hit.matched_cols <=1) continue; // adding this might get to intransparent... analogous statement in PrintAlignments
+ nhits++;
+ sprintf(str,"%3i %-30.30s ",nhits,hit.longname);
+
+
+#ifdef WINDOWS
+ if (par.trans) // Transitive scoring
+ fprintf(outf,"%-34.34s %5.1f %8.2G %8.2G %6.1f %5.1f %4i ",str,hit.Probab,hit.E1val,hit.Eval,hit.score,hit.score_ss,hit.matched_cols);
+ else // Normal scoring
+ fprintf(outf,"%-34.34s %5.1f %8.2G %8.2G %6.1f %5.1f %4i ",str,hit.Probab,hit.Eval,hit.Pval,hit.score,hit.score_ss,hit.matched_cols);
+#else
+ if (par.trans) // Transitive scoring
+ fprintf(outf,"%-34.34s %5.1f %7.2G %7.2G %6.1f %5.1f %4i ",str,hit.Probab,hit.E1val,hit.Eval,hit.score,hit.score_ss,hit.matched_cols);
+ else // Normal scoring
+ fprintf(outf,"%-34.34s %5.1f %7.2G %7.2G %6.1f %5.1f %4i ",str,hit.Probab,hit.Eval,hit.Pval,hit.score,hit.score_ss,hit.matched_cols);
+#endif
+
+ sprintf(str,"%4i-%-4i ",hit.i1,hit.i2);
+ fprintf(outf,"%-10.10s",str);
+ sprintf(str,"%4i-%-4i",hit.j1,hit.j2);
+ fprintf(outf,"%-9.9s(%i)\n",str,hit.L);
+ } //end print hit list
+ fprintf(outf,"\n");
+ if (strcmp(outfile,"stdout")) fclose(outf);
+}
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Print alignments of query sequences against hit sequences
+ */
+int
+HitList::PrintAlignments(
+
+
+#ifdef CLUSTALO
+ char **ppcFirstProf, char **ppcSecndProf,
+#endif
+ HMM& q, char* outfile, char outformat)
+{
+ Hit hit;
+ FullAlignment qt_ali(par.nseqdis+10); // maximum 10 annotation (pseudo) sequences (ss_dssp, sa_dssp, ss_pred, ss_conf, consens,...)
+ int nhits=0;
+
+#ifndef CLUSTALO_NOFILE
+ FILE* outf=NULL;
+ if (strcmp(outfile,"stdout"))
+ {
+ if (outformat==0)
+ outf=fopen(outfile,"a"); //append to summary hitlist
+ else
+ outf=fopen(outfile,"w"); //open for writing
+ if (!outf) OpenFileError(outfile);
+ }
+ else
+ outf = stdout;
+#endif
+
+ Reset();
+ while (!End()) // print hit list
+ {
+ if (nhits>=par.B) break; //max number of lines reached?
+ hit = ReadNext();
+ if (nhits>=par.b && hit.Probab < par.p) break;
+ if (nhits>=par.b && hit.Eval > par.E) continue;
+ // // adding this might get to intransparent...
+ // // analogous statement in PrintHitlist and hhalign.C
+ // if (hit.matched_cols <=1) continue;
+ nhits++;
+
+ // Build double alignment of query against template sequences
+ int iBuildRet = qt_ali.Build(q,hit);
+ if (iBuildRet != OK){ /* FS, r241 -> r243 */
+ fprintf(stderr, "%s:%s:%d: qt_ali.Build failed\n",
+ __FUNCTION__, __FILE__, __LINE__);
+ return FAILURE;
+ }
+
+#ifndef CLUSTALO
+ // Print out alignment
+ if (outformat==0) // HHR format
+ {
+ fprintf(outf,"No %-3i\n",nhits);
+ qt_ali.PrintHeader(outf,q,hit);
+ qt_ali.PrintHHR(outf,hit);
+ }
+ else if (outformat==1) // FASTA format
+ {
+ fprintf(outf,"# No %-3i\n",nhits);
+ qt_ali.PrintFASTA(outf,hit);
+ }
+ else if(outformat==2) // A2M format
+ {
+ fprintf(outf,"# No %-3i\n",nhits);
+ qt_ali.PrintA2M(outf,hit);
+ }
+ else // A3m format
+ {
+ fprintf(outf,"# No %-3i\n",nhits);
+ qt_ali.PrintA3M(outf,hit);
+ }
+#else
+ qt_ali.OverWriteSeqs(ppcFirstProf, ppcSecndProf);
+#endif
+
+ qt_ali.FreeMemory();
+ }
+#ifndef CLUSTALO_NOFILE
+ if (strcmp(outfile,"stdout")) fclose(outf);
+#endif
+
+ return OK;
+
+} /* this is the end of HitList::PrintAlignments() */
+
+
+
+
+
+////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Return the ROC_5 score for optimization
+ * (changed 28.3.08 by Michael & Johannes)
+ */
+void
+HitList::Optimize(HMM& q, char* buffer)
+{
+ const int NFAM =5; // calculate ROC_5 score
+ const int NSFAM=5; // calculate ROC_5 score
+ int roc=0; // ROC score
+ int fam=0; // number of hits from same family (at current threshold)
+ int not_fam=0; // number of hits not from same family
+ int sfam=0; // number of hits from same suporfamily (at current threshold)
+ int not_sfam=0; // number of hits not from same superfamily
+ Hit hit;
+
+ SortList();
+ Reset();
+ while (!End())
+ {
+ hit = ReadNext();
+ if (!strcmp(hit.fam,q.fam)) fam++; // query and template from same superfamily? => positive
+ else if (not_fam<NFAM) // query and template from different family? => negative
+ {
+ not_fam++;
+ roc += fam;
+ }
+ if (!strcmp(hit.sfam,q.sfam)) sfam++; // query and template from same superfamily? => positive
+ else if (not_sfam<NSFAM) // query and template from different superfamily? => negative
+ {
+ not_sfam++;
+ roc += sfam;
+ }
+// printf("qfam=%s tfam=%s qsfam=%s tsfam=%s fam=%-2i not_fam=%3i sfam=%-3i not_sfam=%-5i roc=%-3i\n",q.fam,hit.fam,q.sfam,hit.sfam,fam,not_fam,sfam,not_sfam,roc);
+ }
+
+ // Write ROC score to file or stdout
+ FILE* buf=NULL;
+ if (strcmp(par.buffer,"stdout"))
+ {
+ buf=fopen(buffer,"w");
+ if (!buf) OpenFileError(par.buffer);
+ }
+ else
+ buf = stdout;
+
+ fprintf(buf,"%f\n",float(roc)/float(fam*NFAM+sfam*NSFAM)); // must be between 0 and 1
+ if (v>=2) printf("ROC=%f\n",float(roc)/float(fam*NFAM+sfam*NSFAM));
+ fclose(buf);
+}
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Print score distribution into file score_dist
+ */
+void
+HitList::PrintScoreFile(HMM& q)
+{
+ int i=0, n;
+ FILE* scoref=NULL;
+ Hit hit;
+ Hash<int> twice(10000); // make sure only one hit per HMM is listed
+ twice.Null(-1);
+
+ if (strcmp(par.scorefile,"stdout"))
+ {
+ scoref=fopen(par.scorefile,"w");
+ if (!scoref)
+ {cerr<<endl<<"WARNING from "<<par.argv[0]<<": could not open \'"<<par.scorefile<<"\'\n"; return;}
+ }
+ else
+ scoref = stdout;
+ Reset();
+ fprintf(scoref,"NAME %s\n",q.longname);
+ fprintf(scoref,"FAM %s\n",q.fam);
+ fprintf(scoref,"FILE %s\n",q.file);
+ fprintf(scoref,"LENG %i\n",q.L);
+ fprintf(scoref,"\n");
+//fprintf(scoref,"TARGET REL LEN COL LOG-PVA S-TOT MS NALI\n");
+
+//For hhformat, the PROBAB field has to start at position 41 !!
+// ----+----1----+----2----+----3----+----4----+----
+ fprintf(scoref,"TARGET FAMILY REL LEN COL LOG-PVA S-AASS PROBAB SCORE\n");
+ // d153l__ 5 185 185 287.82 464.22 100.00
+ // d1qsaa2 3 168 124 145.55 239.22 57.36
+ while (!End())
+ {
+ i++;
+ hit = ReadNext();
+ if (twice[hit.name]==1) continue; // better hit with same HMM has been listed already
+ twice.Add(hit.name,1);
+ //if template and query are from the same superfamily
+ if (!strcmp(hit.name,q.name)) n=5;
+ else if (!strcmp(hit.fam,q.fam)) n=4;
+ else if (!strcmp(hit.sfam,q.sfam)) n=3;
+ else if (!strcmp(hit.fold,q.fold)) n=2;
+ else if (!strcmp(hit.cl,q.cl)) n=1;
+ else n=0;
+ fprintf(scoref,"%-10s %-10s %1i %3i %3i %s %7.2f %6.2f %7.2f\n",hit.name,hit.fam,n,hit.L,hit.matched_cols,sprintg(-1.443*hit.logPval,7),-hit.score_aass,hit.Probab,hit.score);
+ }
+ fclose(scoref);
+}
+
+
+inline double
+logPvalue_HHblast(double s, double corr)
+{
+ return -s*(1.0-0.5*corr) + (1.0-corr)*log(1.0+s);
+// return -s*(1.0-0.5*corr) + log( 1.0+(1.0-corr)*s );
+// return -s*(1.0-0.5*corr) + log( 1.0+(1.0-corr)*(1.0-0.5*corr)*s );
+}
+
+inline double
+Pvalue_HHblast(double s, double corr)
+{
+ return exp(-s*(1.0-0.5*corr)) * pow(1.0+s,1.0-corr);
+// return exp(-s*(1.0-0.5*corr)) * ( 1.0+(1.0-corr)*s );
+// return exp(-s*(1.0-0.5*corr)) * ( 1.0+(1.0-corr)*(1.0-0.5*corr)*s );
+}
+
+inline double
+logLikelihood_HHblast(double s, double corr)
+{
+ if (s<0.0) { s=0.0; if (corr<1E-5) corr=1E-5; else if (corr>0.99999) corr=0.99999; }
+ else { if (corr<0.0) corr=0.0; else if (corr>1.0) corr=1.0; }
+ return -s*(1.0-0.5*corr) - corr*log(1.0+s) + log(s*(1.0-0.5*corr)+0.5*corr);
+ // return -s*(1.0-0.5*corr) + log( s*(1.0-corr)*(1.0-0.5*corr)+0.5*corr );
+ // return -s*(1.0-0.5*corr) + log((s*(1.0-corr)*(1.0-0.5*corr)+corr)*(1.0-0.5*corr));
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Evaluate the *negative* log likelihood for the order statistic of the uniform distribution
+ * for the best 10% of hits (vertex v = (corr,offset) )
+ * The k'th order statistic for X~Uniform is p:=X^(k)~Beta(k,n-k+1) = const*p^(k-1)*(1-p)^(n-k)
+ * Needed to fit the correlation and score offset in HHblast
+*/
+double
+HitList::RankOrderFitCorr(double* v)
+{
+ double sum=0.0;
+// printf("%8.2G %8.2G %i\n",v[0],v[1],Nprof);
+ int i1 = imin(Nprof,imax(50,int(0.05*Nprof)));
+ for (int i=0; i<i1; i++)
+ {
+ double p = Pvalue_HHblast(score[i]+v[1],v[0]);
+// sum -= (1.0-double(i)/double(i1)) * weight[i] * ( double(i)*log(p) + (Nprof-i-1.0)*log(1.0-p) );
+ float diff = p-(float(i)+1.0)/(Nprof+1.0);
+ sum += (1.0-double(i)/double(i1)) * weight[i]*diff*diff*(Nprof+1.0)*(Nprof+1.0)*(Nprof+2.0)/(i+10.0)/(Nprof-i);
+// printf("%-3i Pval=%7.5f Preal=%7.5f diff=%7.5f sum=%7.5f\n",i,p,float(i+1)/(1.0+Nprof),diff,sum);
+ }
+ return sum;
+}
+
+/**
+ * @brief Static wrapper-function for calling the nonstatic member function RankOrderFitCorr()
+ * ( see http://www.newty.de/fpt/callback.html#member )
+ */
+double
+HitList::RankOrderFitCorr_static(void* pt2hitlist, double* v)
+{
+ HitList* mySelf = (HitList*) pt2hitlist; // explicitly cast to a pointer to Hitlist
+ return mySelf->RankOrderFitCorr(v); // call member function
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Evaluate the *negative* log likelihood of the data at the vertex v = (corr,offset)
+ * Needed to fit the correlation and score offset in HHblast
+ */
+double
+HitList::LogLikelihoodCorr(double* v)
+{
+ double sum=0.0;
+// printf("%8.2G %8.2G %i\n",v[0],v[1],Nprof);
+ for (int i=0; i<Nprof; i++)
+ {
+ sum -= weight[i]*logLikelihood_HHblast(score[i]+v[1],v[0]);
+// printf("%-3i Pval=%7.5f Preal=%7.5f diff=%7.5f rmsd=%7.5f sum=%7.5f\n",i,Pvalue_HHblast(score[i],v[0]),float(i)/(1.0+Nprof),x,sqrt(sum/sumw),sum);
+ }
+ return sum;
+}
+
+/**
+ * @brief Static wrapper-function for calling the nonstatic member function LogLikelihoodCorr()
+ * ( see http://www.newty.de/fpt/callback.html#member )
+ */
+double
+HitList::LogLikelihoodCorr_static(void* pt2hitlist, double* v)
+{
+ HitList* mySelf = (HitList*) pt2hitlist; // explicitly cast to a pointer to Hitlist
+ return mySelf->LogLikelihoodCorr(v); // call member function
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Evaluate the *negative* log likelihood of the data at the vertex v = (lamda,mu)
+ * p(s) = lamda * exp{ -exp[-lamda*(s-mu)] - lamda*(s-mu) } = lamda * exp( -exp(-x) - x)
+ */
+double
+HitList::LogLikelihoodEVD(double* v)
+{
+ double sum=0.0, sumw=0.0;
+ for (int i=0; i<Nprof; i++)
+ {
+ double x = v[0]*(score[i]-v[1]);
+ sum += weight[i]*(exp(-x)+x);
+ sumw += weight[i];
+ }
+ return sum - sumw*log(v[0]);
+}
+
+/**
+ * @brief Static wrapper-function for calling the nonstatic member function LogLikelihoodEVD()
+ * ( see http://www.newty.de/fpt/callback.html#member )
+ */
+double
+HitList::LogLikelihoodEVD_static(void* pt2hitlist, double* v)
+{
+ HitList* mySelf = (HitList*) pt2hitlist; // explicitly cast to a pointer to Hitlist
+ return mySelf->LogLikelihoodEVD(v); // call member function
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Subroutine to FindMin: try new point given by highest point ihigh and fac and replace ihigh if it is lower
+ */
+double
+HitList::TryPoint(const int ndim, double* p, double* y, double* psum, int ihigh, double fac, double (*Func)(void* pt2hitlist, double* v))
+{
+ // New point p_try = p_c + fac*(p_high-p_c),
+ // where p_c = ( sum_i (p_i) - p_high)/ndim is the center of ndim other points
+ // => p_try = fac1*sum_i(p_i) + fac2*p_high
+ double fac1=(1.-fac)/ndim;
+ double fac2=fac-fac1;
+ double ptry[ndim]; //new point to try out
+ double ytry; //function value of new point
+ int j; //index for the ndim parameters
+
+ for (j=0; j<ndim; j++)
+ ptry[j]=psum[j]*fac1+p[ihigh*ndim+j]*fac2;
+ ytry = (*Func)(this,ptry);
+ if (ytry<=y[ihigh])
+ {
+// if (v>=4) printf("Trying: %-7.3f %-7.3f %-7.3f -> accept\n",ptry[0],ptry[1],ytry);
+ y[ihigh]=ytry;
+ for (j=0; j<ndim; j++)
+ {
+ psum[j] += ptry[j]-p[ihigh*ndim+j]; //update psum[j]
+ p[ihigh*ndim+j]=ptry[j]; //replace p[ihigh] with ptry
+ } //Note: ihigh is now not highest point anymore!
+ }
+// else if (v>=4) printf("Trying: %-7.3f %-7.3f %-7.3f -> reject\n",ptry[0],ptry[1],ytry);
+
+ return ytry;
+}
+
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Find minimum with simplex method of Nelder and Mead (1965)
+ */
+float
+HitList::FindMin(const int ndim, double* p, double* y, double tol, int& nfunc, double (*Func)(void* pt2hitlist, double* v))
+{
+ const int MAXNFUNC=99; //maximum allowed number of function evaluations
+ int ihigh; //index of highest point on simplex
+ int inext; //index of second highest point on simplex
+ int ilow; //index of lowest point on simplex
+ int i; //index for the ndim+1 points
+ int j; //index for the ndim parameters
+ double rtol; //tolerance: difference of function value between highest and lowest point of simplex
+ double temp; //dummy
+ double ytry; //function value of trial point
+ double psum[ndim]; //psum[j] = j'th coordinate of sum vector (sum over all vertex vectors)
+
+ nfunc=0; //number of function evaluations =0
+ //Calculate sum vector psum[j]
+ for (j=0; j<ndim; j++)
+ {
+ psum[j]=p[j];
+ for (i=1; i<ndim+1; i++)
+ psum[j]+=p[i*ndim+j];
+ }
+
+ // Repeat finding better points in simplex until rtol<tol
+ while(1)
+ {
+ // Find indices for highest, next highest and lowest point
+ ilow=0;
+ if (y[0]>y[1]) {inext=1; ihigh=0;} else {inext=0; ihigh=1;}
+ for (i=0; i<ndim+1; i++)
+ {
+ if (y[i]<=y[ilow]) ilow=i;
+ if (y[i]>y[ihigh]) {inext=ihigh; ihigh=i;}
+ else if (y[i]>y[inext] && i!= ihigh) inext=i;
+ }
+
+ // If tolerance in y is smaller than tol swap lowest point to index 0 and break -> return
+ rtol = 2.*fabs(y[ihigh]-y[ilow]) / (fabs(y[ihigh])+fabs(y[ilow])+1E-10);
+ if (rtol<tol)
+ {
+ temp=y[ilow]; y[ilow]=y[0]; y[0]=temp;
+ for (j=0; j<ndim; j++)
+ {
+ temp=p[ilow*ndim+j]; p[ilow*ndim+j]=p[j]; p[j]=temp;
+ }
+ break;
+ }
+
+ // Max number of function evaluations exceeded?
+ if (nfunc>=MAXNFUNC )
+ {
+ if (v) fprintf(stderr,"\nWARNING: maximum likelihood fit of score distribution did not converge.\n");
+ return 1;
+ }
+
+ nfunc+=2;
+ // Point-reflect highest point on the center of gravity p_c of the other ndim points of the simplex
+ if (v>=3) printf("%3i %-7.3f %-7.3f %-12.8f %-9.3E\n",nfunc,p[ilow*ndim],p[ilow*ndim+1],y[ilow],rtol);
+// if (v>=2) printf(" %3i %-9.3E %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f\n",nfunc,rtol,p[ilow*ndim],p[ilow*ndim+1],y[ilow],p[inext*ndim],p[inext*ndim+1],y[inext],p[ihigh*ndim],p[ihigh*ndim+1],y[ihigh]);
+ ytry = TryPoint(ndim,p,y,psum,ihigh,-1.0,Func); //reflect highest point on p_c
+
+ if (ytry<=y[ilow])
+ {
+ ytry = TryPoint(ndim,p,y,psum,ihigh,2.0,Func); //expand: try new point 2x further away from p_c
+// if (v>=2) printf("Expanded: %3i %-9.3E %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f\n",nfunc,rtol,p[ilow*ndim],p[ilow*ndim+1],y[ilow],p[inext*ndim],p[inext*ndim+1],y[inext],p[ihigh*ndim],p[ihigh*ndim+1],y[ihigh]);
+ }
+ else if (ytry>=y[inext])
+ {
+ // The new point is worse than the second worst point
+ temp=y[ihigh];
+ ytry=TryPoint(ndim,p,y,psum,ihigh,0.5,Func); //contract simplex by 0.5 along (p_high-p_c
+// if (v>=2) printf("Compressed:%3i %-9.3E %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f\n",nfunc,rtol,p[ilow*ndim],p[ilow*ndim+1],y[ilow],p[inext*ndim],p[inext*ndim+1],y[inext],p[ihigh*ndim],p[ihigh*ndim+1],y[ihigh]);
+ if (ytry>=temp)
+ {
+ // Trial point is larger than worst point => contract simplex by 0.5 towards lowest point
+ for (i=0; i<ndim+1; i++)
+ {
+ if (i!=ilow)
+ {
+ for (j=0; j<ndim; j++)
+ p[i*ndim+j]=0.5*(p[i*ndim+j]+p[ilow+j]);
+ y[i] = (*Func)(this,p+i*ndim);
+// y[i] = (*Func)(p+i*ndim);
+ }
+ }
+ nfunc+=ndim;
+// if (v>=2) printf("Contracted:%3i %-9.3E %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f %-7.3f\n",nfunc,rtol,p[ilow*ndim],p[ilow*ndim+1],y[ilow],p[inext*ndim],p[inext*ndim+1],y[inext],p[ihigh*ndim],p[ihigh*ndim+1],y[ihigh]);
+
+ //Calculate psum[j]
+ for (j=0; j<ndim; j++)
+ {
+ psum[j]=p[j];
+ for (i=1; i<ndim+1; i++)
+ psum[j]+=p[i*ndim+j];
+ }
+ }
+ }
+ else nfunc--;
+ }
+ return (float)rtol;
+}
+
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Do a maximum likelihod fit of the scores with an EV distribution with parameters lamda and mu
+ */
+void
+HitList::MaxLikelihoodEVD(HMM& q, int nbest)
+{
+ double tol=1E-6; // Maximum relative tolerance when minimizing -log(P)/N (~likelihood)
+ static char first_call=1;
+ static Hash<int> size_fam(MAXPROF/10); // Hash counts number of HMMs in family
+ static Hash<int> size_sfam(MAXPROF/10); // Hash counts number of families in superfamily
+ Hash<int> excluded(50); // Hash containing names of superfamilies to be excluded from fit
+ size_fam.Null(0); // Set int value to return when no data can be retrieved
+ size_sfam.Null(0); // Set int value to return when no data can be retrieved
+ excluded.Null(0); // Set int value to return when no data can be retrieved
+ Hit hit;
+
+ double mu; // EVD[mu,lam](x) = exp(-exp(-(x-mu)/lam)) = P(score<=x)
+ double vertex[2*3]; // three vertices of the simplex in lamda-mu plane
+ double yvertex[3]; // log likelihood values at the three vertices of the simplex
+ int nfunc=0; // number of function calls
+ double sum_weights=0.0;
+ float sum_scores=0.0;
+ float rtol;
+
+ if (first_call==1)
+ {
+ first_call=0;
+ // Count how many HMMs are in each family; set number of multiple hits per template nrep
+ if (v>=4) printf(" count number of profiles in each family and families in each superfamily ...\n");
+ Reset();
+ while (!End())
+ {
+ hit = ReadNext();
+ if (!size_fam.Contains(hit.fam)) (*size_sfam(hit.sfam))++; //Add one to hash element for superfamily
+ (*size_fam(hit.fam))++; //Add one to hash element for family
+ // printf("size(%s)=%i name=%s\n",hit.fam,*size_fam(hit.fam),hit.name)
+ }
+ fams=size_fam.Size();
+ sfams=size_sfam.Size();
+ if (v>=3)
+ printf("%-3i HMMs from %i families and %i superfamilies searched. Found %i hits\n",N_searched,fams,sfams,Size());
+ }
+
+ // Query has SCOP family identifier?
+ if (q.fam && q.fam[0]>='a' && q.fam[0]<='k' && q.fam[1]=='.')
+ {
+ char sfamid[NAMELEN];
+ char* ptr_in_fam=q.fam;
+ while ((ptr_in_fam=strwrd(sfamid,ptr_in_fam,'-')))
+ {
+ char* ptr=strrchr(sfamid,'.');
+ if (ptr) *ptr='\0';
+ excluded.Add(sfamid);
+// fprintf(stderr,"Exclude SCOP superfamily %s ptr_in_fam='%s'\n",sfamid,ptr_in_fam);
+ }
+ }
+ // Exclude best superfamilies from fit
+ else if (nbest>0)
+ {
+ if (sfams<97+nbest) return;
+
+ // Find the nbest best-scoring superfamilies for exclusion from first ML fit
+ if (v>=4) printf(" find %i best-scoring superfamilies to exclude from first fit ...\n",nbest);
+ hit = Smallest();
+ excluded.Add(hit.sfam);
+// printf("Exclude in first round: %s %8.2f %s\n",hit.name,hit.score_aass,hit.sfam);
+ while (excluded.Size()<nbest)
+ {
+ Reset();
+ while (!End() && excluded.Contains(ReadNext().sfam)) ;
+ hit=ReadCurrent();
+ while (!End())
+ {
+ if (ReadNext()<hit && !excluded.Contains(ReadCurrent().sfam))
+ hit=ReadCurrent();
+ }
+ excluded.Add(hit.sfam);
+// printf("Exclude in first round: %s %8.2f %s %i %i\n",hit.name,hit.score_aass,hit.sfam,excluded.Size(),excluded.Contains(hit.sfam));
+ }
+ tol = 0.01/size_sfam.Size(); // tol=1/N would lead to delta(log-likelihood)~1 (where N ~ number of superfamilies) since (1+1/N)^N = e
+ }
+ else
+ {
+ // Find the best-scoring superfamilies from first fit for exclusion from second ML fit
+ if (v>=4) printf(" find best-scoring superfamilies to exclude from second fit ...\n");
+ Reset();
+ while (!End())
+ {
+ hit = ReadNext();
+ if (hit.Eval < 0.05) excluded.Add(hit.sfam); // changed from 0.5 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+ }
+ tol = 0.001/size_sfam.Size(); // tol=1/N would lead to delta(log-likelihood)~1 (where N ~ number of superfamilies) since (1+1/N)^N = e
+ }
+
+ // Put scores into score[] and weights into weight[]
+ if (v>=3) printf(" generate scores and weights array for ML fitting ...\n");
+ Nprof=0;
+ Reset();
+ while (!End())
+ {
+ hit = ReadNext();
+ if (hit.irep > 1) continue; //Use only best hit per template
+ if (Nprof>=MAXPROF) break;
+
+ char sfamid[NAMELEN];
+ char* ptr_in_fam=hit.fam;
+ while ((ptr_in_fam=strwrd(sfamid,ptr_in_fam,'-')))
+ {
+ char* ptr=strrchr(sfamid,'.');
+ if (ptr) *ptr='\0';
+ if (excluded.Contains(sfamid)) break; //HMM is among superfamilies to be excluded
+ }
+ if (excluded.Contains(sfamid)) {
+ if (v>=3) fprintf(stderr,"Exclude hit %s (family %s contains %s)\n",hit.name,hit.fam,sfamid);
+ continue;
+ }
+// ScopID(hit.cl,hit.fold,hit.sfam,hit.fam); //Get scop superfamily code for template
+// if (*hit.sfam=='\0' || excluded.Contains(hit.sfam)) continue; // skip HMM
+
+ score[Nprof] = hit.score;
+ weight[Nprof]=1./size_fam[hit.fam]/size_sfam[hit.sfam];
+ sum_scores +=hit.score*weight[Nprof];
+ sum_weights+=weight[Nprof];
+
+ //DEBUG
+// if (v>=4) printf("%-10.10s %-12.12s %-3i %-12.12s %-3i %6.4f %6.4f %7.1f\n",hit.name,hit.fam,size_fam[hit.fam],hit.sfam,size_sfam[hit.sfam],1./size_fam[hit.fam]/size_sfam[hit.sfam],sum,hit.score);
+ Nprof++;
+ }
+ //DEBUG
+ if (v>=3)
+ printf("%i hits used for score distribution\n",Nprof);
+ // for (int i=0; i<Nprof; i++) printf("%3i score=%8.3f weight=%7.5f\n",i,score[i],weight[i]);
+
+ // Set simplex vertices and function values
+ mu = sum_scores/sum_weights - 0.584/LAMDA;
+ if (par.loc) // fit only in local mode; in global mode use fixed value LAMDA and mu mean score
+ {
+ double (*Func)(void*, double*);
+ Func = HitList::LogLikelihoodEVD_static;
+
+ if (nbest>0) {vertex[0]=LAMDA; vertex[1]=mu;} /////////////////////////////////////////// DEBUG
+ else {vertex[0]=q.lamda; vertex[1]=mu;}
+ vertex[2]=vertex[0]+0.1; vertex[3]=vertex[1];
+ vertex[4]=vertex[0]; vertex[5]=vertex[1]+0.2;
+ yvertex[0]=Func(this,vertex );
+ yvertex[1]=Func(this,vertex+2);
+ yvertex[2]=Func(this,vertex+4);
+
+ // Find lam and mu that minimize negative log likelihood of data
+ if (v>=3) printf("Fitting to EVD by maximum likelihood...\niter lamda mu -log(P)/N tol\n");
+ rtol = FindMin(2,vertex,yvertex,tol,nfunc,Func);
+ if (v>=3) printf("%3i %-7.3f %-7.2f %-7.3f %-7.1E\n\n",nfunc,vertex[0],vertex[1],yvertex[0]-(1.5772-log(vertex[0])),rtol);
+// printf("HHsearch lamda=%-6.3f mu=%-6.3f\n",vertex[0],vertex[1]);
+ }
+ else
+ {
+ vertex[0]=LAMDA_GLOB; vertex[1]=mu;
+ }
+
+ // Set lamda and mu of profile
+ q.lamda = vertex[0];
+ q.mu = vertex[1];
+
+ // Set P-values and E-values
+ // CHECK UPDATE FROM score=-logpval to score=-logpval+SSSCORE2NATLOG*score_ss !!!!
+ Reset();
+ while (!End())
+ {
+ hit = ReadNext();
+
+ // Calculate total score in raw score units: P-value = 1- exp(-exp(-lamda*(Saa-mu)))
+ hit.weight=1./size_fam[hit.fam]/size_sfam[hit.sfam]; // needed for transitive scoring
+ hit.logPval = logPvalue(hit.score,vertex);
+ hit.Pval=Pvalue(hit.score,vertex);
+ hit.Eval=exp(hit.logPval+log(N_searched));
+// hit.score_aass = hit.logPval/0.45-3.0 - hit.score_ss; // median(lamda)~0.45, median(mu)~4.0 in EVDs for scop20.1.63 HMMs
+ hit.score_aass = -q.lamda*(hit.score-q.mu)/0.45-3.0 - fmin(hit.score_ss,fmax(0.0,0.5*hit.score-5.0)); // median(lamda)~0.45, median(mu)~3.0 in EVDs for scop20.1.63 HMMs
+ hit.Probab = Probab(hit);
+ if (nbest>0 && par.loc) // correct length correction (not needed for second round of fitting, since lamda very similar)
+ if (par.idummy==0) ////////////////////////////////////////////
+ hit.score += log(q.L*hit.L)*(1/LAMDA-1/vertex[0]);
+ hit.score_sort = hit.score_aass;
+ Overwrite(hit); // copy hit object into current position of hitlist
+
+ if (nbest==0 && par.trans==1) // if in transitive scoring mode (weights file given)
+ TransitiveScoring();
+ else if (nbest==0 && par.trans==2) // if in transitive scoring mode (weights file given)
+ TransitiveScoring2();
+ else if (nbest==0 && par.trans==3) // if in transitive scoring mode (weights file given)
+ TransitiveScoring3();
+ else if (nbest==0 && par.trans==4) // if in transitive scoring mode (weights file given)
+ TransitiveScoring4();
+ }
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Calculate correlation and score offset for HHblast composite E-values
+ */
+void
+HitList::CalculateHHblastCorrelation(HMM& q)
+{
+ int nfunc=0; // number of function calls
+ double tol; // Maximum relative tolerance when minimizing -log(P)/N (~likelihood)
+ double vertex[2*3]; // three vertices of the simplex in lamda-mu plane
+ double yvertex[3]; // log likelihood values at the three vertices of the simplex
+ Hit hit;
+ Hash<int> excluded(50); // Hash containing names of superfamilies to be excluded from fit
+ excluded.Null(0); // Set int value to return when no data can be retrieved
+
+ // Set sum of HHsearch and PSI-BLAST score for calculating correlation
+ Reset();
+ while (!End())
+ {
+ hit = ReadNext();
+ hit.score_sort = hit.logPval + blast_logPvals->Show(hit.name); // if template not in hash, return log Pval = 0, i.e. Pvalue = 1!
+ Overwrite(hit); // copy hit object into current position of hitlist
+ }
+
+ // Query has SCOP family identifier?
+ if (q.fam && q.fam[0]>='a' && q.fam[0]<='k' && q.fam[1]=='.')
+ {
+ char sfamid[NAMELEN];
+ char* ptr_in_fam=q.fam;
+ while ((ptr_in_fam=strwrd(sfamid,ptr_in_fam,'-')))
+ {
+ char* ptr=strrchr(sfamid,'.');
+ if (ptr) *ptr='\0';
+ excluded.Add(sfamid);
+ fprintf(stderr,"Exclude SCOP superfamily %s ptr_in_fam='%s'\n",sfamid,ptr_in_fam);
+ }
+ }
+
+ // Resort list by sum of log P-values
+ ResortList(); // use InsertSort to resort list according to sum of minus-log-Pvalues
+ Nprof=0;
+ Reset();
+ ReadNext(); // skip best hit
+ while (!End())
+ {
+ hit = ReadNext();
+ if (hit.irep>=2) continue; // use only best alignments
+// if (hit.Eval<0.005) {if (v>=3) printf("Fitting HHblast correlation coefficient: skipping %s with Evalue=%9.1g\n",hit.name,hit.Eval); continue;}
+ if (Nprof>=MAXPROF) break;
+
+ char sfamid[NAMELEN];
+ char* ptr_in_fam=hit.fam;
+ while ((ptr_in_fam=strwrd(sfamid,ptr_in_fam,'-')))
+ {
+ char* ptr=strrchr(sfamid,'.');
+ if (ptr) *ptr='\0';
+ if (excluded.Contains(sfamid)) break; //HMM is among superfamilies to be excluded
+ }
+ if (excluded.Contains(sfamid)) {
+ if (v>=1) fprintf(stderr,"Exclude hit %s (family %s contains %s)\n",hit.name,hit.fam,sfamid);
+ continue;
+ }
+ score[Nprof] = -hit.score_sort;
+ weight[Nprof] = 1.0; // = hit.weight;
+// printf("%3i %-12.12s %7.3f + %7.3f = %7.3f \n",Nprof,hit.name,hit.logPval,blast_logPvals->Show(hit.name),-hit.score_sort); //////////////////////
+ printf("%3i %7.3f %7.3f\n",Nprof,hit.Pval,exp(blast_logPvals->Show(hit.name))); //////////////////////
+ Nprof++;
+ }
+
+ // Fit correlation
+ vertex[0]=0.5; vertex[1]=0.2;
+ vertex[2]=vertex[0]+0.2; vertex[3]=vertex[1];
+ vertex[4]=vertex[0]; vertex[5]=vertex[1]+0.2;
+
+ yvertex[0]=RankOrderFitCorr(vertex );
+ yvertex[1]=RankOrderFitCorr(vertex+2);
+ yvertex[2]=RankOrderFitCorr(vertex+4);
+// yvertex[0]=LogLikelihoodCorr(vertex );
+// yvertex[1]=LogLikelihoodCorr(vertex+2);
+// yvertex[2]=LogLikelihoodCorr(vertex+4);
+ tol = 1e-6;
+ v=3;//////////////////////////////////
+ // Find correlation and offset that minimize mean square deviation of reported composite Pvalues from actual
+ if (v>=2) printf("Fitting correlation coefficient for HHblast...\niter corr offset logLikelihood tol\n");
+ float rtol = FindMin(2,vertex,yvertex,tol,nfunc, HitList::RankOrderFitCorr_static);
+ if (v>=2) printf("%3i %-7.3f %-7.2f %-7.3f %-7.1E\n\n",nfunc,vertex[0],vertex[1],yvertex[0],rtol);
+ if (vertex[0]<0) vertex[0]=0.0;
+
+ // Print correlation and offset for profile
+ printf("HHblast correlation=%-6.3f score offset=%-6.3f\n",vertex[0],vertex[1]);
+ v=2;//////////////////////////////////
+}
+
+
+/**
+ * @brief Calculate HHblast composite E-values
+ */
+inline double
+corr_HHblast(float Nq, float Nt)
+{
+ return 0.5;
+}
+
+/**
+ * @brief Calculate HHblast composite E-values
+ */
+inline double
+offset_HHblast(float Nq, float Nt)
+{
+ return 0.0;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Calculate HHblast composite E-values
+ */
+void
+HitList::CalculateHHblastEvalues(HMM& q)
+{
+ Hit hit;
+ float corr, offset; // correlation coefficient and offset for calculating composite HHblast P-values
+
+ Reset();
+ while (!End())
+ {
+ hit = ReadNext();
+ corr = corr_HHblast(q.Neff_HMM,hit.Neff_HMM);
+ offset = offset_HHblast(q.Neff_HMM,hit.Neff_HMM);
+ hit.score_sort = hit.logPval + blast_logPvals->Show(hit.name);
+ hit.logPval = logPvalue_HHblast(-hit.score_sort+offset,corr); // overwrite logPval from HHsearch with composite logPval from HHblast
+ hit.Pval = Pvalue_HHblast(-hit.score_sort+offset,corr); // overwrite P-value from HHsearch with composite P-value from HHblast
+ hit.Eval = exp(hit.logPval+log(N_searched)); // overwrite E-value from HHsearch with composite E-value from HHblast
+ hit.Probab = Probab(hit);
+ Overwrite(hit); // copy hit object into current position of hitlist
+ }
+ ResortList(); // use InsertSort to resort list according to sum of minus-log-Pvalues
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Read file generated by blastpgp (default output) and store P-values in hash
+ */
+void
+HitList::ReadBlastFile(HMM& q)
+{
+ char line[LINELEN]=""; // input line
+ int Ndb; // number of sequences in database
+ int Ldb=0; // size of database in number of amino acids
+ char* templ;
+ int i;
+ if (!blast_logPvals) { blast_logPvals = new(Hash<float>); blast_logPvals->New(16381,0); }
+
+ FILE* blaf = NULL;
+ if (!strcmp(par.blafile,"stdin")) blaf=stdin;
+ else
+ {
+ blaf = fopen(par.blafile,"rb");
+ if (!blaf) OpenFileError(par.blafile);
+ }
+
+ // Read number of sequences and size of database
+ while (fgetline(line,LINELEN-1,blaf) && !strstr(line,"sequences;"));
+ if (!strstr(line,"sequences;")) FormatError(par.blafile,"No 'Database:' string found.");
+ char* ptr=line;
+ Ndb = strint(ptr);
+ if (Ndb==INT_MIN) FormatError(par.blafile,"No integer for number of sequences in database found.");
+ while ((i=strint(ptr))>INT_MIN) Ldb = 1000*Ldb + i;
+ if (Ldb==0) FormatError(par.blafile,"No integer for size of database found.");
+ printf("\nNumber of sequences in database = %i Size of database = %i\n",Ndb,Ldb);
+
+ // Read all E-values and sequence lengths
+ while (fgetline(line,LINELEN-1,blaf))
+ {
+ if (line[0]=='>')
+ {
+ // Read template name
+ templ = new(char[255]);
+ ptr = line+1;
+ strwrd(templ,ptr);
+ if (!blast_logPvals->Contains(templ)) // store logPval only for best HSP with template
+ {
+ // Read length
+ while (fgetline(line,LINELEN-1,blaf) && !strstr(line,"Length ="));
+ ptr = line+18;
+ int length = strint(ptr);
+ // Read E-value
+ fgetline(line,LINELEN-1,blaf);
+ fgetline(line,LINELEN-1,blaf);
+ float EvalDB; // E-value[seq-db] = Evalue for comparison Query vs. database, from PSI-BLAST
+ float EvalQT; // E-value[seq-seq] = Evalue for comparison Query vs. template (seq-seq)
+ double logPval;
+ ptr = strstr(line+20,"Expect =");
+ if (!ptr) FormatError(par.blafile,"No 'Expect =' string found.");
+ if (sscanf(ptr+8,"%g",&EvalDB)<1)
+ {
+ ptr[7]='1';
+ if (sscanf(ptr+7,"%g",&EvalDB)<1)
+ FormatError(par.blafile,"No Evalue found after 'Expect ='.");
+ }
+ // Calculate P-value[seq-seq] = 1 - exp(-E-value[seq-seq]) = 1 - exp(-Lt/Ldb*E-value[seq-db])
+ EvalQT = length/double(Ldb)*double(EvalDB);
+ if (EvalQT>1E-3) logPval = log(1.0-exp(-EvalQT)); else logPval=log(double(EvalQT)+1.0E-99);
+ blast_logPvals->Add(templ,logPval);
+ printf("template=%-10.10s length=%-3i EvalDB=%8.2g EvalQT=%8.2g P-value=%8.2g log Pval=%8.2g\n",templ,length,EvalDB,EvalQT,exp(logPval),logPval);
+ }
+ else {
+ delete[] templ; templ = NULL;
+ }
+ }
+ }
+ fclose(blaf);
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Calculate output of hidden neural network units
+ */
+inline float
+calc_hidden_output(const float* weights, const float* bias, float Lqnorm, float Ltnorm, float Nqnorm, float Ntnorm)
+{
+ float res;
+ // Calculate activation of hidden unit = sum of all inputs * weights + bias
+ res = Lqnorm*weights[0] + Ltnorm*weights[1] + Nqnorm*weights[2] + Ntnorm*weights[3] + *bias;
+ res = 1.0 / (1.0 + exp(-(res ))); // logistic function
+ return res;
+}
+
+////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Neural network regressions of lamda for EVD
+ */
+inline float
+lamda_NN(float Lqnorm, float Ltnorm, float Nqnorm, float Ntnorm)
+{
+ const int inputs = 4;
+ const int hidden = 4;
+ const float biases[] = {-0.73195, -1.43792, -1.18839, -3.01141}; // bias for all hidden units
+ const float weights[] = { // Weights for the neural networks (column = start unit, row = end unit)
+ -0.52356, -3.37650, 1.12984, -0.46796,
+ -4.71361, 0.14166, 1.66807, 0.16383,
+ -0.94895, -1.24358, -1.20293, 0.95434,
+ -0.00318, 0.53022, -0.04914, -0.77046,
+ 2.45630, 3.02905, 2.53803, 2.64379
+ };
+ float lamda=0.0;
+ for (int h = 0; h<hidden; h++) {
+ lamda += calc_hidden_output( weights+inputs*h, biases+h, Lqnorm,Ltnorm,Nqnorm,Ntnorm ) * weights[hidden*inputs+h];
+ }
+ return lamda;
+}
+
+////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Neural network regressions of mu for EVD
+ */
+inline float
+mu_NN(float Lqnorm, float Ltnorm, float Nqnorm, float Ntnorm)
+{
+ const int inputs = 4;
+ const int hidden = 6;
+ const float biases[] = {-4.25264, -3.63484, -5.86653, -4.78472, -2.76356, -2.21580}; // bias for all hidden units
+ const float weights[] = { // Weights for the neural networks (column = start unit, row = end unit)
+ 1.96172, 1.07181, -7.41256, 0.26471,
+ 0.84643, 1.46777, -1.04800, -0.51425,
+ 1.42697, 1.99927, 0.64647, 0.27834,
+ 1.34216, 1.64064, 0.35538, -8.08311,
+ 2.30046, 1.31700, -0.46435, -0.46803,
+ 0.90090, -3.53067, 0.59212, 1.47503,
+ -1.26036, 1.52812, 1.58413, -1.90409, 0.92803, -0.66871
+ };
+ float mu=0.0;
+ for (int h = 0; h<hidden; h++) {
+ mu += calc_hidden_output( weights+inputs*h, biases+h, Lqnorm,Ltnorm,Nqnorm,Ntnorm ) * weights[hidden*inputs+h];
+ }
+ return 20.0*mu;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Calculate Pvalues as a function of query and template lengths and diversities
+ */
+void
+HitList::CalculatePvalues(HMM& q)
+{
+ Hit hit;
+ float lamda=0.4, mu=3.0;
+ const float log1000=log(1000.0);
+
+ if (par.idummy!=2)
+ {
+ printf("WARNING: idummy should have been ==2 (no length correction)\n");
+ exit(4);
+ }
+
+ if(N_searched==0) N_searched=1;
+ if (v>=2)
+ printf("Calculate Pvalues as a function of query and template lengths and diversities...\n");
+ Reset();
+ while (!End())
+ {
+ hit = ReadNext();
+
+ if (par.loc)
+ {
+ lamda = lamda_NN( log(q.L)/log1000, log(hit.L)/log1000, q.Neff_HMM/10.0, hit.Neff_HMM/10.0 );
+ mu = mu_NN( log(q.L)/log1000, log(hit.L)/log1000, q.Neff_HMM/10.0, hit.Neff_HMM/10.0 );
+// if (v>=3 && nhits++<20)
+// printf("hit=%-10.10s Lq=%-4i Lt=%-4i Nq=%5.2f Nt=%5.2f => lamda=%-6.3f mu=%-6.3f\n",hit.name,q.L,hit.L,q.Neff_HMM,hit.Neff_HMM,lamda,mu);
+ }
+ else
+ {
+ printf("WARNING: global calibration not yet implemented!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
+ }
+ hit.logPval = logPvalue(hit.score,lamda,mu);
+ hit.Pval = Pvalue(hit.score,lamda,mu);
+ hit.Eval=exp(hit.logPval+log(N_searched));
+// hit.score_aass = hit.logPval/LAMDA-3.0 - hit.score_ss; // median(lamda)~0.45, median(mu)~3.0 in EVDs for scop20.1.63 HMMs
+ // P-value = 1- exp(-exp(-lamda*(Saa-mu))) => -lamda*(Saa-mu) = log(-log(1-Pvalue))
+ hit.score_aass = (hit.logPval<-10.0? hit.logPval : log(-log(1-hit.Pval)) )/0.45 - fmin(lamda*hit.score_ss,fmax(0.0,0.2*(hit.score-8.0)))/0.45 - 3.0;
+ hit.score_sort = hit.score_aass;
+ hit.Probab = Probab(hit);
+ Overwrite(hit);
+ }
+ SortList();
+ Reset();
+ return;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Calculate Pvalues from calibration of 0: query HMM, 1:template HMMs, 2: both
+ */
+void
+HitList::GetPvalsFromCalibration(HMM& q)
+{
+ Hit hit;
+ char warn=0;
+ if(N_searched==0) N_searched=1;
+ if (v>=2)
+ {
+ switch (par.calm)
+ {
+ case 0:
+ printf("Using lamda=%-5.3f and mu=%-5.2f from calibrated query HMM %s. \n",q.lamda,q.mu,q.name);
+ printf("Note that HMMs need to be recalibrated when changing HMM-HMM alignment options.\n");
+ break;
+ case 1:
+ printf("Using score distribution parameters lamda and mu from database HMMs \n");
+ break;
+ case 2:
+ printf("Combining score distribution parameters lamda and mu from query and database HMMs\n");
+ printf("Note that HMMs need to be recalibrated when changing HMM-HMM alignment options.\n");
+ break;
+ }
+ }
+ Reset();
+ while (!End())
+ {
+ hit = ReadNext();
+ if (par.calm==0 || (hit.logPvalt==0) )
+ {
+ hit.logPval = logPvalue(hit.score,q.lamda,q.mu);
+ hit.Pval = Pvalue(hit.score,q.lamda,q.mu);
+ if (par.calm>0 && warn++<1 && v>=1)
+ printf("Warning: some template HMM (e.g. %s) are not calibrated. Using query calibration.\n",hit.name);
+ }
+ else if (par.calm==1)
+ {
+ hit.logPval = hit.logPvalt;
+ hit.Pval = hit.Pvalt;
+ }
+ else if (par.calm==2)
+ {
+ hit.logPval = 0.5*( logPvalue(hit.score,q.lamda,q.mu) + hit.logPvalt);
+ hit.Pval = sqrt( Pvalue(hit.score,q.lamda,q.mu) * hit.Pvalt);
+ if (v>=5) printf("Score: %7.1f lamda: %7.1f mu: %7.1f P-values: query-calibrated: %8.2G template-calibrated: %8.2G geometric mean: %8.2G\n",hit.score,q.lamda,q.mu,Pvalue(hit.score,q.lamda,q.mu),hit.Pvalt,hit.Pval);
+ }
+
+ hit.Eval=exp(hit.logPval+log(N_searched));
+// hit.score_aass = hit.logPval/LAMDA-3.0 - hit.score_ss; // median(lamda)~0.45, median(mu)~3.0 in EVDs for scop20.1.63 HMMs
+ // P-value = 1- exp(-exp(-lamda*(Saa-mu))) => -lamda*(Saa-mu) = log(-log(1-Pvalue))
+ hit.score_aass = (hit.logPval<-10.0? hit.logPval : log(-log(1-hit.Pval)) ) / 0.45-3.0 - fmin(hit.score_ss,fmax(0.0,0.5*hit.score-5.0));
+ hit.score_sort = hit.score_aass;
+ hit.Probab = Probab(hit);
+ Overwrite(hit);
+ }
+ SortList();
+ Reset();
+ return;
+}
+
+
+
+
+
+
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+// Transitive scoring
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////////////////////
+
+
+
+
+
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Calculate P-values and Probabilities from transitive scoring over whole database
+ */
+void
+HitList::TransitiveScoring()
+{
+ void PrintMatrix(float** V, int N);
+ void PrintMatrix(double** V, int N);
+
+ float** Z; // matrix of intra-db Z-scores Z_kl
+ float** C; // covariance matrix for Z_k: C_kl = sum_m=1^N (Z_km * Z_lm)
+ char** fold; // fold name of HMM k
+ char** fam; // family of HMM k
+ float* Prob; // probability of HMM k
+ float* Zq; // Zq[k] = Z-score between query and database HMM k
+ float* Ztq; // Ztq[k] = transitive Z-score from query to database HMM k: Ztq[k] = sum_l[ w_ql * Z_lk] / normalization_q
+ float* Zrq; // Zrq[k] = transitive Z-score from database HMM k to query: Zrq[k] = sum_l[ w_kl * Z_lq] / normalization_k
+ float* w; // unnormalized weight matrix; w[l] is w_ql or w_kl, respectively
+ int* ll; // ll[m] is the m'th index l for which Z_lq, Z_lk > Zmin_trans
+ int N; // dimension of weight matrix is NxN
+ int M; // number of HMMs l with Z_ql>Ztrans_min (or Z_lk>Ztrans_min, respectively)
+ int k,l,m,n; // indices for database HMMs
+ char name[NAMELEN];
+ Hash<int> index(MAXPROF+7); // index{name} = index of HMM name in {1,...,N}
+ index.Null(-1); // Set int value to return when no data can be retrieved
+ Hash<int> excluded(13); // Hash containing names of superfamilies to be excluded from fit
+ excluded.Null(0); // Set int value to return when no data can be retrieved
+ Hit hit;
+ size_t unused; /* disable fread gcc warning */
+
+ // Read weights matrix W with index hash and names array
+ fprintf(stderr,"Reading in weights file\n");
+ FILE* wfile = fopen(par.wfile,"rb");
+ if (v>=1 && wfile==NULL)
+ {
+ fprintf(stderr,"Error: %s could not be opened: (N_searched=%i) ",par.wfile,N_searched);
+ perror("fopen");
+ fprintf(stderr,"Skipping caclulation of transitive P-values\n");
+ par.trans=0;
+ return;
+ }
+ unused = fread(&N,sizeof(int),1,wfile); // read matrix dimension (i.e. number of HMMs in database)
+ if (v>=1 && N!=N_searched)
+ {
+ fprintf(stderr,"Error: Number %i of HMMs in weight file is different from number %i of HMMs in searched databases. \n",N,N_searched);
+ fprintf(stderr,"Skipping caclulation of transitive P-values\n");
+ par.trans=0;
+ return;
+ }
+ if (v>=2) fprintf(stderr,"Calculating transitive P-values for %i HMMs\n",N);
+ // Read names of HMMs (to specify mapping of HMM to matrix indices)
+ for (k=0; k<N; k++)
+ {
+ unused = fread(name,sizeof(char),IDLEN,wfile);
+ index.Add(name,k);
+ }
+ // Read symmetric Z-scores matrix
+ Z = new(float*[N]);
+ for (k=0; k<N; k++)
+ {
+ Z[k] = new(float[N]);
+ for (l=0; l<k; l++) Z[k][l] = Z[l][k];
+ unused = fread(Z[k]+k,sizeof(float),N-k,wfile);
+ }
+ // Read symmetric covariance matrix
+ C = new(float*[N]);
+ for (k=0; k<N; k++)
+ {
+ C[k] = new(float[N]);
+ for (l=0; l<k; l++) C[k][l] = C[l][k];
+ unused = fread(C[k]+k,sizeof(float),N-k,wfile);
+ }
+ fclose(wfile);
+
+ // Allocate memory
+ Zq = new(float[N]);
+ Ztq = new(float[N]);
+ Zrq = new(float[N]);
+ fold = new(char*[N]);
+ fam = new(char*[N]);
+ Prob = new(float[N]);
+ ll = new(int[N]);
+ w = new(float[N]);
+
+ // Transform P-values to normally distributed Z-scores and store in Zq vector
+ fprintf(stderr,"Transform P-values to Z-scores\n");
+ float Zmax_neg = Score2Z( -log(MINEVALEXCL) + log(N_searched) ); // calculate Z-score corresponding to E-value MINEVALEXCL
+ float Zmin_trans = Score2Z( -log(par.Emax_trans) + log(N_searched) ); // calculate Z-score corresponding to E-value par.Emax_trans
+ printf("Zmax = %6.2f Zmin = %6.2f \n",Zmax_neg,Zmin_trans);
+
+ Reset();
+ while (!End())
+ {
+ hit = ReadNext();
+ if (hit.irep>1) continue;
+ k = index.Show(hit.name);
+ if (k<0) {fprintf(stderr,"Error: no index found in weights file for domain %s\n",hit.name); exit(1);}
+ if (hit.logPvalt<0)
+ Zq[k] = 0.5*Score2Z(fabs(hit.logPval)) + 0.5*Score2Z(fabs(hit.logPvalt)); // Zq[k] = 0.5*(Zkq + Zqk)
+ else
+ Zq[k] = Score2Z(fabs(hit.logPval)); // Zq[k] = Zqk
+// printf("%4i %-10.10s logPvalt=%9g Zq=%9f\n",k,hit.name,hit.logPvalt,Zq[k]);
+// if (isnan(Zq[k])) {
+// fprintf(stderr,"Error: a floating point exception occurred. Skipping transitive scoring\n");
+// printf("%4i %-10.10s logPval=%9g logPvalt=%9g Zq=%9f\n",k,hit.name,hit.logPval,hit.logPvalt,Zq[k]);
+// par.trans=0;
+// return;
+// }
+ if (Zq[k]>Zmax_neg) excluded.Add(hit.fold);
+ fold[k] = new(char[IDLEN]);
+ fam[k] = new(char[IDLEN]);
+ strcpy(fold[k],hit.fold);
+ strcpy(fam[k],hit.fam);
+ weight[k] = hit.weight;
+ Prob[k] = hit.Probab;
+ }
+
+ if (v>=3)
+ {
+ excluded.Reset();
+ while (!excluded.End())
+ {
+ excluded.ReadNext(name);
+ printf("Excluded fold %s from fitting to Ztq\n",name);
+ }
+ }
+
+
+ ////////////////////////////////////////////////////////////////
+ // Calculate transitive score (query->l) Zt[l]
+
+ // Construct vector ll of indices l for which Z_lq > Zmin_trans
+ m = 0;
+ for (l=0; l<N; l++)
+ if (Zq[l]>=Zmin_trans) ll[m++]=l;
+ M = m; // number of indices l for which Z_lq,Z_lk > Zmin_trans
+
+// for (m=0; m<M; m++)
+// fprintf(stderr,"m=%-4i l=%-4i %-10.10s Zq[l]=%7f\n",m,ll[m],fam[ll[m]],Zq[ll[m]]);
+
+ if (M<=1)
+ for (k=0; k<N; k++) Ztq[k]=0.0;
+ else
+ {
+ // Generate submatrix of C for indices l for which Z_lq,Z_lk > Zmin_trans
+ double** Csub = new(double*[M]);
+ double** Cinv = new(double*[M]);
+ for (m=0; m<M; m++)
+ {
+ Csub[m] = new(double[M]);
+ Cinv[m] = new(double[M]);
+ for (n=0; n<M; n++)
+ Csub[m][n] = double(C[ll[m]][ll[n]]);
+ }
+
+ if (v>=3)
+ {
+ fprintf(stderr,"Covariance matrix\n");
+ PrintMatrix(Csub,M);
+ }
+
+ // Invert Csub
+ fprintf(stderr,"Calculate inverse of covariance submatrix\n");
+ InvertMatrix(Cinv,Csub,M);
+
+ if (v>=3)
+ {
+ fprintf(stderr,"Inverse covariance matrix\n");
+ PrintMatrix(Cinv,M);
+ }
+
+ // Calculate weights w[l]
+ for (m=0; m<M; m++)
+ {
+ double sum = 0.0;
+ for (n=0; n<M; n++)
+ sum += 1.0 * Cinv[m][n];
+ w[m] = fmax(sum,0.0);
+ }
+ for (l=0; l<M; l++){
+ delete[](Cinv[l]); (Cinv[l]) = NULL;
+ }
+ delete[](Cinv); (Cinv) = NULL;
+
+ // Calculate Ztq[k] for all HMMs k
+ fprintf(stderr,"Calculate Ztq vector of transitive Z-scores\n");
+ float norm = NormalizationFactor(Csub,w,M);
+ for (k=0; k<N; k++)
+ {
+ double sumZ = 0.0;
+ for (m=0; m<M; m++)
+ sumZ += w[m] * Z[ll[m]][k];
+ Ztq[k] = sumZ/norm;
+ }
+
+ for (l=0; l<M; l++){
+ delete[](Csub[l]); (Csub[l]) = NULL;
+ }
+ delete[](Csub); (Csub) = NULL;
+ }
+
+ ////////////////////////////////////////////////////////////////
+ // Calculate reverse transitive score (l->query-) Zrq[l]
+
+ fprintf(stderr,"Calculate Zrq vector of transitive Z-scores\n");
+ for (k=0; k<N; k++)
+ {
+ // Construct vector ll of indices l for which Z_lk > Zmin_tran
+ m = 0;
+ for (l=0; l<N; l++)
+ if (Z[l][k]+Z[k][l]>=2*Zmin_trans) ll[m++]=l;
+ int M = m; // number of indices l for which Z_lq,Z_lk > Zmin_tran
+
+
+// fprintf(stderr,"\nfam[k]: %s\n",fam[k]);
+// for (m=0; m<M; m++)
+// printf(stderr,"m=%-4i k=%-4i l=%-4i %-10.10s Zq[l]=%7f Z_lk=%7f \n",m,k,ll[m],fold[ll[m]],Zq[ll[m]],Z[k][ll[m]]);
+
+ if (M<=1)
+ {
+ Zrq[k] = Zq[k];
+ }
+ else
+ {
+ // Generate submatrix of C for indices l for which Z_lq,Z_lk > Zmin_trans
+ double** Csub = new(double*[M]);
+ for (m=0; m<M; m++)
+ {
+ Csub[m] = new(double[M]);
+ for (n=0; n<M; n++)
+ Csub[m][n] = double(C[ll[m]][ll[n]]);
+ }
+// fprintf(stderr,"Covariance matrix\n");
+// PrintMatrix(Csub,M);
+
+ if (M==2)
+ {
+ for (m=0; m<M; m++) w[m] = 1.0/M;
+ }
+ else
+ {
+
+ double** Cinv = new(double*[M]);
+ for (m=0; m<M; m++) Cinv[m] = new(double[M]);
+
+ // Invert Csub
+ InvertMatrix(Cinv,Csub,M);
+
+ // fprintf(stderr,"Inverse covariance matrix\n");
+ // PrintMatrix(Cinv,M);
+
+ // Calculate weights w[l]
+ for (m=0; m<M; m++)
+ {
+ double sum = 0.0;
+ for (n=0; n<M; n++)
+ sum += 1.0 * Cinv[m][n];
+ w[m] = fmax(sum,0.0);
+ }
+
+// for (m=0; m<M; m++) fprintf(stderr,"w[%i]=%8.2g\n",m,w[m]);
+
+ for (l=0; l<M; l++){
+ delete[](Cinv[l]); (Cinv[l]) = NULL;
+ }
+ delete[](Cinv); (Cinv) = NULL;
+ }
+
+ // Calculate Zrq[k] and normalize
+ float norm = NormalizationFactor(Csub,w,M);
+ double sumZ = 0.0;
+ for (m=0; m<M; m++)
+ sumZ += w[m] * Zq[ll[m]];
+ Zrq[k] = sumZ/norm;
+
+ for (l=0; l<M; l++){
+ delete[](Csub[l]); (Csub[l]) = NULL;
+ }
+ delete[](Csub); (Csub) = NULL;
+ }
+
+// fprintf(stderr,"\nZq[k]=%8.2g Zq1[k]=%8.2g\n",Zq[k],Zrq[k]);
+ }
+
+ // Total Z-score = weighted sum over original Z-score, forward transitive and reverse transitive Z-score
+ for (k=0; k<N; k++)
+ {
+ float Zqtot = Zq[k] + par.wtrans*(Ztq[k]+Zrq[k]);
+// if (isnan(Zqtot))
+// {
+// fprintf(stderr,"Error: a floating point exception occurred. Skipping transitive scoring\n");
+// printf("%4i %-10.10s Zq=%6.2f Ztq=%6.2f Zrq=%6.2f Zqtot=%6.2f\n",k,fam[k],Zq[k],Ztq[k],Zrq[k],Zqtot);
+// par.trans=0;
+// return;
+// }
+ if (v>=2 && Zq[k] + Zqtot > 2*Zmin_trans) {
+ printf("%4i %-10.10s Zq=%6.2f Ztq=%6.2f Zrq=%6.2f -> Zqtot=%6.2f\n",k,fam[k],Zq[k],Ztq[k],Zrq[k],Zqtot);
+ }
+ Ztq[k] = Zqtot;
+ }
+
+ // Calculate mean and standard deviation of Z1q
+ fprintf(stderr,"Calculate mean and standard deviation of Ztq\n");
+ double sumw=0.0;
+ double sumZ=0.0;
+ double sumZ2=0.0;
+ for (k=0; k<N; k++)
+ {
+ if (excluded.Contains(fold[k])) continue;
+ sumw += weight[k];
+ sumZ += weight[k]*Ztq[k];
+ sumZ2 += weight[k]*Ztq[k]*Ztq[k];
+// if (isnan(sumZ))
+// {
+// fprintf(stderr,"Error: a floating point exception occurred. Skipping transitive scoring\n");
+// printf("%4i %-10.10s Zq=%9f Zrq=%9f Ztq=%9f\n",k,fam[k],Zq[k],Zrq[k],Ztq[k]);
+// par.trans=0;
+// return;
+// }
+ }
+ float mu = sumZ/sumw;
+ float sigma = sqrt(sumZ2/sumw-mu*mu);
+ if (v>=2) printf("mu(Ztq)=%6.3f sigma(Ztq)=%6.2f\n",mu,sigma);
+ sigma *= 1.01;// correct different fitting of EVD and normal variables
+
+ // Normalize Ztq and calculate P1-values
+ fprintf(stderr,"Normalize Ztq and calculate P1-values\n");
+ Reset();
+ while (!End())
+ {
+ hit = ReadNext();
+ hit.logPval = -Z2Score((Ztq[index.Show(hit.name)]-mu)/sigma);
+ hit.E1val = N_searched*(hit.logPval<-100.0? 0.0 : exp(hit.logPval));
+ // P-value = 1- exp(-exp(-lamda*(Saa-mu))) => -lamda*(Saa-mu) = log(-log(1-Pvalue))
+ hit.score_aass = (hit.logPval<-10.0? hit.logPval : log(-log(1-exp(hit.logPval))) ) / 0.45-3.0 - hit.score_ss;
+ hit.Probab = Probab(hit);
+ hit.score_sort = hit.logPval;
+ Overwrite(hit); // copy hit object into current position of hitlist
+ }
+
+ for (k=0; k<N; k++){
+ delete[](Z[k]); (Z[k]) = NULL;
+ }
+ for (k=0; k<N; k++){
+ delete[](C[k]); (C[k]) = NULL;
+ }
+ for (k=0; k<N; k++){
+ delete[](fold[k]); (fold[k]) = NULL;
+ }
+ for (k=0; k<N; k++){
+ delete[](fam[k]); (fam[k]) = NULL;
+ }
+ delete[](C); (C) = NULL;
+ delete[](Z); (Z) = NULL;
+ delete[](fold); (fold) = NULL;
+ delete[](fam); (fam) = NULL;
+ delete[](Prob); (Prob) = NULL;
+ delete[](ll); (ll) = NULL;
+ delete[](Zq); (Zq) = NULL;
+ delete[](Ztq); (Ztq) = NULL;
+}
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Calculate P-values and Probabilities from transitive scoring over whole database
+ */
+void
+HitList::TransitiveScoring2()
+{
+ void PrintMatrix(float** V, int N);
+ void PrintMatrix(double** V, int N);
+
+ float** Z; // matrix of intra-db Z-scores Z_kl
+ float** C; // covariance matrix for Z_k: C_kl = sum_m=1^N (Z_km * Z_lm)
+ char** fold; // fold name of HMM k
+ char** fam; // family of HMM k
+ float* Prob; // probability of HMM k
+ float* Zq; // Zq[k] = Z-score between query and database HMM k
+ float* Ztq; // Ztq[k] = transitive Z-score from query to database HMM k: Ztq[k] = sum_l[ w_ql * Z_lk] / normalization_q
+ float* Zrq; // Zrq[k] = transitive Z-score from database HMM k to query: Zrq[k] = sum_l[ w_kl * Z_lq] / normalization_k
+ float* w; // unnormalized weight matrix; w[l] is w_ql or w_kl, respectively
+ int* ll; // ll[m] is the m'th index l for which Z_lq, Z_lk > Zmin_trans
+ int N; // dimension of weight matrix is NxN
+ int M; // number of HMMs l with Z_ql>Ztrans_min (or Z_lk>Ztrans_min, respectively)
+ int k,l,m,n; // indices for database HMMs
+ char name[NAMELEN];
+ Hash<int> index(MAXPROF+7); // index{name} = index of HMM name in {1,...,N}
+ index.Null(-1); // Set int value to return when no data can be retrieved
+ Hash<int> excluded(13); // Hash containing names of superfamilies to be excluded from fit
+ excluded.Null(0); // Set int value to return when no data can be retrieved
+ Hit hit;
+ size_t unused; /* disable fread gcc warning */
+
+ // Read weights matrix W with index hash and names array
+ fprintf(stderr,"Reading in weights file\n");
+ FILE* wfile = fopen(par.wfile,"rb");
+ if (v>=1 && wfile==NULL)
+ {
+ fprintf(stderr,"Error: %s could not be opened: (N_searched=%i) ",par.wfile,N_searched);
+ perror("fopen");
+ fprintf(stderr,"Skipping caclulation of transitive P-values\n");
+ par.trans=0;
+ return;
+ }
+ unused = fread(&N,sizeof(int),1,wfile); // read matrix dimension (i.e. number of HMMs in database)
+ if (v>=1 && N!=N_searched)
+ {
+ fprintf(stderr,"Error: Number %i of HMMs in weight file is different from number %i of HMMs in searched databases. \n",N,N_searched);
+ fprintf(stderr,"Skipping caclulation of transitive P-values\n");
+ par.trans=0;
+ return;
+ }
+ if (v>=2) fprintf(stderr,"Calculating transitive P-values for %i HMMs\n",N);
+ // Read names of HMMs (to specify mapping of HMM to matrix indices)
+ for (k=0; k<N; k++)
+ {
+ unused = fread(name,sizeof(char),IDLEN,wfile);
+ index.Add(name,k);
+ }
+ // Read symmetric Z-scores matrix
+ Z = new(float*[N]);
+ for (k=0; k<N; k++)
+ {
+ Z[k] = new(float[N]);
+ for (l=0; l<k; l++) Z[k][l] = Z[l][k];
+ unused = fread(Z[k]+k,sizeof(float),N-k,wfile);
+ }
+ // Read symmetric covariance matrix
+ C = new(float*[N]);
+ for (k=0; k<N; k++)
+ {
+ C[k] = new(float[N]);
+ for (l=0; l<k; l++) C[k][l] = C[l][k];
+ unused = fread(C[k]+k,sizeof(float),N-k,wfile);
+ }
+ fclose(wfile);
+
+ // Allocate memory
+ Zq = new(float[N]);
+ Ztq = new(float[N]);
+ Zrq = new(float[N]);
+ fold = new(char*[N]);
+ fam = new(char*[N]);
+ Prob = new(float[N]);
+ ll = new(int[N]);
+ w = new(float[N]);
+
+ // Transform P-values to normally distributed Z-scores and store in Zq vector
+ fprintf(stderr,"Transform P-values to Z-scores\n");
+ float Zmax_neg = Score2Z( -log(MINEVALEXCL) + log(N_searched) ); // calculate Z-score corresponding to E-value MINEVALEXCL
+ float Zmin_trans = Score2Z( -log(par.Emax_trans) + log(N_searched) ); // calculate Z-score corresponding to E-value par.Emax_trans
+ printf("Zmax = %6.2f Zmin = %6.2f \n",Zmax_neg,Zmin_trans);
+
+ Reset();
+ while (!End())
+ {
+ hit = ReadNext();
+ if (hit.irep>1) continue;
+ k = index.Show(hit.name);
+ if (k<0) {fprintf(stderr,"Error: no index found in weights file for domain %s\n",hit.name); exit(1);}
+ if (hit.logPvalt<0)
+ Zq[k] = 0.5*Score2Z(fabs(hit.logPval)) + 0.5*Score2Z(fabs(hit.logPvalt)); // Zq[k] = 0.5*(Zkq + Zqk)
+ else
+ Zq[k] = Score2Z(fabs(hit.logPval)); // Zq[k] = Zqk
+// printf("%4i %-10.10s logPvalt=%9g Zq=%9f\n",k,hit.name,hit.logPvalt,Zq[k]);
+// if (isnan(Zq[k]))
+// {
+// fprintf(stderr,"Error: a floating point exception occurred. Skipping transitive scoring\n");
+// printf("%4i %-10.10s logPval=%9g logPvalt=%9g Zq=%9f\n",k,hit.name,hit.logPval,hit.logPvalt,Zq[k]);
+// par.trans=0;
+// return;
+// }
+ if (Zq[k]>Zmax_neg) excluded.Add(hit.fold);
+ fold[k] = new(char[IDLEN]);
+ fam[k] = new(char[IDLEN]);
+ strcpy(fold[k],hit.fold);
+ strcpy(fam[k],hit.fam);
+ weight[k] = hit.weight;
+ Prob[k] = hit.Probab;
+ }
+
+ if (v>=3)
+ {
+ excluded.Reset();
+ while (!excluded.End())
+ {
+ excluded.ReadNext(name);
+ printf("Excluded fold %s from fitting to Ztq\n",name);
+ }
+ }
+
+
+ ////////////////////////////////////////////////////////////////
+ // Calculate transitive score (query->l) Zt[l]
+
+ // Construct vector ll of indices l for which Z_lq > Zmin_trans
+ m = 0;
+ for (l=0; l<N; l++)
+ if (Zq[l]>=Zmin_trans) ll[m++]=l;
+ M = m; // number of indices l for which Z_lq,Z_lk > Zmin_trans
+
+// for (m=0; m<M; m++)
+// fprintf(stderr,"m=%-4i l=%-4i %-10.10s Zq[l]=%7f\n",m,ll[m],fam[ll[m]],Zq[ll[m]]);
+
+ if (M<=1)
+ for (k=0; k<N; k++) Ztq[k]=0.0;
+ else
+ {
+ // Generate submatrix of C for indices l for which Z_lq,Z_lk > Zmin_trans
+ double** Csub = new(double*[M]);
+ double** Cinv = new(double*[M]);
+ for (m=0; m<M; m++)
+ {
+ Csub[m] = new(double[M]);
+ Cinv[m] = new(double[M]);
+ for (n=0; n<M; n++)
+ Csub[m][n] = double(C[ll[m]][ll[n]]);
+ }
+
+ if (v>=3)
+ {
+ fprintf(stderr,"Covariance matrix\n");
+ PrintMatrix(Csub,M);
+ }
+
+// // Invert Csub
+// fprintf(stderr,"Calculate inverse of covariance submatrix\n");
+// InvertMatrix(Cinv,Csub,M);
+
+// if (v>=3)
+// {
+// fprintf(stderr,"Inverse covariance matrix\n");
+// PrintMatrix(Cinv,M);
+// }
+
+
+ // Calculate weights w[l]
+ for (m=0; m<M; m++)
+ {
+ double sum = 0.0;
+ for (n=0; n<M; n++)
+ sum += 1.0 * Csub[m][n];
+ printf("w[%4i] = %-8.5f\n",ll[m],1.0/sum);
+ w[m] = (sum>0? Zq[ll[m]] / sum : 0.0);
+ }
+ for (l=0; l<M; l++){
+ delete[](Cinv[l]); (Cinv[l]) = NULL;
+ }
+ delete[](Cinv); (Cinv) = NULL;
+
+ // Calculate Ztq[k] for all HMMs k
+ fprintf(stderr,"Calculate Ztq vector of transitive Z-scores\n");
+ float norm = NormalizationFactor(Csub,w,M);
+ for (k=0; k<N; k++)
+ {
+ double sumZ = 0.0;
+ for (m=0; m<M; m++)
+ sumZ += w[m] * Z[ll[m]][k];
+ Ztq[k] = sumZ/norm;
+ }
+
+ for (l=0; l<M; l++){
+ delete[](Csub[l]); (Csub[l]) = NULL;
+ }
+ delete[](Csub); (Csub) = NULL;
+ }
+
+ ////////////////////////////////////////////////////////////////
+ // Calculate reverse transitive score (l->query-) Zrq[l]
+
+ fprintf(stderr,"Calculate Zrq vector of transitive Z-scores\n");
+ for (k=0; k<N; k++)
+ {
+ // Construct vector ll of indices l for which Z_lk > Zmin_tran
+ m = 0;
+ for (l=0; l<N; l++)
+ if (Z[l][k]+Z[k][l]>=2*Zmin_trans) ll[m++]=l;
+ int M = m; // number of indices l for which Z_lq,Z_lk > Zmin_tran
+
+
+// fprintf(stderr,"\nfam[k]: %s\n",fam[k]);
+// for (m=0; m<M; m++)
+// printf(stderr,"m=%-4i k=%-4i l=%-4i %-10.10s Zq[l]=%7f Z_lk=%7f \n",m,k,ll[m],fold[ll[m]],Zq[ll[m]],Z[k][ll[m]]);
+
+ if (M<=1)
+ {
+ Zrq[k] = Zq[k];
+ }
+ else
+ {
+ // Generate submatrix of C for indices l for which Z_lq,Z_lk > Zmin_trans
+ double** Csub = new(double*[M]);
+ for (m=0; m<M; m++)
+ {
+ Csub[m] = new(double[M]);
+ for (n=0; n<M; n++)
+ Csub[m][n] = double(C[ll[m]][ll[n]]);
+ }
+// fprintf(stderr,"Covariance matrix\n");
+// PrintMatrix(Csub,M);
+
+ if (M<=2)
+ {
+ for (m=0; m<M; m++) w[m] = 1.0/M;
+ }
+ else
+ {
+
+ double** Cinv = new(double*[M]);
+ for (m=0; m<M; m++) Cinv[m] = new(double[M]);
+
+// // Invert Csub
+// InvertMatrix(Cinv,Csub,M);
+
+// // fprintf(stderr,"Inverse covariance matrix\n");
+// // PrintMatrix(Cinv,M);
+
+ // Calculate weights w[l]
+ for (m=0; m<M; m++)
+ {
+ double sum = 0.0;
+ for (n=0; n<M; n++)
+ sum += 1.0 * Csub[m][n];
+ w[m] = (sum>0? Z[ll[m]][k] / sum : 0.0);
+ }
+
+// for (m=0; m<M; m++) fprintf(stderr,"w[%i]=%8.2g\n",m,w[m]);
+
+ for (l=0; l<M; l++){
+ delete[](Cinv[l]); (Cinv[l]) = NULL;
+ }
+ delete[](Cinv); (Cinv) = NULL;
+ }
+
+ // Calculate Zrq[k] and normalize
+ float norm = NormalizationFactor(Csub,w,M);
+ double sumZ = 0.0;
+ for (m=0; m<M; m++)
+ sumZ += w[m] * Zq[ll[m]];
+ Zrq[k] = sumZ/norm;
+
+ for (l=0; l<M; l++){
+ delete[](Csub[l]); (Csub[l]) = NULL;
+ }
+ delete[](Csub); (Csub) = NULL;
+ }
+
+// fprintf(stderr,"\nZq[k]=%8.2g Zq1[k]=%8.2g\n",Zq[k],Zrq[k]);
+ }
+
+ // Total Z-score = weighted sum over original Z-score, forward transitive and reverse transitive Z-score
+ for (k=0; k<N; k++)
+ {
+ float Zqtot = Zq[k] + par.wtrans*(Ztq[k]+Zrq[k]);
+// if (isnan(Zqtot))
+// {
+// fprintf(stderr,"Error: a floating point exception occurred. Skipping transitive scoring\n");
+// printf("%4i %-10.10s Zq=%6.2f Ztq=%6.2f Zrq=%6.2f Zqtot=%6.2f\n",k,fam[k],Zq[k],Ztq[k],Zrq[k],Zqtot);
+// par.trans=0;
+// return;
+// }
+ if (v>=2 && Zq[k] + Zqtot > 2*Zmin_trans) {
+ printf("%4i %-10.10s Zq=%6.2f Ztq=%6.2f Zrq=%6.2f -> Zqtot=%6.2f\n",k,fam[k],Zq[k],Ztq[k],Zrq[k],Zqtot);
+ }
+ Ztq[k] = Zqtot;
+ }
+
+ // Calculate mean and standard deviation of Z1q
+ fprintf(stderr,"Calculate mean and standard deviation of Ztq\n");
+ double sumw=0.0;
+ double sumZ=0.0;
+ double sumZ2=0.0;
+ for (k=0; k<N; k++)
+ {
+ if (excluded.Contains(fold[k])) continue;
+ sumw += weight[k];
+ sumZ += weight[k]*Ztq[k];
+ sumZ2 += weight[k]*Ztq[k]*Ztq[k];
+// if (isnan(sumZ))
+// {
+// fprintf(stderr,"Error: a floating point exception occurred. Skipping transitive scoring\n");
+// printf("%4i %-10.10s Zq=%9f Zrq=%9f Ztq=%9f\n",k,fam[k],Zq[k],Zrq[k],Ztq[k]);
+// par.trans=0;
+// return;
+// }
+ }
+ float mu = sumZ/sumw;
+ float sigma = sqrt(sumZ2/sumw-mu*mu);
+ if (v>=2) printf("mu(Ztq)=%6.3f sigma(Ztq)=%6.2f\n",mu,sigma);
+ sigma *= 1.01;// correct different fitting of EVD and normal variables
+
+ // Normalize Ztq and calculate P1-values
+ fprintf(stderr,"Normalize Ztq and calculate P1-values\n");
+ Reset();
+ while (!End())
+ {
+ hit = ReadNext();
+ hit.logPval = -Z2Score((Ztq[index.Show(hit.name)]-mu)/sigma);
+ hit.E1val = N_searched*(hit.logPval<-100? 0.0 : exp(hit.logPval));
+ // P-value = 1- exp(-exp(-lamda*(Saa-mu))) => -lamda*(Saa-mu) = log(-log(1-Pvalue))
+ hit.score_aass = (hit.logPval<-10.0? hit.logPval : log(-log(1-exp(hit.logPval))) ) / 0.45-3.0 - hit.score_ss;
+ hit.Probab = Probab(hit);
+ hit.score_sort = hit.logPval;
+ Overwrite(hit); // copy hit object into current position of hitlist
+ }
+
+ for (k=0; k<N; k++){
+ delete[](Z[k]); (Z[k]) = NULL;
+ }
+ for (k=0; k<N; k++){
+ delete[](C[k]); (C[k]) = NULL;
+ }
+ for (k=0; k<N; k++){
+ delete[](fold[k]); (fold[k]) = NULL;
+ }
+ for (k=0; k<N; k++){
+ delete[](fam[k]); (fam[k]) = NULL;
+ }
+ delete[](C); (C) = NULL;
+ delete[](Z); (Z) = NULL;
+ delete[](fold); (fold) = NULL;
+ delete[](fam); (fam) = NULL;
+ delete[](Prob); (Prob) = NULL;
+ delete[](ll); (ll) = NULL;
+ delete[](Zq); (Zq) = NULL;
+ delete[](Ztq); (Ztq) = NULL;
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Calculate P-values and Probabilities from transitive scoring over whole database
+ * Like TransitiveScoring(),
+ * but in transitive scoring, Z1_qk = sum_l w_l*Z_lk, use all l:E_ql<=E_qk
+ * and in reverse scoring, Z1_kr = sum_l w_l*Z_lq, use all l:E_kl<=E_kq
+ */
+void
+HitList::TransitiveScoring3()
+{
+ void PrintMatrix(float** V, int N);
+ void PrintMatrix(double** V, int N);
+
+ float** Z; // matrix of intra-db Z-scores Z_kl
+ float** C; // covariance matrix for Z_k: C_kl = sum_m=1^N (Z_km * Z_lm)
+ char** fold; // fold name of HMM k
+ char** fam; // family of HMM k
+ float* Prob; // probability of HMM k
+ float* Zq; // Zq[k] = Z-score between query and database HMM k
+ float* Ztq; // Ztq[k] = transitive Z-score from query to database HMM k: Ztq[k] = sum_l[ w_ql * Z_lk] / normalization_q
+ float* Zrq; // Zrq[k] = transitive Z-score from database HMM k to query: Zrq[k] = sum_l[ w_kl * Z_lq] / normalization_k
+ float* w; // unnormalized weight matrix; w[l] is w_ql or w_kl, respectively
+ int* ll; // ll[m] is the m'th index l for which Z_lq, Z_lk > Zmin_trans
+ int N; // dimension of weight matrix is NxN
+ int M; // number of HMMs l with Z_ql>Ztrans_min (or Z_lk>Ztrans_min, respectively)
+ int k,l,m,n; // indices for database HMMs
+ char name[NAMELEN];
+ Hash<int> index(MAXPROF+7); // index{name} = index of HMM name in {1,...,N}
+ index.Null(-1); // Set int value to return when no data can be retrieved
+ Hash<int> excluded(13); // Hash containing names of superfamilies to be excluded from fit
+ excluded.Null(0); // Set int value to return when no data can be retrieved
+ Hit hit;
+ size_t unused; /* disable fread gcc warning */
+
+ // Read weights matrix W with index hash and names array
+ fprintf(stderr,"Reading in weights file\n");
+ FILE* wfile = fopen(par.wfile,"rb");
+ if (v>=1 && wfile==NULL)
+ {
+ fprintf(stderr,"Error: %s could not be opened: (N_searched=%i) ",par.wfile,N_searched);
+ perror("fopen");
+ fprintf(stderr,"Skipping caclulation of transitive P-values\n");
+ par.trans=0;
+ return;
+ }
+ unused = fread(&N,sizeof(int),1,wfile); // read matrix dimension (i.e. number of HMMs in database)
+ if (v>=1 && N!=N_searched)
+ {
+ fprintf(stderr,"Error: Number %i of HMMs in weight file is different from number %i of HMMs in searched databases. \n",N,N_searched);
+ fprintf(stderr,"Skipping caclulation of transitive P-values\n");
+ par.trans=0;
+ return;
+ }
+ if (v>=2) fprintf(stderr,"Calculating transitive P-values for %i HMMs\n",N);
+ // Read names of HMMs (to specify mapping of HMM to matrix indices)
+ for (k=0; k<N; k++)
+ {
+ unused = fread(name,sizeof(char),IDLEN,wfile);
+ index.Add(name,k);
+ }
+ // Read symmetric Z-scores matrix
+ Z = new(float*[N]);
+ for (k=0; k<N; k++)
+ {
+ Z[k] = new(float[N]);
+ for (l=0; l<k; l++) Z[k][l] = Z[l][k];
+ unused = fread(Z[k]+k,sizeof(float),N-k,wfile);
+ }
+ // Read symmetric covariance matrix
+ C = new(float*[N]);
+ for (k=0; k<N; k++)
+ {
+ C[k] = new(float[N]);
+ for (l=0; l<k; l++) C[k][l] = C[l][k];
+ unused = fread(C[k]+k,sizeof(float),N-k,wfile);
+ }
+ fclose(wfile);
+
+ // Allocate memory
+ Zq = new(float[N]);
+ Ztq = new(float[N]);
+ Zrq = new(float[N]);
+ fold = new(char*[N]);
+ fam = new(char*[N]);
+ Prob = new(float[N]);
+ ll = new(int[N]);
+ w = new(float[N]);
+
+ // Transform P-values to normally distributed Z-scores and store in Zq vector
+ fprintf(stderr,"Transform P-values to Z-scores\n");
+ float Zmax_neg = Score2Z( -log(MINEVALEXCL) + log(N_searched) ); // calculate Z-score corresponding to E-value MINEVALEXCL
+ float Zmin_trans = Score2Z( -log(par.Emax_trans) + log(N_searched) ); // calculate Z-score corresponding to E-value par.Emax_trans
+ printf("Zmax = %6.2f Zmin = %6.2f \n",Zmax_neg,Zmin_trans);
+
+ Reset();
+ while (!End())
+ {
+ hit = ReadNext();
+ if (hit.irep>1) continue;
+ k = index.Show(hit.name);
+ if (k<0) {fprintf(stderr,"Error: no index found in weights file for domain %s\n",hit.name); exit(1);}
+ if (hit.logPvalt<0)
+ Zq[k] = 0.5*Score2Z(fabs(hit.logPval)) + 0.5*Score2Z(fabs(hit.logPvalt)); // Zq[k] = 0.5*(Zkq + Zqk)
+ else
+ Zq[k] = Score2Z(fabs(hit.logPval)); // Zq[k] = Zqk
+// printf("%4i %-10.10s logPvalt=%9g Zq=%9f\n",k,hit.name,hit.logPvalt,Zq[k]);
+// if (isnan(Zq[k]))
+// {
+// fprintf(stderr,"Error: a floating point exception occurred. Skipping transitive scoring\n");
+// printf("%4i %-10.10s logPval=%9g logPvalt=%9g Zq=%9f\n",k,hit.name,hit.logPval,hit.logPvalt,Zq[k]);
+// par.trans=0;
+// return;
+// }
+ if (Zq[k]>Zmax_neg) excluded.Add(hit.fold);
+ fold[k] = new(char[IDLEN]);
+ fam[k] = new(char[IDLEN]);
+ strcpy(fold[k],hit.fold);
+ strcpy(fam[k],hit.fam);
+ weight[k] = hit.weight;
+ Prob[k] = hit.Probab;
+ }
+
+ if (v>=3)
+ {
+ excluded.Reset();
+ while (!excluded.End())
+ {
+ excluded.ReadNext(name);
+ printf("Excluded fold %s from fitting to Ztq\n",name);
+ }
+ }
+
+
+ ////////////////////////////////////////////////////////////////
+ // Calculate transitive score (query->l) Ztq[l]
+
+ fprintf(stderr,"Calculate Ztq vector of transitive Z-scores\n");
+ for (k=0; k<N; k++)
+ {
+ // Construct vector ll of indices l for which Z_lq OR Z_lk >= max(Z_kq,Zmin_trans)
+ float Zmink = fmax(Zq[k],Zmin_trans);
+ for (m=l=0; l<N; l++)
+ if (Zq[l]>=Zmink) ll[m++]=l;
+ M = m; // number of indices l for which Z_lq OR Z_lk >= max(Z_kq,Zmin_trans)
+
+// for (m=0; m<M; m++)
+// fprintf(stderr,"m=%-4i l=%-4i %-10.10s Zq[l]=%7f\n",m,ll[m],fam[ll[m]],Zq[ll[m]]);
+
+ if (M<=1)
+ {
+ Ztq[k]=Zq[k];
+ }
+ else
+ {
+ // Generate submatrix of C for indices l for which Z_lq,Z_lk > Zmin_trans
+ double** Csub = new(double*[M]);
+ double** Cinv = new(double*[M]);
+ for (m=0; m<M; m++)
+ {
+ Csub[m] = new(double[M]);
+ Cinv[m] = new(double[M]);
+ for (n=0; n<M; n++)
+ Csub[m][n] = double(C[ll[m]][ll[n]]);
+ }
+
+// fprintf(stderr,"Covariance matrix\n");
+// PrintMatrix(Csub,M);
+
+ // Invert Csub
+// fprintf(stderr,"Calculate inverse of covariance submatrix\n");
+ InvertMatrix(Cinv,Csub,M);
+
+// fprintf(stderr,"Inverse covariance matrix\n");
+// PrintMatrix(Cinv,M);
+
+ // Calculate weights w[l]
+ for (m=0; m<M; m++)
+ {
+ double sum = 0.0;
+ for (n=0; n<M; n++)
+ sum += 1.0 * Cinv[m][n]; // signal ~ sum_l w_l*Z_lq !
+ w[m] = fmax(sum,0.0);
+ }
+ for (l=0; l<M; l++){
+ delete[](Cinv[l]); (Cinv[l]) = NULL;
+ }
+ delete[](Cinv); (Cinv) = NULL;
+
+ // Calculate Ztq[k]
+ float norm = NormalizationFactor(Csub,w,M);
+ double sumZ = 0.0;
+ for (m=0; m<M; m++)
+ sumZ += w[m] * fmin(Zq[ll[m]],Z[ll[m]][k]);
+// sumZ += w[m] * Z[ll[m]][k];
+ Ztq[k] = sumZ/norm;
+
+ for (l=0; l<M; l++){
+ delete[](Csub[l]); (Csub[l]) = NULL;
+ }
+ delete[](Csub); (Csub) = NULL;
+ }
+ }
+
+ ////////////////////////////////////////////////////////////////
+ // Calculate reverse transitive score (l->query-) Zrq[l]
+
+ fprintf(stderr,"Calculate Zrq vector of transitive Z-scores\n");
+ for (k=0; k<N; k++)
+ {
+ // Construct vector ll of indices l for which Z_lk > Zmin_tran
+ float Zmink = fmax(Zq[k],Zmin_trans);
+ for (m=l=0; l<N; l++)
+ if (Z[l][k]>=Zmink) ll[m++]=l;
+ int M = m; // number of indices l for which Z_lq,Z_lk > Zmin_tran
+
+
+// fprintf(stderr,"\nfam[k]: %s\n",fam[k]);
+// for (m=0; m<M; m++)
+// printf(stderr,"m=%-4i k=%-4i l=%-4i %-10.10s Zq[l]=%7f Z_lk=%7f \n",m,k,ll[m],fold[ll[m]],Zq[ll[m]],Z[k][ll[m]]);
+
+ if (M<=1)
+ {
+ Zrq[k] = Zq[k];
+ }
+ else
+ {
+ // Generate submatrix of C for indices l for which Z_lq,Z_lk > Zmin_trans
+ double** Csub = new(double*[M]);
+ for (m=0; m<M; m++)
+ {
+ Csub[m] = new(double[M]);
+ for (n=0; n<M; n++)
+ Csub[m][n] = double(C[ll[m]][ll[n]]);
+ }
+// fprintf(stderr,"Covariance matrix\n");
+// PrintMatrix(Csub,M);
+
+ if (M==2)
+ {
+ for (m=0; m<M; m++) w[m] = 1.0/M;
+ }
+ else
+ {
+
+ double** Cinv = new(double*[M]);
+ for (m=0; m<M; m++) Cinv[m] = new(double[M]);
+
+ // Invert Csub
+ InvertMatrix(Cinv,Csub,M);
+
+ // fprintf(stderr,"Inverse covariance matrix\n");
+ // PrintMatrix(Cinv,M);
+
+ // Calculate weights w[l]
+ for (m=0; m<M; m++)
+ {
+ double sum = 0.0;
+ for (n=0; n<M; n++)
+ sum += 1.0 * Cinv[m][n]; // signal ~ sum_l w_l*Z_lq !
+ w[m] = fmax(sum,0.0);
+ }
+// for (m=0; m<M; m++) fprintf(stderr,"w[%i]=%8.2g\n",m,w[m]);
+ for (l=0; l<M; l++){
+ delete[](Cinv[l]); (Cinv[l]) = NULL;
+ }
+ delete[](Cinv); (Cinv) = NULL;
+ }
+
+ // Calculate Zrq[k] and normalize
+ float norm = NormalizationFactor(Csub,w,M);
+ double sumZ = 0.0;
+ for (m=0; m<M; m++)
+ sumZ += w[m] * fmin(Zq[ll[m]],Z[ll[m]][k]);
+// sumZ += w[m] * Zq[ll[m]];
+ Zrq[k] = sumZ/norm;
+
+ for (l=0; l<M; l++){
+ delete[](Csub[l]); (Csub[l]) = NULL;
+ }
+ delete[](Csub); (Csub) = NULL;
+ }
+
+// fprintf(stderr,"\nZq[k]=%8.2g Zq1[k]=%8.2g\n",Zq[k],Zrq[k]);
+ }
+
+ // Total Z-score = weighted sum over original Z-score, forward transitive and reverse transitive Z-score
+ for (k=0; k<N; k++)
+ {
+
+ float Zqtot = Zq[k] + par.wtrans*(Ztq[k]+Zrq[k]);
+// if (isnan(Zqtot))
+// {
+// fprintf(stderr,"Error: a floating point exception occurred. Skipping transitive scoring\n");
+// printf("%4i %-10.10s Zq=%6.2f Ztq=%6.2f Zrq=%6.2f -> Zqtot=%6.2f\n",k,fam[k],Zq[k],Ztq[k],Zrq[k],Zqtot);
+// par.trans=0;
+// return;
+// }
+ if (v>=3 && Zqtot > 2*Zmin_trans) {
+ printf("%4i %-10.10s Zq=%6.2f Ztq=%6.2f Zrq=%6.2f -> Zqtot=%6.2f\n",k,fam[k],Zq[k],Ztq[k],Zrq[k],Zqtot);
+ }
+ Ztq[k] = Zqtot;
+ }
+
+ // Calculate mean and standard deviation of Z1q
+ fprintf(stderr,"Calculate mean and standard deviation of Ztq\n");
+ double sumw=0.0;
+ double sumZ=0.0;
+ double sumZ2=0.0;
+ for (k=0; k<N; k++)
+ {
+ if (excluded.Contains(fold[k])) continue;
+ sumw += weight[k];
+ sumZ += weight[k]*Ztq[k];
+ sumZ2 += weight[k]*Ztq[k]*Ztq[k];
+// if (isnan(sumZ))
+// {
+// fprintf(stderr,"Error: a floating point exception occurred. Skipping transitive scoring\n");
+// printf("%4i %-10.10s Zq=%9f Zrq=%9f Ztq=%9f\n",k,fam[k],Zq[k],Zrq[k],Ztq[k]);
+// par.trans=0;
+// return;
+// }
+ }
+ float mu = sumZ/sumw;
+ float sigma = sqrt(sumZ2/sumw-mu*mu);
+ if (v>=2) printf("mu(Ztq)=%6.3f sigma(Ztq)=%6.2f\n",mu,sigma);
+ sigma *= 1.01;// correct different fitting of EVD and normal variables
+
+ // Normalize Ztq and calculate P1-values
+ fprintf(stderr,"Normalize Ztq and calculate P1-values\n");
+ Reset();
+ while (!End())
+ {
+ hit = ReadNext();
+ hit.logPval = -Z2Score((Ztq[index.Show(hit.name)]-mu)/sigma);
+ hit.E1val = N_searched*(hit.logPval<-100? 0.0 : exp(hit.logPval));
+ // P-value = 1- exp(-exp(-lamda*(Saa-mu))) => -lamda*(Saa-mu) = log(-log(1-Pvalue))
+ hit.score_aass = (hit.logPval<-10.0? hit.logPval : log(-log(1-exp(hit.logPval))) ) / 0.45-3.0 - hit.score_ss;
+ hit.Probab = Probab(hit);
+ hit.score_sort = hit.logPval;
+ Overwrite(hit); // copy hit object into current position of hitlist
+ }
+
+ for (k=0; k<N; k++){
+ delete[](Z[k]); (Z[k]) = NULL;
+ }
+ for (k=0; k<N; k++){
+ delete[](C[k]); (C[k]) = NULL;
+ }
+ for (k=0; k<N; k++){
+ delete[](fold[k]); (fold[k]) = NULL;
+ }
+ for (k=0; k<N; k++){
+ delete[](fam[k]); (fam[k]) = NULL;
+ }
+ delete[](C); (C) = NULL;
+ delete[](Z); (Z) = NULL;
+ delete[](fold); (fold) = NULL;
+ delete[](fam); (fam) = NULL;
+ delete[](Prob); (Prob) = NULL;
+ delete[](ll); (ll) = NULL;
+ delete[](Zq); (Zq) = NULL;
+ delete[](Ztq); (Ztq) = NULL;
+
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Calculate P-values and Probabilities from transitive scoring over whole database
+ * Best tested scheme. Use fmin(Zq[ll[m]],Z[ll[m]][k])
+ * and fast approximation for weights (not inverse covariance matrix)
+ */
+void
+HitList::TransitiveScoring4()
+{
+ void PrintMatrix(float** V, int N);
+ void PrintMatrix(double** V, int N);
+
+ float** Z; // matrix of intra-db Z-scores Z_kl
+ float** C; // covariance matrix for Z_k: C_kl = sum_m=1^N (Z_km * Z_lm)
+ char** fold; // fold name of HMM k
+ char** fam; // family of HMM k
+ float* Prob; // probability of HMM k
+ float* Zq; // Zq[k] = Z-score between query and database HMM k
+ float* Ztq; // Ztq[k] = transitive Z-score from query to database HMM k: Ztq[k] = sum_l[ w_ql * Z_lk] / normalization_q
+ float* Zrq; // Zrq[k] = transitive Z-score from database HMM k to query: Zrq[k] = sum_l[ w_kl * Z_lq] / normalization_k
+ float* w; // unnormalized weight matrix; w[l] is w_ql or w_kl, respectively
+ int* ll; // ll[m] is the m'th index l for which Z_lq, Z_lk > Zmin_trans
+ int N; // dimension of weight matrix is NxN
+ int M; // number of HMMs l with Z_ql>Ztrans_min (or Z_lk>Ztrans_min, respectively)
+ int k,l,m,n; // indices for database HMMs
+ char name[NAMELEN];
+ Hash<int> index(MAXPROF+7); // index{name} = index of HMM name in {1,...,N}
+ index.Null(-1); // Set int value to return when no data can be retrieved
+ Hash<int> excluded(13); // Hash containing names of superfamilies to be excluded from fit
+ excluded.Null(0); // Set int value to return when no data can be retrieved
+ Hit hit;
+ size_t unused; /* disable fread gcc warning */
+
+ // Read weights matrix W with index hash and names array
+ fprintf(stderr,"Reading in weights file\n");
+ FILE* wfile = fopen(par.wfile,"rb");
+ if (v>=1 && wfile==NULL)
+ {
+ fprintf(stderr,"Error: %s could not be opened: (N_searched=%i) ",par.wfile,N_searched);
+ perror("fopen");
+ fprintf(stderr,"Skipping caclulation of transitive P-values\n");
+ par.trans=0;
+ return;
+ }
+ unused = fread(&N,sizeof(int),1,wfile); // read matrix dimension (i.e. number of HMMs in database)
+ if (v>=1 && N!=N_searched)
+ {
+ fprintf(stderr,"Error: Number %i of HMMs in weight file is different from number %i of HMMs in searched databases. \n",N,N_searched);
+ fprintf(stderr,"Skipping caclulation of transitive P-values\n");
+ par.trans=0;
+ return;
+ }
+ if (v>=2) fprintf(stderr,"Calculating transitive P-values for %i HMMs\n",N);
+ // Read names of HMMs (to specify mapping of HMM to matrix indices)
+ for (k=0; k<N; k++)
+ {
+ unused = fread(name,sizeof(char),IDLEN,wfile);
+ index.Add(name,k);
+ }
+ // Read symmetric Z-scores matrix
+ Z = new(float*[N]);
+ for (k=0; k<N; k++)
+ {
+ Z[k] = new(float[N]);
+ for (l=0; l<k; l++) Z[k][l] = Z[l][k];
+ unused = fread(Z[k]+k,sizeof(float),N-k,wfile);
+ }
+ // Read symmetric covariance matrix
+ C = new(float*[N]);
+ for (k=0; k<N; k++)
+ {
+ C[k] = new(float[N]);
+ for (l=0; l<k; l++) C[k][l] = C[l][k];
+ unused = fread(C[k]+k,sizeof(float),N-k,wfile);
+ }
+ fclose(wfile);
+
+ // Allocate memory
+ Zq = new(float[N]);
+ Ztq = new(float[N]);
+ Zrq = new(float[N]);
+ fold = new(char*[N]);
+ fam = new(char*[N]);
+ Prob = new(float[N]);
+ ll = new(int[N]);
+ w = new(float[N]);
+
+ // Transform P-values to normally distributed Z-scores and store in Zq vector
+ fprintf(stderr,"Transform P-values to Z-scores\n");
+ float Zmax_neg = Score2Z( -log(MINEVALEXCL) + log(N_searched) ); // calculate Z-score corresponding to E-value MINEVALEXCL
+ float Zmin_trans = Score2Z( -log(par.Emax_trans) + log(N_searched) ); // calculate Z-score corresponding to E-value par.Emax_trans
+ printf("Zmax = %6.2f Zmin = %6.2f \n",Zmax_neg,Zmin_trans);
+
+ Reset();
+ while (!End())
+ {
+ hit = ReadNext();
+ if (hit.irep>1) continue;
+ k = index.Show(hit.name);
+ if (k<0) {fprintf(stderr,"Error: no index found in weights file for domain %s\n",hit.name); exit(1);}
+ if (hit.logPvalt<0)
+ Zq[k] = 0.5*Score2Z(fabs(hit.logPval)) + 0.5*Score2Z(fabs(hit.logPvalt)); // Zq[k] = 0.5*(Zkq + Zqk)
+ else
+ Zq[k] = Score2Z(fabs(hit.logPval)); // Zq[k] = Zqk
+// printf("%4i %-10.10s logPvalt=%9g Zq=%9f\n",k,hit.name,hit.logPvalt,Zq[k]);
+// if (isnan(Zq[k])) {
+// fprintf(stderr,"Error: a floating point exception occurred. Skipping transitive scoring\n");
+// printf("%4i %-10.10s logPval=%9g logPvalt=%9g Zq=%9f\n",k,hit.name,hit.logPval,hit.logPvalt,Zq[k]);
+// par.trans=0;
+// return;
+// }
+ if (Zq[k]>Zmax_neg) excluded.Add(hit.fold);
+ fold[k] = new(char[IDLEN]);
+ fam[k] = new(char[IDLEN]);
+ strcpy(fold[k],hit.fold);
+ strcpy(fam[k],hit.fam);
+ weight[k] = hit.weight;
+ Prob[k] = hit.Probab;
+ }
+
+ if (v>=3)
+ {
+ excluded.Reset();
+ while (!excluded.End())
+ {
+ excluded.ReadNext(name);
+ printf("Excluded fold %s from fitting to Ztq\n",name);
+ }
+ }
+
+ ////////////////////////////////////////////////////////////////
+ // Calculate transitive score (query->l) Zt[l]
+
+ // Construct vector ll of indices l for which Z_lq > Zmin_trans
+ m = 0;
+ for (l=0; l<N; l++)
+ if (Zq[l]>=Zmin_trans) ll[m++]=l;
+ M = m; // number of indices l for which Z_lq,Z_lk > Zmin_trans
+
+// for (m=0; m<M; m++)
+// fprintf(stderr,"m=%-4i l=%-4i %-10.10s Zq[l]=%7f\n",m,ll[m],fam[ll[m]],Zq[ll[m]]);
+
+ if (M<=1)
+ for (k=0; k<N; k++) Ztq[k]=0.0;
+ else
+ {
+ // Generate submatrix of C for indices l for which Z_lq,Z_lk > Zmin_trans
+ double** Csub = new(double*[M]);
+ for (m=0; m<M; m++)
+ {
+ Csub[m] = new(double[M]);
+ for (n=0; n<M; n++)
+ Csub[m][n] = double(C[ll[m]][ll[n]]);
+ }
+
+ if (v>=3)
+ {
+ fprintf(stderr,"Covariance matrix\n");
+ PrintMatrix(Csub,M);
+ }
+
+
+ // Calculate weights w[l]
+ for (m=0; m<M; m++)
+ {
+ double sum = 0.0;
+ for (n=0; n<M; n++)
+ sum += fmax(0.0,Csub[m][n]);
+ printf("w[%4i] = %-8.5f\n",ll[m],1.0/sum);
+ w[m] = 1.0/sum;
+ }
+
+ // Calculate Ztq[k] for all HMMs k
+ fprintf(stderr,"Calculate Ztq vector of transitive Z-scores\n");
+ float norm = NormalizationFactor(Csub,w,M);
+ for (k=0; k<N; k++)
+ {
+ double sumZ = 0.0;
+ for (m=0; m<M; m++)
+ sumZ += w[m] * fmin(Zq[ll[m]],Z[ll[m]][k]);
+ Ztq[k] = sumZ/norm;
+ }
+
+ for (l=0; l<M; l++){
+ delete[](Csub[l]); (Csub[l]) = NULL;
+ }
+ delete[](Csub); (Csub) = NULL;
+ }
+
+ ////////////////////////////////////////////////////////////////
+ // Calculate reverse transitive score (l->query-) Zrq[l]
+
+ fprintf(stderr,"Calculate Zrq vector of transitive Z-scores\n");
+ for (k=0; k<N; k++)
+ {
+ // Construct vector ll of indices l for which Z_lk > Zmin_tran
+ m = 0;
+ for (l=0; l<N; l++)
+ if (Z[k][l]>=Zmin_trans) ll[m++]=l;
+ int M = m; // number of indices l for which Z_lq,Z_lk > Zmin_tran
+
+
+// fprintf(stderr,"\nfam[k]: %s\n",fam[k]);
+// for (m=0; m<M; m++)
+// printf(stderr,"m=%-4i k=%-4i l=%-4i %-10.10s Zq[l]=%7f Z_lk=%7f \n",m,k,ll[m],fold[ll[m]],Zq[ll[m]],Z[k][ll[m]]);
+
+ if (M<=1)
+ {
+ Zrq[k] = Zq[k];
+ }
+ else
+ {
+ // Generate submatrix of C for indices l for which Z_lq,Z_lk > Zmin_trans
+ double** Csub = new(double*[M]);
+ for (m=0; m<M; m++)
+ {
+ Csub[m] = new(double[M]);
+ for (n=0; n<M; n++)
+ Csub[m][n] = double(C[ll[m]][ll[n]]);
+ }
+// fprintf(stderr,"Covariance matrix\n");
+// PrintMatrix(Csub,M);
+
+ // Calculate weights w[l]
+ for (m=0; m<M; m++)
+ {
+ double sum = 0.0;
+ for (n=0; n<M; n++)
+ sum += fmax(0.0,Csub[m][n]);
+ w[m] = 1.0/sum;
+ }
+
+// for (m=0; m<M; m++) fprintf(stderr,"w[%i]=%8.2g\n",m,w[m]);
+
+
+ // Calculate Zrq[k] and normalize
+ float norm = NormalizationFactor(Csub,w,M);
+ double sumZ = 0.0;
+ for (m=0; m<M; m++)
+ sumZ += w[m] * fmin(Zq[ll[m]],Z[ll[m]][k]);
+ Zrq[k] = sumZ/norm;
+
+ for (l=0; l<M; l++){
+ delete[](Csub[l]); (Csub[l]) = NULL;
+ }
+ delete[](Csub); (Csub) = NULL;
+ }
+
+// fprintf(stderr,"\nZq[k]=%8.2g Zq1[k]=%8.2g\n",Zq[k],Zrq[k]);
+ }
+
+ // Total Z-score = weighted sum over original Z-score, forward transitive and reverse transitive Z-score
+ for (k=0; k<N; k++)
+ {
+ float Zqtot = Zq[k] + par.wtrans*(Ztq[k]+Zrq[k]);
+// if (isnan(Zqtot))
+// {
+// fprintf(stderr,"Error: a floating point exception occurred. Skipping transitive scoring\n");
+// printf("%4i %-10.10s Zq=%6.2f Ztq=%6.2f Zrq=%6.2f Zqtot=%6.2f\n",k,fam[k],Zq[k],Ztq[k],Zrq[k],Zqtot);
+// par.trans=0;
+// return;
+// }
+ if (v>=3 && Zq[k] + Zqtot > 2*Zmin_trans) {
+ printf("%4i %-10.10s Zq=%6.2f Ztq=%6.2f Zrq=%6.2f -> Zqtot=%6.2f\n",k,fam[k],Zq[k],Ztq[k],Zrq[k],Zqtot);
+ }
+ Ztq[k] = Zqtot;
+ }
+
+ // Calculate mean and standard deviation of Z1q
+ fprintf(stderr,"Calculate mean and standard deviation of Ztq\n");
+ double sumw=0.0;
+ double sumZ=0.0;
+ double sumZ2=0.0;
+ for (k=0; k<N; k++)
+ {
+ if (excluded.Contains(fold[k])) continue;
+ sumw += weight[k];
+ sumZ += weight[k]*Ztq[k];
+ sumZ2 += weight[k]*Ztq[k]*Ztq[k];
+// if (isnan(sumZ))
+// {
+// fprintf(stderr,"Error: a floating point exception occurred. Skipping transitive scoring\n");
+// printf("%4i %-10.10s Zq=%9f Zrq=%9f Ztq=%9f\n",k,fam[k],Zq[k],Zrq[k],Ztq[k]);
+// par.trans=0;
+// return;
+// }
+ }
+ float mu = sumZ/sumw;
+ float sigma = sqrt(sumZ2/sumw-mu*mu);
+ if (v>=2) printf("mu(Ztq)=%6.3f sigma(Ztq)=%6.2f\n",mu,sigma);
+ sigma *= 1.01;// correct different fitting of EVD and normal variables
+
+ // Normalize Ztq and calculate P1-values
+ fprintf(stderr,"Normalize Ztq and calculate P1-values\n");
+ Reset();
+ while (!End())
+ {
+ hit = ReadNext();
+ hit.logPval = -Z2Score((Ztq[index.Show(hit.name)]-mu)/sigma);
+ hit.E1val = N_searched*(hit.logPval<-100? 0.0 : exp(hit.logPval));
+ // P-value = 1- exp(-exp(-lamda*(Saa-mu))) => -lamda*(Saa-mu) = log(-log(1-Pvalue))
+ hit.score_aass = (hit.logPval<-10.0? hit.logPval : log(-log(1-exp(hit.logPval))) ) / 0.45-3.0 - hit.score_ss;
+ hit.Probab = Probab(hit);
+ hit.score_sort = hit.logPval;
+ Overwrite(hit); // copy hit object into current position of hitlist
+ }
+
+ for (k=0; k<N; k++){
+ delete[](Z[k]); (Z[k]) = NULL;
+ }
+ for (k=0; k<N; k++){
+ delete[](C[k]); (C[k]) = NULL;
+ }
+ for (k=0; k<N; k++){
+ delete[](fold[k]); (fold[k]) = NULL;
+ }
+ for (k=0; k<N; k++){
+ delete[](fam[k]); (fam[k]) = NULL;
+ }
+ delete[](C); (C) = NULL;
+ delete[](Z); (Z) = NULL;
+ delete[](fold); (fold) = NULL;
+ delete[](fam); (fam) = NULL;
+ delete[](Prob); (Prob) = NULL;
+ delete[](ll); (ll) = NULL;
+ delete[](Zq); (Zq) = NULL;
+ delete[](Ztq); (Ztq) = NULL;
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Score2Z transforms the -log(P-value) score into a Z-score for 0 < S
+ * Score2Z(S) = sqrt(2)*dierfc(2*e^(-S)), where dierfc is the inverse of the complementary error function
+ */
+double
+HitList::Score2Z(double S)
+{
+ double s, t, u, w, x, y, z;
+ if (S<=0) return double(-100000);
+ y = ( S>200 ? 0.0 : 2.0*exp(-S) );
+ if (y > 1)
+ {
+ z = (S<1e-6? 2*S : 2-y);
+ w = 0.916461398268964 - log(z);
+ }
+ else
+ {
+ z = y;
+ w = 0.916461398268964 - (0.69314718056-S);
+ }
+
+ u = sqrt(w);
+ s = (log(u) + 0.488826640273108) / w;
+ t = 1 / (u + 0.231729200323405);
+
+ x = u * (1 - s * (s * 0.124610454613712 + 0.5)) -
+ ((((-0.0728846765585675 * t + 0.269999308670029) * t +
+ 0.150689047360223) * t + 0.116065025341614) * t +
+ 0.499999303439796) * t;
+ t = 3.97886080735226 / (x + 3.97886080735226);
+ u = t - 0.5;
+ s = (((((((((0.00112648096188977922 * u +
+ 1.05739299623423047e-4) * u - 0.00351287146129100025) * u -
+ 7.71708358954120939e-4) * u + 0.00685649426074558612) * u +
+ 0.00339721910367775861) * u - 0.011274916933250487) * u -
+ 0.0118598117047771104) * u + 0.0142961988697898018) * u +
+ 0.0346494207789099922) * u + 0.00220995927012179067;
+ s = ((((((((((((s * u - 0.0743424357241784861) * u -
+ 0.105872177941595488) * u + 0.0147297938331485121) * u +
+ 0.316847638520135944) * u + 0.713657635868730364) * u +
+ 1.05375024970847138) * u + 1.21448730779995237) * u +
+ 1.16374581931560831) * u + 0.956464974744799006) * u +
+ 0.686265948274097816) * u + 0.434397492331430115) * u +
+ 0.244044510593190935) * t -
+ (z==0? 0: z * exp(x * x - 0.120782237635245222));
+ x += s * (x * s + 1);
+ if (y > 1) {
+ x = -x;
+ }
+ return double (1.41421356237*x);
+}
+
+/////////////////////////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Z2Score transforms the Z-score into a -log(P-value) value
+ * Z2Score(Z) = log(2) - log( erfc(Z/sqrt(2)) ) , where derfc is the complementary error function
+ */
+double
+HitList::Z2Score(double Z)
+{
+ double t, u, x, y;
+ x = 0.707106781188*Z;
+ if (x>10) return 0.69314718056 - (-x*x - log( (1-0.5/x/x)/x/1.772453851) );
+ t = 3.97886080735226 / (fabs(x) + 3.97886080735226);
+ u = t - 0.5;
+ y = (((((((((0.00127109764952614092 * u + 1.19314022838340944e-4) * u -
+ 0.003963850973605135) * u - 8.70779635317295828e-4) * u +
+ 0.00773672528313526668) * u + 0.00383335126264887303) * u -
+ 0.0127223813782122755) * u - 0.0133823644533460069) * u +
+ 0.0161315329733252248) * u + 0.0390976845588484035) * u +
+ 0.00249367200053503304;
+ y = ((((((((((((y * u - 0.0838864557023001992) * u -
+ 0.119463959964325415) * u + 0.0166207924969367356) * u +
+ 0.357524274449531043) * u + 0.805276408752910567) * u +
+ 1.18902982909273333) * u + 1.37040217682338167) * u +
+ 1.31314653831023098) * u + 1.07925515155856677) * u +
+ 0.774368199119538609) * u + 0.490165080585318424) * u +
+ 0.275374741597376782) * t * (x>10? 0.0 : exp(-x * x));
+ return 0.69314718056 - log( x < 0 ? 2 - y : y );
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief
+ */
+void
+PrintMatrix(float** V, int N)
+{
+ int k,l;
+ for (k=0; k<N; k++)
+ {
+ fprintf(stderr,"k=%4i \n",k);
+ for (l=0; l<N; l++)
+ {
+ fprintf(stderr,"%4i:%6.3f ",l,V[k][l]);
+ if ((l+1)%10==0) fprintf(stderr,"\n");
+ }
+ fprintf(stderr,"\n");
+ }
+ fprintf(stderr,"\n");
+}
+
+/////////////////////////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief
+ */
+void
+PrintMatrix(double** V, int N)
+{
+ int k,l;
+ for (k=0; k<N; k++)
+ {
+ fprintf(stderr,"k=%4i \n",k);
+ for (l=0; l<N; l++)
+ {
+ fprintf(stderr,"%4i:%6.3f ",l,V[k][l]);
+ if ((l+1)%10==0) fprintf(stderr,"\n");
+ }
+ fprintf(stderr,"\n");
+ }
+ fprintf(stderr,"\n");
+}
+
+/////////////////////////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief
+ */
+void
+HitList::Normalize(float* Ztq, char** fold, Hash<int>& excluded)
+{
+ double sumw=0.0;
+ double sumZ=0.0;
+ double sumZ2=0.0;
+ for (int k=0; k<N_searched; k++)
+ {
+ if (excluded.Contains(fold[k])) continue;
+ sumw += weight[k];
+ sumZ += weight[k]*Ztq[k];
+ sumZ2 += weight[k]*Ztq[k]*Ztq[k];
+ }
+ float mu = sumZ/sumw;
+ float sigma = sqrt(sumZ2/sumw-mu*mu);
+ printf("Transitive score Ztq: mu=%8.3g sigma=%8.3g\n",mu,sigma);
+ for (int k=0; k<N_searched; k++) Ztq[k] = (Ztq[k]-mu)/sigma;
+ return;
+}
+
+/////////////////////////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Calculate standard deviation of Z1 = sum_m [ w_m * Z_m ], where Csub_mn = cov(Z_m,Z_n)
+ */
+float
+HitList::NormalizationFactor(double** Csub, float* w, int M)
+ {
+ double sum=0.0;
+ for (int m=0; m<M; m++)
+ {
+ double summ=0.0;
+ for (int n=0; n<M; n++) summ += Csub[m][n]*w[n];
+ sum += w[m]*summ;
+ }
+ return sqrt(sum);
+ }
+
+/////////////////////////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Calculate inverse of matrix A and store result in B
+ */
+void
+HitList::InvertMatrix(double** B, double** A, int N)
+{
+ if (N==0)
+ {
+ printf("Error: InvertMatrix called with matrix of dimension 0\n");
+ exit(6);
+ }
+ if (N==1)
+ {
+ B[0][0] = (A[0][0]==0.0? 0 :1.0/A[0][0]);
+ return;
+ }
+
+ int k,l,m;
+ double** V = new(double*[N]);
+ double* s = new(double[N]);
+ for (k=0; k<N; k++) V[k] = new(double[N]);
+
+ // Copy original matrix A into B since B will be overwritten by SVD()
+ for (k=0; k<N; k++)
+ for (l=0; l<N; l++)
+ B[k][l] = A[k][l];
+
+ SVD(B, N, s, V); // U replaces B on output; s[] contains singluar values
+
+ // Calculate inverse of A: A^-1 = V * diag(1/s) * U^t
+ double** U = B;
+ // Calculate V[k][m] -> V[k][m] *diag(1/s)
+ for (k=0; k<N; k++)
+ for (m=0; m<N; m++)
+ if (s[m]!=0.0) V[k][m] /= s[m]; else V[k][m] = 0.0;
+ // Calculate V[k][l] -> (V * U^t)_kl
+ for (k=0; k<N; k++)
+ {
+ if (v>=4 && k%100==0) printf("%i\n",k);
+ for (l=0; l<N; l++)
+ {
+ s[l] = 0.0; // use s[] as temporary memory to avoid overwriting B[k][] as long as it is needed
+ for (m=0; m<N; m++)
+ s[l] += V[k][m]*U[l][m];
+ }
+ for (l=0; l<N; l++) V[k][l]=s[l];
+ }
+ for (k=0; k<N; k++)
+ for (l=0; l<N; l++)
+ B[k][l] = V[k][l];
+
+ for (k=0; k<N; k++){
+ delete[](V[k]); (V[k]) = NULL;
+ }
+ delete[](V); (V) = NULL;
+ return;
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief
+ */
+void
+HitList::TransposeMatrix(double** V, int N)
+{
+ int k,l;
+ for (k=0; k<N; k++) // transpose Z for efficiency of ensuing matrix multiplication
+ for (l=0; l<k; l++)
+ {
+ double buf = V[k][l];
+ V[k][l] = V[l][k];
+ V[l][k] = buf;
+ }
+}
+
+/////////////////////////////////////////////////////////////////////////////////////////////////////////
+static double sqrarg;
+#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 : sqrarg*sqrarg)
+static double maxarg1,maxarg2;
+#define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1) > (maxarg2) ? (maxarg1) : (maxarg2))
+static int iminarg1,iminarg2;
+#define IMIN(a,b) (iminarg1=(a),iminarg2=(b),(iminarg1) < (iminarg2) ? (iminarg1) : (iminarg2))
+#define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a))
+
+/**
+ * @brief This is a version of the Golub and Reinsch algorithm for singular value decomposition for a quadratic
+ * (n x n) matrix A. It is sped up by transposing A amd V matrices at various places in the algorithm.
+ * On a 400x400 matrix it runs in 1.6 s or 2.3 times faster than the original (n x m) version.
+ * On a 4993x4993 matrix it runs in 2h03 or 4.5 times faster than the original (n x m) version.
+ *
+ * Given a matrix a[0..n-1][0..n-1], this routine computes its singular value decomposition, A = U · W · V^t .
+ * The matrix U replaces a on output. The diagonal matrix of singular values W is out-put as a vector w[0..n-1].
+ * The matrix V (not the transpose V^t) is output as V[0..n-1][0..n-1] ./
+ */
+void
+HitList::SVD(double **A, int n, double w[], double **V)
+{
+ int m=n; // in general algorithm A is an (m x n) matrix instead of (n x n)
+
+ double pythag(double a, double b);
+ int flag,i,its,j,jj,k,l=1,nm=1;
+ double anorm,c,f,g,h,s,scale,x,y,z,*rv1;
+ rv1=new(double[n]);
+ g=scale=anorm=0.0;
+
+ // Householder reduction to bidiagonal form.
+ if (v>=5) printf("\nHouseholder reduction to bidiagonal form\n");
+ for (i=0;i<n;i++) {
+ if (v>=4 && i%100==0) printf("i=%i\n",i);
+ if (v>=4) fprintf(stderr,".");
+ l=i+1;
+ rv1[i]=scale*g;
+ g=s=scale=0.0;
+ if (i < m) {
+ for (k=i;k<m;k++) scale += fabs(A[k][i]);
+ if (scale) {
+ for (k=i;k<m;k++) {
+ A[k][i] /= scale;
+ s += A[k][i]*A[k][i];
+ }
+ f=A[i][i];
+ g = -SIGN(sqrt(s),f);
+ h=f*g-s;
+ A[i][i]=f-g;
+ for (j=l;j<n;j++) {
+ for (s=0.0,k=i;k<m;k++) s += A[k][i]*A[k][j];
+ f=s/h;
+ for (k=i;k<m;k++) A[k][j] += f*A[k][i];
+ }
+ for (k=i;k<m;k++) A[k][i] *= scale;
+ }
+ }
+ w[i]=scale *g;
+ g=s=scale=0.0;
+ if (i < m && i != n-1) {
+ for (k=l;k<n;k++) scale += fabs(A[i][k]);
+ if (scale) {
+ for (k=l;k<n;k++) {
+ A[i][k] /= scale;
+ s += A[i][k]*A[i][k];
+ }
+ f=A[i][l];
+ g = -SIGN(sqrt(s),f);
+ h=f*g-s;
+ A[i][l]=f-g;
+ for (k=l;k<n;k++) rv1[k]=A[i][k]/h;
+ for (j=l;j<m;j++) {
+ for (s=0.0,k=l;k<n;k++) s += A[j][k]*A[i][k];
+ for (k=l;k<n;k++) A[j][k] += s*rv1[k];
+ }
+ for (k=l;k<n;k++) A[i][k] *= scale;
+ }
+ }
+ anorm=FMAX(anorm,(fabs(w[i])+fabs(rv1[i])));
+ }
+ // Accumulation of right-hand transformations.
+ if (v>=5) printf("\nAccumulation of right-hand transformations\n");
+ TransposeMatrix(V,n);
+ for (i=n-1;i>=0;i--) {
+ if (v>=4 && i%100==0) printf("i=%i\n",i);
+ if (v>=4) fprintf(stderr,".");
+ if (i < n-1) {
+ if (g) {
+ // Double division to avoid possible underflow.
+ for (j=l;j<n;j++)
+ V[i][j]=(A[i][j]/A[i][l])/g;
+ for (j=l;j<n;j++) {
+ for (s=0.0,k=l;k<n;k++) s += A[i][k]*V[j][k];
+ for (k=l;k<n;k++) V[j][k] += s*V[i][k];
+ }
+ }
+ for (j=l;j<n;j++) V[j][i]=V[i][j]=0.0;
+ }
+ V[i][i]=1.0;
+ g=rv1[i];
+ l=i;
+ }
+ // Accumulation of left-hand transformations.
+ if (v>=5) printf("\nAccumulation of left-hand transformations\n");
+ TransposeMatrix(A,n);
+ for (i=IMIN(m,n)-1;i>=0;i--) {
+ if (v>=4 && i%100==0) printf("i=%i\n",i);
+ if (v>=4) fprintf(stderr,".");
+ l=i+1;
+ g=w[i];
+ for (j=l;j<n;j++) A[j][i]=0.0;
+ if (g) {
+ g=1.0/g;
+ for (j=l;j<n;j++) {
+ for (s=0.0,k=l;k<m;k++) s += A[i][k]*A[j][k];
+ f=(s/A[i][i])*g;
+ for (k=i;k<m;k++) A[j][k] += f*A[i][k];
+ }
+ for (j=i;j<m;j++) A[i][j] *= g;
+ } else for (j=i;j<m;j++) A[i][j]=0.0;
+ ++A[i][i];
+ }
+
+ // Diagonalization of the bidiagonal form: Loop over singular values, and over allowed iterations.
+ if (v>=5) printf("\nDiagonalization of the bidiagonal form\n");
+ for (k=n-1;k>=0;k--) {
+ if (v>=4 && k%100==0) printf("k=%i\n",k);
+ if (v>=4) fprintf(stderr,".");
+ for (its=1;its<=30;its++) {
+ flag=1;
+ // Test for splitting. Note that rv1[1] is always zero.
+ for (l=k;l>=0;l--) {
+ nm=l-1;
+ if ((double)(fabs(rv1[l])+anorm) == anorm) {
+ flag=0;
+ break;
+ }
+ if ((double)(fabs(w[nm])+anorm) == anorm) break;
+ }
+ if (flag) {
+ // Cancellation of rv1[l], if l > 1.
+ c=0.0;
+ s=1.0;
+ for (i=l;i<=k;i++) {
+ f=s*rv1[i];
+ rv1[i]=c*rv1[i];
+ if ((double)(fabs(f)+anorm) == anorm) break;
+ g=w[i];
+ h=pythag(f,g);
+ w[i]=h;
+ h=1.0/h;
+ c=g*h;
+ s = -f*h;
+ for (j=0;j<m;j++) {
+ y=A[nm][j];
+ z=A[i][j];
+ A[nm][j]=y*c+z*s;
+ A[i][j]=z*c-y*s;
+ }
+ }
+ }
+ z=w[k];
+ // Convergence.
+ if (l == k) {
+ // Singular value is made nonnegative.
+ if (z < 0.0) {
+ w[k] = -z;
+ for (j=0;j<n;j++) V[k][j] = -V[k][j];
+ }
+ break;
+ }
+ if (its == 30) {printf("Error in SVD: no convergence in 30 iterations\n"); exit(7);}
+ // Shift from bottom 2-by-2 minor.
+ x=w[l];
+ nm=k-1;
+ y=w[nm];
+ g=rv1[nm];
+ h=rv1[k];
+ f=((y-z)*(y+z)+(g-h)*(g+h))/(2.0*h*y);
+ g=pythag(f,1.0);
+ f=((x-z)*(x+z)+h*((y/(f+SIGN(g,f)))-h))/x;
+ // Next QR transformation:
+ c=s=1.0;
+ for (j=l;j<=nm;j++) {
+ i=j+1;
+ g=rv1[i];
+ y=w[i];
+ h=s*g;
+ g=c*g;
+ z=pythag(f,h);
+ rv1[j]=z;
+ c=f/z;
+ s=h/z;
+ f=x*c+g*s;
+ g = g*c-x*s;
+ h=y*s;
+ y *= c;
+ for (jj=0;jj<n;jj++) {
+ x=V[j][jj];
+ z=V[i][jj];
+ V[j][jj]=x*c+z*s;
+ V[i][jj]=z*c-x*s;
+ }
+ z=pythag(f,h);
+ // Rotation can be arbitrary if z = 0.
+ w[j]=z;
+ if (z) {
+ z=1.0/z;
+ c=f*z;
+ s=h*z;
+ }
+ f=c*g+s*y;
+ x=c*y-s*g;
+
+ for (jj=0;jj<m;jj++) {
+ y=A[j][jj];
+ z=A[i][jj];
+ A[j][jj]=y*c+z*s;
+ A[i][jj]=z*c-y*s;
+ }
+ }
+ rv1[l]=0.0;
+ rv1[k]=f;
+ w[k]=x;
+ }
+ }
+ TransposeMatrix(V,n);
+ TransposeMatrix(A,n);
+ delete[](rv1); (rv1) = NULL;
+}
+
+/**
+ * @brief Computes (a2 + b2 )^1/2 without destructive underflow or overflow.
+ */
+double
+pythag(double a, double b)
+{
+ double absa,absb;
+ absa=fabs(a);
+ absb=fabs(b);
+ if (absa > absb)
+ return absa*sqrt(1.0+SQR(absb/absa));
+ else
+ return (absb == 0.0 ? 0.0 : absb*sqrt(1.0+SQR(absa/absb)));
+}
+
+
+/* @* HitList::ClobberGlobal(void)
+ */
+void
+HitList::ClobberGlobal(void){
+
+
+ /* @<variables local to HitList::ClobberGlobal@> */
+ class List<Hit>::ListEl<Hit> *pvIter = head;
+
+ /* NOTE: no free/delete-ing of data to be done here
+ hitlist only holds a shallow copy of hit;
+ hit is being cleared off properly.
+ just reset everything to 0/0.0/NULL.
+ The only important thing to do at this stage
+ is to attach head and tail and set size = 0
+ (FS, 2010-02-18)
+
+ NOTE: I only ever saw 1 (one) in-between element,
+ but there may ctually be a real linked list
+ of more than 1 element (FS, 2010-02-18)
+ */
+
+ // printf("POINTER:\t%p\t=HEAD\n", head);
+ while (pvIter->next != tail){
+
+ // printf("POINTER:\t%p->\t%p\n", pvIter, pvIter->next);
+ pvIter = pvIter->next;
+
+#if 1
+ pvIter->data.longname = pvIter->data.name =
+ pvIter->data.file = pvIter->data.dbfile = NULL;
+ pvIter->data.sname = NULL;
+ pvIter->data.seq = NULL;
+ pvIter->data.self = 0;
+ pvIter->data.i = pvIter->data.j = NULL;
+ pvIter->data.states = NULL;
+ pvIter->data.S = pvIter->data.S_ss = pvIter->data.P_posterior = NULL;
+ pvIter->data.Xcons = NULL;
+ pvIter->data.sum_of_probs = 0.0;
+ pvIter->data.Neff_HMM = 0.0;
+ pvIter->data.score_ss = pvIter->data.Pval = pvIter->data.logPval =
+ pvIter->data.Eval = pvIter->data.Probab = pvIter->data.Pforward = 0.0;
+ pvIter->data.nss_conf = pvIter->data.nfirst =
+ pvIter->data.i1 = pvIter->data.i2 = pvIter->data.j1 = pvIter->data.j2 =
+ pvIter->data.matched_cols = pvIter->data.ssm1 = pvIter->data.ssm2 = 0;
+#endif
+ }
+ // printf("POINTER:\t\t\t%p=TAIL\n", tail);
+
+
+ head->next = tail;
+ tail->prev = head;
+ size = 0;
+
+ /* @= */
+ return;
+
+} /* this is the end of HitList::ClobberGlobal() */
+
+
+/*
+ * EOF hhhitlist-C.h
+ */
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhhitlist.h 243 2011-05-31 13:49:19Z fabian $
+ */
+
+// hhhitlist.h
+
+//////////////////////////////////////////////////////////////////////////////
+// HitList is a list of hits of type Hit
+// which can be operated upon by several anaylsis methods
+//////////////////////////////////////////////////////////////////////////////
+class HitList : public List<Hit>
+{
+private:
+ double score[MAXPROF]; // HHsearch score of each HMM for ML fit
+ double weight[MAXPROF]; // weight of each HMM = 1/(size_fam[tfam]*size_sfam[hit.sfam]) for ML fit
+ int Nprof; // Number of HMMs for ML fit
+
+public:
+ int fams; // number of families found found in hitlist
+ int sfams; // number of superfamilies found in hitlist
+ int N_searched; // number of sequences searched from HMM database
+ Hash<float>* blast_logPvals;/* Hash containing names and log(P-values)
+ read from BLAST file (needed for HHblast) */
+
+ HitList() {blast_logPvals=NULL;}
+ ~HitList() {if (blast_logPvals) delete blast_logPvals;}
+
+ // Print summary listing of hits
+ void PrintHitList(HMM& q, char* outfile);
+
+#ifdef CLUSTALO
+ void ClobberGlobal(void);
+#endif
+
+ // Print alignments of query sequences against hit sequences
+ int PrintAlignments(
+#ifdef CLUSTALO
+ char **ppcFirstProf, char **ppcSecndProf,
+#endif
+ HMM& q, char* outfile, char outformat=0);
+
+ // Return a figure of merit for distinction of the score with positive from the scores with negatives
+ void Optimize(HMM& q, char* buffer);
+
+ // Print score distribution into file score_dist
+ void PrintScoreFile(HMM& q);
+
+ // Log likelihood for fitting the EVD to the score distribution
+ double RankOrderFitCorr(double* v);
+ // Static wrapper-function for calling the nonstatic member function RankOrderFitCorr()
+ static double RankOrderFitCorr_static(void* pt2hitlist, double* v);
+
+ // Log likelihood for fitting the EVD to the score distribution
+ double LogLikelihoodCorr(double* v);
+ // Static wrapper-function for calling the nonstatic member function LogLikelihoodCorr()
+ static double LogLikelihoodCorr_static(void* pt2hitlist, double* v);
+
+ // Log likelihood for fitting the EVD to the score distribution
+ double LogLikelihoodEVD(double* v);
+ // Static wrapper-function for calling the nonstatic member function LogLikelihoodEVD()
+ static double LogLikelihoodEVD_static(void* pt2hitlist, double* v);
+
+
+ // Subroutine to FindMin: new point given by highest point ihigh, fac and replaces ihigh if it is lower
+ double TryPoint(int ndim, double* p, double* y, double* psum, int ihigh, double fac, double (*Func)(void* pt2hitlist, double* v));
+
+ // Find minimum with simplex method of Nelder and Mead (1965)
+ float FindMin(int ndim, double* p, double* y, double tol, int& nfunc, double (*Func)(void* pt2hitlist, double* v));
+
+ // Do a maximum likelihood fit of the scores with an EV distribution with parameters lamda and mu
+ void MaxLikelihoodEVD(HMM& q, int nbest);
+
+ // Calculate correlation and score offset for HHblast composite E-values
+ void CalculateHHblastCorrelation(HMM& q);
+
+ // Calculate HHblast composite E-values
+ void CalculateHHblastEvalues(HMM& q);
+
+ // Calculate Pvalues as a function of query and template lengths and diversities
+ void CalculatePvalues(HMM& q);
+
+ // Set P-values, E-values and scores according to q.lamda and q.mu (if calibration from database scan is impossible)
+ void GetPvalsFromCalibration(HMM& q);
+
+ // HHblast: read PSI-BLAST E-values to determine correlation
+ void ReadBlastFile(HMM& q);
+
+ // Print first 20 hits of hitlist
+ void Debug()
+ {
+ Hit hit;
+ int i=0;
+ Reset();
+ printf("TARGET FAMILY LEN COL LOG-PVA S-AASS PROBAB SCORE_SORT\n");
+ while (++i<=20 && !End())
+ {
+ hit = ReadNext();
+ printf("%-10.10s %-10.10s %3i %3i %s %7.2f %6.2f %6.2f\n",hit.name,hit.fam,hit.L,hit.matched_cols,sprintg(-1.443*hit.logPval,7),-hit.score_aass,hit.Probab,hit.score_sort);
+ }
+ }
+
+ // Calculate P-values and Probabilities from transitive scoring over whole database
+ void TransitiveScoring();
+ void TransitiveScoring2();
+ void TransitiveScoring3();
+ void TransitiveScoring4();
+
+ // Score2Z transforms the -log(P-value) score into a Z-score for 0 < S
+ double Score2Z(double S);
+
+ // Z2Score transforms the Z-score into a -log(P-value) value
+ double Z2Score(double Z);
+
+ // Matrix manipulation
+ void PrintMatrix(float** V, int N);
+ void PrintMatrix(double** V, int N);
+ float NormalizationFactor(double** Csub,float* w, int M);
+ void Normalize(float* Ztq, char** fold, Hash<int>& excluded);
+ void InvertMatrix(double** B, double** A, int N);
+ void TransposeMatrix(double** V, int N);
+ void SVD(double **A, int n, double w[], double **V);
+
+};
+
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhhmm-C.h 224 2011-03-23 12:13:33Z fabian $
+ */
+
+
+// hhhmm.C
+
+#ifndef MAIN
+#define MAIN
+#include <iostream> // cin, cout, cerr
+#include <fstream> // ofstream, ifstream
+#include <stdio.h> // printf
+using std::cout;
+using std::cerr;
+using std::endl;
+using std::ios;
+using std::ifstream;
+using std::ofstream;
+#include <stdlib.h> // exit
+#include <string> // strcmp, strstr
+#include <math.h> // sqrt, pow
+#include <limits.h> // INT_MIN
+#include <float.h> // FLT_MIN
+#include <time.h> // clock
+#include <ctype.h> // islower, isdigit etc
+#include "util-C.h" // imax, fmax, iround, iceil, ifloor, strint, strscn, strcut, substr, uprstr, uprchr, Basename etc.
+#include "list.h" // list data structure
+#include "hash.h" // hash data structure
+#include "hhdecl-C.h"
+#include "hhutil-C.h" // imax, fmax, iround, iceil, ifloor, strint, strscn, strcut, substr, uprstr, uprchr, Basename etc.
+#endif
+
+// #ifndef WNLIB
+// #define WNLIB
+// #include "wnconj.h" // Will Naylor's wnlib for optimization in C
+// #endif
+
+//////////////////////////////////////////////////////////////////////////////
+//// Class HMM
+//////////////////////////////////////////////////////////////////////////////
+
+//////////////////////////////////////////////////////////////////////////////
+// Object constructor
+//////////////////////////////////////////////////////////////////////////////
+HMM::HMM(int maxseqdis, int maxres)
+{
+ sname = new char*[maxseqdis]; // names of stored sequences
+ for (int i = 0; i < maxseqdis; i++){ sname[i] = NULL;}
+ seq = new char*[maxseqdis]; // residues of stored sequences (first at pos 1!)
+ for (int i = 0; i < maxseqdis; i++){ seq[i] = NULL;}
+ Neff_M = new float[maxres]; // Neff_M[i] = diversity of subalignment of seqs that have residue in col i
+ Neff_I = new float[maxres]; // Neff_I[i] = diversity of subalignment of seqs that have insert in col i
+ Neff_D = new float[maxres]; // Neff_D[i] = diversity of subalignment of seqs that have delete in col i
+ longname = new char[DESCLEN]; // Full name of first sequence of original alignment (NAME field)
+ ss_dssp = new char[maxres]; // secondary structure determined by dssp 0:- 1:H 2:E 3:C 4:S 5:T 6:G 7:B
+ sa_dssp = new char[maxres]; // solvent accessibility state determined by dssp 0:- 1:A (absolutely buried) 2:B 3:C 4:D 5:E (exposed)
+ ss_pred = new char[maxres]; // predicted secondary structure 0:- 1:H 2:E 3:C
+ ss_conf = new char[maxres]; // confidence value of prediction 0:- 1:0 ... 10:9
+ Xcons = NULL; // create only when needed: consensus sequence in internal representation (A=0 R=1 N=2 D=3 ...)
+ l = new int[maxres]; // l[i] = pos. of j'th match state in aligment
+ /* FS introduced sentinel, NULL terminates loop in destructor, FS, r221->222 */
+ f = new float*[maxres+1]; f[maxres] = NULL; // f[i][a] = prob of finding amino acid a in column i WITHOUT pseudocounts
+ g = new float*[maxres+1]; g[maxres] = NULL; // f[i][a] = prob of finding amino acid a in column i WITH pseudocounts
+ p = new float*[maxres+1]; p[maxres] = NULL; // p[i][a] = prob of finding amino acid a in column i WITH OPTIMUM pseudocounts
+ tr = new float*[maxres+1]; tr[maxres] = NULL; // log2 of transition probabilities M2M M2I M2D I2M I2I D2M D2D M2M_GAPOPEN GAPOPEN GAPEXTD
+// tr_lin = new float*[maxres]; // linear transition probabilities M2M M2I M2D I2M I2I D2M D2D M2M_GAPOPEN GAPOPEN GAPEXTD
+ for (int i=0; i<maxres; i++) {f[i]=new(float[NAA+3]);}
+ for (int i=0; i<maxres; i++) {g[i]=new(float[NAA]);}
+ for (int i=0; i<maxres; i++) {p[i]=new(float[NAA]);}
+ for (int i=0; i<maxres; i++) {tr[i]=new(float[NTRANS]);}
+// for (int i=0; i<maxres; i++) tr_lin[i]=new(float[NTRANS]);
+ L=0;
+ Neff_HMM=0;
+ n_display=N_in=N_filtered=0;
+ nss_dssp=nsa_dssp=nss_pred=nss_conf=nfirst=ncons=-1;
+// lamda_hash.New(37,0.0); // Set size and NULL element for hash
+// mu_hash.New(37,0.0); // Set size and NULL element for hash
+ lamda=0.0; mu=0.0;
+ name[0]=longname[0]=fam[0]='\0';
+ trans_lin=0; // transition probs in log space
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Object destructor
+//////////////////////////////////////////////////////////////////////////////
+HMM::~HMM()
+{
+ //Delete name and seq matrices
+ if (NULL != sname){
+ for (int k=0; (k < n_display) && (NULL != sname[k]); k++){
+ delete[] sname[k]; sname[k] = NULL;
+ }
+ delete[] sname; sname = NULL;
+ }
+ if (NULL != seq){
+ for (int k=0; (k < n_display) && (NULL != seq[k]); k++){
+ delete[] seq[k]; seq[k] = NULL;
+ }
+ delete[] seq; seq = NULL;
+ }
+ delete[] Neff_M; Neff_M = NULL;
+ delete[] Neff_D; Neff_D = NULL;
+ delete[] Neff_I; Neff_I = NULL;
+ delete[] longname; longname = NULL;
+ delete[] ss_dssp; ss_dssp = NULL;
+ delete[] sa_dssp; sa_dssp = NULL;
+ delete[] ss_pred; ss_pred = NULL;
+ delete[] ss_conf; ss_conf = NULL;
+ delete[] Xcons; Xcons = NULL;
+ delete[] l; l = NULL;
+ for (int i=0; i</*MAXRES*/par.maxResLen; i++){
+ if (f[i]){
+ delete[] f[i]; f[i] = NULL;
+ }
+ else break;
+ }
+ for (int i=0; i</*MAXRES*/par.maxResLen; i++){
+ if (g[i]){
+ delete[] g[i]; g[i] = NULL;
+ }
+ else break;
+ }
+ for (int i=0; i</*MAXRES*/par.maxResLen; i++){
+ if (p[i]){
+ delete[] p[i]; p[i] = NULL;
+ }
+ else break;
+ }
+ for (int i=0; i</*MAXRES*/par.maxResLen; i++){
+ if (tr[i]){
+ delete[] tr[i]; tr[i] = NULL;
+ }
+ else break;
+ }
+ // for (int i=0; i</*MAXRES*/par.maxResLen; i++) if (tr_lin[i]) delete[] tr_lin[i]; else break;
+ delete[] f; f = NULL;
+ delete[] g; g = NULL;
+ delete[] p; p = NULL;
+ delete[] tr; tr = NULL;
+// delete[] tr_lin;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+// Deep-copy constructor
+//////////////////////////////////////////////////////////////////////////////
+HMM& HMM::operator=(HMM& q)
+{
+ L=q.L;
+ for (int i=0; i<=L+1; ++i)
+ {
+ for (int a=0; a<NAA; ++a)
+ {
+ f[i][a]=q.f[i][a];
+ g[i][a]=q.g[i][a];
+ p[i][a]=q.p[i][a];
+ }
+ for (int a=0; a<NTRANS; ++a)
+ tr[i][a]=q.tr[i][a];
+ ss_dssp[i]=q.ss_dssp[i];
+ sa_dssp[i]=q.sa_dssp[i];
+ ss_pred[i]=q.ss_pred[i];
+ ss_conf[i]=q.ss_conf[i];
+ l[i]=q.l[i];
+ }
+ if (q.Xcons)
+ for (int i=0; i<=L+1; ++i)
+ Xcons[i] =q.Xcons[i];
+
+ n_display=q.n_display;
+ for (int k=0; k<n_display; k++) {
+ sname[k]=new(char[strlen(q.sname[k])+1]);
+ if (!sname[k]) MemoryError("array of names for sequences to display");
+ strcpy(sname[k],q.sname[k]);
+ }
+ for (int k=0; k<n_display; k++) {
+ seq[k]=new(char[strlen(q.seq[k])+1]);
+ if (!seq[k]) MemoryError("array of names for sequences to display");
+ strcpy(seq[k],q.seq[k]);
+ }
+ ncons=q.ncons;
+ nfirst=q.nfirst;
+ nss_dssp=q.nss_dssp;
+ nsa_dssp=q.nsa_dssp;
+ nss_pred=q.nss_pred;
+ nss_conf=q.nss_conf;
+
+ for (int i=0; i<=L+1; ++i) Neff_M[i]=q.Neff_M[i];
+ for (int i=0; i<=L+1; ++i) Neff_I[i]=q.Neff_I[i];
+ for (int i=0; i<=L+1; ++i) Neff_D[i]=q.Neff_D[i];
+ Neff_HMM=q.Neff_HMM;
+
+ strcpy(longname,q.longname);
+ strcpy(name,q.name);
+ strcpy(fam,q.fam);
+ strcpy(sfam,q.sfam);
+ strcpy(fold,q.fold);
+ strcpy(cl,q.cl);
+ strcpy(file,q.file);
+
+ lamda=q.lamda;
+ mu=q.mu;
+
+ for (int a=0; a<NAA; ++a) pav[a]=q.pav[a];
+ N_in=q.N_in;
+ N_filtered=q.N_filtered;
+ trans_lin=q.trans_lin;
+ return (HMM&) (*this);
+}
+
+
+///////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Read an HMM from an HHsearch .hhm file; return 0 at end of file
+ */
+int
+HMM::Read(FILE* dbf, char* path)
+{
+ char line[LINELEN]=""; // input line
+ char str3[8]="",str4[8]=""; // first 3 and 4 letters of input line
+ char* ptr; // pointer for string manipulation
+ int i=0; // index for match state (first=1)
+ int a; // amino acid index
+ static int warn=0;
+
+ trans_lin=0;
+ L=0;
+ Neff_HMM=0;
+ n_display=N_in=N_filtered=0;
+ nss_dssp=nsa_dssp=nss_pred=nss_conf=nfirst=ncons=-1;
+ lamda=mu=0.0;
+ trans_lin=0; // transition probs in log space
+ name[0]=longname[0]=fam[0]='\0';
+ //If at the end of while-loop L is still 0 then we have reached end of db file
+
+ //Do not delete name and seq vectors because their adresses are transferred to hitlist as part of a hit!!
+
+ while (fgetline(line,LINELEN-1,dbf) && !(line[0]=='/' && line[1]=='/'))
+ {
+
+ if (strscn(line)==NULL) continue; // skip lines that contain only white space
+ substr(str3,line,0,2); // copy the first three characters into str3
+ substr(str4,line,0,3); // copy the first four characters into str4
+
+ if (!strncmp("HH",line,2)) continue;
+
+ if (!strcmp("NAME",str4))
+ {
+ ptr=strscn(line+4); //advance to first non-white-space character
+ if (ptr)
+ {
+ strncpy(longname,ptr,DESCLEN-1); //copy full name to longname
+ longname[DESCLEN-1]='\0';
+ strncpy(name,ptr,NAMELEN-1); //copy longname to name...
+ strcut(name); //...cut after first word...
