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fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = subsample.cpp; sourceTree = ""; }; @@ -447,9 +498,13 @@ A7C3DC0A14FE457500FE1924 /* cooccurrencecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cooccurrencecommand.h; sourceTree = ""; }; A7C3DC0D14FE469500FE1924 /* trialSwap2.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = trialSwap2.cpp; sourceTree = ""; }; A7C3DC0E14FE469500FE1924 /* trialswap2.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = trialswap2.h; sourceTree = ""; }; + A7C7DAB615DA75760059B0CF /* sffmultiplecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sffmultiplecommand.h; sourceTree = ""; }; + A7C7DAB815DA758B0059B0CF /* sffmultiplecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sffmultiplecommand.cpp; sourceTree = ""; }; A7D755D71535F665009BF21A /* treereader.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treereader.h; sourceTree = ""; }; A7D755D91535F679009BF21A /* treereader.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treereader.cpp; sourceTree = ""; }; A7DAAFA3133A254E003956EB /* commandparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = commandparameter.h; sourceTree = ""; }; + A7E0243C15B4520A00A5F046 /* sparsedistancematrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sparsedistancematrix.cpp; sourceTree = ""; }; + A7E0243F15B4522000A5F046 /* sparsedistancematrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sparsedistancematrix.h; sourceTree = ""; }; A7E9B64F12D37EC300DA6239 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = ""; }; A7E9B65012D37EC300DA6239 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = ""; }; A7E9B65112D37EC300DA6239 /* aligncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = aligncommand.cpp; sourceTree = ""; }; @@ -797,17 +852,11 @@ A7E9B7B312D37EC400DA6239 /* readcluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcluster.h; sourceTree = ""; }; A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readcolumn.cpp; sourceTree = ""; }; A7E9B7B512D37EC400DA6239 /* readcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcolumn.h; sourceTree = ""; }; - A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistcommand.cpp; sourceTree = ""; }; - A7E9B7B712D37EC400DA6239 /* readdistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcommand.h; sourceTree = ""; }; A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = ""; }; - A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = ""; }; - A7E9B7BC12D37EC400DA6239 /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = ""; }; A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = ""; }; A7E9B7BE12D37EC400DA6239 /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = ""; }; A7E9B7BF12D37EC400DA6239 /* readtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtree.cpp; sourceTree = ""; }; A7E9B7C012D37EC400DA6239 /* readtree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtree.h; sourceTree = ""; }; - A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = ""; }; - A7E9B7C212D37EC400DA6239 /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = ""; }; A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removegroupscommand.cpp; sourceTree = ""; }; A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removegroupscommand.h; sourceTree = ""; }; A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removelineagecommand.cpp; sourceTree = ""; }; @@ -1126,6 +1175,7 @@ A7E9B79B12D37EC400DA6239 /* progress.cpp */, A7E9B79C12D37EC400DA6239 /* progress.hpp */, A7E9B7A512D37EC400DA6239 /* rarecalc.cpp */, + A7386C191619C9FB00651424 /* randomforest */, A7E9B7A612D37EC400DA6239 /* rarecalc.h */, A7E9B7A712D37EC400DA6239 /* raredisplay.cpp */, A7E9B7A812D37EC400DA6239 /* raredisplay.h */, @@ -1167,6 +1217,30 @@ name = Products; sourceTree = ""; }; + A7386C191619C9FB00651424 /* randomforest */ = { + isa = PBXGroup; + children = ( + A7386C1B1619CACB00651424 /* abstractdecisiontree.hpp */, + A7386C241619E52200651424 /* abstractdecisiontree.cpp */, + A7386C1C1619CACB00651424 /* abstractrandomforest.hpp */, + A7386C26161A0F9C00651424 /* abstractrandomforest.cpp */, + A7386C1D1619CACB00651424 /* decisiontree.hpp */, + A7386C28161A110700651424 /* decisiontree.cpp */, + A7386C1E1619CACB00651424 /* macros.h */, + A7386C1F1619CACB00651424 /* randomforest.hpp */, + A77E1937161B201E00DB1A2A /* randomforest.cpp */, + A7386C201619CACB00651424 /* rftreenode.hpp */, + A77E193A161B289600DB1A2A /* rftreenode.cpp */, + 83F25B0A163B031200ABE73D /* forest.cpp */, + 83F25B0B163B031200ABE73D /* forest.h */, + 834D9D561656D7C400E7FAB9 /* regularizedrandomforest.cpp */, + 834D9D571656D7C400E7FAB9 /* regularizedrandomforest.h */, + 834D9D5A1656DEC700E7FAB9 /* regularizeddecisiontree.cpp */, + 834D9D5B1656DEC700E7FAB9 /* regularizeddecisiontree.h */, + ); + name = randomforest; + sourceTree = ""; + }; A7D161E7149F7F50000523E8 /* fortran */ = { isa = PBXGroup; children = ( @@ -1223,6 +1297,8 @@ A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */, A7E9B69312D37EC400DA6239 /* classifyseqscommand.h */, A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */, + A7386C221619CCE600651424 /* classifysharedcommand.h */, + A7386C211619CCE600651424 /* classifysharedcommand.cpp */, A7EEB0F714F29C1B00344B83 /* classifytreecommand.h */, A7EEB0F414F29BFD00344B83 /* classifytreecommand.cpp */, A7E9B69712D37EC400DA6239 /* clearcutcommand.h */, @@ -1315,6 +1391,8 @@ A7A067191562946F0095C8C5 /* listotulabelscommand.cpp */, A7E9B73E12D37EC400DA6239 /* listseqscommand.h */, A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */, + A73901051588C3EF00ED2ED6 /* loadlogfilecommand.h */, + A73901071588C40900ED2ED6 /* loadlogfilecommand.cpp */, A7FA10001302E096003860FE /* mantelcommand.h */, A7FA10011302E096003860FE /* mantelcommand.cpp */, A724D2B4153C8600000A826F /* makebiomcommand.h */, @@ -1373,12 +1451,6 @@ A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */, A7E9B7AF12D37EC400DA6239 /* rarefactsharedcommand.h */, A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */, - A7E9B7B712D37EC400DA6239 /* readdistcommand.h */, - A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */, - A7E9B7BC12D37EC400DA6239 /* readotucommand.h */, - A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */, - A7E9B7C212D37EC400DA6239 /* readtreecommand.h */, - A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */, A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */, A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */, A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */, @@ -1411,6 +1483,8 @@ A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */, A7E9B7E412D37EC400DA6239 /* sffinfocommand.h */, A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */, + A7C7DAB615DA75760059B0CF /* sffmultiplecommand.h */, + A7C7DAB815DA758B0059B0CF /* sffmultiplecommand.cpp */, A7E9B7F312D37EC400DA6239 /* sharedcommand.h */, A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */, A7E9B82812D37EC400DA6239 /* shhhercommand.h */, @@ -1471,8 +1545,6 @@ A7E9B67112D37EC400DA6239 /* canberra.h */, A7E9B67612D37EC400DA6239 /* chao1.cpp */, A7E9B67712D37EC400DA6239 /* chao1.h */, - A7E9B6A412D37EC400DA6239 /* cmdargs.cpp */, - A7E9B6A512D37EC400DA6239 /* cmdargs.h */, A7E9B6BB12D37EC400DA6239 /* coverage.cpp */, A7E9B6BC12D37EC400DA6239 /* coverage.h */, A7E9B6CA12D37EC400DA6239 /* dist.h */, @@ -1626,10 +1698,12 @@ A7E9B66312D37EC400DA6239 /* blastalign.hpp */, A7E9B66412D37EC400DA6239 /* blastdb.cpp */, A7E9B66512D37EC400DA6239 /* blastdb.hpp */, + A74D59A6159A1E3600043046 /* counttable.h */, + A74D59A3159A1E2000043046 /* counttable.cpp */, + A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */, A7E9B6BD12D37EC400DA6239 /* database.cpp */, A7E9B6BE12D37EC400DA6239 /* database.hpp */, A7E9B6BF12D37EC400DA6239 /* datavector.hpp */, - A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */, A7E9B6CE12D37EC400DA6239 /* distancedb.hpp */, A7E9B6DE12D37EC400DA6239 /* fastamap.cpp */, A7E9B6DF12D37EC400DA6239 /* fastamap.h */, @@ -1661,6 +1735,8 @@ A7E9B7D012D37EC400DA6239 /* sabundvector.hpp */, A7E9B7DB12D37EC400DA6239 /* sequence.cpp */, A7E9B7DC12D37EC400DA6239 /* sequence.hpp */, + A741FAD415D168A00067BCC5 /* sequencecountparser.h */, + A741FAD115D1688E0067BCC5 /* sequencecountparser.cpp */, A7E9B7DD12D37EC400DA6239 /* sequencedb.cpp */, A7E9B7DE12D37EC400DA6239 /* sequencedb.h */, A7F9F5CD141A5E500032F693 /* sequenceparser.h */, @@ -1677,6 +1753,8 @@ A7E9B81412D37EC400DA6239 /* sharedsabundvector.h */, A7E9B83912D37EC400DA6239 /* sparsematrix.cpp */, A7E9B83A12D37EC400DA6239 /* sparsematrix.hpp */, + A7E0243F15B4522000A5F046 /* sparsedistancematrix.h */, + A7E0243C15B4520A00A5F046 /* sparsedistancematrix.cpp */, A7E9B85112D37EC400DA6239 /* suffixdb.cpp */, A7E9B85212D37EC400DA6239 /* suffixdb.hpp */, A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */, @@ -1725,10 +1803,18 @@ A7E9BA4B12D3966900DA6239 /* classifier */ = { isa = PBXGroup; children = ( - A7E9B65A12D37EC300DA6239 /* bayesian.cpp */, + A721AB67161C570F009860A1 /* alignnode.h */, + A721AB66161C570F009860A1 /* alignnode.cpp */, + A721AB69161C570F009860A1 /* aligntree.h */, + A721AB68161C570F009860A1 /* aligntree.cpp */, A7E9B65B12D37EC300DA6239 /* bayesian.h */, + A7E9B65A12D37EC300DA6239 /* bayesian.cpp */, A7E9B68E12D37EC400DA6239 /* classify.cpp */, A7E9B68F12D37EC400DA6239 /* classify.h */, + A721AB6E161C572A009860A1 /* kmernode.h */, + A721AB6D161C572A009860A1 /* kmernode.cpp */, + A721AB70161C572A009860A1 /* kmertree.h */, + A721AB6F161C572A009860A1 /* kmertree.cpp */, A7E9B73812D37EC400DA6239 /* knn.h */, A7E9B73712D37EC400DA6239 /* knn.cpp */, A7E9B78D12D37EC400DA6239 /* phylosummary.cpp */, @@ -1737,6 +1823,8 @@ A7E9B79012D37EC400DA6239 /* phylotree.h */, A7E9B85D12D37EC400DA6239 /* taxonomyequalizer.cpp */, A7E9B85E12D37EC400DA6239 /* taxonomyequalizer.h */, + A721AB74161C573B009860A1 /* taxonomynode.h */, + A721AB73161C573B009860A1 /* taxonomynode.cpp */, ); name = classifier; sourceTree = ""; @@ -1746,6 +1834,8 @@ children = ( A7E9B69412D37EC400DA6239 /* clearcut.cpp */, A7E9B69512D37EC400DA6239 /* clearcut.h */, + A7E9B6A412D37EC400DA6239 /* cmdargs.cpp */, + A7E9B6A512D37EC400DA6239 /* cmdargs.h */, A7E9B6B312D37EC400DA6239 /* common.h */, A7E9B6CF12D37EC400DA6239 /* distclearcut.cpp */, A7E9B6D012D37EC400DA6239 /* distclearcut.h */, @@ -2030,11 +2120,8 @@ A7E9B92912D37EC400DA6239 /* readblast.cpp in Sources */, A7E9B92A12D37EC400DA6239 /* readcluster.cpp in Sources */, A7E9B92B12D37EC400DA6239 /* readcolumn.cpp in Sources */, - A7E9B92C12D37EC400DA6239 /* readdistcommand.cpp in Sources */, - A7E9B92E12D37EC400DA6239 /* readotucommand.cpp in Sources */, A7E9B92F12D37EC400DA6239 /* readphylip.cpp in Sources */, A7E9B93012D37EC400DA6239 /* readtree.cpp in Sources */, - A7E9B93112D37EC400DA6239 /* readtreecommand.cpp in Sources */, A7E9B93212D37EC400DA6239 /* removegroupscommand.cpp in Sources */, A7E9B93312D37EC400DA6239 /* removelineagecommand.cpp in Sources */, A7E9B93412D37EC400DA6239 /* removeotuscommand.cpp in Sources */, @@ -2192,6 +2279,25 @@ A7A0671F1562AC3E0095C8C5 /* makecontigscommand.cpp in Sources */, A70056E6156A93D000924A2D /* getotulabelscommand.cpp in Sources */, A70056EB156AB6E500924A2D /* removeotulabelscommand.cpp in Sources */, + A73901081588C40900ED2ED6 /* loadlogfilecommand.cpp in Sources */, + A74D59A4159A1E2000043046 /* counttable.cpp in Sources */, + A7E0243D15B4520A00A5F046 /* sparsedistancematrix.cpp in Sources */, + A741FAD215D1688E0067BCC5 /* sequencecountparser.cpp in Sources */, + A7C7DAB915DA758B0059B0CF /* sffmultiplecommand.cpp in Sources */, + A7386C231619CCE600651424 /* classifysharedcommand.cpp in Sources */, + A7386C251619E52300651424 /* abstractdecisiontree.cpp in Sources */, + A7386C27161A0F9D00651424 /* abstractrandomforest.cpp in Sources */, + A7386C29161A110800651424 /* decisiontree.cpp in Sources */, + A77E1938161B201E00DB1A2A /* randomforest.cpp in Sources */, + A77E193B161B289600DB1A2A /* rftreenode.cpp in Sources */, + A721AB6A161C570F009860A1 /* alignnode.cpp in Sources */, + A721AB6B161C570F009860A1 /* aligntree.cpp in Sources */, + A721AB71161C572A009860A1 /* kmernode.cpp in Sources */, + A721AB72161C572A009860A1 /* kmertree.cpp in Sources */, + A721AB77161C573B009860A1 /* taxonomynode.cpp in Sources */, + 83F25B0C163B031200ABE73D /* forest.cpp in Sources */, + 834D9D581656D7C400E7FAB9 /* regularizedrandomforest.cpp in Sources */, + 834D9D5C1656DEC800E7FAB9 /* regularizeddecisiontree.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -2204,9 +2310,12 @@ ALWAYS_SEARCH_USER_PATHS = NO; COPY_PHASE_STRIP = NO; DEPLOYMENT_LOCATION = YES; + DSTROOT = TARGET_BUILD_DIR; + "DSTROOT[sdk=*]" = TARGET_BUILD_DIR; GCC_DYNAMIC_NO_PIC = NO; GCC_MODEL_TUNING = G5; - GCC_OPTIMIZATION_LEVEL = 0; + GCC_OPTIMIZATION_LEVEL = 3; + "INSTALL_PATH[sdk=*]" = TARGET_BUILD_DIR; PRODUCT_NAME = mothur; SDKROOT = macosx10.6; SKIP_INSTALL = NO; @@ -2219,7 +2328,9 @@ ALWAYS_SEARCH_USER_PATHS = NO; DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym"; DEPLOYMENT_LOCATION = YES; + DSTROOT = TARGET_BUILD_DIR; GCC_MODEL_TUNING = G5; + GCC_OPTIMIZATION_LEVEL = 3; GCC_WARN_UNUSED_VALUE = YES; PRODUCT_NAME = mothur; SKIP_INSTALL = NO; @@ -2235,11 +2346,11 @@ GCC_ENABLE_SSE3_EXTENSIONS = NO; GCC_ENABLE_SSE41_EXTENSIONS = NO; GCC_ENABLE_SSE42_EXTENSIONS = NO; - GCC_OPTIMIZATION_LEVEL = 0; + GCC_OPTIMIZATION_LEVEL = 3; GCC_PREPROCESSOR_DEFINITIONS = ( "MOTHUR_FILES=\"\\\"../release\\\"\"", - "VERSION=\"\\\"1.25.0\\\"\"", - "RELEASE_DATE=\"\\\"5/01/2012\\\"\"", + "VERSION=\"\\\"1.28.0\\\"\"", + "RELEASE_DATE=\"\\\"11/2/2012\\\"\"", ); "GCC_VERSION[arch=*]" = ""; GCC_WARN_ABOUT_MISSING_NEWLINE = YES; @@ -2272,10 +2383,10 @@ GCC_C_LANGUAGE_STANDARD = gnu99; GCC_GENERATE_DEBUGGING_SYMBOLS = NO; GCC_MODEL_TUNING = ""; - GCC_OPTIMIZATION_LEVEL = 0; + GCC_OPTIMIZATION_LEVEL = 3; GCC_PREPROCESSOR_DEFINITIONS = ( - "VERSION=\"\\\"1.25.0\\\"\"", - "RELEASE_DATE=\"\\\"4/30/2012\\\"\"", + "VERSION=\"\\\"1.28.0\\\"\"", + "RELEASE_DATE=\"\\\"11/2/2012\\\"\"", ); GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; @@ -2311,7 +2422,7 @@ 1DEB928708733DD80010E9CD /* Release */, ); defaultConfigurationIsVisible = 0; - defaultConfigurationName = Release; + defaultConfigurationName = Debug; }; 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = { isa = XCConfigurationList; @@ -2320,7 +2431,7 @@ 1DEB928B08733DD80010E9CD /* Release */, ); defaultConfigurationIsVisible = 0; - defaultConfigurationName = Release; + defaultConfigurationName = Debug; }; /* End XCConfigurationList section */ };