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
6 # we do not use GNU-style files: NEWS README AUTHORS ChangeLog
7 AUTOMAKE_OPTIONS = foreign
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@/
17 # LDADD = foofiles/libfoo.a
19 bin_PROGRAMS = clustalw2
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 \
55 ./tree/UPGMA/RootedGuideTree.cpp \
56 ./tree/UPGMA/RootedTreeOutput.cpp \
58 ./tree/ClusterTree.cpp \
59 ./tree/AlignmentSteps.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 \
68 ./tree/UnRootedClusterTree.h \
69 ./tree/RandomGenerator.cpp \
71 ./tree/ClusterTreeOutput.h \
72 ./tree/RandomGenerator.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 \
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 \
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 \
139 ./clustalw_version.h \