+ }
+ else
+ {
+ strcpy(longname,"undefined");
+ strcpy(name,"undefined");
+ }
+ if (v>=4) cout<<"Reading in HMM "<<name<<":\n";
+ }
+
+ else if (!strcmp("FAM",str3))
+ {
+ ptr=strscn(line+3); //advance to first non-white-space character
+ if (ptr) strncpy(fam,ptr,IDLEN-1); else strcpy(fam,""); //copy family name to basename
+ ScopID(cl,fold,sfam,fam); //get scop classification from basename (e.g. a.1.2.3.4)
+ }
+
+ else if (!strcmp("FILE",str4))
+ {
+ if (path) strncpy(file,path,NAMELEN-1); else *file='\0'; // copy path to file variable
+ ptr=strscn(line+4); //advance to first non-white-space character
+ if (ptr)
+ strncat(file,ptr,NAMELEN-1-strlen(file)); // append file name read from file to path
+ else strcat(file,"*");
+ }
+
+ else if (!strcmp("LENG",str4))
+ {
+ ptr=line+4;
+ L=strint(ptr); //read next integer (number of match states)
+ }
+ else if (!strcmp("FILT",str4) || !strcmp("NSEQ",str4))
+ {
+ ptr=line+4;
+ N_filtered=strint(ptr); //read next integer: number of sequences after filtering
+ N_in=strint(ptr); //read next integer: number of sequences in alignment
+ }
+
+ else if (!strcmp("NEFF",str4) || !strcmp("NAA",str3)) sscanf(line+6,"%f",&Neff_HMM);
+
+ else if (!strcmp("EVD",str3))
+ {
+// char key[IDLEN];
+ sscanf(line+6,"%f %f",&lamda,&mu);
+// sscanf(line+22,"%s",key);
+// lamda_hash.Add(key,lamda);
+// mu_hash.Add(key,mu);
+ }
+
+ else if (!strcmp("DESC",str4)) continue;
+ else if (!strcmp("COM",str3)) continue;
+ else if (!strcmp("DATE",str4)) continue;
+
+ /////////////////////////////////////////////////////////////////////////////////////
+ // Read template sequences that should get displayed in output alignments
+ else if (!strcmp("SEQ",str3))
+ {
+ //char cur_seq[MAXCOL]=""; //Sequence currently read in
+ char *cur_seq = new(char[par.maxColCnt]); //Sequence currently read in
+ int k; // sequence index; start with -1; after reading name of n'th sequence-> k=n
+ int h; // index for character in input line
+ int l=1; // index of character in sequence seq[k]
+ int i=1; // index of match states in ss_dssp[i] and ss_pred[i] sequence
+ int n_seq=0; // number of sequences to be displayed EXCLUDING ss sequences
+ cur_seq[0]='-'; // overwrite '\0' character at beginning to be able to do strcpy(*,cur_seq)
+ k=-1;
+ while (fgetline(line,LINELEN-1,dbf) && line[0]!='#')
+ {
+ if (v>=4) cout<<"Read from file:"<<line<<"\n"; //DEBUG
+ if (line[0]=='>') //line contains sequence name
+ {
+ if (k>=MAXSEQDIS-1) //maximum number of allowable sequences exceeded
+ {while (fgetline(line,LINELEN-1,dbf) && line[0]!='#'); break;}
+ k++;
+ if (!strncmp(line,">ss_dssp",8)) nss_dssp=k;
+ else if (!strncmp(line,">sa_dssp",8)) nsa_dssp=k;
+ else if (!strncmp(line,">ss_pred",8)) nss_pred=k;
+ else if (!strncmp(line,">ss_conf",8)) nss_conf=k;
+ else if (!strncmp(line,">Cons-",6) || !strncmp(line,">Consensus",10)) ncons=k;
+ else
+ {
+ if (nfirst==-1) nfirst=k;
+ if (n_seq>=par.nseqdis)
+ {while (fgetline(line,LINELEN-1,dbf) && line[0]!='#'); k--; break;}
+ n_seq++;
+ }
+
+ //If this is not the first sequence then store residues of previous sequence
+ if (k>0) {
+ seq[k-1]=new(char[strlen(cur_seq)+1]);
+ if (!seq[k-1]) MemoryError("array of sequences to display");
+ strcpy(seq[k-1],cur_seq);
+ }
+
+ // store sequence name
+ strcut(line+1); //find next white-space character and overwrite it with end-of-string character
+ sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0'
+ if (!sname[k]) MemoryError("array of names for sequences to display");
+ strcpy(sname[k],line+1); //store sequence name in **name
+ l=1; i=1;
+ }
+ else //line contains sequence residues
+ {
+ if (k==-1)
+ {
+ cerr<<endl<<"WARNING: Ignoring following line while reading HMM"<<name<<":\n\'"<<line<<"\'\n";
+ continue;
+ }
+
+ h=0; //counts characters in current line
+
+ // Check whether all characters are correct; store into cur_seq
+ if (k==nss_dssp) // lines with dssp secondary structure states (. - H E C S T G B)
+ {
+ while (h<LINELEN && line[h]>'\0' && l</*MAXCOL*/par.maxColCnt-1)
+ {
+ if (ss2i(line[h])>=0 && line[h]!='.')
+ {
+ char c=ss2ss(line[h]);
+ cur_seq[l]=c;
+ if (c!='.' && !(c>='a' && c<='z')) ss_dssp[i++]=ss2i(c);
+ l++;
+ }
+ else if (v && ss2i(line[h])==-2)
+ cerr<<endl<<"WARNING: invalid symbol \'"<<line[h]<<"\' at pos. "<<h<<" in line '"<<line<<"' of HMM "<<name<<"\n";
+ h++;
+ }
+ }
+ if (k==nsa_dssp) // lines with dssp secondary solvent accessibility (- A B C D E)
+ {
+ while (h<LINELEN && line[h]>'\0' && l</*MAXCOL*/par.maxColCnt-1)
+ {
+ if (sa2i(line[h])>=0)
+ {
+ char c=line[h];
+ cur_seq[l]=c;
+ if (c!='.' && !(c>='a' && c<='z')) sa_dssp[i++]=sa2i(c);
+ l++;
+ }
+ else if (v && sa2i(line[h])==-2)
+ cerr<<endl<<"WARNING: invalid symbol \'"<<line[h]<<"\' at pos. "<<h<<" in line '"<<line<<"' of HMM "<<name<<"\n";
+ h++;
+ }
+ }
+ else if (k==nss_pred) // lines with predicted secondary structure (. - H E C)
+ {
+ while (h<LINELEN && line[h]>'\0' && l</*MAXCOL*/par.maxColCnt-1)
+ {
+ if (ss2i(line[h])>=0 && ss2i(line[h])<=3 && line[h]!='.')
+ {
+ char c=ss2ss(line[h]);
+ cur_seq[l]=c;
+ if (c!='.' && !(c>='a' && c<='z')) ss_pred[i++]=ss2i(c);
+ l++;
+ }
+ else if (v && ss2i(line[h])==-2)
+ cerr<<endl<<"WARNING: invalid symbol \'"<<line[h]<<"\' at pos. "<<h<<" in line '"<<line<<"' of HMM "<<name<<"\n";
+ h++;
+ }
+ }
+ else if (k==nss_conf) // lines with confidence values should contain only 0-9, '-', or '.'
+ {
+ while (h<LINELEN && line[h]>'\0' && l</*MAXCOL*/par.maxColCnt-1)
+ {
+ if (line[h]=='-' || (line[h]>='0' && line[h]<='9'))
+ {
+ cur_seq[l]=line[h];
+ ss_conf[l]=cf2i(line[h]);
+ l++;
+ }
+ else if (v && cf2i(line[h])==-2)
+ cerr<<endl<<"WARNING: invalid symbol \'"<<line[h]<<"\' at pos. "<<h<<" in line '"<<line<<"' of HMM "<<name<<"\n";
+ h++;
+ }
+ }
+ else // normal line containing residues
+ {
+ while (h<LINELEN && line[h]>'\0' && l</*MAXCOL*/par.maxColCnt-1)
+ {
+ if (aa2i(line[h])>=0 && line[h]!='.') // ignore '.' and white-space characters ' ', \t and \n (aa2i()==-1)
+ {cur_seq[l]=line[h]; l++;}
+ else if (aa2i(line[h])==-2 && v)
+ cerr<<endl<<"WARNING: invalid symbol \'"<<line[h]<<"\' at pos. "<<h<<" in line '"<<line<<"' of HMM "<<name<<"\n";
+ h++;
+ }
+ }
+ cur_seq[l]='\0'; //Ensure that cur_seq ends with a '\0' character
+
+ } //end else
+ } //while(getline)
+ //If this is not the first sequence some residues have already been read in
+ if (k>=0) {
+ seq[k]=new(char[strlen(cur_seq)+1]);
+ if (!seq[k]) MemoryError("array of sequences to display");
+ strcpy(seq[k],cur_seq);
+ }
+ n_display=k+1;
+
+ // DEBUG
+ if (v>=4)
+ {
+ printf("nss_dssp=%i nsa_dssp=%i nss_pred=%i nss_conf=%i nfirst=%i\n",nss_dssp,nsa_dssp,nss_pred,nss_conf,nfirst);
+ for (k=0; k<n_display; k++)
+ {
+ int j;
+ cout<<">"<<sname[k]<<"(k="<<k<<")\n";
+ if (k==nss_dssp) {for (j=1; j<=L; j++) cout<<char(i2ss(ss_dssp[j]));}
+ else if (k==nsa_dssp) {for (j=1; j<=L; j++) cout<<char(i2sa(sa_dssp[j]));}
+ else if (k==nss_pred) {for (j=1; j<=L; j++) cout<<char(i2ss(ss_pred[j]));}
+ else if (k==nss_conf) {for (j=1; j<=L; j++) cout<<int(ss_conf[j]-1);}
+ else {for (j=1; j<=L; j++) cout<<seq[k][j];}
+ cout<<"\n";
+ }
+ }
+
+ } //end if("SEQ")
+
+ /////////////////////////////////////////////////////////////////////////////////////
+ // Read average amino acid frequencies for HMM
+ else if (!strcmp("FREQ",str4))
+ {
+ fprintf(stderr,"Error: hhm file has obsolete format.\n");
+ fprintf(stderr,"Please use hhmake version > 1.1 to generate hhm files.\n");
+ exit(1);
+ }
+
+ else if (!strcmp("AVER",str4)) {} // AVER line scrapped
+ else if (!strcmp("NULL",str4))
+ {
+ ptr=line+4;
+ for (a=0; a<20 && ptr; ++a)
+ //s2[a]: transform amino acids Sorted by alphabet -> internal numbers for amino acids
+ pb[s2a[a]] = (float) fpow2(float(-strinta(ptr))/HMMSCALE);
+ if (!ptr) return Warning(dbf,line,name);
+ if (v>=4)
+ {
+ printf("\nNULL ");
+ for (a=0; a<20; ++a) printf("%5.1f ",100.*pb[s2a[a]]);
+ printf("\n");
+ }
+ }
+
+ /////////////////////////////////////////////////////////////////////////////////////
+ // Read transition probabilities from start state
+ else if (!strcmp("HMM",str3))
+ {
+ fgetline(line,LINELEN-1,dbf); // Skip line with amino acid labels
+ fgetline(line,LINELEN-1,dbf); // Skip line with transition labels
+ ptr=line;
+ for (a=0; a<=D2D && ptr; ++a)
+ tr[0][a] = float(-strinta(ptr))/HMMSCALE; //store transition probabilites as log2 values
+ // strinta returns next integer in string and puts ptr to first char
+ // after the integer. Returns -99999 if '*' is found.
+ // ptr is set to 0 if no integer is found after ptr.
+ Neff_M[0] = float(strinta(ptr))/HMMSCALE; // Read eff. number of sequences with M->? transition
+ Neff_I[0] = float(strinta(ptr))/HMMSCALE; // Read eff. number of sequences with I->? transition
+ Neff_D[0] = float(strinta(ptr))/HMMSCALE; // Read eff. number of sequences with D->? transition
+ if (!ptr) return Warning(dbf,line,name);
+
+ /////////////////////////////////////////////////////////////////////////////////////
+ // Read columns of HMM
+ int next_i=0; // index of next column
+ while (fgetline(line,LINELEN-2,dbf) && !(line[0]=='/' && line[1]=='/') && line[0]!='#')
+ {
+ if (strscn(line)==NULL) continue; // skip lines that contain only white space
+
+ // Read in AA probabilities
+ ptr=line+1;
+ int prev_i = next_i;
+ next_i = strint(ptr); ++i;
+ if (v && next_i!=prev_i+1)
+ if (++warn<=5)
+ {
+ cerr<<endl<<"WARNING: in HMM "<<name<<" state "<<prev_i<<" is followed by state "<<next_i<<"\n";
+ if (warn==5) cerr<<endl<<"WARNING: further warnings while reading HMMs will be suppressed.\n";
+ }
+ if (i>L)
+ {
+ cerr<<endl<<"WARNING: in HMM "<<name<<" there are more columns than the stated length "<<L<<". Skipping HMM\n";
+ return 2;
+ }
+ if (i>=/*MAXRES*/par.maxResLen-2)
+ {
+ fgetline(line,LINELEN-1,dbf); // Skip line
+ continue;
+ }
+
+ for (a=0; a<20 && ptr; ++a)
+// f[i][s2a[a]] = (float)pow(2.,float(-strinta(ptr))/HMMSCALE);
+ f[i][s2a[a]] = fpow2(float(-strinta(ptr))/HMMSCALE); // speed-up ~5 s for 10000 SCOP domains
+
+ //s2a[a]: transform amino acids Sorted by alphabet -> internal numbers for amino acids
+ l[i]=strint(ptr);
+ if (!ptr) return Warning(dbf,line,name);
+ if (v>=4)
+ {
+ printf("%s",line);
+ printf("%6i ",i);
+ for (a=0; a<20; ++a) printf("%5.1f ",100*f[i][s2a[a]]);
+ printf("%5i",l[i]);
+ printf("\n");
+ }
+
+ // Read transition probabilities
+ fgetline(line,LINELEN-1,dbf); // Skip line with amino acid labels
+ if (line[0]!=' ' && line[0]!='\t') return Warning(dbf,line,name);
+ ptr=line;
+ for (a=0; a<=D2D && ptr; ++a)
+ tr[i][a] = float(-strinta(ptr))/HMMSCALE; //store transition prob's as log2-values
+ Neff_M[i] = float(strinta(ptr))/HMMSCALE; // Read eff. number of sequences with M->? transition
+ Neff_I[i] = float(strinta(ptr))/HMMSCALE; // Read eff. number of sequences with I->? transition
+ Neff_D[i] = float(strinta(ptr))/HMMSCALE; // Read eff. number of sequences with D->? transition
+ if (!ptr) return Warning(dbf,line,name);
+ if (v>=4)
+ {
+ printf(" ");
+ for (a=0; a<=D2D; ++a) printf("%5.1f ",100*fpow2(tr[i][a]));
+ printf("%5.1f %5.1f %5.1f \n",Neff_M[i],Neff_I[i],Neff_D[i]);
+ }
+ }
+ if (line[0]=='/' && line[1]=='/') break;
+ }
+ else if (v) cerr<<endl<<"WARNING: Ignoring line\n\'"<<line<<"\'\nin HMM "<<name<<"\n";
+
+ } //while(getline)
+
+ if (L==0) return 0; //End of db file -> stop reading in
+
+ // Set coefficients of EVD (= 0.0 if not calibrated for these parameters)
+// lamda = lamda_hash.Show(par.Key());
+// mu = mu_hash.Show(par.Key());
+ if (lamda && v>=3) printf("HMM %s is already calibrated: lamda=%-5.3f, mu=%-5.2f\n",name,lamda,mu);
+
+ if (v && i!=L) cerr<<endl<<"Warning: in HMM "<<name<<" there are only "<<i<<" columns while the stated length is "<<L<<"\n";
+ if (v && i>/*MAXRES*/par.maxResLen-2) {i=/*MAXRES*/par.maxResLen-2; cerr<<endl<<"WARNING: maximum number "<</*MAXRES*/par.maxResLen-2<<" of residues exceeded while reading HMM "<<name<<"\n";}
+ if (v && !i) cerr<<endl<<"WARNING: HMM "<<name<<" contains no match states. Check the alignment that gave rise to this HMM.\n";
+ if (v>=2) cout<<"Read in HMM "<<name<<" with "<<L<<" match states and effective number of sequences = "<<Neff_HMM<<"\n";
+ L = i;
+
+ // Set emission probabilities of zero'th (begin) state and L+1st (end) state to background probabilities
+ for (a=0; a<20; ++a) f[0][a]=f[L+1][a]=pb[a];
+ Neff_M[L+1]=1.0f;
+ Neff_I[L+1]=Neff_D[L+1]=0.0f;
+
+ return 1; //return status: ok
+
+} /* this is the end of HMM::Read() */
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Read an HMM from a HMMer .hmm file; return 0 at end of file
+ */
+int
+HMM::ReadHMMer(FILE* dbf, char* filestr)
+{
+ char line[LINELEN]=""; // input line
+ char desc[DESCLEN]=""; // description of family
+ char str4[5]=""; // first 4 letters of input line
+ char* ptr; // pointer for string manipulation
+ int i=0; // index for match state (first=1)
+ int a; // amino acid index
+ char dssp=0; // 1 if a consensus SS has been found in the transition prob lines
+ char annot=0; // 1 if at least one annotation character in insert lines is ne '-' or ' '
+ int k=0; // index for seq[k]
+ static char ignore_hmmer_cal = 0;
+ char* annotchr; // consensus amino acids in ASCII format, or, in HMMER format, the reference annotation character in insert line
+ //annotchr = new char[MAXRES]; // consensus amino acids in ASCII format, or, in HMMER format, the reference annotation character in insert line
+ annotchr = new char[par.maxResLen]; // consensus amino acids in ASCII format, or, in HMMER format, the reference annotation character in insert line
+ static int warn=0;
+ int iAlpha = 20; /* size of alphabet, default is protein = 20 */
+ double dAlphaInv = 1.00 / (double)(iAlpha); /* weight of AA */
+
+ trans_lin=0;
+ L=0;
+ Neff_HMM=0;
+ n_display=N_in=N_filtered=0;
+ nss_dssp=nsa_dssp=nss_pred=nss_conf=nfirst=ncons=-1;
+ lamda=mu=0.0;
+ trans_lin=0; // transition probs in log space
+ name[0]=longname[0]=desc[0]=fam[0]='\0';
+ //If at the end of while-loop L is still 0 then we have reached end of db file
+
+ // Do not delete name and seq vectors because their adresses are transferred to hitlist as part of a hit!!
+
+ while (fgetline(line,LINELEN-1,dbf) && !(line[0]=='/' && line[1]=='/'))
+ {
+
+ if (strscn(line)==NULL) continue; // skip lines that contain only white space
+ if (!strncmp("HMMER",line,5)) continue;
+
+ substr(str4,line,0,3); // copy the first four characters into str4
+
+ if (!strcmp("NAME",str4) && name[0]=='\0')
+ {
+ ptr=strscn(line+4); // advance to first non-white-space character
+ strncpy(name,ptr,NAMELEN-1); // copy full name to name
+ strcut(name); // ...cut after first word...
+ if (v>=4) cout<<"Reading in HMM "<<name<<":\n";
+ }
+
+ else if (!strcmp("ACC ",str4))
+ {
+ ptr=strscn(line+4); // advance to first non-white-space character
+ strncpy(longname,ptr,DESCLEN-1); // copy Accession id to longname...
+ }
+
+ else if (!strcmp("DESC",str4))
+ {
+ ptr=strscn(line+4); // advance to first non-white-space character
+ if (ptr)
+ {
+ strncpy(desc,ptr,DESCLEN-1); // copy description to name...
+ desc[DESCLEN-1]='\0';
+ strcut(ptr); // ...cut after first word...
+ }
+ if (!ptr || ptr[1]!='.' || strchr(ptr+3,'.')==NULL) strcpy(fam,""); else strcpy(fam,ptr); // could not find two '.' in name?
+ }
+
+ else if (!strcmp("LENG",str4))
+ {
+ ptr=line+4;
+ L=strint(ptr); //read next integer (number of match states)
+ }
+
+ else if (!strcmp("ALPH",str4)) {
+
+ ptr=strscn(line+4);
+
+ if (0 == strcmp(ptr, "Amino")){
+ iAlpha = 20;
+ }
+ else if (0 == strcmp(ptr, "Nucleic")){
+ iAlpha = 4;
+ printf("%s:%s:%d: WARNING: HMM reading does not work for DNA/RNA\n",
+ __FUNCTION__, __FILE__, __LINE__);
+ }
+ else {
+ return Warning(dbf,line,name);
+ }
+ dAlphaInv = 1.00 / (double)(iAlpha);
+ //continue;
+ }
+ else if (!strcmp("RF ",str4)) continue;
+ else if (!strcmp("CS ",str4)) continue;
+ else if (!strcmp("MAP ",str4)) continue;
+ else if (!strcmp("COM ",str4)) continue;
+ else if (!strcmp("NSEQ",str4))
+ {
+ ptr=line+4;
+ N_in=N_filtered=strint(ptr); //read next integer: number of sequences after filtering
+ }
+
+ else if (!strcmp("DATE",str4)) continue;
+ else if (!strncmp("CKSUM ",line,5)) continue;
+ else if (!strcmp("GA ",str4)) continue;
+ else if (!strcmp("TC ",str4)) continue;
+ else if (!strcmp("NC ",str4)) continue;
+
+ else if (!strncmp("SADSS",line,5))
+ {
+ if (nsa_dssp<0)
+ {
+ nsa_dssp=k++;
+ seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
+ sname[nsa_dssp] = new(char[15]);
+ strcpy(seq[nsa_dssp]," ");
+ strcpy(sname[nsa_dssp],"sa_dssp");
+
+ }
+ ptr=strscn(line+5);
+ if (ptr)
+ {
+ strcut(ptr);
+ if (strlen(seq[nsa_dssp])+strlen(ptr)>=(unsigned)(/*MAXRES*/par.maxResLen))
+ printf("\nWARNING: HMM %s has SADSS records with more than %i residues.\n",name,/*MAXRES*/par.maxResLen);
+ else strcat(seq[nsa_dssp],ptr);
+ }
+ }
+
+ else if (!strncmp("SSPRD",line,5))
+ {
+ if (nss_pred<0)
+ {
+ nss_pred=k++;
+ seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]);
+ sname[nss_pred] = new(char[15]);
+ strcpy(seq[nss_pred]," ");
+ strcpy(sname[nss_pred],"ss_pred");
+
+ }
+ ptr=strscn(line+5);
+ if (ptr)
+ {
+ strcut(ptr);
+ if (strlen(seq[nss_pred])+strlen(ptr)>=(unsigned)(/*MAXRES*/par.maxResLen))
+ printf("\nWARNING: HMM %s has SSPRD records with more than %i residues.\n",name,/*MAXRES*/par.maxResLen);
+ else strcat(seq[nss_pred],ptr);
+ }
+ }
+
+ else if (!strncmp("SSCON",line,5))
+ {
+ if (nss_conf<0)
+ {
+ nss_conf=k++;
+ seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]);
+ sname[nss_conf] = new(char[15]);
+ strcpy(seq[nss_conf]," ");
+ strcpy(sname[nss_conf],"ss_conf");
+ }
+ ptr=strscn(line+5);
+ if (ptr)
+ {
+ strcut(ptr);
+ if (strlen(seq[nss_conf])+strlen(ptr)>=(unsigned)(/*MAXRES*/par.maxResLen))
+ printf("\nWARNING: HMM %s has SSPRD records with more than %i residues.\n",name,/*MAXRES*/par.maxResLen);
+ else strcat(seq[nss_conf],ptr);
+ }
+ }
+
+ else if (!strncmp("SSCIT",line,5)) continue;
+ else if (!strcmp("XT ",str4)) continue;
+ else if (!strcmp("NULT",str4)) continue;
+
+ else if (!strcmp("NULE",str4))
+ {
+ ptr=line+4;
+ for (a=0; (a < iAlpha) && ptr; ++a){
+ /* FIXME: FS introduced alphabet size (was '20')
+ and dAlphaInv (was '0.05' = 1/20) */
+ //s2a[a]: transform amino acids Sorted by alphabet -> internal numbers for amino acids
+ pb[s2a[a]] = (float) dAlphaInv * fpow2(float(strinta(ptr,-99999))/HMMSCALE); /* dAlphaInv */
+ }
+ for (a = iAlpha; a < 20; a++){
+ pb[s2a[a]] = 0.0;
+ }
+ if (!ptr) return Warning(dbf,line,name);
+ if (v>=4)
+ {
+ printf("\nNULL ");
+ for (a=0; a<iAlpha; ++a) { /* FIXME: FS introduced iAlpha, was '20' */
+ printf("%5.1f ",100.*pb[s2a[a]]);
+ }
+ printf("\n");
+ }
+ }
+
+ else if (!strcmp("EVD ",str4))
+ {
+ char* ptr=line+4;
+ ptr = strscn(ptr);
+ sscanf(ptr,"%f",&lamda);
+ ptr = strscn(ptr);
+ sscanf(ptr,"%f",&mu);
+ if (lamda<0)
+ {
+ if (v>=2 && ignore_hmmer_cal==0)
+ cerr<<endl<<"Warning: some HMMs have been calibrated with HMMER's 'hmmcalibrate'. These calibrations will be ignored\n";
+ ignore_hmmer_cal=1;
+ mu = lamda = 0.0;
+ }
+ }
+
+ /////////////////////////////////////////////////////////////////////////////////////
+ // Read transition probabilities from start state
+ else if (!strncmp("HMM",line,3))
+ {
+ fgetline(line,LINELEN-1,dbf); // Skip line with amino acid labels
+ fgetline(line,LINELEN-1,dbf); // Skip line with transition labels
+ ptr=line;
+ for (a=0; a<=M2D && ptr; ++a)
+ tr[0][a] = float(strinta(ptr,-99999))/HMMSCALE; //store transition probabilites as log2 values
+ // strinta returns next integer in string and puts ptr to first char
+ // after the integer. Returns -99999 if '*' is found.
+ // ptr is set to 0 if no integer is found after ptr.
+ tr[0][I2M] = tr[0][D2M] = 0.0;
+ tr[0][I2I] = tr[0][D2D] = -99999.0;
+ if (!ptr) return Warning(dbf,line,name);
+ if (v>=4)
+ {
+ printf(" ");
+ for (a=0; a<=D2D && ptr; ++a) printf("%5.1f ",100*fpow2(tr[i][a]));
+ printf("\n");
+ }
+
+ // Prepare to store DSSP states (if there are none, delete afterwards)
+ nss_dssp=k++;
+ seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
+ sname[nss_dssp] = new(char[15]);
+ strcpy(sname[nss_dssp],"ss_dssp");
+
+ /////////////////////////////////////////////////////////////////////////////////////
+ // Read columns of HMM
+ int next_i=0; // index of next column
+ while (fgetline(line,LINELEN-1,dbf) && !(line[0]=='/' && line[1]=='/') && line[0]!='#')
+ {
+ if (strscn(line)==NULL) continue; // skip lines that contain only white space
+
+ // Read in AA probabilities
+ ptr=line;
+ int prev_i = next_i;
+ next_i = strint(ptr); ++i;
+ if (v && next_i!=prev_i+1)
+ if (++warn<5)
+ {
+ cerr<<endl<<"WARNING: in HMM "<<name<<" state "<<prev_i<<" is followed by state "<<next_i<<"\n";
+ if (warn==5) cerr<<endl<<"WARNING: further warnings while reading HMMs will be suppressed.\n";
+ }
+ if (i>L)
+ {
+ cerr<<endl<<"Error: in HMM "<<name<<" there are more columns than the stated length "<<L<<"\n";
+ return 2;
+ }
+ if (i>L && v)
+ cerr<<endl<<"WARNING: in HMM "<<name<<" there are more columns than the stated length "<<L<<"\n";
+ if (i>=/*MAXRES*/par.maxResLen-2)
+ {
+ fgetline(line,LINELEN-1,dbf); // Skip two lines
+ fgetline(line,LINELEN-1,dbf);
+ continue;
+ }
+
+ for (a=0; (a<iAlpha) && ptr; ++a){ /* FIXME: FS introduced iAlpha, was '20' */
+ f[i][s2a[a]] = (float) pb[s2a[a]]*fpow2(float(strinta(ptr,-99999))/HMMSCALE);
+ //s2a[a]: transform amino acids Sorted by alphabet -> internal numbers for amino acids
+ }
+ for (a = iAlpha; a < 20; a++){
+ f[i][s2a[a]] = 0.0;
+ }
+ if (!ptr) return Warning(dbf,line,name);
+ if (v>=4)
+ {
+ printf("%6i ",i);
+ for (a=0; a<iAlpha; ++a) { /* FIXME: FS introduced iAlpha, was '20' */
+ printf("%5.1f ",100*f[i][s2a[a]]);
+ }
+ printf("\n");
+ }
+
+ // Read insert emission line
+ fgetline(line,LINELEN-1,dbf);
+ ptr = strscn(line);
+ if (!ptr) return Warning(dbf,line,name);
+ annotchr[i]=uprchr(*ptr);
+ if (*ptr!='-' && *ptr!=' ') annot=1;
+
+ // Read annotation character and seven transition probabilities
+ fgetline(line,LINELEN-1,dbf);
+ ptr = strscn(line);
+ switch (*ptr)
+ {
+ case 'H':
+ ss_dssp[i]=1;
+ seq[nss_dssp][i]=*ptr;
+ dssp=1;
+ break;
+ case 'E':
+ ss_dssp[i]=2;
+ seq[nss_dssp][i]=*ptr;
+ dssp=1;
+ break;
+ case 'C':
+ ss_dssp[i]=3;
+ seq[nss_dssp][i]=*ptr;
+ dssp=1;
+ break;
+ case 'S':
+ ss_dssp[i]=4;
+ seq[nss_dssp][i]=*ptr;
+ dssp=1;
+ break;
+ case 'T':
+ ss_dssp[i]=5;
+ seq[nss_dssp][i]=*ptr;
+ dssp=1;
+ break;
+ case 'G':
+ ss_dssp[i]=6;
+ seq[nss_dssp][i]=*ptr;
+ dssp=1;
+ break;
+ case 'B':
+ ss_dssp[i]=7;
+ seq[nss_dssp][i]=*ptr;
+ dssp=1;
+ break;
+ case 'I':
+ dssp=1;
+ case '~':
+ ss_dssp[i]=3;
+ seq[nss_dssp][i]=*ptr;
+ break;
+ case '-':
+ default:
+ ss_dssp[i]=0;
+ seq[nss_dssp][i]=*ptr;
+ break;
+
+ }
+
+ ptr+=2;
+ for (a=0; a<=D2D && ptr; ++a)
+ tr[i][a] = float(strinta(ptr,-99999))/HMMSCALE; //store transition prob's as log2-values
+ if (!ptr) return Warning(dbf,line,name);
+ if (v>=4)
+ {
+ printf(" ");
+ for (a=0; a<=D2D; ++a) printf("%5.1f ",100*fpow2(tr[i][a]));
+ printf("\n");
+ }
+ }
+
+ if (line[0]=='/' && line[1]=='/') break;
+
+ } /* strncmp("HMM") */
+
+ } //while(getline)
+
+ if (L==0) return 0; //End of db file -> stop reading in
+
+ // Set coefficients of EVD (= 0.0 if not calibrated for these parameters)
+ // lamda = lamda_hash.Show(par.Key());
+ // mu = mu_hash.Show(par.Key());
+ if (lamda && v>=2) printf("HMM %s is already calibrated: lamda=%-5.3f, mu=%-5.2f\n",name,lamda,mu);
+
+ if (v && i!=L) cerr<<endl<<"Warning: in HMM "<<name<<" there are only "<<i<<" columns while the stated length is "<<L<<"\n";
+ if (v && i>=/*MAXRES*/par.maxResLen-2) {i=/*MAXRES*/par.maxResLen-2; cerr<<endl<<"WARNING: maximum number "<</*MAXRES*/par.maxResLen-2<<" of residues exceeded while reading HMM "<<name<<"\n";}
+ if (v && !i) cerr<<endl<<"WARNING: HMM "<<name<<" contains no match states. Check the alignment that gave rise to this HMM.\n";
+ L = i;
+
+ if (strlen(longname)>0) strcat(longname," ");
+ strncat(longname,name,DESCLEN-strlen(longname)-1); // longname = ACC NAME DESC
+ if (strlen(name)>0) strcat(longname," ");
+ strncat(longname,desc,DESCLEN-strlen(longname)-1);
+ longname[DESCLEN-1]='\0';
+ ScopID(cl,fold,sfam,fam);// get scop classification from basename (e.g. a.1.2.3.4)
+ RemoveExtension(file,filestr); // copy name of dbfile without extension into 'file'
+
+ // Secondary structure
+ if (!dssp)
+ {
+ // remove dssp sequence
+ // memory that had been allocated in case ss_dssp was given needs to be freed
+ delete[] seq[nss_dssp]; seq[nss_dssp] = NULL;
+ // memory that had been allocated in case ss_dssp was given needs to be freed
+ delete[] sname[nss_dssp]; sname[nss_dssp] = NULL;
+ nss_dssp=-1;
+ k--;
+ }
+ if (nss_pred>=0)
+ {
+ for (i=1; i<=L; ++i) ss_pred[i] = ss2i(seq[nss_pred][i]);
+ if (nss_conf>=0)
+ for (i=1; i<=L; ++i) ss_conf[i] = cf2i(seq[nss_conf][i]);
+ else
+ for (i=1; i<=L; ++i) ss_conf[i] = 5;
+ }
+
+ // Copy query (first sequence) and consensus residues?
+ if (par.showcons)
+ {
+ sname[k]=new(char[10]);
+ strcpy(sname[k],"Consensus");
+ sname[k+1]=new(char[strlen(longname)+1]);
+ strcpy(sname[k+1],longname);
+ seq[k]=new(char[L+2]);
+ seq[k][0]=' ';
+ seq[k][L+1]='\0';
+ seq[k+1]=new(char[L+2]);
+ seq[k+1][0]=' ';
+ seq[k+1][L+1]='\0';
+ for (i=1; i<=L; ++i)
+ {
+ float pmax=0.0;
+ int amax=0;
+ for (a=0; a<NAA; ++a)
+ if (f[i][a]>pmax) {amax=a; pmax=f[i][a];}
+ if (pmax>0.6) seq[k][i]=i2aa(amax);
+ else if (pmax>0.4) seq[k][i]=lwrchr(i2aa(amax));
+ else seq[k][i]='x';
+ seq[k+1][i]=i2aa(amax);
+ }
+ ncons=k++; // nfirst is set later!
+ }
+ else
+ {
+ sname[k]=new(char[strlen(longname)+1]);
+ /* FIXME valgrind says bytes get lost here during hmm iteration --
+ fixed in HMM::ClobberGlobal(), I (FS) think */
+ strcpy(sname[k],longname);
+ seq[k]=new(char[L+2]);
+ seq[k][0]=' ';
+ seq[k][L+1]='\0';
+ }
+
+ if (annot) // read in some annotation characters?
+ {
+ annotchr[0]=' ';
+ annotchr[L+1]='\0';
+ strcpy(seq[k],annotchr); // overwrite the consensus sequence with the annotation characters
+ }
+ else if (!par.showcons) // we have not yet calculated the consensus, but we need it now as query (first sequence)
+ {
+ /* FIXME: FS set ncons=k
+ don't understand why it is not set but seem to need it */
+ ncons = k;
+ for (i=1; i<=L; ++i)
+ {
+ float pmax=0.0;
+ int amax=0;
+ for (a=0; a<NAA; ++a)
+ if (f[i][a]>pmax) {amax=a; pmax=f[i][a];}
+ seq[k][i]=i2aa(amax);
+ }
+ }
+// printf("%i query name=%s seq=%s\n",n,sname[n],seq[n]);
+ nfirst=k++;
+
+ n_display=k;
+
+ // Calculate overall Neff_HMM
+ Neff_HMM=0;
+ for (i=1; i<=L; ++i)
+ {
+ float S=0.0;
+ for (a=0; a<iAlpha; ++a) { /* FIXME: FS introduced iAlpha, was '20' */
+ if (f[i][a]>1E-10) S-=f[i][a]*fast_log2(f[i][a]);
+ }
+ Neff_HMM+=(float) fpow2(S);
+ }
+ Neff_HMM/=L;
+ for (i=0; i<=L; ++i) Neff_M[i] = Neff_I[i] = Neff_D[i] = 10.0; // to add only little additional pseudocounts!
+ if (v>=2)
+ cout<<"Read in HMM "<<name<<" with "<<L<<" match states and effective number of sequences = "<<Neff_HMM<<"\n";
+
+ // Set emission probabilities of zero'th (begin) state and L+1st (end) state to background probabilities
+ for (a=0; a<iAlpha; ++a) { /* FIXME: FS introduced iAlpha, was '20' */
+ f[0][a]=f[L+1][a]=pb[a];
+ }
+ delete[] annotchr; annotchr = NULL;
+
+ return 1; //return status: ok
+
+} /* this is the end of HMM::ReadHMMer() */
+
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Read an HMM from a HMMER3 .hmm file; return 0 at end of file
+ */
+int
+HMM::ReadHMMer3(FILE* dbf, char* filestr)
+{
+ char line[LINELEN]=""; // input line
+ char desc[DESCLEN]=""; // description of family
+ char str4[5]=""; // first 4 letters of input line
+ char* ptr; // pointer for string manipulation
+ int i=0; // index for match state (first=1)
+ int a; // amino acid index
+ char dssp=0; // 1 if a consensus SS has been found in the transition prob lines
+ char annot=0; // 1 if at least one annotation character in insert lines is ne '-' or ' '
+ int k=0; // index for seq[k]
+ char* annotchr; // consensus amino acids in ASCII format, or, in HMMER format, the reference annotation character in insert line
+ //annotchr = new char[MAXRES]; // consensus amino acids in ASCII format, or, in HMMER format, the reference annotation character in insert line
+ annotchr = new char[par.maxResLen]; // consensus amino acids in ASCII format, or, in HMMER format, the reference annotation character in insert line
+ static int warn=0;
+ int iAlpha = 20; /* size of alphabet, default is protein = 20 */
+ double dAlphaInv = 1.00 / (double)(iAlpha); /* weight of AA */
+
+ trans_lin=0;
+ L=0;
+ Neff_HMM=0;
+ n_seqs=n_display=N_in=N_filtered=0;
+ nss_dssp=nsa_dssp=nss_pred=nss_conf=nfirst=ncons=-1;
+ lamda=mu=0.0;
+ trans_lin=0; // transition probs in log space
+ name[0]=longname[0]=desc[0]=fam[0]='\0';
+ //If at the end of while-loop L is still 0 then we have reached end of db file
+
+ // Do not delete name and seq vectors because their adresses are transferred to hitlist as part of a hit!!
+
+
+ while (fgetline(line,LINELEN-1,dbf) && !(line[0]=='/' && line[1]=='/'))
+ {
+
+ if (strscn(line)==NULL) continue; // skip lines that contain only white space
+ if (!strncmp("HMMER",line,5)) continue;
+
+ substr(str4,line,0,3); // copy the first four characters into str4
+
+ if (!strcmp("NAME",str4) && name[0]=='\0')
+ {
+ ptr=strscn(line+4); // advance to first non-white-space character
+ strncpy(name,ptr,NAMELEN-1); // copy full name to name
+ strcut(name); // ...cut after first word...
+ if (v>=4) cout<<"Reading in HMM "<<name<<":\n";
+ }
+
+ else if (!strcmp("ACC ",str4))
+ {
+ ptr=strscn(line+4); // advance to first non-white-space character
+ strncpy(longname,ptr,DESCLEN-1); // copy Accession id to longname...
+ }
+
+ else if (!strcmp("DESC",str4))
+ {
+ ptr=strscn(line+4); // advance to first non-white-space character
+ if (ptr)
+ {
+ strncpy(desc,ptr,DESCLEN-1); // copy description to name...
+ desc[DESCLEN-1]='\0';
+ strcut(ptr); // ...cut after first word...
+ }
+ if (!ptr || ptr[1]!='.' || strchr(ptr+3,'.')==NULL) strcpy(fam,""); else strcpy(fam,ptr); // could not find two '.' in name?
+ }
+
+ else if (!strcmp("LENG",str4))
+ {
+ ptr=line+4;
+ L=strint(ptr); //read next integer (number of match states)
+ }
+
+ else if (!strcmp("ALPH",str4)) {
+
+ ptr=strscn(line+4);
+
+ if (0 == strcmp(ptr, "amino")){
+ iAlpha = 20;
+ }
+ else if (0 == strcmp(ptr, "Nucleic")){
+ iAlpha = 4;
+ printf("%s:%s:%d: WARNING: HMM reading does not work for DNA/RNA\n",
+ __FUNCTION__, __FILE__, __LINE__);
+ }
+ else {
+ return Warning(dbf,line,name);
+ }
+ dAlphaInv = 1.00 / (double)(iAlpha);
+ //continue;
+ }
+ else if (!strcmp("RF ",str4)) continue;
+ else if (!strcmp("CS ",str4)) continue;
+ else if (!strcmp("MAP ",str4)) continue;
+ else if (!strcmp("COM ",str4)) continue;
+ else if (!strcmp("NSEQ",str4))
+ {
+ ptr=line+4;
+ N_in=N_filtered=strint(ptr); //read next integer: number of sequences after filtering
+ }
+
+ else if (!strcmp("DATE",str4)) continue;
+ else if (!strncmp("CKSUM ",line,5)) continue;
+ else if (!strcmp("GA ",str4)) continue;
+ else if (!strcmp("TC ",str4)) continue;
+ else if (!strcmp("NC ",str4)) continue;
+
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ // Still needed???
+
+ else if (!strncmp("SADSS",line,5))
+ {
+ if (nsa_dssp<0)
+ {
+ nsa_dssp=k++;
+ seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
+ sname[nsa_dssp] = new(char[15]);
+ strcpy(seq[nsa_dssp]," ");
+ strcpy(sname[nsa_dssp],"sa_dssp");
+
+ }
+ ptr=strscn(line+5);
+ if (ptr)
+ {
+ strcut(ptr);
+ if (strlen(seq[nsa_dssp])+strlen(ptr)>=(unsigned)(/*MAXRES*/par.maxResLen))
+ printf("\nWARNING: HMM %s has SADSS records with more than %i residues.\n",name,/*MAXRES*/par.maxResLen);
+ else strcat(seq[nsa_dssp],ptr);
+ }
+ }
+
+ else if (!strncmp("SSPRD",line,5))
+ {
+ if (nss_pred<0)
+ {
+ nss_pred=k++;
+ seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]);
+ sname[nss_pred] = new(char[15]);
+ strcpy(seq[nss_pred]," ");
+ strcpy(sname[nss_pred],"ss_pred");
+
+ }
+ ptr=strscn(line+5);
+ if (ptr)
+ {
+ strcut(ptr);
+ if (strlen(seq[nss_pred])+strlen(ptr)>=(unsigned)(/*MAXRES*/par.maxResLen))
+ printf("\nWARNING: HMM %s has SSPRD records with more than %i residues.\n",name,/*MAXRES*/par.maxResLen);
+ else strcat(seq[nss_pred],ptr);
+ }
+ }
+
+ else if (!strncmp("SSCON",line,5))
+ {
+ if (nss_conf<0)
+ {
+ nss_conf=k++;
+ seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]);
+ sname[nss_conf] = new(char[15]);
+ strcpy(seq[nss_conf]," ");
+ strcpy(sname[nss_conf],"ss_conf");
+ }
+ ptr=strscn(line+5);
+ if (ptr)
+ {
+ strcut(ptr);
+ if (strlen(seq[nss_conf])+strlen(ptr)>=(unsigned)(/*MAXRES*/par.maxResLen))
+ printf("\nWARNING: HMM %s has SSPRD records with more than %i residues.\n",name,/*MAXRES*/par.maxResLen);
+ else strcat(seq[nss_conf],ptr);
+ }
+ }
+
+ else if (!strncmp("SSCIT",line,5)) continue;
+ else if (!strcmp("XT ",str4)) continue;
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ else if (!strncmp("STATS LOCAL",line,11)) continue;
+
+ else if (!strcmp("EFFN",str4))
+ {
+ ptr=line+4;
+ float effn = strflt(ptr);
+ // Calculate Neff_HMM by using f(x) = ax^0.1 + bx^0.5 + cx + d (fitted with scop25 dataset)
+ Neff_HMM = -1.403534 * pow(effn, 0.1) + 4.428118 * pow(effn, 0.5) - 0.2885410 * effn - 1.108568;
+ }
+
+ /////////////////////////////////////////////////////////////////////////////////////
+ // Read transition probabilities from start state
+ else if (!strncmp("HMM",line,3))
+ {
+ fgetline(line,LINELEN-1,dbf); // Skip line with amino acid labels
+ fgetline(line,LINELEN-1,dbf); // Skip line with transition labels
+ ptr=strscn(line);
+
+ if (!strncmp("COMPO",ptr,5))
+ {
+ ptr=ptr+5;
+ for (a=0; a<20 && ptr; ++a)
+ //s2a[a]: transform amino acids Sorted by alphabet -> internal numbers for amino acids
+ pb[s2a[a]] = (float) exp(-1.0*strflta(ptr,99999));
+ if (!ptr) return Warning(dbf,line,name);
+ if (v>=4)
+ {
+ printf("\nNULL ");
+ for (a=0; a<20; ++a) printf("%6.3g ",100.*pb[s2a[a]]);
+ printf("\n");
+ }
+ fgetline(line,LINELEN-1,dbf); // Read next line
+ }
+
+ fgetline(line,LINELEN-1,dbf); // Skip line with 0-states insert probabilities
+
+ ptr = strscn(line);
+ for (a=0; a<=D2D && ptr; ++a)
+ tr[0][a] = log2((float) exp(-1.0*strflta(ptr,99999))); //store transition probabilites as log2 values
+ // strinta returns next integer in string and puts ptr to first char
+ // after the integer. Returns -99999 if '*' is found.
+ // ptr is set to 0 if no integer is found after ptr.
+ if (!ptr) return Warning(dbf,line,name);
+ if (v>=4)
+ {
+ printf(" ");
+ for (a=0; a<=D2D && ptr; ++a) printf("%6.3g ",100*fpow2(tr[i][a]));
+ printf("\n");
+ }
+
+ // Prepare to store DSSP states (if there are none, delete afterwards)
+ nss_dssp=k++;
+ seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
+ sname[nss_dssp] = new(char[15]);
+ strcpy(sname[nss_dssp],"ss_dssp");
+
+ /////////////////////////////////////////////////////////////////////////////////////
+ // Read columns of HMM
+ int next_i=0; // index of next column
+ while (fgetline(line,LINELEN-1,dbf) && !(line[0]=='/' && line[1]=='/') && line[0]!='#')
+ {
+ if (strscn(line)==NULL) continue; // skip lines that contain only white space
+
+ // Read in AA probabilities
+ ptr=line;
+ int prev_i = next_i;
+ next_i = strint(ptr); ++i;
+ if (v && next_i!=prev_i+1)
+ if (++warn<5)
+ {
+ cerr<<endl<<"WARNING: in HMM "<<name<<" state "<<prev_i<<" is followed by state "<<next_i<<"\n";
+ if (warn==5) cerr<<endl<<"WARNING: further warnings while reading HMMs will be suppressed.\n";
+ }
+ if (i>L)
+ {
+ cerr<<endl<<"Error: in HMM "<<name<<" there are more columns than the stated length "<<L<<"\n";
+ return 2;
+ }
+ if (i>L && v)
+ cerr<<endl<<"WARNING: in HMM "<<name<<" there are more columns than the stated length "<<L<<"\n";
+ if (i>=/*MAXRES*/par.maxResLen-2)
+ {
+ fgetline(line,LINELEN-1,dbf); // Skip two lines
+ fgetline(line,LINELEN-1,dbf);
+ continue;
+ }
+
+ for (a=0; a<iAlpha && ptr; ++a){ /* FIXME: FS introduced iAlpha, was '20' */
+ f[i][s2a[a]] = (float) exp(-1.0*strflta(ptr,99999));
+ //s2a[a]: transform amino acids Sorted by alphabet -> internal numbers for amino acids
+ }
+ for (a = iAlpha; a < 20; a++){
+ f[i][s2a[a]] = 0.0;
+ }
+ if (!ptr) return Warning(dbf,line,name);
+ if (v>=4)
+ {
+ printf("%6i ",i);
+ for (a=0; a<iAlpha; ++a) printf("%6.3g ",100*f[i][s2a[a]]);
+ printf("\n");
+ }
+
+ // Ignore MAP annotation
+ ptr = strscn(line); //find next word
+ ptr = strscn_ws(line); // ignore word
+
+ // Read RF and CS annotation
+ ptr = strscn(line);
+ if (!ptr) return Warning(dbf,line,name);
+ annotchr[i]=uprchr(*ptr);
+ if (*ptr!='-' && *ptr!=' ') annot=1;
+
+ ptr = strscn(line);
+ switch (*ptr)
+ {
+ case 'H':
+ ss_dssp[i]=1;
+ seq[nss_dssp][i]=*ptr;
+ dssp=1;
+ break;
+ case 'E':
+ ss_dssp[i]=2;
+ seq[nss_dssp][i]=*ptr;
+ dssp=1;
+ break;
+ case 'C':
+ ss_dssp[i]=3;
+ seq[nss_dssp][i]=*ptr;
+ dssp=1;
+ break;
+ case 'S':
+ ss_dssp[i]=4;
+ seq[nss_dssp][i]=*ptr;
+ dssp=1;
+ break;
+ case 'T':
+ ss_dssp[i]=5;
+ seq[nss_dssp][i]=*ptr;
+ dssp=1;
+ break;
+ case 'G':
+ ss_dssp[i]=6;
+ seq[nss_dssp][i]=*ptr;
+ dssp=1;
+ break;
+ case 'B':
+ ss_dssp[i]=7;
+ seq[nss_dssp][i]=*ptr;
+ dssp=1;
+ break;
+ case 'I':
+ dssp=1;
+ case '~':
+ ss_dssp[i]=3;
+ seq[nss_dssp][i]=*ptr;
+ break;
+ case '-': // no SS available from any template
+ case '.': // no clear consensus SS structure
+ case 'X': // no clear consensus SS structure
+ ss_dssp[i]=0;
+ seq[nss_dssp][i]='-';
+ break;
+ default:
+ ss_dssp[i]=0;
+ seq[nss_dssp][i]=*ptr;
+ break;
+ }
+
+ // Read insert emission line
+ fgetline(line,LINELEN-1,dbf);
+
+ // Read seven transition probabilities
+ fgetline(line,LINELEN-1,dbf);
+
+ ptr+=2;
+ for (a=0; a<=D2D && ptr; ++a)
+ tr[i][a] = log2((float) exp(-1.0*strflta(ptr,99999))); //store transition prob's as log2-values
+ if (!ptr) return Warning(dbf,line,name);
+ if (v>=4)
+ {
+ printf(" ");
+ for (a=0; a<=D2D; ++a) printf("%6.3g ",100*fpow2(tr[i][a]));
+ printf("\n");
+ }
+ }
+
+ if (line[0]=='/' && line[1]=='/') break;
+
+ } /* strncmp("HMM") */
+
+ } //while(getline)
+
+ if (L==0) return 0; //End of db file -> stop reading in
+
+ if (v && i!=L) cerr<<endl<<"Warning: in HMM "<<name<<" there are only "<<i<<" columns while the stated length is "<<L<<"\n";
+ if (v && i>=/*MAXRES*/par.maxResLen-2) {i=/*MAXRES*/par.maxResLen-2; cerr<<endl<<"WARNING: maximum number "<</*MAXRES*/par.maxResLen-2<<" of residues exceeded while reading HMM "<<name<<"\n";}
+ if (v && !i) cerr<<endl<<"WARNING: HMM "<<name<<" contains no match states. Check the alignment that gave rise to this HMM.\n";
+ L = i;
+
+ if (strlen(longname)>0) strcat(longname," ");
+ strncat(longname,name,DESCLEN-strlen(longname)-1); // longname = ACC NAME DESC
+ if (strlen(name)>0) strcat(longname," ");
+ strncat(longname,desc,DESCLEN-strlen(longname)-1);
+ longname[DESCLEN-1]='\0';
+ ScopID(cl,fold,sfam,fam);// get scop classification from basename (e.g. a.1.2.3.4)
+ RemoveExtension(file,filestr); // copy name of dbfile without extension into 'file'
+
+ // Secondary structure
+ if (!dssp)
+ {
+ // remove dssp sequence
+ delete[] seq[nss_dssp]; // memory that had been allocated in case ss_dssp was given needs to be freed
+ delete[] sname[nss_dssp]; // memory that had been allocated in case ss_dssp was given needs to be freed
+ nss_dssp=-1;
+ k--;
+ }
+ else { seq[nss_dssp][0]='-'; seq[nss_dssp][L+1]='\0'; }
+
+ if (nss_pred>=0)
+ {
+ for (i=1; i<=L; ++i) ss_pred[i] = ss2i(seq[nss_pred][i]);
+ if (nss_conf>=0)
+ for (i=1; i<=L; ++i) ss_conf[i] = cf2i(seq[nss_conf][i]);
+ else
+ for (i=1; i<=L; ++i) ss_conf[i] = 5;
+ }
+
+ // Copy query (first sequence) and consensus residues?
+ if (par.showcons)
+ {
+ sname[k]=new(char[10]);
+ strcpy(sname[k],"Consensus");
+ sname[k+1]=new(char[strlen(longname)+1]);
+ strcpy(sname[k+1],longname);
+ seq[k]=new(char[L+2]);
+ seq[k][0]=' ';
+ seq[k][L+1]='\0';
+ seq[k+1]=new(char[L+2]);
+ seq[k+1][0]=' ';
+ seq[k+1][L+1]='\0';
+ for (i=1; i<=L; ++i)
+ {
+ float pmax=0.0;
+ int amax=0;
+ for (a=0; a<NAA; ++a)
+ if (f[i][a]>pmax) {amax=a; pmax=f[i][a];}
+ if (pmax>0.6) seq[k][i]=i2aa(amax);
+ else if (pmax>0.4) seq[k][i]=lwrchr(i2aa(amax));
+ else seq[k][i]='x';
+ seq[k+1][i]=i2aa(amax);
+ }
+ ncons=k++; // nfirst is set later!
+ }
+ else
+ {
+ sname[k]=new(char[strlen(longname)+1]);
+ strcpy(sname[k],longname);
+ seq[k]=new(char[L+2]);
+ seq[k][0]=' ';
+ seq[k][L+1]='\0';
+ }
+
+ if (annot) // read in some annotation characters?
+ {
+ annotchr[0]=' ';
+ annotchr[L+1]='\0';
+ strcpy(seq[k],annotchr); // overwrite the consensus sequence with the annotation characters
+ }
+ else if (!par.showcons) // we have not yet calculated the consensus, but we need it now as query (first sequence)
+ {
+ for (i=1; i<=L; ++i)
+ {
+ float pmax=0.0;
+ int amax=0;
+ for (a=0; a<NAA; ++a)
+ if (f[i][a]>pmax) {amax=a; pmax=f[i][a];}
+ seq[k][i]=i2aa(amax);
+ }
+ }
+ // printf("%i query name=%s seq=%s\n",n,sname[n],seq[n]);
+ nfirst=k++;
+
+ n_display=k;
+ n_seqs=k;
+
+ // If no effektive number of sequences is given, calculate Neff_HMM by given profile
+ if (Neff_HMM == 0) {
+ for (i=1; i<=L; ++i)
+ {
+ float S=0.0;
+ for (a=0; a<20; ++a)
+ if (f[i][a]>1E-10) S-=f[i][a]*fast_log2(f[i][a]);
+ Neff_HMM+=(float) fpow2(S);
+ }
+ Neff_HMM/=L;
+ }
+
+ for (i=0; i<=L; ++i) Neff_M[i] = Neff_I[i] = Neff_D[i] = 10.0; // to add only little additional pseudocounts!
+ Neff_M[L+1]=1.0f;
+ Neff_I[L+1]=Neff_D[L+1]=0.0f;
+
+ if (v>=2)
+ cout<<"Read in HMM "<<name<<" with "<<L<<" match states and effective number of sequences = "<<Neff_HMM<<"\n";
+
+ ///////////////////////////////////////////////////////////////////
+
+ // Set emission probabilities of zero'th (begin) state and L+1st (end) state to background probabilities
+ for (a=0; a<20; ++a) f[0][a]=f[L+1][a]=pb[a];
+ delete[] annotchr;
+
+ has_pseudocounts=true;
+
+ return 1; //return status: ok
+
+
+} /* this is the end of HMM::ReadHMMer3() */
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Add transition pseudocounts to HMM (and calculate lin-space transition probs)
+ */
+void
+HMM::AddTransitionPseudocounts(float gapd, float gape, float gapf, float gapg, float gaph, float gapi, float gapb)
+{
+ int i; //position in alignment
+ float sum;
+ float pM2M, pM2I, pM2D, pI2I, pI2M, pD2D, pD2M;
+ float p0,p1,p2;
+ if (par.gapb<=0) return;
+ if (trans_lin==1) {fprintf(stderr,"Error: Adding transition pseudocounts to linear representation of %s not allowed. Please report this error to the HHsearch developers.\n",name); exit(6);}
+ if (trans_lin==2) {fprintf(stderr,"Error: Adding transition pseudocounts twice is %s not allowed. Please report this error to the HHsearch developers.\n",name); exit(6);}
+ trans_lin=2;
+
+ // Calculate pseudocount transition probabilities
+ pM2D=pM2I=gapd*0.0286; //a-priori probability for inserts and deletions
+ pM2M=1-pM2D-pM2I;
+ // gape=0 -> pI2I=0 gape=1 -> pI2I=0.75 gape=inf -> pI2I=1.
+ pI2I=1.0*gape/(gape-1+1.0/0.75);
+ pI2M=1-pI2I;
+ // gape=0 -> pD2D=0 gape=1 -> pD2D=0.75 gape=inf -> pD2D=1.
+ pD2D=1.0*gape/(gape-1+1.0/0.75);
+ pD2M=1-pD2D;
+
+ for (i=0; i<=L; ++i) //for all columns in HMM
+ {
+ // Transitions from M state
+ p0 = (Neff_M[i]-1)*fpow2(tr[i][M2M]) + gapb*pM2M;
+ p1 = (Neff_M[i]-1)*fpow2(tr[i][M2D]) + gapb*pM2D;
+ p2 = (Neff_M[i]-1)*fpow2(tr[i][M2I]) + gapb*pM2I;
+ if (i==0) p1=p2=0; //from M(0) no transition to D(1) and I(0) possible
+ if (i==L) p1=p2=0; //from M(L) no transition to D(L+1) and I(L+1) possible
+ sum = p0+p1+p2+FLT_MIN;
+
+// p0 = p0/sum ;
+// p1 = pow(p1/sum,gapf);
+// p2 = pow(p2/sum,gapg);
+// sum = p0+p1+p2+FLT_MIN;
+// tr[i][M2M] = fast_log2(p0/sum);
+// tr[i][M2D] = fast_log2(p1/sum);
+// tr[i][M2I] = fast_log2(p2/sum);
+
+ tr[i][M2M] = fast_log2(p0/sum);
+ tr[i][M2D] = fast_log2(p1/sum)*gapf;
+ tr[i][M2I] = fast_log2(p2/sum)*gapg;
+
+ // Transitions from I state
+ p0 = Neff_I[i]*fpow2(tr[i][I2M]) + gapb*pI2M;
+ p1 = Neff_I[i]*fpow2(tr[i][I2I]) + gapb*pI2I;
+ sum = p0+p1+FLT_MIN;
+
+// p0 = pow(p0/sum,gapg);
+// p1 = pow(p1/sum,gapi);
+// sum = p0+p1+FLT_MIN;
+// tr[i][I2M] = fast_log2(p0/sum);
+// tr[i][I2I] = fast_log2(p1/sum);
+
+ tr[i][I2M] = fast_log2(p0/sum);
+ tr[i][I2I] = fast_log2(p1/sum)*gapi;
+
+ // Transitions from D state
+ p0 = Neff_D[i]*fpow2(tr[i][D2M]) + gapb*pD2M;
+ p1 = Neff_D[i]*fpow2(tr[i][D2D]) + gapb*pD2D;
+ if (i==L) p1=0; //from D(L) no transition to D(L+1) possible
+ sum = p0+p1+FLT_MIN;
+
+// p0 = pow(p0/sum,gapf);
+// p1 = pow(p1/sum,gaph);
+// sum = p0+p1+FLT_MIN;
+// tr[i][D2M] = fast_log2(p0/sum);
+// tr[i][D2D] = fast_log2(p1/sum);
+
+ tr[i][D2M] = fast_log2(p0/sum);
+ tr[i][D2D] = fast_log2(p1/sum)*gaph;
+
+ // SS-dependent gap penalties
+ tr[i][M2M_GAPOPEN]=tr[i][M2M];
+ tr[i][GAPOPEN]=0.0;
+ tr[i][GAPEXTD]=0.0;
+ }
+
+ if (v>=4)
+ {
+ printf("\nPseudocount transition probabilities:\n");
+ printf("pM2M=%4.1f%%, pM2I=%4.1f%%, pM2D=%4.1f%%, ",100*pM2M,100*pM2I,100*pM2D);
+ printf("pI2M=%4.1f%%, pI2I=%4.1f%%, ",100*pI2M,100*pI2I);
+ printf("pD2M=%4.1f%%, pD2D=%4.1f%% ",100*pD2M,100*pD2D);
+ printf("tau = %4.1f%%\n\n",100.*gapb/(Neff_HMM-1+gapb));
+ printf("Listing transition probabilities WITH pseudocounts:\n");
+ printf(" i dssp pred sacc M->M M->I M->D I->M I->I D->M D->D\n");
+
+ for (i=1; i<=L; ++i) //for all columns in HMM
+ {
+ printf("%4i %1c %1c %1c %6.3f %6.3f %6.3f ",i,i2ss(ss_dssp[i]),i2ss(ss_pred[i]),i2sa(sa_dssp[i]),fpow2(tr[i][M2M]),fpow2(tr[i][M2I]),fpow2(tr[i][M2D]));
+ printf("%6.3f %6.3f ",fpow2(tr[i][I2M]),fpow2(tr[i][I2I]));
+ printf("%6.3f %6.3f ",fpow2(tr[i][D2M]),fpow2(tr[i][D2D]));
+ printf("%1i %2i %1i\n",ss_pred[i],ss_conf[i],ss_dssp[i]);
+ }
+ printf("\n");
+ printf("nss_dssp=%i nss_pred=%i\n",nss_dssp,nss_pred);
+ }
+ return;
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Use secondary structure-dependent gap penalties
+ * on top of the HMM transition penalties
+ */
+void
+HMM::UseSecStrucDependentGapPenalties()
+{
+ int i; // column in HMM
+ int ii;
+ //unsigned char iis[MAXRES]; // inside-integer array
+ unsigned char iis[par.maxResLen]; // inside-integer array
+ float d; // Additional penalty for opening gap whithin SS element
+ float e; // Additional penalty for extending gap whithin SS element
+
+ // Determine inside-integers:
+ // CCSTCCCHHHHHHHHHHHCCCCCEEEEECCSBGGGCCCCEECC
+ // 0000000123444432100000012210000000000001000
+ ii=0;
+ for (i=0; i<=L; ++i) // forward run
+ {
+ if (ss_dssp[i]==1 || ss_dssp[i]==2) {ii+=(ii<par.ssgapi);} else ii=0;
+ iis[i]=ii;
+ } for (i=0; i<=L; ++i)
+ ii=0;
+ iis[0]=iis[L]=0;
+ for (i=L; i>=0; i--) // backward run
+ {
+ if (ss_dssp[i]==1 || ss_dssp[i]==2) {ii+=(ii<par.ssgapi);} else ii=0;
+ iis[i-1]=imin(ii,iis[i-1]);
+ }
+
+ // Add SS-dependent gap penalties to HMM transition penalties
+ for (i=0; i<=L; ++i) //for all columns in HMM
+ {
+ d=-iis[i]*par.ssgapd;
+ e=-iis[i]*par.ssgape;
+ tr[i][GAPOPEN]=d;
+ tr[i][GAPEXTD]=e;
+ tr[i][M2M_GAPOPEN]+=d;
+ tr[i][M2I]+=d;
+ tr[i][I2M]+=d;
+ tr[i][I2I]+=e;
+ tr[i][M2D]+=d;
+ tr[i][D2M]+=d;
+ tr[i][D2D]+=e;
+ }
+
+ if (v>=3)
+ {
+ printf("Col SS II\n");
+ for (i=0; i<=L; ++i) printf("%3i %c %2i\n",i,i2ss(ss_dssp[i]),iis[i]);
+ }
+ return;
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Generate an amino acid frequency matrix g[][] with full pseudocount admixture (tau=1)
+ */
+void
+HMM::PreparePseudocounts()
+{
+ for (int i=0; i<=L+1; ++i)
+ for (int a=0; a<20; ++a)
+ g[i][a] = // produces fast code
+ R[a][0]*f[i][0] +R[a][1]*f[i][1] +R[a][2]*f[i][2] +R[a][3]*f[i][3] +R[a][4]*f[i][4]
+ +R[a][5]*f[i][5] +R[a][6]*f[i][6] +R[a][7]*f[i][7] +R[a][8]*f[i][8] +R[a][9]*f[i][9]
+ +R[a][10]*f[i][10]+R[a][11]*f[i][11]+R[a][12]*f[i][12]+R[a][13]*f[i][13]+R[a][14]*f[i][14]
+ +R[a][15]*f[i][15]+R[a][16]*f[i][16]+R[a][17]*f[i][17]+R[a][18]*f[i][18]+R[a][19]*f[i][19];
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Add amino acid pseudocounts to HMM and calculate average protein aa probabilities pav[a]
+ * Pseudocounts: t.p[i][a] = (1-tau)*f[i][a] + tau*g[i][a]
+ */
+void
+HMM::AddAminoAcidPseudocounts(char pcm, float pca, float pcb, float pcc)
+{
+ int i; //position in HMM
+ int a; //amino acid (0..19)
+ float sum;
+ float tau; //tau = pseudocount admixture
+
+ for (a=0; a<20; ++a) pav[a]=pb[a]*100.0f/Neff_HMM; // initialize vector of average aa freqs with pseudocounts
+
+ // Calculate amino acid frequencies p[i][a] = (1-tau(i))*f[i][a] + tau(i)*g[i][a]
+ switch (pcm)
+ {
+ case 0: //no pseudocounts whatsoever: tau=0
+ for (i=1; i<=L; ++i)
+ for (a=0; a<20; ++a)
+ pav[a] += ( p[i][a]=f[i][a] );
+ break;
+ case 1: //constant pseudocounts (for optimization): tau = pca
+ tau = pca;
+ for (i=1; i<=L; ++i)
+ for (a=0; a<20; ++a)
+ pav[a] += ( p[i][a] = (1.-tau)*f[i][a] + tau * g[i][a] );
+ break;
+ case 2: //divergence-dependent pseudocounts
+ case 4: //divergence-dependent pseudocounts and rate matrix rescaling
+ if (par.pcc==1.0f)
+ for (i=1; i<=L; ++i)
+ {
+ tau = fmin(1.0, pca/(1. + Neff_M[i]/pcb ) );
+ for (a=0; a<20; ++a)
+ pav[a] += ( p[i][a] = (1.-tau)*f[i][a] + tau * g[i][a] );
+ }
+ else
+ for (i=1; i<=L; ++i)
+ {
+ tau = fmin(1.0, pca/(1. + pow((Neff_M[i])/pcb,pcc)));
+ for (a=0; a<20; ++a)
+ pav[a] += ( p[i][a] = (1.-tau)*f[i][a] + tau * g[i][a] );
+ }
+ break;
+ case 3: // constant-divergence pseudocounts
+ for (i=1; i<=L; ++i)
+ {
+ float x = Neff_M[i]/pcb;
+ pca = 0.793 + 0.048*(pcb-10.0);
+ tau = fmax(0.0, pca*(1-x + pcc*x*(1-x)) );
+ for (a=0; a<20; ++a)
+ pav[a] += ( p[i][a] = (1.-tau)*f[i][a] + tau * g[i][a] );
+ }
+ if (v>=2) { printf("Divergence before / after addition of amino acid pseudocounts: %5.2f / %5.2f\n",Neff_HMM, CalcNeff()); }
+ break;
+ } //end switch (pcm)
+
+
+ // Normalize vector of average aa frequencies pav[a]
+ NormalizeTo1(pav,NAA);
+
+ for (a=0; a<20; ++a)
+ p[0][a] = p[L+1][a] = pav[a];
+
+ // DEBUGGING output
+ if (v>=3)
+ {
+ switch (pcm)
+ {
+ case 0:
+ cout<<"No pseudocounts added (-pcm 0)\n";
+ return;
+ case 1:
+ cout<<"Adding constant AA pseudocount admixture of "<<pca<<" to HMM "<<name<<"\n";
+ break;
+ case 2:
+ cout<<"Adding divergence-dependent AA pseudocounts (-pcm 2) with admixture of "
+ <<pca/(1.+pow((Neff_HMM-1.)/pcb,pcc))<<" to HMM "<<name<<"\n";
+ break;
+ } //end switch (pcm)
+ cout<<"\nAverage amino acid frequencies WITH pseudocounts in HMM: \nProf: ";
+ for (a=0; a<20; ++a) printf("%4.1f ",100*pav[a]);
+ cout<<"\n";
+ if (v>=4)
+ {
+ cout<<"\nAmino acid frequencies WITHOUT pseudocounts:\n A R N D C Q E G H I L K M F P S T W Y V\n";
+ for (i=1; i<=L; ++i)
+ {
+ printf("%3i: ",i);
+ sum=0;
+ for (a=0; a<20; ++a)
+ {
+ sum+=f[i][a];
+ printf("%4.1f ",100*f[i][a]);
+ }
+ printf(" sum=%5.3f\n",sum);
+ }
+ cout<<"\nAmino acid frequencies WITH pseudocounts:\n A R N D C Q E G H I L K M F P S T W Y V\n";
+ for (i=1; i<=L; ++i)
+ {
+ printf("%3i: ",i);
+ sum=0;
+ for (a=0; a<20; ++a)
+ {
+ sum+=p[i][a];
+ printf("%4.1f ",100*p[i][a]);
+ }
+ printf(" sum=%5.3f\n",sum);
+ }
+ }
+ }
+ return;
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Factor Null model into HMM t
+ */
+void
+HMM::IncludeNullModelInHMM(HMM& q, HMM& t)
+{
+
+ int i,j; //query and template match state indices
+ int a; //amino acid index
+
+ switch (par.columnscore)
+ {
+ default:
+ case 0: // Null model with background prob. from database
+ for (a=0; a<20; ++a) pnul[a]=pb[a];
+ break;
+
+ case 1: // Null model with background prob. equal average from query and template
+ for (a=0; a<20; ++a) pnul[a]=0.5*(q.pav[a]+t.pav[a]);
+ break;
+
+ case 2: // Null model with background prob. from template protein
+ for (a=0; a<20; ++a) pnul[a]=t.pav[a];
+ break;
+
+ case 3: // Null model with background prob. from query protein
+ for (a=0; a<20; ++a) pnul[a]=q.pav[a];
+ break;
+
+ case 4: // Null model with background prob. equal average from query and template
+ for (a=0; a<20; ++a) pnul[a]=sqrt(q.pav[a]*t.pav[a]);
+ break;
+
+ case 10: // Separated column scoring for Stochastic Backtracing (STILL USED??)
+ for (i=0; i<=q.L+1; ++i)
+ {
+ float sum = 0.0;
+ for (a=0; a<20; ++a) sum += pb[a]*q.p[i][a];
+ sum = 1.0/sqrt(sum);
+ for (a=0; a<20; ++a) q.p[i][a]*=sum;
+ }
+ for (j=0; j<=t.L+1; j++)
+ {
+ float sum = 0.0;
+ for (a=0; a<20; ++a) sum += pb[a]*t.p[j][a];
+ sum = 1.0/sqrt(sum);
+ for (a=0; a<20; ++a) t.p[j][a]*=sum;
+ }
+ break;
+
+ case 11: // log co-emission probability (no null model)
+ for (a=0; a<20; ++a) pnul[a]=0.05;
+ break;
+
+ }
+
+ // !!!!! ATTENTION!!!!!!! after this t.p is not the same as after adding pseudocounts !!!
+ //Introduce amino acid weights into template (for all but SOP scores)
+ if (par.columnscore!=10)
+ for (a=0; a<20; ++a)
+ for (j=0; j<=t.L+1; j++)
+ t.p[j][a]/=pnul[a];
+
+ if (v>=5)
+ {
+ cout<<"\nAverage amino acid frequencies\n";
+ cout<<" A R N D C Q E G H I L K M F P S T W Y V\n";
+ cout<<"Q: ";
+ for (a=0; a<20; ++a) printf("%4.1f ",100*q.pav[a]);
+ cout<<"\nT: ";
+ for (a=0; a<20; ++a) printf("%4.1f ",100*t.pav[a]);
+ cout<<"\nNull: ";
+ for (a=0; a<20; ++a) printf("%4.1f ",100*pnul[a]);
+ cout<<"\npb: ";
+ for (a=0; a<20; ++a) printf("%4.1f ",100*pb[a]);
+ }
+
+
+ return;
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Write HMM to output file
+ */
+void
+HMM::WriteToFile(char* outfile)
+{
+ const int SEQLEN=100; // number of residues per line for sequences to be displayed
+ int i,a;
+
+ if (trans_lin) {fprintf(stderr,"Error: Writing transition pseudocounts in linear representation not allowed. Please report this error to the HHsearch developers.\n"); exit(6);}
+
+ FILE *outf=NULL;
+ if (strcmp(outfile,"stdout"))
+ {
+ if (par.append) outf=fopen(outfile,"a"); else outf=fopen(outfile,"w");
+ if (!outf) OpenFileError(outfile);
+ }
+ else
+ outf = stdout;
+ if (v>=2) cout<<"Writing HMM to "<<outfile<<"\n";
+
+// fprintf(outf,"HHsearch HHM format 1.5\n");
+ fprintf(outf,"HHsearch 1.5\n"); // format specification
+ fprintf(outf,"NAME %s\n",longname); // name of first sequence
+ fprintf(outf,"FAM %s\n",fam); // family name
+ char file_nopath[NAMELEN];
+ RemovePath(file_nopath,file);
+ fprintf(outf,"FILE %s\n",file_nopath); // base name of alignment file
+
+ // Print command line
+ fprintf(outf,"COM ");
+ for (int i=0; i<par.argc; i++)
+ if (strlen(par.argv[i])<=100)
+ fprintf(outf,"%s ",par.argv[i]);
+ else
+ fprintf(outf,"<%i characters> ",(int)strlen(par.argv[i]));
+ fprintf(outf,"\n");
+
+ // print out date stamp
+ time_t* tp=new(time_t);
+ *tp=time(NULL);
+ fprintf(outf,"DATE %s",ctime(tp));
+ delete tp; tp = NULL; /* really? FS */
+
+ // Print out some statistics of alignment
+ fprintf(outf,"LENG %i match states, %i columns in multiple alignment\n",L,l[L]);
+ fprintf(outf,"FILT %i out of %i sequences passed filter (-id %i -cov %i -qid %i -qsc %.2f -diff %i)\n",N_filtered,N_in,par.max_seqid,par.coverage,par.qid,par.qsc,par.Ndiff);
+ fprintf(outf,"NEFF %-4.1f\n",Neff_HMM);
+
+ // Print selected sequences from alignment (including secondary structure and confidence values, if known)
+ fprintf(outf,"SEQ\n");
+ for (int n=0; n<n_display; n++)
+ {
+ fprintf(outf,">%s\n",sname[n]);
+ //first sequence character starts at 1; 0 not used.
+ for(unsigned int j=0; j<strlen(seq[n]+1); j+=SEQLEN) fprintf(outf,"%-.*s\n",SEQLEN,seq[n]+1+j);
+ }
+ fprintf(outf,"#\n");
+
+ // print null model background probabilities from substitution matrix
+ fprintf(outf,"NULL ");
+ for (a=0; a<20; ++a) fout(outf,-iround(fast_log2(pb[s2a[a]])*HMMSCALE ));
+ fprintf(outf,"\n");
+
+ // print table header line with amino acids
+ fprintf(outf,"HMM ");
+ for (a=0; a<20; ++a) fprintf(outf,"%1c\t",i2aa(s2a[a]));
+ fprintf(outf,"\n");
+
+ // print table header line with state transitions
+ fprintf(outf," M->M\tM->I\tM->D\tI->M\tI->I\tD->M\tD->D\tNeff\tNeff_I\tNeff_D\n");
+
+ // print out transition probabilities from begin state (virtual match state)
+ fprintf(outf," ");
+ for (a=0; a<=D2D; ++a) fout(outf,-iround(tr[0][a]*HMMSCALE));
+ fout(outf,iround(Neff_M[0]*HMMSCALE));
+ fout(outf,iround(Neff_I[0]*HMMSCALE));
+ fout(outf,iround(Neff_D[0]*HMMSCALE));
+ fprintf(outf,"\n");
+
+ // Start loop for printing HMM columns
+ int h=1;
+ for (i=1; i<=L; ++i)
+ {
+
+ while(islower(seq[nfirst][h]) && seq[nfirst][h]) h++;
+ fprintf(outf,"%1c %-4i ",seq[nfirst][h++],i);
+
+ // Print emission probabilities for match state
+ for (a=0; a<20; ++a) fout(outf,-iround(fast_log2(p[i][s2a[a]])*HMMSCALE ));
+ fprintf(outf,"%-i",l[i]);
+ fprintf(outf,"\n");
+
+ // Print transition probabilities
+ fprintf(outf," ");
+ for (a=0; a<=D2D; ++a) fout(outf,-iround(tr[i][a]*HMMSCALE));
+ fout(outf,iround(Neff_M[i]*HMMSCALE));
+ fout(outf,iround(Neff_I[i]*HMMSCALE));
+ fout(outf,iround(Neff_D[i]*HMMSCALE));
+ fprintf(outf,"\n\n");
+ } // end for(i)-loop for printing HMM columns
+
+ fprintf(outf,"//\n");
+ fclose(outf);
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Write HMM to output file
+ */
+void
+HMM::InsertCalibration(char* infile)
+{
+ char* line = new(char[LINELEN]); // input line
+ char** lines = new(char*[3*L+100000]);
+ int nline=0;
+ int l;
+ char done=0; // inserted new 'EVD mu sigma' line?
+
+ // Read from infile all lines and insert the EVD line with lamda and mu coefficients
+ ifstream inf;
+ inf.open(infile, ios::in);
+ if (!inf) OpenFileError(infile);
+ if (v>=2) cout<<"Recording calibration coefficients in "<<infile<<"\n";
+
+ while (inf.getline(line,LINELEN) && !(line[0]=='/' && line[1]=='/') && nline<2*/*MAXRES*/par.maxResLen)
+ {
+
+ // Found an EVD lamda mu line? -> remove
+ while (!done && !strncmp(line,"EVD ",3) && !(line[0]=='/' && line[1]=='/') && nline<2*/*MAXRES*/par.maxResLen)
+ inf.getline(line,LINELEN);
+ if ((line[0]=='/' && line[1]=='/') || nline>=2*/*MAXRES*/par.maxResLen)
+ {fprintf(stderr,"Error: wrong format in %s. Expecting hhm format\n",infile); exit(1);}
+
+ // Found the SEQ line? -> insert calibration before this line
+ if (!done && (!strncmp("SEQ",line,3) || !strncmp("HMM",line,3)) && (isspace(line[3]) || line[3]=='\0'))
+ {
+ done=1;
+ lines[nline]=new(char[128]);
+ if (!lines[nline]) MemoryError("space to read in HHM file for calibration");
+ sprintf(lines[nline],"EVD %-7.4f %-7.4f",lamda,mu);
+ nline++;
+ }
+ lines[nline]=new(char[strlen(line)+1]);
+ if (!lines[nline]) MemoryError("space to read in HHM file for calibration");
+ strcpy (lines[nline],line);
+ nline++;
+ }
+ inf.close();
+
+ // Write to infile all lines
+ FILE* infout=fopen(infile,"w");
+ if (!infout) {
+ cerr<<endl<<"WARNING in "<<program_name<<": no calibration coefficients written to "<<infile<<":\n";
+ cerr<<"Could not open file for writing.\n";
+ return;
+ }
+ for (l=0; l<nline; l++) {
+ fprintf(infout,"%s\n",lines[l]);
+ delete[] lines[l]; lines[l] = NULL;
+ }
+ fprintf(infout,"//\n");
+ fclose(infout);
+ delete[] line; line = NULL;
+ delete[] lines; lines = NULL;
+ return;
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Write HMM to output file in HMMER format
+ */
+void
+HMM::WriteToFileHMMER(char* outfile)
+{
+ const int INTSCALE=1000; //scaling factor in HMMER files
+ const float pBD=0.50;
+ const int LOG2pBD=iround(fast_log2(pBD)*INTSCALE);
+ const int LOG2pBM=iround(fast_log2(1-pBD)*INTSCALE);
+ const float pJB=1.0/350;
+ const int LOG2pJB=iround(fast_log2(pJB)*INTSCALE);
+ const int LOG2pJJ=iround(fast_log2(1-pJB)*INTSCALE);
+ const float pEJ=0.5;
+ const int LOG2pEJ=iround(fast_log2(pEJ)*INTSCALE);
+ const int LOG2pEC=iround(fast_log2(1-pEJ)*INTSCALE);
+ char c;
+ int i,a;
+
+ if (trans_lin) {fprintf(stderr,"Error: Writing transition pseudocounts in linear representation not allowed. Please report this error to the HHsearch developers.\n"); exit(6);}
+
+ FILE *outf=NULL;
+ if (strcmp(outfile,"stdout"))
+ {
+ if (par.append) outf=fopen(outfile,"a"); else outf=fopen(outfile,"w");
+ if (!outf) OpenFileError(outfile);
+ }
+ else
+ outf = stdout;
+ if (v>=2) cout<<"Writing HMM to "<<outfile<<"\n";
+
+ fprintf(outf,"HMMER2.0 [hhmake %s]\n",VERSION_AND_DATE);
+ fprintf(outf,"NAME %s\n",file); // base name of alignment file
+ fprintf(outf,"DESC %s\n",longname);
+ fprintf(outf,"LENG %i\n",L);
+ fprintf(outf,"ALPH Amino\n"); // amino acid seuqences (not DNA)
+ fprintf(outf,"RF yes\n"); // reference annotation flag
+ fprintf(outf,"CS yes\n"); // consensus structure annotation flag
+ fprintf(outf,"MAP yes\n"); // write MA column number after each line of aa probabilities
+
+ fprintf(outf,"COM "); // print out command line
+ for (i=0; i<=par.argc-1; ++i) fprintf(outf,"%s ",par.argv[i]); fprintf(outf,"\n");
+
+ fprintf(outf,"NSEQ %i\n",N_filtered); // print number of sequences after filtering
+
+ // Date stamp
+ time_t* tp=new(time_t);
+ *tp=time(NULL);
+ fprintf(outf,"DATE %s",ctime(tp));
+ delete tp; tp = NULL; /* really? FS */
+
+ // Print out secondary structure
+ if (nss_dssp>=0)
+ fprintf(outf,"SSDSS %s\n",seq[nss_dssp]);
+ if (nsa_dssp>=0)
+ fprintf(outf,"SADSS %s\n",seq[nsa_dssp]);
+ if (nss_pred>=0)
+ fprintf(outf,"SSPRD %s\n",seq[nss_pred]);
+ if (nss_conf>=0)
+ fprintf(outf,"SSCNF %s\n",seq[nss_conf]);
+
+
+ // Special Plan7 transitions that control repeated detection of profile HMM within sequence
+ fprintf(outf,"XT %6i %6i %6i %6i %6i %6i %6i %6i\n",LOG2pJB,LOG2pJJ,LOG2pEC,LOG2pEJ,LOG2pJB,LOG2pJJ,LOG2pJB,LOG2pJJ);
+ fprintf(outf,"NULT -4 -8455\n");
+
+
+ // Null model background probabilities from substitution matrix
+ fprintf(outf,"NULE ");
+ for (a=0; a<20; ++a)
+ {
+ float lg2=fast_log2(pb[s2a[a]]*20.0);
+ if (lg2<-99.999) fprintf(outf," *"); else fprintf(outf," %6i",iround(lg2*INTSCALE));
+ }
+ fprintf(outf,"\n");
+
+ // Table header line with amino acids
+ fprintf(outf,"HMM ");
+ for (a=0; a<20; ++a) fprintf(outf," %1c ",i2aa(s2a[a]));
+ fprintf(outf,"\n");
+
+ // Table header line with state transitions
+ fprintf(outf," m->m m->i m->d i->m i->i d->m d->d b->m m->e\n");
+
+ // Transition probabilities from begin state
+ fprintf(outf," %6i * %6i\n",LOG2pBM,LOG2pBD);
+
+ // Start loop for printing HMM columns
+ int h=1, hss=1;
+ for (i=1; i<=L; ++i)
+ {
+
+ // Emission probabilities for match state
+ fprintf(outf," %5i",i);
+ for (a=0; a<20; ++a) fprintf(outf," %6i",imax(-9999,iround(fast_log2(p[i][s2a[a]]/pb[s2a[a]])*INTSCALE)));
+ fprintf(outf," %5i",l[i]);
+ fprintf(outf,"\n");
+
+ // Emission probabilities (relative to null model) for insert state
+ while(islower(seq[nfirst][h]) && seq[nfirst][h]) h++;
+ if (i==L)
+ fprintf(outf," %1c * * * * * * * * * * * * * * * * * * * *\n",seq[nfirst][h++]);
+ else
+ fprintf(outf," %1c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0\n",seq[nfirst][h++]);
+
+ // Transition probabilities
+ if (nss_dssp>=0)
+ {
+ while(islower(seq[nss_dssp][hss]) && seq[nss_dssp][hss]) hss++;
+ c=seq[nss_dssp][hss++];
+ }
+ else c=' ';
+ fprintf(outf," %1c",c);
+ if (i==1)
+ {
+ for (a=0; a<=D2D; ++a) fprintf(outf," %6i",imax(-9999,iround(tr[i][a]*INTSCALE)));
+ fprintf(outf," %6i *\n",LOG2pBM);
+ }
+ else if (i==L)
+ {
+ for (a=0; a<=D2D; ++a) fprintf(outf," *");
+ fprintf(outf," * 0\n");
+ }
+ else
+ {
+ for (a=0; a<=D2D; ++a) fprintf(outf," %6i",imax(-9999,iround(tr[i][a]*INTSCALE)));
+ fprintf(outf," * *\n");
+ }
+ }
+
+ fprintf(outf,"//\n");
+ fclose(outf);
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Transform log to lin transition probs
+ */
+void
+HMM::Log2LinTransitionProbs(float beta)
+{
+ if (trans_lin==1) return;
+ trans_lin=1;
+ for (int i=0; i<=L; ++i)
+ {
+ for (int a=0; a<NTRANS; ++a)
+ tr[i][a] = fpow2(beta*tr[i][a]);
+/* FIXME valgrind says: "Conditional jump or move depends on
+ * uninitialised value(s)" when using hmm iteration
+ */
+ }
+}
+
+
+/**
+ * @brief Set query columns in His-tags etc to Null model distribution
+ */
+void
+HMM::NeutralizeTags()
+{
+ char* qseq = seq[nfirst];
+ char* pt;
+ int a,i;
+
+ if (NULL == qseq){
+ return;
+ }
+
+ // Neutralize His tag
+ if ( (pt=strstr(qseq,"HHHHH")) )
+ {
+ int i0 = pt-qseq+1;
+ if (v>=2) printf("Neutralized His-tag at position %i\n",i0);
+ for (i=imax(i0-5,1); i<i0; ++i) // neutralize leading 5 columns
+ for (a=0; a<NAA; ++a) p[i][a]=pb[a];
+ for (; (*pt)!='H'; ++i,++pt) // neutralize His columns
+ for (a=0; a<NAA; ++a) p[i][a]=pb[a];
+ i0=i;
+ for (; i<imin(i0+5,L+1); ++i) // neutralize trailing 5 columns
+ for (a=0; a<NAA; ++a) p[i][a]=pb[a];
+ if (v>=3) printf("start:%i end:%i\n",imax(i0-5,1),i-1);
+ }
+
+ // Neutralize C-myc tag
+ if ( (pt=strstr(qseq,"EQKLISEEDL")) )
+ {
+ if (v>=2) printf("Neutralized C-myc-tag at position %i\n",int(pt-qseq)+1);
+ for (i=pt-qseq+1; i<=pt-qseq+10; ++i)
+ for (a=0; a<NAA; ++a) p[i][a]=pb[a];
+ }
+ // Neutralize FLAG tag
+ if ( (pt=strstr(qseq,"DYKDDDDK")) )
+ {
+ if (v>=2) printf("Neutralized FLAG-tag at position %i\n",int(pt-qseq)+1);
+ for (i=pt-qseq+1; i<=pt-qseq+8; ++i)
+ for (a=0; a<NAA; ++a) p[i][a]=pb[a];
+ }
+}
+
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Calculate effective number of sequences using profiles INCLUDING pseudocounts
+ */
+float
+HMM::CalcNeff()
+{
+ float Neff=0;
+ for (int i=1; i<=L; ++i)
+ for (int a=0; a<20; ++a)
+ if (p[i][a]>1E-10) Neff-=p[i][a]*fast_log2(p[i][a]);
+ return fpow2(Neff/L);
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Calculate consensus of HMM (needed to merge HMMs later)
+ */
+void
+HMM::CalculateConsensus()
+{
+ int i; // position in query
+ int a; // amino acid
+ if (!Xcons) Xcons = new char[/*MAXRES*/par.maxResLen+2];
+ for (i=1; i<=L; ++i)
+ {
+ float max=f[i][0]-pb[0];
+ for (a=1; a<20; ++a)
+ if (f[i][a]-pb[a]>max) Xcons[i]=a;
+ }
+ Xcons[0]=Xcons[L+1]=ENDGAP;
+}
+
+// /////////////////////////////////////////////////////////////////////////////////////
+// // Store linear transition probabilities
+// /////////////////////////////////////////////////////////////////////////////////////
+// void HMM::StoreLinearTransitionProbs()
+// {
+// int i; // position in query
+// for (i=0; i<=L+1; ++i) if (!tr_lin[i]) tr_lin[i] = new(float[NTRANS]);
+// for (i=0; i<=L+1; ++i)
+// {
+// tr_lin[i][M2M] = fpow2(tr[i][M2M]);
+// tr_lin[i][M2I] = fpow2(tr[i][M2I]);
+// tr_lin[i][M2D] = fpow2(tr[i][M2D]);
+// tr_lin[i][D2M] = fpow2(tr[i][M2D]);
+// tr_lin[i][D2D] = fpow2(tr[i][D2D]);
+// tr_lin[i][I2M] = fpow2(tr[i][I2M]);
+// tr_lin[i][I2I] = fpow2(tr[i][I2I]);
+// }
+// }
+
+
+// #define Weff(Neff) (1.0+par.neffa*(Neff-1.0)+(par.neffb-4.0*par.neffa)/16.0*(Neff-1.0)*(Neff-1.0))
+
+// /////////////////////////////////////////////////////////////////////////////////////
+// // Initialize f[i][a] with query HMM
+// /////////////////////////////////////////////////////////////////////////////////////
+// void HMM::MergeQueryHMM(HMM& q, float wk[])
+// {
+// int i; // position in query
+// int a; // amino acid
+// float Weff_M, Weff_D, Weff_I;
+// for (i=1; i<=L; i++)
+// {
+// Weff_M = Weff(q.Neff_M[i]-1.0);
+// Weff_D = Weff(q.Neff_D[i]-1.0);
+// Weff_I = Weff(q.Neff_I[i]-1.0);
+// for (a=0; a<20; a++) f[i][a] = q.f[i][a]*wk[i]*Weff_M;
+// tr_lin[i][M2M] = q.tr_lin[i][M2M]*wk[i]*Weff_M;
+// tr_lin[i][M2I] = q.tr_lin[i][M2I]*wk[i]*Weff_M;
+// tr_lin[i][M2D] = q.tr_lin[i][M2D]*wk[i]*Weff_M;
+// tr_lin[i][D2M] = q.tr_lin[i][D2M]*wk[i]*Weff_D;
+// tr_lin[i][D2D] = q.tr_lin[i][D2D]*wk[i]*Weff_D;
+// tr_lin[i][I2M] = q.tr_lin[i][I2M]*wk[i]*Weff_I;
+// tr_lin[i][I2I] = q.tr_lin[i][I2I]*wk[i]*Weff_I;
+// }
+// }
+
+
+
+// /////////////////////////////////////////////////////////////////////////////////////
+// // Normalize probabilities in total merged super-HMM
+// /////////////////////////////////////////////////////////////////////////////////////
+// void HMM::NormalizeHMMandTransitionsLin2Log()
+// {
+// int i; // position in query
+// int a; // amino acid
+// for (i=0; i<=L+1; i++)
+// {
+// float sum=0.0;
+// for (a=0; a<20; a++) sum += f[i][a];
+// for (a=0; a<20; a++) f[i][a]/=sum;
+// sum = tr_lin[i][M2M] + tr_lin[i][M2I] + tr_lin[i][M2D];
+// tr_lin[i][M2M] /= sum;
+// tr_lin[i][M2I] /= sum;
+// tr_lin[i][M2D] /= sum;
+// tr[i][M2M] = fast_log2(tr_lin[i][M2M]);
+// tr[i][M2I] = fast_log2(tr_lin[i][M2I]);
+// tr[i][M2D] = fast_log2(tr_lin[i][M2D]);
+// sum = tr_lin[i][D2M] + tr_lin[i][D2D];
+// tr_lin[i][D2M] /= sum;
+// tr_lin[i][D2D] /= sum;
+// tr[i][D2M] = fast_log2(tr_lin[i][D2M]);
+// tr[i][D2D] = fast_log2(tr_lin[i][D2D]);
+// sum = tr_lin[i][I2M] + tr_lin[i][I2I];
+// tr_lin[i][I2M] /= sum;
+// tr_lin[i][I2I] /= sum;
+// tr[i][I2M] = fast_log2(tr_lin[i][I2M]);
+// tr[i][I2I] = fast_log2(tr_lin[i][I2I]);
+// }
+// }
+
+
+// UNCOMMENT TO ACTIVATE COMPOSITIONALLY BIASED PSEUDOCOUNTS BY RESCALING THE RATE MATRIX
+
+// /////////////////////////////////////////////////////////////////////////////////////
+// //// Function to minimize
+// /////////////////////////////////////////////////////////////////////////////////////
+// double RescaleMatrixFunc(double x[])
+// {
+// double sum=0.0;
+// for (int a=0; a<20; ++a)
+// {
+// double za=0.0;
+// for (int b=0; b<20; ++b) za+=P[a][b]*x[b];
+// sum += (x[a]*za-qav[a])*(x[a]*za-qav[a]);
+// }
+// return sum;
+// }
+
+// /////////////////////////////////////////////////////////////////////////////////////
+// //// Gradient of function to minimize
+// /////////////////////////////////////////////////////////////////////////////////////
+// void RescaleMatrixFuncGrad(double grad[], double x[])
+// {
+// double z[20] = {0.0};
+// double w[20];
+// double tmp;
+// for (int a=0; a<20; ++a)
+// for (int b=0; b<20; ++b) z[a] += P[a][b]*x[b];
+
+// for (int a=0; a<20; ++a) w[a] = x[a]*z[a]-qav[a];
+// for (int a=0; a<20; ++a)
+// {
+// tmp = w[a]*z[a];
+// for (int b=0; b<20; ++b) tmp += P[a][b]*x[b]*w[b];
+// grad[a] = 2.0*tmp;
+// }
+// return;
+// }
+
+
+// /////////////////////////////////////////////////////////////////////////////////////
+// //// Rescale a substitution matrix to biased aa frequencies in global vector qav[a]
+// /////////////////////////////////////////////////////////////////////////////////////
+// void HMM::RescaleMatrix()
+// {
+// int a,b;
+// int code;
+// double x[21]; // scaling factor
+// double val_min;
+// const int len=20;
+// const int max_iterations=50;
+
+// if (v>=2) printf("Adjusting rate matrix to query amino acid composition ...\n");
+
+// // Put amino acid frequencies into global array (needed to call WNLIB's conjugate gradient method)
+// for (a=0; a<20; ++a) qav[a] = pav[a];
+
+// // Initialize scaling factors x[a]
+// for (a=0; a<20; ++a) x[a]=pow(qav[a]/pb[a],0.73); // Initialize
+
+// // Call conjugate gradient minimization method from WNLIB
+// wn_conj_gradient_method(&code,&val_min,x,len,&RescaleMatrixFunc,&RescaleMatrixFuncGrad,max_iterations);
+
+
+// // Calculate z[a] = sum_b Pab*xb
+// float sum_err=0.0f;
+// float sum = 0.0f;
+// for (a=0; a<20; ++a)
+// {
+// float za=0.0f; // za = sum_b Pab*xb
+// for (b=0; b<20; ++b) za+=P[a][b]*x[b];
+// sum_err += (x[a]*za/qav[a]-1)*(x[a]*za/qav[a]-1);
+// sum += x[a]*za;
+// }
+// if (sum_err>1e-3 & v>=1) fprintf(stderr,"WARNING: adjusting rate matrix by CG resulted in residual error of %5.3f.\n",sum_err);
+
+// // Rescale rate matrix
+// for (a=0; a<20; ++a)
+// for (b=0; b<20; ++b)
+// {
+// P[a][b] *= x[a]*x[b]/sum;
+// R[a][b] = P[a][b]/qav[b];
+// }
+
+// // How well approximated?
+// if (v>=3)
+// {
+// // Calculate z[a] = sum_b Pab*xb
+// float z[21];
+// for (a=0; a<20; ++a)
+// for (z[a]=0.0, b=0; b<20; ++b) z[a]+=P[a][b];
+// printf("Adjust A R N D C Q E G H I L K M F P S T W Y V\nErr? ");
+// for (a=0; a<20; ++a) printf("%4.0f ",1000*z[a]/qav[a]);
+// cout<<endl<<"xa ";
+// for (a=0; a<20; ++a) fprintf(stdout,"%4.2f ",x[a]);
+// cout<<endl;
+// }
+
+// // Evaluate sequence identity underlying substitution matrix
+// if (v>=3)
+// {
+// float id=0.0f;
+// float entropy=0.0f;
+// float entropy_qav=0.0f;
+// float mut_info=0.0f;
+// for (a=0; a<20; ++a) id += P[a][a];
+// for (a=0; a<20; ++a) entropy_qav-=qav[a]*fast_log2(qav[a]);
+// for (a=0; a<20; ++a)
+// for (b=0; b<20; ++b)
+// {
+// entropy-=P[a][b]*fast_log2(R[a][b]);
+// mut_info += P[a][b]*fast_log2(P[a][b]/qav[a]/qav[b]);
+// }
+
+// fprintf(stdout,"Rescaling rate matrix: sequence identity = %2.0f%%; entropy per column = %4.2f bits (out of %4.2f); mutual information = %4.2f bits\n",100*id,entropy,entropy_qav,mut_info);
+// }
+// return;
+// }
+
+
+/* @* HMM::ClobberGlobal (eg, q,t)
+ */
+void
+HMM::ClobberGlobal(void){
+
+ for (int i = 0; i < n_display; i++){
+ if (sname[i]){
+ delete[] sname[i]; sname[i] = NULL;
+ }
+ if (seq[i]){
+ delete[] seq[i]; seq[i] = NULL;
+ }
+ }
+ Neff_M[0] = Neff_I[0] = Neff_D[0] = 0.0;
+ longname[0] = '\0'; file[0] = '\0';
+ ss_dssp[0] = sa_dssp[0] = ss_pred[0] = ss_conf[0] = '\0';
+ Xcons = NULL;
+ l[0] = 0;
+ L = 0;
+ Neff_HMM = 0;
+ n_display = N_in = N_filtered = 0;
+ nss_dssp = nsa_dssp = nss_pred = nss_conf = nfirst = ncons = -1;
+ lamda = 0.0; mu = 0.0;
+ name[0] = longname[0] = fam[0] = '\0';
+
+ for (int i = 0; i < NAA; i++){
+ pav[i] = 0;
+ }
+
+ /* @= */
+ return;
+
+} /* this is the end of ClobberGlobal() */
+
+
+/*
+ * EOF hhhmm-C.h
+ */
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhhmm.h 165 2010-12-22 16:24:48Z fabian $
+ */
+
+// hhhmm.h
+
+
+class HMM
+{
+ public:
+ HMM(int maxseqdis=MAXSEQDIS, int maxres=/*MAXRES*/par.maxResLen);
+ ~HMM();
+ HMM& operator=(HMM&);
+
+ int n_display; // number of sequences stored for display of alignment (INCLUDING >ss_ and >cf_ sequences)
+ int n_seqs; // number of sequences read in (INCLUDING >ss_ and >cf_ sequences)
+ char** sname; // names of stored sequences
+ char** seq; // residues of stored sequences (first at pos 1!)
+ int ncons; // index of consensus sequence
+ int nfirst; // index of first sequence (query sequence of HMM)
+ int nss_dssp; // index of seq[] with secondary structure by dssp
+ int nsa_dssp; // index of seq[] with solvent accessibility by dssp
+ int nss_pred; // index of seq[] with predicted secondary structure
+ int nss_conf; // index of seq[] with confidence values for secondary structure prediction
+
+ int L; // length of HMM = number of match states; set in declaration of HMM object
+ int N_in; // number of sequences in alignment
+ int N_filtered; // number of sequences after filtering
+ float* Neff_M; // Neff_M[i] = diversity of subalignment of seqs that have residue in col i
+ float* Neff_I; // Neff_I[i] = diversity of subalignment of seqs that have insert in col i
+ float* Neff_D; // Neff_D[i] = diversity of subalignment of seqs that have delete in col i
+ float Neff_HMM; // average number of Neff over total length of HMM
+
+ char* longname; // Full name of first sequence of original alignment (NAME field)
+ char name[NAMELEN]; // HMM name = first word in longname in lower case
+ char file[NAMELEN]; // Basename (with path, without extension) of alignment file that was used to construct the HMM
+ char fam[NAMELEN]; // family ID (derived from name) (FAM field)
+ char sfam[NAMELEN]; // superfamily ID (derived from name)
+ char fold[NAMELEN]; // fold ID (derived from name)
+ char cl[NAMELEN]; // class ID (derived from name)
+
+ float lamda, mu; // coefficients for aa score distribution of HMM using parameters in 'Parameters par'
+ bool has_pseudocounts; // set to true if HMM contains pseudocounts
+
+ // Make a flat copy of q
+ void FlatCopyTo(HMM& t);
+
+ // Read an HMM from a HHsearch .hhm file and return 0 at end of file
+ int Read(FILE* dbf, char* path=NULL);
+
+ // Read an HMM from a HMMer .hmm file; return 0 at end of file
+ int ReadHMMer(FILE* dbf, char* filestr=NULL);
+
+ // Read an HMM from a HMMer3 .hmm file; return 0 at end of file
+ int ReadHMMer3(FILE* dbf, char* filestr=NULL);
+
+ // Add transition pseudocounts to HMM
+ void AddTransitionPseudocounts(float gapd=par.gapd, float gape=par.gape, float gapf=par.gapf, float gapg=par.gapg, float gaph=par.gaph, float gapi=par.gapi, float gapb=par.gapb);
+
+ // Use secondary structure-dependent gap penalties on top of the HMM transition penalties
+ void UseSecStrucDependentGapPenalties();
+
+ // Generate an amino acid frequency matrix g[][] with full pseudocount admixture (tau=1)
+ void PreparePseudocounts();
+
+ // Add amino acid pseudocounts to HMM: t.p[i][a] = (1-tau)*f[i][a] + tau*g[i][a]
+ void AddAminoAcidPseudocounts(char pcm=par.pcm, float pca=par.pca, float pcb=par.pcb, float pcc=par.pcc);
+
+ // Add no amino acid pseudocounts to HMM: copy t.p[i][a] = f[i][a]
+ void NoAminoAcidPseudocounts() {for(int i=1; i<=L; i++) for(int a=0; a<20; a++) p[i][a]=f[i][a];};
+
+ // Factor Null model into HMM t
+ void IncludeNullModelInHMM(HMM& q, HMM& t);
+
+ // Write HMM to output file
+ void WriteToFile(char* outfile);
+
+ // Insert calibration line 'EVD lamda mu hashvalue' into HMM file
+ void InsertCalibration(char* infile);
+
+ // Write HMM to output file in HMMER format
+ void WriteToFileHMMER(char* outfile);
+
+ // Transform log to lin transition probs
+ void Log2LinTransitionProbs(float beta=1.0);
+
+ // Set query columns in His-tags etc to Null model distribution
+ void NeutralizeTags();
+
+ // Calculate effective number of sequences using profiles INCLUDING pseudocounts
+ float CalcNeff();
+
+ // Calculate consensus of HMM (needed to merge HMMs later)
+ void CalculateConsensus();
+
+ // Store linear transition probabilities
+ void StoreLinearTransitionProbs();
+
+ // Initialize f[i][a] with query HMM
+ void MergeQueryHMM(HMM& q, float wk[]);
+
+ // Normalize probabilities in total merged super-HMM
+ void NormalizeHMMandTransitionsLin2Log();
+
+ // Rescale rate matrices P[a][b], R[a][b] according to HMM av. aa composition in pav[a]
+ void RescaleMatrix();
+
+#ifdef CLUSTALO
+ void ClobberGlobal(void);
+ char cQT; /* query or template */
+#endif
+
+private:
+ float** f; // f[i][a] = prob of finding amino acid a in column i WITHOUT pseudocounts
+ float** g; // f[i][a] = prob of finding amino acid a in column i WITH pseudocounts
+ float** p; // p[i][a] = prob of finding amino acid a in column i WITH OPTIMUM pseudocounts
+ float** tr; // log2 of transition probabilities M2M M2I M2D I2M I2I D2M D2D M2M_GAPOPEN GAPOPEN GAPEXTD
+/* float** tr_lin; // transition probs in log space */
+ char trans_lin; // transition probs are given in log or lin space? (0: p_tr 1: log(p_tr)
+
+ char* ss_dssp; // secondary structure determined by dssp 0:- 1:H 2:E 3:C 4:S 5:T 6:G 7:B
+ char* sa_dssp; // solvent accessibility state determined by dssp 0:- 1:A (absolutely buried) 2:B 3:C 4:D 5:E (exposed)
+ char* ss_pred; // predicted secondary structure 0:- 1:H 2:E 3:C
+ char* ss_conf; // confidence value of prediction 0:- 1:0 ... 10:9
+ char* Xcons; // consensus sequence in internal representation (A=0 R=1 N=2 D=3 ...)
+ float pav[NAA]; // pav[a] = average freq of amino acids in HMM (including subst matrix pseudocounts)
+ float pnul[NAA]; // null model probabilities used in comparison (only set in template/db HMMs)
+ int* l; // l[i] = pos. of j'th match state in aligment
+/* char trans_lin; // transition probs are given in log or lin space? (0: p_tr 1: log(p_tr) */
+
+ // Utility for Read()
+ int Warning(FILE* dbf, char line[], char name[])
+ {
+ if (v) cerr<<"\nWARNING: could not read line\n\'"<<line<<"\'\nin HMM "<<name<<" in "<<file<<"\n";
+ while (fgetline(line,LINELEN,dbf) && !(line[0]=='/' && line[1]=='/'));
+ if (line) return 2; //return status: skip HMM
+ return 0; //return status: end of database file
+ }
+
+ friend class Hit;
+ friend class Alignment;
+ friend class HMMshadow;
+};
+
+class HMMshadow {
+
+ public:
+ float *Neff_M;
+ float *Neff_I;
+ float *Neff_D;
+ float **f;
+ float **g;
+ float **p;
+ float **tr;
+ float pav[20];
+
+ void copyHMMtoShadow(const HMM &hmm) {
+ Neff_M = hmm.Neff_M;
+ Neff_I = hmm.Neff_I;
+ Neff_D = hmm.Neff_D;
+ f = hmm.f;
+ g = hmm.g;
+ p = hmm.p;
+ tr = hmm.tr;
+ memcpy(pav, hmm.pav, 20*sizeof(float));
+ }
+
+ void copyShadowToHMM(const HMM &hmm, const hmm_light rShadow) {
+
+ int i, j;
+
+ for (i = 0; i < rShadow.L+1; i++){
+ hmm.Neff_M[i] = rShadow.Neff_M[i];
+ hmm.Neff_I[i] = rShadow.Neff_I[i];
+ hmm.Neff_D[i] = rShadow.Neff_D[i];
+ for (j = 0; j < 20; j++){
+ hmm.f[i][j] = rShadow.f[i][j];
+ hmm.g[i][j] = rShadow.g[i][j];
+ hmm.p[i][j] = rShadow.p[i][j];
+ }
+ for (j = 0; j < 7; j++){
+ hmm.tr[i][j] = rShadow.tr[i][j];
+ }
+ memcpy((void *)hmm.pav, rShadow.pav, 20*sizeof(float));
+ }
+ } /* this is the end of copyShadowToHMM() */
+
+} /* class HMMshadow */;
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhmatrices-C.h 199 2011-02-21 18:24:49Z fabian $
+ */
+
+// Substitution matrices and their background frequencies
+
+// The following background frequencies were calculated by the formula pa = (P[a,b]/(pa*pb))^(-1) * (1,...,1)
+// For the Blousum50-matrix this becomes pb[a]= SUM_(b=1,20) (2^(BLOSUM50[a,b]/3))^(-1)
+// A R N D C Q E G H I L K M F P S T W Y V
+// Gonnet 7.68,5.14,4.02,5.41,1.89,3.27,5.99,7.56,3.69,5.06,10.01,5.97,2.20,3.50,4.54,4.67,7.12,1.25,3.95,7.28
+// BLOSUM50 8.24,6.24,4.46,4.77,2.03,2.90,6.78,6.69,2.53,6.89,10.7 ,5.04,1.49,4.93,3.97,5.95,6.13,1.34,3.45,6.28
+
+const float Gonnet[]={
+// A R N D C Q E G H I L K M F P S T W Y V
+ 10227, 3430, 2875, 3869, 1625, 2393, 4590, 6500, 2352, 3225, 5819, 4172, 1435, 1579, 3728, 4610, 6264, 418, 1824, 5709, // A
+ 3430, 7780, 2209, 2589, 584, 2369, 3368, 3080, 2173, 1493, 3093, 5701, 763, 859, 1893, 2287, 3487, 444, 1338, 2356, // R
+ 2875, 2209, 3868, 3601, 501, 1541, 2956, 3325, 1951, 1065, 2012, 2879, 532, 688, 1480, 2304, 3204, 219, 1148, 1759, // N
+ 3869, 2589, 3601, 8618, 488, 2172, 6021, 4176, 2184, 1139, 2151, 3616, 595, 670, 2086, 2828, 3843, 204, 1119, 2015, // D
+ 1625, 584, 501, 488, 5034, 355, 566, 900, 516, 741, 1336, 591, 337, 549, 419, 901, 1197, 187, 664, 1373, // C
+ 2393, 2369, 1541, 2172, 355, 1987, 2891, 1959, 1587, 1066, 2260, 2751, 570, 628, 1415, 1595, 2323, 219, 871, 1682, // Q
+ 4590, 3368, 2956, 6021, 566, 2891, 8201, 3758, 2418, 1624, 3140, 4704, 830, 852, 2418, 2923, 4159, 278, 1268, 2809, // E
+ 6500, 3080, 3325, 4176, 900, 1959, 3758,26066, 2016, 1354, 2741, 3496, 741, 797, 2369, 3863, 4169, 375, 1186, 2569, // G
+ 2352, 2173, 1951, 2184, 516, 1587, 2418, 2016, 5409, 1123, 2380, 2524, 600, 1259, 1298, 1642, 2446, 383, 876, 1691, // H
+ 3225, 1493, 1065, 1139, 741, 1066, 1624, 1354, 1123, 6417, 9630, 1858, 1975, 2225, 1260, 1558, 3131, 417, 1697, 7504, // I
+ 5819, 3093, 2012, 2151, 1336, 2260, 3140, 2741, 2380, 9630,25113, 3677, 4187, 5540, 2670, 2876, 5272, 1063, 3945,11005, // L
+ 4172, 5701, 2879, 3616, 591, 2751, 4704, 3496, 2524, 1858, 3677, 7430, 949, 975, 2355, 2847, 4340, 333, 1451, 2932, // K
+ 1435, 763, 532, 595, 337, 570, 830, 741, 600, 1975, 4187, 949, 1300, 1111, 573, 743, 1361, 218, 828, 2310, // M
+ 1579, 859, 688, 670, 549, 628, 852, 797, 1259, 2225, 5540, 975, 1111, 6126, 661, 856, 1498, 1000, 4464, 2602, // F
+ 3728, 1893, 1480, 2086, 419, 1415, 2418, 2369, 1298, 1260, 2670, 2355, 573, 661,11834, 2320, 3300, 179, 876, 2179, // P
+ 4610, 2287, 2304, 2828, 901, 1595, 2923, 3863, 1642, 1558, 2876, 2847, 743, 856, 2320, 3611, 4686, 272, 1188, 2695, // S
+ 6264, 3487, 3204, 3843, 1197, 2323, 4159, 4169, 2446, 3131, 5272, 4340, 1361, 1498, 3300, 4686, 8995, 397, 1812, 5172, // T
+ 418, 444, 219, 204, 187, 219, 278, 375, 383, 417, 1063, 333, 218, 1000, 179, 272, 397, 4101, 1266, 499, // W
+ 1824, 1338, 1148, 1119, 664, 871, 1268, 1186, 876, 1697, 3945, 1451, 828, 4464, 876, 1188, 1812, 1266, 9380, 2227, // Y
+ 5709, 2356, 1759, 2015, 1373, 1682, 2809, 2569, 1691, 7504,11005, 2932, 2310, 2602, 2179, 2695, 5172, 499, 2227,11569};// V
+
+const float Blosum30[]= {
+// A R N D C Q E G H I L K M F P S T W Y V
+ 0.0096,
+ 0.0038,0.0109,
+ 0.0031,0.0019,0.0055,
+ 0.0043,0.0026,0.0027,0.0095,
+ 0.0014,0.0011,0.0010,0.0010,0.0070,
+ 0.0031,0.0031,0.0014,0.0018,0.0007,0.0039,
+ 0.0044,0.0031,0.0024,0.0037,0.0018,0.0028,0.0094,
+ 0.0052,0.0032,0.0032,0.0035,0.0011,0.0020,0.0035,0.0173,
+ 0.0016,0.0014,0.0011,0.0011,0.0004,0.0010,0.0018,0.0015,0.0060,
+ 0.0040,0.0022,0.0024,0.0018,0.0012,0.0016,0.0023,0.0036,0.0012,0.0072,
+ 0.0056,0.0039,0.0032,0.0043,0.0023,0.0027,0.0051,0.0051,0.0022,0.0066,0.0139,
+ 0.0044,0.0043,0.0027,0.0032,0.0010,0.0021,0.0053,0.0039,0.0013,0.0026,0.0044,0.0063,
+ 0.0018,0.0012,0.0009,0.0008,0.0004,0.0007,0.0012,0.0013,0.0008,0.0014,0.0027,0.0017,0.0012,
+ 0.0027,0.0023,0.0017,0.0011,0.0008,0.0010,0.0016,0.0022,0.0008,0.0027,0.0055,0.0023,0.0008,0.0077,
+ 0.0028,0.0021,0.0012,0.0021,0.0007,0.0015,0.0030,0.0030,0.0014,0.0017,0.0027,0.0029,0.0005,0.0011,0.0091,
+ 0.0056,0.0035,0.0028,0.0034,0.0013,0.0021,0.0038,0.0051,0.0017,0.0033,0.0047,0.0042,0.0010,0.0027,0.0024,0.0075,
+ 0.0040,0.0019,0.0024,0.0024,0.0009,0.0016,0.0023,0.0028,0.0010,0.0027,0.0046,0.0025,0.0010,0.0016,0.0020,0.0041,0.0046,
+ 0.0005,0.0007,0.0002,0.0004,0.0003,0.0004,0.0007,0.0011,0.0002,0.0005,0.0009,0.0006,0.0002,0.0007,0.0004,0.0005,0.0003,0.0027,
+ 0.0014,0.0022,0.0008,0.0015,0.0004,0.0011,0.0016,0.0016,0.0010,0.0018,0.0045,0.0017,0.0007,0.0024,0.0011,0.0017,0.0014,0.0009,0.0044,
+ 0.0056,0.0031,0.0022,0.0027,0.0012,0.0015,0.0026,0.0033,0.0012,0.0063,0.0074,0.0030,0.0015,0.0032,0.0017,0.0036,0.0036,0.0005,0.0024,0.0083};
+
+const float Blosum40[]= {
+// A R N D C Q E G H I L K M F P S T W Y V
+ 0.0148,
+ 0.0029,0.0109,
+ 0.0029,0.0019,0.0069,
+ 0.0032,0.0021,0.0031,0.0126,
+ 0.0015,0.0007,0.0007,0.0009,0.0093,
+ 0.0026,0.0024,0.0017,0.0016,0.0004,0.0048,
+ 0.0040,0.0026,0.0023,0.0048,0.0010,0.0032,0.0118,
+ 0.0066,0.0023,0.0035,0.0031,0.0012,0.0020,0.0028,0.0260,
+ 0.0014,0.0012,0.0013,0.0014,0.0003,0.0010,0.0015,0.0014,0.0060,
+ 0.0037,0.0017,0.0017,0.0016,0.0008,0.0012,0.0018,0.0024,0.0009,0.0105,
+ 0.0050,0.0030,0.0021,0.0027,0.0015,0.0023,0.0036,0.0034,0.0017,0.0082,0.0209,
+ 0.0041,0.0051,0.0027,0.0030,0.0010,0.0026,0.0045,0.0035,0.0013,0.0023,0.0037,0.0099,
+ 0.0017,0.0010,0.0007,0.0007,0.0003,0.0007,0.0010,0.0013,0.0007,0.0018,0.0037,0.0012,0.0018,
+ 0.0022,0.0016,0.0013,0.0013,0.0008,0.0008,0.0015,0.0021,0.0009,0.0031,0.0055,0.0018,0.0011,0.0105,
+ 0.0027,0.0014,0.0014,0.0019,0.0005,0.0013,0.0026,0.0028,0.0008,0.0020,0.0021,0.0023,0.0007,0.0010,0.0151,
+ 0.0060,0.0025,0.0030,0.0030,0.0013,0.0026,0.0034,0.0052,0.0013,0.0025,0.0034,0.0034,0.0011,0.0019,0.0022,0.0089,
+ 0.0040,0.0019,0.0022,0.0024,0.0011,0.0015,0.0025,0.0029,0.0009,0.0028,0.0039,0.0029,0.0011,0.0019,0.0022,0.0043,0.0070,
+ 0.0007,0.0005,0.0003,0.0003,0.0001,0.0004,0.0005,0.0008,0.0002,0.0005,0.0009,0.0005,0.0002,0.0008,0.0003,0.0004,0.0003,0.0045,
+ 0.0019,0.0016,0.0010,0.0011,0.0004,0.0010,0.0014,0.0017,0.0012,0.0020,0.0031,0.0017,0.0010,0.0032,0.0009,0.0015,0.0014,0.0008,0.0060,
+ 0.0054,0.0023,0.0017,0.0022,0.0012,0.0014,0.0025,0.0028,0.0008,0.0083,0.0082,0.0027,0.0018,0.0031,0.0018,0.0032,0.0040,0.0005,0.0020,0.0113};
+
+const float Blosum50[]= {
+// A R N D C Q E G H I L K M F P S T W Y V
+ 0.0192,
+ 0.0027,0.0152,
+ 0.0024,0.0020,0.0101,
+ 0.0026,0.0019,0.0035,0.0161,
+ 0.0015,0.0005,0.0006,0.0005,0.0091,
+ 0.0022,0.0025,0.0016,0.0017,0.0004,0.0057,
+ 0.0034,0.0029,0.0023,0.0048,0.0006,0.0033,0.0141,
+ 0.0062,0.0020,0.0031,0.0028,0.0009,0.0017,0.0023,0.0316,
+ 0.0012,0.0013,0.0015,0.0011,0.0003,0.0010,0.0013,0.0011,0.0064,
+ 0.0035,0.0015,0.0013,0.0012,0.0008,0.0011,0.0015,0.0018,0.0007,0.0140,
+ 0.0048,0.0028,0.0017,0.0018,0.0014,0.0019,0.0026,0.0027,0.0013,0.0104,0.0304,
+ 0.0033,0.0064,0.0027,0.0026,0.0006,0.0029,0.0043,0.0028,0.0014,0.0017,0.0027,0.0130,
+ 0.0016,0.0009,0.0007,0.0005,0.0004,0.0008,0.0008,0.0009,0.0005,0.0022,0.0042,0.0010,0.0029,
+ 0.0020,0.0012,0.0009,0.0008,0.0006,0.0007,0.0012,0.0015,0.0009,0.0030,0.0058,0.0012,0.0012,0.0154,
+ 0.0022,0.0011,0.0011,0.0015,0.0004,0.0011,0.0019,0.0019,0.0006,0.0013,0.0017,0.0018,0.0005,0.0007,0.0171,
+ 0.0062,0.0025,0.0032,0.0028,0.0011,0.0022,0.0030,0.0044,0.0012,0.0021,0.0029,0.0031,0.0010,0.0016,0.0018,0.0111,
+ 0.0039,0.0021,0.0026,0.0022,0.0010,0.0015,0.0024,0.0025,0.0009,0.0029,0.0038,0.0026,0.0011,0.0015,0.0016,0.0047,0.0100,
+ 0.0005,0.0004,0.0002,0.0002,0.0001,0.0003,0.0004,0.0005,0.0002,0.0005,0.0008,0.0004,0.0003,0.0009,0.0002,0.0003,0.0004,0.0059,
+ 0.0015,0.0013,0.0009,0.0009,0.0004,0.0009,0.0012,0.0012,0.0013,0.0018,0.0027,0.0013,0.0007,0.0039,0.0006,0.0013,0.0012,0.0008,0.0077,
+ 0.0054,0.0020,0.0015,0.0016,0.0013,0.0014,0.0020,0.0022,0.0007,0.0107,0.0092,0.0022,0.0021,0.0030,0.0016,0.0029,0.0041,0.0005,0.0018,0.0164};
+
+const float Blosum65[]= {
+// A R N D C Q E G H I L K M F P S T W Y V
+ 0.0222,
+ 0.0022,0.0181,
+ 0.0019,0.0019,0.0148,
+ 0.0021,0.0015,0.0037,0.0225,
+ 0.0016,0.0004,0.0004,0.0004,0.0127,
+ 0.0018,0.0024,0.0015,0.0016,0.0003,0.0076,
+ 0.0029,0.0025,0.0021,0.0049,0.0003,0.0034,0.0168,
+ 0.0057,0.0016,0.0027,0.0024,0.0007,0.0013,0.0018,0.0396,
+ 0.0010,0.0013,0.0014,0.0009,0.0002,0.0010,0.0013,0.0009,0.0096,
+ 0.0031,0.0012,0.0009,0.0011,0.0012,0.0008,0.0012,0.0013,0.0006,0.0191,
+ 0.0043,0.0023,0.0013,0.0014,0.0016,0.0016,0.0019,0.0020,0.0009,0.0115,0.0388,
+ 0.0032,0.0062,0.0024,0.0024,0.0005,0.0030,0.0040,0.0024,0.0012,0.0015,0.0024,0.0166,
+ 0.0013,0.0007,0.0005,0.0004,0.0004,0.0007,0.0006,0.0007,0.0003,0.0025,0.0052,0.0008,0.0045,
+ 0.0016,0.0009,0.0007,0.0007,0.0005,0.0005,0.0008,0.0011,0.0008,0.0030,0.0056,0.0009,0.0012,0.0186,
+ 0.0021,0.0009,0.0008,0.0011,0.0003,0.0008,0.0014,0.0013,0.0005,0.0009,0.0013,0.0015,0.0004,0.0005,0.0195,
+ 0.0065,0.0022,0.0030,0.0027,0.0011,0.0018,0.0029,0.0037,0.0011,0.0017,0.0024,0.0030,0.0008,0.0012,0.0016,0.0137,
+ 0.0037,0.0017,0.0022,0.0019,0.0009,0.0013,0.0021,0.0022,0.0007,0.0027,0.0033,0.0023,0.0010,0.0012,0.0013,0.0048,0.0133,
+ 0.0004,0.0003,0.0002,0.0001,0.0002,0.0002,0.0002,0.0004,0.0002,0.0004,0.0007,0.0003,0.0002,0.0009,0.0001,0.0003,0.0003,0.0074,
+ 0.0013,0.0009,0.0007,0.0006,0.0004,0.0006,0.0008,0.0008,0.0016,0.0015,0.0023,0.0010,0.0006,0.0043,0.0004,0.0010,0.0009,0.0010,0.0113,
+ 0.0049,0.0015,0.0011,0.0012,0.0014,0.0011,0.0016,0.0017,0.0006,0.0120,0.0094,0.0019,0.0023,0.0025,0.0012,0.0023,0.0035,0.0004,0.0015,0.0206};
+
+
+const float Blosum80[]= {
+// A R N D C Q E G H I L K M F P S T W Y V
+ 0.0252,
+ 0.0020,0.0210,
+ 0.0016,0.0017,0.0166,
+ 0.0018,0.0013,0.0037,0.0262,
+ 0.0015,0.0003,0.0004,0.0003,0.0172,
+ 0.0017,0.0024,0.0014,0.0014,0.0003,0.0094,
+ 0.0028,0.0023,0.0019,0.0048,0.0003,0.0035,0.0208,
+ 0.0053,0.0015,0.0025,0.0022,0.0006,0.0011,0.0017,0.0463,
+ 0.0009,0.0012,0.0012,0.0008,0.0002,0.0011,0.0012,0.0008,0.0104,
+ 0.0027,0.0010,0.0007,0.0008,0.0011,0.0007,0.0010,0.0009,0.0004,0.0220,
+ 0.0036,0.0018,0.0011,0.0011,0.0014,0.0014,0.0015,0.0016,0.0008,0.0111,0.0442,
+ 0.0029,0.0061,0.0022,0.0020,0.0004,0.0028,0.0036,0.0020,0.0010,0.0012,0.0019,0.0190,
+ 0.0011,0.0006,0.0004,0.0003,0.0004,0.0007,0.0006,0.0005,0.0003,0.0025,0.0052,0.0007,0.0053,
+ 0.0014,0.0007,0.0006,0.0006,0.0005,0.0005,0.0006,0.0009,0.0007,0.0027,0.0052,0.0007,0.0010,0.0211,
+ 0.0021,0.0009,0.0007,0.0009,0.0003,0.0007,0.0012,0.0010,0.0004,0.0007,0.0012,0.0012,0.0003,0.0004,0.0221,
+ 0.0064,0.0020,0.0029,0.0024,0.0010,0.0017,0.0026,0.0034,0.0010,0.0015,0.0021,0.0026,0.0007,0.0010,0.0014,0.0167,
+ 0.0036,0.0015,0.0020,0.0016,0.0009,0.0012,0.0019,0.0019,0.0007,0.0024,0.0028,0.0020,0.0009,0.0011,0.0011,0.0048,0.0156,
+ 0.0003,0.0002,0.0001,0.0001,0.0001,0.0002,0.0002,0.0003,0.0001,0.0003,0.0006,0.0002,0.0002,0.0007,0.0001,0.0002,0.0002,0.0087,
+ 0.0011,0.0007,0.0006,0.0005,0.0003,0.0005,0.0006,0.0006,0.0016,0.0013,0.0020,0.0008,0.0005,0.0046,0.0003,0.0009,0.0008,0.0010,0.0148,
+ 0.0046,0.0013,0.0009,0.0010,0.0013,0.0010,0.0015,0.0014,0.0005,0.0123,0.0089,0.0015,0.0022,0.0022,0.0010,0.0021,0.0033,0.0004,0.0012,0.0246};
+
+
+// prediction accuracy of Psipred:
+// Ppred[cf][B][A] = P(A,B,cf)/P(A)/P(B,cf) = P(A|B,cf)/P(A)
+// A = observed ss state B = predicted ss state cf = confidence value of prediction
+//float Ppred[MAXCF][NSSPRED][NDSSP]=
+const float Ppred[]=
+ {
+//pred/obs - H E ~ S T G B
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=-
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // H
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // E
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // ~
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=0
+ 1.000, 1.128, 0.519, 0.834, 0.957, 1.488, 2.106, 1.085 , // H
+ 1.000, 0.233, 2.240, 1.216, 0.913, 0.519, 0.923, 1.759 , // E
+ 1.000, 0.640, 1.017, 1.122, 1.069, 1.242, 2.140, 1.999 , // ~
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=1
+ 1.000, 1.251, 0.485, 0.771, 0.847, 1.371, 2.266, 0.864 , // H
+ 1.000, 0.222, 2.542, 1.069, 0.804, 0.428, 0.671, 1.728 , // E
+ 1.000, 0.474, 1.103, 1.295, 1.232, 1.214, 1.835, 1.989 , // ~
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=2
+ 1.000, 1.383, 0.426, 0.637, 0.778, 1.349, 2.436, 0.824 , // H
+ 1.000, 0.202, 2.769, 0.999, 0.714, 0.320, 0.551, 1.566 , // E
+ 1.000, 0.395, 1.005, 1.407, 1.376, 1.336, 1.725, 2.063 , // ~
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=3
+ 1.000, 1.531, 0.369, 0.552, 0.682, 1.280, 2.420, 0.698 , // H
+ 1.000, 0.169, 2.970, 0.954, 0.556, 0.273, 0.489, 1.504 , // E
+ 1.000, 0.352, 0.843, 1.515, 1.542, 1.456, 1.684, 1.958 , // ~
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=4
+ 1.000, 1.750, 0.305, 0.444, 0.537, 1.134, 2.295, 0.600 , // H
+ 1.000, 0.124, 3.179, 0.847, 0.513, 0.228, 0.413, 1.897 , // E
+ 1.000, 0.282, 0.718, 1.664, 1.630, 1.577, 1.625, 1.877 , // ~
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=5
+ 1.000, 1.952, 0.250, 0.353, 0.456, 0.982, 2.050, 0.466 , // H
+ 1.000, 0.102, 3.464, 0.699, 0.453, 0.174, 0.284, 1.357 , // E
+ 1.000, 0.227, 0.574, 1.782, 1.846, 1.681, 1.418, 1.885 , // ~
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=6
+ 1.000, 2.183, 0.171, 0.263, 0.319, 0.792, 1.933, 0.345 , // H
+ 1.000, 0.079, 3.712, 0.612, 0.281, 0.133, 0.196, 1.089 , // E
+ 1.000, 0.173, 0.458, 1.915, 2.007, 1.766, 1.220, 1.704 , // ~
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=7
+ 1.000, 2.389, 0.132, 0.192, 0.224, 0.605, 1.605, 0.183 , // H
+ 1.000, 0.053, 3.997, 0.449, 0.201, 0.072, 0.141, 0.919 , // E
+ 1.000, 0.109, 0.328, 2.013, 2.304, 1.882, 0.960, 1.512 , // ~
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=8
+ 1.000, 2.668, 0.065, 0.098, 0.144, 0.354, 1.059, 0.102 , // H
+ 1.000, 0.029, 4.285, 0.284, 0.113, 0.044, 0.059, 0.522 , // E
+ 1.000, 0.053, 0.200, 2.099, 2.444, 2.133, 0.671, 1.290 , // ~
+ 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=9
+ 1.000, 2.966, 0.009, 0.023, 0.036, 0.113, 0.214, 0.017 , // H
+ 1.000, 0.010, 4.555, 0.119, 0.027, 0.010, 0.013, 0.209 , // E
+ 1.000, 0.026, 0.101, 2.576, 1.853, 2.204, 0.308, 0.499 // ~
+ };
+
+// float Ppred[]=
+// {
+// //pred/obs - H E ~ S T G B
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=-
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=0
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=1
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=2
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=3
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=4
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=5
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=6
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=7
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=8
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~
+// 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000, 1.000 , // - conf=9
+// 1.000, 2.000, 0.500, 1.000, 1.000, 1.000, 1.000, 0.500, // H
+// 1.000, 0.500, 2.000, 0.500, 1.000, 1.000, 0.500, 1.000, // E
+// 1.000, 1.000, 1.000, 2.000, 2.000, 2.000, 1.000, 1.000, // ~
+
+
+float Pobs[]={0, 0.3268,0.2119,0.2061,0.0913,0.1143,0.0376,0.0120};
+
+float Pevo_full[]=
+ {
+// - H E C
+ 1.00, 0.00, 0.00, 0.00,
+ 0.00, 0.94, 0.00, 0.04,
+ 0.00, 0.00, 0.92, 0.04,
+ 0.00, 0.06, 0.08, 0.92
+ };
+
+//psipred accuracy for confidence values 0-9
+const float p_acc[]={0.00,0.47,0.53,0.56,0.58,0.62,0.69,0.74,0.82,0.88,0.96};
+
+/**
+ * @brief
+ */
+void
+SetBlosumMatrix(const float BlosumXX[])
+{
+ int a,b,n=0;
+ if (v>=3) printf("Using the BLOSUM%2i matrix\n",par.matrix);
+ for (a=0; a<20; ++a)
+ for (pb[a]=0.0f, b=0; b<=a; ++b,++n)
+ P[a][b] = BlosumXX[n];
+ for (a=0; a<19; a++)
+ for (b=a+1; b<20; ++b)
+ P[a][b] = P[b][a];
+ for (a=0; a<20; ++a) P[a][20]=P[20][a]=1.0f;
+ return;
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Set (global variable) substitution matrix with derived matrices and background frequencies
+ */
+void
+SetSubstitutionMatrix()
+{
+ int a,b;
+ switch (par.matrix)
+ {
+ default:
+ case 0: //Gonnet matrix
+ if (v>=3) cout<<"Using the Gonnet matrix ";
+ for (a=0; a<20; ++a)
+ for (pb[a]=0.0f, b=0; b<20; ++b)
+ P[a][b] = 0.000001f*Gonnet[a*20+b];
+ for (a=0; a<20; ++a) P[a][20]=P[20][a]=1.0f;
+ break;
+
+ case 30: //BLOSUM30
+ SetBlosumMatrix(Blosum30);
+ break;
+ case 40: //BLOSUM40
+ SetBlosumMatrix(Blosum40);
+ break;
+ case 50: //BLOSUM50
+ SetBlosumMatrix(Blosum50);
+ break;
+ case 65: //BLOSUM65
+ SetBlosumMatrix(Blosum65);
+ break;
+ case 80: //BLOSUM80
+ SetBlosumMatrix(Blosum80);
+ break;
+ }
+
+ // Check transition probability matrix, renormalize P and calculate pb[a]
+ float sumab=0.0f;
+ for (a=0; a<20; a++)
+ for (b=0; b<20; ++b) sumab+=P[a][b];
+ for (a=0; a<20; a++)
+ for (b=0; b<20; ++b) P[a][b]/=sumab;
+ for (a=0; a<20; a++)
+ for (pb[a]=0.0f, b=0; b<20; ++b) pb[a]+=P[a][b];
+
+ //Compute similarity matrix for amino acid pairs (for calculating consensus sequence)
+ for (a=0; a<20; ++a)
+ for (b=0; b<20; ++b)
+ Sim[a][b] = P[a][b]*P[a][b]/P[a][a]/P[b][b];
+
+ //Precompute matrix R for amino acid pseudocounts:
+ for (a=0; a<20; ++a)
+ for (b=0; b<20; ++b)
+ R[a][b] = P[a][b]/pb[b]; //R[a][b]=P(a|b)
+
+ //Precompute matrix R for amino acid pseudocounts:
+ for (a=0; a<20; ++a)
+ for (b=0; b<20; ++b)
+ S[a][b] = log2(R[a][b]/pb[a]); // S[a][b] = log2(P(a,b)/P(a)/P(b))
+
+ // Evaluate sequence identity underlying substitution matrix
+ if (v>=3)
+ {
+ float id=0.0f;
+ float entropy=0.0f;
+ float entropy_pb=0.0f;
+ float mut_info=0.0f;
+ for (a=0; a<20; ++a) id+=P[a][a];
+ for (a=0; a<20; ++a) entropy_pb-=pb[a]*log2(pb[a]);
+ for (a=0; a<20; ++a)
+ for (b=0; b<20; ++b)
+ {
+ entropy-=P[a][b]*log2(R[a][b]);
+ mut_info += P[a][b]*S[a][b];
+ }
+
+ printf(": sequence identity = %2.0f%%; entropy per column = %4.2f bits (out of %4.2f); mutual information = %4.2f bits\n",100*id,entropy,entropy_pb,mut_info);
+ }
+
+ if (v>=4) //Debugging: probability matrix and dissimilarity matrix
+ {
+ cout<<"Check matrix: before renormalization sum P(a,b)= "<<sumab<<"...\n";//PRINT
+ cout<<" A R N D C Q E G H I L K M F P S T W Y V\n";
+ cout<<"p[] ";
+ for (a=0; a<20; a++) printf("%4.1f ",100*pb[a]);
+ cout<<endl<<"\nSubstitution matrix log2( P(a,b)/p(a)/p(b) ) (in bits):\n";
+ cout<<" A R N D C Q E G H I L K M F P S T W Y V\n";
+ for (b=0; b<20; b++)
+ {
+ cout<<i2aa(b)<<" ";
+ for (a=0; a<20; a++) printf("%4.1f ",S[a][b]);
+ cout<<endl;
+ }
+ cout<<endl<<"\nOdds matrix P(a,b)/p(a)/p(b):\n";
+ cout<<" A R N D C Q E G H I L K M F P S T W Y V\n";
+ for (b=0; b<20; b++)
+ {
+ cout<<i2aa(b)<<" ";
+ for (a=0; a<20; a++) printf("%4.1f ",P[b][a]/pb[a]/pb[b]);
+ cout<<endl;
+ }
+ cout<<endl<<"\nMatrix of conditional probabilities P(a|b) = P(a,b)/p(b) (in %):\n";
+ cout<<" A R N D C Q E G H I L K M F P S T W Y V\n";
+ for (b=0; b<20; b++)
+ {
+ cout<<i2aa(b)<<" ";
+ for (a=0; a<20; a++) printf("%4.1f ",100*R[b][a]);
+ cout<<endl;
+ }
+ cout<<endl<<"\nProbability matrix P(a,b) (in %):\n";
+ cout<<" A R N D C Q E G H I L K M F P S T W Y V\n";
+ for (b=0; b<20; b++)
+ {
+ cout<<i2aa(b)<<" ";
+ for (a=0; a<20; a++) printf("%5.0f ",1000000*P[b][a]);
+ cout<<endl;
+ }
+ cout<<endl<<"Similarity matrix P(a,b)^2/P(a,a,)/P(b,b) (in %):\n";
+ cout<<" A R N D C Q E G H I L K M F P S T W Y V\n";
+ for (b=0; b<20; b++)
+ {
+ cout<<i2aa(b)<<" ";
+ for (a=0; a<20; a++) printf("%4.0f ",100*Sim[b][a]);
+ cout<<endl;
+ }
+ cout<<endl;
+
+
+ }
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Set secondary structure substitution matrix
+ */
+void
+SetSecStrucSubstitutionMatrix()
+{
+ int A; //observed ss state (determined dssp)
+ int B,BB; //predicted ss states (by psipred)
+ int cf,ccf; //confidence value of prediction
+ float P73[NDSSP][NSSPRED][MAXCF]; //P73[cf][B][A] = P(A,B,cf)/P(A)/P(B,cf) = P(A|B,cf)/P(A)
+ float sum;
+
+ // S73[A][B][cf][b] = score for matching observed ss state A in query with state B in template
+ // predicted with confidence cf, when query and template columns are diverged by b units
+ for (cf=0; cf<MAXCF; cf++)
+ for (A=0; A<NDSSP; A++)
+ for (B=0; B<NSSPRED; B++)
+ {
+ P73[A][B][cf] = 1.-par.ssa + par.ssa*Ppred[cf*NSSPRED*NDSSP + B*NDSSP + A];
+ S73[A][B][cf] = log2(P73[A][B][cf]);
+ }
+
+ for (B=0; B<NSSPRED; B++)
+ for (cf=0; cf<MAXCF; cf++)
+ for (BB=0; BB<NSSPRED; BB++)
+ for (ccf=0; ccf<MAXCF; ccf++)
+ {
+ sum=0;
+ for (A=1; A<NDSSP; A++)
+ sum += P73[A][B][cf] * P73[A][BB][ccf] * Pobs[A];
+ S33[B][cf][BB][ccf] = log2(sum);
+ }
+} /* this is the end of SetSecStrucSubstitutionMatrix() */
+
+
+
+/*
+ * EOF hhmatrices-C.h
+ */
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: hhutil-C.h 246 2011-06-15 12:41:04Z fabian $
+ */
+
+//////////////////////////////////////////////////////////////////////////////
+// Transform a character to lower case and '.' to '-' and vice versa
+//////////////////////////////////////////////////////////////////////////////
+
+
+inline char
+MatchChr(char c) {return ((c>='a' && c<='z')? c-'a'+'A' : (c=='.'? '-':c) );}
+
+inline char
+InsertChr(char c) {return ((c>='A' && c<='Z')? c+'a'-'A' : ((c>='0' && c<='9') || c=='-')? '.':c );}
+
+inline int
+WordChr(char c) {return (int)((c>='A' && c<='Z') || (c>='a' && c<='z'));}
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Transforms the one-letter amino acid code into an integer between 0 and 22
+ */
+inline char
+aa2i(char c)
+{
+ //A R N D C Q E G H I L K M F P S T W Y V
+ if (c>='a' && c<='z') c+='A'-'a';
+ switch (c)
+ {
+ case 'A': return 0;
+ case 'R': return 1;
+ case 'N': return 2;
+ case 'D': return 3;
+ case 'C': return 4;
+ case 'Q': return 5;
+ case 'E': return 6;
+ case 'G': return 7;
+ case 'H': return 8;
+ case 'I': return 9;
+ case 'L': return 10;
+ case 'K': return 11;
+ case 'M': return 12;
+ case 'F': return 13;
+ case 'P': return 14;
+ case 'S': return 15;
+ case 'T': return 16;
+ case 'W': return 17;
+ case 'Y': return 18;
+ case 'V': return 19;
+ case 'X': return ANY;
+ case 'J': return ANY;
+ case 'O': return ANY;
+ case 'U': return 4; //Selenocystein -> Cystein
+ case 'B': return 3; //D (or N)
+ case 'Z': return 6; //E (or Q)
+ case '-': return GAP;
+ case '.': return GAP;
+ case '_': return GAP;
+ }
+ if (c>=0 && c<=32) return -1; // white space and control characters
+ return -2;
+}
+
+///////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Transforms integers between 0 and 22 into the one-letter amino acid code
+ */
+inline char
+i2aa(char c)
+{
+ //A R N D C Q E G H I L K M F P S T W Y V
+ switch (c)
+ {
+ case 0: return 'A';
+ case 1: return 'R';
+ case 2: return 'N';
+ case 3: return 'D';
+ case 4: return 'C';
+ case 5: return 'Q';
+ case 6: return 'E';
+ case 7: return 'G';
+ case 8: return 'H';
+ case 9: return 'I';
+ case 10: return 'L';
+ case 11: return 'K';
+ case 12: return 'M';
+ case 13: return 'F';
+ case 14: return 'P';
+ case 15: return 'S';
+ case 16: return 'T';
+ case 17: return 'W';
+ case 18: return 'Y';
+ case 19: return 'V';
+ case ANY: return 'X';
+ case GAP: return '-';
+ case ENDGAP: return '-';
+ }
+ return '?';
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Transforms the dssp/psipred secondary structure code into an integer number
+ */
+inline char
+ss2i(char c)
+{
+ //- H E C S T G B
+ if (c>='a' && c<='z') c+='A'-'a';
+ switch (c)
+ {
+ case '.': return 0;
+ case '-': return 0;
+ case 'X': return 0;
+ case 'H': return 1;
+ case 'E': return 2;
+ case 'C': return 3;
+ case '~': return 3;
+ case 'S': return 4;
+ case 'T': return 5;
+ case 'G': return 6;
+ case 'B': return 7;
+ case 'I': return 3;
+ case ' ': return -1;
+ case '\t': return -1;
+ case '\n': return -1;
+ }
+ return -2;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Transforms integers between 0 and 8 into the dssp/psipred secondary structure code
+ */
+inline char
+i2ss(int c)
+{
+ //- H E C S T G B
+ switch (c)
+ {
+ case 0: return '-';
+ case 1: return 'H';
+ case 2: return 'E';
+ case 3: return 'C';
+ case 4: return 'S';
+ case 5: return 'T';
+ case 6: return 'G';
+ case 7: return 'B';
+ case 8: return 'I';
+ }
+ return '?';
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Transforms the solvend accessiblity code into an integer number
+ */
+inline char
+sa2i(char c)
+{
+ //- A B C D E
+ if (c>='a' && c<='z') c+='A'-'a';
+ switch (c)
+ {
+ case '.': return 0;
+ case '-': return 0;
+ case 'A': return 1;
+ case 'B': return 2;
+ case 'C': return 3;
+ case 'D': return 4;
+ case 'E': return 5;
+ case 'F': return 6;
+ case ' ': return -1;
+ case '\t': return -1;
+ case '\n': return -1;
+ }
+ return -2;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Transforms integers between 0 and 5 into the solvent accessibility code
+ */
+inline char i2sa(int c)
+{
+ //- H E C S T G B
+ switch (c)
+ {
+ case 0: return '-';
+ case 1: return 'A';
+ case 2: return 'B';
+ case 3: return 'C';
+ case 4: return 'D';
+ case 5: return 'E';
+ case 6: return 'F';
+ }
+ return '?';
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Transforms alternative secondary structure symbols into symbols
+ */
+inline char
+ss2ss(char c)
+{
+ //- H E C S T G B
+ switch (c)
+ {
+ case '~': return 'C';
+ case 'I': return 'C';
+ case 'i': return 'c';
+ case 'H':
+ case 'E':
+ case 'C':
+ case 'S':
+ case 'T':
+ case 'G':
+ case 'B':
+ case 'h':
+ case 'e':
+ case 'c':
+ case 's':
+ case 't':
+ case 'g':
+ case 'b':
+ case '.':
+ return c;
+ }
+ return '-';
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Transforms confidence values of psipred into internal code
+ */
+inline char
+cf2i(char c)
+{
+ switch (c)
+ {
+ case '-': return 0;
+ case '.': return 0;
+ case '0': return 1;
+ case '1': return 2;
+ case '2': return 3;
+ case '3': return 4;
+ case '4': return 5;
+ case '5': return 6;
+ case '6': return 7;
+ case '7': return 8;
+ case '8': return 9;
+ case '9': return 10;
+ }
+ return 0;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Transforms internal representation of psipred confidence values into printable chars
+ */
+inline char
+i2cf(char c)
+{
+ switch (c)
+ {
+ case 0: return '-';
+ case 1: return '0';
+ case 2: return '1';
+ case 3: return '2';
+ case 4: return '3';
+ case 5: return '4';
+ case 6: return '5';
+ case 7: return '6';
+ case 8: return '7';
+ case 9: return '8';
+ case 10: return '9';
+ }
+ return '-';
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Fast lookup of log2(1+2^(-x)) for x>=0 (precision < 0.35%)
+ */
+inline float
+fast_addscore(float x)
+{
+ static float val[2001]; // val[i]=log2(1+2^(-x))
+ static char initialized;
+ if (x>20) return 0.0;
+ if (x<0)
+ {
+ fprintf(stderr,"Error in function fast_addscore: argument %g is negative\n",x);
+ exit(7);
+ }
+ if (!initialized) //First fill in the log2-vector
+ {
+ for (int i=0; i<=2000; i++) val[i]=log2(1.0+pow(2,-0.01*(i+0.5)));
+ initialized=1;
+ }
+ return val[(int)(100.0*x)];
+}
+
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Little utilities for output
+ */
+inline void
+fout(FILE* outf, int d)
+{
+ if (d>=99999) fprintf(outf,"*\t"); else fprintf(outf,"%i\t",d);
+ return;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Errors
+ */
+int
+FormatError(const char infile[], const char details[]="")
+{
+ cerr<<"Error in "<</*par.argv[0],FS*/__FILE__<<": wrong format while reading file \'"<<infile<<". "<<details<<"\n";
+ exit(1);
+}
+
+int
+OpenFileError(const char outfile[])
+{
+ cerr<<endl<<"Error in "<</*par.argv[0],FS*/__FILE__<<": could not open file \'"<<outfile<<"\'\n";
+ exit(2);
+}
+
+int
+MemoryError(const char arrayname[])
+{
+ cerr<<"Error in "<</*par.argv[0],FS*/__FILE__<<": Memory overflow while creating \'"<<arrayname<<"\'. Please report this bug to developers\n";
+ exit(3);
+}
+
+int
+InternalError(const char errstr[])
+{
+ cerr<<"Error in "<</*par.argv[0],FS*/__FILE__<<": "<<errstr<<". Please report this bug to developers\n";
+ exit(6);
+}
+
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Takes family code (eg. a.1.2.3) and returns strings 'a', 'a.1', and 'a.1.2'
+ */
+inline void
+ScopID(char cl[], char fold[], char sfam[], const char fam[])
+{
+ char* ptr;
+
+ //get scop class ID
+ strcpy(cl,fam);
+ ptr = strchr(cl,'.'); //return adress of next '.' in name
+ if(ptr) ptr[0]='\0';
+
+ //get scop fold ID
+ strcpy(fold,fam);
+ ptr = strchr(fold,'.'); //return adress of next '.' in name
+ if(ptr) ptr = strchr(ptr+1,'.'); //return adress of next '.' in name
+ if(ptr) ptr[0]='\0';
+
+ //get scop superfamily ID
+ strcpy(sfam,fam);
+ ptr = strchr(sfam,'.'); //return adress of next '.' in name
+ if(ptr) ptr = strchr(ptr+1,'.'); //return adress of next '.' in name
+ if(ptr) ptr = strchr(ptr+1,'.'); //return adress of next '.' in name
+ if(ptr) ptr[0]='\0';
+ return;
+}
+
+//////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Read up to n lines of outfile and write to screen (STDERR)
+ */
+void
+WriteToScreen(char* outfile, int n)
+{
+ char line[LINELEN]="";
+ ifstream outf;
+ outf.open(outfile, ios::in);
+ if (!outf) {OpenFileError(outfile);}
+ cout<<"\n";
+ for(; n>0 && outf.getline(line,LINELEN); n--) cout<<line<<"\n";
+ outf.close();
+ cout<<"\n";
+}
+
+inline void
+WriteToScreen(char* outfile) {WriteToScreen(outfile,INT_MAX);}
+
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Read .hhdefaults file into array argv_conf (beginning at argv_conf[1])
+ */
+void
+ReadDefaultsFile(int& argc_conf, char** argv_conf)
+{
+ char line[LINELEN]="";
+ char filename[NAMELEN];
+ char* c_first; //pointer to first character of argument string
+ char* c; //pointer to scan line read in for end of argument
+ // ifstream configf;
+ FILE* configf=NULL;
+ argc_conf=1; //counts number of arguments read in
+
+ // Open config file
+ strcpy(filename,"./.hhdefaults");
+ configf = fopen(filename,"r");
+ if (!configf && getenv("HOME"))
+ {
+ strcpy(filename,getenv("HOME"));
+ strcat(filename,"/.hhdefaults");
+ configf = fopen(filename,"r");
+ if (!configf)
+ {
+ if (v>=3) cerr<<"Warning: could not find ./.hhdefaults or "<<filename<<"\n";
+ return;
+ }
+ }
+ else if (!configf) return; // only webserver has no home directory => need no warning
+
+ // Scan file until line 'program_nameANYTHING'
+ while (fgets(line,LINELEN,configf))
+ if (!strncmp(line,program_name,6)) break;
+ // Found line 'program_nameANYTHING'?
+ if (!strncmp(line,program_name,6))
+ {
+ // Read in options until end-of-file or empty line
+ while (fgets(line,LINELEN,configf) && strcmp(line,"\n"))
+ {
+ // Analyze line
+ c=line;
+ do
+ {
+ // Find next word
+ while (*c==' ' || *c=='\t') c++; //Advance until next non-white space
+ if (*c=='\0' || *c=='\n' || *c=='#') break; //Is next word empty string?
