X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=0f03784a89e8beafb1aeec97a0e650aa20092e6d;hb=7bf581f8c46b08eb3bb40715dac94695edee4a67;hp=dae9fe3c9f0ba8bc02939e20c54fccc85e206da0;hpb=956cdff34f2d609a7736838b1631cd7957580b8b;p=mothur.git diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index dae9fe3..0f03784 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -7,6 +7,20 @@ objects = { /* Begin PBXFileReference section */ + 7E4EBD43122018FB00D85E7B /* simpsoneven.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = simpsoneven.h; sourceTree = ""; }; + 7E4EBD44122018FB00D85E7B /* simpsoneven.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = simpsoneven.cpp; sourceTree = ""; }; + 7E5B28DC121FEFCC0005339C /* shannoneven.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannoneven.h; sourceTree = ""; }; + 7E5B28DD121FEFCC0005339C /* shannoneven.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannoneven.cpp; sourceTree = ""; }; + 7E5B2917121FF53C0005339C /* heip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heip.h; sourceTree = ""; }; + 7E5B2918121FF53C0005339C /* heip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heip.cpp; sourceTree = ""; }; + 7E5B294A121FFADC0005339C /* smithwilson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = smithwilson.h; sourceTree = ""; }; + 7E5B294B121FFADC0005339C /* smithwilson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = smithwilson.cpp; sourceTree = ""; }; + 7E84528511EF4BEB00564975 /* seqerrorcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqerrorcommand.h; sourceTree = ""; }; + 7E84528611EF4BEB00564975 /* seqerrorcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqerrorcommand.cpp; sourceTree = ""; }; + 7E85BD1C11EB5E9B00FD37C0 /* qualityscores.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qualityscores.h; sourceTree = ""; }; + 7E85BD1D11EB5E9B00FD37C0 /* qualityscores.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qualityscores.cpp; sourceTree = ""; }; + 7E962A40121F76B1007464B5 /* invsimpson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = invsimpson.h; sourceTree = ""; }; + 7E962A41121F76B1007464B5 /* invsimpson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = invsimpson.cpp; sourceTree = ""; }; 7EA299BA11E384940022D8D3 /* sensspeccommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sensspeccommand.h; sourceTree = ""; }; 7EA299BB11E384940022D8D3 /* sensspeccommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sensspeccommand.cpp; sourceTree = ""; }; 7EC61A0911BEA6AF00F668D9 /* weightedlinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weightedlinkage.cpp; sourceTree = ""; }; @@ -16,6 +30,7 @@ A7118EE611CFCAC000CFDE03 /* degapseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = degapseqscommand.cpp; sourceTree = ""; }; A7118F0F11CFD5DC00CFDE03 /* getrelabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getrelabundcommand.h; sourceTree = ""; }; A7118F1011CFD5DC00CFDE03 /* getrelabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getrelabundcommand.cpp; sourceTree = ""; }; + A71BA75F1225694E00C57506 /* clearcut.