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/* getsharedotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsharedotucommand.h; sourceTree = SOURCE_ROOT; }; + A7E4A782106913F900688F62 /* getsharedotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsharedotucommand.cpp; sourceTree = SOURCE_ROOT; }; + A7E4A822106A9AD700688F62 /* maligner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = maligner.h; sourceTree = SOURCE_ROOT; }; + A7E4A823106A9AD700688F62 /* maligner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = maligner.cpp; sourceTree = SOURCE_ROOT; }; C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = ""; }; EB1216860F619B83004A865F /* bergerparker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bergerparker.h; sourceTree = SOURCE_ROOT; }; EB1216870F619B83004A865F /* bergerparker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bergerparker.cpp; sourceTree = SOURCE_ROOT; }; @@ -524,8 +591,11 @@ 373C68DC0FC1C38D00137ACD /* blastalign.hpp */, 373C68DB0FC1C38D00137ACD /* blastalign.cpp */, 37D928A60F2133C0001D4494 /* calculators */, + 374F2FE81006346600E97C66 /* chimera */, 37D927C20F21331F001D4494 /* cluster.hpp */, 37D927C10F21331F001D4494 /* cluster.cpp */, + A729ACE210849BBE00139801 /* hcluster.h */, + A729ACE310849BBE00139801 /* hcluster.cpp */, 37D928A90F2133E5001D4494 /* commands */, 37D927C60F21331F001D4494 /* collect.h */, 37D927C50F21331F001D4494 /* collect.cpp */, @@ -551,14 +621,14 @@ 373C68BA0FC1C1A600137ACD /* gotohoverlap.cpp */, 375873ED0F7D646F0040F377 /* heatmap.h */, 375873EE0F7D646F0040F377 /* heatmap.cpp */, + 378598720FDD4C1500EF9D03 /* heatmapsim.h */, + 378598730FDD4C1500EF9D03 /* heatmapsim.cpp */, 37D927E60F21331F001D4494 /* inputdata.h */, 37D927E50F21331F001D4494 /* inputdata.cpp */, 7E412F420F8D213C00381DD0 /* libshuff.h */, 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */, 37E3ED800F4D9D0D00B5DF02 /* mothur.h */, 37D927EF0F21331F001D4494 /* mothur.cpp */, - 37D927F10F21331F001D4494 /* nameassignment.hpp */, - 37D927F00F21331F001D4494 /* nameassignment.cpp */, 373C691E0FC1C98600137ACD /* nast.hpp */, 373C691D0FC1C98600137ACD /* nast.cpp */, 373C692A0FC1C9EB00137ACD /* nastreport.hpp */, @@ -568,6 +638,8 @@ 373C68E40FC1C4A500137ACD /* noalign.hpp */, 373C68E30FC1C4A500137ACD /* noalign.cpp */, 37D927F60F21331F001D4494 /* observable.h */, + 3785990E0FDD7E8E00EF9D03 /* optionparser.h */, + 3785990F0FDD7E8E00EF9D03 /* optionparser.cpp */, 373C68C40FC1C25F00137ACD /* overlap.hpp */, 373C68C30FC1C25F00137ACD /* overlap.cpp */, 37D927FC0F21331F001D4494 /* progress.hpp */, @@ -578,8 +650,6 @@ 37D928050F21331F001D4494 /* rarefact.cpp */, 37D928090F21331F001D4494 /* rarefactioncurvedata.h */, 3796441D0FB9B9650081FDB6 /* read */, - 37D928210F21331F001D4494 /* shared.h */, - 37D928200F21331F001D4494 /* shared.cpp */, 211C38310F961DD400FEE541 /* sharedutilities.h */, 211C38300F961DD400FEE541 /* sharedutilities.cpp */, 37D928420F21331F001D4494 /* singlelinkage.cpp */, @@ -601,9 +671,36 @@ name = Products; sourceTree = ""; }; + 374F2FE81006346600E97C66 /* chimera */ = { + isa = PBXGroup; + children = ( + 374F2FD51006320200E97C66 /* chimera.h */, + 372095C1103196D70004D347 /* chimera.cpp */, + 374F2FE9100634B600E97C66 /* bellerophon.h */, + 374F2FEA100634B600E97C66 /* bellerophon.cpp */, + A75B887C104C16860083C454 /* ccode.h */, + A75B887B104C16860083C454 /* ccode.cpp */, + A7283FF61056CAE100D0CC69 /* chimeracheckrdp.h */, + A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */, + A7B04491106CC3E60046FC83 /* chimeraslayer.h */, + A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */, + 372A55531017922B00C5194B /* decalc.h */, + 372A55541017922B00C5194B /* decalc.cpp */, + A7E4A822106A9AD700688F62 /* maligner.h */, + A7E4A823106A9AD700688F62 /* maligner.cpp */, + 