-2010-06-17 Release 0.0.1 (Dubliniensis)
+2016-12-20 Release 1.2.4 (AndreaGiacomo, r317)
+
+ - made code gcc-6 compliant
+
+ (no new command-line flags)
+
+2016-07-20 Release 1.2.3 (AndreaGiacomo, r313)
+
+ - fixed consensus line in ClustalW format, 'H' in NHQK not recognised as strong (bug in Squid)
+
+ (no new command-line flags)
+
+2016-07-01 Release 1.2.2 (AndreaGiacomo, r310)
+
+ - fixed a memory leak in hhalign
+ - parallelised hhalign
+ - increased MAC-RAM default from 2GB to 8GB
+
+ (no new command-line flags)
+
+2014-02-28 Release 1.2.1 (AndreaGiacomo, r292)
+
+ - corrected Clustal format consensus line
+ - label justification (multi-bit)
+
+2013-06-12 Release 1.2.0 (AndreaGiacomo, r284)
+
+ --is-profile disable check if profile, force profile (default no)
+ --use-kimura use Kimura distance correction for aligned sequences (default no)
+ --percent-id convert distances into percent identities (default no)
+
+ fixed bug in --output-order=tree-order for pair-wise alignment
+
+ Kimura distance correction no longer default for protein
+
+ fixed bug in Viterbi algorithm (predominantly affected long nucleotide but also protein, to lesser extent)
+
+ Viterbi is less (~10x) memory hungry than MAC but still scales quadratically with length:
+
+ 2GB of RAM (ClustalO default) can align sequences of 6.5k residues with MAC and 18k with Viterbi
+
+ 8GB of RAM (EBI limit) can align sequences of 12.5k residues with MAC and 37k with Viterbi
+
+ A Viterbi alignment of sequences of 100k residues will require 59GB of RAM
+
+
+2013-05-16 Release 1.1.1 (r281)
+
+ --cluster-size=<n> soft maximum of sequences in sub-clusters
+ --clustering-out=<file> Clustering output file
+ --residuenumber, --resno in Clustal format print residue numbers (default no)
+ --wrap=<n> number of residues before line-wrap in output
+ --output-order={input-order,tree-order} MSA output order like in input/guide-tree
+
+ turned off Kimura correction for DNA/RNA
+
+ enable distance matrix output after initial mBed but subsequent full distance calculation
+
+ enable termination after distance/guide-tree calculation (--max-hmm-iterations=-1)
+
+ longer sequence labels
+
+2012-04-25 Release 1.1.0 (FilumVitae, r275)
+
+ DNA and RNA support now added. Sequence type can be specified manually
+ using --seqtype={Protein|DNA|RNA}
+
+2012-03-27 Release 1.0.4 (r273)
+
+ zipped input now supported
+
+2011-09-07 Release 1.0.3 (r263)
+
+Bugs fixed:
+
+ input failed if first line in fasta file was empty
+
+ input failed if Clustal formatted file had trailing residue numbers
+
+ '*' character was causing problems, did not get filtered out by squid
+
+ --outfmt=fasta was not recognized
+
+ '~' gap characters were not recognized in MSF format
+
+ amended README re sequence/profile alignment
+
+ disallowed empty sequences
+
+ doxygen documentation fixes and fix of API example
+
+ introduced MAC-RAM flag to set amount of RAM given to MAC (in MB)
+
+2011-06-23 Release 1.0.2
+
+2011-06-17 Release 1.0.0 (DeshilHollesEamus, r250)
+
+2011-04-14 Release 0.2.0 (IbiMeVidebunt, r238)
+
+2011-03-23 Release 0.1.1 (OppidumLeonis, r224)
+
+2011-02-22 Release 0.1.0 (OppidumLeonis, r200)
+
+2010-08-10 Release 0.0.3 (Thamesis, r120)
+
+2010-06-17 Release 0.0.1 (Dubliniensis, r81)
First "release" as program has been able for a while to perform
all basic tasks without problems.
# This could be handy for archiving the generated documentation or
# if some version control system is used.
-PROJECT_NUMBER = 1.0.2
+PROJECT_NUMBER = 1.2.4
# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
# base path where the generated documentation will be put.
-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.
+Copyright (C) 1994-1996, 1999-2002, 2004-2013 Free Software Foundation,
+Inc.
Copying and distribution of this file, with or without modification,
are permitted in any medium without royalty provided the copyright
Basic Installation
==================
- Briefly, the shell commands `./configure; make; make install' should
-configure, build, and install this package. The following
+ Briefly, the shell command `./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
and if that doesn't work, install pre-built binaries of GCC for HP-UX.
+ HP-UX `make' updates targets which have the same time stamps as
+their prerequisites, which makes it generally unusable when shipped
+generated files such as `configure' are involved. Use GNU `make'
+instead.
+
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
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:
+an Autoconf limitation. Until the limitation is lifted, you can use
+this workaround:
- CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash
+ CONFIG_SHELL=/bin/bash ./configure CONFIG_SHELL=/bin/bash
`configure' Invocation
======================
`configure' also accepts some other, not widely useful, options. Run
`configure --help' for more details.
-
--- /dev/null
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+# Makefile. Generated from Makefile.in by configure.
+
+# 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.
+
+
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\r
\r
CLUSTAL-OMEGA is a general purpose multiple sequence alignment program\r
-for proteins.\r
+for protein and DNA/RNA.\r
\r
\r
+If you like Clustal-Omega please cite: Sievers F, Wilm A, Dineen D,\r
+ Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding\r
+ J, Thompson JD, Higgins DG. Fast, scalable generation of\r
+ high-quality protein multiple sequence alignments using Clustal\r
+ Omega. Mol Syst Biol. 2011 Oct 11;7:539. doi:\r
+ 10.1038/msb.2011.75. PMID: 21988835.\r
+If you don't like Clustal-Omega, please let us know why (and cite us\r
+anyway).\r
+\r
+Check http://www.clustal.org for more information and updates.\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
+program for protein and DNA/RNA. It produces high quality MSAs and is\r
+capable of handling data-sets of hundreds of thousands of sequences in\r
+reasonable 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
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
+In its current form Clustal-Omega has been extensivly tested for\r
+protein sequences, DNA/RNA support has been added since version 1.1.0.\r
\r
\r
\r
--profile2, --p2=<file>\r
Pre-aligned multiple sequence file (aligned columns will be kept fixed)\r
\r
+--is-profile\r
+ disable check if profile, force profile (default no)\r
+\r
+-t, --seqtype={Protein, RNA, DNA} \r
+ Force a sequence type (default: auto)\r
+\r
+--infmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]} \r
+ Forced sequence input file format (default: auto)\r
+\r
\r
For sequence and profile input Clustal-Omega uses the Squid library\r
from Sean Eddy [3].\r
\r
Use this option to align two alignments (profiles) together.\r
\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
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
+Sequences that all have the same lengths but do not contain a single\r
+gap are by default not recognised as a profile. If these sequences are\r
+indeed a profile and not just a collection of unaligned sequences that\r
+happen to have the same length, then specify the --is-profile flag.\r
+\r
\r
Invalid combinations of the above are:\r
\r
selex,\r
stockholm\r
\r
+Clustal-Omega accepts gzip-ed input.\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
+Since version 1.1.0 the Clustal-Omega alignment engine can process\r
+DNA/RNA. Clustal-Omega tries to guess the sequence type (protein,\r
+DNA/RNA), but this can be over-ruled with the --seqtype (-t) flag.\r
\r
\r
CLUSTERING:\r
--full-iter\r
Use full distance matrix for guide-tree calculation during iteration (mBed is default)\r
\r
+ --cluster-size=<n> \r
+ soft maximum of sequences in sub-clusters\r
+\r
+ --clustering-out=<file> \r
+ Clustering output file\r
+\r
+ --use-kimura\r
+ use Kimura distance correction for aligned sequences (default no)\r
+\r
+ --percent-id\r
+ convert distances into percent identities (default no)\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
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
+and ClustalW2 [5,6]. If the protein sequences inputted via -i are\r
+aligned, then Clustal-Omega uses pairwise aligned identities, these\r
+distances can be Kimura-corrected [7] by specifying --use-kimura. The\r
+distances between aligned DNA/RNA sequences are determined from the\r
+alignment, no Kimura correction can be used. The computational effort\r
+(time/memory) to calculate and store a full distance matrix grows\r
+quadratically with the number of sequences. Clustal-Omega can improve\r
+this scalability to N*log(N) by employing a fast clustering algorithm\r
+called mBed [2]; this option is automatically invoked (default). If a\r
+full distance matrix evaluation is desired, then the --full flag has\r
+to be set. The mBed mode calculates a reduced set of pair-wise\r
+distances. These distances are used in a k-means algorithm, that\r
+clusters at most 100 sequences. For each cluster a full distance\r
+matrix is calculated. No full distance matrix (of all input sequences)\r
+is calculated in mBed mode. If there are less than 100 sequences in\r
+the input, then in effect a full distance matrix is calculated in mBed\r
+mode, however, no distance matrix can be outputted (see below). The\r
+default cluster size of 100 can be over-written by specifying the\r
+--cluster-size flag.\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
+can be written to file. This is only possible in --full or --full-iter\r
+mode. The guide trees by default are used internally to guide the\r
+multiple alignment and are then discarded. By specifying the\r
+--guidetree-out option these internal guide trees can be written out\r
+to file. Conversely, the distance calculation and/or guide tree\r
+building stage can be skipped, by reading in a pre-calculated distance\r
+matrix 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
+respectively. By default, distance matrix and guide tree files are not\r
+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
+guide-trees. It is possible to perform an initial mBed (not-full)\r
+distance calculation and a subsequent full distance calculation by\r
+specifying the --full-iter flag (see section ITERATION). In this case\r
+a distance matrix can be outputted.\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
+The distance measure used at this stage is a full alignment distance\r
+(as opposed the initial pairwise k-tuple distance); distances of\r
+protein sequences can be Kimura corrected [7], DNA/RNA distances are\r
+not. By default, Clustal-Omega constructs a reduced distance matrix at\r
+this stage using the mBed algorithm, which will then be used to create\r
+an improved (iterated) new guide tree. To turn off mBed-like\r
+clustering at this stage the --full-iter flag has to be set. While\r
+full alignment distances in general are much faster to calculate than\r
+k-tuple distances, time and memory requirements still scale\r
+quadratically with the number of sequences and --full-iter clustering\r
+should only be considered for smaller cases (<< 10,000 sequences) or\r
+if response time and resources are not an issue.\r
+\r
+The default cluster size in mBed mode is 100. This means that\r
+sequences are grouped into clusters with a soft maximum of 100\r
+sequences, full distance matrices are calculated for these clusters,\r
+guide-trees are calculated for the clusters and the clusters are then\r
+strung together with an over-arching guide-tree. It is possible to\r
+change the cluster-size with the --cluster-size flag. The clustering\r
+can be outputted to file. The output is comprised of the cluster\r
+index, a running index for the sequences within each cluster, the\r
+running index for the sequence within the input file, the name of the\r
+sequence and the bi-section sequence (see EXAMPLES). \r
+\r
+Clustal-Omega uses pair-distances. Between unaligned sequences these\r
+are so called k-tuple distance, between aligned sequences they are\r
+full alignment distances, as employed by Squid. These values range\r
+between 0.0 (identical) and 1.0 (completely different). The distances\r
+are used to construct the guide-tree and are by default outputted if\r
+--distmat-out is specified (and --full and/or --full-iter are\r
+set). For full alignment distances there is a so called Kimura\r
+correction [7] which more closely reflects evolutionary\r
+distance. Kimura-corrected distances range from 0.0 (identical) to\r
+theoretically infinity (completely different). In practice there\r
+appears to be a maximum value. In Clustal-Omega these Kimura-corrected\r
+distance can be outputted for protein if the --use-kimura flag is\r
+specified. Kimura correction is not available for DNA/RNA. Up to and\r
+including version 1.1.1 Kimura-corrected distances were outputted by\r
+default (where possible). Since version 1.2.0 the default is to output\r
+uncorrected distances.\r
+\r
+\r
+Pair-distances closely correspond to percentage pair-wise identities\r
+through i=100*(1-d), where i is the percentage pair-wise identity and\r
+d is the pair-wise distance. Percentage pair-wise identities can be\r
+outputted in Clustal-Omega instead of the distance matrix by\r
+specifying the --percent-id flag as well as --distmat-out, --full\r
+and/or --full-iter. Percentage pair-wise identities cannot be\r
+outputted if --use-kimura is specified.\r
\r
\r
ALIGNMENT OUTPUT:\r
\r
- -o, --out, --outfile={file,-} Multiple sequence alignment output file (default: stdout)\r
+ -o, --out, --outfile={file,-} \r
+ Multiple sequence alignment output file (default: stdout)\r
+\r
+ --outfmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]} \r
+ MSA output file format (default: fasta)\r
+\r
+ --residuenumber, --resno \r
+ in Clustal format print residue numbers (default no)\r
\r
- --outfmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]} MSA output file format (default: fasta)\r
+ --wrap=<n> \r
+ number of residues before line-wrap in output\r
+\r
+ --output-order={input-order,tree-order} \r
+ MSA output order like in input/guide-tree\r
\r
\r
By default Clustal-Omega writes its results (alignments) to stdout. An\r
\r
* for Vienna format set: --outfmt=vie or --outfmt=vienna\r
\r
+In ClustalW one could print the residue number of the last residue in\r
+each line in Clustal-Format. This feature can be turned on by setting\r
+the --resno or --residuenumber flag.\r
+\r
+The line lengths in Clustal Format is usually 60 residues, in Fasta\r
+format it is usually 60 or 80 residues. This value can be set using\r
+the --wrap flag.\r
+\r
+By default the order of sequences in the output is the same as in the\r
+input (--output-order=input-order). This can be changed to the order\r
+in which the sequences appear in the guide-tree by setting\r
+--output-order=tree-order.\r
+\r
\r
ITERATION:\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
+its guide tree. The hope is that the full alignment distances, that\r
+can be derived from the initial alignment, will give rise to a better\r
+guide 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
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
+used to re-calculate a new guide tree (using full alignment distances)\r
+and to create a HMM. The new guide tree and the HMM are then used to\r
+produce 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
--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
+--iter. If any iteration is desired, then --iter has to be\r
+set. Conversely, if no alignment is desired but only distance\r
+calculation and tree construction, then --max-hmm-iterations=-1 will\r
+terminate the calculation before the alignment stage; --iter does not\r
+have to be specified in this case.\r
\r
\r
LIMITS (will exit early, if exceeded):\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
+using a full distance matrix.\r
\r
\r
./clustalo -i globin.sto --dealign\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
+built from the (preliminary) full alignment distances of the initial\r
+alignment. The un-aligned sequences are then aligned (for the second\r
+time but this time) using pseudo-count information from the HMM\r
+created after the initial alignment (and using the new guide\r
+tree). This second alignment is then again converted into a HMM and a\r
+new guide tree is constructed. The un-aligned sequences are then\r
+aligned (for a third time), again using pseudo-count information of\r
+the HMM from the previous step and the most recent guide tree. The\r
+final alignment is written to screen.\r
\r
\r
./clustalo -i globin.fa --iter=5 --max-guidetree-iterations=1\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
+built from the (preliminary) full alignment distances of the initial\r
+alignment. The un-aligned sequences are then aligned (for the second\r
+time but this time) using pseudo-count information from the HMM\r
+created after the initial alignment (and using the new guide\r
+tree). For the last 4 iterations the guide tree is left unchanged and\r
+only HMM iteration is performed. This means that intermediate\r
+alignments are converted to HMMs, and these intermediate HMMs are used\r
+to guide the MSA during subsequent iteration stages.\r
\r
\r
./clustalo -i globin.fa -o globin.a2m -v\r
intermediate alignment will have profited from the bigger profile.\r
\r
\r
+./clustalo -i globin.fa --clustering-out=globin.aux --cluster-size=3\r
+\r
+globin.fa contains 7 sequences. Usually a full distance matrix is\r
+created for less than 100 sequences. This is over-written by\r
+specifying --cluster-size=3. Clustal-Omega attempts to create clusters\r
+of no more than 3 sequences. This clustering is recorded in the file\r
+globin.aux which looks like\r
+\r
+ Cluster 0: object 0 has index 0 (=seq P1|HBB_HUMAN ) 00\r
+ Cluster 0: object 1 has index 1 (=seq P1|HBB_HORSE ) 00\r
+ Cluster 1: object 0 has index 4 (=seq P1|MYG_PHYCA ) 1\r
+ Cluster 1: object 1 has index 5 (=seq P1|GLB5_PETMA ) 1\r
+ Cluster 1: object 2 has index 6 (=seq P1|LGB2_LUPLU ) 1\r
+ Cluster 2: object 0 has index 2 (=seq P1|HBA_HUMAN ) 01\r
+ Cluster 2: object 1 has index 3 (=seq P1|HBA_HORSE ) 01\r
+\r
+There are 3 clusters, named Cluster~0, Cluster~1 and\r
+Cluster~2. Cluster~0 has 2 sequences, which are sequence 0 and 1 from\r
+the input file, named P1|HBB_HUMAN and P1|HBB_HORSE. Cluster~1 has 3\r
+sequences, sequences 4,5,6 from the input file and Cluster~2 has 2\r
+sequences, sequences 2 and 3 from the input file. The binary string at\r
+the end of each line encode the bi-section that led to this\r
+clustering. The first digit indicated the initial split. The '0'\r
+indicates that in the first split sequences 0,1,2,3 were grouped\r
+together and the '1' that sequences 4,5,6 were grouped together. The\r
+size of Cluster~1 does not exceed --cluster-size, so it does not need\r
+to be broken up. The Cluster (with the initial '0') containing\r
+sequences 0,1,2,3 is comprised of 4 sequences; this number exceeds\r
+--cluster-size, so that it will have to be broken up. This second\r
+split is indicated by the second digit of the binary string. The\r
+second '0' indicates that sequences 0,1 fall into one Cluster (which\r
+will ultimately be Cluster~0), and the second '1' indicates that\r
+sequences 2,3 fall into another cluster (ultimately Cluster~2).\r
+\r
\r
LITERATURE:\r
\r
--- /dev/null
+s/^#undef *\([ABCDEFGHIJKLMNOPQRSTUVWXYZ_]\)/#undef CLUSTAL_OMEGA_\1/
+s/^#undef *\([abcdefghijklmnopqrstuvwxyz]\)/#undef _clustal_omega_\1/
+s/^#define *\([ABCDEFGHIJKLMNOPQRSTUVWXYZ_][abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789_]*\)\(.*\)/#ifndef CLUSTAL_OMEGA_\1\
+#define CLUSTAL_OMEGA_\1\2\
+#endif/
+s/^#define *\([abcdefghijklmnopqrstuvwxyz][abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789_]*\)\(.*\)/#ifndef _clustal_omega_\1\
+#define _clustal_omega_\1\2\
+#endif/
AU_DEFUN([fp_WITH_DMALLOC], [AM_WITH_DMALLOC])
-# Copyright (C) 1996, 1997, 2000, 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,
-# 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($@)])
-
# Do all the work for Automake. -*- Autoconf -*-
# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004,
--- /dev/null
+prefix=/usr/local
+exec_prefix=${prefix}
+libdir=${exec_prefix}/lib
+includedir=${prefix}/include
+
+Name: clustal-omega
+Description: Clustal Omega library.
+Version: 1.2.4
+Requires:
+Libs: -L${libdir} -lclustalo
+Cflags: -I${includedir}/clustalo/
+
--- /dev/null
+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 configure 1.2.4, which was
+generated by GNU Autoconf 2.63. Invocation command line was
+
+ $ ./configure
+
+## --------- ##
+## Platform. ##
+## --------- ##
+
+hostname = ningal.cluster.lifesci.dundee.ac.uk
+uname -m = x86_64
+uname -r = 2.6.32-642.6.1.el6.x86_64
+uname -s = Linux
+uname -v = #1 SMP Wed Oct 5 00:36:12 UTC 2016
+
+/usr/bin/uname -p = unknown
+/bin/uname -X = unknown
+
+/bin/arch = x86_64
+/usr/bin/arch -k = unknown
+/usr/convex/getsysinfo = unknown
+/usr/bin/hostinfo = unknown
+/bin/machine = unknown
+/usr/bin/oslevel = unknown
+/bin/universe = unknown
+
+PATH: /gridware/sge/bin/lx-amd64
+PATH: /homes/fmmarquesmadeira/.local/anaconda/envs/python3/bin
+PATH: /gridware/sge/bin/lx-amd64
+PATH: /usr/lib64/qt-3.3/bin
+PATH: /usr/local/bin
+PATH: /bin
+PATH: /usr/bin
+PATH: /usr/local/sbin
+PATH: /usr/sbin
+PATH: /sbin
+PATH: /opt/dell/srvadmin/bin
+PATH: /homes/fmmarquesmadeira/.local/anaconda/bin
+PATH: /homes/fmmarquesmadeira/.local/bin/stamp4.4.2/bin/linux
+PATH: /homes/fmmarquesmadeira/.local/bin/mustang3.2.2/bin
+PATH: /homes/fmmarquesmadeira/.local/bin/mafft7.273/bin
+PATH: /homes/fmmarquesmadeira/.local/bin/foldx_Linux/bin
+PATH: /homes/fmmarquesmadeira/NOBACK/lib/oxbench_1_3//bin
+PATH: /homes/fmmarquesmadeira/.local/bin/Intellij/bin
+
+
+## ----------- ##
+## Core tests. ##
+## ----------- ##
+
+configure:2083:
+
+ Welcome to Clustal Omega - version 1.2.4 (AndreaGiacomo)
+
+ +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
+
+
+configure:2194: checking for a BSD-compatible install
+configure:2262: result: /usr/bin/install -c
+configure:2273: checking whether build environment is sane
+configure:2316: result: yes
+configure:2341: checking for a thread-safe mkdir -p
+configure:2380: result: /bin/mkdir -p
+configure:2393: checking for gawk
+configure:2409: found /bin/gawk
+configure:2420: result: gawk
+configure:2431: checking whether make sets $(MAKE)
+configure:2453: result: yes
+configure:2669: checking for style of include used by make
+configure:2697: result: GNU
+configure:2767: checking for gcc
+configure:2783: found /usr/bin/gcc
+configure:2794: result: gcc
+configure:3026: checking for C compiler version
+configure:3034: gcc --version >&5
+gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-17)
+Copyright (C) 2010 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.
+
+configure:3038: $? = 0
+configure:3045: gcc -v >&5
+Using built-in specs.
+Target: x86_64-redhat-linux
+Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
+Thread model: posix
+gcc version 4.4.7 20120313 (Red Hat 4.4.7-17) (GCC)
+configure:3049: $? = 0
+configure:3056: gcc -V >&5
+gcc: '-V' option must have argument
+configure:3060: $? = 1
+configure:3083: checking for C compiler default output file name
+configure:3105: gcc conftest.c >&5
+configure:3109: $? = 0
+configure:3147: result: a.out
+configure:3166: checking whether the C compiler works
+configure:3176: ./a.out
+configure:3180: $? = 0
+configure:3199: result: yes
+configure:3206: checking whether we are cross compiling
+configure:3208: result: no
+configure:3211: checking for suffix of executables
+configure:3218: gcc -o conftest conftest.c >&5
+configure:3222: $? = 0
+configure:3248: result:
+configure:3254: checking for suffix of object files
+configure:3280: gcc -c conftest.c >&5
+configure:3284: $? = 0
+configure:3309: result: o
+configure:3313: checking whether we are using the GNU C compiler
+configure:3342: gcc -c conftest.c >&5
+configure:3349: $? = 0
+configure:3366: result: yes
+configure:3375: checking whether gcc accepts -g
+configure:3405: gcc -c -g conftest.c >&5
+configure:3412: $? = 0
+configure:3513: result: yes
+configure:3530: checking for gcc option to accept ISO C89
+configure:3604: gcc -c -g -O2 conftest.c >&5
+configure:3611: $? = 0
+configure:3634: result: none needed
+configure:3654: checking dependency style of gcc
+configure:3745: result: gcc3
+configure:3766: checking how to run the C preprocessor
+configure:3806: gcc -E conftest.c
+configure:3813: $? = 0
+configure:3844: gcc -E conftest.c
+conftest.c:10:28: error: ac_nonexistent.h: No such file or directory
+configure:3851: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| /* end confdefs.h. */
+| #include <ac_nonexistent.h>
+configure:3884: result: gcc -E
+configure:3913: gcc -E conftest.c
+configure:3920: $? = 0
+configure:3951: gcc -E conftest.c
+conftest.c:10:28: error: ac_nonexistent.h: No such file or directory
+configure:3958: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| /* end confdefs.h. */
+| #include <ac_nonexistent.h>
+configure:3998: checking for grep that handles long lines and -e
+configure:4058: result: /bin/grep
+configure:4063: checking for egrep
+configure:4127: result: /bin/grep -E
+configure:4132: checking for ANSI C header files
+configure:4162: gcc -c -g -O2 conftest.c >&5
+configure:4169: $? = 0
+configure:4268: gcc -o conftest -g -O2 conftest.c >&5
+configure:4272: $? = 0
+configure:4278: ./conftest
+configure:4282: $? = 0
+configure:4300: result: yes
+configure:4324: checking for sys/types.h
+configure:4345: gcc -c -g -O2 conftest.c >&5
+configure:4352: $? = 0
+configure:4369: result: yes
+configure:4324: checking for sys/stat.h
+configure:4345: gcc -c -g -O2 conftest.c >&5
+configure:4352: $? = 0
+configure:4369: result: yes
+configure:4324: checking for stdlib.h
+configure:4345: gcc -c -g -O2 conftest.c >&5
+configure:4352: $? = 0
+configure:4369: result: yes
+configure:4324: checking for string.h
+configure:4345: gcc -c -g -O2 conftest.c >&5
+configure:4352: $? = 0
+configure:4369: result: yes
+configure:4324: checking for memory.h
+configure:4345: gcc -c -g -O2 conftest.c >&5
+configure:4352: $? = 0
+configure:4369: result: yes
+configure:4324: checking for strings.h
+configure:4345: gcc -c -g -O2 conftest.c >&5
+configure:4352: $? = 0
+configure:4369: result: yes
+configure:4324: checking for inttypes.h
+configure:4345: gcc -c -g -O2 conftest.c >&5
+configure:4352: $? = 0
+configure:4369: result: yes
+configure:4324: checking for stdint.h
+configure:4345: gcc -c -g -O2 conftest.c >&5
+configure:4352: $? = 0
+configure:4369: result: yes
+configure:4324: checking for unistd.h
+configure:4345: gcc -c -g -O2 conftest.c >&5
+configure:4352: $? = 0
+configure:4369: result: yes
+configure:4394: checking minix/config.h usability
+configure:4411: gcc -c -g -O2 conftest.c >&5
+conftest.c:53:26: error: minix/config.h: No such file or directory
+configure:4418: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #define STDC_HEADERS 1
+| #define HAVE_SYS_TYPES_H 1
+| #define HAVE_SYS_STAT_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STRINGS_H 1
+| #define HAVE_INTTYPES_H 1
+| #define HAVE_STDINT_H 1
+| #define HAVE_UNISTD_H 1
+| /* end confdefs.h. */
+| #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
+| #include <minix/config.h>
+configure:4432: result: no
+configure:4436: checking minix/config.h presence
+configure:4451: gcc -E conftest.c
+conftest.c:20:26: error: minix/config.h: No such file or directory
+configure:4458: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #define STDC_HEADERS 1
+| #define HAVE_SYS_TYPES_H 1
+| #define HAVE_SYS_STAT_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STRINGS_H 1
+| #define HAVE_INTTYPES_H 1
+| #define HAVE_STDINT_H 1
+| #define HAVE_UNISTD_H 1
+| /* end confdefs.h. */
+| #include <minix/config.h>
+configure:4472: result: no
+configure:4505: checking for minix/config.h
+configure:4512: result: no
+configure:4543: checking whether it is safe to define __EXTENSIONS__
+configure:4571: gcc -c -g -O2 conftest.c >&5
+configure:4578: $? = 0
+configure:4593: result: yes
+configure:4627: checking build system type
+configure:4645: result: x86_64-unknown-linux-gnu
+configure:4667: checking host system type
+configure:4682: result: x86_64-unknown-linux-gnu
+configure:4708: checking whether make sets $(MAKE)
+configure:4730: result: yes
+configure:4770: checking for a sed that does not truncate output
+configure:4836: result: /bin/sed
+configure:4854: checking for fgrep
+configure:4918: result: /bin/grep -F
+configure:4953: checking for ld used by gcc
+configure:5020: result: /usr/bin/ld
+configure:5029: checking if the linker (/usr/bin/ld) is GNU ld
+configure:5044: result: yes
+configure:5056: checking for BSD- or MS-compatible name lister (nm)
+configure:5105: result: /usr/bin/nm -B
+configure:5223: checking the name lister (/usr/bin/nm -B) interface
+configure:5230: gcc -c -g -O2 conftest.c >&5
+configure:5233: /usr/bin/nm -B "conftest.o"
+configure:5236: output
+0000000000000000 B some_variable
+configure:5243: result: BSD nm
+configure:5246: checking whether ln -s works
+configure:5250: result: yes
+configure:5258: checking the maximum length of command line arguments
+configure:5378: result: 1966080
+configure:5395: checking whether the shell understands some XSI constructs
+configure:5405: result: yes
+configure:5409: checking whether the shell understands "+="
+configure:5415: result: yes
+configure:5450: checking for /usr/bin/ld option to reload object files
+configure:5457: result: -r
+configure:5526: checking for objdump
+configure:5542: found /usr/bin/objdump
+configure:5553: result: objdump
+configure:5585: checking how to recognize dependent libraries
+configure:5781: result: pass_all
+configure:5841: checking for ar
+configure:5857: found /usr/bin/ar
+configure:5868: result: ar
+configure:5946: checking for strip
+configure:5962: found /usr/bin/strip
+configure:5973: result: strip
+configure:6045: checking for ranlib
+configure:6061: found /usr/bin/ranlib
+configure:6072: result: ranlib
+configure:6162: checking command to parse /usr/bin/nm -B output from gcc object
+configure:6280: gcc -c -g -O2 conftest.c >&5
+configure:6283: $? = 0
+configure:6287: /usr/bin/nm -B conftest.o \| sed -n -e 's/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' \> conftest.nm
+configure:6290: $? = 0
+configure:6344: gcc -o conftest -g -O2 conftest.c conftstm.o >&5
+configure:6347: $? = 0
+configure:6385: result: ok
+configure:6480: gcc -c -g -O2 conftest.c >&5
+configure:6483: $? = 0
+configure:7250: checking for dlfcn.h
+configure:7271: gcc -c -g -O2 conftest.c >&5
+configure:7278: $? = 0
+configure:7295: result: yes
+configure:7481: checking for objdir
+configure:7496: result: .libs
+configure:7792: checking if gcc supports -fno-rtti -fno-exceptions
+configure:7810: gcc -c -g -O2 -fno-rtti -fno-exceptions conftest.c >&5
+cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C
+configure:7814: $? = 0
+configure:7827: result: no
+configure:7847: checking for gcc option to produce PIC
+configure:8119: result: -fPIC -DPIC
+configure:8131: checking if gcc PIC flag -fPIC -DPIC works
+configure:8149: gcc -c -g -O2 -fPIC -DPIC -DPIC conftest.c >&5
+configure:8153: $? = 0
+configure:8166: result: yes
+configure:8190: checking if gcc static flag -static works
+configure:8218: result: yes
+configure:8233: checking if gcc supports -c -o file.o
+configure:8254: gcc -c -g -O2 -o out/conftest2.o conftest.c >&5
+configure:8258: $? = 0
+configure:8280: result: yes
+configure:8288: checking if gcc supports -c -o file.o
+configure:8335: result: yes
+configure:8368: checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
+configure:9443: result: yes
+configure:9480: checking whether -lc should be explicitly linked in
+configure:9485: gcc -c -g -O2 conftest.c >&5
+configure:9488: $? = 0
+configure:9503: gcc -shared conftest.o -v -Wl,-soname -Wl,conftest -o conftest 2\>\&1 \| /bin/grep -lc \>/dev/null 2\>\&1
+configure:9506: $? = 0
+configure:9518: result: no
+configure:9682: checking dynamic linker characteristics
+configure:10125: gcc -o conftest -g -O2 -Wl,-rpath -Wl,/foo conftest.c >&5
+configure:10132: $? = 0
+configure:10377: result: GNU/Linux ld.so
+configure:10479: checking how to hardcode library paths into programs
+configure:10504: result: immediate
+configure:11337: checking whether stripping libraries is possible
+configure:11342: result: yes
+configure:11377: checking if libtool supports shared libraries
+configure:11379: result: yes
+configure:11382: checking whether to build shared libraries
+configure:11403: result: yes
+configure:11406: checking whether to build static libraries
+configure:11410: result: yes
+configure:11462: checking for a BSD-compatible install
+configure:11530: result: /usr/bin/install -c
+configure:11598: checking for gcc
+configure:11625: result: gcc
+configure:11857: checking for C compiler version
+configure:11865: gcc --version >&5
+gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-17)
+Copyright (C) 2010 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.
+
+configure:11869: $? = 0
+configure:11876: gcc -v >&5
+Using built-in specs.
+Target: x86_64-redhat-linux
+Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
+Thread model: posix
+gcc version 4.4.7 20120313 (Red Hat 4.4.7-17) (GCC)
+configure:11880: $? = 0
+configure:11887: gcc -V >&5
+gcc: '-V' option must have argument
+configure:11891: $? = 1
+configure:11894: checking whether we are using the GNU C compiler
+configure:11947: result: yes
+configure:11956: checking whether gcc accepts -g
+configure:12094: result: yes
+configure:12111: checking for gcc option to accept ISO C89
+configure:12215: result: none needed
+configure:12235: checking dependency style of gcc
+configure:12326: result: gcc3
+configure:12347: checking how to run the C preprocessor
+configure:12465: result: gcc -E
+configure:12494: gcc -E conftest.c
+configure:12501: $? = 0
+configure:12532: gcc -E conftest.c
+conftest.c:27:28: error: ac_nonexistent.h: No such file or directory
+configure:12539: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #define STDC_HEADERS 1
+| #define HAVE_SYS_TYPES_H 1
+| #define HAVE_SYS_STAT_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STRINGS_H 1
+| #define HAVE_INTTYPES_H 1
+| #define HAVE_STDINT_H 1
+| #define HAVE_UNISTD_H 1
+| #define __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| /* end confdefs.h. */
+| #include <ac_nonexistent.h>
+configure:12641: checking for g++
+configure:12657: found /usr/bin/g++
+configure:12668: result: g++
+configure:12695: checking for C++ compiler version
+configure:12703: g++ --version >&5
+g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-17)
+Copyright (C) 2010 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.
+
+configure:12707: $? = 0
+configure:12714: g++ -v >&5
+Using built-in specs.
+Target: x86_64-redhat-linux
+Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
+Thread model: posix
+gcc version 4.4.7 20120313 (Red Hat 4.4.7-17) (GCC)
+configure:12718: $? = 0
+configure:12725: g++ -V >&5
+g++: '-V' option must have argument
+configure:12729: $? = 1
+configure:12732: checking whether we are using the GNU C++ compiler
+configure:12761: g++ -c conftest.cpp >&5
+configure:12768: $? = 0
+configure:12785: result: yes
+configure:12794: checking whether g++ accepts -g
+configure:12824: g++ -c -g conftest.cpp >&5
+configure:12831: $? = 0
+configure:12932: result: yes
+configure:12957: checking dependency style of g++
+configure:13048: result: gcc3
+configure:13176: checking for C++ compiler version
+configure:13184: g++ --version >&5
+g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-17)
+Copyright (C) 2010 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.
+
+configure:13188: $? = 0
+configure:13195: g++ -v >&5
+Using built-in specs.
+Target: x86_64-redhat-linux
+Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
+Thread model: posix
+gcc version 4.4.7 20120313 (Red Hat 4.4.7-17) (GCC)
+configure:13199: $? = 0
+configure:13206: g++ -V >&5
+g++: '-V' option must have argument
+configure:13210: $? = 1
+configure:13213: checking whether we are using the GNU C++ compiler
+configure:13266: result: yes
+configure:13275: checking whether g++ accepts -g
+configure:13413: result: yes
+configure:13438: checking dependency style of g++
+configure:13529: result: gcc3
+configure:13552: checking how to run the C++ preprocessor
+configure:13588: g++ -E conftest.cpp
+configure:13595: $? = 0
+configure:13626: g++ -E conftest.cpp
+conftest.cpp:27:28: error: ac_nonexistent.h: No such file or directory
+configure:13633: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #define STDC_HEADERS 1
+| #define HAVE_SYS_TYPES_H 1
+| #define HAVE_SYS_STAT_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STRINGS_H 1
+| #define HAVE_INTTYPES_H 1
+| #define HAVE_STDINT_H 1
+| #define HAVE_UNISTD_H 1
+| #define __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| /* end confdefs.h. */
+| #include <ac_nonexistent.h>
+configure:13666: result: g++ -E
+configure:13695: g++ -E conftest.cpp
+configure:13702: $? = 0
+configure:13733: g++ -E conftest.cpp
+conftest.cpp:27:28: error: ac_nonexistent.h: No such file or directory
+configure:13740: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #define STDC_HEADERS 1
+| #define HAVE_SYS_TYPES_H 1
+| #define HAVE_SYS_STAT_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STRINGS_H 1
+| #define HAVE_INTTYPES_H 1
+| #define HAVE_STDINT_H 1
+| #define HAVE_UNISTD_H 1
+| #define __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| /* end confdefs.h. */
+| #include <ac_nonexistent.h>
+configure:13916: checking for ld used by g++
+configure:13983: result: /usr/bin/ld -m elf_x86_64
+configure:13992: checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld
+configure:14007: result: yes
+configure:14062: checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
+configure:15037: result: yes
+configure:15065: g++ -c -g -O2 conftest.cpp >&5
+configure:15068: $? = 0
+configure:15250: checking for g++ option to produce PIC
+configure:15567: result: -fPIC -DPIC
+configure:15576: checking if g++ PIC flag -fPIC -DPIC works
+configure:15594: g++ -c -g -O2 -fPIC -DPIC -DPIC conftest.cpp >&5
+configure:15598: $? = 0
+configure:15611: result: yes
+configure:15632: checking if g++ static flag -static works
+configure:15660: result: yes
+configure:15672: checking if g++ supports -c -o file.o
+configure:15693: g++ -c -g -O2 -o out/conftest2.o conftest.cpp >&5
+configure:15697: $? = 0
+configure:15719: result: yes
+configure:15724: checking if g++ supports -c -o file.o
+configure:15771: result: yes
+configure:15801: checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries
+configure:15830: result: yes
+configure:15967: checking dynamic linker characteristics
+configure:16358: g++ -o conftest -g -O2 -Wl,-rpath -Wl,/foo conftest.cpp >&5
+configure:16365: $? = 0
+configure:16610: result: GNU/Linux ld.so
+configure:16661: checking how to hardcode library paths into programs
+configure:16686: result: immediate
+configure:16731: checking how to run the C++ preprocessor
+configure:16845: result: g++ -E
+configure:16874: g++ -E conftest.cpp
+configure:16881: $? = 0
+configure:16912: g++ -E conftest.cpp
+conftest.cpp:27:28: error: ac_nonexistent.h: No such file or directory
+configure:16919: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #define STDC_HEADERS 1
+| #define HAVE_SYS_TYPES_H 1
+| #define HAVE_SYS_STAT_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STRINGS_H 1
+| #define HAVE_INTTYPES_H 1
+| #define HAVE_STDINT_H 1
+| #define HAVE_UNISTD_H 1
+| #define __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| /* end confdefs.h. */
+| #include <ac_nonexistent.h>
+configure:17113: checking for ANSI C header files
+configure:17281: result: yes
+configure:17319: checking assert.h usability
+configure:17336: gcc -c -g -O2 conftest.c >&5
+configure:17343: $? = 0
+configure:17357: result: yes
+configure:17361: checking assert.h presence
+configure:17376: gcc -E conftest.c
+configure:17383: $? = 0
+configure:17397: result: yes
+configure:17430: checking for assert.h
+configure:17439: result: yes
+configure:17319: checking ctype.h usability
+configure:17336: gcc -c -g -O2 conftest.c >&5
+configure:17343: $? = 0
+configure:17357: result: yes
+configure:17361: checking ctype.h presence
+configure:17376: gcc -E conftest.c
+configure:17383: $? = 0
+configure:17397: result: yes
+configure:17430: checking for ctype.h
+configure:17439: result: yes
+configure:17319: checking float.h usability
+configure:17336: gcc -c -g -O2 conftest.c >&5
+configure:17343: $? = 0
+configure:17357: result: yes
+configure:17361: checking float.h presence
+configure:17376: gcc -E conftest.c
+configure:17383: $? = 0
+configure:17397: result: yes
+configure:17430: checking for float.h
+configure:17439: result: yes
+configure:17319: checking limits.h usability
+configure:17336: gcc -c -g -O2 conftest.c >&5
+configure:17343: $? = 0
+configure:17357: result: yes
+configure:17361: checking limits.h presence
+configure:17376: gcc -E conftest.c
+configure:17383: $? = 0
+configure:17397: result: yes
+configure:17430: checking for limits.h
+configure:17439: result: yes
+configure:17319: checking math.h usability
+configure:17336: gcc -c -g -O2 conftest.c >&5
+configure:17343: $? = 0
+configure:17357: result: yes
+configure:17361: checking math.h presence
+configure:17376: gcc -E conftest.c
+configure:17383: $? = 0
+configure:17397: result: yes
+configure:17430: checking for math.h
+configure:17439: result: yes
+configure:17308: checking for memory.h
+configure:17315: result: yes
+configure:17319: checking stdarg.h usability
+configure:17336: gcc -c -g -O2 conftest.c >&5
+configure:17343: $? = 0
+configure:17357: result: yes
+configure:17361: checking stdarg.h presence
+configure:17376: gcc -E conftest.c
+configure:17383: $? = 0
+configure:17397: result: yes
+configure:17430: checking for stdarg.h
+configure:17439: result: yes
+configure:17319: checking stdio.h usability
+configure:17336: gcc -c -g -O2 conftest.c >&5
+configure:17343: $? = 0
+configure:17357: result: yes
+configure:17361: checking stdio.h presence
+configure:17376: gcc -E conftest.c
+configure:17383: $? = 0
+configure:17397: result: yes
+configure:17430: checking for stdio.h
+configure:17439: result: yes
+configure:17308: checking for stdlib.h
+configure:17315: result: yes
+configure:17308: checking for string.h
+configure:17315: result: yes
+configure:17319: checking time.h usability
+configure:17336: gcc -c -g -O2 conftest.c >&5
+configure:17343: $? = 0
+configure:17357: result: yes
+configure:17361: checking time.h presence
+configure:17376: gcc -E conftest.c
+configure:17383: $? = 0
+configure:17397: result: yes
+configure:17430: checking for time.h
+configure:17439: result: yes
+configure:17308: checking for unistd.h
+configure:17315: result: yes
+configure:17457: checking for an ANSI C-conforming const
+configure:17532: gcc -c -g -O2 conftest.c >&5
+configure:17539: $? = 0
+configure:17554: result: yes
+configure:17564: checking for size_t
+configure:17592: gcc -c -g -O2 conftest.c >&5
+configure:17599: $? = 0
+configure:17626: gcc -c -g -O2 conftest.c >&5
+conftest.c: In function 'main':
+conftest.c:79: error: expected expression before ')' token
+configure:17633: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #define STDC_HEADERS 1
+| #define HAVE_SYS_TYPES_H 1
+| #define HAVE_SYS_STAT_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STRINGS_H 1
+| #define HAVE_INTTYPES_H 1
+| #define HAVE_STDINT_H 1
+| #define HAVE_UNISTD_H 1
+| #define __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| #define CLUSTALO 1
+| #define PACKAGE_CODENAME "AndreaGiacomo"
+| #define LINUX 1
+| #define STDC_HEADERS 1
+| #define HAVE_ASSERT_H 1
+| #define HAVE_CTYPE_H 1
+| #define HAVE_FLOAT_H 1
+| #define HAVE_LIMITS_H 1
+| #define HAVE_MATH_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STDARG_H 1
+| #define HAVE_STDIO_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_TIME_H 1
+| #define HAVE_UNISTD_H 1
+| /* end confdefs.h. */
+| #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
+| int
+| main ()
+| {
+| if (sizeof ((size_t)))
+| return 0;
+| ;
+| return 0;
+| }
+configure:17656: result: yes
+configure:17668: checking for inline
+configure:17694: gcc -c -g -O2 conftest.c >&5
+configure:17701: $? = 0
+configure:17719: result: inline
+configure:17746: checking for log in -lm
+configure:17781: gcc -o conftest -g -O2 conftest.c -lm >&5
+conftest.c:50: warning: conflicting types for built-in function 'log'
+configure:17788: $? = 0
+configure:17809: result: yes
+configure:17824: checking for log2 in -lm
+configure:17859: gcc -o conftest -g -O2 conftest.c -lm -lm >&5
+conftest.c:51: warning: conflicting types for built-in function 'log2'
+configure:17866: $? = 0
+configure:17887: result: yes
+configure:17918: checking argtable2.h usability
+configure:17935: gcc -c -g -O2 conftest.c >&5
+configure:17942: $? = 0
+configure:17956: result: yes
+configure:17960: checking argtable2.h presence
+configure:17975: gcc -E conftest.c
+configure:17982: $? = 0
+configure:17996: result: yes
+configure:18029: checking for argtable2.h
+configure:18038: result: yes
+configure:18058: checking for arg_parse in -largtable2
+configure:18093: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:18100: $? = 0
+configure:18121: result: yes
+configure:18274: checking for OpenMP flag of C compiler
+configure:18320: gcc -o conftest -g -O2 -fopenmp conftest.c -largtable2 -lm >&5
+configure:18327: $? = 0
+configure:18350: result: -fopenmp
+configure:18399: checking whether byte ordering is bigendian
+configure:18424: gcc -c -g -O2 conftest.c >&5
+conftest.c:49: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'a'
+configure:18431: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #define STDC_HEADERS 1
+| #define HAVE_SYS_TYPES_H 1
+| #define HAVE_SYS_STAT_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STRINGS_H 1
+| #define HAVE_INTTYPES_H 1
+| #define HAVE_STDINT_H 1
+| #define HAVE_UNISTD_H 1
+| #define __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| #define CLUSTALO 1
+| #define PACKAGE_CODENAME "AndreaGiacomo"
+| #define LINUX 1
+| #define STDC_HEADERS 1
+| #define HAVE_ASSERT_H 1
+| #define HAVE_CTYPE_H 1
+| #define HAVE_FLOAT_H 1
+| #define HAVE_LIMITS_H 1
+| #define HAVE_MATH_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STDARG_H 1
+| #define HAVE_STDIO_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_TIME_H 1
+| #define HAVE_UNISTD_H 1
+| #define HAVE_LIBM 1
+| #define HAVE_LOG2 1
+| #define HAVE_ARGTABLE2_H 1
+| #define HAVE_LIBARGTABLE2 1
+| #define HAVE_OPENMP 1
+| /* end confdefs.h. */
+| #ifndef __APPLE_CC__
+| not a universal capable compiler
+| #endif
+| typedef int dummy;
+|
+configure:18481: gcc -c -g -O2 conftest.c >&5
+configure:18488: $? = 0
+configure:18520: gcc -c -g -O2 conftest.c >&5
+conftest.c: In function 'main':
+conftest.c:55: error: 'not' undeclared (first use in this function)
+conftest.c:55: error: (Each undeclared identifier is reported only once
+conftest.c:55: error: for each function it appears in.)
+conftest.c:55: error: expected ';' before 'big'
+configure:18527: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #define STDC_HEADERS 1
+| #define HAVE_SYS_TYPES_H 1
+| #define HAVE_SYS_STAT_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STRINGS_H 1
+| #define HAVE_INTTYPES_H 1
+| #define HAVE_STDINT_H 1
+| #define HAVE_UNISTD_H 1
+| #define __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| #define CLUSTALO 1
+| #define PACKAGE_CODENAME "AndreaGiacomo"
+| #define LINUX 1
+| #define STDC_HEADERS 1
+| #define HAVE_ASSERT_H 1
+| #define HAVE_CTYPE_H 1
+| #define HAVE_FLOAT_H 1
+| #define HAVE_LIMITS_H 1
+| #define HAVE_MATH_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STDARG_H 1
+| #define HAVE_STDIO_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_TIME_H 1
+| #define HAVE_UNISTD_H 1
+| #define HAVE_LIBM 1
+| #define HAVE_LOG2 1
+| #define HAVE_ARGTABLE2_H 1
+| #define HAVE_LIBARGTABLE2 1
+| #define HAVE_OPENMP 1
+| /* end confdefs.h. */
+| #include <sys/types.h>
+| #include <sys/param.h>
+|
+| int
+| main ()
+| {
+| #if BYTE_ORDER != BIG_ENDIAN
+| not big endian
+| #endif
+|
+| ;
+| return 0;
+| }
+configure:18779: result: no
+configure:18809: checking for ntohs
+configure:18865: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:18872: $? = 0
+configure:18894: result: yes
+configure:18809: checking for ntohl
+configure:18865: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:18872: $? = 0
+configure:18894: result: yes
+configure:18809: checking for ntons
+configure:18865: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+/tmp/ccMjUguw.o: In function `main':
+/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/conftest.c:84: undefined reference to `ntons'
+collect2: ld returned 1 exit status
+configure:18872: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #define STDC_HEADERS 1
+| #define HAVE_SYS_TYPES_H 1
+| #define HAVE_SYS_STAT_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STRINGS_H 1
+| #define HAVE_INTTYPES_H 1
+| #define HAVE_STDINT_H 1
+| #define HAVE_UNISTD_H 1
+| #define __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| #define CLUSTALO 1
+| #define PACKAGE_CODENAME "AndreaGiacomo"
+| #define LINUX 1
+| #define STDC_HEADERS 1
+| #define HAVE_ASSERT_H 1
+| #define HAVE_CTYPE_H 1
+| #define HAVE_FLOAT_H 1
+| #define HAVE_LIMITS_H 1
+| #define HAVE_MATH_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STDARG_H 1
+| #define HAVE_STDIO_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_TIME_H 1
+| #define HAVE_UNISTD_H 1
+| #define HAVE_LIBM 1
+| #define HAVE_LOG2 1
+| #define HAVE_ARGTABLE2_H 1
+| #define HAVE_LIBARGTABLE2 1
+| #define HAVE_OPENMP 1
+| #define HAVE_NTOHS 1
+| #define HAVE_NTOHL 1
+| /* end confdefs.h. */
+| /* Define ntons to an innocuous variant, in case <limits.h> declares ntons.
+| For example, HP-UX 11i <limits.h> declares gettimeofday. */
+| #define ntons innocuous_ntons
+|
+| /* System header to define __stub macros and hopefully few prototypes,
+| which can conflict with char ntons (); 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 ntons
+|
+| /* 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 ntons ();
+| /* 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_ntons || defined __stub___ntons
+| choke me
+| #endif
+|
+| int
+| main ()
+| {
+| return ntons ();
+| ;
+| return 0;
+| }
+configure:18894: result: no
+configure:18809: checking for ntonl
+configure:18865: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+/tmp/ccc48aZC.o: In function `main':
+/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/conftest.c:84: undefined reference to `ntonl'
+collect2: ld returned 1 exit status
+configure:18872: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #define STDC_HEADERS 1
+| #define HAVE_SYS_TYPES_H 1
+| #define HAVE_SYS_STAT_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STRINGS_H 1
+| #define HAVE_INTTYPES_H 1
+| #define HAVE_STDINT_H 1
+| #define HAVE_UNISTD_H 1
+| #define __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| #define CLUSTALO 1
+| #define PACKAGE_CODENAME "AndreaGiacomo"
+| #define LINUX 1
+| #define STDC_HEADERS 1
+| #define HAVE_ASSERT_H 1
+| #define HAVE_CTYPE_H 1
+| #define HAVE_FLOAT_H 1
+| #define HAVE_LIMITS_H 1
+| #define HAVE_MATH_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STDARG_H 1
+| #define HAVE_STDIO_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_TIME_H 1
+| #define HAVE_UNISTD_H 1
+| #define HAVE_LIBM 1
+| #define HAVE_LOG2 1
+| #define HAVE_ARGTABLE2_H 1
+| #define HAVE_LIBARGTABLE2 1
+| #define HAVE_OPENMP 1
+| #define HAVE_NTOHS 1
+| #define HAVE_NTOHL 1
+| /* end confdefs.h. */
+| /* Define ntonl to an innocuous variant, in case <limits.h> declares ntonl.
+| For example, HP-UX 11i <limits.h> declares gettimeofday. */
+| #define ntonl innocuous_ntonl
+|
+| /* System header to define __stub macros and hopefully few prototypes,
+| which can conflict with char ntonl (); 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 ntonl
+|
+| /* 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 ntonl ();
+| /* 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_ntonl || defined __stub___ntonl
+| choke me
+| #endif
+|
+| int
+| main ()
+| {
+| return ntonl ();
+| ;
+| return 0;
+| }
+configure:18894: result: no
+configure:18911: checking size of unsigned short
+configure:19216: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:19220: $? = 0
+configure:19226: ./conftest
+configure:19230: $? = 0
+configure:19256: result: 2
+configure:19270: checking size of unsigned int
+configure:19575: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:19579: $? = 0
+configure:19585: ./conftest
+configure:19589: $? = 0
+configure:19615: result: 4
+configure:19629: checking size of unsigned long
+configure:19934: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:19938: $? = 0
+configure:19944: ./conftest
+configure:19948: $? = 0
+configure:19974: result: 8
+configure:19988: checking size of unsigned long long
+configure:20293: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:20297: $? = 0
+configure:20303: ./conftest
+configure:20307: $? = 0
+configure:20333: result: 8
+configure:20349: checking for stroul
+configure:20405: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+/tmp/ccLKPuKy.o: In function `main':
+/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/conftest.c:88: undefined reference to `stroul'
+collect2: ld returned 1 exit status
+configure:20412: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #define STDC_HEADERS 1
+| #define HAVE_SYS_TYPES_H 1
+| #define HAVE_SYS_STAT_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STRINGS_H 1
+| #define HAVE_INTTYPES_H 1
+| #define HAVE_STDINT_H 1
+| #define HAVE_UNISTD_H 1
+| #define __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| #define CLUSTALO 1
+| #define PACKAGE_CODENAME "AndreaGiacomo"
+| #define LINUX 1
+| #define STDC_HEADERS 1
+| #define HAVE_ASSERT_H 1
+| #define HAVE_CTYPE_H 1
+| #define HAVE_FLOAT_H 1
+| #define HAVE_LIMITS_H 1
+| #define HAVE_MATH_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STDARG_H 1
+| #define HAVE_STDIO_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_TIME_H 1
+| #define HAVE_UNISTD_H 1
+| #define HAVE_LIBM 1
+| #define HAVE_LOG2 1
+| #define HAVE_ARGTABLE2_H 1
+| #define HAVE_LIBARGTABLE2 1
+| #define HAVE_OPENMP 1
+| #define HAVE_NTOHS 1
+| #define HAVE_NTOHL 1
+| #define SIZEOF_UNSIGNED_SHORT 2
+| #define SIZEOF_UNSIGNED_INT 4
+| #define SIZEOF_UNSIGNED_LONG 8
+| #define SIZEOF_UNSIGNED_LONG_LONG 8
+| /* end confdefs.h. */
+| /* Define stroul to an innocuous variant, in case <limits.h> declares stroul.
+| For example, HP-UX 11i <limits.h> declares gettimeofday. */
+| #define stroul innocuous_stroul
+|
+| /* System header to define __stub macros and hopefully few prototypes,
+| which can conflict with char stroul (); 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 stroul
+|
+| /* 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 stroul ();
+| /* 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_stroul || defined __stub___stroul
+| choke me
+| #endif
+|
+| int
+| main ()
+| {
+| return stroul ();
+| ;
+| return 0;
+| }
+configure:20434: result: no
+configure:20349: checking for strtoull
+configure:20405: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:20412: $? = 0
+configure:20434: result: yes
+configure:20451: checking for ftello
+configure:20507: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:20514: $? = 0
+configure:20536: result: yes
+configure:20451: checking for fseeko
+configure:20507: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:20514: $? = 0
+configure:20536: result: yes
+configure:20553: checking for ftello64
+configure:20609: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:20616: $? = 0
+configure:20638: result: yes
+configure:20553: checking for fseeko64
+configure:20609: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:20616: $? = 0
+configure:20638: result: yes
+configure:20655: checking for ftell64
+configure:20711: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+/tmp/ccIKIivi.o: In function `main':
+/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/conftest.c:93: undefined reference to `ftell64'
+collect2: ld returned 1 exit status
+configure:20718: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #define STDC_HEADERS 1
+| #define HAVE_SYS_TYPES_H 1
+| #define HAVE_SYS_STAT_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STRINGS_H 1
+| #define HAVE_INTTYPES_H 1
+| #define HAVE_STDINT_H 1
+| #define HAVE_UNISTD_H 1
+| #define __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| #define CLUSTALO 1
+| #define PACKAGE_CODENAME "AndreaGiacomo"
+| #define LINUX 1
+| #define STDC_HEADERS 1
+| #define HAVE_ASSERT_H 1
+| #define HAVE_CTYPE_H 1
+| #define HAVE_FLOAT_H 1
+| #define HAVE_LIMITS_H 1
+| #define HAVE_MATH_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STDARG_H 1
+| #define HAVE_STDIO_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_TIME_H 1
+| #define HAVE_UNISTD_H 1
+| #define HAVE_LIBM 1
+| #define HAVE_LOG2 1
+| #define HAVE_ARGTABLE2_H 1
+| #define HAVE_LIBARGTABLE2 1
+| #define HAVE_OPENMP 1
+| #define HAVE_NTOHS 1
+| #define HAVE_NTOHL 1
+| #define SIZEOF_UNSIGNED_SHORT 2
+| #define SIZEOF_UNSIGNED_INT 4
+| #define SIZEOF_UNSIGNED_LONG 8
+| #define SIZEOF_UNSIGNED_LONG_LONG 8
+| #define HAVE_STRTOULL 1
+| #define HAVE_FTELLO 1
+| #define HAVE_FSEEKO 1
+| #define HAVE_FTELLO64 1
+| #define HAVE_FSEEKO64 1
+| /* end confdefs.h. */
+| /* Define ftell64 to an innocuous variant, in case <limits.h> declares ftell64.
+| For example, HP-UX 11i <limits.h> declares gettimeofday. */
+| #define ftell64 innocuous_ftell64
+|
+| /* System header to define __stub macros and hopefully few prototypes,
+| which can conflict with char ftell64 (); 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 ftell64
+|
+| /* 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 ftell64 ();
+| /* 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_ftell64 || defined __stub___ftell64
+| choke me
+| #endif
+|
+| int
+| main ()
+| {
+| return ftell64 ();
+| ;
+| return 0;
+| }
+configure:20740: result: no
+configure:20655: checking for fseek64
+configure:20711: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+/tmp/cc95kpLo.o: In function `main':
+/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/conftest.c:93: undefined reference to `fseek64'
+collect2: ld returned 1 exit status
+configure:20718: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #define STDC_HEADERS 1
+| #define HAVE_SYS_TYPES_H 1
+| #define HAVE_SYS_STAT_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STRINGS_H 1
+| #define HAVE_INTTYPES_H 1
+| #define HAVE_STDINT_H 1
+| #define HAVE_UNISTD_H 1
+| #define __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| #define CLUSTALO 1
+| #define PACKAGE_CODENAME "AndreaGiacomo"
+| #define LINUX 1
+| #define STDC_HEADERS 1
+| #define HAVE_ASSERT_H 1
+| #define HAVE_CTYPE_H 1
+| #define HAVE_FLOAT_H 1
+| #define HAVE_LIMITS_H 1
+| #define HAVE_MATH_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STDARG_H 1
+| #define HAVE_STDIO_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_TIME_H 1
+| #define HAVE_UNISTD_H 1
+| #define HAVE_LIBM 1
+| #define HAVE_LOG2 1
+| #define HAVE_ARGTABLE2_H 1
+| #define HAVE_LIBARGTABLE2 1
+| #define HAVE_OPENMP 1
+| #define HAVE_NTOHS 1
+| #define HAVE_NTOHL 1
+| #define SIZEOF_UNSIGNED_SHORT 2
+| #define SIZEOF_UNSIGNED_INT 4
+| #define SIZEOF_UNSIGNED_LONG 8
+| #define SIZEOF_UNSIGNED_LONG_LONG 8
+| #define HAVE_STRTOULL 1
+| #define HAVE_FTELLO 1
+| #define HAVE_FSEEKO 1
+| #define HAVE_FTELLO64 1
+| #define HAVE_FSEEKO64 1
+| /* end confdefs.h. */
+| /* Define fseek64 to an innocuous variant, in case <limits.h> declares fseek64.