+ c_first=c;
+ while (*c!=' ' && *c!='\t' && *c!='#' && *c!='\0' && *c!='\n' ) c++; //Advance until next white space or '#'
+ if (*c=='\0' || *c=='\n' || *c=='#') //Is end of line reached?
+ {
+ *c='\0';
+ argv_conf[argc_conf]=new(char[strlen(c_first)+1]);
+ strcpy(argv_conf[argc_conf++],c_first);
+ break;
+ }
+ *c='\0';
+ argv_conf[argc_conf]=new(char[strlen(c_first)+1]);
+ strcpy(argv_conf[argc_conf++],c_first);
+ printf("Argument: %s\n",c_first);
+ c++;
+ } while (1);
+ } //end read line
+ if (v>=3)
+ {
+ cout<<"Arguments read in from .hhdefaults:";
+ for (int argc=1; argc<argc_conf; argc++) cout<<(argv_conf[argc][0]=='-'? " ":"")<<argv_conf[argc]<<" ";
+ cout<<"\n";
+ }
+ else if (v>=3) cout<<"Read in "<<argc_conf<<" default arguments for "<<program_name<<" from "<<filename<<"\n";
+ }
+ else //found no line 'program_name anything"
+ {
+ if (v>=3) cerr<<endl<<"Warning: no default options for \'"<<program_name<<"\' found in "<<filename<<"\n";
+ return; //no line 'program_name anything' found
+ }
+// configf.close();
+ fclose(configf);
+}
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Set default parameter values
+ */
+void
+SetDefaults()
+{
+
+ par.append=0; // overwrite output file
+ par.outformat=0; // 0: hhr 1: FASTA 2:A2M 3:A3M
+ par.p=20.0f; // minimum threshold for inclusion in hit list and alignment listing
+ par.E=1e6f; // maximum threshold for inclusion in hit list and alignment listing
+ par.b=10; // min number of alignments
+ par.B=500; // max number of alignments
+ par.z=10; // min number of lines in hit list
+ par.Z=500; // max number of lines in hit list
+ par.e=1e-3f; // maximum E-value for inclusion in output alignment, output HMM, and PSI-BLAST checkpoint model
+ par.showcons=1; // show consensus sequence
+ par.showdssp=1; // show predicted secondary structure
+ par.showpred=1; // show dssp secondary structure
+ par.cons=0; // show first non-SS sequence as main representative sequence (not consensus)
+ par.nseqdis=1; // maximum number of query sequences for output alignment
+ par.mark=0; // 1: only marked sequences (or first) get displayed; 0: most divergent ones get displayed
+ par.aliwidth=80; // number of characters per line in output alignments for HMM search
+ par.max_seqid=90; // default for maximum sequence identity threshold
+ par.qid=0; // default for minimum sequence identity with query
+ par.qsc=-20.0f; // default for minimum score per column with query
+ par.coverage=0; // default for minimum coverage threshold
+ par.Ndiff=100; // pick Ndiff most different sequences from alignment
+ par.coverage_core=80; // Minimum coverage for sequences in core alignment
+ par.qsc_core=0.3f; // Minimum score per column of core sequence with query
+ par.coresc=-20.0f; // Minimum score per column with core alignment (HMM)
+
+ par.M=1; // match state assignment is by A2M/A3M
+ par.Mgaps=50; // Above this percentage of gaps, columns are assigned to insert states (for par.M=2)
+ par.calibrate=0; // default: no calibration
+ par.calm=0; // derive P-values from: 0:query calibration 1:template calibration 2:both
+ par.mode=0; //
+
+ par.wg=0; // 0: use local sequence weights 1: use local ones
+
+ par.matrix=0; // Subst.matrix 0: Gonnet, 1: HSDM, 2: BLOSUM50 3: BLOSUM62
+ par.pcm=2; // pseudocount mode: default=divergence-dependent (but not column-specific)
+#if 1 /* Nelder-Meade on Baliscore */
+ par.pca=1.712190f; // default values for substitution matrix pseudocounts
+ par.pcb=1.039640f; // significant reduction of pcs by Neff_M starts around Neff_M-1=pcb
+ par.pcc=0.878067f; // pcs are reduced prop. to 1/Neff^pcc
+ par.pcw=0.0f; // wc>0 weighs columns according to their intra-clomun similarity
+
+ par.gapb=1.405220; // default values for transition pseudocounts
+ par.gapd=1.316760; // gap open penalty pseudocount; 0.25 corresponds to 7.1*gapf bits
+ par.gape=1.793780; // gap extension penalty pseudocount
+ par.gapf=1.034710; // factor for increasing gap open penalty for deletes
+ par.gapg=0.894772; // factor for increasing gap open penalty for inserts
+ par.gaph=0.544072; // factor for increasing gap extension penalty for deletes
+ par.gapi=0.862559; // factor for increasing gap extension penalty for inserts
+#else /* Soeding's default*/
+ par.pca=1.0f; // default values for substitution matrix pseudocounts
+ par.pcb=1.5f; // significant reduction of pcs by Neff_M starts around Neff_M-1=pcb
+ par.pcc=1.0f; // pcs are reduced prop. to 1/Neff^pcc
+ par.pcw=0.0f; // wc>0 weighs columns according to their intra-clomun similarity
+
+ par.gapb=1.0; // default values for transition pseudocounts
+ par.gapd=0.15; // gap open penalty pseudocount; 0.25 corresponds to 7.1*gapf bits
+ par.gape=1.0; // gap extension penalty pseudocount
+ par.gapf=0.6; // factor for increasing gap open penalty for deletes
+ par.gapg=0.6; // factor for increasing gap open penalty for inserts
+ par.gaph=0.6; // factor for increasing gap extension penalty for deletes
+ par.gapi=0.6; // factor for increasing gap extension penalty for inserts
+#endif
+
+#if 0
+ /* Viterbi parameters optimised on Sabre (R228), FS, r228 -> r229 */
+ par.pcaV=1.245150f; // default values for substitution matrix pseudocounts
+ par.pcbV=1.682110f; // significant reduction of pcs by Neff_M starts around Neff_M-1=pcb
+ par.pccV=1.483840f; // pcs are reduced prop. to 1/Neff^pcc
+ par.pcwV=0.0f; // wc>0 weighs columns according to their intra-clomun similarity
+
+ par.gapbV=0.818625; // default values for transition pseudocounts
+ par.gapdV=0.666110; // gap open penalty pseudocount; 0.25 corresponds to 7.1*gapf bits
+ par.gapeV=1.028050; // gap extension penalty pseudocount
+ par.gapfV=0.710760; // factor for increasing gap open penalty for deletes
+ par.gapgV=1.649800; // factor for increasing gap open penalty for inserts
+ par.gaphV=0.470604; // factor for increasing gap extension penalty for deletes
+ par.gapiV=0.829479; // factor for increasing gap extension penalty for inserts
+#elif 1
+ /* Viterbi parameters optimised on Balibase, r244 -> r245 */
+ par.pcaV=1.333860f; // default values for substitution matrix pseudocounts
+ par.pcbV=1.934480f; // significant reduction of pcs by Neff_M starts around Neff_M-1=pcb
+ par.pccV=1.655610f; // pcs are reduced prop. to 1/Neff^pcc
+ par.pcwV=0.0f; // wc>0 weighs columns according to their intra-clomun similarity
+
+ par.gapbV=0.334525; // default values for transition pseudocounts
+ par.gapdV=0.074534; // gap open penalty pseudocount; 0.25 corresponds to 7.1*gapf bits
+ par.gapeV=0.320336; // gap extension penalty pseudocount
+ par.gapfV=0.151634; // factor for increasing gap open penalty for deletes
+ par.gapgV=0.641516; // factor for increasing gap open penalty for inserts
+ par.gaphV=0.266434; // factor for increasing gap extension penalty for deletes
+ par.gapiV=0.598414; // factor for increasing gap extension penalty for inserts
+#else /* Soeding default*/
+ par.pcaV=1.0f; // default values for substitution matrix pseudocounts
+ par.pcbV=1.5f; // significant reduction of pcs by Neff_M starts around Neff_M-1=pcb
+ par.pccV=1.0f; // pcs are reduced prop. to 1/Neff^pcc
+ par.pcwV=0.0f; // wc>0 weighs columns according to their intra-clomun similarity
+
+ par.gapbV=1.0; // default values for transition pseudocounts
+ par.gapdV=0.15; // gap open penalty pseudocount; 0.25 corresponds to 7.1*gapf bits
+ par.gapeV=1.0; // gap extension penalty pseudocount
+ par.gapfV=0.6; // factor for increasing gap open penalty for deletes
+ par.gapgV=0.6; // factor for increasing gap open penalty for inserts
+ par.gaphV=0.6; // factor for increasing gap extension penalty for deletes
+ par.gapiV=0.6; // factor for increasing gap extension penalty for inserts
+#endif
+
+ par.ssm=2; // ss scoring mode: 0:no ss score 1:score after alignment 2:score during alignment
+ par.ssw=0.11f; // weight of ss scoring
+ par.ssa=1.0f; // weight of ss evolution matrix
+ par.shift=-0.01f; // Shift match score up
+ par.mact=0.3001f; // Score threshold for MAC alignment in local mode (set to 0.5001 to track user modification)
+ par.corr=0.1f; // Weight of correlations of scores for |i-j|<=4
+ par.wstruc=1.0f; // Weight of structure scores
+
+ par.egq=0.0f; // no charge for end gaps as default
+ par.egt=0.0f; // no charge for end gaps as default
+
+ par.trans=0; // no transitive scoring as default
+ par.Emax_trans=100.0f; // use intermediate HMMs with E-values up to 100 between query and database HMM
+ par.Emax_trans=100.0f; // use intermediate HMMs with E-values up to 100 between query and database HMM
+ par.wtrans=1.0f; // Ztot[k] = Zq[k] + wtrans * (Zforward[k]+Zreverse[k])
+ par.ssgap=0; // 1: add secondary structure-dependent gap penalties 0:off
+ par.ssgapd=1.0f; // secondary structure-dependent gap-opening penalty (per residue)
+ par.ssgape=0.0f; // secondary structure-dependent gap-extension penalty (per residue)
+ par.ssgapi=4; // max. number of inside-integer(ii); gap-open-penalty= -ii*ssgapd
+
+ par.loc=1; // local vs. global alignment as default
+ par.altali=2; // find up to two (possibly overlapping) subalignments
+ par.forward=0; // 0: Viterbi algorithm; 1: Viterbi+stochastic sampling; 3:Maximum Accuracy (MAC) algorithm
+ par.realign=1; // realign with MAC algorithm
+
+ par.repmode=0; // repeats score independently of one another
+ par.columnscore=1; // Default column score is 1: null model pnul = 1/2 * (q_av(a)+p_av(a))
+ par.min_overlap=0; // automatic minimum overlap used
+ par.opt=0; // Default = optimization mode off
+ par.readdefaultsfile=0; // Default = do not read a defaults file ./.hhdefaults or HOME/.hhdefaults
+ par.maxdbstrlen=200; // maximum length of database string to be printed in 'Command' line of hhr file
+ par.mode=0;
+ par.idummy=par.jdummy=0; //
+
+ par.notags=1; // neutralize His-tags, FLAG-tags, C-myc-tags
+
+ // Initialize strings
+ strcpy(par.infile,"stdin");
+ strcpy(par.outfile,"");
+ strcpy(par. pairwisealisfile,"");
+ strcpy(par.buffer,"buffer.txt");
+ strcpy(par.scorefile,"");
+ strcpy(par.wfile,"");
+ strcpy(par.alnfile,"");
+ strcpy(par.hhmfile,"");
+ strcpy(par.psifile,"");
+ par.exclstr=NULL;
+
+#if 0 /* read parameter file from home-dir */
+#include "hhutil-C-help.h"
+#endif /* read parameter file from home-dir */
+
+ return;
+} /** this is the end of SetDefaults() **/
+
+/*
+ * EOF hhutil-C.h
+ */
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: list-C.h 143 2010-10-14 13:11:14Z andreas $
+ */
+
+// list.C
+// Class for double-linked list
+
+
+
+#ifndef JLIST
+#define JLIST
+
+#ifndef MAIN
+#include <iostream> // cin, cout
+#include <stdlib.h> //
+#include <stdio.h> //
+using std::cout;
+using std::cerr;
+#endif
+
+#include "list.h"
+
+////////////////////////////////////////////////////////////////////////////
+// Double-linked list implementation with head and tail dummy elements
+// We set head->prev=head and tail->next=tail.
+// This makes sure that repeated current=current->next; ends up in tail
+// and repeated current=current->prev; ends up in head.
+// head and tail optionally contain a NULL element of Typ defined by method Null(Typ)
+////////////////////////////////////////////////////////////////////////////
+
+
+
+////////////////////////////////////////////////////////////////////////////
+// Constructors and destructor
+
+////////////////////////////////////////////////////////////////////////////
+// Creates empty List with two dummy elements
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+List<Typ>::List()
+{
+ head=new ListEl<Typ>();
+ if (!head) { cerr<<"Could not create new element\n"; return; }
+ tail=new ListEl<Typ>(head,NULL);
+ if (!tail) { cerr<<"Could not create new element\n"; return; }
+ tail->next = tail;
+ head->prev = head;
+ head->next = tail;
+ current = head;
+ size=0;
+}
+
+////////////////////////////////////////////////////////////////////////////
+// Creates List with one element
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+List<Typ>::List(Typ d)
+{
+ head=new ListEl<Typ>();
+ if (!head) { cerr<<"Could not create new element\n"; return; }
+ tail=new ListEl<Typ>();
+ if (!tail) { cerr<<"Could not create new element\n"; return; }
+ ListEl<Typ>* el = new ListEl<Typ>(d,head,tail);
+ if (!el) { cerr<<"Could not create new element\n"; return; }
+ head->prev = head;
+ head->next = el;
+ tail->prev = el;
+ tail->next = tail;
+ current = head;
+ size=1;
+}
+
+////////////////////////////////////////////////////////////////////////////
+// Destructor deletes List object
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+List<Typ>::~List()
+{
+ ListEl<Typ>* n=head->next;
+ while(head!=n)
+ {
+ delete(head); head = NULL;
+ head=n;
+ n=head->next;
+ }
+ delete(head); head = NULL;
+}
+
+////////////////////////////////////////////////////////////////////////////
+// Flat copy
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+List<Typ>& List<Typ>::operator=(List<Typ>& l)
+{
+ head = l.head;
+ tail = l.tail;
+ current = l.current;
+ size = l.size;
+}
+
+
+////////////////////////////////////////////////////////////////////////////
+// Reverse order of list
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+void List<Typ>::Reverse()
+{
+ ListEl<Typ> *n; // next list element; also for swapping
+ ListEl<Typ> *c; // current element to be sorted in. Everything to the left is already sorted
+ if (Size()<=1) return;
+ for (c=head; c!=tail; c=n)
+ {
+ // Swap prev and next pointers of all list elements
+ n = c->next;
+ c->next = c->prev;
+ c->prev = n;
+ }
+
+ // Swap prev and next pointers of tail
+ tail->next = tail->prev;
+ tail->prev = tail;
+
+ // Swap head an tail
+ n = head;
+ head = tail;
+ tail = n;
+}
+
+
+
+
+////////////////////////////////////////////////////////////////////////////
+// Methods that act at the end of the list
+
+////////////////////////////////////////////////////////////////////////////
+// Insert Element after LAST of list (and return address of data element)
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+Typ* List<Typ>::Push(Typ d)
+{
+ ListEl<Typ>* t=new ListEl<Typ>(d,tail->prev,tail);
+ if (!t) { cerr<<"Could not create new element\n"; return 0; }
+ tail->prev->next=t;
+ tail->prev = t;
+ size++;
+ return &(t->data);
+}
+
+////////////////////////////////////////////////////////////////////////////
+// Remove and return LAST element of list. Returns head->data if empty
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+Typ List<Typ>::Pop()
+{
+ if (!size) return head->data;
+ ListEl<Typ>* t=tail->prev;
+ if (current==t) current=tail;
+ Typ d=t->data;
+ t->prev->next=tail;
+ tail->prev=t->prev;
+ delete t; t = NULL;
+ size--;
+ return d;
+}
+
+
+
+////////////////////////////////////////////////////////////////////////////
+// Methods that act at the beginning of the list
+
+////////////////////////////////////////////////////////////////////////////
+// Insert element as FIRST element of list (and return address of data element)
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+Typ* List<Typ>::Enqueue(Typ d)
+{
+ ListEl<Typ>* h = new ListEl<Typ>(d,head,head->next);
+ if (!h) { cerr<<"Could not create new element\n"; return 0; }
+ h->next->prev = h;
+ head->next=h;
+ size++;
+ return &(h->data);
+}
+
+////////////////////////////////////////////////////////////////////////////
+// Remove element at BEGINNING of list
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+Typ List<Typ>::Dequeue()
+{
+ if (!size) return head->data;
+ ListEl<Typ>* h=head->next;
+ if (current==h) current=head;
+ Typ d=h->data;
+ h->next->prev=head;
+ head->next=h->next;
+ delete h; h = NULL;
+ size--;
+ return d;
+}
+
+////////////////////////////////////////////////////////////////////////////
+// Methods that work with 'current' position in the list
+
+////////////////////////////////////////////////////////////////////////////
+// Reads next element; advances current position by 1
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+inline Typ List<Typ>::ReadNext()
+{
+ current = current->next;
+ return current->data;
+}
+
+////////////////////////////////////////////////////////////////////////////
+// Reads current element again (NULL if nothing read yet)
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+inline Typ List<Typ>::ReadCurrent()
+{
+ return current->data;
+}
+
+////////////////////////////////////////////////////////////////////////////
+// Reads previous element; moves current position back by 1
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+inline Typ List<Typ>::ReadPrevious()
+{
+ current = current->prev;
+ return current->data;
+}
+
+////////////////////////////////////////////////////////////////////////////
+// Reads next element; advances current position by 1
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+inline Typ* List<Typ>::ReadNextAddress()
+{
+ current = current->next;
+ if (current==tail) return NULL;
+ return &(current->data);
+}
+
+////////////////////////////////////////////////////////////////////////////
+// Reads address of current element again, returns NULL if at end of list
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+inline Typ* List<Typ>::ReadCurrentAddress()
+{
+ if (current==tail) return NULL;
+ return &(current->data);
+}
+
+////////////////////////////////////////////////////////////////////////////
+// Sets current position to k and reads k'th element (first=1)
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+Typ List<Typ>::Read(int pos)
+{
+ if (pos>size) {current = tail; return tail->data;}
+ if (pos<=0) {current = head; return head->data;}
+ current = head->next;
+ for (; pos>1; pos--) current = current->next; //If pos==2 do 1 iteration
+ return current->data;
+}
+
+////////////////////////////////////////////////////////////////////////////
+// Inserts element d AFTER current element and sets current element to inserted
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+void List<Typ>::Insert(Typ d)
+{
+ ListEl<Typ>* el = new ListEl<Typ>(d,current,current->next);
+ if (!el) { cerr<<"Could not create new element\n"; return; }
+ (current->next)->prev = el;
+ current->next = el;
+ current=el;
+ size++;
+}
+
+////////////////////////////////////////////////////////////////////////////
+// Deletes current element and returns content of deleted element. Current element
+// will be previous one after Delete(). After Reset() delete first element (not 0'th)
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+Typ List<Typ>::Delete()
+{
+ Typ d;
+ ListEl<Typ>* p;
+ if (!size || current==tail) return tail->data;
+ if (current==head) current = head->next; // After Reset() delete first element (not 0'th)
+ (current->prev)->next = current->next;
+ (current->next)->prev = current->prev;
+ d = current->data;
+ p = current->prev;
+ delete current; current = NULL;
+ current = p;
+ size--;
+ return d;
+}
+
+////////////////////////////////////////////////////////////////////////////
+// Methods that return useful information about the list
+
+////////////////////////////////////////////////////////////////////////////
+// Get current position within list (0 <= pos <= Size+1)
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+int List<Typ>::GetPos()
+{
+ int pos=0;
+ ListEl<Typ>* el;
+ for (el = head; el!=current; el=el->next) pos++;
+ return pos;
+}
+
+////////////////////////////////////////////////////////////////////////////
+//print out list
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+void List<Typ>::PrintList()
+{
+ int j=0;
+ ListEl<Typ>* c=current;
+ Reset();
+ printf("List: ");
+ while (!End())
+ {
+ j++;
+ cout<<j<<" "<<ReadNext()<<" ";
+ if (!(j%10)) cout<<"\n ";
+ }
+ cout<<"\n";
+ current=c;
+}
+
+////////////////////////////////////////////////////////////////////////////
+// Get largest data element
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+Typ List<Typ>::Largest()
+{
+ Typ* result= &((tail->prev)->data);
+ Reset();
+ while (!End())
+ {
+ if (*result<ReadNext()) result=ReadCurrentAddress();
+ }
+ return *result;
+}
+
+////////////////////////////////////////////////////////////////////////////
+// Get smallest data element
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+Typ List<Typ>::Smallest()
+{
+ Typ* result= &((tail->prev)->data);
+ Reset();
+ while (!End())
+ {
+ if (ReadNext()<*result) result=ReadCurrentAddress();
+ }
+ return *result;
+}
+
+/////////////////////////////////////////////////////////////////////////////
+// Methods that manipulate the list as a whole
+
+////////////////////////////////////////////////////////////////////////////
+// Copies list 0 into list object
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+void List<Typ>::Copy(List<Typ>* list)
+{
+ if (list==this) return;
+ while (!End()) Pop(); //empty list
+ list->Reset();
+ while (!list->End()) Push(list->ReadNext());
+}
+
+////////////////////////////////////////////////////////////////////////////
+// Appends a copy of list2 to class object
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+void List<Typ>::AppendCopy(List<Typ>* list2)
+{
+ List<Typ>* cpy=new List<Typ>;
+ cpy->Copy(list2);
+ Append(cpy);
+ delete cpy; cpy = NULL;
+}
+
+////////////////////////////////////////////////////////////////////////////
+// Appends list2 to class object
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+void List<Typ>::Append(List<Typ>* list)
+{
+ if (this==list) { AppendCopy(list); return;}
+ (tail->prev)->next = list->head->next;
+ (list->head->next)->prev = tail->prev;
+ if (current==tail) current=tail->prev;
+ ListEl<Typ>* t=tail;
+ tail = list->tail;
+ size += list->size;
+
+// Reuse old tail as new tail t for list2 and initialize pointers for empty list
+ list->tail=t;
+ list->head->next=t;
+ t->prev=list->head;
+ t->next=t;
+ list->head->prev=list->head;
+ t->data=list->head->data;
+ list->current=list->head;
+ list->size = 0;
+}
+
+////////////////////////////////////////////////////////////////////////////
+// Use QUICKSORT to sort list in ascending order between two list elements
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+void List<Typ>::SortList(ListEl<Typ>* left, ListEl<Typ>* right, int sz)
+{
+ if (sz<=1) return; // when SortList() is called, left=head->next, right=tail->prev
+ ListEl<Typ> *l=left->prev, *r=right->next;
+
+ // Choose *random* pivot element!!
+ // (Otherwise, complexity for an already sorted list is N^2 => recursive calls may lead to stack overflow)
+ ListEl<Typ> *c=left;
+ for (int i=1; i<(int)(float(rand())*sz/(RAND_MAX+0.999)); i++) c = c->next;
+ SwapContent(left,c);
+
+ Typ pivot = left->data;
+// Typ* pivot= &(left->data);
+ int sz0=sz+1;
+ // cout<<"Sorting between "<<left->data<<" and "<<right->data<<". Pivot="<<pivot<<endl;
+ while(1)
+ {
+// PrintList();
+ do {r=r->prev; sz0--;} while (pivot < r->data);
+ do l=l->next; while (l->data < pivot);
+ if (l==r || l->prev==r) break;
+ SwapContent(l,r);
+ }
+ SortList(left,r,sz0);
+ SortList(r->next,right,sz-sz0);
+ pivot = tail->data; // to avoid calling the destructor of Typ on some real data element
+ }
+
+////////////////////////////////////////////////////////////////////////////
+// Use QUICKSORT to sort list of POINTERS by comparing the objects the pointers point to
+////////////////////////////////////////////////////////////////////////////
+template <class Typ>
+void List<Typ>::SortPointerList(ListEl<Typ>* left, ListEl<Typ>* right)
+{
+ if (right==left || right->next==left) return;
+ ListEl<Typ> *l=left->prev, *r=right->next;
+ Typ pivot=left->data;
+// cout<<"Sorting between "<<left->data<<" and "<<right->data<<". Pivot="<<pivot<<endl;
+ while(1)
+ {
+// PrintList();
+ do
+ {
+ r=r->prev;
+// cout<<"r=r->prev. r->data="<<r->data<<endl;
+ } while(*pivot < *(r->data));
+ do
+ {
+ l=l->next;
+// cout<<"l=l->next l->data="<<l->data<<endl;
+ } while (*(l->data) < *pivot);
+ if (l==r || l->prev==r) break;
+ SwapContent(l,r);
+ }
+ SortPointerList(left,r);
+ SortPointerList(r->next,right);
+}
+
+// Use INSERTSORT to sort list in asscending order between two list elements. Use only for presorted lists, otherwise time O(N^2)!
+template <class Typ>
+void List<Typ>::ResortList()
+{
+ ListEl<Typ> *c; // current element to be sorted in. Everything to the left is already sorted
+ ListEl<Typ> *n; // next element to be sorted in
+ ListEl<Typ> *p; // pointer for looping through sorted part of list
+ ListEl<Typ> *pnext; // for swapping
+ if (Size()<=1) return;
+ c=head->next->next;
+ while (c!=tail)
+ {
+ p=c->prev;
+ n=c->next;
+ if (c->data < p->data)
+ {
+ do {p=p->prev;} while (p!=head && c->data < p->data);
+ // Connect c->prev to c->next ...
+ c->next->prev=c->prev;
+ c->prev->next=c->next;
+ // ... and insert c between p and p->next ...
+ pnext=p->next;
+ p->next=c;
+ c->next=pnext;
+ pnext->prev=c;
+ c->prev=p;
+ }
+ c=n;
+ }
+}
+
+
+#endif /* JLIST */
+
+
+// //Main program: test class List
+
+// int main()
+// {
+// int p;
+// List<int>* plist=new List<int>(11);
+// List<int> list(22);
+
+// plist->Push(24);
+// plist->Push(18);
+// plist->Push(3);
+// plist->Enqueue(17);
+// plist->Enqueue(29);
+// printf("List 1 with pushed and enqueued elements:\n");
+// plist->PrintList();
+
+// list.Push(222);
+// printf("List 1 with list 2 appended:\n");
+// plist->Append(&list);
+// plist->PrintList();
+
+// printf("Pushing one element three times into list 2:\n");
+// list.Push(333);
+// list.Push(444);
+// list.Push(555);
+// printf("Printing plist and list with three elements:\n");
+// list.PrintList();
+// plist->PrintList();
+
+// printf("list.Copy(plist). Printing list 1 and 2:\n");
+// list.Copy(plist);
+// plist->PrintList();
+// list.PrintList();
+
+// printf("Appending list 1 to itself:\n");
+// plist->Append(plist);
+// plist->PrintList();
+
+// cout<<"Popping "<<plist->Pop()<<"\n";
+// cout<<"Popping "<<plist->Pop()<<"\n";
+// plist->PrintList();
+
+// cout<<"Dequeing "<<plist->Dequeue()<<"\n";
+// cout<<"Dequeing "<<plist->Dequeue()<<"\n";
+// plist->PrintList();
+
+// cout<<"Reversing list\n";
+// plist->Reverse();
+// plist->PrintList();
+
+// cout<<"Reversing to original list\n";
+// plist->Reverse();
+// plist->PrintList();
+
+// for (p=plist->Reset(); p>=5;p--)
+// {cout<<plist->GetPos()<<": "<<plist->Read(p)<<"\n";}
+
+// cout<<"Deleting "<<plist->Delete()<<"\n";
+// cout<<"Deleting "<<plist->Delete()<<"\n";
+// plist->PrintList();
+
+// plist->Append(plist);
+// plist->PrintList();
+// cout<<"List 1 sorted:\n";
+// plist->SortList();
+// plist->PrintList();
+
+// }
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: list.h 143 2010-10-14 13:11:14Z andreas $
+ */
+
+// list.h
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Double-linked list implementation with head and tail dummy elements
+// We set head->prev=head and tail->next=tail.
+// This makes sure that repeated current=current->next; ends up in tail
+// and repeated current=current->prev; ends up in head.
+// head and tail optionally contain a NULL element of Typ defined by method Null(Typ)
+//////////////////////////////////////////////////////////////////////////////
+
+template<class Typ>
+class List
+{
+protected:
+template<class Typ1>
+class ListEl //elements of List; essentially a data structure
+ {
+ public:
+ Typ1 data; //Typ is type of data to be stored in list
+ ListEl* prev; //points to previous list element
+ ListEl* next; //points to next list element
+ ListEl() : prev(0), next(0) {}
+ ListEl(Typ1 d) : data(d), prev(0), next(0) {}
+ ListEl(ListEl* p, ListEl* n) : prev(p), next(n) {}
+ ListEl(Typ1 d, ListEl* p, ListEl* n) : data(d), prev(p), next(n) {}
+ };
+
+ ListEl<Typ>* head; //points to dummy element at beginning of list
+ ListEl<Typ>* tail; //points to dummy element at end of list
+ ListEl<Typ>* current; //current element position within list
+ int size; //Number of elements in list
+
+ // Use QUICKSORT to sort list in asscending order between two list elements
+ void SortList(ListEl<Typ>*, ListEl<Typ>*, int);
+ // Use QUICKSORT to sort list of pointers by comparing elements they point to
+ void SortPointerList(ListEl<Typ>*, ListEl<Typ>*);
+
+ // Swap two list elements by making a flat copy (don't need two copies of data)
+ // Warning: Gets slow if Typ is composite type with many variables (>=5)
+ void SwapContent(ListEl<Typ>* e1, ListEl<Typ>* e2)
+ { Typ d; if (e1!=e2) {d=e1->data; e1->data=e2->data; e2->data=d;} }
+
+public:
+//////////////////////////////////////////////////////////////////////////////
+// General methods
+ List();
+ List(Typ d);
+ ~List();
+ List<Typ>& operator=(List<Typ>&);
+
+ // Set Null element that will be returned when trying to read from an empty list
+ void Null(Typ null) {head->data = tail->data = null;}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Methods that act at the end of the list
+
+ // Insert Element after LAST element of list (and return address of data element)
+ Typ* Push(Typ);
+
+ // Remove and return LAST element of list. Returns head->data if list empty
+ Typ Pop();
+
+ // return LAST element of list. Returns null element in head->data if list empty
+ Typ ReadLast() {return tail->prev->data;}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Methods that act at the beginning of the list
+
+ // Insert element as FIRST element of list (and return address of data element)
+ Typ* Enqueue(Typ);
+
+ // Remove and return element at BEGINNING of list. Returns head->data if list empty
+ Typ Dequeue();
+
+ // return FIRST element of list. Returns null element in head->data if list empty
+ Typ ReadFirst() {if (size) return head->next->data; else return head->data;}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Methods that work with 'current' position in the list
+
+ // Advances current position by 1 and reads next element; returns head->data if at end of list.
+ Typ ReadNext();
+
+ // Reads current element again
+ Typ ReadCurrent();
+
+ // Moves current position back by 1 and reads previous element; returns head->data if at beginning of list.
+ Typ ReadPrevious();
+
+ // Advances current position by 1 and reads address of next element; returns NULL if at end of list.
+ Typ* ReadNextAddress();
+
+ // Reads address of current element again, returns NULL if at end of list
+ Typ* ReadCurrentAddress();
+
+ // Sets current position to k and reads k'th element (first=1). Returns head->data if current points to no data element
+ Typ Read(int);
+
+ // Inserts element AFTER CURRENT element; current element will be set to inserted element
+ void Insert(Typ);
+
+ // Removes and returns element at CURRENT position. New position is one BEFORE current position.
+ // Returns head->data if current points to no data element. After Reset() delete first element (not 0'th)
+ Typ Delete();
+
+ // Overwrites data at current position with new data
+ void Overwrite(Typ d) {current->data=d;}
+
+ // Reset current position to 0 (one BEFORE the first)
+ int Reset() {current = head; return size;}
+
+ // Reset current position to End (one AFTER the last)
+ int SetToEnd() {current = tail; return size;}
+
+
+//////////////////////////////////////////////////////////////////////////////
+// Methods that return information about the list
+
+ // Return number of list elements (size>=0)
+ int Size() {return size;}
+
+ // return true if end of list, i.e. ReadNext would give tail->data (i.e. current position >= Size)
+ char End() {return (current==tail || current==tail->prev);}
+ char End(void* curr) {return ( curr == tail || curr == tail->prev);}
+
+ // return true if start of list, i.e. ReadPrevious would give head->data (i.e. current position <=1)
+ char Start() {return (current==head || current==head->next);}
+
+ // Get current position within list (0 <= pos <= Size+1)
+ int GetPos();
+
+ //print out list (elements assumed int)
+ void PrintList();
+
+ // Get largest data element (Null element for empty list)
+ Typ Largest();
+
+ // Get smallest data element (Null element for empty list)
+ Typ Smallest();
+
+//////////////////////////////////////////////////////////////////////////////
+// Methods that manipulate the list as a whole
+
+ // Reverse list
+ void Reverse();
+
+ // Copies list into list object
+ void Copy(List<Typ>* list);
+
+ // Appends a copy of list to class object
+ void AppendCopy(List<Typ>* list);
+
+ // Appends list to class object list
+ void Append(List<Typ>* list);
+
+ // Use QUICKSORT to sort list in ascending order. Use only for UNSORTED lists, otherwise time O(N^2) instead of O(N*log(N))
+/* void SortList() {if (size>1) SortList(head->next, tail->prev);} */
+ void SortList() {if (size>1) SortList(head->next, tail->prev, size);}
+ void QuickSort() {if (size>1) SortList(head->next, tail->prev, size);}
+
+ // Use QUICKSORT to sort list of pointers in ascending order. Use only for UNSORTED lists, otherwwise time O(N^2)!
+ void SortPointerList() {if (size>1) SortPointerList(head->next, tail->prev);}
+ void QuickSortPointer() {if (size>1) SortPointerList(head->next, tail->prev);}
+
+ // Use INSERTSORT to sort list in asscending order. Use only for PRESORTED lists, otherwise time O(N^2)!
+ void ResortList();
+};
+
+
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: util-C.h 155 2010-11-17 12:18:47Z fabian $
+ */
+
+// Utility subroutines
+
+
+#ifndef MAIN
+#include <iostream> // cin, cout, cerr
+#include <fstream> // ofstream, ifstream
+#include <cstdio> // printf
+#include <stdlib.h> // exit
+#include <time.h> // clock
+#endif
+#include <sys/time.h>
+
+/////////////////////////////////////////////////////////////////////////////////////
+// Arithmetics
+/////////////////////////////////////////////////////////////////////////////////////
+
+//// max and min
+inline double dmax(double x, double y) { return (x>y? x : y);}
+inline double dmin(double x, double y) { return (x<y? x : y);}
+inline int imax(int x, int y) { return (x>y? x : y);}
+inline int imin(int x, int y) { return (x<y? x : y);}
+inline int iabs(int x) { return (x>=0? x : -x);}
+
+// Rounding up, rounding down and rounding to nearest integer
+inline int iceil(double x) {return int(ceil(x));}
+inline int ifloor(double x) {return int(floor(x));}
+inline int iround(double x) {return int(floor(x+0.5));}
+
+//// Generalized mean: d=0: sqrt(x*y) d=1: (x+y)/2 d->-inf: min(x,y) d->+inf: max(x,y)
+inline double fmean(double x, double y, double d) { return pow( (pow(x,d)+pow(y,d))/2 ,1./d);}
+
+// log base 2
+inline float log2(float x) {return (x<=0? (float)(-100000):1.442695041*log(x));}
+inline float log10(float x) {return (x<=0? (float)(-100000):0.434294481*log(x));}
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+// fast log base 2
+/////////////////////////////////////////////////////////////////////////////////////
+
+// This function returns log2 with a max abolute deviation of +/- 1.5E-5 (typically 0.8E-5).
+// It takes 1.42E-8 s whereas log2(x) takes 9.5E-7 s. It is hence 9.4 times faster.
+// It makes use of the representation of 4-byte floating point numbers:
+// seee eeee emmm mmmm mmmm mmmm mmmm mmmm
+// s is the sign,
+// the following 8 bits, eee eee e, give the exponent + 127 (in hex: 0x7f).
+// The following 23 bits, m, give the mantisse, the binary digits behind the decimal point.
+// In summary: x = (-1)^s * 1.mmmmmmmmmmmmmmmmmmmmmm * 2^(eeeeeee-127)
+// The expression (((*(int *)&x) & 0x7f800000 ) >>23 )-0x7f is the exponent eeeeeeee, i.e.
+// the largest integer that is smaller than log2(x) (e.g. -1 for 0.9). *(int *)&x is an integer which
+// contains the bytes as the floating point variable x is represented in memory.
+// Check: assert( sizeof(f) == sizeof(int) );
+// Check: assert( sizeof(f) == 4 );
+inline float fast_log2(float x)
+{
+ static float lg2[1025]; // lg2[i] = log2[1+x/1024]
+ static float diff[1025]; // diff[i]= (lg2[i+1]-lg2[i])/8096 (for interpolation)
+ static char initialized;
+ if (x<=0) return -100000;
+ if (!initialized) //First fill in the arrays lg2[i] and diff[i]
+ {
+ float prev = 0.0f;
+ lg2[0] = 0.0f;
+ for (int i=1; i<=1024; ++i)
+ {
+ lg2[i] = log(float(1024+i))*1.442695041-10.0f;
+ diff[i-1] = (lg2[i]-prev)*1.2352E-4;
+ prev = lg2[i];
+ }
+ initialized=1;
+ }
+ int a = (((*((int *)&x)) & 0x7F800000) >>23 )-0x7f;
+ int b = ((*((int *)&x)) & 0x007FE000) >>13;
+ int c = ((*((int *)&x)) & 0x00001FFF);
+ return a + lg2[b] + diff[b]*(float)(c);
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+// fast 2^x
+// ATTENTION: need to compile with g++ -fno-strict-aliasing when using -O2 or -O3!!!
+// Relative deviation < 1.5E-4
+/////////////////////////////////////////////////////////////////////////////////////
+inline float fpow2(float x)
+{
+ if (x>=128) return FLT_MAX;
+ if (x<=-128) return FLT_MIN;
+ int *px = (int*)(&x); // store address of float as pointer to long
+ float tx = (x-0.5f) + (3<<22); // temporary value for truncation: x-0.5 is added to a large integer (3<<22)
+ int lx = *((int*)&tx) - 0x4b400000; // integer value of x
+ float dx = x-(float)(lx); // float remainder of x
+ x = 1.0f + dx*(0.6960656421638072f // cubic apporoximation of 2^x
+ + dx*(0.224494337302845f // for x in the range [0, 1]
+ + dx*(0.07944023841053369f)));
+ *px += (lx<<23); // add integer power of 2 to exponent
+ return x;
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+// ATTENTION:
+// Can't be used with -O2/-O3 optimization on some compilers !
+// Works with g++ version 4.1, but not with 3.4, in which case it returns values
+// that are a factor 1.002179942 too low
+//
+// Fast pow2 routine (Johannes Soeding)
+// Same speed as fpow2(), but *relative* deviation < 1.2E-7
+// Makes use of the binary representation of floats in memory:
+// x = (-1)^s * 1.mmmmmmmmmmmmmmmmmmmmmm * 2^(eeeeeee-127)
+// is represented as
+// 31 23 7654 3210
+// seee eeee emmm mmmm mmmm mmmm mmmm mmmm
+// s is the sign, the 8 bits eee eee e are the exponent + 127 (in hex: 0x7f),
+// and the following 23 bits m give the mantisse.
+// We decompose the argument x = a + b, with integer a and 0 <= b < 1
+// Therefore 2^x = 2^a * 2^b where a is the binary exponent of 2^x
+// and 1 <= 2^b < 2, i.e. 2^b determines the mantisse uniquely.
+// To calculate 2^b, we split b into the first 10 bits and the last 13 bits,
+// b = b' + c, and then look up the mantisse of 2^b' in a precomputed table.
+// We use the residual c to interpolate between the mantisse for 2^b' and 2(b'+1/1024)
+/////////////////////////////////////////////////////////////////////////////////////
+inline float fast_pow2(float x)
+{
+ if (x<=-127) return 5.9E-39;
+ if (x>=128) return 3.4E38;
+ static char initialized=0;
+ static unsigned int pow2[1025];
+ static unsigned int diff[1025];
+ static int y = 0;
+ if (!initialized) //First fill in the pow2-vector
+ {
+ float f;
+ unsigned int prev = 0;
+ pow2[0] = 0;
+ for (int b=1; b<1024; b++)
+ {
+ f=pow(2.0,float(b)/1024.0);
+ pow2[b]=(*((unsigned int *)(&f)) & 0x7FFFFF); // store the mantisse of 2^(1+b/1024)
+ diff[b-1]=pow2[b]-prev;
+ prev=pow2[b];
+ }
+ pow2[1024]=0x7FFFFF;
+ diff[1023]=pow2[1024]-prev;
+ initialized=1;
+ }
+
+ int *px = (int *)(&x); // store address of float as pointer to int
+ int E = ((*px & 0x7F800000)>>23)-127; // E is exponent of x and is <=6
+ unsigned int M=(*px & 0x007FFFFF) | 0x00800000; // M is the mantisse 1.mmm mmmm mmmm mmmm mmmm mmmm
+ int a,b,c;
+ if (x>=0)
+ {
+ if (E>=0) {
+ a = 0x3F800000 + ((M<<E) & 0x7F800000); // a is exponent of 2^x, beginning at bit 23
+ b = ((M<<E) & 0x007FE000)>>13;
+ c = ((M<<E) & 0x00001FFF);
+ } else {
+ a = 0x3F800000; // a = exponent of 2^x = 0
+ b = ((M>>(-E)) & 0x007FE000)>>13;
+ c = ((M>>(-E)) & 0x00001FFF);
+ }
+ }
+ else
+ {
+ if (E>=0) {
+ a = 0x3F000000 - ((M<<E) & 0x7F800000); // a is exponent of 2^x
+ b = (0x00800000-(int)((M<<E) & 0x007FFFFF)) >>13;
+ c = (0x00800000-(int)((M<<E) & 0x007FFFFF)) & 0x00001FFF;
+ } else {
+ a = 0x3F000000; // a = exponent of 2^x = -1
+ b = (0x00800000-(int)((M>>(-E)) & 0x007FFFFF)) >>13;
+ c = (0x00800000-(int)((M>>(-E)) & 0x007FFFFF)) & 0x00001FFF;
+ }
+ }
+/* printf("x=%0X\n",*px); */
+/* printf("E=%0X\n",E); */
+/* printf("M=%0X\n",M); */
+/* printf("a=%0X\n",a); */
+/* printf("b=%0X\n",b); */
+ y = a | (pow2[b] + ((diff[b]*c)>>13) );
+ /* printf("2^x=%0X\n",*px); */
+ return *((float*)&y);
+}
+
+
+
+// Normalize a float array such that it sums to one
+// If it sums to 0 then assign def_array elements to array (optional)
+inline float NormalizeTo1(float* array, int length, float* def_array=NULL)
+{
+ float sum=0.0f;
+ int k;
+ for (k=0; k<length; k++) sum+=array[k];
+ if (sum!=0.0f)
+ {
+ float fac=1.0/sum;
+ for (k=0; k<length; k++) array[k]*=fac;
+ }
+ else if (def_array)
+ for (k=0; k<length; k++) array[k]=def_array[k];
+ return sum;
+}
+
+// Normalize a float array such that it sums to x
+// If it sums to 0 then assign def_array elements to array (optional)
+inline float NormalizeToX(float* array, int length, float x, float* def_array=NULL)
+{
+ float sum=0.0;
+ int k;
+ for (k=0; k<length; k++) sum+=array[k];
+ if (sum)
+ {
+ float fac=x/sum;
+ for (k=0; k<length; k++) array[k]*=fac;
+ }
+ else if (def_array)
+ for (k=0; k<length; k++) array[k]=def_array[k];
+ return sum;
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+// Similar to spintf("%*g,w,val), but displays maximum number of digits within width w
+/////////////////////////////////////////////////////////////////////////////////////
+inline char* sprintg(float val, int w)
+{
+ static char str[100];
+ float log10val = log10(fabs(val));
+ int neg = (val<0? 1: 0);
+ if (log10val >= w-neg-1 || -log10val > 3)
+ {
+ // positive exponential 1.234E+06
+ // negative exponential 1.234E-06
+ int d = w-6-neg;
+ sprintf(str,"%*.*e",w,d<1?1:d,val);
+ }
+ else
+ {
+ int d = log10val>0? w-2-neg-int(log10val): w-2-neg;
+ sprintf(str,"%#*.*f",w,d,val);
+ }
+ return str;
+}
+
+/////////////////////////////////////////////////////////////////////////////////////
+// String utilities
+/////////////////////////////////////////////////////////////////////////////////////
+
+//the integer. If no integer is found, returns INT_MIN and sets ptr to NULL /* MR1 */
+inline int strtoi(const char*& ptr)
+{
+ int i;
+ const char* ptr0=ptr;
+ if (!ptr) return INT_MIN;
+ while (*ptr!='\0' && !(*ptr>='0' && *ptr<='9')) ptr++;
+ if (*ptr=='\0') {
+ ptr=0;
+ return INT_MIN;
+ }
+ if (*(ptr-1)=='-' && ptr>ptr0) i=-atoi(ptr); else i=atoi(ptr);
+ while (*ptr>='0' && *ptr<='9') ptr++;
+ return i;
+}
+
+
+//Same as strint, but interpretes '*' as default /* MR1 */
+inline int strtoi_(const char*& ptr, int deflt=INT_MAX)
+{
+ int i;
+ if (!ptr) return INT_MIN;
+ while (*ptr!='\0' && !(*ptr>='0' && *ptr<='9') && *ptr!='*') ptr++;
+ if (*ptr=='\0') {
+ ptr=0;
+ return INT_MIN;
+ }
+ if (*ptr=='*') {
+ ptr++;
+ return deflt;
+ }
+ if (*(ptr-1)=='-') i=atoi(ptr-1);
+ else i=atoi(ptr);
+ while (*ptr>='0' && *ptr<='9') ptr++;
+ return i;
+}
+
+
+// Returns leftmost integer in ptr and sets the pointer to first char after
+// the integer. If no integer is found, returns INT_MIN and sets pt to NULL
+int strint(char*& ptr)
+{
+ int i;
+ char* ptr0=ptr;
+ if (!ptr) return INT_MIN;
+ while (*ptr!='\0' && !(*ptr>='0' && *ptr<='9')) ptr++;
+ if (*ptr=='\0')
+ {
+ ptr=0;
+ return INT_MIN;
+ }
+ if (*(ptr-1)=='-' && ptr>ptr0) i=-atoi(ptr); else i=atoi(ptr);
+ while (*ptr>='0' && *ptr<='9') ptr++;
+ return i;
+}
+
+// Same as strint, but interpretes '*' as default
+int strinta(char*& ptr, int deflt=99999)
+{
+ int i;
+ if (!ptr) return INT_MIN;
+ while (*ptr!='\0' && !(*ptr>='0' && *ptr<='9') && *ptr!='*') ptr++;
+ if (*ptr=='\0')
+ {
+ ptr=0;
+ return INT_MIN;
+ }
+ if (*ptr=='*')
+ {
+ ptr++;
+ return deflt;
+ }
+ if (*(ptr-1)=='-') i=atoi(ptr-1);
+ else i=atoi(ptr);
+ while (*ptr>='0' && *ptr<='9') ptr++;
+ return i;
+}
+
+// Returns leftmost float in ptr and sets the pointer to first char after
+// the float. If no float is found, returns FLT_MIN and sets pt to NULL /* MR1 */
+float strflt(char*& ptr)
+{
+ float i;
+ char* ptr0=ptr;
+ if (!ptr) return FLT_MIN;
+ while (*ptr!='\0' && !(*ptr>='0' && *ptr<='9')) ptr++;
+ if (*ptr=='\0')
+ {
+ ptr=0;
+ return FLT_MIN;
+ }
+ if (ptr>ptr0 && *(ptr-1)=='-') i=-atof(ptr); else i=atof(ptr);
+ while ((*ptr>='0' && *ptr<='9') || *ptr=='.') ptr++;
+ return i;
+}
+
+// Same as strint, but interpretes '*' as default /* MR1 */
+float strflta(char*& ptr, float deflt=99999)
+{
+ float i;
+ if (!ptr) return FLT_MIN;
+ while (*ptr!='\0' && !(*ptr>='0' && *ptr<='9') && *ptr!='*') ptr++;
+ if (*ptr=='\0')
+ {
+ ptr=0;
+ return FLT_MIN;
+ }
+ if (*ptr=='*')
+ {
+ ptr++;
+ return deflt;
+ }
+ if (*(ptr-1)=='-') i=-atof(ptr);
+ else i=atof(ptr);
+ while ((*ptr>='0' && *ptr<='9') || *ptr=='.') ptr++;
+ return i;
+}
+
+
+// Removes the newline and other control characters at the end of a string (if present)
+// and returns the new length of the string (-1 if str is NULL)
+inline int chomp(char str[])
+{
+ if (!str) return -1;
+ int l=0;
+ for (l=strlen(str)-1; l>=0 && str[l]<32; l--);
+ str[++l]='\0';
+ return l;
+}
+
+// Emulates the ifstream::getline method; similar to fgets(str,maxlen,FILE*),
+// but removes the newline at the end and returns NULL if at end of file or read error
+inline char* fgetline(char str[], const int maxlen, FILE* file)
+{
+ if (!fgets(str,maxlen,file)) return NULL;
+ if (chomp(str)+1>=maxlen) // if line is cut after maxlen characters...
+ while (fgetc(file)!='\n'); // ... read in rest of line
+ return(str);
+}
+
+// copies substring str[a,b] into substr and returns substr
+char *substr(char* substr, char* str, int a, int b)
+{
+ if (b<a) {int i=b; b=a; a=i;}
+ if (b-a>1000)
+ {printf("Function substr: >1000 chars to copy. Exiting.\n"); exit(6);}
+ char* dest=substr;
+ char* source=str+a;
+ char* send=str+b;
+ while (*source!='\0' && source<=send) *(dest++) = *(source++);
+ *dest='\0';
+ return substr;
+}
+
+
+// Returns pointer to first non-white-space character in str OR to NULL if none found
+inline char* strscn(char* str)
+{
+ if (!str) return NULL;
+ char* ptr=str;
+ while (*ptr!='\0' && *ptr<=32) ptr++;
+ return (*ptr=='\0')? NULL: ptr;
+}
+
+// Returns pointer to first white-space character in str OR to NULL if none found /* MR1 */
+inline char* strscn_ws(char* str)
+{
+ if (!str) return NULL;
+ char* ptr=str;
+ while (*ptr!='\0' && *ptr>32) ptr++;
+ return (*ptr=='\0')? NULL: ptr;
+}
+
+//Returns pointer to first non-white-space character in str OR to NULL if none found /* MR1 */
+inline const char* strscn_c(const char* str)
+{
+ if (!str) return NULL;
+ const char* ptr=str;
+ while (*ptr!='\0' && isspace(*ptr)) ptr++;
+ return (*ptr=='\0') ? NULL : ptr;
+}
+
+// Returns pointer to first non-white-space character in str OR to end of string '\0' if none found
+inline char* strscn_(char* str)
+{
+ if (!str) return NULL;
+ char* ptr=str;
+ while (*ptr!='\0' && *ptr<=32) ptr++;
+ return ptr;
+}
+
+// Returns pointer to first non-c character in str OR to NULL if none found
+inline char* strscn(char* str, const char c)
+{
+ if (!str) return NULL;
+ char* ptr=str;
+ while (*ptr!='\0' && *ptr==c) ptr++;
+ return (*ptr=='\0')? NULL: ptr;
+}
+
+// Returns pointer to first non-c character in str OR to end of string '\0' if none found
+inline char* strscn_(char* str, const char c)
+{
+ if (!str) return NULL;
+ char* ptr=str;
+ while (*ptr!='\0' && *ptr==c) ptr++;
+ return ptr;
+}
+
+// Cuts string at first white space character found by overwriting it with '\0'.
+// Returns pointer to next non-white-space char OR to NULL if no such char found
+inline char* strcut(char* str)
+{
+ if (!str) return NULL;
+ char* ptr=str;
+ while (*ptr!='\0' && *ptr>32) ptr++;
+ if (*ptr=='\0') return NULL;
+ *ptr='\0';
+ ptr++;
+ while (*ptr!='\0' && *ptr<=32) ptr++;
+ return (*ptr=='\0')? NULL:ptr;
+}
+
+// Cuts string at first white space character found by overwriting it with '\0'.
+// Returns pointer to next non-white-space char OR to end of string '\0' if none found
+inline char* strcut_(char* str)
+{
+ if (!str) return NULL;
+ char* ptr=str;
+ while (*ptr!='\0' && *ptr>32) ptr++;
+ if (*ptr=='\0') return ptr;
+ *ptr='\0';
+ ptr++;
+ while (*ptr!='\0' && *ptr<=32) ptr++;
+ return ptr;
+}
+
+// Cuts string at first occurence of charcter c, by overwriting it with '\0'.
+// Returns pointer to next char not equal c, OR to NULL if none found
+inline char* strcut(char* str, const char c)
+{
+ if (!str) return NULL;
+ char* ptr=str;
+ while (*ptr!='\0' && *ptr!=c) ptr++;
+ if (*ptr=='\0') return NULL;
+ *ptr='\0';
+ ptr++;
+ while (*ptr!='\0' && *ptr==c) ptr++;
+ return (*ptr=='\0')? NULL:ptr;
+}
+
+// Cuts string at first occurence of charcter c, by overwriting it with '\0'.
+// Returns pointer to next char not equal c, OR to end of string '\0' if none found
+inline char* strcut_(char* str, const char c)
+{
+ if (!str) return NULL;
+ char* ptr=str;
+ while (*ptr!='\0' && *ptr!=c) ptr++;
+ if (*ptr=='\0') return ptr;
+ *ptr='\0';
+ ptr++;
+ while (*ptr!='\0' && *ptr==c) ptr++;
+ return ptr;
+}
+
+// Cuts string at first occurence of substr, by overwriting the first letter with '\0'.
+// Returns pointer to next char after occurence of substr, OR to NULL if no such char found
+inline char* strcut(char* str, const char* substr)
+{
+ char* ptr; //present location in str being compared to substr
+ const char* sptr=substr; //present location in substr being compared to substr
+ // while not at end of str and not all of substr is matched yet
+ while (1)
+ {
+ for (ptr=str, sptr=substr; *ptr==*sptr && *ptr!='\0'; ptr++, sptr++) ;
+ if (*sptr=='\0') {*str='\0'; return ptr;}
+ if (*ptr=='\0') return NULL;
+ str++;
+ }
+}
+
+// Cuts string at first occurence of substr, by overwriting the first letter with '\0'.
+// Returns pointer to next char after occurence of substr, OR to end of string '\0' if no such char found
+inline char* strcut_(char* str, const char* substr)
+{
+ char* ptr; //present location in str being compared to substr
+ const char* sptr=substr; //present location in substr being compared to str
+ // while not at end of str and not all of substr is matched yet
+ while (1)
+ {
+ for (ptr=str, sptr=substr; *ptr==*sptr && *ptr!='\0'; ptr++, sptr++) ;
+ if (*sptr=='\0') {*str='\0'; return ptr;}
+ if (*ptr=='\0') return ptr;
+ str++;
+ }
+}
+
+// Copies first word in ptr to str. In other words, copies first block of non whitespace characters,
+// beginning at ptr, to str. If a word is found, returns address of second word in ptr or, if no second
+// word is found, returns address to end of word ('\0' character) in ptr string. If no word is found
+// in ptr NULL is returned.
+inline char* strwrd(char* str, char* ptr)
+{
+ ptr=strscn(ptr); // advance to beginning of next word
+ if (ptr)
+ {
+ while (*ptr!='\0' && *ptr>32) *(str++) = *(ptr++);
+ *str='\0';
+ while (*ptr!='\0' && *ptr<=32) ptr++;
+ return ptr;
+ }
+ else return NULL;
+}
+
+// Copies first word ***delimited by char c*** in ptr to str. In other words, copies first block of non-c characters,
+// beginning at ptr, to str. If a word is found, returns address of second word in ptr or, if no second
+// word is found, returns address to end of word ('\0' character) in ptr string. If no word is found
+// in ptr NULL is returned.
+inline char* strwrd(char* str, char* ptr, const char c)
+{
+ ptr=strscn(ptr,c); // advance to beginning of next word
+ if (ptr)
+ {
+ while (*ptr!='\0' && *ptr!=c) *(str++) = *(ptr++);
+ *str='\0';
+ while (*ptr!='\0' && *ptr==c) ptr++;
+ return ptr;
+ }
+ else return NULL;
+}
+
+// Similar to Perl's tr/abc/ABC/: Replaces all chars in str found in one list with characters from the second list
+// Returns the number of replaced charactrs
+int strtr(char* str, const char oldchars[], const char newchars[])
+{
+ char* ptr;
+ const char *plist;
+ int ntr=0;
+ for (ptr=str; *ptr!='\0'; ptr++)
+ for (plist=oldchars; *plist!='\0'; plist++)
+ if (*ptr==*plist)
+ {
+ *ptr=newchars[plist-oldchars];
+ ntr++;
+ break;
+ }
+ return ntr;
+}
+
+// Similar to Perl's tr/abc//d: deletes all chars in str found in the list
+// Returns number of removed characters
+int strtrd(char* str, const char chars[])
+{
+ char* ptr0=str;
+ char* ptr1=str;
+ const char *plist;
+ while (*ptr1!='\0')
+ {
+ for (plist=chars; *plist!='\0'; plist++)
+ if (*ptr1==*plist) break;
+ if (*plist=='\0') {*ptr0=*ptr1; ptr0++;}
+ ptr1++;
+ }
+ return ptr1-ptr0;
+}
+
+// Similar to Perl's tr/a-z//d: deletes all chars in str found in the list
+// Returns number of removed characters
+int strtrd(char* str, char char1, char char2)
+{
+ char* ptr0=str;
+ char* ptr1=str;
+ while (*ptr1!='\0')
+ {
+ if (*ptr1>=char1 && *ptr1<=char2) {*ptr0=*ptr1; ptr0++;}
+ ptr1++;
+ }
+ return ptr1-ptr0;
+}
+
+// transforms str into an all uppercase string
+char* uprstr(char* str)
+{
+ char* s=str;
+ while (*s !='\0') {if (*s>='a' && *s<='z') *s+='A'-'a';s++;}
+ return(str);
+}
+
+// transforms str into an all uppercase string
+char* lwrstr(char* str)
+{
+ char* s=str;
+ while (*s !='\0') {if (*s>='A' && *s<='Z') *s+='a'-'A'; s++;}
+ return(str);
+}
+
+// transforms chr into an uppercase character
+inline char uprchr(char chr)
+{
+ return (chr>='a' && chr<='z')? chr+'A'-'a' : chr;
+}
+
+// transforms chr into an lowercase character
+inline char lwrchr(char chr)
+{
+ return (chr>='A' && chr<='Z')? chr-'A'+'a' : chr;
+}
+
+
+// Replaces first occurence of str1 by str2 in str. Returns pointer to first occurence or NULL if not found
+// ATTENTION: if str2 is longer than str1, allocated memory of str must be long enough!!
+inline char* strsubst(char* str, const char str1[], const char str2[])
+{
+ char* ptr = strstr(str,str1);
+ strcpy(ptr,str2);
+ return ptr;
+}
+
+// Gives elapsed time since first call to this function
+inline void ElapsedTimeSinceFirstCall(const char str[])
+{
+ timeval t;
+ static double tfirst=0;
+ if (tfirst==0)
+ {
+ gettimeofday(&t, NULL);
+ tfirst = 1E-6*t.tv_usec + t.tv_sec;
+ }
+ gettimeofday(&t, NULL);
+ printf("Elapsed time since first call:%12.3fs %s\n",1E-6*t.tv_usec + t.tv_sec - tfirst,str);
+}
+
+// Gives elapsed time since last call to this function
+inline void ElapsedTimeSinceLastCall(const char str[])
+{
+ timeval t;
+ static double tlast=0.0;
+ if (tlast==0.0)
+ {
+ gettimeofday(&t, NULL);
+ tlast = 1.0E-6*t.tv_usec + t.tv_sec;
+ }
+ gettimeofday(&t, NULL);
+ printf("Elapsed time since last call:%12.3fs %s\n",1.0E-6*t.tv_usec + t.tv_sec - tlast,str);
+ tlast = 1.0E-6*t.tv_usec + t.tv_sec;
+}
+
+inline char* RemovePath(char outname[], char filename[])
+{
+ char* ptr;
+#ifdef WINDOWS
+ ptr=strrchr(filename,92); //return adress for LAST \ (backslash) in name
+#else
+ ptr=strrchr(filename,'/'); //return adress for LAST / in name
+#endif
+ if (!ptr) ptr=filename; else ptr++;
+ strcpy(outname,ptr);
+ return outname;
+}
+
+inline char* RemoveExtension(char outname[], char filename[])
+{
+ char *ptr1;
+ ptr1=strrchr(filename,'.'); //return adress for LAST '.' in name
+ if (ptr1) {*ptr1='\0'; strcpy(outname,filename); *ptr1='.';} else strcpy(outname,filename);
+ return outname;
+}
+
+inline char* RemovePathAndExtension(char outname[], char filename[])
+{
+ char *ptr, *ptr1;
+#ifdef WINDOWS
+ ptr=strrchr(filename,92); //return adress for LAST \ (backslash) in name
+#else
+ ptr=strrchr(filename,'/'); //return adress for LAST / in name
+#endif
+ if (!ptr) ptr=filename; else ptr++;
+ ptr1=strrchr(filename,'.'); //return adress for LAST '.' in name
+ if (ptr1) {*ptr1='\0'; strcpy(outname,ptr); *ptr1='.';} else strcpy(outname,ptr);
+ return outname;
+}
+
+inline char* Extension(char extension[], char filename[])
+{
+ char* ptr;
+ ptr=strrchr(filename,'.'); //return adress for LAST '.' in name
+ if (ptr) strcpy(extension,ptr+1); else *extension='\0';
+ return extension;
+}
+
+// Path includes last '/'
+inline char* Pathname(char pathname[], char filename[])
+{
+ char* ptr;
+ char chr;
+#ifdef WINDOWS
+ ptr=strrchr(filename,92); //return adress for LAST \ (backslash) in name
+#else
+ ptr=strrchr(filename,'/'); //return adress for LAST / in name
+#endif
+ if (ptr) {chr=*(++ptr); *ptr='\0'; strcpy(pathname,filename); *ptr=chr;} else *pathname='\0';
+ return pathname;
+}
+
+// Swaps two integer elements in array k
+inline void swapi(int k[], int i, int j)
+{
+ int temp;
+ temp=k[i]; k[i]=k[j]; k[j]=temp;
+}
+
+// QSort sorting routine. time complexity of O(N ln(N)) on average
+// Sorts the index array k between elements i='left' and i='right' in such a way that afterwards
+// v[k[i]] is sorted downwards (up=-1) or upwards (up=+1)
+void QSortInt(int v[], int k[], int left, int right, int up=+1)
+{
+ int i;
+ int last; // last element to have been swapped
+
+ if (left>=right) return; // do nothing if less then 2 elements to sort
+ // Put pivot element in the middle of the sort range to the side (to position 'left') ...
+ swapi(k,left,(left+right)/2);
+ last=left;
+ // ... and swap all elements i SMALLER than the pivot
+ // with an element that is LARGER than the pivot (element last+1):
+ if (up==1)
+ {
+ for (i=left+1; i<=right; i++)
+ if (v[k[i]]<v[k[left]]) swapi(k,++last,i);
+ }
+ else
+ for (i=left+1; i<=right; i++)
+ if (v[k[i]]>v[k[left]]) swapi(k,++last,i);
+
+ // Put the pivot to the right of the elements which are SMALLER, left to elements which are LARGER
+ swapi(k,left,last);
+
+ // Sort the elements left from the pivot and right from the pivot
+ QSortInt(v,k,left,last-1,up);
+ QSortInt(v,k,last+1,right,up);
+}
+
+// QSort sorting routine. time complexity of O(N ln(N)) on average
+// Sorts the index array k between elements i='left' and i='right' in such a way that afterwards
+// v[k[i]] is sorted downwards (up=-1) or upwards (up=+1)
+void QSortFloat(float v[], int k[], int left, int right, int up=+1)
+{
+ int i;
+ int last; // last element to have been swapped
+ void swapi(int k[], int i, int j);
+
+ if (left>=right) return; // do nothing if less then 2 elements to sort
+ // Put pivot element in the middle of the sort range to the side (to position 'left') ...
+ swapi(k,left,(left+right)/2);
+ last=left;
+ // ... and swap all elements i SMALLER than the pivot
+ // with an element that is LARGER than the pivot (element last+1):
+ if (up==1)
+ {
+ for (i=left+1; i<=right; i++)
+ if (v[k[i]]<v[k[left]]) swapi(k,++last,i);
+ }
+ else
+ for (i=left+1; i<=right; i++)
+ if (v[k[i]]>v[k[left]]) swapi(k,++last,i);
+
+ // Put the pivot to the right of the elements which are SMALLER, left to elements which are LARGER
+ swapi(k,left,last);
+
+ // Sort the elements left from the pivot and right from the pivot
+ QSortFloat(v,k,left,last-1,up);
+ QSortFloat(v,k,last+1,right,up);
+}
+
+/**
+ * @brief comparison function for qsort,
+ * sorts floating point numbers ascendingly
+ *
+ * @param cv1 ponter to 1st entry to be sorted
+ * @param cv2 ponter to 2nd entry to be sorted
+ *
+ * @return 0 if entries are equal,
+ * +/-1 if 1st greater/smaller than 2nd
+ */
+int CompFltAsc(const void *cv1, const void *cv2){
+
+ float f1 = *(float *)cv1;
+ float f2 = *(float *)cv2;
+
+ if (f1 > f2) { return +1; }
+ else if (f1 < f2) { return -1; }
+ else { return 0; }
+
+} /* this is the end of CompFltAsc() */
+
+//Return random number in the range [0,1]
+inline float frand() { return rand()/(RAND_MAX+1.0); }
+
+
+/////////////////////////////////////////////////////////////////////////////////////
+//// Execute system command
+/////////////////////////////////////////////////////////////////////////////////////
+void runSystem(std::string cmd, int v = 2)
+{
+ if (v>2)
+ cout << "Command: " << cmd << "!\n";
+ int res = system(cmd.c_str());
+ if (res!=0)
+ {
+ cerr << endl << "ERROR when executing: " << cmd << "!\n";
+ exit(1);
+ }
+
+}
--- /dev/null
+// See KMeans.h\r
+//\r
+// Author: David Arthur (darthur@gmail.com), 2009\r
+\r
+// Includes\r
+\r
+#ifdef CLUSTALO\r
+/* previously in KMeans.h */\r
+#include "KmUtils.h"\r
+#include <iostream>\r
+#include <stdio.h>\r
+\r
+// Sets preferences for how much logging is done and where it is outputted, when k-means is run.\r
+void ClearKMeansLogging();\r
+void AddKMeansLogging(std::ostream *out, bool verbose);\r
+\r
+/*\r
+// Runs k-means++ on the given set of points. Set RunKMeans for info on the parameters.\r
+*/\r
+Scalar\r
+RunKMeansPlusPlus(int n, int k, int d, Scalar *points, int attempts,\r
+ Scalar *centers, int *assignments);\r
+\r
+Scalar\r
+RunKMeans(int n, int k, int d, Scalar *points, int attempts,\r
+ Scalar *centers, int *assignments);\r
+#else\r
+#include "KMeans.h"\r
+#endif\r
+#include "KmTree.h"\r
+#include <sstream>\r
+#include <time.h>\r
+#include <vector>\r
+\r
+#ifdef CLUSTALO\r
+extern "C" double\r
+KMeans(int n, int k, int d, Scalar *points, int attempts, int use_lloyds_method,\r
+ double *centers, int *assignments)\r
+{\r
+ if (use_lloyds_method) {\r
+ /*fprintf(stderr, "FIXME using LLoyd's method\n");*/\r
+ return RunKMeans(n, k, d, points, attempts,\r
+ centers, assignments);\r
+ } else {\r
+ /*fprintf(stderr, "FIXME using KMeansPP method\n");*/\r
+ return RunKMeansPlusPlus(n, k, d, points, attempts,\r
+ centers, assignments);\r
+ }\r
+}\r
+#endif\r
+\r
+using namespace std;\r
+\r
+// Logging\r
+static vector<ostream*> gLogOutputs;\r
+static vector<ostream*> gVerboseLogOutputs;\r
+#define LOG(verbose, text) { \\r
+ vector<ostream*> &outputs = (verbose? gVerboseLogOutputs : gLogOutputs); \\r
+ if (outputs.size() > 0) { \\r
+ ostringstream string_stream; \\r
+ string_stream << text; \\r
+ for (int i = 0; i < (int)outputs.size(); i++) \\r
+ *(outputs[i]) << string_stream.str(); \\r
+ } \\r
+}\r
+void AddKMeansLogging(std::ostream *out, bool verbose) {\r
+ if (verbose)\r
+ gVerboseLogOutputs.push_back(out);\r
+ gLogOutputs.push_back(out);\r
+}\r
+void ClearKMeansLogging() {\r
+ gLogOutputs.clear();\r
+ gVerboseLogOutputs.clear();\r
+}\r
+\r
+// Returns the number of seconds since the program began execution.\r
+static double GetSeconds() {\r
+ return double(clock()) / CLOCKS_PER_SEC;\r
+}\r
+\r
+// See KMeans.h\r
+// Performs one full execution of k-means, logging any relevant information, and tracking meta\r
+// statistics for the run. If min or max values are negative, they are treated as unset.\r
+// best_centers and best_assignment can be 0, in which case they are not set.\r
+static void RunKMeansOnce(const KmTree &tree, int n, int k, int d, Scalar *points, Scalar *centers,\r
+ Scalar *min_cost, Scalar *max_cost, Scalar *total_cost,\r
+ double start_time, double *min_time, double *max_time,\r
+ double *total_time, Scalar *best_centers, int *best_assignment) {\r
+ const Scalar kEpsilon = Scalar(1e-8); // Used to determine when to terminate k-means\r
+\r
+ // Do iterations of k-means until the cost stabilizes\r
+ Scalar old_cost = 0;\r
+ bool is_done = false;\r
+ for (int iteration = 0; !is_done; iteration++) {\r
+ Scalar new_cost = tree.DoKMeansStep(k, centers, 0);\r
+ is_done = (iteration > 0 && new_cost >= (1 - kEpsilon) * old_cost);\r
+ old_cost = new_cost;\r
+ LOG(true, "Completed iteration #" << (iteration+1) << ", cost=" << new_cost << "..." << endl);\r
+ }\r
+ double this_time = GetSeconds() - start_time;\r
+\r
+ // Log the clustering we found\r
+ LOG(false, "Completed run: cost=" << old_cost << " (" << this_time << " seconds)" << endl);\r
+\r
+ // Handle a new min cost, updating best_centers and best_assignment as appropriate\r
+ if (*min_cost < 0 || old_cost < *min_cost) {\r
+ *min_cost = old_cost;\r
+ if (best_assignment != 0)\r
+ tree.DoKMeansStep(k, centers, best_assignment);\r
+ if (best_centers != 0)\r
+ memcpy(best_centers, centers, sizeof(Scalar)*k*d);\r
+ }\r
+\r
+ // Update all other aggregate stats\r
+ if (*max_cost < old_cost) *max_cost = old_cost;\r
+ *total_cost += old_cost;\r
+ if (*min_time < 0 || *min_time > this_time)\r
+ *min_time = this_time;\r
+ if (*max_time < this_time) *max_time = this_time;\r
+ *total_time += this_time;\r
+}\r
+\r
+// Outputs all meta-stats for a set of k-means or k-means++ runs.\r
+void LogMetaStats(Scalar min_cost, Scalar max_cost, Scalar total_cost,\r
+ double min_time, double max_time, double total_time, int num_attempts) {\r
+ LOG(false, "Aggregate info over " << num_attempts << " runs:" << endl);\r
+ LOG(false, " Cost: min=" << min_cost << " average=" << (total_cost / num_attempts)\r
+ << " max=" << max_cost << endl);\r
+ LOG(false, " Time: min=" << min_time << " average=" << (total_time / num_attempts)\r
+ << " max=" << max_time << endl << endl);\r
+}\r
+\r
+// See KMeans.h\r
+Scalar RunKMeans(int n, int k, int d, Scalar *points, int attempts,\r
+ Scalar *ret_centers, int *ret_assignment) {\r
+ KM_ASSERT(k >= 1);\r
+ \r
+ // Create the tree and log\r
+ LOG(false, "Running k-means..." << endl);\r
+ KmTree tree(n, d, points);\r
+ LOG(false, "Done preprocessing..." << endl);\r
+\r
+ // Initialization\r
+ Scalar *centers = (Scalar*)malloc(sizeof(Scalar)*k*d);\r
+ int *unused_centers = (int*)malloc(sizeof(int)*n);\r
+ KM_ASSERT(centers != 0 && unused_centers != 0);\r
+ Scalar min_cost = -1, max_cost = -1, total_cost = 0;\r
+ double min_time = -1, max_time = -1, total_time = 0;\r
+ \r
+ // Handle k > n\r
+ if (k > n) {\r
+ memset(centers + n*d, -1, (k-d)*sizeof(Scalar));\r
+ k = n;\r
+ }\r
+\r
+ // Run all the attempts\r
+ for (int attempt = 0; attempt < attempts; attempt++) {\r
+ double start_time = GetSeconds();\r
+\r
+ // Choose centers uniformly at random\r
+ for (int i = 0; i < n; i++)\r
+ unused_centers[i] = i;\r
+ int num_unused_centers = n;\r
+ for (int i = 0; i < k; i++) {\r
+ int j = GetRandom(num_unused_centers--);\r
+ memcpy(centers + i*d, points + unused_centers[j]*d, d*sizeof(Scalar));\r
+ unused_centers[j] = unused_centers[num_unused_centers];\r
+ }\r
+ \r
+ // Run k-means\r
+ RunKMeansOnce(tree, n, k, d, points, centers, &min_cost, &max_cost, &total_cost, start_time,\r
+ &min_time, &max_time, &total_time, ret_centers, ret_assignment);\r
+ }\r
+ LogMetaStats(min_cost, max_cost, total_cost, min_time, max_time, total_time, attempts);\r
+\r
+ // Clean up and return\r
+ free(unused_centers);\r
+ free(centers);\r
+ return min_cost;\r
+}\r
+\r
+// See KMeans.h\r
+Scalar RunKMeansPlusPlus(int n, int k, int d, Scalar *points, int attempts,\r
+ Scalar *ret_centers, int *ret_assignment) {\r
+ KM_ASSERT(k >= 1);\r
+\r
+ // Create the tree and log\r
+ LOG(false, "Running k-means++..." << endl);\r
+ KmTree tree(n, d, points);\r
+ LOG(false, "Done preprocessing..." << endl);\r
+\r
+ // Initialization\r
+ Scalar *centers = (Scalar*)malloc(sizeof(Scalar)*k*d);\r
+ KM_ASSERT(centers != 0);\r
+ Scalar min_cost = -1, max_cost = -1, total_cost = 0;\r
+ double min_time = -1, max_time = -1, total_time = 0;\r
+\r
+ // Run all the attempts\r
+ for (int attempt = 0; attempt < attempts; attempt++) {\r
+ double start_time = GetSeconds();\r
+\r
+ // Choose centers using k-means++ seeding\r
+ tree.SeedKMeansPlusPlus(k, centers);\r
+ \r
+ // Run k-means\r
+ RunKMeansOnce(tree, n, k, d, points, centers, &min_cost, &max_cost, &total_cost, start_time,\r
+ &min_time, &max_time, &total_time, ret_centers, ret_assignment);\r
+ }\r
+ LogMetaStats(min_cost, max_cost, total_cost, min_time, max_time, total_time, attempts);\r
+\r
+ // Clean up and return\r
+ free(centers);\r
+ return min_cost;\r
+}\r
--- /dev/null
+#ifndef CLUSTALO\r
+// BEWARE: BETA VERSION\r
+// --------------------\r
+//\r
+// The main set of utilities for runnning k-means and k-means++ on arbitrary data sets.\r
+//\r
+// Author: David Arthur (darthur@gmail.com), 2009\r
+#endif\r
+\r
+#ifndef KMEANS_H__\r
+#define KMEANS_H__\r
+\r
+#ifndef CLUSTALO\r
+// Includes\r
+#include "KmUtils.h"\r
+#include <iostream>\r
+\r
+// Sets preferences for how much logging is done and where it is outputted, when k-means is run.\r
+void ClearKMeansLogging();\r
+void AddKMeansLogging(std::ostream *out, bool verbose);\r
+\r
+// Runs k-means on the given set of points.\r
+// - n: The number of points in the data set\r
+// - k: The number of clusters to look for\r
+// - d: The number of dimensions that the data set lives in\r
+// - points: An array of size n*d where points[d*i + j] gives coordinate j of point i\r
+// - attempts: The number of times to independently run k-means with different starting centers.\r
+// The best result is always returned (as measured by the cost function).\r
+// - centers: This can either be null or an array of size k*d. In the latter case, it will be\r
+// filled with the locations of all final cluster centers. Specifically\r
+// centers[d*i + j] will give coordinate j of center i. If the cluster is unused, it\r
+// will contain NaN instead.\r
+// - assignments: This can either be null or an array of size n. In the latter case, it will be\r
+// filled with the cluster that each point is assigned to (an integer between 0\r
+// and k-1 inclusive).\r
+// The final cost of the clustering is also returned.\r
+// The final cost of the clustering is also returned.\r
+Scalar RunKMeans(int n, int k, int d, Scalar *points, int attempts,\r
+ Scalar *centers, int *assignments);\r
+\r
+// Runs k-means++ on the given set of points. Set RunKMeans for info on the parameters.\r
+Scalar RunKMeansPlusPlus(int n, int k, int d, Scalar *points, int attempts,\r
+ Scalar *centers, int *assignments);\r
+\r
+#else\r
+\r
+/* CLUSTALO PATCH:\r
+ * same as above, with one addition: if use_lloyds_method is false, kmpp will be used\r
+ * otherwise the 'classical' i.e. Looyd's method will be used\r
+ */\r
+extern double\r
+KMeans(int n, int k, int d, double *points, int attempts, int use_lloyds_method,\r
+ double *centers, int *assignments);\r
+\r
+#endif\r
+#endif\r
--- /dev/null
+// See KmTree.cpp
+//
+// Author: David Arthur (darthur@gmail.com), 2009
+
+// Includes
+#include "KmTree.h"
+#include <iostream>
+#include <stdlib.h>
+#include <stdio.h>
+using namespace std;
+
+KmTree::KmTree(int n, int d, Scalar *points): n_(n), d_(d), points_(points) {
+ // Initialize memory
+ // DD: need to cast to long otherwise malloc will fail
+ // if we need more than 2 gigabytes or so
+ int node_size = sizeof(Node) + d_ * 3 * sizeof(Scalar);
+ node_data_ = (char*)malloc((2*(long unsigned int)n-1) * node_size);
+ point_indices_ = (int*)malloc(n * sizeof(int));
+ for (int i = 0; i < n; i++)
+ point_indices_[i] = i;
+ KM_ASSERT(node_data_ != 0 && point_indices_ != 0);
+
+ // Calculate the bounding box for the points
+ Scalar *bound_v1 = PointAllocate(d_);
+ Scalar *bound_v2 = PointAllocate(d_);
+ KM_ASSERT(bound_v1 != 0 && bound_v2 != 0);
+ PointCopy(bound_v1, points, d_);
+ PointCopy(bound_v2, points, d_);
+ for (int i = 1; i < n; i++)
+ for (int j = 0; j < d; j++) {
+ if (bound_v1[j] > points[i*d_ + j]) bound_v1[j] = points[i*d_ + j];
+ if (bound_v2[j] < points[i*d_ + j]) bound_v1[j] = points[i*d_ + j];
+ }
+
+ // Build the tree
+ char *temp_node_data = node_data_;
+ top_node_ = BuildNodes(points, 0, n-1, &temp_node_data);
+
+ // Cleanup
+ PointFree(bound_v1);
+ PointFree(bound_v2);
+}
+
+KmTree::~KmTree() {
+ free(point_indices_);
+ free(node_data_);
+}
+
+Scalar KmTree::DoKMeansStep(int k, Scalar *centers, int *assignment) const {
+ // Create an invalid center for comparison purposes
+ Scalar *bad_center = PointAllocate(d_);
+ KM_ASSERT(bad_center != 0);
+ memset(bad_center, 0xff, d_ * sizeof(Scalar));
+
+ // Allocate data
+ Scalar *sums = (Scalar*)calloc(k * d_, sizeof(Scalar));
+ int *counts = (int*)calloc(k, sizeof(int));
+ int num_candidates = 0;
+ int *candidates = (int*)malloc(k * sizeof(int));
+ KM_ASSERT(sums != 0 && counts != 0 && candidates != 0);
+ for (int i = 0; i < k; i++)
+ if (memcmp(centers + i*d_, bad_center, d_ * sizeof(Scalar)) != 0)
+ candidates[num_candidates++] = i;
+
+ // Find nodes
+ Scalar result = DoKMeansStepAtNode(top_node_, num_candidates, candidates, centers, sums,
+ counts, assignment);
+
+ // Set the new centers
+ for (int i = 0; i < k; i++) {
+ if (counts[i] > 0) {
+ PointScale(sums + i*d_, Scalar(1) / counts[i], d_);
+ PointCopy(centers + i*d_, sums + i*d_, d_);
+ } else {
+ memcpy(centers + i*d_, bad_center, d_ * sizeof(Scalar));
+ }
+ }
+
+ // Cleanup memory
+ PointFree(bad_center);
+ free(candidates);
+ free(counts);
+ free(sums);
+ return result;
+}
+
+// Helper functions for constructor
+// ================================
+
+// Build a kd tree from the given set of points
+KmTree::Node *KmTree::BuildNodes(Scalar *points, int first_index, int last_index,
+ char **next_node_data) {
+ // Allocate the node
+ Node *node = (Node*)(*next_node_data);
+ (*next_node_data) += sizeof(Node);
+ node->sum = (Scalar*)(*next_node_data);
+ (*next_node_data) += sizeof(Scalar) * d_;
+ node->median = (Scalar*)(*next_node_data);
+ (*next_node_data) += sizeof(Scalar) * d_;
+ node->radius = (Scalar*)(*next_node_data);
+ (*next_node_data) += sizeof(Scalar) * d_;
+
+ // Fill in basic info
+ node->num_points = (last_index - first_index + 1);
+ node->first_point_index = first_index;
+
+ // Calculate the bounding box
+ Scalar *first_point = points + point_indices_[first_index] * d_;
+ Scalar *bound_p1 = PointAllocate(d_);
+ Scalar *bound_p2 = PointAllocate(d_);
+ KM_ASSERT(bound_p1 != 0 && bound_p2 != 0);
+ PointCopy(bound_p1, first_point, d_);
+ PointCopy(bound_p2, first_point, d_);
+ for (int i = first_index+1; i <= last_index; i++)
+ for (int j = 0; j < d_; j++) {
+ Scalar c = points[point_indices_[i]*d_ + j];
+ if (bound_p1[j] > c) bound_p1[j] = c;
+ if (bound_p2[j] < c) bound_p2[j] = c;
+ }
+
+ // Calculate bounding box stats and delete the bounding box memory
+ Scalar max_radius = -1;
+ int split_d = -1;
+ for (int j = 0; j < d_; j++) {
+ node->median[j] = (bound_p1[j] + bound_p2[j]) / 2;
+ node->radius[j] = (bound_p2[j] - bound_p1[j]) / 2;
+ if (node->radius[j] > max_radius) {
+ max_radius = node->radius[j];
+ split_d = j;
+ }
+ }
+ PointFree(bound_p2);
+ PointFree(bound_p1);
+
+ // If the max spread is 0, make this a leaf node
+ if (max_radius == 0) {
+ node->lower_node = node->upper_node = 0;
+ PointCopy(node->sum, first_point, d_);
+ if (last_index != first_index)
+ PointScale(node->sum, Scalar(last_index - first_index + 1), d_);
+ node->opt_cost = 0;
+ return node;
+ }
+
+ // Partition the points around the midpoint in this dimension. The partitioning is done in-place
+ // by iterating from left-to-right and right-to-left in the same way that partioning is done for
+ // quicksort.
+ Scalar split_pos = node->median[split_d];
+ int i1 = first_index, i2 = last_index, size1 = 0;
+ while (i1 <= i2) {
+ bool is_i1_good = (points[point_indices_[i1]*d_ + split_d] < split_pos);
+ bool is_i2_good = (points[point_indices_[i2]*d_ + split_d] >= split_pos);
+ if (!is_i1_good && !is_i2_good) {
+ int temp = point_indices_[i1];
+ point_indices_[i1] = point_indices_[i2];
+ point_indices_[i2] = temp;
+ is_i1_good = is_i2_good = true;
+ }
+ if (is_i1_good) {
+ i1++;
+ size1++;
+ }
+ if (is_i2_good) {
+ i2--;
+ }
+ }
+
+ // Create the child nodes
+ KM_ASSERT(size1 >= 1 && size1 <= last_index - first_index);
+ node->lower_node = BuildNodes(points, first_index, first_index + size1 - 1, next_node_data);
+ node->upper_node = BuildNodes(points, first_index + size1, last_index, next_node_data);
+
+ // Calculate the new sum and opt cost
+ PointCopy(node->sum, node->lower_node->sum, d_);
+ PointAdd(node->sum, node->upper_node->sum, d_);
+ Scalar *center = PointAllocate(d_);
+ KM_ASSERT(center != 0);
+ PointCopy(center, node->sum, d_);
+ PointScale(center, Scalar(1) / node->num_points, d_);
+ node->opt_cost = GetNodeCost(node->lower_node, center) + GetNodeCost(node->upper_node, center);
+ PointFree(center);
+ return node;
+}
+
+// Returns the total contribution of all points in the given kd-tree node, assuming they are all
+// assigned to a center at the given location. We need to return:
+//
+// sum_{x \in node} ||x - center||^2.
+//
+// If c denotes the center of mass of the points in this node and n denotes the number of points in
+// it, then this quantity is given by
+//
+// n * ||c - center||^2 + sum_{x \in node} ||x - c||^2
+//
+// The sum is precomputed for each node as opt_cost. This formula follows from expanding both sides
+// as dot products. See Kanungo/Mount for more info.
+Scalar KmTree::GetNodeCost(const Node *node, Scalar *center) const {
+ Scalar dist_sq = 0;
+ for (int i = 0; i < d_; i++) {
+ Scalar x = (node->sum[i] / node->num_points) - center[i];
+ dist_sq += x*x;
+ }
+ return node->opt_cost + node->num_points * dist_sq;
+}
+
+// Helper functions for DoKMeans step
+// ==================================
+
+// A recursive version of DoKMeansStep. This determines which clusters all points that are rooted
+// node will be assigned to, and updates sums, counts and assignment (if not null) accordingly.
+// candidates maintains the set of cluster indices which could possibly be the closest clusters
+// for points in this subtree.
+Scalar KmTree::DoKMeansStepAtNode(const Node *node, int k, int *candidates, Scalar *centers,
+ Scalar *sums, int *counts, int *assignment) const {
+ // Determine which center the node center is closest to
+ Scalar min_dist_sq = PointDistSq(node->median, centers + candidates[0]*d_, d_);
+ int closest_i = candidates[0];
+ for (int i = 1; i < k; i++) {
+ Scalar dist_sq = PointDistSq(node->median, centers + candidates[i]*d_, d_);
+ if (dist_sq < min_dist_sq) {
+ min_dist_sq = dist_sq;
+ closest_i = candidates[i];
+ }
+ }
+
+ // If this is a non-leaf node, recurse if necessary
+ if (node->lower_node != 0) {
+ // Build the new list of candidates
+ int new_k = 0;
+ int *new_candidates = (int*)malloc(k * sizeof(int));
+ KM_ASSERT(new_candidates != 0);
+ for (int i = 0; i < k; i++)
+ if (!ShouldBePruned(node->median, node->radius, centers, closest_i, candidates[i]))
+ new_candidates[new_k++] = candidates[i];
+
+ // Recurse if there's at least two
+ if (new_k > 1) {
+ Scalar result = DoKMeansStepAtNode(node->lower_node, new_k, new_candidates, centers,
+ sums, counts, assignment) +
+ DoKMeansStepAtNode(node->upper_node, new_k, new_candidates, centers,
+ sums, counts, assignment);
+ free(new_candidates);
+ return result;
+ } else {
+ free(new_candidates);
+ }
+ }
+
+ // Assigns all points within this node to a single center
+ PointAdd(sums + closest_i*d_, node->sum, d_);
+ counts[closest_i] += node->num_points;
+ if (assignment != 0) {
+ for (int i = node->first_point_index; i < node->first_point_index + node->num_points; i++)
+ assignment[point_indices_[i]] = closest_i;
+ }
+ return GetNodeCost(node, centers + closest_i*d_);
+}
+
+// Determines whether every point in the box is closer to centers[best_index] than to
+// centers[test_index].
+//
+// If x is a point, c_0 = centers[best_index], c = centers[test_index], then:
+// (x-c).(x-c) < (x-c_0).(x-c_0)
+// <=> (c-c_0).(c-c_0) < 2(x-c_0).(c-c_0)
+//
+// The right-hand side is maximized for a vertex of the box where for each dimension, we choose
+// the low or high value based on the sign of x-c_0 in that dimension.
+bool KmTree::ShouldBePruned(Scalar *box_median, Scalar *box_radius, Scalar *centers,
+ int best_index, int test_index) const {
+ if (best_index == test_index)
+ return false;
+
+ Scalar *best = centers + best_index*d_;
+ Scalar *test = centers + test_index*d_;
+ Scalar lhs = 0, rhs = 0;
+ for (int i = 0; i < d_; i++) {
+ Scalar component = test[i] - best[i];
+ lhs += component * component;
+ if (component > 0)
+ rhs += (box_median[i] + box_radius[i] - best[i]) * component;
+ else
+ rhs += (box_median[i] - box_radius[i] - best[i]) * component;
+ }
+ return (lhs >= 2*rhs);
+}
+
+Scalar KmTree::SeedKMeansPlusPlus(int k, Scalar *centers) const {
+ Scalar *dist_sq = (Scalar*)malloc(n_ * sizeof(Scalar));
+ KM_ASSERT(dist_sq != 0);
+
+ // Choose an initial center uniformly at random
+ SeedKmppSetClusterIndex(top_node_, 0);
+ int i = GetRandom(n_);
+ memcpy(centers, points_ + point_indices_[i]*d_, d_*sizeof(Scalar));
+ Scalar total_cost = 0;
+ for (int j = 0; j < n_; j++) {
+ dist_sq[j] = PointDistSq(points_ + point_indices_[j]*d_, centers, d_);
+ total_cost += dist_sq[j];
+ }
+
+ // Repeatedly choose more centers
+ for (int new_cluster = 1; new_cluster < k; new_cluster++) {
+ while (1) {
+ Scalar cutoff = (rand() / Scalar(RAND_MAX)) * total_cost;
+ Scalar cur_cost = 0;
+ for (i = 0; i < n_; i++) {
+ cur_cost += dist_sq[i];
+ if (cur_cost >= cutoff)
+ break;
+ }
+ if (i < n_)
+ break;
+ }
+ memcpy(centers + new_cluster*d_, points_ + point_indices_[i]*d_, d_*sizeof(Scalar));
+ total_cost = SeedKmppUpdateAssignment(top_node_, new_cluster, centers, dist_sq);
+ }
+
+ // Clean up and return
+ free(dist_sq);
+ return total_cost;
+}
+
+// Helper functions for SeedKMeansPlusPlus
+// =======================================
+
+// Sets kmpp_cluster_index to 0 for all nodes
+void KmTree::SeedKmppSetClusterIndex(const Node *node, int value) const {
+ node->kmpp_cluster_index = value;
+ if (node->lower_node != 0) {
+ SeedKmppSetClusterIndex(node->lower_node, value);
+ SeedKmppSetClusterIndex(node->upper_node, value);
+ }
+}
+
+Scalar KmTree::SeedKmppUpdateAssignment(const Node *node, int new_cluster, Scalar *centers,
+ Scalar *dist_sq) const {
+ // See if we can assign all points in this node to one cluster
+ if (node->kmpp_cluster_index >= 0) {
+ if (ShouldBePruned(node->median, node->radius, centers, node->kmpp_cluster_index, new_cluster))
+ return GetNodeCost(node, centers + node->kmpp_cluster_index*d_);
+ if (ShouldBePruned(node->median, node->radius, centers, new_cluster,
+ node->kmpp_cluster_index)) {
+ SeedKmppSetClusterIndex(node, new_cluster);
+ for (int i = node->first_point_index; i < node->first_point_index + node->num_points; i++)
+ dist_sq[i] = PointDistSq(points_ + point_indices_[i]*d_, centers + new_cluster*d_, d_);
+ return GetNodeCost(node, centers + new_cluster*d_);
+ }
+
+ // It may be that the a leaf-node point is equidistant from the new center or old
+ if (node->lower_node == 0)
+ return GetNodeCost(node, centers + node->kmpp_cluster_index*d_);
+ }
+
+ // Recurse
+ Scalar cost = SeedKmppUpdateAssignment(node->lower_node, new_cluster, centers, dist_sq) +
+ SeedKmppUpdateAssignment(node->upper_node, new_cluster, centers, dist_sq);
+ int i1 = node->lower_node->kmpp_cluster_index, i2 = node->upper_node->kmpp_cluster_index;
+ if (i1 == i2 && i1 != -1)
+ node->kmpp_cluster_index = i1;
+ else
+ node->kmpp_cluster_index = -1;
+ return cost;
+}
--- /dev/null
+// BEWARE: BETA VERSION\r
+// --------------------\r
+//\r
+// A k-d tree that vastly speeds up an iteration of k-means (in any number of dimensions). The main\r
+// idea for this data structure is from Kanungo/Mount. This is used internally by Kmeans.cpp, and\r
+// will most likely not need to be used directly.\r
+//\r
+// The stucture works as follows:\r
+// - All data points are placed into a tree where we choose child nodes by partitioning all data\r
+// points along a plane parallel to the axis.\r
+// - We maintain for each node, the bounding box of all data points stored at that node.\r
+// - To do a k-means iteration, we need to assign points to clusters and calculate the sum and\r
+// the number of points assigned to each cluster. For each node in the tree, we can rule out\r
+// some cluster centers as being too far away from every single point in that bounding box.\r
+// Once only one cluster is left, all points in the node can be assigned to that cluster in\r
+// batch.\r
+//\r
+// Author: David Arthur (darthur@gmail.com), 2009\r
+\r
+#ifndef KM_TREE_H__\r
+#define KM_TREE_H__\r
+\r
+// Includes\r
+#include "KmUtils.h"\r
+\r
+// KmTree class definition\r
+class KmTree {\r
+ public:\r
+ // Constructs a tree out of the given n data points living in R^d.\r
+ KmTree(int n, int d, Scalar *points);\r
+ ~KmTree();\r
+\r
+ // Given k cluster centers, this runs a full k-means iterations, choosing the next set of\r
+ // centers and returning the cost function for this set of centers. If assignment is not null,\r
+ // it should be an array of size n that will be filled with the index of the cluster (0 - k-1)\r
+ // that each data point is assigned to. The new center values will overwrite the old ones.\r
+ Scalar DoKMeansStep(int k, Scalar *centers, int *assignment) const;\r
+\r
+ // Choose k initial centers for k-means using the kmeans++ seeding procedure. The resulting\r
+ // centers are returned via the centers variable, which should be pre-allocated to size k*d.\r
+ // The cost of the initial clustering is returned.\r
+ Scalar SeedKMeansPlusPlus(int k, Scalar *centers) const;\r
+\r
+ private:\r
+ struct Node {\r
+ int num_points; // Number of points stored in this node\r
+ int first_point_index; // The smallest point index stored in this node\r
+ Scalar *median, *radius; // Bounding box center and half side-lengths\r
+ Scalar *sum; // Sum of the points stored in this node\r
+ Scalar opt_cost; // Min cost for putting all points in this node in 1 cluster\r
+ Node *lower_node, *upper_node; // Child nodes\r
+ mutable int kmpp_cluster_index; // The cluster these points are assigned to or -1 if variable\r
+ };\r
+\r
+ // Helper functions for constructor\r
+ Node *BuildNodes(Scalar *points, int first_index, int last_index, char **next_node_data);\r
+ Scalar GetNodeCost(const Node *node, Scalar *center) const;\r
+\r
+ // Helper functions for DoKMeans step\r
+ Scalar DoKMeansStepAtNode(const Node *node, int k, int *candidates, Scalar *centers,\r
+ Scalar *sums, int *counts, int *assignment) const;\r
+ bool ShouldBePruned(Scalar *box_median, Scalar *box_radius, Scalar *centers, int best_index,\r
+ int test_index) const;\r
+\r
+ // Helper functions for SeedKMeansPlusPlus\r
+ void SeedKmppSetClusterIndex(const Node *node, int index) const;\r
+ Scalar SeedKmppUpdateAssignment(const Node *node, int new_cluster, Scalar *centers,\r
+ Scalar *dist_sq) const;\r
+\r
+ int n_, d_;\r
+ Scalar *points_;\r
+ Node *top_node_;\r
+ char *node_data_;\r
+ int *point_indices_;\r
+};\r
+\r
+#endif\r
--- /dev/null
+// See KmUtils.h\r
+//\r
+// Author: David Arthur (darthur@gmail.com), 2009\r
+\r
+#include "KmUtils.h"\r
+#include <iostream>\r
+using namespace std;\r
+\r
+int __KMeansAssertionFailure(const char *file, int line, const char *expression) {\r
+ cout << "ASSERTION FAILURE, " << file << " line " << line << ":" << endl;\r
+ cout << " " << expression << endl;\r
+ exit(-1);\r
+}\r
--- /dev/null
+// BEWARE: BETA VERSION\r
+// --------------------\r
+//\r
+// Utilities for arbitrary dimensional points in space. All points are treated as simple value\r
+// arrays. This is done for two reasons:\r
+// - Using value arrays instead of a point class makes all point operations very explicit, which\r
+// makes their usage easier to optimize.\r
+// - A value array is about as universal a format as possible, which makes it easier for\r
+// people to use the k-means code in any project.\r
+// Also contains assertion code that can be disabled if desired.\r
+//\r
+// Author: David Arthur (darthur@gmail.com), 2009\r
+\r
+#ifndef KM_UTILS_H__\r
+#define KM_UTILS_H__\r
+\r
+// Includes\r
+#ifndef CLUSTALO\r
+#include <malloc.h>\r
+#endif\r
+#include <memory.h>\r
+#include <stdlib.h>\r
+\r
+// The data-type used for a single coordinate for points\r
+typedef double Scalar;\r
+\r
+// Point utilities\r
+// ===============\r
+\r
+// Point creation and deletion\r
+inline Scalar *PointAllocate(int d) {\r
+ return (Scalar*)malloc(d * sizeof(Scalar));\r
+}\r
+\r
+inline void PointFree(Scalar *p) {\r
+ free(p);\r
+}\r
+\r
+inline void PointCopy(Scalar *p1, const Scalar *p2, int d) {\r
+ memcpy(p1, p2, d * sizeof(Scalar));\r
+}\r
+\r
+// Point vector tools\r
+inline void PointAdd(Scalar *p1, const Scalar *p2, int d) {\r
+ for (int i = 0; i < d; i++)\r
+ p1[i] += p2[i];\r
+}\r
+\r
+inline void PointScale(Scalar *p, Scalar scale, int d) {\r
+ for (int i = 0; i < d; i++)\r
+ p[i] *= scale;\r
+}\r
+\r
+inline Scalar PointDistSq(const Scalar *p1, const Scalar *p2, int d) {\r
+ Scalar result = 0;\r
+ for (int i = 0; i < d; i++)\r
+ result += (p1[i] - p2[i]) * (p1[i] - p2[i]);\r
+ return result;\r
+}\r
+\r
+// Assertions\r
+// ==========\r
+\r
+// Comment out ENABLE_KMEANS_ASSERTS to turn off ASSERTS for added speed.\r
+#define ENABLE_KMEANS_ASSERTS\r
+#ifdef ENABLE_KMEANS_ASSERTS\r
+int __KMeansAssertionFailure(const char *file, int line, const char *expression);\r
+#define KM_ASSERT(expression) \\r
+ (void)((expression) != 0? 0 : __KMeansAssertionFailure(__FILE__, __LINE__, #expression))\r
+#else\r
+#define KM_ASSERT(expression)\r
+#endif\r
+\r
+// Miscellaneous utilities\r
+// =======================\r
+\r
+// Returns a random integer chosen uniformly from the range [0, n-1]. Note that RAND_MAX could be\r
+// less than n. On Visual Studio, it is only 32767. For larger values of RAND_MAX, we need to be\r
+// careful of overflow.\r
+inline int GetRandom(int n) {\r
+ int u = rand() * RAND_MAX + rand();\r
+ return ((u % n) + n) % n;\r
+}\r
+\r
+#endif\r
--- /dev/null
+# Replaces squids own automake files
+#
+# Some useful automake documentation:
+# http://www.openismus.com/documents/linux/automake/automake.shtml
+# http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html
+
+#SUBDIRS =
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+
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+AM_CXXFLAGS = -DCLUSTALO @AM_CXXFLAGS@
+
+noinst_LTLIBRARIES = libkmpp.la
+
+libkmpp_la_SOURCES = KMeans.cpp KMeans.h \
+ KmTree.cpp KmTree.h \
+ KmUtils.cpp KmUtils.h
--- /dev/null
+# Makefile.in generated by automake 1.10.2 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+@SET_MAKE@
+
+# Replaces squids own automake files
+#
+# Some useful automake documentation:
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+# http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html
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+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
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+
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+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
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+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
--- /dev/null
+/*********************************************************************
+ * Clustal Omage - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: main.cpp 234 2011-04-13 05:26:16Z andreas $
+ */
+
+/*
+ * We are using a mix of C and C++, which means that linking has to be
+ * done with a C++ compiler. By using this "fake" main c++ function,
+ * automake is convinced to use a C++ compiler for linking.
+ *
+ */
+
+#ifdef HAVE_CONFIG_H
+ #include "config.h"
+#endif
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+extern "C" {
+#include "mymain.h"
+#include "clustal/util.h"
+#include "squid/squid.h"
+}
+
+
+/**
+ * @brief Convert an old Clustal command line parameter in the form of
+ * [-/]param[=value] to new parameter if possible
+ *
+ * @param[out] iNewArgC_p
+ * "argc" which will be incremented for each successfully converted option
+ * @param[out] ppcNewArgV_p
+ * "argv" to which each successfully converted options will be added
+ * (caller has to free)
+ * @param[in] pcOldArg
+ * The old parameter and value command line option
+ *
+ */
+void
+ConvertOldCmdLineArg(int *iNewArgC_p, char ***ppcNewArgV_p, char *pcOldArg)
+{
+ char *pcOldParam, *pcOldValue, *pcOldArgCopy;
+ char zcNotImplementedMsg[] = "WARNING: Invalid old command line option";
+
+ pcOldArgCopy = CkStrdup(pcOldArg);
+ pcOldParam = strtok(pcOldArgCopy, "=");
+ pcOldValue = strtok(NULL, "=");
+
+
+ /* go through all options in order of appearance in clustalw2 -help
+ *
+ */
+
+ /* data
+ *
+ */
+ if (STR_NC_EQ("INFILE", &pcOldParam[1])) {
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-i");
+ if (NULL != pcOldValue)
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
+
+ } else if (STR_NC_EQ("PROFILE1", &pcOldParam[1])) {
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--profile1");
+ if (NULL != pcOldValue)
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
+
+ } else if (STR_NC_EQ("PROFILE2", &pcOldParam[1])) {
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--profile2");
+ if (NULL != pcOldValue)
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
+
+ /* verbs
+ *
+ */
+
+ /* missing:
+ * OPTIONS
+ */
+
+ } else if (STR_NC_EQ("HELP", &pcOldParam[1])
+ || STR_NC_EQ("CHECK", &pcOldParam[1])) {
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-h");
+
+ } else if (STR_NC_EQ("FULLHELP", &pcOldParam[1])) {
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-h");
+
+ } else if (STR_NC_EQ("ALIGN", &pcOldParam[1])) {
+ char msg[] = "WARNING: The ALIGN option is default in Clustal Omega";
+ fprintf(stderr, "%s\n", msg);
+
+ /* missing:
+ * TREE
+ * PIM
+ * BOOTSTRAP
+ * CONVERT
+ */
+
+ /* parameters
+ *
+ */
+ } else if (STR_NC_EQ("INTERACTIVE", &pcOldParam[1])) {
+ char msg[] = "WARNING: There is no interactive command-line menu in Clustal Omega";
+ fprintf(stderr, "%s\n", msg);
+ /* trigger help */
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-h");
+
+ } else if (STR_NC_EQ("QUICKTREE", &pcOldParam[1])) {
+ char msg[] = "WARNING: The QUICKTREE (i.e. k-tuple distance) option is default in Clustal Omega";
+ fprintf(stderr, "%s\n", msg);
+
+ } else if (STR_NC_EQ("TYPE", &pcOldParam[1])) {
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-t");
+ if (NULL != pcOldValue)
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
+
+ /* NEGATIVE */
+
+ } else if (STR_NC_EQ("OUTFILE", &pcOldParam[1])) {
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-o");
+ if (NULL != pcOldValue)
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
+
+
+ } else if (STR_NC_EQ("OUTPUT", &pcOldParam[1])) {
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--outfmt");
+ if (NULL != pcOldValue)
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
+
+ /* missing:
+ * OUTORDER
+ * CASE
+ * SEQNOS
+ * SEQNO_RANGE
+ * RANGE
+ */
+
+ } else if (STR_NC_EQ("MAXSEQLEN", &pcOldParam[1])) {
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--maxseqlen");
+ if (NULL != pcOldValue)
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
+
+ } else if (STR_NC_EQ("QUIET", &pcOldParam[1])) {
+ char msg[] = "WARNING: The QUIET option is default in Clustal Omega";
+ fprintf(stderr, "%s\n", msg);
+
+ /* missing:
+ * STATS
+ */
+
+ /* fast pariwise alignment
+ *
+ */
+
+ /* missing:
+ * KTUPLE
+ * TOPDIAGS
+ * WINDOW
+ * PAIRGAP
+ * SCORE
+ */
+
+ /* slow pairwise alignments
+ *
+ */
+
+ /* missing:
+ * PWMATRIX
+ * PWDNAMATRIX
+ * PWGAPOPEN
+ * PWGAPEXT
+ */
+
+ /* multiple alignments
+ *
+ */
+ } else if (STR_NC_EQ("NEWTREE", &pcOldParam[1])) {
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--guidetree-out");
+ if (NULL != pcOldValue)
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
+
+ } else if (STR_NC_EQ("USETREE", &pcOldParam[1])) {
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--guidetree-in");
+ if (NULL != pcOldValue)
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
+
+ /* missing:
+ * MATRIX
+ * DNAMATRIX
+ * GAPOPEN
+ * GAPEXT
+ * ENDGAPS
+ * GAPDIST
+ * NOGAP
+ * NOHGAP
+ * HGAPRESIDUES
+ * MAXDIV
+ * TYPE already handled above
+ * TRANSWEIGHT
+ * ITERATION
+ * NUMITER
+ * NOWEIGHTS
+ */
+
+ /* profile alignments
+ *
+ */
+
+ /* missing:
+ * PROFILE
+ * NEWTREE1
+ * NEWTREE2
+ * USETREE1
+ * USETREE2
+ */
+
+ /* sequence to profile alignments
+ *
+ */
+ } else if (STR_NC_EQ("SEQUENCES", &pcOldParam[1])) {
+ fprintf(stderr, "WARNING: %s: %s\n", zcNotImplementedMsg, pcOldArg);
+
+ /* SEQUENCES and NEWTREE already handled above */
+
+ /* structure alignments
+ *
+ */
+
+ /* missing:
+ * NOSECSTR1
+ * NOSECSTR2
+ * SECSTROUT
+ * HELIXGAP
+ * STRANDGAP
+ * LOOPGAP
+ * TERMINALGAP
+ * HELIXENDIN
+ * HELIXENDOUT
+ * STRANDENDIN
+ * STRANDENDOUT
+ */
+
+ /* trees
+ *
+ */
+
+ /* missing:
+ * OUTPUTTREE
+ * SEED
+ * KIMURA
+ * TOSSGAPS
+ * BOOTLABELS
+ */
+#if 0
+ } else if (STR_NC_EQ("CLUSTERING", &pcOldParam[1])) {
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-c");
+ if (NULL != pcOldValue)
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(pcOldValue);
+#endif
+
+ } else {
+ fprintf(stderr,
+ "WARNING: Unsupported old command line option '%s' will be ignored\n",
+ pcOldArg);
+ }
+
+ /* FIXME: if not outfile was given, than the old default was to create a
+ * filename based on the input filename but with its extension replaced by
+ * aln. If the input already had the extension aln then the input was
+ * overwritten. What to do here? Strictly mimic the old behaviour?
+ */
+
+ free(pcOldArgCopy);
+}
+/* end ConvertOldCmdLineArg */
+
+
+
+/**
+ * @brief Convert old command line usage to new one. Mix of old and
+ * new style will be tolerated
+ *
+ * @param[out] iNewArgC_p
+ * The updated "argc"
+ * @param[out] ppcNewArgV_p
+ * The updated "argv". Caller has to free.
+ * @param[in] argc
+ * Original "argc"
+ * @param[in] argv
+ * Original argv
+ *
+ * @note old style parameters look like this:
+ * [/-]param[=value]
+ * new style parameters:
+ * -p [value]
+ * --param [value]
+ *
+ */
+void
+ConvertOldCmdline(int *iNewArgC_p, char ***ppcNewArgV_p, int argc, char **argv)
+{
+ bool bOldCmdlineDetected = false;
+ int i; /* aux */
+
+ /* we can have at most 2*argc converted arguments, plus the few
+ * that we set by default (.e.g --force)
+ */
+ (*ppcNewArgV_p) = (char **) CKCALLOC(argc*2+10, sizeof(char*));
+
+ /* copy first arg which is program name */
+ (*ppcNewArgV_p)[0] = CkStrdup(argv[0]);
+ *iNewArgC_p = 1;
+
+ for (i=1; i<argc; i++) {
+ bool bNewStyle = false;
+
+ if (strlen(argv[i])<=2) {
+ /* e.g. -i (param) or just numbers (value) */
+ bNewStyle = true;
+
+ } else if (strlen(argv[i])>2) {
+ if (argv[i][0] == '-' && argv[i][1] == '-') {
+ /* new style long opts */
+ bNewStyle = true;
+
+ } else if (argv[i][0]=='/' && (NULL!=strchr(&argv[i][1], '/'))) {
+ /* Slash used to be a valid replacement for dash in
+ * Clustal<=2, but could also be file in new style. If
+ * we find at least two slashes, one at the beginning,
+ * it should be a filename and therefore new style */
+ bNewStyle = true;
+
+ } else if (argv[i][0] != '/' && argv[i][0] != '-') {
+ /* old style opts always start with slash or dash */
+ bNewStyle = true;
+
+ }
+ }
+
+ /* copy and continue if new style arg or attempt to convert
+ * old style arg
+ */
+ if (bNewStyle) {
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup(argv[i]);
+ } else {
+ ConvertOldCmdLineArg(iNewArgC_p, ppcNewArgV_p, argv[i]);
+ /*LOG_DEBUG("old command line arg: %s", argv[i]);*/
+ bOldCmdlineDetected = true;
+ }
+ }
+
+ if (bOldCmdlineDetected) {
+ bool bOutfileOptSet = FALSE;
+ bool bOutFormatOptSet = FALSE;
+
+
+ /* old clustal used to write to a file called in.aln by
+ * default. set if not
+ * explicitely requested otherwisee
+ */
+ for (i=0; i<*iNewArgC_p; i++) {
+ const char *pcOpt = "-o";
+ if (strlen(pcOpt) <= strlen((*ppcNewArgV_p)[i])) {
+ if (0 == strncmp((*ppcNewArgV_p)[i], pcOpt, strlen(pcOpt))) {
+ bOutfileOptSet = TRUE;
+ break;
+ }
+ }
+ }
+ if (FALSE == bOutfileOptSet) {
+#ifdef TOO_LAZY_TO_IMPLEMENT_JUST_USING_DEFAULT_NAME_INSTEAD
+ char *pcDotPos = NULL;
+ char *pcInfileOpt = NULL;
+
+ /* get infile arg and find last dot in it. if found replace
+ * everything after with "aln", otherwise just add "aln"
+ */
+ for (i=0; i<*iNewArgC_p; i++) {
+ const char *pcOpt = "-i";
+ if (strlen(pcOpt) <= strlen((*ppcNewArgV_p)[i])) {
+ if (0 == strncmp((*ppcNewArgV_p)[i], pcOpt, strlen(pcOpt))) {
+ if (*iNewArgC_p<= i+1) {
+ fprintf(stderr,
+ "Oups...error while trying to convert old commandline (%s).\n",
+ "No more arguments left after -i");
+ exit(1);
+ }
+ pcInfileOpt = (*ppcNewArgV_p)[i+1];
+ break;
+ }
+ }
+ }
+ if (NULL == pcInfileOpt) {
+ fprintf(stderr,
+ "Oups...error while trying to convert old commandline (%s)\n",
+ "No infile opt found");
+ exit(1);
+ }
+
+ fprintf(stderr, "FIXME: unfinished\n");
+ exit(1);
+#endif
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-o");
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("clustal.aln");
+ }
+
+
+ /* old clustal used the clustal format by default. set if not
+ * explicitely requested otherwisee
+ */
+ for (i=0; i<*iNewArgC_p; i++) {
+ const char *pcOpt = "--outfmt";
+ if (strlen(pcOpt) <= strlen((*ppcNewArgV_p)[i])) {
+ if (0 == strncmp((*ppcNewArgV_p)[i], pcOpt, strlen(pcOpt))) {
+ bOutFormatOptSet = TRUE;
+ break;
+ }
+ }
+ }
+ if (FALSE == bOutFormatOptSet) {
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--outfmt=clustal");
+ }
+
+
+ /* old clustal was verbose by default
+ */
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("-v");
+
+ /* old clustal used to overwrite files by default
+ */
+ (*ppcNewArgV_p)[(*iNewArgC_p)++] = CkStrdup("--force");
+
+ fprintf(stderr,
+ "WARNING: Your old-style command-line options were converted to: ");
+ for (i=0; i<*iNewArgC_p; i++) {
+ fprintf(stderr, " %s", (*ppcNewArgV_p)[i]);
+ }
+ fprintf(stderr, "\n");
+ }
+
+}
+/* end ConvertOldCmdline */
+
+
+
+int
+main(int argc, char **argv)
+{
+ int new_argc = 0;
+ char **new_argv = NULL;
+ int i; /* aux */
+
+ ConvertOldCmdline(&new_argc, &new_argv, argc, argv);
+
+ MyMain(new_argc, new_argv);
+
+ for (i=0; i<new_argc; i++) {
+ free(new_argv[i]);
+ }
+ free(new_argv);
+
+ return 0;
+}
--- /dev/null
+/* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
+
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: mymain.c 255 2011-06-22 15:59:07Z fabian $
+ */
+
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include <stdio.h>
+#include <string.h>
+#include <assert.h>
+#include <unistd.h>
+#include <argtable2.h>
+#include <ctype.h>
+#include <limits.h>
+#include <libgen.h> /* for basename only */
+
+/* clustal */
+#include "clustal-omega.h"
+
+#include "mymain.h"
+
+/* hhalign (parameters) */
+#include "hhalign/general.h"
+
+typedef struct {
+
+ /* Sequence input
+ */
+ /** sequence type (from cmdline arg) */
+ int iSeqType;
+ /** sequence input file. not directly used by Align() */
+ char *pcSeqInfile;
+ /** Dealign sequences on input. Otherwise we use the alignment
+ * info for background-HMM creation */
+ bool bDealignInputSeqs;
+
+ /* profiles: : pre-aligned sequences, whose alignment will not be changed
+ */
+ /** profile 1: pre-aligned sequence input. not directly used by Align() */
+ char *pcProfile1Infile ;
+ /** profile 2: pre-aligned sequence input. not directly used by Align() */
+ char *pcProfile2Infile;
+
+ /** Input limitations
+ */
+ /** maximum allowed number of input sequences */
+ int iMaxNumSeq;
+ /** maximum allowed input sequence length */
+ int iMaxSeqLen;
+
+ /* Alignment output
+ */
+ /** alignment output file */
+ char *pcAlnOutfile;
+ /** alignment output format */
+ int iAlnOutFormat;
+ /** force overwriting of files */
+ bool bForceFileOverwrite;
+
+ /* multithreading
+ */
+ /** number of threads */
+ int iThreads;
+
+ /* logging
+ */
+ char *pcLogFile;
+
+ opts_t aln_opts;
+
+ /* changes here will have to be reflected in SetDefaultUserOpts(),
+ * FreeUserOpts(), PrintUserOpts() and UserOptsLogicCheck() etc
+ */
+} cmdline_opts_t;
+
+
+
+/* log-file used for non-essential logging in prLog */
+FILE *prLogFile = NULL;
+
+
+
+/**
+ * @brief Sets default user/commandline options
+ *
+ * @param[out] opts
+ * The option structure to initialise
+ *
+ */
+void
+SetDefaultUserOpts(cmdline_opts_t *opts)
+{
+
+ assert(NULL != opts);
+
+ opts->iSeqType = SEQTYPE_UNKNOWN;
+ opts->pcSeqInfile = NULL;
+ opts->bDealignInputSeqs = FALSE;
+ opts->pcProfile1Infile = NULL;
+ opts->pcProfile2Infile = NULL;
+
+ opts->iMaxNumSeq = INT_MAX;
+ opts->iMaxSeqLen = INT_MAX;
+
+ opts->pcAlnOutfile = NULL;
+ opts->iAlnOutFormat = MSAFILE_A2M;
+ opts->bForceFileOverwrite = FALSE;
+
+#ifdef HAVE_OPENMP
+ /* defaults to # of CPUs */
+ opts->iThreads = omp_get_max_threads();
+#else
+ opts->iThreads = 1;
+#endif
+
+ opts->pcLogFile = NULL;
+
+ SetDefaultAlnOpts(& opts->aln_opts);
+}
+/* end of SetDefaultAlnOpts() */
+
+
+
+
+/**
+ * @brief FIXME add doc
+ *
+ */
+void
+PrintUserOpts(FILE *prFile, cmdline_opts_t *opts) {
+
+ /* keep in same order as in struct. FIXME could this be derived from argtable?
+ */
+ /* we only allow protein anyway: fprintf(prFile, "seq-type = %s\n", SeqTypeToStr(opts->iSeqType)); */
+ fprintf(prFile, "option: seq-in = %s\n",
+ NULL != opts->pcSeqInfile? opts->pcSeqInfile: "(null)");
+ fprintf(prFile, "option: dealign = %d\n", opts->bDealignInputSeqs);
+ fprintf(prFile, "option: profile1 = %s\n",
+ NULL != opts->pcProfile1Infile? opts->pcProfile1Infile: "(null)");
+ fprintf(prFile, "option: profile2 = %s\n",
+ NULL != opts->pcProfile2Infile? opts->pcProfile2Infile: "(null)");
+ fprintf(prFile, "option: max-num-seq = %d\n", opts->iMaxNumSeq);
+ fprintf(prFile, "option: max-seq-len = %d\n", opts->iMaxSeqLen);
+ fprintf(prFile, "option: aln-out-file = %s\n",
+ NULL != opts->pcAlnOutfile? opts->pcAlnOutfile: "(null)");
+ fprintf(prFile, "option: aln-out-format = %s\n", SeqfileFormat2String(opts->iAlnOutFormat));
+ fprintf(prFile, "option: force-file-overwrite = %d\n", opts->bForceFileOverwrite);
+ fprintf(prFile, "option: threads = %d\n", opts->iThreads);
+ fprintf(prFile, "option: logFile = %s\n", opts->pcLogFile);
+}
+/* end of PrintUserOpts */
+
+
+
+/**
+ * @brief Frees user opt members allocated during parsing
+ *
+ * @param[out] user_opts
+ * user options whose members are to free
+ *
+ * @see ParseCommandLine()
+ *
+ */
+void
+FreeUserOpts(cmdline_opts_t *user_opts)
+{
+
+ if (NULL != user_opts->pcSeqInfile) {
+ CKFREE(user_opts->pcSeqInfile);
+ }
+ if (NULL != user_opts->pcProfile1Infile) {
+ CKFREE(user_opts->pcProfile1Infile);
+ }
+ if (NULL != user_opts->pcProfile2Infile) {
+ CKFREE(user_opts->pcProfile2Infile);
+ }
+ if (NULL != user_opts->pcAlnOutfile) {
+ CKFREE(user_opts->pcAlnOutfile);
+ }
+ if (NULL != user_opts->pcLogFile) {
+ CKFREE(user_opts->pcLogFile);
+ }
+
+ FreeAlnOpts(& user_opts->aln_opts);
+
+ return;
+}
+/* end of FreeUserOpts() */
+
+
+
+
+/**
+ * @brief Do quick&dirty logic check of used options and call Log(&rLog, LOG_FATAL, ) in case
+ * of any inconsistencies
+ *
+ * @param[in] opts
+ * option structure to check
+ *
+ */
+void
+UserOptsLogicCheck(cmdline_opts_t *opts)
+{
+ /* sequence input
+ *
+ */
+ if (NULL == opts->pcSeqInfile) {
+ if (NULL == opts->pcProfile1Infile && NULL == opts->pcProfile2Infile) {
+ Log(&rLog, LOG_FATAL, "No sequence input was provided. For more information try: --help");
+ }
+ } else {
+ if (NULL != opts->pcProfile1Infile && NULL != opts->pcProfile2Infile) {
+ Log(&rLog, LOG_FATAL, "Can't align two profile alignments AND a 'normal' sequence file");
+ }
+ }
+ /* if a profile was given it should always be no 1, not 2 */
+ if (NULL == opts->pcProfile1Infile && NULL != opts->pcProfile2Infile) {
+ Log(&rLog, LOG_FATAL, "Got a second profile, but no first one.");
+ }
+
+ /* alignment output
+ */
+ if (rLog.iLogLevelEnabled < LOG_WARN && NULL==opts->pcAlnOutfile && NULL==opts->pcLogFile) {
+ Log(&rLog, LOG_FATAL, "%s %s",
+ "You requested alignment output to stdout and verbose logging.",
+ " Alignment and log messages would get mixed up.");
+ }
+ /* distance matrix output impossible in mbed mode, only have clusters, FS, r254 -> */
+ if ( (NULL != opts->aln_opts.pcDistmatOutfile) && (TRUE == opts->aln_opts.bUseMbed) ) {
+ Log(&rLog, LOG_FATAL, "Distance Matrix output not possible in mBed mode.");
+ }
+}
+/* end of UserOptsLogicCheck */
+
+
+
+/**
+ * @brief Parse command line parameters. Will exit if help/usage etc
+ * are called or or call Log(&rLog, LOG_FATAL, ) if an error was detected.
+ *
+ * @param[out] user_opts
+ * User parameter struct, with defaults already set.
+ * @param[in] argc
+ * mains argc
+ * @param[in] argv
+ * mains argv
+ *
+ */
+void
+ParseCommandLine(cmdline_opts_t *user_opts, int argc, char **argv)
+{
+
+ /* argtable command line parsing:
+ * see
+ * http://argtable.sourceforge.net/doc/argtable2-intro.html
+ *
+ * basic structure is: arg_xxxN:
+ * xxx can be int, lit, db1, str, rex, file or date
+ * If N = 0, arguments may appear zero-or-once; N = 1 means
+ * exactly once, N = n means up to maxcount times
+ *
+ *
+ * @note: changes here, might also affect main.cpp:ConvertOldCmdLine()
+ *
+ */
+
+ struct arg_rem *rem_seq_input = arg_rem(NULL, "\nSequence Input:");
+ struct arg_file *opt_seqin = arg_file0("i", "in,infile",
+ "{<file>,-}",
+ "Multiple sequence input file (- for stdin)");
+ struct arg_file *opt_hmm_in = arg_filen(NULL, "hmm-in", "<file>",
+ /*min*/ 0, /*max*/ 128,
+ "HMM input files");
+ struct arg_lit *opt_dealign = arg_lit0(NULL, "dealign",
+ "Dealign input sequences");
+ struct arg_str *opt_seqtype = arg_str0("t", "seqtype",
+ "{Protein,RNA,DNA}",
+ "Force a sequence type (default: auto)");
+ struct arg_file *opt_profile1 = arg_file0(NULL, "profile1,p1",
+ "<file>",
+ "Pre-aligned multiple sequence file (aligned columns will be kept fix)");
+ struct arg_file *opt_profile2 = arg_file0(NULL, "profile2,p2",
+ "<file>",
+ "Pre-aligned multiple sequence file (aligned columns will be kept fix)");
+
+
+ struct arg_rem *rem_guidetree = arg_rem(NULL, "\nClustering:");
+ struct arg_str *opt_pairdist = arg_str0("p", "pairdist",
+ "{ktuple}",
+ "Pairwise alignment distance measure");
+ struct arg_file *opt_distmat_in = arg_file0(NULL, "distmat-in",
+ "<file>",
+ "Pairwise distance matrix input file (skips distance computation)");
+ struct arg_file *opt_distmat_out = arg_file0(NULL, "distmat-out",
+ "<file>",
+ "Pairwise distance matrix output file");
+ struct arg_file *opt_guidetree_in = arg_file0(NULL, "guidetree-in",
+ "<file>",
+ "Guide tree input file (skips distance computation and guide-tree clustering step)");
+ struct arg_file *opt_guidetree_out = arg_file0(NULL, "guidetree-out",
+ "<file>",
+ "Guide tree output file");
+ /* AW: mbed is default since at least R253
+ struct arg_lit *opt_mbed = arg_lit0(NULL, "mbed",
+ "Fast, Mbed-like clustering for guide-tree calculation");
+ struct arg_lit *opt_mbed_iter = arg_lit0(NULL, "mbed-iter",
+ "Use Mbed-like clustering also during iteration");
+ */
+ /* Note: might be better to use arg_str (mbed=YES/NO) but I don't want to introduce an '=' into pipeline, FS, r250 -> */
+ struct arg_lit *opt_full = arg_lit0(NULL, "full",
+ "Use full distance matrix for guide-tree calculation (might be slow; mBed is default)");
+ struct arg_lit *opt_full_iter = arg_lit0(NULL, "full-iter",
+ "Use full distance matrix for guide-tree calculation during iteration (might be slowish; mBed is default)");
+
+ struct arg_str *opt_clustering = arg_str0("c", "clustering",
+ "{UPGMA}",
+ "Clustering method for guide tree");
+
+
+ struct arg_rem *rem_aln_output = arg_rem(NULL, "\nAlignment Output:");
+ struct arg_file *opt_outfile = arg_file0("o", "out,outfile",
+ "{file,-}",
+ "Multiple sequence alignment output file (default: stdout)");
+ struct arg_str *opt_outfmt = arg_str0(NULL, "outfmt",
+ "{a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]}",
+ "MSA output file format (default: fasta)");
+
+
+ struct arg_rem *rem_iteration = arg_rem(NULL, "\nIteration:");
+ struct arg_str *opt_num_iterations = arg_str0(NULL, "iterations,iter",
+ /* FIXME "{<n>,auto}", "Number of combined guide-tree/HMM iterations"); */
+ "<n>", "Number of (combined guide-tree/HMM) iterations");
+ struct arg_int *opt_max_guidetree_iterations = arg_int0(NULL, "max-guidetree-iterations",
+ "<n>", "Maximum number guidetree iterations");
+ struct arg_int *opt_max_hmm_iterations = arg_int0(NULL, "max-hmm-iterations",
+ "<n>", "Maximum number of HMM iterations");
+
+
+ struct arg_rem *rem_limits = arg_rem(NULL, "\nLimits (will exit early, if exceeded):");
+ struct arg_int *opt_max_seq = arg_int0(NULL, "maxnumseq", "<n>",
+ "Maximum allowed number of sequences");
+ struct arg_int *opt_max_seqlen = arg_int0(NULL, "maxseqlen", "<l>",
+ "Maximum allowed sequence length");
+
+
+ struct arg_rem *rem_misc = arg_rem(NULL, "\nMiscellaneous:");
+
+ struct arg_lit *opt_autooptions = arg_lit0(NULL, "auto",
+ "Set options automatically (might overwrite some of your options)");
+ struct arg_int *opt_threads = arg_int0(NULL, "threads", "<n>",
+ "Number of processors to use");
+ struct arg_file *opt_logfile = arg_file0("l", "log",
+ "<file>",
+ "Log all non-essential output to this file");
+ struct arg_lit *opt_help = arg_lit0("h", "help",
+ "Print this help and exit");
+ struct arg_lit *opt_version = arg_lit0(NULL, "version",
+ "Print version information and exit");
+ struct arg_lit *opt_long_version = arg_lit0(NULL, "long-version",
+ "Print long version information and exit");
+ struct arg_lit *opt_verbose = arg_litn("v", "verbose",
+ 0, 3,
+ "Verbose output (increases if given multiple times)");
+ struct arg_lit *opt_force = arg_lit0(NULL, "force",
+ "Force file overwriting");
+ struct arg_int *opt_macram = arg_int0(NULL, "MAC-RAM", "<n>", /* keep this quiet for the moment, FS r240 -> */
+ NULL/*"maximum amount of RAM to use for MAC algorithm (in MB)"*/);
+
+
+ struct arg_end *opt_end = arg_end(10); /* maximum number of errors
+ * to store */
+
+ void *argtable[] = {rem_seq_input,
+ opt_seqin,
+ opt_hmm_in,
+ opt_dealign,
+#if 0
+ /* unused since we only support protein for now */
+ opt_seqtype,
+#endif
+ opt_profile1,
+ opt_profile2,
+
+ rem_guidetree,
+#if 0
+ /* no other options then default available or not implemented */
+ opt_pairdist,
+#endif
+ opt_distmat_in,
+ opt_distmat_out,
+ opt_guidetree_in,
+ opt_guidetree_out,
+ opt_full, /* FS, r250 -> */
+ opt_full_iter, /* FS, r250 -> */
+#if 0
+ /* no other options then default available */
+ opt_clustering,
+#endif
+ rem_aln_output,
+ opt_outfile,
+ opt_outfmt,
+
+ rem_iteration,
+ opt_num_iterations,
+ opt_max_guidetree_iterations,
+ opt_max_hmm_iterations,
+
+ rem_limits,
+ opt_max_seq,
+ opt_max_seqlen,
+
+ rem_misc,
+ opt_autooptions,
+ opt_threads,
+ opt_logfile,
+ opt_help,
+ opt_verbose,
+ opt_version,
+ opt_long_version,
+ opt_force,
+ opt_macram, /* FS, r240 -> r241 */
+
+ opt_end};
+ int nerrors;
+
+
+ /* Verify the argtable[] entries were allocated sucessfully
+ */
+ if (arg_nullcheck(argtable)) {
+ Log(&rLog, LOG_FATAL, "insufficient memory (for argtable allocation)");
+ }
+
+ /* Parse the command line as defined by argtable[]
+ */
+ nerrors = arg_parse(argc, argv, argtable);
+
+ /* Special case: '--help' takes precedence over error reporting
+ */
+ if (opt_help->count > 0) {
+ printf("%s - %s (%s)\n", PACKAGE_NAME, PACKAGE_VERSION, PACKAGE_CODENAME);
+
+ printf("\n");
+ printf("Check http://www.clustal.org for more information and updates.\n");
+
+ /*printf("\n");
+ printf("FIXME more info e.g. how it works, pointers to references etc...\n");
+ FIXME which paper to cite etc
+ */
+
+
+ printf("\n");
+ printf("Usage: %s", basename(argv[0]));
+ arg_print_syntax(stdout,argtable, "\n");
+
+ printf("\n");
+ printf("A typical invocation would be: %s -i my-in-seqs.fa -o my-out-seqs.fa -v\n",
+ basename(argv[0]));
+ printf("See below for a list of all options.\n");
+
+ arg_print_glossary(stdout, argtable, " %-25s %s\n");
+ arg_freetable(argtable, sizeof(argtable)/sizeof(argtable[0]));
+ exit(EXIT_SUCCESS);
+ }
+
+ /* Special case: '--version' takes precedence over error reporting
+ */
+ if (opt_version->count > 0) {
+ printf("%s\n", PACKAGE_VERSION);
+ arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
+ exit(EXIT_SUCCESS);
+ }
+
+ /* Special case: '--long-version' takes precedence over error reporting
+ */
+ if (opt_long_version->count > 0) {
+ char zcLongVersion[1024];
+ PrintLongVersion(zcLongVersion, sizeof(zcLongVersion));
+ printf("%s\n", zcLongVersion);
+ arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
+ exit(EXIT_SUCCESS);
+ }
+
+ /* If the parser returned any errors then display them and exit
+ */
+ if (nerrors > 0) {
+ /* Display the error details contained in the arg_end struct.*/
+ arg_print_errors(stdout, opt_end, PACKAGE);
+ fprintf(stderr, "For more information try: %s --help\n", argv[0]);
+ arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
+ exit(EXIT_FAILURE);
+ }
+
+
+ /* ------------------------------------------------------------
+ *
+ * Command line successfully parsed. Now transfer values to
+ * user_opts. While doing so, make sure that given input files
+ * exist and given output files are writable do not exist, or if
+ * they do, should be overwritten.
+ *
+ * No logic checks here! They are done in a different function
+ *
+ * ------------------------------------------------------------*/
+
+
+ /* not part of user_opts because it declared in src/util.h */
+ if (0 == opt_verbose->count) {
+ rLog.iLogLevelEnabled = LOG_WARN;
+ } else if (1 == opt_verbose->count) {
+ rLog.iLogLevelEnabled = LOG_INFO;
+ } else if (2 == opt_verbose->count) {
+ rLog.iLogLevelEnabled = LOG_VERBOSE;
+ } else if (3 == opt_verbose->count) {
+ rLog.iLogLevelEnabled = LOG_DEBUG;
+ }
+
+ user_opts->aln_opts.bAutoOptions = opt_autooptions->count;
+
+ user_opts->bDealignInputSeqs = opt_dealign->count;
+
+ /* NOTE: full distance matrix used to be default - there was
+ --mbed flag but no --full flag after r250 decided that mBed
+ should be default - now need --full flag to turn off mBed.
+ wanted to retain mBed Boolean, so simply added --full flag. if
+ both flags set (erroneously) want --mbed to overwrite --full,
+ therefore do --full 1st, the --mbed, FS, r250 */
+ if (opt_full->count){
+ user_opts->aln_opts.bUseMbed = FALSE;
+ }
+
+ if (opt_full_iter->count){
+ user_opts->aln_opts.bUseMbedForIteration = FALSE;
+ }
+
+ user_opts->bForceFileOverwrite = opt_force->count;
+
+
+
+ /* log-file
+ */
+ if (opt_logfile->count > 0) {
+ user_opts->pcLogFile = CkStrdup(opt_logfile->filename[0]);
+
+ /* warn if already exists or not writable */
+ if (FileExists(user_opts->pcLogFile) && ! user_opts->bForceFileOverwrite) {
+ Log(&rLog, LOG_FATAL, "%s '%s'. %s",
+ "Cowardly refusing to overwrite already existing file",
+ user_opts->pcLogFile,
+ "Use --force to force overwriting.");
+ }
+ if (! FileIsWritable(user_opts->pcLogFile)) {
+ Log(&rLog, LOG_FATAL, "Sorry, I do not have permission to write to file '%s'.",
+ user_opts->pcLogFile);
+ }
+ }
+
+
+ /* normal sequence input (no profile)
+ */
+ if (opt_seqin->count > 0) {
+ user_opts->pcSeqInfile = CkStrdup(opt_seqin->filename[0]);
+ }
+
+ /* Input limitations
+ */
+ /* maximum number of sequences */
+ if (opt_max_seq->count > 0) {
+ user_opts->iMaxNumSeq = opt_max_seq->ival[0];
+ }
+
+ /* maximum sequence length */
+ if (opt_max_seqlen->count > 0) {
+ user_opts->iMaxSeqLen = opt_max_seqlen->ival[0];
+ }
+
+ /* Sequence type
+ */
+ if (opt_seqtype->count > 0) {
+ if (STR_NC_EQ(opt_seqtype->sval[0], "protein")) {
+ user_opts->iSeqType = SEQTYPE_PROTEIN;
+ } else if (STR_NC_EQ(opt_seqtype->sval[0], "rna")) {
+ user_opts->iSeqType = SEQTYPE_RNA;
+ } else if (STR_NC_EQ(opt_seqtype->sval[0], "dna")) {
+ user_opts->iSeqType = SEQTYPE_DNA;
+ } else {
+ Log(&rLog, LOG_FATAL, "Unknown sequence type '%s'", opt_seqtype->sval[0]);
+ }
+ }
+
+ /* Profile input
+ */
+ if (opt_profile1->count > 0) {
+ user_opts->pcProfile1Infile = CkStrdup(opt_profile1->filename[0]);
+ if (! FileExists(user_opts->pcProfile1Infile)) {
+ Log(&rLog, LOG_FATAL, "File '%s' does not exist.", user_opts->pcProfile1Infile);
+ }
+ }
+
+ if (opt_profile2->count > 0) {
+ user_opts->pcProfile2Infile = CkStrdup(opt_profile2->filename[0]);
+ if (! FileExists(user_opts->pcProfile2Infile)) {
+ Log(&rLog, LOG_FATAL, "File '%s' does not exist.", user_opts->pcProfile2Infile);
+ }
+ }
+
+
+ /* HMM input
+ */
+ user_opts->aln_opts.iHMMInputFiles = 0;
+ user_opts->aln_opts.ppcHMMInput = NULL;
+ if (opt_hmm_in->count>0) {
+ int iAux;
+ user_opts->aln_opts.iHMMInputFiles = opt_hmm_in->count;
+ user_opts->aln_opts.ppcHMMInput = (char **) CKMALLOC(
+ user_opts->aln_opts.iHMMInputFiles * sizeof(char*));
+ for (iAux=0; iAux<opt_hmm_in->count; iAux++) {
+ user_opts->aln_opts.ppcHMMInput[iAux] = CkStrdup(opt_hmm_in->filename[iAux]);
+ if (! FileExists(user_opts->aln_opts.ppcHMMInput[iAux])) {
+ Log(&rLog, LOG_FATAL, "File '%s' does not exist.", user_opts->aln_opts.ppcHMMInput[iAux]);
+ }
+ }
+ }
+
+
+ /* Pair distance method
+ */
+ if (opt_pairdist->count > 0) {
+ if (STR_NC_EQ(opt_pairdist->sval[0], "ktuple")) {
+ user_opts->aln_opts.iPairDistType = PAIRDIST_KTUPLE;
+ } else {
+ Log(&rLog, LOG_FATAL, "Unknown pairdist method '%s'", opt_pairdist->sval[0]);
+ }
+ }
+
+
+ /* Distance matrix input
+ */
+ if (opt_distmat_in->count > 0) {
+ user_opts->aln_opts.pcDistmatInfile = CkStrdup(opt_distmat_in->filename[0]);
+ if (! FileExists(user_opts->aln_opts.pcDistmatInfile)) {
+ Log(&rLog, LOG_FATAL, "File '%s' does not exist.", user_opts->aln_opts.pcDistmatInfile);
+ }
+ }
+
+
+ /* Distance matrix output
+ */
+ if (opt_distmat_out->count > 0) {
+ user_opts->aln_opts.pcDistmatOutfile = CkStrdup(opt_distmat_out->filename[0]);
+
+ /* warn if already exists or not writable */
+ if (FileExists(user_opts->aln_opts.pcDistmatOutfile) && ! user_opts->bForceFileOverwrite) {
+ Log(&rLog, LOG_FATAL, "%s '%s'. %s",
+ "Cowardly refusing to overwrite already existing file",
+ user_opts->aln_opts.pcDistmatOutfile,
+ "Use --force to force overwriting.");
+ }
+ if (! FileIsWritable(user_opts->aln_opts.pcDistmatOutfile)) {
+ Log(&rLog, LOG_FATAL, "Sorry, I do not have permission to write to file '%s'.",
+ user_opts->aln_opts.pcDistmatOutfile);
+ }
+ }
+
+ /* Clustering
+ *
+ */
+ if (opt_clustering->count > 0) {
+ if (STR_NC_EQ(opt_clustering->sval[0], "upgma")) {
+ user_opts->aln_opts.iClusteringType = CLUSTERING_UPGMA;
+ } else {
+ Log(&rLog, LOG_FATAL, "Unknown guide-tree clustering method '%s'", opt_clustering->sval[0]);
+ }
+ }
+
+
+ /* Guidetree input
+ */
+ if (opt_guidetree_in->count > 0) {
+ user_opts->aln_opts.pcGuidetreeInfile = CkStrdup(opt_guidetree_in->filename[0]);
+ if (! FileExists(user_opts->aln_opts.pcGuidetreeInfile)) {
+ Log(&rLog, LOG_FATAL, "File '%s' does not exist.", user_opts->aln_opts.pcGuidetreeInfile);
+ }
+ }
+
+
+ /* Guidetree output
+ */
+ if (opt_guidetree_out->count > 0) {
+ user_opts->aln_opts.pcGuidetreeOutfile = CkStrdup(opt_guidetree_out->filename[0]);
+
+ /* warn if already exists or not writable */
+ if (FileExists(user_opts->aln_opts.pcGuidetreeOutfile) && ! user_opts->bForceFileOverwrite) {
+ Log(&rLog, LOG_FATAL, "%s '%s'. %s",
+ "Cowardly refusing to overwrite already existing file",
+ user_opts->aln_opts.pcGuidetreeOutfile,
+ "Use --force to force overwriting.");
+ }
+ if (! FileIsWritable(user_opts->aln_opts.pcGuidetreeOutfile)) {
+ Log(&rLog, LOG_FATAL, "Sorry, I do not have permission to write to file '%s'.",
+ user_opts->aln_opts.pcGuidetreeOutfile);
+ }
+ }
+
+
+ /* max guidetree iterations
+ */
+ if (opt_max_guidetree_iterations->count > 0) {
+ user_opts->aln_opts.iMaxGuidetreeIterations = opt_max_guidetree_iterations->ival[0];
+ }
+
+
+ /* max guidetree iterations
+ */
+ if (opt_max_hmm_iterations->count > 0) {
+ user_opts->aln_opts.iMaxHMMIterations = opt_max_hmm_iterations->ival[0];
+ }
+
+ /* number of iterations
+ */
+ if (opt_num_iterations->count > 0) {
+ if (STR_NC_EQ(opt_num_iterations->sval[0], "auto")) {
+ Log(&rLog, LOG_FATAL, "Automatic iteration not supported at the moment.");
+ user_opts->aln_opts.bIterationsAuto = TRUE;
+
+ } else {
+ int iAux;
+ user_opts->aln_opts.bIterationsAuto = FALSE;
+ for (iAux=0; iAux<(int)strlen(opt_num_iterations->sval[0]); iAux++) {
+ if (! isdigit(opt_num_iterations->sval[0][iAux])) {
+ Log(&rLog, LOG_FATAL, "Couldn't iteration parameter: %s",
+ opt_num_iterations->sval[0]);
+ }
+ }
+ user_opts->aln_opts.iNumIterations = atoi(opt_num_iterations->sval[0]);
+ }
+ }
+
+
+ /* Alignment output
+ */
+ if (opt_outfile->count > 0) {
+ user_opts->pcAlnOutfile = CkStrdup(opt_outfile->filename[0]);
+
+ /* warn if already exists or not writable */
+ if (FileExists(user_opts->pcAlnOutfile) && ! user_opts->bForceFileOverwrite) {
+ Log(&rLog, LOG_FATAL, "%s '%s'. %s",
+ "Cowardly refusing to overwrite already existing file",
+ user_opts->pcAlnOutfile,
+ "Use --force to force overwriting.");
+ }
+ if (! FileIsWritable(user_opts->pcAlnOutfile)) {
+ Log(&rLog, LOG_FATAL, "Sorry, I do not have permission to write to file '%s'.",
+ user_opts->pcAlnOutfile);
+ }
+ }
+
+
+ /* Output format
+ */
+ if (opt_outfmt->count > 0) {
+ /* avoid gcc warning about discarded qualifier */
+ char *tmp = (char *)opt_outfmt->sval[0];
+ user_opts->iAlnOutFormat = String2SeqfileFormat(tmp);
+ if (SQFILE_UNKNOWN == user_opts->iAlnOutFormat) {
+ Log(&rLog, LOG_FATAL, "Unknown output format '%s'", opt_outfmt->sval[0]);
+ }
+ }
+
+ /* Number of threads
+ */
+#ifdef HAVE_OPENMP
+ if (opt_threads->count > 0) {
+ if (opt_threads->ival[0] <= 0) {
+ Log(&rLog, LOG_FATAL, "Changing number of threads to %d doesn't make sense.",
+ opt_threads->ival[0]);
+ }
+ user_opts->iThreads = opt_threads->ival[0];
+ }
+
+#else
+ if (opt_threads->count > 0) {
+ if (opt_threads->ival[0] > 1) {
+ Log(&rLog, LOG_FATAL, "Cannot change number of threads to %d. %s was build without OpenMP support.",
+ opt_threads->ival[0], PACKAGE_NAME);
+ }
+ }
+#endif
+
+
+ /* max MAC RAM (maximum amount of RAM set aside for MAC algorithm)
+ */
+ if (opt_macram->count > 0) { /* FS, r240 -> r241 */
+ user_opts->aln_opts.iMacRam = opt_macram->ival[0];
+ }
+
+
+
+ arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
+
+ UserOptsLogicCheck(user_opts);
+
+ return;
+}
+/* end of ParseCommandLine() */
+
+
+
+
+/**
+ *
+ * @brief the 'real' main function
+ *
+ */
+int
+MyMain(int argc, char **argv)
+{
+ mseq_t *prMSeq = NULL;
+ mseq_t *prMSeqProfile1 = NULL;
+ mseq_t *prMSeqProfile2 = NULL;
+ cmdline_opts_t cmdline_opts;
+ hhalign_para rHhalignPara = {0};
+
+ /* Must happen first: setup logger */
+ LogDefaultSetup(&rLog);
+
+ /*Log(&rLog, LOG_WARN, "This is a non-public realase of %s. Please do not distribute.", PACKAGE_NAME);*/
+ Log(&rLog, LOG_WARN, "This is a beta version of %s, for protein only.", PACKAGE_NAME); /* FS, r237 -> 238 */
+
+ SetDefaultUserOpts(&(cmdline_opts));
+
+ ParseCommandLine(&cmdline_opts, argc, argv);
+
+ if (NULL != cmdline_opts.pcLogFile) {
+ prLogFile = fopen(cmdline_opts.pcLogFile, "w");
+ LogSetFP(&rLog, LOG_INFO, prLogFile);
+ LogSetFP(&rLog, LOG_VERBOSE, prLogFile);
+ LogSetFP(&rLog, LOG_DEBUG, prLogFile);
+ }
+
+ InitClustalOmega(cmdline_opts.iThreads);
+
+ if (rLog.iLogLevelEnabled < LOG_INFO) {
+ PrintUserOpts(LogGetFP(&rLog, LOG_INFO), & cmdline_opts);
+ PrintAlnOpts(LogGetFP(&rLog, LOG_INFO), & (cmdline_opts.aln_opts));
+ }
+ /* write relevant command-line options for hhalign
+ *
+ */
+ rHhalignPara.iMacRamMB = cmdline_opts.aln_opts.iMacRam;
+
+ /* Read sequence file
+ *
+ */
+ if (NULL != cmdline_opts.pcSeqInfile) {
+ NewMSeq(&prMSeq);
+ if (ReadSequences(prMSeq, cmdline_opts.pcSeqInfile,
+ cmdline_opts.iSeqType,
+ cmdline_opts.iMaxNumSeq, cmdline_opts.iMaxSeqLen)) {
+ Log(&rLog, LOG_FATAL, "Reading sequence file '%s' failed", cmdline_opts.pcSeqInfile);
+ }
+#if TRACE
+ {
+ int iAux;
+ for (iAux=0; iAux<prMSeq->nseqs; iAux++) {
+ Log(&rLog, LOG_FORCED_DEBUG, "seq no %d: seq = %s", iAux, prMSeq->seq[iAux]);
+ LogSqInfo(&prMSeq->sqinfo[iAux]);
+ }
+ }
+#endif
+ }
+ /* k-tuple pairwise distance calculation seg-faults if
+ * only one sequence, simply exit early.
+ * note that for profile/profile alignment prMSeq is NULL
+ * FS, r222->r223 */
+ if (prMSeq && (prMSeq->nseqs <= 1)){
+ Log(&rLog, LOG_FATAL, "File '%s' contains %d sequence%s, nothing to align",
+ cmdline_opts.pcSeqInfile, prMSeq->nseqs, 1==prMSeq->nseqs?"":"s");
+ }
+
+ /* Dealign if requested and neccessary
+ */
+ if (NULL != prMSeq) {
+ if (TRUE == prMSeq->aligned && cmdline_opts.bDealignInputSeqs) {
+ Log(&rLog, LOG_INFO, "Dealigning already aligned input sequences as requested.");
+ DealignMSeq(prMSeq);
+ }
+ }
+
+
+ /* Read profile1
+ *
+ */
+ if (NULL != cmdline_opts.pcProfile1Infile) {
+ NewMSeq(&prMSeqProfile1);
+ if (ReadSequences(prMSeqProfile1, cmdline_opts.pcProfile1Infile,
+ cmdline_opts.iSeqType,
+ cmdline_opts.iMaxNumSeq, cmdline_opts.iMaxSeqLen)) {
+ Log(&rLog, LOG_FATAL, "Reading sequences from profile file '%s' failed",
+ cmdline_opts.pcProfile1Infile);
+ }
+ /* FIXME: commented out. FS, r240 -> r241
+ * for explanation see below */
+ /*if (1==prMSeqProfile1->nseqs) {
+ Log(&rLog, LOG_FATAL, "'%s' contains only one sequence and can therefore not be used as a profile",
+ cmdline_opts.pcProfile1Infile);
+ }*/
+ if (FALSE == prMSeqProfile1->aligned) {
+ Log(&rLog, LOG_FATAL, "Sequences in '%s' are not aligned, i.e. this is not a profile",
+ cmdline_opts.pcProfile1Infile);
+ }
+ }
+
+
+
+ /* Read profile2
+ *
+ */
+ if (NULL != cmdline_opts.pcProfile2Infile) {
+ NewMSeq(&prMSeqProfile2);
+ if (ReadSequences(prMSeqProfile2, cmdline_opts.pcProfile2Infile,
+ cmdline_opts.iSeqType,
+ cmdline_opts.iMaxNumSeq, cmdline_opts.iMaxSeqLen)) {
+ Log(&rLog, LOG_FATAL, "Reading sequences from profile file '%s' failed",
+ cmdline_opts.pcProfile2Infile);
+ }
+ /* FIXME: there is no (clean) way to align a single sequence to a profile.