374F301110063B6F00E97C66 /* pintail.h */, + 374F301210063B6F00E97C66 /* pintail.cpp */, + A7B0450C106CEEC90046FC83 /* slayer.h */, + A7B0450D106CEEC90046FC83 /* slayer.cpp */, + ); + name = chimera; + sourceTree = ""; + }; 3796441D0FB9B9650081FDB6 /* read */ = { isa = PBXGroup; children = ( + A751ACE81098B283003D0911 /* readcluster.h */, + A751ACE91098B283003D0911 /* readcluster.cpp */, 375AA1340F9E433D008EF9B8 /* readcolumn.h */, 375AA1330F9E433D008EF9B8 /* readcolumn.cpp */, 37D928130F21331F001D4494 /* readmatrix.hpp */, @@ -642,6 +739,7 @@ 37C753F40FB34C0300DBD02E /* eachgapignore.h */, 373C69960FC1E63600137ACD /* efron.cpp */, 373C69970FC1E63600137ACD /* efron.h */, + 379D3D6B0FF917F40068C1C0 /* filters.h */, EB9303F70F53517300E8EF26 /* geom.h */, EB9303F80F53517300E8EF26 /* geom.cpp */, 378C1AF10FB0644D004D63F5 /* goodscoverage.h */, @@ -745,8 +843,10 @@ 37D927C70F21331F001D4494 /* collectcommand.cpp */, 37D927CC0F21331F001D4494 /* collectsharedcommand.h */, 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */, - 377326640FAF16E0007ABB8B /* concensuscommand.h */, - 377326630FAF16E0007ABB8B /* concensuscommand.cpp */, + 377326640FAF16E0007ABB8B /* consensuscommand.h */, + 377326630FAF16E0007ABB8B /* consensuscommand.cpp */, + 379D3D4F0FF90E090068C1C0 /* chimeraseqscommand.h */, + 379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */, 37B28F660F27590100808A62 /* deconvolutecommand.h */, 37B28F670F27590100808A62 /* deconvolutecommand.cpp */, 37C753CC0FB3415200DBD02E /* distancecommand.h */, @@ -759,24 +859,36 @@ A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */, A70B53A90F4CD7AD0064797E /* getlinecommand.h */, A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */, + A73329CD1083B3B3003B10C5 /* getlistcountcommand.h */, + A73329CE1083B3B3003B10C5 /* getlistcountcommand.cpp */, 370B88050F8A4EE4005AB382 /* getoturepcommand.h */, 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */, 3749273D0FD5956B0031C06B /* getrabundcommand.h */, 3749273E0FD5956B0031C06B /* getrabundcommand.cpp */, 3749271B0FD58C840031C06B /* getsabundcommand.h */, 3749271C0FD58C840031C06B /* getsabundcommand.cpp */, + 37B73CA41004D89A008C4B41 /* getseqscommand.h */, + 37B73CA51004D89A008C4B41 /* getseqscommand.cpp */, + A7E4A781106913F900688F62 /* getsharedotucommand.h */, + A7E4A782106913F900688F62 /* getsharedotucommand.cpp */, + A729ACCE10848E6100139801 /* hclustercommand.h */, + A729ACCF10848E6100139801 /* hclustercommand.cpp */, 375873F10F7D64800040F377 /* heatmapcommand.h */, 375873F00F7D64800040F377 /* heatmapcommand.cpp */, + 378598640FDD497000EF9D03 /* heatmapsimcommand.h */, + 378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */, 37D927E40F21331F001D4494 /* helpcommand.h */, 37D927E30F21331F001D4494 /* helpcommand.cpp */, 375873F40F7D648F0040F377 /* libshuffcommand.h */, 375873F30F7D648F0040F377 /* libshuffcommand.cpp */, + 37B73C741004BEFD008C4B41 /* listseqscommand.h */, + 37B73C751004BEFD008C4B41 /* listseqscommand.cpp */, 21E859D60FC4632E005E1A48 /* matrixoutputcommand.h */, 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */, - 375873F60F7D649C0040F377 /* nocommands.cpp */, + 7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */, + 7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */, 375873F70F7D649C0040F377 /* nocommands.h */, - 37D927FA0F21331F001D4494 /* parselistcommand.h */, - 37D927F90F21331F001D4494 /* parselistcommand.cpp */, + 375873F60F7D649C0040F377 /* nocommands.cpp */, 3792946E0F2E191800B9034A /* parsimonycommand.h */, 3792946F0F2E191800B9034A /* parsimonycommand.cpp */, 37D927FE0F21331F001D4494 /* quitcommand.h */, @@ -791,18 +903,28 @@ 372E126F0F26365B0095CF7E /* readotucommand.cpp */, 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */, 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */, + 