+| For example, HP-UX 11i <limits.h> declares gettimeofday. */
+| #define fseek64 innocuous_fseek64
+|
+| /* System header to define __stub macros and hopefully few prototypes,
+| which can conflict with char fseek64 (); 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 fseek64
+|
+| /* 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 fseek64 ();
+| /* 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_fseek64 || defined __stub___fseek64
+| choke me
+| #endif
+|
+| int
+| main ()
+| {
+| return fseek64 ();
+| ;
+| return 0;
+| }
+configure:20740: result: no
+configure:20753: checking for off_t
+configure:20781: gcc -c -g -O2 conftest.c >&5
+configure:20788: $? = 0
+configure:20815: gcc -c -g -O2 conftest.c >&5
+conftest.c: In function 'main':
+conftest.c:95: error: expected expression before ')' token
+configure:20822: $? = 1
+configure: failed program was:
+| /* confdefs.h. */
+| #define PACKAGE_NAME "Clustal Omega"
+| #define PACKAGE_TARNAME "clustal-omega"
+| #define PACKAGE_VERSION "1.2.4"
+| #define PACKAGE_STRING "Clustal Omega 1.2.4"
+| #define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+| #define PACKAGE "clustal-omega"
+| #define VERSION "1.2.4"
+| #define STDC_HEADERS 1
+| #define HAVE_SYS_TYPES_H 1
+| #define HAVE_SYS_STAT_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STRINGS_H 1
+| #define HAVE_INTTYPES_H 1
+| #define HAVE_STDINT_H 1
+| #define HAVE_UNISTD_H 1
+| #define __EXTENSIONS__ 1
+| #define _ALL_SOURCE 1
+| #define _GNU_SOURCE 1
+| #define _POSIX_PTHREAD_SEMANTICS 1
+| #define _TANDEM_SOURCE 1
+| #define HAVE_DLFCN_H 1
+| #define LT_OBJDIR ".libs/"
+| #define CLUSTALO 1
+| #define PACKAGE_CODENAME "AndreaGiacomo"
+| #define LINUX 1
+| #define STDC_HEADERS 1
+| #define HAVE_ASSERT_H 1
+| #define HAVE_CTYPE_H 1
+| #define HAVE_FLOAT_H 1
+| #define HAVE_LIMITS_H 1
+| #define HAVE_MATH_H 1
+| #define HAVE_MEMORY_H 1
+| #define HAVE_STDARG_H 1
+| #define HAVE_STDIO_H 1
+| #define HAVE_STDLIB_H 1
+| #define HAVE_STRING_H 1
+| #define HAVE_TIME_H 1
+| #define HAVE_UNISTD_H 1
+| #define HAVE_LIBM 1
+| #define HAVE_LOG2 1
+| #define HAVE_ARGTABLE2_H 1
+| #define HAVE_LIBARGTABLE2 1
+| #define HAVE_OPENMP 1
+| #define HAVE_NTOHS 1
+| #define HAVE_NTOHL 1
+| #define SIZEOF_UNSIGNED_SHORT 2
+| #define SIZEOF_UNSIGNED_INT 4
+| #define SIZEOF_UNSIGNED_LONG 8
+| #define SIZEOF_UNSIGNED_LONG_LONG 8
+| #define HAVE_STRTOULL 1
+| #define HAVE_FTELLO 1
+| #define HAVE_FSEEKO 1
+| #define HAVE_FTELLO64 1
+| #define HAVE_FSEEKO64 1
+| /* end confdefs.h. */
+| #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
+| int
+| main ()
+| {
+| if (sizeof ((off_t)))
+| return 0;
+| ;
+| return 0;
+| }
+configure:20845: result: yes
+configure:20861: checking size of fpos_t
+configure:21166: gcc -o conftest -g -O2 conftest.c -largtable2 -lm >&5
+configure:21170: $? = 0
+configure:21176: ./conftest
+configure:21180: $? = 0
+configure:21206: result: 16
+configure:21249: checking if malloc debugging is wanted
+configure:21269: result: no
+configure:21293: checking whether to build with debug information
+configure:21302: result: no
+configure:21476: creating ./config.status
+
+## ---------------------- ##
+## Running config.status. ##
+## ---------------------- ##
+
+This file was extended by Clustal Omega config.status 1.2.4, which was
+generated by GNU Autoconf 2.63. Invocation command line was
+
+ CONFIG_FILES =
+ CONFIG_HEADERS =
+ CONFIG_LINKS =
+ CONFIG_COMMANDS =
+ $ ./config.status
+
+on ningal.cluster.lifesci.dundee.ac.uk
+
+config.status:1097: creating Makefile
+config.status:1097: creating src/Makefile
+config.status:1097: creating clustalo.pc
+config.status:1097: creating Doxyfile
+config.status:1097: creating src/clustal/Makefile
+config.status:1097: creating src/hhalign/Makefile
+config.status:1097: creating src/kmpp/Makefile
+config.status:1097: creating src/squid/Makefile
+config.status:1097: creating src/config.h
+config.status:1319: src/config.h is unchanged
+config.status:1371: executing src/clustal-omega-config.h commands
+config.status:1411: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines
+config.status:1433: src/clustal-omega-config.h is unchanged
+config.status:1371: executing depfiles commands
+config.status:1371: executing libtool commands
+
+## ---------------- ##
+## Cache variables. ##
+## ---------------- ##
+
+ac_cv_build=x86_64-unknown-linux-gnu
+ac_cv_c_bigendian=no
+ac_cv_c_compiler_gnu=yes
+ac_cv_c_const=yes
+ac_cv_c_inline=inline
+ac_cv_cxx_compiler_gnu=yes
+ac_cv_env_CCC_set=
+ac_cv_env_CCC_value=
+ac_cv_env_CC_set=
+ac_cv_env_CC_value=
+ac_cv_env_CFLAGS_set=
+ac_cv_env_CFLAGS_value=
+ac_cv_env_CPPFLAGS_set=
+ac_cv_env_CPPFLAGS_value=
+ac_cv_env_CPP_set=
+ac_cv_env_CPP_value=
+ac_cv_env_CXXCPP_set=
+ac_cv_env_CXXCPP_value=
+ac_cv_env_CXXFLAGS_set=
+ac_cv_env_CXXFLAGS_value=
+ac_cv_env_CXX_set=
+ac_cv_env_CXX_value=
+ac_cv_env_LDFLAGS_set=
+ac_cv_env_LDFLAGS_value=
+ac_cv_env_LIBS_set=
+ac_cv_env_LIBS_value=
+ac_cv_env_build_alias_set=
+ac_cv_env_build_alias_value=
+ac_cv_env_host_alias_set=
+ac_cv_env_host_alias_value=
+ac_cv_env_target_alias_set=
+ac_cv_env_target_alias_value=
+ac_cv_func_fseek64=no
+ac_cv_func_fseeko64=yes
+ac_cv_func_fseeko=yes
+ac_cv_func_ftell64=no
+ac_cv_func_ftello64=yes
+ac_cv_func_ftello=yes
+ac_cv_func_ntohl=yes
+ac_cv_func_ntohs=yes
+ac_cv_func_ntonl=no
+ac_cv_func_ntons=no
+ac_cv_func_stroul=no
+ac_cv_func_strtoull=yes
+ac_cv_header_argtable2_h=yes
+ac_cv_header_assert_h=yes
+ac_cv_header_ctype_h=yes
+ac_cv_header_dlfcn_h=yes
+ac_cv_header_float_h=yes
+ac_cv_header_inttypes_h=yes
+ac_cv_header_limits_h=yes
+ac_cv_header_math_h=yes
+ac_cv_header_memory_h=yes
+ac_cv_header_minix_config_h=no
+ac_cv_header_stdarg_h=yes
+ac_cv_header_stdc=yes
+ac_cv_header_stdint_h=yes
+ac_cv_header_stdio_h=yes
+ac_cv_header_stdlib_h=yes
+ac_cv_header_string_h=yes
+ac_cv_header_strings_h=yes
+ac_cv_header_sys_stat_h=yes
+ac_cv_header_sys_types_h=yes
+ac_cv_header_time_h=yes
+ac_cv_header_unistd_h=yes
+ac_cv_host=x86_64-unknown-linux-gnu
+ac_cv_lib_argtable2_arg_parse=yes
+ac_cv_lib_m_log2=yes
+ac_cv_lib_m_log=yes
+ac_cv_objext=o
+ac_cv_path_EGREP='/bin/grep -E'
+ac_cv_path_FGREP='/bin/grep -F'
+ac_cv_path_GREP=/bin/grep
+ac_cv_path_SED=/bin/sed
+ac_cv_path_install='/usr/bin/install -c'
+ac_cv_path_mkdir=/bin/mkdir
+ac_cv_prog_AWK=gawk
+ac_cv_prog_CPP='gcc -E'
+ac_cv_prog_CXXCPP='g++ -E'
+ac_cv_prog_ac_ct_AR=ar
+ac_cv_prog_ac_ct_CC=gcc
+ac_cv_prog_ac_ct_CXX=g++
+ac_cv_prog_ac_ct_OBJDUMP=objdump
+ac_cv_prog_ac_ct_RANLIB=ranlib
+ac_cv_prog_ac_ct_STRIP=strip
+ac_cv_prog_cc_c89=
+ac_cv_prog_cc_g=yes
+ac_cv_prog_cxx_g=yes
+ac_cv_prog_make_make_set=yes
+ac_cv_safe_to_define___extensions__=yes
+ac_cv_sizeof_fpos_t=16
+ac_cv_sizeof_unsigned_int=4
+ac_cv_sizeof_unsigned_long=8
+ac_cv_sizeof_unsigned_long_long=8
+ac_cv_sizeof_unsigned_short=2
+ac_cv_type_off_t=yes
+ac_cv_type_size_t=yes
+am_cv_CC_dependencies_compiler_type=gcc3
+am_cv_CXX_dependencies_compiler_type=gcc3
+ax_cv_c_openmp=-fopenmp
+lt_cv_deplibs_check_method=pass_all
+lt_cv_file_magic_cmd='$MAGIC_CMD'
+lt_cv_file_magic_test_file=
+lt_cv_ld_reload_flag=-r
+lt_cv_nm_interface='BSD nm'
+lt_cv_objdir=.libs
+lt_cv_path_LD=/usr/bin/ld
+lt_cv_path_LDCXX='/usr/bin/ld -m elf_x86_64'
+lt_cv_path_NM='/usr/bin/nm -B'
+lt_cv_prog_compiler_c_o=yes
+lt_cv_prog_compiler_c_o_CXX=yes
+lt_cv_prog_compiler_pic_works=yes
+lt_cv_prog_compiler_pic_works_CXX=yes
+lt_cv_prog_compiler_rtti_exceptions=no
+lt_cv_prog_compiler_static_works=yes
+lt_cv_prog_compiler_static_works_CXX=yes
+lt_cv_prog_gnu_ld=yes
+lt_cv_prog_gnu_ldcxx=yes
+lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p'\'''
+lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\) $/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"\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/^[ABCDGIRSTW]* \([^ ]*\) \(lib[^ ]*\)$/ {"\2", (void *) \&\2},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"lib\2", (void *) \&\2},/p'\'''
+lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\'''
+lt_cv_sys_max_cmd_len=1966080
+
+## ----------------- ##
+## Output variables. ##
+## ----------------- ##
+
+ACLOCAL='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run aclocal-1.10'
+AMDEPBACKSLASH='\'
+AMDEP_FALSE='#'
+AMDEP_TRUE=''
+AMTAR='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run tar'
+AM_CFLAGS=' -O3'
+AM_CXXFLAGS=' -O3'
+AM_LDFLAGS=''
+AR='ar'
+AUTOCONF='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run autoconf'
+AUTOHEADER='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run autoheader'
+AUTOMAKE='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run automake-1.10'
+AWK='gawk'
+CC='gcc'
+CCDEPMODE='depmode=gcc3'
+CFLAGS='-g -O2'
+CPP='gcc -E'
+CPPFLAGS=''
+CXX='g++'
+CXXCPP='g++ -E'
+CXXDEPMODE='depmode=gcc3'
+CXXFLAGS='-g -O2'
+CYGPATH_W='echo'
+DEFS='-DHAVE_CONFIG_H'
+DEPDIR='.deps'
+DSYMUTIL=''
+DUMPBIN=''
+ECHO_C=''
+ECHO_N='-n'
+ECHO_T=''
+EGREP='/bin/grep -E'
+EXEEXT=''
+FGREP='/bin/grep -F'
+GREP='/bin/grep'
+INSTALL_DATA='${INSTALL} -m 644'
+INSTALL_PROGRAM='${INSTALL}'
+INSTALL_SCRIPT='${INSTALL}'
+INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
+LD='/usr/bin/ld -m elf_x86_64'
+LDFLAGS=''
+LIBOBJS=''
+LIBS='-largtable2 -lm '
+LIBTOOL='$(SHELL) $(top_builddir)/libtool'
+LIPO=''
+LN_S='ln -s'
+LTLIBOBJS=''
+MAKEINFO='${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run makeinfo'
+MKDIR_P='/bin/mkdir -p'
+NM='/usr/bin/nm -B'
+NMEDIT=''
+OBJDUMP='objdump'
+OBJEXT='o'
+OPENMP_CFLAGS='-fopenmp'
+OPENMP_CXXFLAGS='-fopenmp'
+OTOOL64=''
+OTOOL=''
+PACKAGE='clustal-omega'
+PACKAGE_BUGREPORT='clustalw@ucd.ie'
+PACKAGE_CODENAME='AndreaGiacomo'
+PACKAGE_NAME='Clustal Omega'
+PACKAGE_STRING='Clustal Omega 1.2.4'
+PACKAGE_TARNAME='clustal-omega'
+PACKAGE_VERSION='1.2.4'
+PATH_SEPARATOR=':'
+RANLIB='ranlib'
+SED='/bin/sed'
+SET_MAKE=''
+SHELL='/bin/sh'
+STRIP='strip'
+VERSION='1.2.4'
+ac_ct_CC='gcc'
+ac_ct_CXX='g++'
+ac_ct_DUMPBIN=''
+am__fastdepCC_FALSE='#'
+am__fastdepCC_TRUE=''
+am__fastdepCXX_FALSE='#'
+am__fastdepCXX_TRUE=''
+am__include='include'
+am__isrc=''
+am__leading_dot='.'
+am__quote=''
+am__tar='${AMTAR} chof - "$$tardir"'
+am__untar='${AMTAR} xf -'
+bindir='${exec_prefix}/bin'
+build='x86_64-unknown-linux-gnu'
+build_alias=''
+build_cpu='x86_64'
+build_os='linux-gnu'
+build_vendor='unknown'
+datadir='${datarootdir}'
+datarootdir='${prefix}/share'
+docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
+dvidir='${docdir}'
+exec_prefix='${prefix}'
+host='x86_64-unknown-linux-gnu'
+host_alias=''
+host_cpu='x86_64'
+host_os='linux-gnu'
+host_vendor='unknown'
+htmldir='${docdir}'
+includedir='${prefix}/include'
+infodir='${datarootdir}/info'
+install_sh='$(SHELL) /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/install-sh'
+libdir='${exec_prefix}/lib'
+libexecdir='${exec_prefix}/libexec'
+localedir='${datarootdir}/locale'
+localstatedir='${prefix}/var'
+lt_ECHO='echo'
+mandir='${datarootdir}/man'
+mkdir_p='/bin/mkdir -p'
+oldincludedir='/usr/include'
+pdfdir='${docdir}'
+prefix='/usr/local'
+program_transform_name='s,x,x,'
+psdir='${docdir}'
+sbindir='${exec_prefix}/sbin'
+sharedstatedir='${prefix}/com'
+sysconfdir='${prefix}/etc'
+target_alias=''
+
+## ----------- ##
+## confdefs.h. ##
+## ----------- ##
+
+#define PACKAGE_NAME "Clustal Omega"
+#define PACKAGE_TARNAME "clustal-omega"
+#define PACKAGE_VERSION "1.2.4"
+#define PACKAGE_STRING "Clustal Omega 1.2.4"
+#define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+#define PACKAGE "clustal-omega"
+#define VERSION "1.2.4"
+#define STDC_HEADERS 1
+#define HAVE_SYS_TYPES_H 1
+#define HAVE_SYS_STAT_H 1
+#define HAVE_STDLIB_H 1
+#define HAVE_STRING_H 1
+#define HAVE_MEMORY_H 1
+#define HAVE_STRINGS_H 1
+#define HAVE_INTTYPES_H 1
+#define HAVE_STDINT_H 1
+#define HAVE_UNISTD_H 1
+#define __EXTENSIONS__ 1
+#define _ALL_SOURCE 1
+#define _GNU_SOURCE 1
+#define _POSIX_PTHREAD_SEMANTICS 1
+#define _TANDEM_SOURCE 1
+#define HAVE_DLFCN_H 1
+#define LT_OBJDIR ".libs/"
+#define CLUSTALO 1
+#define PACKAGE_CODENAME "AndreaGiacomo"
+#define LINUX 1
+#define STDC_HEADERS 1
+#define HAVE_ASSERT_H 1
+#define HAVE_CTYPE_H 1
+#define HAVE_FLOAT_H 1
+#define HAVE_LIMITS_H 1
+#define HAVE_MATH_H 1
+#define HAVE_MEMORY_H 1
+#define HAVE_STDARG_H 1
+#define HAVE_STDIO_H 1
+#define HAVE_STDLIB_H 1
+#define HAVE_STRING_H 1
+#define HAVE_TIME_H 1
+#define HAVE_UNISTD_H 1
+#define HAVE_LIBM 1
+#define HAVE_LOG2 1
+#define HAVE_ARGTABLE2_H 1
+#define HAVE_LIBARGTABLE2 1
+#define HAVE_OPENMP 1
+#define HAVE_NTOHS 1
+#define HAVE_NTOHL 1
+#define SIZEOF_UNSIGNED_SHORT 2
+#define SIZEOF_UNSIGNED_INT 4
+#define SIZEOF_UNSIGNED_LONG 8
+#define SIZEOF_UNSIGNED_LONG_LONG 8
+#define HAVE_STRTOULL 1
+#define HAVE_FTELLO 1
+#define HAVE_FSEEKO 1
+#define HAVE_FTELLO64 1
+#define HAVE_FSEEKO64 1
+#define SIZEOF_FPOS_T 16
+#define NDEBUG /**/
+
+configure: exit 0
--- /dev/null
+#! /bin/sh
+# Generated by configure.
+# 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=${CONFIG_SHELL-/bin/sh}
+## --------------------- ##
+## M4sh Initialization. ##
+## --------------------- ##
+
+# Be more Bourne compatible
+DUALCASE=1; export DUALCASE # for MKS sh
+if test -n "${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 1.2.4, 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 $@
+
+on `(hostname || uname -n) 2>/dev/null | sed 1q`
+"
+
+# Files that config.status was made for.
+config_files=" Makefile src/Makefile clustalo.pc Doxyfile src/clustal/Makefile src/hhalign/Makefile src/kmpp/Makefile src/squid/Makefile"
+config_headers=" src/config.h"
+config_commands=" src/clustal-omega-config.h depfiles libtool"
+
+ac_cs_usage="\
+\`$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>."
+
+ac_cs_version="\
+Clustal Omega config.status 1.2.4
+configured by ./configure, generated by GNU Autoconf 2.63,
+ with options \"\"
+
+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='/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo'
+srcdir='.'
+INSTALL='/usr/bin/install -c'
+MKDIR_P='/bin/mkdir -p'
+AWK='gawk'
+test -n "$AWK" || AWK=awk
+# 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
+
+if $ac_cs_recheck; then
+ set X '/bin/sh' './configure' $ac_configure_extra_args --no-create --no-recursion
+ shift
+ $as_echo "running CONFIG_SHELL=/bin/sh $*" >&6
+ CONFIG_SHELL='/bin/sh'
+ export CONFIG_SHELL
+ exec "$@"
+fi
+
+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
+
+#
+# INIT-COMMANDS
+#
+PACKAGE="clustal-omega"
+AMDEP_TRUE="" 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='s/\(["`$\\]\)/\\\1/g'
+double_quote_subst='s/\(["`\\]\)/\\\1/g'
+delay_variable_subst='s/\\\\\\\\\\\$/\\\\\\$/g'
+macro_version='2.2.6'
+macro_revision='1.3012'
+enable_shared='yes'
+enable_static='yes'
+pic_mode='default'
+enable_fast_install='yes'
+host_alias=''
+host='x86_64-unknown-linux-gnu'
+host_os='linux-gnu'
+build_alias=''
+build='x86_64-unknown-linux-gnu'
+build_os='linux-gnu'
+SED='/bin/sed'
+Xsed='/bin/sed -e 1s/^X//'
+GREP='/bin/grep'
+EGREP='/bin/grep -E'
+FGREP='/bin/grep -F'
+LD='/usr/bin/ld -m elf_x86_64'
+NM='/usr/bin/nm -B'
+LN_S='ln -s'
+max_cmd_len='1966080'
+ac_objext='o'
+exeext=''
+lt_unset='unset'
+lt_SP2NL='tr \040 \012'
+lt_NL2SP='tr \015\012 \040\040'
+reload_flag=' -r'
+reload_cmds='$LD$reload_flag -o $output$reload_objs'
+OBJDUMP='objdump'
+deplibs_check_method='pass_all'
+file_magic_cmd='$MAGIC_CMD'
+AR='ar'
+AR_FLAGS='cru'
+STRIP='strip'
+RANLIB='ranlib'
+old_postinstall_cmds='chmod 644 $oldlib~$RANLIB $oldlib'
+old_postuninstall_cmds=''
+old_archive_cmds='$AR $AR_FLAGS $oldlib$oldobjs~$RANLIB $oldlib'
+CC='gcc'
+CFLAGS='-g -O2'
+compiler='g++'
+GCC='yes'
+lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([ABCDGIRSTW][ABCDGIRSTW]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p'\'''
+lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[ABCDGIRSTW]* .* \(.*\)$/extern char \1;/p'\'''
+lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\) $/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"\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/^[ABCDGIRSTW]* \([^ ]*\) \(lib[^ ]*\)$/ {"\2", (void *) \&\2},/p'\'' -e '\''s/^[ABCDGIRSTW]* \([^ ]*\) \([^ ]*\)$/ {"lib\2", (void *) \&\2},/p'\'''
+objdir='.libs'
+SHELL='/bin/sh'
+ECHO='echo'
+MAGIC_CMD='file'
+lt_prog_compiler_no_builtin_flag=' -fno-builtin'
+lt_prog_compiler_wl='-Wl,'
+lt_prog_compiler_pic=' -fPIC -DPIC'
+lt_prog_compiler_static='-static'
+lt_cv_prog_compiler_c_o='yes'
+need_locks='no'
+DSYMUTIL=''
+NMEDIT=''
+LIPO=''
+OTOOL=''
+OTOOL64=''
+libext='a'
+shrext_cmds='.so'
+extract_expsyms_cmds=''
+archive_cmds_need_lc='no'
+enable_shared_with_static_runtimes='no'
+export_dynamic_flag_spec='${wl}--export-dynamic'
+whole_archive_flag_spec='${wl}--whole-archive$convenience ${wl}--no-whole-archive'
+compiler_needs_object='no'
+old_archive_from_new_cmds=''
+old_archive_from_expsyms_cmds=''
+archive_cmds='$CC -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname -o $lib'
+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 -shared $libobjs $deplibs $compiler_flags ${wl}-soname $wl$soname ${wl}-version-script ${wl}$output_objdir/$libname.ver -o $lib'
+module_cmds=''
+module_expsym_cmds=''
+with_gnu_ld='yes'
+allow_undefined_flag=''
+no_undefined_flag=''
+hardcode_libdir_flag_spec='${wl}-rpath ${wl}$libdir'
+hardcode_libdir_flag_spec_ld=''
+hardcode_libdir_separator=''
+hardcode_direct='no'
+hardcode_direct_absolute='no'
+hardcode_minus_L='no'
+hardcode_shlibpath_var='unsupported'
+hardcode_automatic='no'
+inherit_rpath='no'
+link_all_deplibs='unknown'
+fix_srcfile_path=''
+always_export_symbols='no'
+export_symbols_cmds='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+exclude_expsyms='_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*'
+include_expsyms=''
+prelink_cmds=''
+file_list_spec=''
+variables_saved_for_relink='PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH'
+need_lib_prefix='no'
+need_version='no'
+version_type='linux'
+runpath_var='LD_RUN_PATH'
+shlibpath_var='LD_LIBRARY_PATH'
+shlibpath_overrides_runpath='no'
+libname_spec='lib$name'
+library_names_spec='${libname}${release}${shared_ext}$versuffix ${libname}${release}${shared_ext}$major $libname${shared_ext}'
+soname_spec='${libname}${release}${shared_ext}$major'
+postinstall_cmds=''
+postuninstall_cmds=''
+finish_cmds='PATH="\$PATH:/sbin" ldconfig -n $libdir'
+finish_eval=''
+hardcode_into_libs='yes'
+sys_lib_search_path_spec='/usr/lib/gcc/x86_64-redhat-linux/4.4.7 /usr/lib64 /lib64'
+sys_lib_dlsearch_path_spec='/lib /usr/lib /usr/lib64/R/lib /usr/lib64/atlas /usr/lib64/mysql /usr/lib64/papi-4.1.3 /usr/lib64/papi-5.1.1/usr/lib /usr/lib64/qt-3.3/lib /opt/dell/srvadmin/lib64 /opt/dell/srvadmin/lib64/openmanage /opt/dell/srvadmin/lib64 /opt/dell/srvadmin/lib64 /opt/dell/srvadmin/lib64/srvadmin-isvc /opt/dell/srvadmin/lib64 /opt/dell/srvadmin/lib64/openmanage /opt/dell/srvadmin/lib64 /opt/dell/srvadmin/lib64/openmanage /usr/lib64/tcl8.5 /usr/lib/wine/ /usr/lib64/wine/ /usr/lib64/xulrunner '
+hardcode_action='immediate'
+enable_dlopen='unknown'
+enable_dlopen_self='unknown'
+enable_dlopen_self_static='unknown'
+old_striplib='strip --strip-debug'
+striplib='strip --strip-unneeded'
+compiler_lib_search_dirs=''
+predep_objects=''
+postdep_objects=''
+predeps=''
+postdeps=''
+compiler_lib_search_path=''
+LD_CXX='/usr/bin/ld -m elf_x86_64'
+old_archive_cmds_CXX='$AR $AR_FLAGS $oldlib$oldobjs~$RANLIB $oldlib'
+compiler_CXX='g++'
+GCC_CXX='yes'
+lt_prog_compiler_no_builtin_flag_CXX=' -fno-builtin'
+lt_prog_compiler_wl_CXX='-Wl,'
+lt_prog_compiler_pic_CXX=' -fPIC -DPIC'
+lt_prog_compiler_static_CXX='-static'
+lt_cv_prog_compiler_c_o_CXX='yes'
+archive_cmds_need_lc_CXX='no'
+enable_shared_with_static_runtimes_CXX='no'
+export_dynamic_flag_spec_CXX='${wl}--export-dynamic'
+whole_archive_flag_spec_CXX='${wl}--whole-archive$convenience ${wl}--no-whole-archive'
+compiler_needs_object_CXX='no'
+old_archive_from_new_cmds_CXX=''
+old_archive_from_expsyms_cmds_CXX=''
+archive_cmds_CXX='$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 $lib'
+module_cmds_CXX=''
+module_expsym_cmds_CXX=''
+with_gnu_ld_CXX='yes'
+allow_undefined_flag_CXX=''
+no_undefined_flag_CXX=''
+hardcode_libdir_flag_spec_CXX='${wl}-rpath ${wl}$libdir'
+hardcode_libdir_flag_spec_ld_CXX=''
+hardcode_libdir_separator_CXX=''
+hardcode_direct_CXX='no'
+hardcode_direct_absolute_CXX='no'
+hardcode_minus_L_CXX='no'
+hardcode_shlibpath_var_CXX='unsupported'
+hardcode_automatic_CXX='no'
+inherit_rpath_CXX='no'
+link_all_deplibs_CXX='no'
+fix_srcfile_path_CXX=''
+always_export_symbols_CXX='no'
+export_symbols_cmds_CXX='$NM $libobjs $convenience | $global_symbol_pipe | $SED '\''s/.* //'\'' | sort | uniq > $export_symbols'
+exclude_expsyms_CXX='_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*'
+include_expsyms_CXX=''
+prelink_cmds_CXX=''
+file_list_spec_CXX=''
+hardcode_action_CXX='immediate'
+compiler_lib_search_dirs_CXX='/usr/lib/gcc/x86_64-redhat-linux/4.4.7 /usr/lib/gcc/x86_64-redhat-linux/4.4.7 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 /lib/../lib64 /usr/lib/../lib64 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../..'
+predep_objects_CXX='/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbeginS.o'
+postdep_objects_CXX='/usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o'
+predeps_CXX=''
+postdeps_CXX='-lstdc++ -lm -lgcc_s -lc -lgcc_s'
+compiler_lib_search_path_CXX='-L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../..'
+
+LTCC='gcc'
+LTCFLAGS='-g -O2'
+compiler='gcc'
+
+# 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" | $Xsed -e 's/\\\\\\\$0 --fallback-echo"$/$0 --fallback-echo"/'`
+ ;;
+esac
+
+ac_aux_dir='.'
+xsi_shell='yes'
+lt_shell_append='yes'
+
+# See if we are running on zsh, and set the options which allow our
+# commands through without removal of \ escapes INIT.
+if test -n "${ZSH_VERSION+set}" ; then
+ setopt NO_GLOB_SUBST
+fi
+
+
+ PACKAGE='clustal-omega'
+ VERSION='1.2.4'
+ TIMESTAMP=''
+ RM='rm -f'
+ ofile='libtool'
+
+
+
+
+
+
+
+# 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" &&
+cat >>"$tmp/subs1.awk" <<\_ACAWK &&
+S["LTLIBOBJS"]=""
+S["LIBOBJS"]=""
+S["AM_LDFLAGS"]=""
+S["AM_CFLAGS"]=" -O3"
+S["AM_CXXFLAGS"]=" -O3"
+S["OPENMP_CXXFLAGS"]="-fopenmp"
+S["OPENMP_CFLAGS"]="-fopenmp"
+S["CXXCPP"]="g++ -E"
+S["am__fastdepCXX_FALSE"]="#"
+S["am__fastdepCXX_TRUE"]=""
+S["CXXDEPMODE"]="depmode=gcc3"
+S["ac_ct_CXX"]="g++"
+S["CXXFLAGS"]="-g -O2"
+S["CXX"]="g++"
+S["OTOOL64"]=""
+S["OTOOL"]=""
+S["LIPO"]=""
+S["NMEDIT"]=""
+S["DSYMUTIL"]=""
+S["lt_ECHO"]="echo"
+S["RANLIB"]="ranlib"
+S["AR"]="ar"
+S["OBJDUMP"]="objdump"
+S["LN_S"]="ln -s"
+S["NM"]="/usr/bin/nm -B"
+S["ac_ct_DUMPBIN"]=""
+S["DUMPBIN"]=""
+S["LD"]="/usr/bin/ld -m elf_x86_64"
+S["FGREP"]="/bin/grep -F"
+S["SED"]="/bin/sed"
+S["LIBTOOL"]="$(SHELL) $(top_builddir)/libtool"
+S["host_os"]="linux-gnu"
+S["host_vendor"]="unknown"
+S["host_cpu"]="x86_64"
+S["host"]="x86_64-unknown-linux-gnu"
+S["build_os"]="linux-gnu"
+S["build_vendor"]="unknown"
+S["build_cpu"]="x86_64"
+S["build"]="x86_64-unknown-linux-gnu"
+S["EGREP"]="/bin/grep -E"
+S["GREP"]="/bin/grep"
+S["CPP"]="gcc -E"
+S["am__fastdepCC_FALSE"]="#"
+S["am__fastdepCC_TRUE"]=""
+S["CCDEPMODE"]="depmode=gcc3"
+S["AMDEPBACKSLASH"]="\\"
+S["AMDEP_FALSE"]="#"
+S["AMDEP_TRUE"]=""
+S["am__quote"]=""
+S["am__include"]="include"
+S["DEPDIR"]=".deps"
+S["OBJEXT"]="o"
+S["EXEEXT"]=""
+S["ac_ct_CC"]="gcc"
+S["CPPFLAGS"]=""
+S["LDFLAGS"]=""
+S["CFLAGS"]="-g -O2"
+S["CC"]="gcc"
+S["am__untar"]="${AMTAR} xf -"
+S["am__tar"]="${AMTAR} chof - \"$$tardir\""
+S["AMTAR"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run tar"
+S["am__leading_dot"]="."
+S["SET_MAKE"]=""
+S["AWK"]="gawk"
+S["mkdir_p"]="/bin/mkdir -p"
+S["MKDIR_P"]="/bin/mkdir -p"
+S["INSTALL_STRIP_PROGRAM"]="$(install_sh) -c -s"
+S["STRIP"]="strip"
+S["install_sh"]="$(SHELL) /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/install-sh"
+S["MAKEINFO"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run makeinfo"
+S["AUTOHEADER"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run autoheader"
+S["AUTOMAKE"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run automake-1.10"
+S["AUTOCONF"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run autoconf"
+S["ACLOCAL"]="${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run aclocal-1.10"
+S["VERSION"]="1.2.4"
+S["PACKAGE"]="clustal-omega"
+S["CYGPATH_W"]="echo"
+S["am__isrc"]=""
+S["INSTALL_DATA"]="${INSTALL} -m 644"
+S["INSTALL_SCRIPT"]="${INSTALL}"
+S["INSTALL_PROGRAM"]="${INSTALL}"
+S["PACKAGE_CODENAME"]="AndreaGiacomo"
+S["target_alias"]=""
+S["host_alias"]=""
+S["build_alias"]=""
+S["LIBS"]="-largtable2 -lm "
+S["ECHO_T"]=""
+S["ECHO_N"]="-n"
+S["ECHO_C"]=""
+S["DEFS"]="-DHAVE_CONFIG_H"
+S["mandir"]="${datarootdir}/man"
+S["localedir"]="${datarootdir}/locale"
+S["libdir"]="${exec_prefix}/lib"
+S["psdir"]="${docdir}"
+S["pdfdir"]="${docdir}"
+S["dvidir"]="${docdir}"
+S["htmldir"]="${docdir}"
+S["infodir"]="${datarootdir}/info"
+S["docdir"]="${datarootdir}/doc/${PACKAGE_TARNAME}"
+S["oldincludedir"]="/usr/include"
+S["includedir"]="${prefix}/include"
+S["localstatedir"]="${prefix}/var"
+S["sharedstatedir"]="${prefix}/com"
+S["sysconfdir"]="${prefix}/etc"
+S["datadir"]="${datarootdir}"
+S["datarootdir"]="${prefix}/share"
+S["libexecdir"]="${exec_prefix}/libexec"
+S["sbindir"]="${exec_prefix}/sbin"
+S["bindir"]="${exec_prefix}/bin"
+S["program_transform_name"]="s,x,x,"
+S["prefix"]="/usr/local"
+S["exec_prefix"]="${prefix}"
+S["PACKAGE_BUGREPORT"]="clustalw@ucd.ie"
+S["PACKAGE_STRING"]="Clustal Omega 1.2.4"
+S["PACKAGE_VERSION"]="1.2.4"
+S["PACKAGE_TARNAME"]="clustal-omega"
+S["PACKAGE_NAME"]="Clustal Omega"
+S["PATH_SEPARATOR"]=":"
+S["SHELL"]="/bin/sh"
+_ACAWK
+cat >>"$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
+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 "$as_me: error: could not setup config files machinery" >&2;}
+ { (exit 1); exit 1; }; }
+fi # test -n "$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 {
+D["PACKAGE_NAME"]=" \"Clustal Omega\""
+D["PACKAGE_TARNAME"]=" \"clustal-omega\""
+D["PACKAGE_VERSION"]=" \"1.2.4\""
+D["PACKAGE_STRING"]=" \"Clustal Omega 1.2.4\""
+D["PACKAGE_BUGREPORT"]=" \"clustalw@ucd.ie\""
+D["PACKAGE"]=" \"clustal-omega\""
+D["VERSION"]=" \"1.2.4\""
+D["STDC_HEADERS"]=" 1"
+D["HAVE_SYS_TYPES_H"]=" 1"
+D["HAVE_SYS_STAT_H"]=" 1"
+D["HAVE_STDLIB_H"]=" 1"
+D["HAVE_STRING_H"]=" 1"
+D["HAVE_MEMORY_H"]=" 1"
+D["HAVE_STRINGS_H"]=" 1"
+D["HAVE_INTTYPES_H"]=" 1"
+D["HAVE_STDINT_H"]=" 1"
+D["HAVE_UNISTD_H"]=" 1"
+D["__EXTENSIONS__"]=" 1"
+D["_ALL_SOURCE"]=" 1"
+D["_GNU_SOURCE"]=" 1"
+D["_POSIX_PTHREAD_SEMANTICS"]=" 1"
+D["_TANDEM_SOURCE"]=" 1"
+D["HAVE_DLFCN_H"]=" 1"
+D["LT_OBJDIR"]=" \".libs/\""
+D["CLUSTALO"]=" 1"
+D["PACKAGE_CODENAME"]=" \"AndreaGiacomo\""
+D["LINUX"]=" 1"
+D["STDC_HEADERS"]=" 1"
+D["HAVE_ASSERT_H"]=" 1"
+D["HAVE_CTYPE_H"]=" 1"
+D["HAVE_FLOAT_H"]=" 1"
+D["HAVE_LIMITS_H"]=" 1"
+D["HAVE_MATH_H"]=" 1"
+D["HAVE_MEMORY_H"]=" 1"
+D["HAVE_STDARG_H"]=" 1"
+D["HAVE_STDIO_H"]=" 1"
+D["HAVE_STDLIB_H"]=" 1"
+D["HAVE_STRING_H"]=" 1"
+D["HAVE_TIME_H"]=" 1"
+D["HAVE_UNISTD_H"]=" 1"
+D["HAVE_LIBM"]=" 1"
+D["HAVE_LOG2"]=" 1"
+D["HAVE_ARGTABLE2_H"]=" 1"
+D["HAVE_LIBARGTABLE2"]=" 1"
+D["HAVE_OPENMP"]=" 1"
+D["HAVE_NTOHS"]=" 1"
+D["HAVE_NTOHL"]=" 1"
+D["SIZEOF_UNSIGNED_SHORT"]=" 2"
+D["SIZEOF_UNSIGNED_INT"]=" 4"
+D["SIZEOF_UNSIGNED_LONG"]=" 8"
+D["SIZEOF_UNSIGNED_LONG_LONG"]=" 8"
+D["HAVE_STRTOULL"]=" 1"
+D["HAVE_FTELLO"]=" 1"
+D["HAVE_FSEEKO"]=" 1"
+D["HAVE_FTELLO64"]=" 1"
+D["HAVE_FSEEKO64"]=" 1"
+D["SIZEOF_FPOS_T"]=" 16"
+D["NDEBUG"]=" /**/"
+ for (key in D) D_is_set[key] = 1
+ FS = "\a"
+}
+/^[\t ]*#[\t ]*(define|undef)[\t ]+[_abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ][_abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789]*([\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
+ { { $as_echo "$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 ||
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+ "libtool":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) $VERSION
+# Libtool was configured on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
+# NOTE: Changes made to this file will be lost: look at ltmain.sh.
+#
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005,
+# 2006, 2007, 2008 Free Software Foundation, Inc.
+# Written by Gordon Matzigkeit, 1996
+#
+# This file is part of GNU Libtool.
+#
+# GNU Libtool is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License as
+# published by the Free Software Foundation; either version 2 of
+# the License, or (at your option) any later version.
+#
+# As a special exception to the GNU General Public License,
+# if you distribute this file as part of a program or library that
+# is built using GNU Libtool, you may include this file under the
+# same distribution terms that you use for the rest of that program.
+#
+# GNU Libtool is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with GNU Libtool; see the file COPYING. If not, a copy
+# can be downloaded from http://www.gnu.org/licenses/gpl.html, or
+# obtained by writing to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+
+# The names of the tagged configurations supported by this script.
+available_tags="CXX "
+
+# ### BEGIN LIBTOOL CONFIG
+
+# Which release of libtool.m4 was used?
+macro_version=$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; }
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.63 for Clustal Omega 1.0.2.
+# Generated by GNU Autoconf 2.63 for Clustal Omega 1.2.4.
#
# Report bugs to <clustalw@ucd.ie>.
#
# 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_VERSION='1.2.4'
+PACKAGE_STRING='Clustal Omega 1.2.4'
PACKAGE_BUGREPORT='clustalw@ucd.ie'
# Factoring default headers for most tests.
# 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.
+\`configure' configures Clustal Omega 1.2.4 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
if test -n "$ac_init_help"; then
case $ac_init_help in
- short | recursive ) echo "Configuration of Clustal Omega 1.0.2:";;
+ short | recursive ) echo "Configuration of Clustal Omega 1.2.4:";;
esac
cat <<\_ACEOF
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
-Clustal Omega configure 1.0.2
+Clustal Omega configure 1.2.4
generated by GNU Autoconf 2.63
Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001,
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
+It was created by Clustal Omega $as_me 1.2.4, which was
generated by GNU Autoconf 2.63. Invocation command line was
$ $0 $@
ac_compiler_gnu=$ac_cv_c_compiler_gnu
-PACKAGE_CODENAME="DeshilHollesEamus"
+PACKAGE_CODENAME="AndreaGiacomo"
# 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
# Define the identity of the package.
PACKAGE='clustal-omega'
- VERSION='1.0.2'
+ VERSION='1.2.4'
cat >>confdefs.h <<_ACEOF
# 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
+This file was extended by Clustal Omega $as_me 1.2.4, which was
generated by GNU Autoconf 2.63. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
_ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_version="\\
-Clustal Omega config.status 1.0.2
+Clustal Omega config.status 1.2.4
configured by $0, generated by GNU Autoconf 2.63,
with options \\"`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\"
# configure.ac for Clustal Omega
#
-# RCS $Id: configure.ac 256 2011-06-23 13:57:28Z fabian $
+# RCS $Id: configure.ac 317 2016-12-16 17:44:50Z fabian $
# release
#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"
+#AC_INIT([Clustal Omega], [1.0.2], [clustalw@ucd.ie])
+#PACKAGE_CODENAME="DeshilHollesEamus"
+#AC_INIT([Clustal Omega], [1.0.3], [clustalw@ucd.ie])
+#PACKAGE_CODENAME="DeshilHollesEamus"
+#AC_INIT([Clustal Omega], [1.0.4], [clustalw@ucd.ie])
+#PACKAGE_CODENAME="DeshilHollesEamus"
+#AC_INIT([Clustal Omega], [1.1.0], [clustalw@ucd.ie])
+#PACKAGE_CODENAME="FilumVitae"
+#AC_INIT([Clustal Omega], [1.1.1], [clustalw@ucd.ie])
+#PACKAGE_CODENAME="FilumVitae"
+#AC_INIT([Clustal Omega], [1.2.0], [clustalw@ucd.ie])
+#PACKAGE_CODENAME="AndreaGiacomo"
+#AC_INIT([Clustal Omega], [1.2.1], [clustalw@ucd.ie])
+#PACKAGE_CODENAME="AndreaGiacomo"
+# r310
+#AC_INIT([Clustal Omega], [1.2.2], [clustalw@ucd.ie])
+#PACKAGE_CODENAME="AndreaGiacomo"
+# r313
+#AC_INIT([Clustal Omega], [1.2.3], [clustalw@ucd.ie])
+#PACKAGE_CODENAME="AndreaGiacomo"
+# r317
+AC_INIT([Clustal Omega], [1.2.4], [clustalw@ucd.ie])
+PACKAGE_CODENAME="AndreaGiacomo"
# 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
# config.h from config.h.in. Type 'touch stamp-h' to add this file to
# your project.
#
-AM_CONFIG_HEADER(src/config.h)
+AC_CONFIG_HEADERS([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
#! /bin/sh
# depcomp - compile a program generating dependencies as side-effects
-scriptversion=2009-04-28.21; # UTC
+scriptversion=2013-05-30.07; # UTC
-# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free
-# Software Foundation, Inc.
+# Copyright (C) 1999-2014 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
case $1 in
'')
- echo "$0: No command. Try \`$0 --help' for more information." 1>&2
- exit 1;
- ;;
+ echo "$0: No command. Try '$0 --help' for more information." 1>&2
+ exit 1;
+ ;;
-h | --h*)
cat <<\EOF
Usage: depcomp [--help] [--version] PROGRAM [ARGS]
Environment variables:
depmode Dependency tracking mode.
- source Source file read by `PROGRAMS ARGS'.
- object Object file output by `PROGRAMS ARGS'.
+ source Source file read by 'PROGRAMS ARGS'.
+ object Object file output by 'PROGRAMS ARGS'.
DEPDIR directory where to store dependencies.
depfile Dependency file to output.
- tmpdepfile Temporary file to use when outputing dependencies.
+ tmpdepfile Temporary file to use when outputting dependencies.
libtool Whether libtool is used (yes/no).
Report bugs to <bug-automake@gnu.org>.
;;
esac
+# Get the directory component of the given path, and save it in the
+# global variables '$dir'. Note that this directory component will
+# be either empty or ending with a '/' character. This is deliberate.
+set_dir_from ()
+{
+ case $1 in
+ */*) dir=`echo "$1" | sed -e 's|/[^/]*$|/|'`;;
+ *) dir=;;
+ esac
+}
+
+# Get the suffix-stripped basename of the given path, and save it the
+# global variable '$base'.
+set_base_from ()
+{
+ base=`echo "$1" | sed -e 's|^.*/||' -e 's/\.[^.]*$//'`
+}
+
+# If no dependency file was actually created by the compiler invocation,
+# we still have to create a dummy depfile, to avoid errors with the
+# Makefile "include basename.Plo" scheme.
+make_dummy_depfile ()
+{
+ echo "#dummy" > "$depfile"
+}
+
+# Factor out some common post-processing of the generated depfile.
+# Requires the auxiliary global variable '$tmpdepfile' to be set.
+aix_post_process_depfile ()
+{
+ # If the compiler actually managed to produce a dependency file,
+ # post-process it.
+ if test -f "$tmpdepfile"; then
+ # Each line is of the form 'foo.o: dependency.h'.
+ # Do two passes, one to just change these to
+ # $object: dependency.h
+ # and one to simply output
+ # dependency.h:
+ # which is needed to avoid the deleted-header problem.
+ { sed -e "s,^.*\.[$lower]*:,$object:," < "$tmpdepfile"
+ sed -e "s,^.*\.[$lower]*:[$tab ]*,," -e 's,$,:,' < "$tmpdepfile"
+ } > "$depfile"
+ rm -f "$tmpdepfile"
+ else
+ make_dummy_depfile
+ fi
+}
+
+# A tabulation character.
+tab=' '
+# A newline character.
+nl='
+'
+# Character ranges might be problematic outside the C locale.
+# These definitions help.
+upper=ABCDEFGHIJKLMNOPQRSTUVWXYZ
+lower=abcdefghijklmnopqrstuvwxyz
+digits=0123456789
+alpha=${upper}${lower}
+
if test -z "$depmode" || test -z "$source" || test -z "$object"; then
echo "depcomp: Variables source, object and depmode must be set" 1>&2
exit 1
rm -f "$tmpdepfile"
+# Avoid interferences from the environment.
+gccflag= dashmflag=
+
# 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
fi
if test "$depmode" = dashXmstdout; then
- # This is just like dashmstdout with a different argument.
- dashmflag=-xM
- depmode=dashmstdout
+ # This is just like dashmstdout with a different argument.
+ dashmflag=-xM
+ depmode=dashmstdout
fi
cygpath_u="cygpath -u -f -"
if test "$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
+ # 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
+
+if test "$depmode" = msvc7msys; then
+ # This is just like msvc7 but w/o cygpath translation.
+ # Just convert the backslash-escaped backslashes to single forward
+ # slashes to satisfy depend.m4
+ cygpath_u='sed s,\\\\,/,g'
+ depmode=msvc7
+fi
+
+if test "$depmode" = xlc; then
+ # IBM C/C++ Compilers xlc/xlC can output gcc-like dependency information.
+ gccflag=-qmakedep=gcc,-MF
+ depmode=gcc
fi
case "$depmode" in
done
"$@"
stat=$?
- if test $stat -eq 0; then :
- else
+ if test $stat -ne 0; then
rm -f "$tmpdepfile"
exit $stat
fi
;;
gcc)
+## Note that this doesn't just cater to obsosete pre-3.x GCC compilers.
+## but also to in-use compilers like IMB xlc/xlC and the HP C compiler.
+## (see the conditional assignment to $gccflag above).
## There are various ways to get dependency output from gcc. Here's
## why we pick this rather obscure method:
## - Don't want to use -MD because we'd like the dependencies to end
## up in a subdir. Having to rename by hand is ugly.
## (We might end up doing this anyway to support other compilers.)
## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
-## -MM, not -M (despite what the docs say).
+## -MM, not -M (despite what the docs say). Also, it might not be
+## supported by the other compilers which use the 'gcc' depmode.
## - Using -M directly means running the compiler twice (even worse
## than renaming).
if test -z "$gccflag"; then
fi
"$@" -Wp,"$gccflag$tmpdepfile"
stat=$?
- if test $stat -eq 0; then :
- else
+ if test $stat -ne 0; then
rm -f "$tmpdepfile"
exit $stat
fi
rm -f "$depfile"
echo "$object : \\" > "$depfile"
- alpha=ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz
-## The second -e expression handles DOS-style file names with drive letters.
+ # The second -e expression handles DOS-style file names with drive
+ # letters.
sed -e 's/^[^:]*: / /' \
-e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
-## This next piece of magic avoids the `deleted header file' problem.
+## This next piece of magic avoids the "deleted header file" problem.
## The problem is that when a header file which appears in a .P file
## is deleted, the dependency causes make to die (because there is
## typically no way to rebuild the header). We avoid this by adding
## dummy dependencies for each header file. Too bad gcc doesn't do
## this for us directly.
- tr ' ' '
-' < "$tmpdepfile" |
-## Some versions of gcc put a space before the `:'. On the theory
+## 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.
+## well. hp depmode also adds that space, but also prefixes the VPATH
+## to the object. Take care to not repeat it in the output.
## 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"
+ tr ' ' "$nl" < "$tmpdepfile" \
+ | sed -e 's/^\\$//' -e '/^$/d' -e "s|.*$object$||" -e '/:$/d' \
+ | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
"$@" -MDupdate "$tmpdepfile"
fi
stat=$?
- if test $stat -eq 0; then :
- else
+ if test $stat -ne 0; then
rm -f "$tmpdepfile"
exit $stat
fi
if test -f "$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
+ # 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"
+ tr ' ' "$nl" < "$tmpdepfile" \
+ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' \
+ | tr "$nl" ' ' >> "$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"
+ tr ' ' "$nl" < "$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" > "$depfile"
+ make_dummy_depfile
fi
rm -f "$tmpdepfile"
;;
+xlc)
+ # 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
+ ;;
+
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 `$object:' at the
+ # current directory. Also, the AIX compiler puts '$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$//' -e 's/\.lo$//'`
+ set_dir_from "$object"
+ set_base_from "$object"
if test "$libtool" = yes; then
tmpdepfile1=$dir$base.u
tmpdepfile2=$base.u
"$@" -M
fi
stat=$?
-
- if test $stat -eq 0; then :
- else
+ if test $stat -ne 0; then
rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
exit $stat
fi
do
test -f "$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" > "$depfile"
+ aix_post_process_depfile
+ ;;
+
+tcc)
+ # tcc (Tiny C Compiler) understand '-MD -MF file' since version 0.9.26
+ # FIXME: That version still under development at the moment of writing.
+ # Make that this statement remains true also for stable, released
+ # versions.
+ # It will wrap lines (doesn't matter whether long or short) with a
+ # trailing '\', as in:
+ #
+ # foo.o : \
+ # foo.c \
+ # foo.h \
+ #
+ # It will put a trailing '\' even on the last line, and will use leading
+ # spaces rather than leading tabs (at least since its commit 0394caf7
+ # "Emit spaces for -MD").
+ "$@" -MD -MF "$tmpdepfile"
+ stat=$?
+ if test $stat -ne 0; then
+ rm -f "$tmpdepfile"
+ exit $stat
fi
+ rm -f "$depfile"
+ # Each non-empty line is of the form 'foo.o : \' or ' dep.h \'.
+ # We have to change lines of the first kind to '$object: \'.
+ sed -e "s|.*:|$object :|" < "$tmpdepfile" > "$depfile"
+ # And for each line of the second kind, we have to emit a 'dep.h:'
+ # dummy dependency, to avoid the deleted-header problem.
+ sed -n -e 's|^ *\(.*\) *\\$|\1:|p' < "$tmpdepfile" >> "$depfile"
rm -f "$tmpdepfile"
;;
-icc)
- # Intel's C compiler understands `-MD -MF file'. However on
- # icc -MD -MF foo.d -c -o sub/foo.o sub/foo.c
- # ICC 7.0 will fill foo.d with something like
- # foo.o: sub/foo.c
- # foo.o: sub/foo.h
- # which is wrong. We want:
- # sub/foo.o: sub/foo.c
- # sub/foo.o: sub/foo.h
- # sub/foo.c:
- # sub/foo.h:
- # ICC 7.1 will output
+## The order of this option in the case statement is important, since the
+## shell code in configure will try each of these formats in the order
+## listed in this file. A plain '-MD' option would be understood by many
+## compilers, so we must ensure this comes after the gcc and icc options.
+pgcc)
+ # Portland's C compiler understands '-MD'.
+ # Will always output deps to 'file.d' where file is the root name of the
+ # source file under compilation, even if file resides in a subdirectory.
+ # The object file name does not affect the name of the '.d' file.
+ # pgcc 10.2 will output
# foo.o: sub/foo.c sub/foo.h
- # and will wrap long lines using \ :
+ # and will wrap long lines using '\' :
# foo.o: sub/foo.c ... \
# sub/foo.h ... \
# ...
+ set_dir_from "$object"
+ # Use the source, not the object, to determine the base name, since
+ # that's sadly what pgcc will do too.
+ set_base_from "$source"
+ tmpdepfile=$base.d
+
+ # For projects that build the same source file twice into different object
+ # files, the pgcc approach of using the *source* file root name can cause
+ # problems in parallel builds. Use a locking strategy to avoid stomping on
+ # the same $tmpdepfile.
+ lockdir=$base.d-lock
+ trap "
+ echo '$0: caught signal, cleaning up...' >&2
+ rmdir '$lockdir'
+ exit 1
+ " 1 2 13 15
+ numtries=100
+ i=$numtries
+ while test $i -gt 0; do
+ # mkdir is a portable test-and-set.
+ if mkdir "$lockdir" 2>/dev/null; then
+ # This process acquired the lock.
+ "$@" -MD
+ stat=$?
+ # Release the lock.
+ rmdir "$lockdir"
+ break
+ else
+ # If the lock is being held by a different process, wait
+ # until the winning process is done or we timeout.
+ while test -d "$lockdir" && test $i -gt 0; do
+ sleep 1
+ i=`expr $i - 1`
+ done
+ fi
+ i=`expr $i - 1`
+ done
+ trap - 1 2 13 15
+ if test $i -le 0; then
+ echo "$0: failed to acquire lock after $numtries attempts" >&2
+ echo "$0: check lockdir '$lockdir'" >&2
+ exit 1
+ fi
- "$@" -MD -MF "$tmpdepfile"
- stat=$?
- if test $stat -eq 0; then :
- else
+ if test $stat -ne 0; then
rm -f "$tmpdepfile"
exit $stat
fi
sed "s,^[^:]*:,$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"
+ sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" \
+ | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
# '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$//'`
+ set_dir_from "$object"
+ set_base_from "$object"
if test "$libtool" = yes; then
tmpdepfile1=$dir$base.d
tmpdepfile2=$dir.libs/$base.d
"$@" +Maked
fi
stat=$?
- if test $stat -eq 0; then :
- else
+ if test $stat -ne 0; then
rm -f "$tmpdepfile1" "$tmpdepfile2"
exit $stat
fi
test -f "$tmpdepfile" && break
done
if test -f "$tmpdepfile"; then
- sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile"
- # Add `dependent.h:' lines.
+ sed -e "s,^.*\.[$lower]*:,$object:," "$tmpdepfile" > "$depfile"
+ # Add 'dependent.h:' lines.
sed -ne '2,${
- s/^ *//
- s/ \\*$//
- s/$/:/
- p
- }' "$tmpdepfile" >> "$depfile"
+ s/^ *//
+ s/ \\*$//
+ s/$/:/
+ p
+ }' "$tmpdepfile" >> "$depfile"
else
- echo "#dummy" > "$depfile"
+ make_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 "$tmpdepfile"
- ;;
+ # The Tru64 compiler uses -MD to generate dependencies as a side
+ # effect. 'cc -MD -o foo.o ...' puts the dependencies into 'foo.o.d'.
+ # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
+ # dependencies in 'foo.d' instead, so we check for that too.
+ # Subdirectories are respected.
+ set_dir_from "$object"
+ set_base_from "$object"
+
+ if test "$libtool" = yes; then
+ # Libtool 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=$dir$base.o.d # libtool 1.5
+ tmpdepfile2=$dir.libs/$base.o.d # Likewise.
+ tmpdepfile3=$dir.libs/$base.d # Compaq CCC V6.2-504
+ "$@" -Wc,-MD
+ else
+ tmpdepfile1=$dir$base.d
+ tmpdepfile2=$dir$base.d
+ tmpdepfile3=$dir$base.d
+ "$@" -MD
+ fi
+
+ stat=$?
+ if test $stat -ne 0; then
+ rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
+ exit $stat
+ fi
+
+ for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
+ do
+ test -f "$tmpdepfile" && break
+ done
+ # Same post-processing that is required for AIX mode.
+ aix_post_process_depfile
+ ;;
+
+msvc7)
+ if test "$libtool" = yes; then
+ showIncludes=-Wc,-showIncludes
+ else
+ showIncludes=-showIncludes
+ fi
+ "$@" $showIncludes > "$tmpdepfile"
+ stat=$?
+ grep -v '^Note: including file: ' "$tmpdepfile"
+ if test $stat -ne 0; then
+ rm -f "$tmpdepfile"
+ exit $stat
+ fi
+ rm -f "$depfile"
+ echo "$object : \\" > "$depfile"
+ # The first sed program below extracts the file names and escapes
+ # backslashes for cygpath. The second sed program outputs the file
+ # name when reading, but also accumulates all include files in the
+ # hold buffer in order to output them again at the end. This only
+ # works with sed implementations that can handle large buffers.
+ sed < "$tmpdepfile" -n '
+/^Note: including file: *\(.*\)/ {
+ s//\1/
+ s/\\/\\\\/g
+ p
+}' | $cygpath_u | sort -u | sed -n '
+s/ /\\ /g
+s/\(.*\)/'"$tab"'\1 \\/p
+s/.\(.*\) \\/\1:/
+H
+$ {
+ s/.*/'"$tab"'/
+ G
+ p
+}' >> "$depfile"
+ echo >> "$depfile" # make sure the fragment doesn't end with a backslash
+ rm -f "$tmpdepfile"
+ ;;
+
+msvc7msys)
+ # 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
+ ;;
#nosideeffect)
# This comment above is used by automake to tell side-effect
shift
fi
- # Remove `-o $object'.
+ # Remove '-o $object'.
IFS=" "
for arg
do
done
test -z "$dashmflag" && dashmflag=-M
- # Require at least two characters before searching for `:'
+ # 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.
+ # a dependency such as 'c:/foo/bar' could be seen as target 'c' otherwise.
"$@" $dashmflag |
- sed 's:^[ ]*[^: ][^:][^:]*\:[ ]*:'"$object"'\: :' > "$tmpdepfile"
+ sed "s|^[$tab ]*[^:$tab ][^:][^:]*:[$tab ]*|$object: |" > "$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"
+ # Some versions of the HPUX 10.20 sed can't process this sed invocation
+ # correctly. Breaking it into two sed invocations is a workaround.
+ tr ' ' "$nl" < "$tmpdepfile" \
+ | sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' \
+ | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile"
;;
touch "$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"
+ # makedepend may prepend the VPATH from the source file name to the object.
+ # No need to regex-escape $object, excess matching of '.' is harmless.
+ sed "s|^.*\($object *:\)|\1|" "$tmpdepfile" > "$depfile"
+ # Some versions of the HPUX 10.20 sed can't process the last invocation
+ # correctly. Breaking it into two sed invocations is a workaround.
+ sed '1,2d' "$tmpdepfile" \
+ | tr ' ' "$nl" \
+ | sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' \
+ | sed -e 's/$/ :/' >> "$depfile"
rm -f "$tmpdepfile" "$tmpdepfile".bak
;;
shift
fi
- # Remove `-o $object'.
+ # Remove '-o $object'.
IFS=" "
for arg
do
esac
done
- "$@" -E |
- sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
- -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' |
- sed '$ s: \\$::' > "$tmpdepfile"
+ "$@" -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"
shift
;;
"-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
- set fnord "$@"
- shift
- shift
- ;;
+ set fnord "$@"
+ shift
+ shift
+ ;;
*)
- set fnord "$@" "$arg"
- 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 '/^\(.*\)$/ s::'"$tab"'\1 \\:p' >> "$depfile"
+ echo "$tab" >> "$depfile"
sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"
rm -f "$tmpdepfile"
;;
#!/bin/sh
# install - install a program, script, or datafile
-scriptversion=2009-04-28.21; # UTC
+scriptversion=2014-09-12.12; # UTC
# This originates from X11R5 (mit/util/scripts/install.sh), which was
# later released in X11R6 (xc/config/util/install.sh) with the
# 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
+# '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.
+tab=' '
nl='
'
-IFS=" "" $nl"
+IFS=" $tab$nl"
-# set DOITPROG to echo to test this script
+# 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=$doit
-fi
+doit_exec=${doit:-exec}
# Put in absolute file names if you don't have them in your path;
# or use environment vars.
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.
dst_arg=
copy_on_change=false
-no_target_directory=
+is_target_a_directory=possibly
usage="\
Usage: $0 [OPTION]... [-T] SRCFILE DSTFILE
-d) dir_arg=true;;
-g) chgrpcmd="$chgrpprog $2"
- shift;;
+ shift;;
--help) echo "$usage"; exit $?;;
-m) mode=$2
- case $mode in
- *' '* | *' '* | *'
-'* | *'*'* | *'?'* | *'['*)
- echo "$0: invalid mode: $mode" >&2
- exit 1;;
- esac
- shift;;
+ case $mode in
+ *' '* | *"$tab"* | *"$nl"* | *'*'* | *'?'* | *'['*)
+ echo "$0: invalid mode: $mode" >&2
+ exit 1;;
+ esac
+ shift;;
-o) chowncmd="$chownprog $2"
- shift;;
+ shift;;
-s) stripcmd=$stripprog;;
- -t) dst_arg=$2
- shift;;
+ -t)
+ is_target_a_directory=always
+ dst_arg=$2
+ # Protect names problematic for 'test' and other utilities.
+ case $dst_arg in
+ -* | [=\(\)!]) dst_arg=./$dst_arg;;
+ esac
+ shift;;
- -T) no_target_directory=true;;
+ -T) is_target_a_directory=never;;
--version) echo "$0 $scriptversion"; exit $?;;
- --) shift
- break;;
+ --) shift
+ break;;
- -*) echo "$0: invalid option: $1" >&2
- exit 1;;
+ -*) echo "$0: invalid option: $1" >&2
+ exit 1;;
*) break;;
esac
shift
done
+# We allow the use of options -d and -T together, by making -d
+# take the precedence; this is for compatibility with GNU install.
+
+if test -n "$dir_arg"; then
+ if test -n "$dst_arg"; then
+ echo "$0: target directory not allowed when installing a directory." >&2
+ exit 1
+ fi
+fi
+
if test $# -ne 0 && test -z "$dir_arg$dst_arg"; then
# When -d is used, all remaining arguments are directories to create.
# When -t is used, the destination is already specified.
fi
shift # arg
dst_arg=$arg
+ # Protect names problematic for 'test' and other utilities.
+ case $dst_arg in
+ -* | [=\(\)!]) dst_arg=./$dst_arg;;
+ esac
done
fi
echo "$0: no input file specified." >&2
exit 1
fi
- # It's OK to call `install-sh -d' without argument.
+ # It's OK to call 'install-sh -d' without argument.
# This can happen when creating conditional directories.
exit 0
fi
if test -z "$dir_arg"; then
- trap '(exit $?); exit' 1 2 13 15
+ if test $# -gt 1 || test "$is_target_a_directory" = always; then
+ if test ! -d "$dst_arg"; then
+ echo "$0: $dst_arg: Is not a directory." >&2
+ exit 1
+ fi
+ fi
+fi
+
+if test -z "$dir_arg"; then
+ do_exit='(exit $ret); exit $ret'
+ trap "ret=129; $do_exit" 1
+ trap "ret=130; $do_exit" 2
+ trap "ret=141; $do_exit" 13
+ trap "ret=143; $do_exit" 15
# Set umask so as not to create temps with too-generous modes.
# However, 'strip' requires both read and write access to temps.
*[0-7])
if test -z "$stripcmd"; then
- u_plus_rw=
+ u_plus_rw=
else
- u_plus_rw='% 200'
+ u_plus_rw='% 200'
fi
cp_umask=`expr '(' 777 - $mode % 1000 ')' $u_plus_rw`;;
*)
if test -z "$stripcmd"; then
- u_plus_rw=
+ u_plus_rw=
else
- u_plus_rw=,u+rw
+ u_plus_rw=,u+rw
fi
cp_umask=$mode$u_plus_rw;;
esac
for src
do
- # Protect names starting with `-'.
+ # Protect names problematic for 'test' and other utilities.
case $src in
- -*) src=./$src;;
+ -* | [=\(\)!]) src=./$src;;
esac
if test -n "$dir_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: $dst_arg: Is a directory" >&2
- exit 1
+ if test "$is_target_a_directory" = never; 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'
- `
-
+ dstdir=`dirname "$dst"`
test -d "$dstdir"
dstdir_status=$?
fi
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-$$
- trap 'ret=$?; rmdir "$tmpdir/d" "$tmpdir" 2>/dev/null; exit $ret' 0
-
- if (umask $mkdir_umask &&
- exec $mkdirprog $mkdir_mode -p -- "$tmpdir/d") >/dev/null 2>&1
- then
- if test -z "$dir_arg" || {
- # Check for POSIX incompatibilities with -m.
- # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
- # other-writeable bit of parent directory when it shouldn't.
- # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
- ls_ld_tmpdir=`ls -ld "$tmpdir"`
- case $ls_ld_tmpdir in
- d????-?r-*) different_mode=700;;
- d????-?--*) different_mode=755;;
- *) false;;
- esac &&
- $mkdirprog -m$different_mode -p -- "$tmpdir" && {
- ls_ld_tmpdir_1=`ls -ld "$tmpdir"`
- test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
- }
- }
- then posix_mkdir=:
- fi
- rmdir "$tmpdir/d" "$tmpdir"
- else
- # Remove any dirs left behind by ancient mkdir implementations.
- rmdir ./$mkdir_mode ./-p ./-- 2>/dev/null
- fi
- trap '' 0;;
- esac;;
+ # Create intermediate dirs using mode 755 as modified by the umask.
+ # This is like FreeBSD 'install' as of 1997-10-28.
+ umask=`umask`
+ case $stripcmd.$umask in
+ # Optimize common cases.
+ *[2367][2367]) mkdir_umask=$umask;;
+ .*0[02][02] | .[02][02] | .[02]) mkdir_umask=22;;
+
+ *[0-7])
+ mkdir_umask=`expr $umask + 22 \
+ - $umask % 100 % 40 + $umask % 20 \
+ - $umask % 10 % 4 + $umask % 2
+ `;;
+ *) mkdir_umask=$umask,go-w;;
+ esac
+
+ # With -d, create the new directory with the user-specified mode.
+ # Otherwise, rely on $mkdir_umask.
+ if test -n "$dir_arg"; then
+ mkdir_mode=-m$mode
+ else
+ mkdir_mode=
+ fi
+
+ posix_mkdir=false
+ case $umask in
+ *[123567][0-7][0-7])
+ # POSIX mkdir -p sets u+wx bits regardless of umask, which
+ # is incompatible with FreeBSD 'install' when (umask & 300) != 0.
+ ;;
+ *)
+ # $RANDOM is not portable (e.g. dash); use it when possible to
+ # lower collision chance
+ tmpdir=${TMPDIR-/tmp}/ins$RANDOM-$$
+ trap 'ret=$?; rmdir "$tmpdir/a/b" "$tmpdir/a" "$tmpdir" 2>/dev/null; exit $ret' 0
+
+ # As "mkdir -p" follows symlinks and we work in /tmp possibly; so
+ # create the $tmpdir first (and fail if unsuccessful) to make sure
+ # that nobody tries to guess the $tmpdir name.
+ if (umask $mkdir_umask &&
+ $mkdirprog $mkdir_mode "$tmpdir" &&
+ exec $mkdirprog $mkdir_mode -p -- "$tmpdir/a/b") >/dev/null 2>&1
+ then
+ if test -z "$dir_arg" || {
+ # Check for POSIX incompatibilities with -m.
+ # HP-UX 11.23 and IRIX 6.5 mkdir -m -p sets group- or
+ # other-writable bit of parent directory when it shouldn't.
+ # FreeBSD 6.1 mkdir -m -p sets mode of existing directory.
+ test_tmpdir="$tmpdir/a"
+ ls_ld_tmpdir=`ls -ld "$test_tmpdir"`
+ case $ls_ld_tmpdir in
+ d????-?r-*) different_mode=700;;
+ d????-?--*) different_mode=755;;
+ *) false;;
+ esac &&
+ $mkdirprog -m$different_mode -p -- "$test_tmpdir" && {
+ ls_ld_tmpdir_1=`ls -ld "$test_tmpdir"`
+ test "$ls_ld_tmpdir" = "$ls_ld_tmpdir_1"
+ }
+ }
+ then posix_mkdir=:
+ fi
+ rmdir "$tmpdir/a/b" "$tmpdir/a" "$tmpdir"
+ else
+ # Remove any dirs left behind by ancient mkdir implementations.
+ rmdir ./$mkdir_mode ./-p ./-- "$tmpdir" 2>/dev/null
+ fi
+ trap '' 0;;
+ esac;;
esac
if
$posix_mkdir && (
- umask $mkdir_umask &&
- $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
+ umask $mkdir_umask &&
+ $doit_exec $mkdirprog $mkdir_mode -p -- "$dstdir"
)
then :
else
# directory the slow way, step by step, checking for races as we go.
case $dstdir in
- /*) prefix='/';;
- -*) prefix='./';;
- *) prefix='';;
+ /*) prefix='/';;
+ [-=\(\)!]*) prefix='./';;
+ *) prefix='';;
esac
- eval "$initialize_posix_glob"
-
oIFS=$IFS
IFS=/
- $posix_glob set -f
+ set -f
set fnord $dstdir
shift
- $posix_glob set +f
+ set +f
IFS=$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/
+ test X"$d" = X && continue
+
+ prefix=$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
+ # 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 -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" &&
- $posix_glob set -f &&
+ old=`LC_ALL=C ls -dlL "$dst" 2>/dev/null` &&
+ new=`LC_ALL=C ls -dlL "$dsttmp" 2>/dev/null` &&
+ set -f &&
set X $old && old=:$2:$4:$5:$6 &&
set X $new && new=:$2:$4:$5:$6 &&
- $posix_glob set +f &&
-
+ set +f &&
test "$old" = "$new" &&
$cmpprog "$dst" "$dsttmp" >/dev/null 2>&1
then
# to itself, or perhaps because mv is so ancient that it does not
# support -f.
{
- # Now remove or move aside any old file at destination location.