+ * if we go down the -i route, it causes a seg-fault in the pair-wise
+ * k-tuple distance calculation. However, single sequences can be
+ * understood as 1-profiles. Therefore we have to allow for 1-profiles.
+ * FS, r240 -> r241
+ */
+ /*if (1==prMSeqProfile2->nseqs) {
+ Log(&rLog, LOG_FATAL, "'%s' contains only one sequence and can therefore not be used as a profile",
+ cmdline_opts.pcProfile2Infile);
+ }*/
+ if (FALSE == prMSeqProfile1->aligned) {
+ Log(&rLog, LOG_FATAL, "Sequences in '%s' are not aligned, i.e. this is not a profile",
+ cmdline_opts.pcProfile2Infile);
+ }
+ }
+
+
+ /* Depending on the input we got perform
+ *
+ * (i) normal alignment: seq + optional profile
+ * or
+ * (ii) profile profile alignment
+ *
+ */
+ if (NULL != prMSeq) {
+ if (Align(prMSeq, prMSeqProfile1, & cmdline_opts.aln_opts, rHhalignPara)) {
+ Log(&rLog, LOG_FATAL, "An error occured during the alignment");
+ }
+
+ if (WriteAlignment(prMSeq, cmdline_opts.pcAlnOutfile,
+ cmdline_opts.iAlnOutFormat)) {
+ Log(&rLog, LOG_FATAL, "Could not save alignment to %s", cmdline_opts.pcAlnOutfile);
+ }
+#if 0
+ {
+ bool bSampling = FALSE; /* better set to TRUE for many sequences */
+ bool bReportAll = TRUE;
+ AliStat(prMSeq, bSampling, bReportAll);
+ }
+#endif
+
+
+ } else if (NULL != prMSeqProfile1 && NULL != prMSeqProfile2) {
+ if (AlignProfiles(prMSeqProfile1, prMSeqProfile2, rHhalignPara)) {
+ Log(&rLog, LOG_FATAL, "An error occured during the alignment");
+ }
+ if (WriteAlignment(prMSeqProfile1, cmdline_opts.pcAlnOutfile,
+ cmdline_opts.iAlnOutFormat)) {
+ Log(&rLog, LOG_FATAL, "Could not save alignment to %s", cmdline_opts.pcAlnOutfile);
+ }
+ }
+
+
+ /* cleanup
+ */
+ if (NULL != prMSeq) {
+ FreeMSeq(&prMSeq);
+ }
+ if (NULL != prMSeqProfile1) {
+ FreeMSeq(&prMSeqProfile1);
+ }
+ if (NULL != prMSeqProfile2) {
+ FreeMSeq(&prMSeqProfile2);
+ }
+
+ FreeUserOpts(&cmdline_opts);
+
+ Log(&rLog, LOG_DEBUG, "Successful program exit");
+
+ if (NULL != cmdline_opts.pcLogFile) {
+ fclose(prLogFile);
+ }
+ return EXIT_SUCCESS;
+}
+/* end of MyMain() */
+
+
--- /dev/null
+/*********************************************************************
+ * Clustal Omega - Multiple sequence alignment
+ *
+ * Copyright (C) 2010 University College Dublin
+ *
+ * Clustal-Omega is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation; either version 2 of the
+ * License, or (at your option) any later version.
+ *
+ * This file is part of Clustal-Omega.
+ *
+ ********************************************************************/
+
+/*
+ * RCS $Id: mymain.h 97 2010-07-12 15:30:26Z andreas $
+ */
+
+
+extern int
+MyMain(int argc, char **argv);
+
+
--- /dev/null
+SQUID - library of functions for biological sequence analysis
+Copyright (C) 1992-2002 Washington University School of Medicine
+
+SQUID is a freely redistributable library of C code functions for
+sequence analysis. SQUID also includes a number of small utility
+programs.
+
+To install squid, see the file:
+ INSTALL -- instructions for installing the programs
+
+If you have any questions about redistributing squid or using
+squid code in your own work, see the files:
+ COPYRIGHT -- copyright notice, and information on my distribution policy
+ LICENSE -- version 2 of the GNU Public License (see COPYRIGHT)
+
+For a web page with more information on squid, see:
+ http://www.genetics.wustl.edu/eddy/software/#squid
+
+You can always download the latest stable release of squid from:
+ ftp://ftp.genetics.wustl.edu/pub/eddy/software/squid.tar.gz
+
+The development codebase is available by anonymous CVS:
+ cvs -d :pserver:anonymous@skynet.wustl.edu:/repository/sre login
+ (password "anonymous")
+ cvs -d :pserver:anonymous@skynet.wustl.edu:/repository/sre checkout squid
+
+If you encounter any bugs in this library, or you have any questions
+or comments, please e-mail me at the address below. Due to limited
+personal time, I may not respond, but I do read all my mail.
+
+ Sean Eddy
+ eddy@genetics.wustl.edu
+
+ HHMI/Dept. of Genetics
+ Washington University School of Medicine
+ 660 South Euclid Box 8232
+ Saint Louis Missouri 63110
+ USA
+
--- /dev/null
+SQUID - a library of functions for biological sequence analysis
+Copyright (C) 1992-2002 Washington University School of Medicine
+All Rights Reserved
+
+This suite of programs is free software. You can redistribute it
+and/or modify it under the terms of the GNU General Public License as
+published by the Free Software Foundation; either version 2 of the
+License, or (at your option) any later version.
+
+In other words, you are free to modify, copy, or redistribute this
+source code and its documentation in any way you like, but you must
+distribute all derivative versions as free software under the same
+terms that I've provided my code to you (i.e. the GNU General Public
+License). This precludes any use of the code in proprietary or
+commercial software unless your source code is made freely available.
+
+If you wish to use SQUID code under a different Open Source license
+that's not compatible with the GPL (like the Artistic License, BSD
+license, or the Netscape Public License), please contact me
+(eddy@genetics.wustl.edu) for permission.
+
+Incorporation into commercial software under non-GPL terms is
+possible, by arranging a license with the Washington University School
+of Medicine Center for Technology Management (CTM). For this purpose,
+the CTM is authorized to negotiate on behalf of the Howard Hughes
+Medical Institute, the other copyright holder on the code. Certain
+third party code modules may have to be removed from a non-GPL
+distribution. Contact Jack Pincus (jhpincus@cris.com) to arrange
+non-GPL licensing terms.
+
+This software is distributed in the hope that it will be useful, but
+WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this HMMER release, in the file LICENSE; if not, write to
+the Free Software Foundation, Inc., 675 Mass. Ave, Cambridge, MA 02139
+USA.
+
+
--- /dev/null
+ GNU GENERAL PUBLIC LICENSE
+ Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+ 675 Mass Ave, Cambridge, MA 02139, USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
+ The licenses for most software are designed to take away your
+freedom to share and change it. By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users. This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it. (Some other Free Software Foundation software is covered by
+the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+ When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+ To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+ For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have. You must make sure that they, too, receive or can get the
+source code. And you must show them these terms so they know their
+rights.
+
+ We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+ Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software. If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
+that any problems introduced by others will not reflect on the original
+authors' reputations.
+
+ Finally, any free program is threatened constantly by software
+patents. We wish to avoid the danger that redistributors of a free
+program will individually obtain patent licenses, in effect making the
+program proprietary. To prevent this, we have made it clear that any
+patent must be licensed for everyone's free use or not licensed at all.
+
+ The precise terms and conditions for copying, distribution and
+modification follow.
+\f
+ GNU GENERAL PUBLIC LICENSE
+ TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+ 0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
+under the terms of this General Public License. The "Program", below,
+refers to any such program or work, and a "work based on the Program"
+means either the Program or any derivative work under copyright law:
+that is to say, a work containing the Program or a portion of it,
+either verbatim or with modifications and/or translated into another
+language. (Hereinafter, translation is included without limitation in
+the term "modification".) Each licensee is addressed as "you".
+
+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope. The act of
+running the Program is not restricted, and the output from the Program
+is covered only if its contents constitute a work based on the
+Program (independent of having been made by running the Program).
+Whether that is true depends on what the Program does.
+
+ 1. You may copy and distribute verbatim copies of the Program's
+source code as you receive it, in any medium, provided that you
+conspicuously and appropriately publish on each copy an appropriate
+copyright notice and disclaimer of warranty; keep intact all the
+notices that refer to this License and to the absence of any warranty;
+and give any other recipients of the Program a copy of this License
+along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and
+you may at your option offer warranty protection in exchange for a fee.
+
+ 2. You may modify your copy or copies of the Program or any portion
+of it, thus forming a work based on the Program, and copy and
+distribute such modifications or work under the terms of Section 1
+above, provided that you also meet all of these conditions:
+
+ a) You must cause the modified files to carry prominent notices
+ stating that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in
+ whole or in part contains or is derived from the Program or any
+ part thereof, to be licensed as a whole at no charge to all third
+ parties under the terms of this License.
+
+ c) If the modified program normally reads commands interactively
+ when run, you must cause it, when started running for such
+ interactive use in the most ordinary way, to print or display an
+ announcement including an appropriate copyright notice and a
+ notice that there is no warranty (or else, saying that you provide
+ a warranty) and that users may redistribute the program under
+ these conditions, and telling the user how to view a copy of this
+ License. (Exception: if the Program itself is interactive but
+ does not normally print such an announcement, your work based on
+ the Program is not required to print an announcement.)
+\f
+These requirements apply to the modified work as a whole. If
+identifiable sections of that work are not derived from the Program,
+and can be reasonably considered independent and separate works in
+themselves, then this License, and its terms, do not apply to those
+sections when you distribute them as separate works. But when you
+distribute the same sections as part of a whole which is a work based
+on the Program, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Program.
+
+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+ 3. You may copy and distribute the Program (or a work based on it,
+under Section 2) in object code or executable form under the terms of
+Sections 1 and 2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable
+ source code, which must be distributed under the terms of Sections
+ 1 and 2 above on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three
+ years, to give any third party, for a charge no more than your
+ cost of physically performing source distribution, a complete
+ machine-readable copy of the corresponding source code, to be
+ distributed under the terms of Sections 1 and 2 above on a medium
+ customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer
+ to distribute corresponding source code. (This alternative is
+ allowed only for noncommercial distribution and only if you
+ received the program in object code or executable form with such
+ an offer, in accord with Subsection b above.)
+
+The source code for a work means the preferred form of the work for
+making modifications to it. For an executable work, complete source
+code means all the source code for all modules it contains, plus any
+associated interface definition files, plus the scripts used to
+control compilation and installation of the executable. However, as a
+special exception, the source code distributed need not include
+anything that is normally distributed (in either source or binary
+form) with the major components (compiler, kernel, and so on) of the
+operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering
+access to copy from a designated place, then offering equivalent
+access to copy the source code from the same place counts as
+distribution of the source code, even though third parties are not
+compelled to copy the source along with the object code.
+\f
+ 4. You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License. Any attempt
+otherwise to copy, modify, sublicense or distribute the Program is
+void, and will automatically terminate your rights under this License.
+However, parties who have received copies, or rights, from you under
+this License will not have their licenses terminated so long as such
+parties remain in full compliance.
+
+ 5. You are not required to accept this License, since you have not
+signed it. However, nothing else grants you permission to modify or
+distribute the Program or its derivative works. These actions are
+prohibited by law if you do not accept this License. Therefore, by
+modifying or distributing the Program (or any work based on the
+Program), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+ 6. Each time you redistribute the Program (or any work based on the
+Program), the recipient automatically receives a license from the
+original licensor to copy, distribute or modify the Program subject to
+these terms and conditions. You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties to
+this License.
+
+ 7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Program at all. For example, if a patent
+license would not permit royalty-free redistribution of the Program by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
+any particular circumstance, the balance of the section is intended to
+apply and the section as a whole is intended to apply in other
+circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system, which is
+implemented by public license practices. Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+\f
+ 8. If the distribution and/or use of the Program is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Program under this License
+may add an explicit geographical distribution limitation excluding
+those countries, so that distribution is permitted only in or among
+countries not thus excluded. In such case, this License incorporates
+the limitation as if written in the body of this License.
+
+ 9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation. If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+ 10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission. For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this. Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software and
+of promoting the sharing and reuse of software generally.
+
+ NO WARRANTY
+
+ 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+ 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+ END OF TERMS AND CONDITIONS
+\f
+ Appendix: How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) 19yy <name of author>
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) 19yy name of author
+ Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary. Here is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ <signature of Ty Coon>, 1 April 1989
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General
+Public License instead of this License.
--- /dev/null
+# Replaces squids own automake files
+#
+# Some useful automake documentation:
+# http://www.openismus.com/documents/linux/automake/automake.shtml
+# http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html
+
+#SUBDIRS =
+EXTRA_DIST = COPYRIGHT LICENSE 00README clustalo.README squid-1.9g.tar.gz
+#LDADD =
+
+# need DCLUSTALO here to enable Clustal specific squid patches
+# CLUSTALO is also defined in ../config.h which is included by squid.h
+# but some files do not include squid.h
+AM_CFLAGS = -DCLUSTALO -DSRE_STRICT_ANSI @AM_CFLAGS@
+
+noinst_LTLIBRARIES = libsquid.la
+
+libsquid_la_SOURCES = a2m.c aligneval.c alignio.c \
+ clustal.c cluster.c \
+ dayhoff.c \
+ eps.c \
+ file.c \
+ getopt.c gki.c gki.h gsi.c gsi.h gsi64.c gsi64.h \
+ hsregex.c \
+ iupac.c \
+ msa.c msa.h msf.c \
+ phylip.c \
+ revcomp.c rk.c rk.h \
+ selex.c seqencode.c shuffle.c sqerror.c sqfuncs.h sqio.c squid.h squidcore.c \
+ sre_ctype.c sre_math.c sre_random.c sre_random.h sre_string.c \
+ ssi.c ssi.h stack.c stockholm.c stockholm.h stopwatch.c stopwatch.h \
+ translate.c types.c vectorops.c \
+ vectorops.h version.h \
+ weight.c
+
+library_includedir=$(includedir)/clustalo/squid
+
+library_include_HEADERS = gki.h gsi64.h msa.h rk.h \
+ squid.h stopwatch.h sqfuncs.h \
+ sre_random.h ssi.h stockholm.h \
+ vectorops.h version.h
+
+
--- /dev/null
+# Makefile.in generated by automake 1.10.2 from Makefile.am.
+# @configure_input@
+
+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002,
+# 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
+# This Makefile.in is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
+# PARTICULAR PURPOSE.
+
+@SET_MAKE@
+
+# Replaces squids own automake files
+#
+# Some useful automake documentation:
+# http://www.openismus.com/documents/linux/automake/automake.shtml
+# http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html
+
+
+VPATH = @srcdir@
+pkgdatadir = $(datadir)/@PACKAGE@
+pkglibdir = $(libdir)/@PACKAGE@
+pkgincludedir = $(includedir)/@PACKAGE@
+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
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+INSTALL_HEADER = $(INSTALL_DATA)
+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = @build@
+host_triplet = @host@
+subdir = src/squid
+DIST_COMMON = $(library_include_HEADERS) $(srcdir)/Makefile.am \
+ $(srcdir)/Makefile.in
+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+am__aclocal_m4_deps = $(top_srcdir)/m4/ax_prefix_config_h.m4 \
+ $(top_srcdir)/m4/libtool.m4 $(top_srcdir)/m4/ltoptions.m4 \
+ $(top_srcdir)/m4/ltsugar.m4 $(top_srcdir)/m4/ltversion.m4 \
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+mkinstalldirs = $(install_sh) -d
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+CONFIG_CLEAN_FILES =
+LTLIBRARIES = $(noinst_LTLIBRARIES)
+libsquid_la_LIBADD =
+am_libsquid_la_OBJECTS = a2m.lo aligneval.lo alignio.lo clustal.lo \
+ cluster.lo dayhoff.lo eps.lo file.lo getopt.lo gki.lo gsi.lo \
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+ revcomp.lo rk.lo selex.lo seqencode.lo shuffle.lo sqerror.lo \
+ sqio.lo squidcore.lo sre_ctype.lo sre_math.lo sre_random.lo \
+ sre_string.lo ssi.lo stack.lo stockholm.lo stopwatch.lo \
+ translate.lo types.lo vectorops.lo weight.lo
+libsquid_la_OBJECTS = $(am_libsquid_la_OBJECTS)
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+ --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) \
+ $(LDFLAGS) -o $@
+SOURCES = $(libsquid_la_SOURCES)
+DIST_SOURCES = $(libsquid_la_SOURCES)
+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`;
+am__vpath_adj = case $$p in \
+ $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \
+ *) f=$$p;; \
+ esac;
+am__strip_dir = `echo $$p | sed -e 's|^.*/||'`;
+am__installdirs = "$(DESTDIR)$(library_includedir)"
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+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = @ACLOCAL@
+AMTAR = @AMTAR@
+#LDADD =
+
+# need DCLUSTALO here to enable Clustal specific squid patches
+# CLUSTALO is also defined in ../config.h which is included by squid.h
+# but some files do not include squid.h
+AM_CFLAGS = -DCLUSTALO -DSRE_STRICT_ANSI @AM_CFLAGS@
+AM_CXXFLAGS = @AM_CXXFLAGS@
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+OPENMP_CFLAGS = @OPENMP_CFLAGS@
+OPENMP_CXXFLAGS = @OPENMP_CXXFLAGS@
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+OTOOL64 = @OTOOL64@
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+PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
+PACKAGE_CODENAME = @PACKAGE_CODENAME@
+PACKAGE_NAME = @PACKAGE_NAME@
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+top_builddir = @top_builddir@
+top_srcdir = @top_srcdir@
+
+#SUBDIRS =
+EXTRA_DIST = COPYRIGHT LICENSE 00README clustalo.README squid-1.9g.tar.gz
+noinst_LTLIBRARIES = libsquid.la
+libsquid_la_SOURCES = a2m.c aligneval.c alignio.c \
+ clustal.c cluster.c \
+ dayhoff.c \
+ eps.c \
+ file.c \
+ getopt.c gki.c gki.h gsi.c gsi.h gsi64.c gsi64.h \
+ hsregex.c \
+ iupac.c \
+ msa.c msa.h msf.c \
+ phylip.c \
+ revcomp.c rk.c rk.h \
+ selex.c seqencode.c shuffle.c sqerror.c sqfuncs.h sqio.c squid.h squidcore.c \
+ sre_ctype.c sre_math.c sre_random.c sre_random.h sre_string.c \
+ ssi.c ssi.h stack.c stockholm.c stockholm.h stopwatch.c stopwatch.h \
+ translate.c types.c vectorops.c \
+ vectorops.h version.h \
+ weight.c
+
+library_includedir = $(includedir)/clustalo/squid
+library_include_HEADERS = gki.h gsi64.h msa.h rk.h \
+ squid.h stopwatch.h sqfuncs.h \
+ sre_random.h ssi.h stockholm.h \
+ vectorops.h version.h
+
+all: all-am
+
+.SUFFIXES:
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+ @for dep in $?; do \
+ case '$(am__configure_deps)' in \
+ *$$dep*) \
+ ( cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh ) \
+ && { if test -f $@; then exit 0; else break; fi; }; \
+ exit 1;; \
+ esac; \
+ done; \
+ echo ' cd $(top_srcdir) && $(AUTOMAKE) --gnu src/squid/Makefile'; \
+ cd $(top_srcdir) && \
+ $(AUTOMAKE) --gnu src/squid/Makefile
+.PRECIOUS: Makefile
+Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
+ @case '$?' in \
+ *config.status*) \
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+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* a2m.c
+ *
+ * reading/writing A2M (aligned FASTA) files.
+ *
+ * RCS $Id: a2m.c 242 2011-05-27 14:04:21Z andreas $ (Original squid RCS Id: a2m.c,v 1.1 1999/07/15 22:26:40 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "squid.h"
+#include "msa.h"
+
+/* Function: ReadA2M()
+ * Date: SRE, Sun Jun 6 17:11:29 1999 [bus from Madison 1999 worm mtg]
+ *
+ * Purpose: Parse an alignment read from an open A2M format
+ * alignment file. A2M is a single alignment format.
+ * Return the alignment, or NULL if we've already
+ * read the alignment.
+ *
+ * Args: afp - open alignment file
+ *
+ * Returns: MSA * - an alignment object.
+ * Caller responsible for an MSAFree()
+ */
+MSA *
+ReadA2M(MSAFILE *afp)
+{
+ MSA *msa;
+ char *buf;
+ char *name;
+ char *desc;
+ char *seq;
+ int idx;
+ int len1, len2;
+
+ if (feof(afp->f)) return NULL;
+
+ name = NULL;
+ msa = MSAAlloc(10, 0);
+ idx = 0;
+ while ((buf = MSAFileGetLine(afp)) != NULL)
+ {
+ if (*buf == '>')
+ {
+ buf++; /* skip the '>' */
+ if ((name = sre_strtok(&buf, WHITESPACE, &len1)) == NULL)
+ Die("Blank name in A2M file %s (line %d)\n", afp->fname, afp->linenumber);
+ desc = sre_strtok(&buf, "\n", &len2);
+
+ idx = GKIStoreKey(msa->index, name);
+ if (idx >= msa->nseqalloc) MSAExpand(msa);
+
+ msa->sqname[idx] = sre_strdup(name, len1);
+ if (desc != NULL) MSASetSeqDescription(msa, idx, desc);
+ msa->nseq++;
+ }
+ else if (name != NULL)
+ {
+ if ((seq = sre_strtok(&buf, WHITESPACE, &len1)) == NULL) continue;
+ msa->sqlen[idx] = sre_strcat(&(msa->aseq[idx]), msa->sqlen[idx], seq, len1);
+ }
+ }
+ if (name == NULL) { MSAFree(msa); return NULL; }
+
+ MSAVerifyParse(msa);
+ return msa;
+}
+
+
+/* Function: WriteA2M()
+ * Date: SRE, Sun Jun 6 17:40:35 1999 [bus from Madison, 1999 worm mtg]
+ *
+ * Purpose: Write an "aligned FASTA" (aka a2m, to UCSC) formatted
+ * alignment.
+ *
+ * Args: fp - open FILE to write to.
+ * msa - alignment to write
+ *
+ * Returns: void
+ */
+void
+#ifdef CLUSTALO
+WriteA2M(FILE *fp, MSA *msa, int vienna)
+#else
+WriteA2M(FILE *fp, MSA *msa)
+#endif
+{
+ int idx; /* sequence index */
+ int pos; /* position in sequence */
+ char buf[64]; /* buffer for individual lines */
+ int cpl = 60; /* char per line; must be < 64 unless buf is bigger */
+
+ buf[cpl] = '\0';
+ for (idx = 0; idx < msa->nseq; idx++)
+ {
+#ifdef CLUSTALO
+ /* most fasta sequences don't have a description, which
+ * leads to a trailing white space in the original code
+ */
+ fprintf(fp, ">%s", msa->sqname[idx]);
+
+ if (msa->sqdesc != NULL && msa->sqdesc[idx] != NULL && !vienna) {
+ fprintf(fp, " %s", msa->sqdesc[idx]);
+ }
+ fprintf(fp, "\n");
+#else
+ fprintf(fp, ">%s %s\n",
+ msa->sqname[idx],
+ (msa->sqdesc != NULL && msa->sqdesc[idx] != NULL) ? msa->sqdesc[idx] : "");
+#endif
+ for (pos = 0; pos < msa->alen; pos+=cpl)
+ {
+ strncpy(buf, &(msa->aseq[idx][pos]), cpl);
+ if (vienna)
+ fprintf(fp, "%s", buf);
+ else
+ fprintf(fp, "%s\n", buf);
+ }
+ if (vienna)
+ fprintf(fp, "\n");
+
+ }
+}
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* aligneval.c
+ *
+ * Comparison of multiple alignments. Three functions are
+ * provided, using subtly different scoring schemes:
+ * CompareMultAlignments() - basic scoring scheme
+ * CompareRefMultAlignments() - only certain "canonical" columns
+ * are scored
+ *
+ * The similarity measure is a fractional alignment identity averaged
+ * over all sequence pairs. The score for all pairs is:
+ * (identically aligned symbols) / (total aligned columns in
+ * known alignment)
+ *
+ * A column c is identically aligned for sequences i, j if:
+ * 1) both i,j have a symbol aligned in column c, and the
+ * same pair of symbols is aligned somewhere in the test
+ * alignment
+ * 2) S[i][c] is aligned to a gap in sequence j, and that symbol
+ * is aligned to a gap in the test alignment
+ * 3) converse of 2)
+ *
+ *
+ * The algorithm is as follows:
+ * 1) For each known/test aligned pair of sequences (k1,k2 and t1,t2)
+ * construct a list for each sequence, in which for every
+ * counted symbol we record the raw index of the symbol in
+ * the other sequence that it aligns to, or -1 if it aligns
+ * to a gap or uncounted symbol.
+ *
+ * 2) Compare the list for k1 to the list for t1 and count an identity
+ * for each correct alignment.
+ *
+ * 3) Repeat 2) for comparing k2 to t2. Note that this means correct sym/sym
+ * alignments count for 2; correct sym/gap alignments count for 1.
+ *
+ * 4) The score is (identities from 2 + identities from 3) /
+ * (totals from 2 + totals from 3).
+ *
+ * Written originally for koala's ss2 pairwise alignment package.
+ *
+ * Sean Eddy, Sun Nov 1 12:45:11 1992
+ * SRE, Thu Jul 29 16:47:18 1993: major revision: all functions replaced by new algorithm
+ * CVS $Id: aligneval.c,v 1.7 2002/10/09 14:26:09 eddy Exp)
+ */
+
+
+#include <stdio.h>
+#include <string.h>
+#include <ctype.h>
+#include "squid.h"
+#include "sre_random.h"
+
+static int make_alilist(char *s1, char *s2, int **ret_s1_list, int *ret_listlen);
+static int make_ref_alilist(int *refcoords, char *k1, char *k2, char *s1, char *s2,
+ int **ret_s1_list, int *ret_listlen);
+static int compare_lists(int *k1, int *k2, int *t1, int *t2, int len1, int len2, float *ret_sc);
+
+
+/* Function: ComparePairAlignments
+ *
+ * Purpose: Calculate and return a number representing how well two different alignments
+ * of a pair of sequences compare. The number is, roughly speaking,
+ * the fraction of columns which are identically aligned.
+ *
+ * For all columns c in which either known1[c] or known2[c]
+ * is a non-gap, count an identity if those same symbols are
+ * aligned somewhere in calc1/calc2. The score is identities/total
+ * columns examined. (i.e. fully gapped columns don't count)
+ *
+ * more explicitly, identities come from:
+ * both known and test aligned pairs have the same symbol in the first sequence aligned to
+ * a gap in the second sequence;
+ * both known and test aligned pairs have the same symbol in the second sequence
+ * aligned to a gap in the first sequence;
+ * the known alignment has symbols aligned at this column, and the test
+ * alignment aligns the same two symbols.
+ *
+ * Args: known1, known2: trusted alignment of two sequences
+ * calc1, calc2: test alignment of two sequences
+ *
+ * Return: Returns -1.0 on internal failure.
+ */
+float
+ComparePairAlignments(char *known1, char *known2, char *calc1, char *calc2)
+{
+ int *klist1;
+ int *klist2;
+ int *tlist1;
+ int *tlist2;
+ int len1, len2;
+ float score;
+
+ if (! make_alilist(calc1, calc2, &tlist1, &len1)) return -1.0;
+ if (! make_alilist(calc2, calc1, &tlist2, &len2)) return -1.0;
+ if (! make_alilist(known1, known2, &klist1, &len1)) return -1.0;
+ if (! make_alilist(known2, known1, &klist2, &len2)) return -1.0;
+ if (! compare_lists(klist1, klist2, tlist1, tlist2, len1, len2, &score)) return -1.0;
+
+ free(klist1);
+ free(klist2);
+ free(tlist1);
+ free(tlist2);
+ return score;
+}
+
+
+
+/* Function: CompareRefPairAlignments()
+ *
+ * Same as above, but the only columns that count are the ones
+ * with indices in *refcoord. *refcoord and the known1, known2
+ * pair must be in sync with each other (come from the same
+ * multiple sequence alignment)
+ *
+ * Args: ref - 0..alen-1 array of 1 or 0
+ * known1,known2 - trusted alignment
+ * calc1, calc2 - test alignment
+ *
+ * Return: the fractional alignment identity on success, -1.0 on failure.
+ */
+float
+CompareRefPairAlignments(int *ref, char *known1, char *known2, char *calc1, char *calc2)
+{
+ int *klist1;
+ int *klist2;
+ int *tlist1;
+ int *tlist2;
+ int len1, len2;
+ float score;
+
+ if (! make_ref_alilist(ref, known1, known2, calc1, calc2, &tlist1, &len1)) return -1.0;
+ if (! make_ref_alilist(ref, known2, known1, calc2, calc1, &tlist2, &len2)) return -1.0;
+ if (! make_ref_alilist(ref, known1, known2, known1, known2, &klist1, &len1)) return -1.0;
+ if (! make_ref_alilist(ref, known2, known1, known2, known1, &klist2, &len2)) return -1.0;
+ if (! compare_lists(klist1, klist2, tlist1, tlist2, len1, len2, &score)) return -1.0;
+
+ free(klist1);
+ free(klist2);
+ free(tlist1);
+ free(tlist2);
+ return score;
+}
+
+/* Function: make_alilist()
+ *
+ * Purpose: Construct a list (array) mapping the raw symbols of s1
+ * onto the indexes of the aligned symbols in s2 (or -1
+ * for gaps in s2). The list (s1_list) will be of the
+ * length of s1's raw sequence.
+ *
+ * Args: s1 - sequence to construct the list for
+ * s2 - sequence s1 is aligned to
+ * ret_s1_list - RETURN: the constructed list (caller must free)
+ * ret_listlen - RETURN: length of the list
+ *
+ * Returns: 1 on success, 0 on failure
+ */
+static int
+make_alilist(char *s1, char *s2, int **ret_s1_list, int *ret_listlen)
+{
+ int *s1_list;
+ int col; /* column position in alignment */
+ int r1, r2; /* raw symbol index at current col in s1, s2 */
+
+ /* Malloc for s1_list. It can't be longer than s1 itself; we just malloc
+ * for that (and waste a wee bit of space)
+ */
+ s1_list = (int *) MallocOrDie (sizeof(int) * strlen(s1));
+ r1 = r2 = 0;
+ for (col = 0; s1[col] != '\0'; col++)
+ {
+ /* symbol in s1? Record what it's aligned to, and bump
+ * the r1 counter.
+ */
+ if (! isgap(s1[col]))
+ {
+ s1_list[r1] = isgap(s2[col]) ? -1 : r2;
+ r1++;
+ }
+
+ /* symbol in s2? bump the r2 counter
+ */
+ if (! isgap(s2[col]))
+ r2++;
+ }
+
+ *ret_listlen = r1;
+ *ret_s1_list = s1_list;
+ return 1;
+}
+
+
+
+/* Function: make_ref_alilist()
+ *
+ * Purpose: Construct a list (array) mapping the raw symbols of s1
+ * which are under canonical columns of the ref alignment
+ * onto the indexes of the aligned symbols in s2 (or -1
+ * for gaps in s2 or noncanonical symbols in s2).
+ *
+ * Args: ref: - array of indices of canonical coords (1 canonical, 0 non)
+ * k1 - s1's known alignment (w/ respect to refcoords)
+ * k2 - s2's known alignment (w/ respect to refcoords)
+ * s1 - sequence to construct the list for
+ * s2 - sequence s1 is aligned to
+ * ret_s1_list - RETURN: the constructed list (caller must free)
+ * ret_listlen - RETURN: length of the list
+ *
+ * Returns: 1 on success, 0 on failure
+ */
+/*ARGSUSED*/
+static int
+make_ref_alilist(int *ref, char *k1, char *k2,
+ char *s1, char *s2, int **ret_s1_list, int *ret_listlen)
+{
+ int *s1_list;
+ int col; /* column position in alignment */
+ int r1, r2; /* raw symbol index at current col in s1, s2 */
+ int *canons1; /* flag array, 1 if position i in s1 raw seq is canonical */
+ int lpos; /* position in list */
+
+ /* Allocations. No arrays can exceed the length of their
+ * appropriate parent (s1 or s2)
+ */
+ s1_list = (int *) MallocOrDie (sizeof(int) * strlen(s1));
+ canons1 = (int *) MallocOrDie (sizeof(int) * strlen(s1));
+
+ /* First we use refcoords and k1,k2 to construct an array of 1's
+ * and 0's, telling us whether s1's raw symbol number i is countable.
+ * It's countable simply if it's under a canonical column.
+ */
+ r1 = 0;
+ for (col = 0; k1[col] != '\0'; col++)
+ {
+ if (! isgap(k1[col]))
+ {
+ canons1[r1] = ref[col] ? 1 : 0;
+ r1++;
+ }
+ }
+
+ /* Now we can construct the list. We don't count pairs if the sym in s1
+ * is non-canonical.
+ * We have to keep separate track of our position in the list (lpos)
+ * from our positions in the raw sequences (r1,r2)
+ */
+ r1 = r2 = lpos = 0;
+ for (col = 0; s1[col] != '\0'; col++)
+ {
+ if (! isgap(s1[col]) && canons1[r1])
+ {
+ s1_list[lpos] = isgap(s2[col]) ? -1 : r2;
+ lpos++;
+ }
+
+ if (! isgap(s1[col]))
+ r1++;
+ if (! isgap(s2[col]))
+ r2++;
+ }
+
+ free(canons1);
+ *ret_listlen = lpos;
+ *ret_s1_list = s1_list;
+ return 1;
+}
+
+/* Function: compare_lists()
+ *
+ * Purpose: Given four alignment lists (k1,k2, t1,t2), calculate the
+ * alignment score.
+ *
+ * Args: k1 - list of k1's alignment to k2
+ * k2 - list of k2's alignment to k1
+ * t1 - list of t1's alignment to t2
+ * t2 - list of t2's alignment to t2
+ * len1 - length of k1, t1 lists (same by definition)
+ * len2 - length of k2, t2 lists (same by definition)
+ * ret_sc - RETURN: identity score of alignment
+ *
+ * Return: 1 on success, 0 on failure.
+ */
+static int
+compare_lists(int *k1, int *k2, int *t1, int *t2, int len1, int len2, float *ret_sc)
+{
+ float id;
+ float tot;
+ int i;
+
+ id = tot = 0.0;
+ for (i = 0; i < len1; i++)
+ {
+ tot += 1.0;
+ if (t1[i] == k1[i]) id += 1.0;
+ }
+
+ for ( i = 0; i < len2; i++)
+ {
+ tot += 1.0;
+ if (k2[i] == t2[i]) id += 1.0;
+ }
+
+ *ret_sc = id / tot;
+ return 1;
+}
+
+
+/* Function: CompareMultAlignments
+ *
+ * Purpose: Invokes pairwise alignment comparison for every possible pair,
+ * and returns the average score over all N(N-1) of them or -1.0
+ * on an internal failure.
+ *
+ * Can be slow for large N, since it's quadratic.
+ *
+ * Args: kseqs - trusted multiple alignment
+ * tseqs - test multiple alignment
+ * N - number of sequences
+ *
+ * Return: average identity score, or -1.0 on failure.
+ */
+float
+CompareMultAlignments(char **kseqs, char **tseqs, int N)
+{
+ int i, j; /* counters for sequences */
+ float score;
+ float tot_score = 0.0;
+ /* do all pairwise comparisons */
+ for (i = 0; i < N; i++)
+ for (j = i+1; j < N; j++)
+ {
+ score = ComparePairAlignments(kseqs[i], kseqs[j], tseqs[i], tseqs[j]);
+ if (score < 0.0) return -1.0;
+ tot_score += score;
+ }
+ return ((tot_score * 2.0) / ((float) N * ((float) N - 1.0)));
+}
+
+
+
+/* Function: CompareRefMultAlignments()
+ *
+ * Purpose: Same as above, except an array of reference coords for
+ * the canonical positions of the known alignment is also
+ * provided.
+ *
+ * Args: ref : 0..alen-1 array of 1/0 flags, 1 if canon
+ * kseqs : trusted alignment
+ * tseqs : test alignment
+ * N : number of sequences
+ *
+ * Return: average identity score, or -1.0 on failure
+ */
+float
+CompareRefMultAlignments(int *ref, char **kseqs, char **tseqs, int N)
+{
+ int i, j; /* counters for sequences */
+ float score;
+ float tot_score = 0.0;
+
+ /* do all pairwise comparisons */
+ for (i = 0; i < N; i++)
+ for (j = i+1; j < N; j++)
+ {
+ score = CompareRefPairAlignments(ref, kseqs[i], kseqs[j], tseqs[i], tseqs[j]);
+ if (score < 0.0) return -1.0;
+ tot_score += score;
+ }
+ return ((tot_score * 2.0)/ ((float) N * ((float) N - 1.0)));
+}
+
+/* Function: PairwiseIdentity()
+ *
+ * Purpose: Calculate the pairwise fractional identity between
+ * two aligned sequences s1 and s2. This is simply
+ * (idents / MIN(len1, len2)).
+ *
+ * Note how many ways there are to calculate pairwise identity,
+ * because of the variety of choices for the denominator:
+ * idents/(idents+mismat) has the disadvantage that artifactual
+ * gappy alignments would have high "identities".
+ * idents/(AVG|MAX)(len1,len2) both have the disadvantage that
+ * alignments of fragments to longer sequences would have
+ * artifactually low "identities".
+ *
+ * Original Case sensitive; also, watch out in nucleic acid alignments;
+ * U/T RNA/DNA alignments will be counted as mismatches!
+ *
+ * Clustal Omega patch: Case insensitive and T and U are treated the same
+ */
+float
+PairwiseIdentity(char *s1, char *s2)
+{
+ int idents; /* total identical positions */
+ int len1, len2; /* lengths of seqs */
+ int x; /* position in aligned seqs */
+
+ idents = len1 = len2 = 0;
+ for (x = 0; s1[x] != '\0' && s2[x] != '\0'; x++)
+ {
+#ifdef CLUSTALO
+ char c1 = toupper(s1[x]);
+ char c2 = toupper(s2[x]);
+ if (c1=='U')
+ c1 = 'T';
+ if (c2=='U')
+ c2 = 'T';
+
+ if (!isgap(c1)) {
+ len1++;
+ if (c1 == c2)
+ idents++;
+ }
+ if (!isgap(c2))
+ len2++;
+#else
+ if (!isgap(s1[x])) {
+ len1++;
+ if (s1[x] == s2[x]) idents++;
+ }
+ if (!isgap(s2[x])) len2++;
+#endif
+ }
+ if (len2 < len1) len1 = len2;
+ return (len1 == 0 ? 0.0 : (float) idents / (float) len1);
+}
+
+
+
+/* Function: AlignmentIdentityBySampling()
+ * Date: SRE, Mon Oct 19 14:29:01 1998 [St. Louis]
+ *
+ * Purpose: Estimate and return the average pairwise
+ * fractional identity of an alignment,
+ * using sampling.
+ *
+ * For use when there's so many sequences that
+ * an all vs. all rigorous calculation will
+ * take too long.
+ *
+ * Case sensitive!
+ *
+ * Args: aseq - aligned sequences
+ * L - length of alignment
+ * N - number of seqs in alignment
+ * nsample - number of samples
+ *
+ * Returns: average fractional identity, 0..1.
+ */
+float
+AlignmentIdentityBySampling(char **aseq, int L, int N, int nsample)
+{
+ int x, i, j; /* counters */
+ float sum;
+
+ if (N < 2) return 1.0;
+
+ sum = 0.;
+ for (x = 0; x < nsample; x++)
+ {
+ i = CHOOSE(N);
+ do { j = CHOOSE(N); } while (j == i); /* make sure j != i */
+ sum += PairwiseIdentity(aseq[i], aseq[j]);
+ }
+ return sum / (float) nsample;
+}
+
+/* Function: MajorityRuleConsensus()
+ * Date: SRE, Tue Mar 7 15:30:30 2000 [St. Louis]
+ *
+ * Purpose: Given a set of aligned sequences, produce a
+ * majority rule consensus sequence. If >50% nonalphabetic
+ * (usually meaning gaps) in the column, ignore the column.
+ *
+ * Args: aseq - aligned sequences, [0..nseq-1][0..alen-1]
+ * nseq - number of sequences
+ * alen - length of alignment
+ *
+ * Returns: ptr to allocated consensus sequence.
+ * Caller is responsible for free'ing this.
+ */
+char *
+MajorityRuleConsensus(char **aseq, int nseq, int alen)
+{
+ char *cs; /* RETURN: consensus sequence */
+ int count[27]; /* counts for a..z and gaps in a column */
+ int idx,apos; /* counters for seq, column */
+ int spos; /* position in cs */
+ int x; /* counter for characters */
+ int sym;
+ int max, bestx;
+
+ cs = MallocOrDie(sizeof(char) * (alen+1));
+
+ for (spos=0,apos=0; apos < alen; apos++)
+ {
+ for (x = 0; x < 27; x++) count[x] = 0;
+
+ for (idx = 0; idx < nseq; idx++)
+ {
+ if (isalpha(aseq[idx][apos])) {
+ sym = toupper(aseq[idx][apos]);
+ count[sym-'A']++;
+ } else {
+ count[26]++;
+ }
+ }
+
+ if ((float) count[26] / (float) nseq <= 0.5) {
+ max = bestx = -1;
+ for (x = 0; x < 26; x++)
+ if (count[x] > max) { max = count[x]; bestx = x; }
+ cs[spos++] = (char) ('A' + bestx);
+ }
+ }
+ cs[spos] = '\0';
+ return cs;
+}
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* alignio.c
+ * SRE, Mon Jul 12 11:57:37 1993
+ * RCS $Id: alignio.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: alignio.c,v 1.11 2002/10/09 14:26:09 eddy Exp)
+ *
+ * Input/output of sequence alignments.
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+#include "squid.h"
+#include "sre_random.h"
+
+/* Function: AllocAlignment()
+ *
+ * Purpose: Allocate space for an alignment, given the number
+ * of sequences and the alignment length in columns.
+ *
+ * Args: nseq - number of sequences
+ * alen - width of alignment
+ * ret_aseq - RETURN: alignment itself
+ * ainfo - RETURN: other info associated with alignment
+ *
+ * Return: (void)
+ * aseq, ainfo free'd by caller: FreeAlignment(aseq, &ainfo).
+ * note that ainfo itself is alloc'ed in caller, usually
+ * just by a "AINFO ainfo" definition.
+ */
+void
+AllocAlignment(int nseq, int alen, char ***ret_aseq, AINFO *ainfo)
+{
+ char **aseq;
+ int idx;
+
+ InitAinfo(ainfo);
+
+ aseq = (char **) MallocOrDie (sizeof(char *) * nseq);
+ for (idx = 0; idx < nseq; idx++)
+ aseq[idx] = (char *) MallocOrDie (sizeof(char) * (alen+1));
+
+ ainfo->alen = alen;
+ ainfo->nseq = nseq;
+
+ ainfo->wgt = (float *) MallocOrDie (sizeof(float) * nseq);
+ FSet(ainfo->wgt, nseq, 1.0);
+
+ ainfo->sqinfo = (SQINFO *) MallocOrDie (sizeof(SQINFO) * nseq);
+ for (idx = 0; idx < nseq; idx++)
+ ainfo->sqinfo[idx].flags = 0;
+
+ *ret_aseq = aseq;
+}
+
+
+/* Function: InitAinfo()
+ * Date: SRE, Tue Jan 19 10:16:02 1999 [St. Louis]
+ *
+ * Purpose: Initialize the fields in ainfo structure to
+ * default (null) values. Does nothing with
+ * fields that are dependent on nseq or alen.
+ *
+ * Args: ainfo - optional info structure for an alignment
+ *
+ * Returns: (void). ainfo is modified.
+ */
+void
+InitAinfo(AINFO *ainfo)
+{
+ ainfo->name = NULL;
+ ainfo->desc = NULL;
+ ainfo->cs = NULL;
+ ainfo->rf = NULL;
+ ainfo->acc = NULL;
+ ainfo->au = NULL;
+ ainfo->flags = 0;
+
+ ainfo->tc1 = ainfo->tc2 = 0.0;
+ ainfo->nc1 = ainfo->nc2 = 0.0;
+ ainfo->ga1 = ainfo->ga2 = 0.0;
+}
+
+
+/* Function: FreeAlignment()
+ *
+ * Purpose: Free the space allocated to alignment, names, and optional
+ * information.
+ *
+ * Args: aseqs - sequence alignment
+ * ainfo - associated alignment data.
+ */
+void
+FreeAlignment(char **aseqs, AINFO *ainfo)
+{
+ int i;
+
+ for (i = 0; i < ainfo->nseq; i++)
+ {
+ if (ainfo->sqinfo[i].flags & SQINFO_SS) free(ainfo->sqinfo[i].ss);
+ if (ainfo->sqinfo[i].flags & SQINFO_SA) free(ainfo->sqinfo[i].sa);
+ }
+ if (ainfo->cs != NULL) free(ainfo->cs);
+ if (ainfo->rf != NULL) free(ainfo->rf);
+ if (ainfo->name != NULL) free(ainfo->name);
+ if (ainfo->desc != NULL) free(ainfo->desc);
+ if (ainfo->acc != NULL) free(ainfo->acc);
+ if (ainfo->au != NULL) free(ainfo->au);
+
+ free(ainfo->sqinfo);
+ free(ainfo->wgt);
+ Free2DArray((void **) aseqs, ainfo->nseq);
+}
+
+
+
+/* Function: SAMizeAlignment()
+ * Date: SRE, Tue Jun 30 09:49:40 1998 [St. Louis]
+ *
+ * Purpose: Make a "best effort" attempt to convert an alignment
+ * to SAM gap format: - in delete col, . in insert col.
+ * Only works if alignment adheres to SAM's upper/lower
+ * case convention, which is true for instance of old
+ * HMMER alignments.
+ *
+ * Args: aseq - alignment to convert
+ * nseq - number of seqs in alignment
+ * alen - length of alignment
+ *
+ * Returns: (void)
+ */
+void
+SAMizeAlignment(char **aseq, int nseq, int alen)
+{
+ int col; /* counter for aligned columns */
+ int i; /* counter for seqs */
+ int sawlower, sawupper, sawgap;
+ char gapchar;
+
+ for (col = 0; col < alen; col++)
+ {
+ sawlower = sawupper = sawgap = 0;
+ /* pass 1: do we see only upper or lower? */
+ for (i = 0; i < nseq; i++)
+ {
+ if (isgap(aseq[i][col])) { sawgap = 1; continue; }
+ if (isupper((int) aseq[i][col])) { sawupper = 1; continue; }
+ if (islower((int) aseq[i][col])) sawlower = 1;
+ }
+ /* select gap character for column */
+ gapchar = '-'; /* default */
+ if (sawlower && ! sawupper) gapchar = '.';
+
+ /* pass 2: set gap char */
+ for (i = 0; i < nseq; i++)
+ if (isgap(aseq[i][col])) aseq[i][col] = gapchar;
+ }
+}
+
+
+/* Function: SAMizeAlignmentByGapFrac()
+ * Date: SRE, Tue Jun 30 10:58:38 1998 [St. Louis]
+ *
+ * Purpose: Convert an alignment to SAM's gap and case
+ * conventions, using gap fraction in a column
+ * to choose match versus insert columns. In match columns,
+ * residues are upper case and gaps are '-'.
+ * In insert columns, residues are lower case and
+ * gaps are '.'
+ *
+ * Args: aseq - aligned sequences
+ * nseq - number of sequences
+ * alen - length of alignment
+ * maxgap - if more gaps than this fraction, column is insert.
+ *
+ * Returns: (void) Characters in aseq may be altered.
+ */
+void
+SAMizeAlignmentByGapFrac(char **aseq, int nseq, int alen, float maxgap)
+{
+ int apos; /* counter over columns */
+ int idx; /* counter over sequences */
+ int ngap; /* number of gaps seen */
+
+ for (apos = 0; apos < alen; apos++)
+ {
+ /* count gaps */
+ ngap = 0;
+ for (idx = 0; idx < nseq; idx++)
+ if (isgap(aseq[idx][apos])) ngap++;
+
+ /* convert to SAM conventions */
+ if ((float) ngap / (float) nseq > maxgap)
+ { /* insert column */
+ for (idx = 0; idx < nseq; idx++)
+ if (isgap(aseq[idx][apos])) aseq[idx][apos] = '.';
+ else aseq[idx][apos] = (char) tolower((int) aseq[idx][apos]);
+ }
+ else
+ { /* match column */
+ for (idx = 0; idx < nseq; idx++)
+ if (isgap(aseq[idx][apos])) aseq[idx][apos] = '-';
+ else aseq[idx][apos] = (char) toupper((int) aseq[idx][apos]);
+ }
+ }
+}
+
+
+
+
+/* Function: MakeAlignedString()
+ *
+ * Purpose: Given a raw string of some type (secondary structure, say),
+ * align it to a given aseq by putting gaps wherever the
+ * aseq has gaps.
+ *
+ * Args: aseq: template for alignment
+ * alen: length of aseq
+ * ss: raw string to align to aseq
+ * ret_s: RETURN: aligned ss
+ *
+ * Return: 1 on success, 0 on failure (and squid_errno is set.)
+ * ret_ss is malloc'ed here and must be free'd by caller.
+ */
+int
+MakeAlignedString(char *aseq, int alen, char *ss, char **ret_s)
+{
+ char *new;
+ int apos, rpos;
+
+ new = (char *) MallocOrDie ((alen+1) * sizeof(char));
+ for (apos = rpos = 0; apos < alen; apos++)
+ if (! isgap(aseq[apos]))
+ {
+ new[apos] = ss[rpos];
+ rpos++;
+ }
+ else
+ new[apos] = '.';
+ new[apos] = '\0';
+
+ if (rpos != strlen(ss))
+ { squid_errno = SQERR_PARAMETER; free(new); return 0; }
+ *ret_s = new;
+ return 1;
+}
+
+
+/* Function: MakeDealignedString()
+ *
+ * Purpose: Given an aligned string of some type (either sequence or
+ * secondary structure, for instance), dealign it relative
+ * to a given aseq. Return a ptr to the new string.
+ *
+ * Args: aseq : template alignment
+ * alen : length of aseq
+ * ss: : string to make dealigned copy of; same length as aseq
+ * ret_s : RETURN: dealigned copy of ss
+ *
+ * Return: 1 on success, 0 on failure (and squid_errno is set)
+ * ret_s is alloc'ed here and must be freed by caller
+ */
+int
+MakeDealignedString(char *aseq, int alen, char *ss, char **ret_s)
+{
+ char *new;
+ int apos, rpos;
+
+ new = (char *) MallocOrDie ((alen+1) * sizeof(char));
+ for (apos = rpos = 0; apos < alen; apos++)
+ if (! isgap(aseq[apos]))
+ {
+ new[rpos] = ss[apos];
+ rpos++;
+ }
+ new[rpos] = '\0';
+ if (alen != strlen(ss))
+ { squid_errno = SQERR_PARAMETER; free(new); return 0; }
+ *ret_s = new;
+ return 1;
+}
+
+
+/* Function: DealignedLength()
+ *
+ * Purpose: Count the number of non-gap symbols in seq.
+ * (i.e. find the length of the unaligned sequence)
+ *
+ * Args: aseq - aligned sequence to count symbols in, \0 terminated
+ *
+ * Return: raw length of seq.
+ */
+int
+DealignedLength(char *aseq)
+{
+ int rlen;
+ for (rlen = 0; *aseq; aseq++)
+ if (! isgap(*aseq)) rlen++;
+ return rlen;
+}
+
+
+/* Function: WritePairwiseAlignment()
+ *
+ * Purpose: Write a nice formatted pairwise alignment out,
+ * with a BLAST-style middle line showing identities
+ * as themselves (single letter) and conservative
+ * changes as '+'.
+ *
+ * Args: ofp - open fp to write to (stdout, perhaps)
+ * aseq1, aseq2 - alignments to write (not necessarily
+ * flushed right with gaps)
+ * name1, name2 - names of sequences
+ * spos1, spos2 - starting position in each (raw) sequence
+ * pam - PAM matrix; positive values define
+ * conservative changes
+ * indent - how many extra spaces to print on left
+ *
+ * Return: 1 on success, 0 on failure
+ */
+int
+WritePairwiseAlignment(FILE *ofp,
+ char *aseq1, char *name1, int spos1,
+ char *aseq2, char *name2, int spos2,
+ int **pam, int indent)
+{
+ char sname1[11]; /* shortened name */
+ char sname2[11];
+ int still_going; /* True if writing another block */
+ char buf1[61]; /* buffer for writing seq1; CPL+1*/
+ char bufmid[61]; /* buffer for writing consensus */
+ char buf2[61];
+ char *s1, *s2; /* ptrs into each sequence */
+ int count1, count2; /* number of symbols we're writing */
+ int rpos1, rpos2; /* position in raw seqs */
+ int rawcount1, rawcount2; /* number of nongap symbols written */
+ int apos;
+
+ strncpy(sname1, name1, 10);
+ sname1[10] = '\0';
+ strtok(sname1, WHITESPACE);
+
+ strncpy(sname2, name2, 10);
+ sname2[10] = '\0';
+ strtok(sname2, WHITESPACE);
+
+ s1 = aseq1;
+ s2 = aseq2;
+ rpos1 = spos1;
+ rpos2 = spos2;
+
+ still_going = TRUE;
+ while (still_going)
+ {
+ still_going = FALSE;
+
+ /* get next line's worth from both */
+ strncpy(buf1, s1, 60); buf1[60] = '\0';
+ strncpy(buf2, s2, 60); buf2[60] = '\0';
+ count1 = strlen(buf1);
+ count2 = strlen(buf2);
+
+ /* is there still more to go? */
+ if ((count1 == 60 && s1[60] != '\0') ||
+ (count2 == 60 && s2[60] != '\0'))
+ still_going = TRUE;
+
+ /* shift seq ptrs by a line */
+ s1 += count1;
+ s2 += count2;
+
+ /* assemble the consensus line */
+ for (apos = 0; apos < count1 && apos < count2; apos++)
+ {
+ if (!isgap(buf1[apos]) && !isgap(buf2[apos]))
+ {
+ if (buf1[apos] == buf2[apos])
+ bufmid[apos] = buf1[apos];
+ else if (pam[buf1[apos] - 'A'][buf2[apos] - 'A'] > 0)
+ bufmid[apos] = '+';
+ else
+ bufmid[apos] = ' ';
+ }
+ else
+ bufmid[apos] = ' ';
+ }
+ bufmid[apos] = '\0';
+
+ rawcount1 = 0;
+ for (apos = 0; apos < count1; apos++)
+ if (!isgap(buf1[apos])) rawcount1++;
+
+ rawcount2 = 0;
+ for (apos = 0; apos < count2; apos++)
+ if (!isgap(buf2[apos])) rawcount2++;
+
+ (void) fprintf(ofp, "%*s%-10.10s %5d %s %5d\n", indent, "",
+ sname1, rpos1, buf1, rpos1 + rawcount1 -1);
+ (void) fprintf(ofp, "%*s %s\n", indent, "",
+ bufmid);
+ (void) fprintf(ofp, "%*s%-10.10s %5d %s %5d\n", indent, "",
+ sname2, rpos2, buf2, rpos2 + rawcount2 -1);
+ (void) fprintf(ofp, "\n");
+
+ rpos1 += rawcount1;
+ rpos2 += rawcount2;
+ }
+
+ return 1;
+}
+
+
+/* Function: MingapAlignment()
+ *
+ * Purpose: Remove all-gap columns from a multiple sequence alignment
+ * and its associated data. The alignment is assumed to be
+ * flushed (all aseqs the same length).
+ */
+int
+MingapAlignment(char **aseqs, AINFO *ainfo)
+{
+ int apos; /* position in original alignment */
+ int mpos; /* position in new alignment */
+ int idx;
+
+ /* We overwrite aseqs, using its allocated memory.
+ */
+ for (apos = 0, mpos = 0; aseqs[0][apos] != '\0'; apos++)
+ {
+ /* check for all-gap in column */
+ for (idx = 0; idx < ainfo->nseq; idx++)
+ if (! isgap(aseqs[idx][apos]))
+ break;
+ if (idx == ainfo->nseq) continue;
+
+ /* shift alignment and ainfo */
+ if (mpos != apos)
+ {
+ for (idx = 0; idx < ainfo->nseq; idx++)
+ aseqs[idx][mpos] = aseqs[idx][apos];
+
+ if (ainfo->cs != NULL) ainfo->cs[mpos] = ainfo->cs[apos];
+ if (ainfo->rf != NULL) ainfo->rf[mpos] = ainfo->rf[apos];
+ }
+ mpos++;
+ }
+ /* null terminate everything */
+ for (idx = 0; idx < ainfo->nseq; idx++)
+ aseqs[idx][mpos] = '\0';
+ ainfo->alen = mpos; /* set new length */
+ if (ainfo->cs != NULL) ainfo->cs[mpos] = '\0';
+ if (ainfo->rf != NULL) ainfo->rf[mpos] = '\0';
+ return 1;
+}
+
+
+
+/* Function: RandomAlignment()
+ *
+ * Purpose: Create a random alignment from raw sequences.
+ *
+ * Ideally, we would like to sample an alignment from the
+ * space of possible alignments according to its probability,
+ * given a prior probability distribution for alignments.
+ * I don't see how to describe such a distribution, let alone
+ * sample it.
+ *
+ * This is a rough approximation that tries to capture some
+ * desired properties. We assume the alignment is generated
+ * by a simple HMM composed of match and insert states.
+ * Given parameters (pop, pex) for the probability of opening
+ * and extending an insertion, we can find the expected number
+ * of match states, M, in the underlying model for each sequence.
+ * We use an average M taken over all the sequences (this is
+ * an approximation. The expectation of M given all the sequence
+ * lengths is a nasty-looking summation.)
+ *
+ * M = len / ( 1 + pop ( 1 + 1/ (1-pex) ) )
+ *
+ * Then, we assign positions in each raw sequence onto the M match
+ * states and M+1 insert states of this "HMM", by rolling random
+ * numbers and inserting the (rlen-M) inserted positions randomly
+ * into the insert slots, taking into account the relative probability
+ * of open vs. extend.
+ *
+ * The resulting alignment has two desired properties: insertions
+ * tend to follow the HMM-like exponential distribution, and
+ * the "sparseness" of the alignment is controllable through
+ * pop and pex.
+ *
+ * Args: rseqs - raw sequences to "align", 0..nseq-1
+ * sqinfo - array of 0..nseq-1 info structures for the sequences
+ * nseq - number of sequences
+ * pop - probability to open insertion (0<pop<1)
+ * pex - probability to extend insertion (0<pex<1)
+ * ret_aseqs - RETURN: alignment (flushed)
+ * ainfo - fill in: alignment info
+ *
+ * Return: 1 on success, 0 on failure. Sets squid_errno to indicate cause
+ * of failure.
+ */
+int
+RandomAlignment(char **rseqs, SQINFO *sqinfo, int nseq, float pop, float pex,
+ char ***ret_aseqs, AINFO *ainfo)
+{
+ char **aseqs; /* RETURN: alignment */
+ int alen; /* length of alignment */
+ int *rlen; /* lengths of each raw sequence */
+ int M; /* length of "model" */
+ int **ins; /* insertion counts, 0..nseq-1 by 0..M */
+ int *master_ins; /* max insertion counts, 0..M */
+ int apos, rpos, idx;
+ int statepos;
+ int count;
+ int minlen;
+
+ /* calculate expected length of model, M
+ */
+ rlen = (int *) MallocOrDie (sizeof(int) * nseq);
+ M = 0;
+ minlen = 9999999;
+ for (idx = 0; idx < nseq; idx++)
+ {
+ rlen[idx] = strlen(rseqs[idx]);
+ M += rlen[idx];
+ minlen = (rlen[idx] < minlen) ? rlen[idx] : minlen;
+ }
+ M = (int) ((float) M / (1.0 + pop * (1.0 + 1.0 / (1.0 - pex))));
+ M /= nseq;
+ if (M > minlen) M = minlen;
+
+ /* make arrays that count insertions in M+1 possible insert states
+ */
+ ins = (int **) MallocOrDie (sizeof(int *) * nseq);
+ master_ins = (int *) MallocOrDie (sizeof(int) * (M+1));
+ for (idx = 0; idx < nseq; idx++)
+ {
+ ins[idx] = (int *) MallocOrDie (sizeof(int) * (M+1));
+ for (rpos = 0; rpos <= M; rpos++)
+ ins[idx][rpos] = 0;
+ }
+ /* normalize */
+ pop = pop / (pop+pex);
+ pex = 1.0 - pop;
+ /* make insertions for individual sequences */
+ for (idx = 0; idx < nseq; idx++)
+ {
+ apos = -1;
+ for (rpos = 0; rpos < rlen[idx]-M; rpos++)
+ {
+ if (sre_random() < pop || apos == -1) /* open insertion */
+ apos = CHOOSE(M+1); /* choose 0..M */
+ ins[idx][apos]++;
+ }
+ }
+ /* calculate master_ins, max inserts */
+ alen = M;
+ for (apos = 0; apos <= M; apos++)
+ {
+ master_ins[apos] = 0;
+ for (idx = 0; idx < nseq; idx++)
+ if (ins[idx][apos] > master_ins[apos])
+ master_ins[apos] = ins[idx][apos];
+ alen += master_ins[apos];
+ }
+
+
+ /* Now, construct alignment
+ */
+ aseqs = (char **) MallocOrDie (sizeof (char *) * nseq);
+ for (idx = 0; idx < nseq; idx++)
+ aseqs[idx] = (char *) MallocOrDie (sizeof(char) * (alen+1));
+ for (idx = 0; idx < nseq; idx++)
+ {
+ apos = rpos = 0;
+
+ for (statepos = 0; statepos <= M; statepos++)
+ {
+ for (count = 0; count < ins[idx][statepos]; count++)
+ aseqs[idx][apos++] = rseqs[idx][rpos++];
+ for (; count < master_ins[statepos]; count++)
+ aseqs[idx][apos++] = ' ';
+
+ if (statepos != M)
+ aseqs[idx][apos++] = rseqs[idx][rpos++];
+ }
+ aseqs[idx][alen] = '\0';
+ }
+ ainfo->flags = 0;
+ ainfo->alen = alen;
+ ainfo->nseq = nseq;
+ ainfo->sqinfo = (SQINFO *) MallocOrDie (sizeof(SQINFO) * nseq);
+ for (idx = 0; idx < nseq; idx++)
+ SeqinfoCopy(&(ainfo->sqinfo[idx]), &(sqinfo[idx]));
+
+ free(rlen);
+ free(master_ins);
+ Free2DArray((void **) ins, nseq);
+ *ret_aseqs = aseqs;
+ return 1;
+}
+
+/* Function: AlignmentHomogenousGapsym()
+ * Date: SRE, Sun Mar 19 19:37:12 2000 [wren, St. Louis]
+ *
+ * Purpose: Sometimes we've got to convert alignments to
+ * a lowest common denominator, and we need
+ * a single specific gap character -- for example,
+ * PSI-BLAST blastpgp -B takes a very simplistic
+ * alignment input format which appears to only
+ * allow '-' as a gap symbol.
+ *
+ * Anything matching the isgap() macro is
+ * converted.
+ *
+ * Args: aseq - aligned character strings, [0..nseq-1][0..alen-1]
+ * nseq - number of aligned strings
+ * alen - length of alignment
+ * gapsym - character to use for gaps.
+ *
+ * Returns: void ("never fails")
+ */
+void
+AlignmentHomogenousGapsym(char **aseq, int nseq, int alen, char gapsym)
+{
+ int i, apos;
+
+ for (i = 0; i < nseq; i++)
+ for (apos = 0; apos < alen; apos++)
+ if (isgap(aseq[i][apos])) aseq[i][apos] = gapsym;
+}
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* clustal.c
+ * SRE, Sun Jun 6 17:50:45 1999 [bus from Madison, 1999 worm mtg]
+ *
+ * Import/export of ClustalV/W multiple sequence alignment
+ * formatted files. Derivative of msf.c; MSF is a pretty
+ * generic interleaved format.
+ *
+ * RCS $Id: clustal.c 228 2011-03-29 14:05:27Z dave $ (Original squid RCS Id: clustal.c,v 1.1 1999/07/15 22:26:53 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+#include "squid.h"
+#include "msa.h"
+
+#ifdef CLUSTALO
+/* needed for PACKAGE_VERSION */
+#include "../config.h"
+
+#ifndef min
+ #define min( a, b ) ( ((a) < (b)) ? (a) : (b) )
+#endif
+
+/*These are all the positively scoring groups that occur in the Gonnet Pam250
+matrix. There are strong and weak groups, defined as strong score >0.5 and
+weak score =<0.5. Strong matching columns to be assigned ':' and weak matches
+assigned '.' in the clustal output format.
+amino_strong = res_cat1
+amino_weak = res_cat2
+*/
+
+char *amino_strong[] = {"STA", "NEQK", "NHQK", "NDEQ", "QHRK", "MILV",
+ "MILF", "HY", "FYW", NULL};
+
+char *amino_weak[] = {"CSA", "ATV", "SAG", "STNK", "STPA", "SGND",
+ "SNDEQK", "NDEQHK", "NEQHRK", "FVLIM", "HFY", NULL};
+
+#endif
+
+#ifdef TESTDRIVE_CLUSTAL
+/*****************************************************************
+ * msf.c test driver:
+ * cc -DTESTDRIVE_CLUSTAL -g -O2 -Wall -o test clustal.c msa.c gki.c sqerror.c sre_string.c file.c hsregex.c sre_math.c sre_ctype.c -lm
+ *
+ */
+int
+main(int argc, char **argv)
+{
+ MSAFILE *afp;
+ MSA *msa;
+ char *file;
+
+ file = argv[1];
+
+ if ((afp = MSAFileOpen(file, MSAFILE_CLUSTAL, NULL)) == NULL)
+ Die("Couldn't open %s\n", file);
+
+ while ((msa = ReadClustal(afp)) != NULL)
+ {
+ WriteClustal(stdout, msa);
+ MSAFree(msa);
+ }
+
+ MSAFileClose(afp);
+ exit(0);
+}
+/******************************************************************/
+#endif /* testdrive_clustal */
+
+
+/* Function: ReadClustal()
+ * Date: SRE, Sun Jun 6 17:53:49 1999 [bus from Madison, 1999 worm mtg]
+ *
+ * Purpose: Parse an alignment read from an open Clustal format
+ * alignment file. Clustal is a single-alignment format.
+ * Return the alignment, or NULL if we have no data.
+ *
+ * Args: afp - open alignment file
+ *
+ * Returns: MSA * - an alignment object
+ * caller responsible for an MSAFree()
+ * NULL if no more alignments
+ *
+ * Diagnostics:
+ * Will Die() here with a (potentially) useful message
+ * if a parsing error occurs.
+ */
+MSA *
+ReadClustal(MSAFILE *afp)
+{
+ MSA *msa;
+ char *s;
+ int slen;
+ int sqidx;
+ char *name;
+ char *seq;
+ char *s2;
+
+ if (feof(afp->f)) return NULL;
+
+ /* Skip until we see the CLUSTAL header
+ */
+ while ((s = MSAFileGetLine(afp)) != NULL)
+ {
+ if (strncmp(s, "CLUSTAL", 7) == 0 &&
+ strstr(s, "multiple sequence alignment") != NULL)
+ break;
+ }
+ if (s == NULL) return NULL;
+
+ msa = MSAAlloc(10, 0);
+
+ /* Now we're in the sequence section.
+ * As discussed above, if we haven't seen a sequence name, then we
+ * don't include the sequence in the alignment.
+ * Watch out for conservation markup lines that contain *.: chars
+ */
+ while ((s = MSAFileGetLine(afp)) != NULL)
+ {
+ if ((name = sre_strtok(&s, WHITESPACE, NULL)) == NULL) continue;
+ if ((seq = sre_strtok(&s, WHITESPACE, &slen)) == NULL) continue;
+ s2 = sre_strtok(&s, "\n", NULL);
+
+ /* The test for a conservation markup line
+ */
+ if (strpbrk(name, ".*:") != NULL && strpbrk(seq, ".*:") != NULL)
+ continue;
+ if (s2 != NULL)
+ Die("Parse failed at line %d, file %s: possibly using spaces as gaps",
+ afp->linenumber, afp->fname);
+
+ /* It's not blank, and it's not a coord line: must be sequence
+ */
+ sqidx = MSAGetSeqidx(msa, name, msa->lastidx+1);
+ msa->lastidx = sqidx;
+ msa->sqlen[sqidx] = sre_strcat(&(msa->aseq[sqidx]), msa->sqlen[sqidx], seq, slen);
+ }
+
+ MSAVerifyParse(msa); /* verifies, and also sets alen and wgt. */
+ return msa;
+}
+
+
+/* Function: WriteClustal()
+ * Date: SRE, Sun Jun 6 18:12:47 1999 [bus from Madison, worm mtg 1999]
+ *
+ * Purpose: Write an alignment in Clustal format to an open file.
+ *
+ * Args: fp - file that's open for writing.
+ * msa - alignment to write.
+ *
+ * Returns: (void)
+ */
+void
+WriteClustal(FILE *fp, MSA *msa)
+{
+ int idx; /* counter for sequences */
+ int len; /* tmp variable for name lengths */
+ int namelen; /* maximum name length used */
+ int pos; /* position counter */
+ char buf[80]; /* buffer for writing seq */
+ int cpl = 60; /* char per line (< 64) */
+
+ /* consensus line stuff */
+ int subpos;
+ char first;
+ int bail;
+ int strong_bins[9];
+ int weak_bins[11];
+ int cons;
+ int bin;
+
+ /* calculate max namelen used */
+ namelen = 0;
+ for (idx = 0; idx < msa->nseq; idx++)
+ if ((len = strlen(msa->sqname[idx])) > namelen)
+ namelen = len;
+
+#ifdef CLUSTALO
+ fprintf(fp, "CLUSTAL O(%s) multiple sequence alignment\n", PACKAGE_VERSION);
+#else
+ fprintf(fp, "CLUSTAL W(1.5) multiple sequence alignment\n");
+#endif
+
+ /*****************************************************
+ * Write the sequences
+ *****************************************************/
+
+#ifdef CLUSTALO
+ fprintf(fp, "\n"); /* original had two blank lines */
+#endif
+
+ for (pos = 0; pos < msa->alen; pos += cpl)
+ {
+ fprintf(fp, "\n"); /* Blank line between sequence blocks */
+ for (idx = 0; idx < msa->nseq; idx++)
+ {
+ strncpy(buf, msa->aseq[idx] + pos, cpl);
+ buf[cpl] = '\0';
+#ifdef CLUSTALO
+ fprintf(fp, "%-*s %s\n", namelen+5, msa->sqname[idx], buf);
+#else
+ fprintf(fp, "%*s %s\n", namelen, msa->sqname[idx], buf);
+#endif
+ }
+#ifdef CLUSTALO
+ /* do consensus dots */
+
+ /* print namelen+5 spaces */
+ for(subpos = 0; subpos <= namelen+5; subpos++)
+ fprintf(fp, " ");
+
+ for(subpos = pos; subpos < min(pos + cpl, msa->alen); subpos++)
+ {
+ /* see if 100% conservation */
+ first = msa->aseq[0][subpos];
+ bail = 0;
+ for (idx = 1; idx < msa->nseq; idx++)
+ {
+ if(msa->aseq[idx][subpos] != first)
+ {
+ bail = 1;
+ break;
+ }
+ }
+ if(!bail)
+ fprintf(fp, "*");
+ else
+ {
+ /* if not then check strong */
+ for(bin = 0; bin < 9; bin++)
+ strong_bins[bin] = 0; /* clear the bins */
+
+ for(idx = 0; idx < msa->nseq; idx++)
+ {
+ switch(msa->aseq[idx][subpos])
+ {
+ case 'S': strong_bins[0]++; break;
+ case 'T': strong_bins[0]++; break;
+ case 'A': strong_bins[0]++; break;
+ case 'N': strong_bins[1]++; strong_bins[2]++; strong_bins[3]++; break;
+ case 'E': strong_bins[1]++; strong_bins[3]++; break;
+ case 'Q': strong_bins[1]++; strong_bins[2]++; strong_bins[3]++; strong_bins[4]++; break;
+ case 'K': strong_bins[1]++; strong_bins[2]++; strong_bins[4]++; break;
+ case 'D': strong_bins[3]++; break;
+ case 'R': strong_bins[4]++; break;
+ case 'H': strong_bins[4]++; strong_bins[7]++; break;
+ case 'M': strong_bins[5]++; strong_bins[6]++; break;
+ case 'I': strong_bins[5]++; strong_bins[6]++; break;
+ case 'L': strong_bins[5]++; strong_bins[6]++; break;
+ case 'V': strong_bins[5]++; break;
+ case 'F': strong_bins[6]++; strong_bins[8]++; break;
+ case 'Y': strong_bins[7]++; strong_bins[8]++; break;
+ case 'W': strong_bins[8]++; break;
+ }
+ }
+ bail = 0;
+ for(bin = 0; bin < 9; bin++)
+ if(strong_bins[bin] == msa->nseq)
+ {
+ bail = 1;
+ break;
+ }
+ if(bail)
+ fprintf(fp, ":");
+ else
+ {
+ /* check weak */
+ for(bin = 0; bin < 11; bin++)
+ weak_bins[bin] = 0; /* clear the bins */
+
+ for(idx = 0; idx < msa->nseq; idx++)
+ {
+ switch(msa->aseq[idx][subpos])
+ {
+ case 'C': weak_bins[0]++; break;
+ case 'S': weak_bins[0]++; weak_bins[2]++; weak_bins[3]++; weak_bins[4]++; weak_bins[5]++; weak_bins[6]++; break;
+ case 'A': weak_bins[0]++; weak_bins[1]++; weak_bins[2]++; weak_bins[4]++; break;
+ case 'T': weak_bins[1]++; weak_bins[3]++; weak_bins[4]++; break;
+ case 'V': weak_bins[1]++; weak_bins[9]++; break;
+ case 'G': weak_bins[2]++; break;
+ case 'N': weak_bins[3]++; weak_bins[5]++; weak_bins[6]++; weak_bins[7]++; weak_bins[8]++; break;
+ case 'K': weak_bins[3]++; weak_bins[6]++; weak_bins[7]++; weak_bins[8]++; break;
+ case 'D': weak_bins[5]++; weak_bins[6]++; weak_bins[7]++; break;
+ case 'E': weak_bins[6]++; weak_bins[7]++; weak_bins[8]++; break;
+ case 'Q': weak_bins[6]++; weak_bins[7]++; weak_bins[8]++; break;
+ case 'H': weak_bins[7]++; weak_bins[8]++; weak_bins[10]++; break;
+ case 'R': weak_bins[8]++; break;
+ case 'F': weak_bins[9]++; weak_bins[10]++; break;
+ case 'L': weak_bins[9]++; break;
+ case 'I': weak_bins[9]++; break;
+ case 'M': weak_bins[9]++; break;
+ case 'Y': weak_bins[10]++; break;
+ }
+ }
+ bail = 0;
+ for(bin = 0; bin < 11; bin++)
+ if(weak_bins[bin] == msa->nseq)
+ {
+ bail = 1;
+ break;
+ }
+ if(bail)
+ fprintf(fp, ".");
+ else
+ fprintf(fp, " ");
+ }
+ }
+ }
+ fprintf(fp,"\n");
+#endif
+ }
+
+ return;
+}
+
+
+
--- /dev/null
+This is a trimmed down and patched version of Sean Eddy's squid library version 1.9
+See squid-1.9g.tar.gz for the original files.
+Downloaded from ftp://selab.janelia.org/pub/software/squid/
+
+changes in source code are all done via #ifdef CLUSTALO, which is set via Makefile
+
+We use our own config header instead of squidconf (see squid.h)
+
+
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* cluster.c
+ * SRE, Sun Jul 18 09:49:47 1993
+ * moved to squid Thu Mar 3 08:42:57 1994
+ * RCS $Id: cluster.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: cluster.c,v 1.3 1999/07/15 22:32:16 eddy Exp)
+ *
+ * almost identical to bord.c, from fd
+ * also now contains routines for constructing difference matrices
+ * from alignments
+ *
+ * "branch ordering": Input a symmetric or upper-right-diagonal
+ * NxN difference matrix (usually constructed by pairwise alignment
+ * and similarity calculations for N sequences). Use the simple
+ * cluster analysis part of the Fitch/Margoliash tree-building algorithm
+ * (as described by Fitch and Margoliash 1967 as well as Feng
+ * and Doolittle 1987) to calculate the topology of an "evolutionary
+ * tree" consistent with the difference matrix. Returns an array
+ * which represents the tree.
+ *
+ * The input difference matrix is just an NxN matrix of floats.
+ * A good match is a small difference score (the algorithm is going
+ * to search for minima among the difference scores). The original difference
+ * matrix remains unchanged by the calculations.
+ *
+ * The output requires some explanation. A phylogenetic
+ * tree is a binary tree, with N "leaves" and N-1 "nodes". The
+ * topology of the tree may be completely described by N-1 structures
+ * containing two pointers; each pointer points to either a leaf
+ * or another node. Here, this is implemented with integer indices
+ * rather than pointers. An array of N-1 pairs of ints is returned.
+ * If the index is in the range (0..N-1), it is a "leaf" -- the
+ * number of one of the sequences. If the index is in the range
+ * (N..2N-2), it is another "node" -- (index-N) is the index
+ * of the node in the returned array.
+ *
+ * If both indices of a member of the returned array point to
+ * nodes, the tree is "compound": composed of more than one
+ * cluster of related sequences.
+ *
+ * The higher-numbered elements of the returned array were the
+ * first constructed, and hence represent the distal tips
+ * of the tree -- the most similar sequences. The root
+ * is node 0.
+ ******************************************************************
+ *
+ * Algorithm
+ *
+ * INITIALIZATIONS:
+ * - copy the difference matrix (otherwise the caller's copy would
+ * get destroyed by the operations of this algorithm). If
+ * it's asymmetric, make it symmetric.
+ * - make a (0..N-1) array of ints to keep track of the indices in
+ * the difference matrix as they get swapped around. Initialize
+ * this matrix to 0..N-1.
+ * - make a (0..N-2) array of int[2] to store the results (the tree
+ * topology). Doesn't need to be initialized.
+ * - keep track of a "N'", the current size of the difference
+ * matrix being operated on.
+ *
+ * PROCESSING THE DIFFERENCE MATRIX:
+ * - for N' = N down to N' = 2 (N-1 steps):
+ * - in the half-diagonal N'xN' matrix, find the indices i,j at which
+ * there's the minimum difference score
+ *
+ * Store the results:
+ * - at position N'-2 of the result array, store coords[i] and
+ * coords[j].
+ *
+ * Move i,j rows, cols to the outside edges of the matrix:
+ * - swap row i and row N'-2
+ * - swap row j and row N'-1
+ * - swap column i and column N'-2
+ * - swap column j and column N'-1
+ * - swap indices i, N'-2 in the index array
+ * - swap indices j, N'-1 in the index array
+ *
+ * Build a average difference score for differences to i,j:
+ * - for all columns, find avg difference between rows i and j and store in row i:
+ * row[i][col] = (row[i][col] + row[j][col]) / 2.0
+ * - copy the contents of row i to column i (it's a symmetric
+ * matrix, no need to recalculate)
+ * - store an index N'+N-2 at position N'-2 of the index array: means
+ * that this row/column is now a node rather than a leaf, and
+ * contains minimum values
+ *
+ * Continue:
+ * - go to the next N'
+ *
+ * GARBAGE COLLECTION & RETURN.
+ *
+ **********************************************************************
+ *
+ * References:
+ *
+ * Feng D-F and R.F. Doolittle. "Progressive sequence alignment as a
+ * prerequisite to correct phylogenetic trees." J. Mol. Evol.
+ * 25:351-360, 1987.
+ *
+ * Fitch W.M. and Margoliash E. "Construction of phylogenetic trees."
+ * Science 155:279-284, 1967.
+ *
+ **********************************************************************
+ *
+ * SRE, 18 March 1992 (bord.c)
+ * SRE, Sun Jul 18 09:52:14 1993 (cluster.c)
+ * added to squid Thu Mar 3 09:13:56 1994
+ **********************************************************************
+ * Mon May 4 09:47:02 1992: keep track of difference scores at each node
+ */
+
+
+#include <stdio.h>
+#include <string.h>
+#include <math.h>
+
+#include "squid.h"
+#include "sqfuncs.h"
+
+#ifdef MEMDEBUG
+#include "dbmalloc.h"
+#endif
+
+/* Function: Cluster()
+ *
+ * Purpose: Cluster analysis on a distance matrix. Constructs a
+ * phylogenetic tree which contains the topology
+ * and info for each node: branch lengths, how many
+ * sequences are included under the node, and which
+ * sequences are included under the node.
+ *
+ * Args: dmx - the NxN distance matrix ( >= 0.0, larger means more diverged)
+ * N - size of mx (number of sequences)
+ * mode - CLUSTER_MEAN, CLUSTER_MAX, or CLUSTER_MIN
+ * ret_tree- RETURN: the tree
+ *
+ * Return: 1 on success, 0 on failure.
+ * The caller is responsible for freeing the tree's memory,
+ * by calling FreePhylo(tree, N).
+ */
+int
+Cluster(float **dmx, int N, enum clust_strategy mode, struct phylo_s **ret_tree)
+{
+ struct phylo_s *tree; /* (0..N-2) phylogenetic tree */
+ float **mx; /* copy of difference matrix */
+ int *coord; /* (0..N-1), indices for matrix coords */
+ int i, j; /* coords of minimum difference */
+ int idx; /* counter over seqs */
+ int Np; /* N', a working copy of N */
+ int row, col; /* loop variables */
+ float min; /* best minimum score found */
+ float *trow; /* tmp pointer for swapping rows */
+ float tcol; /* tmp storage for swapping cols */
+ float *diff; /* (0..N-2) difference scores at nodes */
+ int swapfoo; /* for SWAP() macro */
+
+ /**************************
+ * Initializations.
+ **************************/
+ /* We destroy the matrix we work on, so make a copy of dmx.
+ */
+ mx = MallocOrDie (sizeof(float *) * N);
+ for (i = 0; i < N; i++)
+ {
+ mx[i] = MallocOrDie (sizeof(float) * N);
+ for (j = 0; j < N; j++)
+ mx[i][j] = dmx[i][j];
+ }
+ /* coord array alloc, (0..N-1) */
+ coord = MallocOrDie (N * sizeof(int));
+ diff = MallocOrDie ((N-1) * sizeof(float));
+ /* init the coord array to 0..N-1 */
+ for (col = 0; col < N; col++) coord[col] = col;
+ for (i = 0; i < N-1; i++) diff[i] = 0.0;
+
+ /* tree array alloc, (0..N-2) */
+ if ((tree = AllocPhylo(N)) == NULL) Die("AllocPhylo() failed");
+
+ /*********************************
+ * Process the difference matrix
+ *********************************/
+
+ /* N-prime, for an NxN down to a 2x2 diffmx */
+ j= 0; /* just to silence gcc uninit warnings */
+ for (Np = N; Np >= 2; Np--)
+ {
+ /* find a minimum on the N'xN' matrix*/
+ min = 999999.;
+ for (row = 0; row < Np; row++)
+ for (col = row+1; col < Np; col++)
+ if (mx[row][col] < min)
+ {
+ min = mx[row][col];
+ i = row;
+ j = col;
+ }
+
+ /* We're clustering row i with col j. write necessary
+ * data into a node on the tree
+ */
+ /* topology info */
+ tree[Np-2].left = coord[i];
+ tree[Np-2].right = coord[j];
+ if (coord[i] >= N) tree[coord[i]-N].parent = N + Np - 2;
+ if (coord[j] >= N) tree[coord[j]-N].parent = N + Np - 2;
+
+ /* keep score info */
+ diff[Np-2] = tree[Np-2].diff = min;
+
+ /* way-simple branch length estimation */
+ tree[Np-2].lblen = tree[Np-2].rblen = min;
+ if (coord[i] >= N) tree[Np-2].lblen -= diff[coord[i]-N];
+ if (coord[j] >= N) tree[Np-2].rblen -= diff[coord[j]-N];
+
+ /* number seqs included at node */
+ if (coord[i] < N)
+ {
+ tree[Np-2].incnum ++;
+ tree[Np-2].is_in[coord[i]] = 1;
+ }
+ else
+ {
+ tree[Np-2].incnum += tree[coord[i]-N].incnum;
+ for (idx = 0; idx < N; idx++)
+ tree[Np-2].is_in[idx] |= tree[coord[i]-N].is_in[idx];
+ }
+
+ if (coord[j] < N)
+ {
+ tree[Np-2].incnum ++;
+ tree[Np-2].is_in[coord[j]] = 1;
+ }
+ else
+ {
+ tree[Np-2].incnum += tree[coord[j]-N].incnum;
+ for (idx = 0; idx < N; idx++)
+ tree[Np-2].is_in[idx] |= tree[coord[j]-N].is_in[idx];
+ }
+
+
+ /* Now build a new matrix, by merging row i with row j and
+ * column i with column j; see Fitch and Margoliash
+ */
+ /* Row and column swapping. */
+ /* watch out for swapping i, j away: */
+ if (i == Np-1 || j == Np-2)
+ SWAP(i,j);
+
+ if (i != Np-2)
+ {
+ /* swap row i, row N'-2 */
+ trow = mx[Np-2]; mx[Np-2] = mx[i]; mx[i] = trow;
+ /* swap col i, col N'-2 */
+ for (row = 0; row < Np; row++)
+ {
+ tcol = mx[row][Np-2];
+ mx[row][Np-2] = mx[row][i];
+ mx[row][i] = tcol;
+ }
+ /* swap coord i, coord N'-2 */
+ SWAP(coord[i], coord[Np-2]);
+ }
+
+ if (j != Np-1)
+ {
+ /* swap row j, row N'-1 */
+ trow = mx[Np-1]; mx[Np-1] = mx[j]; mx[j] = trow;
+ /* swap col j, col N'-1 */
+ for (row = 0; row < Np; row++)
+ {
+ tcol = mx[row][Np-1];
+ mx[row][Np-1] = mx[row][j];
+ mx[row][j] = tcol;
+ }
+ /* swap coord j, coord N'-1 */
+ SWAP(coord[j], coord[Np-1]);
+ }
+
+ /* average i and j together; they're now
+ at Np-2 and Np-1 though */
+ i = Np-2;
+ j = Np-1;
+ /* merge by saving avg of cols of row i and row j */
+ for (col = 0; col < Np; col++)
+ {
+ switch (mode) {
+ case CLUSTER_MEAN: mx[i][col] =(mx[i][col]+ mx[j][col]) / 2.0; break;
+ case CLUSTER_MIN: mx[i][col] = MIN(mx[i][col], mx[j][col]); break;
+ case CLUSTER_MAX: mx[i][col] = MAX(mx[i][col], mx[j][col]); break;
+ default: mx[i][col] =(mx[i][col]+ mx[j][col]) / 2.0; break;
+ }
+ }
+ /* copy those rows to columns */
+ for (col = 0; col < Np; col++)
+ mx[col][i] = mx[i][col];
+ /* store the node index in coords */
+ coord[Np-2] = Np+N-2;
+ }
+
+ /**************************
+ * Garbage collection and return
+ **************************/
+ Free2DArray((void **) mx, N);
+ free(coord);
+ free(diff);
+ *ret_tree = tree;
+ return 1;
+}
+
+/* Function: AllocPhylo()
+ *
+ * Purpose: Allocate space for a phylo_s array. N-1 structures
+ * are allocated, one for each node; in each node, a 0..N
+ * is_in flag array is also allocated and initialized to
+ * all zeros.
+ *
+ * Args: N - size; number of sequences being clustered
+ *
+ * Return: pointer to the allocated array
+ *
+ */
+struct phylo_s *
+AllocPhylo(int N)
+{
+ struct phylo_s *tree;
+ int i;
+
+ if ((tree = (struct phylo_s *) malloc ((N-1) * sizeof(struct phylo_s))) == NULL)
+ return NULL;
+
+ for (i = 0; i < N-1; i++)
+ {
+ tree[i].diff = 0.0;
+ tree[i].lblen = tree[i].rblen = 0.0;
+ tree[i].left = tree[i].right = tree[i].parent = -1;
+ tree[i].incnum = 0;
+ if ((tree[i].is_in = (char *) calloc (N, sizeof(char))) == NULL)
+ return NULL;
+ }
+ return tree;
+}
+
+
+/* Function: FreePhylo()
+ *
+ * Purpose: Free a clustree array that was built to cluster N sequences.
+ *
+ * Args: tree - phylogenetic tree to free
+ * N - size of clustree; number of sequences it clustered
+ *
+ * Return: (void)
+ */
+void
+FreePhylo(struct phylo_s *tree, int N)
+{
+ int idx;
+
+ for (idx = 0; idx < N-1; idx++)
+ free(tree[idx].is_in);
+ free(tree);
+}
+
+
+/* Function: MakeDiffMx()
+ *
+ * Purpose: Given a set of aligned sequences, construct
+ * an NxN fractional difference matrix. (i.e. 1.0 is
+ * completely different, 0.0 is exactly identical).
+ *
+ * Args: aseqs - flushed, aligned sequences
+ * num - number of aseqs
+ * ret_dmx - RETURN: difference matrix
+ *
+ * Return: 1 on success, 0 on failure.
+ * Caller must free diff matrix with FMX2Free(dmx)
+ */
+void
+MakeDiffMx(char **aseqs, int num, float ***ret_dmx)
+{
+ float **dmx; /* RETURN: distance matrix */
+ int i,j; /* counters over sequences */
+
+ /* Allocate 2D float matrix
+ */
+ dmx = FMX2Alloc(num, num);
+
+ /* Calculate distances; symmetric matrix
+ * record difference, not identity (1 - identity)
+ */
+ for (i = 0; i < num; i++)
+ for (j = i; j < num; j++)
+ dmx[i][j] = dmx[j][i] = 1.0 - PairwiseIdentity(aseqs[i], aseqs[j]);
+
+ *ret_dmx = dmx;
+ return;
+}
+
+/* Function: MakeIdentityMx()
+ *
+ * Purpose: Given a set of aligned sequences, construct
+ * an NxN fractional identity matrix. (i.e. 1.0 is
+ * completely identical, 0.0 is completely different).
+ * Virtually identical to MakeDiffMx(). It's
+ * less confusing to have two distinct functions, I find.
+ *
+ * Args: aseqs - flushed, aligned sequences
+ * num - number of aseqs
+ * ret_imx - RETURN: identity matrix (caller must free)
+ *
+ * Return: 1 on success, 0 on failure.
+ * Caller must free imx using FMX2Free(imx)
+ */
+void
+MakeIdentityMx(char **aseqs, int num, float ***ret_imx)
+{
+ float **imx; /* RETURN: identity matrix */
+ int i,j; /* counters over sequences */
+
+ /* Allocate 2D float matrix
+ */
+ imx = FMX2Alloc(num, num);
+
+ /* Calculate distances, symmetric matrix
+ */
+ for (i = 0; i < num; i++)
+ for (j = i; j < num; j++)
+ imx[i][j] = imx[j][i] = PairwiseIdentity(aseqs[i], aseqs[j]);
+
+ *ret_imx = imx;
+ return;
+}
+
+
+
+/* Function: PrintNewHampshireTree()
+ *
+ * Purpose: Print out a tree in the "New Hampshire" standard
+ * format. See PHYLIP's draw.doc for a definition of
+ * the New Hampshire format.
+ *
+ * Like a CFG, we generate the format string left to
+ * right by a preorder tree traversal.
+ *
+ * Args: fp - file to print to
+ * ainfo- alignment info, including sequence names
+ * tree - tree to print
+ * N - number of leaves
+ *
+ */
+void
+PrintNewHampshireTree(FILE *fp, AINFO *ainfo, struct phylo_s *tree, int N)
+{
+ struct intstack_s *stack;
+ int code;
+ float *blen;
+ int docomma;
+
+ blen = (float *) MallocOrDie (sizeof(float) * (2*N-1));
+ stack = InitIntStack();
+ PushIntStack(stack, N); /* push root on stack */
+ docomma = FALSE;
+
+ /* node index code:
+ * 0..N-1 = leaves; indexes of sequences.
+ * N..2N-2 = interior nodes; node-N = index of node in tree structure.
+ * code N is the root.
+ * 2N..3N-2 = special flags for closing interior nodes; node-2N = index in tree
+ */
+ while (PopIntStack(stack, &code))
+ {
+ if (code < N) /* we're a leaf. */
+ {
+ /* 1) print name:branchlength */
+ if (docomma) fputs(",", fp);
+ fprintf(fp, "%s:%.5f", ainfo->sqinfo[code].name, blen[code]);
+ docomma = TRUE;
+ }
+
+ else if (code < 2*N) /* we're an interior node */
+ {
+ /* 1) print a '(' */
+ if (docomma) fputs(",\n", fp);
+ fputs("(", fp);
+ /* 2) push on stack: ), rchild, lchild */
+ PushIntStack(stack, code+N);
+ PushIntStack(stack, tree[code-N].right);
+ PushIntStack(stack, tree[code-N].left);
+ /* 3) record branch lengths */
+ blen[tree[code-N].right] = tree[code-N].rblen;
+ blen[tree[code-N].left] = tree[code-N].lblen;
+ docomma = FALSE;
+ }
+
+ else /* we're closing an interior node */
+ {
+ /* print a ):branchlength */
+ if (code == 2*N) fprintf(fp, ");\n");
+ else fprintf(fp, "):%.5f", blen[code-N]);
+ docomma = TRUE;
+ }
+ }
+
+ FreeIntStack(stack);
+ free(blen);
+ return;
+}
+
+
+/* Function: PrintPhylo()
+ *
+ * Purpose: Debugging output of a phylogenetic tree structure.
+ */
+void
+PrintPhylo(FILE *fp, AINFO *ainfo, struct phylo_s *tree, int N)
+{
+ int idx;
+
+ for (idx = 0; idx < N-1; idx++)
+ {
+ fprintf(fp, "Interior node %d (code %d)\n", idx, idx+N);
+ fprintf(fp, "\tParent: %d (code %d)\n", tree[idx].parent-N, tree[idx].parent);
+ fprintf(fp, "\tLeft: %d (%s) %f\n",
+ tree[idx].left < N ? tree[idx].left-N : tree[idx].left,
+ tree[idx].left < N ? ainfo->sqinfo[tree[idx].left].name : "interior",
+ tree[idx].lblen);
+ fprintf(fp, "\tRight: %d (%s) %f\n",
+ tree[idx].right < N ? tree[idx].right-N : tree[idx].right,
+ tree[idx].right < N ? ainfo->sqinfo[tree[idx].right].name : "interior",
+ tree[idx].rblen);
+ fprintf(fp, "\tHeight: %f\n", tree[idx].diff);
+ fprintf(fp, "\tIncludes:%d seqs\n", tree[idx].incnum);
+ }
+}
+
+
+
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* dayhoff.c
+ *
+ * Routines for dealing with PAM matrices.
+ *
+ * Includes:
+ * ParsePAMFile() -- read a PAM matrix from disk.
+ *
+ *
+ * SRE - Fri Apr 2 11:23:45 1993
+ * RCS $Id: dayhoff.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: dayhoff.c,v 1.5 2002/07/03 15:03:39 eddy Exp)
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <math.h>
+#include <ctype.h>
+#include "squid.h"
+
+/* Function: ParsePAMFile()
+ *
+ * Purpose: Given a pointer to an open file containing a PAM matrix,
+ * parse the file and allocate and fill a 2D array of
+ * floats containing the matrix. The PAM file is
+ * assumed to be in the format that NCBI distributes
+ * with BLAST. BLOSUM matrices also work fine, as
+ * produced by Henikoff's program "MATBLAS".
+ *
+ * Parses both old format and new format BLAST matrices.
+ * Old format just had rows of integers.
+ * New format includes a leading character on each row.
+ *
+ * The PAM matrix is a 27x27 matrix, 0=A..25=Z,26=*.
+ * Note that it's not a 20x20 matrix as you might expect;
+ * this is for speed of indexing as well as the ability
+ * to deal with ambiguous characters.
+ *
+ * Args: fp - open PAM file
+ * ret_pam - RETURN: pam matrix, integers
+ * ret_scale - RETURN: scale factor for converting
+ * to real Sij. For instance, PAM120 is
+ * given in units of ln(2)/2. This may
+ * be passed as NULL if the caller
+ * doesn't care.
+ *
+ * Returns: 1 on success; 0 on failure and sets squid_errno to
+ * indicate the cause. ret_pam is allocated here and
+ * must be freed by the caller (use FreePAM).
+ */
+int
+ParsePAMFile(FILE *fp, int ***ret_pam, float *ret_scale)
+{
+ int **pam;
+ char buffer[512]; /* input buffer from fp */
+ int order[27]; /* order of fields, obtained from header */
+ int nsymbols; /* total number of symbols in matrix */
+ char *sptr;
+ int idx;
+ int row, col;
+ float scale;
+ int gotscale = FALSE;
+
+ scale = 0.0; /* just to silence gcc uninit warnings */
+ if (fp == NULL) { squid_errno = SQERR_NODATA; return 0; }
+
+ /* Look at the first non-blank, non-comment line in the file.
+ * It gives single-letter codes in the order the PAM matrix
+ * is arrayed in the file.
+ */
+ do {
+ if (fgets(buffer, 512, fp) == NULL)
+ { squid_errno = SQERR_NODATA; return 0; }
+
+ /* Get the scale factor from the header.
+ * For BLOSUM files, we assume the line looks like:
+ * BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+ * and we assume that the fraction is always 1/x;
+ *
+ * For PAM files, we assume the line looks like:
+ * PAM 120 substitution matrix, scale = ln(2)/2 = 0.346574
+ * and we assume that the number following the final '=' is our scale
+ */
+ if (strstr(buffer, "BLOSUM Clustered Scoring Matrix") != NULL &&
+ (sptr = strchr(buffer, '/')) != NULL)
+ {
+ sptr++;
+ if (! isdigit((int) (*sptr))) { squid_errno = SQERR_FORMAT; return 0; }
+ scale = (float) (log(2.0) / atof(sptr));
+ gotscale = TRUE;
+ }
+ else if (strstr(buffer, "substitution matrix,") != NULL)
+ {
+ while ((sptr = strrchr(buffer, '=')) != NULL) {
+ sptr += 2;
+ if (IsReal(sptr)) {
+ scale = atof(sptr);
+ gotscale = TRUE;
+ break;
+ }
+ }
+ }
+ } while ((sptr = strtok(buffer, " \t\n")) == NULL || *sptr == '#');
+
+ idx = 0;
+ do {
+ order[idx] = (int) *sptr - (int) 'A';
+ if (order[idx] < 0 || order[idx] > 25) order[idx] = 26;
+ idx++;
+ } while ((sptr = strtok(NULL, " \t\n")) != NULL);
+ nsymbols = idx;
+
+ /* Allocate a pam matrix. For speed of indexing, we use
+ * a 27x27 matrix so we can do lookups using the ASCII codes
+ * of amino acid single-letter representations, plus one
+ * extra field to deal with the "*" (terminators).
+ */
+ if ((pam = (int **) calloc (27, sizeof(int *))) == NULL)
+ Die("calloc failed");
+ for (idx = 0; idx < 27; idx++)
+ if ((pam[idx] = (int *) calloc (27, sizeof(int))) == NULL)
+ Die("calloc failed");
+
+ /* Parse the rest of the file.
+ */
+ for (row = 0; row < nsymbols; row++)
+ {
+ if (fgets(buffer, 512, fp) == NULL)
+ { squid_errno = SQERR_NODATA; return 0; }
+
+ if ((sptr = strtok(buffer, " \t\n")) == NULL)
+ { squid_errno = SQERR_NODATA; return 0; }
+ for (col = 0; col < nsymbols; col++)
+ {
+ if (sptr == NULL) { squid_errno = SQERR_NODATA; return 0; }
+
+ /* Watch out for new BLAST format, with leading characters
+ */
+ if (*sptr == '*' || isalpha((int) *sptr))
+ col--; /* hack hack */
+ else
+ pam [order[row]] [order[col]] = atoi(sptr);
+
+ sptr = strtok(NULL, " \t\n");
+ }
+ }
+
+ /* Return
+ */
+ if (ret_scale != NULL)
+ {
+ if (gotscale) *ret_scale = scale;
+ else
+ {
+#ifdef CLUSTALO
+ Warning("Failed to parse PAM matrix scale factor. Defaulting to ln(2)/2!");
+#else
+ Warn("Failed to parse PAM matrix scale factor. Defaulting to ln(2)/2!");
+#endif
+ *ret_scale = log(2.0) / 2.0;
+ }
+ }
+ *ret_pam = pam;
+ return 1;
+}
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* eps.c
+ * SRE, Thu Jun 21 18:02:31 2001 [St. Louis]
+ *
+ * Some crude support for Encapsulated PostScript (EPS) output,
+ * DSC compliant.
+ *
+ * CVS $Id: eps.c,v 1.4 2002/02/24 19:39:27 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "squid.h"
+#include "msa.h"
+
+/* Function: EPSWriteSmallMSA()
+ * Date: SRE, Thu Jun 21 18:15:21 2001 [St. Louis]
+ *
+ * Purpose: Write an alignment in singleblock, Stockholm/SELEX like
+ * format to an open file. Very crude.
+ * Currently fails if the alignment is >50 columns long, because
+ * it doesn't think it will fit on a single page.
+ *
+ * Args: fp - open file for writing
+ * msa - alignment to write
+ *
+ * Returns: (void)
+ */
+void
+EPSWriteSmallMSA(FILE *fp, MSA *msa)
+{
+ int namewidth; /* namewidth in PostScript units */
+ int fontwidth; /* width of a character in this font */
+ int hspace; /* horizontal space between aligned chars */
+ int vspace; /* vertical space between sequences */
+ char *font; /* font name, e.g. "Courier" */
+ int fontsize; /* font size in pts */
+ int i,j; /* counter over sequences, columns */
+ int len; /* tmp var holding length of something */
+ int width, height; /* width and height of bounding box */
+ int xpos, ypos; /* x,y position */
+
+ /* Set some font characteristics; done here, so it'll
+ * be easy to change. Magic numbers for Courier 12 determined
+ * by trial and error.
+ */
+ fontwidth = 8;
+ hspace = 9;
+ vspace = 15;
+ font = sre_strdup("Courier", -1);
+ fontsize = 12;
+
+ /* Find the width of the longest sequence name in characters.
+ */
+ namewidth = 0;
+ for (i = 0; i < msa->nseq; i++)
+ if ((len = (int) strlen(msa->sqname[i])) > namewidth)
+ namewidth = len;
+ namewidth += 1; /* add a space to separate name & aligned seq */
+ namewidth *= fontwidth;
+
+ /* Determine bounding box
+ */
+ if (msa->alen > 50) Die("No EPS fmt if alignment is >50 columns");
+ width = namewidth + hspace*msa->alen;
+ if (width > 612) Die("Alignment too wide to write in EPS");
+ height = vspace*msa->nseq;
+ if (height > 792) Die("Too many seqs to write in EPS");
+
+ /* Magic EPS header, bare-bones DSC-compliant.
+ */
+ fprintf(fp, "%%!PS-Adobe-3.0 EPSF-3.0\n");
+ fprintf(fp, "%%%%BoundingBox: %d %d %d %d\n", 0, 0, width, height);
+ fprintf(fp, "%%%%Pages: 1\n");
+ fprintf(fp, "%%%%EndComments\n");
+
+ /* More postscript magic before we start the alignment
+ */
+ fprintf(fp, "/%s findfont\n", font);
+ fprintf(fp, "%d scalefont\n", fontsize);
+ fprintf(fp, "setfont\n");
+ fprintf(fp, "newpath\n");
+
+ /* Write the alignment in PostScript in a single block
+ */
+ for (i = 0; i < msa->nseq; i++)
+ {
+ ypos = (msa->nseq-i-1)*vspace;
+ /* name first */
+ fprintf(fp, "%d %d moveto\n", 0, ypos);
+ fprintf(fp, "(%s) show\n", msa->sqname[i]);
+ /* now seq */
+ xpos = namewidth;
+ for (j = 0; j < msa->alen; j++)
+ {
+ fprintf(fp, "%d %d moveto\n", xpos, ypos);
+ fprintf(fp, "(%c) show\n", msa->aseq[i][j]);
+ xpos+= hspace;
+ }
+ }
+
+ free(font);
+}
+
+
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+
+/* file.c
+ * SRE, Wed Jun 19 11:19:22 1996
+ *
+ * File operation utilities, dealing with pathnames, directories,
+ * and environment variables.
+ *
+ * The goal is to have these be platform-independent but they
+ * currently are UNIX-specific: i.e. this file is currently POSIX compliant
+ * but it is NOT ANSI C compliant. (The sole offender is getenv().)
+ *
+ * RCS $Id: file.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: file.c,v 1.8 2002/03/07 03:18:02 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "squid.h"
+#include "sqfuncs.h"
+
+/*
+ * VMS: #define DIRSLASH ']'
+ * MacOS: #define DIRSLASH ':'
+ * DOS: #define DIRSLASH '\\'
+ *
+ * The code assumes that '.' is used for file name extensions,
+ * such as "foo.bar".
+ */
+#define DIRSLASH '/' /* UNIX directory paths have /foo/bar */
+
+
+
+/* Function: FileDirname()
+ *
+ * Purpose: Returns the path from a filename:
+ * "/foo/bar/baz" -> "/foo/bar"
+ * "foo/bar" -> "foo"
+ * "foo" -> "."
+ * "/" -> "/"
+ * i.e. the string will be non-NULL; it will
+ * contain the string up to but not including the
+ * last '/' character; returns "." if
+ * there are no '/' characters, and returns "/"
+ * if the last slash is the first character.
+ * Modeled on Tcl's "file dirname" command.
+ *
+ * Args: file - name of file "/foo/bar/baz".
+ *
+ * Return: ptr to malloc'ed string "/foo/bar".
+ */
+char *
+FileDirname(char *file)
+{
+ char *dirname;
+ char *lastslash;
+ int len;
+
+ lastslash = strrchr(file, DIRSLASH);
+ len = (lastslash == NULL) ? 0 : (int) (lastslash - file);
+ dirname = (char *) MallocOrDie (sizeof(char) * (len+2));
+ if (len > 0) strncpy(dirname, file, len);
+ else if (*file != DIRSLASH) { *dirname = '.'; len = 1; }
+ else { *dirname = DIRSLASH; len = 1; }
+ dirname[len] = '\0';
+ return dirname;
+}
+
+
+/* Function: FileTail()
+ *
+ * Purpose: Return everything after the DIRSLASH:
+ * "/foo/bar/baz.1" -> "baz.1"
+ * "foo/bar" -> "bar"
+ * "foo" -> "foo"
+ * "/" -> ""
+ * If noextension is TRUE, removes a trailing ".foo" extension
+ * too.
+ *
+ * Args: file - name of file "/foo/bar/baz.1"
+ * noextension - TRUE to also remove extensions
+ *
+ * Return: ptr to malloc'ed string "baz.1"
+ */
+char *
+FileTail(char *file, int noextension)
+{
+ char *tail;
+ char *lastslash;
+ char *lastdot;
+ /* remove directory prefix */
+ lastslash = strrchr(file, DIRSLASH);
+ tail = (char *) MallocOrDie (sizeof(char) * (strlen(file)+1));
+ if (lastslash == NULL) strcpy(tail, file);
+ else strcpy(tail, lastslash+1);
+ /* remove trailing suffix */
+ if (noextension) {
+ if ((lastdot = strrchr(tail, '.')) != NULL)
+ *lastdot = '\0';
+ }
+
+ return tail;
+}
+
+
+/* Function: FileSameDirectory()
+ * Date: SRE, Wed Mar 6 20:03:23 2002 [St. Louis]
+ *
+ * Purpose: Given a path to one file, and the
+ * name of another file in the same directory,
+ * concat the path from file1 onto file2, and
+ * return the result. Caller must free the ptr
+ * that's returned.
+ *
+ * Written for SSI - SSI indices contain filenames
+ * without paths, and we will need to convert that
+ * to a full path.
+ *
+ * Args: file1 - a path to a file, e.g. "/foo/bar/baz.1"
+ * file2 - a simple filename, e.g. "quux.2"
+ *
+ * Returns: path to file2: e.g. "/foo/bar/quux.2"
+ * Returns NULL if file2 already has a path, and the result
+ * would be a different place.
+ */
+char *
+FileSameDirectory(char *file1, char *file2)
+{
+ char *path;
+ char *tail;
+ char *result;
+ int seems_ok = 1;
+
+ path = FileDirname(file1);
+ tail = FileTail(file2, FALSE);
+ if (strcmp(file2, tail) != 0) seems_ok = 0; /* ut-oh, file2 *had* a path */
+ result = FileConcat(path, tail);
+ if (! seems_ok && strcmp(result, file2) != 0) {
+ free(result); result = NULL;
+ }
+ free(path);
+ free(tail);
+ return result;
+}
+
+/* Function: FileConcat()
+ *
+ * Purpose: Concatenate a directory path and a file name,
+ * returning a pointer to a malloc'ed string with the
+ * full filename. This isn't just a string concat,
+ * because we're careful about the dir slash.
+ */
+char *
+FileConcat(char *dir, char *file)
+{
+ char *full;
+
+ full = (char *) MallocOrDie (sizeof(char) * (strlen(dir)+strlen(file)+2));
+ if (*file == DIRSLASH) strcpy(full, file); /* file = "/foo", ignore directory. */
+ else sprintf(full, "%s%c%s", dir, DIRSLASH, file);
+ return full;
+}
+
+
+/* Function: FileAddSuffix()
+ * Date: SRE, Wed Aug 1 11:19:33 2001 [Pasadena]
+ *
+ * Purpose: Add a suffix to a filename, return a malloc'ed
+ * string containing the new filename.sfx name.
+ * Example:
+ * FileAddSuffix("genbank", "ssi")
+ * returns "genbank.ssi".
+ */
+char *
+FileAddSuffix(char *filename, char *sfx)
+{
+ char *new;
+ new = MallocOrDie(strlen(filename) + strlen(sfx) + 2);
+ sprintf(new, "%s.%s", filename, sfx);
+ return new;
+}
+
+/* Function: EnvFileOpen()
+ * Date: Sun Feb 12 10:55:29 1995
+ *
+ * Purpose: Open a file, given a file name and an environment
+ * variable that contains a directory path. Files
+ * are opened read-only. Does not look at current directory
+ * unless "." is explicitly in the path specified by env.
+ *
+ * For instance:
+ * fp = EnvFileOpen("BLOSUM45", "BLASTMAT", NULL);
+ * or:
+ * fp = EnvFileOpen("swiss", "BLASTDB", NULL);
+ *
+ * Environment variables may contain a colon-delimited
+ * list of more than one path; e.g.
+ * setenv BLASTDB /nfs/databases/foo:/nfs/databases/bar
+ *
+ * Sometimes a group of files may be found in
+ * one directory; for instance, an index file with a
+ * database. The caller can EnvFileOpen() the main
+ * file, and ask to get the name of the
+ * directory back in ret_dir, so it can construct
+ * the other auxiliary file names and fopen() them. (If it called
+ * EnvFileOpen(), it might get confused by
+ * file name clashes and open files in different
+ * directories.
+ *
+ * Args: fname - name of file to open
+ * env - name of environment variable containing path
+ * ret_dir - if non-NULL, RETURN: name of dir that was used.
+ *
+ * Return: FILE * to open file, or NULL on failure -- same as fopen()
+ * Caller must free ret_dir if it passed a non-NULL address.
+ */
+FILE *
+EnvFileOpen(char *fname, char *env, char **ret_dir)
+{
+ FILE *fp;
+ char *path;
+ char *s; /* ptr to indiv element in env list */
+ char full[1024]; /* constructed file name */
+
+ if (env == NULL) return NULL;
+ if ((path = Strdup(getenv(env))) == NULL) return NULL;
+
+ fp = NULL;
+ s = strtok(path, ":");
+ while (s != NULL)
+ {
+ if (((int) strlen(fname) + (int) strlen(s) + 2) > 1024)
+ { free(path); return NULL; }
+ sprintf(full, "%s%c%s", s, DIRSLASH, fname);
+ if ((fp = fopen(full, "r")) != NULL) break;
+ s = strtok(NULL, ":");
+ }
+
+ /* Return the path we used, if caller wants it
+ */
+ if (ret_dir != NULL) *ret_dir = Strdup(s);
+ free(path);
+
+ return fp;
+}
+
+
+/* Function: FileExists()
+ *
+ * Purpose: Return TRUE if filename exists.
+ * Testing fopen() is the only possible platform-independent test
+ * I'm aware of.
+ */
+int
+FileExists(char *filename)
+{
+ FILE *fp;
+ if ((fp = fopen(filename, "r"))) { fclose(fp); return TRUE; }
+ return FALSE;
+}
+
+
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* RCS $Id: getopt.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: getopt.c,v 1.7 2001/02/21 21:09:10 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+
+#include "squid.h"
+
+/* Function: Getopt()
+ *
+ * Purpose: Portable command line option parsing with abbreviated
+ * option switches. Replaces UNIX getopt(). Using UNIX getopt()
+ * hinders portability to non-UNIX platforms, and getopt()
+ * is also limited to single letter options.
+ *
+ * Getopt() implements a superset of UNIX getopt().
+ * All of getopt()'s single-character switch behavior
+ * is emulated, and "--" by itself terminates the options.
+ * Additionally, Getopt() provides extended switches
+ * like "--youroptionhere", and Getopt() type checks
+ * arguments.
+ *
+ * Extended options must start with "--", as in "--option1".
+ * Normal options must start with "-", as in "-o".
+ * Normal options may be concatenated, as in "-a -b" == "-ab".
+ *
+ * See bottom of this .c file after #fdef GETOPT_TESTDRIVER
+ * for an example of calling Getopt().
+ *
+ * Args: argc - from main(). number of elems in argv.
+ * argv - from main(). argv[0] is the name of the command.
+ * opt - array of opt_s structures, defining option switches
+ * nopts - number of switches in opt
+ * usage - a (possibly long) string to print if usage error.
+ * ret_optind - RETURN: the index in argv[] of the next
+ * valid command-line token.
+ * ret_optname- RETURN: ptr to the name of option switch
+ * seen, or NULL if no option was seen.
+ * ret_optarg - RETURN: ptr to the optional argument, if any;
+ * NULL if option takes no argument.
+ *
+ * Return: 1 if a valid option was parsed.
+ * 0 if no option was found, and command-line parsing is complete.
+ * Die()'s here if an error is detected.
+ */
+int
+Getopt(int argc, char **argv, struct opt_s *opt, int nopts, char *usage,
+ int *ret_optind, char **ret_optname, char **ret_optarg)
+{
+ int i;
+ int arglen;
+ int nmatch;
+ static int optind = 1; /* init to 1 on first call */
+ static char *optptr = NULL; /* ptr to next valid switch */
+ int opti = 0; /* init only to silence gcc uninit warnings */
+
+ /* Check to see if we've run out of options.
+ * A '-' by itself is an argument (e.g. "read from stdin")
+ * not an option.
+ */
+ if (optind >= argc || argv[optind][0] != '-' || strcmp(argv[optind], "-") == 0)
+ {
+ *ret_optind = optind;
+ *ret_optarg = NULL;
+ *ret_optname = NULL;
+ return 0;
+ }
+
+ /* Check to see if we're being told that this is the end
+ * of the options with the special "--" flag.
+ */
+ if (strcmp(argv[optind], "--") == 0)
+ {
+ optind++;
+ *ret_optind = optind;
+ *ret_optname = NULL;
+ *ret_optarg = NULL;
+ return 0;
+ }
+
+ /* We have a real option. Find which one it is.
+ * We handle single letter switches "-o" separately
+ * from full switches "--option", based on the "-" vs. "--"
+ * prefix -- single letter switches can be concatenated
+ * as long as they don't have arguments.
+ */
+ /* full option */
+ if (optptr == NULL && strncmp(argv[optind], "--", 2) == 0)
+ {
+ /* Use optptr to parse argument in options of form "--foo=666"
+ */
+ if ((optptr = strchr(argv[optind], '=')) != NULL)
+ { *optptr = '\0'; optptr++; }
+
+ arglen = strlen(argv[optind]);
+ nmatch = 0;
+ for (i = 0; i < nopts; i++)
+ if (opt[i].single == FALSE &&
+ strncmp(opt[i].name, argv[optind], arglen) == 0)
+ {
+ nmatch++;
+ opti = i;
+ if (arglen == strlen(opt[i].name)) break; /* exact match, stop now */
+ }
+ if (nmatch > 1 && arglen != strlen(opt[i].name))
+ Die("Option \"%s\" is ambiguous; please be more specific.\n%s",
+ argv[optind], usage);
+ if (nmatch == 0)
+ Die("No such option \"%s\".\n%s", argv[optind], usage);
+
+ *ret_optname = opt[opti].name;
+
+ /* Set the argument, if there is one
+ */
+ if (opt[opti].argtype != sqdARG_NONE)
+ {
+ if (optptr != NULL)
+ { /* --foo=666 style */
+ *ret_optarg = optptr;
+ optptr = NULL;
+ optind++;
+ }
+ else if (optind+1 >= argc)
+ Die("Option %s requires an argument\n%s", opt[opti].name, usage);
+ else /* "--foo 666" style */
+ {
+ *ret_optarg = argv[optind+1];
+ optind+=2;
+ }
+ }
+ else /* sqdARG_NONE */
+ {
+ if (optptr != NULL)
+ Die("Option %s does not take an argument\n%s", opt[opti].name, usage);
+ *ret_optarg = NULL;
+ optind++;
+ }
+ }
+ else /* else, a single letter option "-o" */
+ {
+ /* find the option */
+ if (optptr == NULL)
+ optptr = argv[optind]+1;
+ for (opti = -1, i = 0; i < nopts; i++)
+ if (opt[i].single == TRUE && *optptr == opt[i].name[1])
+ { opti = i; break; }
+ if (opti == -1)
+ Die("No such option \"%c\".\n%s", *optptr, usage);
+ *ret_optname = opt[opti].name;
+
+ /* set the argument, if there is one */
+ if (opt[opti].argtype != sqdARG_NONE)
+ {
+ if (*(optptr+1) != '\0') /* attached argument */
+ {
+ *ret_optarg = optptr+1;
+ optind++;
+ }
+ else if (optind+1 < argc) /* unattached argument */
+ {
+ *ret_optarg = argv[optind+1];
+ optind+=2;
+ }
+ else Die("Option %s requires an argument\n%s", opt[opti].name, usage);
+
+ optptr = NULL; /* can't concatenate after an argument */
+ }
+ else /* sqdARG_NONE */
+ {
+ *ret_optarg = NULL;
+ if (*(optptr+1) != '\0') /* concatenation */
+ optptr++;
+ else
+ {
+ optind++; /* move to next field */
+ optptr = NULL;
+ }
+ }
+
+ }
+
+ /* Type check the argument, if there is one
+ */
+ if (opt[opti].argtype != sqdARG_NONE)
+ {
+ if (opt[opti].argtype == sqdARG_INT && ! IsInt(*ret_optarg))
+ Die("Option %s requires an integer argument\n%s",
+ opt[opti].name, usage);
+ else if (opt[opti].argtype == sqdARG_FLOAT && ! IsReal(*ret_optarg))
+ Die("Option %s requires a numerical argument\n%s",
+ opt[opti].name, usage);
+ else if (opt[opti].argtype == sqdARG_CHAR && strlen(*ret_optarg) != 1)
+ Die("Option %s requires a single-character argument\n%s",
+ opt[opti].name, usage);
+ /* sqdARG_STRING is always ok, no type check necessary */
+ }
+
+ *ret_optind = optind;
+ return 1;
+}
+
+
+
+#ifdef GETOPT_TESTDRIVER
+/* cc -DGETOPT_TESTDRIVER -L ~/lib/squid.linux/ getopt.c -lsquid
+ */
+struct opt_s OPTIONS[] = {
+ { "--test1", FALSE, sqdARG_INT },
+ { "--test2", FALSE, sqdARG_FLOAT },
+ { "--test3", FALSE, sqdARG_STRING },
+ { "--test4", FALSE, sqdARG_CHAR },
+ { "-a", TRUE, sqdARG_NONE },
+ { "-b", TRUE, sqdARG_INT },
+};
+#define NOPTIONS (sizeof(OPTIONS) / sizeof(struct opt_s))
+
+int
+main(int argc, char **argv)
+{
+ int optind;
+ char *optarg;
+ char *optname;
+
+ while (Getopt(argc, argv, OPTIONS, NOPTIONS, "Usage/help here",
+ &optind, &optname, &optarg))
+ {
+ printf("Option: index: %d name: %s argument: %s\n",
+ optind, optname, optarg);
+ }
+ while (optind < argc)
+ {
+ printf("Argument: index: %d name: %s\n", optind, argv[optind]);
+ optind++;
+ }
+
+
+}
+
+
+#endif /*GETOPT_TESTDRIVER*/
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* gki.c
+ * SRE, Sat May 1 14:49:08 1999
+ *
+ * "generic key index" module: emulation of Perl hashes.
+ * Maps keys (ASCII char strings) to array index. Dynamically
+ * resizes the hash table.
+ *
+ * Limitations:
+ * - hash table can only grow; no provision for deleting keys
+ * or downsizing the hash table.
+ * - Maximum hash table size set at 100003. Performance
+ * will degrade for key sets much larger than this.
+ * - Assumes that integers are 32 bits (or greater).
+ *
+ * Defines a typedef'd structure:
+ * gki - a key index hash table.
+ * Provides functions:
+ * GKIInit() - start a hash table.
+ * GKIStoreKey() - store a new key, get a unique index.
+ * GKIKeyIndex() - retrieve an existing key's index.
+ * GKIFree() - free a hash table.
+ * GKIStatus() - Debugging: prints internal status of a hash struct
+ *
+ *
+ * Note that there are no dependencies on squid; the gki.c/gki.h
+ * pair are base ANSI C and can be reused anywhere.
+ *****************************************************************
+ *
+ * API for storing/reading stuff:
+ * moral equivalent of Perl's $foo{$key} = whatever, $bar{$key} = whatever:
+ * #include "gki.h"
+ *
+ * gki *hash;
+ * int idx;
+ * char *key;
+ *
+ * hash = GKIInit();
+ * (Storing:)
+ * (foreach key) {
+ * idx = GKIStoreKey(hash, key);
+ * (reallocate foo, bar as needed)
+ * foo[idx] = whatever;
+ * bar[idx] = whatever;
+ * }
+ * (Reading:)
+ * (foreach key) {
+ * idx = GKIKeyIndex(hash, key);
+ * if (idx == -1) {no_such_key; }
+ * (do something with) foo[idx];
+ * (do something with) bar[idx];
+ * }
+ * GKIFree();
+ *
+ *****************************************************************
+ *
+ * Timings on wrasse for 45402 keys in /usr/dict/words using
+ * Tests/test_gki:
+ * 250 msec store (6 usec/store)
+ * 140 msec retrieve (3 usec/retrieve)
+ * and using the 13408 names of Pfam's GP120.full alignment:
+ * 70 msec store (5 usec/store)
+ * 50 msec retrieve (4 usec/retrieve)
+ *
+ * RCS $Id: gki.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: gki.c,v 1.3 2000/12/21 23:42:59 eddy Exp)
+ */
+
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <limits.h>
+#include "squid.h"
+#include "gki.h"
+
+/*
+ * Best hash table sizes are prime numbers (see Knuth vol 3, Sorting
+ * and Searching).
+ * gki_primes[] defines the ascending order of hash table sizes
+ * that we use in upsizing the hash table dynamically.
+ * useful site for testing primes:
+ * http://www.idbsu.edu/people/jbrennan/algebra/numbers/sieve.html
+ * Because of the way gki_hashvalue works, the largest number
+ * must be < INT_MAX / 128 / 128 : 131072 on a 32 bit machine.
+ */
+static int gki_primes[] = { 101, 1009, 10007, 100003 };
+#define GKI_NPRIMES 4
+#define GKI_ALPHABETSIZE 128
+
+static GKI *gki_alloc(int primelevel);
+static int gki_hashvalue(GKI *hash, char *key);
+static int gki_upsize(GKI *old);
+
+
+/* Function: GKIInit()
+ * Date: SRE, Sat May 1 11:12:24 1999 [May Day geek-out]
+ *
+ * Purpose: Initialize a hash table for key indexing.
+ * Simply a wrapper around a level 0 gki_alloc().
+ *
+ * Args: (void)
+ *
+ * Returns: An allocated hash table structure.
+ * Caller frees with GKIFree().
+ */
+GKI *
+GKIInit(void)
+{
+ GKI *hash;
+ hash = gki_alloc(0);
+ return hash;
+}
+
+/* Function: GKIFree()
+ * Date: SRE, Sat May 1 11:13:26 1999 [May Day geek-out]
+ *
+ * Purpose: Free a key index hash table.
+ *
+ * Args: hash - the gki structure
+ *
+ * Returns: (void).
+ * hash table is destroyed.
+ */
+void
+GKIFree(GKI *hash)
+{
+ struct gki_elem *ptr;
+ int i;
+
+ if (hash == NULL) return; /* tolerate a NULL */
+
+ for (i = 0; i < hash->nhash; i++)
+ while (hash->table[i] != NULL)
+ {
+ ptr = hash->table[i]->nxt;
+ /* NULL keys can occur after we've gki_upsize'd */
+ if (hash->table[i]->key != NULL) free(hash->table[i]->key);
+ free(hash->table[i]);
+ hash->table[i] = ptr;
+ }
+ free(hash->table);
+ free(hash);
+}
+
+/* Function: GKIStoreKey()
+ * Date: SRE, Sat May 1 11:16:48 1999 [May Day geek-out]
+ *
+ * Purpose: Store a key in the key index hash table.
+ * Associate it with a unique "key index", counting
+ * from 0. (It's this index that lets us map
+ * the hashed keys to indexed C arrays, (clumsily)
+ * emulating Perl's hashes.)
+ *
+ * Does *not* check to see if the key's already
+ * in the table, so it's possible to store multiple
+ * copies of a key with different indices; probably
+ * not what you want, so if you're not sure the
+ * key is unique, check the table first with
+ * GKIKeyIndex().
+ *
+ * Args: hash - GKI structure to store the key in
+ * key - string to store
+ *
+ * Returns: the new key's index. Since it's always the
+ * last one in the current array, this index is
+ * just hash->nkeys-1.
+ * On a malloc failure, returns -1.
+ * hash table is modified.
+ */
+int
+GKIStoreKey(GKI *hash, char *key)
+{
+ int val;
+ struct gki_elem *ptr;
+
+ val = gki_hashvalue(hash, key);
+
+ ptr = hash->table[val];
+ hash->table[val] = MallocOrDie(sizeof(struct gki_elem));
+ hash->table[val]->key = MallocOrDie(sizeof(char) * (strlen(key)+1));
+ strcpy(hash->table[val]->key, key);
+
+ hash->table[val]->idx = hash->nkeys;
+ hash->table[val]->nxt = ptr;
+
+ hash->nkeys++;
+ /* time to upsize? */
+ if (hash->nkeys > 3*hash->nhash && hash->primelevel < GKI_NPRIMES-1)
+ gki_upsize(hash);
+
+ return hash->nkeys-1;
+}
+
+/* Function: GKIKeyIndex()
+ * Date: SRE, Sat May 1 11:20:42 1999 [May Day geek-out]
+ *
+ * Purpose: Look up a key in the hash table. Return
+ * its index (0..nkeys-1), else -1 if the key
+ * isn't in the hash (yet).
+ *
+ * Args: hash - the GKI hash table to search in
+ * key - the key to look up
+ *
+ * Returns: -1 if key is not found;
+ * index of key if it is found (range 0..nkeys-1).
+ * hash table is unchanged.
+ */
+int
+GKIKeyIndex(GKI *hash, char *key)
+{
+ struct gki_elem *ptr;
+ int val;
+
+ val = gki_hashvalue(hash, key);
+ for (ptr = hash->table[val]; ptr != NULL; ptr = ptr->nxt)
+ if (strcmp(key, ptr->key) == 0) return ptr->idx;
+ return -1;
+}
+
+/* Function: GKIStatus()
+ * Date: SRE, Sat May 1 11:11:13 1999 [St. Louis]
+ *
+ * Purpose: (DEBUGGING) How are we doing? Calculate some
+ * simple statistics for the hash table.
+ *
+ * Args: hash - the GKI hash table to look at
+ *
+ * Returns: (void)
+ * Prints diagnostics on stdout.
+ * hash table is unchanged.
+ */
+void
+GKIStatus(GKI *hash)
+{
+ struct gki_elem *ptr;
+ int i;
+ int nkeys;
+ int nempty = 0;
+ int maxkeys = -1;
+ int minkeys = INT_MAX;
+
+ for (i = 0; i < hash->nhash; i++)
+ {
+ nkeys = 0;
+ for (ptr = hash->table[i]; ptr != NULL; ptr = ptr->nxt)
+ nkeys++;
+
+ if (nkeys == 0) nempty++;
+ if (nkeys > maxkeys) maxkeys = nkeys;
+ if (nkeys < minkeys) minkeys = nkeys;
+ }
+
+ printf("Total keys: %d\n", hash->nkeys);
+ printf("Hash table size: %d\n", hash->nhash);
+ printf("Average occupancy: %.1f\n", (float) hash->nkeys / (float) hash->nhash);
+ printf("Unoccupied slots: %d\n", nempty);
+ printf("Most in one slot: %d\n", maxkeys);
+ printf("Least in one slot: %d\n", minkeys);
+
+}
+
+
+/* Function: gki_alloc()
+ * Date: SRE, Sat May 1 11:55:47 1999 [May Day geek-out]
+ *
+ * Purpose: Allocate a hash table structure with the
+ * size given by primelevel.
+ *
+ * Args: primelevel - level 0..GKI_NPRIMES-1, specifying
+ * the size of the table; see gki_primes[]
+ * array.
+ *
+ * Returns: An allocated hash table structure.
+ * Caller frees with GKIFree().
+ */
+static GKI *
+gki_alloc(int primelevel)
+{
+ GKI *hash;
+ int i;
+
+ if (primelevel < 0 || primelevel >= GKI_NPRIMES)
+ Die("bad primelevel in gki_alloc()");
+ hash = MallocOrDie(sizeof(GKI));
+
+ hash->primelevel = primelevel;
+ hash->nhash = gki_primes[hash->primelevel];
+ hash->table = MallocOrDie(sizeof(struct gki_elem) * hash->nhash);
+ for (i = 0; i < hash->nhash; i++)
+ hash->table[i] = NULL;
+ hash->nkeys = 0;
+ return hash;
+}
+
+
+/* Function: gki_hashvalue()
+ * Date: SRE, Sat May 1 11:14:10 1999 [May Day geek-out]
+ *
+ * Purpose: Calculate the hash value for a key. Usually
+ * we expect a one-word key, but the function will
+ * hash any ASCII string effectively. The hash function
+ * is a simple one (see p. 233 of Sedgewick,
+ * Algorithms in C).
+ * Slightly optimized: does two characters at a time
+ * before doing the modulo; this gives us a significant
+ * speedup.
+ *
+ * Args: hash - the gki structure (we need to know the hash table size)
+ * key - a string to calculate the hash value for
+ *
+ * Returns: a hash value, in the range 0..hash->nhash-1.
+ * hash table is unmodified.
+ */
+static int
+gki_hashvalue(GKI *hash, char *key)
+{
+ int val = 0;
+
+ for (; *key != '\0'; key++)
+ {
+ val = GKI_ALPHABETSIZE*val + *key;
+ if (*(++key) == '\0') { val = val % hash->nhash; break; }
+ val = (GKI_ALPHABETSIZE*val + *key) % hash->nhash;
+ }
+ return val;
+}
+
+/* Function: gki_upsize()
+ * Date: SRE, Sat May 1 11:46:07 1999 [May Day geek-out]
+ *
+ * Purpose: Grow the hash table to the next available size.
+ *
+ * Args: old - the GKI hash table to reallocate.
+ *
+ * Returns: 1 on success (the hash table is changed);
+ * 0 on failure; the table is already at its maximum size,
+ * and the hash table is returned unchanged.
+ */
+static int
+gki_upsize(GKI *old)
+{
+ GKI *new;
+ int i;
+ struct gki_elem *optr;
+ struct gki_elem *nptr;
+ int val;
+
+ if (old->primelevel >= GKI_NPRIMES-1) return 0;
+ new = gki_alloc(old->primelevel+1);
+
+ /* Read the old, store in the new, while *not changing*
+ * any key indices. Because of the way the lists are
+ * treated as LIFO stacks, all the lists are reversed
+ * in the new structure.
+ */
+ for (i = 0; i < old->nhash; i++)
+ {
+ optr = old->table[i];
+ while (optr != NULL)
+ {
+ val = gki_hashvalue(new, optr->key);
+
+ nptr = new->table[val];
+ new->table[val] = optr;
+ optr = optr->nxt;
+ new->table[val]->nxt = nptr;
+ }
+ }
+ free(old->table);
+
+ /* Now swap within the interior of the structures, so the old
+ * structure is updated to the new structure.
+ * (nkeys is identical, so we don't need to swap that element.)
+ */
+ old->primelevel = new->primelevel;
+ old->nhash = new->nhash;
+ old->table = new->table;
+ free(new);
+ return 1;
+}
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+#ifndef SQUID_GKI_INCLUDED
+#define SQUID_GKI_INCLUDED
+
+/* gki.h
+ * SRE, Sat May 1 15:07:22 1999
+ *
+ * Declarations of structures, functions for generic key index
+ * module: emulation of Perl hashes. See gki.c.
+ *
+ * RCS $Id: gki.h 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: gki.h,v 1.2 1999/07/15 22:30:45 eddy Exp)
+ */
+
+/* gki_elem:
+ * key, array index pairs are kept in linked list structures.
+ */
+struct gki_elem {
+ char *key;
+ int idx;
+ struct gki_elem *nxt;
+};
+
+/* gki:
+ * a dynamically resized hash structure;
+ * contains a hash table and associated data
+ */
+typedef struct {
+ struct gki_elem **table;
+
+ int primelevel;
+ int nhash;
+ int nkeys;
+} GKI;
+
+GKI *GKIInit(void);
+void GKIFree(GKI *hash);
+int GKIHashValue(GKI *hash, char *key);
+int GKIStoreKey(GKI *hash, char *key);
+int GKIKeyIndex(GKI *hash, char *key);
+void GKIStatus(GKI *hash);
+
+#endif /* SQUID_GKI_INCLUDED */
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* gsi.c
+ * Interfaces for GSI "generic sequence index" files.
+ * broken away from sqio.c and extended: SRE, Wed Aug 5 10:32:53 1998
+ *
+ *
+ * GSI definition:
+ * 1 + <nfiles> + <nkeys> total records.
+ * Each record = 38 bytes.
+ *
+ * one header record : <"GSI" (32)> <nfiles (2)> <nkeys (4)>
+ * <nfiles> file records : <filename (32)> <fileno (2)> <fmt (4)>
+ * <nkeys> key records : <key (32)> <fileno (2)> <offset(4)>
+ *
+ * Matches up with my Perl scripts that create GSI files.
+ *
+ * RCS $Id: gsi.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: gsi.c,v 1.5 2001/08/04 20:15:42 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#ifndef SEEK_SET
+#include <unistd.h> /* needed for poor crippled SunOS */
+#endif
+
+#include "squid.h"
+#include "gsi.h"
+
+
+/*****************************************************************
+ * GSI index file access routines
+ *****************************************************************/
+
+/* Function: GSIOpen()
+ *
+ * Purpose: Open a GSI file. Returns the number of records in
+ * the file and a file pointer. Returns NULL on failure.
+ * The file pointer should be fclose()'d normally.
+ */
+GSIFILE *
+GSIOpen(char *gsifile)
+{
+ GSIFILE *gsi;
+ char magic[GSI_KEYSIZE];
+
+ gsi = (GSIFILE *) MallocOrDie (sizeof(GSIFILE));
+ if ((gsi->gsifp = fopen(gsifile, "r")) == NULL)
+ { free(gsi); squid_errno = SQERR_NOFILE; return NULL; }
+
+ if (! fread(magic, sizeof(char), GSI_KEYSIZE, gsi->gsifp))
+ { free(gsi); squid_errno = SQERR_NODATA; return NULL; }
+ if (strcmp(magic, "GSI") != 0)
+ { free(gsi); squid_errno = SQERR_FORMAT; return NULL; }
+
+ if (! fread(&(gsi->nfiles), sizeof(sqd_uint16), 1, gsi->gsifp))
+ { free(gsi); squid_errno = SQERR_NODATA; return NULL; }
+ if (! fread(&(gsi->recnum), sizeof(sqd_uint32), 1, gsi->gsifp))
+ { free(gsi); squid_errno = SQERR_NODATA; return NULL; }
+
+ gsi->nfiles = sre_ntoh16(gsi->nfiles); /* convert from network short */
+ gsi->recnum = sre_ntoh32(gsi->recnum); /* convert from network long */
+
+ return gsi;
+}
+
+/* Function: GSIGetRecord()
+ *
+ * Purpose: Each non-header record of a GSI index files consists
+ * of 38 bytes: 32 bytes of character string, a 2 byte
+ * short, and a 4 byte long. This function returns the
+ * three values.
+ *
+ * Args: gsi - open GSI index file, correctly positioned at a record
+ * f1 - char[32], allocated by caller (or NULL if unwanted)
+ * f2 - pointer to short (or NULL if unwanted)
+ * f3 - pointer to long (or NULL if unwanted)
+ *
+ * Return: 0 on failure and sets squid_errno.
+ */
+int
+GSIGetRecord(GSIFILE *gsi, char *f1, sqd_uint16 *f2, sqd_uint32 *f3)
+{
+ if (f1 == NULL) fseek(gsi->gsifp, GSI_KEYSIZE, SEEK_CUR);
+ else if (! fread(f1, GSI_KEYSIZE, 1, gsi->gsifp))
+ { squid_errno = SQERR_NODATA; return 0; }
+
+ if (f2 == NULL) fseek(gsi->gsifp, sizeof(sqd_uint16), SEEK_CUR);
+ else if (! fread(f2, sizeof(sqd_uint16), 1, gsi->gsifp))
+ { squid_errno = SQERR_NODATA; return 0; }
+
+ if (f3 == NULL) fseek(gsi->gsifp, sizeof(sqd_uint32), SEEK_CUR);
+ else if (! fread(f3, sizeof(sqd_uint32), 1, gsi->gsifp))
+ { squid_errno = SQERR_NODATA; return 0; }
+
+ if (f2 != NULL) *f2 = sre_ntoh16(*f2);
+ if (f3 != NULL) *f3 = sre_ntoh32(*f3);
+
+ return 1;
+}
+
+
+/* Function: GSIGetOffset()
+ *
+ * Purpose: From a key (sequence name), find a disk offset
+ * in an open general sequence index file by binary
+ * search. Presumably GSI indexing could be even faster
+ * if we used hashing.
+ *
+ * Args: gsi - GSI index file, opened by GSIOpen()
+ * key - name of key to retrieve indices for
+ * ret_seqfile - pre-alloced char[32] array for seqfile name
+ * ret_fmt - format of seqfile
+ * ret_offset - return: disk offset in seqfile.
+ */
+int
+GSIGetOffset(GSIFILE *gsi, char *key, char *ret_seqfile,
+ int *ret_format, long *ret_offset)
+{
+ sqd_uint32 left, right, mid;
+ int cmp;
+ char name[GSI_KEYSIZE + 1];
+ sqd_uint32 offset;
+ sqd_uint16 filenum;
+ sqd_uint32 fmt;
+
+ name[GSI_KEYSIZE] = '\0';
+
+ left = gsi->nfiles + 1;
+ right = gsi->nfiles + gsi->recnum;
+ mid = (left + right) / 2;
+ fseek(gsi->gsifp, mid * GSI_RECSIZE, SEEK_SET);
+
+ while (GSIGetRecord(gsi, name, &filenum, &offset))
+ {
+ cmp = strcmp(name, key);
+ if (cmp == 0) break; /* found it! */
+ else if (left >= right) return 0; /* oops, missed it; fail. */
+ else if (cmp < 0) left = mid + 1; /* it's right of mid */
+ else if (cmp > 0) right = mid - 1; /* it's left of mid */
+ mid = (left + right) / 2;
+ fseek(gsi->gsifp, mid * GSI_RECSIZE, SEEK_SET);
+ }
+
+ /* Using file number, look up the sequence file and format.
+ */
+ fseek(gsi->gsifp, filenum * GSI_RECSIZE, SEEK_SET);
+ GSIGetRecord(gsi, ret_seqfile, NULL, &fmt);
+ *ret_format = (int) fmt;
+ *ret_offset = (long) offset;
+
+ return 1;
+}
+
+/* Function: GSIClose()
+ *
+ * Purpose: Close an open GSI sequence index file.
+ */
+void
+GSIClose(GSIFILE *gsi)
+{
+ fclose(gsi->gsifp);
+ free(gsi);
+}
+
+
+/*****************************************************************
+ * GSI index construction routines
+ * SRE, Wed Nov 10 11:49:14 1999 [St. Louis]
+ *
+ * API:
+ * g = GSIAllocIndex();
+ *
+ * [foreach filename, <32 char, no directory path]
+ * GSIAddFileToIndex(g, filename);
+ * filenum++;
+ * [foreach key, <32 char, w/ filenum 1..nfiles, w/ 32bit offset]
+ * GSIAddKeyToIndex(g, key, filenum, offset);
+ *
+ * GSISortIndex(g);
+ * GSIWriteIndex(fp, g);
+ * GSIFreeIndex(g);
+ *****************************************************************/
+struct gsiindex_s *
+GSIAllocIndex(void)
+{
+ struct gsiindex_s *g;
+
+ g = MallocOrDie(sizeof(struct gsiindex_s));
+ g->filenames = MallocOrDie(sizeof(char *) * 10);
+ g->fmt = MallocOrDie(sizeof(int) * 10);
+ g->elems = MallocOrDie(sizeof(struct gsikey_s) * 100);
+ g->nfiles = 0;
+ g->nkeys = 0;
+ return g;
+}
+void
+GSIFreeIndex(struct gsiindex_s *g)
+{
+ int i;
+ for (i = 0; i < g->nfiles; i++) free(g->filenames[i]);
+ free(g->filenames);
+ free(g->fmt);
+ free(g->elems);
+ free(g);
+}
+void
+GSIAddFileToIndex(struct gsiindex_s *g, char *filename, int fmt)
+{
+ int len;
+
+ len = strlen(filename);
+ if (len >= GSI_KEYSIZE) Die("File name too long to be indexed.");
+ g->filenames[g->nfiles] = sre_strdup(filename, len);
+ g->fmt[g->nfiles] = fmt;
+ g->nfiles++;
+ if (g->nfiles % 10 == 0) {
+ g->filenames = ReallocOrDie(g->filenames, sizeof(char *) * (g->nfiles + 10));
+ g->fmt = ReallocOrDie(g->fmt, sizeof(int) * (g->nfiles + 10));
+ }
+}
+void
+GSIAddKeyToIndex(struct gsiindex_s *g, char *key, int filenum, long offset)
+{
+ if (strlen(key) >= GSI_KEYSIZE) Die("key too long in GSI index");
+ if (filenum > SQD_UINT16_MAX) Die("too many files in GSI index");
+ if (offset > SQD_UINT32_MAX) Die("offset too big in GSI index");
+
+ strncpy(g->elems[g->nkeys].key, key, GSI_KEYSIZE-1);
+ g->elems[g->nkeys].key[GSI_KEYSIZE-1] = '\0';
+ g->elems[g->nkeys].filenum = (sqd_uint16) filenum;
+ g->elems[g->nkeys].offset = (sqd_uint32) offset;
+ g->nkeys++;
+
+ if (g->nkeys % 100 == 0)
+ g->elems = ReallocOrDie(g->elems, sizeof(struct gsikey_s) * (g->nkeys + 100));
+}
+static int
+gsi_keysorter(const void *k1, const void *k2)
+{
+ struct gsikey_s *key1;
+ struct gsikey_s *key2;
+ key1 = (struct gsikey_s *) k1;
+ key2 = (struct gsikey_s *) k2;
+ return strcmp(key1->key, key2->key);
+}
+void
+GSISortIndex(struct gsiindex_s *g)
+{
+ qsort((void *) g->elems, g->nkeys, sizeof(struct gsikey_s), gsi_keysorter);
+}
+void
+GSIWriteIndex(FILE *fp, struct gsiindex_s *g)
+{
+ sqd_uint32 i;
+
+ /* Range checking.
+ */
+ /* AW: gcc says: comparison always false die to limited range of data type */
+#ifndef CLUSTALO
+ if (g->nfiles > SQD_UINT16_MAX) Die("Too many files in GSI index.");
+#endif
+ if (g->nkeys > SQD_UINT32_MAX) Die("Too many keys in GSI index.");
+
+ GSIWriteHeader(fp, g->nfiles, g->nkeys);
+ for (i = 0; i < g->nfiles; i++)
+ GSIWriteFileRecord(fp, g->filenames[i], i+1, g->fmt[i]);
+ for (i = 0; i < g->nkeys; i++)
+ GSIWriteKeyRecord(fp, g->elems[i].key, g->elems[i].filenum, g->elems[i].offset);
+}
+
+
+
+
+
+/* Function: GSIWriteHeader()
+ * Date: SRE, Wed Aug 5 10:36:02 1998 [St. Louis]
+ *
+ * Purpose: Write the first record to an open GSI file:
+ * "GSI" <nfiles> <nkeys>
+ *
+ * Args: fp - open file to write to.
+ * nfiles - number of files indexed
+ * nkeys - number of keys indexed
+ *
+ * Returns: void
+ */
+void
+GSIWriteHeader(FILE *fp, int nfiles, long nkeys)
+{
+ char key[GSI_KEYSIZE];
+ sqd_uint16 f1;
+ sqd_uint32 f2;
+
+ /* beware potential range errors!
+ */
+ if (nfiles > SQD_UINT16_MAX) Die("GSI: nfiles out of range");
+ if (nkeys > SQD_UINT32_MAX) Die("GSI: nkeys out of range");
+
+ f1 = (sqd_uint16) nfiles;
+ f2 = (sqd_uint32) nkeys;
+ f1 = sre_hton16(f1);
+ f2 = sre_hton32(f2);
+ strcpy(key, "GSI");
+
+ if (fwrite(key, 1, GSI_KEYSIZE, fp) < GSI_KEYSIZE) PANIC;
+ if (fwrite(&f1, 2, 1, fp) < 1) PANIC;
+ if (fwrite(&f2, 4, 1, fp) < 1) PANIC;
+}
+
+
+/* Function: GSIWriteFileRecord()
+ * Date: SRE, Wed Aug 5 10:45:51 1998 [St. Louis]
+ *
+ * Purpose: Write a file record to an open GSI file.
+ *
+ * Args: fp - open GSI file
+ * fname - file name (max 31 characters)
+ * idx - file number
+ * fmt - file format (e.g. kPearson, etc.)
+ *
+ * Returns: 0 on failure. 1 on success.
+ */
+int
+GSIWriteFileRecord(FILE *fp, char *fname, int idx, int fmt)
+{
+ sqd_uint16 f1;
+ sqd_uint32 f2;
+
+ if (strlen(fname) >= GSI_KEYSIZE) return 0;
+ if (idx > SQD_UINT16_MAX) Die("GSI: file index out of range");
+ if (fmt > SQD_UINT32_MAX) Die("GSI: format index out of range");
+
+ f1 = (sqd_uint16) idx;
+ f2 = (sqd_uint32) fmt;
+ f1 = sre_hton16(f1);
+ f2 = sre_hton32(f2);
+
+ if (fwrite(fname, 1, GSI_KEYSIZE, fp) < GSI_KEYSIZE) PANIC;
+ if (fwrite(&f1, 2, 1, fp) < 1) PANIC;
+ if (fwrite(&f2, 4, 1, fp) < 1) PANIC;
+ return 1;
+}
+
+
+/* Function: GSIWriteKeyRecord()
+ * Date: SRE, Wed Aug 5 10:52:30 1998 [St. Louis]
+ *
+ * Purpose: Write a key record to a GSI file.
+ *
+ * Args: fp - open GSI file for writing
+ * key - key (max 31 char + \0)
+ * fileidx - which file number to find this key in
+ * offset - offset for this key
+ *
+ * Returns: 1 on success, else 0.
+ * will fail if key >= 32 chars, for instance.
+ */
+int
+GSIWriteKeyRecord(FILE *fp, char *key, int fileidx, long offset)
+{
+ sqd_uint16 f1;
+ sqd_uint32 f2;
+
+ if (strlen(key) >= GSI_KEYSIZE) return 0;
+ if (fileidx > SQD_UINT16_MAX) Die("GSI: file index out of range");
+ if (offset > SQD_UINT32_MAX) Die("GSI: offset out of range");
+
+ f1 = (sqd_uint16) fileidx;
+ f2 = (sqd_uint32) offset;
+ f1 = sre_hton16(f1);
+ f2 = sre_hton32(f2);
+
+ if (fwrite(key, 1, GSI_KEYSIZE, fp) < GSI_KEYSIZE) PANIC;
+ if (fwrite(&f1, 2, 1, fp) < 1) PANIC;
+ if (fwrite(&f2, 4, 1, fp) < 1) PANIC;
+ return 1;
+}
+
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+#ifndef GSIH_INCLUDED
+#define GSIH_INCLUDED
+
+/* gsi.h
+ * Database indexing (GSI format support)
+ * RCS $Id: gsi.h 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: gsi.h,v 1.3 2001/08/04 20:15:42 eddy Exp)
+ *
+ * A GSI (generic sequence index) file is composed of
+ * recnum + nfiles + 1 records. Each record contains
+ * three fields; key, file number, and disk offset.
+ * Record 0 contains:
+ * [ "GSI" ] [ nfiles ] [ recnum ]
+ * Records 1..nfiles map file names to file numbers, and contain:
+ * [ filename ] [ file number, 1..nfiles ] [ 0 (unused) ]
+ * Records nfiles+1 to recnum+nfiles+1 provide disk offset
+ * and file number indices for every key:
+ * [ key ] [ file number ] [ offset]
+ *
+ * Because the file is binary, we take some (but not
+ * complete) care to improve portability amongst platforms.
+ * This means using network order integers (see ntohl())
+ * and defining types for 16 and 32 bit integers.