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clearcut.cpp; sourceTree = ""; }; A71D924211AEB42400D00CBC /* clustersplitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clustersplitcommand.cpp; sourceTree = ""; }; A71D924311AEB42400D00CBC /* clustersplitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clustersplitcommand.h; sourceTree = ""; }; A71D924411AEB42400D00CBC /* splitabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitabundcommand.cpp; sourceTree = ""; }; @@ -46,6 +61,10 @@ A7825503116519F70002E2DD /* chimerabellerophoncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerabellerophoncommand.cpp; sourceTree = ""; }; A78434881162224F00100BE0 /* chimeraccodecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraccodecommand.h; sourceTree = ""; }; A78434891162224F00100BE0 /* chimeraccodecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraccodecommand.cpp; sourceTree = ""; }; + A798626D1240D91B005FC847 /* normalizesharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = normalizesharedcommand.h; sourceTree = ""; }; + A798626E1240D91B005FC847 /* normalizesharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = normalizesharedcommand.cpp; sourceTree = ""; }; + A7AE6302121C3408001DE6FC /* sharedrabundfloatvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundfloatvector.h; sourceTree = ""; }; + A7AE6303121C3408001DE6FC /* sharedrabundfloatvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrabundfloatvector.cpp; sourceTree = ""; }; A7BBDA7B11B5694E006E6551 /* classifyotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifyotucommand.h; sourceTree = ""; }; A7BBDA7C11B5694E006E6551 /* classifyotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifyotucommand.cpp; sourceTree = ""; }; A7D215C811996C6E00F13F13 /* clearcutcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clearcutcommand.h; sourceTree = ""; }; @@ -450,8 +469,29 @@ A7DA217A113FECD400BF472F /* weighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = weighted.h; sourceTree = ""; }; A7DA217B113FECD400BF472F /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = ""; }; A7DA217C113FECD400BF472F /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = ""; }; + A7DF0AD4121EBB14004A03EA /* clearcut.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clearcut.h; sourceTree = ""; }; + A7DF0AD5121EBB14004A03EA /* cmdargs.cpp */ = {isa = PBXFileReference; explicitFileType = sourcecode.cpp.cpp; fileEncoding = 4; path = cmdargs.cpp; sourceTree = ""; }; + A7DF0AD6121EBB14004A03EA /* cmdargs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cmdargs.h; sourceTree = ""; }; + A7DF0AD7121EBB14004A03EA /* common.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = common.h; sourceTree = ""; }; + A7DF0AD8121EBB14004A03EA /* dayhoff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dayhoff.h; sourceTree = ""; }; + A7DF0AD9121EBB14004A03EA /* distclearcut.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distclearcut.cpp; sourceTree = ""; }; + A7DF0ADA121EBB14004A03EA /* distclearcut.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distclearcut.h; sourceTree = ""; }; + A7DF0ADB121EBB14004A03EA /* dmat.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = dmat.cpp; sourceTree = ""; }; + A7DF0ADC121EBB14004A03EA /* dmat.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dmat.h; sourceTree = ""; }; + A7DF0ADD121EBB14004A03EA /* fasta.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fasta.cpp; sourceTree = ""; }; + A7DF0ADE121EBB14004A03EA /* fasta.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fasta.h; sourceTree = ""; }; + A7DF0ADF121EBB14004A03EA /* getopt_long.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getopt_long.cpp; sourceTree = ""; }; + A7DF0AE0121EBB14004A03EA /* getopt_long.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getopt_long.h; sourceTree = ""; }; + A7DF0AE1121EBB14004A03EA /* prng.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = prng.cpp; sourceTree = ""; }; + A7DF0AE2121EBB14004A03EA /* prng.