- # We try this two ways since rm can't unlink itself on some
- # systems and the destination file might be busy for other
- # reasons. In this case, the final cleanup might fail but the new
- # file should still install successfully.
- {
- test ! -f "$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" "$dst"
+ # Now remove or move aside any old file at destination location.
+ # We try this two ways since rm can't unlink itself on some
+ # systems and the destination file might be busy for other
+ # reasons. In this case, the final cleanup might fail but the new
+ # file should still install successfully.
+ {
+ test ! -f "$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
--- /dev/null
+#! /bin/sh
+
+# libtool - Provide generalized library-building support services.
+# Generated automatically by config.status (clustal-omega) 1.2.4
+# Libtool was configured on host ningal.cluster.lifesci.dundee.ac.uk:
+# 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=2.2.6
+macro_revision=1.3012
+
+# Whether or not to build shared libraries.
+build_libtool_libs=yes
+
+# Whether or not to build static libraries.
+build_old_libs=yes
+
+# What type of objects to build.
+pic_mode=default
+
+# Whether or not to optimize for fast installation.
+fast_install=yes
+
+# The host system.
+host_alias=
+host=x86_64-unknown-linux-gnu
+host_os=linux-gnu
+
+# The build system.
+build_alias=
+build=x86_64-unknown-linux-gnu
+build_os=linux-gnu
+
+# A sed program that does not truncate output.
+SED="/bin/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="/bin/grep"
+
+# An ERE matcher.
+EGREP="/bin/grep -E"
+
+# A literal string matcher.
+FGREP="/bin/grep -F"
+
+# A BSD- or MS-compatible name lister.
+NM="/usr/bin/nm -B"
+
+# Whether we need soft or hard links.
+LN_S="ln -s"
+
+# What is the maximum length of a command?
+max_cmd_len=1966080
+
+# Object file suffix (normally "o").
+objext=o
+
+# Executable file suffix (normally "").
+exeext=
+
+# whether the shell understands "unset".
+lt_unset=unset
+
+# turn spaces into newlines.
+SP2NL="tr \\040 \\012"
+
+# turn newlines into spaces.
+NL2SP="tr \\015\\012 \\040\\040"
+
+# How to create reloadable object files.
+reload_flag=" -r"
+reload_cmds="\$LD\$reload_flag -o \$output\$reload_objs"
+
+# An object symbol dumper.
+OBJDUMP="objdump"
+
+# Method to check whether dependent libraries are shared objects.
+deplibs_check_method="pass_all"
+
+# Command to use when deplibs_check_method == "file_magic".
+file_magic_cmd="\$MAGIC_CMD"
+
+# The archiver.
+AR="ar"
+AR_FLAGS="cru"
+
+# A symbol stripping program.
+STRIP="strip"
+
+# Commands used to install an old-style archive.
+RANLIB="ranlib"
+old_postinstall_cmds="chmod 644 \$oldlib~\$RANLIB \$oldlib"
+old_postuninstall_cmds=""
+
+# A C compiler.
+LTCC="gcc"
+
+# LTCC compiler flags.
+LTCFLAGS="-g -O2"
+
+# Take the output of nm and produce a listing of raw symbols and C names.
+global_symbol_pipe="sed -n -e 's/^.*[ ]\\([ABCDGIRSTW][ABCDGIRSTW]*\\)[ ][ ]*\\([_A-Za-z][_A-Za-z0-9]*\\)\$/\\1 \\2 \\2/p'"
+
+# Transform the output of nm in a proper C declaration.
+global_symbol_to_cdecl="sed -n -e 's/^T .* \\(.*\\)\$/extern int \\1();/p' -e 's/^[ABCDGIRSTW]* .* \\(.*\\)\$/extern char \\1;/p'"
+
+# Transform the output of nm in a C name address pair.
+global_symbol_to_c_name_address="sed -n -e 's/^: \\([^ ]*\\) \$/ {\\\"\\1\\\", (void *) 0},/p' -e 's/^[ABCDGIRSTW]* \\([^ ]*\\) \\([^ ]*\\)\$/ {\"\\2\", (void *) \\&\\2},/p'"
+
+# Transform the output of nm in a C name address pair when lib prefix is needed.
+global_symbol_to_c_name_address_lib_prefix="sed -n -e 's/^: \\([^ ]*\\) \$/ {\\\"\\1\\\", (void *) 0},/p' -e 's/^[ABCDGIRSTW]* \\([^ ]*\\) \\(lib[^ ]*\\)\$/ {\"\\2\", (void *) \\&\\2},/p' -e 's/^[ABCDGIRSTW]* \\([^ ]*\\) \\([^ ]*\\)\$/ {\"lib\\2\", (void *) \\&\\2},/p'"
+
+# The name of the directory that contains temporary libtool files.
+objdir=.libs
+
+# Shell to use when invoking shell scripts.
+SHELL="/bin/sh"
+
+# An echo program that does not interpret backslashes.
+ECHO="echo"
+
+# Used to examine libraries when file_magic_cmd begins with "file".
+MAGIC_CMD=file
+
+# Must we lock files when doing compilation?
+need_locks="no"
+
+# Tool to manipulate archived DWARF debug symbol files on Mac OS X.
+DSYMUTIL=""
+
+# Tool to change global to local symbols on Mac OS X.
+NMEDIT=""
+
+# Tool to manipulate fat objects and archives on Mac OS X.
+LIPO=""
+
+# ldd/readelf like tool for Mach-O binaries on Mac OS X.
+OTOOL=""
+
+# ldd/readelf like tool for 64 bit Mach-O binaries on Mac OS X 10.4.
+OTOOL64=""
+
+# Old archive suffix (normally "a").
+libext=a
+
+# Shared library suffix (normally ".so").
+shrext_cmds=".so"
+
+# The commands to extract the exported symbol list from a shared archive.
+extract_expsyms_cmds=""
+
+# Variables whose values should be saved in libtool wrapper scripts and
+# restored at link time.
+variables_saved_for_relink="PATH LD_LIBRARY_PATH LD_RUN_PATH GCC_EXEC_PREFIX COMPILER_PATH LIBRARY_PATH"
+
+# Do we need the "lib" prefix for modules?
+need_lib_prefix=no
+
+# Do we need a version for libraries?
+need_version=no
+
+# Library versioning type.
+version_type=linux
+
+# Shared library runtime path variable.
+runpath_var=LD_RUN_PATH
+
+# Shared library path variable.
+shlibpath_var=LD_LIBRARY_PATH
+
+# Is shlibpath searched before the hard-coded library search path?
+shlibpath_overrides_runpath=no
+
+# Format of library name prefix.
+libname_spec="lib\$name"
+
+# 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="\${libname}\${release}\${shared_ext}\$versuffix \${libname}\${release}\${shared_ext}\$major \$libname\${shared_ext}"
+
+# The coded name of the library, if different from the real name.
+soname_spec="\${libname}\${release}\${shared_ext}\$major"
+
+# Command to use after installation of a shared archive.
+postinstall_cmds=""
+
+# Command to use after uninstallation of a shared archive.
+postuninstall_cmds=""
+
+# Commands used to finish a libtool library installation in a directory.
+finish_cmds="PATH=\\\"\\\$PATH:/sbin\\\" ldconfig -n \$libdir"
+
+# As "finish_cmds", except a single script fragment to be evaled but
+# not shown.
+finish_eval=""
+
+# Whether we should hardcode library paths into libraries.
+hardcode_into_libs=yes
+
+# Compile-time system search path for libraries.
+sys_lib_search_path_spec="/usr/lib/gcc/x86_64-redhat-linux/4.4.7 /usr/lib64 /lib64"
+
+# Run-time system search path for libraries.
+sys_lib_dlsearch_path_spec="/lib /usr/lib /usr/lib64/R/lib /usr/lib64/atlas /usr/lib64/mysql /usr/lib64/papi-4.1.3 /usr/lib64/papi-5.1.1/usr/lib /usr/lib64/qt-3.3/lib /opt/dell/srvadmin/lib64 /opt/dell/srvadmin/lib64/openmanage /opt/dell/srvadmin/lib64 /opt/dell/srvadmin/lib64 /opt/dell/srvadmin/lib64/srvadmin-isvc /opt/dell/srvadmin/lib64 /opt/dell/srvadmin/lib64/openmanage /opt/dell/srvadmin/lib64 /opt/dell/srvadmin/lib64/openmanage /usr/lib64/tcl8.5 /usr/lib/wine/ /usr/lib64/wine/ /usr/lib64/xulrunner "
+
+# Whether dlopen is supported.
+dlopen_support=unknown
+
+# Whether dlopen of programs is supported.
+dlopen_self=unknown
+
+# Whether dlopen of statically linked programs is supported.
+dlopen_self_static=unknown
+
+# Commands to strip libraries.
+old_striplib="strip --strip-debug"
+striplib="strip --strip-unneeded"
+
+
+# The linker used to build libraries.
+LD="/usr/bin/ld -m elf_x86_64"
+
+# Commands used to build an old-style archive.
+old_archive_cmds="\$AR \$AR_FLAGS \$oldlib\$oldobjs~\$RANLIB \$oldlib"
+
+# A language specific compiler.
+CC="gcc"
+
+# Is the compiler the GNU compiler?
+with_gcc=yes
+
+# Compiler flag to turn off builtin functions.
+no_builtin_flag=" -fno-builtin"
+
+# How to pass a linker flag through the compiler.
+wl="-Wl,"
+
+# Additional compiler flags for building library objects.
+pic_flag=" -fPIC -DPIC"
+
+# Compiler flag to prevent dynamic linking.
+link_static_flag="-static"
+
+# Does compiler simultaneously support -c and -o options?
+compiler_c_o="yes"
+
+# Whether or not to add -lc for building shared libraries.
+build_libtool_need_lc=no
+
+# Whether or not to disallow shared libs when runtime libs are static.
+allow_libtool_libs_with_static_runtimes=no
+
+# Compiler flag to allow reflexive dlopens.
+export_dynamic_flag_spec="\${wl}--export-dynamic"
+
+# Compiler flag to generate shared objects directly from archives.
+whole_archive_flag_spec="\${wl}--whole-archive\$convenience \${wl}--no-whole-archive"
+
+# Whether the compiler copes with passing no objects directly.
+compiler_needs_object="no"
+
+# Create an old-style archive from a shared archive.
+old_archive_from_new_cmds=""
+
+# Create a temporary old-style archive to link instead of a shared archive.
+old_archive_from_expsyms_cmds=""
+
+# Commands used to build a shared archive.
+archive_cmds="\$CC -shared \$libobjs \$deplibs \$compiler_flags \${wl}-soname \$wl\$soname -o \$lib"
+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 -shared \$libobjs \$deplibs \$compiler_flags \${wl}-soname \$wl\$soname \${wl}-version-script \${wl}\$output_objdir/\$libname.ver -o \$lib"
+
+# Commands used to build a loadable module if different from building
+# a shared archive.
+module_cmds=""
+module_expsym_cmds=""
+
+# Whether we are building with GNU ld or not.
+with_gnu_ld="yes"
+
+# Flag that allows shared libraries with undefined symbols to be built.
+allow_undefined_flag=""
+
+# Flag that enforces no undefined symbols.
+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="\${wl}-rpath \${wl}\$libdir"
+
+# If ld is used when linking, flag to hardcode $libdir into a binary
+# during linking. This must work even if $libdir does not exist.
+hardcode_libdir_flag_spec_ld=""
+
+# Whether we need a single "-rpath" flag with a separated argument.
+hardcode_libdir_separator=""
+
+# Set to "yes" if using DIR/libNAME${shared_ext} during linking hardcodes
+# DIR into the resulting binary.
+hardcode_direct=no
+
+# 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=no
+
+# Set to "yes" if using the -LDIR flag during linking hardcodes DIR
+# into the resulting binary.
+hardcode_minus_L=no
+
+# Set to "yes" if using SHLIBPATH_VAR=DIR during linking hardcodes DIR
+# into the resulting binary.
+hardcode_shlibpath_var=unsupported
+
+# 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=no
+
+# Set to yes if linker adds runtime paths of dependent libraries
+# to runtime path list.
+inherit_rpath=no
+
+# Whether libtool must link a program against all its dependency libraries.
+link_all_deplibs=unknown
+
+# Fix the shell variable $srcfile for the compiler.
+fix_srcfile_path=""
+
+# Set to "yes" if exported symbols are required.
+always_export_symbols=no
+
+# The commands to list exported symbols.
+export_symbols_cmds="\$NM \$libobjs \$convenience | \$global_symbol_pipe | \$SED 's/.* //' | sort | uniq > \$export_symbols"
+
+# Symbols that should not be listed in the preloaded symbols.
+exclude_expsyms="_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*"
+
+# Symbols that must always be exported.
+include_expsyms=""
+
+# Commands necessary for linking programs (against libraries) with templates.
+prelink_cmds=""
+
+# Specify filename containing input files.
+file_list_spec=""
+
+# How to hardcode a shared library path into an executable.
+hardcode_action=immediate
+
+# The directories searched by this compiler when creating a shared library.
+compiler_lib_search_dirs=""
+
+# Dependencies to place before and after the objects being linked to
+# create a shared library.
+predep_objects=""
+postdep_objects=""
+predeps=""
+postdeps=""
+
+# The library search path used internally by the compiler when linking
+# a shared library.
+compiler_lib_search_path=""
+
+# ### END LIBTOOL CONFIG
+
+# 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.
+
+# 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}
+}
+
+
+# func_append var value
+# Append VALUE to the end of shell variable VAR.
+func_append ()
+{
+ eval "$1+=\$2"
+}
+# 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
+
+
+# ### BEGIN LIBTOOL TAG CONFIG: CXX
+
+# The linker used to build libraries.
+LD="/usr/bin/ld -m elf_x86_64"
+
+# Commands used to build an old-style archive.
+old_archive_cmds="\$AR \$AR_FLAGS \$oldlib\$oldobjs~\$RANLIB \$oldlib"
+
+# A language specific compiler.
+CC="g++"
+
+# Is the compiler the GNU compiler?
+with_gcc=yes
+
+# Compiler flag to turn off builtin functions.
+no_builtin_flag=" -fno-builtin"
+
+# How to pass a linker flag through the compiler.
+wl="-Wl,"
+
+# Additional compiler flags for building library objects.
+pic_flag=" -fPIC -DPIC"
+
+# Compiler flag to prevent dynamic linking.
+link_static_flag="-static"
+
+# Does compiler simultaneously support -c and -o options?
+compiler_c_o="yes"
+
+# Whether or not to add -lc for building shared libraries.
+build_libtool_need_lc=no
+
+# Whether or not to disallow shared libs when runtime libs are static.
+allow_libtool_libs_with_static_runtimes=no
+
+# Compiler flag to allow reflexive dlopens.
+export_dynamic_flag_spec="\${wl}--export-dynamic"
+
+# Compiler flag to generate shared objects directly from archives.
+whole_archive_flag_spec="\${wl}--whole-archive\$convenience \${wl}--no-whole-archive"
+
+# Whether the compiler copes with passing no objects directly.
+compiler_needs_object="no"
+
+# Create an old-style archive from a shared archive.
+old_archive_from_new_cmds=""
+
+# Create a temporary old-style archive to link instead of a shared archive.
+old_archive_from_expsyms_cmds=""
+
+# Commands used to build a shared archive.
+archive_cmds="\$CC -shared -nostdlib \$predep_objects \$libobjs \$deplibs \$postdep_objects \$compiler_flags \${wl}-soname \$wl\$soname -o \$lib"
+archive_expsym_cmds="\$CC -shared -nostdlib \$predep_objects \$libobjs \$deplibs \$postdep_objects \$compiler_flags \${wl}-soname \$wl\$soname \${wl}-retain-symbols-file \$wl\$export_symbols -o \$lib"
+
+# Commands used to build a loadable module if different from building
+# a shared archive.
+module_cmds=""
+module_expsym_cmds=""
+
+# Whether we are building with GNU ld or not.
+with_gnu_ld="yes"
+
+# Flag that allows shared libraries with undefined symbols to be built.
+allow_undefined_flag=""
+
+# Flag that enforces no undefined symbols.
+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="\${wl}-rpath \${wl}\$libdir"
+
+# If ld is used when linking, flag to hardcode $libdir into a binary
+# during linking. This must work even if $libdir does not exist.
+hardcode_libdir_flag_spec_ld=""
+
+# Whether we need a single "-rpath" flag with a separated argument.
+hardcode_libdir_separator=""
+
+# Set to "yes" if using DIR/libNAME${shared_ext} during linking hardcodes
+# DIR into the resulting binary.
+hardcode_direct=no
+
+# 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=no
+
+# Set to "yes" if using the -LDIR flag during linking hardcodes DIR
+# into the resulting binary.
+hardcode_minus_L=no
+
+# Set to "yes" if using SHLIBPATH_VAR=DIR during linking hardcodes DIR
+# into the resulting binary.
+hardcode_shlibpath_var=unsupported
+
+# 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=no
+
+# Set to yes if linker adds runtime paths of dependent libraries
+# to runtime path list.
+inherit_rpath=no
+
+# Whether libtool must link a program against all its dependency libraries.
+link_all_deplibs=no
+
+# Fix the shell variable $srcfile for the compiler.
+fix_srcfile_path=""
+
+# Set to "yes" if exported symbols are required.
+always_export_symbols=no
+
+# The commands to list exported symbols.
+export_symbols_cmds="\$NM \$libobjs \$convenience | \$global_symbol_pipe | \$SED 's/.* //' | sort | uniq > \$export_symbols"
+
+# Symbols that should not be listed in the preloaded symbols.
+exclude_expsyms="_GLOBAL_OFFSET_TABLE_|_GLOBAL__F[ID]_.*"
+
+# Symbols that must always be exported.
+include_expsyms=""
+
+# Commands necessary for linking programs (against libraries) with templates.
+prelink_cmds=""
+
+# Specify filename containing input files.
+file_list_spec=""
+
+# How to hardcode a shared library path into an executable.
+hardcode_action=immediate
+
+# The directories searched by this compiler when creating a shared library.
+compiler_lib_search_dirs="/usr/lib/gcc/x86_64-redhat-linux/4.4.7 /usr/lib/gcc/x86_64-redhat-linux/4.4.7 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 /lib/../lib64 /usr/lib/../lib64 /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.."
+
+# Dependencies to place before and after the objects being linked to
+# create a shared library.
+predep_objects="/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crti.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtbeginS.o"
+postdep_objects="/usr/lib/gcc/x86_64-redhat-linux/4.4.7/crtendS.o /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crtn.o"
+predeps=""
+postdeps="-lstdc++ -lm -lgcc_s -lc -lgcc_s"
+
+# The library search path used internally by the compiler when linking
+# a shared library.
+compiler_lib_search_path="-L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../.."
+
+# ### END LIBTOOL TAG CONFIG: CXX
#! /bin/sh
-# Common stub for a few missing GNU programs while installing.
+# Common wrapper for a few potentially missing GNU programs.
-scriptversion=2009-04-28.21; # UTC
+scriptversion=2013-10-28.13; # 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.
+# Copyright (C) 1996-2014 Free Software Foundation, Inc.
+# Originally written 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 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"
+ 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
+case $1 in
-msg="missing on your system"
+ --is-lightweight)
+ # Used by our autoconf macros to check whether the available missing
+ # script is modern enough.
+ exit 0
+ ;;
-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
- ;;
+ --run)
+ # Back-compat with the calling convention used by older automake.
+ shift
+ ;;
-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.
+Run 'PROGRAM [ARGUMENT]...', returning a proper advice when this fails due
+to PROGRAM being missing or too old.
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]
+ aclocal autoconf autoheader autom4te automake makeinfo
+ bison yacc flex lex help2man
-Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and
-\`g' are ignored when checking the name.
+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 $?
;;
-*)
- echo 1>&2 "$0: Unknown \`$1' option"
- echo 1>&2 "Try \`$0 --help' for more information"
+ 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 \`$1' program."
- exit 1
- ;;
-esac
+# Run the given program, remember its exit status.
+"$@"; st=$?
+
+# If it succeeded, we are done.
+test $st -eq 0 && exit 0
+
+# Also exit now if we it failed (or wasn't found), and '--version' was
+# passed; such an option is passed most likely to detect whether the
+# program is present and works.
+case $2 in --version|--help) exit $st;; esac
+
+# Exit code 63 means version mismatch. This often happens when the user
+# tries to use an ancient version of a tool on a file that requires a
+# minimum version.
+if test $st -eq 63; then
+ msg="probably too old"
+elif test $st -eq 127; then
+ # Program was missing.
+ msg="missing on your system"
+else
+ # Program was found and executed, but failed. Give up.
+ exit $st
+fi
-exit 0
+perl_URL=http://www.perl.org/
+flex_URL=http://flex.sourceforge.net/
+gnu_software_URL=http://www.gnu.org/software
+
+program_details ()
+{
+ case $1 in
+ aclocal|automake)
+ echo "The '$1' program is part of the GNU Automake package:"
+ echo "<$gnu_software_URL/automake>"
+ echo "It also requires GNU Autoconf, GNU m4 and Perl in order to run:"
+ echo "<$gnu_software_URL/autoconf>"
+ echo "<$gnu_software_URL/m4/>"
+ echo "<$perl_URL>"
+ ;;
+ autoconf|autom4te|autoheader)
+ echo "The '$1' program is part of the GNU Autoconf package:"
+ echo "<$gnu_software_URL/autoconf/>"
+ echo "It also requires GNU m4 and Perl in order to run:"
+ echo "<$gnu_software_URL/m4/>"
+ echo "<$perl_URL>"
+ ;;
+ esac
+}
+
+give_advice ()
+{
+ # Normalize program name to check for.
+ normalized_program=`echo "$1" | sed '
+ s/^gnu-//; t
+ s/^gnu//; t
+ s/^g//; t'`
+
+ printf '%s\n' "'$1' is $msg."
+
+ configure_deps="'configure.ac' or m4 files included by 'configure.ac'"
+ case $normalized_program in
+ autoconf*)
+ echo "You should only need it if you modified 'configure.ac',"
+ echo "or m4 files included by it."
+ program_details 'autoconf'
+ ;;
+ autoheader*)
+ echo "You should only need it if you modified 'acconfig.h' or"
+ echo "$configure_deps."
+ program_details 'autoheader'
+ ;;
+ automake*)
+ echo "You should only need it if you modified 'Makefile.am' or"
+ echo "$configure_deps."
+ program_details 'automake'
+ ;;
+ aclocal*)
+ echo "You should only need it if you modified 'acinclude.m4' or"
+ echo "$configure_deps."
+ program_details 'aclocal'
+ ;;
+ autom4te*)
+ echo "You might have modified some maintainer files that require"
+ echo "the 'autom4te' program to be rebuilt."
+ program_details 'autom4te'
+ ;;
+ bison*|yacc*)
+ echo "You should only need it if you modified a '.y' file."
+ echo "You may want to install the GNU Bison package:"
+ echo "<$gnu_software_URL/bison/>"
+ ;;
+ lex*|flex*)
+ echo "You should only need it if you modified a '.l' file."
+ echo "You may want to install the Fast Lexical Analyzer package:"
+ echo "<$flex_URL>"
+ ;;
+ help2man*)
+ echo "You should only need it if you modified a dependency" \
+ "of a man page."
+ echo "You may want to install the GNU Help2man package:"
+ echo "<$gnu_software_URL/help2man/>"
+ ;;
+ makeinfo*)
+ echo "You should only need it if you modified a '.texi' file, or"
+ echo "any other file indirectly affecting the aspect of the manual."
+ echo "You might want to install the Texinfo package:"
+ echo "<$gnu_software_URL/texinfo/>"
+ echo "The spurious makeinfo call might also be the consequence of"
+ echo "using a buggy 'make' (AIX, DU, IRIX), in which case you might"
+ echo "want to install GNU make:"
+ echo "<$gnu_software_URL/make/>"
+ ;;
+ *)
+ echo "You might have modified some files without having the proper"
+ echo "tools for further handling them. Check the 'README' file, it"
+ echo "often tells you about the needed prerequisites for installing"
+ echo "this package. You may also peek at any GNU archive site, in"
+ echo "case some other package contains this missing '$1' program."
+ ;;
+ esac
+}
+
+give_advice "$1" | sed -e '1s/^/WARNING: /' \
+ -e '2,$s/^/ /' >&2
+
+# Propagate the correct exit status (expected to be 127 for a program
+# not found, 63 for a program that failed due to version mismatch).
+exit $st
# Local variables:
# eval: (add-hook 'write-file-hooks 'time-stamp)
--- /dev/null
+clustal-omega.lo: clustal-omega.c config.h /usr/include/assert.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h clustal-omega.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h \
+ clustal-omega-config.h hhalign/general.h hhalign/../clustal/log.h \
+ /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h hhalign/hhfunc.h clustal/log.h clustal/util.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/bits/string.h \
+ /usr/include/bits/string2.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/stdlib.h /usr/include/strings.h clustal/symmatrix.h \
+ clustal/seq.h squid/squid.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h config.h squid/msa.h squid/gki.h squid/ssi.h \
+ squid/squid.h squid/sqfuncs.h squid/sre_random.h squid/vectorops.h \
+ clustal/util.h clustal/tree.h clustal/symmatrix.h clustal/muscle_tree.h \
+ clustal/seq.h clustal/mbed.h clustal/weights.h clustal/pair_dist.h \
+ clustal/hhalign_wrapper.h
+
+config.h:
+
+/usr/include/assert.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+clustal-omega.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h:
+
+clustal-omega-config.h:
+
+hhalign/general.h:
+
+hhalign/../clustal/log.h:
+
+/usr/include/stdio.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+hhalign/hhfunc.h:
+
+clustal/log.h:
+
+clustal/util.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h:
+
+/usr/include/limits.h:
+
+/usr/include/bits/posix1_lim.h:
+
+/usr/include/bits/local_lim.h:
+
+/usr/include/linux/limits.h:
+
+/usr/include/bits/posix2_lim.h:
+
+/usr/include/bits/xopen_lim.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/strings.h:
+
+clustal/symmatrix.h:
+
+clustal/seq.h:
+
+squid/squid.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+config.h:
+
+squid/msa.h:
+
+squid/gki.h:
+
+squid/ssi.h:
+
+squid/squid.h:
+
+squid/sqfuncs.h:
+
+squid/sre_random.h:
+
+squid/vectorops.h:
+
+clustal/util.h:
+
+clustal/tree.h:
+
+clustal/symmatrix.h:
+
+clustal/muscle_tree.h:
+
+clustal/seq.h:
+
+clustal/mbed.h:
+
+clustal/weights.h:
+
+clustal/pair_dist.h:
+
+clustal/hhalign_wrapper.h:
--- /dev/null
+main.o: main.cpp config.h /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/xlocale.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/string.h mymain.h clustal/util.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
+ /usr/include/strings.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h squid/squid.h \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h config.h squid/msa.h \
+ squid/gki.h squid/ssi.h squid/squid.h squid/sqfuncs.h squid/sre_random.h \
+ squid/vectorops.h
+
+config.h:
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/string.h:
+
+mymain.h:
+
+clustal/util.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h:
+
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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:
/* The package code name */
#ifndef CLUSTAL_OMEGA_PACKAGE_CODENAME
-#define CLUSTAL_OMEGA_PACKAGE_CODENAME "DeshilHollesEamus"
+#define CLUSTAL_OMEGA_PACKAGE_CODENAME "AndreaGiacomo"
#endif
/* Define to the full name of this package. */
/* 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"
+#define CLUSTAL_OMEGA_PACKAGE_STRING "Clustal Omega 1.2.4"
#endif
/* Define to the one symbol short name of this package. */
/* Define to the version of this package. */
#ifndef CLUSTAL_OMEGA_PACKAGE_VERSION
-#define CLUSTAL_OMEGA_PACKAGE_VERSION "1.0.2"
+#define CLUSTAL_OMEGA_PACKAGE_VERSION "1.2.4"
#endif
/* The size of `fpos_t', as computed by sizeof. */
/* Version number of package */
#ifndef CLUSTAL_OMEGA_VERSION
-#define CLUSTAL_OMEGA_VERSION "1.0.2"
+#define CLUSTAL_OMEGA_VERSION "1.2.4"
#endif
/* Define if using the dmalloc debugging malloc package */
********************************************************************/
/*
- * RCS $Id: clustal-omega.c 254 2011-06-21 13:07:50Z andreas $
+ * RCS $Id: clustal-omega.c 304 2016-06-13 13:39:13Z fabian $
*/
#ifdef HAVE_CONFIG_H
#include "clustal-omega.h"
#include "hhalign/general.h"
+#include "clustal/hhalign_wrapper.h"
/* The following comment block contains the frontpage/mainpage of the doxygen
* documentation. Please add some more info. FIXME add more
*
* 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++.
+ * use a C++ compiler, no matter if your program was written in C or C++. See
+ * below (\ref pkgconfig_subsubsec)) on how to figure out compiler flags with
+ * pkg-config.
*
- * First compile (no linking) your source (for an example see section "\ref
- * example_src_subsubsec"):
+ * Assuming Clustal Omega was installed in system-wide default directory (e.g.
+ * /usr), first compile (don't link yet) your source (for example code see
+ * section \ref example_src_subsubsec) and then link against libclustalo:
*
* @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
+ * Voila! Now you have your own alignment program based on Clustal Omega which
+ * can be run with
*
* @code
* $ ./clustalo-api-test <your-sequence-input>
* @endcode
*
*
- * To compile your source use:
+ * To compile your source use as above but this time using proper flags:
*
* @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)
+ * $ gcc -c -ansi -Wall $(pkg-config --cflags clustalo) clustalo-api-test.c
+ * $ g++ -ansi -Wall -o clustalo-api-test $(pkg-config --libs clustalo) clustalo-api-test.o
* @endcode
*
*
*/
-
-
-/* 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
prOpts->pcDistmatInfile = NULL;
prOpts->pcDistmatOutfile = NULL;
-
+
+ prOpts->iClustersizes = 100; /* FS, r274 -> */
+ prOpts->iTransitivity = 0; /* FS, r290 -> */
+ prOpts->pcClustfile = NULL; /* FS, r274 -> */
+ prOpts->pcPosteriorfile = NULL; /* FS, r288 -> */
prOpts->iClusteringType = CLUSTERING_UPGMA;
prOpts->iPairDistType = PAIRDIST_KTUPLE;
prOpts->bUseMbed = TRUE; /* FS, r250 -> */
prOpts->bUseMbedForIteration = TRUE; /* FS, r250 -> */
+ prOpts->bPileup = FALSE; /* FS, r288 -> */
prOpts->pcGuidetreeOutfile = NULL;
prOpts->pcGuidetreeInfile = NULL;
-
+ prOpts->bPercID = FALSE;
+
prOpts->ppcHMMInput = NULL;
prOpts->iHMMInputFiles = 0;
-
+ prOpts->pcHMMBatch = NULL; /* FS, r291 -> */
+
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 */
+
+ SetDefaultHhalignPara(& prOpts->rHhalignPara);
}
/* end of SetDefaultAlnOpts() */
*/
}
- if (prOpts->iMacRam < 512) {
-
- Log(&rLog, LOG_INFO, "Memory for MAC Algorithm quite low, Viterbi Algorithm may be triggered.");
-
- if (prOpts->iMacRam < 1) {
-
+ if (prOpts->rHhalignPara.iMacRamMB < 512) {
+ Log(&rLog, LOG_WARN, "Memory for MAC Algorithm quite low, Viterbi Algorithm may be triggered.");
+ if (prOpts->rHhalignPara.iMacRamMB < 1) {
Log(&rLog, LOG_WARN, "Viterbi Algorithm always turned on, increase MAC-RAM to turn on MAC.");
}
}
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: pile-up = %d\n", prOpts->bPileup);
fprintf(prFile, "option: guidetree-outfile = %s\n",
NULL != prOpts->pcGuidetreeOutfile? prOpts->pcGuidetreeOutfile: "(null)");
fprintf(prFile, "option: guidetree-infile = %s\n",
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);
+ fprintf(prFile, "option: iMacRamMB = %d\n", prOpts->rHhalignPara.iMacRamMB);
+ fprintf(prFile, "option: percent-id = %d\n", prOpts->bPercID);
+ fprintf(prFile, "option: use-kimura = %d\n", prOpts->bUseKimura);
+ fprintf(prFile, "option: clustering-out = %s\n", prOpts->pcClustfile);
+ fprintf(prFile, "option: posterior-out = %s\n", prOpts->pcPosteriorfile);
+
}
/* end of PrintAlnOpts() */
retcode = FAILURE;
goto cleanup_and_return;
}
- if (WriteAlignment(prMSeq, tmp_aln, MSAFILE_A2M)) {
+#define LINE_WRAP 60
+ if (WriteAlignment(prMSeq, tmp_aln, MSAFILE_A2M, LINE_WRAP, FALSE)) {
Log(&rLog, LOG_ERROR, "Could not save alignment to %s", tmp_aln);
retcode = FAILURE;
goto cleanup_and_return;
retcode = FAILURE;
goto cleanup_and_return;
}
- if (WriteAlignment(prMSeq, tmp_aln, MSAFILE_STOCKHOLM)) {
+#define LINE_WRAP 60
+ if (WriteAlignment(prMSeq, tmp_aln, MSAFILE_STOCKHOLM, LINE_WRAP, FALSE)) {
Log(&rLog, LOG_ERROR, "Could not save alignment to %s", tmp_aln);
retcode = FAILURE;
goto cleanup_and_return;
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)
+ int iClusteringType, int iClustersizes,
+ char *pcGuidetreeInfile, char *pcGuidetreeOutfile, char *pcClusterFile,
+ bool bUseMbed, bool bPercID)
{
/* pairwise distance matrix (tmat in 1.83) */
symmatrix_t *distmat = NULL;
if (2==prMSeq->nseqs) {
Log(&rLog, LOG_VERBOSE,
"Have only two sequences: No need to compute pairwise score and compute a tree.");
-
+
+ if (NULL != pcDistmatOutfile){
+ Log(&rLog, LOG_WARN, "Have only two sequences: Will not calculate/print distance matrix.");
+ }
+
(*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;
} else {
if (bUseMbed) {
- if (Mbed(&prTree, prMSeq, iPairDistType, pcGuidetreeOutfile)) {
+ if (NULL != pcDistmatInfile) {
+ Log(&rLog, LOG_ERROR, "Can't input distance matrix when in mbed mode.");
+ return FAILURE;
+ }
+ if (Mbed(&prTree, prMSeq, iPairDistType, pcGuidetreeOutfile, iClustersizes, pcClusterFile)) {
Log(&rLog, LOG_ERROR, "mbed execution failed.");
return FAILURE;
}
}
} else {
- if (PairDistances(&distmat, prMSeq, iPairDistType,
+ if (PairDistances(&distmat, prMSeq, iPairDistType, bPercID,
0, prMSeq->nseqs, 0, prMSeq->nseqs,
pcDistmatInfile, pcDistmatOutfile)) {
Log(&rLog, LOG_ERROR, "Couldn't compute pair distances");
Log(&rLog, LOG_FATAL, "INTERNAL ERROR %s",
"clustering method should have been checked before");
}
- }
- }
+ } /* did not use mBed */
+ } /* had to calculate tree (did not read from file) */
+
#if USE_WEIGHTS
/* derive sequence weights from tree
* @param[in] prMSeqProfile
* optional profile to align against
* @param[in] prOpts
- * alignmemnt options to use
+ * alignment options to use
*
* @return 0 on success, -1 on failure
*
int
Align(mseq_t *prMSeq,
mseq_t *prMSeqProfile,
- opts_t *prOpts,
- hhalign_para rHhalignPara) {
+ opts_t *prOpts) { /* Note DEVEL 291: at this stage pppcHMMBNames is set but ppiHMMBindex is not */
/* HMM
*/
/* last dAlnScore for iteration */
double dLastAlnScore = -666.666;
+ /* HMM batch file */
+ char **ppcHMMbatch = NULL; /* names of unique HMM files */
+ int iHMMbatch = 0; /* number of unique HMM files */
+
int i, j; /* aux */
assert(NULL != prMSeq);
#endif
+ if (TRUE == prOpts->bPileup){
+ PileUp(prMSeq, prOpts->rHhalignPara, prOpts->iClustersizes);
+ return 0;
+ }
+
- /* Read backgrounds HMMs and store in prHMMs
+ /* Read backgrounds HMMs and store in prHMMs (Devel 291)
*
*/
- if (0 < prOpts->iHMMInputFiles) {
+ if (NULL != prOpts->pcHMMBatch){
+ int i, j, k;
+
+ for (i = 0; i < prMSeq->nseqs; i++){
+
+ if (NULL != prMSeq->pppcHMMBNames[i]){
+ for (j = 0; NULL != prMSeq->pppcHMMBNames[i][j]; j++){
+
+ for (k = 0; k < iHMMbatch; k++){
+ if (0 == strcmp(ppcHMMbatch[k], prMSeq->pppcHMMBNames[i][j])){
+ prMSeq->ppiHMMBindex[i][j] = k;
+ break; /* HMM already registered */
+ }
+ } /* went through HMM batch files already identified */
+ if (k == iHMMbatch){
+ FILE *pfHMM = NULL;
+ if (NULL == (pfHMM = fopen(prMSeq->pppcHMMBNames[i][j], "r"))){
+ prMSeq->ppiHMMBindex[i][j] = -1;
+ Log(&rLog, LOG_WARN, "Background HMM %s for %s (%d/%d) does not exist",
+ prMSeq->pppcHMMBNames[i][j], prMSeq->sqinfo[i].name, i, j);
+ }
+ else {
+ fclose(pfHMM); pfHMM = NULL;
+ ppcHMMbatch = (char **)realloc(ppcHMMbatch, (iHMMbatch+1)*sizeof(char *));
+ ppcHMMbatch[iHMMbatch] = strdup(prMSeq->pppcHMMBNames[i][j]);
+ prMSeq->ppiHMMBindex[i][j] = k;
+ iHMMbatch++;
+ }
+ }
+
+ } /* j = 0; NULL != prMSeq->pppcHMMBNames[i][j] */
+ } /* NULL != prMSeq->pppcHMMBNames[i] */
+ else {
+ /* void */
+ }
+ } /* 0 <= i < prMSeq->nseqs */
+
+ } /* there was a HMM batch file */
+
+
+ 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));
+ prHMMs = (hmm_light *) CKMALLOC( (prOpts->iHMMInputFiles) * sizeof(hmm_light));
for (iHMMInfileIndex=0; iHMMInfileIndex<prOpts->iHMMInputFiles; iHMMInfileIndex++) {
char *pcHMMInput = prOpts->ppcHMMInput[iHMMInfileIndex];
CKFREE(prOpts->ppcHMMInput);
} /* there were background HMM files */
+ /** read HMMs specific to individual sequences
+ */
+ if (iHMMbatch > 0){
+ int i;
+
+ prHMMs = (hmm_light *) realloc( prHMMs, (prOpts->iHMMInputFiles + iHMMbatch + 1) * sizeof(hmm_light));
+
+ for (i = 0; i < iHMMbatch; i++){
+ char *pcHMMInput = ppcHMMbatch[i];
+
+ if (OK != readHMMWrapper(&prHMMs[i + prOpts->iHMMInputFiles], pcHMMInput)){
+ Log(&rLog, LOG_ERROR, "Processing of HMM file %s failed", pcHMMInput);
+ return -1;
+ }
+
+ } /* 0 <= i < iHMMbatch */
+
+ } /* there were HMM batch files */
/* If the input ("non-profile") sequences are aligned, then turn
Log(&rLog, LOG_INFO,
"Input sequences are aligned. Will turn alignment into HMM and add it to the user provided background HMMs.");
+ /* certain gap parameters ('~' MSF) cause problems,
+ sanitise them; FS, r258 -> r259 */
+ SanitiseUnknown(prMSeq);
if (OK !=
#if INDIRECT_HMM
AlnToHMM(&rHMMLocal, prMSeq)
#else
- AlnToHMM2(&rHMMLocal, prMSeq->seq, prMSeq->nseqs)
+ AlnToHMM2(&rHMMLocal, prOpts->rHhalignPara, prMSeq->seq, prMSeq->nseqs)
#endif
) {
Log(&rLog, LOG_ERROR, "Couldn't convert aligned input sequences to HMM. Will try to continue");
#if INDIRECT_HMM
AlnToHMM(&rHMMLocal, prMSeqProfile)
#else
- AlnToHMM2(&rHMMLocal, prMSeqProfile->seq, prMSeqProfile->nseqs)
+ AlnToHMM2(&rHMMLocal, prOpts->rHhalignPara, prMSeqProfile->seq, prMSeqProfile->nseqs)
#endif
) {
Log(&rLog, LOG_ERROR, "Couldn't convert profile1 to HMM. Will try to continue");
/* 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 ( (SEQTYPE_PROTEIN == prMSeq->seqtype) && (TRUE == prOpts->bUseKimura) ){
+ Log(&rLog, LOG_INFO, "%s %s",
+ "Input sequences are aligned.",
+ "Will use Kimura distances of aligned sequences.");
+ prOpts->iPairDistType = PAIRDIST_SQUIDID_KIMURA;
+ }
+ else {
+ prOpts->iPairDistType = PAIRDIST_SQUIDID;
+ }
}
#if 0
if (OK != AlignmentOrder(&piOrderLR, &pdSeqWeights, prMSeq,
prOpts->iPairDistType,
prOpts->pcDistmatInfile, prOpts->pcDistmatOutfile,
- prOpts->iClusteringType,
- prOpts->pcGuidetreeInfile, prOpts->pcGuidetreeOutfile,
- prOpts->bUseMbed)) {
+ prOpts->iClusteringType, prOpts->iClustersizes,
+ prOpts->pcGuidetreeInfile, prOpts->pcGuidetreeOutfile, prOpts->pcClustfile,
+ prOpts->bUseMbed, prOpts->bPercID)) {
Log(&rLog, LOG_ERROR, "AlignmentOrder() failed. Cannot continue");
return -1;
}
#endif
+ /* if max-hmm-iter is set < 0 then do not perform alignment
+ * there is a problem/feature(?) that the un-aligned sequences are output
+ */
+ if (prOpts->iMaxHMMIterations < 0){
+ Log(&rLog, LOG_VERBOSE,
+ "iMaxHMMIterations < 0 (%d), will not perform alignment", prOpts->iMaxHMMIterations);
+ if (NULL != piOrderLR){
+ free(piOrderLR); piOrderLR = NULL;
+ }
+ return 0;
+ }
+
+
/* 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);
+ prHMMs, prOpts->iHMMInputFiles, -1, prOpts->rHhalignPara);
dLastAlnScore = dAlnScore;
Log(&rLog, LOG_VERBOSE,
"Alignment score for first alignment = %f", dAlnScore);
char zcIntermediate[1000] = {0};
char *pcFormat = "fasta";
sprintf(zcIntermediate, "clustalo-aln-iter~%d~", iIterationCounter);
- if (WriteAlignment(prMSeq, zcIntermediate, MSAFILE_A2M)) {
+#define LINE_WRAP 60
+ if (WriteAlignment(prMSeq, zcIntermediate, MSAFILE_A2M, LINE_WRAP)) {
Log(&rLog, LOG_ERROR, "Could not save alignment to %s", zcIntermediate);
return -1;
}
CKFREE(piOrderLR);
if (NULL != pdSeqWeights)
CKFREE(pdSeqWeights);
+ Log(&rLog, LOG_INFO, "Computing new guide tree (iteration step %d)");
if (AlignmentOrder(&piOrderLR, &pdSeqWeights, prMSeq,
- PAIRDIST_SQUIDID_KIMURA /* override */, NULL, prOpts->pcDistmatOutfile,
- prOpts->iClusteringType, NULL, prOpts->pcGuidetreeOutfile,
- prOpts->bUseMbedForIteration)) {
+ ((SEQTYPE_PROTEIN == prMSeq->seqtype) && (TRUE == prOpts->bUseKimura)) ? PAIRDIST_SQUIDID_KIMURA : PAIRDIST_SQUIDID,
+ NULL, prOpts->pcDistmatOutfile,
+ prOpts->iClusteringType, prOpts->iClustersizes,
+ NULL, prOpts->pcGuidetreeOutfile, prOpts->pcClustfile,
+ prOpts->bUseMbedForIteration, prOpts->bPercID)) {
Log(&rLog, LOG_ERROR, "AlignmentOrder() failed. Cannot continue");
return -1;
}
/* new local hmm iteration
*
*/
+ /* non-residue/gap characters will crash AlnToHMM2(),
+ therefore sanitise unknown characters, FS, r259 -> r260 */
+ SanitiseUnknown(prMSeq);
if (iIterationCounter < prOpts->iMaxHMMIterations) {
+ Log(&rLog, LOG_INFO, "Computing HMM from alignment");
+
if (OK !=
#if INDIRECT_HMM
AlnToHMM(&rHMMLocal, prMSeq)
#else
- AlnToHMM2(&rHMMLocal, prMSeq->seq, prMSeq->nseqs)
+ AlnToHMM2(&rHMMLocal, prOpts->rHhalignPara, prMSeq->seq, prMSeq->nseqs)
#endif
) {
Log(&rLog, LOG_ERROR, "Couldn't convert alignment to HMM. Will stop iterating now...");
/* align the sequences (again)
*/
dAlnScore = HHalignWrapper(prMSeq, piOrderLR, pdSeqWeights,
- 2*prMSeq->nseqs -1/* nodes */, &rHMMLocal, 1, -1, rHhalignPara);
+ 2*prMSeq->nseqs -1/* nodes */, &rHMMLocal, 1, -1,
+ prOpts->rHhalignPara);
Log(&rLog, LOG_VERBOSE,
"Alignment score for alignmnent in hmm-iteration no %d = %f (last score = %f)",
iIterationCounter+1, dAlnScore, dLastAlnScore);
*
*/
if (NULL != prMSeqProfile) {
- if (AlignProfiles(prMSeq, prMSeqProfile, rHhalignPara)) {
+ if (AlignProfiles(prMSeq, prMSeqProfile, prOpts->rHhalignPara)) {
Log(&rLog, LOG_ERROR, "An error occured during the profile/profile alignment");
return -1;
}
}
+ if (NULL != prOpts->pcPosteriorfile){
+
+ hmm_light rHMMLocal = {0};
+
+ if (OK !=
+#if INDIRECT_HMM
+ AlnToHMM(&rHMMLocal, prMSeq)
+#else
+ AlnToHMM2(&rHMMLocal, prOpts->rHhalignPara, prMSeq->seq, prMSeq->nseqs)
+#endif
+ ) {
+ Log(&rLog, LOG_ERROR, "Couldn't convert alignment to HMM. Will not do posterior probabilities...");
+ }
+ PosteriorProbabilities(prMSeq, rHMMLocal, prOpts->rHhalignPara, prOpts->pcPosteriorfile);
+ FreeHMMstruct(&rHMMLocal);
+ }
if (NULL != piOrderLR) {
CKFREE(piOrderLR);
* here.
* @param[in] prMSeqProfile2
* First profile/aligned set of sequences
+ * @param[in] rHhalignPara
+ * FIXME
*
* @return 0 on success, -1 on failure
*
*/
int
AlignProfiles(mseq_t *prMSeqProfile1,
- mseq_t *prMSeqProfile2, hhalign_para rHhalignPara) {
+ mseq_t *prMSeqProfile2, hhalign_para rHhalignPara) {
double dAlnScore;
}
/* end of AlignProfiles() */
+/**
+ * @brief read pseudo-count 'fudge' parameters from file
+ *
+ * @param[out] rHhalignPara_p
+ * structure that holds several hhalign parameters
+ * @param[in] pcPseudoFile
+ * name of file with pseudo-count information.
+ * format must be collection of pairs of lines where one line specifies name of parameter
+ * (gapb,gapd,gape,gapf,gapg,gaph,gapi,pca,pcb,pcc,gapbV,gapdV,gapeV,gapfV,gapgV,gaphV,gapiV,pcaV,pcbV,pccV)
+ * followed by second line with the (double) value of this parameter.
+ *
+ * order of parameters is not fixed, not all parameters have to be set
+ */
+int ReadPseudoCountParams(hhalign_para *rHhalignPara_p, char *pcPseudoFile){
+
+
+ FILE *pfIn = NULL;
+ char zcLine[1000] = {0};
+ char zcFudge[1000] = {0};
+ double dVal = 0.00;
+ char *pcToken = NULL;
+ char *pcEnd = NULL;
+
+ if (NULL == (pfIn = fopen(pcPseudoFile, "r"))){
+ Log(&rLog, LOG_FATAL, "File %s with pseudo-count parameters does not exist", pcPseudoFile);
+ }
+ else {
+ while (NULL != fgets(zcLine, 1000, pfIn)){
+
+ if (NULL == (pcToken = strtok(zcLine, " \040\t\n"))){
+ Log(&rLog, LOG_FATAL, "no token specifying pseudo-count parameter in file %s\n"
+ , pcPseudoFile
+ );
+ }
+ strcpy(zcFudge, pcToken);
+
+ if (NULL == fgets(zcLine, 1000, pfIn)){
+ Log(&rLog, LOG_FATAL, "no line with parameter in file %s associated with %s\n"
+ , pcPseudoFile, zcFudge
+ );
+ }
+ else {
+ if (NULL == (pcToken = strtok(zcLine, " \040\t\n"))){
+ Log(&rLog, LOG_FATAL, "no token in 2nd line in file %s associated with %s\n"
+ , pcPseudoFile, zcFudge
+ );
+ }
+ else {
+ dVal = (double)strtod(pcToken, &pcEnd);
+ if ('\0' != *pcEnd){
+ Log(&rLog, LOG_FATAL, "token in file %s associated with %s not valid double (%s)\n"
+ , pcPseudoFile, zcFudge, pcToken
+ );
+ }
+ }
+ }
+#if 0
+ printf("%s:%s:%d: read file %s: fudge = %s, val = %f\n"
+ , __FUNCTION__, __FILE__, __LINE__
+ , pcPseudoFile, zcFudge, dVal
+ );
+#endif
+
+ if (0 == strcmp(zcFudge, "gapb")){
+ rHhalignPara_p->gapb = dVal;
+ }
+ else if (0 == strcmp(zcFudge, "gapd")){
+ rHhalignPara_p->gapd = dVal;
+ }
+ else if (0 == strcmp(zcFudge, "gape")){
+ rHhalignPara_p->gape = dVal;
+ }
+ else if (0 == strcmp(zcFudge, "gapf")){
+ rHhalignPara_p->gapf = dVal;
+ }
+ else if (0 == strcmp(zcFudge, "gapg")){
+ rHhalignPara_p->gapg = dVal;
+ }
+ else if (0 == strcmp(zcFudge, "gaph")){
+ rHhalignPara_p->gaph = dVal;
+ }
+ else if (0 == strcmp(zcFudge, "gapi")){
+ rHhalignPara_p->gapi = dVal;
+ }
+ else if (0 == strcmp(zcFudge, "pca")){
+ rHhalignPara_p->pca = dVal;
+ }
+ else if (0 == strcmp(zcFudge, "pcb")){
+ rHhalignPara_p->pcb = dVal;
+ }
+ else if (0 == strcmp(zcFudge, "pcc")){
+ rHhalignPara_p->pcc = dVal;
+ }
+ else if (0 == strcmp(zcFudge, "gapbV")){
+ rHhalignPara_p->gapbV = dVal;
+ }
+ else if (0 == strcmp(zcFudge, "gapdV")){
+ rHhalignPara_p->gapdV = dVal;
+ }
+ else if (0 == strcmp(zcFudge, "gapeV")){
+ rHhalignPara_p->gapeV = dVal;
+ }
+ else if (0 == strcmp(zcFudge, "gapfV")){
+ rHhalignPara_p->gapfV = dVal;
+ }
+ else if (0 == strcmp(zcFudge, "gapgV")){
+ rHhalignPara_p->gapgV = dVal;
+ }
+ else if (0 == strcmp(zcFudge, "gaphV")){
+ rHhalignPara_p->gaphV = dVal;
+ }
+ else if (0 == strcmp(zcFudge, "gapiV")){
+ rHhalignPara_p->gapiV = dVal;
+ }
+ else if (0 == strcmp(zcFudge, "pcaV")){
+ rHhalignPara_p->pcaV = dVal;
+ }
+ else if (0 == strcmp(zcFudge, "pcbV")){
+ rHhalignPara_p->pcbV = dVal;
+ }
+ else if (0 == strcmp(zcFudge, "pccV")){
+ rHhalignPara_p->pccV = dVal;
+ }
+ else {
+ Log(&rLog, LOG_FATAL, "%s not a valid pseudo-count parameter\n"
+ "must be one of [gapb,gapd,gape,gapf,gapg,gaph,gapi,pca,pcb,pcc,gapbV,gapdV,gapeV,gapfV,gapgV,gaphV,gapiV,pcaV,pcbV,pccV]\n"
+ , zcFudge);
+ } /* switched between parameters */
+
+ } /* while !EOF */
+ fclose(pfIn); pfIn = NULL;
+
+ } /* there was a parameter file */
+#if 0
+ printf("%s:%s:%d: gapb=%g,gapd=%g,gape=%g,gapf=%g,gapg=%g,gaph=%g,gapi=%g,pca=%g,pcb=%g,pcc=%g\n"
+ , __FUNCTION__, __FILE__, __LINE__
+ , rHhalignPara_p->gapb, rHhalignPara_p->gapd, rHhalignPara_p->gape, rHhalignPara_p->gapf, rHhalignPara_p->gapg, rHhalignPara_p->gaph, rHhalignPara_p->gapi, rHhalignPara_p->pca, rHhalignPara_p->pcb, rHhalignPara_p->pcc
+ );
+#endif
+#if 0
+ printf("%s:%s:%d: gapbV=%g,gapdV=%g,gapeV=%g,gapfV=%g,gapgV=%g,gaphV=%g,gapiV=%g,pcaV=%g,pcbV=%g,pccV=%g\n"
+ , __FUNCTION__, __FILE__, __LINE__
+ , rHhalignPara_p->gapbV, rHhalignPara_p->gapdV, rHhalignPara_p->gapeV, rHhalignPara_p->gapfV, rHhalignPara_p->gapgV, rHhalignPara_p->gaphV, rHhalignPara_p->gapiV, rHhalignPara_p->pcaV, rHhalignPara_p->pcbV, rHhalignPara_p->pccV
+ );
+#endif
+
+ return 0;
+
+} /* this is the end of ReadPseudoCountParams() */
+
+
+/*
+ * EOF clustal-omega.c
+ */
#ifdef HAVE_OPENMP
#include <omp.h>
#endif
+#include <stdbool.h>
#include "clustal-omega-config.h"
extern int iNumberOfThreads;
+/* output order */
+enum {INPUT_ORDER = 0, TREE_ORDER};
+
/** user/commandline options
*
*/
/** clustering type (from cmdline arg) */
int iClusteringType;
+ /** number of sequences in cluster */
+ int iClustersizes;
+ /** file with clustering information */
+ char *pcClustfile;
+ /** use transitivity */
+ int iTransitivity;
+ /** file with posterior probability information */
+ char *pcPosteriorfile;
/** pairwise distance method */
int iPairDistType;
/** use mbed-like clustering */
bool bUseMbed;
/** use mbed-like clustering also during iteration */
bool bUseMbedForIteration;
+ /** pile-up flag */
+ bool bPileup;
/** guidetree output file */
char *pcGuidetreeOutfile;
/** guidetree input file */
char *pcGuidetreeInfile;
-
+ /** use Kimura corrected distance */
+ bool bUseKimura;
+ /** print percentage identity */
+ bool bPercID;
+
/* HMMs
*/
/** HMM input files. index range: 0..iHMMInputFiles */
/** number of provided HMM input files. not really a user
option but need for ppcHMMInput */
int iHMMInputFiles;
+ /** HMM batch-file, specify HMMs for individual sequences. FS, r291 -> */
+ char *pcHMMBatch;
/* Iteration
*/
/** max number of guidetree iterations */
int iMaxGuidetreeIterations;
- /** max MAC RAM (maximum amount of RAM set aside for MAC algorithm) */
- int iMacRam; /* FS, r240 -> */
+ hhalign_para rHhalignPara;
/* changes here will have to be reflected in FreeAlnOpts(),
* SetDefaultAlnOpts(), AlnOptsLogicCheck() etc
-
-
extern void
PrintLongVersion(char *pcStr, int iSize);
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);
+ int iClusteringType, int iClustersizes,
+ char *pcGuidetreeInfile, char *pcGuidetreeOutfile, char *pcClusterFile,
+ bool bUseMBed, bool bPercID);
extern int
Align(mseq_t *prMSeq,
mseq_t *prMSeqProfile,
- opts_t *prOpts,
- hhalign_para rHhalignPara);
+ opts_t *prOpts);
extern int
AlignProfiles(mseq_t *prMSeqProfile1,
mseq_t *prMSeqProfile2, hhalign_para rHhalignPara);
#endif
+extern int
+ReadPseudoCountParams(hhalign_para *rHhalignPara_p, char *pcPseudoFile);
--- /dev/null
+# clustal-omega.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/clustal-omega.o'
+
+# Name of the non-PIC object
+non_pic_object='clustal-omega.o'
+
--- /dev/null
+hhalign_wrapper.lo: hhalign_wrapper.c ../../src/config.h \
+ /usr/include/stdlib.h /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/xlocale.h \
+ /usr/include/sys/types.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/time.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/string.h /usr/include/bits/string.h \
+ /usr/include/bits/string2.h /usr/include/assert.h /usr/include/ctype.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h seq.h \
+ ../../src/squid/squid.h /usr/include/stdio.h /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h ../../src/squid/msa.h ../../src/squid/gki.h \
+ ../../src/squid/ssi.h ../../src/squid/squid.h ../../src/squid/sqfuncs.h \
+ ../../src/squid/sre_random.h ../../src/squid/vectorops.h util.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
+ /usr/include/strings.h tree.h symmatrix.h muscle_tree.h progress.h \
+ ../../src/squid/stopwatch.h /usr/include/sys/times.h \
+ ../../src/hhalign/general.h ../../src/hhalign/../clustal/log.h \
+ ../../src/hhalign/hhfunc.h ../../src/hhalign/hhalign.h
+
+../../src/config.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/string.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/assert.h:
+
+/usr/include/ctype.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h:
+
+seq.h:
+
+../../src/squid/squid.h:
+
+/usr/include/stdio.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/squid/msa.h:
+
+../../src/squid/gki.h:
+
+../../src/squid/ssi.h:
+
+../../src/squid/squid.h:
+
+../../src/squid/sqfuncs.h:
+
+../../src/squid/sre_random.h:
+
+../../src/squid/vectorops.h:
+
+util.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h:
+
+/usr/include/limits.h:
+
+/usr/include/bits/posix1_lim.h:
+
+/usr/include/bits/local_lim.h:
+
+/usr/include/linux/limits.h:
+
+/usr/include/bits/posix2_lim.h:
+
+/usr/include/bits/xopen_lim.h:
+
+/usr/include/strings.h:
+
+tree.h:
+
+symmatrix.h:
+
+muscle_tree.h:
+
+progress.h:
+
+../../src/squid/stopwatch.h:
+
+/usr/include/sys/times.h:
+
+../../src/hhalign/general.h:
+
+../../src/hhalign/../clustal/log.h:
+
+../../src/hhalign/hhfunc.h:
+
+../../src/hhalign/hhalign.h:
--- /dev/null
+ktuple_pair.lo: ktuple_pair.c ../../src/config.h /usr/include/stdio.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/stdlib.h /usr/include/ctype.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h /usr/include/assert.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h \
+ ../../src/squid/squid.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h ../../src/squid/msa.h \
+ ../../src/squid/gki.h ../../src/squid/ssi.h ../../src/squid/squid.h \
+ ../../src/squid/sqfuncs.h ../../src/squid/sre_random.h \
+ ../../src/squid/vectorops.h util.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
+ /usr/include/strings.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h symmatrix.h \
+ seq.h ktuple_pair.h progress.h ../../src/squid/stopwatch.h \
+ /usr/include/sys/times.h log.h
+
+../../src/config.h:
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/ctype.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/assert.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:
+
+../../src/squid/squid.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/squid/msa.h:
+
+../../src/squid/gki.h:
+
+../../src/squid/ssi.h:
+
+../../src/squid/squid.h:
+
+../../src/squid/sqfuncs.h:
+
+../../src/squid/sre_random.h:
+
+../../src/squid/vectorops.h:
+
+util.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h:
+
+/usr/include/limits.h:
+
+/usr/include/bits/posix1_lim.h:
+
+/usr/include/bits/local_lim.h:
+
+/usr/include/linux/limits.h:
+
+/usr/include/bits/posix2_lim.h:
+
+/usr/include/bits/xopen_lim.h:
+
+/usr/include/strings.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h:
+
+symmatrix.h:
+
+seq.h:
+
+ktuple_pair.h:
+
+progress.h:
+
+../../src/squid/stopwatch.h:
+
+/usr/include/sys/times.h:
+
+log.h:
--- /dev/null
+list.lo: list.c ../../src/config.h /usr/include/assert.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h /usr/include/string.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/bits/string.h \
+ /usr/include/bits/string2.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/stdlib.h list.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h
+
+../../src/config.h:
+
+/usr/include/assert.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/include/string.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/stdlib.h:
+
+list.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
--- /dev/null
+log.lo: log.c ../../src/config.h /usr/include/stdio.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/xlocale.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/assert.h log.h
+
+../../src/config.h:
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/assert.h:
+
+log.h:
--- /dev/null
+mbed.lo: mbed.c ../../src/config.h /usr/include/assert.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h mbed.h \
+ muscle_tree.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h util.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
+ /usr/include/string.h /usr/include/xlocale.h /usr/include/bits/string.h \
+ /usr/include/bits/string2.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/stdlib.h /usr/include/strings.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h seq.h \
+ ../../src/squid/squid.h /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h ../../src/squid/msa.h \
+ ../../src/squid/gki.h ../../src/squid/ssi.h ../../src/squid/squid.h \
+ ../../src/squid/sqfuncs.h ../../src/squid/sre_random.h \
+ ../../src/squid/vectorops.h pair_dist.h symmatrix.h ktuple_pair.h \
+ progress.h ../../src/squid/stopwatch.h /usr/include/sys/times.h tree.h \
+ queue.h list.h log.h ../../src/kmpp/KMeans.h
+
+../../src/config.h:
+
+/usr/include/assert.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h:
+
+mbed.h:
+
+muscle_tree.h:
+
+/usr/include/stdio.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+util.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h:
+
+/usr/include/limits.h:
+
+/usr/include/bits/posix1_lim.h:
+
+/usr/include/bits/local_lim.h:
+
+/usr/include/linux/limits.h:
+
+/usr/include/bits/posix2_lim.h:
+
+/usr/include/bits/xopen_lim.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/strings.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h:
+
+seq.h:
+
+../../src/squid/squid.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/squid/msa.h:
+
+../../src/squid/gki.h:
+
+../../src/squid/ssi.h:
+
+../../src/squid/squid.h:
+
+../../src/squid/sqfuncs.h:
+
+../../src/squid/sre_random.h:
+
+../../src/squid/vectorops.h:
+
+pair_dist.h:
+
+symmatrix.h:
+
+ktuple_pair.h:
+
+progress.h:
+
+../../src/squid/stopwatch.h:
+
+/usr/include/sys/times.h:
+
+tree.h:
+
+queue.h:
+
+list.h:
+
+log.h:
+
+../../src/kmpp/KMeans.h:
--- /dev/null
+muscle_tree.lo: muscle_tree.c /usr/include/stdlib.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/stdio.h /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h /usr/include/assert.h \
+ /usr/include/ctype.h util.h /usr/include/strings.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h log.h \
+ muscle_tree.h
+
+/usr/include/stdlib.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/stdio.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h:
+
+/usr/include/limits.h:
+
+/usr/include/bits/posix1_lim.h:
+
+/usr/include/bits/local_lim.h:
+
+/usr/include/linux/limits.h:
+
+/usr/include/bits/posix2_lim.h:
+
+/usr/include/assert.h:
+
+/usr/include/ctype.h:
+
+util.h:
+
+/usr/include/strings.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h:
+
+log.h:
+
+muscle_tree.h:
--- /dev/null
+muscle_upgma.lo: muscle_upgma.c /usr/include/stdlib.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/stdio.h /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/assert.h util.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h /usr/include/string.h \
+ /usr/include/xlocale.h /usr/include/bits/string.h \
+ /usr/include/bits/string2.h /usr/include/strings.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h log.h \
+ symmatrix.h seq.h ../../src/squid/squid.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h ../../src/clustal-omega-config.h \
+ ../../src/squid/msa.h ../../src/squid/gki.h ../../src/squid/ssi.h \
+ ../../src/squid/squid.h ../../src/squid/sqfuncs.h \
+ ../../src/squid/sre_random.h ../../src/squid/vectorops.h muscle_tree.h \
+ muscle_upgma.h
+
+/usr/include/stdlib.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/stdio.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/assert.h:
+
+util.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h:
+
+/usr/include/limits.h:
+
+/usr/include/bits/posix1_lim.h:
+
+/usr/include/bits/local_lim.h:
+
+/usr/include/linux/limits.h:
+
+/usr/include/bits/posix2_lim.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/strings.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h:
+
+log.h:
+
+symmatrix.h:
+
+seq.h:
+
+../../src/squid/squid.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/clustal-omega-config.h:
+
+../../src/squid/msa.h:
+
+../../src/squid/gki.h:
+
+../../src/squid/ssi.h:
+
+../../src/squid/squid.h:
+
+../../src/squid/sqfuncs.h:
+
+../../src/squid/sre_random.h:
+
+../../src/squid/vectorops.h:
+
+muscle_tree.h:
+
+muscle_upgma.h:
--- /dev/null
+pair_dist.lo: pair_dist.c ../../src/config.h /usr/include/stdlib.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/xlocale.h \
+ /usr/include/sys/types.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/time.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/ctype.h /usr/include/assert.h \
+ ../../src/clustal-omega.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h \
+ ../../src/clustal-omega-config.h ../../src/hhalign/general.h \
+ ../../src/hhalign/../clustal/log.h /usr/include/stdio.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h ../../src/hhalign/hhfunc.h \
+ ../../src/clustal/log.h ../../src/clustal/util.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
+ /usr/include/string.h /usr/include/bits/string.h \
+ /usr/include/bits/string2.h /usr/include/strings.h \
+ ../../src/clustal/symmatrix.h ../../src/clustal/seq.h \
+ ../../src/squid/squid.h /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h ../../src/squid/msa.h \
+ ../../src/squid/gki.h ../../src/squid/ssi.h ../../src/squid/squid.h \
+ ../../src/squid/sqfuncs.h ../../src/squid/sre_random.h \
+ ../../src/squid/vectorops.h ../../src/clustal/util.h \
+ ../../src/clustal/tree.h ../../src/clustal/symmatrix.h \
+ ../../src/clustal/muscle_tree.h ../../src/clustal/seq.h \
+ ../../src/clustal/mbed.h ../../src/clustal/weights.h \
+ ../../src/clustal/pair_dist.h ../../src/clustal/hhalign_wrapper.h \
+ ktuple_pair.h seq.h symmatrix.h progress.h ../../src/squid/stopwatch.h \
+ /usr/include/sys/times.h pair_dist.h util.h
+
+../../src/config.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/ctype.h:
+
+/usr/include/assert.h:
+
+../../src/clustal-omega.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/omp.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h:
+
+../../src/clustal-omega-config.h:
+
+../../src/hhalign/general.h:
+
+../../src/hhalign/../clustal/log.h:
+
+/usr/include/stdio.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+../../src/hhalign/hhfunc.h:
+
+../../src/clustal/log.h:
+
+../../src/clustal/util.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h:
+
+/usr/include/limits.h:
+
+/usr/include/bits/posix1_lim.h:
+
+/usr/include/bits/local_lim.h:
+
+/usr/include/linux/limits.h:
+
+/usr/include/bits/posix2_lim.h:
+
+/usr/include/bits/xopen_lim.h:
+
+/usr/include/string.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/strings.h:
+
+../../src/clustal/symmatrix.h:
+
+../../src/clustal/seq.h:
+
+../../src/squid/squid.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/squid/msa.h:
+
+../../src/squid/gki.h:
+
+../../src/squid/ssi.h:
+
+../../src/squid/squid.h:
+
+../../src/squid/sqfuncs.h:
+
+../../src/squid/sre_random.h:
+
+../../src/squid/vectorops.h:
+
+../../src/clustal/util.h:
+
+../../src/clustal/tree.h:
+
+../../src/clustal/symmatrix.h:
+
+../../src/clustal/muscle_tree.h:
+
+../../src/clustal/seq.h:
+
+../../src/clustal/mbed.h:
+
+../../src/clustal/weights.h:
+
+../../src/clustal/pair_dist.h:
+
+../../src/clustal/hhalign_wrapper.h:
+
+ktuple_pair.h:
+
+seq.h:
+
+symmatrix.h:
+
+progress.h:
+
+../../src/squid/stopwatch.h:
+
+/usr/include/sys/times.h:
+
+pair_dist.h:
+
+util.h:
--- /dev/null
+progress.lo: progress.c ../../src/config.h /usr/include/stdlib.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/xlocale.h \
+ /usr/include/sys/types.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/time.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/stdio.h /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/assert.h util.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
+ /usr/include/string.h /usr/include/bits/string.h \
+ /usr/include/bits/string2.h /usr/include/strings.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h log.h \
+ progress.h ../../src/squid/stopwatch.h /usr/include/sys/times.h
+
+../../src/config.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/stdio.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/assert.h:
+
+util.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h:
+
+/usr/include/limits.h:
+
+/usr/include/bits/posix1_lim.h:
+
+/usr/include/bits/local_lim.h:
+
+/usr/include/linux/limits.h:
+
+/usr/include/bits/posix2_lim.h:
+
+/usr/include/bits/xopen_lim.h:
+
+/usr/include/string.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/strings.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h:
+
+log.h:
+
+progress.h:
+
+../../src/squid/stopwatch.h:
+
+/usr/include/sys/times.h:
--- /dev/null
+seq.lo: seq.c ../../src/config.h /usr/include/assert.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h ../../src/squid/squid.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/xlocale.h /usr/include/sys/types.h /usr/include/time.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h ../../src/squid/msa.h \
+ ../../src/squid/gki.h ../../src/squid/ssi.h ../../src/squid/squid.h \
+ ../../src/squid/sqfuncs.h ../../src/squid/sre_random.h \
+ ../../src/squid/vectorops.h /usr/include/ctype.h util.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
+ /usr/include/string.h /usr/include/bits/string.h \
+ /usr/include/bits/string2.h /usr/include/strings.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h log.h seq.h
+
+../../src/config.h:
+
+/usr/include/assert.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+../../src/squid/squid.h:
+
+/usr/include/stdio.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/squid/msa.h:
+
+../../src/squid/gki.h:
+
+../../src/squid/ssi.h:
+
+../../src/squid/squid.h:
+
+../../src/squid/sqfuncs.h:
+
+../../src/squid/sre_random.h:
+
+../../src/squid/vectorops.h:
+
+/usr/include/ctype.h:
+
+util.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h:
+
+/usr/include/limits.h:
+
+/usr/include/bits/posix1_lim.h:
+
+/usr/include/bits/local_lim.h:
+
+/usr/include/linux/limits.h:
+
+/usr/include/bits/posix2_lim.h:
+
+/usr/include/bits/xopen_lim.h:
+
+/usr/include/string.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/strings.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h:
+
+log.h:
+
+seq.h:
--- /dev/null
+symmatrix.lo: symmatrix.c ../../src/config.h /usr/include/stdlib.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/xlocale.h \
+ /usr/include/sys/types.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/time.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/stdio.h /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/ctype.h /usr/include/string.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/assert.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h symmatrix.h \
+ seq.h ../../src/squid/squid.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h ../../src/squid/msa.h ../../src/squid/gki.h \
+ ../../src/squid/ssi.h ../../src/squid/squid.h ../../src/squid/sqfuncs.h \
+ ../../src/squid/sre_random.h ../../src/squid/vectorops.h util.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
+ /usr/include/strings.h
+
+../../src/config.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/stdio.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/ctype.h:
+
+/usr/include/string.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/assert.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h:
+
+symmatrix.h:
+
+seq.h:
+
+../../src/squid/squid.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/squid/msa.h:
+
+../../src/squid/gki.h:
+
+../../src/squid/ssi.h:
+
+../../src/squid/squid.h:
+
+../../src/squid/sqfuncs.h:
+
+../../src/squid/sre_random.h:
+
+../../src/squid/vectorops.h:
+
+util.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h:
+
+/usr/include/limits.h:
+
+/usr/include/bits/posix1_lim.h:
+
+/usr/include/bits/local_lim.h:
+
+/usr/include/linux/limits.h:
+
+/usr/include/bits/posix2_lim.h:
+
+/usr/include/bits/xopen_lim.h:
+
+/usr/include/strings.h:
--- /dev/null
+tree.lo: tree.c ../../src/config.h /usr/include/stdlib.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/xlocale.h \
+ /usr/include/sys/types.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h /usr/include/time.h \
+ /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/string.h /usr/include/bits/string.h \
+ /usr/include/bits/string2.h /usr/include/assert.h util.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
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--- /dev/null
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--- /dev/null
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+ progress.c progress.h \
+ queue.h \
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+ symmatrix.c symmatrix.h \
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+include ./$(DEPDIR)/list.Plo
+include ./$(DEPDIR)/log.Plo
+include ./$(DEPDIR)/mbed.Plo
+include ./$(DEPDIR)/muscle_tree.Plo
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+include ./$(DEPDIR)/pair_dist.Plo
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+include ./$(DEPDIR)/weights.Plo
+
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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:
********************************************************************/
/*
- * RCS $Id: hhalign_wrapper.c 256 2011-06-23 13:57:28Z fabian $
+ * RCS $Id: hhalign_wrapper.c 306 2016-06-13 13:49:04Z fabian $
*/
#ifdef HAVE_CONFIG_H
#include <string.h>
#include <assert.h>
#include <ctype.h>
+#include <stdbool.h>
#include "seq.h"
#include "tree.h"
#define TRACE 0
/**
+ * @brief FIXME
+ *
+ * @note prHalignPara has to point to an already allocated instance
+ *
+ */
+void SetDefaultHhalignPara(hhalign_para *prHhalignPara)
+{
+ prHhalignPara->iMacRamMB = 8000; /* default|give just under 8GB to MAC algorithm, FS, 2016-04-18, went from 2GB to 8GB */
+ prHhalignPara->bIsDna = false; /* protein mode unless we say otherwise */
+ prHhalignPara->bIsRna = false;
+ prHhalignPara->pca = -UNITY;
+ prHhalignPara->pcb = -UNITY;
+ prHhalignPara->pcc = -UNITY;
+ prHhalignPara->pcw = -UNITY;
+ prHhalignPara->gapb = -UNITY;
+ prHhalignPara->gapd = -UNITY;
+ prHhalignPara->gape = -UNITY;
+ prHhalignPara->gapf = -UNITY;
+ prHhalignPara->gapg = -UNITY;
+ prHhalignPara->gaph = -UNITY;
+ prHhalignPara->gapi = -UNITY;
+ prHhalignPara->pcaV = -UNITY;
+ prHhalignPara->pcbV = -UNITY;
+ prHhalignPara->pccV = -UNITY;
+ prHhalignPara->pcwV = -UNITY;
+ prHhalignPara->gapbV = -UNITY;
+ prHhalignPara->gapdV = -UNITY;
+ prHhalignPara->gapeV = -UNITY;
+ prHhalignPara->gapfV = -UNITY;
+ prHhalignPara->gapgV = -UNITY;
+ prHhalignPara->gaphV = -UNITY;
+ prHhalignPara->gapiV = -UNITY;
+
+}
+/*** end: SetDefaultHhalignPara() ***/
+
+
+
+/**
* @brief get rid of unknown residues
*
* @note HHalignWrapper can be entered in 2 different ways: (i) all
{
int iS; /* iterator for sequence */
- int iR; /* iterator for residue */
- int iLen; /* length of sequence */
+ /*int iR;*/ /* iterator for residue */
+ /*int iLen;*/ /* length of sequence */
char *pcRes = NULL;
for (pcRes = mseq->seq[iS]; '\0' != *pcRes; pcRes++){
if (isgap(*pcRes)){
+ /* don't like MSF gap characters ('~'),
+ sanitise them (and '.' and ' '); FS, r258 -> r259 */
+ *pcRes = '-';
continue;
}
/**
* @brief re-attach leading and trailing gaps to alignment
*
- * @param[in,out] prMSeq,
+ * @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
/**
+ * @brief PosteriorProbabilities() calculates posterior probabilities
+ * of aligning a single sequences on-to an alignment containing this sequence
+ *
+ * @param[in] prMSeq
+ * holds the aligned sequences [in]
+ * @param[in] rHMMalignment
+ * HMM of the alignment in prMSeq
+ * @param[in] rHhalignPara
+ * various parameters read from commandline, needed by hhalign()
+ * @param[in] pcPosteriorfile
+ * name of file into which posterior probability information is written
+ *
+ * @return score of the alignment FIXME what is this?