+ *
+ * Because we use 32-bit offsets, ftell(), and fseek(),
+ * there is an implicit 2 Gb file size maximum.
+ * AFAIK neither ANSI C nor POSIX provide a portable solution
+ * to this problem. fsetpos(), fgetpos() use an
+ * opaque fpos_t datatype that we can't write portably
+ * to a disk file. Suggestions welcomed.
+ */
+#define GSI_KEYSIZE 32 /* keys are 32 bytes long */
+#define GSI_RECSIZE 38 /* 32 + 2 + 4 bytes */
+#define SQD_UINT16_MAX 65535 /* 2^16-1 */
+#define SQD_UINT32_MAX 4294967295U/* 2^32-1 */
+
+struct gsi_s {
+ FILE *gsifp; /* open GSI index file */
+ sqd_uint16 nfiles; /* number of files = 16 bit int */
+ sqd_uint32 recnum; /* number of records = 32 bit int */
+};
+typedef struct gsi_s GSIFILE;
+
+struct gsikey_s {
+ char key[GSI_KEYSIZE];
+ sqd_uint16 filenum;
+ sqd_uint32 offset;
+};
+struct gsiindex_s {
+ char **filenames;
+ int *fmt;
+ sqd_uint16 nfiles;
+
+ struct gsikey_s *elems;
+ int nkeys;
+};
+
+
+/* from gsi.c
+ */
+extern GSIFILE *GSIOpen(char *gsifile);
+extern int GSIGetRecord(GSIFILE *gsi, char *f1, sqd_uint16 *f2, sqd_uint32 *f3);
+extern int GSIGetOffset(GSIFILE *gsi, char *key, char *sqfile,
+ int *fmt, long *ret_offset);
+extern void GSIClose(GSIFILE *gsi);
+extern struct gsiindex_s *GSIAllocIndex(void);
+extern void GSIFreeIndex(struct gsiindex_s *g);
+extern void GSIAddFileToIndex(struct gsiindex_s *g, char *filename, int fmt);
+extern void GSIAddKeyToIndex(struct gsiindex_s *g, char *key, int filenum, long offset);
+extern void GSISortIndex(struct gsiindex_s *g);
+extern void GSIWriteIndex(FILE *fp, struct gsiindex_s *g);
+extern void GSIWriteHeader(FILE *fp, int nfiles, long nkeys);
+extern int GSIWriteFileRecord(FILE *fp, char *fname, int idx, int fmt);
+extern int GSIWriteKeyRecord(FILE *fp, char *key, int fileidx, long offset);
+
+#endif /*GSIH_INCLUDED*/
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+#ifdef USE_GSI64
+
+/* gsi64.c
+ * Updated interfaces for GSI64 64-bit "generic sequence index" files.
+ * See gsi.c for old interfaces.
+ * This is a temporary hack! Needed for human genome project.
+ */
+
+/* 1 + <nfiles> + <nkeys> total records.
+ * Each record = 42 bytes.
+ *
+ * one header record : <"GSI64" (32)> <nfiles (2)> <nkeys (8)>
+ * <nfiles> file records : <filename (32)> <fileno (2)> <fmt (8)>
+ * <nkeys> key records : <key (32)> <fileno (2)> <offset(8)>
+ *
+ * CVS $Id: gsi64.c,v 1.2 2000/12/21 23:42:59 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#ifndef SEEK_SET
+#include <unistd.h> /* needed for poor crippled SunOS */
+#endif
+
+#include "squid.h"
+#include "gsi64.h"
+
+/*****************************************************************
+ * GSI64 index file access routines
+ *****************************************************************/
+
+/* Function: GSI64Open()
+ *
+ * Purpose: Open a GSI64 file. Returns the number of records in
+ * the file and a file pointer. Returns NULL on failure.
+ * The file pointer should be fclose()'d normally.
+ */
+GSI64FILE *
+GSI64Open(char *gsifile)
+{
+ GSI64FILE *gsi;
+ char magic[GSI64_KEYSIZE];
+
+ gsi = (GSI64FILE *) MallocOrDie (sizeof(GSI64FILE));
+ if ((gsi->gsifp = fopen(gsifile, "r")) == NULL)
+ { free(gsi); squid_errno = SQERR_NOFILE; return NULL; }
+
+ if (! fread(magic, sizeof(char), GSI64_KEYSIZE, gsi->gsifp))
+ { free(gsi); squid_errno = SQERR_NODATA; return NULL; }
+ if (strcmp(magic, "GSI64") != 0)
+ { free(gsi); squid_errno = SQERR_FORMAT; return NULL; }
+
+ if (! fread(&(gsi->nfiles), sizeof(sqd_uint16), 1, gsi->gsifp))
+ { free(gsi); squid_errno = SQERR_NODATA; return NULL; }
+ if (! fread(&(gsi->recnum), sizeof(sqd_uint64), 1, gsi->gsifp))
+ { free(gsi); squid_errno = SQERR_NODATA; return NULL; }
+
+#if 0 /* HACK! we don't byteswap */
+ gsi->nfiles = sre_ntohs(gsi->nfiles); /* convert from network short */
+ gsi->recnum = sre_ntohl(gsi->recnum); /* convert from network long */
+#endif
+
+ return gsi;
+}
+
+/* Function: GSI64GetRecord()
+ *
+ * Purpose: Each non-header record of a GSI64 index file consists
+ * of 42 bytes: 32 bytes of character string, a 2 byte
+ * short, and an 8 byte long long. This function returns the
+ * three values.
+ *
+ * Args: gsi - open GSI64 index file, correctly positioned at a record
+ * f1 - char[32], allocated by caller (or NULL if unwanted)
+ * f2 - pointer to short (or NULL if unwanted)
+ * f3 - pointer to long long (or NULL if unwanted)
+ *
+ * Return: 0 on failure and sets squid_errno.
+ */
+int
+GSI64GetRecord(GSI64FILE *gsi, char *f1, sqd_uint16 *f2, sqd_uint64 *f3)
+{
+ if (f1 == NULL) fseek64(gsi->gsifp, GSI64_KEYSIZE, SEEK_CUR);
+ else if (! fread(f1, GSI64_KEYSIZE, 1, gsi->gsifp))
+ { squid_errno = SQERR_NODATA; return 0; }
+
+ if (f2 == NULL) fseek64(gsi->gsifp, sizeof(sqd_uint16), SEEK_CUR);
+ else if (! fread(f2, sizeof(sqd_uint16), 1, gsi->gsifp))
+ { squid_errno = SQERR_NODATA; return 0; }
+
+ if (f3 == NULL) fseek64(gsi->gsifp, sizeof(sqd_uint64), SEEK_CUR);
+ else if (! fread(f3, sizeof(sqd_uint64), 1, gsi->gsifp))
+ { squid_errno = SQERR_NODATA; return 0; }
+
+#if 0 /* no byteswap yet! HACK! */
+ if (f2 != NULL) *f2 = sre_ntohs(*f2);
+ if (f3 != NULL) *f3 = sre_ntohl(*f3);
+#endif
+
+ return 1;
+}
+
+
+/* Function: GSI64GetOffset()
+ *
+ * Purpose: From a key (sequence name), find a disk offset
+ * in an open general sequence index file by binary
+ * search. Presumably GSI64 indexing could be even faster
+ * if we used hashing.
+ *
+ * Args: gsi - GSI64 index file, opened by GSI64Open()
+ * key - name of key to retrieve indices for
+ * ret_seqfile - pre-alloced char[32] array for seqfile name
+ * ret_fmt - format of seqfile
+ * ret_offset - return: disk offset in seqfile.
+ */
+int
+GSI64GetOffset(GSI64FILE *gsi, char *key, char *ret_seqfile,
+ int *ret_format, long long *ret_offset)
+{
+ sqd_uint64 left, right, mid;
+ int cmp;
+ char name[GSI64_KEYSIZE + 1];
+ sqd_uint64 offset;
+ sqd_uint16 filenum;
+ sqd_uint64 fmt;
+
+ name[GSI64_KEYSIZE] = '\0';
+
+ left = gsi->nfiles + 1;
+ right = gsi->nfiles + gsi->recnum;
+ mid = (left + right) / 2;
+ fseek64(gsi->gsifp, mid * GSI64_RECSIZE, SEEK_SET);
+
+ while (GSI64GetRecord(gsi, name, &filenum, &offset))
+ {
+ cmp = strcmp(name, key);
+ if (cmp == 0) break; /* found it! */
+ else if (left >= right) return 0; /* oops, missed it; fail. */
+ else if (cmp < 0) left = mid + 1; /* it's right of mid */
+ else if (cmp > 0) right = mid - 1; /* it's left of mid */
+ mid = (left + right) / 2;
+ fseek64(gsi->gsifp, mid * GSI64_RECSIZE, SEEK_SET);
+ }
+
+ /* Using file number, look up the sequence file and format.
+ */
+ fseek64(gsi->gsifp, filenum * GSI64_RECSIZE, SEEK_SET);
+ GSI64GetRecord(gsi, ret_seqfile, NULL, &fmt);
+ *ret_format = (int) fmt;
+ *ret_offset = (long long) offset;
+
+ return 1;
+}
+
+/* Function: GSI64Close()
+ *
+ * Purpose: Close an open GSI64 sequence index file.
+ */
+void
+GSI64Close(GSI64FILE *gsi)
+{
+ fclose(gsi->gsifp);
+ free(gsi);
+}
+
+
+/*****************************************************************
+ * GSI64 index construction routines
+ * SRE, Wed Nov 10 11:49:14 1999 [St. Louis]
+ *
+ * API:
+ * g = GSI64AllocIndex();
+ *
+ * [foreach filename, <32 char, no directory path]
+ * GSI64AddFileToIndex(g, filename);
+ * filenum++;
+ * [foreach key, <32 char, w/ filenum 1..nfiles, w/ 64bit offset]
+ * GSI64AddKeyToIndex(g, key, filenum, offset);
+ *
+ * GSI64SortIndex(g);
+ * GSI64WriteIndex(fp, g);
+ * GSI64FreeIndex(g);
+ *****************************************************************/
+struct gsi64index_s *
+GSI64AllocIndex(void)
+{
+ struct gsi64index_s *g;
+
+ g = MallocOrDie(sizeof(struct gsi64index_s));
+ g->filenames = MallocOrDie(sizeof(char *) * 10);
+ g->fmt = MallocOrDie(sizeof(int) * 10);
+ g->elems = MallocOrDie(sizeof(struct gsi64key_s) * 100);
+ g->nfiles = 0;
+ g->nkeys = 0;
+ return g;
+}
+void
+GSI64FreeIndex(struct gsi64index_s *g)
+{
+ int i;
+ for (i = 0; i < g->nfiles; i++) free(g->filenames[i]);
+ free(g->filenames);
+ free(g->fmt);
+ free(g->elems);
+ free(g);
+}
+void
+GSI64AddFileToIndex(struct gsi64index_s *g, char *filename, int fmt)
+{
+ int len;
+
+ len = strlen(filename);
+ if (len >= GSI64_KEYSIZE) Die("File name too long to be indexed.");
+ g->filenames[g->nfiles] = sre_strdup(filename, len);
+ g->fmt[g->nfiles] = fmt;
+ g->nfiles++;
+ if (g->nfiles % 10 == 0) {
+ g->filenames = ReallocOrDie(g->filenames, sizeof(char *) * (g->nfiles + 10));
+ g->fmt = ReallocOrDie(g->fmt, sizeof(int) * (g->nfiles + 10));
+ }
+}
+void
+GSI64AddKeyToIndex(struct gsi64index_s *g, char *key, int filenum, long long offset)
+{
+ if (strlen(key) >= GSI64_KEYSIZE) Die("key too long in GSI64 index");
+ if (filenum > SQD_UINT16_MAX) Die("too many files in GSI64 index");
+ if (offset > SQD_UINT64_MAX) Die("offset too big in GSI64 index");
+
+ strncpy(g->elems[g->nkeys].key, key, GSI64_KEYSIZE-1);
+ g->elems[g->nkeys].key[GSI64_KEYSIZE-1] = '\0';
+ g->elems[g->nkeys].filenum = (sqd_uint16) filenum;
+ g->elems[g->nkeys].offset = (sqd_uint64) offset;
+ g->nkeys++;
+
+ if (g->nkeys % 100 == 0)
+ g->elems = ReallocOrDie(g->elems, sizeof(struct gsi64key_s) * (g->nkeys + 100));
+}
+static int
+gsi_keysorter(const void *k1, const void *k2)
+{
+ struct gsi64key_s *key1;
+ struct gsi64key_s *key2;
+ key1 = (struct gsi64key_s *) k1;
+ key2 = (struct gsi64key_s *) k2;
+ return strcmp(key1->key, key2->key);
+}
+void
+GSI64SortIndex(struct gsi64index_s *g)
+{
+ qsort((void *) g->elems, g->nkeys, sizeof(struct gsi64key_s), gsi_keysorter);
+}
+void
+GSI64WriteIndex(FILE *fp, struct gsi64index_s *g)
+{
+ sqd_uint16 i;
+ sqd_uint64 j;
+
+ /* Range checking.
+ */
+ if (g->nfiles > SQD_UINT16_MAX) Die("Too many files in GSI64 index.");
+ if (g->nkeys > SQD_UINT64_MAX) Die("Too many keys in GSI64 index.");
+
+ GSI64WriteHeader(fp, g->nfiles, g->nkeys);
+ for (i = 0; i < g->nfiles; i++)
+ GSI64WriteFileRecord(fp, g->filenames[i], i+1, g->fmt[i]);
+ for (j = 0; j < g->nkeys; j++)
+ GSI64WriteKeyRecord(fp, g->elems[j].key, g->elems[j].filenum, g->elems[j].offset);
+}
+
+
+
+
+
+/* Function: GSI64WriteHeader()
+ * Date: SRE, Wed Aug 5 10:36:02 1998 [St. Louis]
+ *
+ * Purpose: Write the first record to an open GSI64 file:
+ * "GSI64" <nfiles> <nkeys>
+ *
+ * Args: fp - open file to write to.
+ * nfiles - number of files indexed
+ * nkeys - number of keys indexed
+ *
+ * Returns: void
+ */
+void
+GSI64WriteHeader(FILE *fp, int nfiles, long long nkeys)
+{
+ char key[GSI64_KEYSIZE];
+ sqd_uint16 f1;
+ sqd_uint64 f2;
+
+ /* beware potential range errors!
+ */
+ if (nfiles > SQD_UINT16_MAX) Die("GSI64: nfiles out of range");
+ if (nkeys > SQD_UINT64_MAX) Die("GSI64: nkeys out of range");
+
+ f1 = (sqd_uint16) nfiles;
+ f2 = (sqd_uint64) nkeys;
+#if 0 /* HACK no byteswap */
+ f1 = sre_htons(f1);
+ f2 = sre_htonl(f2);
+#endif
+ strcpy(key, "GSI64");
+
+ if (fwrite(key, 1, GSI64_KEYSIZE, fp) < GSI64_KEYSIZE) PANIC;
+ if (fwrite(&f1, 2, 1, fp) < 1) PANIC;
+ if (fwrite(&f2, 8, 1, fp) < 1) PANIC;
+}
+
+
+/* Function: GSI64WriteFileRecord()
+ * Date: SRE, Wed Aug 5 10:45:51 1998 [St. Louis]
+ *
+ * Purpose: Write a file record to an open GSI64 file.
+ *
+ * Args: fp - open GSI64 file
+ * fname - file name (max 31 characters)
+ * idx - file number
+ * fmt - file format (e.g. kPearson, etc.)
+ *
+ * Returns: 0 on failure. 1 on success.
+ */
+int
+GSI64WriteFileRecord(FILE *fp, char *fname, int idx, int fmt)
+{
+ sqd_uint16 f1;
+ sqd_uint64 f2;
+
+ if (strlen(fname) >= GSI64_KEYSIZE) return 0;
+ if (idx > SQD_UINT16_MAX) Die("GSI64: file index out of range");
+ if (fmt > SQD_UINT64_MAX) Die("GSI64: format index out of range");
+
+ f1 = (sqd_uint16) idx;
+ f2 = (sqd_uint64) fmt;
+#if 0 /* hack : no byteswap */
+ f1 = sre_htons(f1);
+ f2 = sre_htonl(f2);
+#endif
+
+ if (fwrite(fname, 1, GSI64_KEYSIZE, fp) < GSI64_KEYSIZE) PANIC;
+ if (fwrite(&f1, 2, 1, fp) < 1) PANIC;
+ if (fwrite(&f2, 8, 1, fp) < 1) PANIC;
+ return 1;
+}
+
+
+/* Function: GSI64WriteKeyRecord()
+ * Date: SRE, Wed Aug 5 10:52:30 1998 [St. Louis]
+ *
+ * Purpose: Write a key record to a GSI64 file.
+ *
+ * Args: fp - open GSI64 file for writing
+ * key - key (max 31 char + \0)
+ * fileidx - which file number to find this key in
+ * offset - offset for this key
+ *
+ * Returns: 1 on success, else 0.
+ * will fail if key >= 32 chars, for instance.
+ */
+int
+GSI64WriteKeyRecord(FILE *fp, char *key, int fileidx, long long offset)
+{
+ sqd_uint16 f1;
+ sqd_uint64 f2;
+
+ if (strlen(key) >= GSI64_KEYSIZE) return 0;
+ if (fileidx > SQD_UINT16_MAX) Die("GSI64: file index out of range");
+ if (offset > SQD_UINT64_MAX) Die("GSI64: offset out of range");
+
+ f1 = (sqd_uint16) fileidx;
+ f2 = (sqd_uint64) offset;
+#if 0 /* HACK! */
+ f1 = sre_htons(f1);
+ f2 = sre_htonl(f2);
+#endif
+
+ if (fwrite(key, 1, GSI64_KEYSIZE, fp) < GSI64_KEYSIZE) PANIC;
+ if (fwrite(&f1, 2, 1, fp) < 1) PANIC;
+ if (fwrite(&f2, 8, 1, fp) < 1) PANIC;
+ return 1;
+}
+
+#endif /*USE_GSI64 */
--- /dev/null
+/*****************************************************************
+ * @LICENSE@
+ *****************************************************************/
+
+#ifndef GSI64H_INCLUDED
+#define GSI64H_INCLUDED
+#ifdef USE_GSI64
+
+/* gsi64.h
+ * Database indexing (GSI64 format support)
+ * CVS $Id: gsi64.h,v 1.2 2000/12/21 23:42:59 eddy Exp)
+ *
+ * A GSI64 (generic sequence index, 64 bit hack) file is composed of
+ * recnum + nfiles + 1 records. Each record contains
+ * three fields; key, file number, and disk offset.
+ * Record 0 contains:
+ * [ "GSI64" ] [ nfiles ] [ recnum ]
+ * Records 1..nfiles map file names to file numbers, and contain:
+ * [ filename ] [ file number, 1..nfiles ] [ 0 (unused) ]
+ * Records nfiles+1 to recnum+nfiles+1 provide disk offset
+ * and file number indices for every key:
+ * [ key ] [ file number ] [ offset]
+ *
+ * Because the file is binary, we take some (but not
+ * complete) care to improve portability amongst platforms.
+ * This means using network order integers (see ntohl())
+ * and defining types for 16 and 64 bit integers.
+ *
+ * A short test program that verifies the sizes of these
+ * data types would be a good idea...
+ *
+ * Because we use 64-bit offsets, ftell64(), and fseek64(),
+ * we rely on the OS actually providing these. This is
+ * a temporary hack for human genome analysis.
+ */
+typedef unsigned long long sqd_uint64; /* 64 bit integer. */
+
+#define GSI64_KEYSIZE 32 /* keys are 32 bytes long */
+#define GSI64_RECSIZE 42 /* 32 + 2 + 8 bytes */
+#define SQD_UINT16_MAX 65535 /* 2^16-1 */
+#define SQD_UINT64_MAX 18446744073709551615LU /* 2^64-1 */
+
+struct gsi64_s {
+ FILE *gsifp; /* open GSI index file */
+ sqd_uint16 nfiles; /* number of files = 16 bit int */
+ sqd_uint64 recnum; /* number of records = 64 bit int */
+};
+typedef struct gsi64_s GSI64FILE;
+
+struct gsi64key_s {
+ char key[GSI64_KEYSIZE];
+ sqd_uint16 filenum;
+ sqd_uint64 offset;
+};
+struct gsi64index_s {
+ char **filenames;
+ int *fmt;
+ sqd_uint16 nfiles;
+
+ struct gsi64key_s *elems;
+ sqd_uint64 nkeys;
+};
+
+
+
+/* if ntohl() and friends are not available, you
+ * can slip replacements in by providing sre_ntohl()
+ * functions. (i.e., there is a possible portability problem here.)
+ */
+#if 0
+#define sre_ntohl(x) ntohl(x);
+#define sre_ntohs(x) ntohs(x);
+#define sre_htonl(x) htonl(x);
+#define sre_htons(x) htons(x);
+#endif
+
+/* from gsi64.c
+ */
+extern GSI64FILE *GSI64Open(char *gsifile);
+extern int GSI64GetRecord(GSI64FILE *gsi, char *f1, sqd_uint16 *f2, sqd_uint64 *f3);
+extern int GSI64GetOffset(GSI64FILE *gsi, char *key, char *sqfile,
+ int *fmt, long long *ret_offset);
+extern void GSI64Close(GSI64FILE *gsi);
+extern struct gsi64index_s *GSI64AllocIndex(void);
+extern void GSI64FreeIndex(struct gsi64index_s *g);
+extern void GSI64AddFileToIndex(struct gsi64index_s *g, char *filename, int fmt);
+extern void GSI64AddKeyToIndex(struct gsi64index_s *g, char *key, int filenum, long long offset);
+extern void GSI64SortIndex(struct gsi64index_s *g);
+extern void GSI64WriteIndex(FILE *fp, struct gsi64index_s *g);
+extern void GSI64WriteHeader(FILE *fp, int nfiles, long long nkeys);
+extern int GSI64WriteFileRecord(FILE *fp, char *fname, int idx, int fmt);
+extern int GSI64WriteKeyRecord(FILE *fp, char *key, int fileidx, long long offset);
+
+#endif /* USE_GSI64 */
+#endif /*GSIH_INCLUDED*/
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/*****************************************************************
+ * This code is an altered version of Henry Spencer's
+ * regex library. Alterations are limited to minor streamlining,
+ * and some name changes to protect the SQUID namespace.
+ * Henry's copyright notice appears below.
+ * You can obtain the original from
+ * ftp://ftp.zoo.toronto.edu/pub/bookregex.tar.Z
+ * Thanks, Henry!
+ *
+ * The magic word for compiling a testdriver: NBA_TEAM_IN_STL
+ * gcc -o test -g -DNBA_TEAM_IN_STL -L. hsregex.c -lsquid -lm
+ *
+ * Usage:
+ * test <pattern> <ntok> <string>
+ *
+ * SRE, Fri Aug 28 11:10:17 1998
+ * CVS $Id: hsregex.c,v 1.7 2001/08/09 17:50:17 eddy Exp)
+ *****************************************************************/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+#include "squid.h"
+
+/* global sqd_parse[] are managed by Strparse().
+ * WARNING: TODO: this code is not threadsafe, and needs to be revised.
+ */
+char *sqd_parse[10];
+
+/* Function: Strparse()
+ *
+ * Purpose: Match a regexp to a string. Returns 1 if pattern matches,
+ * else 0.
+ *
+ * Much like Perl, Strparse() makes copies of the matching
+ * substrings available via globals, sqd_parse[].
+ * sqd_parse[0] contains a copy of the complete matched
+ * text. sqd_parse[1-9] contain copies of up to nine
+ * different substrings matched within parentheses.
+ * The memory for these strings is internally managed and
+ * volatile; the next call to Strparse() may destroy them.
+ * If the caller needs the matched substrings to persist
+ * beyond a new Strparse() call, it must make its own
+ * copies.
+ *
+ * A minor drawback of the memory management is that
+ * there will be a small amount of unfree'd memory being
+ * managed by Strparse() when a program exits; this may
+ * confuse memory debugging (Purify, dbmalloc). The
+ * general cleanup function SqdClean() is provided;
+ * you can call this before exiting.
+ *
+ * Uses an extended POSIX regular expression interface.
+ * A copylefted GNU implementation is included in the squid
+ * implementation (gnuregex.c) for use on non-POSIX compliant
+ * systems. POSIX 1003.2-compliant systems (all UNIX,
+ * some WinNT, I believe) can omit the GNU code if necessary.
+ *
+ * I built this for ease of use, not speed nor efficiency.
+ *
+ * Example: Strparse("foo-...-baz", "foo-bar-baz") returns 0
+ * Strparse("foo-(...)-baz", "foo-bar-baz")
+ * returns 0; sqd_parse[0] is "foo-bar-baz";
+ * sqd_parse[1] is "bar".
+ *
+ * A real example:
+ * s = ">gnl|ti|3 G10P69425RH2.T0 {SUB 81..737} /len=657"
+ * pat = "SUB ([0-9]+)"
+ * Strparse(pat, s, 1)
+ * returns 1; sqd_parse[1] is "81".
+ *
+ * Args: rexp - regular expression, extended POSIX form
+ * s - string to match against
+ * ntok - number of () substrings we will save (maximum NSUBEXP-1)
+ *
+ * Return: 1 on match, 0 if no match
+ */
+int
+Strparse(char *rexp, char *s, int ntok)
+{
+ sqd_regexp *pat;
+ int code;
+ int len;
+ int i;
+ /* sanity check */
+ if (ntok >= NSUBEXP ) Die("Strparse(): ntok must be <= %d", NSUBEXP-1);
+
+ /* Free previous global substring buffers
+ */
+ for (i = 0; i <= ntok; i++)
+ if (sqd_parse[i] != NULL)
+ {
+ free(sqd_parse[i]);
+ sqd_parse[i] = NULL;
+ }
+
+ /* Compile and match the pattern, using our modified
+ * copy of Henry Spencer's regexp library
+ */
+ if ((pat = sqd_regcomp(rexp)) == NULL)
+ Die("regexp compilation failed.");
+ code = sqd_regexec(pat, s);
+
+ /* Fill the global substring buffers
+ */
+ if (code == 1)
+ for (i = 0; i <= ntok; i++)
+ if (pat->startp[i] != NULL && pat->endp[i] != NULL)
+ {
+ len = pat->endp[i] - pat->startp[i];
+ sqd_parse[i] = (char *) MallocOrDie(sizeof(char) * (len+1));
+ strncpy(sqd_parse[i], pat->startp[i], len);
+ sqd_parse[i][len] = '\0';
+ }
+
+ free(pat);
+ return code;
+}
+
+/* Function: SqdClean()
+ * Date: SRE, Wed Oct 29 12:52:08 1997 [TWA 721]
+ *
+ * Purpose: Clean up any squid library allocations before exiting
+ * a program, so we don't leave unfree'd memory around
+ * and confuse a malloc debugger like Purify or dbmalloc.
+ */
+void
+SqdClean(void)
+{
+ int i;
+
+ /* Free global substring buffers that Strparse() uses
+ */
+ for (i = 0; i <= 9; i++)
+ if (sqd_parse[i] != NULL) {
+ free(sqd_parse[i]);
+ sqd_parse[i] = NULL;
+ }
+}
+
+
+
+/* all code below is:
+ * Copyright (c) 1986, 1993, 1995 by University of Toronto.
+ * Written by Henry Spencer. Not derived from licensed software.
+ *
+ * Permission is granted to anyone to use this software for any
+ * purpose on any computer system, and to redistribute it in any way,
+ * subject to the following restrictions:
+ *
+ * 1. The author is not responsible for the consequences of use of
+ * this software, no matter how awful, even if they arise
+ * from defects in it.
+ *
+ * 2. The origin of this software must not be misrepresented, either
+ * by explicit claim or by omission.
+ *
+ * 3. Altered versions must be plainly marked as such, and must not
+ * be misrepresented (by explicit claim or omission) as being
+ * the original software.
+ *
+ * 4. This notice must not be removed or altered.
+ */
+
+/*
+ * sqd_regcomp and sqd_regexec -- sqd_regsub and sqd_regerror are elsewhere
+ */
+
+/*
+ * The first byte of the regexp internal "program" is actually this magic
+ * number; the start node begins in the second byte.
+ */
+#define SQD_REGMAGIC 0234
+
+/*
+ * The "internal use only" fields in regexp.h are present to pass info from
+ * compile to execute that permits the execute phase to run lots faster on
+ * simple cases. They are:
+ *
+ * regstart char that must begin a match; '\0' if none obvious
+ * reganch is the match anchored (at beginning-of-line only)?
+ * regmust string (pointer into program) that match must include, or NULL
+ * regmlen length of regmust string
+ *
+ * Regstart and reganch permit very fast decisions on suitable starting points
+ * for a match, cutting down the work a lot. Regmust permits fast rejection
+ * of lines that cannot possibly match. The regmust tests are costly enough
+ * that sqd_regcomp() supplies a regmust only if the r.e. contains something
+ * potentially expensive (at present, the only such thing detected is * or +
+ * at the start of the r.e., which can involve a lot of backup). Regmlen is
+ * supplied because the test in sqd_regexec() needs it and sqd_regcomp() is computing
+ * it anyway.
+ */
+
+/*
+ * Structure for regexp "program". This is essentially a linear encoding
+ * of a nondeterministic finite-state machine (aka syntax charts or
+ * "railroad normal form" in parsing technology). Each node is an opcode
+ * plus a "next" pointer, possibly plus an operand. "Next" pointers of
+ * all nodes except BRANCH implement concatenation; a "next" pointer with
+ * a BRANCH on both ends of it is connecting two alternatives. (Here we
+ * have one of the subtle syntax dependencies: an individual BRANCH (as
+ * opposed to a collection of them) is never concatenated with anything
+ * because of operator precedence.) The operand of some types of node is
+ * a literal string; for others, it is a node leading into a sub-FSM. In
+ * particular, the operand of a BRANCH node is the first node of the branch.
+ * (NB this is *not* a tree structure: the tail of the branch connects
+ * to the thing following the set of BRANCHes.) The opcodes are:
+ */
+
+/* definition number opnd? meaning */
+#define END 0 /* no End of program. */
+#define BOL 1 /* no Match beginning of line. */
+#define EOL 2 /* no Match end of line. */
+#define ANY 3 /* no Match any character. */
+#define ANYOF 4 /* str Match any of these. */
+#define ANYBUT 5 /* str Match any but one of these. */
+#define BRANCH 6 /* node Match this, or the next..\&. */
+#define BACK 7 /* no "next" ptr points backward. */
+#define EXACTLY 8 /* str Match this string. */
+#define NOTHING 9 /* no Match empty string. */
+#define STAR 10 /* node Match this 0 or more times. */
+#define PLUS 11 /* node Match this 1 or more times. */
+#define OPEN 20 /* no Sub-RE starts here. */
+ /* OPEN+1 is number 1, etc. */
+#define CLOSE 30 /* no Analogous to OPEN. */
+
+/*
+ * Opcode notes:
+ *
+ * BRANCH The set of branches constituting a single choice are hooked
+ * together with their "next" pointers, since precedence prevents
+ * anything being concatenated to any individual branch. The
+ * "next" pointer of the last BRANCH in a choice points to the
+ * thing following the whole choice. This is also where the
+ * final "next" pointer of each individual branch points; each
+ * branch starts with the operand node of a BRANCH node.
+ *
+ * BACK Normal "next" pointers all implicitly point forward; BACK
+ * exists to make loop structures possible.
+ *
+ * STAR,PLUS '?', and complex '*' and '+', are implemented as circular
+ * BRANCH structures using BACK. Simple cases (one character
+ * per match) are implemented with STAR and PLUS for speed
+ * and to minimize recursive plunges.
+ *
+ * OPEN,CLOSE ...are numbered at compile time.
+ */
+
+/*
+ * A node is one char of opcode followed by two chars of "next" pointer.
+ * "Next" pointers are stored as two 8-bit pieces, high order first. The
+ * value is a positive offset from the opcode of the node containing it.
+ * An operand, if any, simply follows the node. (Note that much of the
+ * code generation knows about this implicit relationship.)
+ *
+ * Using two bytes for the "next" pointer is vast overkill for most things,
+ * but allows patterns to get big without disasters.
+ */
+#define OP(p) (*(p))
+#define NEXT(p) (((*((p)+1)&0177)<<8) + (*((p)+2)&0377))
+#define OPERAND(p) ((p) + 3)
+
+/*
+ * Utility definitions.
+ */
+#define FAIL(m) { sqd_regerror(m); return(NULL); }
+#define ISREPN(c) ((c) == '*' || (c) == '+' || (c) == '?')
+#define META "^$.[()|?+*\\"
+
+/*
+ * Flags to be passed up and down.
+ */
+#define HASWIDTH 01 /* Known never to match null string. */
+#define SIMPLE 02 /* Simple enough to be STAR/PLUS operand. */
+#define SPSTART 04 /* Starts with * or +. */
+#define WORST 0 /* Worst case. */
+
+/*
+ * Work-variable struct for sqd_regcomp().
+ */
+struct comp {
+ char *regparse; /* Input-scan pointer. */
+ int regnpar; /* () count. */
+ char *regcode; /* Code-emit pointer; ®dummy = don't. */
+ char regdummy[3]; /* NOTHING, 0 next ptr */
+ long regsize; /* Code size. */
+};
+#define EMITTING(cp) ((cp)->regcode != (cp)->regdummy)
+
+/*
+ * Forward declarations for sqd_regcomp()'s friends.
+ */
+static char *reg(struct comp *cp, int paren, int *flagp);
+static char *regbranch(struct comp *cp, int *flagp);
+static char *regpiece(struct comp *cp, int *flagp);
+static char *regatom(struct comp *cp, int *flagp);
+static char *regnode(struct comp *cp, int op);
+static char *regnext(char *node);
+static void regc(struct comp *cp, int c);
+static void reginsert(struct comp *cp, int op, char *opnd);
+static void regtail(struct comp *cp, char *p, char *val);
+static void regoptail(struct comp *cp, char *p, char *val);
+
+/*
+ - sqd_regcomp - compile a regular expression into internal code
+ *
+ * We can't allocate space until we know how big the compiled form will be,
+ * but we can't compile it (and thus know how big it is) until we've got a
+ * place to put the code. So we cheat: we compile it twice, once with code
+ * generation turned off and size counting turned on, and once "for real".
+ * This also means that we don't allocate space until we are sure that the
+ * thing really will compile successfully, and we never have to move the
+ * code and thus invalidate pointers into it. (Note that it has to be in
+ * one piece because free() must be able to free it all.)
+ *
+ * Beware that the optimization-preparation code in here knows about some
+ * of the structure of the compiled regexp.
+ */
+sqd_regexp *
+sqd_regcomp(exp)
+const char *exp;
+{
+ register sqd_regexp *r;
+ register char *scan;
+ int flags;
+ struct comp co;
+
+ if (exp == NULL)
+ FAIL("NULL argument to sqd_regcomp");
+
+ /* First pass: determine size, legality. */
+ co.regparse = (char *)exp;
+ co.regnpar = 1;
+ co.regsize = 0L;
+ co.regdummy[0] = NOTHING;
+ co.regdummy[1] = co.regdummy[2] = 0;
+ co.regcode = co.regdummy;
+ regc(&co, SQD_REGMAGIC);
+ if (reg(&co, 0, &flags) == NULL)
+ return(NULL);
+
+ /* Small enough for pointer-storage convention? */
+ if (co.regsize >= 0x7fffL) /* Probably could be 0xffffL. */
+ FAIL("regexp too big");
+
+ /* Allocate space. */
+ r = (sqd_regexp *)malloc(sizeof(sqd_regexp) + (size_t)co.regsize);
+ if (r == NULL)
+ FAIL("out of space");
+
+ /* Second pass: emit code. */
+ co.regparse = (char *)exp;
+ co.regnpar = 1;
+ co.regcode = r->program;
+ regc(&co, SQD_REGMAGIC);
+ if (reg(&co, 0, &flags) == NULL)
+ return(NULL);
+
+ /* Dig out information for optimizations. */
+ r->regstart = '\0'; /* Worst-case defaults. */
+ r->reganch = 0;
+ r->regmust = NULL;
+ r->regmlen = 0;
+ scan = r->program+1; /* First BRANCH. */
+ if (OP(regnext(scan)) == END) { /* Only one top-level choice. */
+ scan = OPERAND(scan);
+
+ /* Starting-point info. */
+ if (OP(scan) == EXACTLY)
+ r->regstart = *OPERAND(scan);
+ else if (OP(scan) == BOL)
+ r->reganch = 1;
+
+ /*
+ * If there's something expensive in the r.e., find the
+ * longest literal string that must appear and make it the
+ * regmust. Resolve ties in favor of later strings, since
+ * the regstart check works with the beginning of the r.e.
+ * and avoiding duplication strengthens checking. Not a
+ * strong reason, but sufficient in the absence of others.
+ */
+ if (flags&SPSTART) {
+ register char *longest = NULL;
+ register size_t len = 0;
+
+ for (; scan != NULL; scan = regnext(scan))
+ if (OP(scan) == EXACTLY && strlen(OPERAND(scan)) >= len) {
+ longest = OPERAND(scan);
+ len = strlen(OPERAND(scan));
+ }
+ r->regmust = longest;
+ r->regmlen = (int)len;
+ }
+ }
+
+ return(r);
+}
+
+/*
+ - reg - regular expression, i.e. main body or parenthesized thing
+ *
+ * Caller must absorb opening parenthesis.
+ *
+ * Combining parenthesis handling with the base level of regular expression
+ * is a trifle forced, but the need to tie the tails of the branches to what
+ * follows makes it hard to avoid.
+ */
+static char *
+reg(cp, paren, flagp)
+register struct comp *cp;
+int paren; /* Parenthesized? */
+int *flagp;
+{
+ register char *ret = NULL; /* SRE: NULL init added to silence gcc */
+ register char *br;
+ register char *ender;
+ register int parno = 0; /* SRE: init added to silence gcc */
+ int flags;
+
+ *flagp = HASWIDTH; /* Tentatively. */
+
+ if (paren) {
+ /* Make an OPEN node. */
+ if (cp->regnpar >= NSUBEXP)
+ FAIL("too many ()");
+ parno = cp->regnpar;
+ cp->regnpar++;
+ ret = regnode(cp, OPEN+parno);
+ }
+
+ /* Pick up the branches, linking them together. */
+ br = regbranch(cp, &flags);
+ if (br == NULL)
+ return(NULL);
+ if (paren)
+ regtail(cp, ret, br); /* OPEN -> first. */
+ else
+ ret = br;
+ *flagp &= ~(~flags&HASWIDTH); /* Clear bit if bit 0. */
+ *flagp |= flags&SPSTART;
+ while (*cp->regparse == '|') {
+ cp->regparse++;
+ br = regbranch(cp, &flags);
+ if (br == NULL)
+ return(NULL);
+ regtail(cp, ret, br); /* BRANCH -> BRANCH. */
+ *flagp &= ~(~flags&HASWIDTH);
+ *flagp |= flags&SPSTART;
+ }
+
+ /* Make a closing node, and hook it on the end. */
+ ender = regnode(cp, (paren) ? CLOSE+parno : END);
+ regtail(cp, ret, ender);
+
+ /* Hook the tails of the branches to the closing node. */
+ for (br = ret; br != NULL; br = regnext(br))
+ regoptail(cp, br, ender);
+
+ /* Check for proper termination. */
+ if (paren && *cp->regparse++ != ')') {
+ FAIL("unterminated ()");
+ } else if (!paren && *cp->regparse != '\0') {
+ if (*cp->regparse == ')') {
+ FAIL("unmatched ()");
+ } else
+ FAIL("internal error: junk on end");
+ /* NOTREACHED */
+ }
+
+ return(ret);
+}
+
+/*
+ - regbranch - one alternative of an | operator
+ *
+ * Implements the concatenation operator.
+ */
+static char *
+regbranch(cp, flagp)
+register struct comp *cp;
+int *flagp;
+{
+ register char *ret;
+ register char *chain;
+ register char *latest;
+ int flags;
+ register int c;
+
+ *flagp = WORST; /* Tentatively. */
+
+ ret = regnode(cp, BRANCH);
+ chain = NULL;
+ while ((c = *cp->regparse) != '\0' && c != '|' && c != ')') {
+ latest = regpiece(cp, &flags);
+ if (latest == NULL)
+ return(NULL);
+ *flagp |= flags&HASWIDTH;
+ if (chain == NULL) /* First piece. */
+ *flagp |= flags&SPSTART;
+ else
+ regtail(cp, chain, latest);
+ chain = latest;
+ }
+ if (chain == NULL) /* Loop ran zero times. */
+ (void) regnode(cp, NOTHING);
+
+ return(ret);
+}
+
+/*
+ - regpiece - something followed by possible [*+?]
+ *
+ * Note that the branching code sequences used for ? and the general cases
+ * of * and + are somewhat optimized: they use the same NOTHING node as
+ * both the endmarker for their branch list and the body of the last branch.
+ * It might seem that this node could be dispensed with entirely, but the
+ * endmarker role is not redundant.
+ */
+static char *
+regpiece(cp, flagp)
+register struct comp *cp;
+int *flagp;
+{
+ register char *ret;
+ register char op;
+ register char *next;
+ int flags;
+
+ ret = regatom(cp, &flags);
+ if (ret == NULL)
+ return(NULL);
+
+ op = *cp->regparse;
+ if (!ISREPN(op)) {
+ *flagp = flags;
+ return(ret);
+ }
+
+ if (!(flags&HASWIDTH) && op != '?')
+ FAIL("*+ operand could be empty");
+ switch (op) {
+ case '*': *flagp = WORST|SPSTART; break;
+ case '+': *flagp = WORST|SPSTART|HASWIDTH; break;
+ case '?': *flagp = WORST; break;
+ }
+
+ if (op == '*' && (flags&SIMPLE))
+ reginsert(cp, STAR, ret);
+ else if (op == '*') {
+ /* Emit x* as (x&|), where & means "self". */
+ reginsert(cp, BRANCH, ret); /* Either x */
+ regoptail(cp, ret, regnode(cp, BACK)); /* and loop */
+ regoptail(cp, ret, ret); /* back */
+ regtail(cp, ret, regnode(cp, BRANCH)); /* or */
+ regtail(cp, ret, regnode(cp, NOTHING)); /* null. */
+ } else if (op == '+' && (flags&SIMPLE))
+ reginsert(cp, PLUS, ret);
+ else if (op == '+') {
+ /* Emit x+ as x(&|), where & means "self". */
+ next = regnode(cp, BRANCH); /* Either */
+ regtail(cp, ret, next);
+ regtail(cp, regnode(cp, BACK), ret); /* loop back */
+ regtail(cp, next, regnode(cp, BRANCH)); /* or */
+ regtail(cp, ret, regnode(cp, NOTHING)); /* null. */
+ } else if (op == '?') {
+ /* Emit x? as (x|) */
+ reginsert(cp, BRANCH, ret); /* Either x */
+ regtail(cp, ret, regnode(cp, BRANCH)); /* or */
+ next = regnode(cp, NOTHING); /* null. */
+ regtail(cp, ret, next);
+ regoptail(cp, ret, next);
+ }
+ cp->regparse++;
+ if (ISREPN(*cp->regparse))
+ FAIL("nested *?+");
+
+ return(ret);
+}
+
+/*
+ - regatom - the lowest level
+ *
+ * Optimization: gobbles an entire sequence of ordinary characters so that
+ * it can turn them into a single node, which is smaller to store and
+ * faster to run. Backslashed characters are exceptions, each becoming a
+ * separate node; the code is simpler that way and it's not worth fixing.
+ */
+static char *
+regatom(cp, flagp)
+register struct comp *cp;
+int *flagp;
+{
+ register char *ret;
+ int flags;
+
+ *flagp = WORST; /* Tentatively. */
+
+ switch (*cp->regparse++) {
+ case '^':
+ ret = regnode(cp, BOL);
+ break;
+ case '$':
+ ret = regnode(cp, EOL);
+ break;
+ case '.':
+ ret = regnode(cp, ANY);
+ *flagp |= HASWIDTH|SIMPLE;
+ break;
+ case '[': {
+ register int range;
+ register int rangeend;
+ register int c;
+
+ if (*cp->regparse == '^') { /* Complement of range. */
+ ret = regnode(cp, ANYBUT);
+ cp->regparse++;
+ } else
+ ret = regnode(cp, ANYOF);
+ if ((c = *cp->regparse) == ']' || c == '-') {
+ regc(cp, c);
+ cp->regparse++;
+ }
+ while ((c = *cp->regparse++) != '\0' && c != ']') {
+ if (c != '-')
+ regc(cp, c);
+ else if ((c = *cp->regparse) == ']' || c == '\0')
+ regc(cp, '-');
+ else {
+ range = (unsigned char)*(cp->regparse-2);
+ rangeend = (unsigned char)c;
+ if (range > rangeend)
+ FAIL("invalid [] range");
+ for (range++; range <= rangeend; range++)
+ regc(cp, range);
+ cp->regparse++;
+ }
+ }
+ regc(cp, '\0');
+ if (c != ']')
+ FAIL("unmatched []");
+ *flagp |= HASWIDTH|SIMPLE;
+ break;
+ }
+ case '(':
+ ret = reg(cp, 1, &flags);
+ if (ret == NULL)
+ return(NULL);
+ *flagp |= flags&(HASWIDTH|SPSTART);
+ break;
+ case '\0':
+ case '|':
+ case ')':
+ /* supposed to be caught earlier */
+ FAIL("internal error: \\0|) unexpected");
+ break;
+ case '?':
+ case '+':
+ case '*':
+ FAIL("?+* follows nothing");
+ break;
+ case '\\':
+ if (*cp->regparse == '\0')
+ FAIL("trailing \\");
+ ret = regnode(cp, EXACTLY);
+ regc(cp, *cp->regparse++);
+ regc(cp, '\0');
+ *flagp |= HASWIDTH|SIMPLE;
+ break;
+ default: {
+ register size_t len;
+ register char ender;
+
+ cp->regparse--;
+ len = strcspn(cp->regparse, META);
+ if (len == 0)
+ FAIL("internal error: strcspn 0");
+ ender = *(cp->regparse+len);
+ if (len > 1 && ISREPN(ender))
+ len--; /* Back off clear of ?+* operand. */
+ *flagp |= HASWIDTH;
+ if (len == 1)
+ *flagp |= SIMPLE;
+ ret = regnode(cp, EXACTLY);
+ for (; len > 0; len--)
+ regc(cp, *cp->regparse++);
+ regc(cp, '\0');
+ break;
+ }
+ }
+
+ return(ret);
+}
+
+/*
+ - regnode - emit a node
+ */
+static char * /* Location. */
+regnode(cp, op)
+register struct comp *cp;
+char op;
+{
+ register char *const ret = cp->regcode;
+ register char *ptr;
+
+ if (!EMITTING(cp)) {
+ cp->regsize += 3;
+ return(ret);
+ }
+
+ ptr = ret;
+ *ptr++ = op;
+ *ptr++ = '\0'; /* Null next pointer. */
+ *ptr++ = '\0';
+ cp->regcode = ptr;
+
+ return(ret);
+}
+
+/*
+ - regc - emit (if appropriate) a byte of code
+ */
+static void
+regc(cp, b)
+register struct comp *cp;
+char b;
+{
+ if (EMITTING(cp))
+ *cp->regcode++ = b;
+ else
+ cp->regsize++;
+}
+
+/*
+ - reginsert - insert an operator in front of already-emitted operand
+ *
+ * Means relocating the operand.
+ */
+static void
+reginsert(cp, op, opnd)
+register struct comp *cp;
+char op;
+char *opnd;
+{
+ register char *place;
+
+ if (!EMITTING(cp)) {
+ cp->regsize += 3;
+ return;
+ }
+
+ (void) memmove(opnd+3, opnd, (size_t)(cp->regcode - opnd));
+ cp->regcode += 3;
+
+ place = opnd; /* Op node, where operand used to be. */
+ *place++ = op;
+ *place++ = '\0';
+ *place++ = '\0';
+}
+
+/*
+ - regtail - set the next-pointer at the end of a node chain
+ */
+static void
+regtail(cp, p, val)
+register struct comp *cp;
+char *p;
+char *val;
+{
+ register char *scan;
+ register char *temp;
+ register int offset;
+
+ if (!EMITTING(cp))
+ return;
+
+ /* Find last node. */
+ for (scan = p; (temp = regnext(scan)) != NULL; scan = temp)
+ continue;
+
+ offset = (OP(scan) == BACK) ? scan - val : val - scan;
+ *(scan+1) = (offset>>8)&0177;
+ *(scan+2) = offset&0377;
+}
+
+/*
+ - regoptail - regtail on operand of first argument; nop if operandless
+ */
+static void
+regoptail(cp, p, val)
+register struct comp *cp;
+char *p;
+char *val;
+{
+ /* "Operandless" and "op != BRANCH" are synonymous in practice. */
+ if (!EMITTING(cp) || OP(p) != BRANCH)
+ return;
+ regtail(cp, OPERAND(p), val);
+}
+
+/*
+ * sqd_regexec and friends
+ */
+
+/*
+ * Work-variable struct for sqd_regexec().
+ */
+struct exec {
+ char *reginput; /* String-input pointer. */
+ char *regbol; /* Beginning of input, for ^ check. */
+ char **regstartp; /* Pointer to startp array. */
+ char **regendp; /* Ditto for endp. */
+};
+
+/*
+ * Forwards.
+ */
+static int regtry(struct exec *ep, sqd_regexp *rp, char *string);
+static int regmatch(struct exec *ep, char *prog);
+static size_t regrepeat(struct exec *ep, char *node);
+
+#ifdef DEBUG
+int regnarrate = 0;
+void regdump();
+static char *regprop();
+#endif
+
+/*
+ - sqd_regexec - match a regexp against a string
+ */
+int
+sqd_regexec(prog, str)
+register sqd_regexp *prog;
+const char *str;
+{
+ register char *string = (char *)str; /* avert const poisoning */
+ register char *s;
+ struct exec ex;
+
+ /* Be paranoid. */
+ if (prog == NULL || string == NULL) {
+ sqd_regerror("NULL argument to sqd_regexec");
+ return(0);
+ }
+
+ /* Check validity of program. */
+ if ((unsigned char)*prog->program != SQD_REGMAGIC) {
+ sqd_regerror("corrupted regexp");
+ return(0);
+ }
+
+ /* If there is a "must appear" string, look for it. */
+ if (prog->regmust != NULL && strstr(string, prog->regmust) == NULL)
+ return(0);
+
+ /* Mark beginning of line for ^ . */
+ ex.regbol = string;
+ ex.regstartp = prog->startp;
+ ex.regendp = prog->endp;
+
+ /* Simplest case: anchored match need be tried only once. */
+ if (prog->reganch)
+ return(regtry(&ex, prog, string));
+
+ /* Messy cases: unanchored match. */
+ if (prog->regstart != '\0') {
+ /* We know what char it must start with. */
+ for (s = string; s != NULL; s = strchr(s+1, prog->regstart))
+ if (regtry(&ex, prog, s))
+ return(1);
+ return(0);
+ } else {
+ /* We don't -- general case. */
+ for (s = string; !regtry(&ex, prog, s); s++)
+ if (*s == '\0')
+ return(0);
+ return(1);
+ }
+ /* NOTREACHED */
+}
+
+/*
+ - regtry - try match at specific point
+ */
+static int /* 0 failure, 1 success */
+regtry(ep, prog, string)
+register struct exec *ep;
+sqd_regexp *prog;
+char *string;
+{
+ register int i;
+ register char **stp;
+ register char **enp;
+
+ ep->reginput = string;
+
+ stp = prog->startp;
+ enp = prog->endp;
+ for (i = NSUBEXP; i > 0; i--) {
+ *stp++ = NULL;
+ *enp++ = NULL;
+ }
+ if (regmatch(ep, prog->program + 1)) {
+ prog->startp[0] = string;
+ prog->endp[0] = ep->reginput;
+ return(1);
+ } else
+ return(0);
+}
+
+/*
+ - regmatch - main matching routine
+ *
+ * Conceptually the strategy is simple: check to see whether the current
+ * node matches, call self recursively to see whether the rest matches,
+ * and then act accordingly. In practice we make some effort to avoid
+ * recursion, in particular by going through "ordinary" nodes (that don't
+ * need to know whether the rest of the match failed) by a loop instead of
+ * by recursion.
+ */
+static int /* 0 failure, 1 success */
+regmatch(ep, prog)
+register struct exec *ep;
+char *prog;
+{
+ register char *scan; /* Current node. */
+ char *next; /* Next node. */
+
+#ifdef DEBUG
+ if (prog != NULL && regnarrate)
+ fprintf(stderr, "%s(\n", regprop(prog));
+#endif
+ for (scan = prog; scan != NULL; scan = next) {
+#ifdef DEBUG
+ if (regnarrate)
+ fprintf(stderr, "%s...\n", regprop(scan));
+#endif
+ next = regnext(scan);
+
+ switch (OP(scan)) {
+ case BOL:
+ if (ep->reginput != ep->regbol)
+ return(0);
+ break;
+ case EOL:
+ if (*ep->reginput != '\0')
+ return(0);
+ break;
+ case ANY:
+ if (*ep->reginput == '\0')
+ return(0);
+ ep->reginput++;
+ break;
+ case EXACTLY: {
+ register size_t len;
+ register char *const opnd = OPERAND(scan);
+
+ /* Inline the first character, for speed. */
+ if (*opnd != *ep->reginput)
+ return(0);
+ len = strlen(opnd);
+ if (len > 1 && strncmp(opnd, ep->reginput, len) != 0)
+ return(0);
+ ep->reginput += len;
+ break;
+ }
+ case ANYOF:
+ if (*ep->reginput == '\0' ||
+ strchr(OPERAND(scan), *ep->reginput) == NULL)
+ return(0);
+ ep->reginput++;
+ break;
+ case ANYBUT:
+ if (*ep->reginput == '\0' ||
+ strchr(OPERAND(scan), *ep->reginput) != NULL)
+ return(0);
+ ep->reginput++;
+ break;
+ case NOTHING:
+ break;
+ case BACK:
+ break;
+ case OPEN+1: case OPEN+2: case OPEN+3:
+ case OPEN+4: case OPEN+5: case OPEN+6:
+ case OPEN+7: case OPEN+8: case OPEN+9: {
+ register const int no = OP(scan) - OPEN;
+ register char *const input = ep->reginput;
+
+ if (regmatch(ep, next)) {
+ /*
+ * Don't set startp if some later
+ * invocation of the same parentheses
+ * already has.
+ */
+ if (ep->regstartp[no] == NULL)
+ ep->regstartp[no] = input;
+ return(1);
+ } else
+ return(0);
+ break;
+ }
+ case CLOSE+1: case CLOSE+2: case CLOSE+3:
+ case CLOSE+4: case CLOSE+5: case CLOSE+6:
+ case CLOSE+7: case CLOSE+8: case CLOSE+9: {
+ register const int no = OP(scan) - CLOSE;
+ register char *const input = ep->reginput;
+
+ if (regmatch(ep, next)) {
+ /*
+ * Don't set endp if some later
+ * invocation of the same parentheses
+ * already has.
+ */
+ if (ep->regendp[no] == NULL)
+ ep->regendp[no] = input;
+ return(1);
+ } else
+ return(0);
+ break;
+ }
+ case BRANCH: {
+ register char *const save = ep->reginput;
+
+ if (OP(next) != BRANCH) /* No choice. */
+ next = OPERAND(scan); /* Avoid recursion. */
+ else {
+ while (OP(scan) == BRANCH) {
+ if (regmatch(ep, OPERAND(scan)))
+ return(1);
+ ep->reginput = save;
+ scan = regnext(scan);
+ }
+ return(0);
+ /* NOTREACHED */
+ }
+ break;
+ }
+ case STAR: case PLUS: {
+ register const char nextch =
+ (OP(next) == EXACTLY) ? *OPERAND(next) : '\0';
+ register size_t no;
+ register char *const save = ep->reginput;
+ register const size_t min = (OP(scan) == STAR) ? 0 : 1;
+
+ for (no = regrepeat(ep, OPERAND(scan)) + 1; no > min; no--) {
+ ep->reginput = save + no - 1;
+ /* If it could work, try it. */
+ if (nextch == '\0' || *ep->reginput == nextch)
+ if (regmatch(ep, next))
+ return(1);
+ }
+ return(0);
+ break;
+ }
+ case END:
+ return(1); /* Success! */
+ break;
+ default:
+ sqd_regerror("regexp corruption");
+ return(0);
+ break;
+ }
+ }
+
+ /*
+ * We get here only if there's trouble -- normally "case END" is
+ * the terminating point.
+ */
+ sqd_regerror("corrupted pointers");
+ return(0);
+}
+
+/*
+ - regrepeat - report how many times something simple would match
+ */
+static size_t
+regrepeat(ep, node)
+register struct exec *ep;
+char *node;
+{
+ register size_t count;
+ register char *scan;
+ register char ch;
+
+ switch (OP(node)) {
+ case ANY:
+ return(strlen(ep->reginput));
+ break;
+ case EXACTLY:
+ ch = *OPERAND(node);
+ count = 0;
+ for (scan = ep->reginput; *scan == ch; scan++)
+ count++;
+ return(count);
+ break;
+ case ANYOF:
+ return(strspn(ep->reginput, OPERAND(node)));
+ break;
+ case ANYBUT:
+ return(strcspn(ep->reginput, OPERAND(node)));
+ break;
+ default: /* Oh dear. Called inappropriately. */
+ sqd_regerror("internal error: bad call of regrepeat");
+ return(0); /* Best compromise. */
+ break;
+ }
+ /* NOTREACHED */
+}
+
+/*
+ - regnext - dig the "next" pointer out of a node
+ */
+static char *
+regnext(p)
+register char *p;
+{
+ register const int offset = NEXT(p);
+
+ if (offset == 0)
+ return(NULL);
+
+ return((OP(p) == BACK) ? p-offset : p+offset);
+}
+
+#ifdef DEBUG
+
+static char *regprop();
+
+/*
+ - regdump - dump a regexp onto stdout in vaguely comprehensible form
+ */
+void
+regdump(r)
+sqd_regexp *r;
+{
+ register char *s;
+ register char op = EXACTLY; /* Arbitrary non-END op. */
+ register char *next;
+
+
+ s = r->program + 1;
+ while (op != END) { /* While that wasn't END last time... */
+ op = OP(s);
+ printf("%2d%s", s-r->program, regprop(s)); /* Where, what. */
+ next = regnext(s);
+ if (next == NULL) /* Next ptr. */
+ printf("(0)");
+ else
+ printf("(%d)", (s-r->program)+(next-s));
+ s += 3;
+ if (op == ANYOF || op == ANYBUT || op == EXACTLY) {
+ /* Literal string, where present. */
+ while (*s != '\0') {
+ putchar(*s);
+ s++;
+ }
+ s++;
+ }
+ putchar('\n');
+ }
+
+ /* Header fields of interest. */
+ if (r->regstart != '\0')
+ printf("start `%c' ", r->regstart);
+ if (r->reganch)
+ printf("anchored ");
+ if (r->regmust != NULL)
+ printf("must have \"%s\"", r->regmust);
+ printf("\n");
+}
+
+/*
+ - regprop - printable representation of opcode
+ */
+static char *
+regprop(op)
+char *op;
+{
+ register char *p;
+ static char buf[50];
+
+ (void) strcpy(buf, ":");
+
+ switch (OP(op)) {
+ case BOL:
+ p = "BOL";
+ break;
+ case EOL:
+ p = "EOL";
+ break;
+ case ANY:
+ p = "ANY";
+ break;
+ case ANYOF:
+ p = "ANYOF";
+ break;
+ case ANYBUT:
+ p = "ANYBUT";
+ break;
+ case BRANCH:
+ p = "BRANCH";
+ break;
+ case EXACTLY:
+ p = "EXACTLY";
+ break;
+ case NOTHING:
+ p = "NOTHING";
+ break;
+ case BACK:
+ p = "BACK";
+ break;
+ case END:
+ p = "END";
+ break;
+ case OPEN+1:
+ case OPEN+2:
+ case OPEN+3:
+ case OPEN+4:
+ case OPEN+5:
+ case OPEN+6:
+ case OPEN+7:
+ case OPEN+8:
+ case OPEN+9:
+ sprintf(buf+strlen(buf), "OPEN%d", OP(op)-OPEN);
+ p = NULL;
+ break;
+ case CLOSE+1:
+ case CLOSE+2:
+ case CLOSE+3:
+ case CLOSE+4:
+ case CLOSE+5:
+ case CLOSE+6:
+ case CLOSE+7:
+ case CLOSE+8:
+ case CLOSE+9:
+ sprintf(buf+strlen(buf), "CLOSE%d", OP(op)-CLOSE);
+ p = NULL;
+ break;
+ case STAR:
+ p = "STAR";
+ break;
+ case PLUS:
+ p = "PLUS";
+ break;
+ default:
+ sqd_regerror("corrupted opcode");
+ break;
+ }
+ if (p != NULL)
+ (void) strcat(buf, p);
+ return(buf);
+}
+#endif
+
+
+/*
+ - sqd_regsub - perform substitutions after a regexp match
+ */
+void
+sqd_regsub(rp, source, dest)
+const sqd_regexp *rp;
+const char *source;
+char *dest;
+{
+ register sqd_regexp * const prog = (sqd_regexp *)rp;
+ register char *src = (char *)source;
+ register char *dst = dest;
+ register char c;
+ register int no;
+ register size_t len;
+
+ if (prog == NULL || source == NULL || dest == NULL) {
+ sqd_regerror("NULL parameter to sqd_regsub");
+ return;
+ }
+ if ((unsigned char)*(prog->program) != SQD_REGMAGIC) {
+ sqd_regerror("damaged regexp");
+ return;
+ }
+
+ while ((c = *src++) != '\0') {
+ if (c == '&')
+ no = 0;
+ else if (c == '\\' && isdigit((int) (*src)))
+ no = *src++ - '0';
+ else
+ no = -1;
+
+ if (no < 0) { /* Ordinary character. */
+ if (c == '\\' && (*src == '\\' || *src == '&'))
+ c = *src++;
+ *dst++ = c;
+ } else if (prog->startp[no] != NULL && prog->endp[no] != NULL &&
+ prog->endp[no] > prog->startp[no]) {
+ len = prog->endp[no] - prog->startp[no];
+ (void) strncpy(dst, prog->startp[no], len);
+ dst += len;
+ if (*(dst-1) == '\0') { /* strncpy hit NUL. */
+ sqd_regerror("damaged match string");
+ return;
+ }
+ }
+ }
+ *dst++ = '\0';
+}
+
+
+void
+sqd_regerror(s)
+char *s;
+{
+ fprintf(stderr, "regexp(3): %s\n", s);
+ exit(EXIT_FAILURE);
+ /* NOTREACHED */
+}
+
+#ifdef NBA_TEAM_IN_STL
+int
+main(int argc, char **argv)
+{
+ char *pat;
+ int ntok;
+ char *s;
+ int status;
+
+ pat = argv[1];
+ ntok = atoi(argv[2]);
+ s = argv[3];
+
+ status = Strparse(pat, s, ntok);
+ if (status == 0) {
+ printf("no match\n");
+ } else {
+ int i;
+ printf("MATCH.\n");
+ for (i = 1; i <= ntok; i++)
+ printf("matched token %1d: %s\n", i, sqd_parse[i]);
+ }
+}
+#endif /*NBA_TEAM_IN_STL*/
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* iupac.c
+ *
+ * Globally defines the IUPAC symbols for nucleic acid sequence
+ * Slowly evolving into a repository of globals. Tue Apr 20 1993
+ *
+ * RCS $Id: iupac.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: iupac.c,v 1.3 2001/02/21 21:09:10 eddy Exp)
+ */
+#include "squid.h"
+
+/* Default expected nucleotide occurrence frequencies, A/C/G/T.
+ * Used (for instance) as the default distribution for
+ * i.i.d. random nucleotide sequences.
+ */
+float dnafq[4] = { 0.25, 0.25, 0.25, 0.25 };
+
+/* Dayhoff f(i) amino acid occurrence frequencies.
+ * From SwissProt 34: 21,210,388 residues
+ * In alphabetic order by single-letter code.
+ * Used (for instance) as the default distribution for
+ * i.i.d. random protein sequences.
+ */
+float aafq[20] = {
+ 0.075520, /* A */
+ 0.016973, /* C */
+ 0.053029, /* D */
+ 0.063204, /* E */
+ 0.040762, /* F */
+ 0.068448, /* G */
+ 0.022406, /* H */
+ 0.057284, /* I */
+ 0.059398, /* K */
+ 0.093399, /* L */
+ 0.023569, /* M */
+ 0.045293, /* N */
+ 0.049262, /* P */
+ 0.040231, /* Q */
+ 0.051573, /* R */
+ 0.072214, /* S */
+ 0.057454, /* T */
+ 0.065252, /* V */
+ 0.012513, /* W */
+ 0.031985 /* Y */
+};
+
+char aa_alphabet[] = AMINO_ALPHABET;
+ /* aa_index converts to pam's 27x27 scheme */
+int aa_index[20] = { 0, 2, 3, 4, 5, 6, 7, 8, 10, 11,
+ 12, 13, 15, 16, 17, 18, 19, 21, 22, 24 };
+
+ /* IUPAC code translations */
+ /* note: sequence chars are UPPER CASE */
+struct iupactype iupac[] = {
+ { 'A', 'T', NTA, NTT, },
+ { 'C', 'G', NTC, NTG, },
+ { 'G', 'C', NTG, NTC, },
+ { 'T', 'A', NTT, NTA, },
+ { 'U', 'A', NTU, NTA, },
+ { 'N', 'N', NTN, NTN, },
+ { ' ', ' ', NTGAP, NTGAP, },
+ { 'R', 'Y', NTR, NTY, },
+ { 'Y', 'R', NTY, NTR, },
+ { 'M', 'K', NTM, NTK, },
+ { 'K', 'M', NTK, NTM, },
+ { 'S', 'S', NTS, NTS, },
+ { 'W', 'W', NTW, NTW, },
+ { 'H', 'D', NTH, NTD, },
+ { 'B', 'V', NTB, NTV, },
+ { 'V', 'B', NTV, NTB, },
+ { 'D', 'H', NTD, NTH, },
+ };
+
+
+char *stdcode1[65] = {
+ "K", /* AAA */
+ "N", /* AAC */
+ "K", /* AAG */
+ "N", /* AAU */
+ "T", /* ACA */
+ "T", /* ACC */
+ "T", /* ACG */
+ "T", /* ACU */
+ "R", /* AGA */
+ "S", /* AGC */
+ "R", /* AGG */
+ "S", /* AGU */
+ "I", /* AUA */
+ "I", /* AUC */
+ "M", /* AUG */
+ "I", /* AUU */
+ "Q", /* CAA */
+ "H", /* CAC */
+ "Q", /* CAG */
+ "H", /* CAU */
+ "P", /* CCA */
+ "P", /* CCC */
+ "P", /* CCG */
+ "P", /* CCU */
+ "R", /* CGA */
+ "R", /* CGC */
+ "R", /* CGG */
+ "R", /* CGU */
+ "L", /* CUA */
+ "L", /* CUC */
+ "L", /* CUG */
+ "L", /* CUU */
+ "E", /* GAA */
+ "D", /* GAC */
+ "E", /* GAG */
+ "D", /* GAU */
+ "A", /* GCA */
+ "A", /* GCC */
+ "A", /* GCG */
+ "A", /* GCU */
+ "G", /* GGA */
+ "G", /* GGC */
+ "G", /* GGG */
+ "G", /* GGU */
+ "V", /* GUA */
+ "V", /* GUC */
+ "V", /* GUG */
+ "V", /* GUU */
+ "*", /* UAA */
+ "Y", /* UAC */
+ "*", /* UAG */
+ "Y", /* UAU */
+ "S", /* UCA */
+ "S", /* UCC */
+ "S", /* UCG */
+ "S", /* UCU */
+ "*", /* UGA */
+ "C", /* UGC */
+ "W", /* UGG */
+ "C", /* UGU */
+ "L", /* UUA */
+ "F", /* UUC */
+ "L", /* UUG */
+ "F", /* UUU */
+ "X", /* unknown */
+};
+
+
+
+
+char *stdcode3[65] = {
+ "Lys", /* AAA */
+ "Asn", /* AAC */
+ "Lys", /* AAG */
+ "Asn", /* AAU */
+ "Thr", /* ACA */
+ "Thr", /* ACC */
+ "Thr", /* ACG */
+ "Thr", /* ACU */
+ "Arg", /* AGA */
+ "Ser", /* AGC */
+ "Arg", /* AGG */
+ "Ser", /* AGU */
+ "Ile", /* AUA */
+ "Ile", /* AUC */
+ "Met", /* AUG */
+ "Ile", /* AUU */
+ "Gln", /* CAA */
+ "His", /* CAC */
+ "Gln", /* CAG */
+ "His", /* CAU */
+ "Pro", /* CCA */
+ "Pro", /* CCC */
+ "Pro", /* CCG */
+ "Pro", /* CCU */
+ "Arg", /* CGA */
+ "Arg", /* CGC */
+ "Arg", /* CGG */
+ "Arg", /* CGU */
+ "Leu", /* CUA */
+ "Leu", /* CUC */
+ "Leu", /* CUG */
+ "Leu", /* CUU */
+ "Glu", /* GAA */
+ "Asp", /* GAC */
+ "Glu", /* GAG */
+ "Asp", /* GAU */
+ "Ala", /* GCA */
+ "Ala", /* GCC */
+ "Ala", /* GCG */
+ "Ala", /* GCU */
+ "Gly", /* GGA */
+ "Gly", /* GGC */
+ "Gly", /* GGG */
+ "Gly", /* GGU */
+ "Val", /* GUA */
+ "Val", /* GUC */
+ "Val", /* GUG */
+ "Val", /* GUU */
+ "***", /* UAA */
+ "Tyr", /* UAC */
+ "***", /* UAG */
+ "Tyr", /* UAU */
+ "Ser", /* UCA */
+ "Ser", /* UCC */
+ "Ser", /* UCG */
+ "Ser", /* UCU */
+ "***", /* UGA */
+ "Cys", /* UGC */
+ "Trp", /* UGG */
+ "Cys", /* UGU */
+ "Leu", /* UUA */
+ "Phe", /* UUC */
+ "Leu", /* UUG */
+ "Trp", /* UUU */
+ "XXX", /* unknown */
+};
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* msa.c
+ * SRE, Mon May 17 10:48:47 1999
+ *
+ * SQUID's interface for multiple sequence alignment
+ * manipulation: access to the MSA object.
+ *
+ * RCS $Id: msa.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: msa.c,v 1.18 2002/10/12 04:40:35 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "squid.h"
+#include "msa.h" /* multiple sequence alignment object support */
+#include "gki.h" /* string indexing hashtable code */
+#include "ssi.h" /* SSI sequence file indexing code */
+
+/* Function: MSAAlloc()
+ * Date: SRE, Tue May 18 10:45:47 1999 [St. Louis]
+ *
+ * Purpose: Allocate an MSA structure, return a pointer
+ * to it.
+ *
+ * Designed to be used in three ways:
+ * 1) We know exactly the dimensions of the alignment:
+ * both nseq and alen.
+ * msa = MSAAlloc(nseq, alen);
+ *
+ * 2) We know the number of sequences but not alen.
+ * (We add sequences later.)
+ * msa = MSAAlloc(nseq, 0);
+ *
+ * 3) We even don't know the number of sequences, so
+ * we'll have to dynamically expand allocations.
+ * We provide a blocksize for the allocation expansion,
+ * and expand when needed.
+ * msa = MSAAlloc(10, 0);
+ * if (msa->nseq == msa->nseqalloc) MSAExpand(msa);
+ *
+ * Args: nseq - number of sequences, or nseq allocation blocksize
+ * alen - length of alignment in columns, or 0
+ *
+ * Returns: pointer to new MSA object, w/ all values initialized.
+ * Note that msa->nseq is initialized to 0, though space
+ * is allocated.
+ *
+ * Diagnostics: "always works". Die()'s on memory allocation failure.
+ *
+ */
+MSA *
+MSAAlloc(int nseq, int alen)
+{
+ MSA *msa;
+ int i;
+
+ msa = MallocOrDie(sizeof(MSA));
+ msa->aseq = MallocOrDie(sizeof(char *) * nseq);
+ msa->sqname = MallocOrDie(sizeof(char *) * nseq);
+ msa->sqlen = MallocOrDie(sizeof(int) * nseq);
+ msa->wgt = MallocOrDie(sizeof(float) * nseq);
+
+ for (i = 0; i < nseq; i++)
+ {
+ msa->sqname[i] = NULL;
+ msa->sqlen[i] = 0;
+ msa->wgt[i] = -1.0;
+
+ if (alen != 0) msa->aseq[i] = MallocOrDie(sizeof(char) * (alen+1));
+ else msa->aseq[i] = NULL;
+ }
+
+ msa->alen = alen;
+ msa->nseq = 0;
+ msa->nseqalloc = nseq;
+ msa->nseqlump = nseq;
+
+ msa->flags = 0;
+ msa->type = kOtherSeq;
+ msa->name = NULL;
+ msa->desc = NULL;
+ msa->acc = NULL;
+ msa->au = NULL;
+ msa->ss_cons = NULL;
+ msa->sa_cons = NULL;
+ msa->rf = NULL;
+ msa->sqacc = NULL;
+ msa->sqdesc = NULL;
+ msa->ss = NULL;
+ msa->sslen = NULL;
+ msa->sa = NULL;
+ msa->salen = NULL;
+ msa->index = GKIInit();
+ msa->lastidx = 0;
+
+ for (i = 0; i < MSA_MAXCUTOFFS; i++) {
+ msa->cutoff[i] = 0.;
+ msa->cutoff_is_set[i] = FALSE;
+ }
+
+ /* Initialize unparsed optional markup
+ */
+ msa->comment = NULL;
+ msa->ncomment = 0;
+ msa->alloc_ncomment = 0;
+
+ msa->gf_tag = NULL;
+ msa->gf = NULL;
+ msa->ngf = 0;
+
+ msa->gs_tag = NULL;
+ msa->gs = NULL;
+ msa->gs_idx = NULL;
+ msa->ngs = 0;
+
+ msa->gc_tag = NULL;
+ msa->gc = NULL;
+ msa->gc_idx = NULL;
+ msa->ngc = 0;
+
+ msa->gr_tag = NULL;
+ msa->gr = NULL;
+ msa->gr_idx = NULL;
+ msa->ngr = 0;
+
+ /* Done. Return the alloced, initialized structure
+ */
+ return msa;
+}
+
+/* Function: MSAExpand()
+ * Date: SRE, Tue May 18 11:06:53 1999 [St. Louis]
+ *
+ * Purpose: Increase the sequence allocation in an MSA
+ * by msa->nseqlump. (Typically used when we're reading
+ * in an alignment sequentially from a file,
+ * so we don't know nseq until we're done.)
+ *
+ * Args: msa - the MSA object
+ *
+ * Returns: (void)
+ *
+ */
+void
+MSAExpand(MSA *msa)
+{
+ int i,j;
+
+ msa->nseqalloc += msa->nseqlump;
+
+ msa->aseq = ReallocOrDie(msa->aseq, sizeof(char *) * msa->nseqalloc);
+ msa->sqname = ReallocOrDie(msa->sqname, sizeof(char *) * msa->nseqalloc);
+ msa->sqlen = ReallocOrDie(msa->sqlen, sizeof(char *) * msa->nseqalloc);
+ msa->wgt = ReallocOrDie(msa->wgt, sizeof(float) * msa->nseqalloc);
+
+ if (msa->ss != NULL) {
+ msa->ss = ReallocOrDie(msa->ss, sizeof(char *) * msa->nseqalloc);
+ msa->sslen = ReallocOrDie(msa->sslen, sizeof(int) * msa->nseqalloc);
+ }
+ if (msa->sa != NULL) {
+ msa->sa = ReallocOrDie(msa->sa, sizeof(char *) * msa->nseqalloc);
+ msa->salen = ReallocOrDie(msa->salen, sizeof(int) * msa->nseqalloc);
+ }
+ if (msa->sqacc != NULL)
+ msa->sqacc = ReallocOrDie(msa->sqacc, sizeof(char *) * msa->nseqalloc);
+ if (msa->sqdesc != NULL)
+ msa->sqdesc =ReallocOrDie(msa->sqdesc,sizeof(char *) * msa->nseqalloc);
+
+ for (i = msa->nseqalloc-msa->nseqlump; i < msa->nseqalloc; i++)
+ {
+ msa->sqname[i] = NULL;
+ msa->wgt[i] = -1.0;
+
+ if (msa->sqacc != NULL) msa->sqacc[i] = NULL;
+ if (msa->sqdesc != NULL) msa->sqdesc[i] = NULL;
+
+ if (msa->alen != 0)
+ msa->aseq[i] = ReallocOrDie(msa->aseq[i], sizeof(char) * (msa->alen+1));
+ else msa->aseq[i] = NULL;
+ msa->sqlen[i] = 0;
+
+ if (msa->ss != NULL) {
+ if (msa->alen != 0)
+ msa->ss[i] = ReallocOrDie(msa->ss[i], sizeof(char) * (msa->alen+1));
+ else msa->ss[i] = NULL;
+ msa->sslen[i] = 0;
+ }
+ if (msa->sa != NULL) {
+ if (msa->alen != 0)
+ msa->sa[i] = ReallocOrDie(msa->ss[i], sizeof(char) * (msa->alen+1));
+ else
+ msa->sa[i] = NULL;
+ msa->salen[i] = 0;
+ }
+ }
+
+ /* Reallocate and re-init for unparsed #=GS tags, if we have some.
+ * gs is [0..ngs-1][0..nseq-1][], so we're reallocing the middle
+ * set of pointers.
+ */
+ if (msa->gs != NULL)
+ for (i = 0; i < msa->ngs; i++)
+ {
+ if (msa->gs[i] != NULL)
+ {
+ msa->gs[i] = ReallocOrDie(msa->gs[i], sizeof(char *) * msa->nseqalloc);
+ for (j = msa->nseqalloc-msa->nseqlump; j < msa->nseqalloc; j++)
+ msa->gs[i][j] = NULL;
+ }
+ }
+
+ /* Reallocate and re-init for unparsed #=GR tags, if we have some.
+ * gr is [0..ngs-1][0..nseq-1][], so we're reallocing the middle
+ * set of pointers.
+ */
+ if (msa->gr != NULL)
+ for (i = 0; i < msa->ngr; i++)
+ {
+ if (msa->gr[i] != NULL)
+ {
+ msa->gr[i] = ReallocOrDie(msa->gr[i], sizeof(char *) * msa->nseqalloc);
+ for (j = msa->nseqalloc-msa->nseqlump; j < msa->nseqalloc; j++)
+ msa->gr[i][j] = NULL;
+ }
+ }
+
+ return;
+}
+
+/* Function: MSAFree()
+ * Date: SRE, Tue May 18 11:20:16 1999 [St. Louis]
+ *
+ * Purpose: Free a multiple sequence alignment structure.
+ *
+ * Args: msa - the alignment
+ *
+ * Returns: (void)
+ */
+void
+MSAFree(MSA *msa)
+{
+ Free2DArray((void **) msa->aseq, msa->nseq);
+ Free2DArray((void **) msa->sqname, msa->nseq);
+ Free2DArray((void **) msa->sqacc, msa->nseq);
+ Free2DArray((void **) msa->sqdesc, msa->nseq);
+ Free2DArray((void **) msa->ss, msa->nseq);
+ Free2DArray((void **) msa->sa, msa->nseq);
+
+ if (msa->sqlen != NULL) free(msa->sqlen);
+ if (msa->wgt != NULL) free(msa->wgt);
+
+ if (msa->name != NULL) free(msa->name);
+ if (msa->desc != NULL) free(msa->desc);
+ if (msa->acc != NULL) free(msa->acc);
+ if (msa->au != NULL) free(msa->au);
+ if (msa->ss_cons != NULL) free(msa->ss_cons);
+ if (msa->sa_cons != NULL) free(msa->sa_cons);
+ if (msa->rf != NULL) free(msa->rf);
+ if (msa->sslen != NULL) free(msa->sslen);
+ if (msa->salen != NULL) free(msa->salen);
+
+ Free2DArray((void **) msa->comment, msa->ncomment);
+ Free2DArray((void **) msa->gf_tag, msa->ngf);
+ Free2DArray((void **) msa->gf, msa->ngf);
+ Free2DArray((void **) msa->gs_tag, msa->ngs);
+ Free3DArray((void ***)msa->gs, msa->ngs, msa->nseq);
+ Free2DArray((void **) msa->gc_tag, msa->ngc);
+ Free2DArray((void **) msa->gc, msa->ngc);
+ Free2DArray((void **) msa->gr_tag, msa->ngr);
+ Free3DArray((void ***)msa->gr, msa->ngr, msa->nseq);
+
+ GKIFree(msa->index);
+ GKIFree(msa->gs_idx);
+ GKIFree(msa->gc_idx);
+ GKIFree(msa->gr_idx);
+
+ free(msa);
+}
+
+
+/* Function: MSASetSeqAccession()
+ * Date: SRE, Mon Jun 21 04:13:33 1999 [Sanger Centre]
+ *
+ * Purpose: Set a sequence accession in an MSA structure.
+ * Handles some necessary allocation/initialization.
+ *
+ * Args: msa - multiple alignment to add accession to
+ * seqidx - index of sequence to attach accession to
+ * acc - accession
+ *
+ * Returns: void
+ */
+void
+MSASetSeqAccession(MSA *msa, int seqidx, char *acc)
+{
+ int x;
+
+ if (msa->sqacc == NULL) {
+ msa->sqacc = MallocOrDie(sizeof(char *) * msa->nseqalloc);
+ for (x = 0; x < msa->nseqalloc; x++)
+ msa->sqacc[x] = NULL;
+ }
+ msa->sqacc[seqidx] = sre_strdup(acc, -1);
+}
+
+/* Function: MSASetSeqDescription()
+ * Date: SRE, Mon Jun 21 04:21:09 1999 [Sanger Centre]
+ *
+ * Purpose: Set a sequence description in an MSA structure.
+ * Handles some necessary allocation/initialization.
+ *
+ * Args: msa - multiple alignment to add accession to
+ * seqidx - index of sequence to attach accession to
+ * desc - description
+ *
+ * Returns: void
+ */
+void
+MSASetSeqDescription(MSA *msa, int seqidx, char *desc)
+{
+ int x;
+
+ if (msa->sqdesc == NULL) {
+ msa->sqdesc = MallocOrDie(sizeof(char *) * msa->nseqalloc);
+ for (x = 0; x < msa->nseqalloc; x++)
+ msa->sqdesc[x] = NULL;
+ }
+ msa->sqdesc[seqidx] = sre_strdup(desc, -1);
+}
+
+
+/* Function: MSAAddComment()
+ * Date: SRE, Tue Jun 1 17:37:21 1999 [St. Louis]
+ *
+ * Purpose: Add an (unparsed) comment line to the MSA structure,
+ * allocating as necessary.
+ *
+ * Args: msa - a multiple alignment
+ * s - comment line to add
+ *
+ * Returns: (void)
+ */
+void
+MSAAddComment(MSA *msa, char *s)
+{
+ /* If this is our first recorded comment, we need to malloc();
+ * and if we've filled available space, we need to realloc().
+ * Note the arbitrary lumpsize of 10 lines per allocation...
+ */
+ if (msa->comment == NULL) {
+ msa->comment = MallocOrDie (sizeof(char *) * 10);
+ msa->alloc_ncomment = 10;
+ }
+ if (msa->ncomment == msa->alloc_ncomment) {
+ msa->alloc_ncomment += 10;
+ msa->comment = ReallocOrDie(msa->comment, sizeof(char *) * msa->alloc_ncomment);
+ }
+
+ msa->comment[msa->ncomment] = sre_strdup(s, -1);
+ msa->ncomment++;
+ return;
+}
+
+/* Function: MSAAddGF()
+ * Date: SRE, Wed Jun 2 06:53:54 1999 [bus to Madison]
+ *
+ * Purpose: Add an unparsed #=GF markup line to the MSA
+ * structure, allocating as necessary.
+ *
+ * Args: msa - a multiple alignment
+ * tag - markup tag (e.g. "AU")
+ * value - free text markup (e.g. "Alex Bateman")
+ *
+ * Returns: (void)
+ */
+void
+MSAAddGF(MSA *msa, char *tag, char *value)
+{
+ /* If this is our first recorded unparsed #=GF line, we need to malloc();
+ * if we've filled availabl space If we already have a hash index, and the GF
+ * Note the arbitrary lumpsize of 10 lines per allocation...
+ */
+ if (msa->gf_tag == NULL) {
+ msa->gf_tag = MallocOrDie (sizeof(char *) * 10);
+ msa->gf = MallocOrDie (sizeof(char *) * 10);
+ msa->alloc_ngf = 10;
+ }
+ if (msa->ngf == msa->alloc_ngf) {
+ msa->alloc_ngf += 10;
+ msa->gf_tag = ReallocOrDie(msa->gf_tag, sizeof(char *) * msa->alloc_ngf);
+ msa->gf = ReallocOrDie(msa->gf, sizeof(char *) * msa->alloc_ngf);
+ }
+
+ msa->gf_tag[msa->ngf] = sre_strdup(tag, -1);
+ msa->gf[msa->ngf] = sre_strdup(value, -1);
+ msa->ngf++;
+
+ return;
+}
+
+
+/* Function: MSAAddGS()
+ * Date: SRE, Wed Jun 2 06:57:03 1999 [St. Louis]
+ *
+ * Purpose: Add an unparsed #=GS markup line to the MSA
+ * structure, allocating as necessary.
+ *
+ * It's possible that we could get more than one
+ * of the same type of GS tag per sequence; for
+ * example, "DR PDB;" structure links in Pfam.
+ * Hack: handle these by appending to the string,
+ * in a \n separated fashion.
+ *
+ * Args: msa - multiple alignment structure
+ * tag - markup tag (e.g. "AC")
+ * sqidx - index of sequence to assoc markup with (0..nseq-1)
+ * value - markup (e.g. "P00666")
+ *
+ * Returns: 0 on success
+ */
+void
+MSAAddGS(MSA *msa, char *tag, int sqidx, char *value)
+{
+ int tagidx;
+ int i;
+
+ /* Is this an unparsed tag name that we recognize?
+ * If not, handle adding it to index, and reallocating
+ * as needed.
+ */
+ if (msa->gs_tag == NULL) /* first tag? init w/ malloc */
+ {
+ msa->gs_idx = GKIInit();
+ tagidx = GKIStoreKey(msa->gs_idx, tag);
+ SQD_DASSERT1((tagidx == 0));
+ msa->gs_tag = MallocOrDie(sizeof(char *));
+ msa->gs = MallocOrDie(sizeof(char **));
+ msa->gs[0] = MallocOrDie(sizeof(char *) * msa->nseqalloc);
+ for (i = 0; i < msa->nseqalloc; i++)
+ msa->gs[0][i] = NULL;
+ }
+ else
+ {
+ /* new tag? */
+ tagidx = GKIKeyIndex(msa->gs_idx, tag);
+ if (tagidx < 0) { /* it's a new tag name; realloc */
+ tagidx = GKIStoreKey(msa->gs_idx, tag);
+ /* since we alloc in blocks of 1,
+ we always realloc upon seeing
+ a new tag. */
+ SQD_DASSERT1((tagidx == msa->ngs));
+ msa->gs_tag = ReallocOrDie(msa->gs_tag, (msa->ngs+1) * sizeof(char *));
+ msa->gs = ReallocOrDie(msa->gs, (msa->ngs+1) * sizeof(char **));
+ msa->gs[msa->ngs] = MallocOrDie(sizeof(char *) * msa->nseqalloc);
+ for (i = 0; i < msa->nseqalloc; i++)
+ msa->gs[msa->ngs][i] = NULL;
+ }
+ }
+
+ if (tagidx == msa->ngs) {
+ msa->gs_tag[tagidx] = sre_strdup(tag, -1);
+ msa->ngs++;
+ }
+
+ if (msa->gs[tagidx][sqidx] == NULL) /* first annotation of this seq with this tag? */
+ msa->gs[tagidx][sqidx] = sre_strdup(value, -1);
+ else {
+ /* >1 annotation of this seq with this tag; append */
+ int len;
+ if ((len = sre_strcat(&(msa->gs[tagidx][sqidx]), -1, "\n", 1)) < 0)
+ Die("failed to sre_strcat()");
+ if (sre_strcat(&(msa->gs[tagidx][sqidx]), len, value, -1) < 0)
+ Die("failed to sre_strcat()");
+ }
+ return;
+}
+
+/* Function: MSAAppendGC()
+ * Date: SRE, Thu Jun 3 06:25:14 1999 [Madison]
+ *
+ * Purpose: Add an unparsed #=GC markup line to the MSA
+ * structure, allocating as necessary.
+ *
+ * When called multiple times for the same tag,
+ * appends value strings together -- used when
+ * parsing multiblock alignment files, for
+ * example.
+ *
+ * Args: msa - multiple alignment structure
+ * tag - markup tag (e.g. "CS")
+ * value - markup, one char per aligned column
+ *
+ * Returns: (void)
+ */
+void
+MSAAppendGC(MSA *msa, char *tag, char *value)
+{
+ int tagidx;
+
+ /* Is this an unparsed tag name that we recognize?
+ * If not, handle adding it to index, and reallocating
+ * as needed.
+ */
+ if (msa->gc_tag == NULL) /* first tag? init w/ malloc */
+ {
+ msa->gc_tag = MallocOrDie(sizeof(char *));
+ msa->gc = MallocOrDie(sizeof(char *));
+ msa->gc_idx = GKIInit();
+ tagidx = GKIStoreKey(msa->gc_idx, tag);
+ SQD_DASSERT1((tagidx == 0));
+ msa->gc[0] = NULL;
+ }
+ else
+ { /* new tag? */
+ tagidx = GKIKeyIndex(msa->gc_idx, tag);
+ if (tagidx < 0) { /* it's a new tag name; realloc */
+ tagidx = GKIStoreKey(msa->gc_idx, tag);
+ /* since we alloc in blocks of 1,
+ we always realloc upon seeing
+ a new tag. */
+ SQD_DASSERT1((tagidx == msa->ngc));
+ msa->gc_tag = ReallocOrDie(msa->gc_tag, (msa->ngc+1) * sizeof(char **));
+ msa->gc = ReallocOrDie(msa->gc, (msa->ngc+1) * sizeof(char **));
+ msa->gc[tagidx] = NULL;
+ }
+ }
+
+ if (tagidx == msa->ngc) {
+ msa->gc_tag[tagidx] = sre_strdup(tag, -1);
+ msa->ngc++;
+ }
+ sre_strcat(&(msa->gc[tagidx]), -1, value, -1);
+ return;
+}
+
+/* Function: MSAGetGC()
+ * Date: SRE, Fri Aug 13 13:25:57 1999 [St. Louis]
+ *
+ * Purpose: Given a tagname for a miscellaneous #=GC column
+ * annotation, return a pointer to the annotation
+ * string.
+ *
+ * Args: msa - alignment and its annotation
+ * tag - name of the annotation
+ *
+ * Returns: ptr to the annotation string. Caller does *not*
+ * free; is managed by msa object still.
+ */
+char *
+MSAGetGC(MSA *msa, char *tag)
+{
+ int tagidx;
+
+ if (msa->gc_idx == NULL) return NULL;
+ if ((tagidx = GKIKeyIndex(msa->gc_idx, tag)) < 0) return NULL;
+ return msa->gc[tagidx];
+}
+
+
+/* Function: MSAAppendGR()
+ * Date: SRE, Thu Jun 3 06:34:38 1999 [Madison]
+ *
+ * Purpose: Add an unparsed #=GR markup line to the
+ * MSA structure, allocating as necessary.
+ *
+ * When called multiple times for the same tag,
+ * appends value strings together -- used when
+ * parsing multiblock alignment files, for
+ * example.
+ *
+ * Args: msa - multiple alignment structure
+ * tag - markup tag (e.g. "SS")
+ * sqidx - index of seq to assoc markup with (0..nseq-1)
+ * value - markup, one char per aligned column
+ *
+ * Returns: (void)
+ */
+void
+MSAAppendGR(MSA *msa, char *tag, int sqidx, char *value)
+{
+ int tagidx;
+ int i;
+
+ /* Is this an unparsed tag name that we recognize?
+ * If not, handle adding it to index, and reallocating
+ * as needed.
+ */
+ if (msa->gr_tag == NULL) /* first tag? init w/ malloc */
+ {
+ msa->gr_tag = MallocOrDie(sizeof(char *));
+ msa->gr = MallocOrDie(sizeof(char **));
+ msa->gr[0] = MallocOrDie(sizeof(char *) * msa->nseqalloc);
+ for (i = 0; i < msa->nseqalloc; i++)
+ msa->gr[0][i] = NULL;
+ msa->gr_idx = GKIInit();
+ tagidx = GKIStoreKey(msa->gr_idx, tag);
+ SQD_DASSERT1((tagidx == 0));
+ }
+ else
+ {
+ /* new tag? */
+ tagidx = GKIKeyIndex(msa->gr_idx, tag);
+ if (tagidx < 0) { /* it's a new tag name; realloc */
+ tagidx = GKIStoreKey(msa->gr_idx, tag);
+ /* since we alloc in blocks of 1,
+ we always realloc upon seeing
+ a new tag. */
+ SQD_DASSERT1((tagidx == msa->ngr));
+ msa->gr_tag = ReallocOrDie(msa->gr_tag, (msa->ngr+1) * sizeof(char *));
+ msa->gr = ReallocOrDie(msa->gr, (msa->ngr+1) * sizeof(char **));
+ msa->gr[msa->ngr] = MallocOrDie(sizeof(char *) * msa->nseqalloc);
+ for (i = 0; i < msa->nseqalloc; i++)
+ msa->gr[msa->ngr][i] = NULL;
+ }
+ }
+
+ if (tagidx == msa->ngr) {
+ msa->gr_tag[tagidx] = sre_strdup(tag, -1);
+ msa->ngr++;
+ }
+ sre_strcat(&(msa->gr[tagidx][sqidx]), -1, value, -1);
+ return;
+}
+
+
+/* Function: MSAVerifyParse()
+ * Date: SRE, Sat Jun 5 14:24:24 1999 [Madison, 1999 worm mtg]
+ *
+ * Purpose: Last function called after a multiple alignment is
+ * parsed. Checks that parse was successful; makes sure
+ * required information is present; makes sure required
+ * information is consistent. Some fields that are
+ * only use during parsing may be freed (sqlen, for
+ * example).
+ *
+ * Some fields in msa may be modified (msa->alen is set,
+ * for example).
+ *
+ * Args: msa - the multiple alignment
+ * sqname, aseq must be set
+ * nseq must be correct
+ * alen need not be set; will be set here.
+ * wgt will be set here if not already set
+ *
+ * Returns: (void)
+ * Will Die() here with diagnostics on error.
+ *
+ * Example:
+ */
+void
+MSAVerifyParse(MSA *msa)
+{
+ int idx;
+
+ if (msa->nseq == 0) Die("Parse error: no sequences were found for alignment %s",
+ msa->name != NULL ? msa->name : "");
+
+ msa->alen = msa->sqlen[0];
+
+ /* We can rely on msa->sqname[] being valid for any index,
+ * because of the way the line parsers always store any name
+ * they add to the index.
+ */
+ for (idx = 0; idx < msa->nseq; idx++)
+ {
+ /* aseq is required. */
+ if (msa->aseq[idx] == NULL)
+ Die("Parse error: No sequence for %s in alignment %s", msa->sqname[idx],
+ msa->name != NULL ? msa->name : "");
+ /* either all weights must be set, or none of them */
+ if ((msa->flags & MSA_SET_WGT) && msa->wgt[idx] == -1.0)
+ Die("Parse error: some weights are set, but %s doesn't have one in alignment %s",
+ msa->sqname[idx],
+ msa->name != NULL ? msa->name : "");
+ /* all aseq must be same length. */
+ if (msa->sqlen[idx] != msa->alen)
+ Die("Parse error: sequence %s: length %d, expected %d in alignment %s",
+ msa->sqname[idx], msa->sqlen[idx], msa->alen,
+ msa->name != NULL ? msa->name : "");
+ /* if SS is present, must have length right */
+ if (msa->ss != NULL && msa->ss[idx] != NULL && msa->sslen[idx] != msa->alen)
+ Die("Parse error: #=GR SS annotation for %s: length %d, expected %d in alignment %s",
+ msa->sqname[idx], msa->sslen[idx], msa->alen,
+ msa->name != NULL ? msa->name : "");
+ /* if SA is present, must have length right */
+ if (msa->sa != NULL && msa->sa[idx] != NULL && msa->salen[idx] != msa->alen)
+ Die("Parse error: #=GR SA annotation for %s: length %d, expected %d in alignment %s",
+ msa->sqname[idx], msa->salen[idx], msa->alen,
+ msa->name != NULL ? msa->name : "");
+ }
+
+ /* if cons SS is present, must have length right */
+ if (msa->ss_cons != NULL && strlen(msa->ss_cons) != msa->alen)
+ Die("Parse error: #=GC SS_cons annotation: length %d, expected %d in alignment %s",
+ strlen(msa->ss_cons), msa->alen,
+ msa->name != NULL ? msa->name : "");
+
+ /* if cons SA is present, must have length right */
+ if (msa->sa_cons != NULL && strlen(msa->sa_cons) != msa->alen)
+ Die("Parse error: #=GC SA_cons annotation: length %d, expected %d in alignment %s",
+ strlen(msa->sa_cons), msa->alen,
+ msa->name != NULL ? msa->name : "");
+
+ /* if RF is present, must have length right */
+ if (msa->rf != NULL && strlen(msa->rf) != msa->alen)
+ Die("Parse error: #=GC RF annotation: length %d, expected %d in alignment %s",
+ strlen(msa->rf), msa->alen,
+ msa->name != NULL ? msa->name : "");
+
+ /* Check that all or no weights are set */
+ if (!(msa->flags & MSA_SET_WGT))
+ FSet(msa->wgt, msa->nseq, 1.0); /* default weights */
+
+ /* Clean up a little from the parser */
+ if (msa->sqlen != NULL) { free(msa->sqlen); msa->sqlen = NULL; }
+ if (msa->sslen != NULL) { free(msa->sslen); msa->sslen = NULL; }
+ if (msa->salen != NULL) { free(msa->salen); msa->salen = NULL; }
+
+ return;
+}
+
+
+
+
+/* Function: MSAFileOpen()
+ * Date: SRE, Tue May 18 13:22:01 1999 [St. Louis]
+ *
+ * Purpose: Open an alignment database file and prepare
+ * for reading one alignment, or sequentially
+ * in the (rare) case of multiple MSA databases
+ * (e.g. Stockholm format).
+ *
+ * Args: filename - name of file to open
+ * if "-", read stdin
+ * if it ends in ".gz", read from pipe to gunzip -dc
+ * format - format of file (e.g. MSAFILE_STOCKHOLM)
+ * env - environment variable for path (e.g. BLASTDB)
+ *
+ * Returns: opened MSAFILE * on success.
+ * NULL on failure:
+ * usually, because the file doesn't exist;
+ * for gzip'ed files, may also mean that gzip isn't in the path.
+ */
+MSAFILE *
+MSAFileOpen(char *filename, int format, char *env)
+{
+ MSAFILE *afp;
+
+ afp = MallocOrDie(sizeof(MSAFILE));
+ if (strcmp(filename, "-") == 0)
+ {
+ afp->f = stdin;
+ afp->do_stdin = TRUE;
+ afp->do_gzip = FALSE;
+ afp->fname = sre_strdup("[STDIN]", -1);
+ afp->ssi = NULL; /* can't index stdin because we can't seek*/
+ }
+#ifndef SRE_STRICT_ANSI
+ /* popen(), pclose() aren't portable to non-POSIX systems; disable */
+ else if (Strparse("^.*\\.gz$", filename, 0))
+ {
+ char cmd[256];
+
+ /* Note that popen() will return "successfully"
+ * if file doesn't exist, because gzip works fine
+ * and prints an error! So we have to check for
+ * existence of file ourself.
+ */
+ if (! FileExists(filename))
+ Die("%s: file does not exist", filename);
+ if (strlen(filename) + strlen("gzip -dc ") >= 256)
+ Die("filename > 255 char in MSAFileOpen()");
+ sprintf(cmd, "gzip -dc %s", filename);
+ if ((afp->f = popen(cmd, "r")) == NULL)
+ return NULL;
+
+ afp->do_stdin = FALSE;
+ afp->do_gzip = TRUE;
+ afp->fname = sre_strdup(filename, -1);
+ /* we can't index a .gz file, because we can't seek in a pipe afaik */
+ afp->ssi = NULL;
+ }
+#endif /*SRE_STRICT_ANSI*/
+ else
+ {
+ char *ssifile;
+ char *dir;
+
+ /* When we open a file, it may be either in the current
+ * directory, or in the directory indicated by the env
+ * argument - and we have to construct the SSI filename accordingly.
+ */
+ if ((afp->f = fopen(filename, "r")) != NULL)
+ {
+ ssifile = MallocOrDie(sizeof(char) * (strlen(filename) + 5));
+ sprintf(ssifile, "%s.ssi", filename);
+ }
+ else if ((afp->f = EnvFileOpen(filename, env, &dir)) != NULL)
+ {
+ char *full;
+ full = FileConcat(dir, filename);
+ ssifile = MallocOrDie(sizeof(char) * (strlen(full) + strlen(filename) + 5));
+ sprintf(ssifile, "%s.ssi", full);
+ free(dir);
+ }
+ else return NULL;
+
+ afp->do_stdin = FALSE;
+ afp->do_gzip = FALSE;
+ afp->fname = sre_strdup(filename, -1);
+ afp->ssi = NULL;
+
+ /* Open the SSI index file. If it doesn't exist, or
+ * it's corrupt, or some error happens, afp->ssi stays NULL.
+ */
+ SSIOpen(ssifile, &(afp->ssi));
+ free(ssifile);
+ }
+
+ /* Invoke autodetection if we haven't already been told what
+ * to expect.
+ */
+ if (format == MSAFILE_UNKNOWN)
+ {
+ if (afp->do_stdin == TRUE || afp->do_gzip)
+ Die("Can't autodetect alignment file format from a stdin or gzip pipe");
+ format = MSAFileFormat(afp);
+ if (format == MSAFILE_UNKNOWN)
+ Die("Can't determine format of multiple alignment file %s", afp->fname);
+ }
+
+ afp->format = format;
+ afp->linenumber = 0;
+ afp->buf = NULL;
+ afp->buflen = 0;
+
+ return afp;
+}
+
+
+/* Function: MSAFilePositionByKey()
+ * MSAFilePositionByIndex()
+ * MSAFileRewind()
+ *
+ * Date: SRE, Tue Nov 9 19:02:54 1999 [St. Louis]
+ *
+ * Purpose: Family of functions for repositioning in
+ * open MSA files; analogous to a similarly
+ * named function series in HMMER's hmmio.c.
+ *
+ * Args: afp - open alignment file
+ * offset - disk offset in bytes
+ * key - key to look up in SSI indices
+ * idx - index of alignment.
+ *
+ * Returns: 0 on failure.
+ * 1 on success.
+ * If called on a non-fseek()'able file (e.g. a gzip'ed
+ * or pipe'd alignment), returns 0 as a failure flag.
+ */
+int
+MSAFileRewind(MSAFILE *afp)
+{
+ if (afp->do_gzip || afp->do_stdin) return 0;
+ rewind(afp->f);
+ return 1;
+}
+int
+MSAFilePositionByKey(MSAFILE *afp, char *key)
+{
+ int fh; /* filehandle is ignored */
+ SSIOFFSET offset; /* offset of the key alignment */
+
+ if (afp->ssi == NULL) return 0;
+ if (SSIGetOffsetByName(afp->ssi, key, &fh, &offset) != 0) return 0;
+ if (SSISetFilePosition(afp->f, &offset) != 0) return 0;
+ return 1;
+}
+int
+MSAFilePositionByIndex(MSAFILE *afp, int idx)
+{
+ int fh; /* filehandled is passed but ignored */
+ SSIOFFSET offset; /* disk offset of desired alignment */
+
+ if (afp->ssi == NULL) return 0;
+ if (SSIGetOffsetByNumber(afp->ssi, idx, &fh, &offset) != 0) return 0;
+ if (SSISetFilePosition(afp->f, &offset) != 0) return 0;
+ return 1;
+}
+
+
+/* Function: MSAFileRead()
+ * Date: SRE, Fri May 28 16:01:43 1999 [St. Louis]
+ *
+ * Purpose: Read the next msa from an open alignment file.
+ * This is a wrapper around format-specific calls.
+ *
+ * Args: afp - open alignment file
+ *
+ * Returns: next alignment, or NULL if out of alignments
+ */
+MSA *
+MSAFileRead(MSAFILE *afp)
+{
+ MSA *msa = NULL;
+
+ switch (afp->format) {
+ case MSAFILE_STOCKHOLM: msa = ReadStockholm(afp); break;
+ case MSAFILE_MSF: msa = ReadMSF(afp); break;
+ case MSAFILE_A2M: msa = ReadA2M(afp); break;
+ case MSAFILE_CLUSTAL: msa = ReadClustal(afp); break;
+ case MSAFILE_SELEX: msa = ReadSELEX(afp); break;
+ case MSAFILE_PHYLIP: msa = ReadPhylip(afp); break;
+ default:
+ Die("MSAFILE corrupted: bad format index");
+ }
+ return msa;
+}
+
+/* Function: MSAFileClose()
+ * Date: SRE, Tue May 18 14:05:28 1999 [St. Louis]
+ *
+ * Purpose: Close an open MSAFILE.
+ *
+ * Args: afp - ptr to an open MSAFILE.
+ *
+ * Returns: void
+ */
+void
+MSAFileClose(MSAFILE *afp)
+{
+#ifndef SRE_STRICT_ANSI /* gzip functionality only on POSIX systems */
+ if (afp->do_gzip) pclose(afp->f);
+#endif
+ if (! afp->do_stdin) fclose(afp->f);
+ if (afp->buf != NULL) free(afp->buf);
+ if (afp->ssi != NULL) SSIClose(afp->ssi);
+ if (afp->fname != NULL) free(afp->fname);
+ free(afp);
+}
+
+char *
+MSAFileGetLine(MSAFILE *afp)
+{
+ char *s;
+ if ((s = sre_fgets(&(afp->buf), &(afp->buflen), afp->f)) == NULL)
+ return NULL;
+ afp->linenumber++;
+ return afp->buf;
+}
+
+void
+MSAFileWrite(FILE *fp, MSA *msa, int outfmt, int do_oneline)
+{
+ switch (outfmt) {
+#ifdef CLUSTALO
+ case MSAFILE_A2M: WriteA2M(stdout, msa, 0); break;
+ case MSAFILE_VIENNA: WriteA2M(stdout, msa, 1); break;
+#else
+ case MSAFILE_A2M: WriteA2M(stdout, msa); break;
+#endif
+ case MSAFILE_CLUSTAL: WriteClustal(stdout, msa); break;
+ case MSAFILE_MSF: WriteMSF(stdout, msa); break;
+ case MSAFILE_PHYLIP: WritePhylip(stdout, msa); break;
+ case MSAFILE_SELEX: WriteSELEX(stdout, msa); break;
+ case MSAFILE_STOCKHOLM:
+ if (do_oneline) WriteStockholmOneBlock(stdout, msa);
+ else WriteStockholm(stdout, msa);
+ break;
+ default:
+ Die("can't write. no such alignment format %d\n", outfmt);
+ }
+}
+
+/* Function: MSAGetSeqidx()
+ * Date: SRE, Wed May 19 15:08:25 1999 [St. Louis]
+ *
+ * Purpose: From a sequence name, return seqidx appropriate
+ * for an MSA structure.
+ *
+ * 1) try to guess the index. (pass -1 if you can't guess)
+ * 2) Look up name in msa's hashtable.
+ * 3) If it's a new name, store in msa's hashtable;
+ * expand allocs as needed;
+ * save sqname.
+ *
+ * Args: msa - alignment object
+ * name - a sequence name
+ * guess - a guess at the right index, or -1 if no guess.
+ *
+ * Returns: seqidx
+ */
+int
+MSAGetSeqidx(MSA *msa, char *name, int guess)
+{
+ int seqidx;
+ /* can we guess? */
+ if (guess >= 0 && guess < msa->nseq && strcmp(name, msa->sqname[guess]) == 0)
+ return guess;
+ /* else, a lookup in the index */
+ if ((seqidx = GKIKeyIndex(msa->index, name)) >= 0)
+ return seqidx;
+ /* else, it's a new name */
+ seqidx = GKIStoreKey(msa->index, name);
+ if (seqidx >= msa->nseqalloc) MSAExpand(msa);
+
+ msa->sqname[seqidx] = sre_strdup(name, -1);
+ msa->nseq++;
+ return seqidx;
+}
+
+
+/* Function: MSAFromAINFO()
+ * Date: SRE, Mon Jun 14 11:22:24 1999 [St. Louis]
+ *
+ * Purpose: Convert the old aseq/ainfo alignment structure
+ * to new MSA structure. Enables more rapid conversion
+ * of codebase to the new world order.
+ *
+ * Args: aseq - [0..nseq-1][0..alen-1] alignment
+ * ainfo - old-style optional info
+ *
+ * Returns: MSA *
+ */
+MSA *
+MSAFromAINFO(char **aseq, AINFO *ainfo)
+{
+ MSA *msa;
+ int i, j;
+
+ msa = MSAAlloc(ainfo->nseq, ainfo->alen);
+ for (i = 0; i < ainfo->nseq; i++)
+ {
+ strcpy(msa->aseq[i], aseq[i]);
+ msa->wgt[i] = ainfo->wgt[i];
+ msa->sqname[i] = sre_strdup(ainfo->sqinfo[i].name, -1);
+ msa->sqlen[i] = msa->alen;
+ GKIStoreKey(msa->index, msa->sqname[i]);
+
+ if (ainfo->sqinfo[i].flags & SQINFO_ACC)
+ MSASetSeqAccession(msa, i, ainfo->sqinfo[i].acc);
+
+ if (ainfo->sqinfo[i].flags & SQINFO_DESC)
+ MSASetSeqDescription(msa, i, ainfo->sqinfo[i].desc);
+
+ if (ainfo->sqinfo[i].flags & SQINFO_SS) {
+ if (msa->ss == NULL) {
+ msa->ss = MallocOrDie(sizeof(char *) * msa->nseqalloc);
+ msa->sslen = MallocOrDie(sizeof(int) * msa->nseqalloc);
+ for (j = 0; j < msa->nseqalloc; j++) {
+ msa->ss[j] = NULL;
+ msa->sslen[j] = 0;
+ }
+ }
+ MakeAlignedString(msa->aseq[i], msa->alen, ainfo->sqinfo[i].ss, &(msa->ss[i]));
+ msa->sslen[i] = msa->alen;
+ }
+
+ if (ainfo->sqinfo[i].flags & SQINFO_SA) {
+ if (msa->sa == NULL) {
+ msa->sa = MallocOrDie(sizeof(char *) * msa->nseqalloc);
+ msa->salen = MallocOrDie(sizeof(int) * msa->nseqalloc);
+ for (j = 0; j < msa->nseqalloc; j++) {
+ msa->sa[j] = NULL;
+ msa->salen[j] = 0;
+ }
+ }
+ MakeAlignedString(msa->aseq[i], msa->alen, ainfo->sqinfo[i].sa, &(msa->sa[i]));
+ msa->salen[i] = msa->alen;
+ }
+ }
+ /* note that sre_strdup() returns NULL when passed NULL */
+ msa->name = sre_strdup(ainfo->name, -1);
+ msa->desc = sre_strdup(ainfo->desc, -1);
+ msa->acc = sre_strdup(ainfo->acc, -1);
+ msa->au = sre_strdup(ainfo->au, -1);
+ msa->ss_cons = sre_strdup(ainfo->cs, -1);
+ msa->rf = sre_strdup(ainfo->rf, -1);
+ if (ainfo->flags & AINFO_TC) {
+ msa->cutoff[MSA_CUTOFF_TC1] = ainfo->tc1; msa->cutoff_is_set[MSA_CUTOFF_TC1] = TRUE;
+ msa->cutoff[MSA_CUTOFF_TC2] = ainfo->tc2; msa->cutoff_is_set[MSA_CUTOFF_TC2] = TRUE;
+ }
+ if (ainfo->flags & AINFO_NC) {
+ msa->cutoff[MSA_CUTOFF_NC1] = ainfo->nc1; msa->cutoff_is_set[MSA_CUTOFF_NC1] = TRUE;
+ msa->cutoff[MSA_CUTOFF_NC2] = ainfo->nc2; msa->cutoff_is_set[MSA_CUTOFF_NC2] = TRUE;
+ }
+ if (ainfo->flags & AINFO_GA) {
+ msa->cutoff[MSA_CUTOFF_GA1] = ainfo->ga1; msa->cutoff_is_set[MSA_CUTOFF_GA1] = TRUE;
+ msa->cutoff[MSA_CUTOFF_GA2] = ainfo->ga2; msa->cutoff_is_set[MSA_CUTOFF_GA2] = TRUE;
+ }
+ msa->nseq = ainfo->nseq;
+ msa->alen = ainfo->alen;
+ return msa;
+}
+
+
+
+
+/* Function: MSAFileFormat()
+ * Date: SRE, Fri Jun 18 14:26:49 1999 [Sanger Centre]
+ *
+ * Purpose: (Attempt to) determine the format of an alignment file.
+ * Since it rewinds the file pointer when it's done,
+ * cannot be used on a pipe or gzip'ed file. Works by
+ * calling SeqfileFormat() from sqio.c, then making sure
+ * that the format is indeed an alignment. If the format
+ * comes back as FASTA, it assumes that the format as A2M
+ * (e.g. aligned FASTA).
+ *
+ * Args: fname - file to evaluate
+ *
+ * Returns: format code; e.g. MSAFILE_STOCKHOLM
+ */
+int
+MSAFileFormat(MSAFILE *afp)
+{
+ int fmt;
+
+ fmt = SeqfileFormat(afp->f);
+
+ if (fmt == SQFILE_FASTA) fmt = MSAFILE_A2M;
+
+ if (fmt != MSAFILE_UNKNOWN && ! IsAlignmentFormat(fmt))
+ Die("File %s does not appear to be an alignment file;\n\
+rather, it appears to be an unaligned file in %s format.\n\
+I'm expecting an alignment file in this context.\n",
+ afp->fname,
+ SeqfileFormat2String(fmt));
+ return fmt;
+}
+
+
+/* Function: MSAMingap()
+ * Date: SRE, Mon Jun 28 18:57:54 1999 [on jury duty, St. Louis Civil Court]
+ *
+ * Purpose: Remove all-gap columns from a multiple sequence alignment
+ * and its associated per-residue data.
+ *
+ * Args: msa - the alignment
+ *
+ * Returns: (void)
+ */
+void
+MSAMingap(MSA *msa)
+{
+ int *useme; /* array of TRUE/FALSE flags for which columns to keep */
+ int apos; /* position in original alignment */
+ int idx; /* sequence index */
+
+ useme = MallocOrDie(sizeof(int) * msa->alen);
+ for (apos = 0; apos < msa->alen; apos++)
+ {
+ for (idx = 0; idx < msa->nseq; idx++)
+ if (! isgap(msa->aseq[idx][apos]))
+ break;
+ if (idx == msa->nseq) useme[apos] = FALSE; else useme[apos] = TRUE;
+ }
+ MSAShorterAlignment(msa, useme);
+ free(useme);
+ return;
+}
+
+/* Function: MSANogap()
+ * Date: SRE, Wed Nov 17 09:59:51 1999 [St. Louis]
+ *
+ * Purpose: Remove all columns from a multiple sequence alignment that
+ * contain any gaps -- used for filtering before phylogenetic
+ * analysis.
+ *
+ * Args: msa - the alignment
+ *
+ * Returns: (void). The alignment is modified, so if you want to keep
+ * the original for something, make a copy.
+ */
+void
+MSANogap(MSA *msa)
+{
+ int *useme; /* array of TRUE/FALSE flags for which columns to keep */
+ int apos; /* position in original alignment */
+ int idx; /* sequence index */
+
+ useme = MallocOrDie(sizeof(int) * msa->alen);
+ for (apos = 0; apos < msa->alen; apos++)
+ {
+ for (idx = 0; idx < msa->nseq; idx++)
+ if (isgap(msa->aseq[idx][apos]))
+ break;
+ if (idx == msa->nseq) useme[apos] = TRUE; else useme[apos] = FALSE;
+ }
+ MSAShorterAlignment(msa, useme);
+ free(useme);
+ return;
+}
+
+
+/* Function: MSAShorterAlignment()
+ * Date: SRE, Wed Nov 17 09:49:32 1999 [St. Louis]
+ *
+ * Purpose: Given an array "useme" (0..alen-1) of TRUE/FALSE flags,
+ * where TRUE means "keep this column in the new alignment":
+ * Remove all columns annotated as "FALSE" in the useme
+ * array.
+ *
+ * Args: msa - the alignment. The alignment is changed, so
+ * if you don't want the original screwed up, make
+ * a copy of it first.
+ * useme - TRUE/FALSE flags for columns to keep: 0..alen-1
+ *
+ * Returns: (void)
+ */
+void
+MSAShorterAlignment(MSA *msa, int *useme)
+{
+ int apos; /* position in original alignment */
+ int mpos; /* position in new alignment */
+ int idx; /* sequence index */
+ int i; /* markup index */
+
+ /* Since we're minimizing, we can overwrite, using already allocated
+ * memory.
+ */
+ for (apos = 0, mpos = 0; apos < msa->alen; apos++)
+ {
+ if (useme[apos] == FALSE) continue;
+
+ /* shift alignment and associated per-column+per-residue markup */
+ if (mpos != apos)
+ {
+ for (idx = 0; idx < msa->nseq; idx++)
+ {
+ msa->aseq[idx][mpos] = msa->aseq[idx][apos];
+ if (msa->ss != NULL && msa->ss[idx] != NULL) msa->ss[idx][mpos] = msa->ss[idx][apos];
+ if (msa->sa != NULL && msa->sa[idx] != NULL) msa->sa[idx][mpos] = msa->sa[idx][apos];
+
+ for (i = 0; i < msa->ngr; i++)
+ if (msa->gr[i][idx] != NULL) msa->gr[i][idx][mpos] = msa->gr[i][idx][apos];
+ }
+
+ if (msa->ss_cons != NULL) msa->ss_cons[mpos] = msa->ss_cons[apos];
+ if (msa->sa_cons != NULL) msa->sa_cons[mpos] = msa->sa_cons[apos];
+ if (msa->rf != NULL) msa->rf[mpos] = msa->rf[apos];
+
+ for (i = 0; i < msa->ngc; i++)
+ msa->gc[i][mpos] = msa->gc[i][apos];
+ }
+ mpos++;
+ }
+
+ msa->alen = mpos; /* set new length */
+ /* null terminate everything */
+ for (idx = 0; idx < msa->nseq; idx++)
+ {
+ msa->aseq[idx][mpos] = '\0';
+ if (msa->ss != NULL && msa->ss[idx] != NULL) msa->ss[idx][mpos] = '\0';
+ if (msa->sa != NULL && msa->sa[idx] != NULL) msa->sa[idx][mpos] = '\0';
+
+ for (i = 0; i < msa->ngr; i++)
+ if (msa->gr[i][idx] != NULL) msa->gr[i][idx][mpos] = '\0';
+ }
+
+ if (msa->ss_cons != NULL) msa->ss_cons[mpos] = '\0';
+ if (msa->sa_cons != NULL) msa->sa_cons[mpos] = '\0';
+ if (msa->rf != NULL) msa->rf[mpos] = '\0';
+
+ for (i = 0; i < msa->ngc; i++)
+ msa->gc[i][mpos] = '\0';
+
+ return;
+}
+
+
+/* Function: MSASmallerAlignment()
+ * Date: SRE, Wed Jun 30 09:56:08 1999 [St. Louis]
+ *
+ * Purpose: Given an array "useme" of TRUE/FALSE flags for
+ * each sequence in an alignment, construct
+ * and return a new alignment containing only
+ * those sequences that are flagged useme=TRUE.
+ *
+ * Used by routines such as MSAFilterAlignment()
+ * and MSASampleAlignment().
+ *
+ * Limitations:
+ * Does not copy unparsed Stockholm markup.
+ *
+ * Does not make assumptions about meaning of wgt;
+ * if you want the new wgt vector renormalized, do
+ * it yourself with FNorm(new->wgt, new->nseq).
+ *
+ * Args: msa -- the original (larger) alignment
+ * useme -- [0..nseq-1] array of TRUE/FALSE flags; TRUE means include
+ * this seq in new alignment
+ * ret_new -- RETURN: new alignment
+ *
+ * Returns: void
+ * ret_new is allocated here; free with MSAFree()
+ */
+void
+MSASmallerAlignment(MSA *msa, int *useme, MSA **ret_new)
+{
+ MSA *new; /* RETURN: new alignment */
+ int nnew; /* number of seqs in new msa (e.g. # of TRUEs) */
+ int oidx, nidx; /* old, new indices */
+ int i;
+
+ nnew = 0;
+ for (oidx = 0; oidx < msa->nseq; oidx++)
+ if (useme[oidx]) nnew++;
+ if (nnew == 0) { *ret_new = NULL; return; }
+
+ new = MSAAlloc(nnew, 0);
+ nidx = 0;
+ for (oidx = 0; oidx < msa->nseq; oidx++)
+ if (useme[oidx])
+ {
+ new->aseq[nidx] = sre_strdup(msa->aseq[oidx], msa->alen);
+ new->sqname[nidx] = sre_strdup(msa->sqname[oidx], msa->alen);
+ GKIStoreKey(new->index, msa->sqname[oidx]);
+ new->wgt[nidx] = msa->wgt[oidx];
+ if (msa->sqacc != NULL)
+ MSASetSeqAccession(new, nidx, msa->sqacc[oidx]);
+ if (msa->sqdesc != NULL)
+ MSASetSeqDescription(new, nidx, msa->sqdesc[oidx]);
+ if (msa->ss != NULL && msa->ss[oidx] != NULL)
+ {
+ if (new->ss == NULL) new->ss = MallocOrDie(sizeof(char *) * new->nseq);
+ new->ss[nidx] = sre_strdup(msa->ss[oidx], -1);
+ }
+ if (msa->sa != NULL && msa->sa[oidx] != NULL)
+ {
+ if (new->sa == NULL) new->sa = MallocOrDie(sizeof(char *) * new->nseq);
+ new->sa[nidx] = sre_strdup(msa->sa[oidx], -1);
+ }
+ nidx++;
+ }
+
+ new->nseq = nnew;
+ new->alen = msa->alen;
+ new->flags = msa->flags;
+ new->type = msa->type;
+ new->name = sre_strdup(msa->name, -1);
+ new->desc = sre_strdup(msa->desc, -1);
+ new->acc = sre_strdup(msa->acc, -1);
+ new->au = sre_strdup(msa->au, -1);
+ new->ss_cons = sre_strdup(msa->ss_cons, -1);
+ new->sa_cons = sre_strdup(msa->sa_cons, -1);
+ new->rf = sre_strdup(msa->rf, -1);
+ for (i = 0; i < MSA_MAXCUTOFFS; i++) {
+ new->cutoff[i] = msa->cutoff[i];
+ new->cutoff_is_set[i] = msa->cutoff_is_set[i];
+ }
+ free(new->sqlen);
+
+ MSAMingap(new);
+ *ret_new = new;
+ return;
+}
+
+
+/*****************************************************************
+ * Retrieval routines
+ *
+ * Access to MSA structure data is possible through these routines.
+ * I'm not doing this because of object oriented design, though
+ * it might work in my favor someday.
+ * I'm doing this because lots of MSA data is optional, and
+ * checking through the chain of possible NULLs is a pain.
+ *****************************************************************/
+
+char *
+MSAGetSeqAccession(MSA *msa, int idx)
+{
+ if (msa->sqacc != NULL && msa->sqacc[idx] != NULL)
+ return msa->sqacc[idx];
+ else
+ return NULL;
+}
+char *
+MSAGetSeqDescription(MSA *msa, int idx)
+{
+ if (msa->sqdesc != NULL && msa->sqdesc[idx] != NULL)
+ return msa->sqdesc[idx];
+ else
+ return NULL;
+}
+char *
+MSAGetSeqSS(MSA *msa, int idx)
+{
+ if (msa->ss != NULL && msa->ss[idx] != NULL)
+ return msa->ss[idx];
+ else
+ return NULL;
+}
+char *
+MSAGetSeqSA(MSA *msa, int idx)
+{
+ if (msa->sa != NULL && msa->sa[idx] != NULL)
+ return msa->sa[idx];
+ else
+ return NULL;
+}
+
+
+/*****************************************************************
+ * Information routines
+ *
+ * Access information about the MSA.
+ *****************************************************************/
+
+/* Function: MSAAverageSequenceLength()
+ * Date: SRE, Sat Apr 6 09:41:34 2002 [St. Louis]
+ *
+ * Purpose: Return the average length of the (unaligned) sequences
+ * in the MSA.
+ *
+ * Args: msa - the alignment
+ *
+ * Returns: average length
+ */
+float
+MSAAverageSequenceLength(MSA *msa)
+{
+ int i;
+ float avg;
+
+ avg = 0.;
+ for (i = 0; i < msa->nseq; i++)
+ avg += (float) DealignedLength(msa->aseq[i]);
+
+ if (msa->nseq == 0) return 0.;
+ else return (avg / msa->nseq);
+}
+
+
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+#ifndef SQUID_MSA_INCLUDED
+#define SQUID_MSA_INCLUDED
+
+/* msa.h
+ * SRE, Mon May 17 10:24:30 1999
+ *
+ * Header file for SQUID's multiple sequence alignment
+ * manipulation code.
+ *
+ * RCS $Id: msa.h 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: msa.h,v 1.12 2002/10/12 04:40:35 eddy Exp)
+ */
+
+#include <stdio.h> /* FILE support */
+#include "gki.h" /* hash table support */
+#include "ssi.h" /* sequence file index support */
+#include "squid.h" /* need SQINFO */
+
+/****************************************************
+ * Obsolete alignment information, AINFO
+ * Superceded by MSA structure further below; but we
+ * need AINFO for the near future for backwards
+ * compatibility.
+ ****************************************************/
+/* Structure: aliinfo_s
+ *
+ * Purpose: Optional information returned from an alignment file.
+ *
+ * flags: always used. Flags for which info is valid/alloced.
+ *
+ * alen: mandatory. Alignments are always flushed right
+ * with gaps so that all aseqs are the same length, alen.
+ * Available for all alignment formats.
+ *
+ * nseq: mandatory. Aligned seqs are indexed 0..nseq-1.
+ *
+ * wgt: 0..nseq-1 vector of sequence weights. Mandatory.
+ * If not explicitly set, weights are initialized to 1.0.
+ *
+ * cs: 0..alen-1, just like the alignment. Contains single-letter
+ * secondary structure codes for consensus structure; "<>^+"
+ * for RNA, "EHL." for protein. May be NULL if unavailable
+ * from seqfile. Only available for SELEX format files.
+ *
+ * rf: 0..alen-1, just like the alignment. rf is an arbitrary string
+ * of characters, used for annotating columns. Blanks are
+ * interpreted as non-canonical columns and anything else is
+ * considered canonical. Only available from SELEX files.
+ *
+ * sqinfo: mandatory. Array of 0..nseq-1
+ * per-sequence information structures, carrying
+ * name, id, accession, coords.
+ *
+ */
+struct aliinfo_s {
+ int flags; /* flags for what info is valid */
+ int alen; /* length of alignment (columns) */
+ int nseq; /* number of seqs in alignment */
+ float *wgt; /* sequence weights [0..nseq-1] */
+ char *cs; /* consensus secondary structure string */
+ char *rf; /* reference coordinate system */
+ struct seqinfo_s *sqinfo; /* name, id, coord info for each sequence */
+
+ /* Pfam/HMMER pick-ups */
+ char *name; /* name of alignment */
+ char *desc; /* description of alignment */
+ char *acc; /* accession of alignment */
+ char *au; /* "author" information */
+ float tc1, tc2; /* trusted score cutoffs (per-seq, per-domain) */
+ float nc1, nc2; /* noise score cutoffs (per-seq, per-domain) */
+ float ga1, ga2; /* gathering cutoffs */
+};
+typedef struct aliinfo_s AINFO;
+#define AINFO_TC (1 << 0)
+#define AINFO_NC (1 << 1)
+#define AINFO_GA (1 << 2)
+
+/*****************************************************************
+ * MSA
+ * SRE, Sun Jun 27 15:03:35 1999 [TW 723 over Greenland]
+ *
+ * Defines the new data structure and API for multiple
+ * sequence alignment i/o.
+ *****************************************************************/
+
+/* The following constants define the Pfam/Rfam cutoff set we'll propagate
+ * from msa's into HMMER and Infernal models.
+ */
+#define MSA_CUTOFF_TC1 0
+#define MSA_CUTOFF_TC2 1
+#define MSA_CUTOFF_GA1 2
+#define MSA_CUTOFF_GA2 3
+#define MSA_CUTOFF_NC1 4
+#define MSA_CUTOFF_NC2 5
+#define MSA_MAXCUTOFFS 6
+
+/* Structure: MSA
+ * SRE, Tue May 18 11:33:08 1999
+ *
+ * Our object for a multiple sequence alignment.
+ */
+typedef struct msa_struct {
+ /* Mandatory information associated with the alignment.
+ */
+ char **aseq; /* the alignment itself, [0..nseq-1][0..alen-1] */
+ char **sqname; /* names of sequences, [0..nseq-1][0..alen-1] */
+ float *wgt; /* sequence weights [0..nseq-1] */
+ int alen; /* length of alignment (columns) */
+ int nseq; /* number of seqs in alignment */
+
+ /* Optional information that we understand, and might have.
+ */
+ int flags; /* flags for what optional info is valid */
+ int type; /* kOtherSeq, kRNA/hmmNUCLEIC, or kAmino/hmmAMINO */
+ char *name; /* name of alignment, or NULL */
+ char *desc; /* description of alignment, or NULL */
+ char *acc; /* accession of alignment, or NULL */
+ char *au; /* "author" information, or NULL */
+ char *ss_cons; /* consensus secondary structure string, or NULL */
+ char *sa_cons; /* consensus surface accessibility string, or NULL */
+ char *rf; /* reference coordinate system, or NULL */
+ char **sqacc; /* accession numbers for individual sequences */
+ char **sqdesc; /* description lines for individual sequences */
+ char **ss; /* per-seq secondary structure annotation, or NULL */
+ char **sa; /* per-seq surface accessibility annotation, or NULL */
+ float cutoff[MSA_MAXCUTOFFS]; /* NC, TC, GA cutoffs propagated to Pfam/Rfam */
+ int cutoff_is_set[MSA_MAXCUTOFFS];/* TRUE if a cutoff is set; else FALSE */
+
+ /* Optional information that we don't understand.
+ * That is, we know what type of information it is, but it's
+ * either (interpreted as) free-text comment, or it's Stockholm
+ * markup with unfamiliar tags.
+ */
+ char **comment; /* free text comments, or NULL */
+ int ncomment; /* number of comment lines */
+ int alloc_ncomment; /* number of comment lines alloc'ed */
+
+ char **gf_tag; /* markup tags for unparsed #=GF lines */
+ char **gf; /* annotations for unparsed #=GF lines */
+ int ngf; /* number of unparsed #=GF lines */
+ int alloc_ngf; /* number of gf lines alloc'ed */
+
+ char **gs_tag; /* markup tags for unparsed #=GS lines */
+ char ***gs; /* [0..ngs-1][0..nseq-1][free text] markup */
+ GKI *gs_idx; /* hash of #=GS tag types */
+ int ngs; /* number of #=GS tag types */
+
+ char **gc_tag; /* markup tags for unparsed #=GC lines */
+ char **gc; /* [0..ngc-1][0..alen-1] markup */
+ GKI *gc_idx; /* hash of #=GC tag types */
+ int ngc; /* number of #=GC tag types */
+
+ char **gr_tag; /* markup tags for unparsed #=GR lines */
+ char ***gr; /* [0..ngr][0..nseq-1][0..alen-1] markup */
+ GKI *gr_idx; /* hash of #=GR tag types */
+ int ngr; /* number of #=GR tag types */
+
+ /* Stuff we need for our own maintenance of the data structure
+ */
+ GKI *index; /* name ->seqidx hash table */
+ int nseqalloc; /* number of seqs currently allocated for */
+ int nseqlump; /* lump size for dynamic expansions of nseq */
+ int *sqlen; /* individual sequence lengths during parsing */
+ int *sslen; /* individual ss lengths during parsing */
+ int *salen; /* individual sa lengths during parsing */
+ int lastidx; /* last index we saw; use for guessing next */
+} MSA;
+#define MSA_SET_WGT (1 << 0) /* track whether wgts were set, or left at default 1.0 */
+
+
+/* Structure: MSAFILE
+ * SRE, Tue May 18 11:36:54 1999
+ *
+ * Defines an alignment file that's open for reading.
+ */
+typedef struct msafile_struct {
+ FILE *f; /* open file pointer */
+ char *fname; /* name of file. used for diagnostic output */
+ int linenumber; /* what line are we on in the file */
+
+ char *buf; /* buffer for line input w/ sre_fgets() */
+ int buflen; /* current allocated length for buf */
+
+ SSIFILE *ssi; /* open SSI index file; or NULL, if none. */
+
+ int do_gzip; /* TRUE if f is a pipe from gzip -dc (need pclose(f)) */
+ int do_stdin; /* TRUE if f is stdin (don't close f, not our problem) */
+ int format; /* format of alignment file we're reading */
+} MSAFILE;
+
+
+/* Alignment file formats.
+ * Must coexist with sqio.c/squid.h unaligned file format codes.
+ * Rules:
+ * - 0 is an unknown/unassigned format
+ * - <100 reserved for unaligned formats
+ * - >100 reserved for aligned formats
+ */
+#define MSAFILE_UNKNOWN 0 /* unknown format */
+#define MSAFILE_STOCKHOLM 101 /* Pfam/HMMER's Stockholm format */
+#define MSAFILE_SELEX 102 /* Obsolete(!): old HMMER/SELEX format */
+#define MSAFILE_MSF 103 /* GCG MSF format */
+#define MSAFILE_CLUSTAL 104 /* Clustal V/W format */
+#define MSAFILE_A2M 105 /* aligned FASTA (A2M is UCSC terminology) */
+#define MSAFILE_PHYLIP 106 /* Felsenstein's PHYLIP format */
+#define MSAFILE_EPS 107 /* Encapsulated PostScript (output only) */
+#ifdef CLUSTALO
+#define MSAFILE_VIENNA 108 /* Vienna: concatenated fasta */
+#endif
+
+#define IsAlignmentFormat(fmt) ((fmt) > 100)
+
+
+/* from msa.c
+ */
+extern MSAFILE *MSAFileOpen(char *filename, int format, char *env);
+extern MSA *MSAFileRead(MSAFILE *afp);
+extern void MSAFileClose(MSAFILE *afp);
+extern void MSAFree(MSA *msa);
+extern void MSAFileWrite(FILE *fp, MSA *msa, int outfmt, int do_oneline);
+
+extern int MSAFileRewind(MSAFILE *afp);
+extern int MSAFilePositionByKey(MSAFILE *afp, char *key);
+extern int MSAFilePositionByIndex(MSAFILE *afp, int idx);
+
+extern int MSAFileFormat(MSAFILE *afp);
+extern MSA *MSAAlloc(int nseq, int alen);
+extern void MSAExpand(MSA *msa);
+extern char *MSAFileGetLine(MSAFILE *afp);
+extern void MSASetSeqAccession(MSA *msa, int seqidx, char *acc);
+extern void MSASetSeqDescription(MSA *msa, int seqidx, char *desc);
+extern void MSAAddComment(MSA *msa, char *s);
+extern void MSAAddGF(MSA *msa, char *tag, char *value);
+extern void MSAAddGS(MSA *msa, char *tag, int seqidx, char *value);
+extern void MSAAppendGC(MSA *msa, char *tag, char *value);
+extern char *MSAGetGC(MSA *msa, char *tag);
+extern void MSAAppendGR(MSA *msa, char *tag, int seqidx, char *value);
+extern void MSAVerifyParse(MSA *msa);
+extern int MSAGetSeqidx(MSA *msa, char *name, int guess);
+
+extern MSA *MSAFromAINFO(char **aseq, AINFO *ainfo);
+
+extern void MSAMingap(MSA *msa);
+extern void MSANogap(MSA *msa);
+extern void MSAShorterAlignment(MSA *msa, int *useme);
+extern void MSASmallerAlignment(MSA *msa, int *useme, MSA **ret_new);
+
+extern char *MSAGetSeqAccession(MSA *msa, int idx);
+extern char *MSAGetSeqDescription(MSA *msa, int idx);
+extern char *MSAGetSeqSS(MSA *msa, int idx);
+extern char *MSAGetSeqSA(MSA *msa, int idx);
+
+extern float MSAAverageSequenceLength(MSA *msa);
+
+/* from a2m.c
+ */
+extern MSA *ReadA2M(MSAFILE *afp);
+#ifdef CLUSTALO
+extern void WriteA2M(FILE *fp, MSA *msa, int vienna);
+#else
+extern void WriteA2M(FILE *fp, MSA *msa);
+#endif
+/* from clustal.c
+ */
+extern MSA *ReadClustal(MSAFILE *afp);
+extern void WriteClustal(FILE *fp, MSA *msa);
+
+/* from eps.c
+ */
+extern void EPSWriteSmallMSA(FILE *fp, MSA *msa);
+
+/* from msf.c
+ */
+extern MSA *ReadMSF(MSAFILE *afp);
+extern void WriteMSF(FILE *fp, MSA *msa);
+
+/* from phylip.c
+ */
+extern MSA *ReadPhylip(MSAFILE *afp);
+extern void WritePhylip(FILE *fp, MSA *msa);
+
+/* from selex.c
+ */
+extern MSA *ReadSELEX(MSAFILE *afp);
+extern void WriteSELEX(FILE *fp, MSA *msa);
+extern void WriteSELEXOneBlock(FILE *fp, MSA *msa);
+
+/* from stockholm.c
+ */
+extern MSA *ReadStockholm(MSAFILE *afp);
+extern void WriteStockholm(FILE *fp, MSA *msa);
+extern void WriteStockholmOneBlock(FILE *fp, MSA *msa);
+
+#endif /*SQUID_MSA_INCLUDED*/
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* msf.c
+ * SRE, Sun Jul 11 16:17:32 1993
+ *
+ * Import/export of GCG MSF multiple sequence alignment
+ * formatted files. Designed using format specifications
+ * kindly provided by Steve Smith of Genetics Computer Group.
+ *
+ * RCS $Id: msf.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: msf.c,v 1.4 2001/04/23 00:35:33 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+#include <time.h>
+#include "squid.h"
+#include "msa.h"
+
+#ifdef TESTDRIVE_MSF
+/*****************************************************************
+ * msf.c test driver:
+ * cc -DTESTDRIVE_MSF -g -O2 -Wall -o test msf.c msa.c gki.c sqerror.c sre_string.c file.c hsregex.c sre_math.c sre_ctype.c sqio.c alignio.c selex.c interleaved.c types.c -lm
+ *
+ */
+int
+main(int argc, char **argv)
+{
+ MSAFILE *afp;
+ MSA *msa;
+ char *file;
+
+ file = argv[1];
+
+ if ((afp = MSAFileOpen(file, MSAFILE_STOCKHOLM, NULL)) == NULL)
+ Die("Couldn't open %s\n", file);
+
+ while ((msa = ReadMSF(afp)) != NULL)
+ {
+ WriteMSF(stdout, msa);
+ MSAFree(msa);
+ }
+
+ MSAFileClose(afp);
+ exit(0);
+}
+/******************************************************************/
+#endif /* testdrive_msf */
+
+
+
+/* Function: ReadMSF()
+ * Date: SRE, Tue Jun 1 08:07:22 1999 [St. Louis]
+ *
+ * Purpose: Parse an alignment read from an open MSF format
+ * alignment file. (MSF is a single-alignment format.)
+ * Return the alignment, or NULL if we've already
+ * read the alignment.
+ *
+ * Args: afp - open alignment file
+ *
+ * Returns: MSA * - an alignment object
+ * caller responsible for an MSAFree()
+ * NULL if no more alignments
+ *
+ * Diagnostics:
+ * Will Die() here with a (potentially) useful message
+ * if a parsing error occurs.
+ */
+MSA *
+ReadMSF(MSAFILE *afp)
+{
+ MSA *msa;
+ char *s;
+ int alleged_alen;
+ int alleged_type;
+ int alleged_checksum;
+ char *tok;
+ char *sp;
+ int slen;
+ int sqidx;
+ char *name;
+ char *seq;
+
+ if (feof(afp->f)) return NULL;
+ if ((s = MSAFileGetLine(afp)) == NULL) return NULL;
+
+ /* The first line is the header.
+ * This is a new-ish GCG feature. Don't count on it, so
+ * we can be a bit more tolerant towards non-GCG software
+ * generating "MSF" files.
+ */
+ msa = MSAAlloc(10, 0);
+ if (strncmp(s, "!!AA_MULTIPLE_ALIGNMENT", 23) == 0) {
+ msa->type = kAmino;
+ if ((s = MSAFileGetLine(afp)) == NULL) return NULL;
+ } else if (strncmp(s, "!!NA_MULTIPLE_ALIGNMENT", 23) == 0) {
+ msa->type = kRNA;
+ if ((s = MSAFileGetLine(afp)) == NULL) return NULL;
+ }
+
+ /* Now we're in the free text comment section of the MSF file.
+ * It ends when we see the "MSF: Type: Check: .." line.
+ * This line must be present.
+ */
+ do
+ {
+ if ((strstr(s, "..") != NULL && strstr(s, "MSF:") != NULL) &&
+ Strparse("^.+MSF: +([0-9]+) +Type: +([PNX]).+Check: +([0-9]+) +\\.\\.", s, 3))
+ {
+ alleged_alen = atoi(sqd_parse[0]);
+ switch (*(sqd_parse[1])) {
+ case 'N' : alleged_type = kRNA; break;
+ case 'P' : alleged_type = kAmino; break;
+ case 'X' : alleged_type = kOtherSeq; break;
+ default : alleged_type = kOtherSeq;
+ }
+ alleged_checksum = atoi(sqd_parse[3]);
+ if (msa->type == kOtherSeq) msa->type = alleged_type;
+ break; /* we're done with comment section. */
+ }
+ if (! IsBlankline(s))
+ MSAAddComment(msa, s);
+ } while ((s = MSAFileGetLine(afp)) != NULL);
+
+ /* Now we're in the name section.
+ * GCG has a relatively poorly documented feature: only sequences that
+ * appear in this list will be read from the alignment section. Commenting
+ * out sequences in the name list (by preceding them with "!") is
+ * allowed as a means of manually defining subsets of sequences in
+ * the alignment section. We can support this feature reasonably
+ * easily because of the hash table for names in the MSA: we
+ * only add names to the hash table when we see 'em in the name section.
+ */
+ while ((s = MSAFileGetLine(afp)) != NULL)
+ {
+ while ((*s == ' ' || *s == '\t') && *s) s++; /* skip leading whitespace */
+
+ if (*s == '\n') continue; /* skip blank lines */
+ else if (*s == '!') MSAAddComment(msa, s);
+ else if ((sp = strstr(s, "Name:")) != NULL)
+ {
+ /* We take the name and the weigh, and that's it */
+ sp += 5;
+ tok = sre_strtok(&sp, " \t", &slen); /* <sequence name> */
+ sqidx = GKIStoreKey(msa->index, tok);
+ if (sqidx >= msa->nseqalloc) MSAExpand(msa);
+ msa->sqname[sqidx] = sre_strdup(tok, slen);
+ msa->nseq++;
+
+ if ((sp = strstr(sp, "Weight:")) == NULL)
+ Die("No Weight: on line %d for %s in name section of MSF file %s\n",
+ afp->linenumber, msa->sqname[sqidx], afp->fname);
+ sp += 7;
+ tok = sre_strtok(&sp, " \t", &slen);
+ msa->wgt[sqidx] = atof(tok);
+ msa->flags |= MSA_SET_WGT;
+ }
+ else if (strncmp(s, "//", 2) == 0)
+ break;
+ else
+ {
+ Die("Invalid line (probably %d) in name section of MSF file %s:\n%s\n",
+ afp->linenumber, afp->fname, s);
+ squid_errno = SQERR_FORMAT; /* NOT THREADSAFE */
+ return NULL;
+ }
+
+ }
+
+ /* And now we're in the sequence section.
+ * As discussed above, if we haven't seen a sequence name, then we
+ * don't include the sequence in the alignment.
+ * Also, watch out for coordinate-only lines.
+ */
+ while ((s = MSAFileGetLine(afp)) != NULL)
+ {
+ sp = s;
+ if ((name = sre_strtok(&sp, " \t", NULL)) == NULL) continue;
+ if ((seq = sre_strtok(&sp, "\n", &slen)) == NULL) continue;
+
+ /* The test for a coord line: digits starting both fields
+ */
+ if (isdigit(*name) && isdigit(*seq))
+ continue;
+
+ /* It's not blank, and it's not a coord line: must be sequence
+ */
+ sqidx = GKIKeyIndex(msa->index, name);
+ if (sqidx < 0) continue; /* not a sequence we recognize */
+
+ msa->sqlen[sqidx] = sre_strcat(&(msa->aseq[sqidx]), msa->sqlen[sqidx], seq, slen);
+ }
+
+ /* We've left blanks in the aseqs; take them back out.
+ */
+ for (sqidx = 0; sqidx < msa->nseq; sqidx++)
+ {
+ if (msa->aseq[sqidx] == NULL)
+ Die("Didn't find a sequence for %s in MSF file %s\n", msa->sqname[sqidx], afp->fname);
+
+ for (s = sp = msa->aseq[sqidx]; *s != '\0'; s++)
+ {
+ if (*s == ' ' || *s == '\t') {
+ msa->sqlen[sqidx]--;
+ } else {
+ *sp = *s;
+ sp++;
+ }
+ }
+ *sp = '\0';
+ }
+
+ MSAVerifyParse(msa); /* verifies, and also sets alen and wgt. */
+ return msa;
+}
+
+
+/* Function: WriteMSF()
+ * Date: SRE, Mon May 31 11:25:18 1999 [St. Louis]
+ *
+ * Purpose: Write an alignment in MSF format to an open file.
+ *
+ * Args: fp - file that's open for writing.
+ * msa - alignment to write.
+ *
+ * Note that msa->type, usually optional, must be
+ * set for WriteMSF to work. If it isn't, a fatal
+ * error is generated.
+ *
+ * Returns: (void)
+ */
+void
+WriteMSF(FILE *fp, MSA *msa)
+{
+ time_t now; /* current time as a time_t */
+ char date[64]; /* today's date in GCG's format "October 3, 1996 15:57" */
+ char **gcg_aseq; /* aligned sequences with gaps converted to GCG format */
+ char **gcg_sqname; /* sequence names with GCG-valid character sets */
+ int idx; /* counter for sequences */
+ char *s; /* pointer into sqname or seq */
+ int len; /* tmp variable for name lengths */
+ int namelen; /* maximum name length used */
+ int pos; /* position counter */
+ char buffer[51]; /* buffer for writing seq */
+ int i; /* another position counter */
+
+ /*****************************************************************
+ * Make copies of sequence names and sequences.
+ * GCG recommends that name characters should only contain
+ * alphanumeric characters, -, or _
+ * Some GCG and GCG-compatible software is sensitive to this.
+ * We silently convert all other characters to '_'.
+ *
+ * For sequences, GCG allows only ~ and . for gaps.
+ * Otherwise, everthing is interpreted as a residue;
+ * so squid's IUPAC-restricted chars are fine. ~ means
+ * an external gap. . means an internal gap.
+ *****************************************************************/
+
+ /* make copies that we can edit */
+ gcg_aseq = MallocOrDie(sizeof(char *) * msa->nseq);
+ gcg_sqname = MallocOrDie(sizeof(char *) * msa->nseq);
+ for (idx = 0; idx < msa->nseq; idx++)
+ {
+ gcg_aseq[idx] = sre_strdup(msa->aseq[idx], msa->alen);
+ gcg_sqname[idx] = sre_strdup(msa->sqname[idx], -1);
+ }
+ /* alter names as needed */
+ for (idx = 0; idx < msa->nseq; idx++)
+ for (s = gcg_sqname[idx]; *s != '\0'; s++)
+ if (! isalnum((int) *s) && *s != '-' && *s != '_')
+ *s = '_';
+ /* alter gap chars in seq */
+ for (idx = 0; idx < msa->nseq; idx++)
+ {
+ for (s = gcg_aseq[idx]; *s != '\0' && isgap(*s); s++)
+ *s = '~';
+ for (; *s != '\0'; s++)
+ if (isgap(*s)) *s = '.';
+ for (pos = msa->alen-1; pos > 0 && isgap(gcg_aseq[idx][pos]); pos--)
+ gcg_aseq[idx][pos] = '~';
+ }
+ /* calculate max namelen used */
+ namelen = 0;
+ for (idx = 0; idx < msa->nseq; idx++)
+ if ((len = strlen(msa->sqname[idx])) > namelen)
+ namelen = len;
+
+ /*****************************************************
+ * Write the MSF header
+ *****************************************************/
+ /* required file type line */
+ if (msa->type == kOtherSeq)
+ msa->type = GuessAlignmentSeqtype(msa->aseq, msa->nseq);
+
+ if (msa->type == kRNA) fprintf(fp, "!!NA_MULTIPLE_ALIGNMENT 1.0\n");
+ else if (msa->type == kDNA) fprintf(fp, "!!NA_MULTIPLE_ALIGNMENT 1.0\n");
+ else if (msa->type == kAmino) fprintf(fp, "!!AA_MULTIPLE_ALIGNMENT 1.0\n");
+ else if (msa->type == kOtherSeq)
+ Die("WriteMSF(): couldn't guess whether that alignment is RNA or protein.\n");
+ else
+ Die("Invalid sequence type %d in WriteMSF()\n", msa->type);
+
+ /* free text comments */
+ if (msa->ncomment > 0)
+ {
+ for (idx = 0; idx < msa->ncomment; idx++)
+ fprintf(fp, "%s\n", msa->comment[idx]);
+ fprintf(fp, "\n");
+ }
+ /* required checksum line */
+ now = time(NULL);
+ if (strftime(date, 64, "%B %d, %Y %H:%M", localtime(&now)) == 0)
+ Die("What time is it on earth? strftime() failed in WriteMSF().\n");
+ fprintf(fp, " %s MSF: %d Type: %c %s Check: %d ..\n",
+ msa->name != NULL ? msa->name : "squid.msf",
+ msa->alen,
+ msa->type == kRNA ? 'N' : 'P',
+ date,
+ GCGMultchecksum(gcg_aseq, msa->nseq));
+ fprintf(fp, "\n");
+
+ /*****************************************************
+ * Names/weights section
+ *****************************************************/
+
+ for (idx = 0; idx < msa->nseq; idx++)
+ {
+ fprintf(fp, " Name: %-*.*s Len: %5d Check: %4d Weight: %.2f\n",
+ namelen, namelen,
+ gcg_sqname[idx],
+ msa->alen,
+ GCGchecksum(gcg_aseq[idx], msa->alen),
+ msa->wgt[idx]);
+ }
+ fprintf(fp, "\n");
+ fprintf(fp, "//\n");
+
+ /*****************************************************
+ * Write the sequences
+ *****************************************************/
+
+ for (pos = 0; pos < msa->alen; pos += 50)
+ {
+ fprintf(fp, "\n"); /* Blank line between sequence blocks */
+
+ /* Coordinate line */
+ len = (pos + 50) > msa->alen ? msa->alen - pos : 50;
+ if (len > 10)
+ fprintf(fp, "%*s %-6d%*s%6d\n", namelen, "",
+ pos+1,
+ len + ((len-1)/10) - 12, "",
+ pos + len);
+ else
+ fprintf(fp, "%*s %-6d\n", namelen, "", pos+1);
+
+ for (idx = 0; idx < msa->nseq; idx++)
+ {
+ fprintf(fp, "%-*s ", namelen, gcg_sqname[idx]);
+ /* get next line's worth of 50 from seq */
+ strncpy(buffer, gcg_aseq[idx] + pos, 50);
+ buffer[50] = '\0';
+ /* draw the sequence line */
+ for (i = 0; i < len; i++)
+ {
+ if (! (i % 10)) fputc(' ', fp);
+ fputc(buffer[i], fp);
+ }
+ fputc('\n', fp);
+ }
+ }
+
+ Free2DArray((void **) gcg_aseq, msa->nseq);
+ Free2DArray((void **) gcg_sqname, msa->nseq);
+ return;
+}
+
+
+
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* phylip.c
+ * SRE, Mon Jun 14 14:08:33 1999 [St. Louis]
+ *
+ * Import/export of PHYLIP interleaved multiple sequence alignment
+ * format files.
