X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2Fclustalw%2Fsrc%2F.deps%2FEMBLFileParser.Po;h=cc3fe04526dfe11acba33f6069de7532d10847f4;hb=7c6018cf87e67d7ac21f5230284ef2162a19320f;hp=35d50b60c8f7993cc02d7eae8fd9e64604c21ec0;hpb=1eab6cadc31107fabe7ef060de1ae91eeb4a025b;p=jabaws.git diff --git a/binaries/src/clustalw/src/.deps/EMBLFileParser.Po b/binaries/src/clustalw/src/.deps/EMBLFileParser.Po index 35d50b6..cc3fe04 100644 --- a/binaries/src/clustalw/src/.deps/EMBLFileParser.Po +++ b/binaries/src/clustalw/src/.deps/EMBLFileParser.Po @@ -1,156 +1,145 @@ -EMBLFileParser.o EMBLFileParser.o: fileInput/EMBLFileParser.cpp config.h \ - fileInput/EMBLFileParser.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++config.h \ - /usr/include/bits/wordsize.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/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/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstring \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h \ - /usr/include/string.h /usr/include/xlocale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/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/bits/stdio_lim.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdlib \ - /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/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/4.1.2/../../../../include/c++/4.1.2/iosfwd \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstdio \ - /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/wchar.h /usr/include/bits/wchar.h /usr/include/gconv.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale \ - /usr/include/locale.h /usr/include/bits/locale.h \ - /usr/include/langinfo.h /usr/include/nl_types.h /usr/include/iconv.h \ - /usr/include/libintl.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ - /usr/include/signal.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/4.1.2/../../../../include/c++/4.1.2/cctype \ - /usr/include/ctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime \ - /usr/include/stdint.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/functexcept.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception_defines.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_pair.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cpp_type_traits.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_types.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator_base_funcs.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/concept_check.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/debug/debug.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/memory \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ext/new_allocator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/new \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/exception \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_construct.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_uninitialized.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_raw_storage_iter.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/limits \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_function.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/atomicity.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/atomic_word.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/algorithm \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algo.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_heap.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_tempbuf.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_string.tcc \ - fileInput/FileParser.h fileInput/../alignment/Sequence.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/vector \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_vector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_bvector.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/vector.tcc \ - fileInput/../alignment/../general/userparams.h \ - fileInput/../alignment/../general/UserParameters.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ostream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ios \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/localefwd.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ios_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_classes.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/streambuf \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/streambuf_iterator.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwctype \ - /usr/include/wctype.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_base.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/ctype_inline.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/codecvt.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/time_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/messages_members.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/basic_ios.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/ostream.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/locale \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/locale_facets.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/typeinfo \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/istream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/istream.tcc \ - fileInput/../alignment/../general/utils.h \ - fileInput/../alignment/../general/Utility.h /usr/include/errno.h \ - /usr/include/bits/errno.h /usr/include/linux/errno.h \ - /usr/include/asm/errno.h /usr/include/asm-x86_64/errno.h \ - /usr/include/asm-generic/errno.h /usr/include/asm-generic/errno-base.h \ - fileInput/../alignment/../general/clustalw.h \ - fileInput/../alignment/../general/general.h \ - fileInput/../alignment/../general/Array2D.h \ - fileInput/../alignment/../general/SquareMat.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional \ - fileInput/../alignment/../general/SymMatrix.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath \ - /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/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/stdexcept \ - fileInput/../alignment/../general/utils.h \ - fileInput/../general/userparams.h fileInput/InFileStream.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/fstream \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/basic_file.h \ - /usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/fstream.tcc +EMBLFileParser.o: fileInput/EMBLFileParser.cpp config.h \ + fileInput/EMBLFileParser.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string \ + /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/bits/stringfwd.h \ + /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/cstddef \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.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/postypes.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar \ + /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/bits/allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new \ + /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/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/iosfwd \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype \ + /usr/include/ctype.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/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.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/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 \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.tcc \ + fileInput/FileParser.h fileInput/../alignment/Sequence.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_construct.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_uninitialized.h \ + /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 \ + fileInput/../alignment/../general/userparams.h \ + fileInput/../alignment/../general/UserParameters.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/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/bits/ios_base.h \ + /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/bits/locale_classes.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/streambuf \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_ios.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwctype \ + /usr/include/wctype.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_base.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/streambuf_iterator.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/ctype_inline.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/locale_facets.tcc \ + /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 \ + fileInput/../alignment/../general/utils.h \ + fileInput/../alignment/../general/Utility.