+ *
+ * @note the PP-loop can be parallelised easily FIXME
+ */
+
+int
+PosteriorProbabilities(mseq_t *prMSeq, hmm_light rHMMalignment, hhalign_para rHhalignPara, char *pcPosteriorfile)
+{
+
+ double dScore = 0.0;
+ int i;
+ int iS; /* iterator for sequences */
+ int iNseq = prMSeq->nseqs; /* number of sequences */
+ int iLenHMM = rHMMalignment.L; /* length of alignment */
+ int iViterbiCount = 0; /* counts how often Viterbi is triggered */
+ char **ppcCopy = NULL;
+ char **ppcRepresent = NULL;
+ char zcAux[10000] = {0};
+ char zcError[10000] = {0};
+ hhalign_scores *prHHscores = NULL;
+ FILE *pfPP = NULL;
+
+ pfPP = fopen(pcPosteriorfile, "w");
+ fprintf(pfPP, "#1.i\t2.name\t\t3.L1\t4.L2\t5.sum\t\t6.sum/L1\t7.HH\n");
+
+
+ prHHscores = CKCALLOC(iNseq, sizeof(hhalign_scores));
+ for (iS = 0; iS < iNseq; iS++){
+ memset(&(prHHscores[iS]), 0, sizeof(hhalign_scores));
+ }
+
+ ppcCopy = CKCALLOC(1, sizeof(char *));
+ ppcCopy[0] = CKCALLOC(2*iLenHMM, sizeof(char));
+ ppcRepresent = CKCALLOC(1, sizeof(char *));
+ ppcRepresent[0] = CKCALLOC(2*iLenHMM, sizeof(char));
+
+ for (i = 0; i < iLenHMM; i++){
+ ppcRepresent[0][i] = rHMMalignment.seq[rHMMalignment.ncons][i+1];
+ }
+
+ /* FIXME: this loop can be parallelised, FS r288 */
+ iViterbiCount = 0;
+ for (iS = 0; iS < iNseq; iS++){
+
+ /* single sequences may very well contain leading/trailing gaps,
+ * this will trigger warning in Transfer:hhalignment-C.h */
+ char *pcIter = NULL;
+ for (pcIter = prMSeq->orig_seq[iS]; ('-' == *pcIter) || ('.' == *pcIter); pcIter++);
+ strcpy(ppcCopy[0], pcIter/*prMSeq->orig_seq[iS]*/);
+ for (pcIter = &ppcCopy[0][strlen(ppcCopy[0])-1]; ('-' == *pcIter) || ('.' == *pcIter); pcIter--);
+ pcIter++;
+ *pcIter = '\0';
+
+ zcError[0] = '\0';
+ hhalign(ppcCopy, 1, NULL,
+ ppcRepresent, 0, NULL,
+ &dScore, &rHMMalignment, &rHMMalignment,
+ NULL, NULL, NULL, NULL,
+ rHhalignPara, &prHHscores[iS], 0/* debug */, FALSE /* Log-Level*/,
+ zcAux, zcError);
+ if (NULL != strstr(zcError, "Viterbi")){
+ iViterbiCount++;
+ }
+
+ } /* 0 <= iS < iNseq */
+ Log(&rLog, LOG_INFO, "Viterbi algorithm triggered %d times (out of %d)", iViterbiCount, iNseq-1);
+
+ for (iS = 0; iS < iNseq; iS++){
+
+ fprintf(pfPP, "%d\t%10s\t%3d"
+ , iS, prMSeq->sqinfo[iS].name, (int)(strlen(prMSeq->orig_seq[iS])));
+ fprintf(pfPP, "\t%3d\t%f\t%f\t%f",
+ prHHscores[iS].L, prHHscores[iS].sumPP, prHHscores[iS].sumPP/strlen(prMSeq->orig_seq[iS]), prHHscores[iS].hhScore);
+ fprintf(pfPP, "\n");
+ } /* 0 <= iS < iNseq */
+
+
+
+ fclose(pfPP); pfPP = NULL;
+ free(ppcRepresent[0]); ppcRepresent[0] = NULL;
+ free(ppcCopy[0]); ppcCopy[0] = NULL;
+ free(ppcRepresent); ppcRepresent = NULL;
+ free(ppcCopy); ppcCopy = NULL;
+ free(prHHscores); prHHscores = NULL;
+
+ return 1;
+
+} /* this is the end of PosteriorProbabilities() */
+
+
+/**
+ * @brief sequentially align (chain) sequences
+ *
+ * @param[in,out] prMSeq
+ * holds the un-aligned sequences (in) and the final alignment (out)
+ * @param[in] rHhalignPara
+ * various parameters needed by hhalign()
+ * @param[in] iClustersize
+ * parameter that controls how often HMM is updated
+ *
+ * @note chained alignment takes much longer than balanced alignment
+ * because at every step ClustalO has to scan all previously aligned residues.
+ * for a balanced tree this takes N*log(N) time but for a chained tree
+ * it takes N^2 time.
+ * This function has a short-cut, that the HMM need not be updated
+ * for every single alignment step, but the HMM from the previous
+ * step(s) can be re-cycled. The HMM is updated (i) at the very first step,
+ * (ii) if a gap has been inserted into the HMM during alignment or
+ * (iii) if the HMM has been used for too many steps without having
+ * been updated. This update-frequency is controlled by the input
+ * parameter iClustersize. iClustersize is the number of sequences used
+ * to build a HMM to allow for one non-updating step. For example,
+ * if iClustersize=100 and a HMM has been build from 100 sequences,
+ * then this HMM can be used once without updating. If the HMM has
+ * been built from 700 sequences (and iClustersize=100) then this
+ * HMM can be used 7-times without having to be updated, etc.
+ * For this reason the initial iClustersize sequences are always
+ * aligned with fully updated HMMs.
+ */
+double
+PileUp(mseq_t *prMSeq, hhalign_para rHhalignPara, int iClustersize)
+{
+ /* @<variables local to PileUp> */
+ int iI; /* iterator for sequences */
+ int iCountPro = 0; /* count how many sequences are already in profile */
+ int *piLeafListSeq = NULL; /* lists required by PrepareAlignment() for attaching sequences pointers to ppcProfileSeq */
+ int *piLeafListPro = NULL; /* -"- ppcProfilePro */
+ double *pdWeightL = NULL; /* argument used by hhalign, not used here */
+ double *pdWeightR = NULL; /* -"- */
+ double *pdWeightP = NULL; /* -"- */
+ char **ppcProfileSeq = NULL; /* pointer to sequences in profile */
+ char **ppcProfilePro = NULL; /* pointer to sequences in profile */
+ double dScore = -1.0; /* alignment score, calculated by hhalign() */
+ hhalign_scores rHHscores = {0}; /* more explicit scores than dScore */
+ hmm_light *prHMM = NULL; /* HMM against which to align single sequence */
+ hmm_light rHMMprofile = {0}; /* HMM calculated externally from profile */
+ int iHHret = -1; /* return value of hhalign() */
+ char zcAux[10000] = {0}; /* auxilliary print string used by hhalign() */
+ char zcError[10000] = {0}; /* error message printed by hhalign() */
+ char *pcConsensPro = NULL, /* auxilliary sequence strings required by hhalign() */
+ *pcReprsntPro = NULL, /* not used here */
+ *pcConsensSeq = NULL, *pcReprsntSeq = NULL;
+ bool bHMM_stale = YES; /* flag if HMM has to be updated */
+ int iSinceLastUpdate = -1; /* counts how often HMM has been used since last update */
+ progress_t *prProgress; /* structure required for progress report */
+ bool bPrintCR = (rLog.iLogLevelEnabled<=LOG_VERBOSE) ? FALSE : TRUE; /* progress report */
+ char **ppcReprsnt = NULL; /* string used to represent HMM */
+ ppcReprsnt = CKCALLOC(1, sizeof(char *));
+
+ /* weights are not really used, but hhalign() expects them */
+ pdWeightL = (double *)CKMALLOC(prMSeq->nseqs * sizeof(double));
+ pdWeightR = (double *)CKMALLOC(prMSeq->nseqs * sizeof(double));
+ pdWeightP = (double *)CKMALLOC(prMSeq->nseqs * sizeof(double));
+
+ /* lists used for attaching ppcProfileSeq/ppcProfilePro to prMSeq */
+ piLeafListSeq = (int *)CKMALLOC(1 * sizeof(int));
+ piLeafListPro = (int *)CKMALLOC(prMSeq->nseqs * sizeof(int));
+
+ ppcProfileSeq = (char **)CKMALLOC(1 * sizeof(char *));
+ ppcProfileSeq[0] = NULL;
+ ppcProfilePro = (char **)CKMALLOC(prMSeq->nseqs * sizeof(char *));
+ for (iI = 0; iI < prMSeq->nseqs; iI++){
+ ppcProfilePro[iI] = NULL;
+ }
+
+ piLeafListPro[0] = 0; /* first sequences in profile is simply un-aligned sequence */
+ iCountPro = 1; /* 'profile' now contains 1 sequence */
+
+ NewProgress(&prProgress, LogGetFP(&rLog, LOG_INFO),
+ "Progressive alignment progress", bPrintCR);
+
+ /* build up the initial alignment:
+ * sequences are chained but hhalign() is used normally,
+ * that is, one sequence is aligned to a profile */
+ for (iI = 1; iI < MIN(prMSeq->nseqs, iClustersize); iI++){
+
+ piLeafListSeq[0] = iI;
+
+ /* PrepareAlignment() connects ppcProfileSeq/ppcProfilePro and prMSeq */
+ PrepareAlignment(prMSeq, ppcProfilePro, ppcProfileSeq,
+ pdWeightL, pdWeightR, pdWeightP,
+ iI, piLeafListPro,
+ 1, piLeafListSeq);
+
+ /* align 1 (5th argument) sequence to the growing profile
+ * (2nd argument number of sequences is iI),
+ * external HMM not used at this stage (prHMM=NULL) */
+ iHHret = hhalign(ppcProfilePro, iI, NULL/*pdWeightL*/,
+ ppcProfileSeq, 1, NULL/*pdWeightR*/,
+ &dScore, prHMM, prHMM,
+ pcConsensPro, pcReprsntPro,
+ pcConsensSeq, pcReprsntSeq,
+ rHhalignPara, &rHHscores,
+ CALL_FROM_REGULAR/* DEBUG ARGUMENT */, rLog.iLogLevelEnabled,
+ zcAux, zcError);
+
+ piLeafListPro[iI] = iI;
+ iCountPro = iI+1;
+ ProgressLog(prProgress, iI, prMSeq->nseqs-1, FALSE); /* FIXME: test! FS, r288 */
+
+ } /* 1 <= iI < MIN(prMSeq->nseqs, iClustersize) */
+
+ /* now align single sequences not to a profile but to a HMM of a potentially old profile */
+ while (iI < prMSeq->nseqs){
+
+ /* if HMM not up-to-date then create new HMM for profile:
+ * HMM is stale (i) at the beginning,
+ * (ii) if a gap has been inserted into the HMM during previous step,
+ * (iii) too many steps after the last up-date */
+ if ( (YES == bHMM_stale) ){
+ FreeHMMstruct(&rHMMprofile);
+ if (OK !=
+ AlnToHMM2(&rHMMprofile, rHhalignPara, prMSeq->seq, iI)
+ ) {
+ Log(&rLog, LOG_ERROR, "Couldn't convert alignment to HMM. Will not proceed with chained alignment, step %d", iI);
+ }
+ bHMM_stale = NO;
+ iSinceLastUpdate = 0;
+ }
+
+ /* align single sequence to HMM */
+ piLeafListSeq[0] = iI;
+
+ PrepareAlignment(prMSeq, ppcProfilePro, ppcProfileSeq,
+ pdWeightL, pdWeightR, pdWeightP,
+ iI, piLeafListPro,
+ 1, piLeafListSeq);
+
+ /* use representative sequence to track where gaps are inserted into HMM */
+ ppcReprsnt[0] = CKREALLOC(ppcReprsnt[0], strlen(ppcProfilePro[0])+strlen(ppcProfileSeq[0])+1);
+ memcpy(ppcReprsnt[0], rHMMprofile.seq[rHMMprofile.ncons]+1, rHMMprofile.L);
+ ppcReprsnt[0][rHMMprofile.L] = '\0';
+
+ /* align 1 (5th argument) sequence to a HMM (2nd argument number of sequences is '0',
+ * not iI as for a profile or '1' for one representative sequence),
+ * external HMM (rHMMprofile calculated by AlnToHMM2()) is used at this stage */
+ prHMM = &rHMMprofile;
+ hhalign(ppcReprsnt, 0, NULL,
+ ppcProfileSeq, 1, NULL,
+ &dScore, prHMM, prHMM,
+ pcConsensPro, pcReprsntPro,
+ pcConsensSeq, pcReprsntSeq,
+ rHhalignPara, &rHHscores,
+ CALL_FROM_ALN_HMM/* DEBUG ARGUMENT */, rLog.iLogLevelEnabled,
+ zcAux, zcError);
+ iSinceLastUpdate++; /* HMM has been used one more time */
+ ProgressLog(prProgress, iI, prMSeq->nseqs-1, FALSE); /* FIXME: test! FS, r288 */
+
+ /* check if gaps have been inserted into HMM.
+ * if this is the case then HMM is stale
+ * and the profile used to create the HMM must get gaps at the same positions.
+ * gaps are shown in the representative sequence */
+ if (rHMMprofile.L != strlen(ppcReprsnt[0])){
+
+ int iSeq; /* iterate through sequences of profile */
+
+ /* manually insert gaps into existing profile,
+ * there should already be enough memory */
+#ifdef HAVE_OPENMP
+ /* all sequences in profile obtain gaps at the same position,
+ * can do this in parallel */
+ #pragma omp parallel for
+#endif
+ for (iSeq = 0; iSeq < iI; iSeq++){
+
+ int iPtrRep, /* points to 'residue' in representative sequence */
+ iPtrPrf; /* points to the corresponding position in the profile */
+
+ for (iPtrRep = strlen(ppcReprsnt[0])-1, iPtrPrf = strlen(ppcProfilePro[iSeq])-1;
+ iPtrRep >= 0; iPtrRep--){
+
+ if ('-' == ppcReprsnt[0][iPtrRep]){ /* gaps are newly introduced into profile */
+ ppcProfilePro[iSeq][iPtrRep] = '-';
+ }
+ else { /* non-gap characters (residues) are shifted towards the back */
+ ppcProfilePro[iSeq][iPtrRep] = ppcProfilePro[iSeq][iPtrPrf];
+ iPtrPrf--;
+ }
+ if (iPtrRep == iPtrPrf){
+ /* if profile and representative seq point to same position then no more gaps */
+ break;
+ }
+ } /* strlen(ppcReprsnt[0])-1 >= iPtrRep >= 0 */
+ ppcProfilePro[iSeq][strlen(ppcReprsnt[0])] = '\0';
+
+ } /* 0 <= iSeq < iI */
+
+ /* make HMM stale */
+ bHMM_stale = YES;
+
+ } /* strlen(represent) != HMM.L (gaps inserted into HMM) */
+
+ /* check if maximum number of sequences exceeded */
+ if ( (iClustersize <= 1) || (iSinceLastUpdate > (double)(rHMMprofile.N_in)/(double)(iClustersize)) ){
+ bHMM_stale = YES;
+ }
+
+
+ piLeafListPro[iI] = iI;
+ iCountPro = iI+1;
+
+ iI++;
+
+ } /* iI < prMSeq->nseqs */
+ ProgressDone(prProgress);
+ FreeProgress(&prProgress);
+
+ FreeHMMstruct(&rHMMprofile);
+ CKFREE(pdWeightL); CKFREE(pdWeightR); CKFREE(pdWeightP);
+ if (NULL != ppcReprsnt){
+ if (NULL != ppcReprsnt[0]){
+ CKFREE(ppcReprsnt[0]);
+ }
+ CKFREE(ppcReprsnt);
+ }
+ CKFREE(piLeafListSeq); CKFREE(piLeafListPro);
+
+ return 0.0;
+
+} /* this is the end of PileUp() */
+
+
+
+
+
+/**
* @brief wrapper for hhalign. This is a frontend function to
* the ported hhalign code.
*
* @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,
double *pdWeightsL = NULL; /* sequence weights of left profile */
double *pdWeightsR = NULL; /* sequence weights of right profile */
int iMergeNodeCounter = 0;
- hmm_light *prHMM = NULL;
+ hmm_light *prHMM = NULL;
+ hmm_light *prHMMleft = NULL;
+ hmm_light *prHMMrght = NULL;
+ hmm_light *prHMMnull = NULL;
bool bPrintCR = (rLog.iLogLevelEnabled<=LOG_VERBOSE) ? FALSE : TRUE;
#if TIMING
char zcStopwatchMsg[1024];
StopwatchZero(stopwatch);
StopwatchStart(stopwatch);
#endif
-
-
- if (NULL != prHMMList) {
+ hhalign_scores rHHscores = {0};
+
+#if 0 /* DEVEL 291 */
+ if (NULL != prHMMList) { /* FIXME DEVEL 291: replace this outer test with iHMMCount>0*/
if (iHMMCount>1) {
Log(&rLog, LOG_WARN, "FIXME: Using only first of %u HMMs (needs implementation)", iHMMCount);
}
- prHMM = &(prHMMList[0]);
+ prHMM = &(prHMMList[0]); /* FIXME DEVEL 291: check for NULL */
} else {
/* FIXME: prHMM not allowed to be NULL and therefore pseudo allocated here */
prHMM = (hmm_light *) CKCALLOC(1, sizeof(hmm_light));
}
+#else
+ prHMMnull = (hmm_light *) CKCALLOC(1, sizeof(hmm_light));
+ if ( (iHMMCount > 0) && (NULL != prHMMList) ){
+ prHMM = &(prHMMList[0]);
+ if (iHMMCount > 1) {
+ Log(&rLog, LOG_WARN, "FIXME: Using only first of %u HMMs (needs implementation)", iHMMCount);
+ }
+ }
+ else {
+ prHMM = prHMMnull; /* prHMM not allowed to be NULL and therefore assigned to pseudo allocated */
+ }
+#endif
assert(NULL!=prMSeq);
* protein
*/
if (SEQTYPE_PROTEIN != prMSeq->seqtype) {
- Log(&rLog, LOG_WARN, "Sequence type is %s. HHalign has only been tested on protein.",
- SeqTypeToStr(prMSeq->seqtype));
+ /*Log(&rLog, LOG_WARN, "%s alignment is still experimental.",
+ SeqTypeToStr(prMSeq->seqtype));*/
+ if(prMSeq->seqtype == SEQTYPE_DNA)
+ rHhalignPara.bIsDna = true;
+ if(prMSeq->seqtype == SEQTYPE_RNA)
+ rHhalignPara.bIsRna = true;
}
/* hhalign produces funny results if sequences contain gaps, so
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 1 /* DEVEL 291 */
+ /*
+ * Note: if there is a HMM-batch file, then prMSeq->ppiHMMBindex is not NULL;
+ * ppiLeafList[iL/iR][0] is the 'lead' sequence in a profile;
+ * prMSeq->ppiHMMBindex[ppiLeafList[iL][0]] are the HMMs associated with the lead sequence;
+ * this could be NULL if there are no HMMs associated with this particular sequence
+ * at the moment only 1st HMM can be used, prMSeq->ppiHMMBindex[ppiLeafList[iL][0]][0];
+ * the index of this HMM can be '-1' if the specified HMM file does not exist
+ * Note: we only use prHMMleft/prHMMrght, even if global HMM (--hmm-in) is specified
+ **/
+ if ( (NULL != prMSeq->ppiHMMBindex) && (NULL != prMSeq->ppiHMMBindex[ppiLeafList[iL][0]]) &&
+ (prMSeq->ppiHMMBindex[ppiLeafList[iL][0]][0] > -1) ){
+ prHMMleft = &(prHMMList[prMSeq->ppiHMMBindex[ppiLeafList[iL][0]][0]]);
+ }
+ else if (iHMMCount > 0){
+ prHMMleft = prHMM;
+ }
+ else {
+ prHMMleft = prHMMnull;
+ }
+ if ( (NULL != prMSeq->ppiHMMBindex) && (NULL != prMSeq->ppiHMMBindex[ppiLeafList[iR][0]]) &&
+ (prMSeq->ppiHMMBindex[ppiLeafList[iR][0]][0] > -1) ){
+ prHMMrght = &(prHMMList[prMSeq->ppiHMMBindex[ppiLeafList[iR][0]][0]]);
+ }
+ else if (iHMMCount > 0){
+ prHMMrght = prHMM;
+ }
+ else {
+ prHMMrght = prHMMnull;
+ }
+#endif
/* align individual sequences to HMM;
* - use representative sequence to get gapping
* 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) ){
+ /*if ( (piLeafCount[iL] <= APPLY_BG_HMM_UP_TO_TREE_DEPTH) && (0 != prHMM->L) ){*/
+ if (0 != prHMMleft->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];
+ pcReprsnt1 = CKCALLOC(prHMMleft->L+strlen(ppcProfile1[0])+1, sizeof(char));
+ for (i = 0; i < prHMMleft->L; i++){
+ pcReprsnt1[i] = prHMMleft->seq[prHMMleft->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));
+ ppcCopy1[j] = CKCALLOC(prHMMleft->L+strlen(ppcProfile1[0])+1, sizeof(char));
for (i = 0; i < (int) strlen(ppcProfile1[0]); i++){
ppcCopy1[j][i] = ppcProfile1[j][i];
}
FS, r236 -> r237
*/
int iLenA = strlen(ppcCopy1[0]);
- int iLenH = prHMM->L;
+ int iLenH = prHMMleft->L;
int iHHret = 0;
if (iLenH < iLenA){
iHHret = hhalign(ppcReprsnt1, 0/* only one representative seq*/, NULL,
ppcCopy1, piLeafCount[iL], pdWeightsL,
- &dScore, prHMM,
+ &dScore, prHMMleft, prHMMleft,
NULL, NULL, NULL, NULL,
- rHhalignPara,
- iAux_FS++, /* DEBUG ARGUMENT */
+ rHhalignPara, &rHHscores,
+ iAux_FS++, /* DEBUG ARGUMENT */ rLog.iLogLevelEnabled,
zcAux, zcError);
}
else {
iHHret = hhalign(ppcCopy1, piLeafCount[iL], pdWeightsL,
ppcReprsnt1, 0/* only one representative seq*/, NULL,
- &dScore, prHMM,
+ &dScore, prHMMleft, prHMMleft,
NULL, NULL, NULL, NULL,
- rHhalignPara,
- iAux_FS++, /* DEBUG ARGUMENT */
+ rHhalignPara, &rHHscores,
+ iAux_FS++, /* DEBUG ARGUMENT */ rLog.iLogLevelEnabled,
zcAux, zcError);
}
- if (0 != iHHret){ /* FS, r255 -> */
+ if ( (0 != iHHret) && (rLog.iLogLevelEnabled <= LOG_VERBOSE) ){ /* 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",
+ "\t#=%d (len=%d), lead-seq=%s, len(HMM)=%d\n%s\nCARRY ON REGARDLESS\n",
__FUNCTION__, __FILE__, __LINE__, iHHret,
- piLeafCount[iL], (int)strlen(ppcCopy1[0]), prMSeq->sqinfo[ppiLeafList[iL][0]].name, (int)strlen(ppcReprsnt1[0]));
+ piLeafCount[iL], (int)strlen(ppcCopy1[0]), prMSeq->sqinfo[ppiLeafList[iL][0]].name,
+ (int)strlen(ppcReprsnt1[0]), zcError);
}
}
pdScores[ppiLeafList[iL][0]] = dScore;
* 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++){
+ pcConsens1 = CKCALLOC(prHMMleft->L+strlen(ppcProfile1[0])+1, sizeof(char));
+ for (i = 0; i < prHMMleft->L; i++){
for (j = 0, pcConsens1[i] = '-'; (j < piLeafCount[iL]) && ('-' == pcConsens1[i]); j++){
pcConsens1[i] = ppcCopy1[j][i];
}
#endif
} /* ( (1 == piLeafCount[iL]) && (0 != prHMM->L) ) */
- if ( (piLeafCount[iR] <= APPLY_BG_HMM_UP_TO_TREE_DEPTH) && (0 != prHMM->L) ){
+ /*if ( (piLeafCount[iR] <= APPLY_BG_HMM_UP_TO_TREE_DEPTH) && (0 != prHMM->L) ){*/
+ if (0 != prHMMrght->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];
+ pcReprsnt2 = CKCALLOC(prHMMrght->L+strlen(ppcProfile2[0])+1, sizeof(char));
+ for (i = 0; i < prHMMrght->L; i++){
+ pcReprsnt2[i] = prHMMrght->seq[prHMMrght->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));
+ ppcCopy2[j] = CKCALLOC(prHMMrght->L+strlen(ppcProfile2[0])+1, sizeof(char));
for (i = 0; i < (int) strlen(ppcProfile2[0]); i++){
ppcCopy2[j][i] = ppcProfile2[j][i];
}
FS, r236 -> r237
*/
int iLenA = strlen(ppcCopy2[0]);
- int iLenH = prHMM->L;
+ int iLenH = prHMMrght->L;
int iHHret = 0;
if (iLenH < iLenA){
iHHret = hhalign(ppcReprsnt2, 0/* only one representative seq */, NULL,
ppcCopy2, piLeafCount[iR], pdWeightsR,
- &dScore, prHMM,
+ &dScore, prHMMrght, prHMMrght,
NULL, NULL, NULL, NULL,
- rHhalignPara,
- iAux_FS++, /* DEBUG ARGUMENT */
+ rHhalignPara, &rHHscores,
+ iAux_FS++, /* DEBUG ARGUMENT */ rLog.iLogLevelEnabled,
zcAux, zcError);
}
else {
iHHret = hhalign(ppcCopy2, piLeafCount[iR], pdWeightsR,
ppcReprsnt2, 0/* only one representative seq */, NULL,
- &dScore, prHMM,
+ &dScore, prHMMrght, prHMMrght,
NULL, NULL, NULL, NULL,
- rHhalignPara,
- iAux_FS++, /* DEBUG ARGUMENT */
+ rHhalignPara, &rHHscores,
+ iAux_FS++, /* DEBUG ARGUMENT */ rLog.iLogLevelEnabled,
zcAux, zcError);
}
- if (0 != iHHret){ /* FS, r255 -> */
+ if ( (0 != iHHret) && (rLog.iLogLevelEnabled <= LOG_VERBOSE) ){ /* 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",
+ "\t#=%d (len=%d), lead-seq=%s, len(HMM)=%d\n%s\nCARRY ON REGARDLESS\n",
__FUNCTION__, __FILE__, __LINE__, iHHret,
- piLeafCount[iR], (int)strlen(ppcCopy2[0]), prMSeq->sqinfo[ppiLeafList[iR][0]].name, (int)strlen(ppcReprsnt2[0]));
+ piLeafCount[iR], (int)strlen(ppcCopy2[0]), prMSeq->sqinfo[ppiLeafList[iR][0]].name,
+ (int)strlen(ppcReprsnt2[0]), zcError);
}
}
pdScores[ppiLeafList[iR][0]] = dScore;
* 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++){
+ pcConsens2 = CKCALLOC(prHMMrght->L+strlen(ppcProfile2[0])+1, sizeof(char));
+ for (i = 0; i < prHMMrght->L; i++){
for (j = 0, pcConsens2[i] = '-'; (j < piLeafCount[iR]) && ('-' == pcConsens2[i]); j++){
pcConsens2[i] = ppcCopy2[j][i];
}
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,
+ &dScore, prHMMleft, prHMMrght,
pcConsens1, pcReprsnt1,
pcConsens2, pcReprsnt2,
- rHhalignPara,
- iAux_FS++, /* DEBUG ARGUMENT */
+ rHhalignPara, &rHHscores,
+ iAux_FS++, /* DEBUG ARGUMENT */ rLog.iLogLevelEnabled,
zcAux, zcError);
if (RETURN_OK != iHHret){ /* FS, r241 -> */
+ /*fprintf(stderr, "%s:%d: emergency EXIT\n", __FILE__, __LINE__); exit(-1);*/
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",
+ "\thh-error-code=%d (mac-ram=%d)\n%s",
__FUNCTION__, __FILE__, __LINE__, piLeafCount[iL], piLeafCount[iR],
prMSeq->sqinfo[ppiLeafList[iL][0]].name, prMSeq->sqinfo[ppiLeafList[iR][0]].name,
- iHHret, rHhalignPara.iMacRamMB);
+ iHHret, rHhalignPara.iMacRamMB, zcError);
/* 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?).
iHHret = hhalign(ppcProfile1, piLeafCount[iL], pdWeightsL,
ppcProfile2, piLeafCount[iR], pdWeightsR,
- &dScore, prHMM,
+ &dScore, prHMMleft, prHMMrght,
pcConsens1, pcReprsnt1,
pcConsens2, pcReprsnt2,
- rHhalignPara,
- iAux_FS++, /* DEBUG ARGUMENT */
+ rHhalignPara, &rHHscores,
+ iAux_FS++, /* DEBUG ARGUMENT */ rLog.iLogLevelEnabled,
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);
+ fprintf(stderr, "%s:%s:%d: problem in alignment, Viterbi did not work\n"
+ "\thh-error-code=%d (mac-ram=%d)\n%s",
+ __FUNCTION__, __FILE__, __LINE__, iHHret, rHhalignPara.iMacRamMB, zcError);
Log(&rLog, LOG_FATAL, "could not perform alignment -- bailing out\n");
}
else {
int iOldMacRam = rHhalignPara.iMacRamMB;
iHHret = hhalign(ppcProfile2, piLeafCount[iR], pdWeightsR,
ppcProfile1, piLeafCount[iL], pdWeightsL,
- &dScore, prHMM,
+ &dScore, prHMMrght, prHMMleft,
pcConsens2, pcReprsnt2,
pcConsens1, pcReprsnt1,
- rHhalignPara,
- iAux_FS++, /* DEBUG ARGUMENT */
+ rHhalignPara, &rHHscores,
+ iAux_FS++, /* DEBUG ARGUMENT */ rLog.iLogLevelEnabled,
zcAux, zcError);
if (RETURN_OK != iHHret){ /* FS, r241 -> r243 */
+ /*fprintf(stderr, "%s:%d: emergency EXIT\n", __FILE__, __LINE__); exit(-1);*/
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",
+ "\thh-error-code=%d (mac-ram=%d)\n%s",
__FUNCTION__, __FILE__, __LINE__, piLeafCount[iL], piLeafCount[iR],
prMSeq->sqinfo[ppiLeafList[iL][0]].name, prMSeq->sqinfo[ppiLeafList[iR][0]].name,
- iHHret, rHhalignPara.iMacRamMB);
+ iHHret, rHhalignPara.iMacRamMB, zcError);
/* 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;
iHHret = hhalign(ppcProfile2, piLeafCount[iR], pdWeightsR,
ppcProfile1, piLeafCount[iL], pdWeightsL,
- &dScore, prHMM,
+ &dScore, prHMMrght, prHMMleft,
pcConsens2, pcReprsnt2,
pcConsens1, pcReprsnt1,
- rHhalignPara,
- iAux_FS++, /* DEBUG ARGUMENT */
+ rHhalignPara, &rHHscores,
+ iAux_FS++, /* DEBUG ARGUMENT */ rLog.iLogLevelEnabled,
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);
+ fprintf(stderr, "%s:%s:%d: problem in alignment, Viterbi did not work\n"
+ "\thh-error-code=%d (mac-ram=%d)\n%s",
+ __FUNCTION__, __FILE__, __LINE__, iHHret, rHhalignPara.iMacRamMB, zcError);
Log(&rLog, LOG_FATAL, "could not perform alignment -- bailing out\n");
}
else {
} /* 1st invocation failed */
} /* 2nd profile was shorter than 1st */
+
+ /*
+ * at this stage have performed alignment of 2 profiles/sequences.
+ * if HMM batch information had been used then have choices:
+ * (i) if HMM info only intended for initial alignment (of sequences) then make both HMMs stale;
+ * (iia) if alignment of 2 profiles/sequences where same HMM used, then retain;
+ * (iib) if alignment of 2 profiles/sequences where different HMMs used, then make both stale;
+ * (iii) some majority voting
+ */
+#if 0 /* always make HMM batch stale (after 1st invocation) */
+ if ( (NULL != prMSeq->ppiHMMBindex) && (NULL != prMSeq->ppiHMMBindex[ppiLeafList[iL][0]]) ){
+ prMSeq->ppiHMMBindex[ppiLeafList[iL][0]][0] = -1;
+ }
+ if ( (NULL != prMSeq->ppiHMMBindex) && (NULL != prMSeq->ppiHMMBindex[ppiLeafList[iR][0]]) ){
+ prMSeq->ppiHMMBindex[ppiLeafList[iR][0]][0] = -1;
+ }
+#else /* retain HMMs if they were the same for both profiles */
+ if (NULL != prMSeq->ppiHMMBindex) {
+ int i;
+
+ if ( (NULL != prMSeq->ppiHMMBindex[ppiLeafList[iL][0]]) && (NULL != prMSeq->ppiHMMBindex[ppiLeafList[iR][0]]) ){
+ if ( prMSeq->ppiHMMBindex[ppiLeafList[iL][0]][0] == -1){
+ prMSeq->ppiHMMBindex[ppiLeafList[iR][0]][0] = -1; /* this is conservative, could do H[iL] = H[iR] */
+ for (i = 0; i < piLeafCount[iR]; i++){
+ prMSeq->ppiHMMBindex[ppiLeafList[iR][i]][0] = -1;
+ }
+ }
+ else if ( prMSeq->ppiHMMBindex[ppiLeafList[iR][0]][0] == -1){
+ prMSeq->ppiHMMBindex[ppiLeafList[iL][0]][0] = -1; /* this is conservative, could do H[iR] = H[iL] */
+ for (i = 0; i < piLeafCount[iL]; i++){
+ prMSeq->ppiHMMBindex[ppiLeafList[iL][i]][0] = -1;
+ }
+ }
+ else if (prMSeq->ppiHMMBindex[ppiLeafList[iL][0]][0] != prMSeq->ppiHMMBindex[ppiLeafList[iR][0]][0]){
+ prMSeq->ppiHMMBindex[ppiLeafList[iL][0]][0] = -1; /* this is NOT conservative, mandatory */
+ for (i = 0; i < piLeafCount[iL]; i++){
+ prMSeq->ppiHMMBindex[ppiLeafList[iL][i]][0] = -1;
+ }
+ prMSeq->ppiHMMBindex[ppiLeafList[iR][0]][0] = -1; /* this is NOT conservative, mandatory */
+ for (i = 0; i < piLeafCount[iR]; i++){
+ prMSeq->ppiHMMBindex[ppiLeafList[iR][i]][0] = -1;
+ }
+ }
+ else {
+ /* void, HMMs should be same */
+ }
+ }
+ } /* there was a HMM batch */
+#endif
+ if (rLog.iLogLevelEnabled <= LOG_DEBUG){
+ int i;
+
+ printf("@@iL=%d, #(iL)=%d, iR=%d, #(iR)=%d\n", iL, piLeafCount[iL], iR, piLeafCount[iR]);
+ for (i = 0; i < piLeafCount[iL]; i++){
+ char *pc = ppcProfile1[i];
+ printf("@@>%s\n", prMSeq->sqinfo[ppiLeafList[iL][i]].name);
+ printf("@@");
+ while('\0' != *pc){
+ printf("%c", toupper(*pc));
+ pc++;
+ }
+ printf("\n");
+ }
+ for (i = 0; i < piLeafCount[iR]; i++){
+ char *pc = ppcProfile2[i];
+ printf("@@>%s\n", prMSeq->sqinfo[ppiLeafList[iR][i]].name);
+ printf("@@");
+ while('\0' != *pc){
+ printf("%c", toupper(*pc));
+ pc++;
+ }
+ printf("\n");
+ }
+ printf("\n");
+ } /* LOG_DEBUG */
+
}
/* free left/right node lists,
* after alignment left/right profiles no longer needed
ppiLeafList[iL] = CKFREE(ppiLeafList[iL]);
ppiLeafList[iR] = CKFREE(ppiLeafList[iR]);
piLeafCount[iL] = piLeafCount[iR] = 0;
-
+
} /* was a merge node */
if (rLog.iLogLevelEnabled <= LOG_DEBUG){
TranslateUnknown2Ambiguity(prMSeq);
ReAttachLeadingGaps(prMSeq, iProfProfSeparator);
+#if 0 /* DEVEL 291 */
if (NULL == prHMMList){
CKFREE(prHMM);
}
+#else
+ CKFREE(prHMMnull);
+#endif
CKFREE(ppcProfile2);
CKFREE(ppcProfile1);
CKFREE(ppiLeafList[piOrderLR[DIFF_NODE*(iNodeCount-1)+PRNT_NODE]]);
********************************************************************/
/*
- * RCS $Id: hhalign_wrapper.h 241 2011-05-04 14:37:17Z fabian $
+ * RCS $Id: hhalign_wrapper.h 289 2013-09-17 10:09:37Z fabian $
*/
+extern void
+SetDefaultHhalignPara(hhalign_para *prHhalignPara);
+
+extern int
+PosteriorProbabilities(mseq_t *prMSeq, hmm_light rHMMalignment, hhalign_para rHhalignPara, char *pcPosteriorfile);
+
+extern double
+PileUp(mseq_t *prMSeq, hhalign_para rHhalignPara, int iClustersize);
extern double
HHalignWrapper(mseq_t *mseq, int *piOrderLR,
double *pdSeqWeights, int iNodeCount,
hmm_light *prHMMList, int iHMMCount,
int iProfProfSeparator, hhalign_para rHhalignPara);
+void
+SanitiseUnknown(mseq_t *mseq);
--- /dev/null
+# hhalign_wrapper.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/hhalign_wrapper.o'
+
+# Name of the non-PIC object
+non_pic_object='hhalign_wrapper.o'
+
********************************************************************/
/*
- * RCS $Id: ktuple_pair.c 230 2011-04-09 15:37:50Z andreas $
+ * RCS $Id: ktuple_pair.c 305 2016-06-13 13:46:02Z fabian $
*
*
* K-Tuple code for pairwise alignment (Wilbur and Lipman, 1983; PMID
/* 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),
#pragma omp critical(ktuple)
#if 0
{
- printf("steps: %d\n", private_step_no);
+ int tid;
+ tid = omp_get_thread_num();
+ printf("%s:%d: tid %d: steps %d\n", __FILE__, __LINE__, tid, private_step_no);
}
#endif
#endif
--- /dev/null
+# ktuple_pair.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/ktuple_pair.o'
+
+# Name of the non-PIC object
+non_pic_object='ktuple_pair.o'
+
--- /dev/null
+# libclustal.la - a libtool library file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# The name that we can dlopen(3).
+dlname=''
+
+# Names of this library.
+library_names=''
+
+# The name of the static archive.
+old_library='libclustal.a'
+
+# Linker flags that can not go in dependency_libs.
+inherited_linker_flags=''
+
+# Libraries that this one depends upon.
+dependency_libs=' -largtable2 -lm'
+
+# Names of additional weak libraries provided by this library
+weak_library_names=''
+
+# Version information for libclustal.
+current=
+age=
+revision=
+
+# Is this an already installed library?
+installed=no
+
+# Should we warn about portability when linking against -modules?
+shouldnotlink=no
+
+# Files to dlopen/dlpreopen
+dlopen=''
+dlpreopen=''
+
+# Directory that this library needs to be installed in:
+libdir=''
--- /dev/null
+# list.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/list.o'
+
+# Name of the non-PIC object
+non_pic_object='list.o'
+
--- /dev/null
+# log.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/log.o'
+
+# Name of the non-PIC object
+non_pic_object='log.o'
+
********************************************************************/
/*
- * RCS $Id: mbed.c 254 2011-06-21 13:07:50Z andreas $
+ * RCS $Id: mbed.c 316 2016-12-16 16:14:39Z fabian $
*
*
- * Reimplementation from scratch of mBed:
- * Blackshields et al. (2010); PMID 20470396
- *
+ * Reimplementation from scratch of mBed (Blackshields et al., 2010;
+ * PMID 20470396) and addition of bisecting K-Means which allows
+ * control over subcluster size
*
*/
#define USE_KMEANS_LLOYDS 0
-#ifndef HAVE_LOG2
-#define log2(x) (log(x) / 0.69314718055994530942)
+//#ifndef HAVE_LOG2
+#ifndef CLUSTAL_OMEGA_HAVE_LOG2
+//#define log2(x) (log(x) / 0.69314718055994530942)
+#define log2(x) ( x<=0 ? (float)(-100000) : 1.442695041*log(x) )
#endif
#define NUMBER_OF_SEEDS(n) pow(log2(((double)n)), 2)
int iSeqIndex;
int iSeedIndex;
/* indices for restoring order */
- int *restore;
+ int *restore = NULL;
/* sorted copy of piSeeds */
- int *piSortedSeeds;
+ int *piSortedSeeds = NULL;
#if TIMING
Stopwatch_t *stopwatch = StopwatchCreate();
* distance function for each seq/seed pair
*
*/
- if (0 != PairDistances(&prDistmat, prMSeq, iPairDistType,
+ /* 4th argument (FALSE) is bPercID, in mBed mode never use percent-identities */
+ if (0 != PairDistances(&prDistmat, prMSeq, iPairDistType, FALSE,
0, iNumSeeds, 0, prMSeq->nseqs,
NULL, NULL)) {
Log(&rLog, LOG_ERROR, "Could not compute pairwise distances for mbed.");
for (iSeqIndex=0; iSeqIndex<prMSeq->nseqs; iSeqIndex++) {
labels[iSeqIndex] = prMSeq->sqinfo[iSeqIndex].name;
}
- SymMatrixPrint(prDistmat, labels, NULL);
+ SymMatrixPrint(prDistmat, labels, NULL, FALSE);
CKFREE(labels);
}
#endif
FreeSymMatrix(&prDistmat);
CKFREE(restore);
+ CKFREE(piSortedSeeds);
#if TIMING
StopwatchStop(stopwatch);
StopwatchDisplay(stdout, "Total time for SeqToVec(): ", stopwatch);
BisectingKmeans(bisecting_kmeans_result_t **prKMeansResult_p,
const int iNObjs, const int iDim, double **ppdVectors,
const int iMinRequiredObjsPerCluster,
- const int iMaxAllowedObjsPerCluster)
+ const int iMaxAllowedObjsPerCluster, char ***ppcClusterSplits_p)
{
int iN, iD;
/* cluster centers for each cluster created at each split */
bool bSmallClusterDetected;
/* queue of clusters which are to be split */
int_queue_t rClusterSplitQueue;
+ /* */
+ int iLog2N2 = 0;
#if TIMING
Stopwatch_t *stopwatch = StopwatchCreate();
}
+ /*
+ * this is an array that encodes where a sequences fell at a bisecting k-means
+ * ppcClusterSplits_p can consume quite a bit of memory,
+ but it is only needed if clustering info is written to file.
+ Use ppcClusterSplits_p as a flag, initialise in the calling function (Mbed)
+ to NULL, if no info written out then leave ppcClusterSplits_p=NULL.
+ If info is to be written out then malloc one char*, so that
+ ppcClusterSplits_p!=NULL. In that case realloc proper amount.
+ Only expect a certain number of splits, iLog2N2.
+ Worst case would be iNObjs but then ppcClusterSplits_p
+ would be quadratic, which is too big for many sequences.
+ */
+ if (NULL != *ppcClusterSplits_p){
+ /* (square) of logarithm (base 2) of number of objects */
+ double dLog2N = log10(iNObjs) / log10(2);
+ iLog2N2 = (int)(dLog2N*dLog2N);
+
+ *ppcClusterSplits_p = (char **)CKREALLOC(*ppcClusterSplits_p, iNObjs*sizeof(char *));
+ (*ppcClusterSplits_p)[0] = (char *)CKMALLOC(iNObjs*iLog2N2);
+ (*ppcClusterSplits_p)[0][0] = '\0';
+ for (iN = 1; iN < iNObjs; iN++){
+ (*ppcClusterSplits_p)[iN] = (*ppcClusterSplits_p)[iN-1] + iLog2N2;
+ (*ppcClusterSplits_p)[iN][0] = '\0';
+ }
+ }
+
/* Starting with the first cluster that now contains all the
* sequences keep splitting until no cluster contains more than
}
#if TRACE
- Log(&rLog, LOG_FOCRED_DEBUG, "Round %d: Will split cluster %d which has %d objects",
- iNRounds, iClusterToSplot, iNObjsInClusterToSplit);
+ Log(&rLog, LOG_FORCED_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++) {
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."
+ "Hope it's not too big and doesn't slow things down."
);
bNaNDetected = TRUE;
break;
if (0 == iThisClusterAssignment) {
iThisClusterIndex = iClusterToSplot;
+ if (*ppcClusterSplits_p && strlen((*ppcClusterSplits_p)[iThisObjIdx])<iLog2N2){
+ strcat((*ppcClusterSplits_p)[iThisObjIdx], "0");
+ }
} else if (1 == iThisClusterAssignment) {
iThisClusterIndex = iNewClusterIdx;
+ if (*ppcClusterSplits_p && strlen((*ppcClusterSplits_p)[iThisObjIdx])<iLog2N2){
+ strcat((*ppcClusterSplits_p)[iThisObjIdx], "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)",
* @param[in] pcGuidetreeOut
* Passed down to GuideTreeUpgma()
*
+ * @note: if the number of sequences is smaller than
+ * MAX_ALLOWED_SEQ_PER_PRECLUSTER then there's no need to do the subclustering
+ * first. In fact it costs some extra time. However, it's insignificant and
+ * for simplicities sake we don't do any special checks
+
+ *
* @return Zero on success, non-zero on error
*
*/
int
Mbed(tree_t **prMbedTree_p, mseq_t *prMSeq, const int iPairDistType,
- const char *pcGuidetreeOut)
+ const char *pcGuidetreeOut, int iClustersizes, const char *pcClusterFile)
{
/* number of seeds */
- int iNumSeeds;
+ int iNumSeeds = 0;
/* seed indices matching prMSeq */
- int *piSeeds;
+ int *piSeeds = NULL;
/* seqs represented as distance vectors */
- double **ppdSeqVec;
+ double **ppdSeqVec = NULL;
/* 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;
+ char **ppcLabels = NULL;
+ int iNodeIndex = 0;
/* mapping of cluster-center tree node indices to corresponding
cluster */
- int *piClusterToTreeNode;
- int iClusterIndex;
+ int *piClusterToTreeNode = NULL;
+ int iClusterIndex = 0;
int iI, iJ;
- FILE *pfOut;
- progress_t *prSubClusterDistanceProgress;
+ FILE *pfOut = NULL;
+ progress_t *prSubClusterDistanceProgress = NULL;
bool bPrintCR = (rLog.iLogLevelEnabled<=LOG_VERBOSE) ? FALSE : TRUE;
+ char **ppcClusterSplits = NULL;
#if FULL_WITHIN_CLUSTER_DISTANCES
Log(&rLog, LOG_DEBUG, "Computing real distances within subclusters for mBed.");
StopwatchStart(stopwatch);
#endif
+ /* ppcClusterSplits can consume quite a bit of memory,
+ however, it is only needed if cluster information is
+ to be written to file. If no pcClusterFile is specified,
+ then ppcClusterSplits does not have to be allocated.
+ Use ppcClusterSplits as a flag, initialise to NULL,
+ if NULL is passed into BisectingKmeans then do NOT malloc,
+ if !NULL is passed in then realloc the appropriate memory */
+ if (NULL != pcClusterFile){
+ ppcClusterSplits = (char **)malloc(sizeof(char*));
+ }
+ else {
+ ppcClusterSplits = NULL;
+ }
+
BisectingKmeans(&prKMeansResult, prMSeq->nseqs, iNumSeeds, ppdSeqVec,
MIN_REQUIRED_SEQ_PER_PRECLUSTER,
- MAX_ALLOWED_SEQ_PER_PRECLUSTER);
+ iClustersizes/*MAX_ALLOWED_SEQ_PER_PRECLUSTER*/, &ppcClusterSplits);
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);
+ iClustersizes/*MAX_ALLOWED_SEQ_PER_PRECLUSTER*/);
+ if (NULL != pcClusterFile){ /* print clustering: FS, r275 -> */
+ FILE *pfClust = NULL;
+ if (NULL == (pfClust = fopen(pcClusterFile, "w"))){
+ Log(&rLog, LOG_FATAL, "Could not open file %s for writing", pcClusterFile);
+ }
+ for (iI = 0; iI < prKMeansResult->iNClusters; iI++) {
+ for (iJ=0; iJ<prKMeansResult->piNObjsPerCluster[iI]; iJ++) {
+ int iRealIndex = prKMeansResult->ppiObjIndicesPerCluster[iI][iJ];
+ fprintf(pfClust, "Cluster %u: object %u has index %u (=seq %s %d~len)\t %s\n",
+ iI, iJ, iRealIndex, prMSeq->sqinfo[iRealIndex].name, prMSeq->sqinfo[iRealIndex].len, ppcClusterSplits[iRealIndex]);
+ }
+ }
+ fclose(pfClust); pfClust = NULL;
+ /* if there is no pcClusterFile then no memory will have been allocated */
+ CKFREE(ppcClusterSplits[0]);
+ CKFREE(ppcClusterSplits);
+ } /* there was a request to write out clustering */
#if PRINT_CLUSTER_DISTRIBUTION
Log(&rLog, LOG_FORCED_DEBUG, "Bisecting Kmeans returned %d clusters", prKMeansResult->iNClusters);
}
#if TRACE
Log(&rLog, LOG_FORCED_DEBUG, "%s", "Distance matrix for pre-cluster centers:");
- SymMatrixPrint(prPreClusterDistmat, ppcLabels, NULL);
+ SymMatrixPrint(prPreClusterDistmat, ppcLabels, NULL, FALSE);
#endif
GuideTreeUpgma(prMbedTree_p,
CKFREE(ppcLabels);
#if TRACE
Log(&rLog, LOG_FORCED_DEBUG, "%s", "Cluster-center guide-tree:");
- LogTree(*prMbedTree_p);
+ LogTree(*prMbedTree_p, stderr);
#endif
"%s\n", "Calling new Mbed use makes only sense if nseq>MAX_ALLOWED_SEQ_PER_PRECLUSTER");
if (TRUE == prMSeq->aligned) {
- iPairDistType = PAIRDIST_SQUIDID_KIMURA;
+ if (SEQTYPE_PROTEIN == prMSeq->seqtype){
+ iPairDistType = PAIRDIST_SQUIDID_KIMURA;
+ }
+ else {
+ iPairDistType = PAIRDIST_SQUIDID;
+ }
} else {
iPairDistType = PAIRDIST_KTUPLE;
}
iOldLogLevel = rLog.iLogLevelEnabled;
rLog.iLogLevelEnabled = LOG_WARN;
/* compute distances, but be quiet */
- if (PairDistances(&prWithinClusterDistances, prSubClusterMSeq, iPairDistType,
+ /* 4th argument (FALSE) is bPercID, in mBed mode never use percent-identities */
+ if (PairDistances(&prWithinClusterDistances, prSubClusterMSeq, iPairDistType, FALSE,
0, prSubClusterMSeq->nseqs, 0, prSubClusterMSeq->nseqs,
NULL, NULL)) {
Log(&rLog, LOG_ERROR, "Couldn't compute pair distances");
#if TRACE
Log(&rLog, LOG_FORCED_DEBUG, "Distance matrix for seqs within sub cluster %d/%d",
iClusterIndex, prKMeansResult->iNClusters);
- SymMatrixPrint(prWithinClusterDistances, ppcLabels, NULL);
+ SymMatrixPrint(prWithinClusterDistances, ppcLabels, NULL, FALSE);
#endif
********************************************************************/
/*
- * RCS $Id: mbed.h 193 2011-02-07 15:45:21Z andreas $
+ * RCS $Id: mbed.h 278 2013-05-16 15:53:45Z fabian $
*/
#ifndef CLUSTALO_MBED_H
extern int
Mbed(tree_t **tree, mseq_t *prMSeq,
- const int iPairDistType, const char *pcGuidetreeOutfile);
+ const int iPairDistType, const char *pcGuidetreeOutfile,
+ int iClustersizes, const char *pcClusterFile);
#endif
--- /dev/null
+# mbed.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/mbed.o'
+
+# Name of the non-PIC object
+non_pic_object='mbed.o'
+
--- /dev/null
+# muscle_tree.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/muscle_tree.o'
+
+# Name of the non-PIC object
+non_pic_object='muscle_tree.o'
+
--- /dev/null
+# muscle_upgma.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/muscle_upgma.o'
+
+# Name of the non-PIC object
+non_pic_object='muscle_upgma.o'
+
********************************************************************/
/*
- * RCS $Id: pair_dist.c 242 2011-05-27 14:04:21Z andreas $
+ * RCS $Id: pair_dist.c 301 2016-06-13 13:32:55Z fabian $
*/
#ifdef HAVE_CONFIG_H
#include "progress.h"
#include "util.h"
+/* Made iend/jend const unsigned long int (originally just int), FS, 2016-04-04
+ */
+
/* 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
static int
SquidIdPairDist(symmatrix_t *tmat, mseq_t *mseq,
- int istart, int iend,
- int jstart, int jend,
+ int istart, const unsigned long int iend,
+ int jstart, const unsigned long int jend,
bool use_KimuraCorrection, progress_t *prProgress,
unsigned long int *ulStepNo, unsigned long int ulTotalStepNo);
*/
int
SquidIdPairDist(symmatrix_t *tmat, mseq_t *mseq,
- int istart, int iend,
- int jstart, int jend,
+ int istart, const unsigned long int iend,
+ int jstart, const unsigned long int jend,
bool use_kimura, progress_t *prProgress,
unsigned long int *ulStepNo, unsigned long int ulTotalStepNo)
{
*
*/
int
-PairDistances(symmatrix_t **distmat, mseq_t *mseq, int pairdist_type,
- int istart, int iend,
- int jstart, int jend,
+PairDistances(symmatrix_t **distmat, mseq_t *mseq, int pairdist_type, bool bPercID,
+ int istart, const unsigned long int iend,
+ int jstart, const unsigned long int jend,
char *fdist_in, char *fdist_out)
{
int uSeqIndex;
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
*
#include "random-dist.h"
#else
if (NULL != fdist_in) {
- Log(&rLog, LOG_FATAL, "FIXME: reading of distance matrix from file not implemented");
+ Log(&rLog, LOG_WARN,
+ "Please use distance matrix input only, if you know exactly what you're doing!");
+ if (SymMatrixRead(fdist_in, distmat, mseq)) {
+ Log(&rLog, LOG_FATAL, "%s", "Reading distance matrix failed");
+ }
} else {
+ if (NewSymMatrix(distmat, iend, jend)!=0) {
+ Log(&rLog, LOG_FATAL, "%s", "Memory allocation for distance matrix failed");
+ }
+
/* 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)
+ if (iChunk == iNumberOfThreads - 1){
iChunkStart = 0;
- else
+ }
+ else if (iend == jend){
iChunkStart = iend - ((double)(iend - istart) * sqrt(((double)iChunk + 1.0)/(double)iNumberOfThreads));
+ }
+ else {
+ iChunkStart = iend - (iend - istart) * (iChunk + 1) / (double)(iNumberOfThreads);
+ }
iChunkStarts[iChunk] = iChunkStart;
iChunkEnds[iChunk] = iChunkEnd;
+ /*printf("%s:%d: C=%d, ie=%d, is=%d, je=%d, js=%d, Cstart=%d, Cend=%d, diff=%d\n",
+ __FILE__, __LINE__, iChunk, iend, istart, jend, jstart, iChunkStart, iChunkEnd, iChunkEnd-iChunkStart);*/
}
if (PAIRDIST_KTUPLE == pairdist_type) {
Log(&rLog, LOG_INFO, "Calculating pairwise ktuple-distances...");
-
+
NewProgress(&prProgress, LogGetFP(&rLog, LOG_INFO),
- "Ktuple-distance calculation progress", bPrintCR);
+ "Ktuple-distance calculation progress", bPrintCR);
#ifdef HAVE_OPENMP
#pragma omp parallel for private(iChunk) schedule(dynamic)
#endif
}
#endif /* random/proper distance calculation */
-
+
/* optional printing of matrix to file
*/
if (NULL != fdist_out) {
names[uSeqIndex] = mseq->sqinfo[uSeqIndex].name;
}
- SymMatrixPrint((*distmat), names, fdist_out);
+ SymMatrixPrint((*distmat), names, fdist_out, bPercID);
Log(&rLog, LOG_INFO, "Pairwise distance matrix written to %s",
fdist_out);
ProgressDone(prProgress);
FreeProgress(&prProgress);
}
-
+
return 0;
}
/*** end: PairDistances() ***/
********************************************************************/
/*
- * RCS $Id: pair_dist.h 193 2011-02-07 15:45:21Z andreas $
+ * RCS $Id: pair_dist.h 302 2016-06-13 13:35:50Z fabian $
*/
#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,
+PairDistances(symmatrix_t **distmat, mseq_t *mseq, const int pairdist_type, bool bPercID,
+ const int istart, const unsigned long int iend,
+ const int jstart, const unsigned long int jend,
char *fdist_in, char *fdist_out);
#endif
--- /dev/null
+# pair_dist.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/pair_dist.o'
+
+# Name of the non-PIC object
+non_pic_object='pair_dist.o'
+
--- /dev/null
+# progress.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/progress.o'
+
+# Name of the non-PIC object
+non_pic_object='progress.o'
+
********************************************************************/
/*
- * RCS $Id: seq.c 245 2011-06-15 12:38:53Z fabian $
+ * RCS $Id: seq.c 298 2014-11-07 12:18:36Z fabian $
*
*
* Module for sequence/alignment IO and misc.