+ *
+ * RCS $Id: phylip.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: phylip.c,v 1.1 1999/07/15 22:29:20 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+#include "squid.h"
+#include "msa.h"
+
+#ifdef TESTDRIVE_PHYLIP
+/*****************************************************************
+ * phylip.c test driver:
+ *
+ */
+int
+main(int argc, char **argv)
+{
+ MSAFILE *afp;
+ MSA *msa;
+ char *file;
+
+ file = argv[1];
+
+ if ((afp = MSAFileOpen(file, MSAFILE_UNKNOWN, NULL)) == NULL)
+ Die("Couldn't open %s\n", file);
+
+ printf("format %d\n", afp->format);
+
+ while ((msa = ReadPhylip(afp)) != NULL)
+ {
+ WritePhylip(stdout, msa);
+ MSAFree(msa);
+ }
+
+ MSAFileClose(afp);
+ exit(0);
+}
+/******************************************************************/
+#endif /* testdrive_phylip */
+
+
+
+/* Function: ReadPhylip()
+ * Date: SRE, Fri Jun 18 12:59:37 1999 [Sanger Centre]
+ *
+ * Purpose: Parse an alignment from an open Phylip format
+ * alignment file. Phylip is a single-alignment format.
+ * Return the alignment, or NULL if we have no data.
+ *
+ * Args: afp - open alignment file
+ *
+ * Returns: MSA * - an alignment object
+ * Caller responsible for an MSAFree()
+ * NULL if no more alignments
+ */
+MSA *
+ReadPhylip(MSAFILE *afp)
+{
+ MSA *msa;
+ char *s, *s1, *s2;
+ char name[11]; /* seq name max len = 10 char */
+ int nseq, alen;
+ int idx; /* index of current sequence */
+ int slen;
+ int nblock;
+
+ if (feof(afp->f)) return NULL;
+
+ /* Skip until we see a nonblank line; it's the header,
+ * containing nseq/alen
+ */
+ nseq = 0; alen = 0;
+ while ((s = MSAFileGetLine(afp)) != NULL)
+ {
+ if ((s1 = sre_strtok(&s, WHITESPACE, NULL)) == NULL) continue;
+ if ((s2 = sre_strtok(&s, WHITESPACE, NULL)) == NULL)
+ Die("Failed to parse nseq/alen from first line of PHYLIP file %s\n", afp->fname);
+ if (! IsInt(s1) || ! IsInt(s2))
+ Die("nseq and/or alen not an integer in first line of PHYLIP file %s\n", afp->fname);
+ nseq = atoi(s1);
+ alen = atoi(s2);
+ break;
+ }
+
+ msa = MSAAlloc(nseq, 0);
+ idx = 0;
+ nblock = 0;
+ while ((s = MSAFileGetLine(afp)) != NULL)
+ {
+ /* ignore blank lines. nonblank lines start w/ nonblank char */
+ if (isspace(*s)) continue;
+ /* First block has seq names */
+ if (nblock == 0) {
+ strncpy(name, s, 10);
+ name[10] = '\0';
+ GKIStoreKey(msa->index, name);
+ msa->sqname[idx] = sre_strdup(name, -1);
+ s += 10;
+ }
+ /* be careful of trailing whitespace on lines */
+ if ((s1 = sre_strtok(&s, WHITESPACE, &slen)) == NULL)
+ Die("Failed to parse sequence at line %d of PHYLIP file %s\n",
+ afp->linenumber, afp->fname);
+ msa->sqlen[idx] = sre_strcat(&(msa->aseq[idx]), msa->sqlen[idx], s1, slen);
+
+ idx++;
+ if (idx == nseq) { idx = 0; nblock++; }
+ }
+ msa->nseq = nseq;
+ MSAVerifyParse(msa); /* verifies; sets alen, wgt; frees sqlen[] */
+ return msa;
+}
+
+
+
+/* Function: WritePhylip()
+ * Date: SRE, Fri Jun 18 12:07:41 1999 [Sanger Centre]
+ *
+ * Purpose: Write an alignment in Phylip format to an open file.
+ *
+ * Args: fp - file that's open for writing.
+ * msa - alignment to write.
+ *
+ * Returns: (void)
+ */
+void
+WritePhylip(FILE *fp, MSA *msa)
+{
+ int idx; /* counter for sequences */
+ int cpl = 50; /* 50 seq char per line */
+ char buf[51]; /* buffer for writing seq */
+ int pos;
+
+ /* First line has nseq, alen
+ */
+ fprintf(fp, " %d %d\n", msa->nseq, msa->alen);
+
+ /* Alignment section.
+ * PHYLIP is a multiblock format, blocks (optionally) separated
+ * by blanks; names only attached to first block. Names are
+ * restricted to ten char; we achieve this by simple truncation (!).
+ * (Do we need to convert gap characters from our ./- convention?)
+ */
+ for (pos = 0; pos < msa->alen; pos += cpl)
+ {
+ if (pos > 0) fprintf(fp, "\n");
+
+ for (idx = 0; idx < msa->nseq; idx++)
+ {
+ strncpy(buf, msa->aseq[idx] + pos, cpl);
+ buf[cpl] = '\0';
+ if (pos > 0) fprintf(fp, "%s\n", buf);
+ else fprintf(fp, "%-10.10s%s\n", msa->sqname[idx], buf);
+ }
+ }
+ return;
+}
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* revcomp.c
+ *
+ * Reverse complement of a IUPAC character string
+ * RCS $Id: revcomp.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: revcomp.c,v 1.5 2002/06/25 20:06:06 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <string.h>
+#include <ctype.h>
+#include "squid.h"
+
+/* Function: revcomp()
+ *
+ * Purpose: Reverse complement seq; store in comp.
+ * Can revcomp "in place" (revcomp(seq, seq)).
+ *
+ * Args: comp - destination for reverse complement of seq
+ * seq - sequence to reverse complement
+ *
+ * Returns: NULL on failure; or a (useless) pointer to comp.
+ */
+char *
+revcomp(char *comp, char *seq)
+{
+ char *s;
+ char c;
+
+ if (comp == NULL) return NULL;
+ if (seq == NULL) return NULL;
+
+ StrReverse(comp, seq);
+ for (s = comp; *s != '\0'; s++)
+ {
+ c = *s;
+ c = sre_toupper(c);
+ switch (c) {
+ case 'A': c = 'T'; break;
+ case 'C': c = 'G'; break;
+ case 'G': c = 'C'; break;
+ case 'T': c = 'A'; break;
+ case 'U': c = 'A'; break;
+ case 'R': c = 'Y'; break;
+ case 'Y': c = 'R'; break;
+ case 'M': c = 'K'; break;
+ case 'K': c = 'M'; break;
+ case 'S': c = 'S'; break;
+ case 'W': c = 'W'; break;
+ case 'H': c = 'D'; break;
+ case 'D': c = 'H'; break;
+ case 'B': c = 'V'; break;
+ case 'V': c = 'B'; break;
+ default: break; /* anything else? leave it; it's prob a gap or an X */
+ }
+ if (islower((int) *s)) c = (char) sre_tolower((int) c);
+ *s = c;
+ }
+ return comp;
+}
+
+#ifdef REVCOMP_TESTDRIVER
+/* gcc -g -DREVCOMP_TESTDRIVER revcomp.c sre_string.c shuffle.c sre_math.c sre_ctype.c sqerror.c -lm
+*/
+int
+main(void)
+{
+ float p[4] = {0.25, 0.25, 0.25, 0.25};
+ char *alphabet = "ACGT";
+ int len = 10;
+ char *seq;
+
+ seq = RandomSequence(alphabet, p, 4, len);
+ printf("%s\n", seq);
+ revcomp(seq, seq);
+ printf("%s\n", seq);
+ free(seq);
+ exit(0);
+}
+#endif
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* rk.c (originally from rnabob's patsearch.c)
+ *
+ * Contains a compiler and a search engine for Rabin-Karp
+ * based primary sequence pattern searching on encoded
+ * sequences.
+ *
+ * See Sedgewick, _Algorithms_, for a general discussion of
+ * the Rabin-Karp algorithm. See the rkcomp or rkexec man
+ * pages for specific details.
+ *
+ * RCS $Id: rk.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: rk.c,v 1.2 1998/10/09 18:07:16 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <string.h>
+#include <ctype.h>
+#include "squid.h" /* seq encoding utilities and typedefs */
+#include "rk.h"
+
+
+#ifdef MEMDEBUG
+#include "dbmalloc.h"
+#endif
+
+Hashseq
+rkcomp(char *probe) /* A,C,G,T/U, N probe string, 0-8 nt long */
+{
+ Hashseq hashprobe = 0;
+ char coded[RK_HASHSIZE + 1];
+ int len;
+ int i;
+ /* check bounds violation on probe */
+ if ((len = strlen(probe)) > RK_HASHSIZE) return 0;
+ /* encode the probe */
+ if (seqencode(coded, probe) == 0) return 0;
+ /* pack the probe into a Hashseq */
+ for (i = 0; i < len; i++)
+ {
+ hashprobe <<= 4;
+ hashprobe |= (Hashseq) coded[i];
+ }
+ /* left adjust as needed */
+ for (; i < RK_HASHSIZE; i++)
+ {
+ hashprobe <<= 4;
+ hashprobe |= (Hashseq) NTN;
+ }
+ /* return the compiled probe */
+ return hashprobe;
+}
+
+int
+rkseq(Hashseq hashprobe, /* up to 8 nt packed into the probe */
+ char *sequence) /* encoded sequence */
+{
+ long i;
+ long pos = 0;
+ Hashseq target = 0;
+
+ /* initialize the target hashseq */
+ for (i = 0; i < RK_HASHSIZE; i++)
+ {
+ if (*(sequence + i) == NTEND)
+ break;
+ target <<= 4;
+ target |= (Hashseq) (*(sequence + i));
+ }
+
+ while (*(sequence + pos + RK_HASHSIZE -1) != NTEND)
+ {
+#ifdef DEBUG
+ printf("hashprobe: ");
+ writehash(hashprobe);
+ printf("\ttarget: ");
+ writehash(target);
+ printf("\nhashprobe & target: ");
+ writehash(hashprobe & target);
+ printf("\n");
+#endif
+ if ((hashprobe & target) == target)
+ return ((int) pos);
+ target <<= 4;
+ target |= (Hashseq) (*(sequence + pos + RK_HASHSIZE));
+ pos++;
+ }
+ /* now we deal with an end effect */
+ for (i = 0; i < RK_HASHSIZE; i++)
+ {
+ target |= (Hashseq) NTN;
+ if ((hashprobe & target) == target)
+ return ((int) pos);
+ target <<=4;
+ pos++;
+ }
+
+ return(-1);
+}
+
+
+#ifdef DEBUG /* Debugging aids */
+
+static void
+writehash(Hashseq hashseq)
+{
+ int idx;
+ int sym;
+
+ if (hashseq/16)
+ writehash(hashseq/16);
+
+ sym = (int) (hashseq % 16);
+ if (sym == 0)
+ putchar('-');
+ else
+ {
+ for (idx = 0; sym != iupac[idx].code && idx < IUPACSYMNUM; idx++);
+ if (idx > IUPACSYMNUM)
+ printf("(%d)", sym);
+ else
+ putchar(iupac[idx].sym);
+ }
+}
+
+#endif
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+#ifndef SQRKH_INCLUDED
+#define SQRKH_INCLUDED
+
+/* rk.h
+ *
+ * Header file for Rabin-Karp pattern searching on encoded
+ * sequence strings.
+ *
+ * Sean Eddy, Thu Oct 1 11:45:42 1992
+ * RCS $Id: rk.h 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: rk.h,v 1.2 1998/10/09 18:07:16 eddy Exp)
+ */
+
+
+ /* expect 32 bits for 8 nt */
+typedef unsigned long Hashseq;
+ /* but we count to be sure...
+ RK_HASHSIZE is the number of nt that fit
+ in one probe */
+#define RK_HASHSIZE (sizeof(Hashseq)*2)
+ /* empirically, how many nt minimum we require
+ in a pattern before we abandon rk and
+ go with something else */
+#define RK_REQUIRE 4
+
+extern int rkseq(Hashseq hashprobe, char *sequence);
+extern Hashseq rkcomp(char *probe); /* compile a Hashseq from a pattern */
+
+
+
+#endif /* SQRKH_INCLUDED */
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* selex.c
+ *
+ * SRE, Mon Jun 14 11:08:38 1999
+ * SELEX obsolete as the preferred HMMER/SQUID format
+ * replaced by Stockholm format
+ * selex support retained for backwards compatibility
+ * kludged to use the MSA interface
+ *
+ * SRE, Mon Jan 30 14:41:49 1995:
+ * #=SA side chain % surface accessibility annotation supported
+ *
+ * SRE, Tue Nov 9 17:40:50 1993:
+ * major revision. #= special comments and aliinfo_s optional
+ * alignment info support added. Support for #=CS (consensus
+ * secondary structure), #=SS (individual secondary structure),
+ * #=RF (reference coordinate system), #=SQ (per-sequence header info),
+ * and #=AU ("author") added.
+ *
+ * Fri Dec 4 17:43:24 1992, SRE:
+ * Reading and writing aligned sequences to/from disk files.
+ * Implements a new, broader specification of SELEX format
+ * and supercedes alignio.c.
+ *
+ * SELEX format is documented in Docs/formats.tex.
+ ****************************************************************************
+ * RCS $Id: selex.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: selex.c,v 1.11 2002/10/12 04:40:35 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+#include <memory.h>
+#include "squid.h"
+#include "msa.h"
+
+static int copy_alignment_line(char *aseq, int apos, int name_rcol,
+ char *buffer, int lcol, int rcol, char gapsym);
+static void actually_write_selex(FILE *fp, MSA *msa, int cpl);
+
+static char commentsyms[] = "%#";
+
+/* Function: ReadSELEX()
+ * Date: SRE, Sun Jun 6 18:24:09 1999 [St. Louis]
+ *
+ * Purpose: Parse an alignment read from an open SELEX format
+ * alignment file. (SELEX is a single alignment format).
+ * Return the alignment, or NULL if we've already read the
+ * alignment or there's no alignment data in the file.
+ *
+ * Limitations: SELEX is the only remaining multipass parser for
+ * alignment files. It cannot read from gzip or from stdin.
+ * It Die()'s here if you try. The reason for this
+ * that SELEX allows space characters as gaps, so we don't
+ * know the borders of an alignment block until we've seen
+ * the whole block. I could rewrite to allow single-pass
+ * parsing (by storing the whole block in memory) but
+ * since SELEX is now legacy, why bother.
+ *
+ * Note that the interface is totally kludged: fastest
+ * possible adaptation of old ReadSELEX() to the new
+ * MSA interface.
+ *
+ * Args: afp - open alignment file
+ *
+ * Returns: MSA * - an alignment object
+ * caller responsible for an MSAFree()
+ * NULL if no alignment data.
+ */
+MSA *
+ReadSELEX(MSAFILE *afp)
+{
+ MSA *msa; /* RETURN: mult seq alignment */
+ FILE *fp; /* ptr to opened seqfile */
+ char **aseqs; /* aligned seqs */
+ int num = 0; /* number of seqs read */
+ char buffer[LINEBUFLEN]; /* input buffer for lines */
+ char bufcpy[LINEBUFLEN]; /* strtok'able copy of buffer */
+ struct block_struc { /** alignment data for a block: */
+ int lcol; /* furthest left aligned sym */
+ int rcol; /* furthest right aligned sym */
+ } *blocks = NULL;
+ int blocknum; /* number of blocks in file */
+ char *nptr; /* ptr to start of name on line */
+ char *sptr; /* ptr into sequence on line */
+ int currnum; /* num. seqs in given block */
+ int currblock; /* index for blocks */
+ int i; /* loop counter */
+ int seqidx; /* counter for seqs */
+ int alen; /* length of alignment */
+ int warn_names; /* becomes TRUE if names don't match between blocks */
+ int headnum; /* seqidx in per-sequence header info */
+ int currlen;
+ int count;
+ int have_cs = 0;
+ int have_rf = 0;
+ AINFO base_ainfo, *ainfo; /* hack: used to be passed ptr to AINFO */
+
+
+ /* Convert from MSA interface to what old ReadSELEX() did:
+ * - copy our open fp, rather than opening file
+ * - verify that we're not reading a gzip or stdin
+ */
+ if (feof(afp->f)) return NULL;
+ if (afp->do_gzip || afp->do_stdin)
+ Die("Can't read a SELEX format alignment from a pipe, stdin, or gzip'ed file");
+ fp = afp->f;
+ ainfo = &base_ainfo;
+
+ /***************************************************
+ * First pass across file.
+ * Count seqs, get names, determine column info
+ * Determine what sorts of info are active in this file.
+ ***************************************************/
+
+ InitAinfo(ainfo);
+ /* get first line of the block
+ * (non-comment, non-blank) */
+ do
+ {
+ if (fgets(buffer, LINEBUFLEN, fp) == NULL)
+ { squid_errno = SQERR_NODATA; return 0; }
+ strcpy(bufcpy, buffer);
+ if (*buffer == '#')
+ {
+ if (strncmp(buffer, "#=CS", 4) == 0) have_cs = 1;
+ else if (strncmp(buffer, "#=RF", 4) == 0) have_rf = 1;
+ }
+ }
+ while ((nptr = strtok(bufcpy, WHITESPACE)) == NULL ||
+ (strchr(commentsyms, *nptr) != NULL));
+
+ blocknum = 0;
+ warn_names = FALSE;
+ while (!feof(fp))
+ {
+ /* allocate for info about this block. */
+ if (blocknum == 0)
+ blocks = (struct block_struc *) MallocOrDie (sizeof(struct block_struc));
+ else
+ blocks = (struct block_struc *) ReallocOrDie (blocks, (blocknum+1) * sizeof(struct block_struc));
+ blocks[blocknum].lcol = LINEBUFLEN+1;
+ blocks[blocknum].rcol = -1;
+
+ currnum = 0;
+ while (nptr != NULL) /* becomes NULL when this block ends. */
+ {
+ /* First block only: save names */
+ if (blocknum == 0)
+ {
+ if (currnum == 0)
+ ainfo->sqinfo = (SQINFO *) MallocOrDie (sizeof(SQINFO));
+ else
+ ainfo->sqinfo = (SQINFO *) ReallocOrDie (ainfo->sqinfo, (currnum + 1) * sizeof(SQINFO));
+
+ ainfo->sqinfo[currnum].flags = 0;
+ SetSeqinfoString(&(ainfo->sqinfo[currnum]), nptr, SQINFO_NAME);
+ }
+ else /* in each additional block: check names */
+ {
+ if (strcmp(ainfo->sqinfo[currnum].name, nptr) != 0)
+ warn_names = TRUE;
+ }
+ currnum++;
+
+ /* check rcol, lcol */
+ if ((sptr = strtok(NULL, WHITESPACE)) != NULL)
+ {
+ /* is this the furthest left we've
+ seen word 2 in this block? */
+ if (sptr - bufcpy < blocks[blocknum].lcol)
+ blocks[blocknum].lcol = sptr - bufcpy;
+ /* look for right side in buffer */
+ for (sptr = buffer + strlen(buffer) - 1;
+ strchr(WHITESPACE, *sptr) != NULL;
+ sptr --)
+ /* do nothing */ ;
+ if (sptr - buffer > blocks[blocknum].rcol)
+ blocks[blocknum].rcol = sptr - buffer;
+ }
+
+ /* get the next line; blank line means end of block */
+ do
+ {
+ if (fgets(buffer, LINEBUFLEN, fp) == NULL)
+ { nptr = NULL; break; }
+ strcpy(bufcpy, buffer);
+
+ if (strncmp(buffer, "#=SS", 4) == 0) ainfo->sqinfo[currnum-1].flags |= SQINFO_SS;
+ else if (strncmp(buffer, "#=SA", 4) == 0) ainfo->sqinfo[currnum-1].flags |= SQINFO_SA;
+ else if (strncmp(buffer, "#=CS", 4) == 0) have_cs = 1;
+ else if (strncmp(buffer, "#=RF", 4) == 0) have_rf = 1;
+
+ if ((nptr = strtok(bufcpy, WHITESPACE)) == NULL)
+ break;
+ } while (strchr(commentsyms, *nptr) != NULL);
+ }
+
+
+ /* check that number of sequences matches expected */
+ if (blocknum == 0)
+ num = currnum;
+ else if (currnum != num)
+ Die("Parse error in ReadSELEX()");
+ blocknum++;
+
+ /* get first line of next block
+ * (non-comment, non-blank) */
+ do
+ {
+ if (fgets(buffer, LINEBUFLEN, fp) == NULL) { nptr = NULL; break; }
+ strcpy(bufcpy, buffer);
+ }
+ while ((nptr = strtok(bufcpy, WHITESPACE)) == NULL ||
+ (strchr(commentsyms, *nptr) != NULL));
+ }
+
+
+ /***************************************************
+ * Get ready for second pass:
+ * figure out the length of the alignment
+ * malloc space
+ * rewind the file
+ ***************************************************/
+
+ alen = 0;
+ for (currblock = 0; currblock < blocknum; currblock++)
+ alen += blocks[currblock].rcol - blocks[currblock].lcol + 1;
+
+ rewind(fp);
+
+ /* allocations. we can't use AllocateAlignment because of
+ * the way we already used ainfo->sqinfo.
+ */
+ aseqs = (char **) MallocOrDie (num * sizeof(char *));
+ if (have_cs)
+ ainfo->cs = (char *) MallocOrDie ((alen+1) * sizeof(char));
+ if (have_rf)
+ ainfo->rf = (char *) MallocOrDie ((alen+1) * sizeof(char));
+
+
+
+ for (i = 0; i < num; i++)
+ {
+ aseqs[i] = (char *) MallocOrDie ((alen+1) * sizeof(char));
+ if (ainfo->sqinfo[i].flags & SQINFO_SS)
+ ainfo->sqinfo[i].ss = (char *) MallocOrDie ((alen+1) * sizeof(char));
+ if (ainfo->sqinfo[i].flags & SQINFO_SA)
+ ainfo->sqinfo[i].sa = (char *) MallocOrDie ((alen+1) * sizeof(char));
+ }
+
+ ainfo->alen = alen;
+ ainfo->nseq = num;
+ ainfo->wgt = (float *) MallocOrDie (sizeof(float) * num);
+ FSet(ainfo->wgt, num, 1.0);
+
+ /***************************************************
+ * Second pass across file. Parse header; assemble sequences
+ ***************************************************/
+ /* We've now made a complete first pass over the file. We know how
+ * many blocks it contains, we know the number of seqs in the first
+ * block, and we know every block has the same number of blocks;
+ * so we can be a bit more cavalier about error-checking as we
+ * make the second pass.
+ */
+
+ /* Look for header
+ */
+ headnum = 0;
+ for (;;)
+ {
+ if (fgets(buffer, LINEBUFLEN, fp) == NULL)
+ Die("Parse error in ReadSELEX()");
+ strcpy(bufcpy, buffer);
+ if ((nptr = strtok(bufcpy, WHITESPACE)) == NULL) continue; /* skip blank lines */
+
+ if (strcmp(nptr, "#=AU") == 0 && (sptr = strtok(NULL, "\n")) != NULL)
+ ainfo->au = Strdup(sptr);
+ else if (strcmp(nptr, "#=ID") == 0 && (sptr = strtok(NULL, "\n")) != NULL)
+ ainfo->name = Strdup(sptr);
+ else if (strcmp(nptr, "#=AC") == 0 && (sptr = strtok(NULL, "\n")) != NULL)
+ ainfo->acc = Strdup(sptr);
+ else if (strcmp(nptr, "#=DE") == 0 && (sptr = strtok(NULL, "\n")) != NULL)
+ ainfo->desc = Strdup(sptr);
+ else if (strcmp(nptr, "#=GA") == 0)
+ {
+ if ((sptr = strtok(NULL, WHITESPACE)) == NULL)
+ Die("Parse error in #=GA line in ReadSELEX()");
+ ainfo->ga1 = atof(sptr);
+
+ if ((sptr = strtok(NULL, WHITESPACE)) == NULL)
+ Die("Parse error in #=GA line in ReadSELEX()");
+ ainfo->ga2 = atof(sptr);
+
+ ainfo->flags |= AINFO_GA;
+ }
+ else if (strcmp(nptr, "#=TC") == 0)
+ {
+ if ((sptr = strtok(NULL, WHITESPACE)) == NULL)
+ Die("Parse error in #=TC line in ReadSELEX()");
+ ainfo->tc1 = atof(sptr);
+
+ if ((sptr = strtok(NULL, WHITESPACE)) == NULL)
+ Die("Parse error in #=TC line in ReadSELEX()");
+ ainfo->tc2 = atof(sptr);
+
+ ainfo->flags |= AINFO_TC;
+ }
+ else if (strcmp(nptr, "#=NC") == 0)
+ {
+ if ((sptr = strtok(NULL, WHITESPACE)) == NULL)
+ Die("Parse error in #=NC line in ReadSELEX()");
+ ainfo->nc1 = atof(sptr);
+
+ if ((sptr = strtok(NULL, WHITESPACE)) == NULL)
+ Die("Parse error in #=NC line in ReadSELEX()");
+ ainfo->nc2 = atof(sptr);
+
+ ainfo->flags |= AINFO_NC;
+ }
+ else if (strcmp(nptr, "#=SQ") == 0) /* per-sequence header info */
+ {
+ /* first field is the name */
+ if ((sptr = strtok(NULL, WHITESPACE)) == NULL)
+ Die("Parse error in #=SQ line in ReadSELEX()");
+ if (strcmp(sptr, ainfo->sqinfo[headnum].name) != 0) warn_names = TRUE;
+
+ /* second field is the weight */
+ if ((sptr = strtok(NULL, WHITESPACE)) == NULL)
+ Die("Parse error in #=SQ line in ReadSELEX()");
+ if (!IsReal(sptr))
+ Die("Parse error in #=SQ line in ReadSELEX(): weight is not a number");
+ ainfo->wgt[headnum] = atof(sptr);
+
+ /* third field is database source id */
+ if ((sptr = strtok(NULL, WHITESPACE)) == NULL)
+ Die("Parse error in #=SQ line in ReadSELEX(): incomplete line");
+ SetSeqinfoString(&(ainfo->sqinfo[headnum]), sptr, SQINFO_ID);
+
+ /* fourth field is database accession number */
+ if ((sptr = strtok(NULL, WHITESPACE)) == NULL)
+ Die("Parse error in #=SQ line in ReadSELEX(): incomplete line");
+ SetSeqinfoString(&(ainfo->sqinfo[headnum]), sptr, SQINFO_ACC);
+
+ /* fifth field is start..stop::olen */
+ if ((sptr = strtok(NULL, ".:")) == NULL)
+ Die("Parse error in #=SQ line in ReadSELEX(): incomplete line");
+ SetSeqinfoString(&(ainfo->sqinfo[headnum]), sptr, SQINFO_START);
+
+ if ((sptr = strtok(NULL, ".:")) == NULL)
+ Die("Parse error in #=SQ line in ReadSELEX(): incomplete line");
+ SetSeqinfoString(&(ainfo->sqinfo[headnum]), sptr, SQINFO_STOP);
+
+ if ((sptr = strtok(NULL, ":\t ")) == NULL)
+ Die("Parse error in #=SQ line in ReadSELEX(): incomplete line");
+ SetSeqinfoString(&(ainfo->sqinfo[headnum]), sptr, SQINFO_OLEN);
+
+ /* rest of line is optional description */
+ if ((sptr = strtok(NULL, "\n")) != NULL)
+ SetSeqinfoString(&(ainfo->sqinfo[headnum]), sptr, SQINFO_DESC);
+
+ headnum++;
+ }
+ else if (strcmp(nptr, "#=CS") == 0) break;
+ else if (strcmp(nptr, "#=RF") == 0) break;
+ else if (strchr(commentsyms, *nptr) == NULL) break; /* non-comment, non-header */
+ }
+
+
+ currlen = 0;
+ for (currblock = 0 ; currblock < blocknum; currblock++)
+ {
+ /* parse the block */
+ seqidx = 0;
+ while (nptr != NULL)
+ {
+ /* Consensus structure */
+ if (strcmp(nptr, "#=CS") == 0)
+ {
+ if (! copy_alignment_line(ainfo->cs, currlen, strlen(nptr)-1,
+ buffer, blocks[currblock].lcol, blocks[currblock].rcol, (char) '.'))
+ Die("Parse error in #=CS line in ReadSELEX()");
+ }
+
+ /* Reference coordinates */
+ else if (strcmp(nptr, "#=RF") == 0)
+ {
+ if (! copy_alignment_line(ainfo->rf, currlen, strlen(nptr)-1,
+ buffer, blocks[currblock].lcol, blocks[currblock].rcol, (char) '.'))
+ Die("Parse error in #=RF line in ReadSELEX()");
+ }
+ /* Individual secondary structure */
+ else if (strcmp(nptr, "#=SS") == 0)
+ {
+ if (! copy_alignment_line(ainfo->sqinfo[seqidx-1].ss, currlen, strlen(nptr)-1,
+ buffer, blocks[currblock].lcol,
+ blocks[currblock].rcol, (char) '.'))
+ Die("Parse error in #=SS line in ReadSELEX()");
+ }
+
+ /* Side chain % surface accessibility code */
+ else if (strcmp(nptr, "#=SA") == 0)
+ {
+ if (! copy_alignment_line(ainfo->sqinfo[seqidx-1].sa, currlen, strlen(nptr)-1,
+ buffer, blocks[currblock].lcol,
+ blocks[currblock].rcol, (char) '.'))
+ Die("Parse error in #=SA line in ReadSELEX()");
+ }
+ /* Aligned sequence; avoid unparsed machine comments */
+ else if (strncmp(nptr, "#=", 2) != 0)
+ {
+ if (! copy_alignment_line(aseqs[seqidx], currlen, strlen(nptr)-1,
+ buffer, blocks[currblock].lcol, blocks[currblock].rcol, (char) '.'))
+ Die("Parse error in alignment line in ReadSELEX()");
+ seqidx++;
+ }
+
+ /* get next line */
+ for (;;)
+ {
+ nptr = NULL;
+ if (fgets(buffer, LINEBUFLEN, fp) == NULL) break; /* EOF */
+ strcpy(bufcpy, buffer);
+ if ((nptr = strtok(bufcpy, WHITESPACE)) == NULL) break; /* blank */
+ if (strncmp(buffer, "#=", 2) == 0) break; /* machine comment */
+ if (strchr(commentsyms, *nptr) == NULL) break; /* data */
+ }
+ } /* end of a block */
+
+ currlen += blocks[currblock].rcol - blocks[currblock].lcol + 1;
+
+ /* get line 1 of next block */
+ for (;;)
+ {
+ if (fgets(buffer, LINEBUFLEN, fp) == NULL) break; /* no data */
+ strcpy(bufcpy, buffer);
+ if ((nptr = strtok(bufcpy, WHITESPACE)) == NULL) continue; /* blank */
+ if (strncmp(buffer, "#=", 2) == 0) break; /* machine comment */
+ if (strchr(commentsyms, *nptr) == NULL) break; /* non-comment */
+ }
+ } /* end of the file */
+
+ /* Lengths in sqinfo are for raw sequence (ungapped),
+ * and SS, SA are 0..rlen-1 not 0..alen-1.
+ * Only the seqs with structures come out of here with lengths set.
+ */
+ for (seqidx = 0; seqidx < num; seqidx++)
+ {
+ int apos, rpos;
+ /* secondary structures */
+ if (ainfo->sqinfo[seqidx].flags & SQINFO_SS)
+ {
+ for (apos = rpos = 0; apos < alen; apos++)
+ if (! isgap(aseqs[seqidx][apos]))
+ {
+ ainfo->sqinfo[seqidx].ss[rpos] = ainfo->sqinfo[seqidx].ss[apos];
+ rpos++;
+ }
+ ainfo->sqinfo[seqidx].ss[rpos] = '\0';
+ }
+ /* Surface accessibility */
+ if (ainfo->sqinfo[seqidx].flags & SQINFO_SA)
+ {
+ for (apos = rpos = 0; apos < alen; apos++)
+ if (! isgap(aseqs[seqidx][apos]))
+ {
+ ainfo->sqinfo[seqidx].sa[rpos] = ainfo->sqinfo[seqidx].sa[apos];
+ rpos++;
+ }
+ ainfo->sqinfo[seqidx].sa[rpos] = '\0';
+ }
+ }
+
+ /* NULL-terminate all the strings */
+ if (ainfo->rf != NULL) ainfo->rf[alen] = '\0';
+ if (ainfo->cs != NULL) ainfo->cs[alen] = '\0';
+ for (seqidx = 0; seqidx < num; seqidx++)
+ aseqs[seqidx][alen] = '\0';
+
+ /* find raw sequence lengths for sqinfo */
+ for (seqidx = 0; seqidx < num; seqidx++)
+ {
+ count = 0;
+ for (sptr = aseqs[seqidx]; *sptr != '\0'; sptr++)
+ if (!isgap(*sptr)) count++;
+ ainfo->sqinfo[seqidx].len = count;
+ ainfo->sqinfo[seqidx].flags |= SQINFO_LEN;
+ }
+
+
+ /***************************************************
+ * Garbage collection and return
+ ***************************************************/
+ free(blocks);
+ if (warn_names)
+#ifdef CLUSTALO
+ Warning("sequences may be in different orders in blocks of %s?", afp->fname);
+#else
+ Warn("sequences may be in different orders in blocks of %s?", afp->fname);
+#endif
+
+ /* Convert back to MSA structure. (Wasteful kludge.)
+ */
+ msa = MSAFromAINFO(aseqs, ainfo);
+ MSAVerifyParse(msa);
+ FreeAlignment(aseqs, ainfo);
+ return msa;
+}
+
+
+/* Function: WriteSELEX()
+ * Date: SRE, Mon Jun 14 13:13:14 1999 [St. Louis]
+ *
+ * Purpose: Write a SELEX file in multiblock format.
+ *
+ * Args: fp - file that's open for writing
+ * msa - multiple sequence alignment object
+ *
+ * Returns: (void)
+ */
+void
+WriteSELEX(FILE *fp, MSA *msa)
+{
+ actually_write_selex(fp, msa, 50); /* 50 char per block */
+}
+
+/* Function: WriteSELEXOneBlock()
+ * Date: SRE, Mon Jun 14 13:14:56 1999 [St. Louis]
+ *
+ * Purpose: Write a SELEX alignment file in Pfam's single-block
+ * format style. A wrapper for actually_write_selex().
+ *
+ * Args: fp - file that's open for writing
+ * msa- alignment to write
+ *
+ * Returns: (void)
+ */
+void
+WriteSELEXOneBlock(FILE *fp, MSA *msa)
+{
+ actually_write_selex(fp, msa, msa->alen); /* one big block */
+}
+
+
+/* Function: actually_write_selex()
+ * Date: SRE, Mon Jun 14 12:54:46 1999 [St. Louis]
+ *
+ * Purpose: Write an alignment in SELEX format to an open
+ * file. This is the function that actually does
+ * the work. The API's WriteSELEX() and
+ * WriteSELEXOneBlock() are wrappers.
+ *
+ * Args: fp - file that's open for writing
+ * msa - alignment to write
+ * cpl - characters to write per line in alignment block
+ *
+ * Returns: (void)
+ */
+static void
+actually_write_selex(FILE *fp, MSA *msa, int cpl)
+{
+ int i;
+ int len = 0;
+ int namewidth;
+ char *buf;
+ int currpos;
+
+ buf = malloc(sizeof(char) * (cpl+101)); /* 100 chars allowed for name, etc. */
+
+ /* Figure out how much space we need for name + markup
+ * to keep the alignment in register, for easier human viewing --
+ * even though Stockholm format doesn't care about visual
+ * alignment.
+ */
+ namewidth = 0;
+ for (i = 0; i < msa->nseq; i++)
+ if ((len = strlen(msa->sqname[i])) > namewidth)
+ namewidth = len;
+ if (namewidth < 6) namewidth = 6; /* minimum space for markup tags */
+
+ /* Free text comments
+ */
+ for (i = 0; i < msa->ncomment; i++)
+ fprintf(fp, "# %s\n", msa->comment[i]);
+ if (msa->ncomment > 0) fprintf(fp, "\n");
+
+ /* Per-file annotation
+ */
+ if (msa->name != NULL) fprintf(fp, "#=ID %s\n", msa->name);
+ if (msa->acc != NULL) fprintf(fp, "#=AC %s\n", msa->acc);
+ if (msa->desc != NULL) fprintf(fp, "#=DE %s\n", msa->desc);
+ if (msa->au != NULL) fprintf(fp, "#=AU %s\n", msa->au);
+
+ /* Thresholds are hacky. Pfam has two. Rfam has one.
+ */
+ if (msa->cutoff_is_set[MSA_CUTOFF_GA1] && msa->cutoff_is_set[MSA_CUTOFF_GA2])
+ fprintf(fp, "#=GA %.1f %.1f\n", msa->cutoff[MSA_CUTOFF_GA1], msa->cutoff[MSA_CUTOFF_GA2]);
+ else if (msa->cutoff_is_set[MSA_CUTOFF_GA1])
+ fprintf(fp, "#=GA %.1f\n", msa->cutoff[MSA_CUTOFF_GA1]);
+ if (msa->cutoff_is_set[MSA_CUTOFF_NC1] && msa->cutoff_is_set[MSA_CUTOFF_NC2])
+ fprintf(fp, "#=NC %.1f %.1f\n", msa->cutoff[MSA_CUTOFF_NC1], msa->cutoff[MSA_CUTOFF_NC2]);
+ else if (msa->cutoff_is_set[MSA_CUTOFF_NC1])
+ fprintf(fp, "#=NC %.1f\n", msa->cutoff[MSA_CUTOFF_NC1]);
+ if (msa->cutoff_is_set[MSA_CUTOFF_TC1] && msa->cutoff_is_set[MSA_CUTOFF_TC2])
+ fprintf(fp, "#=TC %.1f %.1f\n", msa->cutoff[MSA_CUTOFF_TC1], msa->cutoff[MSA_CUTOFF_TC2]);
+ else if (msa->cutoff_is_set[MSA_CUTOFF_TC1])
+ fprintf(fp, "#=TC %.1f\n", msa->cutoff[MSA_CUTOFF_TC1]);
+
+ /* Per-sequence annotation
+ */
+ for (i = 0; i < msa->nseq; i++)
+ fprintf(fp, "#=SQ %-*.*s %6.4f %s %s %d..%d::%d %s\n",
+ namewidth, namewidth, msa->sqname[i],
+ msa->wgt[i],
+ "-", /* MSA has no ID field */
+ (msa->sqacc != NULL && msa->sqacc[i] != NULL) ? msa->sqacc[i] : "-",
+ 0, 0, 0, /* MSA has no start, stop, olen field */
+ (msa->sqdesc != NULL && msa->sqdesc[i] != NULL) ? msa->sqdesc[i] : "-");
+ fprintf(fp, "\n");
+
+ /* Alignment section:
+ */
+ for (currpos = 0; currpos < msa->alen; currpos += cpl)
+ {
+ if (currpos > 0) fprintf(fp, "\n");
+
+ if (msa->ss_cons != NULL) {
+ strncpy(buf, msa->ss_cons + currpos, cpl);
+ buf[cpl] = '\0';
+ fprintf(fp, "%-*.*s %s\n", namewidth, namewidth, "#=CS", buf);
+ }
+ if (msa->rf != NULL) {
+ strncpy(buf, msa->rf + currpos, cpl);
+ buf[cpl] = '\0';
+ fprintf(fp, "%-*.*s %s\n", namewidth, namewidth, "#=RF", buf);
+ }
+ for (i = 0; i < msa->nseq; i++)
+ {
+ strncpy(buf, msa->aseq[i] + currpos, cpl);
+ buf[cpl] = '\0';
+ fprintf(fp, "%-*.*s %s\n", namewidth, namewidth, msa->sqname[i], buf);
+
+ if (msa->ss != NULL && msa->ss[i] != NULL) {
+ strncpy(buf, msa->ss[i] + currpos, cpl);
+ buf[cpl] = '\0';
+ fprintf(fp, "%-*.*s %s\n", namewidth, namewidth, "#=SS", buf);
+ }
+ if (msa->sa != NULL && msa->sa[i] != NULL) {
+ strncpy(buf, msa->sa[i] + currpos, cpl);
+ buf[cpl] = '\0';
+ fprintf(fp, "%-*.*s %s\n", namewidth, namewidth, "#=SA", buf);
+ }
+ }
+ }
+ free(buf);
+}
+
+
+/* Function: copy_alignment_line()
+ *
+ * Purpose: Given a line from an alignment file, and bounds lcol,rcol
+ * on what part of it may be sequence, save the alignment into
+ * aseq starting at position apos.
+ *
+ * name_rcol is set to the rightmost column this aseqs's name
+ * occupies; if name_rcol >= lcol, we have a special case in
+ * which the name intrudes into the sequence zone.
+ */
+static int
+copy_alignment_line(char *aseq, int apos, int name_rcol,
+ char *buffer, int lcol, int rcol, char gapsym)
+{
+ char *s1, *s2;
+ int i;
+
+ s1 = aseq + apos;
+ s2 = buffer; /* be careful that buffer doesn't end before lcol! */
+ for (i = 0; i < lcol; i++)
+ if (*s2) s2++;
+
+ for (i = lcol; i <= rcol; i++)
+ {
+ if (*s2 == '\t') {
+#ifdef CLUSTALO
+ Warning("TAB characters will corrupt a SELEX alignment! Please remove them first.");
+#else
+ Warn("TAB characters will corrupt a SELEX alignment! Please remove them first.");
+#endif
+ return 0;
+ }
+ if (name_rcol >= i) /* name intrusion special case: pad left w/ gaps */
+ *s1 = gapsym;
+ /* short buffer special case: pad right w/ gaps */
+ else if (*s2 == '\0' || *s2 == '\n')
+ *s1 = gapsym;
+
+ else if (*s2 == ' ') /* new: disallow spaces as gap symbols */
+ *s1 = gapsym;
+
+ else /* normal case: copy buffer into aseq */
+ *s1 = *s2;
+
+ s1++;
+ if (*s2) s2++;
+ }
+ return 1;
+}
+
+
+
+
+
+/* Function: DealignAseqs()
+ *
+ * Given an array of (num) aligned sequences aseqs,
+ * strip the gaps. Store the raw sequences in a new allocated array.
+ *
+ * Caller is responsible for free'ing the memory allocated to
+ * rseqs.
+ *
+ * Returns 1 on success. Returns 0 and sets squid_errno on
+ * failure.
+ */
+int
+DealignAseqs(char **aseqs, int num, char ***ret_rseqs)
+{
+ char **rseqs; /* de-aligned sequence array */
+ int idx; /* counter for sequences */
+ int depos; /* position counter for dealigned seq*/
+ int apos; /* position counter for aligned seq */
+ int seqlen; /* length of aligned seq */
+
+ /* alloc space */
+ rseqs = (char **) MallocOrDie (num * sizeof(char *));
+ /* main loop */
+ for (idx = 0; idx < num; idx++)
+ {
+ seqlen = strlen(aseqs[idx]);
+ /* alloc space */
+ rseqs[idx] = (char *) MallocOrDie ((seqlen + 1) * sizeof(char));
+
+ /* strip gaps */
+ depos = 0;
+ for (apos = 0; aseqs[idx][apos] != '\0'; apos++)
+ if (!isgap(aseqs[idx][apos]))
+ {
+ rseqs[idx][depos] = aseqs[idx][apos];
+ depos++;
+ }
+ rseqs[idx][depos] = '\0';
+ }
+ *ret_rseqs = rseqs;
+ return 1;
+}
+
+
+/* Function: IsSELEXFormat()
+ *
+ * Return TRUE if filename may be in SELEX format.
+ *
+ * Accuracy is sacrificed for speed; a TRUE return does
+ * *not* guarantee that the file will pass the stricter
+ * error-checking of ReadSELEX(). All it checks is that
+ * the first 500 non-comment lines of a file are
+ * blank, or if there's a second "word" on the line
+ * it looks like sequence (i.e., it's not kOtherSeq).
+ *
+ * Returns TRUE or FALSE.
+ */
+int
+IsSELEXFormat(char *filename)
+{
+ FILE *fp; /* ptr to open sequence file */
+ char buffer[LINEBUFLEN];
+ char *sptr; /* ptr to first word */
+ int linenum;
+
+
+ if ((fp = fopen(filename, "r")) == NULL)
+ { squid_errno = SQERR_NOFILE; return 0; }
+
+ linenum = 0;
+ while (linenum < 500 &&
+ fgets(buffer, LINEBUFLEN, fp) != NULL)
+ {
+ linenum++;
+ /* dead giveaways for extended SELEX */
+ if (strncmp(buffer, "#=AU", 4) == 0) goto DONE;
+ else if (strncmp(buffer, "#=ID", 4) == 0) goto DONE;
+ else if (strncmp(buffer, "#=AC", 4) == 0) goto DONE;
+ else if (strncmp(buffer, "#=DE", 4) == 0) goto DONE;
+ else if (strncmp(buffer, "#=GA", 4) == 0) goto DONE;
+ else if (strncmp(buffer, "#=TC", 4) == 0) goto DONE;
+ else if (strncmp(buffer, "#=NC", 4) == 0) goto DONE;
+ else if (strncmp(buffer, "#=SQ", 4) == 0) goto DONE;
+ else if (strncmp(buffer, "#=SS", 4) == 0) goto DONE;
+ else if (strncmp(buffer, "#=CS", 4) == 0) goto DONE;
+ else if (strncmp(buffer, "#=RF", 4) == 0) goto DONE;
+
+ /* a comment? */
+ if (strchr(commentsyms, *buffer) != NULL) continue;
+
+ /* a blank line? */
+ if ((sptr = strtok(buffer, WHITESPACE)) == NULL) continue;
+
+ /* a one-word line (name only)
+ is possible, though rare */
+ if ((sptr = strtok(NULL, "\n")) == NULL) continue;
+
+ if (Seqtype(sptr) == kOtherSeq) {fclose(fp); return 0;}
+ }
+
+ DONE:
+ fclose(fp);
+ return 1;
+}
+
+
+
+
+
+
+
+
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* seqencode.c
+ *
+ * Routines for creating and manipulating encoded sequence strings.
+ * RCS $Id: seqencode.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: seqencode.c,v 1.3 1999/05/02 21:55:27 eddy Exp)
+ */
+#include <stdio.h>
+#include <string.h>
+#include <ctype.h>
+#include "squid.h"
+
+
+#ifdef MEMDEBUG
+#include "dbmalloc.h"
+#endif
+ /* seqcmp()
+ returns 0 if s1 == s2
+ mismatch number otherwise */
+int
+seqcmp(char *s1, char *s2, int allow)
+{
+ int mmat = 0;
+
+ while ((*s1 != NTEND) && (*s2 != NTEND) && (mmat <= allow))
+ {
+ if (!(ntmatch(*s1, *s2)))
+ mmat++;;
+ s1++;
+ s2++;
+ }
+ while ((*s1++ != NTEND) && (mmat <= allow))
+ mmat++;
+ return(mmat);
+}
+ /* seqncmp()
+ same as seqcmp but it looks at,
+ at most, n positions */
+int
+seqncmp(char *s1, char *s2, int n, int allow)
+{
+ int mmat = 0;
+
+ while ((*s2 != NTEND) &&
+ (n-- != 0))
+ {
+ if ((!(ntmatch(*s1, *s2))) &&
+ (++mmat > allow))
+ return(mmat);
+ s1++;
+ s2++;
+ }
+ while ((n-- != 0) && (*s1++ != NTEND) && (mmat <= allow))
+ mmat++;
+ return (mmat);
+}
+
+ /* seqencode()
+ given a character text string str (A,C,G,T),
+ convert to an encoded seq string;
+ return 1 for success, 0 if fail */
+int
+seqencode(char *codeseq, /* pre-allocated space for answer */
+ char *str) /* character string to convert */
+{
+ char *ptr;
+ int idx;
+
+ ptr = codeseq;
+ while (*str != '\0')
+ {
+ if (islower((int) (*str))) *str = (char) toupper((int) (*str));
+ for (idx = 0; *str != iupac[idx].sym && idx <= IUPACSYMNUM; idx++)
+ ;
+ if (idx > IUPACSYMNUM)
+ {
+ *ptr = (char) NTEND;
+ return 0;
+ }
+ else
+ *ptr = iupac[idx].code;
+ ptr++;
+ str++;
+ }
+ *ptr = NTEND;
+ return 1;
+}
+
+
+int
+coded_revcomp(char *comp, char *seq)
+{
+ long bases;
+ char *bckp, *fwdp;
+ int idx;
+ long pos;
+
+ bases = strlen(seq);
+
+ fwdp = comp;
+ bckp = seq + bases -1;
+ for (pos = 0; pos < bases; pos++)
+ {
+ for (idx = 0; *bckp != iupac[idx].code && idx < IUPACSYMNUM; idx++);
+ if (idx > IUPACSYMNUM)
+ {
+ *fwdp = NTEND;
+ return 0;
+ }
+ else
+ *fwdp = iupac[idx].comp;
+ fwdp++;
+ bckp--;
+ }
+ *fwdp = NTEND;
+ return(1);
+}
+
+int
+seqdecode(char *str, char *codeseq)
+{
+ int idx;
+ int pos;
+
+ pos = 0;
+ while (*codeseq != NTEND)
+ {
+ for (idx = 0; *codeseq != iupac[idx].code && idx < IUPACSYMNUM; idx++)
+ ;
+ if (idx > IUPACSYMNUM)
+ {
+ str[pos] = 'X';
+ return 0;
+ }
+ else
+ str[pos] = iupac[idx].sym;
+ codeseq++;
+ pos++;
+ }
+ str[pos] = '\0';
+ return 1;
+}
+
+int
+seqndecode(
+ char *str, /* pre-allocated string to write into */
+ char *codeseq, /* sequence to decode */
+ int n) /* how many bases to decode */
+{
+ int idx;
+ int pos = 0;
+
+ while (--n >= 0)
+ {
+ for (idx = 0; *codeseq != iupac[idx].code && idx < IUPACSYMNUM; idx++);
+ if (idx > IUPACSYMNUM)
+ {
+ str[pos] = 'X';
+ return 0;
+ }
+ else
+ str[pos] = iupac[idx].sym;
+ codeseq++;
+ pos++;
+ }
+ str[pos] = '\0';
+ return 1;
+}
+
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* shuffle.c
+ *
+ * Routines for randomizing sequences.
+ *
+ * All routines are alphabet-independent (DNA, protein, RNA, whatever);
+ * they assume that input strings are purely alphabetical [a-zA-Z], and
+ * will return strings in all upper case [A-Z].
+ *
+ * All return 1 on success, and 0 on failure; 0 status invariably
+ * means the input string was not alphabetical.
+ *
+ * StrShuffle() - shuffled string, preserve mono-symbol composition.
+ * StrDPShuffle() - shuffled string, preserve mono- and di-symbol composition.
+ *
+ * StrMarkov0() - random string, same zeroth order Markov properties.
+ * StrMarkov1() - random string, same first order Markov properties.
+ *
+ * StrReverse() - simple reversal of string
+ * StrRegionalShuffle() - mono-symbol shuffled string in regional windows
+ *
+ * There are also similar routines for shuffling alignments:
+ *
+ * AlignmentShuffle() - alignment version of StrShuffle().
+ * AlignmentBootstrap() - sample with replacement; a bootstrap dataset.
+ * QRNAShuffle() - shuffle a pairwise alignment, preserving all gap positions.
+ *
+ * CVS $Id: shuffle.c,v 1.6 2002/10/09 14:26:09 eddy Exp)
+ */
+
+#include <string.h>
+#include <ctype.h>
+
+#include "squid.h"
+#include "sre_random.h"
+
+/* Function: StrShuffle()
+ *
+ * Purpose: Returns a shuffled version of s2, in s1.
+ * (s1 and s2 can be identical, to shuffle in place.)
+ *
+ * Args: s1 - allocated space for shuffled string.
+ * s2 - string to shuffle.
+ *
+ * Return: 1 on success.
+ */
+int
+StrShuffle(char *s1, char *s2)
+{
+ int len;
+ int pos;
+ char c;
+
+ if (s1 != s2) strcpy(s1, s2);
+ for (len = strlen(s1); len > 1; len--)
+ {
+ pos = CHOOSE(len);
+ c = s1[pos];
+ s1[pos] = s1[len-1];
+ s1[len-1] = c;
+ }
+ return 1;
+}
+
+/* Function: StrDPShuffle()
+ * Date: SRE, Fri Oct 29 09:15:17 1999 [St. Louis]
+ *
+ * Purpose: Returns a shuffled version of s2, in s1.
+ * (s1 and s2 may be identical; i.e. a string
+ * may be shuffled in place.) The shuffle is a
+ * "doublet-preserving" (DP) shuffle. Both
+ * mono- and di-symbol composition are preserved.
+ *
+ * Done by searching for a random Eulerian
+ * walk on a directed multigraph.
+ * Reference: S.F. Altschul and B.W. Erickson, Mol. Biol.
+ * Evol. 2:526-538, 1985. Quoted bits in my comments
+ * are from Altschul's outline of the algorithm.
+ *
+ * Args: s1 - RETURN: the string after it's been shuffled
+ * (space for s1 allocated by caller)
+ * s2 - the string to be shuffled
+ *
+ * Returns: 0 if string can't be shuffled (it's not all [a-zA-z]
+ * alphabetic.
+ * 1 on success.
+ */
+int
+StrDPShuffle(char *s1, char *s2)
+{
+ int len;
+ int pos; /* a position in s1 or s2 */
+ int x,y; /* indices of two characters */
+ char **E; /* edge lists: E[0] is the edge list from vertex A */
+ int *nE; /* lengths of edge lists */
+ int *iE; /* positions in edge lists */
+ int n; /* tmp: remaining length of an edge list to be shuffled */
+ char sf; /* last character in s2 */
+ char Z[26]; /* connectivity in last edge graph Z */
+ int keep_connecting; /* flag used in Z connectivity algorithm */
+ int is_eulerian; /* flag used for when we've got a good Z */
+
+ /* First, verify that the string is entirely alphabetic.
+ */
+ len = strlen(s2);
+ for (pos = 0; pos < len; pos++)
+ if (! isalpha(s2[pos])) return 0;
+
+ /* "(1) Construct the doublet graph G and edge ordering E
+ * corresponding to S."
+ *
+ * Note that these also imply the graph G; and note,
+ * for any list x with nE[x] = 0, vertex x is not part
+ * of G.
+ */
+ E = MallocOrDie(sizeof(char *) * 26);
+ nE = MallocOrDie(sizeof(int) * 26);
+ for (x = 0; x < 26; x++)
+ {
+ E[x] = MallocOrDie(sizeof(char) * (len-1));
+ nE[x] = 0;
+ }
+
+ x = toupper(s2[0]) - 'A';
+ for (pos = 1; pos < len; pos++)
+ {
+ y = toupper(s2[pos]) - 'A';
+ E[x][nE[x]] = y;
+ nE[x]++;
+ x = y;
+ }
+
+ /* Now we have to find a random Eulerian edge ordering.
+ */
+ sf = toupper(s2[len-1]) - 'A';
+ is_eulerian = 0;
+ while (! is_eulerian)
+ {
+ /* "(2) For each vertex s in G except s_f, randomly select
+ * one edge from the s edge list of E(S) to be the
+ * last edge of the s list in a new edge ordering."
+ *
+ * select random edges and move them to the end of each
+ * edge list.
+ */
+ for (x = 0; x < 26; x++)
+ {
+ if (nE[x] == 0 || x == sf) continue;
+
+ pos = CHOOSE(nE[x]);
+ y = E[x][pos];
+ E[x][pos] = E[x][nE[x]-1];
+ E[x][nE[x]-1] = y;
+ }
+
+ /* "(3) From this last set of edges, construct the last-edge
+ * graph Z and determine whether or not all of its
+ * vertices are connected to s_f."
+ *
+ * a probably stupid algorithm for looking at the
+ * connectivity in Z: iteratively sweep through the
+ * edges in Z, and build up an array (confusing called Z[x])
+ * whose elements are 1 if x is connected to sf, else 0.
+ */
+ for (x = 0; x < 26; x++) Z[x] = 0;
+ Z[(int) sf] = keep_connecting = 1;
+
+ while (keep_connecting) {
+ keep_connecting = 0;
+ for (x = 0; x < 26; x++)
+ {
+ y = E[x][nE[x]-1]; /* xy is an edge in Z */
+ if (Z[x] == 0 && Z[y] == 1) /* x is connected to sf in Z */
+ {
+ Z[x] = 1;
+ keep_connecting = 1;
+ }
+ }
+ }
+
+ /* if any vertex in Z is tagged with a 0, it's
+ * not connected to sf, and we won't have a Eulerian
+ * walk.
+ */
+ is_eulerian = 1;
+ for (x = 0; x < 26; x++)
+ {
+ if (nE[x] == 0 || x == sf) continue;
+ if (Z[x] == 0) {
+ is_eulerian = 0;
+ break;
+ }
+ }
+
+ /* "(4) If any vertex is not connected in Z to s_f, the
+ * new edge ordering will not be Eulerian, so return to
+ * (2). If all vertices are connected in Z to s_f,
+ * the new edge ordering will be Eulerian, so
+ * continue to (5)."
+ *
+ * e.g. note infinite loop while is_eulerian is FALSE.
+ */
+ }
+
+ /* "(5) For each vertex s in G, randomly permute the remaining
+ * edges of the s edge list of E(S) to generate the s
+ * edge list of the new edge ordering E(S')."
+ *
+ * Essentially a StrShuffle() on the remaining nE[x]-1 elements
+ * of each edge list; unfortunately our edge lists are arrays,
+ * not strings, so we can't just call out to StrShuffle().
+ */
+ for (x = 0; x < 26; x++)
+ for (n = nE[x] - 1; n > 1; n--)
+ {
+ pos = CHOOSE(n);
+ y = E[x][pos];
+ E[x][pos] = E[x][n-1];
+ E[x][n-1] = y;
+ }
+
+ /* "(6) Construct sequence S', a random DP permutation of
+ * S, from E(S') as follows. Start at the s_1 edge list.
+ * At each s_i edge list, add s_i to S', delete the
+ * first edge s_i,s_j of the edge list, and move to
+ * the s_j edge list. Continue this process until
+ * all edge lists are exhausted."
+ */
+ iE = MallocOrDie(sizeof(int) * 26);
+ for (x = 0; x < 26; x++) iE[x] = 0;
+
+ pos = 0;
+ x = toupper(s2[0]) - 'A';
+ while (1)
+ {
+ s1[pos++] = 'A' + x; /* add s_i to S' */
+
+ y = E[x][iE[x]];
+ iE[x]++; /* "delete" s_i,s_j from edge list */
+
+ x = y; /* move to s_j edge list. */
+
+ if (iE[x] == nE[x])
+ break; /* the edge list is exhausted. */
+ }
+ s1[pos++] = 'A' + sf;
+ s1[pos] = '\0';
+
+ /* Reality checks.
+ */
+ if (x != sf) Die("hey, you didn't end on s_f.");
+ if (pos != len) Die("hey, pos (%d) != len (%d).", pos, len);
+
+ /* Free and return.
+ */
+ Free2DArray((void **) E, 26);
+ free(nE);
+ free(iE);
+ return 1;
+}
+
+
+/* Function: StrMarkov0()
+ * Date: SRE, Fri Oct 29 11:08:31 1999 [St. Louis]
+ *
+ * Purpose: Returns a random string s1 with the same
+ * length and zero-th order Markov properties
+ * as s2.
+ *
+ * s1 and s2 may be identical, to randomize s2
+ * in place.
+ *
+ * Args: s1 - allocated space for random string
+ * s2 - string to base s1's properties on.
+ *
+ * Returns: 1 on success; 0 if s2 doesn't look alphabetical.
+ */
+int
+StrMarkov0(char *s1, char *s2)
+{
+ int len;
+ int pos;
+ float p[26]; /* symbol probabilities */
+
+ /* First, verify that the string is entirely alphabetic.
+ */
+ len = strlen(s2);
+ for (pos = 0; pos < len; pos++)
+ if (! isalpha(s2[pos])) return 0;
+
+ /* Collect zeroth order counts and convert to frequencies.
+ */
+ FSet(p, 26, 0.);
+ for (pos = 0; pos < len; pos++)
+ p[(int)(toupper(s2[pos]) - 'A')] += 1.0;
+ FNorm(p, 26);
+
+ /* Generate a random string using those p's.
+ */
+ for (pos = 0; pos < len; pos++)
+ s1[pos] = FChoose(p, 26) + 'A';
+ s1[pos] = '\0';
+
+ return 1;
+}
+
+
+/* Function: StrMarkov1()
+ * Date: SRE, Fri Oct 29 11:22:20 1999 [St. Louis]
+ *
+ * Purpose: Returns a random string s1 with the same
+ * length and first order Markov properties
+ * as s2.
+ *
+ * s1 and s2 may be identical, to randomize s2
+ * in place.
+ *
+ * Args: s1 - allocated space for random string
+ * s2 - string to base s1's properties on.
+ *
+ * Returns: 1 on success; 0 if s2 doesn't look alphabetical.
+ */
+int
+StrMarkov1(char *s1, char *s2)
+{
+ int len;
+ int pos;
+ int x,y;
+ int i; /* initial symbol */
+ float p[26][26]; /* symbol probabilities */
+
+ /* First, verify that the string is entirely alphabetic.
+ */
+ len = strlen(s2);
+ for (pos = 0; pos < len; pos++)
+ if (! isalpha(s2[pos])) return 0;
+
+ /* Collect first order counts and convert to frequencies.
+ */
+ for (x = 0; x < 26; x++) FSet(p[x], 26, 0.);
+
+ i = x = toupper(s2[0]) - 'A';
+ for (pos = 1; pos < len; pos++)
+ {
+ y = toupper(s2[pos]) - 'A';
+ p[x][y] += 1.0;
+ x = y;
+ }
+ for (x = 0; x < 26; x++)
+ FNorm(p[x], 26);
+
+ /* Generate a random string using those p's.
+ */
+ x = i;
+ s1[0] = x + 'A';
+ for (pos = 1; pos < len; pos++)
+ {
+ y = FChoose(p[x], 26);
+ s1[pos] = y + 'A';
+ x = y;
+ }
+ s1[pos] = '\0';
+
+ return 1;
+}
+
+
+
+/* Function: StrReverse()
+ * Date: SRE, Thu Nov 20 10:54:52 1997 [St. Louis]
+ *
+ * Purpose: Returns a reversed version of s2, in s1.
+ * (s1 and s2 can be identical, to reverse in place)
+ *
+ * Args: s1 - allocated space for reversed string.
+ * s2 - string to reverse.
+ *
+ * Return: 1.
+ */
+int
+StrReverse(char *s1, char *s2)
+{
+ int len;
+ int pos;
+ char c;
+
+ len = strlen(s2);
+ for (pos = 0; pos < len/2; pos++)
+ { /* swap ends */
+ c = s2[len-pos-1];
+ s1[len-pos-1] = s2[pos];
+ s1[pos] = c;
+ }
+ if (len%2) { s1[pos] = s2[pos]; } /* copy middle residue in odd-len s2 */
+ s1[len] = '\0';
+ return 1;
+}
+
+/* Function: StrRegionalShuffle()
+ * Date: SRE, Thu Nov 20 11:02:34 1997 [St. Louis]
+ *
+ * Purpose: Returns a regionally shuffled version of s2, in s1.
+ * (s1 and s2 can be identical to regionally
+ * shuffle in place.) See [Pearson88].
+ *
+ * Args: s1 - allocated space for regionally shuffled string.
+ * s2 - string to regionally shuffle
+ * w - window size (typically 10 or 20)
+ *
+ * Return: 1.
+ */
+int
+StrRegionalShuffle(char *s1, char *s2, int w)
+{
+ int len;
+ char c;
+ int pos;
+ int i, j;
+
+ if (s1 != s2) strcpy(s1, s2);
+ len = strlen(s1);
+
+ for (i = 0; i < len; i += w)
+ for (j = MIN(len-1, i+w-1); j > i; j--)
+ {
+ pos = i + CHOOSE(j-i);
+ c = s1[pos];
+ s1[pos] = s1[j];
+ s1[j] = c;
+ }
+ return 1;
+}
+
+
+/* Function: AlignmentShuffle()
+ * Date: SRE, Sun Apr 22 18:37:15 2001 [St. Louis]
+ *
+ * Purpose: Returns a shuffled version of ali2, in ali1.
+ * (ali1 and ali2 can be identical, to shuffle
+ * in place.) The alignment columns are shuffled,
+ * preserving % identity within the columns.
+ *
+ * Args: ali1 - allocated space for shuffled alignment
+ * [0..nseq-1][0..alen-1]
+ * ali2 - alignment to be shuffled
+ * nseq - number of sequences in the alignment
+ * alen - length of alignment, in columns.
+ *
+ * Returns: int
+ */
+int
+AlignmentShuffle(char **ali1, char **ali2, int nseq, int alen)
+{
+ int i;
+ int pos;
+ char c;
+
+ if (ali1 != ali2)
+ {
+ for (i = 0; i < nseq; i++) strcpy(ali1[i], ali2[i]);
+ }
+
+ for (i = 0; i < nseq; i++)
+ ali1[i][alen] = '\0';
+
+ for (; alen > 1; alen--)
+ {
+ pos = CHOOSE(alen);
+ for (i = 0; i < nseq; i++)
+ {
+ c = ali1[i][pos];
+ ali1[i][pos] = ali1[i][alen-1];
+ ali1[i][alen-1] = c;
+ }
+ }
+
+ return 1;
+}
+
+/* Function: AlignmentBootstrap()
+ * Date: SRE, Sun Apr 22 18:49:14 2001 [St. Louis]
+ *
+ * Purpose: Returns a bootstrapped alignment sample in ali1,
+ * constructed from ali2 by sampling columns with
+ * replacement.
+ *
+ * Unlike the other shuffling routines, ali1 and
+ * ali2 cannot be the same. ali2 is left unchanged.
+ * ali1 must be a properly allocated space for an
+ * alignment the same size as ali2.
+ *
+ * Args: ali1 - allocated space for bootstrapped alignment
+ * [0..nseq-1][0..alen-1]
+ * ali2 - alignment to be bootstrapped
+ * nseq - number of sequences in the alignment
+ * alen - length of alignment, in columns.
+ *
+ * Returns: 1 on success.
+ */
+int
+AlignmentBootstrap(char **ali1, char **ali2, int nseq, int alen)
+{
+ int pos;
+ int col;
+ int i;
+
+ for (pos = 0; pos < alen; pos++)
+ {
+ col = CHOOSE(alen);
+ for (i = 0; i < nseq; i++)
+ ali1[i][pos] = ali2[i][col];
+ }
+ for (i = 0; i < nseq; i++)
+ ali1[i][alen] = '\0';
+
+ return 1;
+}
+
+
+/* Function: QRNAShuffle()
+ * Date: SRE, Mon Dec 10 10:14:12 2001 [St. Louis]
+ *
+ * Purpose: Shuffle a pairwise alignment x,y while preserving the
+ * position of gaps; return the shuffled alignment in xs,
+ * ys.
+ *
+ * Works by doing three separate
+ * shuffles, of (1) columns with residues in both
+ * x and y, (2) columns with residue in x and gap in y,
+ * and (3) columns with gap in x and residue in y.
+ *
+ * xs,x and ys,y may be identical: that is, to shuffle
+ * an alignment "in place", destroying the original
+ * alignment, just call:
+ * QRNAShuffle(x,y,x,y);
+ *
+ * Args: xs, ys: allocated space for shuffled pairwise ali of x,y [L+1]
+ * x, y: pairwise alignment to be shuffled [0..L-1]
+ *
+ * Returns: 1 on success, 0 on failure.
+ * The shuffled alignment is returned in xs, ys.
+ */
+int
+QRNAShuffle(char *xs, char *ys, char *x, char *y)
+{
+ int L;
+ int *xycol, *xcol, *ycol;
+ int nxy, nx, ny;
+ int i;
+ int pos, c;
+ char xsym, ysym;
+
+ if (xs != x) strcpy(xs, x);
+ if (ys != y) strcpy(ys, y);
+
+ /* First, construct three arrays containing lists of the column positions
+ * of the three types of columns. (If a column contains gaps in both x and y,
+ * we've already simply copied it to the shuffled sequence.)
+ */
+ L = strlen(x);
+ xycol = MallocOrDie(sizeof(int) * L);
+ xcol = MallocOrDie(sizeof(int) * L);
+ ycol = MallocOrDie(sizeof(int) * L);
+ nxy = nx = ny = 0;
+
+ for (i = 0; i < L; i++)
+ {
+ if (isgap(x[i]) && isgap(y[i])) { continue; }
+ else if (! isgap(x[i]) && ! isgap(y[i])) { xycol[nxy] = i; nxy++; }
+ else if (isgap(x[i])) { ycol[ny] = i; ny++; }
+ else if (isgap(y[i])) { xcol[nx] = i; nx++; }
+ }
+
+ /* Second, shuffle the sequences indirectly, via shuffling these arrays.
+ * Yow, careful with those indices, and with order of the statements...
+ */
+ for (; nxy > 1; nxy--) {
+ pos = CHOOSE(nxy);
+ xsym = xs[xycol[pos]]; ysym = ys[xycol[pos]]; c = xycol[pos];
+ xs[xycol[pos]] = xs[xycol[nxy-1]]; ys[xycol[pos]] = ys[xycol[nxy-1]]; xycol[pos] = xycol[nxy-1];
+ xs[xycol[nxy-1]] = xsym; ys[xycol[nxy-1]] = ysym; xycol[pos] = xycol[nxy-1];
+ }
+ for (; nx > 1; nx--) {
+ pos = CHOOSE(nx);
+ xsym = xs[xcol[pos]]; ysym = ys[xcol[pos]]; c = xcol[pos];
+ xs[xcol[pos]] = xs[xcol[nx-1]]; ys[xcol[pos]] = ys[xcol[nx-1]]; xcol[pos] = xcol[nx-1];
+ xs[xcol[nx-1]] = xsym; ys[xcol[nx-1]] = ysym; xcol[nx-1] = c;
+ }
+ for (; ny > 1; ny--) {
+ pos = CHOOSE(ny);
+ xsym = xs[ycol[pos]]; ysym = ys[ycol[pos]]; c = ycol[pos];
+ xs[ycol[pos]] = xs[ycol[ny-1]]; ys[ycol[pos]] = ys[ycol[ny-1]]; ycol[pos] = ycol[ny-1];
+ xs[ycol[ny-1]] = xsym; ys[ycol[ny-1]] = ysym; ycol[ny-1] = c;
+ }
+
+ free(xycol); free(xcol); free(ycol);
+ return 1;
+}
+
+
+#ifdef TESTDRIVER
+/*
+ * cc -g -o testdriver -DTESTDRIVER -L. shuffle.c -lsquid -lm
+ */
+int
+main(int argc, char **argv)
+{
+ char s1[100];
+ char s2[100];
+
+ sre_srandom(42);
+ strcpy(s2, "GGGGGGGGGGCCCCCCCCCC");
+ /* strcpy(s2, "AGACATAAAGTTCCGTACTGCCGGGAT");
+ */
+ StrDPShuffle(s1, s2);
+ printf("DPshuffle: %s\n", s1);
+ StrMarkov0(s1,s2);
+ printf("Markov 0 : %s\n", s1);
+ StrMarkov1(s1,s2);
+ printf("Markov 1 : %s\n", s1);
+
+ strcpy(s1, "ACGTACGT--------ACGTACGT----ACGTACGT");
+ strcpy(s2, "ACGTACGTACGTACGT------------ACGTACGT");
+ QRNAShuffle(s1,s2,s1,s2);
+ printf("QRNA : %s\n", s1);
+ printf(" : %s\n", s2);
+
+ return 0;
+}
+#endif
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* sqerror.c
+ *
+ * error handling for the squid library
+ * RCS $Id: sqerror.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: sqerror.c,v 1.4 1999/07/15 22:28:31 eddy Exp)
+ */
+
+ /* a global errno equivalent */
+int squid_errno;
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdarg.h>
+
+#ifdef MEMDEBUG
+#include "dbmalloc.h"
+#endif
+
+/* Function: Die()
+ *
+ * Purpose: Print an error message and die. The arguments
+ * are formatted exactly like arguments to printf().
+ *
+ * Return: None. Exits the program.
+ */
+/* VARARGS0 */
+void
+Die(char *format, ...)
+{
+ va_list argp;
+ /* format the error mesg */
+ fprintf(stderr, "\nFATAL: ");
+ va_start(argp, format);
+ vfprintf(stderr, format, argp);
+ va_end(argp);
+ fprintf(stderr, "\n");
+ fflush(stderr);
+ /* exit */
+ exit(1);
+}
+
+
+
+/* Function: Warn()
+ *
+ * Purpose: Print an error message and return. The arguments
+ * are formatted exactly like arguments to printf().
+ *
+ * Return: (void)
+ */
+/* VARARGS0 */
+void
+#ifdef CLUSTALO
+Warning(char *format, ...)
+#else
+Warn(char *format, ...)
+#endif
+{
+ va_list argp;
+ /* format the error mesg */
+ fprintf(stderr, "WARNING: ");
+ va_start(argp, format);
+ vfprintf(stderr, format, argp);
+ va_end(argp);
+ fprintf(stderr, "\n");
+ fflush(stderr);
+}
+
+/* Function: Panic()
+ *
+ * Purpose: Die from a lethal error that's not my problem,
+ * but instead a failure of a StdC/POSIX call that
+ * shouldn't fail. Call perror() to get the
+ * errno flag, then die.
+ *
+ * Usually called by the PANIC macro which adds
+ * the __FILE__ and __LINE__ information; see
+ * structs.h.
+ *
+ * Inspired by code in Donald Lewine's book, _POSIX
+ * Programmer's Guide_.
+ */
+void
+Panic(char *file, int line)
+{
+ (void) fprintf(stderr, "\nPANIC [%s line %d] ", file, line);
+ (void) perror("Unusual error");
+ exit(EXIT_FAILURE);
+}
+
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+#ifndef SQFUNCSH_INCLUDED
+#define SQFUNCSH_INCLUDED
+/* sqfuncs.h
+ *
+ * Prototypes for squid library functions;
+ * also makes a good reference list for what the package contains.
+ *
+ * Warning: squid is a slowly evolving beast. Some functions are
+ * obsolete. Some functions are probably just wrong, dating to
+ * a primordial era before I knew anything about what I was doing.
+ * Some functions are both obsolete and wrong but still necessary
+ * to get legacy code to compile.
+ *
+ * CVS $Id: sqfuncs.h,v 1.28 2002/10/09 14:26:09 eddy Exp)
+ */
+
+/*
+ * from aligneval.c
+ */
+extern float ComparePairAlignments(char *known1, char *known2, char *calc1, char *calc2);
+extern float CompareRefPairAlignments(int *ref, char *known1, char *known2, char *calc1, char *calc2);
+extern float CompareMultAlignments(char **kseqs, char **tseqs, int N);
+extern float CompareRefMultAlignments(int *ref, char **kseqs, char **tseqs, int N);
+extern float PairwiseIdentity(char *s1, char *s2);
+extern float AlignmentIdentityBySampling(char **aseq, int L, int N, int nsample);
+extern char *MajorityRuleConsensus(char **aseq, int nseq, int alen);
+
+/*
+ * from alignio.c
+ */
+extern void AllocAlignment(int nseq, int alen, char ***ret_aseq, AINFO *ainfo);
+extern void InitAinfo(AINFO *ainfo);
+extern void FreeAlignment(char **aseqs, AINFO *ainfo);
+extern void SAMizeAlignment(char **aseq, int nseq, int alen);
+extern void SAMizeAlignmentByGapFrac(char **aseq, int nseq, int alen, float maxgap);
+extern int MakeAlignedString(char *aseq, int alen, char *ss, char **ret_s);
+extern int MakeDealignedString(char *aseq, int alen, char *ss, char **ret_s);
+extern int DealignedLength(char *aseq);
+extern int WritePairwiseAlignment(FILE *ofp, char *aseq1, char *name1, int spos1,
+ char *aseq2, char *name2, int spos2,
+ int **pam, int indent);
+extern int MingapAlignment(char **aseqs, AINFO *ainfo);
+extern int RandomAlignment(char **rseqs, SQINFO *sqinfo, int nseq, float pop, float pex,
+ char ***ret_aseqs, AINFO *ainfo);
+extern void AlignmentHomogenousGapsym(char **aseq, int nseq, int alen, char gapsym);
+
+/* from cluster.c
+ */
+extern int Cluster(float **mx, int N, enum clust_strategy mode, struct phylo_s **ret_tree);
+extern struct phylo_s *AllocPhylo(int N);
+extern void FreePhylo(struct phylo_s *tree, int N);
+extern void MakeDiffMx(char **aseqs, int num, float ***ret_dmx);
+extern void MakeIdentityMx(char **aseqs, int num, float ***ret_imx);
+extern void PrintNewHampshireTree(FILE *fp, AINFO *ainfo, struct phylo_s *tree, int N);
+extern void PrintPhylo(FILE *fp, AINFO *ainfo, struct phylo_s *tree, int N);
+
+/*
+ * from dayhoff.c
+ */
+extern int ParsePAMFile(FILE *fp, int ***ret_pam, float *ret_scale);
+extern void ScalePAM(int **pam, int scale);
+
+
+/* from file.c
+ */
+extern char *FileDirname(char *filename);
+extern char *FileTail(char *file, int noextension);
+extern char *FileSameDirectory(char *full, char *file);
+extern char *FileConcat(char *dir, char *file);
+extern char *FileAddSuffix(char *filename, char *sfx);
+extern FILE *EnvFileOpen(char *fname, char *env, char **ret_dir);
+extern int FileExists(char *filename);
+
+
+/* from getopt.c
+ */
+extern int Getopt(int argc, char **argv,
+ struct opt_s *opt, int nopts, char *usage,
+ int *ret_optind, char **ret_optname, char **ret_optarg);
+
+
+/* from hsregex.c
+ * Henry Spencer's regex() code
+ */
+extern int Strparse(char *rexp, char *s, int ntok);
+extern void SqdClean(void);
+extern sqd_regexp *sqd_regcomp(const char *re);
+extern int sqd_regexec(sqd_regexp *rp, const char *s);
+extern void sqd_regsub(const sqd_regexp *rp, const char *src, char *dst);
+extern void sqd_regerror(char *message);
+
+/* from interleaved.c
+ */
+extern int IsInterleavedFormat(int format);
+extern int ReadInterleaved(char *seqfile,
+ int (*skip_header)(FILE *),
+ int (*parse_header)(FILE *, AINFO *),
+ int (*is_dataline)(char *, char *),
+ char ***ret_aseqs, AINFO *ainfo);
+extern int ReadAlignment(char *seqfile, int format, char ***ret_aseqs, AINFO *ainfo);
+
+
+/* from revcomp.c
+ */
+extern char *revcomp(char *comp, char *seq);
+
+/*
+ * from selex.c
+ */
+extern int DealignAseqs(char **aseqs, int num, char ***ret_rseqs);
+extern int IsSELEXFormat(char *filename);
+extern int TruncateNames(char **names, int N); /* OBSOLETE? */
+
+/*
+ * from seqencode.c
+ */
+extern int seqcmp(char *s1, char *s2, int allow);
+extern int seqncmp(char *s1, char *s2, int n, int allow);
+extern int seqencode(char *codeseq,char *str);
+extern int coded_revcomp(char *comp, char *seq);
+extern int seqdecode(char *str, char *codeseq);
+extern int seqndecode(char *str, char *codeseq, int n);
+
+/*
+ * from shuffle.c
+ */
+extern int StrShuffle(char *s1, char *s2);
+extern int StrDPShuffle(char *s1, char *s2);
+extern int StrMarkov0(char *s1, char *s2);
+extern int StrMarkov1(char *s1, char *s2);
+extern int StrReverse(char *s1, char *s2);
+extern int StrRegionalShuffle(char *s1, char *s2, int w);
+extern int AlignmentShuffle(char **ali1, char **ali2, int nseq, int alen);
+extern int AlignmentBootstrap(char **ali1, char **ali2, int nseq, int alen);
+extern int QRNAShuffle(char *xs, char *ys, char *x, char *y);
+
+/*
+ * from sqerror.c
+ */
+extern void Die(char *format, ...);
+#ifdef CLUSTALO
+extern void Warning(char *format, ...);
+#else
+extern void Warn(char *format, ...);
+#endif
+extern void Panic(char *file, int line);
+
+
+/*
+ * from sqio.c
+ */
+extern void FreeSequence(char *seq, SQINFO *sqinfo);
+extern int SetSeqinfoString(SQINFO *sqinfo, char *sptr, int flag);
+extern void SeqinfoCopy(SQINFO *sq1, SQINFO *sq2);
+extern void ToDNA(char *seq);
+extern void ToRNA(char *seq);
+extern void ToIUPAC(char *seq, int is_aseq);
+extern int ReadMultipleRseqs(char *seqfile, int fformat, char ***ret_rseqs,
+ SQINFO **ret_sqinfo, int *ret_num);
+extern SQFILE *SeqfileOpen(char *filename, int format, char *env);
+extern SQFILE *SeqfileOpenForIndexing(char *filename, int format, char *env, int ssimode);
+extern int SeqfileFormat(FILE *fp);
+extern void SeqfilePosition(SQFILE *sfp, SSIOFFSET *offset);
+extern void SeqfileRewind(SQFILE *sfp);
+extern void SeqfileClose(SQFILE *sfp);
+
+extern int ReadSeq(SQFILE *fp, int format, char **ret_seq, SQINFO *sqinfo);
+extern int GCGBinaryToSequence(char *seq, int len);
+extern int GCGchecksum(char *seq, int seqlen);
+extern int GCGMultchecksum(char **seqs, int nseq);
+extern void WriteSimpleFASTA(FILE *fp, char *seq, char *name, char *desc);
+extern int WriteSeq(FILE *outf, int outfmt, char *seq, SQINFO *sqinfo);
+extern int Seqtype(char *seq);
+extern int GuessAlignmentSeqtype(char **aseq, int nseq);
+extern int String2SeqfileFormat(char *s);
+extern char *SeqfileFormat2String(int code);
+extern SQINFO *MSAToSqinfo(MSA *msa);
+
+/* from squidcore.c
+ */
+extern void Banner(FILE *fp, char *banner);
+
+
+/* from sre_ctype.c
+ */
+extern int sre_tolower(int c);
+extern int sre_toupper(int c);
+
+/* from sre_math.c
+ */
+extern int Linefit(float *x, float *y, int N,
+ float *ret_a, float *ret_b, float *ret_r);
+extern void WeightedLinefit(float *x, float *y, float *var, int N,
+ float *ret_m, float *ret_b);
+extern double Gammln(double xx);
+extern float **FMX2Alloc(int rows, int cols);
+extern void FMX2Free(float **mx);
+extern double **DMX2Alloc(int rows, int cols);
+extern void DMX2Free(double **mx);
+extern void FMX2Multiply(float **A, float **B, float **C, int m, int p, int n);
+extern double IncompleteGamma(double a, double x);
+
+/* from sre_string.c
+ */
+#ifdef NOSTR
+extern char *strstr(char *s, char *subs);
+#endif
+extern char *Strdup(char *s);
+extern void StringChop(char *s);
+extern int Strinsert(char *s1, char c, int pos);
+extern int Strdelete(char *s1, int pos);
+extern void s2lower(char *s);
+extern void s2upper(char *s);
+extern void *sre_malloc(char *file, int line, size_t size);
+extern void *sre_realloc(char *file, int line, void *p, size_t size);
+extern void Free2DArray(void **p, int dim1);
+extern void Free3DArray(void ***p, int dim1, int dim2);
+extern char *RandomSequence(char *alphabet, float *p, int n, int len);
+extern char *sre_fgets(char **buf, int *n, FILE *fp);
+extern int sre_strcat(char **dest, int ldest, char *src, int lsrc);
+extern char *sre_strtok(char **s, char *delim, int *len);
+extern char *sre_strdup(char *s, int n);
+extern char *sre_strncat(char *s1, char *s2, int n);
+extern int IsBlankline(char *s);
+
+/* from stack.c
+ */
+extern struct intstack_s *InitIntStack(void);
+extern void PushIntStack(struct intstack_s *stack, int data);
+extern int PopIntStack(struct intstack_s *stack, int *ret_data);
+extern void ReverseIntStack(struct intstack_s *stack);
+extern int FreeIntStack( struct intstack_s *stack );
+
+/*
+ * from translate.c
+ */
+extern char *Translate(char *seq, char **code);
+
+/*
+ * from types.c
+ */
+extern int IsInt(char *s);
+extern int IsReal(char *s);
+extern void Byteswap(char *swap, int nbytes);
+#ifndef USE_HOST_BYTESWAP_FUNCTIONS
+extern sqd_uint16 sre_ntoh16(sqd_uint16 netshort);
+extern sqd_uint32 sre_ntoh32(sqd_uint32 netlong);
+extern sqd_uint16 sre_hton16(sqd_uint16 hostshort);
+extern sqd_uint32 sre_hton32(sqd_uint32 hostlong);
+#endif /*!USE_HOST_BYTESWAP_FUNCTIONS*/
+extern sqd_uint64 sre_ntoh64(sqd_uint64 net_int64);
+extern sqd_uint64 sre_hton64(sqd_uint64 host_int64);
+
+/*
+ * from weight.c
+ */
+extern void GSCWeights(char **aseq, int nseq, int alen, float *wgt);
+extern void VoronoiWeights(char **aseq, int nseq, int alen, float *wgt);
+extern void BlosumWeights(char **aseq, int nseq, int alen, float blosumlevel, float *wgt);
+extern void PositionBasedWeights(char **aseq, int nseq, int alen, float *wgt);
+extern void FilterAlignment(MSA *msa, float cutoff, MSA **ret_new);
+extern void SampleAlignment(MSA *msa, int sample, MSA **ret_new);
+extern void SingleLinkCluster(char **aseq, int nseq, int alen, float maxid,
+ int **ret_c, int *ret_nc);
+#endif /* SQFUNCSH_INCLUDED */
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* File: sqio.c
+ * From: ureadseq.c in Don Gilbert's sequence i/o package
+ *
+ * Reads and writes nucleic/protein sequence in various
+ * formats. Data files may have multiple sequences.
+ *
+ * Heavily modified from READSEQ package
+ * Copyright (C) 1990 by D.G. Gilbert
+ * Biology Dept., Indiana University, Bloomington, IN 47405
+ * email: gilbertd@bio.indiana.edu
+ * Thanks Don!
+ *
+ * SRE: Modifications as noted. Fri Jul 3 09:44:54 1992
+ * Packaged for squid, Thu Oct 1 10:07:11 1992
+ * ANSI conversion in full swing, Mon Jul 12 12:22:21 1993
+ *
+ * CVS $Id: sqio.c,v 1.29 2002/08/26 23:10:52 eddy Exp)
+ *
+ *****************************************************************
+ * Basic API for single sequence reading:
+ *
+ * SQFILE *sqfp;
+ * char *seqfile;
+ * int format; - see squid.h for formats; example: SQFILE_FASTA
+ * char *seq;
+ * SQINFO sqinfo;
+ *
+ * if ((sqfp = SeqfileOpen(seqfile, format, "BLASTDB")) == NULL)
+ * Die("Failed to open sequence database file %s\n%s\n", seqfile, usage);
+ * while (ReadSeq(sqfp, sqfp->format, &seq, &sqinfo)) {
+ * do_stuff;
+ * FreeSequence(seq, &sqinfo);
+ * }
+ * SeqfileClose(sqfp);
+ *
+ *****************************************************************
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+
+#ifndef SEEK_SET
+#include <unistd.h>
+#endif
+
+#include "squid.h"
+#include "msa.h"
+#include "ssi.h"
+
+static void SeqfileGetLine(SQFILE *V);
+
+#define kStartLength 500
+
+static char *aminos = "ABCDEFGHIKLMNPQRSTVWXYZ*";
+static char *primenuc = "ACGTUN";
+static char *protonly = "EFIPQZ";
+
+static SQFILE *seqfile_open(char *filename, int format, char *env, int ssimode);
+
+/* Function: SeqfileOpen()
+ *
+ * Purpose : Open a sequence database file and prepare for reading
+ * sequentially.
+ *
+ * Args: filename - name of file to open
+ * format - format of file
+ * env - environment variable for path (e.g. BLASTDB)
+ * ssimode - -1, SSI_OFFSET_I32, or SSI_OFFSET_I64
+ *
+ * Returns opened SQFILE ptr, or NULL on failure.
+ */
+SQFILE *
+SeqfileOpen(char *filename, int format, char *env)
+{
+ return seqfile_open(filename, format, env, -1);
+}
+SQFILE *
+SeqfileOpenForIndexing(char *filename, int format, char *env, int ssimode)
+{
+ return seqfile_open(filename, format, env, ssimode);
+}
+static SQFILE *
+seqfile_open(char *filename, int format, char *env, int ssimode)
+{
+ SQFILE *dbfp;
+
+ dbfp = (SQFILE *) MallocOrDie (sizeof(SQFILE));
+
+ dbfp->ssimode = ssimode;
+ dbfp->rpl = -1; /* flag meaning "unset" */
+ dbfp->lastrpl = 0;
+ dbfp->maxrpl = 0;
+ dbfp->bpl = -1; /* flag meaning "unset" */
+ dbfp->lastbpl = 0;
+ dbfp->maxbpl = 0;
+
+ /* Open our file handle.
+ * Three possibilities:
+ * 1. normal file open
+ * 2. filename = "-"; read from stdin
+ * 3. filename = "*.gz"; read thru pipe from gzip
+ * If we're reading from stdin or a pipe, we can't reliably
+ * back up, so we can't do two-pass parsers like the interleaved alignment
+ * formats.
+ */
+ if (strcmp(filename, "-") == 0)
+ {
+ dbfp->f = stdin;
+ dbfp->do_stdin = TRUE;
+ dbfp->do_gzip = FALSE;
+ dbfp->fname = sre_strdup("[STDIN]", -1);
+ }
+#ifndef SRE_STRICT_ANSI
+ /* popen(), pclose() aren't portable to non-POSIX systems; disable */
+ else if (Strparse("^.*\\.gz$", filename, 0))
+ {
+ char cmd[256];
+
+ /* Note that popen() will return "successfully"
+ * if file doesn't exist, because gzip works fine
+ * and prints an error! So we have to check for
+ * existence of file ourself.
+ */
+ if (! FileExists(filename))
+ Die("%s: file does not exist", filename);
+
+ if (strlen(filename) + strlen("gzip -dc ") >= 256)
+ Die("filename > 255 char in SeqfileOpen()");
+ sprintf(cmd, "gzip -dc %s", filename);
+ if ((dbfp->f = popen(cmd, "r")) == NULL)
+ return NULL;
+
+ dbfp->do_stdin = FALSE;
+ dbfp->do_gzip = TRUE;
+ dbfp->fname = sre_strdup(filename, -1);
+ }
+#endif /*SRE_STRICT_ANSI*/
+ else
+ {
+ if ((dbfp->f = fopen(filename, "r")) == NULL &&
+ (dbfp->f = EnvFileOpen(filename, env, NULL)) == NULL)
+ return NULL;
+
+ dbfp->do_stdin = FALSE;
+ dbfp->do_gzip = FALSE;
+ dbfp->fname = sre_strdup(filename, -1);
+ }
+
+
+ /* Invoke autodetection if we haven't already been told what
+ * to expect.
+ */
+ if (format == SQFILE_UNKNOWN)
+ {
+ if (dbfp->do_stdin == TRUE || dbfp->do_gzip)
+ Die("Can't autodetect sequence file format from a stdin or gzip pipe");
+ format = SeqfileFormat(dbfp->f);
+ if (format == SQFILE_UNKNOWN)
+ Die("Can't determine format of sequence file %s", dbfp->fname);
+ }
+
+ /* The hack for sequential access of an interleaved alignment file:
+ * read the alignment in, we'll copy sequences out one at a time.
+ */
+ dbfp->msa = NULL;
+ dbfp->afp = NULL;
+ dbfp->format = format;
+ dbfp->linenumber = 0;
+ dbfp->buf = NULL;
+ dbfp->buflen = 0;
+ if (IsAlignmentFormat(format))
+ {
+ /* We'll be reading from the MSA interface. Copy our data
+ * to the MSA afp's structure.
+ */
+ dbfp->afp = MallocOrDie(sizeof(MSAFILE));
+ dbfp->afp->f = dbfp->f; /* just a ptr, don't close */
+ dbfp->afp->do_stdin = dbfp->do_stdin;
+ dbfp->afp->do_gzip = dbfp->do_gzip;
+ dbfp->afp->fname = dbfp->fname; /* just a ptr, don't free */
+ dbfp->afp->format = dbfp->format; /* e.g. format */
+ dbfp->afp->linenumber = dbfp->linenumber; /* e.g. 0 */
+ dbfp->afp->buf = NULL;
+ dbfp->afp->buflen = 0;
+
+ if ((dbfp->msa = MSAFileRead(dbfp->afp)) == NULL)
+ Die("Failed to read any alignment data from file %s", dbfp->fname);
+ /* hack: overload/reuse msa->lastidx; indicates
+ next seq to return upon a ReadSeq() call */
+ dbfp->msa->lastidx = 0;
+
+ return dbfp;
+ }
+
+ /* Load the first line.
+ */
+ SeqfileGetLine(dbfp);
+ return dbfp;
+}
+
+/* Function: SeqfilePosition()
+ *
+ * Purpose: Move to a particular offset in a seqfile.
+ * Will not work on alignment files.
+ */
+void
+SeqfilePosition(SQFILE *sqfp, SSIOFFSET *offset)
+{
+ if (sqfp->do_stdin || sqfp->do_gzip || IsAlignmentFormat(sqfp->format))
+ Die("SeqfilePosition() failed: in a nonrewindable data file or stream");
+
+ if (SSISetFilePosition(sqfp->f, offset) != 0)
+ Die("SSISetFilePosition failed, but that shouldn't happen.");
+ SeqfileGetLine(sqfp);
+}
+
+
+/* Function: SeqfileRewind()
+ *
+ * Purpose: Set a sequence file back to the first sequence.
+ *
+ * Won't work on alignment files. Although it would
+ * seem that it could (just set msa->lastidx back to 0),
+ * that'll fail on "multiple multiple" alignment file formats
+ * (e.g. Stockholm).
+ */
+void
+SeqfileRewind(SQFILE *sqfp)
+{
+ if (sqfp->do_stdin || sqfp->do_gzip)
+ Die("SeqfileRewind() failed: in a nonrewindable data file or stream");
+
+ rewind(sqfp->f);
+ SeqfileGetLine(sqfp);
+}
+
+/* Function: SeqfileLineParameters()
+ * Date: SRE, Thu Feb 15 17:00:41 2001 [St. Louis]
+ *
+ * Purpose: After all the sequences have been read from the file,
+ * but before closing it, retrieve overall bytes-per-line and
+ * residues-per-line info. If non-zero, these mean that
+ * the file contains homogeneous sequence line lengths (except
+ * the last line in each record).
+ *
+ * If either of bpl or rpl is determined to be inhomogeneous,
+ * both are returned as 0.
+ *
+ * Args: *sqfp - an open but fully read sequence file
+ * ret_bpl - RETURN: bytes per line, or 0 if inhomogeneous
+ * ret_rpl - RETURN: residues per line, or 0 if inhomogenous.
+ *
+ * Returns: void
+ */
+void
+SeqfileLineParameters(SQFILE *V, int *ret_bpl, int *ret_rpl)
+{
+ if (V->rpl > 0 && V->maxrpl == V->rpl &&
+ V->bpl > 0 && V->maxbpl == V->bpl) {
+ *ret_bpl = V->bpl;
+ *ret_rpl = V->rpl;
+ } else {
+ *ret_bpl = 0;
+ *ret_rpl = 0;
+ }
+}
+
+
+void
+SeqfileClose(SQFILE *sqfp)
+{
+ /* note: don't test for sqfp->msa being NULL. Now that
+ * we're holding afp open and allowing access to multi-MSA
+ * databases (e.g. Stockholm format, Pfam), msa ends
+ * up being NULL when we run out of alignments.
+ */
+ if (sqfp->afp != NULL) {
+ if (sqfp->msa != NULL) MSAFree(sqfp->msa);
+ if (sqfp->afp->buf != NULL) free(sqfp->afp->buf);
+ free(sqfp->afp);
+ }
+#ifndef SRE_STRICT_ANSI /* gunzip functionality only on POSIX systems */
+ if (sqfp->do_gzip) pclose(sqfp->f);
+#endif
+ else if (! sqfp->do_stdin) fclose(sqfp->f);
+ if (sqfp->buf != NULL) free(sqfp->buf);
+ if (sqfp->fname != NULL) free(sqfp->fname);
+ free(sqfp);
+}
+
+
+/* Function: SeqfileGetLine()
+ * Date: SRE, Tue Jun 22 09:15:49 1999 [Sanger Centre]
+ *
+ * Purpose: read a line from a sequence file into V->buf
+ * If the fgets() is NULL, sets V->buf[0] to '\0'.
+ *
+ * Args: V
+ *
+ * Returns: void
+ */
+static void
+SeqfileGetLine(SQFILE *V)
+{
+ if (V->ssimode >= 0)
+ if (0 != SSIGetFilePosition(V->f, V->ssimode, &(V->ssioffset)))
+ Die("SSIGetFilePosition() failed");
+ if (sre_fgets(&(V->buf), &(V->buflen), V->f) == NULL)
+ *(V->buf) = '\0';
+ V->linenumber++;
+}
+
+
+void
+FreeSequence(char *seq, SQINFO *sqinfo)
+{
+ if (seq != NULL) free(seq); /* FS, r244, here is potential problem in profile/profile */
+ if (sqinfo->flags & SQINFO_SS){
+ if (NULL != sqinfo->ss){ /* FS, r244 -> r245 */
+ free(sqinfo->ss);
+ }
+ }
+ if (sqinfo->flags & SQINFO_SA){
+ if (NULL != sqinfo->sa){ /* FS, r244 -> r245 */
+ free(sqinfo->sa);
+ }
+ }
+}
+
+int
+SetSeqinfoString(SQINFO *sqinfo, char *sptr, int flag)
+{
+ int len;
+ int pos;
+
+ /* silently ignore NULL. */
+ if (sptr == NULL) return 1;
+
+ while (*sptr == ' ') sptr++; /* ignore leading whitespace */
+ for (pos = strlen(sptr)-1; pos >= 0; pos--)
+ if (! isspace((int) sptr[pos])) break;
+ sptr[pos+1] = '\0'; /* ignore trailing whitespace */
+
+ switch (flag) {
+ case SQINFO_NAME:
+ if (*sptr != '-')
+ {
+ strncpy(sqinfo->name, sptr, SQINFO_NAMELEN-1);
+ sqinfo->name[SQINFO_NAMELEN-1] = '\0';
+ sqinfo->flags |= SQINFO_NAME;
+ }
+ break;
+
+ case SQINFO_ID:
+ if (*sptr != '-')
+ {
+ strncpy(sqinfo->id, sptr, SQINFO_NAMELEN-1);
+ sqinfo->id[SQINFO_NAMELEN-1] = '\0';
+ sqinfo->flags |= SQINFO_ID;
+ }
+ break;
+
+ case SQINFO_ACC:
+ if (*sptr != '-')
+ {
+ strncpy(sqinfo->acc, sptr, SQINFO_NAMELEN-1);
+ sqinfo->acc[SQINFO_NAMELEN-1] = '\0';
+ sqinfo->flags |= SQINFO_ACC;
+ }
+ break;
+
+ case SQINFO_DESC:
+ if (*sptr != '-')
+ {
+ if (sqinfo->flags & SQINFO_DESC) /* append? */
+ {
+ len = strlen(sqinfo->desc);
+ if (len < SQINFO_DESCLEN-2) /* is there room? */
+ {
+ strncat(sqinfo->desc, " ", SQINFO_DESCLEN-1-len); len++;
+ strncat(sqinfo->desc, sptr, SQINFO_DESCLEN-1-len);
+ }
+ }
+ else /* else copy */
+ strncpy(sqinfo->desc, sptr, SQINFO_DESCLEN-1);
+ sqinfo->desc[SQINFO_DESCLEN-1] = '\0';
+ sqinfo->flags |= SQINFO_DESC;
+ }
+ break;
+
+ case SQINFO_START:
+ if (!IsInt(sptr)) { squid_errno = SQERR_FORMAT; return 0; }
+ sqinfo->start = atoi(sptr);
+ if (sqinfo->start != 0) sqinfo->flags |= SQINFO_START;
+ break;
+
+ case SQINFO_STOP:
+ if (!IsInt(sptr)) { squid_errno = SQERR_FORMAT; return 0; }
+ sqinfo->stop = atoi(sptr);
+ if (sqinfo->stop != 0) sqinfo->flags |= SQINFO_STOP;
+ break;
+
+ case SQINFO_OLEN:
+ if (!IsInt(sptr)) { squid_errno = SQERR_FORMAT; return 0; }
+ sqinfo->olen = atoi(sptr);
+ if (sqinfo->olen != 0) sqinfo->flags |= SQINFO_OLEN;
+ break;
+
+ default:
+ Die("Invalid flag %d to SetSeqinfoString()", flag);
+ }
+ return 1;
+}
+
+void
+SeqinfoCopy(SQINFO *sq1, SQINFO *sq2)
+{
+ sq1->flags = sq2->flags;
+ if (sq2->flags & SQINFO_NAME) strcpy(sq1->name, sq2->name);
+ if (sq2->flags & SQINFO_ID) strcpy(sq1->id, sq2->id);
+ if (sq2->flags & SQINFO_ACC) strcpy(sq1->acc, sq2->acc);
+ if (sq2->flags & SQINFO_DESC) strcpy(sq1->desc, sq2->desc);
+ if (sq2->flags & SQINFO_LEN) sq1->len = sq2->len;
+ if (sq2->flags & SQINFO_START) sq1->start = sq2->start;
+ if (sq2->flags & SQINFO_STOP) sq1->stop = sq2->stop;
+ if (sq2->flags & SQINFO_OLEN) sq1->olen = sq2->olen;
+ if (sq2->flags & SQINFO_TYPE) sq1->type = sq2->type;
+ if (sq2->flags & SQINFO_SS) sq1->ss = Strdup(sq2->ss);
+ if (sq2->flags & SQINFO_SA) sq1->sa = Strdup(sq2->sa);
+}
+
+/* Function: ToDNA()
+ *
+ * Purpose: Convert a sequence to DNA.
+ * U --> T
+ */
+void
+ToDNA(char *seq)
+{
+ for (; *seq != '\0'; seq++)
+ {
+ if (*seq == 'U') *seq = 'T';
+ else if (*seq == 'u') *seq = 't';
+ }
+}
+
+/* Function: ToRNA()
+ *
+ * Purpose: Convert a sequence to RNA.
+ * T --> U
+ */
+void
+ToRNA(char *seq)
+{
+ for (; *seq != '\0'; seq++)
+ {
+ if (*seq == 'T') *seq = 'U';
+ else if (*seq == 't') *seq = 'u';
+ }
+}
+
+
+/* Function: ToIUPAC()
+ *
+ * Purpose: Convert X's, o's, other junk in a nucleic acid sequence to N's,
+ * to comply with IUPAC code. If is_aseq is TRUE, will allow gap
+ * characters though, so we can call ToIUPAC() on aligned seqs.
+ *
+ * NUCLEOTIDES is defined in squid.h as:
+ * "ACGTUNRYMKSWHBVDacgtunrymkswhbvd"
+ * gap chars allowed by isgap() are defined in squid.h as:
+ * " ._-~"
+ *
+ * WU-BLAST's pressdb will
+ * choke on X's, for instance, necessitating conversion
+ * of certain genome centers' data.
+ */
+void
+ToIUPAC(char *seq, int is_aseq)
+{
+ if (is_aseq) {
+ for (; *seq != '\0'; seq++)
+ if (strchr(NUCLEOTIDES, *seq) == NULL && ! isgap(*seq)) *seq = 'N';
+ } else {
+ for (; *seq != '\0'; seq++)
+ if (strchr(NUCLEOTIDES, *seq) == NULL) *seq = 'N';
+ }
+}
+
+
+/* Function: addseq()
+ *
+ * Purpose: Add a line of sequence to the growing string in V.
+ *
+ * In the seven supported unaligned formats, all sequence
+ * lines may contain whitespace that must be filtered out;
+ * four formats (PIR, EMBL, Genbank, GCG) include coordinates
+ * that must be filtered out. Thus an (!isdigit && !isspace)
+ * test on each character before we accept it.
+ */
+static void
+addseq(char *s, struct ReadSeqVars *V)
+{
+ char *s0;
+ char *sq;
+ int rpl; /* valid residues per line */
+ int bpl; /* characters per line */
+
+ if (V->ssimode == -1)
+ { /* Normal mode: keeping the seq */
+ /* Make sure we have enough room. We know that s is <= buflen,
+ * so just make sure we've got room for a whole new buflen worth
+ * of sequence.
+ */
+ if (V->seqlen + V->buflen > V->maxseq) {
+ V->maxseq += MAX(V->buflen, kStartLength);
+ V->seq = ReallocOrDie (V->seq, V->maxseq+1);
+ }
+
+ sq = V->seq + V->seqlen;
+ while (*s != 0) {
+#ifdef CLUSTALO
+ if (! isdigit((int) *s) && ! isspace((int) *s) && isprint((int) *s)) {
+#else
+ if (! isdigit((int) *s) && ! isspace((int) *s)) {
+#endif
+ *sq = *s;
+ sq++;
+ }
+ s++;
+ }
+ V->seqlen = sq - V->seq;
+ }
+ else /* else: indexing mode, discard the seq */
+ {
+ s0 = s;
+ rpl = 0;
+ while (*s != 0) {
+ if (! isdigit((int) *s) && ! isspace((int) *s)) {
+ rpl++;
+ }
+ s++;
+ }
+ V->seqlen += rpl;
+ bpl = s - s0;
+
+ /* Keep track of the global rpl, bpl for the file.
+ * This is overly complicated because we have to
+ * allow the last line of each record (e.g. the last addseq() call
+ * on each sequence) to have a different length - and sometimes
+ * we'll have one-line sequence records, too. Thus we only
+ * do something with the global V->rpl when we have *passed over*
+ * a line - we keep the last line's rpl in last_rpl. And because
+ * a file might consist entirely of single-line records, we keep
+ * a third guy, maxrpl, that tells us the maximum rpl of any line
+ * in the file. If we reach the end of file and rpl is still unset,
+ * we'll set it to maxrpl. If we reach eof and rpl is set, but is
+ * less than maxrpl, that's a weird case where a last line in some
+ * record is longer than every other line.
+ */
+ if (V->rpl != 0) { /* 0 means we already know rpl is invalid */
+ if (V->lastrpl > 0) { /* we're on something that's not the first line */
+ if (V->rpl > 0 && V->lastrpl != V->rpl) V->rpl = 0;
+ else if (V->rpl == -1) V->rpl = V->lastrpl;
+ }
+ V->lastrpl = rpl;
+ if (rpl > V->maxrpl) V->maxrpl = rpl; /* make sure we check max length of final lines */
+ }
+ if (V->bpl != 0) { /* 0 means we already know bpl is invalid */
+ if (V->lastbpl > 0) { /* we're on something that's not the first line */
+ if (V->bpl > 0 && V->lastbpl != V->bpl) V->bpl = 0;
+ else if (V->bpl == -1) V->bpl = V->lastbpl;
+ }
+ V->lastbpl = bpl;
+ if (bpl > V->maxbpl) V->maxbpl = bpl; /* make sure we check max length of final lines */
+ }
+ } /* end of indexing mode of addseq(). */
+
+}
+
+static void
+readLoop(int addfirst, int (*endTest)(char *,int *), struct ReadSeqVars *V)
+{
+ int addend = 0;
+ int done = 0;
+
+ V->seqlen = 0;
+ V->lastrpl = V->lastbpl = 0;
+ if (addfirst) {
+ if (V->ssimode >= 0) V->d_off = V->ssioffset;
+ addseq(V->buf, V);
+ } else if (V->ssimode >= 0)
+ if (0 != SSIGetFilePosition(V->f, V->ssimode, &(V->d_off)))
+ Die("SSIGetFilePosition() failed");
+
+ do {
+ SeqfileGetLine(V);
+ /* feof() alone is a bug; files not necessarily \n terminated */
+ if (*(V->buf) == '\0' && feof(V->f))
+ done = TRUE;
+ done |= (*endTest)(V->buf, &addend);
+ if (addend || !done)
+ addseq(V->buf, V);
+ } while (!done);
+}
+
+
+static int
+endPIR(char *s, int *addend)
+{
+ *addend = 0;
+ if ((strncmp(s, "///", 3) == 0) ||
+ (strncmp(s, "ENTRY", 5) == 0))
+ return 1;
+ else
+ return 0;
+}
+
+static void
+readPIR(struct ReadSeqVars *V)
+{
+ char *sptr;
+ /* load first line of entry */
+ while (!feof(V->f) && strncmp(V->buf, "ENTRY", 5) != 0) {
+ SeqfileGetLine(V);
+ }
+ if (feof(V->f)) return;
+ if (V->ssimode >= 0) V->r_off = V->ssioffset;
+
+ if ((sptr = strtok(V->buf + 15, "\n\t ")) != NULL)
+ {
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
+ }
+ do {
+ SeqfileGetLine(V);
+ if (!feof(V->f) && strncmp(V->buf, "TITLE", 5) == 0)
+ SetSeqinfoString(V->sqinfo, V->buf+15, SQINFO_DESC);
+ else if (!feof(V->f) && strncmp(V->buf, "ACCESSION", 9) == 0)
+ {
+ if ((sptr = strtok(V->buf+15, " \t\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
+ }
+ } while (! feof(V->f) && (strncmp(V->buf,"SEQUENCE", 8) != 0));
+ SeqfileGetLine(V); /* skip next line, coords */
+
+ readLoop(0, endPIR, V);
+
+ /* reading a real PIR-CODATA database file, we keep the source coords
+ */
+ V->sqinfo->start = 1;
+ V->sqinfo->stop = V->seqlen;
+ V->sqinfo->olen = V->seqlen;
+ V->sqinfo->flags |= SQINFO_START | SQINFO_STOP | SQINFO_OLEN;
+
+ /* get next line
+ */
+ while (!feof(V->f) && strncmp(V->buf, "ENTRY", 5) != 0) {
+ SeqfileGetLine(V);
+ }
+}
+
+
+
+static int
+endIG(char *s, int *addend)
+{
+ *addend = 1; /* 1 or 2 occur in line w/ bases */
+ return((strchr(s,'1')!=NULL) || (strchr(s,'2')!=NULL));
+}
+
+static void
+readIG(struct ReadSeqVars *V)
+{
+ char *nm;
+ /* position past ';' comments */
+ do {
+ SeqfileGetLine(V);
+ } while (! (feof(V->f) || ((*V->buf != 0) && (*V->buf != ';')) ));
+
+ if (!feof(V->f))
+ {
+ if ((nm = strtok(V->buf, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
+
+ readLoop(0, endIG, V);
+ }
+
+ while (!(feof(V->f) || ((*V->buf != '\0') && (*V->buf == ';'))))
+ SeqfileGetLine(V);
+}
+
+static int
+endStrider(char *s, int *addend)
+{
+ *addend = 0;
+ return (strstr( s, "//") != NULL);
+}
+
+static void
+readStrider(struct ReadSeqVars *V)
+{
+ char *nm;
+
+ while ((!feof(V->f)) && (*V->buf == ';'))
+ {
+ if (strncmp(V->buf,"; DNA sequence", 14) == 0)
+ {
+ if ((nm = strtok(V->buf+16, ",\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
+ }
+ SeqfileGetLine(V);
+ }
+
+ if (! feof(V->f))
+ readLoop(1, endStrider, V);
+
+ /* load next line
+ */
+ while ((!feof(V->f)) && (*V->buf != ';'))
+ SeqfileGetLine(V);
+}
+
+
+static int
+endGB(char *s, int *addend)
+{
+ *addend = 0;
+ return ((strstr(s,"//") != NULL) || (strstr(s,"LOCUS") == s));
+}
+
+static void
+readGenBank(struct ReadSeqVars *V)
+{
+ char *sptr;
+ int in_definition;
+
+ /* We'll map three genbank identifiers onto names:
+ * LOCUS -> sqinfo.name
+ * ACCESSION -> sqinfo.acc [primary accession only]
+ * VERSION -> sqinfo.id
+ * We don't currently store the GI number, or secondary accessions.
+ */
+ while (strncmp(V->buf, "LOCUS", 5) != 0) {
+ SeqfileGetLine(V);
+ }
+ if (V->ssimode >= 0) V->r_off = V->ssioffset;
+
+ if ((sptr = strtok(V->buf+12, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+
+ in_definition = FALSE;
+ while (! feof(V->f))
+ {
+ SeqfileGetLine(V);
+ if (! feof(V->f) && strstr(V->buf, "DEFINITION") == V->buf)
+ {
+ if ((sptr = strtok(V->buf+12, "\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
+ in_definition = TRUE;
+ }
+ else if (! feof(V->f) && strstr(V->buf, "ACCESSION") == V->buf)
+ {
+ if ((sptr = strtok(V->buf+12, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
+ in_definition = FALSE;
+ }
+ else if (! feof(V->f) && strstr(V->buf, "VERSION") == V->buf)
+ {
+ if ((sptr = strtok(V->buf+12, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
+ in_definition = FALSE;
+ }
+ else if (strncmp(V->buf,"ORIGIN", 6) != 0)
+ {
+ if (in_definition)
+ SetSeqinfoString(V->sqinfo, V->buf, SQINFO_DESC);
+ }
+ else
+ break;
+ }
+
+ readLoop(0, endGB, V);
+
+ /* reading a real GenBank database file, we keep the source coords
+ */
+ V->sqinfo->start = 1;
+ V->sqinfo->stop = V->seqlen;
+ V->sqinfo->olen = V->seqlen;
+ V->sqinfo->flags |= SQINFO_START | SQINFO_STOP | SQINFO_OLEN;
+
+
+ while (!(feof(V->f) || ((*V->buf!=0) && (strstr(V->buf,"LOCUS") == V->buf))))
+ SeqfileGetLine(V);
+ /* SRE: V->s now holds "//", so sequential
+ reads are wedged: fixed Tue Jul 13 1993 */
+ while (!feof(V->f) && strstr(V->buf, "LOCUS ") != V->buf)
+ SeqfileGetLine(V);
+}
+
+static int
+endGCGdata(char *s, int *addend)
+{
+ *addend = 0;
+ return (*s == '>');
+}
+
+static void
+readGCGdata(struct ReadSeqVars *V)
+{
+ int binary = FALSE; /* whether data are binary or not */
+ int blen = 0; /* length of binary sequence */
+
+ /* first line contains ">>>>" followed by name */
+ if (Strparse(">>>>([^ ]+) .+2BIT +Len: ([0-9]+)", V->buf, 2))
+ {
+ binary = TRUE;
+ SetSeqinfoString(V->sqinfo, sqd_parse[1], SQINFO_NAME);
+ blen = atoi(sqd_parse[2]);
+ }
+ else if (Strparse(">>>>([^ ]+) .+ASCII +Len: [0-9]+", V->buf, 1))
+ SetSeqinfoString(V->sqinfo, sqd_parse[1], SQINFO_NAME);
+ else
+ Die("bogus GCGdata format? %s", V->buf);
+
+ /* second line contains free text description */
+ SeqfileGetLine(V);
+ SetSeqinfoString(V->sqinfo, V->buf, SQINFO_DESC);
+
+ if (binary) {
+ /* allocate for blen characters +3... (allow for 3 bytes of slop) */
+ if (blen >= V->maxseq) {
+ V->maxseq = blen;
+ if ((V->seq = (char *) realloc (V->seq, sizeof(char)*(V->maxseq+4)))==NULL)
+ Die("malloc failed");
+ }
+ /* read (blen+3)/4 bytes from file */
+ if (fread(V->seq, sizeof(char), (blen+3)/4, V->f) < (size_t) ((blen+3)/4))
+ Die("fread failed");
+ V->seqlen = blen;
+ /* convert binary code to seq */
+ GCGBinaryToSequence(V->seq, blen);
+ }
+ else readLoop(0, endGCGdata, V);
+
+ while (!(feof(V->f) || ((*V->buf != 0) && (*V->buf == '>'))))
+ SeqfileGetLine(V);
+}
+
+static int
+endPearson(char *s, int *addend)
+{
+ *addend = 0;
+ return(*s == '>');
+}
+
+static void
+readPearson(struct ReadSeqVars *V)
+{
+ char *sptr;
+
+ if (V->ssimode >= 0) V->r_off = V->ssioffset;
+
+ if (*V->buf != '>')
+ Die("\
+File %s does not appear to be in FASTA format at line %d.\n\
+You may want to specify the file format on the command line.\n\
+Usually this is done with an option --informat <fmt>.\n",
+ V->fname, V->linenumber);
+
+ if ((sptr = strtok(V->buf+1, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+ if ((sptr = strtok(NULL, "\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
+
+ readLoop(0, endPearson, V);
+
+ while (!(feof(V->f) || ((*V->buf != 0) && (*V->buf == '>')))) {
+ SeqfileGetLine(V);
+ }
+}
+
+
+static int
+endEMBL(char *s, int *addend)
+{
+ *addend = 0;
+ /* Some people (Berlin 5S rRNA database, f'r instance) use
+ * an extended EMBL format that attaches extra data after
+ * the sequence -- watch out for that. We use the fact that
+ * real EMBL sequence lines begin with five spaces.
+ *
+ * We can use this as the sole end test because readEMBL() will
+ * advance to the next ID line before starting to read again.
+ */
+ return (strncmp(s," ",5) != 0);
+/* return ((strstr(s,"//") != NULL) || (strstr(s,"ID ") == s)); */
+}
+
+static void
+readEMBL(struct ReadSeqVars *V)
+{
+ char *sptr;
+
+ /* make sure we have first line */
+ while (!feof(V->f) && strncmp(V->buf, "ID ", 4) != 0) {
+ SeqfileGetLine(V);
+ }
+ if (V->ssimode >= 0) V->r_off = V->ssioffset;
+
+ if ((sptr = strtok(V->buf+5, "\n\t ")) != NULL)
+ {
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
+ }
+
+ do {
+ SeqfileGetLine(V);
+ if (!feof(V->f) && strstr(V->buf, "AC ") == V->buf)
+ {
+ if ((sptr = strtok(V->buf+5, "; \t\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
+ }
+ else if (!feof(V->f) && strstr(V->buf, "DE ") == V->buf)
+ {
+ if ((sptr = strtok(V->buf+5, "\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
+ }
+ } while (! feof(V->f) && strncmp(V->buf,"SQ",2) != 0);
+
+ readLoop(0, endEMBL, V);
+
+ /* Hack for Staden experiment files: convert - to N
+ */
+ if (V->ssimode == -1) /* if we're in ssi mode, we're not keeping the seq */
+ for (sptr = V->seq; *sptr != '\0'; sptr++)
+ if (*sptr == '-') *sptr = 'N';
+
+ /* reading a real EMBL database file, we keep the source coords
+ */
+ V->sqinfo->start = 1;
+ V->sqinfo->stop = V->seqlen;
+ V->sqinfo->olen = V->seqlen;
+ V->sqinfo->flags |= SQINFO_START | SQINFO_STOP | SQINFO_OLEN;
+
+ /* load next record's ID line */
+ while (!feof(V->f) && strncmp(V->buf, "ID ", 4) != 0) {
+ SeqfileGetLine(V);
+ }
+
+}
+
+
+static int
+endZuker(char *s, int *addend)
+{
+ *addend = 0;
+ return( *s == '(' );
+}
+
+static void
+readZuker(struct ReadSeqVars *V)
+{
+ char *sptr;
+
+ SeqfileGetLine(V); /*s == "seqLen seqid string..."*/
+
+ if ((sptr = strtok(V->buf+6, " \t\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+
+ if ((sptr = strtok(NULL, "\n")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC);
+
+ readLoop(0, endZuker, V);
+
+ while (!(feof(V->f) | ((*V->buf != '\0') & (*V->buf == '('))))
+ SeqfileGetLine(V);
+}
+
+static void
+readUWGCG(struct ReadSeqVars *V)
+{
+ char *si;
+ char *sptr;
+ int done;
+
+ V->seqlen = 0;
+
+ /*writeseq: " %s Length: %d (today) Check: %d ..\n" */
+ /*drop above or ".." from id*/
+ if ((si = strstr(V->buf," Length: ")) != NULL) *si = 0;
+ else if ((si = strstr(V->buf,"..")) != NULL) *si = 0;
+
+ if ((sptr = strtok(V->buf, "\n\t ")) != NULL)
+ SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+
+ do {
+ done = feof(V->f);
+ SeqfileGetLine(V);
+ if (! done) addseq(V->buf, V);
+ } while (!done);
+}
+
+
+/* Function: ReadSeq()
+ *
+ * Purpose: Read next sequence from an open database file.
+ * Return the sequence and associated info.
+ *
+ * Args: fp - open sequence database file pointer
+ * format - format of the file (previously determined
+ * by call to SeqfileFormat()).
+ * Currently unused, since we carry it in V.
+ * ret_seq - RETURN: sequence
+ * sqinfo - RETURN: filled in w/ other information
+ *
+ * Limitations: uses squid_errno, so it's not threadsafe.
+ *
+ * Return: 1 on success, 0 on failure.
+ * ret_seq and some field of sqinfo are allocated here,
+ * The preferred call mechanism to properly free the memory is:
+ *
+ * SQINFO sqinfo;
+ * char *seq;
+ *
+ * ReadSeq(fp, format, &seq, &sqinfo);
+ * ... do something...
+ * FreeSequence(seq, &sqinfo);
+ */
+int
+ReadSeq(SQFILE *V, int format, char **ret_seq, SQINFO *sqinfo)
+{
+ int gotuw;
+
+ squid_errno = SQERR_OK;
+
+ /* Here's the hack for sequential access of sequences from
+ * the multiple sequence alignment formats
+ */
+ if (IsAlignmentFormat(V->format))
+ {
+ if (V->msa->lastidx >= V->msa->nseq)
+ { /* out of data. try to read another alignment */
+ MSAFree(V->msa);
+ if ((V->msa = MSAFileRead(V->afp)) == NULL)
+ return 0;
+ V->msa->lastidx = 0;
+ }
+ /* copy and dealign the appropriate aligned seq */
+/* AW: stopping squid from dealigning sequences and corresponding info */
+#ifdef CLUSTALO
+ V->seq = sre_strdup(V->msa->aseq[V->msa->lastidx], V->msa->alen);
+#else
+ MakeDealignedString(V->msa->aseq[V->msa->lastidx], V->msa->alen,
+ V->msa->aseq[V->msa->lastidx], &(V->seq));
+#endif
+ V->seqlen = strlen(V->seq);
+
+ /* Extract sqinfo stuff for this sequence from the msa.
+ * Tedious; code that should be cleaned.
+ */
+ sqinfo->flags = 0;
+ if (V->msa->sqname[V->msa->lastidx] != NULL)
+ SetSeqinfoString(sqinfo, V->msa->sqname[V->msa->lastidx], SQINFO_NAME);
+ if (V->msa->sqacc != NULL && V->msa->sqacc[V->msa->lastidx] != NULL)
+ SetSeqinfoString(sqinfo, V->msa->sqacc[V->msa->lastidx], SQINFO_ACC);
+ if (V->msa->sqdesc != NULL && V->msa->sqdesc[V->msa->lastidx] != NULL)
+ SetSeqinfoString(sqinfo, V->msa->sqdesc[V->msa->lastidx], SQINFO_DESC);
+ if (V->msa->ss != NULL && V->msa->ss[V->msa->lastidx] != NULL) {
+/* AW: stopping squid from dealigning sequences and corresponding info */
+#ifdef CLUSTALO
+ sqinfo->ss = sre_strdup(V->msa->ss[V->msa->lastidx], V->msa->alen);
+#else
+ MakeDealignedString(V->msa->aseq[V->msa->lastidx], V->msa->alen,
+ V->msa->ss[V->msa->lastidx], &(sqinfo->ss));
+#endif
+ sqinfo->flags |= SQINFO_SS;
+ }
+ if (V->msa->sa != NULL && V->msa->sa[V->msa->lastidx] != NULL) {
+/* AW: stopping squid from dealigning sequences and corresponding info */
+#ifdef CLUSTALO
+ sqinfo->sa = sre_strdup(V->msa->sa[V->msa->lastidx], V->msa->alen);
+#else
+ MakeDealignedString(V->msa->aseq[V->msa->lastidx], V->msa->alen,
+ V->msa->sa[V->msa->lastidx], &(sqinfo->sa));
+#endif
+ sqinfo->flags |= SQINFO_SA;
+ }
+ V->msa->lastidx++;
+ }
+ else {
+ if (feof(V->f)) return 0;
+
+ if (V->ssimode == -1) { /* normal mode */
+ V->seq = (char*) calloc (kStartLength+1, sizeof(char));
+ V->maxseq = kStartLength;
+ } else { /* index mode: discarding seq */
+ V->seq = NULL;
+ V->maxseq = 0;
+ }
+ V->seqlen = 0;
+ V->sqinfo = sqinfo;
+ V->sqinfo->flags = 0;
+
+ switch (V->format) {
+ case SQFILE_IG : readIG(V); break;
+ case SQFILE_STRIDER : readStrider(V); break;
+ case SQFILE_GENBANK : readGenBank(V); break;
+ case SQFILE_FASTA : readPearson(V); break;
+ case SQFILE_EMBL : readEMBL(V); break;
+ case SQFILE_ZUKER : readZuker(V); break;
+ case SQFILE_PIR : readPIR(V); break;
+ case SQFILE_GCGDATA : readGCGdata(V); break;
+
+ case SQFILE_GCG :
+ do { /* skip leading comments on GCG file */
+ gotuw = (strstr(V->buf,"..") != NULL);
+ if (gotuw) readUWGCG(V);
+ SeqfileGetLine(V);
+ } while (! feof(V->f));
+ break;
+
+ case SQFILE_IDRAW: /* SRE: no attempt to read idraw postscript */
+ default:
+ squid_errno = SQERR_FORMAT;
+ free(V->seq);
+ return 0;
+ }
+ if (V->seq != NULL) /* (it can be NULL in indexing mode) */
+ V->seq[V->seqlen] = 0; /* stick a string terminator on it */
+ }
+
+ /* Cleanup
+ */
+ sqinfo->len = V->seqlen;
+ sqinfo->flags |= SQINFO_LEN;
+ *ret_seq = V->seq;
+ if (squid_errno == SQERR_OK) return 1; else return 0;
+}
+
+/* Function: SeqfileFormat()
+ * Date: SRE, Tue Jun 22 10:58:58 1999 [Sanger Centre]
+ *
+ * Purpose: Determine format of an open file.
+ * Returns format code.
+ * Rewinds the file.
+ *
+ * Autodetects the following unaligned formats:
+ * SQFILE_FASTA
+ * SQFILE_GENBANK
+ * SQFILE_EMBL
+ * SQFILE_GCG
+ * SQFILE_GCGDATA
+ * SQFILE_PIR
+ * Also autodetects the following alignment formats:
+ * MSAFILE_STOCKHOLM
+ * MSAFILE_MSF
+ * MSAFILE_CLUSTAL
+ * MSAFILE_SELEX
+ * MSAFILE_PHYLIP
+ *
+ * Can't autodetect MSAFILE_A2M, calls it SQFILE_FASTA.
+ * MSAFileFormat() does the opposite.
+ *
+ * Args: sfp - open SQFILE
+ *
+ * Return: format code, or SQFILE_UNKNOWN if unrecognized
+ */
+int
+SeqfileFormat(FILE *fp)
+{
+ char *buf;
+ int len;
+ int fmt = SQFILE_UNKNOWN;
+ int ndataline;
+ char *bufcpy, *s, *s1, *s2;
+ int has_junk;
+
+ buf = NULL;
+ len = 0;
+ ndataline = 0;
+ has_junk = FALSE;
+ while (sre_fgets(&buf, &len, fp) != NULL)
+ {
+ if (IsBlankline(buf)) continue;
+
+ /* Well-behaved formats identify themselves in first nonblank line.
+ */
+ if (ndataline == 0)
+ {
+ if (strncmp(buf, ">>>>", 4) == 0 && strstr(buf, "Len: "))
+ { fmt = SQFILE_GCGDATA; goto DONE; }
+
+ if (buf[0] == '>')
+ { fmt = SQFILE_FASTA; goto DONE; }
+
+ if (strncmp(buf, "!!AA_SEQUENCE", 13) == 0 ||
+ strncmp(buf, "!!NA_SEQUENCE", 13) == 0)
+ { fmt = SQFILE_GCG; goto DONE; }
+
+ if (strncmp(buf, "# STOCKHOLM 1.", 14) == 0)
+ { fmt = MSAFILE_STOCKHOLM; goto DONE; }
+
+ if (strncmp(buf, "CLUSTAL", 7) == 0 &&
+ strstr(buf, "multiple sequence alignment") != NULL)
+ { fmt = MSAFILE_CLUSTAL; goto DONE; }
+
+ if (strncmp(buf, "!!AA_MULTIPLE_ALIGNMENT", 23) == 0 ||
+ strncmp(buf, "!!NA_MULTIPLE_ALIGNMENT", 23) == 0)
+ { fmt = MSAFILE_MSF; goto DONE; }
+
+ /* PHYLIP id: also just a good bet */
+ bufcpy = sre_strdup(buf, -1);
+ s = bufcpy;
+ if ((s1 = sre_strtok(&s, WHITESPACE, NULL)) != NULL &&
+ (s2 = sre_strtok(&s, WHITESPACE, NULL)) != NULL &&
+ IsInt(s1) &&
+ IsInt(s2))
+ { free(bufcpy); fmt = MSAFILE_PHYLIP; goto DONE; }
+ free(bufcpy);
+ }
+
+ /* We trust that other formats identify themselves soon.
+ */
+ /* dead giveaways for extended SELEX */
+ if (strncmp(buf, "#=AU", 4) == 0 ||
+ strncmp(buf, "#=ID", 4) == 0 ||
+ strncmp(buf, "#=AC", 4) == 0 ||
+ strncmp(buf, "#=DE", 4) == 0 ||
+ strncmp(buf, "#=GA", 4) == 0 ||
+ strncmp(buf, "#=TC", 4) == 0 ||
+ strncmp(buf, "#=NC", 4) == 0 ||
+ strncmp(buf, "#=SQ", 4) == 0 ||
+ strncmp(buf, "#=SS", 4) == 0 ||
+ strncmp(buf, "#=CS", 4) == 0 ||
+ strncmp(buf, "#=RF", 4) == 0)
+ { fmt = MSAFILE_SELEX; goto DONE; }
+
+ if (strncmp(buf, "///", 3) == 0 || strncmp(buf, "ENTRY ", 6) == 0)
+ { fmt = SQFILE_PIR; goto DONE; }
+
+ /* a ha, diagnostic of an (old) MSF file */
+ if ((strstr(buf, "..") != NULL) &&
+ (strstr(buf, "MSF:") != NULL) &&
+ (strstr(buf, "Check:")!= NULL))
+ { fmt = MSAFILE_MSF; goto DONE; }
+
+ /* unaligned GCG (must follow MSF test!) */
+ if (strstr(buf, " Check: ") != NULL && strstr(buf, "..") != NULL)
+ { fmt = SQFILE_GCG; goto DONE; }
+
+ if (strncmp(buf,"LOCUS ",6) == 0 || strncmp(buf,"ORIGIN ",6) == 0)
+ { fmt = SQFILE_GENBANK; goto DONE; }
+
+ if (strncmp(buf,"ID ",5) == 0 || strncmp(buf,"SQ ",5) == 0)
+ { fmt = SQFILE_EMBL; goto DONE; }
+
+ /* But past here, we're being desperate. A simple SELEX file is
+ * very difficult to detect; we can only try to disprove it.
+ */
+ s = buf;
+ if ((s1 = sre_strtok(&s, WHITESPACE, NULL)) == NULL) continue; /* skip blank lines */
+ if (strchr("#%", *s1) != NULL) continue; /* skip comment lines */
+
+ /* Disproof 1. Noncomment, nonblank lines in a SELEX file
+ * must have at least two space-delimited fields (name/seq)
+ */
+ if ((s2 = sre_strtok(&s, WHITESPACE, NULL)) == NULL)
+ has_junk = TRUE;
+
+ /* Disproof 2.
+ * The sequence field should look like a sequence.
+ */
+ if (s2 != NULL && Seqtype(s2) == kOtherSeq)
+ has_junk = TRUE;
+
+ ndataline++;
+ if (ndataline == 300) break; /* only look at first 300 lines */
+ }
+
+ if (ndataline == 0)
+ Die("Sequence file contains no data");
+
+ /* If we've made it this far, we've run out of data, but there
+ * was at least one line of it; check if we've
+ * disproven SELEX. If not, cross our fingers, pray, and guess SELEX.
+ */
+ if (has_junk == TRUE) fmt = SQFILE_UNKNOWN;
+ else fmt = MSAFILE_SELEX;
+
+ DONE:
+ if (buf != NULL) free(buf);
+ rewind(fp);
+ return fmt;
+}
+
+/* Function: GCGBinaryToSequence()
+ *
+ * Purpose: Convert a GCG 2BIT binary string to DNA sequence.
+ * 0 = C 1 = T 2 = A 3 = G
+ * 4 nts/byte
+ *
+ * Args: seq - binary sequence. Converted in place to DNA.
+ * len - length of DNA. binary is (len+3)/4 bytes
+ */
+int
+GCGBinaryToSequence(char *seq, int len)
+{
+ int bpos; /* position in binary */
+ int spos; /* position in sequence */
+ char twobit;
+ int i;
+
+ for (bpos = (len-1)/4; bpos >= 0; bpos--)
+ {
+ twobit = seq[bpos];
+ spos = bpos*4;
+
+ for (i = 3; i >= 0; i--)
+ {
+ switch (twobit & 0x3) {
+ case 0: seq[spos+i] = 'C'; break;
+ case 1: seq[spos+i] = 'T'; break;
+ case 2: seq[spos+i] = 'A'; break;
+ case 3: seq[spos+i] = 'G'; break;
+ }
+ twobit = twobit >> 2;
+ }
+ }
+ seq[len] = '\0';
+ return 1;
+}
+
+
+/* Function: GCGchecksum()
+ * Date: SRE, Mon May 31 11:13:21 1999 [St. Louis]
+ *
+ * Purpose: Calculate a GCG checksum for a sequence.
+ * Code provided by Steve Smith of Genetics
+ * Computer Group.
+ *
+ * Args: seq - sequence to calculate checksum for.
+ * may contain gap symbols.
+ * len - length of sequence (usually known,
+ * so save a strlen() call)
+ *
+ * Returns: GCG checksum.
+ */
+int
+GCGchecksum(char *seq, int len)
+{
+ int i; /* position in sequence */
+ int chk = 0; /* calculated checksum */
+
+ for (i = 0; i < len; i++)
+ chk = (chk + (i % 57 + 1) * (sre_toupper((int) seq[i]))) % 10000;
+ return chk;
+}
+
+
+/* Function: GCGMultchecksum()
+ *
+ * Purpose: GCG checksum for a multiple alignment: sum of
+ * individual sequence checksums (including their
+ * gap characters) modulo 10000.
+ *
+ * Implemented using spec provided by Steve Smith of
+ * Genetics Computer Group.
+ *
+ * Args: seqs - sequences to be checksummed; aligned or not
+ * nseq - number of sequences
+ *
+ * Return: the checksum, a number between 0 and 9999
+ */
+int
+GCGMultchecksum(char **seqs, int nseq)
+{
+ int chk = 0;
+ int idx;
+
+ for (idx = 0; idx < nseq; idx++)
+ chk = (chk + GCGchecksum(seqs[idx], strlen(seqs[idx]))) % 10000;
+ return chk;
+}
+
+
+
+
+/* Function: Seqtype()
+ *
+ * Purpose: Returns a (very good) guess about type of sequence:
+ * kDNA, kRNA, kAmino, or kOtherSeq.
+ *
+ * Modified from, and replaces, Gilbert getseqtype().
+ */
+int
+Seqtype(char *seq)
+{
+ int saw; /* how many non-gap characters I saw */
+ char c;
+ int po = 0; /* count of protein-only */
+ int nt = 0; /* count of t's */
+ int nu = 0; /* count of u's */
+ int na = 0; /* count of nucleotides */
+ int aa = 0; /* count of amino acids */
+ int no = 0; /* count of others */
+
+ /* Look at the first 300 non-gap characters
+ */
+
+#ifdef CLUSTALO
+ /* VGGNGDDYLSGGTGNDTL is recognized as unknown using squid's default
+ * approach.
+ * We change it to the following:
+
+ * 1. counting: ignore gaps and not alpha characters. if protein-only then
+ * count as such (po). otherwise decide if amino-acid (aa) or nucleic-acid
+ * (na) or unknown (no)
+ *
+ * 2. determine type: if we saw more unknown than aa or na, return unknown.
+ * if encountered protein-only return protein-only. otherwise decide based
+ * on majority. (if aa==na return na)
+ */
+ for (saw = 0; *seq != '\0' && saw < 300; seq++) {
+ c = sre_toupper((int) *seq);
+ int unknown = 1;
+
+ if (isgap(c) || ! isalpha((int) c)) {
+ continue;
+ }
+
+ if (strchr(protonly, c)) {
+ po++;
+ unknown = 0;
+ }
+
+ if (strchr(aminos,c)) {
+ aa++;
+ unknown = 0;
+ }
+
+ if (strchr(primenuc,c)) {
+ na++;
+ unknown = 0;
+
+ if (c == 'T')
+ nt++;
+ else if (c == 'U')
+ nu++;
+ }
+
+ if (unknown) {
+ no ++;
+ }
+
+ saw++;
+ }
+
+ if (no > aa && no > na)
+ return kOtherSeq;
+
+ if (po > 0 || aa>na)
+ return kAmino;
+
+ if (na >= aa) {
+ if (nu > nt)
+ return kRNA;
+ else
+ return kDNA;
+ }
+
+ return kOtherSeq;
+
+
+#else
+ for (saw = 0; *seq != '\0' && saw < 300; seq++)
+ {
+ c = sre_toupper((int) *seq);
+ if (! isgap(c))
+ {
+ if (strchr(protonly, c)) po++;
+ else if (strchr(primenuc,c)) {
+ na++;
+ if (c == 'T') nt++;
+ else if (c == 'U') nu++;
+ }
+ else if (strchr(aminos,c)) aa++;
+ else if (isalpha((int) c)) no++;
+ saw++;
+ }
+ }
+
+ if (no > 0) return kOtherSeq;
+ else if (po > 0) return kAmino;
+ else if (na > aa) {
+ if (nu > nt) return kRNA;
+ else return kDNA;
+ }
+ else return kAmino; /* ooooh. risky. */
+#endif
+
+}
+
+
+/* Function: GuessAlignmentSeqtype()
+ * Date: SRE, Wed Jul 7 09:42:34 1999 [St. Louis]
+ *
+ * Purpose: Try to guess whether an alignment is protein
+ * or nucleic acid; return a code for the
+ * type (kRNA, kDNA, or kAmino).
+ *
+ * Args: aseq - array of aligned sequences. (Could also
+ * be an rseq unaligned sequence array)
+ * nseq - number of aseqs
+ *
+ * Returns: kRNA, kDNA, kAmino;
+ * kOtherSeq if inconsistency is detected.
+ */
+int
+GuessAlignmentSeqtype(char **aseq, int nseq)
+{
+ int idx;
+ int nrna = 0;
+ int ndna = 0;
+ int namino = 0;
+ int nother = 0;
+
+ for (idx = 0; idx < nseq; idx++)
+ switch (Seqtype(aseq[idx])) {
+ case kRNA: nrna++; break;
+ case kDNA: ndna++; break;
+ case kAmino: namino++; break;
+ default: nother++;
+ }
+
+ /* Unambiguous decisions:
+ */
+ if (nother) return kOtherSeq;
+ if (namino == nseq) return kAmino;
+ if (ndna == nseq) return kDNA;
+ if (nrna == nseq) return kRNA;
+
+ /* Ambiguous decisions:
+ */
+ if (namino == 0) return kRNA; /* it's nucleic acid, but seems mixed RNA/DNA */
+ return kAmino; /* some amino acid seen; others probably short seqs, some
+ of which may be entirely ACGT (ala,cys,gly,thr). We
+ could be a little more sophisticated: U would be a giveaway
+ that we're not in protein seqs */
+}
+
+/* Function: WriteSimpleFASTA()
+ * Date: SRE, Tue Nov 16 18:06:00 1999 [St. Louis]
+ *
+ * Purpose: Just write a FASTA format sequence to a file;
+ * minimal interface, mostly for quick and dirty programs.
+ *
+ * Args: fp - open file handle (stdout, possibly)
+ * seq - sequence to output
+ * name - name for the sequence
+ * desc - optional description line, or NULL.
+ *
+ * Returns: void
+ */
+void
+WriteSimpleFASTA(FILE *fp, char *seq, char *name, char *desc)
+{
+ char buf[61];
+ int len;
+ int pos;
+
+ len = strlen(seq);
+ buf[60] = '\0';
+ fprintf(fp, ">%s %s\n", name, desc != NULL ? desc : "");
+ for (pos = 0; pos < len; pos += 60)
+ {
+ strncpy(buf, seq+pos, 60);
+ fprintf(fp, "%s\n", buf);
+ }
+}
+
+int
+WriteSeq(FILE *outf, int outform, char *seq, SQINFO *sqinfo)
+{
+ int numline = 0;
+ int lines = 0, spacer = 0, width = 50, tab = 0;
+ int i, j, l, l1, ibase;
+ char endstr[10];
+ char s[100]; /* buffer for sequence */
+ char ss[100]; /* buffer for structure */
+ int checksum = 0;
+ int seqlen;
+ int which_case; /* 0 = do nothing. 1 = upper case. 2 = lower case */
+ int dostruc; /* TRUE to print structure lines*/
+
+ which_case = 0;
+ dostruc = FALSE;
+ seqlen = (sqinfo->flags & SQINFO_LEN) ? sqinfo->len : strlen(seq);
+
+ if (IsAlignmentFormat(outform))
+ Die("Tried to write an aligned format with WriteSeq() -- bad, bad.");
+
+
+ strcpy( endstr,"");
+ l1 = 0;
+ checksum = GCGchecksum(seq, seqlen);
+
+ switch (outform) {
+ case SQFILE_UNKNOWN: /* no header, just sequence */
+ strcpy(endstr,"\n"); /* end w/ extra blank line */
+ break;
+
+ case SQFILE_GENBANK:
+ fprintf(outf,"LOCUS %s %d bp\n",
+ sqinfo->name, seqlen);
+ fprintf(outf,"ACCESSION %s\n",
+ (sqinfo->flags & SQINFO_ACC) ? sqinfo->acc : ".");
+ fprintf(outf,"DEFINITION %s\n",
+ (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : ".");
+ fprintf(outf,"VERSION %s\n",
+ (sqinfo->flags & SQINFO_ID) ? sqinfo->id : ".");
+ fprintf(outf,"ORIGIN \n");
+ spacer = 11;
+ numline = 1;
+ strcpy(endstr, "\n//");
+ break;
+
+ case SQFILE_GCGDATA:
+ fprintf(outf, ">>>>%s 9/95 ASCII Len: %d\n", sqinfo->name, seqlen);
+ fprintf(outf, "%s\n", (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : "-");
+ break;
+
+ case SQFILE_PIR:
+ fprintf(outf, "ENTRY %s\n",
+ (sqinfo->flags & SQINFO_ID) ? sqinfo->id : sqinfo->name);
+ fprintf(outf, "TITLE %s\n",
+ (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : "-");
+ fprintf(outf, "ACCESSION %s\n",
+ (sqinfo->flags & SQINFO_ACC) ? sqinfo->acc : "-");
+ fprintf(outf, "SUMMARY #Length %d #Checksum %d\n",
+ sqinfo->len, checksum);
+ fprintf(outf, "SEQUENCE\n");
+ fprintf(outf, " 5 10 15 20 25 30\n");
+ spacer = 2; /* spaces after every residue */
+ numline = 1; /* number lines w/ coords */
+ width = 30; /* 30 aa per line */
+ strcpy(endstr, "\n///");
+ break;
+
+ case SQFILE_SQUID:
+ fprintf(outf, "NAM %s\n", sqinfo->name);
+ if (sqinfo->flags & (SQINFO_ID | SQINFO_ACC | SQINFO_START | SQINFO_STOP | SQINFO_OLEN))
+ fprintf(outf, "SRC %s %s %d..%d::%d\n",
+ (sqinfo->flags & SQINFO_ID) ? sqinfo->id : "-",
+ (sqinfo->flags & SQINFO_ACC) ? sqinfo->acc : "-",
+ (sqinfo->flags & SQINFO_START) ? sqinfo->start : 0,
+ (sqinfo->flags & SQINFO_STOP) ? sqinfo->stop : 0,
+ (sqinfo->flags & SQINFO_OLEN) ? sqinfo->olen : 0);
+ if (sqinfo->flags & SQINFO_DESC)
+ fprintf(outf, "DES %s\n", sqinfo->desc);
+ if (sqinfo->flags & SQINFO_SS)
+ {
+ fprintf(outf, "SEQ +SS\n");
+ dostruc = TRUE; /* print structure lines too */
+ }
+ else
+ fprintf(outf, "SEQ\n");
+ numline = 1; /* number seq lines w/ coords */
+ strcpy(endstr, "\n++");
+ break;
+
+ case SQFILE_EMBL:
+ fprintf(outf,"ID %s\n",
+ (sqinfo->flags & SQINFO_ID) ? sqinfo->id : sqinfo->name);
+ fprintf(outf,"AC %s\n",
+ (sqinfo->flags & SQINFO_ACC) ? sqinfo->acc : "-");
+ fprintf(outf,"DE %s\n",
+ (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : "-");
+ fprintf(outf,"SQ %d BP\n", seqlen);
+ strcpy(endstr, "\n//"); /* 11Oct90: bug fix*/
+ tab = 5; /** added 31jan91 */
+ spacer = 11; /** added 31jan91 */
+ break;
+
+ case SQFILE_GCG:
+ fprintf(outf,"%s\n", sqinfo->name);
+ if (sqinfo->flags & SQINFO_ACC)
+ fprintf(outf,"ACCESSION %s\n", sqinfo->acc);
+ if (sqinfo->flags & SQINFO_DESC)
+ fprintf(outf,"DEFINITION %s\n", sqinfo->desc);
+ fprintf(outf," %s Length: %d (today) Check: %d ..\n",
+ sqinfo->name, seqlen, checksum);
+ spacer = 11;
+ numline = 1;
+ strcpy(endstr, "\n"); /* this is insurance to help prevent misreads at eof */
+ break;
+
+ case SQFILE_STRIDER: /* ?? map ?*/
+ fprintf(outf,"; ### from DNA Strider ;-)\n");
+ fprintf(outf,"; DNA sequence %s, %d bases, %d checksum.\n;\n",
+ sqinfo->name, seqlen, checksum);
+ strcpy(endstr, "\n//");
+ break;
+
+ /* SRE: Don had Zuker default to Pearson, which is not
+ intuitive or helpful, since Zuker's MFOLD can't read
+ Pearson format. More useful to use kIG */
+ case SQFILE_ZUKER:
+ which_case = 1; /* MFOLD requires upper case. */
+ /*FALLTHRU*/
+ case SQFILE_IG:
+ fprintf(outf,";%s %s\n",
+ sqinfo->name,
+ (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : "");
+ fprintf(outf,"%s\n", sqinfo->name);
+ strcpy(endstr,"1"); /* == linear dna */
+ break;
+
+ case SQFILE_RAW: /* Raw: no header at all. */
+ break;
+
+ default :
+ case SQFILE_FASTA:
+ fprintf(outf,">%s %s\n", sqinfo->name,
+ (sqinfo->flags & SQINFO_DESC) ? sqinfo->desc : "");
+ break;
+ }
+
+ if (which_case == 1) s2upper(seq);
+ if (which_case == 2) s2lower(seq);
+
+
+ width = MIN(width,100);
+ for (i=0, l=0, ibase = 1, lines = 0; i < seqlen; ) {
+ if (l1 < 0) l1 = 0;
+ else if (l1 == 0) {
+ if (numline) fprintf(outf,"%8d ",ibase);
+ for (j=0; j<tab; j++) fputc(' ',outf);
+ }
+ if ((spacer != 0) && ((l+1) % spacer == 1))
+ { s[l] = ' '; ss[l] = ' '; l++; }
+ s[l] = seq[i];
+ ss[l] = (sqinfo->flags & SQINFO_SS) ? sqinfo->ss[i] : '.';
+ l++; i++;
+ l1++; /* don't count spaces for width*/
+ if (l1 == width || i == seqlen) {
+ s[l] = ss[l] = '\0';
+ l = 0; l1 = 0;
+ if (dostruc)
+ {
+ fprintf(outf, "%s\n", s);
+ if (numline) fprintf(outf," ");
+ for (j=0; j<tab; j++) fputc(' ',outf);
+ if (i == seqlen) fprintf(outf,"%s%s\n",ss,endstr);
+ else fprintf(outf,"%s\n",ss);
+ }
+ else
+ {
+ if (i == seqlen) fprintf(outf,"%s%s\n",s,endstr);
+ else fprintf(outf,"%s\n",s);
+ }
+ lines++;
+ ibase = i+1;
+ }
+ }
+ return lines;
+}
+
+
+/* Function: ReadMultipleRseqs()
+ *
+ * Purpose: Open a data file and
+ * parse it into an array of rseqs (raw, unaligned
+ * sequences).