37B73CBE1004EB38008C4B41 /* removeseqscommand.h */, + 37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */, + 7E09C5120FDA79C5002ECAE5 /* reversecommand.h */, + 7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */, + A70DECD71063D8B40057C03C /* secondarystructurecommand.h */, + A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */, 371B30B30FD7EE67000414CA /* screenseqscommand.h */, 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */, - 3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */, 3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */, + 3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */, 37D928270F21331F001D4494 /* sharedcommand.h */, 37D928260F21331F001D4494 /* sharedcommand.cpp */, 37D928470F21331F001D4494 /* summarycommand.h */, 37D928460F21331F001D4494 /* summarycommand.cpp */, 37D9284B0F21331F001D4494 /* summarysharedcommand.h */, 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */, + 37B73CCD1004F5E0008C4B41 /* systemcommand.h */, + 37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */, 211C38370F961E1F00FEE541 /* treegroupscommand.h */, 211C38360F961E1F00FEE541 /* treegroupscommand.cpp */, + 7E09C5340FDA7F65002ECAE5 /* trimseqscommand.h */, + 7E09C5350FDA7F65002ECAE5 /* trimseqscommand.cpp */, 3746109B0F40657600460C57 /* unifracunweightedcommand.h */, 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */, 374610760F40645300460C57 /* unifracweightedcommand.h */, @@ -839,6 +961,8 @@ 37D927EB0F21331F001D4494 /* kmerdb.cpp */, 37D927EE0F21331F001D4494 /* listvector.hpp */, 37D927ED0F21331F001D4494 /* listvector.cpp */, + 37D927F10F21331F001D4494 /* nameassignment.hpp */, + 37D927F00F21331F001D4494 /* nameassignment.cpp */, 37D927F80F21331F001D4494 /* ordervector.hpp */, 37D927F70F21331F001D4494 /* ordervector.cpp */, 37D928000F21331F001D4494 /* rabundvector.hpp */, @@ -878,12 +1002,8 @@ 37D928B10F213472001D4494 /* errorcheckor */ = { isa = PBXGroup; children = ( - 37D927DA0F21331F001D4494 /* errorchecking.h */, - 37D927D90F21331F001D4494 /* errorchecking.cpp */, 37D928500F21331F001D4494 /* validcalculator.h */, 37D9284F0F21331F001D4494 /* validcalculator.cpp */, - 37D928520F21331F001D4494 /* validcommands.h */, - 37D928510F21331F001D4494 /* validcommands.cpp */, 37D928540F21331F001D4494 /* validparameter.h */, 37D928530F21331F001D4494 /* validparameter.cpp */, ); @@ -955,7 +1075,6 @@ 37D928610F21331F001D4494 /* completelinkage.cpp in Sources */, 37D928620F21331F001D4494 /* database.cpp in Sources */, 37D928630F21331F001D4494 /* engine.cpp in Sources */, - 37D928640F21331F001D4494 /* errorchecking.cpp in Sources */, 37D928650F21331F001D4494 /* fastamap.cpp in Sources */, 37D928660F21331F001D4494 /* fileoutput.cpp in Sources */, 37D928670F21331F001D4494 /* globaldata.cpp in Sources */, @@ -970,7 +1089,6 @@ 37D928700F21331F001D4494 /* nameassignment.cpp in Sources */, 37D928720F21331F001D4494 /* npshannon.cpp in Sources */, 37D928730F21331F001D4494 /* ordervector.cpp in Sources */, - 37D928740F21331F001D4494 /* parselistcommand.cpp in Sources */, 37D928750F21331F001D4494 /* progress.cpp in Sources */, 37D928760F21331F001D4494 /* quitcommand.cpp in Sources */, 37D928770F21331F001D4494 /* rabundvector.cpp in Sources */, @@ -982,7 +1100,6 @@ 37D928840F21331F001D4494 /* sabundvector.cpp in Sources */, 37D928850F21331F001D4494 /* sequence.cpp in Sources */, 37D928860F21331F001D4494 /* shannon.cpp in Sources */, - 37D928870F21331F001D4494 /* shared.cpp in Sources */, 37D928880F21331F001D4494 /* sharedace.cpp in Sources */, 37D928890F21331F001D4494 /* sharedchao1.cpp in Sources */, 37D9288A0F21331F001D4494 /* sharedcommand.cpp in Sources */, @@ -1005,7 +1122,6 @@ 37D9289B0F21331F001D4494 /* summarysharedcommand.cpp in Sources */, 37D9289C0F21331F001D4494 /* uvest.cpp in Sources */, 37D9289D0F21331F001D4494 /* validcalculator.cpp in Sources */, - 37D9289E0F21331F001D4494 /* validcommands.cpp in Sources */, 37D9289F0F21331F001D4494 /* validparameter.cpp in Sources */, 372E12700F26365B0095CF7E /* readotucommand.cpp in Sources */, 372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */, @@ -1060,7 +1176,7 @@ 375AA13B0F9E433D008EF9B8 /* readphylip.cpp in Sources */, 7EC3D4550FA0FFF900338DA5 /* coverage.cpp in Sources */, 7EC3D4560FA0FFF900338DA5 /* whittaker.cpp in Sources */, - 377326650FAF16E0007ABB8B /* concensuscommand.cpp in Sources */, + 377326650FAF16E0007ABB8B /* consensuscommand.cpp in Sources */, 378C1B030FB0644E004D63F5 /* filterseqscommand.cpp in Sources */, 378C1B040FB0644E004D63F5 /* goodscoverage.cpp in Sources */, 378C1B0A0FB0644E004D63F5 /* sequencedb.cpp in Sources */, @@ -1091,6 +1207,32 @@ 3799A9500FD6A58C00E33EDE /* distancedb.cpp in Sources */, 3799A9510FD6A58C00E33EDE /* seqsummarycommand.cpp in Sources */, 371B30B40FD7EE67000414CA /* screenseqscommand.cpp in Sources */, + 7E09C5140FDA79C5002ECAE5 /* reversecommand.cpp in Sources */, + 7E09C5360FDA7F65002ECAE5 /* trimseqscommand.cpp in Sources */, + 378598660FDD497000EF9D03 /* heatmapsimcommand.cpp in Sources */, + 378598740FDD4C1500EF9D03 /* heatmapsim.cpp in Sources */, + 378599100FDD7E8E00EF9D03 /* optionparser.cpp in Sources */, + 7E5A17AF0FE57292003C6A03 /* mergefilecommand.cpp in Sources */, + 379D3D510FF90E090068C1C0 /* chimeraseqscommand.cpp in Sources */, + 37B73C761004BEFD008C4B41 /* listseqscommand.cpp in Sources */, + 37B73CA61004D89A008C4B41 /* getseqscommand.cpp in Sources */, + 37B73CC01004EB38008C4B41 /* removeseqscommand.cpp in Sources */, + 37B73CCF1004F5E0008C4B41 /* systemcommand.cpp in Sources */, + 374F2FEB100634B600E97C66 /* bellerophon.cpp in Sources */, + 374F301310063B6F00E97C66 /* pintail.cpp in Sources */, + 372A55551017922B00C5194B /* decalc.cpp in Sources */, + 372095C2103196D70004D347 /* chimera.cpp in Sources */, + A75B887E104C16860083C454 /* ccode.cpp in Sources */, + A7283FF81056CAE100D0CC69 /* chimeracheckrdp.cpp in Sources */, + A70DECD91063D8B40057C03C /* secondarystructurecommand.cpp in Sources */, + A7E4A783106913F900688F62 /* getsharedotucommand.cpp in Sources */, + A7E4A824106A9AD700688F62 /* maligner.cpp in Sources */, + A7B04493106CC3E60046FC83 /* chimeraslayer.cpp in Sources */, + A7B0450E106CEEC90046FC83 /* slayer.cpp in Sources */, + A73329CF1083B3B3003B10C5 /* getlistcountcommand.cpp in Sources */, + A729ACD010848E6100139801 /* hclustercommand.cpp in Sources */, + A729ACE410849BBE00139801 /* hcluster.cpp in Sources */, + A751ACEA1098B283003D0911 /* readcluster.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -1129,10 +1271,15 @@ isa = XCBuildConfiguration; buildSettings = { GCC_OPTIMIZATION_LEVEL = 3; + GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; + GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO; + GCC_WARN_PEDANTIC = NO; GCC_WARN_UNUSED_VARIABLE = YES; + OTHER_CPLUSPLUSFLAGS = ""; PREBINDING = NO; SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk"; + WARNING_CFLAGS = ""; }; name = Debug; }; @@ -1144,10 +1291,25 @@ i386, ); GCC_OPTIMIZATION_LEVEL = 3; + GCC_WARN_ABOUT_MISSING_NEWLINE = YES; + GCC_WARN_ABOUT_MISSING_PROTOTYPES = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; + GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO; + GCC_WARN_MISSING_PARENTHESES = YES; + GCC_WARN_PEDANTIC = YES; + GCC_WARN_UNUSED_FUNCTION = YES; + GCC_WARN_UNUSED_PARAMETER = NO; + GCC_WARN_UNUSED_VALUE = YES; GCC_WARN_UNUSED_VARIABLE = YES; + OTHER_CPLUSPLUSFLAGS = ( + "-ansi", + "-pedantic", + "-wall", + ); PREBINDING = NO; SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk"; + SYMROOT = /Users/johnwestcott/Desktop; + WARNING_CFLAGS = ""; }; name = Release; };