#include "util.h"
#include "log.h"
#include "seq.h"
+/*#include "../../mymemmonitor.h"*/
-
-#define ALLOW_ONLY_PROTEIN 0 /* requested by Hamish, FS, r244 -> r245 */
-
+#define ALLOW_ONLY_PROTEIN 0 // DD
*/
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;
/**
- * @brief convert int-encoded seqtype to string
+ * @brief convert int-encoded iSeqType to string
*
- * @param[in] seqtype int-encoded sequence type
+ * @param[in] iSeqType int-encoded sequence type
*
* @return character pointer describing the sequence type
*
*/
const char*
-SeqTypeToStr(int seqtype)
+SeqTypeToStr(int iSeqType)
{
- switch (seqtype) {
+ switch (iSeqType) {
case SEQTYPE_DNA:
return "DNA";
case SEQTYPE_RNA:
}
return "Will never get here";
}
-/*** end: seqtype_to_str ***/
+/*** end: SeqTypeToStr ***/
* 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
+ * @param[in] iSeqType
* int-encoded sequence type. Set to
* SEQTYPE_UNKNOWN for autodetect (guessed from first sequence)
* @param[in] iMaxNumSeq
* - If supported by squid, gzipped files can be read as well.
*/
int
-ReadSequences(mseq_t *prMSeq, char *seqfile, int seqtype,
- int iMaxNumSeq, int iMaxSeqLen)
+ReadSequences(mseq_t *prMSeq, char *seqfile,
+ int iSeqType, int iSeqFmt, bool bIsProfile, bool bDealignInputSeqs,
+ int iMaxNumSeq, int iMaxSeqLen, char *pcHMMBatch)
{
- int fmt = SQFILE_UNKNOWN; /* file format: auto detect if unknown */
SQFILE *dbfp; /* sequence file descriptor */
- char *cur_seq;
- SQINFO cur_sqinfo;
+ char *cur_seq = NULL;
+ SQINFO cur_sqinfo = {0};
int iSeqIdx; /* sequence counter */
int iSeqPos; /* sequence string position counter */
/* Try to work around inability to autodetect from a pipe or .gz:
* assume FASTA format
*/
- if (SQFILE_UNKNOWN == fmt &&
+ if (SQFILE_UNKNOWN == iSeqFmt &&
(Strparse("^.*\\.gz$", seqfile, 0) || strcmp(seqfile, "-") == 0)) {
- fmt = SQFILE_FASTA;
+ iSeqFmt = SQFILE_FASTA;
}
/* Using squid routines to read input. taken from seqstat_main.c. we don't
*
*/
- if (NULL == (dbfp = SeqfileOpen(seqfile, fmt, NULL))) {
+ if (NULL == (dbfp = SeqfileOpen(seqfile, iSeqFmt, NULL))) {
Log(&rLog, LOG_ERROR, "Failed to open sequence file %s for reading", seqfile);
return -1;
}
*/
while (ReadSeq(dbfp, dbfp->format,
&cur_seq,
- &cur_sqinfo)) {
-
+ &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);
cur_sqinfo.name, strlen(cur_seq), iMaxSeqLen);
return -1;
}
+ if ((int)strlen(cur_seq)==0) {
+ Log(&rLog, LOG_ERROR, "Sequence '%s' has 0 residues",
+ cur_sqinfo.name);
+ return -1;
+ }
/* FIXME: use modified version of AddSeq() that allows handing down SqInfo
*/
prMSeq->sqinfo = (SQINFO *)
- CKREALLOC(prMSeq->sqinfo, (prMSeq->nseqs+1) * sizeof(SQINFO));
+ CKREALLOC(prMSeq->sqinfo, (prMSeq->nseqs+1) * sizeof(SQINFO));
+ memset(&prMSeq->sqinfo[prMSeq->nseqs], 0, sizeof(SQINFO));
SeqinfoCopy(&prMSeq->sqinfo[prMSeq->nseqs], &cur_sqinfo);
#ifdef TRACE
/* override with given sequence type but check with
* automatically detected type and warn if necessary
*/
- if (SEQTYPE_UNKNOWN != seqtype) {
- if (prMSeq->seqtype != seqtype) {
+ if (SEQTYPE_UNKNOWN != iSeqType) {
+ if (prMSeq->seqtype != iSeqType) {
Log(&rLog, LOG_WARN, "Overriding automatically determined seq-type %s to %s as requested",
- SeqTypeToStr(prMSeq->seqtype), SeqTypeToStr(seqtype));
- prMSeq->seqtype = seqtype;
+ SeqTypeToStr(prMSeq->seqtype), SeqTypeToStr(iSeqType));
+ prMSeq->seqtype = iSeqType;
}
}
/* if type could not be determined and was not set return error */
- if (SEQTYPE_UNKNOWN == seqtype && SEQTYPE_UNKNOWN == prMSeq->seqtype) {
+ if (SEQTYPE_UNKNOWN == iSeqType && SEQTYPE_UNKNOWN == prMSeq->seqtype) {
Log(&rLog, LOG_ERROR, "Couldn't guess sequence type from first sequence");
FreeSequence(cur_seq, &cur_sqinfo);
SeqfileClose(dbfp);
prMSeq->nseqs++;
- FreeSequence(cur_seq, &cur_sqinfo);
+ FreeSequence(cur_seq, &cur_sqinfo);
}
SeqfileClose(dbfp);
-#if ALLOW_ONLY_PROTEIN
+/*#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
+#endif*/
/* Check if sequences are aligned */
- prMSeq->aligned = SeqsAreAligned(prMSeq);
+ prMSeq->aligned = SeqsAreAligned(prMSeq, bIsProfile, bDealignInputSeqs);
/* keep original sequence as copy and convert "working" sequence
}
}
-
+ /* order in which sequences appear in guide-tree
+ * only allocate if different output-order desired */
+ prMSeq->tree_order = NULL;
+
prMSeq->filename = CkStrdup(seqfile);
Log(&rLog, LOG_INFO, "Read %d sequences (type: %s) from %s",
prMSeq->nseqs, SeqTypeToStr(prMSeq->seqtype), prMSeq->filename);
+ prMSeq->pppcHMMBNames = NULL;
+ prMSeq->ppiHMMBindex = NULL;
+
+ /* read HMM-batch file if existent */
+ if (NULL != pcHMMBatch) {
+
+ enum {MAXLINE=10000};
+ FILE *pfHMMBatch = NULL;
+ char zcScanline[MAXLINE] = {0};
+ char *pcToken = NULL;
+ char *pcSeqName = NULL;
+ int iSeq = 0;
+
+ /* check that file exists */
+ if (NULL == (pfHMMBatch = fopen(pcHMMBatch, "r"))){
+ Log(&rLog, LOG_ERROR, "Failed to open HMM-batch file %s for reading", pcHMMBatch);
+ return -1;
+ }
+
+ /* initialise names and indices */
+ prMSeq->pppcHMMBNames = (char ***)CKMALLOC(prMSeq->nseqs * sizeof(char **));
+ for (iSeq = 0; iSeq < prMSeq->nseqs; iSeq++){
+ prMSeq->pppcHMMBNames[iSeq] = NULL;
+ }
+ prMSeq->ppiHMMBindex = (int **)CKMALLOC(prMSeq->nseqs * sizeof(int *));
+ for (iSeq = 0; iSeq < prMSeq->nseqs; iSeq++){
+ prMSeq->ppiHMMBindex[iSeq] = (int *)CKMALLOC(1 * sizeof(int));
+ prMSeq->ppiHMMBindex[iSeq][0] = -1;
+ }
+
+ /* read batch file line-by-line */
+ while (NULL != fgets(zcScanline, MAXLINE, pfHMMBatch)){
+
+ pcToken = strtok(zcScanline, " \040\t\n");
+ if (NULL == pcToken){
+ continue;
+ }
+ else {
+ pcSeqName = pcToken;
+ }
+ /* identify sequence label from batch file in labels read from sequence file */
+ for (iSeq = 0; iSeq < prMSeq->nseqs; iSeq++){
+ int iHMM = 0;
+
+ if (0 == strcmp(pcSeqName, prMSeq->sqinfo[iSeq].name)){
+
+ while (NULL != (pcToken = strtok(NULL, " \040\t\n"))){
+ prMSeq->pppcHMMBNames[iSeq] = (char **)CKREALLOC(prMSeq->pppcHMMBNames[iSeq],
+ (iHMM+2) * sizeof(char *));
+ prMSeq->pppcHMMBNames[iSeq][iHMM] = CkStrdup(pcToken);
+ prMSeq->ppiHMMBindex[iSeq] = (int *)CKREALLOC(prMSeq->ppiHMMBindex[iSeq],
+ (iHMM+2) * sizeof(int));
+ prMSeq->ppiHMMBindex[iSeq][iHMM] = 0;
+ iHMM++;
+ prMSeq->pppcHMMBNames[iSeq][iHMM] = NULL;
+ prMSeq->ppiHMMBindex[iSeq][iHMM] = 0;
+ }
+ break;
+ }
+
+ } /* 0 <= iSeq < prMSeq->nseqs */
+ if (iSeq >= prMSeq->nseqs) {
+ Log(&rLog, LOG_WARN,
+ "sequence %s not found in input sequences (%s), will be ignored",
+ pcSeqName, seqfile);
+ }
+
+ } /* !EOF */
+
+ fclose(pfHMMBatch); pfHMMBatch = NULL;
+
+ } /* there was a HMM batch file */
+ else {
+ prMSeq->pppcHMMBNames = NULL;
+ prMSeq->ppiHMMBindex = NULL;
+ } /* there was no HMM batch file */
+
return 0;
}
/*** end: ReadSequences ***/
(*prMSeq)->seqtype = SEQTYPE_UNKNOWN;
(*prMSeq)->sqinfo = NULL;
(*prMSeq)->filename = NULL;
+ (*prMSeq)->tree_order = NULL;
+ (*prMSeq)->pppcHMMBNames = NULL;
+ (*prMSeq)->ppiHMMBindex = NULL;
}
/*** end: NewMSeq ***/
CKFREE((*mseq)->sqinfo);
}
+ /* FIXME (FS): problem with freeing tree_order */
+ if ((*mseq)->tree_order){
+ CKFREE((*mseq)->tree_order);
+ }
+
+ if (NULL != (*mseq)->pppcHMMBNames){ /* FS, r291 -> */
+ for (i = 0; (*mseq)->pppcHMMBNames[i] && (i < (*mseq)->nseqs); i++){
+ int iIter = 0;
+ for (iIter = 0; NULL != (*mseq)->pppcHMMBNames[i][iIter]; iIter++){
+ CKFREE((*mseq)->pppcHMMBNames[i][iIter]);
+ }
+ }
+ }
(*mseq)->seqtype = SEQTYPE_UNKNOWN;
(*mseq)->nseqs = 0;
* The name of the output file
* @param[in] outfmt
* The alignment output format (defined in squid.h)
+ * @param[in] iWrap
+ * length of line for Clustal/Fasta format
*
* @return Non-zero on error
*
*
*/
int
-WriteAlignment(mseq_t *mseq, const char *pcAlnOutfile, int outfmt)
+WriteAlignment(mseq_t *mseq, const char *pcAlnOutfile, int outfmt, int iWrap, bool bResno)
{
int i; /* aux */
MSA *msa; /* squid's alignment structure */
* 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 */
+ char *this_name = NULL; /* mseq sequence name */
+ char *this_seq = NULL; /* mseq sequence */
+ SQINFO *this_sqinfo = NULL; /* mseq sequence name */
+ int iI;
+
+ /* mseq->tree_order encodes to order in which sequences are listed in the guide-tree,
+ if the user wants the sequence output in the input-order then mseq->tree_order==NULL,
+ otherwise mseq->tree_order!=NULL, containing the indices of the sequences, FS, r274 -> */
+ iI = (NULL == mseq->tree_order) ? i : mseq->tree_order[i];
+
+ this_name = mseq->sqinfo[iI].name; /* mseq sequence name */
+ this_seq = mseq->seq[iI]; /* mseq sequence */
+ this_sqinfo = &mseq->sqinfo[iI]; /* mseq sequence name */
key = GKIStoreKey(msa->index, this_name);
msa->sqname[key] = sre_strdup(this_name, strlen(this_name));
*/
msa->nseq++;
- }
+
+ } /* 0 <= i < mseq->nseqs */
/* FIXME Would like to, but can't use MSAVerifyParse(msa) here, as it
switch (outfmt) {
case MSAFILE_A2M:
- WriteA2M(pfOut, msa, 0);
+ /*WriteA2M(pfOut, msa, 0);*/
+ WriteA2M(pfOut, msa, iWrap);
break;
case MSAFILE_VIENNA:
- WriteA2M(pfOut, msa, 1);
+ /*WriteA2M(pfOut, msa, 1);*/
+ WriteA2M(pfOut, msa, INT_MAX);
break;
case MSAFILE_CLUSTAL:
- WriteClustal(pfOut, msa);
+ WriteClustal(pfOut, msa, iWrap, TRUE==bResno ? 1 : 0, mseq->seqtype);
break;
case MSAFILE_MSF:
WriteMSF(pfOut, msa);
*
*/
bool
-SeqsAreAligned(mseq_t *prMSeq)
+SeqsAreAligned(mseq_t *prMSeq, bool bIsProfile, bool bDealignInputSeqs)
{
bool bGapFound, bSameLength;
int iSeqIdx; /* sequence counter */
*/
bGapFound = FALSE;
bSameLength = TRUE;
- for (iSeqIdx=0; iSeqIdx<prMSeq->nseqs; iSeqIdx++) {
- if (FALSE == bGapFound) {
+ for (iSeqIdx=0; (iSeqIdx < prMSeq->nseqs); iSeqIdx++) {
+ if ( (FALSE == bGapFound) ){
for (iSeqPos=0;
iSeqPos<prMSeq->sqinfo[iSeqIdx].len && false==bGapFound;
iSeqPos++) {
break;
}
}
- }
+ } /* gap not (yet) found */
if (iSeqIdx>0) {
if (prMSeq->sqinfo[iSeqIdx].len != prMSeq->sqinfo[iSeqIdx-1].len) {
break;
}
}
- }
+ } /* 0 <= iSeqIdx < prMSeq->nseqs */
#if 0
Log(&rLog, LOG_FORCED_DEBUG, "bSameLength=%d bGapFound=%d", bSameLength, bGapFound);
#endif
- if (TRUE == bSameLength && TRUE == bGapFound) {
+
+#if 0
+ if ( (TRUE == bSameLength) && ((TRUE == bGapFound) || (TRUE == bIsProfile)) ) {
return TRUE;
} else {
+ if ((FALSE == bSameLength) && (TRUE == bGapFound) && (FALSE == bDealignInputSeqs)){
+ Log(&rLog, LOG_FORCED_DEBUG, "Potential Problem: Gaps encountered but not all sequences have same length, consider using --dealign");
+ }
return FALSE;
}
+#else
+ if (FALSE == bSameLength){
+ /* if sequences don't have same lengths they can never be profile */
+ if (TRUE == bGapFound){
+ Log(&rLog, LOG_FORCED_DEBUG, "Potential Problem: sequences (N=%d) don't have same lengths but contain gaps, consider using --dealign", prMSeq->nseqs);
+ }
+ return FALSE;
+ }
+ else { /* here all sequences have same lengths */
+ if (TRUE == bGapFound){
+ /* if at least one sequence contains gaps (and all have the same lengths)
+ then we can be sure it is a profile */
+ return TRUE;
+ }
+ /* here all sequences have same lengths but no sequences contain any gaps */
+ else if (TRUE == bIsProfile){
+ /* if the user says it is a profile then it is */
+ return TRUE;
+ }
+ else {
+ return FALSE;
+ }
+ }
+#endif
-}
+}
/*** end: SeqsAreAligned() ***/
* MSeq structure to which to append to
* @param[out] prMSeqToAdd
* MSeq structure which is to append
- *
*
*/
void
}
(*prMSeqDest_p)->nseqs = iNewNSeq;
-
- (*prMSeqDest_p)->aligned = SeqsAreAligned(*prMSeqDest_p);
+
+#if 0
+ /* 2nd arg is bIsProfile, which when set TRUE skips
+ * the check for gaps. here always check for gaps,
+ * so set FALSE (main reason is that it is easier), FS, r282 -> */
+ /* had a problem at this stage, therefore dispense with gap check, FS, r290 -> */
+ /* 3rd argument is dealignment flag, do not dealign profiles */
+ (*prMSeqDest_p)->aligned = SeqsAreAligned(*prMSeqDest_p, TRUE/*FALSE*/, FALSE);
+#else
+ (*prMSeqDest_p)->aligned = TRUE;
+#endif
return;
}
********************************************************************/
/*
- * RCS $Id: seq.h 234 2011-04-13 05:26:16Z andreas $
+ * RCS $Id: seq.h 296 2014-10-07 12:15:41Z fabian $
*/
#ifndef CLUSTALO_SEQ_H
*/
char **orig_seq;
+ /** order in which sequences appear in guide-tree
+ */
+ int *tree_order;
+
/**
* @brief Squid's sequence info structure.
* Index range: 0--nseq-1.
*
*/
SQINFO *sqinfo;
+
+ /* HMM batch information */
+ char ***pppcHMMBNames;
+ int **ppiHMMBindex;
} mseq_t;
extern void
SeqTypeToStr(int seqtype);
extern int
-ReadSequences(mseq_t *prMSeq_p, char *pcSeqFile, int iSeqType,
- int iMaxNumSeq, int iMaxSeqLen);
+ReadSequences(mseq_t *prMSeq_p, char *pcSeqFile,
+ int iSeqType, int iSeqFmt, bool bIsProfile, bool bDealignInputSeqs,
+ int iMaxNumSeq, int iMaxSeqLen, char *pcHMMBatch);
extern void
NewMSeq(mseq_t **mseq);
FindSeqName(char *seqname, mseq_t *mseq);
extern int
-WriteAlignment(mseq_t *mseq, const char *aln_outfile, int msafile_format);
+WriteAlignment(mseq_t *mseq, const char *aln_outfile, int msafile_format, int iWrap, bool bResno);
extern void
DealignSeq(char *seq);
JoinMSeqs(mseq_t **prMSeqDest_p, mseq_t *prMSeqToAdd);
bool
-SeqsAreAligned(mseq_t *prMSeq);
+SeqsAreAligned(mseq_t *prMSeq, bool bIsProfile, bool bDealignInputSeqs);
#endif
--- /dev/null
+# seq.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/seq.o'
+
+# Name of the non-PIC object
+non_pic_object='seq.o'
+
********************************************************************/
/*
- * RCS $Id: symmatrix.c 230 2011-04-09 15:37:50Z andreas $
+ * RCS $Id: symmatrix.c 303 2016-06-13 13:37:47Z fabian $
*
*
* Functions for symmetric (square) matrices including diagonal.
#include <ctype.h>
#include <string.h>
#include <assert.h>
+#include <stdbool.h>
#include "symmatrix.h"
+#include "util.h"
#if 0
#define DEBUG
fprintf(stderr, "Couldn't allocate memory (%s|%s)\n",
__FILE__, __FUNCTION__);
return -1;
+ }
+ else {
+ (*symmat)->nrows = nrows;
+ (*symmat)->ncols = ncols;
}
(*symmat)->data = (double **) malloc(nrows * sizeof(double *));
*symmat = NULL;
return -1;
}
+
+#ifdef HAVE_OPENMP
+ /* one malloc for the full matrix data structure
+ assumes ncols >= nrows (asserted above) */
+ double *mat_data;
+ int elements_to_date=0;
+ if ((mat_data = (double *)malloc(((nrows+1)*nrows/2 + (ncols-nrows)*nrows) * sizeof(double))) == NULL) {
+ fprintf(stderr, "Couldn't allocate MPI memory (%s|%s)\n", __FILE__, __FUNCTION__);
+ free((*symmat)->data);
+ free(*symmat);
+ *symmat = NULL;
+ return -1;
+ }
+ for (i=0; i<nrows; i++) {
+ (*symmat)->data[i] = &mat_data[elements_to_date];
+ elements_to_date += ncols-i;
+#ifdef TRACE
+ fprintf(stderr, "DEBUG(%s|%s():%d) initialising symmat with the number of the beast\n",
+ __FILE__, __FUNCTION__, __LINE__);
+#endif
+ {
+ int j;
+ for (j=0; j<ncols-i; j++) {
+#ifdef TRACE
+ (*symmat)->data[i][j] = -666.0;
+#else
+ (*symmat)->data[i][j] = 0.0;
+#endif
+ }
+ }
+ }
+#else /* not HAVE_OPENMP */
for (i=0; i<nrows; i++) {
(*symmat)->data[i] = (double *) calloc((ncols-i), sizeof(double));
if (NULL == (*symmat)->data[i]) {
}
#endif
}
+#endif /* HAVE_OPENMP */
- (*symmat)->nrows = nrows;
- (*symmat)->ncols = ncols;
-
return 0;
}
/*** end: new_symmatrix ***/
void
FreeSymMatrix(symmatrix_t **symmat)
{
+#ifndef HAVE_OPENMP
int i;
+#endif
if (NULL != (*symmat)) {
if (NULL != (*symmat)->data) {
+#ifdef HAVE_OPENMP
+ free((*symmat)->data[0]);
+#else
for (i=0; i<(*symmat)->nrows; i++) {
free((*symmat)->data[i]);
}
+#endif
free((*symmat)->data);
}
}
*
*/
void
-SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path)
+SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path, bool bPercID)
{
FILE *fp = NULL;
int i, j; /* aux */
/* 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));
+ if (TRUE == bPercID){
+ for (j=0; j<symmat->ncols; j++) {
+ fprintf(fp, " %f", 100*(1.00-SymMatrixGetValue(symmat, i, j)));
+ }
+ }
+ else{
+ for (j=0; j<symmat->ncols; j++) {
+ fprintf(fp, " %f", SymMatrixGetValue(symmat, i, j));
+ }
}
fprintf(fp, "%s", "\n");
}
*
* @param[in] pcFileIn
* distance matrix filename
+ * @param[in] prMSeq
+ * optional mseq pointer. only used for consistency checking of names/labels
* @param[out] prSymMat_p
* the symmatrix_t. will be allocated here.
* @return:
* FIXME untested code
*/
int
-SymMatrixRead(char *pcFileIn, symmatrix_t **prSymMat_p)
+SymMatrixRead(char *pcFileIn, symmatrix_t **prSymMat_p, mseq_t *prMSeq)
{
FILE *prFilePointer;
char *buf;
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");
-
+ /* could pass down prMSeq for label checking if non NULL */
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__);
while (isspace(szToken[strlen(szToken)-1])) {
szToken[strlen(szToken)-1]='\0';
}
- /* FIXME save label? */
+ if (strcmp(szToken, prMSeq->sqinfo[iNParsedSeq-1].name) != 0) {
+ fprintf(stderr, "Sequence ordering in mseq and distmat differ (expected %s and got %s from distmat %s)n",
+ prMSeq->sqinfo[iNParsedSeq-1].name, szToken, pcFileIn);
+ iRetCode = -1;
+ goto closefile_and_freebuf;
+ }
szToken = strtok(NULL, " \t");
}
/* from here on it's only parsing of distances */
********************************************************************/
/*
- * RCS $Id: symmatrix.h 216 2011-03-19 10:11:53Z andreas $
+ * RCS $Id: symmatrix.h 288 2013-07-29 13:15:50Z andreas $
*/
/**
#ifndef CLUSTALO_SYMMATRIX_H
#define CLUSTALO_SYMMATRIX_H
+/* ugly, but necessary for cross-checking of names in distmat and
+ * mseq */
+#include "seq.h"
+
+
/**
* @brief symmetric matrix structure
FreeSymMatrix(symmatrix_t **symmat);
extern void
-SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path);
+SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path, bool bPercID);
extern int
-SymMatrixRead(char *pcFileIn, symmatrix_t **prSymMat_p);
+SymMatrixRead(char *pcFileIn, symmatrix_t **prSymMat_p, mseq_t *prMSeq);
#endif
--- /dev/null
+# symmatrix.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/symmatrix.o'
+
+# Name of the non-PIC object
+non_pic_object='symmatrix.o'
+
********************************************************************/
/*
- * RCS $Id: tree.c 230 2011-04-09 15:37:50Z andreas $
+ * RCS $Id: tree.c 278 2013-05-16 15:53:45Z fabian $
*/
#ifdef HAVE_CONFIG_H
{
int tree_nodeindex = 0;
int order_index = 0;
-
+ int iLeafCount = 0;
+
assert(NULL!=tree);
assert(NULL!=mseq);
assert(IsRooted(tree));
do {
if (IsLeaf(tree_nodeindex, tree)) {
int leafid = GetLeafId(tree_nodeindex, tree);
- if (leafid >= mseq->nseqs)
+ if (leafid >= mseq->nseqs){
Log(&rLog, LOG_FATAL, "Sequence index out of range during tree traversal (leafid=%d nseqs=%d)",
- leafid, mseq->nseqs);
-
+ leafid, mseq->nseqs);
+ }
+ if (NULL != mseq->tree_order){
+ mseq->tree_order[iLeafCount] = leafid;
+ iLeafCount++;
+ }
+
/* this is a leaf node,
* indicate this by registering same leafid for left/right
*/
--- /dev/null
+# tree.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/tree.o'
+
+# Name of the non-PIC object
+non_pic_object='tree.o'
+
--- /dev/null
+# util.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/util.o'
+
+# Name of the non-PIC object
+non_pic_object='util.o'
+
--- /dev/null
+# weights.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/weights.o'
+
+# Name of the non-PIC object
+non_pic_object='weights.o'
+
********************************************************************/
/*
- * RCS $Id: clustalo-api-test.c 213 2011-03-11 16:10:15Z andreas $
+ * RCS $Id: clustalo-api-test.c 280 2013-05-16 16:04:12Z fabian $
*/
#include <stdio.h>
+/* see clustal-omega.c for documentation */
+
/* Include clustal-omega's header. That's all you need
*
* If you developing in C++, use the following instead:
char *pcSeqInfile;
int iAux;
- /* use LOGLEVEL_QUIET to make Clustal shut up */
- iVerbosityLevel = LOGLEVEL_INFO;
+
+ /* Must happen first: setup logger */
+ LogDefaultSetup(&rLog);
SetDefaultAlnOpts(&rAlnOpts);
/* Get sequence input file name from command line
*/
if (argc!=2) {
- Fatal("Need sequence file as argument");
+ Log(&rLog, LOG_FATAL, "Need sequence file as argument");
}
pcSeqInfile = argv[1];
if (ReadSequences(prMSeq, pcSeqInfile,
SEQTYPE_UNKNOWN,
INT_MAX, INT_MAX)) {
- Fatal("Reading sequence file '%s' failed", pcSeqInfile);
+ Log(&rLog, LOG_FATAL, "Reading sequence file '%s' failed", pcSeqInfile);
}
/* Dump some info about the sequences
*/
for (iAux=0; iAux<prMSeq->nseqs; iAux++) {
- Info(LOGLEVEL_INFO,
+ Log(&rLog, LOG_INFO,
"Sequence no %d has the following name: %s",
iAux, prMSeq->sqinfo[iAux].name);
- Info(LOGLEVEL_INFO,
+ Log(&rLog, LOG_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");
+ if (Align(prMSeq, NULL, &rAlnOpts)) {
+ Log(&rLog, LOG_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");
+#define LINE_WRAP 60
+ if (WriteAlignment(prMSeq, NULL, MSAFILE_A2M, LINE_WRAP)) {
+ Log(&rLog, LOG_FATAL, "Could not save alignment");
}
FreeMSeq(&prMSeq);
- Info(LOGLEVEL_INFO, "Successfull program exit");
+ Log(&rLog, LOG_INFO, "Successfull program exit");
return EXIT_SUCCESS;
}
--- /dev/null
+/* 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 */
+#define CLUSTALO 1
+
+/* 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. */
+#define HAVE_ARGTABLE2_H 1
+
+/* Define to 1 if you have the <assert.h> header file. */
+#define HAVE_ASSERT_H 1
+
+/* Define to 1 if you have the <ctype.h> header file. */
+#define HAVE_CTYPE_H 1
+
+/* Define to 1 if you have the <dlfcn.h> header file. */
+#define HAVE_DLFCN_H 1
+
+/* Define to 1 if you have the <float.h> header file. */
+#define HAVE_FLOAT_H 1
+
+/* Define to 1 if you have the `fseek64' function. */
+/* #undef HAVE_FSEEK64 */
+
+/* Define to 1 if you have the `fseeko' function. */
+#define HAVE_FSEEKO 1
+
+/* Define to 1 if you have the `fseeko64' function. */
+#define HAVE_FSEEKO64 1
+
+/* Define to 1 if you have the `ftell64' function. */
+/* #undef HAVE_FTELL64 */
+
+/* Define to 1 if you have the `ftello' function. */
+#define HAVE_FTELLO 1
+
+/* Define to 1 if you have the `ftello64' function. */
+#define HAVE_FTELLO64 1
+
+/* Define to 1 if you have the <inttypes.h> header file. */
+#define HAVE_INTTYPES_H 1
+
+/* Define to 1 if you have the `argtable2' library (-largtable2). */
+#define HAVE_LIBARGTABLE2 1
+
+/* Define to 1 if you have the `m' library (-lm). */
+#define HAVE_LIBM 1
+
+/* Define to 1 if you have the <limits.h> header file. */
+#define HAVE_LIMITS_H 1
+
+/* Has log2() */
+#define HAVE_LOG2 1
+
+/* Define to 1 if you have the <math.h> header file. */
+#define HAVE_MATH_H 1
+
+/* Define to 1 if you have the <memory.h> header file. */
+#define HAVE_MEMORY_H 1
+
+/* Define to 1 if you have the `ntohl' function. */
+#define HAVE_NTOHL 1
+
+/* Define to 1 if you have the `ntohs' function. */
+#define HAVE_NTOHS 1
+
+/* 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 */
+#define HAVE_OPENMP 1
+
+/* Define to 1 if you have the <stdarg.h> header file. */
+#define HAVE_STDARG_H 1
+
+/* Define to 1 if you have the <stdint.h> header file. */
+#define HAVE_STDINT_H 1
+
+/* Define to 1 if you have the <stdio.h> header file. */
+#define HAVE_STDIO_H 1
+
+/* Define to 1 if you have the <stdlib.h> header file. */
+#define HAVE_STDLIB_H 1
+
+/* Define to 1 if you have the <strings.h> header file. */
+#define HAVE_STRINGS_H 1
+
+/* Define to 1 if you have the <string.h> header file. */
+#define HAVE_STRING_H 1
+
+/* Define to 1 if you have the `stroul' function. */
+/* #undef HAVE_STROUL */
+
+/* Define to 1 if you have the `strtoull' function. */
+#define HAVE_STRTOULL 1
+
+/* Define to 1 if you have the <sys/stat.h> header file. */
+#define HAVE_SYS_STAT_H 1
+
+/* Define to 1 if you have the <sys/types.h> header file. */
+#define HAVE_SYS_TYPES_H 1
+
+/* Define to 1 if you have the <time.h> header file. */
+#define HAVE_TIME_H 1
+
+/* Define to 1 if you have the <unistd.h> header file. */
+#define HAVE_UNISTD_H 1
+
+/* This is a LINUX system */
+#define LINUX 1
+
+/* Define to the sub-directory in which libtool stores uninstalled libraries.
+ */
+#define LT_OBJDIR ".libs/"
+
+/* This is a MinGW system */
+/* #undef MINGW */
+
+/* No-debug Mode */
+#define NDEBUG /**/
+
+/* Some strange OS */
+/* #undef OTHEROS */
+
+/* Name of package */
+#define PACKAGE "clustal-omega"
+
+/* Define to the address where bug reports for this package should be sent. */
+#define PACKAGE_BUGREPORT "clustalw@ucd.ie"
+
+/* The package code name */
+#define PACKAGE_CODENAME "AndreaGiacomo"
+
+/* Define to the full name of this package. */
+#define PACKAGE_NAME "Clustal Omega"
+
+/* Define to the full name and version of this package. */
+#define PACKAGE_STRING "Clustal Omega 1.2.4"
+
+/* Define to the one symbol short name of this package. */
+#define PACKAGE_TARNAME "clustal-omega"
+
+/* Define to the version of this package. */
+#define PACKAGE_VERSION "1.2.4"
+
+/* The size of `fpos_t', as computed by sizeof. */
+#define SIZEOF_FPOS_T 16
+
+/* The size of `unsigned int', as computed by sizeof. */
+#define SIZEOF_UNSIGNED_INT 4
+
+/* The size of `unsigned long', as computed by sizeof. */
+#define SIZEOF_UNSIGNED_LONG 8
+
+/* The size of `unsigned long long', as computed by sizeof. */
+#define SIZEOF_UNSIGNED_LONG_LONG 8
+
+/* The size of `unsigned short', as computed by sizeof. */
+#define SIZEOF_UNSIGNED_SHORT 2
+
+/* 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. */
+#define STDC_HEADERS 1
+
+/* 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 */
+#define VERSION "1.2.4"
+
+/* 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 */
--- /dev/null
+hhalign.lo: hhalign.cpp \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
+ /usr/include/bits/wordsize.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/wchar.h /usr/include/xlocale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
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+ /usr/include/bits/typesizes.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
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+ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \
+ /usr/include/bits/sched.h /usr/include/bits/time.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \
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+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/sys/types.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/sys/sysmacros.h /usr/include/alloca.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
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+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h /usr/include/bits/xopen_lim.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h general.h \
+ ../clustal/log.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h util-C.h \
+ /usr/include/sys/time.h ../config.h list-C.h list.h hash-C.h hash.h \
+ hhdecl-C.h hhutil-C.h hhmatrices-C.h hhhmm.h hhhit.h hhalignment.h \
+ hhhalfalignment.h hhfullalignment.h hhhitlist.h hhhmm-C.h \
+ hhalignment-C.h ../../src/config.h hhhit-C.h hhhalfalignment-C.h \
+ hhfullalignment-C.h hhhitlist-C.h hhfunc-C.h
+
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+/usr/include/wchar.h:
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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new:
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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream:
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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc:
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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h:
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+/usr/include/libio.h:
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+/usr/include/bits/stdio_lim.h:
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+/usr/include/bits/sys_errlist.h:
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+/usr/include/bits/stdio.h:
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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h:
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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc:
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+/usr/include/string.h:
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+/usr/include/bits/waitstatus.h:
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+/usr/include/sys/types.h:
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+/usr/include/bits/select.h:
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+/usr/include/bits/sigset.h:
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+/usr/include/sys/sysmacros.h:
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+/usr/include/alloca.h:
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+/usr/include/math.h:
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+/usr/include/bits/huge_val.h:
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+/usr/include/bits/huge_valf.h:
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+/usr/include/bits/huge_vall.h:
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+/usr/include/bits/inf.h:
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+/usr/include/bits/mathdef.h:
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+/usr/include/bits/mathcalls.h:
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+/usr/include/bits/mathinline.h:
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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h:
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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h:
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+/usr/include/limits.h:
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+/usr/include/bits/local_lim.h:
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+/usr/include/linux/limits.h:
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+/usr/include/bits/xopen_lim.h:
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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h:
+
+general.h:
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+../clustal/log.h:
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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h:
+
+util-C.h:
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+/usr/include/sys/time.h:
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+../config.h:
+
+list-C.h:
+
+list.h:
+
+hash-C.h:
+
+hash.h:
+
+hhdecl-C.h:
+
+hhutil-C.h:
+
+hhmatrices-C.h:
+
+hhhmm.h:
+
+hhhit.h:
+
+hhalignment.h:
+
+hhhalfalignment.h:
+
+hhfullalignment.h:
+
+hhhitlist.h:
+
+hhhmm-C.h:
+
+hhalignment-C.h:
+
+../../src/config.h:
+
+hhhit-C.h:
+
+hhhalfalignment-C.h:
+
+hhfullalignment-C.h:
+
+hhhitlist-C.h:
+
+hhfunc-C.h:
--- /dev/null
+# libhhalign.la - a libtool library file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# The name that we can dlopen(3).
+dlname=''
+
+# Names of this library.
+library_names=''
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********************************************************************/
/*
- * RCS $Id: general.h 247 2011-06-16 11:41:15Z fabian $
+ * RCS $Id: general.h 290 2013-09-20 15:18:12Z fabian $
*/
#include "../clustal/log.h"
+#include <stdbool.h>
/*
***** Omega definitions************************************
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
+enum {CALL_FROM_DONT_KNOW = -1, CALL_FROM_ALN_HMM, CALL_FROM_REGULAR};
/*#define MIN(a,b) ((a)<(b)?(a):(b))*/
typedef struct {
int iMacRamMB; /* dedicated amount of RAM for Maximum Accuracy (in MB) */
+ bool bIsDna; /* indicates we're in nucleotide mode */
+ bool bIsRna; /* indicates we're in nucleotide mode */
+ double pca;
+ double pcb;
+ double pcc;
+ double pcw;
+ double gapb;
+ double gapd;
+ double gape;
+ double gapf;
+ double gapg;
+ double gaph;
+ double gapi;
+ double pcaV;
+ double pcbV;
+ double pccV;
+ double pcwV;
+ double gapbV;
+ double gapdV;
+ double gapeV;
+ double gapfV;
+ double gapgV;
+ double gaphV;
+ double gapiV;
} hhalign_para;
+/* 'scores' passed out from hhalign */
+typedef struct{
+
+ double forwardProb;
+ double backwardProb;
+ double hhScore;
+ double sumPP;
+ double *PP;
+ int L;
+
+} hhalign_scores;
+
+
typedef struct {
/***public***/
int n_display;
********************************************************************/
/*
- * RCS $Id: hash-C.h 143 2010-10-14 13:11:14Z andreas $
+ * RCS $Id: hash-C.h 309 2016-06-13 14:10:11Z fabian $
*/
// hash.C
// * 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 $
+ * RCS $Id: hash-C.h 309 2016-06-13 14:10:11Z fabian $
*/
#ifndef HASH
#endif
#include "hash.h"
-
+//#include "new_new.h" /* memory tracking */
//////////////////////////////////////////////////////////////////////////////
********************************************************************/
/*
- * RCS $Id: hhalign.cpp 250 2011-06-17 13:06:20Z fabian $
+ * RCS $Id: hhalign.cpp 309 2016-06-13 14:10:11Z fabian $
*/
/* hhalign.C:
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() */
-
-
-
-
+bool nucleomode = false;
////////////////////////////////////////////////////////////////////////////
// Help functions
* @param[in] rHhalignPara,
* various parameters passed down from commandline
* e.g., iMaxRamMB
+ * @param[out] rHHscores
+ * qualify goodness of alignment
*
* iFlag,zcAux,zcError are debugging arguments
*
extern "C" int
hhalign(char **ppcFirstProf, int iFirstCnt, double *pdWeightsL,
char **ppcSecndProf, int iSecndCnt, double *pdWeightsR,
- double *dScore_p, hmm_light *prHMM,
+ double *dScore_p, hmm_light *prHMM, hmm_light *prHMM2,
char *pcPrealigned1, char *pcRepresent1,
char *pcPrealigned2, char *pcRepresent2,
- hhalign_para rHhalignPara,
- int iFlag,
+ hhalign_para rHhalignPara, hhalign_scores *rHHscores,
+ int iFlag, int iVerbosity,
char zcAux[], char zcError[]) {
int Nali; /* number of normally backtraced alignments
in dot plot */
- SetDefaults();
+ SetDefaults(rHhalignPara);
strcpy(par.tfile,""); /* FS, Initialise Argument */
strcpy(par.alnfile,"");
par.p=0.0 ; /* minimum threshold for inclusion in hit list
// Set (global variable) substitution matrix and derived matrices
- SetSubstitutionMatrix();
-
+ // DD: new experimental matrices and params for nucleotides
+ if(rHhalignPara.bIsDna)
+ {
+ nucleomode = true;
+ SetDnaDefaults(rHhalignPara);
+ SetDnaSubstitutionMatrix();
+ }
+ else if(rHhalignPara.bIsRna)
+ {
+ nucleomode = true;
+ SetRnaDefaults(rHhalignPara);
+ SetRnaSubstitutionMatrix();
+ }
+ else
+ SetSubstitutionMatrix();
// Set secondary structure substitution matrix
SetSecStrucSubstitutionMatrix();
tL = strlen(ppcSecndProf[0]);
}
else {
- tL = prHMM->L;
+ tL = prHMM2->L;
}
// longest allowable length of database HMM
int Lmaxmem=(int)((float)MEMSPACE_DYNPROG/qL/6/8);
if (par.forward==2 && tL+2>=Lmaxmem) {
+ sprintf(zcError, "%s:%s:%d: switch to Viterbi (qL=%d, tL=%d, MAC-RAM=%d\n)",
+ __FUNCTION__, __FILE__, __LINE__, qL, tL, rHhalignPara.iMacRamMB);
if (v>=1)
cerr<<"WARNING: Not sufficient memory to realign with MAC algorithm. Using Viterbi algorithm."<<endl;
par.forward=0;
}
-
// Read input file (HMM, HHM, or alignment format), and add pseudocounts etc.
q.cQT = 'q';
if (OK != ReadAndPrepare(INTERN_ALN_2_HMM,
and add pseudocounts etc. */
t.cQT = 't';
if (OK != ReadAndPrepare(INTERN_ALN_2_HMM,
- ppcSecndProf, iSecndCnt, prHMM,
+ ppcSecndProf, iSecndCnt, prHMM2,
pcPrealigned2, pcRepresent2, pdWeightsR,
infile, t)) {
sprintf(zcError, "%s:%s:%d: Problem Reading/Preparing t-profile (len=%d)\n",
// Factor Null model into HMM t
t.IncludeNullModelInHMM(q,t);
+ /* alignment will fail if one profile does not contain useful characters, FS, r259 -> r260 */
+ if ( (q.L <= 0) || (t.L <= 0) ){
+ sprintf(zcError, "%s:%s:%d: Problem Reading/Preparing profiles (len(q)=%d/len(t)=%d)\n",
+ __FUNCTION__, __FILE__, __LINE__, q.L, t.L);
+ iRetVal = RETURN_FROM_RNP;
+ goto this_is_the_end;
+ }
+
/* switch at this stage is ineffectual as log/lin already decided in RnP().
FS, r228 -> r229 */
/*const float MEMSPACE_DYNPROG = 512*1024*1024;
/* 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");
- }
+ 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");
}
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;
}
int iPrAliRtn = hitlist.PrintAlignments(
#ifdef CLUSTALO
- ppcFirstProf, ppcSecndProf,
+ ppcFirstProf, ppcSecndProf, zcAux, zcError,
#endif
q, par.pairwisealisfile, par.outformat);
- if (OK != iPrAliRtn){
- fprintf(stderr, "%s:%s:%d: Could not print alignments\n",
+ if ( (OK != iPrAliRtn) ){
+ sprintf(zcAux, "%s:%s:%d: Could not print alignments\n",
__FUNCTION__, __FILE__, __LINE__);
+ strcat(zcError, zcAux);
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;
hitlist.PrintHitList(q, par.outfile);
hitlist.PrintAlignments(
#ifdef CLUSTALO
- ppcFirstProf, ppcSecndProf,
+ ppcFirstProf, ppcSecndProf, zcAux, zcError,
#endif
q, par.outfile);
if (v>=2) {
q.name,t.name,par.hitrank,hit.score,hit.Pval);
}
-
+ rHHscores->hhScore = hit.score;
+ rHHscores->forwardProb = hit.Pforward;
+ rHHscores->sumPP = hit.sum_of_probs;
+
+ /* next few lines commented out as they caused segfaults in RNA mode */
+ /* rHHscores->PP = (double *)malloc((hit.L+GOOD_MEASURE) * sizeof(double));*/
+ rHHscores->L = hit.L;
+/* for (int i = 0; i < hit.L; i++){
+ cout << "rHHscores->PP[i]" << rHHscores->PP[i] << endl;
+ cout << "hit.P_posterior[i+1]" << hit.P_posterior[i+1] << endl;
+ rHHscores->PP[i] = hit.P_posterior[i+1];
+ } */
+
+
this_is_the_end:
// Delete memory for dynamic programming matrix
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++){
t.ClobberGlobal();
}
hitlist.ClobberGlobal();
-
+
return iRetVal;
} /* this is the end of hhalign() //end main */
********************************************************************/
/*
- * RCS $Id: hhalign.h 241 2011-05-04 14:37:17Z fabian $
+ * RCS $Id: hhalign.h 296 2014-10-07 12:15:41Z fabian $
*/
extern int
hhalign(char **ppcFirstProf, int iFirstCnt, double *pdWeightsL,
char **ppcSecndProf, int iSecndCnt, double *pdWeightsR,
- double *dScore_p, hmm_light *prHMM,
+ double *dScore_p, hmm_light *prHMM, hmm_light *prHMM2,
char *pcPrealigned1, char *pcRepresent1,
char *pcPrealigned2, char *pcRepresent2,
- hhalign_para rHhalignPara,
- int iFlag,
+ hhalign_para rHhalignPara, hhalign_scores *rHHscores,
+ int iFlag, int iVerbosity,
char zcAux[], char zcError[]);
--- /dev/null
+# hhalign.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/hhalign.o'
+
+# Name of the non-PIC object
+non_pic_object='hhalign.o'
+
********************************************************************/
/*
- * RCS $Id: hhalignment-C.h 236 2011-04-14 11:30:04Z fabian $
+ * RCS $Id: hhalignment-C.h 316 2016-12-16 16:14:39Z fabian $
*/
#include "hhhmm.h"
#endif
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+//#include "new_new.h" /* memory tracking */
+
enum {KEEP_NOT = 0, KEEP_CONDITIONALLY, KEEP_ALWAYS};
//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 */
+ 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
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_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;
}
// Create space for residues and paste new sequence in
- seq[k]=new(char[strlen(cur_seq)+2]);
+ seq[k]=new char[strlen(cur_seq)+2];
if (!seq[k]) MemoryError("array for input sequences");
- X[k]=new(char[strlen(cur_seq)+2]);
+ 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]);
+ I[k]=new short unsigned int[strlen(cur_seq)+2];
if (!I[k]) MemoryError("array for input sequences");
strcpy(seq[k],cur_seq);
}
// 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]);
+ 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)
if (k>=0) //if at least one sequence was read in
{
- seq[k]=new(char[strlen(cur_seq)+2]);
+ seq[k]=new char[strlen(cur_seq)+2];
if (!seq[k]) MemoryError("array for input sequences");
- X[k]=new(char[strlen(cur_seq)+2]);
+ 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]);
+ I[k]=new short unsigned int[strlen(cur_seq)+2];
if (!I[k]) MemoryError("array for input sequences");
strcpy(seq[k],cur_seq);
}
/*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 */
+ 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 */
i--;
if (L!=i && L!=/*MAXRES*/par.maxResLen-2 && !unequal_lengths) unequal_lengths=k; //sequences have different lengths
L=imin(L,i);
- }
+ } // end for (k)
if (unequal_lengths) break;
//Replace GAP with ENDGAP for all end gaps /* MR1 */
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]);
+ 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]);
+ if (nres==NULL) nres=new int[N_in];
+#if 0
+//#ifdef HAVE_OPENMP
+#pragma omp parallel for schedule(static), private(l)
+#endif
for (k=0; k<N_in; k++)
{
if (!keep[k]) continue;
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)
+#if 0
+//#ifdef HAVE_OPENMP
+#pragma omp parallel for schedule(static)
+#endif
for (k=0; k<N_in; k++)
if (keep[k] && (X[k][l]<20) )
{
}
// Add up percentage of gaps
+#if 0
+//#ifdef HAVE_OPENMP
+#pragma omp parallel for schedule(static) private(k)
+#endif
for (l=1; l<=L; l++)
{
float res=0;
}
i++;
this->l[i]=l;
+#if 0
+//#ifdef HAVE_OPENMP
+#pragma omp parallel for schedule(static)
+#endif
for (k=0; k<N_in; k++)
{
if (keep[k])
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]);
+ match_state = new char[par.maxColCnt];
// Determine number of columns L in alignment
L=strlen(seq[0]+1);
if (par.mark) return n_display;
- char *dummy = new(char[N_in+1]);
+ char *dummy = new char[N_in+1];
int vtmp=v, seqid;
v=0;
n_display=0;
{
// 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
+ 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 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
+ 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;
}
// Determine number of residues nres[k]?
- if ( (nres==NULL) || (sizeof(nres)<N_in*sizeof(int)) )
+ // KB: memory leak as sizeof(nres) just gives the size of an int pointer
+ //if ( (nres==NULL) || (sizeof(nres)<N_in*sizeof(int)) )
+ if (nres==NULL)
{
- nres=new(int[N_in]);
+ 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;
// 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
+ 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
}
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]));
- }
+ } // end for (k)
if (seqid1>seqid2)
{
// printf("\n");
// Loop over all candidate sequences kk (-> k)
+#if 0
+//#ifdef HAVE_OPENMP
+#pragma omp parallel for schedule(static) private(k, i, diff_min_frac, jj, j, first_kj, last_kj, cov_kj, diff_suff, diff)
+#endif
for (kk=0; kk<N_in; kk++)
{
if (inkk[kk]) continue; // seq k already accepted
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;}
+// if (seqid>=100) {in[k]=inkk[kk]=1; n++; continue;}
+ if (seqid>=100) {
+ in[k]=inkk[kk]=1;
+#if 0
+//#ifdef HAVE_OPENMP
+#pragma omp atomic
+#endif
+ n++;
+ continue;
+ }
float seqidk=seqid1;
for (i=first[k]; i<=last[k]; i++)
if (idmaxwin[i]>seqidk) seqidk=idmaxwin[i];
if (jj>=kk) // did loop reach end? => accept k. Otherwise reject k (the shorter of the two)
{
in[k]=inkk[kk]=1;
+#if 0
+//#ifdef HAVE_OPENMP
+#pragma omp atomic
+#endif
n++;
- for (i=first[k]; i<=last[k]; i++) N[i]++; // update number of sequences at position i
+ for (i=first[k]; i<=last[k]; i++) {
+#if 0
+//#ifdef HAVE_OPENMP
+#pragma omp atomic
+#endif
+ N[i]++; // update number of sequences at position i
+ }
// printf("%i %20.20s accepted\n",k,sname[k]);
}
// else
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)
+ 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 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
+ 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
// 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
+ 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;
// Determine number of residues nres[k]?
if (nres==NULL)
{
- nres=new(int[N_in]);
+ 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 (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 0
+//#ifdef HAVE_OPENMP
if(par.wg != 1)
{
#pragma omp parallel sections
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]);
+ 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]);
+ 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]);
+ 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
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]);
+ 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]);
+ 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]);
}
//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
+ 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]);
+ wi = new float[N_in+2];
// Global weights?
if (par.wg==1)
- for (k=0; k<N_in; k++) wi[k]=wg[k];
+ 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;
+ n = new int*[L+2];
+//#if 0
+#ifdef HAVE_OPENMP
+#pragma omp parallel for schedule(static) private(a)
+#endif
+ for (j=1; j<=L; j++) {
+ n[j]=new(int[NAA+3]);
+ 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];
- }
- }
+ {
+ 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++;
+//#if 0
+#ifdef HAVE_OPENMP
+#pragma omp parallel for schedule(static)
+#endif
+ 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--;
+//#if 0
+#ifdef HAVE_OPENMP
+#pragma omp parallel for schedule(static)
+#endif
+ 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
+//#if 0
+#ifdef HAVE_OPENMP
+#pragma omp parallel for schedule(static) private(naa, a, k)
+#endif
+ 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;
+//#if 0
+#ifdef HAVE_OPENMP
+#pragma omp atomic
+#endif
+ 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]);}
+//#if 0
+#ifdef HAVE_OPENMP
+#pragma omp atomic
+#endif
+ wi[k]+=1.0/float(n[j][ (int)X[k][j] ]*naa);
+ }
+ }
+ } // end for (j)
+
+ // 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;
+//#if 0
+#ifdef HAVE_OPENMP
+#pragma omp parallel for schedule(static) private(a, k, fj)
+#endif
+ 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)
+//#if 0
+#ifdef HAVE_OPENMP
+#pragma omp atomic
+#endif
+ Neff[i]-=fj[a]*fast_log2(fj[a]);
+ }
+ if (ncol>0)
+ Neff[i]=pow(2.0,Neff[i]/ncol);
+ else
+ Neff[i]=1.0;
+ } // end change
+
+ else //no update was necessary; copy values for i-1
+ {
+ Neff[i]=Neff[i-1];
+ }
+ } // end par.wg==0
// 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];
+ 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)
+ {
+ 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);
+ 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
+ // 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[j]);
+ (n[j]) = NULL;
}
delete[](n); (n) = NULL;
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];
+ 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)
- {
+ {
+//#if 0
+#ifdef HAVE_OPENMP
+#pragma omp parallel for schedule(static) private(a)
+#endif
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);
- }
+ {
+ 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]);
+//#if 0
+#ifdef HAVE_OPENMP
+#pragma omp atomic
+#endif
+ 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
+ float scale=Log2((Nlim-q.Neff_HMM)/(Nlim-1.0)); // for calculating Neff for those seqs with inserts at specific pos
+//#if 0
+#ifdef HAVE_OPENMP
+#pragma omp parallel for schedule(static) private(k)
+#endif
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]);
- }
- }
+ {
+ 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+=Neff[i];
+ q.Neff_M[i]=Neff[i];
+ if (q.Neff_M[i] == 0) {
+ q.Neff_M[i] = 1;
+ } /* MR1 */
+ }
q.Neff_HMM/=L;
- }
+ } // end par.wg==1
delete[] Neff; Neff = NULL;
//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
+ 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 Nlim=0.0; // only for global weights
float scale=0.0; // only for global weights
- wi = new(float[N_in+2]);
+ 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
+ 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]);
+ n = new int*[L+2];
for (j=1; j<=L; j++) n[j]=new(int[NAA+3]);
//////////////////////////////////////////////////////////////////////////////////////////////
// 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);
+ 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
//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
+ 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 Nlim=0.0; // only for global weights
float scale=0.0; // only for global weights
- wi = new(float[N_in+2]); /* FIXME: FS */
+ 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];
+ 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
+ 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;
-
-
+ n = new int*[L+2];
+//#if 0
+#ifdef HAVE_OPENMP
+#pragma omp parallel for schedule(static) private(a)
+#endif
+ for (j=1; j<=L; j++) {
+ n[j]=new(int[NAA+3]);
+ 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
{
- 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++;
+//#if 0
+#ifdef HAVE_OPENMP
+#pragma omp parallel for schedule(static)
+#endif
+ 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--;
+//#if 0
+#ifdef HAVE_OPENMP
+#pragma omp parallel for schedule(static)
+#endif
+ 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
+//#if 0
+#ifdef HAVE_OPENMP
+#pragma omp parallel for schedule(static) private(naa, a, k)
+#endif
+ for (j=1; j<=L; j++)
{
- change=0;
- // Check all sequences k and update n[j][a] and ri[j] if necessary
+ if (n[j][ENDGAP]>MAXENDGAPFRAC*nseqi) continue;
+ naa=0;
+ for (a=0; a<20; a++)
+ if(n[j][a])
+ naa++;
+ if (naa==0) continue;
+//#if 0
+#ifdef HAVE_OPENMP
+#pragma omp atomic
+#endif
+ ncol++;
for (k=0; k<N_in; k++)
+ {
+ if (in[k] && X[k][i]==GAP && X[k][j]<ANY)
{
- 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 (!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]);}
+//#if 0
+#ifdef HAVE_OPENMP
+#pragma omp atomic
+#endif
+ wi[k]+=1.0/float(n[j][ (int)X[k][j] ]*naa);
}
+ }
+ } // end for (j)
+ // 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;
+//#if 0
+#ifdef HAVE_OPENMP
+#pragma omp parallel for schedule(static) private(a, k, fj)
+#endif
+ 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)
+//#if 0
+#ifdef HAVE_OPENMP
+#pragma omp atomic
+#endif
+ Neff[i]-=fj[a]*fast_log2(fj[a]);
+ }
+ if (ncol>0) Neff[i]=pow(2.0,Neff[i]/ncol); else Neff[i]=1.0;
- // 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];
- }
+ 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)
+ // 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?
+ 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
{
- 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;
- }
+ 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);
+ // 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.Neff_D[0]=99.999;
// Assign Neff_D[i]
- for (i=1; i<=L; 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[i]);
+ (n[i]) = NULL;
}
+
delete[](n); (n) = NULL;
+ delete[](wi); wi = NULL;/* FIXME: FS */
delete[] Neff; Neff = NULL;
return;
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* imatch=new int[hit.j2+1];
int step = hit.nsteps;
for (j=hit.j1; j<=hit.j2; j++)
{
iprev=i; lprev=l;
if (h>=maxcol-1000) // too few columns? Reserve double space
{
- char* new_seq=new(char[2*maxcol]);
+ 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;
cur_seq[h++]='\0';
keep[N_in] = display[N_in] = KEEP_CONDITIONALLY;
- seq[N_in]=new(char[h]);
+ 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]);
+ X[N_in]=new char[h];
if (!X[N_in]) MemoryError("array for input sequences");
- I[N_in]=new(short unsigned int[h]);
+ 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]);
+ 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++;
{
int i; // position in query and target
if (L<=0) InternalError("L is not set in AddSequence()");
- X[N_in]=new(char[L+2]);
+ 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;
{
// Initialization
- n = new(int*[L+2]);
+ 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;
/* @<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]);
+ 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]){
********************************************************************/
/*
- * RCS $Id: hhfullalignment-C.h 243 2011-05-31 13:49:19Z fabian $
+ * RCS $Id: hhfullalignment-C.h 315 2016-12-15 17:18:30Z fabian $
*/
// hhfullalignment.C
#include "hhhit.h"
#include "hhhalfalignment.h"
#endif
+//#include "new_new.h" /* memory tracking */
* @brief Build full alignment -> qa->s[k][h] and ta->s[k][h]
*/
int
-FullAlignment::Build(HMM& q, Hit& hit)
+FullAlignment::Build(HMM& q, Hit& hit, char zcError[])
{
int step;
char prev_state=MM, state=MM;
}
}
else {
- fprintf(stderr,
+ sprintf(zcError,
"+-------------------------------+\n"
"| both sequences truncated left |\n"
"+-------------------------------+\n"
}
}
else{
- fprintf(stderr,
+ sprintf(zcError,
"+--------------------------------+\n"
"| both sequences truncated right |\n"
"+--------------------------------+\n"
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]);
+ 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];
********************************************************************/
/*
- * RCS $Id: hhfullalignment.h 243 2011-05-31 13:49:19Z fabian $
+ * RCS $Id: hhfullalignment.h 284 2013-06-12 10:10:11Z fabian $
*/
//////////////////////////////////////////////////////////////////////////////
FullAlignment(int maxseqdis=MAXSEQDIS);
~FullAlignment();
void FreeMemory();
- int Build(HMM& q, Hit& hit);
+ int Build(HMM& q, Hit& hit, char zcError[]);
void PrintHeader(FILE* outf, HMM& q, Hit& hit);
void PrintHHR(FILE* outf, Hit& hit);
void PrintA2M(FILE* outf, Hit& hit);
********************************************************************/
/*
- * RCS $Id: hhfunc-C.h 256 2011-06-23 13:57:28Z fabian $
+ * RCS $Id: hhfunc-C.h 309 2016-06-13 14:10:11Z fabian $
*/
/*
// hhfunc.C
+//#include "new_new.h" /* memory tracking */
/**
* AddBackgroundFrequencies()
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 */
+ //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 / 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 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",
*
* @param[in] iRnPtype
* type of read/prepare
- * enum {INTERN_ALN_2_HMM = 0, READ_ALN_2_HMM, READ_HMM_2_HMM};
+ * enum {INTERN_ALN_2_HMM = 0, READ_ALN_2_HMM, READ_HMM_2_HMM, INTERN_HMM_2_HMM};
* @param[in] ppcProf
* alignment
* @param[in] iCnt
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];
cout<<"WARNING! Use of HMMER3 format as input results in dramatically loss of sensitivity!\n";
}
- // Read 'query HMMER file
+ // Read 'query HMMER file
rewind(inf);
q.ReadHMMer3(inf,path);
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;
*
*/
extern "C" int
-AlnToHMM2(hmm_light *rHMM_p,
- char **ppcSeq, int iN){
-
+AlnToHMM2(hmm_light *rHMM_p, hhalign_para rHhalignPara,
+ char **ppcSeq, int iN){
if (0 == par.M){
- SetDefaults();
+ SetDefaults(rHhalignPara);
SetSubstitutionMatrix();
par.cons = 1;
par.M = 2;
} /* (0 <= iA < AMINOACIDS) */
rHMM_p->seq[rHMM_p->ncons][i] = i2aa(iAmax);
} /* (0 <= i < rHMM_p->L) */
-
+ rHMM_p->seq[rHMM_p->ncons][i] = '\0'; /* FS, r291 -> */
} /* ncons not set */
********************************************************************/
/*
- * RCS $Id: hhfunc.h 143 2010-10-14 13:11:14Z andreas $
+ * RCS $Id: hhfunc.h 290 2013-09-20 15:18:12Z fabian $
*/
int readHMMWrapper(hmm_light *rHMM_p,
char *pcHMM_input);
void FreeHMMstruct(hmm_light *prHMM);
-int AlnToHMM2(hmm_light *rHMM_p,
+int AlnToHMM2(hmm_light *rHMM_p, hhalign_para rHhalignPara,
char **ppcSeq, int iN);
int HHMake_Wrapper(char *tmp_aln, char *hmm_out);
********************************************************************/
/*
- * RCS $Id: hhhalfalignment-C.h 227 2011-03-28 17:03:09Z fabian $
+ * RCS $Id: hhhalfalignment-C.h 315 2016-12-15 17:18:30Z fabian $
*/
// hhfullalignment.C
#include "hhalignment.h" // class Alignment
#include "hhhit.h"
#endif
+//#include "new_new.h" /* memory tracking */
/////////////////////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////////////////////
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]
+ 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]
}
/////////////////////////////////////////////////////////////////////////////////////
********************************************************************/
/*
- * RCS $Id: hhhit-C.h 245 2011-06-15 12:38:53Z fabian $
+ * RCS $Id: hhhit-C.h 316 2016-12-16 16:14:39Z fabian $
*/
// hhhit.C
#include "hhalignment.h" // class Alignment
#include "hhhitlist.h" // class HitList
#endif
+//#include "new_new.h" /* memory tracking */
#define CALCULATE_MAX6(max, var1, var2, var3, var4, var5, var6, varb) \
if (var1>var2) { max=var1; varb=STOP;} \
delete[] dbfile; dbfile = NULL;
for (int k=0; k<n_display; k++)
{
- //delete[] sname[k]; sname[k] = NULL;
+ delete[] sname[k]; sname[k] = NULL; /* this seems to be the long lost piece of memory, FS, 2016-06-09 */
delete[] seq[k]; seq[k] = NULL;
}
- //delete[] sname; sname = NULL;
+ delete[] sname; sname = NULL; /* this seems to be the long lost piece of memory, FS, 2016-06-09 */
delete[] seq; seq = NULL;
}
}
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]);
+ 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]);
+ 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);
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;
+
+ if (NULL != bMM){ /* FS, r259 -> r260 */
+ 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;
+ }
}
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?