+ *
+ * Caller is responsible for free'ing memory allocated
+ * to ret_rseqs, ret_weights, and ret_names.
+ *
+ * Weights are currently only supported for MSF format.
+ * Sequences read from all other formats will be assigned
+ * weights of 1.0. If the caller isn't interested in
+ * weights, it passes NULL as ret_weights.
+ *
+ * Returns 1 on success. Returns 0 on failure and sets
+ * squid_errno to indicate the cause.
+ */
+int
+ReadMultipleRseqs(char *seqfile,
+ int fformat,
+ char ***ret_rseqs,
+ SQINFO **ret_sqinfo,
+ int *ret_num)
+{
+ SQINFO *sqinfo; /* array of sequence optional info */
+ SQFILE *dbfp; /* open ptr for sequential access of file */
+ char **rseqs; /* sequence array */
+ int numalloced; /* num of seqs currently alloced for */
+ int num;
+
+
+ num = 0;
+ numalloced = 16;
+ rseqs = (char **) MallocOrDie (numalloced * sizeof(char *));
+ sqinfo = (SQINFO *) MallocOrDie (numalloced * sizeof(SQINFO));
+ if ((dbfp = SeqfileOpen(seqfile, fformat, NULL)) == NULL) return 0;
+
+ while (ReadSeq(dbfp, dbfp->format, &rseqs[num], &(sqinfo[num])))
+ {
+ num++;
+ if (num == numalloced) /* more seqs coming, alloc more room */
+ {
+ numalloced += 16;
+ rseqs = (char **) ReallocOrDie (rseqs, numalloced*sizeof(char *));
+ sqinfo = (SQINFO *) ReallocOrDie (sqinfo, numalloced * sizeof(SQINFO));
+ }
+ }
+ SeqfileClose(dbfp);
+
+ *ret_rseqs = rseqs;
+ *ret_sqinfo = sqinfo;
+ *ret_num = num;
+ return 1;
+}
+
+
+/* Function: String2SeqfileFormat()
+ * Date: SRE, Sun Jun 27 15:25:54 1999 [TW 723 over Canadian Shield]
+ *
+ * Purpose: Convert a string (e.g. from command line option arg)
+ * to a format code. Case insensitive. Return
+ * MSAFILE_UNKNOWN/SQFILE_UNKNOWN if string is bad.
+ * Uses codes defined in squid.h (unaligned formats) and
+ * msa.h (aligned formats).
+ *
+ * Args: s - string to convert; e.g. "stockholm"
+ *
+ * Returns: format code; e.g. MSAFILE_STOCKHOLM
+ */
+int
+String2SeqfileFormat(char *s)
+{
+ char *s2;
+ int code = SQFILE_UNKNOWN;
+
+ if (s == NULL) return SQFILE_UNKNOWN;
+ s2 = sre_strdup(s, -1);
+ s2upper(s2);
+
+ if (strcmp(s2, "FASTA") == 0) code = SQFILE_FASTA;
+#ifdef CLUSTALO
+ if (strcmp(s2, "FA") == 0) code = SQFILE_FASTA;
+ else if (strcmp(s2, "VIENNA") == 0) code = SQFILE_VIENNA;
+ else if (strcmp(s2, "VIE") == 0) code = SQFILE_VIENNA;
+#endif
+ else if (strcmp(s2, "GENBANK") == 0) code = SQFILE_GENBANK;
+#ifdef CLUSTALO
+ else if (strcmp(s2, "GB") == 0) code = SQFILE_GENBANK;
+#endif
+ else if (strcmp(s2, "EMBL") == 0) code = SQFILE_EMBL;
+ else if (strcmp(s2, "GCG") == 0) code = SQFILE_GCG;
+ else if (strcmp(s2, "GCGDATA") == 0) code = SQFILE_GCGDATA;
+ else if (strcmp(s2, "RAW") == 0) code = SQFILE_RAW;
+ else if (strcmp(s2, "IG") == 0) code = SQFILE_IG;
+ else if (strcmp(s2, "STRIDER") == 0) code = SQFILE_STRIDER;
+ else if (strcmp(s2, "IDRAW") == 0) code = SQFILE_IDRAW;
+ else if (strcmp(s2, "ZUKER") == 0) code = SQFILE_ZUKER;
+ else if (strcmp(s2, "PIR") == 0) code = SQFILE_PIR;
+ else if (strcmp(s2, "SQUID") == 0) code = SQFILE_SQUID;
+ else if (strcmp(s2, "STOCKHOLM") == 0) code = MSAFILE_STOCKHOLM;
+#ifdef CLUSTALO
+ else if (strcmp(s2, "ST") == 0) code = MSAFILE_STOCKHOLM;
+ else if (strcmp(s2, "STK") == 0) code = MSAFILE_STOCKHOLM;
+#endif
+ else if (strcmp(s2, "SELEX") == 0) code = MSAFILE_SELEX;
+ else if (strcmp(s2, "MSF") == 0) code = MSAFILE_MSF;
+ else if (strcmp(s2, "CLUSTAL") == 0) code = MSAFILE_CLUSTAL;
+#ifdef CLUSTALO
+ else if (strcmp(s2, "CLU") == 0) code = MSAFILE_CLUSTAL;
+#endif
+ else if (strcmp(s2, "A2M") == 0) code = MSAFILE_A2M;
+ else if (strcmp(s2, "PHYLIP") == 0) code = MSAFILE_PHYLIP;
+#ifdef CLUSTALO
+ else if (strcmp(s2, "PHY") == 0) code = MSAFILE_PHYLIP;
+#endif
+ else if (strcmp(s2, "EPS") == 0) code = MSAFILE_EPS;
+#ifdef CLUSTALO
+ else code = SQFILE_UNKNOWN;
+#endif
+ free(s2);
+ return code;
+}
+char *
+SeqfileFormat2String(int code)
+{
+ switch (code) {
+ case SQFILE_UNKNOWN: return "unknown";
+ case SQFILE_FASTA: return "FASTA";
+#ifdef CLUSTALO
+ case SQFILE_VIENNA: return "Vienna";
+#endif
+ case SQFILE_GENBANK: return "Genbank";
+ case SQFILE_EMBL: return "EMBL";
+ case SQFILE_GCG: return "GCG";
+ case SQFILE_GCGDATA: return "GCG data library";
+ case SQFILE_RAW: return "raw";
+ case SQFILE_IG: return "Intelligenetics";
+ case SQFILE_STRIDER: return "MacStrider";
+ case SQFILE_IDRAW: return "Idraw Postscript";
+ case SQFILE_ZUKER: return "Zuker";
+ case SQFILE_PIR: return "PIR";
+ case SQFILE_SQUID: return "SQUID";
+ case MSAFILE_STOCKHOLM: return "Stockholm";
+ case MSAFILE_SELEX: return "SELEX";
+ case MSAFILE_MSF: return "MSF";
+ case MSAFILE_CLUSTAL: return "Clustal";
+ case MSAFILE_A2M: return "a2m";
+ case MSAFILE_PHYLIP: return "Phylip";
+ case MSAFILE_EPS: return "EPS";
+ default:
+ Die("Bad code passed to MSAFormat2String()");
+ }
+ /*NOTREACHED*/
+ return NULL;
+}
+
+
+/* Function: MSAToSqinfo()
+ * Date: SRE, Tue Jul 20 14:36:56 1999 [St. Louis]
+ *
+ * Purpose: Take an MSA and generate a SQINFO array suitable
+ * for use in annotating the unaligned sequences.
+ * Return the array.
+ *
+ * Permanent temporary code. sqinfo was poorly designed.
+ * it must eventually be replaced, but the odds
+ * of this happening soon are nil, so I have to deal.
+ *
+ * Args: msa - the alignment
+ *
+ * Returns: ptr to allocated sqinfo array.
+ * Freeing is ghastly: free in each individual sqinfo[i]
+ * with FreeSequence(NULL, &(sqinfo[i])), then
+ * free(sqinfo).
+ */
+SQINFO *
+MSAToSqinfo(MSA *msa)
+{
+ int idx;
+ SQINFO *sqinfo;
+
+ sqinfo = MallocOrDie(sizeof(SQINFO) * msa->nseq);
+
+ for (idx = 0; idx < msa->nseq; idx++)
+ {
+ sqinfo[idx].flags = 0;
+ SetSeqinfoString(&(sqinfo[idx]),
+ msa->sqname[idx], SQINFO_NAME);
+ SetSeqinfoString(&(sqinfo[idx]),
+ MSAGetSeqAccession(msa, idx), SQINFO_ACC);
+ SetSeqinfoString(&(sqinfo[idx]),
+ MSAGetSeqDescription(msa, idx), SQINFO_DESC);
+
+ if (msa->ss != NULL && msa->ss[idx] != NULL) {
+ MakeDealignedString(msa->aseq[idx], msa->alen,
+ msa->ss[idx], &(sqinfo[idx].ss));
+ sqinfo[idx].flags |= SQINFO_SS;
+ }
+
+ if (msa->sa != NULL && msa->sa[idx] != NULL) {
+ MakeDealignedString(msa->aseq[idx], msa->alen,
+ msa->sa[idx], &(sqinfo[idx].sa));
+ sqinfo[idx].flags |= SQINFO_SA;
+ }
+
+ sqinfo[idx].len = DealignedLength(msa->aseq[idx]);
+ sqinfo[idx].flags |= SQINFO_LEN;
+ }
+ return sqinfo;
+}
+
+
+
+/* cc -o sqio_test -DA_QUIET_DAY -L. sqio.c -lsquid */
+#ifdef A_QUIET_DAY
+#include "ssi.h"
+int
+main(int argc, char **argv)
+{
+ FILE *fp;
+ char *filename;
+ char *buf;
+ int len;
+ int mode = 3;
+ SSIOFFSET off;
+
+ filename = argv[1];
+
+ if (mode == 1) {
+ buf = malloc(sizeof(char) * 256);
+ if ((fp = fopen(filename, "r")) == NULL)
+ Die("open of %s failed", filename);
+ while (fgets(buf, 255, fp) != NULL)
+ ;
+ fclose(fp);
+ free(buf);
+ } else if (mode == 2) {
+ if ((fp = fopen(filename, "r")) == NULL)
+ Die("open of %s failed", filename);
+ buf = NULL; len = 0;
+ while (sre_fgets(&buf, &len, fp) != NULL)
+ SSIGetFilePosition(fp, SSI_OFFSET_I32, &off);
+ fclose(fp);
+ free(buf);
+ } else if (mode == 3) {
+ SQFILE *dbfp;
+ SQINFO info;
+
+ if ((dbfp = SeqfileOpen(filename, SQFILE_FASTA, NULL)) == NULL)
+ Die("open of %s failed", filename);
+ while (ReadSeq(dbfp, dbfp->format, &buf, &info)) {
+ SSIGetFilePosition(dbfp->f, SSI_OFFSET_I32, &off);
+ FreeSequence(buf, &info);
+ }
+ SeqfileClose(dbfp);
+ }
+
+}
+
+
+#endif
--- /dev/null
+/* Generated automatically from squid.h.in by configure. */
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+#ifndef SQUIDH_INCLUDED
+#define SQUIDH_INCLUDED
+
+/* squid.h
+ * Header file for my library of sequence functions.
+ *
+ * CVS $Id: squid.h.in,v 1.5 2002/10/09 14:26:09 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <math.h>
+#include <stdlib.h>
+#include <unistd.h> /* for sysconf() #define's */
+
+
+#if DEBUGLEVEL > 0
+#include <assert.h> /* for SQD_DASSERT1(), etc. */
+#endif
+
+/* include clustal's config.h */
+#ifdef CLUSTALO
+#include "config.h"
+#define CLUSTALO 1
+#else
+#include "clustal-omega-config.h"
+#define CLUSTALO 1
+#endif
+
+#ifdef CLUSTALO
+/* we don't want squidconf.h but our own config header. but, there are
+ * some checks, espcially at the end of squidconf.h might be
+ * necessary for squid to work. They follow after the inclusion of
+ * config.h
+ */
+#undef DEBUG
+
+/* squidconf.h checks:
+ */
+#if defined HAVE_NTOHL && defined HAVE_NTOHS && defined HAVE_HTONS && defined HAVE_HTONL
+#define USE_HOST_BYTESWAP_FUNCTIONS 1
+#endif
+/* On 64-bit machines like Alphas, strtoull doesn't exist, strotul will work
+ */
+#if SIZEOF_UNSIGNED_LONG == 8 && defined HAVE_STRTOUL && ! defined HAVE_STRTOULL
+#define strtoull strtoul
+#endif
+
+#if defined HAVE_FTELLO && defined HAVE_FSEEKO && SIZEOF_OFF_T == 8
+#define HAS_64BIT_FILE_OFFSETS 1
+#elif defined HAVE_FTELLO64 && defined HAVE_FSEEKO64 && SIZEOF_OFF64_T == 8
+#define HAS_64BIT_FILE_OFFSETS 1
+#elif defined HAVE_FTELL64 && defined HAVE_FSEEK64
+#define HAS_64BIT_FILE_OFFSETS 1
+#elif defined ARITHMETIC_FPOS_T && SIZEOF_FPOS_T == 8
+#define HAS_64BIT_FILE_OFFSETS 1
+#else
+#undef HAS_64BIT_FILE_OFFSETS
+#endif
+
+/* The following check seems like nonsense to me (AW), therefore */
+#if 0
+/* Stuff to work around Tru64 not having strtoull() -
+ * on systems with 64-bit longs, we can use strtoul()
+ */
+#undef HAVE_STRTOULL
+#if ! defined HAVE_STRTOULL && SIZEOF_UNSIGNED_LONG == 8
+#define strtoull strtoul
+#endif
+#endif
+
+#else /* CLUSTALO */
+#include "squidconf.h" /* #define's generated by ./configure script */
+#endif
+
+/*****************************************************************
+ * Integers of guaranteed size. (used for instance in gsi.c, gsi2.c)
+ * These are set by the ./configure script; if they show up as FIXME,
+ * they must be manually edited to appropriate type definitions. You
+ * do need 64-bit integers in the current code; email me if this
+ * prevents you from compiling SQUID and tell me your system (I don't
+ * know of any systems that don't have 64-bit integers these days).
+ *****************************************************************/
+typedef unsigned short sqd_uint16;
+typedef unsigned int sqd_uint32;
+typedef unsigned long sqd_uint64;
+
+#ifdef USE_HOST_BYTESWAP_FUNCTIONS
+#include <sys/types.h> /* only for ntohl() and friends. */
+#include <netinet/in.h> /* only for ntohl() and friends. */
+#define sre_ntoh16(x) ntohs(x);
+#define sre_ntoh32(x) ntohl(x);
+#define sre_hton16(x) htons(x);
+#define sre_hton32(x) htonl(x);
+#endif /* USE_HOST_BYTESWAP_FUNCTIONS */
+
+/* Library version info is made available as a global to
+ * any interested program. These are defined in iupac.c
+ * with the other globals.
+ */
+extern char squid_version[]; /* version number */
+extern char squid_date[]; /* date of release */
+extern int squid_errno; /* error codes */
+
+
+
+/****************************************************
+ * Error codes returned by squid library functions (squid_errno)
+ ****************************************************/
+
+#define SQERR_OK 0 /* no error */
+#define SQERR_UNKNOWN 1 /* generic error, unidentified */
+#define SQERR_NODATA 2 /* unexpectedly NULL stream */
+#define SQERR_MEM 3 /* malloc or realloc failed */
+#define SQERR_NOFILE 4 /* file not found */
+#define SQERR_FORMAT 5 /* file format not recognized */
+#define SQERR_PARAMETER 6 /* bad parameter passed to func */
+#define SQERR_DIVZERO 7 /* error in sre_math.c */
+#define SQERR_INCOMPAT 8 /* incompatible parameters */
+#define SQERR_EOD 9 /* end-of-data (often normal) */
+
+/****************************************************
+ * Single sequence information
+ ****************************************************/
+#define SQINFO_NAMELEN 64
+#define SQINFO_DESCLEN 128
+
+struct seqinfo_s {
+ int flags; /* what extra data are available */
+ char name[SQINFO_NAMELEN];/* up to 63 characters of name */
+ char id[SQINFO_NAMELEN]; /* up to 63 char of database identifier */
+ char acc[SQINFO_NAMELEN]; /* up to 63 char of database accession # */
+ char desc[SQINFO_DESCLEN];/* up to 127 char of description */
+ int len; /* length of this seq */
+ int start; /* (1..len) start position on source seq */
+ int stop; /* (1..len) end position on source seq */
+ int olen; /* original length of source seq */
+ int type; /* kRNA, kDNA, kAmino, or kOther */
+ char *ss; /* 0..len-1 secondary structure string */
+ char *sa; /* 0..len-1 % side chain surface access. */
+};
+typedef struct seqinfo_s SQINFO;
+
+#define SQINFO_NAME (1 << 0)
+#define SQINFO_ID (1 << 1)
+#define SQINFO_ACC (1 << 2)
+#define SQINFO_DESC (1 << 3)
+#define SQINFO_START (1 << 4)
+#define SQINFO_STOP (1 << 5)
+#define SQINFO_LEN (1 << 6)
+#define SQINFO_TYPE (1 << 7)
+#define SQINFO_OLEN (1 << 8)
+#define SQINFO_SS (1 << 9)
+#define SQINFO_SA (1 << 10)
+
+
+/****************************************************
+ * Sequence alphabet: see also iupac.c
+ ****************************************************/
+ /* IUPAC symbols defined globally in iupac.c */
+struct iupactype {
+ char sym; /* character representation */
+ char symcomp; /* complement (regular char */
+ char code; /* my binary rep */
+ char comp; /* binary encoded complement */
+};
+extern struct iupactype iupac[];
+#define IUPACSYMNUM 17
+
+extern char *stdcode1[]; /* 1-letter amino acid translation code */
+extern char *stdcode3[]; /* 3-letter amino acid translation code */
+extern float dnafq[]; /* nucleotide occurrence frequencies */
+extern float aafq[]; /* amino acid occurrence frequencies */
+extern char aa_alphabet[]; /* amino acid alphabet */
+extern int aa_index[]; /* convert 0..19 indices to 0..26 */
+
+ /* valid symbols in IUPAC code */
+#define NUCLEOTIDES "ACGTUNRYMKSWHBVDacgtunrymkswhbvd"
+#define AMINO_ALPHABET "ACDEFGHIKLMNPQRSTVWY"
+#define DNA_ALPHABET "ACGT"
+#define RNA_ALPHABET "ACGU"
+#define WHITESPACE " \t\n"
+
+#define isgap(c) ((c) == ' ' || (c) == '.' || (c) == '_' || (c) == '-' || (c) == '~')
+
+
+/****************************************************
+ * Sequence i/o: originally from Don Gilbert's readseq
+ ****************************************************/
+#include "msa.h" /* for multiple sequence alignment support */
+
+ /* buffer size for reading in lines from sequence files*/
+#define LINEBUFLEN 4096
+
+/* sequence types parsed by Seqtype() */
+/* note that these must match hmmAMINO and hmmNUCLEIC in HMMER */
+#define kOtherSeq 0 /* hmmNOTSETYET */
+#define kDNA 1
+#define kRNA 2 /* hmmNUCLEIC */
+#define kAmino 3 /* hmmAMINO */
+
+/* Unaligned sequence file formats recognized
+ * Coexists with definitions of multiple alignment formats in msa.h:
+ * >100 reserved for alignment formats
+ * <100 reserved for unaligned formats
+ * 0 reserved for unknown
+ *
+ * Some "legacy" formats are supported only when explicitly
+ * requested; not autodetected by SeqfileFormat().
+ *
+ * DON'T REASSIGN THESE CODES. They're written into
+ * GSI index files. You can use new ones, but reassigning
+ * the sense of old ones will break GSI indices.
+ * Alignment format codes were reassigned with the creation
+ * of msa.c, but before Stockholm format, there were no
+ * indexed alignment databases.
+ */
+#define SQFILE_UNKNOWN 0 /* unknown format */
+#define SQFILE_IG 1 /* Intelligenetics (!) */
+#define SQFILE_GENBANK 2 /* GenBank flatfile */
+ /* 3 was A2M. Now an alignment format */
+#define SQFILE_EMBL 4 /* EMBL or Swissprot flatfile */
+#define SQFILE_GCG 5 /* GCG single sequence files */
+#define SQFILE_STRIDER 6 /* MacStrider (!!) */
+#define SQFILE_FASTA 7 /* FASTA format: default */
+#define SQFILE_ZUKER 8 /* Zuker MFOLD format (legacy) */
+#define SQFILE_IDRAW 9 /* Idraw-style PostScript (legacy) */
+ /* 10 was SELEX. Now alignment format */
+ /* 11 was MSF. Now alignment format */
+#define SQFILE_PIR 12 /* PIR format */
+#define SQFILE_RAW 13 /* raw sequence */
+#define SQFILE_SQUID 14 /* my obsolete squid format */
+ /* 15 was kXPearson, extended FASTA; withdrawn */
+#define SQFILE_GCGDATA 16 /* GCG data library file */
+ /* 17 was Clustal. Now alignment format*/
+#ifdef CLUSTALO
+#define SQFILE_VIENNA 18 /* Vienna format: concatenated fasta */
+#endif
+#define IsUnalignedFormat(fmt) ((fmt) && (fmt) < 100)
+
+#include "ssi.h"
+
+struct ReadSeqVars {
+ FILE *f; /* open file pointer */
+ char *fname; /* name of file; used for diagnostics */
+ int linenumber; /* what line are we on in the file */
+
+ char *buf; /* dynamically allocated sre_fgets() buffer */
+ int buflen; /* allocation length for buf */
+
+ int ssimode; /* SSI_OFFSET_I32 or SSI_OFFSET_I64 */
+ SSIOFFSET ssioffset; /* disk offset to last line read into buf */
+ SSIOFFSET r_off; /* offset to start of record */
+ SSIOFFSET d_off; /* offset to start of sequence data */
+
+ int rpl; /* residues per data line for this file; -1 if unset, 0 if invalid */
+ int lastrpl; /* rpl on last line seen */
+ int maxrpl; /* max rpl on any line of the file */
+ int bpl; /* bytes per data line; -1 if unset, 0 if invalid */
+ int lastbpl; /* bpl on last line seen */
+ int maxbpl; /* max bpl on any line of the file */
+
+ char *seq; /* growing sequence during parse */
+ SQINFO *sqinfo; /* name, id, etc, gathered during parse */
+ char *sp;
+ int seqlen; /* current sequence length */
+ int maxseq; /* current allocation length for seq */
+
+ int format; /* format of seqfile we're reading. */
+ int do_gzip; /* TRUE if f is a pipe from gzip -dc */
+ int do_stdin; /* TRUE if f is stdin */
+
+ /* An (important) hack for sequential access of multiple alignment files:
+ * we read the whole alignment in,
+ * and then copy it one sequence at a time into seq and sqinfo.
+ * It is active if msa is non NULL.
+ * msa->lastidx is reused/overloaded: used to keep track of what
+ * seq we'll return next.
+ * afp->format is the real format, while SQFILE->format is kMSA.
+ * Because we keep it in the SQFILE structure,
+ * ReadSeq() and friends are always reentrant for multiple seqfiles.
+ */
+ MSA *msa;
+ MSAFILE *afp;
+};
+typedef struct ReadSeqVars SQFILE;
+
+
+/****************************************************
+ * Cluster analysis and phylogenetic tree support
+ ****************************************************/
+
+/* struct phylo_s - a phylogenetic tree
+ *
+ * For N sequences, there will generally be an array of 0..N-2
+ * phylo_s structures representing the nodes of a tree.
+ * [0] is the root. The indexes of left and
+ * right children are somewhat confusing so be careful. The
+ * indexes can have values of 0..2N-2. If they are 0..N-1, they
+ * represent pointers to individual sequences. If they are
+ * >= N, they represent pointers to a phylo_s structure
+ * at (index - N).
+ */
+struct phylo_s {
+ int parent; /* index of parent, N..2N-2, or -1 for root */
+ int left; /* index of one of the branches, 0..2N-2 */
+ int right; /* index of other branch, 0..2N-2 */
+ float diff; /* difference score between seqs */
+ float lblen; /* left branch length */
+ float rblen; /* right branch length */
+ char *is_in; /* 0..N-1 flag array, 1 if seq included */
+ int incnum; /* number of seqs included at this node */
+};
+
+
+/* Strategies for cluster analysis; cluster by mean distance,
+ * minimum distance, or maximum distance.
+ */
+enum clust_strategy { CLUSTER_MEAN, CLUSTER_MAX, CLUSTER_MIN };
+
+/****************************************************
+ * Generic data structure support
+ ****************************************************/
+
+/* a struct intstack_s implements a pushdown stack for storing
+ * single integers.
+ */
+struct intstack_s {
+ int data;
+ struct intstack_s *nxt;
+};
+
+/****************************************************
+ * Binary nucleotide alphabet support
+ ****************************************************/
+
+/* Binary encoding of the IUPAC code for nucleotides
+ *
+ * four-bit "word", permitting rapid degenerate matching
+ * A C G T/U
+ * 0 0 1 0
+ */
+#define NTA 8
+#define NTC 4
+#define NTG 2
+#define NTT 1
+#define NTU 1
+#define NTN 15 /* A|C|G|T */
+#define NTR 10 /* A|G */
+#define NTY 5 /* C|T */
+#define NTM 12 /* A|C */
+#define NTK 3 /* G|T */
+#define NTS 6 /* C|G */
+#define NTW 9 /* A|T */
+#define NTH 13 /* A|C|T */
+#define NTB 7 /* C|G|T */
+#define NTV 14 /* A|C|G */
+#define NTD 11 /* A|G|T */
+#define NTGAP 16 /* GAP */
+#define NTEND 0 /* null string terminator */
+
+/* ntmatch(): bitwise comparison of two nuc's
+ * note that it's sensitive to the order;
+ * probe may be degenerate but target should not be
+ */
+#define ntmatch(probe, target) ((probe & target) == target)
+
+/****************************************************
+ * Support for a portable, flexible Getopt()
+ ****************************************************/
+
+/* Structure: opt_s
+ *
+ * Structure for declaring options to a main().
+ */
+struct opt_s {
+ char *name; /* name of option, e.g. "--option1" or "-o" */
+ int single; /* TRUE if a single letter option */
+ int argtype; /* for typechecking, e.g. sqdARG_INT */
+};
+ /* acceptable argtype's... */
+#define sqdARG_NONE 0 /* no argument */
+#define sqdARG_INT 1 /* something that atoi() can grok */
+#define sqdARG_FLOAT 2 /* something that atof() can grok */
+#define sqdARG_CHAR 3 /* require single character or digit */
+#define sqdARG_STRING 4 /* anything goes */
+
+/****************************************************
+ * Support for convenient Perl-y regexp matching
+ * See hsregexp.c for copyright notice: this code is derived
+ * from Henry Spencer's freely distributed regexp library.
+ ****************************************************/
+
+#define NSUBEXP 10
+typedef struct sqd_regexp {
+ char *startp[NSUBEXP];
+ char *endp[NSUBEXP];
+ char regstart; /* Internal use only. */
+ char reganch; /* Internal use only. */
+ char *regmust; /* Internal use only. */
+ int regmlen; /* Internal use only. */
+ char program[1]; /* Unwarranted chumminess with compiler. */
+} sqd_regexp;
+
+/* Strparse() defines and manages these.
+ * sqd_parse[0] contains the substring that matched the pattern.
+ * sqd_parse[1-9] contain substrings matched with ()'s.
+ */
+extern char *sqd_parse[10];
+
+/****************************************************
+ * Portable detection of multiprocessor # of CPUs.
+ * #include <unistd.h>
+ * long foo = SQD_NPROC;
+ * returns the number of available processors.
+ * if foo == -1, we failed.
+ ****************************************************/
+
+/* Our problem here is that POSIX apparently doesn't specify
+ * a standard for how to get sysconf() to report the number of
+ * processors on-line. _SC_NPROCESSORS_ONLN is specified
+ * by SVR4.0MP. Thanks to W. Gish for help here.
+ */
+#undef SQD_NPROC
+#ifdef _SC_NPROCESSORS_ONLN /* Sun Solaris, Digital UNIX */
+#define SQD_NPROC sysconf(_SC_NPROCESSORS_ONLN)
+#else
+#ifdef _SC_NPROC_ONLN /* Silicon Graphics IRIX */
+#define SQD_NPROC sysconf(_SC_NPROC_ONLN)
+#else /* FreeBSD, Linux don't support getting ncpu via sysconf() */
+#define SQD_NPROC -1
+#endif
+#endif
+
+/****************************************************
+ * Three levels of debugging printf's and assert's
+ * level 1: little impact on verbosity or performance
+ * level 2: moderate impact
+ * level 3: high impact
+ * Example:
+ * SQD_DPRINTF3(("Matrix row %d col %d = %f\n", i, j, val));
+ * Note the double parentheses; these are important.
+ ****************************************************/
+
+#ifndef DEBUGLEVEL
+#define DEBUGLEVEL 0
+#endif
+
+#if (DEBUGLEVEL >= 1)
+#define SQD_DPRINTF1(x) printf x
+#define SQD_DASSERT1(x) assert x
+#else
+#define SQD_DPRINTF1(x)
+#define SQD_DASSERT1(x)
+#endif
+#if (DEBUGLEVEL >= 2)
+#define SQD_DPRINTF2(x) printf x
+#define SQD_DASSERT2(x) assert x
+#else
+#define SQD_DPRINTF2(x)
+#define SQD_DASSERT2(x)
+#endif
+#if (DEBUGLEVEL >= 3)
+#define SQD_DPRINTF3(x) printf x
+#define SQD_DASSERT3(x) assert x
+#else
+#define SQD_DPRINTF3(x)
+#define SQD_DASSERT3(x)
+#endif
+
+/* PANIC is called for failures of Std C/POSIX functions,
+ * instead of my own functions. Panic() calls perror() and exits
+ * abnormally.
+ */
+#define PANIC Panic(__FILE__, __LINE__)
+
+/* Malloc/realloc calls are wrapped
+ */
+#define MallocOrDie(x) sre_malloc(__FILE__, __LINE__, (x))
+#define ReallocOrDie(x,y) sre_realloc(__FILE__, __LINE__, (x), (y))
+
+/****************************************************
+ * Miscellaneous macros and defines
+ ****************************************************/
+
+#define SQDCONST_E 2.71828182845904523536028747135
+#define SQDCONST_PI 3.14159265358979323846264338328
+
+ /* must declare swapfoo to use SWAP() */
+#define SWAP(a,b) {swapfoo = b; b = a; a = swapfoo;}
+#define ScalarsEqual(a,b) (fabs((a)-(b)) < 1e-7)
+
+#ifndef MIN
+#define MIN(a,b) (((a)<(b))?(a):(b))
+#endif
+#ifndef MAX
+#define MAX(a,b) (((a)>(b))?(a):(b))
+#endif
+
+/* For convenience and (one hopes) clarity in boolean tests:
+ */
+#ifndef TRUE
+#define TRUE 1
+#endif
+#ifndef FALSE
+#define FALSE 0
+#endif
+
+/* Somewhere, there is a universe in which Unix vendors comply
+ * with the ANSI C standard. Unfortunately, it is not ours:
+ */
+#ifndef EXIT_SUCCESS
+#define EXIT_SUCCESS 0
+#endif
+#ifndef EXIT_FAILURE
+#define EXIT_FAILURE 1
+#endif
+
+#include "sqfuncs.h" /* squid function declarations */
+#include "sre_random.h" /* random number generator and samplers */
+#include "vectorops.h" /* vector operations */
+#endif /* SQUIDH_INCLUDED */
--- /dev/null
+/************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ ************************************************************/
+
+/* squidcore.c
+ * SRE, Sun Jun 20 17:19:04 1999 [Graeme's kitchen]
+ *
+ * Core functions for SQUID library.
+ * RCS $Id: squidcore.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: squidcore.c,v 1.1 1999/07/15 22:24:41 eddy Exp)
+ */
+
+#include <stdio.h>
+#include "version.h"
+
+/* Function: Banner()
+ * Date: SRE, Sun Jun 20 17:19:41 1999 [Graeme's kitchen]
+ *
+ * Purpose: Print a package version and copyright banner.
+ * Used by all the main()'s.
+ *
+ * Expects to be able to pick up defined macros:
+ * macro example
+ * ------ --------------
+ * PACKAGE "HMMER"
+ * RELEASE "2.0.42"
+ * RELEASEDATE "April 1 1999"
+ * COPYRIGHT "Copyright (C) 1992-1999 Washington University School of Medicine"
+ * LICENSE "HMMER is freely distributed under the GNU General Public License (GPL)."
+ *
+ * This gives us a general mechanism to update release information
+ * without changing multiple points in the code; we can also override
+ * SQUID release data with another package's release data (e.g.
+ * HMMER) just by redefining macros.
+ *
+ * Args: fp - where to print it
+ * banner - one-line program description, e.g.:
+ * "foobar - make bars from foo with elan"
+ * Returns: (void)
+ */
+void
+Banner(FILE *fp, char *banner)
+{
+ fprintf(fp, "%s\n%s %s (%s)\n%s\n%s\n", banner, PACKAGE, RELEASE, RELEASEDATE, COPYRIGHT, LICENSE);
+ fprintf(fp, "- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n");
+}
+
+
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* sre_ctype.c
+ *
+ * For portability. Some systems have functions tolower, toupper
+ * as macros (for instance, MIPS M-2000 RISC/os!)
+ *
+ * RCS $Id: sre_ctype.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: sre_ctype.c,v 1.3 2001/09/02 23:43:19 eddy Exp)
+ */
+
+#include <ctype.h>
+#include "squid.h"
+
+int
+sre_tolower(int c)
+{
+ if (isupper(c)) return tolower(c);
+ else return c;
+}
+
+int
+sre_toupper(int c)
+{
+ if (islower(c)) return toupper(c);
+ else return c;
+}
+
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* sre_math.c
+ *
+ * Portability for and extensions to C math library.
+ * RCS $Id: sre_math.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: sre_math.c,v 1.12 2002/10/09 14:26:09 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include "squid.h"
+
+
+/* Function: Linefit()
+ *
+ * Purpose: Given points x[0..N-1] and y[0..N-1], fit to
+ * a straight line y = a + bx.
+ * a, b, and the linear correlation coefficient r
+ * are filled in for return.
+ *
+ * Args: x - x values of data
+ * y - y values of data
+ * N - number of data points
+ * ret_a - RETURN: intercept
+ * ret_b - RETURN: slope
+ * ret_r - RETURN: correlation coefficient
+ *
+ * Return: 1 on success, 0 on failure.
+ */
+int
+Linefit(float *x, float *y, int N, float *ret_a, float *ret_b, float *ret_r)
+{
+ float xavg, yavg;
+ float sxx, syy, sxy;
+ int i;
+
+ /* Calculate averages, xavg and yavg
+ */
+ xavg = yavg = 0.0;
+ for (i = 0; i < N; i++)
+ {
+ xavg += x[i];
+ yavg += y[i];
+ }
+ xavg /= (float) N;
+ yavg /= (float) N;
+
+ sxx = syy = sxy = 0.0;
+ for (i = 0; i < N; i++)
+ {
+ sxx += (x[i] - xavg) * (x[i] - xavg);
+ syy += (y[i] - yavg) * (y[i] - xavg);
+ sxy += (x[i] - xavg) * (y[i] - yavg);
+ }
+ *ret_b = sxy / sxx;
+ *ret_a = yavg - xavg*(*ret_b);
+ *ret_r = sxy / (sqrt(sxx) * sqrt(syy));
+ return 1;
+}
+
+
+/* Function: WeightedLinefit()
+ *
+ * Purpose: Given points x[0..N-1] and y[0..N-1] with
+ * variances (measurement errors) var[0..N-1],
+ * fit to a straight line y = mx + b.
+ *
+ * Method: Algorithm from Numerical Recipes in C, [Press88].
+ *
+ * Return: (void)
+ * ret_m contains slope; ret_b contains intercept
+ */
+void
+WeightedLinefit(float *x, float *y, float *var, int N, float *ret_m, float *ret_b)
+{
+ int i;
+ double s;
+ double sx, sy;
+ double sxx, sxy;
+ double delta;
+ double m, b;
+
+ s = sx = sy = sxx = sxy = 0.;
+ for (i = 0; i < N; i++)
+ {
+ s += 1./var[i];
+ sx += x[i] / var[i];
+ sy += y[i] / var[i];
+ sxx += x[i] * x[i] / var[i];
+ sxy += x[i] * y[i] / var[i];
+ }
+
+ delta = s * sxx - (sx * sx);
+ b = (sxx * sy - sx * sxy) / delta;
+ m = (s * sxy - sx * sy) / delta;
+
+ *ret_m = m;
+ *ret_b = b;
+}
+
+
+/* Function: Gammln()
+ *
+ * Returns the natural log of the gamma function of x.
+ * x is > 0.0.
+ *
+ * Adapted from a public domain implementation in the
+ * NCBI core math library. Thanks to John Spouge and
+ * the NCBI. (According to the NCBI, that's Dr. John
+ * "Gammas Galore" Spouge to you, pal.)
+ */
+double
+Gammln(double x)
+{
+ int i;
+ double xx, tx;
+ double tmp, value;
+ static double cof[11] = {
+ 4.694580336184385e+04,
+ -1.560605207784446e+05,
+ 2.065049568014106e+05,
+ -1.388934775095388e+05,
+ 5.031796415085709e+04,
+ -9.601592329182778e+03,
+ 8.785855930895250e+02,
+ -3.155153906098611e+01,
+ 2.908143421162229e-01,
+ -2.319827630494973e-04,
+ 1.251639670050933e-10
+ };
+
+ /* Protect against x=0. We see this in Dirichlet code,
+ * for terms alpha = 0. This is a severe hack but it is effective
+ * and (we think?) safe. (due to GJM)
+ */
+ if (x <= 0.0) return 999999.;
+
+ xx = x - 1.0;
+ tx = tmp = xx + 11.0;
+ value = 1.0;
+ for (i = 10; i >= 0; i--) /* sum least significant terms first */
+ {
+ value += cof[i] / tmp;
+ tmp -= 1.0;
+ }
+ value = log(value);
+ tx += 0.5;
+ value += 0.918938533 + (xx+0.5)*log(tx) - tx;
+ return value;
+}
+
+
+/* 2D matrix operations
+ */
+float **
+FMX2Alloc(int rows, int cols)
+{
+ float **mx;
+ int r;
+
+ mx = (float **) MallocOrDie(sizeof(float *) * rows);
+ mx[0] = (float *) MallocOrDie(sizeof(float) * rows * cols);
+ for (r = 1; r < rows; r++)
+ mx[r] = mx[0] + r*cols;
+ return mx;
+}
+void
+FMX2Free(float **mx)
+{
+ free(mx[0]);
+ free(mx);
+}
+double **
+DMX2Alloc(int rows, int cols)
+{
+ double **mx;
+ int r;
+
+ mx = (double **) MallocOrDie(sizeof(double *) * rows);
+ mx[0] = (double *) MallocOrDie(sizeof(double) * rows * cols);
+ for (r = 1; r < rows; r++)
+ mx[r] = mx[0] + r*cols;
+ return mx;
+}
+void
+DMX2Free(double **mx)
+{
+ free(mx[0]);
+ free(mx);
+}
+/* Function: FMX2Multiply()
+ *
+ * Purpose: Matrix multiplication.
+ * Multiply an m x p matrix A by a p x n matrix B,
+ * giving an m x n matrix C.
+ * Matrix C must be a preallocated matrix of the right
+ * size.
+ */
+void
+FMX2Multiply(float **A, float **B, float **C, int m, int p, int n)
+{
+ int i, j, k;
+
+ for (i = 0; i < m; i++)
+ for (j = 0; j < n; j++)
+ {
+ C[i][j] = 0.;
+ for (k = 0; k < p; k++)
+ C[i][j] += A[i][p] * B[p][j];
+ }
+}
+
+
+/* Function: IncompleteGamma()
+ *
+ * Purpose: Returns 1 - P(a,x) where:
+ * P(a,x) = \frac{1}{\Gamma(a)} \int_{0}^{x} t^{a-1} e^{-t} dt
+ * = \frac{\gamma(a,x)}{\Gamma(a)}
+ * = 1 - \frac{\Gamma(a,x)}{\Gamma(a)}
+ *
+ * Used in a chi-squared test: for a X^2 statistic x
+ * with v degrees of freedom, call:
+ * p = IncompleteGamma(v/2., x/2.)
+ * to get the probability p that a chi-squared value
+ * greater than x could be obtained by chance even for
+ * a correct model. (i.e. p should be large, say
+ * 0.95 or more).
+ *
+ * Method: Based on ideas from Numerical Recipes in C, Press et al.,
+ * Cambridge University Press, 1988.
+ *
+ * Args: a - for instance, degrees of freedom / 2 [a > 0]
+ * x - for instance, chi-squared statistic / 2 [x >= 0]
+ *
+ * Return: 1 - P(a,x).
+ */
+double
+IncompleteGamma(double a, double x)
+{
+ int iter; /* iteration counter */
+
+ if (a <= 0.) Die("IncompleteGamma(): a must be > 0");
+ if (x < 0.) Die("IncompleteGamma(): x must be >= 0");
+
+ /* For x > a + 1 the following gives rapid convergence;
+ * calculate 1 - P(a,x) = \frac{\Gamma(a,x)}{\Gamma(a)}:
+ * use a continued fraction development for \Gamma(a,x).
+ */
+ if (x > a+1)
+ {
+ double oldp; /* previous value of p */
+ double nu0, nu1; /* numerators for continued fraction calc */
+ double de0, de1; /* denominators for continued fraction calc */
+
+ nu0 = 0.; /* A_0 = 0 */
+ de0 = 1.; /* B_0 = 1 */
+ nu1 = 1.; /* A_1 = 1 */
+ de1 = x; /* B_1 = x */
+
+ oldp = nu1;
+ for (iter = 1; iter < 100; iter++)
+ {
+ /* Continued fraction development:
+ * set A_j = b_j A_j-1 + a_j A_j-2
+ * B_j = b_j B_j-1 + a_j B_j-2
+ * We start with A_2, B_2.
+ */
+ /* j = even: a_j = iter-a, b_j = 1 */
+ /* A,B_j-2 are in nu0, de0; A,B_j-1 are in nu1,de1 */
+ nu0 = nu1 + ((double)iter - a) * nu0;
+ de0 = de1 + ((double)iter - a) * de0;
+
+ /* j = odd: a_j = iter, b_j = x */
+ /* A,B_j-2 are in nu1, de1; A,B_j-1 in nu0,de0 */
+ nu1 = x * nu0 + (double) iter * nu1;
+ de1 = x * de0 + (double) iter * de1;
+
+ /* rescale */
+ if (de1 != 0.)
+ {
+ nu0 /= de1;
+ de0 /= de1;
+ nu1 /= de1;
+ de1 = 1.;
+ }
+ /* check for convergence */
+ if (fabs((nu1-oldp)/nu1) < 1.e-7)
+ return nu1 * exp(a * log(x) - x - Gammln(a));
+
+ oldp = nu1;
+ }
+ Die("IncompleteGamma(): failed to converge using continued fraction approx");
+ }
+ else /* x <= a+1 */
+ {
+ double p; /* current sum */
+ double val; /* current value used in sum */
+
+ /* For x <= a+1 we use a convergent series instead:
+ * P(a,x) = \frac{\gamma(a,x)}{\Gamma(a)},
+ * where
+ * \gamma(a,x) = e^{-x}x^a \sum_{n=0}{\infty} \frac{\Gamma{a}}{\Gamma{a+1+n}} x^n
+ * which looks appalling but the sum is in fact rearrangeable to
+ * a simple series without the \Gamma functions:
+ * = \frac{1}{a} + \frac{x}{a(a+1)} + \frac{x^2}{a(a+1)(a+2)} ...
+ * and it's obvious that this should converge nicely for x <= a+1.
+ */
+
+ p = val = 1. / a;
+ for (iter = 1; iter < 10000; iter++)
+ {
+ val *= x / (a+(double)iter);
+ p += val;
+
+ if (fabs(val/p) < 1.e-7)
+ return 1. - p * exp(a * log(x) - x - Gammln(a));
+ }
+ Die("IncompleteGamma(): failed to converge using series approx");
+ }
+ /*NOTREACHED*/
+ return 0.;
+}
+
--- /dev/null
+/* sre_random.c
+ *
+ * Portable random number generator, and sampling routines.
+ *
+ * SRE, Tue Oct 1 15:24:11 2002 [St. Louis]
+ * CVS $Id: sre_random.c,v 1.1 2002/10/09 14:26:09 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include "sre_random.h"
+
+static int sre_randseed = 42; /* default seed for sre_random() */
+
+/* Function: sre_random()
+ *
+ * Purpose: Return a uniform deviate x, 0.0 <= x < 1.0.
+ *
+ * sre_randseed is a static variable, set
+ * by sre_srandom(). When it is non-zero,
+ * we re-seed.
+ *
+ * Implements L'Ecuyer's algorithm for combining output
+ * of two linear congruential generators, plus a Bays-Durham
+ * shuffle. This is essentially ran2() from Numerical Recipes,
+ * sans their nonhelpful Rand/McNally-esque code obfuscation.
+ *
+ * Overflow errors are avoided by Schrage's algorithm:
+ * az % m = a(z%q) - r(z/q) (+m if <0)
+ * where q=m/a, r=m%a
+ *
+ * Requires that long int's have at least 32 bits.
+ * This function uses statics and is NOT THREADSAFE.
+ *
+ * Reference: Press et al. Numerical Recipes in C, 1992.
+ *
+ * Reliable and portable, but slow. Benchmarks on wrasse,
+ * using Linux gcc and Linux glibc rand() (see randspeed, in Testsuite):
+ * sre_random(): 0.5 usec/call
+ * rand(): 0.2 usec/call
+ */
+double
+sre_random(void)
+{
+ static long rnd1; /* random number from LCG1 */
+ static long rnd2; /* random number from LCG2 */
+ static long rnd; /* random number we return */
+ static long tbl[64]; /* table for Bays/Durham shuffle */
+ long x,y;
+ int i;
+
+ /* Magic numbers a1,m1, a2,m2 from L'Ecuyer, for 2 LCGs.
+ * q,r derive from them (q=m/a, r=m%a) and are needed for Schrage's algorithm.
+ */
+ long a1 = 40014;
+ long m1 = 2147483563;
+ long q1 = 53668;
+ long r1 = 12211;
+
+ long a2 = 40692;
+ long m2 = 2147483399;
+ long q2 = 52774;
+ long r2 = 3791;
+
+ if (sre_randseed > 0)
+ {
+ rnd1 = sre_randseed;
+ rnd2 = sre_randseed;
+ /* Fill the table for Bays/Durham */
+ for (i = 0; i < 64; i++) {
+ x = a1*(rnd1%q1); /* LCG1 in action... */
+ y = r1*(rnd1/q1);
+ rnd1 = x-y;
+ if (rnd1 < 0) rnd1 += m1;
+
+ x = a2*(rnd2%q2); /* LCG2 in action... */
+ y = r2*(rnd2/q2);
+ rnd2 = x-y;
+ if (rnd2 < 0) rnd2 += m2;
+
+ tbl[i] = rnd1-rnd2;
+ if (tbl[i] < 0) tbl[i] += m1;
+ }
+ sre_randseed = 0; /* drop the flag. */
+ }/* end of initialization*/
+
+
+ x = a1*(rnd1%q1); /* LCG1 in action... */
+ y = r1*(rnd1/q1);
+ rnd1 = x-y;
+ if (rnd1 < 0) rnd1 += m1;
+
+ x = a2*(rnd2%q2); /* LCG2 in action... */
+ y = r2*(rnd2/q2);
+ rnd2 = x-y;
+ if (rnd2 < 0) rnd2 += m2;
+
+ /* Choose our random number from the table... */
+ i = (int) (((double) rnd / (double) m1) * 64.);
+ rnd = tbl[i];
+ /* and replace with a new number by L'Ecuyer. */
+ tbl[i] = rnd1-rnd2;
+ if (tbl[i] < 0) tbl[i] += m1;
+
+ return ((double) rnd / (double) m1);
+}
+
+/* Function: sre_srandom()
+ *
+ * Purpose: Initialize with a random seed. Seed must be
+ * >= 0 to work; we silently enforce this.
+ */
+void
+sre_srandom(int seed)
+{
+ if (seed < 0) seed = -1 * seed;
+ if (seed == 0) seed = 42;
+ sre_randseed = seed;
+}
+
+/* Function: sre_random_positive()
+ * Date: SRE, Wed Apr 17 13:34:32 2002 [St. Louis]
+ *
+ * Purpose: Assure 0 < x < 1 (positive uniform deviate)
+ */
+double
+sre_random_positive(void)
+{
+ double x;
+ do { x = sre_random(); } while (x == 0.0);
+ return x;
+}
+
+/* Function: ExponentialRandom()
+ * Date: SRE, Mon Sep 6 21:24:29 1999 [St. Louis]
+ *
+ * Purpose: Pick an exponentially distributed random variable
+ * 0 > x >= infinity
+ *
+ * Args: (void)
+ *
+ * Returns: x
+ */
+double
+ExponentialRandom(void)
+{
+ double x;
+
+ do x = sre_random(); while (x == 0.0);
+ return -log(x);
+}
+
+/* Function: Gaussrandom()
+ *
+ * Pick a Gaussian-distributed random variable
+ * with some mean and standard deviation, and
+ * return it.
+ *
+ * Based on RANLIB.c public domain implementation.
+ * Thanks to the authors, Barry W. Brown and James Lovato,
+ * University of Texas, M.D. Anderson Cancer Center, Houston TX.
+ * Their implementation is from Ahrens and Dieter, "Extensions
+ * of Forsythe's method for random sampling from the normal
+ * distribution", Math. Comput. 27:927-937 (1973).
+ *
+ * Impenetrability of the code is to be blamed on its FORTRAN/f2c lineage.
+ *
+ */
+double
+Gaussrandom(double mean, double stddev)
+{
+ static double a[32] = {
+ 0.0,3.917609E-2,7.841241E-2,0.11777,0.1573107,0.1970991,0.2372021,0.2776904, 0.3186394,0.36013,0.4022501,0.4450965,0.4887764,0.5334097,0.5791322,
+ 0.626099,0.6744898,0.7245144,0.7764218,0.8305109,0.8871466,0.9467818,
+ 1.00999,1.077516,1.150349,1.229859,1.318011,1.417797,1.534121,1.67594,
+ 1.862732,2.153875
+ };
+ static double d[31] = {
+ 0.0,0.0,0.0,0.0,0.0,0.2636843,0.2425085,0.2255674,0.2116342,0.1999243,
+ 0.1899108,0.1812252,0.1736014,0.1668419,0.1607967,0.1553497,0.1504094,
+ 0.1459026,0.14177,0.1379632,0.1344418,0.1311722,0.128126,0.1252791,
+ 0.1226109,0.1201036,0.1177417,0.1155119,0.1134023,0.1114027,0.1095039
+ };
+ static double t[31] = {
+ 7.673828E-4,2.30687E-3,3.860618E-3,5.438454E-3,7.0507E-3,8.708396E-3,
+ 1.042357E-2,1.220953E-2,1.408125E-2,1.605579E-2,1.81529E-2,2.039573E-2,
+ 2.281177E-2,2.543407E-2,2.830296E-2,3.146822E-2,3.499233E-2,3.895483E-2,
+ 4.345878E-2,4.864035E-2,5.468334E-2,6.184222E-2,7.047983E-2,8.113195E-2,
+ 9.462444E-2,0.1123001,0.136498,0.1716886,0.2276241,0.330498,0.5847031
+ };
+ static double h[31] = {
+ 3.920617E-2,3.932705E-2,3.951E-2,3.975703E-2,4.007093E-2,4.045533E-2,
+ 4.091481E-2,4.145507E-2,4.208311E-2,4.280748E-2,4.363863E-2,4.458932E-2,
+ 4.567523E-2,4.691571E-2,4.833487E-2,4.996298E-2,5.183859E-2,5.401138E-2,
+ 5.654656E-2,5.95313E-2,6.308489E-2,6.737503E-2,7.264544E-2,7.926471E-2,
+ 8.781922E-2,9.930398E-2,0.11556,0.1404344,0.1836142,0.2790016,0.7010474
+ };
+ static long i;
+ static double snorm,u,s,ustar,aa,w,y,tt;
+
+ u = sre_random();
+ s = 0.0;
+ if(u > 0.5) s = 1.0;
+ u += (u-s);
+ u = 32.0*u;
+ i = (long) (u);
+ if(i == 32) i = 31;
+ if(i == 0) goto S100;
+ /*
+ * START CENTER
+ */
+ ustar = u-(double)i;
+ aa = *(a+i-1);
+S40:
+ if(ustar <= *(t+i-1)) goto S60;
+ w = (ustar-*(t+i-1))**(h+i-1);
+S50:
+ /*
+ * EXIT (BOTH CASES)
+ */
+ y = aa+w;
+ snorm = y;
+ if(s == 1.0) snorm = -y;
+ return (stddev*snorm + mean);
+S60:
+ /*
+ * CENTER CONTINUED
+ */
+ u = sre_random();
+ w = u*(*(a+i)-aa);
+ tt = (0.5*w+aa)*w;
+ goto S80;
+S70:
+ tt = u;
+ ustar = sre_random();
+S80:
+ if(ustar > tt) goto S50;
+ u = sre_random();
+ if(ustar >= u) goto S70;
+ ustar = sre_random();
+ goto S40;
+S100:
+ /*
+ * START TAIL
+ */
+ i = 6;
+ aa = *(a+31);
+ goto S120;
+S110:
+ aa += *(d+i-1);
+ i += 1;
+S120:
+ u += u;
+ if(u < 1.0) goto S110;
+ u -= 1.0;
+S140:
+ w = u**(d+i-1);
+ tt = (0.5*w+aa)*w;
+ goto S160;
+S150:
+ tt = u;
+S160:
+ ustar = sre_random();
+ if(ustar > tt) goto S50;
+ u = sre_random();
+ if(ustar >= u) goto S150;
+ u = sre_random();
+ goto S140;
+}
+
+
+/* Functions: DChoose(), FChoose()
+ *
+ * Purpose: Make a random choice from a normalized distribution.
+ * DChoose() is for double-precision vectors;
+ * FChoose() is for single-precision float vectors.
+ * Returns the number of the choice.
+ */
+int
+DChoose(double *p, int N)
+{
+ double roll; /* random fraction */
+ double sum; /* integrated prob */
+ int i; /* counter over the probs */
+
+ roll = sre_random();
+ sum = 0.0;
+ for (i = 0; i < N; i++)
+ {
+ sum += p[i];
+ if (roll < sum) return i;
+ }
+ return (int) (sre_random() * N); /* bulletproof */
+}
+int
+FChoose(float *p, int N)
+{
+ float roll; /* random fraction */
+ float sum; /* integrated prob */
+ int i; /* counter over the probs */
+
+ roll = sre_random();
+ sum = 0.0;
+ for (i = 0; i < N; i++)
+ {
+ sum += p[i];
+ if (roll < sum) return i;
+ }
+ return (int) (sre_random() * N); /* bulletproof */
+}
+
+
--- /dev/null
+/* sre_random.h
+ * Header file for sre_random.c
+ *
+ * SRE, Tue Oct 1 15:24:29 2002
+ * CVS $Id: sre_random.h,v 1.1 2002/10/09 14:26:09 eddy Exp)
+ */
+
+extern double sre_random(void);
+extern void sre_srandom(int seed);
+extern double sre_random_positive(void);
+extern double ExponentialRandom(void);
+extern double Gaussrandom(double mean, double stddev);
+extern int DChoose(double *p, int N);
+extern int FChoose(float *p, int N);
+
+#define CHOOSE(a) ((int) (sre_random() * (a)))
+
+
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* sre_string.c
+ *
+ * my library of extra string functions. Some for portability
+ * across UNIXes
+ *
+ * RCS $Id: sre_string.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: sre_string.c,v 1.11 2001/06/07 16:59:37 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <stdarg.h>
+#include <ctype.h>
+#include "squid.h"
+
+/* Function: Strdup()
+ *
+ * Purpose: Implementation of the common (but non-ANSI) function
+ * strdup(). Robust against being passed a NULL pointer.
+ *
+ */
+char *
+Strdup(char *s)
+{
+ char *new;
+ if (s == NULL) return NULL;
+ if ((new = (char *) malloc (strlen(s) +1)) == NULL) return NULL;
+ strcpy(new, s);
+ return new;
+}
+
+/* Function: StringChop()
+ * Date: SRE, Wed Oct 29 12:10:02 1997 [TWA 721]
+ *
+ * Purpose: Chop trailing whitespace off of a string.
+ */
+void
+StringChop(char *s)
+{
+ int i;
+
+ i = strlen(s) - 1; /* set i at last char in string */
+ while (i >= 0 && isspace((int) s[i])) i--; /* i now at last non-whitespace char, or -1 */
+ s[i+1] = '\0';
+}
+
+int
+Strinsert(char *s1, /* string to insert a char into */
+ char c, /* char to insert */
+ int pos) /* position in s1 to insert c at */
+{
+ char oldc;
+ char *s;
+
+ for (s = s1 + pos; c; s++)
+ {
+ /* swap current char for inserted one */
+ oldc = *s; /* pick up current */
+ *s = c; /* put down inserted one */
+ c = oldc; /* old becomes next to insert */
+ }
+ *s = '\0';
+
+ return 1;
+}
+
+
+int
+Strdelete(char *s1, /* string to delete a char from */
+ int pos) /* position of char to delete 0..n-1 */
+{
+ char *s;
+
+ for (s = s1 + pos; *s; s++)
+ *s = *(s + 1);
+
+ return 1;
+}
+
+void
+s2lower(char *s)
+{
+ for (; *s != '\0'; s++)
+ *s = sre_tolower((int) *s);
+}
+
+void
+s2upper(char *s)
+{
+ for (; *s != '\0'; s++)
+ *s = sre_toupper((int) *s);
+}
+
+
+void *
+sre_malloc(char *file, int line, size_t size)
+{
+ void *ptr;
+
+ SQD_DPRINTF3(("MALLOC: %d bytes (file %s line %d)\n", size, file, line));
+ if ((ptr = malloc (size)) == NULL)
+ Die("malloc of %ld bytes failed: file %s line %d", size, file, line);
+ return ptr;
+}
+
+void *
+sre_realloc(char *file, int line, void *p, size_t size)
+{
+ void *ptr;
+
+ if ((ptr = realloc(p, size)) == NULL)
+ Die("realloc of %ld bytes failed: file %s line %d", size, file, line);
+ return ptr;
+}
+
+
+
+/* Function: Free2DArray(), Free3DArray()
+ * Date: SRE, Tue Jun 1 14:47:14 1999 [St. Louis]
+ *
+ * Purpose: Convenience functions for free'ing 2D
+ * and 3D pointer arrays. Tolerates any of the
+ * pointers being NULL, to allow "sparse"
+ * arrays.
+ *
+ * Args: p - array to be freed
+ * dim1 - n for first dimension
+ * dim2 - n for second dimension
+ *
+ * e.g. a 2d array is indexed p[0..dim1-1][]
+ * a 3D array is indexed p[0..dim1-1][0..dim2-1][]
+ *
+ * Returns: void
+ *
+ * Diagnostics: (void)
+ * "never fails"
+ */
+void
+Free2DArray(void **p, int dim1)
+{
+ int i;
+
+ if (p != NULL) {
+ for (i = 0; i < dim1; i++)
+ if (p[i] != NULL) free(p[i]);
+ free(p);
+ }
+}
+void
+Free3DArray(void ***p, int dim1, int dim2)
+{
+ int i, j;
+
+ if (p != NULL) {
+ for (i = 0; i < dim1; i++)
+ if (p[i] != NULL) {
+ for (j = 0; j < dim2; j++)
+ if (p[i][j] != NULL) free(p[i][j]);
+ free(p[i]);
+ }
+ free(p);
+ }
+}
+
+
+/* Function: RandomSequence()
+ *
+ * Purpose: Generate an iid symbol sequence according
+ * to some alphabet, alphabet_size, probability
+ * distribution, and length. Return the
+ * sequence.
+ *
+ * Args: alphabet - e.g. "ACGT"
+ * p - probability distribution [0..n-1]
+ * n - number of symbols in alphabet
+ * len - length of generated sequence
+ *
+ * Return: ptr to random sequence, or NULL on failure.
+ */
+char *
+RandomSequence(char *alphabet, float *p, int n, int len)
+{
+ char *s;
+ int x;
+
+ s = (char *) MallocOrDie (sizeof(char) * (len+1));
+ for (x = 0; x < len; x++)
+ s[x] = alphabet[FChoose(p,n)];
+ s[x] = '\0';
+ return s;
+}
+
+/* Function: sre_fgets()
+ * Date: SRE, Thu May 13 10:56:28 1999 [St. Louis]
+ *
+ * Purpose: Dynamic allocation version of fgets(),
+ * capable of reading unlimited line lengths.
+ *
+ * Args: buf - ptr to a string (may be reallocated)
+ * n - ptr to current allocated length of buf,
+ * (may be changed)
+ * fp - open file ptr for reading
+ *
+ * Before the first call to sre_fgets(),
+ * buf should be initialized to NULL and n to 0.
+ * They're a linked pair, so don't muck with the
+ * allocation of buf or the value of n while
+ * you're still doing sre_fgets() calls with them.
+ *
+ * Returns: ptr to the buffer on success.
+ * NULL on EOF (buf isn't to be used in this case)
+ * sre_fgets() *always* results in an allocation
+ * in buf.
+ *
+ * The reason to have it return a ptr to buf
+ * is that it makes wrapper macros easy; see
+ * MSAFileGetLine() for an example.
+ *
+ * Example: char *buf;
+ * int n;
+ * FILE *fp;
+ *
+ * fp = fopen("my_file", "r");
+ * buf = NULL;
+ * n = 0;
+ * while (sre_fgets(&buf, &n, fp) != NULL)
+ * {
+ * do stuff with buf;
+ * }
+ */
+char *
+sre_fgets(char **buf, int *n, FILE *fp)
+{
+ char *s;
+ int len;
+ int pos;
+
+ if (*n == 0)
+ {
+ *buf = MallocOrDie(sizeof(char) * 128);
+ *n = 128;
+ }
+
+ /* Simple case 1. We're sitting at EOF, or there's an error.
+ * fgets() returns NULL, so we return NULL.
+ */
+ if (fgets(*buf, *n, fp) == NULL) return NULL;
+
+ /* Simple case 2. fgets() got a string, and it reached EOF.
+ * return success status, so caller can use
+ * the last line; on the next call we'll
+ * return the 0 for the EOF.
+ */
+ if (feof(fp)) return *buf;
+
+ /* Simple case 3. We got a complete string, with \n,
+ * and don't need to extend the buffer.
+ */
+ len = strlen(*buf);
+ if ((*buf)[len-1] == '\n') return *buf;
+
+ /* The case we're waiting for. We have an incomplete string,
+ * and we have to extend the buffer one or more times. Make
+ * sure we overwrite the previous fgets's \0 (hence +(n-1)
+ * in first step, rather than 128, and reads of 129, not 128).
+ */
+ pos = (*n)-1;
+ while (1) {
+ *n += 128;
+ *buf = ReallocOrDie(*buf, sizeof(char) * (*n));
+ s = *buf + pos;
+ if (fgets(s, 129, fp) == NULL) return *buf;
+ len = strlen(s);
+ if (s[len-1] == '\n') return *buf;
+ pos += 128;
+ }
+ /*NOTREACHED*/
+}
+
+/* Function: sre_strcat()
+ * Date: SRE, Thu May 13 09:36:32 1999 [St. Louis]
+ *
+ * Purpose: Dynamic memory version of strcat().
+ * appends src to the string that dest points to,
+ * extending allocation for dest if necessary.
+ *
+ * One timing experiment (100 successive appends of
+ * 1-255 char) shows sre_strcat() has about a 20%
+ * overhead relative to strcat(). However, if optional
+ * length info is passed, sre_strcat() is about 30%
+ * faster than strcat().
+ *
+ * Args: dest - ptr to string (char **), '\0' terminated
+ * ldest - length of dest, if known; or -1 if length unknown.
+ * src - string to append to dest, '\0' terminated
+ * lsrc - length of src, if known; or -1 if length unknown.
+ *
+ * dest may be NULL, in which case this is
+ * the equivalent of dest = Strdup(src).
+ *
+ * src may also be NULL, in which case
+ * dest is unmodified (but why would you want to pass
+ * a NULL src?)
+ *
+ * if both dest and src are NULL, dest is
+ * unmodified; it stays NULL.
+ *
+ * the length parameters are optional. If a -1
+ * is passed, sre_strcat() will call strlen() to
+ * determine the length itself. Passing length
+ * info saves the strlen() calls and can speed things
+ * up if lots of successive appends need to be done.
+ *
+ * Returns: new length of dest (>=0 on success);
+ * dest is (probably) reallocated, and modified
+ * to a longer string, '\0' terminated.
+ */
+int
+sre_strcat(char **dest, int ldest, char *src, int lsrc)
+{
+ int len1, len2;
+
+ if (ldest < 0) len1 = ((*dest == NULL) ? 0 : strlen(*dest));
+ else len1 = ldest;
+
+ if (lsrc < 0) len2 = (( src == NULL) ? 0 : strlen(src));
+ else len2 = lsrc;
+
+ if (len2 == 0) return len1;
+
+ if (*dest == NULL) *dest = MallocOrDie(sizeof(char) * (len2+1));
+ else *dest = ReallocOrDie(*dest, sizeof(char) * (len1+len2+1));
+
+ memcpy((*dest)+len1, src, len2+1);
+ return len1+len2;
+}
+
+/* Function: sre_strtok()
+ * Date: SRE, Wed May 19 16:30:20 1999 [St. Louis]
+ *
+ * Purpose: Thread-safe version of strtok().
+ *
+ * Returns ptr to next token in a string: skips
+ * until it reaches a character that is not in the delim
+ * string, and sets beginning of token. Skips to
+ * next delim character (or '\0') to set the end; replaces that
+ * character with '\0'.
+ * If there's still more string left, sets s to point to next
+ * character after the '\0' that was written, so successive
+ * calls extract tokens in succession. If there was no string
+ * left, s points at the terminal '\0'.
+ *
+ * If no token is found, returns NULL.
+ *
+ * Also returns the length of the token, which
+ * may save us a strlen() call in some applications.
+ *
+ * Limitations:
+ * *s can't be a constant string, since we write to it.
+ *
+ * Example:
+ * char *tok;
+ * int len;
+ * char *s;
+ * char buf[50] = "This is a sentence.";
+ *
+ * s = buf;
+ * tok = sre_strtok(&s, " ", &len);
+ * tok is "This"; s is "is a sentence."; len is 4.
+ * tok = sre_strtok(&s, " ", &len);
+ * tok is "is"; s is " a sentence."; len is 2.
+ * tok = sre_strtok(&s, " ", &len);
+ * tok is "a"; s is "sentence."; len is 1.
+ * tok = sre_strtok(&s, " ", &len);
+ * tok is "sentence."; s is "\0"; len is 9.
+ * tok = sre_strtok(&s, " ", &len);
+ * tok is NULL; s is "\0", len is undefined.
+ *
+ * Args: s - a tmp, modifiable ptr to string
+ * delim - characters that delimits tokens
+ * len - RETURN: length of token; pass NULL if not wanted
+ *
+ * Returns: ptr to next token, or NULL if there aren't any.
+ */
+char *
+sre_strtok(char **s, char *delim, int *len)
+{
+ char *begin, *end;
+ int n;
+
+ begin = *s;
+ begin += strspn(begin, delim);
+ if (! *begin) return NULL;
+
+ n = strcspn(begin, delim);
+ end = begin + n;
+ if (*end == '\0') { *s = end;}
+ else {
+ *end = '\0';
+ *s = end+1;
+ }
+
+ if (len != NULL) *len = n;
+ return begin;
+}
+
+
+
+/* Function: sre_strdup()
+ * Date: SRE, Wed May 19 17:57:28 1999 [St. Louis]
+ *
+ * Purpose: A version of the common but non-ANSI strdup()
+ * function. Can pass len, if known, to save a
+ * strlen() call.
+ *
+ * Args: s - string to duplicate
+ * n - length of string, if known; -1 if unknown.
+ *
+ * Returns: allocated copy of string.
+ * NULL on failure.
+ */
+char *
+sre_strdup(char *s, int n)
+{
+ char *new;
+
+ if (s == NULL) return NULL;
+ if (n < 0) n = strlen(s);
+ new = MallocOrDie (sizeof(char) * (n+1));
+ strcpy(new, s);
+ return new;
+}
+
+
+/* Function: sre_strncpy()
+ * Date: SRE, Tue Jun 22 10:10:46 1999 [Sanger Centre]
+ *
+ * Purpose: a strncpy() that makes sure it adds a trailing \0.
+ *
+ * Args: s1 - string to copy to (allocated n+1 or larger)
+ * s2 - string to copy from
+ * n - number of chars to copy
+ *
+ * Returns: s1.
+ * Done only for consistency with strncpy(). Not clear
+ * why it's useful for a strncpy() to return s1.
+ */
+char *
+sre_strncpy(char *s1, char *s2, int n)
+{
+ strncpy(s1,s2,n);
+ s1[n] = '\0';
+ return s1;
+}
+
+/* Function: IsBlankline()
+ * Date: SRE, Fri Jun 18 14:36:08 1999 [St. Louis]
+ *
+ * Purpose: Returns TRUE if string consists solely of whitespace.
+ *
+ * Args: s - string to check
+ */
+int
+IsBlankline(char *s)
+{
+ for (; *s != '\0'; s++)
+ if (! isspace(*s)) return FALSE;
+ return TRUE;
+}
+
+
+
+#ifdef CUBS_WIN
+/* A timing test for sre_strcat()
+ * cc -O2 -g sre_string.c sre_ctype.c sqerror.c sre_math.c hsregex.c -lm
+ * 15.200u - 5.360u = 9.84u if sre_strcat() with no length info passed
+ * 13.660u - 5.360u = 8.30u if strcat(), with a single malloc().
+ * 11.370u - 5.360u = 6.01u if sre_strcat() with length info passed.
+ */
+int main(void)
+{
+ float p[4] = {0.25, 0.25, 0.25, 0.25};
+ int buflen;
+ int len;
+ int nappends;
+ int nstrings;
+ char *s1 = NULL;
+ char *s2;
+ int i;
+
+ nappends = 100;
+ nstrings = 1000;
+ while (nstrings--)
+ {
+ /* s1 = malloc(sizeof(char) * (255*nappends+1));
+ s1[0] = '\0';
+ */
+
+ s1 = NULL;
+ len = 0;
+ for (i = 0; i < nappends; i++)
+ {
+ buflen = CHOOSE(255) + 1;
+ s2 = RandomSequence("ACGT", p, 4, buflen);
+
+ /* strcat(s1,s2); */
+ if ((len = sre_strcat(&s1, len, s2, buflen)) < 0) exit(1);
+ free(s2);
+ }
+ free(s1);
+ }
+ exit(0);
+}
+#endif /*CUBS_WIN*/
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <unistd.h>
+#include "squid.h"
+#include "ssi.h"
+#ifdef CLUSTALO
+#include <limits.h>
+#endif
+
+static sqd_uint32 v20magic = 0xf3f3e9b1; /* SSI 1.0: "ssi1" + 0x80808080 */
+static sqd_uint32 v20swap = 0xb1e9f3f3; /* byteswapped */
+
+static int read_i16(FILE *fp, sqd_uint16 *ret_result);
+static int read_i32(FILE *fp, sqd_uint32 *ret_result);
+static int read_i64(FILE *fp, sqd_uint64 *ret_result);
+static int read_offset(FILE *fp, char mode, SSIOFFSET *ret_offset);
+static int write_i16(FILE *fp, sqd_uint16 n);
+static int write_i32(FILE *fp, sqd_uint32 n);
+static int write_i64(FILE *fp, sqd_uint64 n);
+static int write_offset(FILE *fp, SSIOFFSET *offset);
+static int binary_search(SSIFILE *sfp, char *key, int klen, SSIOFFSET *base,
+ sqd_uint32 recsize, sqd_uint32 maxidx);
+static int indexfile_position(SSIFILE *sfp, SSIOFFSET *base, sqd_uint32 len,
+ sqd_uint32 n);
+static void clear_ssifile(SSIFILE *sfp);
+static sqd_uint64 current_index_size(SSIINDEX *g);
+static int activate_external_sort(SSIINDEX *g);
+static int load_indexfile(SSIFILE *sfp);
+static int parse_pkey_info(char *buf, char mode, struct ssipkey_s *pkey);
+static int parse_skey_info(char *buf, struct ssiskey_s *skey);
+
+/* Function: SSIOpen()
+ * Date: SRE, Sun Dec 31 12:40:03 2000 [St. Louis]
+ *
+ * Purpose: Opens the SSI index file {filename} and returns
+ * a SSIFILE * stream thru {ret_sfp}.
+ * The caller must eventually close this stream using
+ * SSIClose(). More than one index file can be open
+ * at once.
+ *
+ * Args: filename - full path to a SSI index file
+ *
+ * Returns: Returns 0 on success, nonzero on failure.
+ */
+int
+SSIOpen(char *filename, SSIFILE **ret_sfp)
+{
+ SSIFILE *sfp = NULL;
+ int status;
+ if ((sfp = malloc(sizeof(SSIFILE))) == NULL) return SSI_ERR_MALLOC;
+ if ((sfp->fp = fopen(filename, "rb")) == NULL) {
+ free(sfp);
+ return SSI_ERR_NOFILE;
+ }
+ status = load_indexfile(sfp);
+ *ret_sfp = sfp;
+ return status;
+}
+/* load_indexfile(): given a SSIFILE structure with an open and positioned
+ * stream (fp) -- but no other data loaded -- read the next SSIFILE
+ * in from disk. We use this routine without its SSIOpen() wrapper
+ * as part of the external mergesort when creating large indices.
+ */
+static int
+load_indexfile(SSIFILE *sfp)
+{
+ sqd_uint32 magic;
+ sqd_uint16 i; /* counter over files */
+ int status; /* overall return status if an error is thrown */
+
+ status = SSI_ERR_BADFORMAT; /* default: almost every kind of error is a bad format error */
+
+ sfp->filename = NULL;
+ sfp->fileformat = NULL;
+ sfp->fileflags = NULL;
+ sfp->bpl = NULL;
+ sfp->rpl = NULL;
+ sfp->nfiles = 0;
+ if (! read_i32(sfp->fp, &magic)) {status = SSI_ERR_BADMAGIC; goto FAILURE; }
+ if (magic != v20magic && magic != v20swap) {status = SSI_ERR_BADMAGIC; goto FAILURE; }
+ if (! read_i32(sfp->fp, &(sfp->flags))) goto FAILURE;
+
+ /* If we have 64-bit offsets, make sure we can deal with them.
+ */
+#ifndef HAS_64BIT_FILE_OFFSETS
+ if ((sfp->flags & SSI_USE64_INDEX) ||
+ (sfp->flags & SSI_USE64))
+ { status = SSI_ERR_NO64BIT; goto FAILURE; }
+#endif
+
+ sfp->imode = (sfp->flags & SSI_USE64_INDEX) ? SSI_OFFSET_I64 : SSI_OFFSET_I32;
+ sfp->smode = (sfp->flags & SSI_USE64) ? SSI_OFFSET_I64 : SSI_OFFSET_I32;
+
+ if (! read_i16(sfp->fp, &(sfp->nfiles))) goto FAILURE;
+ if (! read_i32(sfp->fp, &(sfp->nprimary))) goto FAILURE;
+ if (! read_i32(sfp->fp, &(sfp->nsecondary))) goto FAILURE;
+ if (! read_i32(sfp->fp, &(sfp->flen))) goto FAILURE;
+ if (! read_i32(sfp->fp, &(sfp->plen))) goto FAILURE;
+ if (! read_i32(sfp->fp, &(sfp->slen))) goto FAILURE;
+ if (! read_i32(sfp->fp, &(sfp->frecsize))) goto FAILURE;
+ if (! read_i32(sfp->fp, &(sfp->precsize))) goto FAILURE;
+ if (! read_i32(sfp->fp, &(sfp->srecsize))) goto FAILURE;
+
+ if (! read_offset(sfp->fp, sfp->imode, &(sfp->foffset))) goto FAILURE;
+ if (! read_offset(sfp->fp, sfp->imode, &(sfp->poffset))) goto FAILURE;
+ if (! read_offset(sfp->fp, sfp->imode, &(sfp->soffset))) goto FAILURE;
+
+ /* Read the file information and keep it.
+ * We expect the number of files to be small, so reading it
+ * once should be advantageous overall. If SSI ever had to
+ * deal with large numbers of files, you'd probably want to
+ * read file information on demand.
+ */
+ if (sfp->nfiles == 0) goto FAILURE;
+ if ((sfp->filename=malloc(sizeof(char *) *sfp->nfiles)) == NULL) {status = SSI_ERR_MALLOC; goto FAILURE; }
+ for (i = 0; i < sfp->nfiles; i++) sfp->filename[i] = NULL;
+ if ((sfp->fileformat=malloc(sizeof(sqd_uint32)*sfp->nfiles)) == NULL) {status = SSI_ERR_MALLOC; goto FAILURE; }
+ if ((sfp->fileflags =malloc(sizeof(sqd_uint32)*sfp->nfiles)) == NULL) {status = SSI_ERR_MALLOC; goto FAILURE; }
+ if ((sfp->bpl =malloc(sizeof(sqd_uint32)*sfp->nfiles)) == NULL) {status = SSI_ERR_MALLOC; goto FAILURE; }
+ if ((sfp->rpl =malloc(sizeof(sqd_uint32)*sfp->nfiles)) == NULL) {status = SSI_ERR_MALLOC; goto FAILURE; }
+
+ for (i = 0; i < sfp->nfiles; i++)
+ {
+ /* We have to explicitly position, because header and file
+ * records may expand in the future; frecsize and foffset
+ * give us forwards compatibility.
+ */
+ if (indexfile_position(sfp, &(sfp->foffset), sfp->frecsize, i) !=0) goto FAILURE;
+ if ((sfp->filename[i] =malloc(sizeof(char)*sfp->flen)) == NULL) {status = SSI_ERR_MALLOC; goto FAILURE; }
+ if (fread(sfp->filename[i],sizeof(char),sfp->flen, sfp->fp)!=sfp->flen) goto FAILURE;
+ if (! read_i32(sfp->fp, &(sfp->fileformat[i]))) goto FAILURE;
+ if (! read_i32(sfp->fp, &(sfp->fileflags[i]))) goto FAILURE;
+ if (! read_i32(sfp->fp, &(sfp->bpl[i]))) goto FAILURE;
+ if (! read_i32(sfp->fp, &(sfp->rpl[i]))) goto FAILURE;
+ }
+
+ /* Success. Return 0.
+ */
+ return 0;
+
+ FAILURE:
+ /* Failure: free the damaged structure, return status code.
+ */
+ SSIClose(sfp);
+ return status;
+}
+
+
+
+/* Function: SSIGetOffsetByName()
+ * Date: SRE, Sun Dec 31 13:55:31 2000 [St. Louis]
+ *
+ * Purpose: Looks up the string {key} in the open index {sfp}.
+ * {key} can be either a primary or secondary key. If {key}
+ * is found, {*ret_fh} contains a unique handle on
+ * the file that contains {key} (suitable for an SSIFileInfo()
+ * call, or for comparison to the handle of the last file
+ * that was opened for retrieval), and {offset} is filled
+ * in with the offset in that file.
+ *
+ * Args: sfp - open index file
+ * key - string to search for
+ * ret_fh - RETURN: handle on file that key is in
+ * ret_offset - RETURN: offset of the start of that key's record
+ *
+ * Returns: 0 on success.
+ * non-zero on error.
+ */
+int
+SSIGetOffsetByName(SSIFILE *sfp, char *key, int *ret_fh,
+ SSIOFFSET *ret_offset)
+{
+ int status;
+ sqd_uint16 fnum;
+
+ /* Look in the primary keys.
+ */
+ status = binary_search(sfp, key, sfp->plen, &(sfp->poffset), sfp->precsize,
+ sfp->nprimary);
+ if (status == 0) {
+ /* We found it as a primary key; get our data & return.
+ */
+ if (! read_i16(sfp->fp, &fnum)) return SSI_ERR_NODATA;
+ *ret_fh = (int) fnum;
+ if (! read_offset(sfp->fp, sfp->smode, ret_offset)) return SSI_ERR_NODATA;
+
+ return 0; /* success! (we don't need the other key data) */
+ } else if (status == SSI_ERR_NO_SUCH_KEY) {
+ /* Not in the primary keys? OK, try the secondary keys.
+ */
+ if (sfp->nsecondary > 0) {
+ char *pkey;
+ status = binary_search(sfp, key, sfp->slen, &(sfp->soffset), sfp->srecsize,
+ sfp->nsecondary);
+ if (status != 0) return status;
+ if ((pkey = malloc(sizeof(char) * sfp->plen)) == NULL) return SSI_ERR_MALLOC;
+ if (fread(pkey, sizeof(char), sfp->plen, sfp->fp) != sfp->plen) return SSI_ERR_NODATA;
+
+ status = SSIGetOffsetByName(sfp, pkey, ret_fh, ret_offset);
+ free(pkey);
+ }
+ return status;
+
+ } else return status;
+ /*NOTREACHED*/
+}
+
+/* Function: SSIGetOffsetByNumber()
+ * Date: SRE, Mon Jan 1 19:42:42 2001 [St. Louis]
+ *
+ * Purpose: Looks up primary key #{n} in the open index {sfp}.
+ * {n} ranges from 0..nprimary-1. When key #{n}
+ * is found, {*ret_fh} contains a unique
+ * handle on the file that contains {key} (suitable
+ * for an SSIFileInfo() call, or for comparison to
+ * the handle of the last file that was opened for retrieval),
+ * and {offset} is filled in with the offset in that file.
+ *
+ * Args: sfp - open index file
+ * n - primary key number to retrieve.
+ * ret_fh - RETURN: handle on file that key is in
+ * ret_offset - RETURN: offset of the start of that key's record
+ *
+ * Returns: 0 on success.
+ * non-zero on error.
+ */
+int
+SSIGetOffsetByNumber(SSIFILE *sfp, int n, int *ret_fh, SSIOFFSET *ret_offset)
+{
+ sqd_uint16 fnum;
+ char *pkey;
+
+ if (n >= sfp->nprimary) return SSI_ERR_NO_SUCH_KEY;
+ if (indexfile_position(sfp, &(sfp->poffset), sfp->precsize, n) != 0)
+ return SSI_ERR_SEEK_FAILED;
+
+ if ((pkey = malloc(sizeof(char) * sfp->plen)) == NULL) return SSI_ERR_MALLOC;
+ if (fread(pkey, sizeof(char), sfp->plen, sfp->fp) != sfp->plen) return SSI_ERR_NODATA;
+ if (! read_i16(sfp->fp, &fnum)) return SSI_ERR_NODATA;
+ if (! read_offset(sfp->fp, sfp->smode, ret_offset)) return SSI_ERR_NODATA;
+ *ret_fh = fnum;
+ free(pkey);
+ return 0;
+}
+
+/* Function: SSIGetSubseqOffset()
+ * Date: SRE, Mon Jan 1 19:49:31 2001 [St. Louis]
+ *
+ * Purpose: Implements SSI_FAST_SUBSEQ.
+ *
+ * Looks up a primary or secondary {key} in the open
+ * index {sfp}. Asks for the nearest offset to a
+ * subsequence starting at position {requested_start}
+ * in the sequence (numbering the sequence 1..L).
+ * If {key} is found, on return, {ret_fh}
+ * contains a unique handle on the file that contains
+ * {key} (suitable for an SSIFileInfo() call, or for
+ * comparison to the handle of the last file that was
+ * opened for retrieval); {record_offset} contains the
+ * disk offset to the start of the record; {data_offset}
+ * contains the disk offset either exactly at the requested
+ * residue, or at the start of the line containing the
+ * requested residue; {ret_actual_start} contains the
+ * coordinate (1..L) of the first valid residue at or
+ * after {data_offset}. {ret_actual_start} is <=
+ * {requested_start}.
+ *
+ * Args: sfp - open index file
+ * key - primary or secondary key to find
+ * requested_start - residue we'd like to start at (1..L)
+ * ret_fh - RETURN: handle for file the key is in
+ * record_offset - RETURN: offset of entire record
+ * data_offset - RETURN: offset of subseq (see above)
+ * ret_actual_start- RETURN: coord (1..L) of residue at data_offset
+ *
+ * Returns: 0 on success, non-zero on failure.
+ */
+int
+SSIGetSubseqOffset(SSIFILE *sfp, char *key, int requested_start,
+ int *ret_fh, SSIOFFSET *record_offset,
+ SSIOFFSET *data_offset, int *ret_actual_start)
+{
+ int status;
+ sqd_uint32 len;
+ int r, b, i, l; /* tmp variables for "clarity", to match docs */
+
+ /* Look up the key. Rely on the fact that SSIGetOffsetByName()
+ * leaves the index file positioned at the rest of the data for this key.
+ */
+ status = SSIGetOffsetByName(sfp, key, ret_fh, record_offset);
+ if (status != 0) return status;
+
+ /* Check that we're allowed to do subseq lookup on that file.
+ */
+ if (! (sfp->fileflags[*ret_fh] & SSI_FAST_SUBSEQ))
+ return SSI_ERR_NO_SUBSEQS;
+
+ /* Read the data we need for subseq lookup
+ */
+ if (! read_offset(sfp->fp, sfp->smode, data_offset)) return SSI_ERR_NODATA;
+ if (! read_i32(sfp->fp, &len)) return SSI_ERR_NODATA;
+
+ /* Set up tmp variables for clarity of equations below,
+ * and to make them match documentation (ssi-format.tex).
+ */
+ r = sfp->rpl[*ret_fh]; /* residues per line */
+ b = sfp->bpl[*ret_fh]; /* bytes per line */
+ i = requested_start; /* start position 1..L */
+ l = (i-1)/r; /* data line # (0..) that the residue is on */
+ if (r == 0 || b == 0) return SSI_ERR_NO_SUBSEQS;
+ if (i < 0 || i > len) return SSI_ERR_RANGE;
+
+ /* When b = r+1, there's nothing but sequence on each data line (and the \0),
+ * and we can find each residue precisely.
+ */
+ if (b == r+1) {
+ if (sfp->smode == SSI_OFFSET_I32) {
+ data_offset->mode = SSI_OFFSET_I32;
+ data_offset->off.i32 = data_offset->off.i32 + l*b + (i-1)%r;
+ } else if (sfp->smode == SSI_OFFSET_I64) {
+ data_offset->mode = SSI_OFFSET_I64;
+ data_offset->off.i64 = data_offset->off.i64 + l*b + (i-1)%r;
+ }
+ *ret_actual_start = requested_start;
+ } else {
+ /* else, there's other stuff on seq lines, so the best
+ * we can do easily is to position at start of relevant line.
+ */
+ if (sfp->smode == SSI_OFFSET_I32) {
+ data_offset->mode = SSI_OFFSET_I32;
+ data_offset->off.i32 = data_offset->off.i32 + l*b;
+ } else if (sfp->smode == SSI_OFFSET_I64) {
+ data_offset->mode = SSI_OFFSET_I64;
+ data_offset->off.i64 = data_offset->off.i64 + l*b;
+ }
+ /* yes, the eq below is = 1 + (i-1)/r*r but it's not = i. that's an integer /. */
+ *ret_actual_start = 1 + l*r;
+ }
+ return 0;
+}
+
+/* Function: SSISetFilePosition()
+ * Date: SRE, Tue Jan 2 09:13:46 2001 [St. Louis]
+ *
+ * Purpose: Uses {offset} to sets the file position for {fp}, usually an
+ * open sequence file, relative to the start of the file.
+ * Hides the details of system-dependent shenanigans necessary for
+ * file positioning in large (>2 GB) files.
+ *
+ * Behaves just like fseek(fp, offset, SEEK_SET) for 32 bit
+ * offsets and <2 GB files.
+ *
+ * Warning: if all else fails, in desperation, it will try to
+ * use fsetpos(). This requires making assumptions about fpos_t
+ * that may be unwarranted... assumptions that ANSI C prohibits
+ * me from making... though I believe the ./configure
+ * script robustly tests whether I can play with fpos_t like this.
+ *
+ * Args: fp - file to position.
+ * offset - SSI offset relative to file start.
+ *
+ * Returns: 0 on success, nonzero on error.
+ */
+int
+SSISetFilePosition(FILE *fp, SSIOFFSET *offset)
+{
+ if (offset->mode == SSI_OFFSET_I32) {
+ if (fseek(fp, offset->off.i32, SEEK_SET) != 0) return SSI_ERR_SEEK_FAILED;
+ }
+#ifndef HAS_64BIT_FILE_OFFSETS
+ else return SSI_ERR_NO64BIT;
+#elif defined HAVE_FSEEKO && SIZEOF_OFF_T == 8
+ else if (fseeko(fp, offset->off.i64, SEEK_SET) != 0) return SSI_ERR_SEEK_FAILED;
+#elif defined HAVE_FSEEKO64 && SIZEOF_OFF64_T == 8
+ else if (fseeko64(fp, offset->off.i64, SEEK_SET) != 0) return SSI_ERR_SEEK_FAILED;
+#elif defined HAVE_FSEEK64
+ else if (fseek64(fp, offset->off.i64, SEEK_SET) != 0) return SSI_ERR_SEEK_FAILED;
+#elif defined ARITHMETIC_FPOS_T && SIZEOF_FPOS_T == 8
+ else if (fsetpos(fp, &(offset->off.i64)) != 0) return SSI_ERR_SEEK_FAILED;
+#endif
+ return 0;
+}
+
+
+/* Function: SSIFileInfo()
+ * Date: SRE, Tue Jan 2 10:31:01 2001 [St. Louis]
+ *
+ * Purpose: Given a file number {fh} in an open index file
+ * {sfp}, retrieve file name {ret_filename} and
+ * the file format {ret_format}.
+ *
+ * {ret_filename} is a pointer to a string maintained
+ * internally by {sfp}. It should not be free'd;
+ * SSIClose(sfp) takes care of it.
+ *
+ * Args: sfp - open index file
+ * fh - handle on file to look up
+ * ret_filename - RETURN: name of file n
+ * ret_format - RETURN: format of file n
+ *
+ * Returns: 0 on success, nonzero on failure.
+ */
+int
+SSIFileInfo(SSIFILE *sfp, int fh, char **ret_filename, int *ret_format)
+{
+ if (fh < 0 || fh >= sfp->nfiles) return SSI_ERR_BADARG;
+ *ret_filename = sfp->filename[fh];
+ *ret_format = sfp->fileformat[fh];
+ return 0;
+}
+
+/* Function: SSIClose()
+ * Date: SRE, Sun Dec 31 14:56:37 2000 [St. Louis]
+ *
+ * Purpose: Close an open {SSIFILE *}.
+ *
+ * Args: sfp - index file to close.
+ *
+ * Returns: (void)
+ */
+void
+SSIClose(SSIFILE *sfp)
+{
+ if (sfp != NULL) {
+ clear_ssifile(sfp);
+ if (sfp->fp != NULL) fclose(sfp->fp);
+ free(sfp);
+ }
+}
+/* clear_ssifile(): free the innards of SSIFILE, without
+ * destroying the structure or closing the stream.
+ */
+static void
+clear_ssifile(SSIFILE *sfp)
+{
+ int i;
+
+ if (sfp->filename != NULL) {
+ for (i = 0; i < sfp->nfiles; i++)
+ if (sfp->filename[i] != NULL) free(sfp->filename[i]);
+ free(sfp->filename);
+ }
+ if (sfp->fileformat != NULL) free(sfp->fileformat);
+ if (sfp->fileflags != NULL) free(sfp->fileflags);
+ if (sfp->bpl != NULL) free(sfp->bpl);
+ if (sfp->rpl != NULL) free(sfp->rpl);
+}
+
+
+/* Function: SSIRecommendMode()
+ * Date: SRE, Fri Feb 16 08:23:47 2001 [St. Louis]
+ *
+ * Purpose: Examines the file and determines whether it should be
+ * indexed with large file support or not; returns
+ * SSI_OFFSET_I32 for most files, SSI_OFFSET_I64 for large
+ * files, or -1 on failure.
+ *
+ * Args: file - name of file to check for size
+ *
+ * Returns: -1 on failure (including case where file is too big)
+ * SSI_OFFSET_I32 for most files (<= 2^31-1 bytes)
+ * SSI_OFFSET_I64 for large files (> 2^31-1 bytes)
+ */
+int
+SSIRecommendMode(char *file)
+{
+#if HAVE_STAT64
+ struct stat64 s1;
+ if (stat64(file, &s1) == 0) {
+ if (s1.st_size <= 2146483647L) return SSI_OFFSET_I32;
+ else return SSI_OFFSET_I64;
+ }
+#else
+ struct stat s2;
+ if (stat(file, &s2) == 0) {
+ if (s2.st_size <= 2146483647L) return SSI_OFFSET_I32;
+ else return SSI_OFFSET_I64;
+ }
+#endif
+ return -1;
+}
+
+
+/* Function: SSICreateIndex()
+ * Date: SRE, Tue Jan 2 11:23:25 2001 [St. Louis]
+ *
+ * Purpose: Creates and initializes a SSI index structure.
+ * Sequence file offset type is specified by {mode}.
+ *
+ * Args: mode - SSI_OFFSET_I32 or SSI_OFFSET_I64, sequence file index mode.
+ *
+ * Returns: ptr to new index structure, or NULL on failure.
+ * Caller is responsible for free'ing the returned
+ * structure with SSIFreeIndex().
+ */
+SSIINDEX *
+SSICreateIndex(int mode)
+{
+ SSIINDEX *g;
+
+ g = NULL;
+ if ((g = malloc(sizeof(SSIINDEX))) == NULL) goto FAILURE;
+ g->smode = mode;
+ g->imode = SSI_OFFSET_I32; /* index always starts as 32-bit; may get upgraded later */
+ g->external = FALSE;
+ g->max_ram = SSI_MAXRAM;
+
+#ifndef HAS_64BIT_FILE_OFFSETS
+ if (mode == SSI_OFFSET_I64)
+ Die("\
+Can't create a 64-bit SSI index on this system, sorry;\n\
+I don't have 64-bit file offset functions available.\n");
+#endif
+
+ g->filenames = NULL;
+ g->fileformat = NULL;
+ g->bpl = NULL;
+ g->rpl = NULL;
+ g->flen = 0;
+ g->nfiles = 0;
+
+ g->pkeys = NULL;
+ g->plen = 0;
+ g->nprimary = 0;
+ g->ptmpfile = "tmp.ssi.1"; /* hardcoded, for now. */
+ g->ptmp = NULL;
+
+ g->skeys = NULL;
+ g->slen = 0;
+ g->nsecondary = 0;
+ g->stmpfile = "tmp.ssi.2"; /* hardcoded, for now. */
+ g->stmp = NULL;
+
+ /* All mallocs must go after NULL initializations, because of the cleanup strategy;
+ * we'll try to free anything non-NULL if a malloc fails.
+ */
+ if ((g->filenames = malloc(sizeof(char *) * SSI_FILE_BLOCK)) == NULL) goto FAILURE;
+ if ((g->fileformat= malloc(sizeof(sqd_uint32) * SSI_FILE_BLOCK)) == NULL) goto FAILURE;
+ if ((g->bpl = malloc(sizeof(sqd_uint32) * SSI_FILE_BLOCK)) == NULL) goto FAILURE;
+ if ((g->rpl = malloc(sizeof(sqd_uint32) * SSI_FILE_BLOCK)) == NULL) goto FAILURE;
+
+ if ((g->pkeys = malloc(sizeof(struct ssipkey_s)* SSI_KEY_BLOCK))== NULL) goto FAILURE;
+ if ((g->skeys = malloc(sizeof(struct ssipkey_s)* SSI_KEY_BLOCK))== NULL) goto FAILURE;
+
+ return g;
+
+ FAILURE:
+ SSIFreeIndex(g); /* free the damaged structure */
+ return NULL;
+}
+
+/* Function: SSIGetFilePosition()
+ * Date: SRE, Tue Jan 2 09:59:26 2001 [St. Louis]
+ *
+ * Purpose: Fills {ret_offset} with the current disk
+ * offset of {fp}, relative to the start of the file.
+ * {mode} is set to either SSI_OFFSET_I32 or
+ * SSI_OFFSET_I64. If {mode} is _I32 (32 bit), just wraps
+ * a call to ftell(); otherwise deals with system-dependent
+ * details of 64-bit file offsets.
+ *
+ * Args: fp - open stream
+ * mode - SSI_OFFSET_I32 or SSI_OFFSET_I64
+ * ret_offset - RETURN: file position
+ *
+ * Returns: 0 on success. nonzero on error.
+ */
+int
+SSIGetFilePosition(FILE *fp, int mode, SSIOFFSET *ret_offset)
+{
+ if (mode == SSI_OFFSET_I32)
+ {
+ ret_offset->mode = SSI_OFFSET_I32;
+ ret_offset->off.i32 = ftell(fp);
+ if (ret_offset->off.i32 == -1) return SSI_ERR_TELL_FAILED;
+ }
+ else if (mode != SSI_OFFSET_I64) abort(); /* only happens on a coding error */
+ else {
+ ret_offset->mode = SSI_OFFSET_I64;
+#ifndef HAS_64BIT_FILE_OFFSETS
+ return SSI_ERR_NO64BIT;
+#elif defined HAVE_FTELLO && SIZEOF_OFF_T == 8
+ if ((ret_offset->off.i64 = ftello(fp)) == -1) return SSI_ERR_TELL_FAILED;
+#elif defined HAVE_FTELLO64 && SIZEOF_OFF64_T == 8
+ if ((ret_offset->off.i64 = ftello64(fp)) == -1) return SSI_ERR_TELL_FAILED;
+#elif defined HAVE_FTELL64
+ if ((ret_offset->off.i64 = ftell64(fp)) == -1) return SSI_ERR_TELL_FAILED;
+#elif defined ARITHMETIC_FPOS_T && SIZEOF_FPOS_T == 8
+ if (fgetpos(fp, &(ret_offset->off.i64)) != 0) return SSI_ERR_TELL_FAILED;
+#endif
+ }
+ return 0;
+}
+
+/* Function: SSIAddFileToIndex()
+ * Date: SRE, Tue Jan 2 12:54:36 2001 [St. Louis]
+ *
+ * Purpose: Adds the sequence file {filename}, which is known to
+ * be in format {fmt}, to the index {g}. Creates and returns
+ * a unique filehandle {fh} for then associating primary keys
+ * with this file using SSIAddPrimaryKeyToIndex().
+ *
+ * Args: g - active index
+ * filename - file to add
+ * fmt - format code for this file (e.g. SQFILE_FASTA)
+ * ret_fh - RETURN: unique handle for this file
+ *
+ * Returns: 0 on success; nonzero on error.
+ */
+int
+SSIAddFileToIndex(SSIINDEX *g, char *filename, int fmt, int *ret_fh)
+{
+ int n;
+
+ if (g->nfiles >= SSI_MAXFILES) return SSI_ERR_TOOMANY_FILES;
+
+ n = strlen(filename);
+ if ((n+1) > g->flen) g->flen = n+1;
+
+ g->filenames[g->nfiles] = FileTail(filename, FALSE);
+ g->fileformat[g->nfiles] = fmt;
+ g->bpl[g->nfiles] = 0;
+ g->rpl[g->nfiles] = 0;
+ *ret_fh = g->nfiles; /* handle is simply = file number */
+ g->nfiles++;
+
+ if (g->nfiles % SSI_FILE_BLOCK == 0) {
+ g->filenames = realloc(g->filenames, sizeof(char *) * (g->nfiles+SSI_FILE_BLOCK));
+ if (g->filenames == NULL) return SSI_ERR_MALLOC;
+ g->fileformat= realloc(g->fileformat, sizeof(sqd_uint32) * (g->nfiles+SSI_FILE_BLOCK));
+ if (g->fileformat == NULL) return SSI_ERR_MALLOC;
+ g->bpl = realloc(g->bpl, sizeof(sqd_uint32) * (g->nfiles+SSI_FILE_BLOCK));
+ if (g->bpl == NULL) return SSI_ERR_MALLOC;
+ g->rpl = realloc(g->rpl, sizeof(sqd_uint32) * (g->nfiles+SSI_FILE_BLOCK));
+ if (g->rpl == NULL) return SSI_ERR_MALLOC;
+ }
+ return 0;
+}
+
+
+/* Function: SSISetFileForSubseq()
+ * Date: SRE, Tue Jan 9 10:02:05 2001 [St. Louis]
+ *
+ * Purpose: Set SSI_FAST_SUBSEQ for the file indicated by
+ * filehandle {fh} in the index {g}, setting
+ * parameters {bpl} and {rpl} to the values given.
+ * {bpl} is the number of bytes per sequence data line.
+ * {rpl} is the number of residues per sequence data line.
+ * Caller must be sure that {bpl} and {rpl} do not change
+ * on any line of any sequence record in the file
+ * (except for the last data line of each record). If
+ * this is not the case in this file, SSI_FAST_SUBSEQ
+ * will not work, and this routine should not be
+ * called.
+ *
+ * Args: g - the active index
+ * fh - handle for file to set SSI_FAST_SUBSEQ on
+ * bpl - bytes per data line
+ * rpl - residues per data line
+ *
+ * Returns: 0 on success; 1 on error.
+ */
+int
+SSISetFileForSubseq(SSIINDEX *g, int fh, int bpl, int rpl)
+{
+ if (fh < 0 || fh >= g->nfiles) return SSI_ERR_BADARG;
+ if (bpl <= 0 || rpl <= 0) return SSI_ERR_BADARG;
+ g->bpl[fh] = bpl;
+ g->rpl[fh] = rpl;
+ return 0;
+}
+
+
+/* Function: SSIAddPrimaryKeyToIndex()
+ * Date: SRE, Tue Jan 2 11:50:54 2001 [St. Louis]
+ *
+ * Purpose: Put primary key {key} in the index {g}, while telling
+ * the index this primary key is in the file associated
+ * with filehandle {fh} (returned by a previous call
+ * to SSIAddFileToIndex()), and its record starts at
+ * position {r_off} in the file.
+ *
+ * {d_off} and {L} are optional; they may be left unset
+ * by passing NULL and 0, respectively. (If one is
+ * provided, both must be provided.) If they are provided,
+ * {d_off} gives the position of the first line of sequence
+ * data in the record, and {L} gives the length of
+ * the sequence in residues. They are used when
+ * SSI_FAST_SUBSEQ is set for this file. If SSI_FAST_SUBSEQ
+ * is not set for the file, {d_off} and {L} will be
+ * ignored by the index reading API even if they are stored
+ * by the index writing API, so it doesn't hurt for the
+ * indexing program to provide them; typically they
+ * won't know whether it's safe to set SSI_FAST_SUBSEQ
+ * for the whole file until the whole file has been
+ * read and every key has already been added to the index.
+ *
+ * Args: g - active index
+ * key - primary key to add
+ * fh - handle on file that this key's in
+ * r_off - offset to start of record
+ * d_off - offset to start of sequence data
+ * L - length of sequence, or 0
+ *
+ * Returns: 0 on success, nonzero on error.
+ */
+int
+SSIAddPrimaryKeyToIndex(SSIINDEX *g, char *key, int fh,
+ SSIOFFSET *r_off, SSIOFFSET *d_off, int L)
+{
+ int n; /* a string length */
+
+ if (fh >= SSI_MAXFILES) return SSI_ERR_TOOMANY_FILES;
+ if (g->nprimary >= SSI_MAXKEYS) return SSI_ERR_TOOMANY_KEYS;
+ if (L > 0 && d_off == NULL) abort(); /* need both. */
+
+ /* Before adding the key: check how big our index is.
+ * If it's getting too large, switch to external mode.
+ */
+ if (!g->external && current_index_size(g) >= g->max_ram)
+ if (activate_external_sort(g) != 0) return SSI_ERR_NOFILE;
+
+ /* Update maximum pkey length, if needed.
+ */
+ n = strlen(key);
+ if ((n+1) > g->plen) g->plen = n+1;
+
+ /* External mode? Simply append to disk...
+ */
+ if (g->external) {
+ if (g->smode == SSI_OFFSET_I32) {
+ fprintf(g->ptmp, "%s\t%d\t%lu\t%lu\t%lu\n",
+ key, fh, (unsigned long) r_off->off.i32,
+ (unsigned long) (d_off == NULL? 0 : d_off->off.i32),
+ (unsigned long) L);
+ } else {
+#ifdef CLUSTALO
+ fprintf(g->ptmp, "%s\t%d\t%llu\t%llu\t%lu\n",
+ key, fh, (unsigned long long)r_off->off.i64,
+ d_off == NULL? 0 : (unsigned long long) d_off->off.i64,
+ (unsigned long) L);
+#else
+ fprintf(g->ptmp, "%s\t%d\t%llu\t%llu\t%lu\n",
+ key, fh, r_off->off.i64,
+ d_off == NULL? 0 : d_off->off.i64,
+ (unsigned long) L);
+#endif
+ }
+ g->nprimary++;
+ return 0;
+ }
+
+ /* Else: internal mode, keep keys in memory...
+ */
+ if ((g->pkeys[g->nprimary].key = sre_strdup(key, n)) == NULL) return SSI_ERR_MALLOC;
+ g->pkeys[g->nprimary].fnum = (sqd_uint16) fh;
+ g->pkeys[g->nprimary].r_off = *r_off;
+ if (d_off != NULL && L > 0) {
+ g->pkeys[g->nprimary].d_off = *d_off;
+ g->pkeys[g->nprimary].len = L;
+ } else {
+ /* yeah, this looks stupid, but look: we have to give a valid
+ looking, non-NULL d_off of some sort, or writes will fail.
+ It's going to be unused anyway. */
+ g->pkeys[g->nprimary].d_off = *r_off;
+ g->pkeys[g->nprimary].len = 0;
+ }
+ g->nprimary++;
+
+ if (g->nprimary % SSI_KEY_BLOCK == 0) {
+ g->pkeys = realloc(g->pkeys, sizeof(struct ssipkey_s) * (g->nprimary+SSI_KEY_BLOCK));
+ if (g->pkeys == NULL) return SSI_ERR_MALLOC;
+ }
+ return 0;
+}
+
+
+/* Function: SSIAddSecondaryKeyToIndex()
+ * Date: SRE, Tue Jan 2 12:44:40 2001 [St. Louis]
+ *
+ * Purpose: Puts secondary key {key} in the index {g}, associating
+ * it with primary key {pkey} that was previously
+ * registered by SSIAddPrimaryKeyToIndex().
+ *
+ * Args: g - active index
+ * key - secondary key to add
+ * pkey - primary key to associate this key with
+ *
+ * Returns: 0 on success, nonzero on failure.
+ */
+int
+SSIAddSecondaryKeyToIndex(SSIINDEX *g, char *key, char *pkey)
+{
+ int n; /* a string length */
+
+ if (g->nsecondary >= SSI_MAXKEYS) return SSI_ERR_TOOMANY_KEYS;
+
+ /* Before adding the key: check how big our index is.
+ * If it's getting too large, switch to external mode.
+ */
+ if (!g->external && current_index_size(g) >= g->max_ram)
+ if (activate_external_sort(g) != 0) return SSI_ERR_NOFILE;
+
+ /* Update maximum secondary key length, if necessary.
+ */
+ n = strlen(key);
+ if ((n+1) > g->slen) g->slen = n+1;
+
+ /* if external mode: write info to disk.
+ */
+ if (g->external) {
+ fprintf(g->stmp, "%s\t%s\n", key, pkey);
+ g->nsecondary++;
+ return 0;
+ }
+
+ /* else, internal mode... store info in memory.
+ */
+ if ((g->skeys[g->nsecondary].key = sre_strdup(key, n)) == NULL) return SSI_ERR_MALLOC;
+ if ((g->skeys[g->nsecondary].pkey = sre_strdup(pkey, -1)) == NULL) return SSI_ERR_MALLOC;
+ g->nsecondary++;
+
+ if (g->nsecondary % SSI_KEY_BLOCK == 0) {
+ g->skeys = realloc(g->skeys, sizeof(struct ssiskey_s) * (g->nsecondary+SSI_KEY_BLOCK));
+ if (g->skeys == NULL) return SSI_ERR_MALLOC;
+ }
+ return 0;
+}
+
+
+
+
+/* Function: SSIWriteIndex()
+ * Date: SRE, Tue Jan 2 13:55:56 2001 [St. Louis]
+ *
+ * Purpose: Writes complete index {g} in SSI format to a
+ * binary file {file}. Does all
+ * the overhead of sorting the primary and secondary keys,
+ * and maintaining the association of secondary keys
+ * with primary keys during and after the sort.
+ *
+ * Args: file - file to write to
+ * g - index to sort & write out.
+ *
+ * Returns: 0 on success, nonzero on error.
+ */
+/* needed for qsort() */
+static int
+pkeysort(const void *k1, const void *k2)
+{
+ struct ssipkey_s *key1;
+ struct ssipkey_s *key2;
+ key1 = (struct ssipkey_s *) k1;
+ key2 = (struct ssipkey_s *) k2;
+ return strcmp(key1->key, key2->key);
+}
+static int
+skeysort(const void *k1, const void *k2)
+{
+ struct ssiskey_s *key1;
+ struct ssiskey_s *key2;
+ key1 = (struct ssiskey_s *) k1;
+ key2 = (struct ssiskey_s *) k2;
+ return strcmp(key1->key, key2->key);
+}
+int
+SSIWriteIndex(char *file, SSIINDEX *g)
+{
+ FILE *fp;
+ int status;
+ int i;
+ sqd_uint32 header_flags, file_flags;
+ sqd_uint32 frecsize, precsize, srecsize;
+ sqd_uint64 foffset, poffset, soffset;
+ char *s, *s2;
+
+ if ((fp = fopen(file,"wb")) == NULL) return SSI_ERR_NOFILE;
+ status = 0;
+
+ /* How big is the index? If it's going to be > 2GB, we need
+ * to flip to 64-bit index mode. 2047 (instead of 2048) gives us
+ * some slop room.
+ * die'ing here is pretty brutal - if we flip to 64-bit index
+ * mode, we hve 100's of millions of keys, so we've processed
+ * a long time before reaching this point. Ah well.
+ */
+ if (current_index_size(g) >= 2047) {
+ g->imode = SSI_OFFSET_I64;
+#ifndef HAS_64BIT_FILE_OFFSETS
+ Die("\
+Can't switch to 64-bit SSI index mode on this system, sorry;\n\
+I don't have 64-bit file offset functions available.\n");
+#endif
+ }
+
+ /* Magic-looking numbers come from adding up sizes
+ * of things in bytes
+ */
+ frecsize = 16 + g->flen;
+ precsize = (g->smode == SSI_OFFSET_I64) ? 22+g->plen : 14+g->plen;
+ srecsize = g->slen + g->plen;
+
+ header_flags = 0;
+ if (g->smode == SSI_OFFSET_I64) header_flags |= SSI_USE64;
+ if (g->imode == SSI_OFFSET_I64) header_flags |= SSI_USE64_INDEX;
+
+ /* Magic-looking numbers again come from adding up sizes
+ * of things in bytes
+ */
+ foffset = (header_flags & SSI_USE64_INDEX) ? 66 : 54;
+ poffset = foffset + frecsize*g->nfiles;
+ soffset = poffset + precsize*g->nprimary;
+
+ /* Sort the keys
+ * If external mode, make system calls to UNIX/POSIX "sort" in place, then
+ * open new sorted files for reading thru ptmp and stmp handles.
+ * If internal mode, call qsort.
+ *
+ * Note that you'd better force a POSIX locale for the sort; else,
+ * some silly distro (e.g. Mandrake Linux >=8.1) may have specified
+ * LC_COLLATE=en_US, and this'll give a sort "bug" in which it doesn't
+ * sort by byte order.
+ */
+ if (g->external) {
+ char cmd[1024];
+
+ fclose(g->ptmp);
+ g->ptmp = NULL;
+ sprintf(cmd, "env LC_ALL=POSIX sort -o %s %s\n", g->ptmpfile, g->ptmpfile);
+ if ((status = system(cmd)) != 0) return SSI_ERR_EXTERNAL_SORT;
+ if ((g->ptmp = fopen(g->ptmpfile, "r")) == NULL) return SSI_ERR_EXTERNAL_SORT;
+
+ fclose(g->stmp);
+ g->stmp = NULL;
+ sprintf(cmd, "env LC_ALL=POSIX sort -o %s %s\n", g->stmpfile, g->stmpfile);
+ if ((status = system(cmd)) != 0) return SSI_ERR_EXTERNAL_SORT;
+ if ((g->stmp = fopen(g->stmpfile, "r")) == NULL) return SSI_ERR_EXTERNAL_SORT;
+ } else {
+ qsort((void *) g->pkeys, g->nprimary, sizeof(struct ssipkey_s), pkeysort);
+ qsort((void *) g->skeys, g->nsecondary, sizeof(struct ssiskey_s), skeysort);
+ }
+
+ /* Write the header
+ */
+ if (! write_i32(fp, v20magic)) return SSI_ERR_FWRITE;
+ if (! write_i32(fp, header_flags)) return SSI_ERR_FWRITE;
+ if (! write_i16(fp, g->nfiles)) return SSI_ERR_FWRITE;
+ if (! write_i32(fp, g->nprimary)) return SSI_ERR_FWRITE;
+ if (! write_i32(fp, g->nsecondary)) return SSI_ERR_FWRITE;
+ if (! write_i32(fp, g->flen)) return SSI_ERR_FWRITE;
+ if (! write_i32(fp, g->plen)) return SSI_ERR_FWRITE;
+ if (! write_i32(fp, g->slen)) return SSI_ERR_FWRITE;
+ if (! write_i32(fp, frecsize)) return SSI_ERR_FWRITE;
+ if (! write_i32(fp, precsize)) return SSI_ERR_FWRITE;
+ if (! write_i32(fp, srecsize)) return SSI_ERR_FWRITE;
+ if (g->imode == SSI_OFFSET_I32) {
+ if (! write_i32(fp, foffset)) return SSI_ERR_FWRITE;
+ if (! write_i32(fp, poffset)) return SSI_ERR_FWRITE;
+ if (! write_i32(fp, soffset)) return SSI_ERR_FWRITE;
+ } else {
+ if (! write_i64(fp, foffset)) return SSI_ERR_FWRITE;
+ if (! write_i64(fp, poffset)) return SSI_ERR_FWRITE;
+ if (! write_i64(fp, soffset)) return SSI_ERR_FWRITE;
+ }
+
+ /* The file section
+ */
+ if ((s = malloc(sizeof(char) * g->flen)) == NULL) return SSI_ERR_MALLOC;
+ for (i = 0; i < g->nfiles; i++)
+ {
+ file_flags = 0;
+ if (g->bpl[i] > 0 && g->rpl[i] > 0) file_flags |= SSI_FAST_SUBSEQ;
+
+ strcpy(s, g->filenames[i]);
+ if (fwrite(s, sizeof(char), g->flen, fp) != g->flen) return SSI_ERR_FWRITE;
+ if (! write_i32(fp, g->fileformat[i])) return SSI_ERR_FWRITE;
+ if (! write_i32(fp, file_flags)) return SSI_ERR_FWRITE;
+ if (! write_i32(fp, g->bpl[i])) return SSI_ERR_FWRITE;
+ if (! write_i32(fp, g->rpl[i])) return SSI_ERR_FWRITE;
+ }
+ free(s);
+
+ /* The primary key section
+ */
+ if ((s = malloc(sizeof(char) * g->plen)) == NULL) return SSI_ERR_MALLOC;
+ if (g->external) {
+ char *buf = NULL;
+ int buflen = 0;
+ struct ssipkey_s pkey;
+ for (i = 0; i < g->nprimary; i++)
+ {
+ if (sre_fgets(&buf, &buflen, g->ptmp) == NULL) return SSI_ERR_NODATA;
+ if (parse_pkey_info(buf, g->smode, &pkey) != 0) return SSI_ERR_BADFORMAT;
+ strcpy(s, pkey.key);
+ if (fwrite(s, sizeof(char), g->plen, fp) != g->plen) return SSI_ERR_FWRITE;
+ if (! write_i16( fp, pkey.fnum)) return SSI_ERR_FWRITE;
+ if (! write_offset(fp, &(pkey.r_off))) return SSI_ERR_FWRITE;
+ if (! write_offset(fp, &(pkey.d_off))) return SSI_ERR_FWRITE;
+ if (! write_i32( fp, pkey.len)) return SSI_ERR_FWRITE;
+ }
+ free(buf);
+ } else {
+ for (i = 0; i < g->nprimary; i++)
+ {
+ strcpy(s, g->pkeys[i].key);
+ if (fwrite(s, sizeof(char), g->plen, fp) != g->plen) return SSI_ERR_FWRITE;
+ if (! write_i16( fp, g->pkeys[i].fnum)) return SSI_ERR_FWRITE;
+ if (! write_offset(fp, &(g->pkeys[i].r_off))) return SSI_ERR_FWRITE;
+ if (! write_offset(fp, &(g->pkeys[i].d_off))) return SSI_ERR_FWRITE;
+ if (! write_i32( fp, g->pkeys[i].len)) return SSI_ERR_FWRITE;
+ }
+ }
+
+ /* The secondary key section
+ */
+ if (g->nsecondary > 0) {
+ if ((s2 = malloc(sizeof(char) * g->slen)) == NULL) return SSI_ERR_MALLOC;
+
+ if (g->external) {
+ struct ssiskey_s skey;
+ char *buf = NULL;
+ int n = 0;
+
+ for (i = 0; i < g->nsecondary; i++)
+ {
+ if (sre_fgets(&buf, &n, g->stmp) == NULL) return SSI_ERR_NODATA;
+ if (parse_skey_info(buf, &skey) != 0) return SSI_ERR_BADFORMAT;
+ strcpy(s2, skey.key);
+ strcpy(s, skey.pkey);
+ if (fwrite(s2, sizeof(char), g->slen, fp) != g->slen) return SSI_ERR_FWRITE;
+ if (fwrite(s, sizeof(char), g->plen, fp) != g->plen) return SSI_ERR_FWRITE;
+ }
+ free(buf);
+ } else {
+ for (i = 0; i < g->nsecondary; i++)
+ {
+ strcpy(s2, g->skeys[i].key);
+ strcpy(s, g->skeys[i].pkey);
+ if (fwrite(s2, sizeof(char), g->slen, fp) != g->slen) return SSI_ERR_FWRITE;
+ if (fwrite(s, sizeof(char), g->plen, fp) != g->plen) return SSI_ERR_FWRITE;
+ }
+ }
+ free(s2);
+ }
+
+ free(s);
+ fclose(fp);
+ return status;
+}
+
+
+/* Function: SSIFreeIndex()
+ * Date: SRE, Tue Jan 2 11:44:08 2001 [St. Louis]
+ *
+ * Purpose: Free an index structure {g}.
+ *
+ * Args: g - ptr to an open index.
+ *
+ * Returns: (void)
+ */
+void
+SSIFreeIndex(SSIINDEX *g)
+{
+ int i;
+ if (g != NULL)
+ {
+ if (g->external == FALSE) {
+ for (i = 0; i < g->nprimary; i++) free(g->pkeys[i].key);
+ for (i = 0; i < g->nsecondary; i++) free(g->skeys[i].key);
+ for (i = 0; i < g->nsecondary; i++) free(g->skeys[i].pkey);
+ if (g->pkeys != NULL) free(g->pkeys);
+ if (g->skeys != NULL) free(g->skeys);
+ } else {
+ if (g->ptmp != NULL) fclose(g->ptmp);
+ if (g->stmp != NULL) fclose(g->stmp);
+#if DEBUGLEVEL == 0
+ remove(g->ptmpfile);
+ remove(g->stmpfile);
+#endif
+ }
+ for (i = 0; i < g->nfiles; i++) free(g->filenames[i]);
+ if (g->filenames != NULL) free(g->filenames);
+ if (g->fileformat != NULL) free(g->fileformat);
+ if (g->bpl != NULL) free(g->bpl);
+ if (g->rpl != NULL) free(g->rpl);
+ free(g);
+ }
+}
+
+
+/* Function: SSIErrorString()
+ * Date: SRE, Tue Jan 2 10:38:10 2001 [St. Louis]
+ *
+ * Purpose: Returns a ptr to an internal string corresponding
+ * to error {n}, a code returned from any of the
+ * functions in the API that return non-zero on error.
+ *
+ * Args: n - error code
+ *
+ * Returns: ptr to an internal string.
+ */
+char *
+SSIErrorString(int n)
+{
+ switch (n) {
+ case SSI_ERR_OK: return "ok (no error)";
+ case SSI_ERR_NODATA: return "no data, fread() failed";
+ case SSI_ERR_NO_SUCH_KEY: return "no such key";
+ case SSI_ERR_MALLOC: return "out of memory, malloc() failed";
+ case SSI_ERR_NOFILE: return "file not found, fopen() failed";
+ case SSI_ERR_BADMAGIC: return "not a SSI file? (bad magic)";
+ case SSI_ERR_BADFORMAT: return "corrupt format? unexpected data";
+ case SSI_ERR_NO64BIT: return "no large file support for this system";
+ case SSI_ERR_SEEK_FAILED: return "failed to reposition on disk";
+ case SSI_ERR_TELL_FAILED: return "failed to get file position on disk";
+ case SSI_ERR_NO_SUBSEQS: return "no fast subseq support for this seqfile";
+ case SSI_ERR_RANGE: return "subseq start is out of range";
+ case SSI_ERR_BADARG: return "an argument is out of range";
+ case SSI_ERR_TOOMANY_FILES: return "number of files exceeds limit";
+ case SSI_ERR_TOOMANY_KEYS: return "number of keys exceeds limit";
+ case SSI_ERR_FWRITE: return "an fwrite() failed";
+ case SSI_ERR_EXTERNAL_SORT: return "some problem with external sorting";
+ default: return "unrecognized code";
+ }
+ /*NOTREACHED*/
+}
+
+static int
+read_i16(FILE *fp, sqd_uint16 *ret_result)
+{
+ sqd_uint16 result;
+ if (fread(&result, sizeof(sqd_uint16), 1, fp) != 1) return 0;
+ *ret_result = sre_ntoh16(result);
+ return 1;
+}
+static int
+write_i16(FILE *fp, sqd_uint16 n)
+{
+ n = sre_hton16(n);
+ if (fwrite(&n, sizeof(sqd_uint16), 1, fp) != 1) return 0;
+ return 1;
+}
+static int
+read_i32(FILE *fp, sqd_uint32 *ret_result)
+{
+ sqd_uint32 result;
+ if (fread(&result, sizeof(sqd_uint32), 1, fp) != 1) return 0;
+ *ret_result = sre_ntoh32(result);
+ return 1;
+}
+static int
+write_i32(FILE *fp, sqd_uint32 n)
+{
+ n = sre_hton32(n);
+ if (fwrite(&n, sizeof(sqd_uint32), 1, fp) != 1) return 0;
+ return 1;
+}
+static int
+read_i64(FILE *fp, sqd_uint64 *ret_result)
+{
+ sqd_uint64 result;
+ if (fread(&result, sizeof(sqd_uint64), 1, fp) != 1) return 0;
+ *ret_result = sre_ntoh64(result);
+ return 1;
+}
+static int
+write_i64(FILE *fp, sqd_uint64 n)
+{
+ n = sre_hton64(n);
+ if (fwrite(&n, sizeof(sqd_uint64), 1, fp) != 1) return 0;
+ return 1;
+}
+static int
+read_offset(FILE *fp, char mode, SSIOFFSET *ret_offset)
+{
+ if (mode == SSI_OFFSET_I32) {
+ ret_offset->mode = SSI_OFFSET_I32;
+ if (! read_i32(fp, &(ret_offset->off.i32))) return 0;
+ } else if (mode == SSI_OFFSET_I64) {
+ ret_offset->mode = SSI_OFFSET_I64;
+ if (! read_i64(fp, &(ret_offset->off.i64))) return 0;
+ } else return 0;
+
+ return 1;
+}
+static int
+write_offset(FILE *fp, SSIOFFSET *offset)
+{
+ if (offset->mode == SSI_OFFSET_I32) return write_i32(fp, offset->off.i32);
+ else if (offset->mode == SSI_OFFSET_I64) return write_i64(fp, offset->off.i64);
+ else abort();
+ /*UNREACHED*/
+ return 1; /* silence bitchy compilers */
+}
+
+static int
+parse_pkey_info(char *buf, char mode, struct ssipkey_s *pkey)
+{
+ char *s, *tok;
+ int n;
+
+ s = buf;
+ if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT;
+ pkey->key = tok;
+ if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT;
+ pkey->fnum = (sqd_uint16) atoi(tok);
+
+ if (mode == SSI_OFFSET_I32) {
+ if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT;
+ pkey->r_off.mode = mode;
+ pkey->r_off.off.i32 = (sqd_uint32) strtoul(tok, NULL, 10);
+ if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT;
+ pkey->d_off.mode = mode;
+ pkey->d_off.off.i32 = (sqd_uint32) strtoul(tok, NULL, 10);
+ }
+#ifdef HAS_64BIT_FILE_OFFSETS
+ else {
+ if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT;
+ pkey->r_off.mode = mode;
+ pkey->r_off.off.i64 = (sqd_uint64) strtoull(tok, NULL, 10);
+ if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT;
+ pkey->d_off.mode = mode;
+ pkey->d_off.off.i64 = (sqd_uint64) strtoull(tok, NULL, 10);
+ }
+#else
+ else {
+ return SSI_ERR_NO64BIT;
+ }
+#endif
+ if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT;
+ pkey->len = (sqd_uint32) strtoul(tok, NULL, 10);
+
+ return 0;
+}
+static int
+parse_skey_info(char *buf, struct ssiskey_s *skey)
+{
+ char *s, *tok;
+ int n;
+
+ s = buf;
+ if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT;
+ skey->key = tok;
+ if ((tok = sre_strtok(&s, "\t\n", &n)) == NULL) return SSI_ERR_BADFORMAT;
+ skey->pkey = tok;
+ return 0;
+}
+
+/* Function: binary_search()
+ * Date: SRE, Sun Dec 31 16:05:03 2000 [St. Louis]
+ *
+ * Purpose: Find a key in a SSI index, by a binary search
+ * in an alphabetically sorted list of keys. If successful,
+ * return 0, and the index file is positioned to read
+ * the rest of the data for that key. Else returns nonzero.
+ *
+ * Args: sfp - an open SSIFILE
+ * key - key to find
+ * klen - key length to allocate (plen or slen from sfp)
+ * base - base offset (poffset or soffset)
+ * recsize - size of each key record in bytes (precsize or srecsize)
+ * maxidx - # of keys (nprimary or nsecondary)
+ *
+ * Returns: 0 on success, and leaves file positioned for reading remaining
+ * data for the key.
+ * Nonzero on failure:
+ * SSI_ERR_NO_SUCH_KEY - that key's not in the index
+ * SSI_ERR_MALLOC - a memory allocation failure
+ * SSI_ERR_NODATA - an fread() failed
+ */
+static int
+binary_search(SSIFILE *sfp, char *key, int klen, SSIOFFSET *base,
+ sqd_uint32 recsize, sqd_uint32 maxidx)
+{
+ char *name;
+ sqd_uint32 left, right, mid;
+ int cmp;
+ int status;
+
+ if (maxidx == 0) return SSI_ERR_NO_SUCH_KEY; /* special case: empty index */
+ if ((name = malloc (sizeof(char)*klen)) == NULL) return SSI_ERR_MALLOC;
+ left = 0;
+ right = maxidx-1;
+ while (1) { /* A binary search: */
+ mid = (left+right) / 2; /* careful here. only works because
+ we limit unsigned vars to signed ranges. */
+ if ((status = indexfile_position(sfp, base, recsize, mid)) != 0)
+ { free(name); return status; }
+ if (fread(name, sizeof(char), klen, sfp->fp) != klen)
+ { free(name); return SSI_ERR_NODATA; }
+ cmp = strcmp(name, key);
+ if (cmp == 0) break; /* found it! */
+ else if (left >= right) /* oops, missed it; fail */
+ { free(name); return SSI_ERR_NO_SUCH_KEY; }
+ else if (cmp < 0) left = mid+1; /* it's right of mid */
+ else if (cmp > 0) {
+ if (mid == 0) { free(name); return SSI_ERR_NO_SUCH_KEY; } /* special case, beware */
+ else right = mid-1; /* it's left of mid */
+ }
+ }
+ free(name);
+ return 0; /* and sfp->fp is positioned... */
+}
+
+/* Function: indexfile_position()
+ * Date: SRE, Mon Jan 1 19:32:49 2001 [St. Louis]
+ *
+ * Purpose: Position the open index file {sfp} at the start
+ * of record {n} in a list of records that starts at
+ * base offset {base}, where each record takes up {l}
+ * bytes. (e.g. the position is byte (base + n*l)).
+ *
+ * Args: sfp - open SSIFILE
+ * base - offset of record 0 (e.g. sfp->foffset)
+ * len - size of each record in bytes (e.g. sfp->frecsize)
+ * n - which record to get (e.g. 0..sfp->nfiles)
+ *
+ * Returns: 0 on success, non-zero on failure.
+ */
+static int
+indexfile_position(SSIFILE *sfp, SSIOFFSET *base, sqd_uint32 len, sqd_uint32 n)
+{
+ SSIOFFSET pos;
+ int status;
+
+ if (base->mode == SSI_OFFSET_I32) {
+ pos.mode = SSI_OFFSET_I32;
+ pos.off.i32 = base->off.i32 + n*len;
+ } else if (base->mode == SSI_OFFSET_I64) {
+ pos.mode = SSI_OFFSET_I64;
+ pos.off.i64 = base->off.i64 + n*len;
+ } else return 0;
+ if ((status = SSISetFilePosition(sfp->fp, &pos)) != 0) return status;
+ return 0;
+}
+
+/* Function: current_index_size()
+ * Date: SRE, Tue Feb 20 18:23:30 2001 [St. Louis]
+ *
+ * Purpose: Calculates the size of the current index,
+ * in megabytes.
+ */
+static sqd_uint64
+current_index_size(SSIINDEX *g)
+{
+ sqd_uint64 frecsize, precsize, srecsize;
+ sqd_uint64 total;
+
+ /* Magic-looking numbers come from adding up sizes
+ * of things in bytes
+ */
+ frecsize = 16 + g->flen;
+ precsize = (g->smode == SSI_OFFSET_I64) ? 22+g->plen : 14+g->plen;
+ srecsize = g->plen+g->slen;
+ total = (66L + /* header size, if 64bit index offsets */
+ frecsize * g->nfiles + /* file section size */
+ precsize * g->nprimary + /* primary key section size */
+ srecsize * g->nsecondary) / /* secondary key section size */
+ 1048576L;
+ return total;
+}
+/* Function: activate_external_sort()
+ * Date: SRE, Mon Feb 4 09:08:08 2002 [St. Louis]
+ *
+ * Purpose: Switch to external sort mode.
+ * Open file handles for external index files (ptmp, stmp).
+ * Flush current index information to these files.
+ * Free current memory, turn over control to the tmpfiles.
+ *
+ * Return: 0 on success; non-zero on failure.
+ */
+static int
+activate_external_sort(SSIINDEX *g)
+{
+ int i;
+ /* it's a bit late to be checking this, but... */
+ if (g->external) return 0; /* we already are external, fool */
+ if (FileExists(g->ptmpfile)) return 1;
+ if (FileExists(g->stmpfile)) return 1;
+ if ((g->ptmp = fopen(g->ptmpfile, "w")) == NULL) return 1;
+ if ((g->stmp = fopen(g->stmpfile, "w")) == NULL) return 1;
+
+ /* Flush the current indices.
+ */
+ SQD_DPRINTF1(("Switching to external sort - flushing ssiindex to disk...\n"));
+ for (i = 0; i < g->nprimary; i++) {
+ if (g->smode == SSI_OFFSET_I32) {
+ fprintf(g->ptmp, "%s\t%u\t%lu\t%lu\t%lu\n",
+ g->pkeys[i].key, g->pkeys[i].fnum,
+ (unsigned long) g->pkeys[i].r_off.off.i32,
+ (unsigned long) g->pkeys[i].d_off.off.i32,
+ (unsigned long) g->pkeys[i].len);
+ } else {
+ fprintf(g->ptmp, "%s\t%u\t%llu\t%llu\t%lu\n",
+ g->pkeys[i].key, g->pkeys[i].fnum,
+ (unsigned long long) g->pkeys[i].r_off.off.i64,
+ (unsigned long long) g->pkeys[i].d_off.off.i64,
+ (unsigned long) g->pkeys[i].len);
+ }
+ }
+ for (i = 0; i < g->nsecondary; i++)
+ fprintf(g->stmp, "%s\t%s\n", g->skeys[i].key, g->skeys[i].pkey);
+
+ /* Free the memory now that we've flushed our lists to disk
+ */
+ for (i = 0; i < g->nprimary; i++) free(g->pkeys[i].key);
+ for (i = 0; i < g->nsecondary; i++) free(g->skeys[i].key);
+ for (i = 0; i < g->nsecondary; i++) free(g->skeys[i].pkey);
+ if (g->pkeys != NULL) free(g->pkeys);
+ if (g->skeys != NULL) free(g->skeys);
+ g->pkeys = NULL;
+ g->skeys = NULL;
+
+ /* Turn control over to external accumulation mode.
+ */
+ g->external = TRUE;
+ return 0;
+}
+
+
+/*****************************************************************
+ * Debugging API
+ *****************************************************************/
+void
+SSIForceExternalSort(SSIINDEX *g)
+{
+ if (activate_external_sort(g) != 0)
+ Die("failed to turn external sorting on.");
+}
+
+
+/*****************************************************************
+ * Test driving mode
+ *****************************************************************/
+#ifdef MUGGINS_LETS_ME_SLEEP
+/* Minimally:
+ cc -g -Wall -o shiva -DDEBUGLEVEL=1 -DMUGGINS_LETS_ME_SLEEP ssi.c sqerror.c sre_string.c types.c sre_ctype.c sre_math.c file.c -lm
+*/
+
+int
+main(int argc, char **argv)
+{
+ char name[32], accession[32];
+ SSIINDEX *ssi;
+ int mode;
+ SSIOFFSET r_off, d_off;
+ FILE *ofp;
+ int i;
+ int fh; /* a file handle */
+ int status; /* return status from a SSI call */
+
+ mode = SSI_OFFSET_I32;
+ if ((ssi = SSICreateIndex(mode)) == NULL)
+ Die("Failed to allocate SSI index");
+
+ /* Generate two FASTA files, tmp.0 and tmp.1, and index them.
+ */
+ if ((ofp = fopen("tmp.0", "w")) == NULL)
+ Die("failed to open tmp.0");
+ if ((status = SSIAddFileToIndex(ssi, "tmp.0", SQFILE_FASTA, &fh)) != 0)
+ Die("SSIAddFileToIndex() failed: %s", SSIErrorString(status));
+ for (i = 0; i < 10; i++) {
+ if ((status = SSIGetFilePosition(ofp, mode, &r_off)) != 0)
+ Die("SSIGetFilePosition() failed: %s", SSIErrorString(status));
+ sprintf(name, "seq%d", i);
+ sprintf(accession, "ac%d", i);
+ fprintf(ofp, ">%s [%s] Description? we don't need no steenking description.\n",
+ name, accession);
+ if ((status = SSIGetFilePosition(ofp, mode, &d_off)) != 0)
+ Die("SSIGetFilePosition() failed: %s", SSIErrorString(status));
+ fprintf(ofp, "AAAAAAAAAA\n");
+ fprintf(ofp, "CCCCCCCCCC\n");
+ fprintf(ofp, "GGGGGGGGGG\n");
+ fprintf(ofp, "TTTTTTTTTT\n");
+
+ if ((status = SSIAddPrimaryKeyToIndex(ssi, name, fh, &r_off, &d_off, 40)) != 0)
+ Die("SSIAddPrimaryKeyToIndex() failed: %s", SSIErrorString(status));
+ if ((status = SSIAddSecondaryKeyToIndex(ssi, accession, name)) != 0)
+ Die("SSIAddSecondaryKeyToIndex() failed: %s", SSIErrorString(status));
+ }
+ SSISetFileForSubseq(ssi, fh, 11, 10);
+ fclose(ofp);
+
+ if ((ofp = fopen("tmp.1", "w")) == NULL)
+ Die("failed to open tmp.1");
+ if ((status = SSIAddFileToIndex(ssi, "tmp.1", SQFILE_FASTA, &fh)) != 0)
+ Die("SSIAddFileToIndex() failed: %s", SSIErrorString(status));
+ for (i = 10; i < 20; i++) {
+ if ((status = SSIGetFilePosition(ofp, mode, &r_off)) != 0)
+ Die("SSIGetFilePosition() failed: %s", SSIErrorString(status));
+ sprintf(name, "seq%d", i);
+ sprintf(accession, "ac%d", i);
+ fprintf(ofp, ">%s [%s] i/o, i/o, it's off to disk we go.\n",
+ name, accession);
+ if ((status = SSIGetFilePosition(ofp, mode, &d_off)) != 0)
+ Die("SSIGetFilePosition() failed: %s", SSIErrorString(status));
+ fprintf(ofp, "AAAAAAAAAA 10\n");
+ fprintf(ofp, "CCCCCCCCCC 20\n");
+ fprintf(ofp, "GGGGGGGGGG 30\n");
+ fprintf(ofp, "TTTTTTTTTT 40\n");
+
+ if ((status = SSIAddPrimaryKeyToIndex(ssi, name, fh, &r_off, &d_off, 40)) != 0)
+ Die("SSIAddPrimaryKeyToIndex() failed: %s", SSIErrorString(status));
+ if ((status = SSIAddSecondaryKeyToIndex(ssi, accession, name)) != 0)
+ Die("SSIAddSecondaryKeyToIndex() failed: %s", SSIErrorString(status));
+ }
+ SSISetFileForSubseq(ssi, fh, 14, 10);
+ fclose(ofp);
+
+ /* Write the index to tmp.ssi
+ */
+ if ((status = SSIWriteIndex("tmp.ssi", ssi)) != 0)
+ Die("SSIWriteIndex() failed: %s", SSIErrorString(status));
+ SSIFreeIndex(ssi);
+
+ /* Now reopen the index and run some tests.
+ */
+ exit(0);
+}
+
+
+#endif /* test driving code */
+
+
+
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+#ifndef SSIH_INCLUDED
+#define SSIH_INCLUDED
+
+/* ssi.h
+ * Database indexing (SSI format support)
+ * CVS $Id: ssi.h,v 1.7 2002/02/24 19:39:27 eddy Exp)
+ *
+ * See: ssi_format.tex in Docs/
+ */
+
+#include <stdio.h>
+#include "squid.h"
+
+/* Limits
+ */
+#define SSI_MAXFILES 32767 /* 2^15-1 */
+#define SSI_MAXKEYS 2147483647L /* 2^31-1 */
+#define SSI_MAXRAM 200 /* allow 200MB indexes before external sort mode */
+
+/* typedef: SSIOFFSET
+ * Use the union to save space, since the two offset types are
+ * mutually exclusive, controlled by "mode"
+ */
+struct ssioffset_s {
+ char mode; /* GSI_OFFSET_I32, for example */
+ union {
+ sqd_uint32 i32; /* an offset that fseek() can use */
+ sqd_uint64 i64; /* an offset that e.g. fseeko64() can use */
+ } off;
+};
+typedef struct ssioffset_s SSIOFFSET;
+#define SSI_OFFSET_I32 0
+#define SSI_OFFSET_I64 1
+
+/* Structure: SSIFILE
+ * xref: SSI API documentation in ssi-format.tex
+ */
+struct ssifile_s {
+ FILE *fp; /* open SSI index file */
+ sqd_uint32 flags; /* optional behavior flags */
+ sqd_uint16 nfiles; /* number of files = 16 bit int */
+ sqd_uint32 nprimary; /* number of primary keys */
+ sqd_uint32 nsecondary; /* number of secondary keys */
+ sqd_uint32 flen; /* length of filenames (inc '\0') */
+ sqd_uint32 plen; /* length of primary keys (inc '\0') */
+ sqd_uint32 slen; /* length of secondary keys (inc '\0') */
+ sqd_uint32 frecsize; /* # bytes in a file record */
+ sqd_uint32 precsize; /* # bytes in a primary key record */
+ sqd_uint32 srecsize; /* # bytes in a secondary key record */
+ SSIOFFSET foffset; /* disk offset, start of file records */
+ SSIOFFSET poffset; /* disk offset, start of pri key recs */
+ SSIOFFSET soffset; /* disk offset, start of sec key recs */
+
+ char imode; /* mode for index file offsets, 32 v. 64 bit */
+ char smode; /* mode for sequence file offsets, 32 v. 64 bit */
+
+ /* File information:
+ */
+ char **filename; /* list of file names [0..nfiles-1] */
+ sqd_uint32 *fileformat; /* file formats */
+ sqd_uint32 *fileflags; /* optional per-file behavior flags */
+ sqd_uint32 *bpl; /* bytes per line in file */
+ sqd_uint32 *rpl; /* residues per line in file */
+};
+typedef struct ssifile_s SSIFILE;
+
+/* optional per-index behavior flags in SSIFILE structure's flags:
+ */
+#define SSI_USE64 1<<0 /* seq offsets are 64-bit */
+#define SSI_USE64_INDEX 1<<1 /* index file offsets are 64-bit */
+
+/* optional per-file behavior flags in fileflags
+ */
+#define SSI_FAST_SUBSEQ 1<<0 /* can do subseq lookup in this file */
+
+/* Structure: SSIINDEX
+ *
+ * Used when building up an index and writing it to disk
+ */
+struct ssipkey_s { /* Primary key data: */
+ char *key; /* key name */
+ sqd_uint16 fnum; /* file number */
+ SSIOFFSET r_off; /* record offset */
+ SSIOFFSET d_off; /* data offset */
+ sqd_uint32 len; /* sequence length */
+};
+struct ssiskey_s { /* Secondary key data: */
+ char *key; /* secondary key name */
+ char *pkey; /* primary key name */
+};
+struct ssiindex_s {
+ int smode; /* sequence mode: SSI_OFFSET_I32 or _I64 */
+ int imode; /* index mode: SSI_OFFSET_I32 or _I64 */
+ int external; /* TRUE if pkeys and skeys are on disk */
+ int max_ram; /* maximum RAM in MB before switching to external */
+
+ char **filenames;
+ sqd_uint32 *fileformat;
+ sqd_uint32 *bpl;
+ sqd_uint32 *rpl;
+ sqd_uint32 flen; /* length of longest filename, inc '\0' */
+ sqd_uint16 nfiles;
+
+ struct ssipkey_s *pkeys;
+ sqd_uint32 plen; /* length of longest pkey, including '\0' */
+ sqd_uint32 nprimary;
+ char *ptmpfile; /* name of tmp file, for external sort mode */
+ FILE *ptmp; /* handle on open ptmpfile */
+
+ struct ssiskey_s *skeys;
+ sqd_uint32 slen; /* length of longest skey, including '\0' */
+ sqd_uint32 nsecondary;
+ char *stmpfile; /* name of tmp file, for external sort mode */
+ FILE *stmp; /* handle on open ptmpfile */
+};
+typedef struct ssiindex_s SSIINDEX;
+
+/* These control malloc and realloc chunk sizes in the index
+ * construction code.
+ */
+#define SSI_FILE_BLOCK 10
+#define SSI_KEY_BLOCK 100
+
+/* Error codes set by the API
+ */
+#define SSI_ERR_OK 0
+#define SSI_ERR_NODATA 1 /* no data? an fread() failed */
+#define SSI_ERR_NO_SUCH_KEY 2 /* that key's not in the index */
+#define SSI_ERR_MALLOC 3
+#define SSI_ERR_NOFILE 4 /* no such file? an fopen() failed */
+#define SSI_ERR_BADMAGIC 5 /* magic number mismatch in GSIOpen() */
+#define SSI_ERR_BADFORMAT 6 /* didn't read what I expected to fread() */
+#define SSI_ERR_NO64BIT 7 /* needed 64-bit support and didn't have it */
+#define SSI_ERR_SEEK_FAILED 8 /* an fseek() (or similar) failed */
+#define SSI_ERR_TELL_FAILED 9 /* an ftell() (or similar) failed */
+#define SSI_ERR_NO_SUBSEQS 10 /* fast subseq is disallowed */
+#define SSI_ERR_RANGE 11 /* subseq requested is out of range */
+#define SSI_ERR_BADARG 12 /* something wrong with a function argument */
+#define SSI_ERR_TOOMANY_FILES 13 /* ran out of range for files in an index */
+#define SSI_ERR_TOOMANY_KEYS 14 /* ran out of range for keys in an index */
+#define SSI_ERR_FWRITE 15
+#define SSI_ERR_EXTERNAL_SORT 16 /* external sort failed */
+
+/* The SSI file reading API:
+ */
+extern int SSIOpen(char *filename, SSIFILE **ret_sfp);
+extern int SSIGetOffsetByName(SSIFILE *sfp, char *key, int *ret_fh,
+ SSIOFFSET *ret_offset);
+extern int SSIGetOffsetByNumber(SSIFILE *sfp, int n, int *ret_fh,
+ SSIOFFSET *ret_offset);
+extern int SSIGetSubseqOffset(SSIFILE *sfp, char *key, int requested_start,
+ int *ret_fh, SSIOFFSET *record_offset,
+ SSIOFFSET *data_offset, int *ret_actual_start);
+extern int SSISetFilePosition(FILE *fp, SSIOFFSET *offset);
+extern int SSIFileInfo(SSIFILE *sfp, int fh, char **ret_filename, int *ret_format);
+extern void SSIClose(SSIFILE *sfp);
+
+/* The SSI index file writing API:
+ */
+extern int SSIRecommendMode(char *file);
+extern SSIINDEX *SSICreateIndex(int mode);
+extern int SSIGetFilePosition(FILE *fp, int mode, SSIOFFSET *ret_offset);
+extern int SSIAddFileToIndex(SSIINDEX *g, char *filename, int fmt, int *ret_fh);
+extern int SSISetFileForSubseq(SSIINDEX *g, int fh, int bpl, int rpl);
+extern int SSIAddPrimaryKeyToIndex(SSIINDEX *g, char *key, int fh,
+ SSIOFFSET *r_off, SSIOFFSET *d_off,
+ int L);
+extern int SSIAddSecondaryKeyToIndex(SSIINDEX *g, char *key, char *pkey);
+extern int SSIWriteIndex(char *file, SSIINDEX *g);
+extern void SSIFreeIndex(SSIINDEX *g);
+
+/* The SSI misc. functions API:
+ */
+extern char *SSIErrorString(int n);
+
+/* The SSI debugging API:
+ */
+extern void SSIForceExternalSort(SSIINDEX *g);
+
+#endif /*SSIH_INCLUDED*/
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* stack.c
+ * SRE, Thu Mar 3 10:08:48 1994
+ *
+ * Implementation of generic stack structures.
+ * RCS $Id: stack.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: stack.c,v 1.2 1998/10/09 18:07:16 eddy Exp)
+ */
+
+#include <stdlib.h>
+#include "squid.h"
+
+#ifdef MEMDEBUG
+#include "dbmalloc.h"
+#endif
+
+
+/************************************************************
+ * intstack_s implementation.
+ *
+ * Functions: InitIntStack() - returns ptr to new stack
+ * PushIntStack() - (void)
+ * PopIntStack() - returns 1 on success, 0 if stack empty
+ * FreeIntStack() - returns number of elements free'd, or 0 if
+ * stack was empty.
+ *
+ * Implementation of the pushdown stack for storing single
+ * integers.
+ *************************************************************/
+struct intstack_s *
+InitIntStack(void)
+{
+ struct intstack_s *stack;
+
+ if ((stack = (struct intstack_s *) malloc (sizeof(struct intstack_s))) == NULL)
+ Die("Memory allocation failure at %s line %d", __FILE__, __LINE__);
+ stack->nxt = NULL;
+ return stack;
+}
+void
+PushIntStack(struct intstack_s *stack, int data)
+{
+ struct intstack_s *new;
+
+ if ((new = (struct intstack_s *) malloc (sizeof(struct intstack_s))) == NULL)
+ Die("Memory allocation failure at %s line %d", __FILE__, __LINE__);
+ new->data = data;
+
+ new->nxt = stack->nxt;
+ stack->nxt = new;
+}
+
+int
+PopIntStack(struct intstack_s *stack, int *ret_data)
+{
+ struct intstack_s *old;
+
+ if (stack->nxt == NULL) return 0;
+
+ old = stack->nxt;
+ stack->nxt = old->nxt;
+
+ *ret_data = old->data;
+ free(old);
+ return 1;
+}
+
+void
+ReverseIntStack(struct intstack_s *stack)
+{
+ struct intstack_s *old;
+ struct intstack_s *new;
+
+ old = stack->nxt;
+ stack->nxt = NULL;
+ while (old != NULL)
+ {
+ new = old; /* remove one from top of old stack */
+ old = old->nxt;
+ new->nxt = stack->nxt; /* push it onto new stack */
+ stack->nxt = new;
+ }
+}
+
+int
+FreeIntStack( struct intstack_s *stack )
+{
+ int data;
+ int count = 0;
+
+ while (PopIntStack(stack, &data))
+ count++;
+ free(stack);
+ return count;
+}
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* stockholm.c
+ * SRE, Fri May 28 15:46:41 1999
+ *
+ * Reading/writing of Stockholm format multiple sequence alignments.