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdlib \ + /usr/include/stdlib.h /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/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/include/string.h /usr/include/errno.h \ + /usr/include/bits/errno.h /usr/include/linux/errno.h \ + /usr/include/asm/errno.h /usr/include/asm-generic/errno.h \ + /usr/include/asm-generic/errno-base.h \ + fileInput/../alignment/../general/clustalw.h \ + fileInput/../alignment/../general/general.h \ + fileInput/../alignment/../general/Array2D.h \ + fileInput/../alignment/../general/SquareMat.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip \ + fileInput/../alignment/../general/SymMatrix.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath \ + /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/c++/4.4.7/bits/cmath.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/stdexcept \ + fileInput/../alignment/../general/utils.h \ + fileInput/../general/userparams.h fileInput/InFileStream.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/fstream \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/codecvt.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstdio \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/basic_file.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++io.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/fstream.tcc \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/memory \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_tempbuf.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_raw_storage_iter.h \ + /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/auto_ptr.h config.h: fileInput/EMBLFileParser.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/string: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/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/c++config.h: /usr/include/bits/wordsize.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/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/os_defines.h: /usr/include/features.h: @@ -160,129 +149,119 @@ fileInput/EMBLFileParser.h: /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/cpu_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/4.1.2/../../../../include/c++/4.1.2/bits/stringfwd.h: +/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/4.1.2/../../../../include/c++/4.1.2/bits/char_traits.h: +/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/4.1.2/../../../../include/c++/4.1.2/cstring: +/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/4.1.2/../../../../include/c++/4.1.2/cstddef: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cstddef: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stddef.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h: -/usr/include/string.h: - -/usr/include/xlocale.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/stl_algobase.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/climits: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/limits.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/syslimits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/functexcept.h: -/usr/include/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception_defines.h: -/usr/include/bits/posix1_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cpp_type_traits.h: -/usr/include/bits/local_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/type_traits.h: -/usr/include/linux/limits.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/numeric_traits.h: -/usr/include/bits/posix2_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_pair.h: -/usr/include/bits/xopen_lim.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/move.h: -/usr/include/bits/stdio_lim.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/4.1.2/../../../../include/c++/4.1.2/cstdlib: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_types.h: -/usr/include/stdlib.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator_base_funcs.h: -/usr/include/bits/waitflags.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_iterator.h: -/usr/include/bits/waitstatus.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/debug/debug.h: -/usr/include/endian.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/postypes.h: -/usr/include/bits/endian.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cwchar: -/usr/include/sys/types.h: - -/usr/include/bits/types.h: +/usr/include/wchar.h: -/usr/include/bits/typesizes.h: +/usr/include/stdio.h: -/usr/include/time.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h: -/usr/include/sys/select.h: - -/usr/include/bits/select.h: +/usr/include/bits/wchar.h: -/usr/include/bits/sigset.h: +/usr/include/xlocale.h: -/usr/include/bits/time.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h: -/usr/include/sys/sysmacros.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h: -/usr/include/bits/pthreadtypes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h: -/usr/include/alloca.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/new: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iosfwd: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/exception: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++locale.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/4.1.2/../../../../include/c++/4.1.2/cstdio: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++locale.h: -/usr/include/stdio.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/clocale: -/usr/include/libio.h: +/usr/include/locale.h: -/usr/include/_G_config.h: +/usr/include/bits/locale.h: -/usr/include/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iosfwd: -/usr/include/bits/wchar.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cctype: -/usr/include/gconv.h: +/usr/include/ctype.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/include/stdarg.h: +/usr/include/bits/types.h: -/usr/include/bits/sys_errlist.h: +/usr/include/bits/typesizes.h: -/usr/include/bits/stdio.h: +/usr/include/endian.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/clocale: +/usr/include/bits/endian.h: -/usr/include/locale.h: +/usr/include/bits/byteswap.h: -/usr/include/bits/locale.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/ostream_insert.h: -/usr/include/langinfo.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cxxabi-forced.h: -/usr/include/nl_types.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_function.h: -/usr/include/iconv.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/binders.h: -/usr/include/libintl.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/basic_string.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/c++io.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/4.1.2/../../../../include/c++/4.1.2/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.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/x86_64-redhat-linux/bits/gthr-default.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/time.h: + /usr/include/bits/sched.h: -/usr/include/signal.h: +/usr/include/bits/time.h: + +/usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -296,143 +275,107 @@ fileInput/EMBLFileParser.h: /usr/include/getopt.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cctype: - -/usr/include/ctype.h: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/postypes.h: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/atomic_word.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cwchar: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/initializer_list: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/ctime: 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/usr/include/asm-generic/errno.h: /usr/include/asm-generic/errno-base.h: @@ -456,13 +397,11 @@ fileInput/../alignment/../general/Array2D.h: fileInput/../alignment/../general/SquareMat.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/iomanip: - -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/functional: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iomanip: fileInput/../alignment/../general/SymMatrix.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cmath: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/cmath: /usr/include/math.h: @@ -482,9 +421,9 @@ fileInput/../alignment/../general/SymMatrix.h: /usr/include/bits/mathinline.h: -/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../include/c++/4.1.2/bits/cmath.tcc: +/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/cmath.tcc: 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