+ 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]);
+ 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);
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;
+
+ if (NULL != F_MM){ /* FS, r259 -> r260 */
+ 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;
}
- 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;
}
/////////////////////////////////////////////////////////////////////////////////////
void
Hit::AllocateBackwardMatrix(int Nq, int Nt)
{
- B_MM=new(double*[Nq]);
+ 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]);
+ 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);
void Hit::DeleteBackwardMatrix(int Nq)
{
- for (int i=0; i<Nq; i++)
- {
- delete[] B_MM[i]; B_MM[i] = NULL; /* is this all? FS */
+
+ if (NULL != B_MM){ /* FS, r259 -> r260 */
+ 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;
}
- delete[] B_MM; B_MM = NULL;
- B_MM=B_MI=B_IM=B_DG=B_GD=NULL;
}
//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;
+ 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=0,j=0; //query and template match state indices
+ float sMM_i_j=0, sMI_i_j=0, sIM_i_j=0, sGD_i_j=0, sDG_i_j=0;
+ float sMM_i_1_j_1=0, sMI_i_1_j_1=0, sIM_i_1_j_1=0, sGD_i_1_j_1=0, sDG_i_1_j_1=0;
+ int jmin=0, jmax=0;
// Reset crossed out cells?
if(irep==1) InitializeForAlignment(q,t);
}
// Calculate log2(P_forward)
- score = log2(Pforward)-10.0f;
- for (i=1; i<=q.L+1; i++) score -= log2(scale[i]);
+ score = Log2(Pforward)-10.0f;
+ for (i=1; i<=q.L+1; i++) score -= Log2(scale[i]);
// state = MM;
if (par.loc)
__FUNCTION__, __FILE__, __LINE__, score, Pforward);
return FAILURE;
}
+ /* alignment might fail if no useful characters in sequence, FS, r259 -> r260 */
+ if ( (q.L <= 0) || (t.L <= 0) ){
+ fprintf(stderr, "%s:%s:%d: length(s) of profile(s) invalid (q.L=%d/t.L=%d)\n",
+ __FUNCTION__, __FILE__, __LINE__, q.L, t.L);
+ 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",
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 (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,
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]);
+ double* scale_cum = new double[q.L+2];
scale_cum[0]=1;
else
{
// float sumF[q.L+t.L];
- double* sumF=new(double[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];;
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 (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,
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 (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,
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;
- }
+ 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");
+ }
- 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;
-}
+ 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;
+} /* this is the end of Hit::InitializeBacktrace() */
/////////////////////////////////////////////////////////////////////////////////////
// Some score functions
********************************************************************/
/*
- * RCS $Id: hhhitlist-C.h 243 2011-05-31 13:49:19Z fabian $
+ * RCS $Id: hhhitlist-C.h 315 2016-12-15 17:18:30Z fabian $
*/
// hhhitlist.C
#include "hhhalfalignment.h"
#include "hhfullalignment.h"
#endif
+//#include "new_new.h" /* memory tracking */
//////////////////////////////////////////////////////////////////////////////
#ifdef CLUSTALO
- char **ppcFirstProf, char **ppcSecndProf,
+ char **ppcFirstProf, char **ppcSecndProf, char zcAux[], char zcError[],
#endif
HMM& q, char* outfile, char outformat)
{
nhits++;
// Build double alignment of query against template sequences
- int iBuildRet = qt_ali.Build(q,hit);
+ int iBuildRet = qt_ali.Build(q,hit, zcError);
if (iBuildRet != OK){ /* FS, r241 -> r243 */
- fprintf(stderr, "%s:%s:%d: qt_ali.Build failed\n",
+ sprintf(zcAux, "%s:%s:%d: qt_ali.Build failed\n",
__FUNCTION__, __FILE__, __LINE__);
+ strcat(zcError, zcAux);
return FAILURE;
}
index.Add(name,k);
}
// Read symmetric Z-scores matrix
- Z = new(float*[N]);
+ Z = new float*[N];
for (k=0; k<N; k++)
{
- Z[k] = new(float[N]);
+ 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]);
+ C = new float*[N];
for (k=0; k<N; k++)
{
- C[k] = new(float[N]);
+ 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]);
+ 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");
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]);
+ 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]);
+ 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]]);
}
else
{
// Generate submatrix of C for indices l for which Z_lq,Z_lk > Zmin_trans
- double** Csub = new(double*[M]);
+ double** Csub = new double*[M];
for (m=0; m<M; m++)
{
- Csub[m] = new(double[M]);
+ Csub[m] = new double[M];
for (n=0; n<M; n++)
Csub[m][n] = double(C[ll[m]][ll[n]]);
}
else
{
- double** Cinv = new(double*[M]);
- for (m=0; m<M; m++) Cinv[m] = new(double[M]);
+ double** Cinv = new double*[M];
+ for (m=0; m<M; m++) Cinv[m] = new double[M];
// Invert Csub
InvertMatrix(Cinv,Csub,M);
index.Add(name,k);
}
// Read symmetric Z-scores matrix
- Z = new(float*[N]);
+ Z = new float*[N];
for (k=0; k<N; k++)
{
- Z[k] = new(float[N]);
+ 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]);
+ C = new float*[N];
for (k=0; k<N; k++)
{
- C[k] = new(float[N]);
+ 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]);
+ 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");
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]);
+ 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]);
+ 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]]);
}
else
{
// Generate submatrix of C for indices l for which Z_lq,Z_lk > Zmin_trans
- double** Csub = new(double*[M]);
+ double** Csub = new double*[M];
for (m=0; m<M; m++)
{
- Csub[m] = new(double[M]);
+ Csub[m] = new double[M];
for (n=0; n<M; n++)
Csub[m][n] = double(C[ll[m]][ll[n]]);
}
else
{
- double** Cinv = new(double*[M]);
- for (m=0; m<M; m++) Cinv[m] = new(double[M]);
+ double** Cinv = new double*[M];
+ for (m=0; m<M; m++) Cinv[m] = new double[M];
// // Invert Csub
// InvertMatrix(Cinv,Csub,M);
index.Add(name,k);
}
// Read symmetric Z-scores matrix
- Z = new(float*[N]);
+ Z = new float*[N];
for (k=0; k<N; k++)
{
- Z[k] = new(float[N]);
+ 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]);
+ C = new float*[N];
for (k=0; k<N; k++)
{
- C[k] = new(float[N]);
+ 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]);
+ 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");
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]);
+ 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]);
+ 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]]);
}
else
{
// Generate submatrix of C for indices l for which Z_lq,Z_lk > Zmin_trans
- double** Csub = new(double*[M]);
+ double** Csub = new double*[M];
for (m=0; m<M; m++)
{
- Csub[m] = new(double[M]);
+ Csub[m] = new double[M];
for (n=0; n<M; n++)
Csub[m][n] = double(C[ll[m]][ll[n]]);
}
else
{
- double** Cinv = new(double*[M]);
- for (m=0; m<M; m++) Cinv[m] = new(double[M]);
+ double** Cinv = new double*[M];
+ for (m=0; m<M; m++) Cinv[m] = new double[M];
// Invert Csub
InvertMatrix(Cinv,Csub,M);
index.Add(name,k);
}
// Read symmetric Z-scores matrix
- Z = new(float*[N]);
+ Z = new float*[N];
for (k=0; k<N; k++)
{
- Z[k] = new(float[N]);
+ 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]);
+ C = new float*[N];
for (k=0; k<N; k++)
{
- C[k] = new(float[N]);
+ 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]);
+ 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");
else
{
// Generate submatrix of C for indices l for which Z_lq,Z_lk > Zmin_trans
- double** Csub = new(double*[M]);
+ double** Csub = new double*[M];
for (m=0; m<M; m++)
{
- Csub[m] = new(double[M]);
+ Csub[m] = new double[M];
for (n=0; n<M; n++)
Csub[m][n] = double(C[ll[m]][ll[n]]);
}
else
{
// Generate submatrix of C for indices l for which Z_lq,Z_lk > Zmin_trans
- double** Csub = new(double*[M]);
+ double** Csub = new double*[M];
for (m=0; m<M; m++)
{
- Csub[m] = new(double[M]);
+ Csub[m] = new double[M];
for (n=0; n<M; n++)
Csub[m][n] = double(C[ll[m]][ll[n]]);
}
}
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]);
+ 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++)
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]);
+ rv1=new double[n];
g=scale=anorm=0.0;
// Householder reduction to bidiagonal form.
}
// printf("POINTER:\t\t\t%p=TAIL\n", tail);
-
+ if ( (NULL != current) && (head != current) ){
+ delete current; /* this seems to be the long lost piece of memory, FS, 2016-04-15 */
+ current = NULL;
+ }
head->next = tail;
tail->prev = head;
size = 0;
********************************************************************/
/*
- * RCS $Id: hhhitlist.h 243 2011-05-31 13:49:19Z fabian $
+ * RCS $Id: hhhitlist.h 284 2013-06-12 10:10:11Z fabian $
*/
// hhhitlist.h
// Print alignments of query sequences against hit sequences
int PrintAlignments(
#ifdef CLUSTALO
- char **ppcFirstProf, char **ppcSecndProf,
+ char **ppcFirstProf, char **ppcSecndProf, char zcAux[], char zcError[],
#endif
HMM& q, char* outfile, char outformat=0);
********************************************************************/
/*
- * RCS $Id: hhhmm-C.h 224 2011-03-23 12:13:33Z fabian $
+ * RCS $Id: hhhmm-C.h 316 2016-12-16 16:14:39Z fabian $
*/
#include "hhdecl-C.h"
#include "hhutil-C.h" // imax, fmax, iround, iceil, ifloor, strint, strscn, strcut, substr, uprstr, uprchr, Basename etc.
#endif
+//#include "new_new.h" /* memory tracking */
// #ifndef WNLIB
// #define WNLIB
//////////////////////////////////////////////////////////////////////////////
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
+ 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
}
n_display=q.n_display;
for (int k=0; k<n_display; k++) {
- sname[k]=new(char[strlen(q.sname[k])+1]);
+ 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]);
+ 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]);
}
else if (!strcmp("SEQ",str3))
{
//char cur_seq[MAXCOL]=""; //Sequence currently read in
- char *cur_seq = new(char[par.maxColCnt]); //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]
//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]);
+ 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'
+ 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;
} //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]);
+ seq[k]=new char[strlen(cur_seq)+1];
if (!seq[k]) MemoryError("array of sequences to display");
strcpy(seq[k],cur_seq);
}
if (nsa_dssp<0)
{
nsa_dssp=k++;
- seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
+ 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");
if (nss_pred<0)
{
nss_pred=k++;
- seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]);
+ 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");
if (nss_conf<0)
{
nss_conf=k++;
- seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]);
+ 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");
// Prepare to store DSSP states (if there are none, delete afterwards)
nss_dssp=k++;
- seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
+ seq[nss_dssp] = new char[/*MAXRES*/par.maxResLen+2];
sname[nss_dssp] = new(char[15]);
strcpy(sname[nss_dssp],"ss_dssp");
{
sname[k]=new(char[10]);
strcpy(sname[k],"Consensus");
- sname[k+1]=new(char[strlen(longname)+1]);
+ sname[k+1]=new char[strlen(longname)+1];
strcpy(sname[k+1],longname);
- seq[k]=new(char[L+2]);
+ seq[k]=new char[L+2];
seq[k][0]=' ';
seq[k][L+1]='\0';
- seq[k+1]=new(char[L+2]);
+ seq[k+1]=new char[L+2];
seq[k+1][0]=' ';
seq[k+1][L+1]='\0';
for (i=1; i<=L; ++i)
}
else
{
- sname[k]=new(char[strlen(longname)+1]);
+ 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]=new char[L+2];
seq[k][0]=' ';
seq[k][L+1]='\0';
}
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 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
if (nsa_dssp<0)
{
nsa_dssp=k++;
- seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
+ 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");
if (nss_pred<0)
{
nss_pred=k++;
- seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]);
+ 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");
if (nss_conf<0)
{
nss_conf=k++;
- seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]);
+ 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);
for (a=0; a<=D2D && ptr; ++a)
- tr[0][a] = log2((float) exp(-1.0*strflta(ptr,99999))); //store transition probabilites as log2 values
+ 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.
// Prepare to store DSSP states (if there are none, delete afterwards)
nss_dssp=k++;
- seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]);
+ seq[nss_dssp] = new char[/*MAXRES*/par.maxResLen+2];
sname[nss_dssp] = new(char[15]);
strcpy(sname[nss_dssp],"ss_dssp");
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
+ 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)
{
{
sname[k]=new(char[10]);
strcpy(sname[k],"Consensus");
- sname[k+1]=new(char[strlen(longname)+1]);
+ sname[k+1]=new char[strlen(longname)+1];
strcpy(sname[k+1],longname);
- seq[k]=new(char[L+2]);
+ seq[k]=new char[L+2];
seq[k][0]=' ';
seq[k][L+1]='\0';
- seq[k+1]=new(char[L+2]);
+ seq[k+1]=new char[L+2];
seq[k+1][0]=' ';
seq[k+1][L+1]='\0';
for (i=1; i<=L; ++i)
}
else
{
- sname[k]=new(char[strlen(longname)+1]);
+ sname[k]=new char[strlen(longname)+1];
strcpy(sname[k],longname);
- seq[k]=new(char[L+2]);
+ seq[k]=new char[L+2];
seq[k][0]=' ';
seq[k][L+1]='\0';
}
HMM::InsertCalibration(char* infile)
{
char* line = new(char[LINELEN]); // input line
- char** lines = new(char*[3*L+100000]);
+ char** lines = new char*[3*L+100000];
int nline=0;
int l;
char done=0; // inserted new 'EVD mu sigma' line?
sprintf(lines[nline],"EVD %-7.4f %-7.4f",lamda,mu);
nline++;
}
- lines[nline]=new(char[strlen(line)+1]);
+ lines[nline]=new char[strlen(line)+1];
if (!lines[nline]) MemoryError("space to read in HHM file for calibration");
strcpy (lines[nline],line);
nline++;
********************************************************************/
/*
- * RCS $Id: hhmatrices-C.h 199 2011-02-21 18:24:49Z fabian $
+ * RCS $Id: hhmatrices-C.h 316 2016-12-16 16:14:39Z fabian $
*/
// Substitution matrices and their background frequencies
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};
+const float mism = 2000; // standard mismatch score
+const float matc = 7000;
+// RNA matrix, Gonnet type format
+const float ribosum[]={
+// A C G T U R Y M K S W B D H V N ? ? ? ?
+ 9500, 600, 700, 900, 900, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // A
+ 600, 4000, 300, 1200, 1200, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // C
+ 700, 300, 3500, 700, 700, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // G
+ 900, 1200, 700, 8200, 8200, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // T
+ 900, 1200, 700, 8200, 8200, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // U
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // R
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // Y
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // M
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // K
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // S
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // W
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // B
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // D
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // H
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // V
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // N
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // ?
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // ?
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // ?
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism};// ?
+
+const float dna_basic[]={
+// A C G T U R Y M K S W B D H V N ? ? ? ?
+ matc, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // A
+ mism, matc, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // C
+ mism, mism, matc, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // G
+ mism, mism, mism, matc, matc, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // T
+ mism, mism, mism, matc, matc, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // U
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // R
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // Y
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // M
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // K
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // S
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // W
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // B
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // D
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // H
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // V
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // N
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // ?
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // ?
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // ?
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism};// ?
+
+const float dave_nucleo[]={
+// A C G T U R Y M K S W B D H V N ? ? ? ?
+ 8000, 1500, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // A
+ 1500, 6500, 1000, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // C
+ mism, 1000, 6500, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // G
+ mism, mism, mism, 7000, 7000, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // T
+ mism, mism, mism, 7000, 7000, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // U
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // R
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // Y
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // M
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // K
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // S
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // W
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // B
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // D
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // H
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // V
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // N
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // ?
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // ?
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, // ?
+ mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism, mism};// ?
+
// 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
//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))
+ 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 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) 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]);
+ entropy-=P[a][b]*Log2(R[a][b]);
mut_info += P[a][b]*S[a][b];
}
}
}
+/////////////////////////////////////////////////////////////////////////////////////
+/**
+ * @brief Set (global variable) substitution matrix with derived matrices and background frequencies
+ */
+void
+SetRnaSubstitutionMatrix()
+{
+ int a,b;
+ for (a=0; a<20; ++a)
+ for (pb[a]=0.0f, b=0; b<20; ++b)
+ P[a][b] = 0.000001f*ribosum[a*20+b];
+ for (a=0; a<20; ++a) P[a][20]=P[20][a]=1.0f;
+
+ // 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 C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\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 C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\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 C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\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 C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\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 C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\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 C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\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 (global variable) substitution matrix with derived matrices and background frequencies
+ */
+void
+SetDnaSubstitutionMatrix()
+{
+ int a,b;
+ for (a=0; a<20; ++a)
+ for (pb[a]=0.0f, b=0; b<20; ++b)
+ P[a][b] = 0.000001f*dna_basic[a*20+b];
+ for (a=0; a<20; ++a) P[a][20]=P[20][a]=1.0f;
+
+ // 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 C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\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 C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\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 C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\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 C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\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 C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\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 C G T U ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?\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;
+
+
+ }
+}
/////////////////////////////////////////////////////////////////////////////////////
/**
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]);
+ S73[A][B][cf] = Log2(P73[A][B][cf]);
}
for (B=0; B<NSSPRED; B++)
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);
+ S33[B][cf][BB][ccf] = Log2(sum);
}
} /* this is the end of SetSecStrucSubstitutionMatrix() */
********************************************************************/
/*
- * RCS $Id: hhutil-C.h 246 2011-06-15 12:41:04Z fabian $
+ * RCS $Id: hhutil-C.h 315 2016-12-15 17:18:30Z fabian $
*/
+#define PARAMETERSFROMFILE 0
+
+extern bool nucleomode;
+
//////////////////////////////////////////////////////////////////////////////
// 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
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)
- {
+ if(!nucleomode)
+ {
+ // proteins!
+ // A R N D C Q E G H I L K M F P S T W Y V
+ 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;
+ }
+ }
+ else
+ {
+ // nucleotides!
+ 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 'C': return 1;
+ case 'G': return 2;
+ case 'T': return 3;
+ case 'U': return 4;
+ case 'N': return ANY;
case '-': return GAP;
case '.': return GAP;
case '_': return GAP;
- }
+ default: return ANY;
+ }
+ }
if (c>=0 && c<=32) return -1; // white space and control characters
return -2;
}
i2aa(char c)
{
//A R N D C Q E G H I L K M F P S T W Y V
+ if(!nucleomode)
+ {
switch (c)
{
case 0: return 'A';
case GAP: return '-';
case ENDGAP: return '-';
}
+ }
+ else
+ {
+ // DNA/RNA
+ switch(c)
+ {
+ case 0: return 'A';
+ case 1: return 'C';
+ case 2: return 'G';
+ case 3: return 'T';
+ case 4: return 'U';
+ case ANY: return 'N';
+ case GAP: return '-';
+ case ENDGAP: return '-';
+ }
+ }
return '?';
}
if (*c=='\0' || *c=='\n' || *c=='#') //Is end of line reached?
{
*c='\0';
- argv_conf[argc_conf]=new(char[strlen(c_first)+1]);
+ 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]);
+ argv_conf[argc_conf]=new char[strlen(c_first)+1];
strcpy(argv_conf[argc_conf++],c_first);
printf("Argument: %s\n",c_first);
c++;
* @brief Set default parameter values
*/
void
-SetDefaults()
+SetDefaults(hhalign_para rHhalignPara)
{
par.append=0; // overwrite output file
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 */
+#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.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
+ 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
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 */
+
+ //#if PARAMETERSFROMFILE /* read parameter file from home-dir */
+ //#include "hhutil-C-help.h"
+ //#endif /* read parameter file from home-dir */
+ if (rHhalignPara.pca >= 0.00){ par.pca = rHhalignPara.pca; }
+ if (rHhalignPara.pcb >= 0.00){ par.pcb = rHhalignPara.pcb; }
+ if (rHhalignPara.pcc >= 0.00){ par.pcc = rHhalignPara.pcc; }
+ if (rHhalignPara.pcw >= 0.00){ par.pcw = rHhalignPara.pcw; }
+ if (rHhalignPara.gapb >= 0.00){ par.gapb = rHhalignPara.gapb; }
+ if (rHhalignPara.gapd >= 0.00){ par.gapd = rHhalignPara.gapd; }
+ if (rHhalignPara.gape >= 0.00){ par.gape = rHhalignPara.gape; }
+ if (rHhalignPara.gapf >= 0.00){ par.gapf = rHhalignPara.gapf; }
+ if (rHhalignPara.gapg >= 0.00){ par.gapg = rHhalignPara.gapg; }
+ if (rHhalignPara.gaph >= 0.00){ par.gaph = rHhalignPara.gaph; }
+ if (rHhalignPara.gapi >= 0.00){ par.gapi = rHhalignPara.gapi; }
+ if (rHhalignPara.pcaV >= 0.00){ par.pcaV = rHhalignPara.pcaV; }
+ if (rHhalignPara.pcbV >= 0.00){ par.pcbV = rHhalignPara.pcbV; }
+ if (rHhalignPara.pccV >= 0.00){ par.pccV = rHhalignPara.pccV; }
+ if (rHhalignPara.pcwV >= 0.00){ par.pcwV = rHhalignPara.pcwV; }
+ if (rHhalignPara.gapbV >= 0.00){ par.gapbV = rHhalignPara.gapbV; }
+ if (rHhalignPara.gapdV >= 0.00){ par.gapdV = rHhalignPara.gapdV; }
+ if (rHhalignPara.gapeV >= 0.00){ par.gapeV = rHhalignPara.gapeV; }
+ if (rHhalignPara.gapfV >= 0.00){ par.gapfV = rHhalignPara.gapfV; }
+ if (rHhalignPara.gapgV >= 0.00){ par.gapgV = rHhalignPara.gapgV; }
+ if (rHhalignPara.gaphV >= 0.00){ par.gaphV = rHhalignPara.gaphV; }
+ if (rHhalignPara.gapiV >= 0.00){ par.gapiV = rHhalignPara.gapiV; }
return;
} /** this is the end of SetDefaults() **/
+void SetRnaDefaults(hhalign_para rHhalignPara)
+{
+ par.pca=1.28f; // default values for substitution matrix pseudocounts
+ par.pcb=1.75f; // significant reduction of pcs by Neff_M starts around Neff_M-1=pcb
+ par.pcc=0.87f; // pcs are reduced prop. to 1/Neff^pcc
+ par.pcw=0.0f; // wc>0 weighs columns according to their intra-clomun similarity
+
+ par.gapb=0.80; // default values for transition pseudocounts
+ par.gapd=0.34; // gap open penalty pseudocount; 0.25 corresponds to 7.1*gapf bits
+ par.gape=2.25; // gap extension penalty pseudocount
+ par.gapf=0.51; // factor for increasing gap open penalty for deletes
+ par.gapg=1.01; // factor for increasing gap open penalty for inserts
+ par.gaph=1.24; // factor for increasing gap extension penalty for deletes
+ par.gapi=0.45; // factor for increasing gap extension penalty for inserts
+
+#if 0 /* these are the parameters determined by Dave (pre r274) */
+ par.pcaV=2.57f; // default values for substitution matrix pseudocounts
+ par.pcbV=2.34f; // significant reduction of pcs by Neff_M starts around Neff_M-1=pcb
+ par.pccV=0.88f; // pcs are reduced prop. to 1/Neff^pcc
+ par.pcwV=0.0f; // wc>0 weighs columns according to their intra-clomun similarity
+
+ par.gapbV=1.41; // default values for transition pseudocounts
+ par.gapdV=1.8; // gap open penalty pseudocount; 0.25 corresponds to 7.1*gapf bits
+ par.gapeV=1.5; // gap extension penalty pseudocount
+ par.gapfV=1.03; // factor for increasing gap open penalty for deletes
+ par.gapgV=0.89; // factor for increasing gap open penalty for inserts
+ par.gaphV=0.54; // factor for increasing gap extension penalty for deletes
+ par.gapiV=0.86; // factor for increasing gap extension penalty for inserts
+#else /* parameters determined for r274, using Bralibase, FS */
+ par.pcaV=1.655620f; // default values for substitution matrix pseudocounts
+ par.pcbV=0.438399f; // significant reduction of pcs by Neff_M starts around Neff_M-1=pcb
+ par.pccV=0.371491f; // pcs are reduced prop. to 1/Neff^pcc
+ par.pcwV=0.0f; // wc>0 weighs columns according to their intra-clomun similarity
+
+ par.gapbV=1.914490; // default values for transition pseudocounts
+ par.gapdV=0.104278; // gap open penalty pseudocount; 0.25 corresponds to 7.1*gapf bits
+ par.gapeV=1.100210; // gap extension penalty pseudocount
+ par.gapfV=0.335152; // factor for increasing gap open penalty for deletes
+ par.gapgV=0.786688; // factor for increasing gap open penalty for inserts
+ par.gaphV=0.667143; // factor for increasing gap extension penalty for deletes
+ par.gapiV=0.711993; // factor for increasing gap extension penalty for inserts
+#endif
+
+ //#if PARAMETERSFROMFILE /* read parameter file from home-dir */
+ //#include "hhutil-C-help.h"
+ //#endif /* read parameter file from home-dir */
+ if (rHhalignPara.pca >= 0.00){ par.pca = rHhalignPara.pca; }
+ if (rHhalignPara.pcb >= 0.00){ par.pcb = rHhalignPara.pcb; }
+ if (rHhalignPara.pcc >= 0.00){ par.pcc = rHhalignPara.pcc; }
+ if (rHhalignPara.pcw >= 0.00){ par.pcw = rHhalignPara.pcw; }
+ if (rHhalignPara.gapb >= 0.00){ par.gapb = rHhalignPara.gapb; }
+ if (rHhalignPara.gapd >= 0.00){ par.gapd = rHhalignPara.gapd; }
+ if (rHhalignPara.gape >= 0.00){ par.gape = rHhalignPara.gape; }
+ if (rHhalignPara.gapf >= 0.00){ par.gapf = rHhalignPara.gapf; }
+ if (rHhalignPara.gapg >= 0.00){ par.gapg = rHhalignPara.gapg; }
+ if (rHhalignPara.gaph >= 0.00){ par.gaph = rHhalignPara.gaph; }
+ if (rHhalignPara.gapi >= 0.00){ par.gapi = rHhalignPara.gapi; }
+ if (rHhalignPara.pcaV >= 0.00){ par.pcaV = rHhalignPara.pcaV; }
+ if (rHhalignPara.pcbV >= 0.00){ par.pcbV = rHhalignPara.pcbV; }
+ if (rHhalignPara.pccV >= 0.00){ par.pccV = rHhalignPara.pccV; }
+ if (rHhalignPara.pcwV >= 0.00){ par.pcwV = rHhalignPara.pcwV; }
+ if (rHhalignPara.gapbV >= 0.00){ par.gapbV = rHhalignPara.gapbV; }
+ if (rHhalignPara.gapdV >= 0.00){ par.gapdV = rHhalignPara.gapdV; }
+ if (rHhalignPara.gapeV >= 0.00){ par.gapeV = rHhalignPara.gapeV; }
+ if (rHhalignPara.gapfV >= 0.00){ par.gapfV = rHhalignPara.gapfV; }
+ if (rHhalignPara.gapgV >= 0.00){ par.gapgV = rHhalignPara.gapgV; }
+ if (rHhalignPara.gaphV >= 0.00){ par.gaphV = rHhalignPara.gaphV; }
+ if (rHhalignPara.gapiV >= 0.00){ par.gapiV = rHhalignPara.gapiV; }
+
+} /* this is the end of SetRnaDefaults() */
+
+void SetDnaDefaults(hhalign_para rHhalignPara)
+{
+ par.pca=2.89f; // default values for substitution matrix pseudocounts
+ par.pcb=1.17f; // significant reduction of pcs by Neff_M starts around Neff_M-1=pcb
+ par.pcc=0.88f; // pcs are reduced prop. to 1/Neff^pcc
+ par.pcw=0.0f; // wc>0 weighs columns according to their intra-clomun similarity
+
+ par.gapb=0.80; // default values for transition pseudocounts
+ par.gapd=0.34; // gap open penalty pseudocount; 0.25 corresponds to 7.1*gapf bits
+ par.gape=2.25; // gap extension penalty pseudocount
+ par.gapf=0.78; // factor for increasing gap open penalty for deletes
+ par.gapg=1.01; // factor for increasing gap open penalty for inserts
+ par.gaph=1.24; // factor for increasing gap extension penalty for deletes
+ par.gapi=0.45; // factor for increasing gap extension penalty for inserts
+
+#if 0 /* these are the parameters determined by Dave (pre r274) */
+ par.pcaV=1.712f; // default values for substitution matrix pseudocounts
+ par.pcbV=1.039f; // significant reduction of pcs by Neff_M starts around Neff_M-1=pcb
+ par.pccV=0.266f; // pcs are reduced prop. to 1/Neff^pcc
+ par.pcwV=0.0f; // wc>0 weighs columns according to their intra-clomun similarity
+
+ par.gapbV=1.405; // default values for transition pseudocounts
+ par.gapdV=1.8; // gap open penalty pseudocount; 0.25 corresponds to 7.1*gapf bits
+ par.gapeV=2.25; // gap extension penalty pseudocount
+ par.gapfV=1.034; // factor for increasing gap open penalty for deletes
+ par.gapgV=2.025; // factor for increasing gap open penalty for inserts
+ par.gaphV=0.544; // factor for increasing gap extension penalty for deletes
+ par.gapiV=1.35; // factor for increasing gap extension penalty for inserts }
+#else /* parameters determined for r274, using mdsa, FS */
+ par.pcaV=2.196; // default values for substitution matrix pseudocounts
+ par.pcbV=0.329; // significant reduction of pcs by Neff_M starts around Neff_M-1=pcb
+ par.pccV=0.393; // pcs are reduced prop. to 1/Neff^pcc
+ par.pcwV=0.0f; // wc>0 weighs columns according to their intra-clomun similarity
+
+ par.gapbV=0.570; // default values for transition pseudocounts
+ par.gapdV=0.048; // gap open penalty pseudocount; 0.25 corresponds to 7.1*gapf bits
+ par.gapeV=1.692; // gap extension penalty pseudocount
+ par.gapfV=0.398; // factor for increasing gap open penalty for deletes
+ par.gapgV=0.121; // factor for increasing gap open penalty for inserts
+ par.gaphV=0.012; // factor for increasing gap extension penalty for deletes
+ par.gapiV=0.645; // factor for increasing gap extension penalty for inserts }
+#endif
+
+ //#if PARAMETERSFROMFILE /* read parameter file from home-dir */
+ //#include "hhutil-C-help.h"
+ //#endif /* read parameter file from home-dir */
+ if (rHhalignPara.pca >= 0.00){ par.pca = rHhalignPara.pca; }
+ if (rHhalignPara.pcb >= 0.00){ par.pcb = rHhalignPara.pcb; }
+ if (rHhalignPara.pcc >= 0.00){ par.pcc = rHhalignPara.pcc; }
+ if (rHhalignPara.pcw >= 0.00){ par.pcw = rHhalignPara.pcw; }
+ if (rHhalignPara.gapb >= 0.00){ par.gapb = rHhalignPara.gapb; }
+ if (rHhalignPara.gapd >= 0.00){ par.gapd = rHhalignPara.gapd; }
+ if (rHhalignPara.gape >= 0.00){ par.gape = rHhalignPara.gape; }
+ if (rHhalignPara.gapf >= 0.00){ par.gapf = rHhalignPara.gapf; }
+ if (rHhalignPara.gapg >= 0.00){ par.gapg = rHhalignPara.gapg; }
+ if (rHhalignPara.gaph >= 0.00){ par.gaph = rHhalignPara.gaph; }
+ if (rHhalignPara.gapi >= 0.00){ par.gapi = rHhalignPara.gapi; }
+ if (rHhalignPara.pcaV >= 0.00){ par.pcaV = rHhalignPara.pcaV; }
+ if (rHhalignPara.pcbV >= 0.00){ par.pcbV = rHhalignPara.pcbV; }
+ if (rHhalignPara.pccV >= 0.00){ par.pccV = rHhalignPara.pccV; }
+ if (rHhalignPara.pcwV >= 0.00){ par.pcwV = rHhalignPara.pcwV; }
+ if (rHhalignPara.gapbV >= 0.00){ par.gapbV = rHhalignPara.gapbV; }
+ if (rHhalignPara.gapdV >= 0.00){ par.gapdV = rHhalignPara.gapdV; }
+ if (rHhalignPara.gapeV >= 0.00){ par.gapeV = rHhalignPara.gapeV; }
+ if (rHhalignPara.gapfV >= 0.00){ par.gapfV = rHhalignPara.gapfV; }
+ if (rHhalignPara.gapgV >= 0.00){ par.gapgV = rHhalignPara.gapgV; }
+ if (rHhalignPara.gaphV >= 0.00){ par.gaphV = rHhalignPara.gaphV; }
+ if (rHhalignPara.gapiV >= 0.00){ par.gapiV = rHhalignPara.gapiV; }
+
+
+} /* this is the end of SetDnaDefaults() */
+
+
/*
* EOF hhutil-C.h
*/
--- /dev/null
+# libhhalign.la - a libtool library file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# The name that we can dlopen(3).
+dlname=''
+
+# Names of this library.
+library_names=''
+
+# The name of the static archive.
+old_library='libhhalign.a'
+
+# Linker flags that can not go in dependency_libs.
+inherited_linker_flags=''
+
+# Libraries that this one depends upon.
+dependency_libs=' -largtable2'
+
+# Names of additional weak libraries provided by this library
+weak_library_names=''
+
+# Version information for libhhalign.
+current=
+age=
+revision=
+
+# Is this an already installed library?
+installed=no
+
+# Should we warn about portability when linking against -modules?
+shouldnotlink=no
+
+# Files to dlopen/dlpreopen
+dlopen=''
+dlpreopen=''
+
+# Directory that this library needs to be installed in:
+libdir=''
********************************************************************/
/*
- * RCS $Id: util-C.h 155 2010-11-17 12:18:47Z fabian $
+ * RCS $Id: util-C.h 316 2016-12-16 16:14:39Z fabian $
*/
// Utility subroutines
#include <time.h> // clock
#endif
#include <sys/time.h>
+//#include "new_new.h" /* memory tracking */
+#include "../config.h"
/////////////////////////////////////////////////////////////////////////////////////
// Arithmetics
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));}
+//#ifndef CLUSTAL_OMEGA_HAVE_LOG2
+//#ifndef HAVE_LOG2
+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));}
+//#endif
/////////////////////////////////////////////////////////////////////////////////////
inline char* sprintg(float val, int w)
{
static char str[100];
- float log10val = log10(fabs(val));
+ float log10val = Log10(fabs(val));
int neg = (val<0? 1: 0);
if (log10val >= w-neg-1 || -log10val > 3)
{
--- /dev/null
+KMeans.lo: KMeans.cpp KmUtils.h /usr/include/memory.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h /usr/include/string.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \
+ /usr/include/locale.h /usr/include/bits/locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
+ /usr/include/ctype.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \
+ /usr/include/bits/setjmp.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h \
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+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h KmTree.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_bvector.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc
+
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+/usr/include/libio.h:
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+/usr/include/bits/stdio_lim.h:
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+/usr/include/bits/sys_errlist.h:
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+/usr/include/bits/stdio.h:
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--- /dev/null
+KmTree.lo: KmTree.cpp KmTree.h KmUtils.h /usr/include/memory.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h /usr/include/string.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \
+ /usr/include/locale.h /usr/include/bits/locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
+ /usr/include/ctype.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
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+ /usr/include/bits/confname.h /usr/include/getopt.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream.tcc \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/istream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/istream.tcc \
+ /usr/include/libio.h /usr/include/_G_config.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h
+
+KmTree.h:
+
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+
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+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
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--- /dev/null
+KmUtils.lo: KmUtils.cpp KmUtils.h /usr/include/memory.h \
+ /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h /usr/include/string.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/cpu_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ostream \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ios \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stringfwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef \
+ /usr/include/wchar.h /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/char_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_algobase.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/concept_check.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/localefwd.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale \
+ /usr/include/locale.h /usr/include/bits/locale.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \
+ /usr/include/ctype.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ios_base.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/atomicity.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/gthr-default.h \
+ /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \
+ /usr/include/bits/setjmp.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h \
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+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_classes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \
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--- /dev/null
+# libkmpp.la - a libtool library file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# The name that we can dlopen(3).
+dlname=''
+
+# Names of this library.
+library_names=''
+
+# The name of the static archive.
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+
+# Linker flags that can not go in dependency_libs.
+inherited_linker_flags=''
+
+# Libraries that this one depends upon.
+dependency_libs=' -largtable2'
+
+# Names of additional weak libraries provided by this library
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+
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+current=
+age=
+revision=
+
+# Is this an already installed library?
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+
+# Should we warn about portability when linking against -modules?
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+
+# Files to dlopen/dlpreopen
+dlopen=''
+dlpreopen=''
+
+# Directory that this library needs to be installed in:
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--- /dev/null
+# KMeans.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/KMeans.o'
+
+# Name of the non-PIC object
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--- /dev/null
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+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
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+
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+
--- /dev/null
+# KmUtils.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
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+
+# Name of the non-PIC object
+non_pic_object='KmUtils.o'
+
--- /dev/null
+# Makefile.in generated by automake 1.10.2 from Makefile.am.
+# src/kmpp/Makefile. Generated from Makefile.in by configure.
+
+# 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.
+
+
+
+# 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
+
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+
+
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+ $(top_srcdir)/m4/libtool.m4 $(top_srcdir)/m4/ltoptions.m4 \
+ $(top_srcdir)/m4/ltsugar.m4 $(top_srcdir)/m4/ltversion.m4 \
+ $(top_srcdir)/m4/lt~obsolete.m4 $(top_srcdir)/m4/ax_openmp.m4 \
+ $(top_srcdir)/configure.ac
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+ $(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/src/config.h
+CONFIG_CLEAN_FILES =
+LTLIBRARIES = $(noinst_LTLIBRARIES)
+libkmpp_la_LIBADD =
+am_libkmpp_la_OBJECTS = KMeans.lo KmTree.lo KmUtils.lo
+libkmpp_la_OBJECTS = $(am_libkmpp_la_OBJECTS)
+DEFAULT_INCLUDES = -I. -I$(top_builddir)/src
+depcomp = $(SHELL) $(top_srcdir)/depcomp
+am__depfiles_maybe = depfiles
+CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
+ $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+LTCXXCOMPILE = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+ --mode=compile $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
+ $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS)
+CXXLD = $(CXX)
+CXXLINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+ --mode=link $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) \
+ $(LDFLAGS) -o $@
+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
+ $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+LTCOMPILE = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+ --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
+ $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+CCLD = $(CC)
+LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+ --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) \
+ $(LDFLAGS) -o $@
+SOURCES = $(libkmpp_la_SOURCES)
+DIST_SOURCES = $(libkmpp_la_SOURCES)
+ETAGS = etags
+CTAGS = ctags
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run aclocal-1.10
+AMTAR = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run tar
+AM_CFLAGS = -O3
+
+# need DCLUSTALO here to enable Clustal specific squid patches
+AM_CXXFLAGS = -DCLUSTALO -O3
+AM_LDFLAGS =
+AR = ar
+AUTOCONF = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run autoconf
+AUTOHEADER = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run autoheader
+AUTOMAKE = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run automake-1.10
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+CXXFLAGS = -g -O2
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+DEFS = -DHAVE_CONFIG_H
+DEPDIR = .deps
+DSYMUTIL =
+DUMPBIN =
+ECHO_C =
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+ECHO_T =
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+EXEEXT =
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+GREP = /bin/grep
+INSTALL = /usr/bin/install -c
+INSTALL_DATA = ${INSTALL} -m 644
+INSTALL_PROGRAM = ${INSTALL}
+INSTALL_SCRIPT = ${INSTALL}
+INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
+LD = /usr/bin/ld -m elf_x86_64
+LDFLAGS =
+LIBOBJS =
+LIBS = -largtable2 -lm
+LIBTOOL = $(SHELL) $(top_builddir)/libtool
+LIPO =
+LN_S = ln -s
+LTLIBOBJS =
+MAKEINFO = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run makeinfo
+MKDIR_P = /bin/mkdir -p
+NM = /usr/bin/nm -B
+NMEDIT =
+OBJDUMP = objdump
+OBJEXT = o
+OPENMP_CFLAGS = -fopenmp
+OPENMP_CXXFLAGS = -fopenmp
+OTOOL =
+OTOOL64 =
+PACKAGE = clustal-omega
+PACKAGE_BUGREPORT = clustalw@ucd.ie
+PACKAGE_CODENAME = AndreaGiacomo
+PACKAGE_NAME = Clustal Omega
+PACKAGE_STRING = Clustal Omega 1.2.4
+PACKAGE_TARNAME = clustal-omega
+PACKAGE_VERSION = 1.2.4
+PATH_SEPARATOR = :
+RANLIB = ranlib
+SED = /bin/sed
+SET_MAKE =
+SHELL = /bin/sh
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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
+# libkmpp.la - a libtool library file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# The name that we can dlopen(3).
+dlname=''
+
+# Names of this library.
+library_names=''
+
+# The name of the static archive.
+old_library='libkmpp.a'
+
+# Linker flags that can not go in dependency_libs.
+inherited_linker_flags=''
+
+# Libraries that this one depends upon.
+dependency_libs=' -largtable2'
+
+# Names of additional weak libraries provided by this library
+weak_library_names=''
+
+# Version information for libkmpp.
+current=
+age=
+revision=
+
+# Is this an already installed library?
+installed=no
+
+# Should we warn about portability when linking against -modules?
+shouldnotlink=no
+
+# Files to dlopen/dlpreopen
+dlopen=''
+dlpreopen=''
+
+# Directory that this library needs to be installed in:
+libdir=''
--- /dev/null
+# libclustalo.la - a libtool library file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# The name that we can dlopen(3).
+dlname=''
+
+# Names of this library.
+library_names=''
+
+# The name of the static archive.
+old_library='libclustalo.a'
+
+# Linker flags that can not go in dependency_libs.
+inherited_linker_flags=''
+
+# Libraries that this one depends upon.
+dependency_libs=' -largtable2 -lm'
+
+# Names of additional weak libraries provided by this library
+weak_library_names=''
+
+# Version information for libclustalo.
+current=0
+age=0
+revision=0
+
+# Is this an already installed library?
+installed=no
+
+# Should we warn about portability when linking against -modules?
+shouldnotlink=no
+
+# Files to dlopen/dlpreopen
+dlopen=''
+dlpreopen=''
+
+# Directory that this library needs to be installed in:
+libdir='/usr/local/lib'
********************************************************************/
/*
- * RCS $Id: main.cpp 234 2011-04-13 05:26:16Z andreas $
+ * RCS $Id: main.cpp 289 2013-09-17 10:09:37Z fabian $
*/
/*
} else {
fprintf(stderr,
- "WARNING: Unsupported old command line option '%s' will be ignored\n",
+ "WARNING: Unsupported old command line option '%s' will be ignored (may change default output stream and format)\n",
pcOldArg);
}
********************************************************************/
/*
- * RCS $Id: mymain.c 255 2011-06-22 15:59:07Z fabian $
+ * RCS $Id: mymain.c 296 2014-10-07 12:15:41Z fabian $
*/
#ifdef HAVE_CONFIG_H
#include "mymain.h"
-/* hhalign (parameters) */
-#include "hhalign/general.h"
-
typedef struct {
/* Sequence input
* info for background-HMM creation */
bool bDealignInputSeqs;
+ /** Sequence input format
+ */
+ int iSeqInFormat;
+
/* 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;
-
+ /** profiles that contain no gaps are rejected, force them */
+ bool bIsProfile;
+ /** up to version 1.1.1 Kimura distance was default, change default, make Kimura optional */
+ /*bool bUseKimura; */
+ /** distance matrix output is default, allow %-ID output */
+ bool bPercentID;
+
/** Input limitations
*/
/** maximum allowed number of input sequences */
/** force overwriting of files */
bool bForceFileOverwrite;
+ /* line wrapping, FS, r274 -> */
+ int iWrap;
+ /* residue number in Clustal format, FS, r274 -> */
+ bool bResno;
+ /* output order, FS, r274 -> */
+ int iOutputOrder;
+
/* multithreading
*/
/** number of threads */
int iThreads;
+ /* pseudo-count file
+ */
+ char *pcPseudoFile;
/* logging
*/
char *pcLogFile;
/* log-file used for non-essential logging in prLog */
FILE *prLogFile = NULL;
+const char *CITATION = " Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG."
+ "\n"
+ " Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega."
+ "\n"
+ " Mol Syst Biol. 2011 Oct 11;7:539. doi: 10.1038/msb.2011.75. PMID: 21988835.";
+
/**
void
SetDefaultUserOpts(cmdline_opts_t *opts)
{
-
assert(NULL != opts);
opts->iSeqType = SEQTYPE_UNKNOWN;
opts->bDealignInputSeqs = FALSE;
opts->pcProfile1Infile = NULL;
opts->pcProfile2Infile = NULL;
-
+ opts->bIsProfile = FALSE;
+ opts->aln_opts.bUseKimura = FALSE;
+ opts->aln_opts.bPercID = FALSE;
+ opts->aln_opts.pcHMMBatch = NULL;
+
opts->iMaxNumSeq = INT_MAX;
opts->iMaxSeqLen = INT_MAX;
opts->pcAlnOutfile = NULL;
opts->iAlnOutFormat = MSAFILE_A2M;
opts->bForceFileOverwrite = FALSE;
+ opts->iWrap = 60;
+ opts->bResno = FALSE;
+ opts->iOutputOrder = INPUT_ORDER;
#ifdef HAVE_OPENMP
/* defaults to # of CPUs */
opts->iThreads = 1;
#endif
+ opts->pcPseudoFile = NULL;
opts->pcLogFile = NULL;
SetDefaultAlnOpts(& opts->aln_opts);
}
-/* end of SetDefaultAlnOpts() */
+/* end of SetDefaultUserOpts() */
/* 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, "seq-type = %s\n", SeqTypeToStr(opts->iSeqType));
+ fprintf(prFile, "seq-in-fmt = %s\n", SeqfileFormat2String(opts->iSeqInFormat));
fprintf(prFile, "option: seq-in = %s\n",
NULL != opts->pcSeqInfile? opts->pcSeqInfile: "(null)");
fprintf(prFile, "option: dealign = %d\n", opts->bDealignInputSeqs);
NULL != opts->pcProfile1Infile? opts->pcProfile1Infile: "(null)");
fprintf(prFile, "option: profile2 = %s\n",
NULL != opts->pcProfile2Infile? opts->pcProfile2Infile: "(null)");
+ /*fprintf(prFile, "option: percent-id = %d\n", opts->aln_opts.bPercID);*/
+ fprintf(prFile, "option: is-profile = %d\n", opts->bIsProfile);
+ /*fprintf(prFile, "option: use-kimura = %d\n", opts->aln_opts.bUseKimura);*/
+
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: line wrap = %d\n", opts->iWrap);
+ fprintf(prFile, "option: print residue numbers = %d\n", opts->bResno);
+ fprintf(prFile, "option: order alignment like input/tree = %d\n", opts->iOutputOrder);
+
fprintf(prFile, "option: threads = %d\n", opts->iThreads);
+ fprintf(prFile, "option: PseudoFile = %s\n", opts->pcPseudoFile);
fprintf(prFile, "option: logFile = %s\n", opts->pcLogFile);
}
/* end of PrintUserOpts */
if (NULL != user_opts->pcLogFile) {
CKFREE(user_opts->pcLogFile);
}
+ if (NULL != user_opts->pcPseudoFile) {
+ CKFREE(user_opts->pcPseudoFile);
+ }
FreeAlnOpts(& user_opts->aln_opts);
"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 -> */
+ /* distance matrix output impossible in mBed mode, only have clusters, FS, r254 -> */
+#if 1
+ /* allow distance matrix output if initial mBed but subsequent full matrix during iteration, FS, r274 -> */
+ if (NULL != opts->aln_opts.pcDistmatOutfile){
+ if ( (TRUE == opts->aln_opts.bUseMbed) && (opts->aln_opts.iNumIterations < 1) ){
+ Log(&rLog, LOG_FATAL, "Distance Matrix output not possible in mBed mode.");
+ }
+ if ( (TRUE == opts->aln_opts.bUseMbed) && (TRUE == opts->aln_opts.bUseMbedForIteration) ){
+ Log(&rLog, LOG_FATAL, "Distance Matrix output not possible in mBed mode.");
+ }
+ if ( (TRUE == opts->aln_opts.bUseMbed) && (opts->aln_opts.iNumIterations > 0) &&
+ (opts->aln_opts.iMaxGuidetreeIterations < 1) ){
+ Log(&rLog, LOG_FATAL, "Distance Matrix output not possible in mBed mode.");
+ }
+ }
+#else
if ( (NULL != opts->aln_opts.pcDistmatOutfile) && (TRUE == opts->aln_opts.bUseMbed) ) {
Log(&rLog, LOG_FATAL, "Distance Matrix output not possible in mBed mode.");
}
+#endif
+
+ /* percentage identity cannot be printed in Kimura mode */
+ if ( (TRUE == opts->aln_opts.bUseKimura) && (TRUE == opts->aln_opts.bPercID) ){
+ Log(&rLog, LOG_FATAL, "Percentage Identity cannot be calculated if Kimura Distances are used.");
+ }
+
+ /* iteration destroys effect of pile-up */
+ if ( (TRUE == opts->aln_opts.bPileup) && (opts->aln_opts.iNumIterations > 0) ){
+ Log(&rLog, LOG_WARN, "Iteration destroys effect of pile-up.");
+ }
+
+ AlnOptsLogicCheck(& opts->aln_opts);
}
/* end of UserOptsLogicCheck */
struct arg_file *opt_hmm_in = arg_filen(NULL, "hmm-in", "<file>",
/*min*/ 0, /*max*/ 128,
"HMM input files");
+ struct arg_file *opt_hmm_batch = arg_file0(NULL, "hmm-batch", "<file>", /* FS, r291 -> */
+ "specify HMMs for individual sequences");
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_lit *opt_isprofile = arg_lit0(NULL, "is-profile",
+ "disable check if profile, force profile (default no)");
+ struct arg_str *opt_seqtype = arg_str0("t", "seqtype",
+ "{Protein, RNA, DNA}",
+ "Force a sequence type (default: auto)");
+/* struct arg_lit *opt_force_protein = arg_lit0(NULL, "protein",
+ "Set sequence type to protein even if Clustal guessed nucleic acid"); */
+ struct arg_str *opt_infmt = arg_str0(NULL, "infmt",
+ "{a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]}",
+ "Forced sequence input file format (default: auto)");
+ struct arg_lit *opt_resno = arg_lit0(NULL, "residuenumber,resno",
+ "in Clustal format print residue numbers (default no)");
struct arg_rem *rem_guidetree = arg_rem(NULL, "\nClustering:");
struct arg_str *opt_pairdist = arg_str0("p", "pairdist",
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_pileup = arg_lit0(NULL, "pileup",
+ "Sequentially align sequences");
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_int *opt_clustersize = arg_int0(NULL, "cluster-size", "<n>",
+ "soft maximum of sequences in sub-clusters"); /* FS, r274 -> */
+
+ struct arg_file *opt_clustfile = arg_file0(NULL, "clustering-out",
+ "<file>",
+ "Clustering output file"); /* FS, r274 -> */
+ struct arg_int *opt_trans = arg_int0(NULL, "trans", "<n>", "use transitivity (default: 0)");
+ struct arg_file *opt_posteriorfile = arg_file0(NULL, "posterior-out",
+ "<file>",
+ "Posterior probability output file"); /* FS, r288 -> */
+ struct arg_lit *opt_usekimura = arg_lit0(NULL, "use-kimura",
+ "use Kimura distance correction for aligned sequences (default no)");
+ struct arg_lit *opt_percentid = arg_lit0(NULL, "percent-id",
+ "convert distances into percent identities (default no)");
+
struct arg_str *opt_clustering = arg_str0("c", "clustering",
"{UPGMA}",
"Clustering method for guide tree");
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_int *opt_wrap = arg_int0(NULL, "wrap", "<n>",
+ "number of residues before line-wrap in output");
+ struct arg_str *opt_output_order = arg_str0(NULL, "output-order",
+ "{input-order,tree-order}",
+ "MSA output order like in input/guide-tree");
struct arg_rem *rem_iteration = arg_rem(NULL, "\nIteration:");
/* 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");
+ "<n>", "Maximum number of guidetree iterations");
struct arg_int *opt_max_hmm_iterations = arg_int0(NULL, "max-hmm-iterations",
"<n>", "Maximum number of HMM iterations");
"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_pseudo = arg_file0(NULL, "pseudo", "<file>",
+ "Input file for pseudo-count parameters");
struct arg_file *opt_logfile = arg_file0("l", "log",
"<file>",
"Log all non-essential output to this file");
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_hmm_batch, /* FS, r291 -> */
opt_dealign,
-#if 0
- /* unused since we only support protein for now */
- opt_seqtype,
-#endif
opt_profile1,
opt_profile2,
-
+ opt_isprofile, /* FS, r282 ->*/
+ opt_seqtype,
+ /* opt_force_protein, */
+ opt_infmt,
rem_guidetree,
#if 0
/* no other options then default available or not implemented */
opt_distmat_out,
opt_guidetree_in,
opt_guidetree_out,
+ opt_pileup, /* FS, r288 -> */
opt_full, /* FS, r250 -> */
opt_full_iter, /* FS, r250 -> */
+ opt_clustersize, /* FS, r274 -> */
+ opt_clustfile, /* FS, r274 -> */
+ opt_trans, /* FS, r290 -> */
+ opt_posteriorfile, /* FS, r288 -> */
+ opt_usekimura, /* FS, r282 ->*/
+ opt_percentid, /* FS, r282 ->*/
#if 0
/* no other options then default available */
opt_clustering,
rem_aln_output,
opt_outfile,
opt_outfmt,
+ opt_resno, /* FS, 274 -> */
+ opt_wrap, /* FS, 274 -> */
+ opt_output_order, /* FS, 274 -> */
rem_iteration,
opt_num_iterations,
rem_misc,
opt_autooptions,
opt_threads,
+ opt_pseudo,
opt_logfile,
opt_help,
opt_verbose,
printf("%s - %s (%s)\n", PACKAGE_NAME, PACKAGE_VERSION, PACKAGE_CODENAME);
printf("\n");
+ printf("If you like Clustal-Omega please cite:\n%s\n", CITATION);
+ printf("If you don't like Clustal-Omega, please let us know why (and cite us anyway).\n");
+ /* printf("You can contact reach us under %s\n", PACKAGE_BUGREPORT); */
+ 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]));
user_opts->aln_opts.bUseMbedForIteration = FALSE;
}
- user_opts->bForceFileOverwrite = opt_force->count;
+ if (opt_pileup->count){
+ user_opts->aln_opts.bPileup = TRUE;
+ }
+ user_opts->bForceFileOverwrite = opt_force->count;
/* log-file
*/
}
+ /* pseudo-count-file
+ */
+ if (opt_pseudo->count > 0) {
+ user_opts->pcPseudoFile = CkStrdup(opt_pseudo->filename[0]);
+ if (! FileExists(user_opts->pcPseudoFile)) {
+ Log(&rLog, LOG_FATAL, "File '%s' does not exist.", user_opts->pcPseudoFile);
+ }
+ }
+
+
/* normal sequence input (no profile)
*/
if (opt_seqin->count > 0) {
user_opts->iMaxSeqLen = opt_max_seqlen->ival[0];
}
+ /* Output format
+ */
+ if (opt_infmt->count > 0) {
+ /* avoid gcc warning about discarded qualifier */
+ char *tmp = (char *)opt_infmt->sval[0];
+ user_opts->iSeqInFormat = String2SeqfileFormat(tmp);
+ } else {
+ user_opts->iSeqInFormat = SQFILE_UNKNOWN;
+ }
+
+
/* Sequence type
*/
if (opt_seqtype->count > 0) {
Log(&rLog, LOG_FATAL, "Unknown sequence type '%s'", opt_seqtype->sval[0]);
}
}
+/* if (opt_force_protein->count > 0) {
+ user_opts->iSeqType = SEQTYPE_PROTEIN;
+ } */
/* Profile input
*/
}
}
+ if (opt_isprofile->count){
+ user_opts->bIsProfile = TRUE;
+ }
+ if (opt_usekimura->count){
+ user_opts->aln_opts.bUseKimura = TRUE;
+ }
+ if (opt_percentid->count){
+ user_opts->aln_opts.bPercID = TRUE;
+ }
+
/* HMM input
*/
}
+ /* HMM Batch, FS, r291 ->
+ */
+ user_opts->aln_opts.pcHMMBatch = NULL;
+ if (opt_hmm_batch->count>0){
+ user_opts->aln_opts.pcHMMBatch = CkStrdup(opt_hmm_batch->filename[0]);
+ if (! FileExists(user_opts->aln_opts.pcHMMBatch)){
+ Log(&rLog, LOG_FATAL, "File '%s' does not exist.", user_opts->aln_opts.pcHMMBatch);
+ }
+ }
+
/* Pair distance method
*/
if (opt_pairdist->count > 0) {
}
}
-
+ if (opt_clustersize->count > 0){ /* FS, r274 -> */
+ if (opt_clustersize->ival[0] > 0){
+ user_opts->aln_opts.iClustersizes = opt_clustersize->ival[0];
+ }
+ }
+
+ if (opt_clustfile->count > 0){ /* FS, r274 -> */
+ user_opts->aln_opts.pcClustfile = CkStrdup(opt_clustfile->filename[0]);
+ /*if (! FileExists(user_opts->aln_opts.pcClustfile)) {
+ Log(&rLog, LOG_FATAL, "File '%s' does not exist.", user_opts->aln_opts.pcClustfile);
+ }*/
+ }
+
+ if (opt_trans->count > 0){ /* FS, r290 -> */
+ user_opts->aln_opts.iTransitivity = opt_trans->ival[0];
+ }
+ if (opt_posteriorfile->count > 0){ /* FS, r288 -> */
+ user_opts->aln_opts.pcPosteriorfile = CkStrdup(opt_posteriorfile->filename[0]);
+ /*if (! FileExists(user_opts->aln_opts.pcPosteriorfile)) {
+ Log(&rLog, LOG_FATAL, "File '%s' does not exist.", user_opts->aln_opts.pcPosteriorfile);
+ }*/
+ }
+
+
/* Guidetree input
*/
if (opt_guidetree_in->count > 0) {
/* 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];
+ user_opts->aln_opts.rHhalignPara.iMacRamMB = opt_macram->ival[0];
}
+ /* Number of residues in output before line-wrap
+ */
+ if (opt_wrap->count > 0) { /* FS, r274 -> */
+ user_opts->iWrap = opt_wrap->ival[0];
+ }
+
+ user_opts->bResno = opt_resno->count;
+
+ /* output-order
+ * like input (INPUT_ORDER = 0) or tree (TREE_ORDER = 1)
+ * if output-order format not valid use INPUT_ORDER
+ */
+ if (opt_output_order->count > 0){
+ user_opts->iOutputOrder = (0 == strcmp(opt_output_order->sval[0], "input-order")) ? INPUT_ORDER :
+ (0 == strcmp(opt_output_order->sval[0], "tree-order")) ? TREE_ORDER : INPUT_ORDER;
+ }
arg_freetable(argtable,sizeof(argtable)/sizeof(argtable[0]));
mseq_t *prMSeq = NULL;
mseq_t *prMSeqProfile1 = NULL;
mseq_t *prMSeqProfile2 = NULL;
- cmdline_opts_t cmdline_opts;
- hhalign_para rHhalignPara = {0};
+ cmdline_opts_t cmdline_opts = {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 */
+ /*Log(&rLog, LOG_WARN, "This is a beta version of %s, for protein only.", PACKAGE_NAME);*/ /* FS, r237 -> 238 */
SetDefaultUserOpts(&(cmdline_opts));
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;
+#if 1
+ if (NULL != cmdline_opts.pcPseudoFile){
+ ReadPseudoCountParams(&cmdline_opts.aln_opts.rHhalignPara, cmdline_opts.pcPseudoFile);
+ }
+#endif
/* 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)) {
+ cmdline_opts.iSeqType, cmdline_opts.iSeqInFormat,
+ cmdline_opts.bIsProfile, cmdline_opts.bDealignInputSeqs,
+ cmdline_opts.iMaxNumSeq, cmdline_opts.iMaxSeqLen, cmdline_opts.aln_opts.pcHMMBatch)) {
Log(&rLog, LOG_FATAL, "Reading sequence file '%s' failed", cmdline_opts.pcSeqInfile);
}
#if TRACE
Log(&rLog, LOG_FATAL, "File '%s' contains %d sequence%s, nothing to align",
cmdline_opts.pcSeqInfile, prMSeq->nseqs, 1==prMSeq->nseqs?"":"s");
}
+ /* if there are fewer sequences than target size of clusters,
+ * then mBed is unnecessary, FS, r283-> */
+ if ( (prMSeq) && (prMSeq->nseqs <= cmdline_opts.aln_opts.iClustersizes) ){
+ cmdline_opts.aln_opts.bUseMbed = FALSE;
+ cmdline_opts.aln_opts.bUseMbedForIteration = FALSE;
+ Log(&rLog, LOG_INFO, "not more sequences (%d) than cluster-size (%d), turn off mBed",
+ prMSeq->nseqs, cmdline_opts.aln_opts.iClustersizes);
+ }
/* Dealign if requested and neccessary
*/
if (NULL != prMSeq) {
- if (TRUE == prMSeq->aligned && cmdline_opts.bDealignInputSeqs) {
+ if (/*TRUE == prMSeq->aligned &&*/ cmdline_opts.bDealignInputSeqs) {
Log(&rLog, LOG_INFO, "Dealigning already aligned input sequences as requested.");
DealignMSeq(prMSeq);
}
if (NULL != cmdline_opts.pcProfile1Infile) {
NewMSeq(&prMSeqProfile1);
if (ReadSequences(prMSeqProfile1, cmdline_opts.pcProfile1Infile,
- cmdline_opts.iSeqType,
- cmdline_opts.iMaxNumSeq, cmdline_opts.iMaxSeqLen)) {
+ cmdline_opts.iSeqType, cmdline_opts.iSeqInFormat,
+ cmdline_opts.bIsProfile, cmdline_opts.bDealignInputSeqs,
+ cmdline_opts.iMaxNumSeq, cmdline_opts.iMaxSeqLen, cmdline_opts.aln_opts.pcHMMBatch)) {
Log(&rLog, LOG_FATAL, "Reading sequences from profile file '%s' failed",
cmdline_opts.pcProfile1Infile);
}
if (NULL != cmdline_opts.pcProfile2Infile) {
NewMSeq(&prMSeqProfile2);
if (ReadSequences(prMSeqProfile2, cmdline_opts.pcProfile2Infile,
- cmdline_opts.iSeqType,
- cmdline_opts.iMaxNumSeq, cmdline_opts.iMaxSeqLen)) {
+ cmdline_opts.iSeqType, cmdline_opts.iSeqInFormat,
+ cmdline_opts.bIsProfile, cmdline_opts.bDealignInputSeqs,
+ cmdline_opts.iMaxNumSeq, cmdline_opts.iMaxSeqLen, cmdline_opts.aln_opts.pcHMMBatch)) {
Log(&rLog, LOG_FATAL, "Reading sequences from profile file '%s' failed",
cmdline_opts.pcProfile2Infile);
}
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) {
+ if (FALSE == prMSeqProfile2->aligned) {
Log(&rLog, LOG_FATAL, "Sequences in '%s' are not aligned, i.e. this is not a profile",
cmdline_opts.pcProfile2Infile);
}
* (ii) profile profile alignment
*
*/
+
if (NULL != prMSeq) {
- if (Align(prMSeq, prMSeqProfile1, & cmdline_opts.aln_opts, rHhalignPara)) {
+
+ if (2 == prMSeq->nseqs){
+ /* if there are only 2 sequences then the order does not matter */
+ /* this is important, because for pair-wise alignment we don't do
+ * tree indexing*, and trying to use tree-indexing during output
+ * will cause a segmentation fault */
+ cmdline_opts.iOutputOrder = INPUT_ORDER;
+ }
+ if (TREE_ORDER == cmdline_opts.iOutputOrder){
+ /* this is a crutch, if tree_order==NULL use input order,
+ * otherwise use guide-tree-order */
+ prMSeq->tree_order = (int *)CKMALLOC(prMSeq->nseqs * sizeof(int));
+ }
+ if (Align(prMSeq, prMSeqProfile1, & cmdline_opts.aln_opts)) {
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 (cmdline_opts.aln_opts.iMaxHMMIterations >= 0){
+ if (WriteAlignment(prMSeq, cmdline_opts.pcAlnOutfile,
+ cmdline_opts.iAlnOutFormat, cmdline_opts.iWrap, cmdline_opts.bResno)) {
+ Log(&rLog, LOG_FATAL, "Could not save alignment to %s", cmdline_opts.pcAlnOutfile);
+ }
}
#if 0
{
} else if (NULL != prMSeqProfile1 && NULL != prMSeqProfile2) {
- if (AlignProfiles(prMSeqProfile1, prMSeqProfile2, rHhalignPara)) {
+ if (AlignProfiles(prMSeqProfile1, prMSeqProfile2,
+ cmdline_opts.aln_opts.rHhalignPara)) {
Log(&rLog, LOG_FATAL, "An error occured during the alignment");
}
if (WriteAlignment(prMSeqProfile1, cmdline_opts.pcAlnOutfile,
- cmdline_opts.iAlnOutFormat)) {
+ cmdline_opts.iAlnOutFormat, cmdline_opts.iWrap, cmdline_opts.bResno)) {
Log(&rLog, LOG_FATAL, "Could not save alignment to %s", cmdline_opts.pcAlnOutfile);
}
}
--- /dev/null
+a2m.lo: a2m.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h squid.h \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h ../../src/config.h \
+ msa.h gki.h ssi.h sqfuncs.h sre_random.h vectorops.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+squid.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+aligneval.lo: aligneval.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/stdlib.h /usr/include/ctype.h \
+ squid.h /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h ../../src/config.h \
+ msa.h gki.h ssi.h sqfuncs.h sre_random.h vectorops.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/ctype.h:
+
+squid.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+alignio.lo: alignio.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/ctype.h squid.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h ../../src/config.h msa.h gki.h ssi.h sqfuncs.h \
+ sre_random.h vectorops.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/ctype.h:
+
+squid.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+clustal.lo: clustal.c \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h \
+ /usr/include/unistd.h /usr/include/features.h /usr/include/sys/cdefs.h \
+ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
+ /usr/include/gnu/stubs-64.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/types.h \
+ /usr/include/bits/typesizes.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h /usr/include/stdio.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/ctype.h squid.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ ../../src/config.h msa.h gki.h ssi.h sqfuncs.h sre_random.h vectorops.h \
+ ../config.h
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdbool.h:
+
+/usr/include/unistd.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+/usr/include/stdio.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/ctype.h:
+
+squid.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
+
+../config.h:
--- /dev/null
+cluster.lo: cluster.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/stdlib.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h squid.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h ../../src/config.h msa.h gki.h ssi.h sqfuncs.h \
+ sre_random.h vectorops.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+squid.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+dayhoff.lo: dayhoff.c /usr/include/stdlib.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/stdio.h /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h /usr/include/ctype.h squid.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h ../../src/config.h msa.h gki.h ssi.h sqfuncs.h \
+ sre_random.h vectorops.h
+
+/usr/include/stdlib.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/stdio.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/ctype.h:
+
+squid.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+eps.lo: eps.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h squid.h \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h ../../src/config.h \
+ msa.h gki.h ssi.h sqfuncs.h sre_random.h vectorops.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
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+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
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+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+squid.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+file.lo: file.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h squid.h \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h ../../src/config.h \
+ msa.h gki.h ssi.h sqfuncs.h sre_random.h vectorops.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
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+
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+
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+
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+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
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+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/stdlib.h:
+
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+
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+
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+
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+
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+
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+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+squid.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+getopt.lo: getopt.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h squid.h \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h ../../src/config.h \
+ msa.h gki.h ssi.h sqfuncs.h sre_random.h vectorops.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
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+/usr/include/bits/string.h:
+
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+
+/usr/include/endian.h:
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+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+squid.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+gki.lo: gki.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h squid.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h ../../src/config.h msa.h gki.h ssi.h sqfuncs.h \
+ sre_random.h vectorops.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
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+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h:
+
+/usr/include/limits.h:
+
+/usr/include/bits/posix1_lim.h:
+
+/usr/include/bits/local_lim.h:
+
+/usr/include/linux/limits.h:
+
+/usr/include/bits/posix2_lim.h:
+
+squid.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+gsi.lo: gsi.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h squid.h \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h ../../src/config.h \
+ msa.h gki.h ssi.h sqfuncs.h sre_random.h vectorops.h gsi.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
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+
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+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
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+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
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+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/stdlib.h:
+
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+/usr/include/bits/waitstatus.h:
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+/usr/include/bits/endian.h:
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+
+/usr/include/time.h:
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+/usr/include/bits/select.h:
+
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+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
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+
+/usr/include/bits/string2.h:
+
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+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
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+
+/usr/include/bits/nan.h:
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+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
+
+gsi.h:
--- /dev/null
+gsi64.lo: gsi64.c
--- /dev/null
+hsregex.lo: hsregex.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/ctype.h squid.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h ../../src/config.h msa.h gki.h ssi.h sqfuncs.h \
+ sre_random.h vectorops.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
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+
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+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
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+
+/usr/include/_G_config.h:
+
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+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
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+
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+
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+
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+
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+
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+
+/usr/include/sys/types.h:
+
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+
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+
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+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
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+
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+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/ctype.h:
+
+squid.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+iupac.lo: iupac.c squid.h /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h ../../src/config.h msa.h gki.h ssi.h sqfuncs.h \
+ sre_random.h vectorops.h
+
+squid.h:
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
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+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+msa.lo: msa.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h squid.h \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h ../../src/config.h \
+ msa.h gki.h ssi.h sqfuncs.h sre_random.h vectorops.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
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+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
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+
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+
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+/usr/include/bits/pthreadtypes.h:
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+/usr/include/xlocale.h:
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+
+/usr/include/bits/string2.h:
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+squid.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+msf.lo: msf.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/ctype.h squid.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h ../../src/config.h msa.h gki.h ssi.h sqfuncs.h \
+ sre_random.h vectorops.h
+
+/usr/include/stdio.h:
+
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+
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+
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+
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+
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+
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+
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+
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+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
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+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+phylip.lo: phylip.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/ctype.h squid.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h ../../src/config.h msa.h gki.h ssi.h sqfuncs.h \
+ sre_random.h vectorops.h
+
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+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+revcomp.lo: revcomp.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/stdlib.h /usr/include/ctype.h \
+ squid.h /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h ../../src/config.h \
+ msa.h gki.h ssi.h sqfuncs.h sre_random.h vectorops.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
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+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/unistd.h:
+
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+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+rk.lo: rk.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/stdlib.h /usr/include/ctype.h \
+ squid.h /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h ../../src/config.h \
+ msa.h gki.h ssi.h sqfuncs.h sre_random.h vectorops.h rk.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
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+
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+
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+
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+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
+
+rk.h:
--- /dev/null
+selex.lo: selex.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/ctype.h /usr/include/memory.h squid.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h ../../src/config.h msa.h gki.h ssi.h sqfuncs.h \
+ sre_random.h vectorops.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
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+
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+
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+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
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+
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+
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+
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+
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+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
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+
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+
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+
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+
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+
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+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
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+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/ctype.h:
+
+/usr/include/memory.h:
+
+squid.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+seqencode.lo: seqencode.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/stdlib.h /usr/include/ctype.h \
+ squid.h /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h ../../src/config.h \
+ msa.h gki.h ssi.h sqfuncs.h sre_random.h vectorops.h
+
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+
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+
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+
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+
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+
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+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
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+
+/usr/include/bits/select.h:
+
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+
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+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
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+ssi.h:
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+sqfuncs.h:
+
+sre_random.h:
+
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--- /dev/null
+shuffle.lo: shuffle.c /usr/include/string.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
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+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/stdlib.h /usr/include/ctype.h squid.h /usr/include/stdio.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h ../../src/config.h msa.h gki.h ssi.h sqfuncs.h \
+ sre_random.h vectorops.h
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+
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+
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+
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+
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+
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+
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+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+sqerror.lo: sqerror.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
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+
+/usr/include/bits/wordsize.h:
+
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+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
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+
+/usr/include/time.h:
+
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+
+/usr/include/bits/select.h:
+
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+
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+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
--- /dev/null
+sqio.lo: sqio.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/ctype.h squid.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h ../../src/config.h msa.h gki.h ssi.h sqfuncs.h \
+ sre_random.h vectorops.h
+
+/usr/include/stdio.h:
+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
+/usr/include/bits/sys_errlist.h:
+
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+
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+
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+
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+
+/usr/include/endian.h:
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+
+/usr/include/bits/byteswap.h:
+
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+
+/usr/include/time.h:
+
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+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/ctype.h:
+
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+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+squidcore.lo: squidcore.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h version.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+version.h:
--- /dev/null
+sre_ctype.lo: sre_ctype.c /usr/include/ctype.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/xlocale.h squid.h \
+ /usr/include/stdio.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h ../../src/config.h \
+ msa.h gki.h ssi.h sqfuncs.h sre_random.h vectorops.h
+
+/usr/include/ctype.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/xlocale.h:
+
+squid.h:
+
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+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/math.h:
+
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+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+sre_math.lo: sre_math.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h squid.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h ../../src/config.h \
+ msa.h gki.h ssi.h sqfuncs.h sre_random.h vectorops.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
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+
+/usr/include/stdlib.h:
+
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+
+/usr/include/bits/waitstatus.h:
+
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+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
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+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
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+
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+
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+
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+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+squid.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+sre_random.lo: sre_random.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h sre_random.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
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+
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+
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+
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+
+/usr/include/bits/stdio.h:
+
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+
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+
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+
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+
+/usr/include/bits/endian.h:
+
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+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
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+
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+
+/usr/include/sys/sysmacros.h:
+
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+
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+
+/usr/include/bits/inf.h:
+
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+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+sre_random.h:
--- /dev/null
+sre_string.lo: sre_string.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/ctype.h squid.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h ../../src/config.h msa.h gki.h ssi.h sqfuncs.h \
+ sre_random.h vectorops.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/ctype.h:
+
+squid.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+ssi.lo: ssi.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/sys/stat.h /usr/include/bits/stat.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h squid.h \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h ../../src/config.h msa.h gki.h ssi.h \
+ sqfuncs.h sre_random.h vectorops.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
+ /usr/include/limits.h /usr/include/bits/posix1_lim.h \
+ /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
+ /usr/include/bits/posix2_lim.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/sys/stat.h:
+
+/usr/include/bits/stat.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+squid.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h:
+
+/usr/include/limits.h:
+
+/usr/include/bits/posix1_lim.h:
+
+/usr/include/bits/local_lim.h:
+
+/usr/include/linux/limits.h:
+
+/usr/include/bits/posix2_lim.h:
--- /dev/null
+stack.lo: stack.c /usr/include/stdlib.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h squid.h /usr/include/stdio.h /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h ../../src/config.h msa.h gki.h ssi.h sqfuncs.h \
+ sre_random.h vectorops.h
+
+/usr/include/stdlib.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+squid.h:
+
+/usr/include/stdio.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+stockholm.lo: stockholm.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/stdlib.h squid.h \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h ../../src/config.h \
+ msa.h gki.h ssi.h sqfuncs.h sre_random.h vectorops.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/string.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/stdlib.h:
+
+squid.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+stopwatch.lo: stopwatch.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/stdlib.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h stopwatch.h \
+ /usr/include/xlocale.h /usr/include/sys/times.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
+
+/usr/include/bits/stdio.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+stopwatch.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/sys/times.h:
--- /dev/null
+translate.lo: translate.c /usr/include/stdio.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/string.h /usr/include/xlocale.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/stdlib.h squid.h \
+ /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/unistd.h \
+ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \
+ /usr/include/bits/confname.h /usr/include/getopt.h ../../src/config.h \
+ msa.h gki.h ssi.h sqfuncs.h sre_random.h vectorops.h
+
+/usr/include/stdio.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/types.h:
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+
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+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
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+
+/usr/include/bits/sys_errlist.h:
+
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+
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+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/stdlib.h:
+
+squid.h:
+
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+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
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+
+/usr/include/bits/mathinline.h:
+
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+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
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+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/unistd.h:
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+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+types.lo: types.c /usr/include/string.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/xlocale.h /usr/include/bits/string.h \
+ /usr/include/bits/string2.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/stdlib.h /usr/include/ctype.h squid.h /usr/include/stdio.h \
+ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h ../../src/config.h msa.h gki.h ssi.h sqfuncs.h \
+ sre_random.h vectorops.h
+
+/usr/include/string.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/xlocale.h:
+
+/usr/include/bits/string.h:
+
+/usr/include/bits/string2.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/stdlib.h:
+
+/usr/include/ctype.h:
+
+squid.h:
+
+/usr/include/stdio.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
+
+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
+
+/usr/include/bits/stdio_lim.h:
+
+/usr/include/bits/sys_errlist.h:
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+/usr/include/bits/stdio.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+vectorops.lo: vectorops.c /usr/include/stdlib.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/sigset.h /usr/include/bits/time.h \
+ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
+ /usr/include/alloca.h /usr/include/math.h /usr/include/bits/huge_val.h \
+ /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
+ /usr/include/bits/inf.h /usr/include/bits/nan.h \
+ /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
+ /usr/include/bits/mathinline.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h vectorops.h
+
+/usr/include/stdlib.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
+
+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/bits/types.h:
+
+/usr/include/bits/typesizes.h:
+
+/usr/include/time.h:
+
+/usr/include/sys/select.h:
+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/math.h:
+
+/usr/include/bits/huge_val.h:
+
+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h:
+
+vectorops.h:
--- /dev/null
+weight.lo: weight.c /usr/include/ctype.h /usr/include/features.h \
+ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
+ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/xlocale.h \
+ /usr/include/string.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/string.h /usr/include/bits/string2.h \
+ /usr/include/stdlib.h squid.h /usr/include/stdio.h /usr/include/libio.h \
+ /usr/include/_G_config.h /usr/include/wchar.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
+ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
+ /usr/include/bits/stdio.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
+ /usr/include/bits/select.h /usr/include/bits/sigset.h \
+ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
+ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
+ /usr/include/unistd.h /usr/include/bits/posix_opt.h \
+ /usr/include/bits/environments.h /usr/include/bits/confname.h \
+ /usr/include/getopt.h ../../src/config.h msa.h gki.h ssi.h sqfuncs.h \
+ sre_random.h vectorops.h
+
+/usr/include/ctype.h:
+
+/usr/include/features.h:
+
+/usr/include/sys/cdefs.h:
+
+/usr/include/bits/wordsize.h:
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+/usr/include/gnu/stubs.h:
+
+/usr/include/gnu/stubs-64.h:
+
+/usr/include/bits/types.h:
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+/usr/include/bits/typesizes.h:
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+/usr/include/endian.h:
+
+/usr/include/bits/endian.h:
+
+/usr/include/bits/byteswap.h:
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+/usr/include/xlocale.h:
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+/usr/include/string.h:
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+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h:
+
+/usr/include/bits/string.h:
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+/usr/include/bits/string2.h:
+
+/usr/include/stdlib.h:
+
+squid.h:
+
+/usr/include/stdio.h:
+
+/usr/include/libio.h:
+
+/usr/include/_G_config.h:
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+/usr/include/wchar.h:
+
+/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h:
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+/usr/include/bits/stdio_lim.h:
+
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+/usr/include/bits/stdio.h:
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+/usr/include/math.h:
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+/usr/include/bits/huge_val.h:
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+/usr/include/bits/huge_valf.h:
+
+/usr/include/bits/huge_vall.h:
+
+/usr/include/bits/inf.h:
+
+/usr/include/bits/nan.h:
+
+/usr/include/bits/mathdef.h:
+
+/usr/include/bits/mathcalls.h:
+
+/usr/include/bits/mathinline.h:
+
+/usr/include/bits/waitflags.h:
+
+/usr/include/bits/waitstatus.h:
+
+/usr/include/sys/types.h:
+
+/usr/include/time.h:
+
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+
+/usr/include/bits/select.h:
+
+/usr/include/bits/sigset.h:
+
+/usr/include/bits/time.h:
+
+/usr/include/sys/sysmacros.h:
+
+/usr/include/bits/pthreadtypes.h:
+
+/usr/include/alloca.h:
+
+/usr/include/unistd.h:
+
+/usr/include/bits/posix_opt.h:
+
+/usr/include/bits/environments.h:
+
+/usr/include/bits/confname.h:
+
+/usr/include/getopt.h:
+
+../../src/config.h:
+
+msa.h:
+
+gki.h:
+
+ssi.h:
+
+sqfuncs.h:
+
+sre_random.h:
+
+vectorops.h:
--- /dev/null
+# libsquid.la - a libtool library file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# The name that we can dlopen(3).