+ *
+ * example of API:
+ *
+ * MSA *msa;
+ * FILE *fp; -- opened for write with fopen()
+ * MSAFILE *afp; -- opened for read with MSAFileOpen()
+ *
+ * while ((msa = ReadStockholm(afp)) != NULL)
+ * {
+ * WriteStockholm(fp, msa);
+ * MSAFree(msa);
+ * }
+ *
+ * RCS $Id: stockholm.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: stockholm.c,v 1.7 2002/10/12 04:40:36 eddy Exp)
+ */
+#include <stdio.h>
+#include <string.h>
+#include "squid.h"
+#include "msa.h"
+
+static int parse_gf(MSA *msa, char *buf);
+static int parse_gs(MSA *msa, char *buf);
+static int parse_gc(MSA *msa, char *buf);
+static int parse_gr(MSA *msa, char *buf);
+static int parse_comment(MSA *msa, char *buf);
+static int parse_sequence(MSA *msa, char *buf);
+static void actually_write_stockholm(FILE *fp, MSA *msa, int cpl);
+
+#ifdef TESTDRIVE_STOCKHOLM
+/*****************************************************************
+ * stockholm.c test driver:
+ * cc -DTESTDRIVE_STOCKHOLM -g -O2 -Wall -o test stockholm.c msa.c gki.c sqerror.c sre_string.c file.c hsregex.c sre_math.c sre_ctype.c -lm
+ *
+ */
+int
+main(int argc, char **argv)
+{
+ MSAFILE *afp;
+ MSA *msa;
+ char *file;
+
+ file = argv[1];
+
+ if ((afp = MSAFileOpen(file, MSAFILE_STOCKHOLM, NULL)) == NULL)
+ Die("Couldn't open %s\n", file);
+
+ while ((msa = ReadStockholm(afp)) != NULL)
+ {
+ WriteStockholm(stdout, msa);
+ MSAFree(msa);
+ }
+
+ MSAFileClose(afp);
+ exit(0);
+}
+/******************************************************************/
+#endif /* testdriver */
+
+
+/* Function: ReadStockholm()
+ * Date: SRE, Fri May 21 17:33:10 1999 [St. Louis]
+ *
+ * Purpose: Parse the next alignment from an open Stockholm
+ * format alignment file. Return the alignment, or
+ * NULL if there are no more alignments in the file.
+ *
+ * Args: afp - open alignment file
+ *
+ * Returns: MSA * - an alignment object.
+ * caller responsible for an MSAFree()
+ * NULL if no more alignments
+ *
+ * Diagnostics:
+ * Will Die() here with a (potentially) useful message
+ * if a parsing error occurs
+ */
+MSA *
+ReadStockholm(MSAFILE *afp)
+{
+ MSA *msa;
+ char *s;
+ int status;
+
+ if (feof(afp->f)) return NULL;
+
+ /* Initialize allocation of the MSA.
+ */
+ msa = MSAAlloc(10, 0);
+
+ /* Check the magic Stockholm header line.
+ * We have to skip blank lines here, else we perceive
+ * trailing blank lines in a file as a format error when
+ * reading in multi-record mode.
+ */
+ do {
+ if ((s = MSAFileGetLine(afp)) == NULL) {
+ MSAFree(msa);
+ return NULL;
+ }
+ } while (IsBlankline(s));
+
+ if (strncmp(s, "# STOCKHOLM 1.", 14) != 0)
+ Die("\
+File %s doesn't appear to be in Stockholm format.\n\
+Assuming there isn't some other problem with your file (it is an\n\
+alignment file, right?), please either:\n\
+ a) use the Babelfish format autotranslator option (-B, usually);\n\
+ b) specify the file's format with the --informat option; or\n\
+ a) reformat the alignment to Stockholm format.\n",
+ afp->fname);
+
+ /* Read the alignment file one line at a time.
+ */
+ while ((s = MSAFileGetLine(afp)) != NULL)
+ {
+ while (*s == ' ' || *s == '\t') s++; /* skip leading whitespace */
+
+ if (*s == '#') {
+ if (strncmp(s, "#=GF", 4) == 0) status = parse_gf(msa, s);
+ else if (strncmp(s, "#=GS", 4) == 0) status = parse_gs(msa, s);
+ else if (strncmp(s, "#=GC", 4) == 0) status = parse_gc(msa, s);
+ else if (strncmp(s, "#=GR", 4) == 0) status = parse_gr(msa, s);
+ else status = parse_comment(msa, s);
+ }
+ else if (strncmp(s, "//", 2) == 0) break;
+ else if (*s == '\n') continue;
+ else status = parse_sequence(msa, s);
+
+ if (status == 0)
+ Die("Stockholm format parse error: line %d of file %s while reading alignment %s",
+ afp->linenumber, afp->fname, msa->name == NULL? "" : msa->name);
+ }
+
+ if (s == NULL && msa->nseq != 0)
+ Die ("Didn't find // at end of alignment %s", msa->name == NULL ? "" : msa->name);
+
+ if (s == NULL && msa->nseq == 0) {
+ /* probably just some junk at end of file */
+ MSAFree(msa);
+ return NULL;
+ }
+
+ MSAVerifyParse(msa);
+ return msa;
+}
+
+
+/* Function: WriteStockholm()
+ * Date: SRE, Mon May 31 19:15:22 1999 [St. Louis]
+ *
+ * Purpose: Write an alignment in standard multi-block
+ * Stockholm format to an open file. A wrapper
+ * for actually_write_stockholm().
+ *
+ * Args: fp - file that's open for writing
+ * msa - alignment to write
+ *
+ * Returns: (void)
+ */
+void
+WriteStockholm(FILE *fp, MSA *msa)
+{
+ actually_write_stockholm(fp, msa, 50); /* 50 char per block */
+}
+
+/* Function: WriteStockholmOneBlock()
+ * Date: SRE, Mon May 31 19:15:22 1999 [St. Louis]
+ *
+ * Purpose: Write an alignment in Pfam's single-block
+ * Stockholm format to an open file. A wrapper
+ * for actually_write_stockholm().
+ *
+ * Args: fp - file that's open for writing
+ * msa - alignment to write
+ *
+ * Returns: (void)
+ */
+void
+WriteStockholmOneBlock(FILE *fp, MSA *msa)
+{
+ actually_write_stockholm(fp, msa, msa->alen); /* one big block */
+}
+
+
+/* Function: actually_write_stockholm()
+ * Date: SRE, Fri May 21 17:39:22 1999 [St. Louis]
+ *
+ * Purpose: Write an alignment in Stockholm format to
+ * an open file. This is the function that actually
+ * does the work. The API's WriteStockholm()
+ * and WriteStockholmOneBlock() are wrappers.
+ *
+ * Args: fp - file that's open for writing
+ * msa - alignment to write
+ * cpl - characters to write per line in alignment block
+ *
+ * Returns: (void)
+ */
+static void
+actually_write_stockholm(FILE *fp, MSA *msa, int cpl)
+{
+ int i, j;
+ int len = 0;
+ int namewidth;
+ int typewidth = 0; /* markup tags are up to 5 chars long */
+ int markupwidth = 0; /* #=GR, #=GC are four char wide + 1 space */
+ char *buf;
+ int currpos;
+ char *s, *tok;
+
+ /* Figure out how much space we need for name + markup
+ * to keep the alignment in register. Required by Stockholm
+ * spec, even though our Stockholm parser doesn't care (Erik's does).
+ */
+ namewidth = 0;
+ for (i = 0; i < msa->nseq; i++)
+ if ((len = strlen(msa->sqname[i])) > namewidth)
+ namewidth = len;
+
+ /* Figure out how much space we need for markup tags
+ * markupwidth = always 4 if we're doing markup: strlen("#=GR")
+ * typewidth = longest markup tag
+ */
+ if (msa->ss != NULL) { markupwidth = 4; typewidth = 2; }
+ if (msa->sa != NULL) { markupwidth = 4; typewidth = 2; }
+ for (i = 0; i < msa->ngr; i++)
+ if ((len = strlen(msa->gr_tag[i])) > typewidth) typewidth = len;
+
+ if (msa->rf != NULL) { markupwidth = 4; if (typewidth < 2) typewidth = 2; }
+ if (msa->ss_cons != NULL) { markupwidth = 4; if (typewidth < 7) typewidth = 7; }
+ if (msa->sa_cons != NULL) { markupwidth = 4; if (typewidth < 7) typewidth = 7; }
+ for (i = 0; i < msa->ngc; i++)
+ if ((len = strlen(msa->gc_tag[i])) > typewidth) typewidth = len;
+
+ buf = MallocOrDie(sizeof(char) * (cpl+namewidth+typewidth+markupwidth+61));
+
+ /* Magic Stockholm header
+ */
+ fprintf(fp, "# STOCKHOLM 1.0\n");
+
+ /* Free text comments
+ */
+ for (i = 0; i < msa->ncomment; i++)
+ fprintf(fp, "# %s\n", msa->comment[i]);
+ if (msa->ncomment > 0) fprintf(fp, "\n");
+
+ /* GF section: per-file annotation
+ */
+ if (msa->name != NULL) fprintf(fp, "#=GF ID %s\n", msa->name);
+ if (msa->acc != NULL) fprintf(fp, "#=GF AC %s\n", msa->acc);
+ if (msa->desc != NULL) fprintf(fp, "#=GF DE %s\n", msa->desc);
+ if (msa->au != NULL) fprintf(fp, "#=GF AU %s\n", msa->au);
+
+ /* Thresholds are hacky. Pfam has two. Rfam has one.
+ */
+ if (msa->cutoff_is_set[MSA_CUTOFF_GA1] && msa->cutoff_is_set[MSA_CUTOFF_GA2])
+ fprintf(fp, "#=GF GA %.1f %.1f\n", msa->cutoff[MSA_CUTOFF_GA1], msa->cutoff[MSA_CUTOFF_GA2]);
+ else if (msa->cutoff_is_set[MSA_CUTOFF_GA1])
+ fprintf(fp, "#=GF GA %.1f\n", msa->cutoff[MSA_CUTOFF_GA1]);
+ if (msa->cutoff_is_set[MSA_CUTOFF_NC1] && msa->cutoff_is_set[MSA_CUTOFF_NC2])
+ fprintf(fp, "#=GF NC %.1f %.1f\n", msa->cutoff[MSA_CUTOFF_NC1], msa->cutoff[MSA_CUTOFF_NC2]);
+ else if (msa->cutoff_is_set[MSA_CUTOFF_NC1])
+ fprintf(fp, "#=GF NC %.1f\n", msa->cutoff[MSA_CUTOFF_NC1]);
+ if (msa->cutoff_is_set[MSA_CUTOFF_TC1] && msa->cutoff_is_set[MSA_CUTOFF_TC2])
+ fprintf(fp, "#=GF TC %.1f %.1f\n", msa->cutoff[MSA_CUTOFF_TC1], msa->cutoff[MSA_CUTOFF_TC2]);
+ else if (msa->cutoff_is_set[MSA_CUTOFF_TC1])
+ fprintf(fp, "#=GF TC %.1f\n", msa->cutoff[MSA_CUTOFF_TC1]);
+
+ for (i = 0; i < msa->ngf; i++)
+ fprintf(fp, "#=GF %-5s %s\n", msa->gf_tag[i], msa->gf[i]);
+ fprintf(fp, "\n");
+
+
+ /* GS section: per-sequence annotation
+ */
+ if (msa->flags & MSA_SET_WGT)
+ {
+ for (i = 0; i < msa->nseq; i++)
+ fprintf(fp, "#=GS %-*.*s WT %.2f\n", namewidth, namewidth, msa->sqname[i], msa->wgt[i]);
+ fprintf(fp, "\n");
+ }
+ if (msa->sqacc != NULL)
+ {
+ for (i = 0; i < msa->nseq; i++)
+ if (msa->sqacc[i] != NULL)
+ fprintf(fp, "#=GS %-*.*s AC %s\n", namewidth, namewidth, msa->sqname[i], msa->sqacc[i]);
+ fprintf(fp, "\n");
+ }
+ if (msa->sqdesc != NULL)
+ {
+ for (i = 0; i < msa->nseq; i++)
+ if (msa->sqdesc[i] != NULL)
+ fprintf(fp, "#=GS %*.*s DE %s\n", namewidth, namewidth, msa->sqname[i], msa->sqdesc[i]);
+ fprintf(fp, "\n");
+ }
+ for (i = 0; i < msa->ngs; i++)
+ {
+ /* Multiannotated GS tags are possible; for example,
+ * #=GS foo DR PDB; 1xxx;
+ * #=GS foo DR PDB; 2yyy;
+ * These are stored, for example, as:
+ * msa->gs[0][0] = "PDB; 1xxx;\nPDB; 2yyy;"
+ * and must be decomposed.
+ */
+ for (j = 0; j < msa->nseq; j++)
+ if (msa->gs[i][j] != NULL)
+ {
+ s = msa->gs[i][j];
+ while ((tok = sre_strtok(&s, "\n", NULL)) != NULL)
+ fprintf(fp, "#=GS %*.*s %5s %s\n", namewidth, namewidth,
+ msa->sqname[j], msa->gs_tag[i], tok);
+ }
+ fprintf(fp, "\n");
+ }
+
+ /* Alignment section:
+ * contains aligned sequence, #=GR annotation, and #=GC annotation
+ */
+ for (currpos = 0; currpos < msa->alen; currpos += cpl)
+ {
+ if (currpos > 0) fprintf(fp, "\n");
+ for (i = 0; i < msa->nseq; i++)
+ {
+ strncpy(buf, msa->aseq[i] + currpos, cpl);
+ buf[cpl] = '\0';
+ fprintf(fp, "%-*.*s %s\n", namewidth+typewidth+markupwidth, namewidth+typewidth+markupwidth,
+ msa->sqname[i], buf);
+
+ if (msa->ss != NULL && msa->ss[i] != NULL) {
+ strncpy(buf, msa->ss[i] + currpos, cpl);
+ buf[cpl] = '\0';
+ fprintf(fp, "#=GR %-*.*s SS %s\n", namewidth, namewidth, msa->sqname[i], buf);
+ }
+ if (msa->sa != NULL && msa->sa[i] != NULL) {
+ strncpy(buf, msa->sa[i] + currpos, cpl);
+ buf[cpl] = '\0';
+ fprintf(fp, "#=GR %-*.*s SA %s\n", namewidth, namewidth, msa->sqname[i], buf);
+ }
+ for (j = 0; j < msa->ngr; j++)
+ if (msa->gr[j][i] != NULL) {
+ strncpy(buf, msa->gr[j][i] + currpos, cpl);
+ buf[cpl] = '\0';
+ fprintf(fp, "#=GR %-*.*s %5s %s\n",
+ namewidth, namewidth, msa->sqname[i], msa->gr_tag[j], buf);
+ }
+ }
+ if (msa->ss_cons != NULL) {
+ strncpy(buf, msa->ss_cons + currpos, cpl);
+ buf[cpl] = '\0';
+ fprintf(fp, "#=GC %-*.*s %s\n", namewidth+typewidth, namewidth+typewidth, "SS_cons", buf);
+ }
+
+ if (msa->sa_cons != NULL) {
+ strncpy(buf, msa->sa_cons + currpos, cpl);
+ buf[cpl] = '\0';
+ fprintf(fp, "#=GC %-*.*s %s\n", namewidth+typewidth, namewidth+typewidth, "SA_cons", buf);
+ }
+
+ if (msa->rf != NULL) {
+ strncpy(buf, msa->rf + currpos, cpl);
+ buf[cpl] = '\0';
+ fprintf(fp, "#=GC %-*.*s %s\n", namewidth+typewidth, namewidth+typewidth, "RF", buf);
+ }
+ for (j = 0; j < msa->ngc; j++) {
+ strncpy(buf, msa->gc[j] + currpos, cpl);
+ buf[cpl] = '\0';
+ fprintf(fp, "#=GC %-*.*s %s\n", namewidth+typewidth, namewidth+typewidth,
+ msa->gc_tag[j], buf);
+ }
+ }
+ fprintf(fp, "//\n");
+ free(buf);
+}
+
+
+
+
+
+/* Format of a GF line:
+ * #=GF <featurename> <text>
+ */
+static int
+parse_gf(MSA *msa, char *buf)
+{
+ char *gf;
+ char *featurename;
+ char *text;
+ char *s;
+
+ s = buf;
+ if ((gf = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
+ if ((featurename = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
+ if ((text = sre_strtok(&s, "\n", NULL)) == NULL) return 0;
+ while (*text && (*text == ' ' || *text == '\t')) text++;
+
+ if (strcmp(featurename, "ID") == 0)
+ msa->name = sre_strdup(text, -1);
+ else if (strcmp(featurename, "AC") == 0)
+ msa->acc = sre_strdup(text, -1);
+ else if (strcmp(featurename, "DE") == 0)
+ msa->desc = sre_strdup(text, -1);
+ else if (strcmp(featurename, "AU") == 0)
+ msa->au = sre_strdup(text, -1);
+ else if (strcmp(featurename, "GA") == 0)
+ { /* Pfam has GA1, GA2. Rfam just has GA1. */
+ s = text;
+ if ((text = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
+ msa->cutoff[MSA_CUTOFF_GA1] = atof(text);
+ msa->cutoff_is_set[MSA_CUTOFF_GA1] = TRUE;
+ if ((text = sre_strtok(&s, WHITESPACE, NULL)) != NULL) {
+ msa->cutoff[MSA_CUTOFF_GA2] = atof(text);
+ msa->cutoff_is_set[MSA_CUTOFF_GA2] = TRUE;
+ }
+ }
+ else if (strcmp(featurename, "NC") == 0)
+ {
+ s = text;
+ if ((text = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
+ msa->cutoff[MSA_CUTOFF_NC1] = atof(text);
+ msa->cutoff_is_set[MSA_CUTOFF_NC1] = TRUE;
+ if ((text = sre_strtok(&s, WHITESPACE, NULL)) != NULL) {
+ msa->cutoff[MSA_CUTOFF_NC2] = atof(text);
+ msa->cutoff_is_set[MSA_CUTOFF_NC2] = TRUE;
+ }
+ }
+ else if (strcmp(featurename, "TC") == 0)
+ {
+ s = text;
+ if ((text = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
+ msa->cutoff[MSA_CUTOFF_TC1] = atof(text);
+ msa->cutoff_is_set[MSA_CUTOFF_TC1] = TRUE;
+ if ((text = sre_strtok(&s, WHITESPACE, NULL)) != NULL) {
+ msa->cutoff[MSA_CUTOFF_TC2] = atof(text);
+ msa->cutoff_is_set[MSA_CUTOFF_TC2] = TRUE;
+ }
+ }
+ else
+ MSAAddGF(msa, featurename, text);
+
+ return 1;
+}
+
+
+/* Format of a GS line:
+ * #=GS <seqname> <featurename> <text>
+ */
+static int
+parse_gs(MSA *msa, char *buf)
+{
+ char *gs;
+ char *seqname;
+ char *featurename;
+ char *text;
+ int seqidx;
+ char *s;
+
+ s = buf;
+ if ((gs = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
+ if ((seqname = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
+ if ((featurename = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
+ if ((text = sre_strtok(&s, "\n", NULL)) == NULL) return 0;
+ while (*text && (*text == ' ' || *text == '\t')) text++;
+
+ /* GS usually follows another GS; guess lastidx+1
+ */
+ seqidx = MSAGetSeqidx(msa, seqname, msa->lastidx+1);
+ msa->lastidx = seqidx;
+
+ if (strcmp(featurename, "WT") == 0)
+ {
+ msa->wgt[seqidx] = atof(text);
+ msa->flags |= MSA_SET_WGT;
+ }
+
+ else if (strcmp(featurename, "AC") == 0)
+ MSASetSeqAccession(msa, seqidx, text);
+
+ else if (strcmp(featurename, "DE") == 0)
+ MSASetSeqDescription(msa, seqidx, text);
+
+ else
+ MSAAddGS(msa, featurename, seqidx, text);
+
+ return 1;
+}
+
+/* Format of a GC line:
+ * #=GC <featurename> <text>
+ */
+static int
+parse_gc(MSA *msa, char *buf)
+{
+ char *gc;
+ char *featurename;
+ char *text;
+ char *s;
+ int len;
+
+ s = buf;
+ if ((gc = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
+ if ((featurename = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
+ if ((text = sre_strtok(&s, WHITESPACE, &len)) == NULL) return 0;
+
+ if (strcmp(featurename, "SS_cons") == 0)
+ sre_strcat(&(msa->ss_cons), -1, text, len);
+ else if (strcmp(featurename, "SA_cons") == 0)
+ sre_strcat(&(msa->sa_cons), -1, text, len);
+ else if (strcmp(featurename, "RF") == 0)
+ sre_strcat(&(msa->rf), -1, text, len);
+ else
+ MSAAppendGC(msa, featurename, text);
+
+ return 1;
+}
+
+/* Format of a GR line:
+ * #=GR <seqname> <featurename> <text>
+ */
+static int
+parse_gr(MSA *msa, char *buf)
+{
+ char *gr;
+ char *seqname;
+ char *featurename;
+ char *text;
+ int seqidx;
+ int len;
+ int j;
+ char *s;
+
+ s = buf;
+ if ((gr = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
+ if ((seqname = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
+ if ((featurename = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
+ if ((text = sre_strtok(&s, WHITESPACE, &len)) == NULL) return 0;
+
+ /* GR usually follows sequence it refers to; guess msa->lastidx */
+ seqidx = MSAGetSeqidx(msa, seqname, msa->lastidx);
+ msa->lastidx = seqidx;
+
+ if (strcmp(featurename, "SS") == 0)
+ {
+ if (msa->ss == NULL)
+ {
+ msa->ss = MallocOrDie(sizeof(char *) * msa->nseqalloc);
+ msa->sslen = MallocOrDie(sizeof(int) * msa->nseqalloc);
+ for (j = 0; j < msa->nseqalloc; j++)
+ {
+ msa->ss[j] = NULL;
+ msa->sslen[j] = 0;
+ }
+ }
+ msa->sslen[seqidx] = sre_strcat(&(msa->ss[seqidx]), msa->sslen[seqidx], text, len);
+ }
+ else if (strcmp(featurename, "SA") == 0)
+ {
+ if (msa->sa == NULL)
+ {
+ msa->sa = MallocOrDie(sizeof(char *) * msa->nseqalloc);
+ msa->salen = MallocOrDie(sizeof(int) * msa->nseqalloc);
+ for (j = 0; j < msa->nseqalloc; j++)
+ {
+ msa->sa[j] = NULL;
+ msa->salen[j] = 0;
+ }
+ }
+ msa->salen[seqidx] = sre_strcat(&(msa->sa[seqidx]), msa->salen[seqidx], text, len);
+ }
+ else
+ MSAAppendGR(msa, featurename, seqidx, text);
+
+ return 1;
+}
+
+
+/* comments are simply stored verbatim, not parsed
+ */
+static int
+parse_comment(MSA *msa, char *buf)
+{
+ char *s;
+ char *comment;
+
+ s = buf + 1; /* skip leading '#' */
+ if (*s == '\n') { *s = '\0'; comment = s; } /* deal with blank comment */
+ else if ((comment = sre_strtok(&s, "\n", NULL)) == NULL) return 0;
+
+ MSAAddComment(msa, comment);
+ return 1;
+}
+
+static int
+parse_sequence(MSA *msa, char *buf)
+{
+ char *s;
+ char *seqname;
+ char *text;
+ int seqidx;
+ int len;
+
+ s = buf;
+ if ((seqname = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0;
+ if ((text = sre_strtok(&s, WHITESPACE, &len)) == NULL) return 0;
+
+ /* seq usually follows another seq; guess msa->lastidx +1 */
+ seqidx = MSAGetSeqidx(msa, seqname, msa->lastidx+1);
+ msa->lastidx = seqidx;
+
+ msa->sqlen[seqidx] = sre_strcat(&(msa->aseq[seqidx]), msa->sqlen[seqidx], text, len);
+ return 1;
+}
+
+
+
--- /dev/null
+#ifndef STOCKHOLM_H_INCLUDED
+#define STOCKHOLM_H_INCLUDED
+
+#include "gki.h"
+
+typedef struct {
+ int *linetype; /* e.g. STOCKHOLM_GF_LINE; always valid */
+ int *featurecode; /* all markup codes: e.g. STOCKHOLM_GF_ID;
+ nonmarkup: always set to STOCKHOLM_UNPARSED */
+ char **featurename; /* all unparsed markup codes: string, e.g. "ID";
+ all other lines: NULL */
+ int *seqidx; /* all GS, GR, GC, sequence lines: which sequence;
+ other lines: 0 */
+ int *len; /* all GR, GC, sequence lines: length of text field;
+ other lines: 0 */
+ char **text; /* all unparsed nonblank lines: rest of data
+ other lines: NULL */
+ int nseqalloc; /* current nseqs allocated for in aseqs and ainfo */
+ int nlines; /* number of lines in this skel */
+ int nlinealloc; /* current # of lines allocated for in this skel */
+ int overall_line; /* line # in file (important in files w/ >1 ali)*/
+} alifile_skeleton;
+
+#define STOCKHOLM_GF_LINE 0
+#define STOCKHOLM_GS_LINE 1
+#define STOCKHOLM_GC_LINE 2
+#define STOCKHOLM_GR_LINE 3
+#define STOCKHOLM_SEQ_LINE 4
+#define STOCKHOLM_BLANK_LINE 5
+#define STOCKHOLM_COMMENT_LINE 6
+
+#define STOCKHOLM_UNPARSED 0
+#define STOCKHOLM_GF_ID 1
+#define STOCKHOLM_GF_AC 2
+#define STOCKHOLM_GF_DE 3
+#define STOCKHOLM_GF_AU 4
+#define STOCKHOLM_GF_GA 5
+#define STOCKHOLM_GF_NC 6
+#define STOCKHOLM_GF_TC 7
+#define STOCKHOLM_GS_WT 100
+#define STOCKHOLM_GS_AC 101
+#define STOCKHOLM_GS_DE 102
+#define STOCKHOLM_GC_CS 200
+#define STOCKHOLM_GC_RF 201
+#define STOCKHOLM_GR_SS 300
+#define STOCKHOLM_GR_SA 301
+
+#define SKEL_NSEQLUMP 10 /* allocate for new seqs in blocks of this size */
+#define SKEL_LUMPSIZE 100 /* allocate for new lines in skel in blocks of this size */
+
+#endif /*STOCKHOLM_H_INCLUDED*/
--- /dev/null
+/************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ ************************************************************/
+
+/* stopwatch.c
+ * SRE, Fri Nov 26 14:54:21 1999 [St. Louis] [HMMER]
+ * SRE, Thu Aug 3 08:11:52 2000 [St. Louis] [moved to SQUID]
+ *
+ * Reporting of cpu/system/elapsed time used by a process.
+ * thanks to Warren Gish for assistance.
+ *
+ * Basic API:
+ *
+ * Stopwatch_t *w;
+ * w = StopwatchCreate();
+ *
+ * StopwatchStart(w);
+ * do_lots_of_stuff;
+ * StopwatchStop(w);
+ * StopwatchDisplay(stdout, "CPU time: ", w);
+ *
+ * StopwatchFree(w);
+ *
+ * Some behavior can be controlled at compile time by #define's:
+ *
+ * SRE_STRICT_ANSI: By default, stopwatch module assumes that a
+ * machine is POSIX-compliant (e.g. has struct tms, sys/times.h,
+ * and times()). If compiled with -DSRE_STRICT_ANSI, reverts to
+ * pure ANSI C conformant implementation. This simpler system
+ * won't report system times, only user and elapsed times.
+ *
+ * SRE_ENABLE_PVM: If compiled with -DSRE_ENABLE_PVM, the
+ * functions StopwatchPVMPack() and StopwatchPVMUnpack()
+ * are compiled, providing PVM communications ability.
+ *
+ * One additional compile-time configuration note:
+ * PTHREAD_TIMES_HACK: Linux pthreads, as of RH6.0/glibc-devel-2.1.1-6,
+ * appears to interact poorly with times() -- usage times in all
+ * but the master thread are lost. A workaround for this bug is
+ * to run stopwatches in each worker thread, and accumulate those
+ * times back into the master stopwatch using StopwatchInclude().
+ * (Just like a PVM implementation has to do.) In HMMER, this
+ * behavior is compiled in with -DPTHREAD_TIMES_HACK. No
+ * changes are made in stopwatch functions themselves, though;
+ * all the extra code is HMMER code. See hmmcalibrate.c for
+ * an example.
+ *
+ * See hmmcalibrate.c for examples of more complex usage
+ * in dealing with pthreads and PVM.
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#ifdef SRE_ENABLE_PVM
+#include <pvm3.h>
+#endif
+
+#include "stopwatch.h"
+
+/* Function: format_time_string()
+ * Date: SRE, Fri Nov 26 15:06:28 1999 [St. Louis]
+ *
+ * Purpose: Given a number of seconds, format into
+ * hh:mm:ss.xx in a provided buffer.
+ *
+ * Args: buf - allocated space (128 is plenty!)
+ * sec - number of seconds
+ * do_frac - TRUE (1) to include hundredths of a sec
+ */
+static void
+format_time_string(char *buf, double sec, int do_frac)
+{
+ int h, m, s, hs;
+
+ h = (int) (sec / 3600.);
+ m = (int) (sec / 60.) - h * 60;
+ s = (int) (sec) - h * 3600 - m * 60;
+ if (do_frac) {
+ hs = (int) (sec * 100.) - h * 360000 - m * 6000 - s * 100;
+ sprintf(buf, "%02d:%02d:%02d.%02d", h,m,s,hs);
+ } else {
+ sprintf(buf, "%02d:%02d:%02d", h,m,s);
+ }
+}
+
+/* Function: StopwatchStart()
+ * Date: SRE, Fri Nov 26 15:07:48 1999 [St. Louis]
+ *
+ * Purpose: Start a stopwatch.
+ *
+ * Args: w - the watch
+ */
+void
+StopwatchStart(Stopwatch_t *w)
+{
+ w->t0 = time(NULL);
+#ifdef SRE_STRICT_ANSI
+ w->cpu0 = clock();
+#else
+ (void) times(&(w->cpu0));
+#endif
+
+ w->elapsed = 0.;
+ w->user = 0.;
+ w->sys = 0.;
+}
+
+/* Function: StopwatchStop()
+ * Date: SRE, Fri Nov 26 15:08:16 1999 [St. Louis]
+ *
+ * Purpose: Stop a stopwatch.
+ *
+ * The implementation allows "split times":
+ * you can stop a watch multiple times, reporting
+ * times at multiple points during program
+ * execution.
+ *
+ * Args: w - the watch
+ */
+void
+StopwatchStop(Stopwatch_t *w)
+{
+ time_t t1;
+#ifdef SRE_STRICT_ANSI
+ clock_t cpu1;
+#else
+ struct tms cpu1;
+ long clk_tck;
+#endif
+
+ t1 = time(NULL);
+ w->elapsed = difftime(t1, w->t0);
+
+#ifdef SRE_STRICT_ANSI
+ cpu1 = clock();
+ w->user = (double) (cpu1- w->cpu0) / (double) CLOCKS_PER_SEC;
+ w->sys = 0.; /* no way to portably get system time in ANSI C */
+
+#else /* assume we're on a POSIX system by default */
+ (void) times(&cpu1);
+
+ clk_tck = sysconf(_SC_CLK_TCK);
+ w->user = (double) (cpu1.tms_utime + cpu1.tms_cutime -
+ w->cpu0.tms_utime - w->cpu0.tms_cutime) /
+ (double) clk_tck;
+
+ w->sys = (double) (cpu1.tms_stime + cpu1.tms_cstime -
+ w->cpu0.tms_stime - w->cpu0.tms_cstime) /
+ (double) clk_tck;
+#endif
+}
+
+/* Function: StopwatchInclude()
+ * Date: SRE, Fri Nov 26 15:09:34 1999 [St. Louis]
+ *
+ * Purpose: Merge the cpu and system times from a slave into
+ * a master stopwatch. Both watches must be
+ * stopped, and should not be stopped again unless
+ * You Know What You're Doing.
+ *
+ * Elapsed time is *not* merged; master is assumed
+ * to be keeping track of the wall clock time,
+ * and the slave/worker watch is ignored.
+ *
+ * Used in two cases:
+ * 1) PVM; merge in the stopwatch(es) from separate
+ * process(es) in a cluster.
+ * 2) Threads, for broken pthreads/times() implementations
+ * that lose track of cpu times used by spawned
+ * threads.
+ *
+ * Args: w1 - the master stopwatch
+ * w2 - the slave/worker watch
+ *
+ */
+void
+StopwatchInclude(Stopwatch_t *w1, Stopwatch_t *w2)
+{
+ w1->user += w2->user;
+ w1->sys += w2->sys;
+}
+
+/* Function: StopwatchAlloc(), StopwatchZero(), StopwatchCopy(),
+ * StopwatchFree()
+ * Date: SRE, Fri Nov 26 15:13:14 1999 [St. Louis]
+ *
+ * Purpose: The usual creation/manipulation/destruction routines
+ * for a stopwatch object.
+ */
+Stopwatch_t *
+StopwatchCreate(void)
+{
+ Stopwatch_t *w;
+ w = malloc(sizeof(Stopwatch_t));
+ return w;
+}
+void
+StopwatchZero(Stopwatch_t *w)
+{
+ w->elapsed = 0.;
+ w->user = 0.;
+ w->sys = 0.;
+}
+void
+StopwatchCopy(Stopwatch_t *w1, Stopwatch_t *w2)
+{
+ w1->t0 = w2->t0;
+#ifdef SRE_STRICT_ANSI
+ w1->cpu0 = w2->cpu0;
+#else
+ w1->cpu0.tms_utime = w2->cpu0.tms_utime;
+ w1->cpu0.tms_stime = w2->cpu0.tms_stime;
+ w1->cpu0.tms_cutime = w2->cpu0.tms_cutime;
+ w1->cpu0.tms_cstime = w2->cpu0.tms_cstime;
+#endif
+ w1->elapsed = w2->elapsed;
+ w1->user = w2->user;
+ w1->sys = w2->sys;
+}
+void
+StopwatchFree(Stopwatch_t *w)
+{
+ free(w);
+}
+
+
+/* Function: StopwatchDisplay()
+ * Date: SRE, Fri Nov 26 15:14:12 1999 [St. Louis]
+ *
+ * Purpose: Output a usage summary line from a *stopped*
+ * stopwatch (the times will reflect the last
+ * time StopwatchStop() was called.)
+ *
+ * For s = "CPU Time: " an example output line is:
+ * CPU Time: 142.55u 7.17s 149.72 Elapsed: 00:02:35.00
+ *
+ * Args: fp - open file for writing (stdout, possibly)
+ * s - prefix for the report line
+ * w - a (recently stopped) stopwatch
+ *
+ */
+void
+StopwatchDisplay(FILE *fp, char *s, Stopwatch_t *w)
+{
+ char buf[128]; /* (safely holds up to 10^14 years) */
+
+ if (s == NULL)
+ fputs("CPU Time: ", fp);
+ else
+ fputs(s, fp);
+
+ format_time_string(buf, w->user+w->sys, 1);
+#ifdef SRE_STRICT_ANSI
+ fprintf(fp, "%.2fu %s ", w->user, buf);
+#else
+ fprintf(fp, "%.2fu %.2fs %s ", w->user, w->sys, buf);
+#endif
+
+ format_time_string(buf, w->elapsed, 0);
+ fprintf(fp, "Elapsed: %s\n", buf);
+}
+
+#ifdef SRE_ENABLE_PVM
+/* Function: StopwatchPVMPack(), StopwatchPVMUnpack()
+ * Date: SRE, Fri Nov 26 15:22:04 1999 [St. Louis]
+ *
+ * Purpose: Transmission of stopwatch data in a PVM
+ * cluster.
+ */
+void
+StopwatchPVMPack(Stopwatch_t *w)
+{
+ pvm_pkdouble(&(w->elapsed), 1, 1);
+ pvm_pkdouble(&(w->user), 1, 1);
+ pvm_pkdouble(&(w->sys), 1, 1);
+}
+void
+StopwatchPVMUnpack(Stopwatch_t *w)
+{
+ pvm_upkdouble(&(w->elapsed), 1, 1);
+ pvm_upkdouble(&(w->user), 1, 1);
+ pvm_upkdouble(&(w->sys), 1, 1);
+}
+#endif /*SRE_ENABLE_PVM*/
+
+
+#ifdef TESTDRIVER
+int
+main(int argc, char **argv)
+{
+ Stopwatch_t stopwatch;
+
+ StopwatchStart(&stopwatch);
+
+ sleep(5);
+
+ StopwatchStop(&stopwatch);
+ StopwatchDisplay(stdout, "CPU Time: ", &stopwatch);
+}
+#endif
--- /dev/null
+/* stopwatch.h
+ * SRE, Fri Nov 26 14:54:21 1999 [St. Louis] [HMMER]
+ * SRE, Thu Aug 3 08:00:35 2000 [St. Louis] [moved to SQUID]
+ * CVS $Id: stopwatch.h,v 1.2 2000/08/03 22:24:38 eddy Exp)
+ *
+ * Header file for stopwatch.c module:
+ * reporting of cpu/system/elapsed time used by a process.
+ * See stopwatch.c comments for documentation of compile-time
+ * configuration options and API.
+ *
+ *****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************
+ */
+#include <stdio.h>
+#include <time.h>
+#ifndef SRE_STRICT_ANSI
+#include <sys/times.h>
+#endif
+
+#ifndef STOPWATCH_H_INCLUDED
+#define STOPWATCH_H_INCLUDED
+
+struct stopwatch_s {
+ time_t t0; /* Wall clock time, ANSI time() */
+#ifdef SRE_STRICT_ANSI
+ clock_t cpu0; /* CPU time, ANSI clock() */
+#else
+ struct tms cpu0; /* CPU/system time, POSIX times()*/
+#endif
+
+ double elapsed; /* elapsed time, seconds */
+ double user; /* CPU time, seconds */
+ double sys; /* system time, seconds */
+};
+typedef struct stopwatch_s Stopwatch_t;
+
+extern void StopwatchStart(Stopwatch_t *w);
+extern void StopwatchStop(Stopwatch_t *w);
+extern void StopwatchInclude(Stopwatch_t *w1, Stopwatch_t *w2);
+extern Stopwatch_t *StopwatchCreate(void);
+extern void StopwatchZero(Stopwatch_t *w);
+extern void StopwatchCopy(Stopwatch_t *w1, Stopwatch_t *w2);
+extern void StopwatchFree(Stopwatch_t *w);
+extern void StopwatchDisplay(FILE *fp, char *s, Stopwatch_t *w);
+
+#ifdef HMMER_PVM
+extern void StopwatchPVMPack(Stopwatch_t *w);
+extern void StopwatchPVMUnpack(Stopwatch_t *w);
+#endif
+
+#endif /*STOPWATCH_H_INCLUDED*/
+
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/*
+ * translate.c - functions for translating nucleic acid sequence
+ * created Tue Jan 12 11:27:29 1993, SRE
+ *
+ * RCS $Id: translate.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: translate.c,v 1.2 1998/10/09 18:07:16 eddy Exp)
+ */
+
+#include <stdio.h>
+#include <string.h>
+#include "squid.h"
+
+
+#ifdef MEMDEBUG
+#include "dbmalloc.h"
+#endif
+
+
+
+/* Function: Translate(char *seq, char **code)
+ *
+ * Given a ptr to the start of a nucleic acid sequence,
+ * and a genetic code, translate the sequence into
+ * amino acid sequence.
+ *
+ * code is an array of 65 strings, representing
+ * the translations of the 64 codons, arranged
+ * in order AAA, AAC, AAG, AAU, ..., UUA, UUC, UUG, UUU.
+ * '*' or '***' is used to represent termination
+ * codons, usually. The final string, code[64],
+ * is the code for an ambiguous amino acid.
+ *
+ * Because of the way space is allocated for the amino
+ * acid sequence, the amino acid strings cannot be
+ * longer than 3 letters each. (I don't foresee using
+ * anything but the single- and triple- letter codes.)
+ *
+ * Returns a ptr to the translation string on success,
+ * or NULL on failure.
+ */
+char *
+Translate(char *seq, char **code)
+{
+ int codon; /* index for codon */
+ char *aaseq; /* RETURN: the translation */
+ char *aaptr; /* ptr into aaseq */
+ int i;
+
+ if (seq == NULL)
+ { squid_errno = SQERR_NODATA; return NULL; }
+ if ((aaseq = (char *) calloc (strlen(seq) + 1, sizeof(char))) == NULL)
+ Die("calloc failed");
+
+ aaptr = aaseq;
+ for (; *seq != '\0' && *(seq+1) != '\0' && *(seq+2) != '\0'; seq += 3)
+ {
+ /* calculate the lookup value for
+ this codon */
+ codon = 0;
+ for (i = 0; i < 3; i++)
+ {
+ codon *= 4;
+ switch (*(seq + i)) {
+ case 'A': case 'a': break;
+ case 'C': case 'c': codon += 1; break;
+ case 'G': case 'g': codon += 2; break;
+ case 'T': case 't': codon += 3; break;
+ case 'U': case 'u': codon += 3; break;
+ default: codon = 64; break;
+ }
+ if (codon == 64) break;
+ }
+
+ strcpy(aaptr, code[codon]);
+ aaptr += strlen(code[codon]);
+ }
+ return aaseq;
+}
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* file: types.c
+ *
+ * Finicky type checkers for strings. Return 1 (TRUE) if ok, 0 elsewise.
+ * Also, finicky type converters (sre_ntoh32() and friends)
+ *
+ * CVS $Id: types.c,v 1.5 2001/01/08 22:58:12 eddy Exp)
+ */
+
+#include <string.h>
+#include <ctype.h>
+#include "squid.h"
+
+/* Function: IsInt()
+ *
+ * Returns TRUE if s points to something that atoi() will parse
+ * completely and convert to an integer.
+ */
+int
+IsInt(char *s)
+{
+ int hex = 0;
+
+ if (s == NULL) {squid_errno = SQERR_PARAMETER; return 0; }
+
+ /* skip whitespace */
+ while (isspace((int) (*s))) s++;
+ /* skip leading sign */
+ if (*s == '-' || *s == '+') s++;
+ /* skip leading conversion signals */
+ if ((strncmp(s, "0x", 2) == 0 && (int) strlen(s) > 2) ||
+ (strncmp(s, "0X", 2) == 0 && (int) strlen(s) > 2))
+ {
+ s += 2;
+ hex = 1;
+ }
+ else if (*s == '0' && (int) strlen(s) > 1)
+ s++;
+ /* examine remainder for garbage chars */
+ if (!hex)
+ while (*s != '\0')
+ {
+ if (!isdigit((int) (*s))) return 0;
+ s++;
+ }
+ else
+ while (*s != '\0')
+ {
+ if (!isxdigit((int) (*s))) return 0;
+ s++;
+ }
+
+ return 1;
+}
+
+
+/* Function: IsReal()
+ *
+ * Purpose: Returns TRUE if s is a string representation
+ * of a valid floating point number.
+ */
+int
+IsReal(char *s)
+{
+ int gotdecimal = 0;
+ int gotexp = 0;
+ int gotreal = 0;
+
+ if (s == NULL) return 0;
+
+ while (isspace((int) (*s))) s++; /* skip leading whitespace */
+ if (*s == '-' || *s == '+') s++; /* skip leading sign */
+
+ /* Examine remainder for garbage. Allowed one '.' and
+ * one 'e' or 'E'; if both '.' and e/E occur, '.'
+ * must be first.
+ */
+ while (*s != '\0')
+ {
+ if (isdigit((int) (*s)))
+ gotreal++;
+ else if (*s == '.')
+ {
+ if (gotdecimal) return 0; /* can't have two */
+ if (gotexp) return 0; /* e/E preceded . */
+ else gotdecimal++;
+ }
+ else if (*s == 'e' || *s == 'E')
+ {
+ if (gotexp) return 0; /* can't have two */
+ else gotexp++;
+ }
+ else if (isspace((int) (*s)))
+ break;
+
+ s++;
+ }
+
+ while (isspace((int) (*s))) s++; /* skip trailing whitespace */
+ if (*s == '\0' && gotreal) return 1;
+ else return 0;
+}
+
+
+/* Function: Byteswap()
+ *
+ * Purpose: Swap between big-endian and little-endian.
+ * For example:
+ * int foo = 0x12345678;
+ * byteswap((char *) &foo, sizeof(int));
+ * printf("%x\n", foo)
+ * gives 78563412.
+ *
+ * I don't fully understand byte-swapping issues.
+ * However, I have tested this on chars through floats,
+ * on various machines:
+ * SGI IRIX 4.0.5, SunOS 4.1.3, DEC Alpha OSF/1, Alliant
+ *
+ * Date: Sun Feb 12 10:26:22 1995
+ */
+void
+Byteswap(char *swap, int nbytes)
+{
+ int x;
+ char byte;
+
+ for (x = 0; x < nbytes / 2; x++)
+ {
+ byte = swap[nbytes - x - 1];
+ swap[nbytes - x - 1] = swap[x];
+ swap[x] = byte;
+ }
+}
+
+
+
+/* Functions: sre_ntoh16(), etc.
+ * Date: SRE, Sun Dec 31 11:26:53 2000 [St. Louis]
+ *
+ * Purpose: Provide functionality of ntohs(), etc; extended
+ * to 64-bit unsigned ints, and explicitly provided
+ * in case a machine doesn't have the ntohs()
+ * family.
+ *
+ * If we're using the host functions,
+ * USE_HOST_BYTESWAP_FUNCTIONS was set to 1 in
+ * squidconf.h, and we #define'd sre_hton16(x)=hton(x), etc.
+ * in squid.h. In doing this, we assumed that the
+ * host functions work on 16- and 32-bit unsigned quantities.
+ * If for some reason that's not true, set
+ * USE_HOST_BYTESWAP_FUNCTIONS to 0.
+ */
+#ifndef USE_HOST_BYTESWAP_FUNCTIONS
+sqd_uint16
+sre_ntoh16(sqd_uint16 netshort)
+{
+#ifdef WORDS_BIGENDIAN
+ return netshort;
+#else
+ Byteswap((char *) &netshort, 2);
+ return netshort;
+#endif
+}
+sqd_uint32
+sre_ntoh32(sqd_uint32 netlong)
+{
+#ifdef WORDS_BIGENDIAN
+ return netlong;
+#else
+ Byteswap((char *) &netlong, 4);
+ return netlong;
+#endif
+}
+sqd_uint16
+sre_hton16(sqd_uint16 hostshort)
+{
+#ifdef WORDS_BIGENDIAN
+ return hostshort;
+#else
+ Byteswap((char *) &hostshort, 2);
+ return hostshort;
+#endif
+}
+sqd_uint32
+sre_hton32(sqd_uint32 hostlong)
+{
+#ifdef WORDS_BIGENDIAN
+ return hostlong;
+#else
+ Byteswap((char *) &hostlong, 4);
+ return hostlong;
+#endif
+}
+#endif /*USE_HOST_BYTESWAP_FUNCTIONS*/
+
+sqd_uint64
+sre_ntoh64(sqd_uint64 net_int64)
+{
+#ifdef WORDS_BIGENDIAN
+ return net_int64;
+#else
+ Byteswap((char *) &net_int64, 8);
+ return net_int64;
+#endif
+}
+sqd_uint64
+sre_hton64(sqd_uint64 host_int64)
+{
+#ifdef WORDS_BIGENDIAN
+ return host_int64;
+#else
+ Byteswap((char *) &host_int64, 8);
+ return host_int64;
+#endif
+}
+
+
+
+
--- /dev/null
+/* vectorops.c
+ * Operations on vectors of floats or doubles.
+ *
+ * DSet(), FSet() - set all items in vector to value.
+ * DScale(), FScale() - multiply all items in vector by scale
+ * DSum(), FSum() - return sum of values in vector
+ * DAdd(), FAdd() - add vec2 to vec1.
+ * DCopy(), FCopy() - set vec1 to be same as vec2.
+ * DDot(), FDot() - return dot product of two vectors.
+ * DMax(), FMax() - return value of maximum element in vector
+ * DMin(), FMin() - return value of minimum element in vector
+ * DArgMax(), FArgMax() - return index of maximum element in vector
+ * DArgMin(), FArgMin() - return index of minimum element in vector
+ *
+ * DNorm(), FNorm() - normalize a probability vector of length n.
+ * DLog(), FLog() - convert to log probabilities
+ * DExp(), FExp() - convert log p's back to probabilities
+ * DLogSum(), FLogSum() - given vector of log p's; return log of summed p's.
+ *
+ * SRE, Tue Oct 1 15:23:25 2002 [St. Louis]
+ * CVS $Id: vectorops.c,v 1.1 2002/10/09 14:26:09 eddy Exp)
+ */
+
+#include <stdlib.h>
+#include <math.h>
+#include <float.h>
+#include "vectorops.h"
+
+void
+DSet(double *vec, int n, double value)
+{
+ int x;
+ for (x = 0; x < n; x++) vec[x] = value;
+}
+
+void
+FSet(float *vec, int n, float value)
+{
+ int x;
+ for (x = 0; x < n; x++) vec[x] = value;
+}
+
+void
+DScale(double *vec, int n, double scale)
+{
+ int x;
+ for (x = 0; x < n; x++) vec[x] *= scale;
+}
+
+void
+FScale(float *vec, int n, float scale)
+{
+ int x;
+ for (x = 0; x < n; x++) vec[x] *= scale;
+}
+
+double
+DSum(double *vec, int n)
+{
+ double sum = 0.;
+ int x;
+ for (x = 0; x < n; x++) sum += vec[x];
+ return sum;
+}
+
+float
+FSum(float *vec, int n)
+{
+ float sum = 0.;
+ int x;
+ for (x = 0; x < n; x++) sum += vec[x];
+ return sum;
+}
+
+void
+DAdd(double *vec1, double *vec2, int n)
+{
+ int x;
+ for (x = 0; x < n; x++) vec1[x] += vec2[x];
+}
+
+void
+FAdd(float *vec1, float *vec2, int n)
+{
+ int x;
+ for (x = 0; x < n; x++) vec1[x] += vec2[x];
+}
+
+void
+DCopy(double *vec1, double *vec2, int n)
+{
+ int x;
+ for (x = 0; x < n; x++) vec1[x] = vec2[x];
+}
+
+void
+FCopy(float *vec1, float *vec2, int n)
+{
+ int x;
+ for (x = 0; x < n; x++) vec1[x] = vec2[x];
+}
+
+double
+DDot(double *vec1, double *vec2, int n)
+{
+ double result = 0.;
+ int x;
+ for (x = 0; x < n; x++) result += vec1[x] * vec2[x];
+ return result;
+}
+
+float
+FDot(float *vec1, float *vec2, int n)
+{
+ float result = 0.;
+ int x;
+ for (x = 0; x < n; x++) result += vec1[x] * vec2[x];
+ return result;
+}
+
+double
+DMax(double *vec, int n)
+{
+ int i;
+ double best;
+
+ best = vec[0];
+ for (i = 1; i < n; i++)
+ if (vec[i] > best) best = vec[i];
+ return best;
+}
+
+float
+FMax(float *vec, int n)
+{
+ int i;
+ float best;
+
+ best = vec[0];
+ for (i = 1; i < n; i++)
+ if (vec[i] > best) best = vec[i];
+ return best;
+}
+
+double
+DMin(double *vec, int n)
+{
+ int i;
+ double best;
+
+ best = vec[0];
+ for (i = 1; i < n; i++)
+ if (vec[i] < best) best = vec[i];
+ return best;
+}
+
+float
+FMin(float *vec, int n)
+{
+ int i;
+ float best;
+
+ best = vec[0];
+ for (i = 1; i < n; i++)
+ if (vec[i] < best) best = vec[i];
+ return best;
+}
+
+double
+DArgMax(double *vec, int n)
+{
+ int i;
+ int best = 0;
+
+ for (i = 1; i < n; i++)
+ if (vec[i] > vec[best]) best = i;
+ return best;
+}
+
+float
+FArgMax(float *vec, int n)
+{
+ int i;
+ int best = 0;
+
+ for (i = 1; i < n; i++)
+ if (vec[i] > vec[best]) best = i;
+ return best;
+}
+
+double
+DArgMin(double *vec, int n)
+{
+ int i;
+ int best = 0;
+ for (i = 1; i < n; i++)
+ if (vec[i] < vec[best]) best = i;
+ return best;
+}
+
+float
+FArgMin(float *vec, int n)
+{
+ int i;
+ int best = 0;
+
+ for (i = 1; i < n; i++)
+ if (vec[i] < vec[best]) best = i;
+ return best;
+}
+
+void
+DNorm(double *vec, int n)
+{
+ int x;
+ double sum;
+
+ sum = DSum(vec, n);
+ if (sum != 0.0) for (x = 0; x < n; x++) vec[x] /= sum;
+ else for (x = 0; x < n; x++) vec[x] = 1. / (double) n;
+}
+
+void
+FNorm(float *vec, int n)
+{
+ int x;
+ float sum;
+
+ sum = FSum(vec, n);
+ if (sum != 0.0) for (x = 0; x < n; x++) vec[x] /= sum;
+ else for (x = 0; x < n; x++) vec[x] = 1. / (float) n;
+}
+
+void
+DLog(double *vec, int n)
+{
+ int x;
+ for (x = 0; x < n; x++)
+ if (vec[x] > 0.) vec[x] = log(vec[x]);
+ else vec[x] = -DBL_MAX;
+}
+
+void
+FLog(float *vec, int n)
+{
+ int x;
+ for (x = 0; x < n; x++)
+ if (vec[x] > 0.) vec[x] = log(vec[x]);
+ else vec[x] = -FLT_MAX;
+}
+
+void
+DExp(double *vec, int n)
+{
+ int x;
+ for (x = 0; x < n; x++) vec[x] = exp(vec[x]);
+}
+
+void
+FExp(float *vec, int n)
+{
+ int x;
+ for (x = 0; x < n; x++) vec[x] = exp(vec[x]);
+}
+
+float
+DLogSum(double *vec, int n)
+{
+ int x;
+ double max, sum;
+
+ max = DMax(vec, n);
+ sum = 0.0;
+ for (x = 0; x < n; x++)
+ if (vec[x] > max - 50.)
+ sum += exp(vec[x] - max);
+ sum = log(sum) + max;
+ return sum;
+}
+
+float
+FLogSum(float *vec, int n)
+{
+ int x;
+ float max, sum;
+
+ max = FMax(vec, n);
+ sum = 0.0;
+ for (x = 0; x < n; x++)
+ if (vec[x] > max - 50.)
+ sum += exp(vec[x] - max);
+ sum = log(sum) + max;
+ return sum;
+}
+
+
+
--- /dev/null
+/* vectorops.h
+ * Header file for vectorops.c
+ *
+ * SRE, Tue Oct 1 15:23:37 2002 [St. Louis]
+ * CVS $Id: vectorops.h,v 1.1 2002/10/09 14:26:09 eddy Exp)
+ */
+
+extern void DSet(double *vec, int n, double value);
+extern void FSet(float *vec, int n, float value);
+extern void DScale(double *vec, int n, double scale);
+extern void FScale(float *vec, int n, float scale);
+extern double DSum(double *vec, int n);
+extern float FSum(float *vec, int n);
+extern void DAdd(double *vec1, double *vec2, int n);
+extern void FAdd(float *vec1, float *vec2, int n);
+extern void DCopy(double *vec1, double *vec2, int n);
+extern void FCopy(float *vec1, float *vec2, int n);
+extern double DDot(double *vec1, double *vec2, int n);
+extern float FDot(float *vec1, float *vec2, int n);
+extern double DMax(double *vec, int n);
+extern float FMax(float *vec, int n);
+extern double DMin(double *vec, int n);
+extern float FMin(float *vec, int n);
+extern double DArgMax(double *vec, int n);
+extern float FArgMax(float *vec, int n);
+extern double DArgMin(double *vec, int n);
+extern float FArgMin(float *vec, int n);
+extern void DNorm(double *vec, int n);
+extern void FNorm(float *vec, int n);
+extern void DLog(double *vec, int n);
+extern void FLog(float *vec, int n);
+extern void DExp(double *vec, int n);
+extern void FExp(float *vec, int n);
+extern float DLogSum(double *vec, int n);
+extern float FLogSum(float *vec, int n);
+
--- /dev/null
+/* version.h -- automatically generated by a Makefile. DO NOT EDIT. */
+#define PACKAGE "SQUID"
+#define RELEASE "1.9g"
+#define RELEASEDATE "Oct 2002"
+#define COPYRIGHT "Copyright (C) 1992-2002 HHMI/Washington University School of Medicine"
+#define LICENSE "Freely distributed under the GNU General Public License (GPL)"
--- /dev/null
+/*****************************************************************
+ * SQUID - a library of functions for biological sequence analysis
+ * Copyright (C) 1992-2002 Washington University School of Medicine
+ *
+ * This source code is freely distributed under the terms of the
+ * GNU General Public License. See the files COPYRIGHT and LICENSE
+ * for details.
+ *****************************************************************/
+
+/* weight.c
+ * SRE, Thu Mar 3 07:56:01 1994
+ *
+ * Calculate weights for sequences in an alignment.
+ * RCS $Id: weight.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: weight.c,v 1.9 2002/10/09 14:26:09 eddy Exp)
+ */
+
+#include <ctype.h>
+#include <string.h>
+#include "squid.h"
+#include "sre_random.h"
+
+static void upweight(struct phylo_s *tree, int nseq, float *lwt, float *rwt, int node);
+static void downweight(struct phylo_s *tree, int nseq, float *lwt, float *rwt,
+ float *fwt, int node);
+static float simple_distance(char *s1, char *s2);
+static int simple_diffmx(char **aseqs,int num, float ***ret_dmx);
+
+/* Function: GSCWeights()
+ *
+ * Purpose: Use Erik's tree-based algorithm to set weights for
+ * sequences in an alignment. upweight() and downweight()
+ * are derived from Graeme Mitchison's code.
+ *
+ * Args: aseq - array of (0..nseq-1) aligned sequences
+ * nseq - number of seqs in alignment
+ * alen - length of alignment
+ * wgt - allocated [0..nseq-1] array of weights to be returned
+ *
+ * Return: (void)
+ * wgt is filled in.
+ */
+void
+GSCWeights(char **aseq, int nseq, int alen, float *wgt)
+{
+ float **dmx; /* distance (difference) matrix */
+ struct phylo_s *tree;
+ float *lwt, *rwt; /* weight on left, right of this tree node */
+ float *fwt; /* final weight assigned to this node */
+ int i;
+
+ /* Sanity check first
+ */
+ if (nseq == 1) { wgt[0] = 1.0; return; }
+
+ /* I use a simple fractional difference matrix derived by
+ * pairwise identity. Perhaps I should include a Poisson
+ * distance correction.
+ */
+ MakeDiffMx(aseq, nseq, &dmx);
+ if (! Cluster(dmx, nseq, CLUSTER_MIN, &tree)) Die("Cluster() failed");
+
+ /* Allocations
+ */
+ lwt = MallocOrDie (sizeof(float) * (2 * nseq - 1));
+ rwt = MallocOrDie (sizeof(float) * (2 * nseq - 1));
+ fwt = MallocOrDie (sizeof(float) * (2 * nseq - 1));
+
+ /* lwt and rwt are the total branch weight to the left and
+ * right of a node or sequence. They are 0..2N-2. 0..N-1 are
+ * the sequences; these have weight 0. N..2N-2 are the actual
+ * tree nodes.
+ */
+ for (i = 0; i < nseq; i++)
+ lwt[i] = rwt[i] = 0.0;
+ /* recursively calculate rwt, lwt, starting
+ at node nseq (the root) */
+ upweight(tree, nseq, lwt, rwt, nseq);
+
+ /* recursively distribute weight across the
+ tree */
+ fwt[nseq] = nseq;
+ downweight(tree, nseq, lwt, rwt, fwt, nseq);
+ /* collect the weights */
+ for (i = 0; i < nseq; i++)
+ wgt[i] = fwt[i];
+
+ FMX2Free(dmx);
+ FreePhylo(tree, nseq);
+ free(lwt); free(rwt); free(fwt);
+}
+
+static void
+upweight(struct phylo_s *tree, int nseq, float *lwt, float *rwt, int node)
+{
+ int ld,rd;
+
+ ld = tree[node-nseq].left;
+ if (ld >= nseq) upweight(tree, nseq, lwt, rwt, ld);
+ rd = tree[node-nseq].right;
+ if (rd >= nseq) upweight(tree, nseq, lwt, rwt, rd);
+ lwt[node] = lwt[ld] + rwt[ld] + tree[node-nseq].lblen;
+ rwt[node] = lwt[rd] + rwt[rd] + tree[node-nseq].rblen;
+}
+
+
+static void
+downweight(struct phylo_s *tree, int nseq, float *lwt, float *rwt, float *fwt, int node)
+{
+ int ld,rd;
+ float lnum, rnum;
+
+ ld = tree[node-nseq].left;
+ rd = tree[node-nseq].right;
+ if (lwt[node] + rwt[node] > 0.0)
+ {
+ fwt[ld] = fwt[node] * (lwt[node] / (lwt[node] + rwt[node]));
+ fwt[rd] = fwt[node] * (rwt[node] / (lwt[node] + rwt[node]));
+ }
+ else
+ {
+ lnum = (ld >= nseq) ? tree[ld-nseq].incnum : 1.0;
+ rnum = (rd >= nseq) ? tree[rd-nseq].incnum : 1.0;
+ fwt[ld] = fwt[node] * lnum / (lnum + rnum);
+ fwt[rd] = fwt[node] * rnum / (lnum + rnum);
+ }
+
+ if (ld >= nseq) downweight(tree, nseq, lwt, rwt, fwt, ld);
+ if (rd >= nseq) downweight(tree, nseq, lwt, rwt, fwt, rd);
+}
+
+
+
+
+/* Function: VoronoiWeights()
+ *
+ * Purpose: Calculate weights using the scheme of Sibbald &
+ * Argos (JMB 216:813-818 1990). The scheme is
+ * slightly modified because the original algorithm
+ * actually doesn't work on gapped alignments.
+ * The sequences are assumed to be protein.
+ *
+ * Args: aseq - array of (0..nseq-1) aligned sequences
+ * nseq - number of sequences
+ * alen - length of alignment
+ * wgt - allocated [0..nseq-1] array of weights to be returned
+ *
+ * Return: void
+ * wgt is filled in.
+ */
+void
+VoronoiWeights(char **aseq, int nseq, int alen, float *wgt)
+{
+ float **dmx; /* distance (difference) matrix */
+ float *halfmin; /* 1/2 minimum distance to other seqs */
+ char **psym; /* symbols seen in each column */
+ int *nsym; /* # syms seen in each column */
+ int symseen[27]; /* flags for observed syms */
+ char *randseq; /* randomly generated sequence */
+ int acol; /* pos in aligned columns */
+ int idx; /* index in sequences */
+ int symidx; /* 0..25 index for symbol */
+ int i; /* generic counter */
+ float min; /* minimum distance */
+ float dist; /* distance between random and real */
+ float challenge, champion; /* for resolving ties */
+ int itscale; /* how many iterations per seq */
+ int iteration;
+ int best; /* index of nearest real sequence */
+
+ /* Sanity check first
+ */
+ if (nseq == 1) { wgt[0] = 1.0; return; }
+
+ itscale = 50;
+
+ /* Precalculate 1/2 minimum distance to other
+ * sequences for each sequence
+ */
+ if (! simple_diffmx(aseq, nseq, &dmx))
+ Die("simple_diffmx() failed");
+ halfmin = MallocOrDie (sizeof(float) * nseq);
+ for (idx = 0; idx < nseq; idx++)
+ {
+ for (min = 1.0, i = 0; i < nseq; i++)
+ {
+ if (i == idx) continue;
+ if (dmx[idx][i] < min) min = dmx[idx][i];
+ }
+ halfmin[idx] = min / 2.0;
+ }
+ Free2DArray((void **) dmx, nseq);
+
+ /* Set up the random sequence generating model.
+ */
+ psym = MallocOrDie (alen * sizeof(char *));
+ nsym = MallocOrDie (alen * sizeof(int));
+ for (acol = 0; acol < alen; acol++)
+ psym[acol] = MallocOrDie (27 * sizeof(char));
+
+/* #ifdef ORIGINAL_SIBBALD_ALGORITHM_IS_BROKEN */
+ for (acol = 0; acol < alen; acol++)
+ {
+ memset(symseen, 0, sizeof(int) * 27);
+ for (idx = 0; idx < nseq; idx++)
+ if (! isgap(aseq[idx][acol]))
+ {
+ if (isupper((int) aseq[idx][acol]))
+ symidx = aseq[idx][acol] - 'A';
+ else
+ symidx = aseq[idx][acol] - 'a';
+ if (symidx >= 0 && symidx < 26)
+ symseen[symidx] = 1;
+ }
+ else
+ symseen[26] = 1; /* a gap */
+
+ for (nsym[acol] = 0, i = 0; i < 26; i++)
+ if (symseen[i])
+ {
+ psym[acol][nsym[acol]] = 'A'+i;
+ nsym[acol]++;
+ }
+ if (symseen[26]) { psym[acol][nsym[acol]] = ' '; nsym[acol]++; }
+ }
+/* #endif ORIGINAL_SIBBALD_ALGORITHM_IS_BROKEN */
+
+ /* Note: the original Sibbald&Argos algorithm calls for
+ * bounding the sampled space using a template-like random
+ * sequence generator. However, this leads to one minor
+ * and one major problem. The minor problem is that
+ * exceptional amino acids in a column can have a
+ * significant effect by altering the amount of sampled
+ * sequence space; the larger the data set, the worse
+ * this problem becomes. The major problem is that
+ * there is no reasonable way to deal with gaps.
+ * Gapped sequences simply inhabit a different dimensionality
+ * and it's pretty painful to imagine calculating Voronoi
+ * volumes when the N in your N-space is varying.
+ * Note that all the examples shown by Sibbald and Argos
+ * are *ungapped* examples.
+ *
+ * The best way I've found to circumvent this problem is
+ * just not to bound the sampled space; count gaps as
+ * symbols and generate completely random sequences.
+ */
+#ifdef ALL_SEQUENCE_SPACE
+ for (acol = 0; acol < alen; acol++)
+ {
+ strcpy(psym[acol], "ACDEFGHIKLMNPQRSTVWY ");
+ nsym[acol] = 21;
+ }
+#endif
+
+ /* Sibbald and Argos algorithm:
+ * 1) assign all seqs weight 0.
+ * 2) generate a "random" sequence
+ * 3) calculate distance to every other sequence
+ * (if we get a distance < 1/2 minimum distance
+ * to other real seqs, we can stop)
+ * 4) if unique closest sequence, increment its weight 1.
+ * if multiple closest seq, choose one randomly
+ * 5) repeat 2-4 for lots of iterations
+ * 6) normalize all weights to sum to nseq.
+ */
+ randseq = MallocOrDie ((alen+1) * sizeof(char));
+
+ best = 42.; /* solely to silence GCC uninit warnings. */
+ FSet(wgt, nseq, 0.0);
+ for (iteration = 0; iteration < itscale * nseq; iteration++)
+ {
+ for (acol = 0; acol < alen; acol++)
+ randseq[acol] = (nsym[acol] == 0) ? ' ' : psym[acol][CHOOSE(nsym[acol])];
+ randseq[acol] = '\0';
+
+ champion = sre_random();
+ for (min = 1.0, idx = 0; idx < nseq; idx++)
+ {
+ dist = simple_distance(aseq[idx], randseq);
+ if (dist < halfmin[idx])
+ {
+ best = idx;
+ break;
+ }
+ if (dist < min)
+ { champion = sre_random(); best = idx; min = dist; }
+ else if (dist == min)
+ {
+ challenge = sre_random();
+ if (challenge > champion)
+ { champion = challenge; best = idx; min = dist; }
+ }
+ }
+ wgt[best] += 1.0;
+ }
+
+ for (idx = 0; idx < nseq; idx++)
+ wgt[idx] = wgt[idx] / (float) itscale;
+
+ free(randseq);
+ free(nsym);
+ free(halfmin);
+ Free2DArray((void **) psym, alen);
+}
+
+
+/* Function: simple_distance()
+ *
+ * Purpose: For two identical-length null-terminated strings, return
+ * the fractional difference between them. (0..1)
+ * (Gaps don't count toward anything.)
+ */
+static float
+simple_distance(char *s1, char *s2)
+{
+ int diff = 0;
+ int valid = 0;
+
+ for (; *s1 != '\0'; s1++, s2++)
+ {
+ if (isgap(*s1) || isgap(*s2)) continue;
+ if (*s1 != *s2) diff++;
+ valid++;
+ }
+ return (valid > 0 ? ((float) diff / (float) valid) : 0.0);
+}
+
+/* Function: simple_diffmx()
+ *
+ * Purpose: Given a set of flushed, aligned sequences, construct
+ * an NxN fractional difference matrix using the
+ * simple_distance rule.
+ *
+ * Args: aseqs - flushed, aligned sequences
+ * num - number of aseqs
+ * ret_dmx - RETURN: difference matrix (caller must free)
+ *
+ * Return: 1 on success, 0 on failure.
+ */
+static int
+simple_diffmx(char **aseqs,
+ int num,
+ float ***ret_dmx)
+{
+ float **dmx; /* RETURN: distance matrix */
+ int i,j; /* counters over sequences */
+
+ /* Allocate
+ */
+ if ((dmx = (float **) malloc (sizeof(float *) * num)) == NULL)
+ Die("malloc failed");
+ for (i = 0; i < num; i++)
+ if ((dmx[i] = (float *) malloc (sizeof(float) * num)) == NULL)
+ Die("malloc failed");
+
+ /* Calculate distances, symmetric matrix
+ */
+ for (i = 0; i < num; i++)
+ for (j = i; j < num; j++)
+ dmx[i][j] = dmx[j][i] = simple_distance(aseqs[i], aseqs[j]);
+
+ /* Return
+ */
+ *ret_dmx = dmx;
+ return 1;
+}
+
+
+
+/* Function: BlosumWeights()
+ * Date: SRE, Fri Jul 16 17:33:59 1999 (St. Louis)
+ *
+ * Purpose: Assign weights to a set of aligned sequences
+ * using the BLOSUM rule:
+ * - do single linkage clustering at some pairwise identity
+ * - in each cluster, give each sequence 1/clustsize
+ * total weight.
+ *
+ * The clusters have no pairwise link >= maxid.
+ *
+ * O(N) in memory. Probably ~O(NlogN) in time; O(N^2)
+ * in worst case, which is no links between sequences
+ * (e.g., values of maxid near 1.0).
+ *
+ * Args: aseqs - alignment
+ * nseq - number of seqs in alignment
+ * alen - # of columns in alignment
+ * maxid - fractional identity (e.g. 0.62 for BLOSUM62)
+ * wgt - [0..nseq-1] array of weights to be returned
+ */
+void
+BlosumWeights(char **aseqs, int nseq, int alen, float maxid, float *wgt)
+{
+ int *c, nc;
+ int *nmem; /* number of seqs in each cluster */
+ int i; /* loop counter */
+
+ SingleLinkCluster(aseqs, nseq, alen, maxid, &c, &nc);
+
+ FSet(wgt, nseq, 1.0);
+ nmem = MallocOrDie(sizeof(int) * nc);
+
+ for (i = 0; i < nc; i++) nmem[i] = 0;
+ for (i = 0; i < nseq; i++) nmem[c[i]]++;
+ for (i = 0; i < nseq; i++) wgt[i] = 1. / (float) nmem[c[i]];
+
+ free(nmem);
+ free(c);
+ return;
+}
+
+
+/* Function: PositionBasedWeights()
+ * Date: SRE, Fri Jul 16 17:47:22 1999 [St. Louis]
+ *
+ * Purpose: Implementation of Henikoff and Henikoff position-based
+ * weights (JMB 243:574-578, 1994) [Henikoff94b].
+ *
+ * A significant advantage of this approach that Steve and Jorja
+ * don't point out is that it is O(N) in memory, unlike
+ * many other approaches like GSC weights or Voronoi.
+ *
+ * A potential disadvantage that they don't point out
+ * is that in the theoretical limit of infinite sequences
+ * in the alignment, weights go flat: eventually every
+ * column has at least one representative of each of 20 aa (or 4 nt)
+ * in it.
+ *
+ * They also don't give a rule for how to handle gaps.
+ * The rule used here seems the obvious and sensible one
+ * (ignore them). This means that longer sequences
+ * initially get more weight; hence a "double
+ * normalization" in which the weights are first divided
+ * by sequence length (to compensate for that effect),
+ * then normalized to sum to nseq.
+ *
+ * Limitations:
+ * Implemented in a way that's alphabet-independent:
+ * it uses the 26 upper case letters as "residues".
+ * Any alphabetic character in aseq is interpreted as
+ * a unique "residue" (case insensitively; lower case
+ * mapped to upper case). All other characters are
+ * interpreted as gaps.
+ *
+ * This way, we don't have to pass around any alphabet
+ * type info (DNA vs. RNA vs. protein) and don't have
+ * to deal with remapping IUPAC degenerate codes
+ * probabilistically. However, on the down side,
+ * a sequence with a lot of degenerate IUPAC characters
+ * will get an artifactually high PB weight.
+ *
+ * Args: aseq - sequence alignment to weight
+ * nseq - number of sequences in alignment
+ * alen - length of alignment
+ * wgt - RETURN: weights filled in (pre-allocated 0..nseq-1)
+ *
+ * Returns: (void)
+ * wgt is allocated (0..nseq-1) by caller, and filled in here.
+ */
+void
+PositionBasedWeights(char **aseq, int nseq, int alen, float *wgt)
+{
+ int rescount[26]; /* count of A-Z residues in a column */
+ int nres; /* number of different residues in col */
+ int idx, pos; /* indices into aseq */
+ int x;
+ float norm;
+
+ FSet(wgt, nseq, 0.0);
+ for (pos = 0; pos < alen; pos++)
+ {
+ for (x = 0; x < 26; x++) rescount[x] = 0;
+ for (idx = 0; idx < nseq; idx++)
+ if (isalpha(aseq[idx][pos]))
+ rescount[toupper(aseq[idx][pos]) - 'A'] ++;
+
+ nres = 0;
+ for (x = 0; x < 26; x++)
+ if (rescount[x] > 0) nres++;
+
+ for (idx = 0; idx < nseq; idx++)
+ if (isalpha(aseq[idx][pos]))
+ wgt[idx] += 1. / (float) (nres * rescount[toupper(aseq[idx][pos]) - 'A']);
+ }
+
+ for (idx = 0; idx < nseq; idx++)
+ wgt[idx] /= (float) DealignedLength(aseq[idx]);
+ norm = (float) nseq / FSum(wgt, nseq);
+ FScale(wgt, nseq, norm);
+ return;
+}
+
+
+
+
+/* Function: FilterAlignment()
+ * Date: SRE, Wed Jun 30 09:19:30 1999 [St. Louis]
+ *
+ * Purpose: Constructs a new alignment by removing near-identical
+ * sequences from a given alignment (where identity is
+ * calculated *based on the alignment*).
+ * Does not affect the given alignment.
+ * Keeps earlier sequence, discards later one.
+ *
+ * Usually called as an ad hoc sequence "weighting" mechanism.
+ *
+ * Limitations:
+ * Unparsed Stockholm markup is not propagated into the
+ * new alignment.
+ *
+ * Args: msa -- original alignment
+ * cutoff -- fraction identity cutoff. 0.8 removes sequences > 80% id.
+ * ret_new -- RETURN: new MSA, usually w/ fewer sequences
+ *
+ * Return: (void)
+ * ret_new must be free'd by caller: MSAFree().
+ */
+void
+FilterAlignment(MSA *msa, float cutoff, MSA **ret_new)
+{
+ int nnew; /* number of seqs in new alignment */
+ int *list;
+ int *useme;
+ float ident;
+ int i,j;
+ int remove;
+
+ /* find which seqs to keep (list) */
+ /* diff matrix; allow ragged ends */
+ list = MallocOrDie (sizeof(int) * msa->nseq);
+ useme = MallocOrDie (sizeof(int) * msa->nseq);
+ for (i = 0; i < msa->nseq; i++) useme[i] = FALSE;
+
+ nnew = 0;
+ for (i = 0; i < msa->nseq; i++)
+ {
+ remove = FALSE;
+ for (j = 0; j < nnew; j++)
+ {
+ ident = PairwiseIdentity(msa->aseq[i], msa->aseq[list[j]]);
+ if (ident > cutoff)
+ {
+ remove = TRUE;
+ printf("removing %12s -- fractional identity %.2f to %s\n",
+ msa->sqname[i], ident,
+ msa->sqname[list[j]]);
+ break;
+ }
+ }
+ if (remove == FALSE) {
+ list[nnew++] = i;
+ useme[i] = TRUE;
+ }
+ }
+
+ MSASmallerAlignment(msa, useme, ret_new);
+ free(list);
+ free(useme);
+ return;
+}
+
+
+/* Function: SampleAlignment()
+ * Date: SRE, Wed Jun 30 10:13:56 1999 [St. Louis]
+ *
+ * Purpose: Constructs a new, smaller alignment by sampling a given
+ * number of sequences at random. Does not change the
+ * alignment nor the order of the sequences.
+ *
+ * If you ask for a sample that is larger than nseqs,
+ * it silently returns the original alignment.
+ *
+ * Not really a weighting method, but this is as good
+ * a place as any to keep it, since it's similar in
+ * construction to FilterAlignment().
+ *
+ * Args: msa -- original alignment
+ * sample -- number of sequences in new alignment (0 < sample <= nseq)
+ * ret_new -- RETURN: new MSA
+ *
+ * Return: (void)
+ * ret_new must be free'd by caller: MSAFree().
+ */
+void
+SampleAlignment(MSA *msa, int sample, MSA **ret_new)
+{
+ int *list; /* array for random selection w/o replace */
+ int *useme; /* array of flags 0..nseq-1: TRUE to use */
+ int i, idx;
+ int len;
+
+ /* Allocations
+ */
+ list = (int *) MallocOrDie (sizeof(int) * msa->nseq);
+ useme = (int *) MallocOrDie (sizeof(int) * msa->nseq);
+ for (i = 0; i < msa->nseq; i++)
+ {
+ list[i] = i;
+ useme[i] = FALSE;
+ }
+
+ /* Sanity check.
+ */
+ if (sample >= msa->nseq) sample = msa->nseq;
+
+ /* random selection w/o replacement */
+ for (len = msa->nseq, i = 0; i < sample; i++)
+ {
+ idx = CHOOSE(len);
+ printf("chose %d: %s\n", list[idx], msa->sqname[list[idx]]);
+ useme[list[idx]] = TRUE;
+ list[idx] = list[--len];
+ }
+
+ MSASmallerAlignment(msa, useme, ret_new);
+ free(list);
+ free(useme);
+ return;
+}
+
+
+/* Function: SingleLinkCluster()
+ * Date: SRE, Fri Jul 16 15:02:57 1999 [St. Louis]
+ *
+ * Purpose: Perform simple single link clustering of seqs in a
+ * sequence alignment. A pairwise identity threshold
+ * defines whether two sequences are linked or not.
+ *
+ * Important: runs in O(N) memory, unlike standard
+ * graph decomposition algorithms that use O(N^2)
+ * adjacency matrices or adjacency lists. Requires
+ * O(N^2) time in worst case (which is when you have
+ * no links at all), O(NlogN) in "average"
+ * case, and O(N) in best case (when there is just
+ * one cluster in a completely connected graph.
+ *
+ * (Developed because hmmbuild could no longer deal
+ * with GP120, a 16,013 sequence alignment.)
+ *
+ * Limitations:
+ * CASE-SENSITIVE. Assumes aseq have been put into
+ * either all lower or all upper case; or at least,
+ * within a column, there's no mixed case.
+ *
+ * Algorithm:
+ * I don't know if this algorithm is published. I
+ * haven't seen it in graph theory books, but that might
+ * be because it's so obvious that nobody's bothered.
+ *
+ * In brief, we're going to do a breadth-first search
+ * of the graph, and we're going to calculate links
+ * on the fly rather than precalculating them into
+ * some sort of standard adjacency structure.
+ *
+ * While working, we keep two stacks of maximum length N:
+ * a : list of vertices that are still unconnected.
+ * b : list of vertices that we've connected to
+ * in our current breadth level, but we haven't
+ * yet tested for other connections to a.
+ * The current length (number of elements in) a and b are
+ * kept in na, nb.
+ *
+ * We store our results in an array of length N:
+ * c : assigns each vertex to a component. for example
+ * c[4] = 1 means that vertex 4 is in component 1.
+ * nc is the number of components. Components
+ * are numbered from 0 to nc-1. We return c and nc
+ * to our caller.
+ *
+ * The algorithm is:
+ *
+ * Initialisation:
+ * a <-- all the vertices
+ * na <-- N
+ * b <-- empty set
+ * nb <-- 0
+ * nc <-- 0
+ *
+ * Then:
+ * while (a is not empty)
+ * pop a vertex off a, push onto b
+ * while (b is not empty)
+ * pop vertex v off b
+ * assign c[v] = nc
+ * for each vertex w in a:
+ * compare v,w. If w is linked to v, remove w
+ * from a, push onto b.
+ * nc++
+ * q.e.d. :)
+ *
+ * Args: aseq - aligned sequences
+ * nseq - number of sequences in aseq
+ * alen - alignment length
+ * maxid - fractional identity threshold 0..1. if id >= maxid, seqs linked
+ * ret_c - RETURN: 0..nseq-1 assignments of seqs to components (clusters)
+ * ret_nc - RETURN: number of components
+ *
+ * Returns: void.
+ * ret_c is allocated here. Caller free's with free(*ret_c)
+ */
+void
+SingleLinkCluster(char **aseq, int nseq, int alen, float maxid,
+ int **ret_c, int *ret_nc)
+{
+ int *a, na; /* stack of available vertices */
+ int *b, nb; /* stack of working vertices */
+ int *c; /* array of results */
+ int nc; /* total number of components */
+ int v,w; /* index of a working vertices */
+ int i; /* loop counter */
+
+ /* allocations and initializations
+ */
+ a = MallocOrDie (sizeof(int) * nseq);
+ b = MallocOrDie (sizeof(int) * nseq);
+ c = MallocOrDie (sizeof(int) * nseq);
+ for (i = 0; i < nseq; i++) a[i] = i;
+ na = nseq;
+ nb = 0;
+ nc = 0;
+
+ /* Main algorithm
+ */
+ while (na > 0)
+ {
+ v = a[na-1]; na--; /* pop a vertex off a, */
+ b[nb] = v; nb++; /* and push onto b */
+ while (nb > 0)
+ {
+ v = b[nb-1]; nb--; /* pop vertex off b */
+ c[v] = nc; /* assign it to component nc */
+ for (i = na-1; i >= 0; i--)/* backwards, becase of deletion/swapping we do*/
+ if (simple_distance(aseq[v], aseq[a[i]]) <= 1. - maxid) /* linked? */
+ {
+ w = a[i]; a[i] = a[na-1]; na--; /* delete w from a (note swap) */
+ b[nb] = w; nb++; /* push w onto b */
+ }
+ }
+ nc++;
+ }
+
+ /* Cleanup and return
+ */
+ free(a);
+ free(b);
+ *ret_c = c;
+ *ret_nc = nc;
+ return;
+}
--- /dev/null
+* Clustal Omega:\r
+Fabian Sievers UCD Dublin, Ireland\r
+Andreas Wilm UCD Dublin, Ireland\r
+David Dineen UCD Dublin, Ireland\r
+Johannes Söding Gene Center Munich, Germany\r
+Michael Remmert Gene Center Munich, Germany\r
+\r
+* Clustal 2\r
+Mark Larkin UCD Dublin, Ireland\r
+\r
+* Clustal 1.X\r
+Toby Gibson EMBL Heidelberg, Germany\r
+Des Higgins UCC Cork, Ireland\r
+Julie Thompson IGBMC Strasbourg, France\r
+\r
+* Contributors:\r
+Chenna Ramu EMBL Heidelberg, Germany\r
+Nigel Brown EMBL Heidelberg, Germany\r
+\r
+\r
--- /dev/null
+ GNU GENERAL PUBLIC LICENSE\r
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+\r
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+\r
+ <signature of Ty Coon>, 1 April 1989\r
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+\r
+This General Public License does not permit incorporating your program into\r
+proprietary programs. If your program is a subroutine library, you may\r
+consider it more useful to permit linking proprietary applications with the\r
+library. If this is what you want to do, use the GNU Lesser General\r
+Public License instead of this License.\r
--- /dev/null
+2010-06-17 Release 0.0.1 (Dubliniensis)\r
+ \r
+ First "release" as program has been able for a while to perform\r
+ all basic tasks without problems.\r
+\r
+ Non-standard features already built-in include:\r
+ HMM-iteration (using HMMER for building an HMM) and guide-tree\r
+ iteration. On top of that HMM input works fine and\r
+ background-frequencies are added to the HHalign process.\r
+ \r
+ Known issues: RNA/DNA alignment is considered buggy. Aligned\r
+ sequences have to be dealigned for HHalign to work properly.\r
+ \r
+ The HMMER version message can be ignored if no HMM-iteration\r
+ was used.\r
--- /dev/null
+The impatient can try:\r
+\r
+$ ./configure\r
+$ make\r
+$ make install\r
+\r
+\r
+Clustal-Omega needs argtable2 (http://argtable.sourceforge.net/). If\r
+argtable2 is installed in a non-standard directory you might have to\r
+point configure to its installation directory. For example, if you are\r
+on a Mac and have argtable installed via MacPorts then you should use\r
+the following command line:\r
+\r
+$ ./configure CFLAGS='-I/opt/local/include' LDFLAGS='-L/opt/local/lib'\r
+\r
+ClustalO will automatically support multi-threading if your compiler\r
+supports OpenMP. For some reason automake's OpenMP detection for\r
+Apple's gcc is broken. You can force OpenMP detection by calling configure \r
+like so:\r
+\r
+$ ./configure OPENMP_CFLAGS='-fopenmp' CFLAGS='-DHAVE_OPENMP'\r
+\r
+You could use a non-Apple gcc installed via MacPorts, adding\r
+\r
+CC=/opt/local/bin/gcc-mp-4.5\r
+\r
+to the configure call (you will have to change the exact string to match\r
+your gcc version).\r
+\r
+See below for generic installation instructions:\r
+\r
+----------------------------------------------------------------------\r
+\r
+\r
+\r
+Installation Instructions\r
+*************************\r
+\r
+Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005,\r
+2006, 2007, 2008, 2009 Free Software Foundation, Inc.\r
+\r
+ Copying and distribution of this file, with or without modification,\r
+are permitted in any medium without royalty provided the copyright\r
+notice and this notice are preserved. This file is offered as-is,\r
+without warranty of any kind.\r
+\r
+Basic Installation\r
+==================\r
+\r
+ Briefly, the shell commands `./configure; make; make install' should\r
+configure, build, and install this package. The following\r
+more-detailed instructions are generic; see the `README' file for\r
+instructions specific to this package. Some packages provide this\r
+`INSTALL' file but do not implement all of the features documented\r
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+necessarily a bug. More recommendations for GNU packages can be found\r
+in *note Makefile Conventions: (standards)Makefile Conventions.\r
+\r
+ The `configure' shell script attempts to guess correct values for\r
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+you can run in the future to recreate the current configuration, and a\r
+file `config.log' containing compiler output (useful mainly for\r
+debugging `configure').\r
+\r
+ It can also use an optional file (typically called `config.cache'\r
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+cache files.\r
+\r
+ If you need to do unusual things to compile the package, please try\r
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+be considered for the next release. If you are using the cache, and at\r
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+may remove or edit it.\r
+\r
+ The file `configure.ac' (or `configure.in') is used to create\r
+`configure' by a program called `autoconf'. You need `configure.ac' if\r
+you want to change it or regenerate `configure' using a newer version\r
+of `autoconf'.\r
+\r
+ The simplest way to compile this package is:\r
+\r
+ 1. `cd' to the directory containing the package's source code and type\r
+ `./configure' to configure the package for your system.\r
+\r
+ Running `configure' might take a while. While running, it prints\r
+ some messages telling which features it is checking for.\r
+\r
+ 2. Type `make' to compile the package.\r
+\r
+ 3. Optionally, type `make check' to run any self-tests that come with\r
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+\r
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+\r
+ 5. Optionally, type `make installcheck' to repeat any self-tests, but\r
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+ This target does not install anything. Running this target as a\r
+ regular user, particularly if the prior `make install' required\r
+ root privileges, verifies that the installation completed\r
+ correctly.\r
+\r
+ 6. You can remove the program binaries and object files from the\r
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+ for the package's developers. If you use it, you may have to get\r
+ all sorts of other programs in order to regenerate files that came\r
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+\r
+ 7. Often, you can also type `make uninstall' to remove the installed\r
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+ GNU Coding Standards.\r
+\r
+ 8. Some packages, particularly those that use Automake, provide `make\r
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+ targets like `make install' and `make uninstall' work correctly.\r
+ This target is generally not run by end users.\r
+\r
+Compilers and Options\r
+=====================\r
+\r
+ Some systems require unusual options for compilation or linking that\r
+the `configure' script does not know about. Run `./configure --help'\r
+for details on some of the pertinent environment variables.\r
+\r
+ You can give `configure' initial values for configuration parameters\r
+by setting variables in the command line or in the environment. Here\r
+is an example:\r
+\r
+ ./configure CC=c99 CFLAGS=-g LIBS=-lposix\r
+\r
+ *Note Defining Variables::, for more details.\r
+\r
+Compiling For Multiple Architectures\r
+====================================\r
+\r
+ You can compile the package for more than one kind of computer at the\r
+same time, by placing the object files for each architecture in their\r
+own directory. To do this, you can use GNU `make'. `cd' to the\r
+directory where you want the object files and executables to go and run\r
+the `configure' script. `configure' automatically checks for the\r
+source code in the directory that `configure' is in and in `..'. This\r
+is known as a "VPATH" build.\r
+\r
+ With a non-GNU `make', it is safer to compile the package for one\r
+architecture at a time in the source code directory. After you have\r
+installed the package for one architecture, use `make distclean' before\r
+reconfiguring for another architecture.\r
+\r
+ On MacOS X 10.5 and later systems, you can create libraries and\r
+executables that work on multiple system types--known as "fat" or\r
+"universal" binaries--by specifying multiple `-arch' options to the\r
+compiler but only a single `-arch' option to the preprocessor. Like\r
+this:\r
+\r
+ ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \\r
+ CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \\r
+ CPP="gcc -E" CXXCPP="g++ -E"\r
+\r
+ This is not guaranteed to produce working output in all cases, you\r
+may have to build one architecture at a time and combine the results\r
+using the `lipo' tool if you have problems.\r
+\r
+Installation Names\r
+==================\r
+\r
+ By default, `make install' installs the package's commands under\r
+`/usr/local/bin', include files under `/usr/local/include', etc. You\r
+can specify an installation prefix other than `/usr/local' by giving\r
+`configure' the option `--prefix=PREFIX', where PREFIX must be an\r
+absolute file name.\r
+\r
+ You can specify separate installation prefixes for\r
+architecture-specific files and architecture-independent files. If you\r
+pass the option `--exec-prefix=PREFIX' to `configure', the package uses\r
+PREFIX as the prefix for installing programs and libraries.\r
+Documentation and other data files still use the regular prefix.\r
+\r
+ In addition, if you use an unusual directory layout you can give\r
+options like `--bindir=DIR' to specify different values for particular\r
+kinds of files. Run `configure --help' for a list of the directories\r
+you can set and what kinds of files go in them. In general, the\r
+default for these options is expressed in terms of `${prefix}', so that\r
+specifying just `--prefix' will affect all of the other directory\r
+specifications that were not explicitly provided.\r
+\r
+ The most portable way to affect installation locations is to pass the\r
+correct locations to `configure'; however, many packages provide one or\r
+both of the following shortcuts of passing variable assignments to the\r
+`make install' command line to change installation locations without\r
+having to reconfigure or recompile.\r
+\r
+ The first method involves providing an override variable for each\r
+affected directory. For example, `make install\r
+prefix=/alternate/directory' will choose an alternate location for all\r
+directory configuration variables that were expressed in terms of\r
+`${prefix}'. Any directories that were specified during `configure',\r
+but not in terms of `${prefix}', must each be overridden at install\r
+time for the entire installation to be relocated. The approach of\r
+makefile variable overrides for each directory variable is required by\r
+the GNU Coding Standards, and ideally causes no recompilation.\r
+However, some platforms have known limitations with the semantics of\r
+shared libraries that end up requiring recompilation when using this\r
+method, particularly noticeable in packages that use GNU Libtool.\r
+\r
+ The second method involves providing the `DESTDIR' variable. For\r
+example, `make install DESTDIR=/alternate/directory' will prepend\r
+`/alternate/directory' before all installation names. The approach of\r
+`DESTDIR' overrides is not required by the GNU Coding Standards, and\r
+does not work on platforms that have drive letters. On the other hand,\r
+it does better at avoiding recompilation issues, and works well even\r
+when some directory options were not specified in terms of `${prefix}'\r
+at `configure' time.\r
+\r
+Optional Features\r
+=================\r
+\r
+ If the package supports it, you can cause programs to be installed\r
+with an extra prefix or suffix on their names by giving `configure' the\r
+option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.\r
+\r
+ Some packages pay attention to `--enable-FEATURE' options to\r
+`configure', where FEATURE indicates an optional part of the package.\r
+They may also pay attention to `--with-PACKAGE' options, where PACKAGE\r
+is something like `gnu-as' or `x' (for the X Window System). The\r
+`README' should mention any `--enable-' and `--with-' options that the\r
+package recognizes.\r
+\r
+ For packages that use the X Window System, `configure' can usually\r
+find the X include and library files automatically, but if it doesn't,\r
+you can use the `configure' options `--x-includes=DIR' and\r
+`--x-libraries=DIR' to specify their locations.\r
+\r
+ Some packages offer the ability to configure how verbose the\r
+execution of `make' will be. For these packages, running `./configure\r
+--enable-silent-rules' sets the default to minimal output, which can be\r
+overridden with `make V=1'; while running `./configure\r
+--disable-silent-rules' sets the default to verbose, which can be\r
+overridden with `make V=0'.\r
+\r
+Particular systems\r
+==================\r
+\r
+ On HP-UX, the default C compiler is not ANSI C compatible. If GNU\r
+CC is not installed, it is recommended to use the following options in\r
+order to use an ANSI C compiler:\r
+\r
+ ./configure CC="cc -Ae -D_XOPEN_SOURCE=500"\r
+\r
+and if that doesn't work, install pre-built binaries of GCC for HP-UX.\r
+\r
+ On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot\r
+parse its `<wchar.h>' header file. The option `-nodtk' can be used as\r
+a workaround. If GNU CC is not installed, it is therefore recommended\r
+to try\r
+\r
+ ./configure CC="cc"\r
+\r
+and if that doesn't work, try\r
+\r
+ ./configure CC="cc -nodtk"\r
+\r
+ On Solaris, don't put `/usr/ucb' early in your `PATH'. This\r
+directory contains several dysfunctional programs; working variants of\r
+these programs are available in `/usr/bin'. So, if you need `/usr/ucb'\r
+in your `PATH', put it _after_ `/usr/bin'.\r
+\r
+ On Haiku, software installed for all users goes in `/boot/common',\r
+not `/usr/local'. It is recommended to use the following options:\r
+\r
+ ./configure --prefix=/boot/common\r
+\r
+Specifying the System Type\r
+==========================\r
+\r
+ There may be some features `configure' cannot figure out\r
+automatically, but needs to determine by the type of machine the package\r
+will run on. Usually, assuming the package is built to be run on the\r
+_same_ architectures, `configure' can figure that out, but if it prints\r
+a message saying it cannot guess the machine type, give it the\r
+`--build=TYPE' option. TYPE can either be a short name for the system\r
+type, such as `sun4', or a canonical name which has the form:\r
+\r
+ CPU-COMPANY-SYSTEM\r
+\r
+where SYSTEM can have one of these forms:\r
+\r
+ OS\r
+ KERNEL-OS\r
+\r
+ See the file `config.sub' for the possible values of each field. If\r
+`config.sub' isn't included in this package, then this package doesn't\r
+need to know the machine type.\r
+\r
+ If you are _building_ compiler tools for cross-compiling, you should\r
+use the option `--target=TYPE' to select the type of system they will\r
+produce code for.\r
+\r
+ If you want to _use_ a cross compiler, that generates code for a\r
+platform different from the build platform, you should specify the\r
+"host" platform (i.e., that on which the generated programs will\r
+eventually be run) with `--host=TYPE'.\r
+\r
+Sharing Defaults\r
+================\r
+\r
+ If you want to set default values for `configure' scripts to share,\r
+you can create a site shell script called `config.site' that gives\r
+default values for variables like `CC', `cache_file', and `prefix'.\r
+`configure' looks for `PREFIX/share/config.site' if it exists, then\r
+`PREFIX/etc/config.site' if it exists. Or, you can set the\r
+`CONFIG_SITE' environment variable to the location of the site script.\r
+A warning: not all `configure' scripts look for a site script.\r
+\r
+Defining Variables\r
+==================\r
+\r
+ Variables not defined in a site shell script can be set in the\r
+environment passed to `configure'. However, some packages may run\r
+configure again during the build, and the customized values of these\r
+variables may be lost. In order to avoid this problem, you should set\r
+them in the `configure' command line, using `VAR=value'. For example:\r
+\r
+ ./configure CC=/usr/local2/bin/gcc\r
+\r
+causes the specified `gcc' to be used as the C compiler (unless it is\r
+overridden in the site shell script).\r
+\r
+Unfortunately, this technique does not work for `CONFIG_SHELL' due to\r
+an Autoconf bug. Until the bug is fixed you can use this workaround:\r
+\r
+ CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash\r
+\r
+`configure' Invocation\r
+======================\r
+\r
+ `configure' recognizes the following options to control how it\r
+operates.\r
+\r
+`--help'\r
+`-h'\r
+ Print a summary of all of the options to `configure', and exit.\r
+\r
+`--help=short'\r
+`--help=recursive'\r
+ Print a summary of the options unique to this package's\r
+ `configure', and exit. The `short' variant lists options used\r
+ only in the top level, while the `recursive' variant lists options\r
+ also present in any nested packages.\r
+\r
+`--version'\r
+`-V'\r
+ Print the version of Autoconf used to generate the `configure'\r
+ script, and exit.\r
+\r
+`--cache-file=FILE'\r
+ Enable the cache: use and save the results of the tests in FILE,\r
+ traditionally `config.cache'. FILE defaults to `/dev/null' to\r
+ disable caching.\r
+\r
+`--config-cache'\r
+`-C'\r
+ Alias for `--cache-file=config.cache'.\r
+\r
+`--quiet'\r
+`--silent'\r
+`-q'\r
+ Do not print messages saying which checks are being made. To\r
+ suppress all normal output, redirect it to `/dev/null' (any error\r
+ messages will still be shown).\r
+\r
+`--srcdir=DIR'\r
+ Look for the package's source code in directory DIR. Usually\r
+ `configure' can determine that directory automatically.\r
+\r
+`--prefix=DIR'\r
+ Use DIR as the installation prefix. *note Installation Names::\r
+ for more details, including other options available for fine-tuning\r
+ the installation locations.\r
+\r
+`--no-create'\r
+`-n'\r
+ Run the configure checks, but stop before creating any output\r
+ files.\r
+\r
+`configure' also accepts some other, not widely useful, options. Run\r
+`configure --help' for more details.\r
+\r
--- /dev/null
+\r
+\r
+CLUSTAL-OMEGA is a general purpose multiple sequence alignment program\r
+for proteins.\r
+\r
+\r
+\r
+INTRODUCTION\r
+\r
+Clustal-Omega is a general purpose multiple sequence alignment (MSA)\r
+program for proteins. It produces high quality MSAs and is capable of\r
+handling data-sets of hundreds of thousands of sequences in reasonable\r
+time.\r
+\r
+In default mode, users give a file of sequences to be aligned and\r
+these are clustered to produce a guide tree and this is used to guide\r
+a "progressive alignment" of the sequences. There are also facilities\r
+for aligning existing alignments to each other, aligning a sequence to\r
+an alignment and for using a hidden Markov model (HMM) to help guide\r
+an alignment of new sequences that are homologous to the sequences\r
+used to make the HMM. This latter procedure is referred to as\r
+"external profile alignment" or EPA.\r
+\r
+Clustal-Omega uses HMMs for the alignment engine, based on the HHalign\r
+package from Johannes Soeding [1]. Guide trees are made using an\r
+enhanced version of mBed [2] which can cluster very large numbers of\r
+sequences in O(N*log(N)) time. Multiple alignment then proceeds by\r
+aligning larger and larger alignments using HHalign, following the\r
+clustering given by the guide tree.\r
+\r
+In its current form Clustal-Omega can only align protein sequences but\r
+not DNA/RNA sequences. It is envisioned that DNA/RNA will become\r
+available in a future version.\r
+\r
+\r
+\r
+SEQUENCE INPUT:\r
+\r
+-i, --in, --infile={<file>,-}\r
+ Multiple sequence input file (- for stdin)\r
+\r
+--hmm-in=<file>\r
+ HMM input files\r
+\r
+--dealign\r
+ Dealign input sequences\r
+\r
+--profile1, --p1=<file>\r
+ Pre-aligned multiple sequence file (aligned columns will be kept fixed)\r
+\r
+--profile2, --p2=<file>\r
+ Pre-aligned multiple sequence file (aligned columns will be kept fixed)\r
+\r
+\r
+For sequence and profile input Clustal-Omega uses the Squid library\r
+from Sean Eddy [3].\r
+\r
+\r
+Clustal-Omega accepts 3 types of sequence input: (i) a sequence file\r
+with un-aligned or aligned sequences, (ii) profiles (a multiple\r
+alignment in a file) of aligned sequences, (iii) a HMM. Valid\r
+combinations of the above are:\r
+\r
+(a) one file with un-aligned or aligned sequences (i); the sequences\r
+ will be aligned, and the alignment will be written out. For this\r
+ mode use the -i flag. If the sequences are aligned (all sequences\r
+ have the same length and at least one sequence has at least one\r
+ gap), then the alignment is turned into a HMM, the sequences are\r
+ de-aligned and the now un-aligned sequences are aligned using the\r
+ HMM as an External Profile for External Profile Alignment (EPA).\r
+ If no EPA is desired use the --dealign flag.\r
+\r
+ Use the above option to make a multiple alignment from a set of\r
+ sequences. A sequence file must contain more than one sequence (at\r
+ least two sequences).\r
+\r
+(b) two profiles (ii)+(ii); the columns in each profile will be kept\r
+ fixed and the alignment of the two profiles will be written\r
+ out. Use the --p1 and --p2 flags for this mode.\r
+\r
+ Use this option to align two alignments (profiles) together.\r
+\r
+(c) one file with un/aligned sequences (i) and one profile (ii); the\r
+ profile is converted into a HMM and the un-aligned sequences will\r
+ be multiply aligned (using the HMM background information) to form\r
+ a profile; this constructed profile is aligned with the input\r
+ profile; the columns in each profile (the original one and the one\r
+ created from the un-aligned sequences) will be kept fixed and the\r
+ alignment of the two profiles will be written out. Use the -i flag\r
+ in conjunction with the --p1 flag for this mode.\r
+ The un/aligned sequences file (i) must contain at least two\r
+ sequences. If a single sequence has to be aligned with a profile\r
+ the profile-profile option (b) has to be used.\r
+\r
+ Use the above option to add new sequences to an existing\r
+ alignment.\r
+\r
+(d) one file with un-aligned sequences (i) and one HMM (iii); the\r
+ un-aligned sequences will be aligned to form a profile, using the\r
+ HMM as an External Profile. So far only one HMM can be input and\r
+ only HMMer2 and HMMer3 formats are allowed. The alignment will be\r
+ written out; the HMM information is discarded. As, at the moment,\r
+ only one HMM can be used, no HMM is produced if the sequences are\r
+ already aligned. Use the -i flag in conjunction with the --hmm-in\r
+ flag for this mode. Multiple HMMs can be inputted, however, in the\r
+ current version all but the first HMM will be ignored.\r
+\r
+ Use this option to make a new multiple alignment of sequences from\r
+ the input file and use the HMM as a guide (EPA).\r
+\r
+\r
+Invalid combinations of the above are:\r
+\r
+(v) an un/aligned sequence file containing just one sequence (i)\r
+\r
+(w) an un/aligned sequence file containing just one sequence and a profile\r
+ (i)+(ii)\r
+\r
+(x) an un/aligned sequence file containing just one sequence and a HMM\r
+ (i)+(iii)\r
+\r
+(y) two or more HMMs (iii)+(iii)+... cannot be aligned to one another.\r
+\r
+(z) one profile (ii) cannot be aligned with a HMM (iii)\r
+\r
+\r
+The following MSA file formats are allowed:\r
+\r
+ a2m=fasta, (vienna)\r
+ clustal,\r
+ msf,\r
+ phylip,\r
+ selex,\r
+ stockholm\r
+\r
+\r
+Prior to MSA, Clustal-Omega de-aligns all sequence input (i). However,\r
+alignment information is automatically converted into a HMM and used\r
+during MSA, unless the --dealign flag is specifically set. Profiles\r
+(ii) are not de-aligned.\r
+\r
+The Clustal-Omega alignment engine can at the moment not process\r
+DNA/RNA. If a sequence input file (i) or a profile (ii) is interpreted\r
+as DNA/RNA the program will terminate during the file input stage.\r
+\r
+\r
+\r
+CLUSTERING:\r
+\r
+ --distmat-in=<file>\r
+ Pairwise distance matrix input file (skips distance computation)\r
+\r
+ --distmat-out=<file>\r
+ Pairwise distance matrix output file\r
+\r
+ --guidetree-in=<file>\r
+ Guide tree input file\r
+ (skips distance computation and guide tree clustering step)\r
+\r
+ --guidetree-out=<file>\r
+ Guide tree output file\r
+\r
+ --full\r
+ Use full distance matrix for guide-tree calculation (slow; mBed is default)\r
+\r
+ --full-iter\r
+ Use full distance matrix for guide-tree calculation during iteration (mBed is default)\r
+\r
+\r
+In order to produce a multiple alignment Clustal-Omega requires a\r
+guide tree which defines the order in which sequences/profiles are\r
+aligned. A guide tree in turn is constructed, based on a distance\r
+matrix. Conventionally, this distance matrix is comprised of all the\r
+pair-wise distances of the sequences. The distance measure\r
+Clustal-Omega uses for pair-wise distances of un-aligned sequences is\r
+the k-tuple measure [4], which was also implemented in Clustal 1.83\r
+and ClustalW2 [5,6]. If the sequences inputted via -i are aligned\r
+Clustal-Omega uses the Kimura-corrected pairwise aligned identities\r
+[7]. The computational effort (time/memory) to calculate and store a\r
+full distance matrix grows quadratically with the number of sequences.\r
+Clustal-Omega can improve this scalability to N*log(N) by employing a\r
+fast clustering algorithm called mBed [2]; this option is\r
+automatically invoked (default). If a full distance matrix evaluation\r
+is desired, then the --full flag has to be set. The mBed mode\r
+calculates a reduced set of pair-wise distances. These distances are\r
+used in a k-means algorithm, that clusters at most 100 sequences. For\r
+each cluster a full distance matrix is calculated. No full distance\r
+matrix (of all input sequences) is calculated in mBed mode. If there\r
+are less than 100 sequences in the input, then in effect a full\r
+distance matrix is calculated in mBed mode, however, no distance\r
+matrix can be outputted (see below).\r
+\r
+\r
+Clustal-Omega uses Muscle's [8] fast UPGMA implementation to construct\r
+its guide trees from the distance matrix. By default, the distance\r
+matrix is used internally to construct the guide tree and is then\r
+discarded. By specifying --distmat-out the internal distance matrix\r
+can be written to file. This is only possible in --full mode. The\r
+guide trees by default are used internally to guide the multiple\r
+alignment and are then discarded. By specifying the --guidetree-out\r
+option these internal guide trees can be written out to\r
+file. Conversely, the distance calculation and/or guide tree building\r
+stage can be skipped, by reading in a pre-calculated distance matrix\r
+and/or pre-calculated guide tree. These options are invoked by\r
+specifying the --distmat-in and/or --guidetree-in flags,\r
+respectively. However, distance matrix reading is disabled in the\r
+current version. By default, distance matrix and guide tree files are\r
+not over-written, if a file with the specified name already exists. In\r
+this case Clustal-Omega aborts during the command-line processing\r
+stage. To force over-writing of already existing files use the --force\r
+flag (see MISCELLANEOUS). In mBed mode a full distance matrix cannot\r
+be outputted, distance matrix output is only possible in --full mode.\r
+mBed or --full distance mode do not affect the ability to write out\r
+guide-trees.\r
+\r
+Guide trees can be iterated to refine the alignment (see section\r
+ITERATION). Clustal-Omega takes the alignment, that was produced\r
+initially and constructs a new distance matrix from this alignment.\r
+The distance measure used at this stage is the Kimura distance [7]. By\r
+default, Clustal-Omega constructs a reduced distance matrix at this\r
+stage using the mBed algorithm, which will then be used to create an\r
+improved (iterated) new guide tree. To turn off mBed-like clustering\r
+at this stage the --full-iter flag has to be set. While Kimura\r
+distances in general are much faster to calculate than k-tuple\r
+distances, time and memory requirements still scale quadratically with\r
+the number of sequences and --full-iter clustering should only be\r
+considered for smaller cases (<< 10,000 sequences).\r
+\r
+\r
+\r
+ALIGNMENT OUTPUT:\r
+\r
+ -o, --out, --outfile={file,-} Multiple sequence alignment output file (default: stdout)\r
+\r
+ --outfmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]} MSA output file format (default: fasta)\r
+\r
+\r
+By default Clustal-Omega writes its results (alignments) to stdout. An\r
+output file can be specified with the -o flag. Output to stdout is not\r
+possible in verbose mode (-v, see MISCELLANEOUS) as verbose/debugging\r
+messages would interfere with the alignment output. By default,\r
+alignment files are not over-written, if a file with the specified\r
+name already exists. In this case Clustal-Omega aborts during the\r
+command-line processing stage. To force over-writing of already\r
+existing files use the --force flag (see MISCELLANEOUS).\r
+\r
+Clustal-Omega can output alignments in various formats by setting the\r
+--outfmt flag:\r
+\r
+ * for Fasta format set: --outfmt=a2m or --outfmt=fa or --outfmt=fasta\r
+\r
+ * for Clustal format set: --outfmt=clu or --outfmt=clustal\r
+\r
+ * for Msf format: set --outfmt= msf\r
+\r
+ * for Phylip format set: --outfmt=phy or --outfmt=phylip\r
+\r
+ * for Selex format set: --outfmt=selex\r
+\r
+ * for Stockholm format set: --outfmt=st or --outfmt=stockholm\r
+\r
+ * for Vienna format set: --outfmt=vie or --outfmt=vienna\r
+\r
+\r
+ITERATION:\r
+\r
+ --iterations, --iter=<n> Number of (combined guide tree/HMM) iterations\r
+\r
+ --max-guidetree-iterations=<n> Maximum guide tree iterations\r
+\r
+ --max-hmm-iterations=<n> Maximum number of HMM iterations\r
+\r
+\r
+By default, Clustal-Omega calculates (or reads in) a guide tree and\r
+performs a multiple alignment in the order specified by this guide\r
+tree. This alignment is then outputted. Clustal-Omega can 'iterate'\r
+its guide tree. The hope is that the (Kimura) distances, that can be\r
+derived from the initial alignment, will give rise to a better guide\r
+tree, and by extension, to a better alignment.\r
+\r
+A similar rationale applies to HMM-iteration. MSAs in general are very\r
+'vulnerable' at their early stages. Sequences that are aligned at an\r
+early stage remain fixed for the rest of the MSA. Another way of\r
+putting this is: 'once a gap, always a gap'. This behaviour can be\r
+mitigated by HMM iteration. An initial alignment is created and turned\r
+into a HMM. This HMM can help in a new round of MSA to 'anticipate'\r
+where residues should align. This is using the HMM as an External\r
+Profile and carrying out iterative EPA. In practice, individual\r
+sequences and profiles are aligned to the External HMM, derived after\r
+the initial alignment. Pseudo-count information is then transferred to\r
+the (internal) HMM, corresponding to the individual\r
+sequence/profile. The now somewhat 'softened' sequences/profiles are\r
+then in turn aligned in the order specified by the guide\r
+tree. Pseudo-count transfer is reduced with the size of the\r
+profile. Individual sequences attain the greatest pseudo-count\r
+transfer, larger profiles less so. Pseudo-count transfer to profiles\r
+larger than, say, 10 is negligible. The effect of HMM iteration is\r
+more pronounced in larger test sets (that is, with more sequences).\r
+\r
+Both, HMM- and guide tree-iteration come at a cost of increasing the\r
+run-time. One round of guide tree iteration adds on (roughly) the time\r
+it took to construct the initial alignment. If, for example, the\r
+initial alignment took 1min, then it will take (roughly) 2min to\r
+iterate the guide tree once, 3min to iterate the guide tree twice, and\r
+so on. HMM-iteration is more costly, as each round of iteration adds\r
+three times the time required for the alignment stage. For example, if\r
+the initial alignment took 1min, then each additional round of HMM\r
+iteration will add on 3min; so 4 iterations will take 13min\r
+(=1min+4*3min). The factor of 3 stems from the fact that at every\r
+stage both intermediate profiles have to be aligned with the\r
+background HMM, and finally the (softened) HMMs have to be aligned as\r
+well. All times are quoted for single processors.\r
+\r
+By default, guide tree iteration and HMM-iteration are coupled. This\r
+means, at each iteration step both, guide tree and HMM, are\r
+re-calculated. This is invoked by setting the --iter flag. For\r
+example, if --iter=1, then first an initial alignment is produced\r
+(without external HMM background information and using k-tuple\r
+distances to calculate the guide tree). This initial alignment is then\r
+used to re-calculate a new guide tree (using Kimura distances) and to\r
+create a HMM. The new guide tree and the HMM are then used to produce\r
+a new MSA.\r
+\r
+Iteration of guide tree and HMM can be de-coupled. This means that the\r
+number of guide tree iterations and HMM iterations can be\r
+different. This can be done by combining the --iter flag with the\r
+--max-guidetree-iterations and/or the --max-hmm-iterations flag. The\r
+number of guide tree iterations is the minimum of --iter and\r
+--max-guidetree-iterations, while the number of HMM iterations is the\r
+minimum of --iter and --max-hmm-iterations. If, for example, HMM\r
+iteration should be performed 5 times but guide tree iteration should\r
+be performed only 3 times, then one should set --iter=5 and\r
+--max-guidetree-iterations=3. All three flags can be specified at the\r
+same time (however, this makes no sense). It is not sufficient just to\r
+specify --max-guidetree-iterations and --max-hmm-iterations but not\r
+--iter. If any iteration is desired --iter has to be set.\r
+\r
+\r
+LIMITS (will exit early, if exceeded):\r
+\r
+ --maxnumseq=<n> Maximum allowed number of sequences\r
+\r
+ --maxseqlen=<l> Maximum allowed sequence length\r
+\r
+Limits can be imposed on the number of sequences in the input file\r
+and/or the lengths of the sequences. This cap can be set with the\r
+--maxnumseq and --maxseqlen flags, respectively. Clustal-Omega will\r
+exit early, if these limits are exceeded.\r
+\r
+\r
+MISCELLANEOUS:\r
+\r
+ --auto Set options automatically (might overwrite some of your options)\r
+\r
+ --threads=<n> Number of processors to use\r
+\r
+ -l, --log=<file> Log all non-essential output to this file\r
+\r
+ -h, --help Print help and exit\r
+\r
+ -v, --verbose Verbose output (increases if given multiple times)\r
+\r
+ --version Print version information and exit\r
+\r
+ --long-version Print long version information and exit\r
+\r
+ --force Force file overwriting\r
+\r
+\r
+Users may feel unsure which options are appropriate in certain\r
+situations even though using ClustalO without any special options\r
+should give you the desired results. The --auto flag tries to\r
+alleviate this problem and selects accuracy/speed flags according to\r
+the number of sequences. For all cases will use mBed and thereby\r
+possibly overwrite the --full option. For more than 1,000 sequences\r
+the iteration is turned off as the effect of iteration is more\r
+noticeable for 'larger' problems. Otherwise iterations are set to 1 if\r
+not already set to a higher value by the user. Expert users may want\r
+to avoid this flag and exercise more fine tuned control by selecting\r
+the appropriate options manually.\r
+\r
+Certain parts of the MSA calculation have been parallelised. Most\r
+noticeably, the distance matrix calculation, and certain aspects of\r
+the HMM building stage. Clustal-Omega uses OpenMP. By default,\r
+Clustal-Omega will attempt to use as many threads as possible. For\r
+example, on a 4-core machine Clustal-Omega will attempt to use 4\r
+threads. The number of threads can be limited by setting the --threads\r
+flag. This may be desirable, for example, in the case of\r
+benchmarking/timing.\r
+\r
+Usually, non-essential (verbose) output is written to screen. This\r
+output can be written to file by specifying the --log flag.\r
+\r
+Help is available by specifying the -h flag.\r
+\r
+By default Clustal-Omega does not print any information to stdout\r
+(other than the final alignment, if no output file is\r
+specified). Information concerning the progress of the alignment can\r
+be obtained by specifying one verbosity flag (-v). This may be\r
+desirable, to verify what Clustal-Omega is actually doing at the\r
+moment. If two verbosity flags (-v -v) are specified, command-line\r
+flags (explicitly and implicitly set) are printed in addition to the\r
+progress report. Triple verbose level (-v -v -v) is the most verbose\r
+level. In addition to single- and double-verbose information much more\r
+information is displayed: input sequences and names, details of the\r
+tree construction and intermediate alignments. Tree construction\r
+information includes pairwise distances. The number of pairwise\r
+distances scales with the square of the number of sequences, and\r
+double verbose mode is probably only useful for a small number of\r
+sequences.\r
+\r
+The current version number of Clustal-Omega can be displayed by\r
+setting the --version flag.\r
+\r
+The current version number of Clustal-Omega as well as the code-name\r
+and the build date can be displayed by setting the --long-version\r
+flag.\r
+\r
+By default, Clustal-Omega does not over-write files. These can be (i)\r
+alignment output, (ii) distance matrix and (iii) guide\r
+tree. Overwriting can be forced by setting the --force flag.\r
+\r
+\r
+EXAMPLES:\r
+\r
+./clustalo -i globin.fa\r
+\r
+Clustal-Omega reads the sequence file globin.fa, aligns the sequences\r
+and prints the result to screen in fasta/a2m format.\r
+\r
+\r
+./clustalo -i globin.fa -o globin.sto --outfmt=st\r
+\r
+If the file globin.sto does not exist, then Clustal-Omega reads the\r
+sequence file globin.fa, aligns the sequences and prints the result to\r
+globin.sto in Stockholm format. If the file globin.sto does exist\r
+already, then Clustal-Omega terminates the alignment process before\r
+reading globin.fa.\r
+\r
+\r
+./clustalo -i globin.fa -o globin.aln --outfmt=clu --force\r
+\r
+Clustal-Omega reads the sequence file globin.fa, aligns the sequences\r
+and prints the result to globin.aln in Clustal format, overwriting the\r
+file globin.aln, if it already exists.\r
+\r
+\r
+./clustalo -i globin.fa --distmat-out=globin.mat --guidetree-out=globin.dnd --force\r
+\r
+Clustal-Omega reads the sequence file globin.fa, aligns the sequences,\r
+prints the result to screen in fasta/a2m format (default), the guide\r
+tree to globin.dnd and the distance matrix to globin.mat, overwriting\r
+those files if they already exist.\r
+\r
+\r
+./clustalo -i globin.fa --guidetree-in=globin.dnd\r
+\r
+Clustal-Omega reads the files globin.fa and globin.dnd, skipping\r
+distance calculation and guide tree creation, using instead the guide\r
+tree specified in globin.dnd.\r
+\r
+\r
+./clustalo -i globin.fa --hmm-in=PF00042.hmm\r
+\r
+Clustal-Omega reads the sequence file globin.fa and the HMM file\r
+PF00042.hmm (in HMMer2 or HMMer3 format). It then performs the\r
+alignment, transferring pseudo-count information contained in\r
+PF00042.hmm to the sequences/profiles during the MSA.\r
+\r
+\r
+./clustalo -i globin.sto\r
+\r
+Clustal-Omega reads the file globin.sto (of aligned sequences in\r
+Stockholm format). It converts the alignment into a HMM, de-aligns the\r
+sequences and re-aligns them, transferring pseudo-count information to\r
+the sequences/profiles during the MSA. The guide tree is constructed\r
+using a full distance matrix of Kimura distances.\r
+\r
+\r
+./clustalo -i globin.sto --dealign\r
+\r
+Clustal-Omega reads the file globin.sto (of aligned sequences in\r
+Stockholm format). It de-aligns the sequences and then re-aligns\r
+them. No HMM is produced in the process, no pseudo-count information\r
+is transferred. Consequently, the output must be the same as for\r
+unaligned output (like in the first example ./clustalo -i globin.fa)\r
+\r
+\r
+./clustalo -i globin.fa --iter=2\r
+\r
+Clustal-Omega reads the file globin.fa, creates a UPGMA guide tree\r
+built from k-tuple distances, and performs an initial alignment. This\r
+initial alignment is converted into a HMM and a new guide tree is\r
+built from the Kimura distances of the initial alignment. The\r
+un-aligned sequences are then aligned (for the second time but this\r
+time) using pseudo-count information from the HMM created after the\r
+initial alignment (and using the new guide tree). This second\r
+alignment is then again converted into a HMM and a new guide tree is\r
+constructed. The un-aligned sequences are then aligned (for a third\r
+time), again using pseudo-count information of the HMM from the\r
+previous step and the most recent guide tree. The final alignment is\r
+written to screen.\r
+\r
+\r
+./clustalo -i globin.fa --iter=5 --max-guidetree-iterations=1\r
+\r
+Clustal-Omega reads the file globin.fa, creates a UPGMA guide tree\r
+built from k-tuple distances, and performs an initial alignment. This\r
+initial alignment is converted into a HMM and a new guide tree is\r
+built from the Kimura distances of the initial alignment. The\r
+un-aligned sequences are then aligned (for the second time but this\r
+time) using pseudo-count information from the HMM created after the\r
+initial alignment (and using the new guide tree). For the last 4\r
+iterations the guide tree is left unchanged and only HMM iteration is\r
+performed. This means that intermediate alignments are converted to\r
+HMMs, and these intermediate HMMs are used to guide the MSA during\r
+subsequent iteration stages.\r
+\r
+\r
+./clustalo -i globin.fa -o globin.a2m -v\r
+\r
+In case the file globin.a2m does not exist, Clustal-Omega reads the\r
+file globin.fa, prints a progress report to screen and writes the\r
+alignment in (default) Fasta format to globin.a2m. The progress report\r
+consists of the number of threads used, the number of sequences read,\r
+the current progress in the k-tuple distance calculation, completion\r
+of the guide tree computation and current progress of the MSA stage.\r
+If the file globin.a2m already exists Clustal-Omega aborts before\r
+reading the file globin.fa. Note that in verbose mode an output file\r
+has to be specified, because progress/debugging information, which is\r
+printed to screen, would interfere with the alignment being printed to\r
+screen.\r
+\r
+\r
+./clustalo -i PF00042_full.fa --dealign --full --outfmt=vie -o PF00042_full.vie --force\r
+\r
+Clustal-Omega reads the file PF00042_full.fa. This file contains\r
+several thousand aligned sequences. --dealign tells Clustal-Omega to\r
+erase all alignment information and re-align the sequences from\r
+scratch. As there are several thousand sequences calculating a full\r
+distance matrix may be slow. Setting the --full flag specifically\r
+selects the full distance mode over the default mBed mode. The\r
+alignment is then written out in Vienna format (fasta format all on\r
+one line, no line breaks per sequence) to file PF00042_full.vie.\r
+\r
+\r
+./clustalo -i PF00042_full.fa --dealign --outfmt=vie -o PF00042_full.vie --force\r
+\r
+Clustal-Omega reads the file PF00042_full.fa. This file contains\r
+several thousand aligned sequences. --dealign tells Clustal-Omega to\r
+erase all alignment information and re-align the sequences from\r
+scratch. Calculating the distance matrix will be done by mBed\r
+(default). Clustal-Omega will calculate pairwise distances to a\r
+small number of reference sequences only. This will give a significant\r
+speed-up. The speed-up is greater for larger families (more\r
+sequences). The alignment is then written out in Vienna format (fasta\r
+format all on one line, no line breaks per sequence) to file\r
+PF00042_full.vie.\r
+\r
+\r
+./clustalo --p1=globin.sto --p2=PF00042_full.vie -o globin+pf00042.fa\r
+\r
+Clustal-Omega reads files globin.sto and PF00042_full.vie of aligned\r
+sequences (profiles). Both profiles are then aligned. The relative\r
+positions of residues in both profiles are not changed during this\r
+alignment, however, columns of gaps may be inserted into the profiles,\r
+respectively. The final alignment is written to file globin+pf00042.fa\r
+in fasta format.\r
+\r
+\r
+./clustalo -i globin.fa --p1=PF00042_full.vie -o pf00042+globin.fa\r
+\r
+Clustal-Omega reads file globin.fa of un-aligned sequences and the\r
+profile (of aligned sequences) in file PF00042_full.vie. A HMM is\r
+created from the profile. This HMM is used to guide the alignment of\r
+the un-aligned sequences in globin.fa. The profile that was generated\r
+during this alignment of un-aligned globin.fa sequences is then\r
+aligned to the input profile PF00042_full.vie. The relative positions\r
+of residues in profile PF00042_full.vie is not changed during this\r
+alignment, however, columns of gaps may be inserted into the\r
+profile. The final alignment is output to file pf00042+globin.fa in\r
+fasta format. The alignment in this example may be slightly different\r
+from the alignment in the previous example, because no HMM guidance\r
+was used generate the profile globin.sto. In this example HMM guidance\r
+was used to align the sequences in globin.fa; the hope being that this\r
+intermediate alignment will have profited from the bigger profile.\r
+\r
+\r
+\r
+LITERATURE:\r
+\r
+[1] Johannes Soding (2005) Protein homology detection by HMM-HMM\r
+ comparison. Bioinformatics 21 (7): 951–960.\r
+\r
+[2] Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG. Sequence\r
+ embedding for fast construction of guide trees for multiple\r
+ sequence alignment. Algorithms Mol Biol. 2010 May 14;5:21.\r
+\r
+[3] http://www.genetics.wustl.edu/eddy/software/#squid\r
+\r
+[4] Wilbur and Lipman, 1983; PMID 6572363\r
+\r
+[5] Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: improving\r
+ the sensitivity of progressive multiple sequence alignment through\r
+ sequence weighting, position-specific gap penalties and weight\r
+ matrix choice. Nucleic Acids Res., 22, 4673-4680.\r
+\r
+[6] Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA,\r
+ McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD,\r
+ Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version\r
+ 2.0. Bioinformatics, 23, 2947-2948.\r
+\r
+[7] Kimura M (1980). "A simple method for estimating evolutionary\r
+ rates of base substitutions through comparative studies of\r
+ nucleotide sequences". Journal of Molecular Evolution 16: 111–120.\r
+\r
+[8] Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high\r
+ accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.\r
+\r
--- /dev/null
+ISSUES: \r
+\r
+-auto \r
+\r
+WARNING: Unsupported old command line option '-auto' will be ignored\r
+WARNING: Your old-style command-line options were converted to: D:\workspace\JABA2\binaries\windows\clustalo\clustalo.exe --outfmt=clustal --log=stat.log --infile=D:\workspace\JABA2\testsrc\testdata\TO1381.fasta --outfile=TO1381.clustal.out -o clustal.aln -v --force\r
+WARNING: This is a beta version of Clustal Omega, for protein only.\r
+For more information try: D:\workspace\JABA2\binaries\windows\clustalo\clustalo.exe --help\r
+\r
#clustalw.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
\r
\r
+###### CLUSTAL OMEGA CONFIGURATION ######\r
+local.clustalo.bin.windows=binaries/windows/clustalo/clustalo.exe\r
+local.clustalo.bin=binaries/src/clustalo/clustalo\r
+#cluster.clustalo.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalo/clustalo\r
+## This parameters specifies the directory where the matrices files are stored \r
+clustalo.presets.file=conf/settings/ClustalPresets.xml\r
+clustalo.parameters.file=conf/settings/ClustalParameters.xml\r
+#clustalo.limits.file=conf/settings/ClustalLimits.xml\r
+#clustalo.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+\r
+\r
###### MUSCLE CONFIGURATION ######\r
local.muscle.bin.windows=binaries/windows/muscle.exe\r
local.muscle.bin=binaries/src/muscle/muscle\r
--- /dev/null
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
+<limits>\r
+ <runnerClassName>compbio.runner.clustal.ClustalW</runnerClassName>\r
+ <limit isDefault="true">\r
+ <seqNumber>1000</seqNumber>\r
+ <seqLength>1000</seqLength>\r
+ </limit>\r
+ <limit isDefault="false">\r
+ <preset># LocalEngineExecutionLimit #</preset>\r
+ <seqNumber>30</seqNumber>\r
+ <seqLength>500</seqLength>\r
+ </limit>\r
+\r
+ <!-- Limits for presets -->\r
+ <limit isDefault="false">\r
+ <preset>Disable gap weighting (Speed-oriented)</preset>\r
+ <seqNumber>1000</seqNumber>\r
+ <seqLength>3000</seqLength>\r
+ </limit>\r
+\r
+</limits>\r
--- /dev/null
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
+<runnerConfig>\r
+ <runnerClassName>compbio.runner.msa.ClustalO</runnerClassName>\r
+ <options>\r
+ <name>Dealign</name>\r
+ <description>Dealign input sequences</description>\r
+ <optionNames>--dealign</optionNames>\r
+ <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
+ </options>\r
+ <options>\r
+ <name>Full distance matrix</name>\r
+ <description>Use full distance matrix for guide-tree calculation (slow; mBed is default)</description>\r
+ <optionNames>--full</optionNames>\r
+ <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
+ </options>\r
+ <options>\r
+ <name>Full distance matrix for each iteration</name>\r
+ <description>Use full distance matrix for guide-tree calculation during iteration (mBed is default)</description>\r
+ <optionNames>--full-iter</optionNames>\r
+ <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
+ </options>\r
+ <prmSeparator>=</prmSeparator>\r
+ <parameters>\r
+ <name>Max Guide tree iterations</name>\r
+ <description>Maximum number of HMM iterations</description>\r
+ <optionNames>--max-hmm-iterations</optionNames>\r
+ <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
+ <defaultValue>1</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>1</min>\r
+ <max>100</max>\r
+ </validValue>\r
+ </parameters>\r
+ <parameters>\r
+ <name>Number of iterations (combined)</name>\r
+ <description>Number of (combined guide tree/HMM) iterations</description>\r
+ <optionNames>--iter</optionNames>\r
+ <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
+ <defaultValue>1</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>1</min>\r
+ <max>100</max>\r
+ </validValue>\r
+ </parameters>\r
+ <parameters>\r
+ <name>Max Guide tree iterations</name>\r
+ <description>Maximum guide tree iterations</description>\r
+ <optionNames>--max-guidetree-iterations</optionNames>\r
+ <furtherDetails>prog_docs/clustalo.txt</furtherDetails>\r
+ <defaultValue>1</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>1</min>\r
+ <max>100</max>\r
+ </validValue>\r
+ </parameters>\r
+</runnerConfig>\r
--- /dev/null
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
+<presets>\r
+ <runnerClassName>compbio.runner.clustal.ClustalW</runnerClassName>\r
+ <preset>\r
+ <name>Disable gap weighting (Speed-oriented)</name>\r
+ <description></description>\r
+ <optlist>\r
+ <option>-NOPGAP</option>\r
+ <option>-NOWEIGHTS</option>\r
+ <option>-NOHGAP</option>\r
+ </optlist>\r
+ </preset>\r
+</presets>\r
--- /dev/null
+/* Copyright (c) 2009 Peter Troshin\r
+ * \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0\r
+ * \r
+ * This library is free software; you can redistribute it and/or modify it under the terms of the\r
+ * Apache License version 2 as published by the Apache Software Foundation\r
+ * \r
+ * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
+ * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
+ * License for more details.\r
+ * \r
+ * A copy of the license is in apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
+ * \r
+ * Any republication or derived work distributed in source code form\r
+ * must include this copyright and license notice.\r
+ */\r
+\r
+package compbio.runner.msa;\r
+\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+import java.util.Arrays;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.data.sequence.Alignment;\r
+import compbio.data.sequence.UnknownFileFormatException;\r
+import compbio.engine.client.SkeletalExecutable;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.runner.Util;\r
+\r
+public class ClustalO extends SkeletalExecutable<ClustalO> {\r
+\r
+ private static Logger log = Logger.getLogger(ClustalO.class);\r
+ private static final String EXEC_STAT_FILE = "stat.log";\r
+ private static final String TREE_FILE_EXT = ".dnd";\r
+\r
+ public static final String KEY_VALUE_SEPARATOR = "=";\r
+\r
+ /**\r
+ * \r
+ * --auto Set options automatically (might overwrite some of your options)\r
+ * \r
+ * --threads=<n> Number of processors to use\r
+ * \r
+ * -l, --log=<file> Log all non-essential output to this file\r
+ */\r
+ public ClustalO() {\r
+ super(KEY_VALUE_SEPARATOR);\r
+ addParameters(Arrays.asList("--outfmt=clustal", "-v", "--log="\r
+ + EXEC_STAT_FILE));\r
+ // set default in, outs and err files\r
+ this.setInput(super.inputFile);\r
+ this.setOutput(super.outputFile);\r
+ this.setError(super.errorFile);\r
+ }\r
+\r
+ @Override\r
+ public ClustalO setOutput(String outFile) {\r
+ super.setOutput(outFile);\r
+ cbuilder.setParam("--outfile=" + outFile);\r
+ return this;\r
+ }\r
+\r
+ @Override\r
+ public ClustalO setInput(String inFile) {\r
+ super.setInput(inFile);\r
+ cbuilder.setParam("--infile=" + inFile);\r
+ return this;\r
+ }\r
+\r
+ @SuppressWarnings("unchecked")\r
+ public Alignment getResults(String workDirectory)\r
+ throws ResultNotAvailableException {\r
+ try {\r
+ return Util.readClustalFile(workDirectory, getOutput());\r
+ } catch (FileNotFoundException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ } catch (IOException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ } catch (UnknownFileFormatException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ } catch (NullPointerException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ }\r
+ }\r
+\r
+ public static String getStatFile() {\r
+ return EXEC_STAT_FILE;\r
+ }\r
+\r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public Class<ClustalO> getType() {\r
+ return (Class<ClustalO>) this.getClass();\r
+ }\r
+\r
+}\r
--- /dev/null
+/* Copyright (c) 2009 Peter Troshin\r
+ * \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 \r
+ * \r
+ * This library is free software; you can redistribute it and/or modify it under the terms of the\r
+ * Apache License version 2 as published by the Apache Software Foundation\r
+ * \r
+ * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
+ * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
+ * License for more details.\r
+ * \r
+ * A copy of the license is in apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
+ * \r
+ * Any republication or derived work distributed in source code form\r
+ * must include this copyright and license notice.\r
+ */\r
+\r
+package compbio.runner.msa;\r
+\r
+import static org.testng.Assert.assertEquals;\r
+import static org.testng.Assert.assertFalse;\r
+import static org.testng.Assert.assertNotNull;\r
+import static org.testng.Assert.assertTrue;\r
+import static org.testng.Assert.fail;\r
+\r
+import java.io.File;\r
+import java.io.FileInputStream;\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+import java.text.ParseException;\r
+import java.util.ArrayList;\r
+import java.util.Collections;\r
+import java.util.List;\r
+\r
+import javax.xml.bind.JAXBException;\r
+import javax.xml.bind.ValidationException;\r
+\r
+import org.ggf.drmaa.DrmaaException;\r
+import org.ggf.drmaa.JobInfo;\r
+import org.testng.annotations.Test;\r
+\r
+import compbio.data.sequence.FastaSequence;\r
+import compbio.engine.AsyncExecutor;\r
+import compbio.engine.Configurator;\r
+import compbio.engine.FilePuller;\r
+import compbio.engine.SyncExecutor;\r
+import compbio.engine.client.ConfExecutable;\r
+import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.engine.client.Executable;\r
+import compbio.engine.client.Executable.ExecProvider;\r
+import compbio.engine.client.RunConfiguration;\r
+import compbio.engine.cluster.drmaa.ClusterUtil;\r
+import compbio.engine.cluster.drmaa.JobRunner;\r
+import compbio.engine.cluster.drmaa.StatisticManager;\r
+import compbio.engine.conf.RunnerConfigMarshaller;\r
+import compbio.engine.local.AsyncLocalRunner;\r
+import compbio.engine.local.LocalExecutorService;\r
+import compbio.engine.local.LocalRunner;\r
+import compbio.metadata.AllTestSuit;\r
+import compbio.metadata.ChunkHolder;\r
+import compbio.metadata.JobExecutionException;\r
+import compbio.metadata.JobStatus;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.LimitsManager;\r
+import compbio.metadata.PresetManager;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.metadata.RunnerConfig;\r
+import compbio.runner.OptionCombinator;\r
+import compbio.runner.Util;\r
+import compbio.util.FileWatcher;\r
+import compbio.util.SysPrefs;\r
+\r
+public class ClustalOTester {\r
+\r
+ static final String clustalConfigFile = AllTestSuit.TEST_DATA_PATH\r
+ + "ClustalParameters.xml";\r
+ public static String test_outfile = "TO1381.clustal.out";\r
+ public static String cluster_test_outfile = "TO1381.clustal.cluster.out";\r
+\r
+ @Test(groups = {AllTestSuit.test_group_cluster,\r
+ AllTestSuit.test_group_runner})\r
+ public void testRunOnCluster() {\r
+ ClustalW clustal = new ClustalW();\r
+ assertFalse(SysPrefs.isWindows,\r
+ "Cluster execution can only be in unix environment");\r
+ clustal.setInput(AllTestSuit.test_input)\r
+ .setOutput(cluster_test_outfile);\r
+\r
+ try {\r
+\r
+ ConfiguredExecutable<ClustalW> confClustal = Configurator\r
+ .configureExecutable(clustal);\r
+ JobRunner runner = JobRunner.getInstance(confClustal);\r
+ // ClusterSession csession = JobRunner.getSession();\r
+ assertNotNull(runner);\r
+ runner.executeJob();\r
+ // assertNotNull("JobId is null", jobId1);\r
+ JobStatus status = runner.getJobStatus();\r
+ assertTrue(status == JobStatus.PENDING\r
+ || status == JobStatus.RUNNING);\r
+ JobInfo info = runner.getJobInfo();\r
+ assertNotNull(info);\r
+ StatisticManager sm = new StatisticManager(info);\r
+ assertNotNull(sm);\r
+ try {\r
+ String exits = sm.getExitStatus();\r
+ assertNotNull("Exit status is null", exits);\r
+ // cut 4 trailing zeros from the number\r
+ int exitsInt = ClusterUtil.CLUSTER_STAT_IN_SEC.parse(exits)\r
+ .intValue();\r
+ assertEquals(0, exitsInt);\r
+ System.out.println(sm.getAllStats());\r
+\r
+ } catch (ParseException e) {\r
+ e.printStackTrace();\r
+ fail("Parse Exception: " + e.getMessage());\r
+ }\r
+ // At present the task directory could not be completely removed\r
+ // @see JobRunner.cleanup()\r
+ assertFalse(runner.cleanup(),\r
+ "Could not remove some files whilst cleaning up ");\r
+ assertTrue(sm.hasExited());\r
+ assertFalse(sm.wasAborted());\r
+ assertFalse(sm.hasDump());\r
+ assertFalse(sm.hasSignaled());\r
+\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail("DrmaaException caught:" + e.getMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail("DrmaaException caught:" + e.getMessage());\r
+ } catch (DrmaaException e) {\r
+ e.printStackTrace();\r
+ fail("DrmaaException caught:" + e.getMessage());\r
+ }\r
+ }\r
+\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void testRunLocally() {\r
+ ClustalO clustal = new ClustalO();\r
+ clustal.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
+ try {\r
+\r
+ // For local execution use relavive\r
+ ConfiguredExecutable<ClustalO> confClustal = Configurator\r
+ .configureExecutable(clustal, Executable.ExecProvider.Local);\r
+ LocalRunner lr = new LocalRunner(confClustal);\r
+ lr.executeJob();\r
+ confClustal = (ConfiguredExecutable<ClustalO>) lr.waitForResult();\r
+ assertNotNull(confClustal.getResults());\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void testConfigurationLoading() {\r
+ try {\r
+ RunnerConfig<ClustalW> clustalConfig = ConfExecutable\r
+ .getRunnerOptions(ClustalW.class);\r
+ assertNotNull(clustalConfig);\r
+ assertTrue(clustalConfig.getArguments().size() > 0);\r
+\r
+ PresetManager<ClustalW> clustalPresets = ConfExecutable\r
+ .getRunnerPresets(ClustalW.class);\r
+ assertNotNull(clustalPresets);\r
+ assertTrue(clustalPresets.getPresets().size() > 0);\r
+ clustalPresets.validate(clustalConfig);\r
+\r
+ LimitsManager<ClustalW> clustalLimits = ConfExecutable\r
+ .getRunnerLimits(ClustalW.class);\r
+ assertNotNull(clustalLimits);\r
+ assertTrue(clustalLimits.getLimits().size() > 0);\r
+ clustalLimits.validate(clustalPresets);\r
+\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ValidationException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void testOptionsLocally() {\r
+ try {\r
+\r
+ RunnerConfigMarshaller<ClustalW> clustalmarsh = new RunnerConfigMarshaller<ClustalW>(\r
+ RunnerConfig.class);\r
+\r
+ RunnerConfig<ClustalW> clustalConfig = clustalmarsh.read(\r
+ new FileInputStream(new File(clustalConfigFile)),\r
+ RunnerConfig.class);\r
+\r
+ OptionCombinator clustalOpc = new OptionCombinator(clustalConfig);\r
+ List<String> options = clustalOpc.getOptionsAtRandom();\r
+ for (int i = 0; i < options.size(); i++) {\r
+ System.out.println("Using options: " + options);\r
+ ClustalW clustal = new ClustalW();\r
+ clustal.setInput(AllTestSuit.test_input)\r
+ .setOutput(test_outfile);\r
+\r
+ // For local execution use relavive\r
+ ConfiguredExecutable<ClustalW> confClustal = Configurator\r
+ .configureExecutable(clustal, ExecProvider.Local);\r
+\r
+ // Add options to the executable\r
+ confClustal.addParameters(options);\r
+\r
+ LocalRunner lr = new LocalRunner(confClustal);\r
+ lr.executeJob();\r
+ confClustal = (ConfiguredExecutable<ClustalW>) lr\r
+ .waitForResult();\r
+ assertNotNull(confClustal.getResults());\r
+ Collections.shuffle(options);\r
+ }\r
+\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (JAXBException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ fail(e.getLocalizedMessage());\r
+ }\r
+ }\r
+\r
+ public static final void main(String[] args) throws JobSubmissionException,\r
+ JobExecutionException, InterruptedException {\r
+ ClustalW clustal = new ClustalW();\r
+ clustal.setInput(AllTestSuit.test_input).setOutput(test_outfile);\r
+ // For local execution use relavive\r
+ ConfiguredExecutable<ClustalW> confClustal = Configurator\r
+ .configureExecutable(clustal);\r
+ AsyncExecutor lr = new AsyncLocalRunner();\r
+ lr.submitJob(confClustal);\r
+ Thread.sleep(3000);\r
+ LocalExecutorService.shutDown();\r
+ }\r
+\r
+ @Test(enabled = false)\r
+ public void testAddParameters() {\r
+ ArrayList<FastaSequence> seqs = new ArrayList<FastaSequence>();\r
+ FastaSequence fs = new FastaSequence("tests1",\r
+ "aqtctcatcatctcatctgcccccgggttatgagtagtacgcatctacg");\r
+ FastaSequence fs2 = new FastaSequence("tests2",\r
+ "aqtctcatcatctcatctgcccccgggttatgagtagtacgcatctacg");\r
+ FastaSequence fs3 = new FastaSequence("tests3",\r
+ "aqtctcatcatctcatctgcccccgggttatgagtagtacgcatctacg");\r
+ seqs.add(fs);\r
+ seqs.add(fs2);\r
+ seqs.add(fs3);\r
+ ClustalW cl = new ClustalW();\r
+ cl.setInput("input.txt").setOutput("output.txt");\r
+ ConfiguredExecutable<ClustalW> confClustal;\r
+ try {\r
+ confClustal = Configurator.configureExecutable(cl);\r
+ Util.writeInput(seqs, confClustal);\r
+\r
+ LocalRunner lr = new LocalRunner(confClustal);\r
+ lr.executeJob();\r
+ confClustal = (ConfiguredExecutable<ClustalW>) lr.waitForResult();\r
+ assertNotNull(confClustal.getResults());\r
+\r
+ assertTrue(confClustal.saveRunConfiguration());\r
+ ConfiguredExecutable<ClustalW> cexec = (ConfiguredExecutable<ClustalW>) confClustal\r
+ .loadRunConfiguration(new FileInputStream(new File(\r
+ confClustal.getWorkDirectory(),\r
+ RunConfiguration.rconfigFile)));\r
+ assertNotNull(cexec);\r
+\r
+ lr = new LocalRunner(cexec);\r
+ lr.executeJob();\r
+ confClustal = (ConfiguredExecutable<ClustalW>) lr.waitForResult();\r
+ assertNotNull(confClustal.getResults());\r
+\r
+ System.out.println("CE:" + cexec);\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void testPersistance() {\r
+ try {\r
+ ClustalW clustal = new ClustalW();\r
+ clustal.setError("errrr.txt").setInput(AllTestSuit.test_input)\r
+ .setOutput("outtt.txt");\r
+ assertEquals(clustal.getInput(), AllTestSuit.test_input);\r
+ assertEquals(clustal.getError(), "errrr.txt");\r
+ assertEquals(clustal.getOutput(), "outtt.txt");\r
+ ConfiguredExecutable<ClustalW> cClustal = Configurator\r
+ .configureExecutable(clustal, Executable.ExecProvider.Local);\r
+\r
+ SyncExecutor sexec = Configurator.getSyncEngine(cClustal);\r
+ sexec.executeJob();\r
+ cClustal = (ConfiguredExecutable<ClustalW>) sexec.waitForResult();\r
+ assertNotNull(cClustal.getResults());\r
+ // Save run configuration\r
+ assertTrue(cClustal.saveRunConfiguration());\r
+\r
+ // See if loaded configuration is the same as saved\r
+ RunConfiguration loadedRun = RunConfiguration\r
+ .load(new FileInputStream(new File(cClustal\r
+ .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
+ assertTrue(((ConfExecutable<ClustalW>) cClustal)\r
+ .getRunConfiguration().equals(loadedRun));\r
+ // Load run configuration as ConfExecutable\r
+ ConfiguredExecutable<ClustalW> resurrectedCclustal = (ConfiguredExecutable<ClustalW>) cClustal\r
+ .loadRunConfiguration(new FileInputStream(new File(cClustal\r
+ .getWorkDirectory(), RunConfiguration.rconfigFile)));\r
+ assertNotNull(resurrectedCclustal);\r
+ // See in details whether executables are the same\r
+ assertEquals(resurrectedCclustal.getExecutable(), clustal);\r
+\r
+ // Finally rerun the job in the new task directory\r
+ ConfiguredExecutable<ClustalW> resclustal = Configurator\r
+ .configureExecutable(resurrectedCclustal.getExecutable(),\r
+ Executable.ExecProvider.Local);\r
+\r
+ sexec = Configurator.getSyncEngine(resclustal,\r
+ Executable.ExecProvider.Local);\r
+ sexec.executeJob();\r
+ cClustal = (ConfiguredExecutable<ClustalW>) sexec.waitForResult();\r
+ assertNotNull(cClustal.getResults());\r
+\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (JobExecutionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (FileNotFoundException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+\r
+ @Test(groups = {AllTestSuit.test_group_runner})\r
+ public void readStatistics() {\r
+ try {\r
+ ClustalW clustal = new ClustalW().setInput(AllTestSuit.test_input)\r
+ .setOutput(test_outfile);\r
+ ConfiguredExecutable<ClustalW> confClustal = Configurator\r
+ .configureExecutable(clustal, Executable.ExecProvider.Local);\r
+\r
+ AsyncExecutor sexec = Configurator.getAsyncEngine(confClustal);\r
+ String jobId = sexec.submitJob(confClustal);\r
+ FilePuller fw = FilePuller.newFilePuller(\r
+ confClustal.getWorkDirectory() + File.separator\r
+ + ClustalW.getStatFile(),\r
+ FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
+ int count = 0;\r
+ long position = 0;\r
+ fw.waitForFile(4);\r
+ while (!(sexec.getJobStatus(jobId) == JobStatus.FINISHED\r
+ || sexec.getJobStatus(jobId) == JobStatus.FAILED || sexec\r
+ .getJobStatus(jobId) == JobStatus.UNDEFINED)\r
+ || fw.hasMoreData()) {\r
+ ChunkHolder ch = fw.pull(position);\r
+ String chunk = ch.getChunk();\r
+ position = ch.getNextPosition();\r
+ System.out.print(chunk);\r
+ count++;\r
+ }\r
+ assertTrue(count > 1);\r
+ ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
+ assertNotNull(al.getResults());\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+\r
+ @Test(groups = {AllTestSuit.test_group_cluster,\r
+ AllTestSuit.test_group_runner})\r
+ public void readStatisticsClusterExecution() {\r
+ try {\r
+ ClustalW clustal = new ClustalW().setInput(AllTestSuit.test_input)\r
+ .setOutput(test_outfile);\r
+ ConfiguredExecutable<ClustalW> confClustal = Configurator\r
+ .configureExecutable(clustal,\r
+ Executable.ExecProvider.Cluster);\r
+\r
+ AsyncExecutor sexec = Configurator.getAsyncEngine(confClustal);\r
+ String jobId = sexec.submitJob(confClustal);\r
+ FilePuller fw = FilePuller.newFilePuller(\r
+ confClustal.getWorkDirectory() + File.separator\r
+ + ClustalW.getStatFile(),\r
+ FileWatcher.MIN_CHUNK_SIZE_BYTES);\r
+ int count = 0;\r
+ long position = 0;\r
+ fw.waitForFile(200);\r
+ /*\r
+ * Under certain circumstances DRMAA could report the status wrongly\r
+ * thus this loop never ends TODO deal with this!\r
+ */\r
+ while (!(sexec.getJobStatus(jobId) == JobStatus.FINISHED || sexec\r
+ .getJobStatus(jobId) == JobStatus.FAILED)\r
+ || fw.hasMoreData()) {\r
+ ChunkHolder ch = fw.pull(position);\r
+ String chunk = ch.getChunk();\r
+ position = ch.getNextPosition();\r
+ System.out.print(chunk);\r
+ count++;\r
+ if (sexec.getJobStatus(jobId) == JobStatus.UNDEFINED) {\r
+ System.out.println("DRMAA reported wrong status for job + "\r
+ + jobId + " continue anyway!");\r
+ break;\r
+ }\r
+ }\r
+ assertTrue(count > 1);\r
+ ConfiguredExecutable<?> al = sexec.getResults(jobId);\r
+ assertNotNull(al.getResults());\r
+ } catch (JobSubmissionException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (ResultNotAvailableException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
+ }\r
+}\r
git://source.jalview.org / jabaws.git / commitdiff