binaries/src/clustalw/src/Makefile.am

   1 # Andreas Wilm (UCD): 2007-12-10
   2 # Generated using the following sites
   3 # http://www.openismus.com/documents/linux/automake/automake.shtml
   4 # http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html
   5
   6 # we do not use GNU-style files: NEWS README AUTHORS ChangeLog
   7 AUTOMAKE_OPTIONS = foreign
   8
   9 SUBDIRS =
  10
  11 #EXTRA_DIST =
  12 # got the following with automake 1.10 (AW 2009-05-19):
  13 # src/Makefile.am:13: `INCLUDES' is the old name for `AM_CPPFLAGS' (or `*_CPPFLAGS')
  14 # deleted next line therefore
  15 # INCLUDES = -I@top_srcdir@/
  16
  17 # LDADD = foofiles/libfoo.a
  18
  19 bin_PROGRAMS = clustalw2
  20
  21 clustalw2_SOURCES =  ./pairwise/PairwiseAlignBase.h \
  22  ./pairwise/FastPairwiseAlign.h \
  23  ./pairwise/FullPairwiseAlign.cpp \
  24  ./pairwise/FullPairwiseAlign.h \
  25  ./pairwise/FastPairwiseAlign.cpp \
  26  ./fileInput/FileParser.h \
  27  ./fileInput/EMBLFileParser.h \
  28  ./fileInput/MSFFileParser.cpp \
  29  ./fileInput/FileReader.cpp \
  30  ./fileInput/PIRFileParser.cpp \
  31  ./fileInput/MSFFileParser.h \
  32  ./fileInput/FileReader.h \
  33  ./fileInput/RSFFileParser.cpp \
  34  ./fileInput/PIRFileParser.h \
  35  ./fileInput/GDEFileParser.cpp \
  36  ./fileInput/RSFFileParser.h \
  37  ./fileInput/GDEFileParser.h \
  38  ./fileInput/InFileStream.cpp \
  39  ./fileInput/ClustalFileParser.cpp \
  40  ./fileInput/PearsonFileParser.cpp \
  41  ./fileInput/InFileStream.h \
  42  ./fileInput/ClustalFileParser.h \
  43  ./fileInput/PearsonFileParser.h \
  44  ./fileInput/FileParser.cpp \
  45  ./fileInput/EMBLFileParser.cpp \
  46  ./tree/UPGMA/RootedClusterTree.cpp \
  47  ./tree/UPGMA/RootedGuideTree.h \
  48  ./tree/UPGMA/UPGMAAlgorithm.cpp \
  49  ./tree/UPGMA/RootedTreeOutput.h \
  50  ./tree/UPGMA/RootedClusterTree.h \
  51  ./tree/UPGMA/Node.cpp \
  52  ./tree/UPGMA/UPGMAAlgorithm.h \
  53  ./tree/UPGMA/upgmadata.h \
  54  ./tree/UPGMA/Node.h \
  55  ./tree/UPGMA/RootedGuideTree.cpp \
  56  ./tree/UPGMA/RootedTreeOutput.cpp \
  57  ./tree/Tree.cpp \
  58  ./tree/ClusterTree.cpp \
  59  ./tree/AlignmentSteps.h \
  60  ./tree/Tree.h \
  61  ./tree/ClusterTree.h \
  62  ./tree/ClusterTreeAlgorithm.h \
  63  ./tree/TreeInterface.cpp \
  64  ./tree/UnRootedClusterTree.cpp \
  65  ./tree/ClusterTreeOutput.cpp \
  66  ./tree/TreeInterface.h \
  67  ./tree/dayhoff.h \
  68  ./tree/UnRootedClusterTree.h \
  69  ./tree/RandomGenerator.cpp \
  70  ./tree/NJTree.cpp \
  71  ./tree/ClusterTreeOutput.h \
  72  ./tree/RandomGenerator.h \
  73  ./tree/NJTree.h \
  74  ./tree/AlignmentSteps.cpp \
  75  ./interface/InteractiveMenu.cpp \
  76  ./interface/CommandLineParser.cpp \
  77  ./interface/InteractiveMenu.h \
  78  ./interface/CommandLineParser.h \
  79  ./substitutionMatrix/SubMatrix.cpp \
  80  ./substitutionMatrix/SubMatrix.h \
  81  ./substitutionMatrix/globalmatrix.h \
  82  ./substitutionMatrix/matrices.h \
  83  ./multipleAlign/Iteration.cpp \
  84  ./multipleAlign/MSA.cpp \
  85  ./multipleAlign/MyersMillerProfileAlign.cpp \
  86  ./multipleAlign/ProfileBase.h \
  87  ./multipleAlign/ProfileStandard.cpp \
  88  ./multipleAlign/LowScoreSegProfile.h \
  89  ./multipleAlign/Iteration.h \
  90  ./multipleAlign/MSA.h \
  91  ./multipleAlign/MyersMillerProfileAlign.h \
  92  ./multipleAlign/ProfileStandard.h \
  93  ./multipleAlign/ProfileWithSub.cpp \
  94  ./multipleAlign/ProfileAlignAlgorithm.h \
  95  ./multipleAlign/ProfileBase.cpp \
  96  ./multipleAlign/ProfileWithSub.h \
  97  ./multipleAlign/LowScoreSegProfile.cpp \
  98  ./general/ClustalWResources.h \
  99  ./general/OutputFile.cpp \
 100  ./general/VectorOutOfRange.h \
 101  ./general/UserParameters.cpp \
 102  ./general/SymMatrix.h \
 103  ./general/Utility.cpp \
 104  ./general/clustalw.h \
 105  ./general/OutputFile.h \
 106  ./general/param.h \
 107  ./general/utils.h \
 108  ./general/UserParameters.h \
 109  ./general/SquareMat.h \
 110  ./general/Utility.h \
 111  ./general/SequenceNotFoundException.h \
 112  ./general/InvalidCombination.cpp \
 113  ./general/Array2D.h \
 114  ./general/RandomAccessLList.h \
 115  ./general/general.h \
 116  ./general/debuglogObject.h \
 117  ./general/statsObject.h \
 118  ./general/userparams.h \
 119  ./general/DebugLog.cpp \
 120  ./general/ClustalWResources.cpp \
 121  ./general/VectorUtility.h \
 122  ./general/VectorOutOfRange.cpp \
 123  ./general/SymMatrix.cpp \
 124  ./general/DebugLog.h \
 125  ./general/Stats.cpp \
 126  ./general/Stats.h \
 127  ./Help.cpp \
 128  ./Help.h \
 129  ./alignment/Alignment.cpp \
 130  ./alignment/AlignmentOutput.cpp \
 131  ./alignment/Alignment.h \
 132  ./alignment/AlignmentOutput.h \
 133  ./alignment/ObjectiveScore.cpp \
 134  ./alignment/Sequence.cpp \
 135  ./alignment/ObjectiveScore.h \
 136  ./alignment/Sequence.h \
 137  ./Clustal.cpp \
 138  ./Clustal.h \
 139  ./clustalw_version.h \
 140  ./main.cpp