+dlname=''
+
+# Names of this library.
+library_names=''
+
+# The name of the static archive.
+old_library='libsquid.a'
+
+# Linker flags that can not go in dependency_libs.
+inherited_linker_flags=''
+
+# Libraries that this one depends upon.
+dependency_libs=' -largtable2 -lm'
+
+# Names of additional weak libraries provided by this library
+weak_library_names=''
+
+# Version information for libsquid.
+current=
+age=
+revision=
+
+# Is this an already installed library?
+installed=no
+
+# Should we warn about portability when linking against -modules?
+shouldnotlink=no
+
+# Files to dlopen/dlpreopen
+dlopen=''
+dlpreopen=''
+
+# Directory that this library needs to be installed in:
+libdir=''
--- /dev/null
+# Makefile.in generated by automake 1.10.2 from Makefile.am.
+# src/squid/Makefile. Generated from Makefile.in by configure.
+
+# 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.
+
+
+
+# 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
+
+
+
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+pkglibdir = $(libdir)/clustal-omega
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+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd
+install_sh_DATA = $(install_sh) -c -m 644
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+transform = $(program_transform_name)
+NORMAL_INSTALL = :
+PRE_INSTALL = :
+POST_INSTALL = :
+NORMAL_UNINSTALL = :
+PRE_UNINSTALL = :
+POST_UNINSTALL = :
+build_triplet = x86_64-unknown-linux-gnu
+host_triplet = x86_64-unknown-linux-gnu
+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 \
+ $(top_srcdir)/m4/lt~obsolete.m4 $(top_srcdir)/m4/ax_openmp.m4 \
+ $(top_srcdir)/configure.ac
+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+ $(ACLOCAL_M4)
+mkinstalldirs = $(install_sh) -d
+CONFIG_HEADER = $(top_builddir)/src/config.h
+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 \
+ gsi64.lo hsregex.lo iupac.lo msa.lo msf.lo phylip.lo \
+ 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)
+DEFAULT_INCLUDES = -I. -I$(top_builddir)/src
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+COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
+ $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
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+ --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \
+ $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
+CCLD = $(CC)
+LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) $(LIBTOOLFLAGS) \
+ --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)"
+library_includeHEADERS_INSTALL = $(INSTALL_HEADER)
+HEADERS = $(library_include_HEADERS)
+ETAGS = etags
+CTAGS = ctags
+DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
+ACLOCAL = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run aclocal-1.10
+AMTAR = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run tar
+#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
+# not using -DSRE_STRICT_ANSI allows to use gzipped files as input and lists user *and* system time during timings
+# not sure if there are any downsides
+# AM_CFLAGS = -DCLUSTALO -DSRE_STRICT_ANSI -O3
+AM_CFLAGS = -DCLUSTALO -O3
+AM_CXXFLAGS = -O3
+AM_LDFLAGS =
+AR = ar
+AUTOCONF = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run autoconf
+AUTOHEADER = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run autoheader
+AUTOMAKE = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run automake-1.10
+AWK = gawk
+CC = gcc
+CCDEPMODE = depmode=gcc3
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+DEPDIR = .deps
+DSYMUTIL =
+DUMPBIN =
+ECHO_C =
+ECHO_N = -n
+ECHO_T =
+EGREP = /bin/grep -E
+EXEEXT =
+FGREP = /bin/grep -F
+GREP = /bin/grep
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+INSTALL_DATA = ${INSTALL} -m 644
+INSTALL_PROGRAM = ${INSTALL}
+INSTALL_SCRIPT = ${INSTALL}
+INSTALL_STRIP_PROGRAM = $(install_sh) -c -s
+LD = /usr/bin/ld -m elf_x86_64
+LDFLAGS =
+LIBOBJS =
+LIBS = -largtable2 -lm
+LIBTOOL = $(SHELL) $(top_builddir)/libtool
+LIPO =
+LN_S = ln -s
+LTLIBOBJS =
+MAKEINFO = ${SHELL} /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/missing --run makeinfo
+MKDIR_P = /bin/mkdir -p
+NM = /usr/bin/nm -B
+NMEDIT =
+OBJDUMP = objdump
+OBJEXT = o
+OPENMP_CFLAGS = -fopenmp
+OPENMP_CXXFLAGS = -fopenmp
+OTOOL =
+OTOOL64 =
+PACKAGE = clustal-omega
+PACKAGE_BUGREPORT = clustalw@ucd.ie
+PACKAGE_CODENAME = AndreaGiacomo
+PACKAGE_NAME = Clustal Omega
+PACKAGE_STRING = Clustal Omega 1.2.4
+PACKAGE_TARNAME = clustal-omega
+PACKAGE_VERSION = 1.2.4
+PATH_SEPARATOR = :
+RANLIB = ranlib
+SED = /bin/sed
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+SHELL = /bin/sh
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+VERSION = 1.2.4
+abs_builddir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/src/squid
+abs_srcdir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo/src/squid
+abs_top_builddir = /homes/fmmarquesmadeira/Projects/jabaws/binaries/src/clustalo
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+target_alias =
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+top_builddir = ../..
+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 \
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+ && { 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*) \
+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh;; \
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+ echo ' cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@ $(am__depfiles_maybe)'; \
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+
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+ cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
+
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+ @list='$(noinst_LTLIBRARIES)'; for p in $$list; do \
+ dir="`echo $$p | sed -e 's|/[^/]*$$||'`"; \
+ test "$$dir" != "$$p" || dir=.; \
+ echo "rm -f \"$${dir}/so_locations\""; \
+ rm -f "$${dir}/so_locations"; \
+ done
+libsquid.la: $(libsquid_la_OBJECTS) $(libsquid_la_DEPENDENCIES)
+ $(LINK) $(libsquid_la_OBJECTS) $(libsquid_la_LIBADD) $(LIBS)
+
+mostlyclean-compile:
+ -rm -f *.$(OBJEXT)
+
+distclean-compile:
+ -rm -f *.tab.c
+
+include ./$(DEPDIR)/a2m.Plo
+include ./$(DEPDIR)/aligneval.Plo
+include ./$(DEPDIR)/alignio.Plo
+include ./$(DEPDIR)/clustal.Plo
+include ./$(DEPDIR)/cluster.Plo
+include ./$(DEPDIR)/dayhoff.Plo
+include ./$(DEPDIR)/eps.Plo
+include ./$(DEPDIR)/file.Plo
+include ./$(DEPDIR)/getopt.Plo
+include ./$(DEPDIR)/gki.Plo
+include ./$(DEPDIR)/gsi.Plo
+include ./$(DEPDIR)/gsi64.Plo
+include ./$(DEPDIR)/hsregex.Plo
+include ./$(DEPDIR)/iupac.Plo
+include ./$(DEPDIR)/msa.Plo
+include ./$(DEPDIR)/msf.Plo
+include ./$(DEPDIR)/phylip.Plo
+include ./$(DEPDIR)/revcomp.Plo
+include ./$(DEPDIR)/rk.Plo
+include ./$(DEPDIR)/selex.Plo
+include ./$(DEPDIR)/seqencode.Plo
+include ./$(DEPDIR)/shuffle.Plo
+include ./$(DEPDIR)/sqerror.Plo
+include ./$(DEPDIR)/sqio.Plo
+include ./$(DEPDIR)/squidcore.Plo
+include ./$(DEPDIR)/sre_ctype.Plo
+include ./$(DEPDIR)/sre_math.Plo
+include ./$(DEPDIR)/sre_random.Plo
+include ./$(DEPDIR)/sre_string.Plo
+include ./$(DEPDIR)/ssi.Plo
+include ./$(DEPDIR)/stack.Plo
+include ./$(DEPDIR)/stockholm.Plo
+include ./$(DEPDIR)/stopwatch.Plo
+include ./$(DEPDIR)/translate.Plo
+include ./$(DEPDIR)/types.Plo
+include ./$(DEPDIR)/vectorops.Plo
+include ./$(DEPDIR)/weight.Plo
+
+.c.o:
+ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $<
+ mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po
+# source='$<' object='$@' libtool=no \
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+# $(COMPILE) -c `$(CYGPATH_W) '$<'`
+
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+ mv -f $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Plo
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+# DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) \
+# $(LTCOMPILE) -c -o $@ $<
+
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+ -rm -f *.lo
+
+clean-libtool:
+ -rm -rf .libs _libs
+install-library_includeHEADERS: $(library_include_HEADERS)
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+ echo "INSTALL_PROGRAM_ENV=STRIPPROG='$(STRIP)'"` install
+mostlyclean-generic:
+
+clean-generic:
+
+distclean-generic:
+ -test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
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+ @echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
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+clean-am: clean-generic clean-libtool clean-noinstLTLIBRARIES \
+ mostlyclean-am
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+distclean: distclean-am
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+mostlyclean-am: mostlyclean-compile mostlyclean-generic \
+ mostlyclean-libtool
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+pdf: pdf-am
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+ps: ps-am
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+.PHONY: CTAGS GTAGS all all-am check check-am clean clean-generic \
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+ distclean-compile distclean-generic distclean-libtool \
+ distclean-tags distdir dvi dvi-am html html-am info info-am \
+ install install-am install-data install-data-am install-dvi \
+ install-dvi-am install-exec install-exec-am install-html \
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+ install-pdf-am install-ps install-ps-am install-strip \
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+ maintainer-clean-generic mostlyclean mostlyclean-compile \
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+ tags uninstall uninstall-am uninstall-library_includeHEADERS
+
+# 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:
# 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@
+# not using -DSRE_STRICT_ANSI allows to use gzipped files as input and lists user *and* system time during timings
+# not sure if there are any downsides
+# AM_CFLAGS = -DCLUSTALO -DSRE_STRICT_ANSI @AM_CFLAGS@
+AM_CFLAGS = -DCLUSTALO @AM_CFLAGS@
noinst_LTLIBRARIES = libsquid.la
# 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@
+# not using -DSRE_STRICT_ANSI allows to use gzipped files as input and lists user *and* system time during timings
+# not sure if there are any downsides
+# AM_CFLAGS = -DCLUSTALO -DSRE_STRICT_ANSI @AM_CFLAGS@
+AM_CFLAGS = -DCLUSTALO @AM_CFLAGS@
AM_CXXFLAGS = @AM_CXXFLAGS@
AM_LDFLAGS = @AM_LDFLAGS@
AR = @AR@
*
* 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)
+ * RCS $Id: a2m.c 297 2014-10-31 13:02:37Z fabian $ (Original squid RCS Id: a2m.c,v 1.1 1999/07/15 22:26:40 eddy Exp)
*/
#include <stdio.h>
*/
void
#ifdef CLUSTALO
-WriteA2M(FILE *fp, MSA *msa, int vienna)
+/*WriteA2M(FILE *fp, MSA *msa, int vienna)*/
+WriteA2M(FILE *fp, MSA *msa, int iWrap)
#else
WriteA2M(FILE *fp, MSA *msa)
#endif
{
int idx; /* sequence index */
int pos; /* position in sequence */
+#ifdef CLUSTALO
+ char *buf; /* buffer for writing seq */
+ int cpl = msa->alen<iWrap ? msa->alen+10 : (iWrap > 0 ? iWrap : 60); /* char per line (< 64) */
+#else
char buf[64]; /* buffer for individual lines */
int cpl = 60; /* char per line; must be < 64 unless buf is bigger */
-
+#endif
+
+#ifdef CLUSTALO
+ if (NULL == (buf = (char *)malloc(cpl+20))){
+ Die("%s:%s:%d: could not malloc %d char for buffer",
+ __FUNCTION__, __FILE__, __LINE__, cpl+20);
+ }
+ else {
+ memset(buf, 0, cpl+20);
+ }
+#endif
+
+
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");
+ /* 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] : "");
+ 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)
+ 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);
+ strncpy(buf, &(msa->aseq[idx][pos]), cpl);
+ /*if (vienna)
+ fprintf(fp, "%s", buf);
+ else*/
+ fprintf(fp, "%s\n", buf);
}
- if (vienna)
- fprintf(fp, "\n");
-
+ /*if (vienna)
+ fprintf(fp, "\n");*/
+
}
-}
+
+#ifdef CLUSTALO
+ free(buf); buf = NULL;
+#endif
+
+} /* this is the end of WriteA2M() */
--- /dev/null
+# a2m.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/a2m.o'
+
+# Name of the non-PIC object
+non_pic_object='a2m.o'
+
--- /dev/null
+# aligneval.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/aligneval.o'
+
+# Name of the non-PIC object
+non_pic_object='aligneval.o'
+
--- /dev/null
+# alignio.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/alignio.o'
+
+# Name of the non-PIC object
+non_pic_object='alignio.o'
+
* 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)
+ * RCS $Id: clustal.c 315 2016-12-15 17:18:30Z fabian $ (Original squid RCS Id: clustal.c,v 1.1 1999/07/15 22:26:53 eddy Exp)
*/
+#include <stdbool.h>
+#include <unistd.h>
+
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
/* needed for PACKAGE_VERSION */
#include "../config.h"
+/* DD: isnumber is in BSD/OSX but not GCC/Linux */
+#ifndef isnumber
+ #define isnumber(c) ( (c>='0') && (c<='9'))
+#endif
+
#ifndef min
#define min( a, b ) ( ((a) < (b)) ? (a) : (b) )
#endif
while ((msa = ReadClustal(afp)) != NULL)
{
+#ifdef CLUSTALO
+#define LINE_WRAP 60
+ WriteClustal(stdout, msa, LINE_WRAP);
+#else
WriteClustal(stdout, msa);
+#endif
MSAFree(msa);
}
*/
if (strpbrk(name, ".*:") != NULL && strpbrk(seq, ".*:") != NULL)
continue;
+#ifdef CLUSTALO
+ /* extra bit at the end of a line might be the unaligned residue
+ count */
+ if (s2 != NULL) {
+ int i;
+ for (i=0; i<strlen(s2); i++) {
+ if (! isnumber(s2[i])) {
+ Die("Parse failed at line %d, file %s: possibly using spaces as gaps",
+ afp->linenumber, afp->fname);
+ }
+ }
+ }
+#else
if (s2 != NULL)
- Die("Parse failed at line %d, file %s: possibly using spaces as gaps",
- afp->linenumber, afp->fname);
-
+ Die("Parse failed at line %d, file %s: possibly using spaces as gaps",
+ afp->linenumber, afp->fname);
+#endif
/* It's not blank, and it's not a coord line: must be sequence
*/
sqidx = MSAGetSeqidx(msa, name, msa->lastidx+1);
return msa;
}
+size_t utf8len(char *s)
+{
+ size_t len = 0;
+ for (; *s; ++s) if ((*s & 0xC0) != 0x80) ++len;
+ return len;
+}
+
/* Function: WriteClustal()
* Date: SRE, Sun Jun 6 18:12:47 1999 [bus from Madison, worm mtg 1999]
* Returns: (void)
*/
void
+#ifdef CLUSTALO
+WriteClustal(FILE *fp, MSA *msa, int iWrap, int bResno, int iSeqType)
+#else
WriteClustal(FILE *fp, MSA *msa)
+#endif
{
int idx; /* counter for sequences */
int len; /* tmp variable for name lengths */
int namelen; /* maximum name length used */
int pos; /* position counter */
+#ifdef CLUSTALO
+ char *buf; /* buffer for writing seq */
+ int cpl = msa->alen<iWrap ? msa->alen+10 : (iWrap > 0 ? iWrap : 60); /* char per line (< 64) */
+#else
char buf[80]; /* buffer for writing seq */
int cpl = 60; /* char per line (< 64) */
+#endif
/* consensus line stuff */
int subpos;
int bail;
int strong_bins[9];
int weak_bins[11];
- int cons;
+ /*int cons;*/
int bin;
+#ifdef CLUSTALO
+ int *piResCnt = NULL;
+#endif
+
+#ifdef CLUSTALO
+ if (1 == bResno){
+
+ if (NULL == (piResCnt = (int *)malloc(msa->nseq * sizeof(int)))){
+ Die("%s:%s:%d: could not malloc %d int for residue count",
+ __FUNCTION__, __FILE__, __LINE__, msa->nseq);
+ }
+ else {
+ memset(piResCnt, 0, msa->nseq * sizeof(int));
+ }
+ } /* do print residue numbers */
+
+ if (NULL == (buf = (char *)malloc(cpl+20))){
+ Die("%s:%s:%d: could not malloc %d char for buffer",
+ __FUNCTION__, __FILE__, __LINE__, cpl+20);
+ }
+ else {
+ memset(buf, 0, cpl+20);
+ }
+
+#endif
+
+
/* calculate max namelen used */
namelen = 0;
- for (idx = 0; idx < msa->nseq; idx++)
- if ((len = strlen(msa->sqname[idx])) > namelen)
- namelen = len;
+ for (idx = 0; idx < msa->nseq; idx++){
+ /*if ((len = strlen(msa->sqname[idx])) > namelen) */ /* strlen() gives problems for unicode, FS, -> 290 */
+ if ((len = utf8len(msa->sqname[idx])) > namelen)
+ {
+ namelen = len;
+ }
+ }
#ifdef CLUSTALO
fprintf(fp, "CLUSTAL O(%s) multiple sequence alignment\n", PACKAGE_VERSION);
strncpy(buf, msa->aseq[idx] + pos, cpl);
buf[cpl] = '\0';
#ifdef CLUSTALO
- fprintf(fp, "%-*s %s\n", namelen+5, msa->sqname[idx], buf);
+ if (1 == bResno){
+ char *pc = NULL;
+ for (pc = buf; *pc != '\0'; pc++){
+ if ( ( (*pc >= 'a') && (*pc <= 'z') ) || ( (*pc >= 'A') && (*pc <= 'Z') ) ){
+ piResCnt[idx]++;
+ }
+ }
+ /* printf("%*s") gives problems for unicode, FS, -> 290 */
+ /*fprintf(fp, "%-*s\t%s\t%d\n", namelen+5, msa->sqname[idx], buf, piResCnt[idx]);*/
+ fprintf(fp, "%s%*s %s\t%d\n", msa->sqname[idx], (int)(namelen+5-utf8len(msa->sqname[idx])), "", buf, piResCnt[idx]);
+ }
+ else {
+ /* printf("%*s") gives problems for unicode, FS, -> 290 */
+ /*fprintf(fp, "%-*s\t%s\n", namelen+5, msa->sqname[idx], buf);*/
+ fprintf(fp, "%s%*s %s\n", msa->sqname[idx], (int)(namelen+5-utf8len(msa->sqname[idx])), "", buf);
+ }
#else
fprintf(fp, "%*s %s\n", namelen, msa->sqname[idx], buf);
#endif
bail = 0;
for (idx = 1; idx < msa->nseq; idx++)
{
- if(msa->aseq[idx][subpos] != first)
+ if(toupper(msa->aseq[idx][subpos]) != toupper(first)) /* toupper makes consensus case-insensitive, FS, r290 -> */
{
bail = 1;
break;
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])
+ for (idx = 0; (iSeqType == kAmino) && (idx < msa->nseq); idx++)
+ { /* do this only for amino acids, no strong/weak consensus for nucleotide, FS, r290 -> */
+ switch(toupper(msa->aseq[idx][subpos])) /* toupper makes consensus case-insensitive, FS, r290 -> */
{
case 'S': strong_bins[0]++; break;
case 'T': strong_bins[0]++; 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 'H': strong_bins[2]++; strong_bins[4]++; strong_bins[7]++; break; /* added bin-2 (NHQK), FS 2016-07-14 */
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;
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])
+ for(idx = 0; (iSeqType == kAmino) && (idx < msa->nseq); idx++)
+ { /* do this only for amino acids, no strong/weak consensus for nucleotide, FS, r290 -> */
+ switch(toupper(msa->aseq[idx][subpos])) /* toupper makes consensus case-insensitive, FS, r290 -> */
{
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 'G': weak_bins[2]++; weak_bins[5]++; break; /* Added bin-5, FS 2016-07-14 */
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;
#endif
}
+#ifdef CLUSTAL
+ free(piResCnt); piResCnt = NULL;
+#endif
+
return;
}
--- /dev/null
+# clustal.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/clustal.o'
+
+# Name of the non-PIC object
+non_pic_object='clustal.o'
+
--- /dev/null
+# cluster.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/cluster.o'
+
+# Name of the non-PIC object
+non_pic_object='cluster.o'
+
--- /dev/null
+# dayhoff.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/dayhoff.o'
+
+# Name of the non-PIC object
+non_pic_object='dayhoff.o'
+
--- /dev/null
+# eps.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/eps.o'
+
+# Name of the non-PIC object
+non_pic_object='eps.o'
+
--- /dev/null
+# file.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/file.o'
+
+# Name of the non-PIC object
+non_pic_object='file.o'
+
--- /dev/null
+# getopt.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/getopt.o'
+
+# Name of the non-PIC object
+non_pic_object='getopt.o'
+
* 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)
+ * RCS $Id: gki.c 293 2014-02-28 18:37:03Z fabian $ (Original squid RCS Id: gki.c,v 1.3 2000/12/21 23:42:59 eddy Exp)
*/
int val;
struct gki_elem *ptr;
- val = gki_hashvalue(hash, key);
+ val = gki_hashvalue(hash, key); if(val<0){val=0;} /* problem for multi-byte characters, FS 291-> */
ptr = hash->table[val];
hash->table[val] = MallocOrDie(sizeof(struct gki_elem));
--- /dev/null
+# gki.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/gki.o'
+
+# Name of the non-PIC object
+non_pic_object='gki.o'
+
--- /dev/null
+# gsi.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/gsi.o'
+
+# Name of the non-PIC object
+non_pic_object='gsi.o'
+
--- /dev/null
+# gsi64.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/gsi64.o'
+
+# Name of the non-PIC object
+non_pic_object='gsi64.o'
+
register char *ret;
register char *chain;
register char *latest;
- int flags;
+ int flags = 0;
register int c;
*flagp = WORST; /* Tentatively. */
register char *ret;
register char op;
register char *next;
- int flags;
+ int flags = 0;
ret = regatom(cp, &flags);
if (ret == NULL)
--- /dev/null
+# hsregex.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/hsregex.o'
+
+# Name of the non-PIC object
+non_pic_object='hsregex.o'
+
--- /dev/null
+# iupac.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/iupac.o'
+
+# Name of the non-PIC object
+non_pic_object='iupac.o'
+
--- /dev/null
+# libsquid.la - a libtool library file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# The name that we can dlopen(3).
+dlname=''
+
+# Names of this library.
+library_names=''
+
+# The name of the static archive.
+old_library='libsquid.a'
+
+# Linker flags that can not go in dependency_libs.
+inherited_linker_flags=''
+
+# Libraries that this one depends upon.
+dependency_libs=' -largtable2 -lm'
+
+# Names of additional weak libraries provided by this library
+weak_library_names=''
+
+# Version information for libsquid.
+current=
+age=
+revision=
+
+# Is this an already installed library?
+installed=no
+
+# Should we warn about portability when linking against -modules?
+shouldnotlink=no
+
+# Files to dlopen/dlpreopen
+dlopen=''
+dlpreopen=''
+
+# Directory that this library needs to be installed in:
+libdir=''
* 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)
+ * RCS $Id: msa.c 297 2014-10-31 13:02:37Z fabian $ (Original squid RCS Id: msa.c,v 1.18 2002/10/12 04:40:35 eddy Exp)
*/
#include <stdio.h>
msa->sslen = NULL;
msa->sa = NULL;
msa->salen = NULL;
+ msa->co = NULL;
+ msa->colen = NULL;
msa->index = GKIInit();
msa->lastidx = 0;
Free2DArray((void **) msa->sqdesc, msa->nseq);
Free2DArray((void **) msa->ss, msa->nseq);
Free2DArray((void **) msa->sa, msa->nseq);
+ Free2DArray((void **) msa->co, msa->nseq);
if (msa->sqlen != NULL) free(msa->sqlen);
if (msa->wgt != NULL) free(msa->wgt);
if (msa->nseq == 0) Die("Parse error: no sequences were found for alignment %s",
msa->name != NULL ? msa->name : "");
- msa->alen = msa->sqlen[0];
+ 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
msa->sqname[idx],
msa->name != NULL ? msa->name : "");
/* all aseq must be same length. */
- if (msa->sqlen[idx] != msa->alen)
+ 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 cons SS is present, must have length right */
- if (msa->ss_cons != NULL && strlen(msa->ss_cons) != msa->alen)
+ if (msa->ss_cons != NULL && strlen(msa->ss_cons) != msa->alen) /* FIXME */
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)
+ if (msa->sa_cons != NULL && strlen(msa->sa_cons) != msa->alen) /* FIXME */
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 : "");
}
+/* @* MSAVerifyParseDub */
+void
+MSAVerifyParseDub(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 : "");
+ /* this is Dublin format, aseq don't have to be same length. */
+ if (msa->sqlen[idx] > msa->alen) {
+ msa->alen = msa->sqlen[idx];
+ }
+ /* if SS is present, must have length right */
+ if (msa->ss != NULL && msa->ss[idx] != NULL && msa->sslen[idx] != msa->sqlen[idx])
+ Die("Parse error: #=GR SS annotation for %s: length %d, expected %d in alignment %s",
+ msa->sqname[idx], msa->sslen[idx], msa->sqlen[idx],
+ 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->sqlen[idx])
+ Die("Parse error: #=GR SA annotation for %s: length %d, expected %d in alignment %s",
+ msa->sqname[idx], msa->salen[idx], msa->sqlen[idx],
+ msa->name != NULL ? msa->name : "");
+
+ /* if CO is present, must have length right */
+ if (msa->co != NULL && msa->co[idx] != NULL && msa->colen[idx] != msa->sqlen[idx])
+ Die("Parse error: #=GR CO annotation for %s: length %d, expected %d in alignment %s",
+ msa->sqname[idx], msa->colen[idx], msa->sqlen[idx],
+ 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; }
+ if (msa->colen != NULL) { free(msa->colen); msa->colen = NULL; }
+
+ return;
+} /* this is the end of MSAVerifyParseDub() */
+
/* Function: MSAFileOpen()
case MSAFILE_CLUSTAL: msa = ReadClustal(afp); break;
case MSAFILE_SELEX: msa = ReadSELEX(afp); break;
case MSAFILE_PHYLIP: msa = ReadPhylip(afp); break;
+ case MSAFILE_DUBLIN: msa = ReadDublin(afp); break; /* -> r296, FS */
default:
Die("MSAFILE corrupted: bad format index");
}
}
void
-MSAFileWrite(FILE *fp, MSA *msa, int outfmt, int do_oneline)
+MSAFileWrite(FILE *fp, MSA *msa, int outfmt, int do_oneline, int iWrap, int bResno, int iSeqType)
{
switch (outfmt) {
#ifdef CLUSTALO
- case MSAFILE_A2M: WriteA2M(stdout, msa, 0); break;
- case MSAFILE_VIENNA: WriteA2M(stdout, msa, 1); break;
+ /*case MSAFILE_A2M: WriteA2M(stdout, msa, 0); break;*/
+ /*case MSAFILE_VIENNA: WriteA2M(stdout, msa, 1); break;*/
+ case MSAFILE_A2M: WriteA2M(stdout, msa, iWrap); break;
+#ifndef INT_MAX
+#define INT_MAX 2147483647
+#endif
+ case MSAFILE_VIENNA: WriteA2M(stdout, msa, INT_MAX); break;
+ case MSAFILE_CLUSTAL: WriteClustal(stdout, msa, iWrap, bResno, iSeqType); break;
#else
case MSAFILE_A2M: WriteA2M(stdout, msa); break;
-#endif
case MSAFILE_CLUSTAL: WriteClustal(stdout, msa); break;
+#endif
case MSAFILE_MSF: WriteMSF(stdout, msa); break;
case MSAFILE_PHYLIP: WritePhylip(stdout, msa); break;
case MSAFILE_SELEX: WriteSELEX(stdout, msa); break;
* 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)
+ * RCS $Id: msa.h 297 2014-10-31 13:02:37Z fabian $ (Original squid RCS Id: msa.h,v 1.12 2002/10/12 04:40:35 eddy Exp)
*/
#include <stdio.h> /* FILE support */
char **sqacc; /* accession numbers for individual sequences */
char **sqdesc; /* description lines for individual sequences */
char **ss; /* per-seq secondary structure annotation, or NULL */
+ char **co; /* per-seq confidence of secondary structure annotation, or NULL, -> r296, FS */
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 */
int *sqlen; /* individual sequence lengths during parsing */
int *sslen; /* individual ss lengths during parsing */
int *salen; /* individual sa lengths during parsing */
+ int *colen; /* individual co 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 */
#define MSAFILE_EPS 107 /* Encapsulated PostScript (output only) */
#ifdef CLUSTALO
#define MSAFILE_VIENNA 108 /* Vienna: concatenated fasta */
+#define MSAFILE_DUBLIN 109 /* Dublin: modified Stockholm format */
#endif
#define IsAlignmentFormat(fmt) ((fmt) > 100)
extern MSA *MSAFileRead(MSAFILE *afp);
extern void MSAFileClose(MSAFILE *afp);
extern void MSAFree(MSA *msa);
+#ifdef CLUSTALO
+extern void MSAFileWrite(FILE *fp, MSA *msa, int outfmt, int do_oneline, int iWrap, int bResno, int iSeqtype);
+#else
extern void MSAFileWrite(FILE *fp, MSA *msa, int outfmt, int do_oneline);
+#endif
extern int MSAFileRewind(MSAFILE *afp);
extern int MSAFilePositionByKey(MSAFILE *afp, char *key);
extern char *MSAGetGC(MSA *msa, char *tag);
extern void MSAAppendGR(MSA *msa, char *tag, int seqidx, char *value);
extern void MSAVerifyParse(MSA *msa);
+extern void MSAVerifyParseDub(MSA *msa);
extern int MSAGetSeqidx(MSA *msa, char *name, int guess);
extern MSA *MSAFromAINFO(char **aseq, AINFO *ainfo);
*/
extern MSA *ReadA2M(MSAFILE *afp);
#ifdef CLUSTALO
-extern void WriteA2M(FILE *fp, MSA *msa, int vienna);
+/*extern void WriteA2M(FILE *fp, MSA *msa, int vienna);*/
+extern void WriteA2M(FILE *fp, MSA *msa, int iWrap);
#else
extern void WriteA2M(FILE *fp, MSA *msa);
#endif
/* from clustal.c
*/
extern MSA *ReadClustal(MSAFILE *afp);
+#ifdef CLUSTALO
+extern void WriteClustal(FILE *fp, MSA *msa, int iWrap, int bResno, int iSeqType);
+#else
extern void WriteClustal(FILE *fp, MSA *msa);
+#endif
/* from eps.c
*/
/* from stockholm.c
*/
+extern MSA *ReadDublin(MSAFILE *afp);
extern MSA *ReadStockholm(MSAFILE *afp);
extern void WriteStockholm(FILE *fp, MSA *msa);
extern void WriteStockholmOneBlock(FILE *fp, MSA *msa);
--- /dev/null
+# msa.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/msa.o'
+
+# Name of the non-PIC object
+non_pic_object='msa.o'
+
* 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)
+ * RCS $Id: msf.c 316 2016-12-16 16:14:39Z fabian $ (Original squid RCS Id: msf.c,v 1.4 2001/04/23 00:35:33 eddy Exp)
*/
#include <stdio.h>
{
MSA *msa;
char *s;
- int alleged_alen;
- int alleged_type;
- int alleged_checksum;
+ int alleged_alen = 0;
+ int alleged_type = 0;
+ int alleged_checksum = 0;
char *tok;
char *sp;
int slen;
--- /dev/null
+# msf.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/msf.o'
+
+# Name of the non-PIC object
+non_pic_object='msf.o'
+
--- /dev/null
+# phylip.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/phylip.o'
+
+# Name of the non-PIC object
+non_pic_object='phylip.o'
+
--- /dev/null
+# revcomp.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/revcomp.o'
+
+# Name of the non-PIC object
+non_pic_object='revcomp.o'
+
--- /dev/null
+# rk.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/rk.o'
+
+# Name of the non-PIC object
+non_pic_object='rk.o'
+
--- /dev/null
+# selex.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/selex.o'
+
+# Name of the non-PIC object
+non_pic_object='selex.o'
+
--- /dev/null
+# seqencode.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/seqencode.o'
+
+# Name of the non-PIC object
+non_pic_object='seqencode.o'
+
--- /dev/null
+# shuffle.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/shuffle.o'
+
+# Name of the non-PIC object
+non_pic_object='shuffle.o'
+
--- /dev/null
+# sqerror.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/sqerror.o'
+
+# Name of the non-PIC object
+non_pic_object='sqerror.o'
+
free(sqinfo->sa);
}
}
-}
+ if (sqinfo->flags & SQINFO_CO){
+ if (NULL != sqinfo->co){ /* FS, r296 -> */
+ free(sqinfo->co);
+ }
+ }
+} /* this is the end of FreeSequence() */
int
SetSeqinfoString(SQINFO *sqinfo, char *sptr, int flag)
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);
+ if (sq2->flags & SQINFO_CO) sq1->co = Strdup(sq2->co);
}
/* Function: ToDNA()
return(*s == '>');
}
+#ifdef CLUSTALO
+static int
+only_whitespace(const char *s) {
+ while (*s != '\0') {
+ if (!isspace((unsigned char)*s))
+ return 0;
+ s++;
+ }
+ return 1;
+}
+#endif
+
static void
readPearson(struct ReadSeqVars *V)
{
if (V->ssimode >= 0) V->r_off = V->ssioffset;
+#ifdef CLUSTALO
+ while (only_whitespace(V->buf)) {
+ SeqfileGetLine(V);
+ }
+
+ if (feof(V->f) || *V->buf != '>')
+#else
if (*V->buf != '>')
+#endif
+#ifdef CLUSTALO
+ 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 --infmt <fmt>.\n",
+ V->fname, V->linenumber);
+#else
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);
-
+#endif
if ((sptr = strtok(V->buf+1, "\n\t ")) != NULL)
SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
if ((sptr = strtok(NULL, "\n")) != NULL)
#endif
sqinfo->flags |= SQINFO_SA;
}
+ if (V->msa->co != NULL && V->msa->co[V->msa->lastidx] != NULL) {
+/* AW: stopping squid from dealigning sequences and corresponding info */
+#ifdef CLUSTALO
+ sqinfo->co = sre_strdup(V->msa->co[V->msa->lastidx], V->msa->alen);
+#else
+ MakeDealignedString(V->msa->aseq[V->msa->lastidx], V->msa->alen,
+ V->msa->co[V->msa->lastidx], &(sqinfo->co));
+#endif
+ sqinfo->flags |= SQINFO_CO;
+ } /* co */
V->msa->lastidx++;
}
else {
strncmp(buf, "!!NA_SEQUENCE", 13) == 0)
{ fmt = SQFILE_GCG; goto DONE; }
+ if (strncmp(buf, "# DUBLIN 1.", 11) == 0) /* -> r296, FS */
+ { fmt = MSAFILE_DUBLIN; goto DONE; }
+
if (strncmp(buf, "# STOCKHOLM 1.", 14) == 0)
{ fmt = MSAFILE_STOCKHOLM; goto DONE; }
if (strcmp(s2, "FASTA") == 0) code = SQFILE_FASTA;
#ifdef CLUSTALO
- if (strcmp(s2, "FA") == 0) code = SQFILE_FASTA;
+ else 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
--- /dev/null
+# sqio.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/sqio.o'
+
+# Name of the non-PIC object
+non_pic_object='sqio.o'
+
/****************************************************
* Single sequence information
****************************************************/
-#define SQINFO_NAMELEN 64
+#define SQINFO_NAMELEN 128 /* increased 64 -> 128, FS, r274 -> */
#define SQINFO_DESCLEN 128
struct seqinfo_s {
int type; /* kRNA, kDNA, kAmino, or kOther */
char *ss; /* 0..len-1 secondary structure string */
char *sa; /* 0..len-1 % side chain surface access. */
+ char *co; /* 0..len-1 secondary struct confidence */
};
typedef struct seqinfo_s SQINFO;
#define SQINFO_OLEN (1 << 8)
#define SQINFO_SS (1 << 9)
#define SQINFO_SA (1 << 10)
+#define SQINFO_CO (1 << 11)
/****************************************************
/* 17 was Clustal. Now alignment format*/
#ifdef CLUSTALO
#define SQFILE_VIENNA 18 /* Vienna format: concatenated fasta */
+#define SQFILE_DUBLIN 19 /* unaligned version of Stockholm */
#endif
#define IsUnalignedFormat(fmt) ((fmt) && (fmt) < 100)
--- /dev/null
+# squidcore.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/squidcore.o'
+
+# Name of the non-PIC object
+non_pic_object='squidcore.o'
+
--- /dev/null
+# sre_ctype.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/sre_ctype.o'
+
+# Name of the non-PIC object
+non_pic_object='sre_ctype.o'
+
--- /dev/null
+# sre_math.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/sre_math.o'
+
+# Name of the non-PIC object
+non_pic_object='sre_math.o'
+
--- /dev/null
+# sre_random.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/sre_random.o'
+
+# Name of the non-PIC object
+non_pic_object='sre_random.o'
+
--- /dev/null
+# sre_string.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/sre_string.o'
+
+# Name of the non-PIC object
+non_pic_object='sre_string.o'
+
--- /dev/null
+# ssi.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/ssi.o'
+
+# Name of the non-PIC object
+non_pic_object='ssi.o'
+
--- /dev/null
+# stack.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/stack.o'
+
+# Name of the non-PIC object
+non_pic_object='stack.o'
+
* 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)
+ * RCS $Id: stockholm.c 297 2014-10-31 13:02:37Z fabian $ (Original squid RCS Id: stockholm.c,v 1.7 2002/10/12 04:40:36 eddy Exp)
*/
#include <stdio.h>
#include <string.h>
return msa;
}
+/* Function: ReadDublin()
+ * Date: 2014-10-15
+ *
+ * Purpose: Parse the next sequences from an open Dublin
+ * format file. Return the sequences, or
+ * NULL if there are no more sequences 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 *
+ReadDublin(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 Dublin 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, "# DUBLIN 1.", 11) != 0)
+ Die("\
+File %s doesn't appear to be in Dublin 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("Dublin 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;
+ }
+
+ MSAVerifyParseDub(msa);
+ return msa;
+
+} /* this is the end of ReadDublin() */
+
/* Function: WriteStockholm()
* Date: SRE, Mon May 31 19:15:22 1999 [St. Louis]
}
msa->salen[seqidx] = sre_strcat(&(msa->sa[seqidx]), msa->salen[seqidx], text, len);
}
+ else if (strcmp(featurename, "CO") == 0)
+ {
+ if (msa->co == NULL)
+ {
+ msa->co = MallocOrDie(sizeof(char *) * msa->nseqalloc);
+ msa->colen = MallocOrDie(sizeof(int) * msa->nseqalloc);
+ for (j = 0; j < msa->nseqalloc; j++)
+ {
+ msa->co[j] = NULL;
+ msa->colen[j] = 0;
+ }
+ }
+ msa->colen[seqidx] = sre_strcat(&(msa->co[seqidx]), msa->colen[seqidx], text, len);
+ }
else
MSAAppendGR(msa, featurename, seqidx, text);
--- /dev/null
+# stockholm.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/stockholm.o'
+
+# Name of the non-PIC object
+non_pic_object='stockholm.o'
+
--- /dev/null
+# stopwatch.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/stopwatch.o'
+
+# Name of the non-PIC object
+non_pic_object='stopwatch.o'
+
--- /dev/null
+# translate.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/translate.o'
+
+# Name of the non-PIC object
+non_pic_object='translate.o'
+
--- /dev/null
+# types.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/types.o'
+
+# Name of the non-PIC object
+non_pic_object='types.o'
+
--- /dev/null
+# vectorops.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/vectorops.o'
+
+# Name of the non-PIC object
+non_pic_object='vectorops.o'
+
--- /dev/null
+# weight.lo - a libtool object file
+# Generated by ltmain.sh (GNU libtool) 2.2.6 Debian-2.2.6a-1ubuntu1
+#
+# Please DO NOT delete this file!
+# It is necessary for linking the library.
+
+# Name of the PIC object.
+pic_object='.libs/weight.o'
+
+# Name of the non-PIC object
+non_pic_object='weight.o'
+
--- /dev/null
+timestamp for src/config.h
echo "Compiling Clustal Omega..."
cd clustalo
-make clean
chmod +x ./configure
./configure
+make clean
make
+chmod +x src/clustalo
cd ..
echo "Compiling Mafft..."
- GNU GENERAL PUBLIC LICENSE\r
- Version 2, June 1991\r
-\r
- Copyright (C) 1989, 1991 Free Software Foundation, Inc.,\r
- 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA\r
- Everyone is permitted to copy and distribute verbatim copies\r
- of this license document, but changing it is not allowed.\r
-\r
- Preamble\r
-\r
- The licenses for most software are designed to take away your\r
-freedom to share and change it. By contrast, the GNU General Public\r
-License is intended to guarantee your freedom to share and change free\r
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-Foundation's software and to any other program whose authors commit to\r
-using it. (Some other Free Software Foundation software is covered by\r
-the GNU Lesser General Public License instead.) You can apply it to\r
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-\r
- When we speak of free software, we are referring to freedom, not\r
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- To protect your rights, we need to make restrictions that forbid\r
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- For example, if you distribute copies of such a program, whether\r
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-rights.\r
-\r
- We protect your rights with two steps: (1) copyright the software, and\r
-(2) offer you this license which gives you legal permission to copy,\r
-distribute and/or modify the software.\r
-\r
- Also, for each author's protection and ours, we want to make certain\r
-that everyone understands that there is no warranty for this free\r
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-\r
- Finally, any free program is threatened constantly by software\r
-patents. We wish to avoid the danger that redistributors of a free\r
-program will individually obtain patent licenses, in effect making the\r
-program proprietary. To prevent this, we have made it clear that any\r
-patent must be licensed for everyone's free use or not licensed at all.\r
-\r
- The precise terms and conditions for copying, distribution and\r
-modification follow.\r
-\r
- GNU GENERAL PUBLIC LICENSE\r
- TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION\r
-\r
- 0. This License applies to any program or other work which contains\r
-a notice placed by the copyright holder saying it may be distributed\r
-under the terms of this General Public License. The "Program", below,\r
-refers to any such program or work, and a "work based on the Program"\r
-means either the Program or any derivative work under copyright law:\r
-that is to say, a work containing the Program or a portion of it,\r
-either verbatim or with modifications and/or translated into another\r
-language. (Hereinafter, translation is included without limitation in\r
-the term "modification".) Each licensee is addressed as "you".\r
-\r
-Activities other than copying, distribution and modification are not\r
-covered by this License; they are outside its scope. The act of\r
-running the Program is not restricted, and the output from the Program\r
-is covered only if its contents constitute a work based on the\r
-Program (independent of having been made by running the Program).\r
-Whether that is true depends on what the Program does.\r
-\r
- 1. You may copy and distribute verbatim copies of the Program's\r
-source code as you receive it, in any medium, provided that you\r
-conspicuously and appropriately publish on each copy an appropriate\r
-copyright notice and disclaimer of warranty; keep intact all the\r
-notices that refer to this License and to the absence of any warranty;\r
-and give any other recipients of the Program a copy of this License\r
-along with the Program.\r
-\r
-You may charge a fee for the physical act of transferring a copy, and\r
-you may at your option offer warranty protection in exchange for a fee.\r
-\r
- 2. You may modify your copy or copies of the Program or any portion\r
-of it, thus forming a work based on the Program, and copy and\r
-distribute such modifications or work under the terms of Section 1\r
-above, provided that you also meet all of these conditions:\r
-\r
- a) You must cause the modified files to carry prominent notices\r
- stating that you changed the files and the date of any change.\r
-\r
- b) You must cause any work that you distribute or publish, that in\r
- whole or in part contains or is derived from the Program or any\r
- part thereof, to be licensed as a whole at no charge to all third\r
- parties under the terms of this License.\r
-\r
- c) If the modified program normally reads commands interactively\r
- when run, you must cause it, when started running for such\r
- interactive use in the most ordinary way, to print or display an\r
- announcement including an appropriate copyright notice and a\r
- notice that there is no warranty (or else, saying that you provide\r
- a warranty) and that users may redistribute the program under\r
- these conditions, and telling the user how to view a copy of this\r
- License. (Exception: if the Program itself is interactive but\r
- does not normally print such an announcement, your work based on\r
- the Program is not required to print an announcement.)\r
-\r
-These requirements apply to the modified work as a whole. If\r
-identifiable sections of that work are not derived from the Program,\r
-and can be reasonably considered independent and separate works in\r
-themselves, then this License, and its terms, do not apply to those\r
-sections when you distribute them as separate works. But when you\r
-distribute the same sections as part of a whole which is a work based\r
-on the Program, the distribution of the whole must be on the terms of\r
-this License, whose permissions for other licensees extend to the\r
-entire whole, and thus to each and every part regardless of who wrote it.\r
-\r
-Thus, it is not the intent of this section to claim rights or contest\r
-your rights to work written entirely by you; rather, the intent is to\r
-exercise the right to control the distribution of derivative or\r
-collective works based on the Program.\r
-\r
-In addition, mere aggregation of another work not based on the Program\r
-with the Program (or with a work based on the Program) on a volume of\r
-a storage or distribution medium does not bring the other work under\r
-the scope of this License.\r
-\r
- 3. You may copy and distribute the Program (or a work based on it,\r
-under Section 2) in object code or executable form under the terms of\r
-Sections 1 and 2 above provided that you also do one of the following:\r
-\r
- a) Accompany it with the complete corresponding machine-readable\r
- source code, which must be distributed under the terms of Sections\r
- 1 and 2 above on a medium customarily used for software interchange; or,\r
-\r
- b) Accompany it with a written offer, valid for at least three\r
- years, to give any third party, for a charge no more than your\r
- cost of physically performing source distribution, a complete\r
- machine-readable copy of the corresponding source code, to be\r
- distributed under the terms of Sections 1 and 2 above on a medium\r
- customarily used for software interchange; or,\r
-\r
- c) Accompany it with the information you received as to the offer\r
- to distribute corresponding source code. (This alternative is\r
- allowed only for noncommercial distribution and only if you\r
- received the program in object code or executable form with such\r
- an offer, in accord with Subsection b above.)\r
-\r
-The source code for a work means the preferred form of the work for\r
-making modifications to it. For an executable work, complete source\r
-code means all the source code for all modules it contains, plus any\r
-associated interface definition files, plus the scripts used to\r
-control compilation and installation of the executable. However, as a\r
-special exception, the source code distributed need not include\r
-anything that is normally distributed (in either source or binary\r
-form) with the major components (compiler, kernel, and so on) of the\r
-operating system on which the executable runs, unless that component\r
-itself accompanies the executable.\r
-\r
-If distribution of executable or object code is made by offering\r
-access to copy from a designated place, then offering equivalent\r
-access to copy the source code from the same place counts as\r
-distribution of the source code, even though third parties are not\r
-compelled to copy the source along with the object code.\r
-\r
- 4. You may not copy, modify, sublicense, or distribute the Program\r
-except as expressly provided under this License. Any attempt\r
-otherwise to copy, modify, sublicense or distribute the Program is\r
-void, and will automatically terminate your rights under this License.\r
-However, parties who have received copies, or rights, from you under\r
-this License will not have their licenses terminated so long as such\r
-parties remain in full compliance.\r
-\r
- 5. You are not required to accept this License, since you have not\r
-signed it. However, nothing else grants you permission to modify or\r
-distribute the Program or its derivative works. These actions are\r
-prohibited by law if you do not accept this License. Therefore, by\r
-modifying or distributing the Program (or any work based on the\r
-Program), you indicate your acceptance of this License to do so, and\r
-all its terms and conditions for copying, distributing or modifying\r
-the Program or works based on it.\r
-\r
- 6. Each time you redistribute the Program (or any work based on the\r
-Program), the recipient automatically receives a license from the\r
-original licensor to copy, distribute or modify the Program subject to\r
-these terms and conditions. You may not impose any further\r
-restrictions on the recipients' exercise of the rights granted herein.\r
-You are not responsible for enforcing compliance by third parties to\r
-this License.\r
-\r
- 7. If, as a consequence of a court judgment or allegation of patent\r
-infringement or for any other reason (not limited to patent issues),\r
-conditions are imposed on you (whether by court order, agreement or\r
-otherwise) that contradict the conditions of this License, they do not\r
-excuse you from the conditions of this License. If you cannot\r
-distribute so as to satisfy simultaneously your obligations under this\r
-License and any other pertinent obligations, then as a consequence you\r
-may not distribute the Program at all. For example, if a patent\r
-license would not permit royalty-free redistribution of the Program by\r
-all those who receive copies directly or indirectly through you, then\r
-the only way you could satisfy both it and this License would be to\r
-refrain entirely from distribution of the Program.\r
-\r
-If any portion of this section is held invalid or unenforceable under\r
-any particular circumstance, the balance of the section is intended to\r
-apply and the section as a whole is intended to apply in other\r
-circumstances.\r
-\r
-It is not the purpose of this section to induce you to infringe any\r
-patents or other property right claims or to contest validity of any\r
-such claims; this section has the sole purpose of protecting the\r
-integrity of the free software distribution system, which is\r
-implemented by public license practices. Many people have made\r
-generous contributions to the wide range of software distributed\r
-through that system in reliance on consistent application of that\r
-system; it is up to the author/donor to decide if he or she is willing\r
-to distribute software through any other system and a licensee cannot\r
-impose that choice.\r
-\r
-This section is intended to make thoroughly clear what is believed to\r
-be a consequence of the rest of this License.\r
-\r
- 8. If the distribution and/or use of the Program is restricted in\r
-certain countries either by patents or by copyrighted interfaces, the\r
-original copyright holder who places the Program under this License\r
-may add an explicit geographical distribution limitation excluding\r
-those countries, so that distribution is permitted only in or among\r
-countries not thus excluded. In such case, this License incorporates\r
-the limitation as if written in the body of this License.\r
-\r
- 9. The Free Software Foundation may publish revised and/or new versions\r
-of the General Public License from time to time. Such new versions will\r
-be similar in spirit to the present version, but may differ in detail to\r
-address new problems or concerns.\r
-\r
-Each version is given a distinguishing version number. If the Program\r
-specifies a version number of this License which applies to it and "any\r
-later version", you have the option of following the terms and conditions\r
-either of that version or of any later version published by the Free\r
-Software Foundation. If the Program does not specify a version number of\r
-this License, you may choose any version ever published by the Free Software\r
-Foundation.\r
-\r
- 10. If you wish to incorporate parts of the Program into other free\r
-programs whose distribution conditions are different, write to the author\r
-to ask for permission. For software which is copyrighted by the Free\r
-Software Foundation, write to the Free Software Foundation; we sometimes\r
-make exceptions for this. Our decision will be guided by the two goals\r
-of preserving the free status of all derivatives of our free software and\r
-of promoting the sharing and reuse of software generally.\r
-\r
- NO WARRANTY\r
-\r
- 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY\r
-FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN\r
-OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES\r
-PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED\r
-OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF\r
-MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS\r
-TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE\r
-PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,\r
-REPAIR OR CORRECTION.\r
-\r
- 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING\r
-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR\r
-REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,\r
-INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING\r
-OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED\r
-TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY\r
-YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER\r
-PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE\r
-POSSIBILITY OF SUCH DAMAGES.\r
-\r
- END OF TERMS AND CONDITIONS\r
-\r
- How to Apply These Terms to Your New Programs\r
-\r
- If you develop a new program, and you want it to be of the greatest\r
-possible use to the public, the best way to achieve this is to make it\r
-free software which everyone can redistribute and change under these terms.\r
-\r
- To do so, attach the following notices to the program. It is safest\r
-to attach them to the start of each source file to most effectively\r
-convey the exclusion of warranty; and each file should have at least\r
-the "copyright" line and a pointer to where the full notice is found.\r
-\r
- <one line to give the program's name and a brief idea of what it does.>\r
- Copyright (C) <year> <name of author>\r
-\r
- This program is free software; you can redistribute it and/or modify\r
- it under the terms of the GNU General Public License as published by\r
- the Free Software Foundation; either version 2 of the License, or\r
- (at your option) any later version.\r
-\r
- This program is distributed in the hope that it will be useful,\r
- but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- GNU General Public License for more details.\r
-\r
- You should have received a copy of the GNU General Public License along\r
- with this program; if not, write to the Free Software Foundation, Inc.,\r
- 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.\r
-\r
-Also add information on how to contact you by electronic and paper mail.\r
-\r
-If the program is interactive, make it output a short notice like this\r
-when it starts in an interactive mode:\r
-\r
- Gnomovision version 69, Copyright (C) year name of author\r
- Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.\r
- This is free software, and you are welcome to redistribute it\r
- under certain conditions; type `show c' for details.\r
-\r
-The hypothetical commands `show w' and `show c' should show the appropriate\r
-parts of the General Public License. Of course, the commands you use may\r
-be called something other than `show w' and `show c'; they could even be\r
-mouse-clicks or menu items--whatever suits your program.\r
-\r
-You should also get your employer (if you work as a programmer) or your\r
-school, if any, to sign a "copyright disclaimer" for the program, if\r
-necessary. Here is a sample; alter the names:\r
-\r
- Yoyodyne, Inc., hereby disclaims all copyright interest in the program\r
- `Gnomovision' (which makes passes at compilers) written by James Hacker.\r
-\r
- <signature of Ty Coon>, 1 April 1989\r
- Ty Coon, President of Vice\r
-\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
+ 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
+ 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 Lesser 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.
+
+ 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.)
+
+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.
+
+ 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.
+
+ 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
+
+ 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) <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.
+
+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) 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
+ 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 Lesser General
+Public License instead of this License.
--- /dev/null
+2016-07-01 Release 1.2.2 (AndreaGiacomo)
+
+ - fixed a memory leak in hhalign
+ - paralleised hhalign
+ - increased MAC-RAM default from 2GB to 8GB
+
+ (no new command-line flags)
+
+2014-02-28 Release 1.2.1 (AndreaGiacomo)
+
+ - corrected Clustal format consensus line
+ - label justification (multi-bit)
+
+2013-06-12 Release 1.2.0 (AndreaGiacomo)
+
+ --is-profile disable check if profile, force profile (default no)
+ --use-kimura use Kimura distance correction for aligned sequences (default no)
+ --percent-id convert distances into percent identities (default no)
+
+ fixed bug in --output-order=tree-order for pair-wise alignment
+
+ Kimura distance correction no longer default for protein
+
+ fixed bug in Viterbi algorithm (predominantly affected long nucleotide but also protein, to lesser extent)
+
+ Viterbi is less (~10x) memory hungry than MAC but still scales quadratically with length:
+
+ 2GB of RAM (ClustalO default) can align sequences of 6.5k residues with MAC and 18k with Viterbi
+
+ 8GB of RAM (EBI limit) can align sequences of 12.5k residues with MAC and 37k with Viterbi
+
+ A Viterbi alignment of sequences of 100k residues will require 59GB of RAM
+
+
+2013-05-16 Release 1.1.1
+
+ --cluster-size=<n> soft maximum of sequences in sub-clusters
+ --clustering-out=<file> Clustering output file
+ --residuenumber, --resno in Clustal format print residue numbers (default no)
+ --wrap=<n> number of residues before line-wrap in output
+ --output-order={input-order,tree-order} MSA output order like in input/guide-tree
+
+ turned off Kimura correction for DNA/RNA
+
+ enable distance matrix output after initial mBed but subsequent full distance calculation
+
+ enable termination after distance/guide-tree calculation (--max-hmm-iterations=-1)
+
+ longer sequence labels
+
+2012-04-25 Release 1.1.0
+
+ DNA and RNA support now added. Sequence type can be specified manually
+ using --seqtype={Protein|DNA|RNA}
+
+2012-03-27 Release 1.0.4
+
+ zipped input now supported
+
+2011-09-07 Release 1.0.3
+
+Bugs fixed:
+
+ input failed if first line in fasta file was empty
+
+ input failed if Clustal formatted file had trailing residue numbers
+
+ '*' character was causing problems, did not get filtered out by squid
+
+ --outfmt=fasta was not recognized
+
+ '~' gap characters were not recognized in MSF format
+
+ amended README re sequence/profile alignment
+
+ disallowed empty sequences
+
+ doxygen documentation fixes and fix of API example
+
+ introduced MAC-RAM flag to set amount of RAM given to MAC (in MB)
+
+2011-06-23 Release 1.0.2
+
+2011-06-17 Release 1.0.0 (DeshilHollesEamus)
+
+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.
-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
+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
+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
+
+
+ On Windows do
+
+ 1. Preparation
+
+ 1.1. Install free MinGW64 on Windows 7. Download
+ mingw-w64-bin_x86_64-mingw_20111101_sezero.zip from
+ http://sourceforge.net/projects/mingw-w64/files/Toolchains
+ targetting Win64/Personal Builds/sezero_4.5_20111101/, extract
+ it, move mingw64 folder to C:\ and rename it to mingw. MinGW64
+ provides tools to develop 64-bit Windows applications using
+ gcc and g++. With MinGW64, some software developed for Linux
+ platform can be built on Windows.
+
+ 1.2. There is a file named pthreads-w64.zip in C:\mingw
+ folder. Extract it under C:\mingw folder.
+
+ 1.3. Download MSYS-1.0.11.exe from
+ http://sourceforge.net/projects/mingw/files/MSYS/Base/msys-core/msys-1.0.11/
+ and install it.
+
+ 1.4. Download Clustal Omega source from
+ http://www.clustal.org/omega/clustal-omega-x.x.x.tar.gz (where
+ x.x.x is the current version)
+
+ 1.5. Copy downloaded file to MSYS. If you installed MSYS in
+ C:\msys and your account is Administrator, copy it to
+ C:\msys\1.0\home\Administrator. You can do it using Windows
+ explorer.
+
+ 1.6. Download argtable2-13.tar.gz from
+ http://argtable.sourceforge.net/ and copy it to MSYS. This is
+ required by Clustal Omega.
+
+ 2. Configuration and Build process
+
+ 2.1. Launch MSYS and extract argtable2 source as tar xfz
+ argtable2-13.tar.gz.
+
+ 2.2. Extract Clustal Omega source as tar xfz
+ clustal-omega-1.2.0.tar.gz.
+
+ 2.3. cd argtable2-13; ./configure; make; make install
+
+ 2.4. cd ~/clustal-omega-1.2.0
+
+ 2.5. ./configure CFLAGS='-I/usr/local/include
+ -DSRE_STRICT_ANSI' LDFLAGS='-L/usr/local/lib'
+
+ 2.6. make; make install
+
+ 2.7. You can find clustalo.exe in /usr/local/bin folder which
+ is C:\msys\1.0\local/bin.
+
+ 2.8. Following DLLs are necessary to run clustalo.exe. Put
+ them in the same folder where clustalo.exe
+ exists. C:\mingw\bin\libcc_sjlj-1.dll,
+ C:\mingw\bin\libgomp-1.dll, C:\mingw\bin\libstdc++-6.dll,
+ C:\mingw\bin\pthreadGC2-w64.dll
+
+ (lifted from
+ http://www.blaststation.com/freestuff/en/howtoBuildx64ClustalO.php,
+ as of 2014-10-14)
+
+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.
+
-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
-below. The lack of an optional feature in a given package is not\r
-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
-various system-dependent variables used during compilation. It uses\r
-those values to create a `Makefile' in each directory of the package.\r
-It may also create one or more `.h' files containing system-dependent\r
-definitions. Finally, it creates a shell script `config.status' that\r
-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
-and enabled with `--cache-file=config.cache' or simply `-C') that saves\r
-the results of its tests to speed up reconfiguring. Caching is\r
-disabled by default to prevent problems with accidental use of stale\r
-cache files.\r
-\r
- If you need to do unusual things to compile the package, please try\r
-to figure out how `configure' could check whether to do them, and mail\r
-diffs or instructions to the address given in the `README' so they can\r
-be considered for the next release. If you are using the cache, and at\r
-some point `config.cache' contains results you don't want to keep, you\r
-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
- the package, generally using the just-built uninstalled binaries.\r
-\r
- 4. Type `make install' to install the programs and any data files and\r
- documentation. When installing into a prefix owned by root, it is\r
- recommended that the package be configured and built as a regular\r
- user, and only the `make install' phase executed with root\r
- privileges.\r
-\r
- 5. Optionally, type `make installcheck' to repeat any self-tests, but\r
- this time using the binaries in their final installed location.\r
- 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
- source code directory by typing `make clean'. To also remove the\r
- files that `configure' created (so you can compile the package for\r
- a different kind of computer), type `make distclean'. There is\r
- also a `make maintainer-clean' target, but that is intended mainly\r
- 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
- with the distribution.\r
-\r
- 7. Often, you can also type `make uninstall' to remove the installed\r
- files again. In practice, not all packages have tested that\r
- uninstallation works correctly, even though it is required by the\r
- GNU Coding Standards.\r
-\r
- 8. Some packages, particularly those that use Automake, provide `make\r
- distcheck', which can by used by developers to test that all other\r
- 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
+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
+
+
+CLUSTAL-OMEGA is a general purpose multiple sequence alignment program
+for protein and DNA/RNA.
+
+
+
+INTRODUCTION
+
+Clustal-Omega is a general purpose multiple sequence alignment (MSA)
+program for protein and DNA/RNA. It produces high quality MSAs and is
+capable of handling data-sets of hundreds of thousands of sequences in
+reasonable time.
+
+In default mode, users give a file of sequences to be aligned and
+these are clustered to produce a guide tree and this is used to guide
+a "progressive alignment" of the sequences. There are also facilities
+for aligning existing alignments to each other, aligning a sequence to
+an alignment and for using a hidden Markov model (HMM) to help guide
+an alignment of new sequences that are homologous to the sequences
+used to make the HMM. This latter procedure is referred to as
+"external profile alignment" or EPA.
+
+Clustal-Omega uses HMMs for the alignment engine, based on the HHalign
+package from Johannes Soeding [1]. Guide trees are made using an
+enhanced version of mBed [2] which can cluster very large numbers of
+sequences in O(N*log(N)) time. Multiple alignment then proceeds by
+aligning larger and larger alignments using HHalign, following the
+clustering given by the guide tree.
+
+In its current form Clustal-Omega has been extensivly tested for
+protein sequences, DNA/RNA support has been added since version 1.1.0.
+
+
+
+SEQUENCE INPUT:
+
+-i, --in, --infile={<file>,-}
+ Multiple sequence input file (- for stdin)
+
+--hmm-in=<file>
+ HMM input files
+
+--dealign
+ Dealign input sequences
+
+--profile1, --p1=<file>
+ Pre-aligned multiple sequence file (aligned columns will be kept fixed)
+
+--profile2, --p2=<file>
+ Pre-aligned multiple sequence file (aligned columns will be kept fixed)
+
+--is-profile
+ disable check if profile, force profile (default no)
+
+-t, --seqtype={Protein, RNA, DNA}
+ Force a sequence type (default: auto)
+
+--infmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]}
+ Forced sequence input file format (default: auto)
+
+
+For sequence and profile input Clustal-Omega uses the Squid library
+from Sean Eddy [3].
+
+
+Clustal-Omega accepts 3 types of sequence input: (i) a sequence file
+with un-aligned or aligned sequences, (ii) profiles (a multiple
+alignment in a file) of aligned sequences, (iii) a HMM. Valid
+combinations of the above are:
+
+(a) one file with un-aligned or aligned sequences (i); the sequences
+ will be aligned, and the alignment will be written out. For this
+ mode use the -i flag. If the sequences are aligned (all sequences
+ have the same length and at least one sequence has at least one
+ gap), then the alignment is turned into a HMM, the sequences are
+ de-aligned and the now un-aligned sequences are aligned using the
+ HMM as an External Profile for External Profile Alignment (EPA).
+ If no EPA is desired use the --dealign flag.
+
+ Use the above option to make a multiple alignment from a set of
+ sequences. A sequence file must contain more than one sequence (at
+ least two sequences).
+
+(b) two profiles (ii)+(ii); the columns in each profile will be kept
+ fixed and the alignment of the two profiles will be written
+ out. Use the --p1 and --p2 flags for this mode.
+
+ Use this option to align two alignments (profiles) together.
+
+
+(c) one file with un/aligned sequences (i) and one profile (ii); the
+ profile is converted into a HMM and the un-aligned sequences will
+ be multiply aligned (using the HMM background information) to form
+ a profile; this constructed profile is aligned with the input
+ profile; the columns in each profile (the original one and the one
+ created from the un-aligned sequences) will be kept fixed and the
+ alignment of the two profiles will be written out. Use the -i flag
+ in conjunction with the --p1 flag for this mode.
+ The un/aligned sequences file (i) must contain at least two
+ sequences. If a single sequence has to be aligned with a profile
+ the profile-profile option (b) has to be used.
+
+ Use the above option to add new sequences to an existing
+ alignment.
+
+(d) one file with un-aligned sequences (i) and one HMM (iii); the
+ un-aligned sequences will be aligned to form a profile, using the
+ HMM as an External Profile. So far only one HMM can be input and
+ only HMMer2 and HMMer3 formats are allowed. The alignment will be
+ written out; the HMM information is discarded. As, at the moment,
+ only one HMM can be used, no HMM is produced if the sequences are
+ already aligned. Use the -i flag in conjunction with the --hmm-in
+ flag for this mode. Multiple HMMs can be inputted, however, in the
+ current version all but the first HMM will be ignored.
+
+ Use this option to make a new multiple alignment of sequences from
+ the input file and use the HMM as a guide (EPA).
+
+Sequences that all have the same lengths but do not contain a single
+gap are by default not recognised as a profile. If these sequences are
+indeed a profile an not just a collection of unaligned sequences that
+happen to have the same length then specify the --is-profile flag.
+
+
+Invalid combinations of the above are:
+
+(v) an un/aligned sequence file containing just one sequence (i)
+
+(w) an un/aligned sequence file containing just one sequence and a profile
+ (i)+(ii)
+
+(x) an un/aligned sequence file containing just one sequence and a HMM
+ (i)+(iii)
+
+(y) two or more HMMs (iii)+(iii)+... cannot be aligned to one another.
+
+(z) one profile (ii) cannot be aligned with a HMM (iii)
+
+
+The following MSA file formats are allowed:
+
+ a2m=fasta, (vienna)
+ clustal,
+ msf,
+ phylip,
+ selex,
+ stockholm
+
+
+Prior to MSA, Clustal-Omega de-aligns all sequence input (i). However,
+alignment information is automatically converted into a HMM and used
+during MSA, unless the --dealign flag is specifically set. Profiles
+(ii) are not de-aligned.
+
+Since version 1.1.0 the Clustal-Omega alignment engine can process
+DNA/RNA. Clustal-Omega tries to guess the sequence type (protein,
+DNA/RNA), but this can be over-ruled with the --seqtype (-t) flag.
+
+
+CLUSTERING:
+
+ --distmat-in=<file>
+ Pairwise distance matrix input file (skips distance computation)
+
+ --distmat-out=<file>
+ Pairwise distance matrix output file
+
+ --guidetree-in=<file>
+ Guide tree input file
+ (skips distance computation and guide tree clustering step)
+
+ --guidetree-out=<file>
+ Guide tree output file
+
+ --full
+ Use full distance matrix for guide-tree calculation (slow; mBed is default)
+
+ --full-iter
+ Use full distance matrix for guide-tree calculation during iteration (mBed is default)
+
+ --cluster-size=<n>
+ soft maximum of sequences in sub-clusters
+
+ --clustering-out=<file>
+ Clustering output file
+
+ --use-kimura
+ use Kimura distance correction for aligned sequences (default no)
+
+ --percent-id
+ convert distances into percent identities (default no)
+
+In order to produce a multiple alignment Clustal-Omega requires a
+guide tree which defines the order in which sequences/profiles are
+aligned. A guide tree in turn is constructed, based on a distance
+matrix. Conventionally, this distance matrix is comprised of all the
+pair-wise distances of the sequences. The distance measure
+Clustal-Omega uses for pair-wise distances of un-aligned sequences is
+the k-tuple measure [4], which was also implemented in Clustal 1.83
+and ClustalW2 [5,6]. If the protein sequences inputted via -i are
+aligned, then Clustal-Omega uses pairwise aligned identities, these
+distances can be Kimura-corrected [7] by specifying --use-kimura. The
+distances between aligned DNA/RNA sequences are determined from the
+alignment, no Kimura correction can be used. The computational effort
+(time/memory) to calculate and store a full distance matrix grows
+quadratically with the number of sequences. Clustal-Omega can improve
+this scalability to N*log(N) by employing a fast clustering algorithm
+called mBed [2]; this option is automatically invoked (default). If a
+full distance matrix evaluation is desired, then the --full flag has
+to be set. The mBed mode calculates a reduced set of pair-wise
+distances. These distances are used in a k-means algorithm, that
+clusters at most 100 sequences. For each cluster a full distance
+matrix is calculated. No full distance matrix (of all input sequences)
+is calculated in mBed mode. If there are less than 100 sequences in
+the input, then in effect a full distance matrix is calculated in mBed
+mode, however, no distance matrix can be outputted (see below).
+
+
+Clustal-Omega uses Muscle's [8] fast UPGMA implementation to construct
+its guide trees from the distance matrix. By default, the distance
+matrix is used internally to construct the guide tree and is then
+discarded. By specifying --distmat-out the internal distance matrix
+can be written to file. This is only possible in --full or --full-iter
+mode. The guide trees by default are used internally to guide the
+multiple alignment and are then discarded. By specifying the
+--guidetree-out option these internal guide trees can be written out
+to file. Conversely, the distance calculation and/or guide tree
+building stage can be skipped, by reading in a pre-calculated distance
+matrix and/or pre-calculated guide tree. These options are invoked by
+specifying the --distmat-in and/or --guidetree-in flags,
+respectively. However, distance matrix reading is disabled in the
+current version. By default, distance matrix and guide tree files are
+not over-written, if a file with the specified name already exists. In
+this case Clustal-Omega aborts during the command-line processing
+stage. To force over-writing of already existing files use the --force
+flag (see MISCELLANEOUS). In mBed mode a full distance matrix cannot
+be outputted, distance matrix output is only possible in --full mode.
+mBed or --full distance mode do not affect the ability to write out
+guide-trees. It is possible to perform an initial mBed (not-full)
+distance calculation and a subsequent full distance calculation (see
+section ITERATION). In this case a distance matrix can be outputted.
+
+Guide trees can be iterated to refine the alignment (see section
+ITERATION). Clustal-Omega takes the alignment, that was produced
+initially and constructs a new distance matrix from this alignment.
+The distance measure used at this stage is a full alignment distance
+(as opposed the initial pairwise k-tuple distance); distances of
+protein sequences can be Kimura corrected [7], DNA/RNA distances are
+not. By default, Clustal-Omega constructs a reduced distance matrix at
+this stage using the mBed algorithm, which will then be used to create
+an improved (iterated) new guide tree. To turn off mBed-like
+clustering at this stage the --full-iter flag has to be set. While
+full alignment distances in general are much faster to calculate than
+k-tuple distances, time and memory requirements still scale
+quadratically with the number of sequences and --full-iter clustering
+should only be considered for smaller cases (<< 10,000 sequences) or
+if response time and resources are not an issue.
+
+The default cluster size in mBed mode is 100. This means that
+sequences are grouped into clusters with a soft maximum of 100
+sequences, full distance matrices are calculated for these clusters,
+guide-trees are calculated for the clusters and the clusters are then
+strung together with an over-arching guide-tree. It is possible to
+change the cluster-size with the --cluster-size flag. The clustering
+can be outputted to file. The output is comprised of the cluster
+index, a running index for the sequences within each cluster, the
+running index for the sequence within the input file, the name of the
+sequence and the bi-section sequence (see EXAMPLES).
+
+Clustal-Omega uses pair-distances. Between unaligned sequences these
+are so called k-tuple distance, between aligned sequences they are
+full alignment distances, as employed by Squid. These values range
+between 0.0 (identical) and 1.0 (completely different). The distances
+are used to construct the guide-tree and are by default outputted if
+--distmat-out is specified (and --full and/or --full-iter are
+set). For full alignment distances there is a so called Kimura
+correction [7] which more closely reflects evolutionary
+distance. Kimura-corrected distances range from 0.0 (identical) to
+theoretically infinity (completely different). In practice there
+appears to be a maximum value. In Clustal-Omega these Kimura-corrected
+distance can be outputted for protein if the --use-kimura flag is
+specified. Kimura correction is not available for DNA/RNA. Up to and
+including version 1.1.1 Kimura-corrected distances were outputted by
+default (where possible). Since version 1.2.0 the default is to output
+uncorrected distances.
+
+
+Pair-distances closely correspond to percentage pair-wise identities
+through i=100*(1-d), where i is the percentage pair-wise identity and
+d is the pair-wise distance. Percentage pair-wise identities can be
+outputted in Clustal-Omega instead of the distance matrix by
+specifying the --percent-id flag as well as --distmat-out, --full
+and/or --full-iter. Percentage pair-wise identities cannot be
+outputted if --use-kimura is specified.
+
+
+ALIGNMENT OUTPUT:
+
+ -o, --out, --outfile={file,-}
+ Multiple sequence alignment output file (default: stdout)
+
+ --outfmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]}
+ MSA output file format (default: fasta)
+
+ --residuenumber, --resno
+ in Clustal format print residue numbers (default no)
+
+ --wrap=<n>
+ number of residues before line-wrap in output
+
+ --output-order={input-order,tree-order}
+ MSA output order like in input/guide-tree
+
+
+By default Clustal-Omega writes its results (alignments) to stdout. An
+output file can be specified with the -o flag. Output to stdout is not
+possible in verbose mode (-v, see MISCELLANEOUS) as verbose/debugging
+messages would interfere with the alignment output. By default,
+alignment files are not over-written, if a file with the specified
+name already exists. In this case Clustal-Omega aborts during the
+command-line processing stage. To force over-writing of already
+existing files use the --force flag (see MISCELLANEOUS).
+
+Clustal-Omega can output alignments in various formats by setting the
+--outfmt flag:
+
+ * for Fasta format set: --outfmt=a2m or --outfmt=fa or --outfmt=fasta
+
+ * for Clustal format set: --outfmt=clu or --outfmt=clustal
+
+ * for Msf format: set --outfmt= msf
+
+ * for Phylip format set: --outfmt=phy or --outfmt=phylip
+
+ * for Selex format set: --outfmt=selex
+
+ * for Stockholm format set: --outfmt=st or --outfmt=stockholm
+
+ * for Vienna format set: --outfmt=vie or --outfmt=vienna
+
+In ClustalW one could print the residue number of the last residue in
+each line in Clustal-Format. This feature can be turned on by setting
+the --resno or --residuenumber flag.
+
+The line lengths in Clustal Format is usually 60 residues, in Fasta
+format it is usually 60 or 80 residues. This value can be set using
+the --wrap flag.
+
+By default the order of sequences in the output is the same as in the
+input (--output-order=input-order). This can be changed to the order
+in which the sequences appear in the guide-tree by setting
+--output-order=tree-order.
+
+
+ITERATION:
+
+ --iterations, --iter=<n> Number of (combined guide tree/HMM) iterations
+
+ --max-guidetree-iterations=<n> Maximum guide tree iterations
+
+ --max-hmm-iterations=<n> Maximum number of HMM iterations
+
+
+By default, Clustal-Omega calculates (or reads in) a guide tree and
+performs a multiple alignment in the order specified by this guide
+tree. This alignment is then outputted. Clustal-Omega can 'iterate'
+its guide tree. The hope is that the full alignment distances, that
+can be derived from the initial alignment, will give rise to a better
+guide tree, and by extension, to a better alignment.
+
+A similar rationale applies to HMM-iteration. MSAs in general are very
+'vulnerable' at their early stages. Sequences that are aligned at an
+early stage remain fixed for the rest of the MSA. Another way of
+putting this is: 'once a gap, always a gap'. This behaviour can be
+mitigated by HMM iteration. An initial alignment is created and turned
+into a HMM. This HMM can help in a new round of MSA to 'anticipate'
+where residues should align. This is using the HMM as an External
+Profile and carrying out iterative EPA. In practice, individual
+sequences and profiles are aligned to the External HMM, derived after
+the initial alignment. Pseudo-count information is then transferred to
+the (internal) HMM, corresponding to the individual
+sequence/profile. The now somewhat 'softened' sequences/profiles are
+then in turn aligned in the order specified by the guide
+tree. Pseudo-count transfer is reduced with the size of the
+profile. Individual sequences attain the greatest pseudo-count
+transfer, larger profiles less so. Pseudo-count transfer to profiles
+larger than, say, 10 is negligible. The effect of HMM iteration is
+more pronounced in larger test sets (that is, with more sequences).
+
+Both, HMM- and guide tree-iteration come at a cost of increasing the
+run-time. One round of guide tree iteration adds on (roughly) the time
+it took to construct the initial alignment. If, for example, the
+initial alignment took 1min, then it will take (roughly) 2min to
+iterate the guide tree once, 3min to iterate the guide tree twice, and
+so on. HMM-iteration is more costly, as each round of iteration adds
+three times the time required for the alignment stage. For example, if
+the initial alignment took 1min, then each additional round of HMM
+iteration will add on 3min; so 4 iterations will take 13min
+(=1min+4*3min). The factor of 3 stems from the fact that at every
+stage both intermediate profiles have to be aligned with the
+background HMM, and finally the (softened) HMMs have to be aligned as
+well. All times are quoted for single processors.
+
+By default, guide tree iteration and HMM-iteration are coupled. This
+means, at each iteration step both, guide tree and HMM, are
+re-calculated. This is invoked by setting the --iter flag. For
+example, if --iter=1, then first an initial alignment is produced
+(without external HMM background information and using k-tuple
+distances to calculate the guide tree). This initial alignment is then
+used to re-calculate a new guide tree (using full alignment distances)
+and to create a HMM. The new guide tree and the HMM are then used to
+produce a new MSA.
+
+Iteration of guide tree and HMM can be de-coupled. This means that the
+number of guide tree iterations and HMM iterations can be
+different. This can be done by combining the --iter flag with the
+--max-guidetree-iterations and/or the --max-hmm-iterations flag. The
+number of guide tree iterations is the minimum of --iter and
+--max-guidetree-iterations, while the number of HMM iterations is the
+minimum of --iter and --max-hmm-iterations. If, for example, HMM
+iteration should be performed 5 times but guide tree iteration should
+be performed only 3 times, then one should set --iter=5 and
+--max-guidetree-iterations=3. All three flags can be specified at the
+same time (however, this makes no sense). It is not sufficient just to
+specify --max-guidetree-iterations and --max-hmm-iterations but not
+--iter. If any iteration is desired, then --iter has to be
+set. Conversely, if no alignment is desired but only distance
+calculation and tree construction, then --max-hmm-iterations=-1 will
+terminate the calculation before the alignment stage; --iter does not
+have to be specified in this case.
+
+
+LIMITS (will exit early, if exceeded):
+
+ --maxnumseq=<n> Maximum allowed number of sequences
+
+ --maxseqlen=<l> Maximum allowed sequence length
+
+Limits can be imposed on the number of sequences in the input file
+and/or the lengths of the sequences. This cap can be set with the
+--maxnumseq and --maxseqlen flags, respectively. Clustal-Omega will
+exit early, if these limits are exceeded.
+
+
+MISCELLANEOUS:
+
+ --auto Set options automatically (might overwrite some of your options)
+
+ --threads=<n> Number of processors to use
+
+ -l, --log=<file> Log all non-essential output to this file
+
+ -h, --help Print help and exit
+
+ -v, --verbose Verbose output (increases if given multiple times)
+
+ --version Print version information and exit
+
+ --long-version Print long version information and exit
+
+ --force Force file overwriting
+
+
+Users may feel unsure which options are appropriate in certain
+situations even though using ClustalO without any special options
+should give you the desired results. The --auto flag tries to
+alleviate this problem and selects accuracy/speed flags according to
+the number of sequences. For all cases will use mBed and thereby
+possibly overwrite the --full option. For more than 1,000 sequences
+the iteration is turned off as the effect of iteration is more
+noticeable for 'larger' problems. Otherwise iterations are set to 1 if
+not already set to a higher value by the user. Expert users may want
+to avoid this flag and exercise more fine tuned control by selecting
+the appropriate options manually.
+
+Certain parts of the MSA calculation have been parallelised. Most
+noticeably, the distance matrix calculation, and certain aspects of
+the HMM building stage. Clustal-Omega uses OpenMP. By default,
+Clustal-Omega will attempt to use as many threads as possible. For
+example, on a 4-core machine Clustal-Omega will attempt to use 4
+threads. The number of threads can be limited by setting the --threads
+flag. This may be desirable, for example, in the case of
+benchmarking/timing.
+
+Usually, non-essential (verbose) output is written to screen. This
+output can be written to file by specifying the --log flag.
+
+Help is available by specifying the -h flag.
+
+By default Clustal-Omega does not print any information to stdout
+(other than the final alignment, if no output file is
+specified). Information concerning the progress of the alignment can
+be obtained by specifying one verbosity flag (-v). This may be
+desirable, to verify what Clustal-Omega is actually doing at the
+moment. If two verbosity flags (-v -v) are specified, command-line
+flags (explicitly and implicitly set) are printed in addition to the
+progress report. Triple verbose level (-v -v -v) is the most verbose
+level. In addition to single- and double-verbose information much more
+information is displayed: input sequences and names, details of the
+tree construction and intermediate alignments. Tree construction
+information includes pairwise distances. The number of pairwise
+distances scales with the square of the number of sequences, and
+double verbose mode is probably only useful for a small number of
+sequences.
+
+The current version number of Clustal-Omega can be displayed by
+setting the --version flag.
+
+The current version number of Clustal-Omega as well as the code-name
+and the build date can be displayed by setting the --long-version
+flag.
+
+By default, Clustal-Omega does not over-write files. These can be (i)
+alignment output, (ii) distance matrix and (iii) guide
+tree. Overwriting can be forced by setting the --force flag.
+
+
+EXAMPLES:
+
+./clustalo -i globin.fa
+
+Clustal-Omega reads the sequence file globin.fa, aligns the sequences
+and prints the result to screen in fasta/a2m format.
+
+
+./clustalo -i globin.fa -o globin.sto --outfmt=st
+
+If the file globin.sto does not exist, then Clustal-Omega reads the
+sequence file globin.fa, aligns the sequences and prints the result to
+globin.sto in Stockholm format. If the file globin.sto does exist
+already, then Clustal-Omega terminates the alignment process before
+reading globin.fa.
+
+
+./clustalo -i globin.fa -o globin.aln --outfmt=clu --force
+
+Clustal-Omega reads the sequence file globin.fa, aligns the sequences
+and prints the result to globin.aln in Clustal format, overwriting the
+file globin.aln, if it already exists.
+
+
+./clustalo -i globin.fa --distmat-out=globin.mat --guidetree-out=globin.dnd --force
+
+Clustal-Omega reads the sequence file globin.fa, aligns the sequences,
+prints the result to screen in fasta/a2m format (default), the guide
+tree to globin.dnd and the distance matrix to globin.mat, overwriting
+those files if they already exist.
+
+
+./clustalo -i globin.fa --guidetree-in=globin.dnd
+
+Clustal-Omega reads the files globin.fa and globin.dnd, skipping
+distance calculation and guide tree creation, using instead the guide
+tree specified in globin.dnd.
+
+
+./clustalo -i globin.fa --hmm-in=PF00042.hmm
+
+Clustal-Omega reads the sequence file globin.fa and the HMM file
+PF00042.hmm (in HMMer2 or HMMer3 format). It then performs the
+alignment, transferring pseudo-count information contained in
+PF00042.hmm to the sequences/profiles during the MSA.
+
+
+./clustalo -i globin.sto
+
+Clustal-Omega reads the file globin.sto (of aligned sequences in
+Stockholm format). It converts the alignment into a HMM, de-aligns the
+sequences and re-aligns them, transferring pseudo-count information to
+the sequences/profiles during the MSA. The guide tree is constructed
+using a full distance matrix.
+
+
+./clustalo -i globin.sto --dealign
+
+Clustal-Omega reads the file globin.sto (of aligned sequences in
+Stockholm format). It de-aligns the sequences and then re-aligns
+them. No HMM is produced in the process, no pseudo-count information
+is transferred. Consequently, the output must be the same as for
+unaligned output (like in the first example ./clustalo -i globin.fa)
+
+
+./clustalo -i globin.fa --iter=2
+
+Clustal-Omega reads the file globin.fa, creates a UPGMA guide tree
+built from k-tuple distances, and performs an initial alignment. This
+initial alignment is converted into a HMM and a new guide tree is
+built from the (preliminary) full alignment distances of the initial
+alignment. The un-aligned sequences are then aligned (for the second
+time but this time) using pseudo-count information from the HMM
+created after the initial alignment (and using the new guide
+tree). This second alignment is then again converted into a HMM and a
+new guide tree is constructed. The un-aligned sequences are then
+aligned (for a third time), again using pseudo-count information of
+the HMM from the previous step and the most recent guide tree. The
+final alignment is written to screen.
+
+
+./clustalo -i globin.fa --iter=5 --max-guidetree-iterations=1
+
+Clustal-Omega reads the file globin.fa, creates a UPGMA guide tree
+built from k-tuple distances, and performs an initial alignment. This
+initial alignment is converted into a HMM and a new guide tree is
+built from the (preliminary) full alignment distances of the initial
+alignment. The un-aligned sequences are then aligned (for the second
+time but this time) using pseudo-count information from the HMM
+created after the initial alignment (and using the new guide
+tree). For the last 4 iterations the guide tree is left unchanged and
+only HMM iteration is performed. This means that intermediate
+alignments are converted to HMMs, and these intermediate HMMs are used
+to guide the MSA during subsequent iteration stages.
+
+
+./clustalo -i globin.fa -o globin.a2m -v
+
+In case the file globin.a2m does not exist, Clustal-Omega reads the
+file globin.fa, prints a progress report to screen and writes the
+alignment in (default) Fasta format to globin.a2m. The progress report
+consists of the number of threads used, the number of sequences read,
+the current progress in the k-tuple distance calculation, completion
+of the guide tree computation and current progress of the MSA stage.
+If the file globin.a2m already exists Clustal-Omega aborts before
+reading the file globin.fa. Note that in verbose mode an output file
+has to be specified, because progress/debugging information, which is
+printed to screen, would interfere with the alignment being printed to
+screen.
+
+
+./clustalo -i PF00042_full.fa --dealign --full --outfmt=vie -o PF00042_full.vie --force
+
+Clustal-Omega reads the file PF00042_full.fa. This file contains
+several thousand aligned sequences. --dealign tells Clustal-Omega to
+erase all alignment information and re-align the sequences from
+scratch. As there are several thousand sequences calculating a full
+distance matrix may be slow. Setting the --full flag specifically
+selects the full distance mode over the default mBed mode. The
+alignment is then written out in Vienna format (fasta format all on
+one line, no line breaks per sequence) to file PF00042_full.vie.
+
+
+./clustalo -i PF00042_full.fa --dealign --outfmt=vie -o PF00042_full.vie --force
+
+Clustal-Omega reads the file PF00042_full.fa. This file contains
+several thousand aligned sequences. --dealign tells Clustal-Omega to
+erase all alignment information and re-align the sequences from
+scratch. Calculating the distance matrix will be done by mBed
+(default). Clustal-Omega will calculate pairwise distances to a
+small number of reference sequences only. This will give a significant
+speed-up. The speed-up is greater for larger families (more
+sequences). The alignment is then written out in Vienna format (fasta
+format all on one line, no line breaks per sequence) to file
+PF00042_full.vie.
+
+
+./clustalo --p1=globin.sto --p2=PF00042_full.vie -o globin+pf00042.fa
+
+Clustal-Omega reads files globin.sto and PF00042_full.vie of aligned
+sequences (profiles). Both profiles are then aligned. The relative
+positions of residues in both profiles are not changed during this
+alignment, however, columns of gaps may be inserted into the profiles,
+respectively. The final alignment is written to file globin+pf00042.fa
+in fasta format.
+
+
+./clustalo -i globin.fa --p1=PF00042_full.vie -o pf00042+globin.fa
+
+Clustal-Omega reads file globin.fa of un-aligned sequences and the
+profile (of aligned sequences) in file PF00042_full.vie. A HMM is
+created from the profile. This HMM is used to guide the alignment of
+the un-aligned sequences in globin.fa. The profile that was generated
+during this alignment of un-aligned globin.fa sequences is then
+aligned to the input profile PF00042_full.vie. The relative positions
+of residues in profile PF00042_full.vie is not changed during this
+alignment, however, columns of gaps may be inserted into the
+profile. The final alignment is output to file pf00042+globin.fa in
+fasta format. The alignment in this example may be slightly different
+from the alignment in the previous example, because no HMM guidance
+was used generate the profile globin.sto. In this example HMM guidance
+was used to align the sequences in globin.fa; the hope being that this
+intermediate alignment will have profited from the bigger profile.
+
+
+./clustalo -i globin.fa --clustering-out=globin.aux --cluster-size=3
+
+globin.fa contains 7 sequences. Usually a full distance matrix is
+created for less than 100 sequences. This is over-written by
+specifying --cluster-size=3. Clustal-Omega attempts to create clusters
+of no more than 3 sequences. This clustering is recorded in the file
+globin.aux which looks like
+
+ Cluster 0: object 0 has index 0 (=seq P1|HBB_HUMAN ) 00
+ Cluster 0: object 1 has index 1 (=seq P1|HBB_HORSE ) 00
+ Cluster 1: object 0 has index 4 (=seq P1|MYG_PHYCA ) 1
+ Cluster 1: object 1 has index 5 (=seq P1|GLB5_PETMA ) 1
+ Cluster 1: object 2 has index 6 (=seq P1|LGB2_LUPLU ) 1
+ Cluster 2: object 0 has index 2 (=seq P1|HBA_HUMAN ) 01
+ Cluster 2: object 1 has index 3 (=seq P1|HBA_HORSE ) 01
+
+There are 3 clusters, named Cluster~0, Cluster~1 and
+Cluster~2. Cluster~0 has 2 sequences, which are sequence 0 and 1 from
+the input file, named P1|HBB_HUMAN and P1|HBB_HORSE. Cluster~1 has 3
+sequences, sequences 4,5,6 from the input file and Cluster~2 has 2
+sequences, sequences 2 and 3 from the input file. The binary string at
+the end of each line encode the bi-section that led to this
+clustering. The first digit indicated the initial split. The '0'
+indicates that in the first split sequences 0,1,2,3 were grouped
+together and the '1' that sequences 4,5,6 were grouped together. The
+size of Cluster~1 does not exceed --cluster-size, so it does need to
+be broken up. The Cluster (with the initial '0') containing sequences
+0,1,2,3 is comprised of 4 sequences; this number exceed
+--cluster-size, so that it will have to be broken up. This second
+split is indicated by the second digit of the binary string. The
+second '0' indicates that sequences 0,1 fall into one Cluster (which
+will ultimately be Cluster~0), and the second '1' indicates that
+sequences 2,3 fall into another cluster (ultimately Cluster~2).
+
+
+LITERATURE:
+
+[1] Johannes Soding (2005) Protein homology detection by HMM-HMM
+ comparison. Bioinformatics 21 (7): 951–960.
+
+[2] Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG. Sequence
+ embedding for fast construction of guide trees for multiple
+ sequence alignment. Algorithms Mol Biol. 2010 May 14;5:21.
+
+[3] http://www.genetics.wustl.edu/eddy/software/#squid
+
+[4] Wilbur and Lipman, 1983; PMID 6572363
+
+[5] Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: improving
+ the sensitivity of progressive multiple sequence alignment through
+ sequence weighting, position-specific gap penalties and weight
+ matrix choice. Nucleic Acids Res., 22, 4673-4680.
+
+[6] Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA,
+ McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD,
+ Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version
+ 2.0. Bioinformatics, 23, 2947-2948.
+
+[7] Kimura M (1980). "A simple method for estimating evolutionary
+ rates of base substitutions through comparative studies of
+ nucleotide sequences". Journal of Molecular Evolution 16: 111–120.
+
+[8] Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high
+ accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.
+
-\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
+
+
+CLUSTAL-OMEGA is a general purpose multiple sequence alignment program
+for proteins.
+
+
+
+INTRODUCTION
+
+Clustal-Omega is a general purpose multiple sequence alignment (MSA)
+program for proteins. It produces high quality MSAs and is capable of
+handling data-sets of hundreds of thousands of sequences in reasonable
+time.
+
+In default mode, users give a file of sequences to be aligned and
+these are clustered to produce a guide tree and this is used to guide
+a "progressive alignment" of the sequences. There are also facilities
+for aligning existing alignments to each other, aligning a sequence to
+an alignment and for using a hidden Markov model (HMM) to help guide
+an alignment of new sequences that are homologous to the sequences
+used to make the HMM. This latter procedure is referred to as
+"external profile alignment" or EPA.
+
+Clustal-Omega uses HMMs for the alignment engine, based on the HHalign
+package from Johannes Soeding [1]. Guide trees are made using an
+enhanced version of mBed [2] which can cluster very large numbers of
+sequences in O(N*log(N)) time. Multiple alignment then proceeds by
+aligning larger and larger alignments using HHalign, following the
+clustering given by the guide tree.
+
+In its current form Clustal-Omega can only align protein sequences but
+not DNA/RNA sequences. It is envisioned that DNA/RNA will become
+available in a future version.
+
+
+
+SEQUENCE INPUT:
+
+-i, --in, --infile={<file>,-}
+ Multiple sequence input file (- for stdin)
+
+--hmm-in=<file>
+ HMM input files
+
+--dealign
+ Dealign input sequences
+
+--profile1, --p1=<file>
+ Pre-aligned multiple sequence file (aligned columns will be kept fixed)
+
+--profile2, --p2=<file>
+ Pre-aligned multiple sequence file (aligned columns will be kept fixed)
+
+
+For sequence and profile input Clustal-Omega uses the Squid library
+from Sean Eddy [3].
+
+
+Clustal-Omega accepts 3 types of sequence input: (i) a sequence file
+with un-aligned or aligned sequences, (ii) profiles (a multiple
+alignment in a file) of aligned sequences, (iii) a HMM. Valid
+combinations of the above are:
+
+(a) one file with un-aligned or aligned sequences (i); the sequences
+ will be aligned, and the alignment will be written out. For this
+ mode use the -i flag. If the sequences are aligned (all sequences
+ have the same length and at least one sequence has at least one
+ gap), then the alignment is turned into a HMM, the sequences are
+ de-aligned and the now un-aligned sequences are aligned using the
+ HMM as an External Profile for External Profile Alignment (EPA).
+ If no EPA is desired use the --dealign flag.
+
+ Use the above option to make a multiple alignment from a set of
+ sequences. A sequence file must contain more than one sequence (at
+ least two sequences).
+
+(b) two profiles (ii)+(ii); the columns in each profile will be kept
+ fixed and the alignment of the two profiles will be written
+ out. Use the --p1 and --p2 flags for this mode.
+
+ Use this option to align two alignments (profiles) together.
+
+(c) one file with un/aligned sequences (i) and one profile (ii); the
+ profile is converted into a HMM and the un-aligned sequences will
+ be multiply aligned (using the HMM background information) to form
+ a profile; this constructed profile is aligned with the input
+ profile; the columns in each profile (the original one and the one
+ created from the un-aligned sequences) will be kept fixed and the
+ alignment of the two profiles will be written out. Use the -i flag
+ in conjunction with the --p1 flag for this mode.
+ The un/aligned sequences file (i) must contain at least two
+ sequences. If a single sequence has to be aligned with a profile
+ the profile-profile option (b) has to be used.
+
+ Use the above option to add new sequences to an existing
+ alignment.
+
+(d) one file with un-aligned sequences (i) and one HMM (iii); the
+ un-aligned sequences will be aligned to form a profile, using the
+ HMM as an External Profile. So far only one HMM can be input and
+ only HMMer2 and HMMer3 formats are allowed. The alignment will be
+ written out; the HMM information is discarded. As, at the moment,
+ only one HMM can be used, no HMM is produced if the sequences are
+ already aligned. Use the -i flag in conjunction with the --hmm-in
+ flag for this mode. Multiple HMMs can be inputted, however, in the
+ current version all but the first HMM will be ignored.
+
+ Use this option to make a new multiple alignment of sequences from
+ the input file and use the HMM as a guide (EPA).
+
+
+Invalid combinations of the above are:
+
+(v) an un/aligned sequence file containing just one sequence (i)
+
+(w) an un/aligned sequence file containing just one sequence and a profile
+ (i)+(ii)
+
+(x) an un/aligned sequence file containing just one sequence and a HMM
+ (i)+(iii)
+
+(y) two or more HMMs (iii)+(iii)+... cannot be aligned to one another.
+
+(z) one profile (ii) cannot be aligned with a HMM (iii)
+
+
+The following MSA file formats are allowed:
+
+ a2m=fasta, (vienna)
+ clustal,
+ msf,
+ phylip,
+ selex,
+ stockholm
+
+
+Prior to MSA, Clustal-Omega de-aligns all sequence input (i). However,
+alignment information is automatically converted into a HMM and used
+during MSA, unless the --dealign flag is specifically set. Profiles
+(ii) are not de-aligned.
+
+The Clustal-Omega alignment engine can at the moment not process
+DNA/RNA. If a sequence input file (i) or a profile (ii) is interpreted
+as DNA/RNA the program will terminate during the file input stage.
+
+
+
+CLUSTERING:
+
+ --distmat-in=<file>
+ Pairwise distance matrix input file (skips distance computation)
+
+ --distmat-out=<file>
+ Pairwise distance matrix output file
+
+ --guidetree-in=<file>
+ Guide tree input file
+ (skips distance computation and guide tree clustering step)
+
+ --guidetree-out=<file>
+ Guide tree output file
+
+ --full
+ Use full distance matrix for guide-tree calculation (slow; mBed is default)
+
+ --full-iter
+ Use full distance matrix for guide-tree calculation during iteration (mBed is default)
+
+
+In order to produce a multiple alignment Clustal-Omega requires a
+guide tree which defines the order in which sequences/profiles are
+aligned. A guide tree in turn is constructed, based on a distance
+matrix. Conventionally, this distance matrix is comprised of all the
+pair-wise distances of the sequences. The distance measure
+Clustal-Omega uses for pair-wise distances of un-aligned sequences is
+the k-tuple measure [4], which was also implemented in Clustal 1.83
+and ClustalW2 [5,6]. If the sequences inputted via -i are aligned
+Clustal-Omega uses the Kimura-corrected pairwise aligned identities
+[7]. The computational effort (time/memory) to calculate and store a
+full distance matrix grows quadratically with the number of sequences.
+Clustal-Omega can improve this scalability to N*log(N) by employing a
+fast clustering algorithm called mBed [2]; this option is
+automatically invoked (default). If a full distance matrix evaluation
+is desired, then the --full flag has to be set. The mBed mode
+calculates a reduced set of pair-wise distances. These distances are
+used in a k-means algorithm, that clusters at most 100 sequences. For
+each cluster a full distance matrix is calculated. No full distance
+matrix (of all input sequences) is calculated in mBed mode. If there
+are less than 100 sequences in the input, then in effect a full
+distance matrix is calculated in mBed mode, however, no distance
+matrix can be outputted (see below).
+
+
+Clustal-Omega uses Muscle's [8] fast UPGMA implementation to construct
+its guide trees from the distance matrix. By default, the distance
+matrix is used internally to construct the guide tree and is then
+discarded. By specifying --distmat-out the internal distance matrix
+can be written to file. This is only possible in --full mode. The
+guide trees by default are used internally to guide the multiple
+alignment and are then discarded. By specifying the --guidetree-out
+option these internal guide trees can be written out to
+file. Conversely, the distance calculation and/or guide tree building
+stage can be skipped, by reading in a pre-calculated distance matrix
+and/or pre-calculated guide tree. These options are invoked by
+specifying the --distmat-in and/or --guidetree-in flags,
+respectively. However, distance matrix reading is disabled in the
+current version. By default, distance matrix and guide tree files are
+not over-written, if a file with the specified name already exists. In
+this case Clustal-Omega aborts during the command-line processing
+stage. To force over-writing of already existing files use the --force
+flag (see MISCELLANEOUS). In mBed mode a full distance matrix cannot
+be outputted, distance matrix output is only possible in --full mode.
+mBed or --full distance mode do not affect the ability to write out
+guide-trees.
+
+Guide trees can be iterated to refine the alignment (see section
+ITERATION). Clustal-Omega takes the alignment, that was produced
+initially and constructs a new distance matrix from this alignment.
+The distance measure used at this stage is the Kimura distance [7]. By
+default, Clustal-Omega constructs a reduced distance matrix at this
+stage using the mBed algorithm, which will then be used to create an
+improved (iterated) new guide tree. To turn off mBed-like clustering
+at this stage the --full-iter flag has to be set. While Kimura
+distances in general are much faster to calculate than k-tuple
+distances, time and memory requirements still scale quadratically with
+the number of sequences and --full-iter clustering should only be
+considered for smaller cases (<< 10,000 sequences).
+
+
+
+ALIGNMENT OUTPUT:
+
+ -o, --out, --outfile={file,-} Multiple sequence alignment output file (default: stdout)
+
+ --outfmt={a2m=fa[sta],clu[stal],msf,phy[lip],selex,st[ockholm],vie[nna]} MSA output file format (default: fasta)
+
+
+By default Clustal-Omega writes its results (alignments) to stdout. An
+output file can be specified with the -o flag. Output to stdout is not
+possible in verbose mode (-v, see MISCELLANEOUS) as verbose/debugging
+messages would interfere with the alignment output. By default,
+alignment files are not over-written, if a file with the specified
+name already exists. In this case Clustal-Omega aborts during the
+command-line processing stage. To force over-writing of already
+existing files use the --force flag (see MISCELLANEOUS).
+
+Clustal-Omega can output alignments in various formats by setting the
+--outfmt flag:
+
+ * for Fasta format set: --outfmt=a2m or --outfmt=fa or --outfmt=fasta
+
+ * for Clustal format set: --outfmt=clu or --outfmt=clustal
+
+ * for Msf format: set --outfmt= msf
+
+ * for Phylip format set: --outfmt=phy or --outfmt=phylip
+
+ * for Selex format set: --outfmt=selex
+
+ * for Stockholm format set: --outfmt=st or --outfmt=stockholm
+
+ * for Vienna format set: --outfmt=vie or --outfmt=vienna
+
+
+ITERATION:
+
+ --iterations, --iter=<n> Number of (combined guide tree/HMM) iterations
+
+ --max-guidetree-iterations=<n> Maximum guide tree iterations
+
+ --max-hmm-iterations=<n> Maximum number of HMM iterations
+
+
+By default, Clustal-Omega calculates (or reads in) a guide tree and
+performs a multiple alignment in the order specified by this guide
+tree. This alignment is then outputted. Clustal-Omega can 'iterate'
+its guide tree. The hope is that the (Kimura) distances, that can be
+derived from the initial alignment, will give rise to a better guide
+tree, and by extension, to a better alignment.
+
+A similar rationale applies to HMM-iteration. MSAs in general are very
+'vulnerable' at their early stages. Sequences that are aligned at an
+early stage remain fixed for the rest of the MSA. Another way of
+putting this is: 'once a gap, always a gap'. This behaviour can be
+mitigated by HMM iteration. An initial alignment is created and turned
+into a HMM. This HMM can help in a new round of MSA to 'anticipate'
+where residues should align. This is using the HMM as an External
+Profile and carrying out iterative EPA. In practice, individual
+sequences and profiles are aligned to the External HMM, derived after
+the initial alignment. Pseudo-count information is then transferred to
+the (internal) HMM, corresponding to the individual
+sequence/profile. The now somewhat 'softened' sequences/profiles are
+then in turn aligned in the order specified by the guide
+tree. Pseudo-count transfer is reduced with the size of the
+profile. Individual sequences attain the greatest pseudo-count
+transfer, larger profiles less so. Pseudo-count transfer to profiles
+larger than, say, 10 is negligible. The effect of HMM iteration is
+more pronounced in larger test sets (that is, with more sequences).
+
+Both, HMM- and guide tree-iteration come at a cost of increasing the
+run-time. One round of guide tree iteration adds on (roughly) the time
+it took to construct the initial alignment. If, for example, the
+initial alignment took 1min, then it will take (roughly) 2min to
+iterate the guide tree once, 3min to iterate the guide tree twice, and
+so on. HMM-iteration is more costly, as each round of iteration adds
+three times the time required for the alignment stage. For example, if
+the initial alignment took 1min, then each additional round of HMM
+iteration will add on 3min; so 4 iterations will take 13min
+(=1min+4*3min). The factor of 3 stems from the fact that at every
+stage both intermediate profiles have to be aligned with the
+background HMM, and finally the (softened) HMMs have to be aligned as
+well. All times are quoted for single processors.
+
+By default, guide tree iteration and HMM-iteration are coupled. This
+means, at each iteration step both, guide tree and HMM, are
+re-calculated. This is invoked by setting the --iter flag. For
+example, if --iter=1, then first an initial alignment is produced
+(without external HMM background information and using k-tuple
+distances to calculate the guide tree). This initial alignment is then
+used to re-calculate a new guide tree (using Kimura distances) and to
+create a HMM. The new guide tree and the HMM are then used to produce
+a new MSA.
+
+Iteration of guide tree and HMM can be de-coupled. This means that the
+number of guide tree iterations and HMM iterations can be
+different. This can be done by combining the --iter flag with the
+--max-guidetree-iterations and/or the --max-hmm-iterations flag. The
+number of guide tree iterations is the minimum of --iter and
+--max-guidetree-iterations, while the number of HMM iterations is the
+minimum of --iter and --max-hmm-iterations. If, for example, HMM
+iteration should be performed 5 times but guide tree iteration should
+be performed only 3 times, then one should set --iter=5 and
+--max-guidetree-iterations=3. All three flags can be specified at the
+same time (however, this makes no sense). It is not sufficient just to
+specify --max-guidetree-iterations and --max-hmm-iterations but not
+--iter. If any iteration is desired --iter has to be set.
+
+
+LIMITS (will exit early, if exceeded):
+
+ --maxnumseq=<n> Maximum allowed number of sequences
+
+ --maxseqlen=<l> Maximum allowed sequence length
+
+Limits can be imposed on the number of sequences in the input file
+and/or the lengths of the sequences. This cap can be set with the
+--maxnumseq and --maxseqlen flags, respectively. Clustal-Omega will
+exit early, if these limits are exceeded.
+
+
+MISCELLANEOUS:
+
+ --auto Set options automatically (might overwrite some of your options)
+
+ --threads=<n> Number of processors to use
+
+ -l, --log=<file> Log all non-essential output to this file
+
+ -h, --help Print help and exit
+
+ -v, --verbose Verbose output (increases if given multiple times)
+
+ --version Print version information and exit
+
+ --long-version Print long version information and exit
+
+ --force Force file overwriting
+
+
+Users may feel unsure which options are appropriate in certain
+situations even though using ClustalO without any special options
+should give you the desired results. The --auto flag tries to
+alleviate this problem and selects accuracy/speed flags according to
+the number of sequences. For all cases will use mBed and thereby
+possibly overwrite the --full option. For more than 1,000 sequences
+the iteration is turned off as the effect of iteration is more
+noticeable for 'larger' problems. Otherwise iterations are set to 1 if
+not already set to a higher value by the user. Expert users may want
+to avoid this flag and exercise more fine tuned control by selecting
+the appropriate options manually.
+
+Certain parts of the MSA calculation have been parallelised. Most
+noticeably, the distance matrix calculation, and certain aspects of
+the HMM building stage. Clustal-Omega uses OpenMP. By default,
+Clustal-Omega will attempt to use as many threads as possible. For
+example, on a 4-core machine Clustal-Omega will attempt to use 4
+threads. The number of threads can be limited by setting the --threads
+flag. This may be desirable, for example, in the case of
+benchmarking/timing.
+
+Usually, non-essential (verbose) output is written to screen. This
+output can be written to file by specifying the --log flag.
+
+Help is available by specifying the -h flag.
+
+By default Clustal-Omega does not print any information to stdout
+(other than the final alignment, if no output file is
+specified). Information concerning the progress of the alignment can
+be obtained by specifying one verbosity flag (-v). This may be
+desirable, to verify what Clustal-Omega is actually doing at the
+moment. If two verbosity flags (-v -v) are specified, command-line
+flags (explicitly and implicitly set) are printed in addition to the
+progress report. Triple verbose level (-v -v -v) is the most verbose
+level. In addition to single- and double-verbose information much more
+information is displayed: input sequences and names, details of the
+tree construction and intermediate alignments. Tree construction
+information includes pairwise distances. The number of pairwise
+distances scales with the square of the number of sequences, and
+double verbose mode is probably only useful for a small number of
+sequences.
+
+The current version number of Clustal-Omega can be displayed by
+setting the --version flag.
+
+The current version number of Clustal-Omega as well as the code-name
+and the build date can be displayed by setting the --long-version
+flag.
+
+By default, Clustal-Omega does not over-write files. These can be (i)
+alignment output, (ii) distance matrix and (iii) guide
+tree. Overwriting can be forced by setting the --force flag.
+
+
+EXAMPLES:
+
+./clustalo -i globin.fa
+
+Clustal-Omega reads the sequence file globin.fa, aligns the sequences
+and prints the result to screen in fasta/a2m format.
+
+
+./clustalo -i globin.fa -o globin.sto --outfmt=st
+
+If the file globin.sto does not exist, then Clustal-Omega reads the
+sequence file globin.fa, aligns the sequences and prints the result to
+globin.sto in Stockholm format. If the file globin.sto does exist
+already, then Clustal-Omega terminates the alignment process before
+reading globin.fa.
+
+
+./clustalo -i globin.fa -o globin.aln --outfmt=clu --force
+
+Clustal-Omega reads the sequence file globin.fa, aligns the sequences
+and prints the result to globin.aln in Clustal format, overwriting the
+file globin.aln, if it already exists.
+
+
+./clustalo -i globin.fa --distmat-out=globin.mat --guidetree-out=globin.dnd --force
+
+Clustal-Omega reads the sequence file globin.fa, aligns the sequences,
+prints the result to screen in fasta/a2m format (default), the guide
+tree to globin.dnd and the distance matrix to globin.mat, overwriting
+those files if they already exist.
+
+
+./clustalo -i globin.fa --guidetree-in=globin.dnd
+
+Clustal-Omega reads the files globin.fa and globin.dnd, skipping
+distance calculation and guide tree creation, using instead the guide
+tree specified in globin.dnd.
+
+
+./clustalo -i globin.fa --hmm-in=PF00042.hmm
+
+Clustal-Omega reads the sequence file globin.fa and the HMM file
+PF00042.hmm (in HMMer2 or HMMer3 format). It then performs the
+alignment, transferring pseudo-count information contained in
+PF00042.hmm to the sequences/profiles during the MSA.
+
+
+./clustalo -i globin.sto
+
+Clustal-Omega reads the file globin.sto (of aligned sequences in
+Stockholm format). It converts the alignment into a HMM, de-aligns the
+sequences and re-aligns them, transferring pseudo-count information to
+the sequences/profiles during the MSA. The guide tree is constructed
+using a full distance matrix of Kimura distances.
+
+
+./clustalo -i globin.sto --dealign
+
+Clustal-Omega reads the file globin.sto (of aligned sequences in
+Stockholm format). It de-aligns the sequences and then re-aligns
+them. No HMM is produced in the process, no pseudo-count information
+is transferred. Consequently, the output must be the same as for
+unaligned output (like in the first example ./clustalo -i globin.fa)
+
+
+./clustalo -i globin.fa --iter=2
+
+Clustal-Omega reads the file globin.fa, creates a UPGMA guide tree
+built from k-tuple distances, and performs an initial alignment. This
+initial alignment is converted into a HMM and a new guide tree is
+built from the Kimura distances of the initial alignment. The
+un-aligned sequences are then aligned (for the second time but this
+time) using pseudo-count information from the HMM created after the
+initial alignment (and using the new guide tree). This second
+alignment is then again converted into a HMM and a new guide tree is
+constructed. The un-aligned sequences are then aligned (for a third
+time), again using pseudo-count information of the HMM from the
+previous step and the most recent guide tree. The final alignment is
+written to screen.
+
+
+./clustalo -i globin.fa --iter=5 --max-guidetree-iterations=1
+
+Clustal-Omega reads the file globin.fa, creates a UPGMA guide tree
+built from k-tuple distances, and performs an initial alignment. This
+initial alignment is converted into a HMM and a new guide tree is
+built from the Kimura distances of the initial alignment. The
+un-aligned sequences are then aligned (for the second time but this
+time) using pseudo-count information from the HMM created after the
+initial alignment (and using the new guide tree). For the last 4
+iterations the guide tree is left unchanged and only HMM iteration is
+performed. This means that intermediate alignments are converted to
+HMMs, and these intermediate HMMs are used to guide the MSA during
+subsequent iteration stages.
+
+
+./clustalo -i globin.fa -o globin.a2m -v
+
+In case the file globin.a2m does not exist, Clustal-Omega reads the
+file globin.fa, prints a progress report to screen and writes the
+alignment in (default) Fasta format to globin.a2m. The progress report
+consists of the number of threads used, the number of sequences read,
+the current progress in the k-tuple distance calculation, completion
+of the guide tree computation and current progress of the MSA stage.
+If the file globin.a2m already exists Clustal-Omega aborts before
+reading the file globin.fa. Note that in verbose mode an output file
+has to be specified, because progress/debugging information, which is
+printed to screen, would interfere with the alignment being printed to
+screen.
+
+
+./clustalo -i PF00042_full.fa --dealign --full --outfmt=vie -o PF00042_full.vie --force
+
+Clustal-Omega reads the file PF00042_full.fa. This file contains
+several thousand aligned sequences. --dealign tells Clustal-Omega to
+erase all alignment information and re-align the sequences from
+scratch. As there are several thousand sequences calculating a full
+distance matrix may be slow. Setting the --full flag specifically
+selects the full distance mode over the default mBed mode. The
+alignment is then written out in Vienna format (fasta format all on
+one line, no line breaks per sequence) to file PF00042_full.vie.
+
+
+./clustalo -i PF00042_full.fa --dealign --outfmt=vie -o PF00042_full.vie --force
+
+Clustal-Omega reads the file PF00042_full.fa. This file contains
+several thousand aligned sequences. --dealign tells Clustal-Omega to
+erase all alignment information and re-align the sequences from
+scratch. Calculating the distance matrix will be done by mBed
+(default). Clustal-Omega will calculate pairwise distances to a
+small number of reference sequences only. This will give a significant
+speed-up. The speed-up is greater for larger families (more
+sequences). The alignment is then written out in Vienna format (fasta
+format all on one line, no line breaks per sequence) to file
+PF00042_full.vie.
+
+
+./clustalo --p1=globin.sto --p2=PF00042_full.vie -o globin+pf00042.fa
+
+Clustal-Omega reads files globin.sto and PF00042_full.vie of aligned
+sequences (profiles). Both profiles are then aligned. The relative
+positions of residues in both profiles are not changed during this
+alignment, however, columns of gaps may be inserted into the profiles,
+respectively. The final alignment is written to file globin+pf00042.fa
+in fasta format.
+
+
+./clustalo -i globin.fa --p1=PF00042_full.vie -o pf00042+globin.fa
+
+Clustal-Omega reads file globin.fa of un-aligned sequences and the
+profile (of aligned sequences) in file PF00042_full.vie. A HMM is
+created from the profile. This HMM is used to guide the alignment of
+the un-aligned sequences in globin.fa. The profile that was generated
+during this alignment of un-aligned globin.fa sequences is then
+aligned to the input profile PF00042_full.vie. The relative positions
+of residues in profile PF00042_full.vie is not changed during this
+alignment, however, columns of gaps may be inserted into the
+profile. The final alignment is output to file pf00042+globin.fa in
+fasta format. The alignment in this example may be slightly different
+from the alignment in the previous example, because no HMM guidance
+was used generate the profile globin.sto. In this example HMM guidance
+was used to align the sequences in globin.fa; the hope being that this
+intermediate alignment will have profited from the bigger profile.
+
+
+
+LITERATURE:
+
+[1] Johannes Soding (2005) Protein homology detection by HMM-HMM
+ comparison. Bioinformatics 21 (7): 951–960.
+
+[2] Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG. Sequence
+ embedding for fast construction of guide trees for multiple
+ sequence alignment. Algorithms Mol Biol. 2010 May 14;5:21.
+
+[3] http://www.genetics.wustl.edu/eddy/software/#squid
+
+[4] Wilbur and Lipman, 1983; PMID 6572363
+
+[5] Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: improving
+ the sensitivity of progressive multiple sequence alignment through
+ sequence weighting, position-specific gap penalties and weight
+ matrix choice. Nucleic Acids Res., 22, 4673-4680.
+
+[6] Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA,
+ McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD,
+ Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version
+ 2.0. Bioinformatics, 23, 2947-2948.
+
+[7] Kimura M (1980). "A simple method for estimating evolutionary
+ rates of base substitutions through comparative studies of
+ nucleotide sequences". Journal of Molecular Evolution 16: 111–120.
+
+[8] Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high
+ accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.
+
-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
+ISSUES:
+
+-auto
+
+WARNING: Unsupported old command line option '-auto' will be ignored
+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
+WARNING: This is a beta version of Clustal Omega, for protein only.
+For more information try: D:\workspace\JABA2\binaries\windows\clustalo\clustalo.exe --help
+
git://source.jalview.org / jabaws.git / commitdiff