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = prng.h; sourceTree = ""; }; A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsesffcommand.cpp; sourceTree = ""; }; A7E8338C115BBDAA00739EC4 /* parsesffcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsesffcommand.h; sourceTree = ""; }; + A7F6C8E1124229F900299875 /* fisher2.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; path = fisher2.c; sourceTree = ""; }; + A7F6C8E2124229F900299875 /* fisher2.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fisher2.h; sourceTree = ""; }; + A7F6C8E3124229F900299875 /* metastats2.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; path = metastats2.c; sourceTree = ""; }; + A7F6C8EA12423C0300299875 /* metastatscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = metastatscommand.h; sourceTree = ""; }; + A7F6C8EB12423C0300299875 /* metastatscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = metastatscommand.cpp; sourceTree = ""; }; + A7F6C9D512425D4600299875 /* metastats.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = metastats.h; sourceTree = ""; }; /* End PBXFileReference section */ /* Begin PBXGroup section */ @@ -469,6 +509,7 @@ A7CB593B11402EF90010EB83 /* calculators */, A7CB594A11402FB40010EB83 /* chimeras */, A7CB594511402F6E0010EB83 /* classifers */, + A7DF0AE5121EBC26004A03EA /* clearcutsource */, A7CB593E11402F110010EB83 /* commands */, A7CB594211402F430010EB83 /* containers */, A7DA2023113FECD400BF472F /* collect.cpp */, @@ -502,6 +543,7 @@ A7DA2082113FECD400BF472F /* inputdata.h */, A7DA208B113FECD400BF472F /* libshuff.cpp */, A7DA208C113FECD400BF472F /* libshuff.h */, + A7F6C8DC1242299300299875 /* metastatsource */, A7DA209E113FECD400BF472F /* mothur.cpp */, A7DA209F113FECD400BF472F /* mothur.h */, A7DA20A0113FECD400BF472F /* mothurout.cpp */, @@ -573,7 +615,11 @@ A7DA2059113FECD400BF472F /* geom.h */, A7DA206C113FECD400BF472F /* goodscoverage.cpp */, A7DA206D113FECD400BF472F /* goodscoverage.h */, + 7E5B2917121FF53C0005339C /* heip.h */, + 7E5B2918121FF53C0005339C /* heip.cpp */, A7DA2080113FECD400BF472F /* ignoregaps.h */, + 7E962A40121F76B1007464B5 /* invsimpson.h */, + 7E962A41121F76B1007464B5 /* invsimpson.cpp */, A7DA2083113FECD400BF472F /* jackknife.cpp */, A7DA2084113FECD400BF472F /* jackknife.h */, A7DA2093113FECD400BF472F /* logsd.cpp */, @@ -591,6 +637,8 @@ A7DA20CF113FECD400BF472F /* qstat.h */, A7DA2104113FECD400BF472F /* shannon.cpp */, A7DA2105113FECD400BF472F /* shannon.h */, + 7E5B28DC121FEFCC0005339C /* shannoneven.h */, + 7E5B28DD121FEFCC0005339C /* shannoneven.cpp */, A7DA2106113FECD400BF472F /* sharedace.cpp */, A7DA2107113FECD400BF472F /* sharedace.h */, A7DA2108113FECD400BF472F /* sharedanderberg.h */, @@ -639,6 +687,10 @@ A7DA213D113FECD400BF472F /* sharedthetayc.h */, A7DA2140113FECD400BF472F /* shen.cpp */, A7DA2141113FECD400BF472F /* shen.h */, + 7E4EBD43122018FB00D85E7B /* simpsoneven.h */, + 7E4EBD44122018FB00D85E7B /* simpsoneven.cpp */, + 7E5B294A121FFADC0005339C /* smithwilson.h */, + 7E5B294B121FFADC0005339C /* smithwilson.cpp */, A7DA2142113FECD400BF472F /* simpson.cpp */, A7DA2143113FECD400BF472F /* simpson.h */, A7DA2149113FECD400BF472F /* sobs.h */, @@ -694,8 +746,8 @@ A7DA2022113FECD400BF472F /* clustercommand.h */, A71D924311AEB42400D00CBC /* clustersplitcommand.h */, A71D924211AEB42400D00CBC /* clustersplitcommand.cpp */, - A7DA2025113FECD400BF472F /* collectcommand.cpp */, A7DA2026113FECD400BF472F /* collectcommand.h */, + A7DA2025113FECD400BF472F /* collectcommand.cpp */, A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */, A7DA202A113FECD400BF472F /* collectsharedcommand.h */, A7DA2031113FECD400BF472F /* consensuscommand.cpp */, @@ -744,10 +796,14 @@ A7DA2099113FECD400BF472F /* matrixoutputcommand.h */, A7DA209A113FECD400BF472F /* mergefilecommand.cpp */, A7DA209B113FECD400BF472F /* mergefilecommand.h */, + A7F6C8EA12423C0300299875 /* metastatscommand.h */, + A7F6C8EB12423C0300299875 /* metastatscommand.cpp */, A7DA209C113FECD400BF472F /* mgclustercommand.cpp */, A7DA209D113FECD400BF472F /* mgclustercommand.h */, A7DA20AC113FECD400BF472F /* nocommands.cpp */, A7DA20AD113FECD400BF472F /* nocommands.h */, + A798626D1240D91B005FC847 /* normalizesharedcommand.h */, + A798626E1240D91B005FC847 /* normalizesharedcommand.cpp */, A7DA20B8113FECD400BF472F /* otuhierarchycommand.cpp */, A7DA20B9113FECD400BF472F /* otuhierarchycommand.h */, A7DA20BC113FECD400BF472F /* parselistscommand.cpp */, @@ -786,6 +842,8 @@ A7DA20FA113FECD400BF472F /* secondarystructurecommand.cpp */, 7EA299BA11E384940022D8D3 /* sensspeccommand.h */, 7EA299BB11E384940022D8D3 /* sensspeccommand.cpp */, + 7E84528511EF4BEB00564975 /* seqerrorcommand.h */, + 7E84528611EF4BEB00564975 /* seqerrorcommand.cpp */, A7DA20FD113FECD400BF472F /* seqsummarycommand.h */, A7DA20FC113FECD400BF472F /* seqsummarycommand.cpp */, A7DA2103113FECD400BF472F /* setdircommand.h */, @@ -848,8 +906,10 @@ A7DA20A3113FECD400BF472F /* nameassignment.hpp */, A7DA20B6113FECD400BF472F /* ordervector.cpp */, A7DA20B7113FECD400BF472F /* ordervector.hpp */, - A7DA20D2113FECD400BF472F /* rabundvector.cpp */, + 7E85BD1C11EB5E9B00FD37C0 /* qualityscores.h */, + 7E85BD1D11EB5E9B00FD37C0 /* qualityscores.cpp */, A7DA20D3113FECD400BF472F /* rabundvector.hpp */, + A7DA20D2113FECD400BF472F /* rabundvector.cpp */, A7DA20F6113FECD400BF472F /* sabundvector.cpp */, A7DA20F7113FECD400BF472F /* sabundvector.hpp */, A7DA20FE113FECD400BF472F /* sequence.cpp */, @@ -862,8 +922,10 @@ A7DA212B113FECD400BF472F /* sharedordervector.h */, A7DA212C113FECD400BF472F /* sharedrabundvector.cpp */, A7DA212D113FECD400BF472F /* sharedrabundvector.h */, - A7DA212E113FECD400BF472F /* sharedsabundvector.cpp */, + A7AE6302121C3408001DE6FC /* sharedrabundfloatvector.h */, + A7AE6303121C3408001DE6FC /* sharedrabundfloatvector.cpp */, A7DA212F113FECD400BF472F /* sharedsabundvector.h */, + A7DA212E113FECD400BF472F /* sharedsabundvector.cpp */, A7DA214C113FECD400BF472F /* sparsematrix.cpp */, A7DA214D113FECD400BF472F /* sparsematrix.hpp */, A7DA214E113FECD400BF472F /* suffixdb.cpp */, @@ -955,6 +1017,40 @@ name = read; sourceTree = ""; }; + A7DF0AE5121EBC26004A03EA /* clearcutsource */ = { + isa = PBXGroup; + children = ( + A7DF0AD4121EBB14004A03EA /* clearcut.h */, + A71BA75F1225694E00C57506 /* clearcut.cpp */, + A7DF0AD7121EBB14004A03EA /* common.h */, + A7DF0AD8121EBB14004A03EA /* dayhoff.h */, + A7DF0AD6121EBB14004A03EA /* cmdargs.h */, + A7DF0AD5121EBB14004A03EA /* cmdargs.cpp */, + A7DF0AD9121EBB14004A03EA /* distclearcut.cpp */, + A7DF0ADA121EBB14004A03EA /* distclearcut.h */, + A7DF0ADB121EBB14004A03EA /* dmat.cpp */, + A7DF0ADC121EBB14004A03EA /* dmat.h */, + A7DF0ADD121EBB14004A03EA /* fasta.cpp */, + A7DF0ADE121EBB14004A03EA /* fasta.h */, + A7DF0ADF121EBB14004A03EA /* getopt_long.cpp */, + A7DF0AE0121EBB14004A03EA /* getopt_long.h */, + A7DF0AE2121EBB14004A03EA /* prng.h */, + A7DF0AE1121EBB14004A03EA /* prng.cpp */, + ); + name = clearcutsource; + sourceTree = ""; + }; + A7F6C8DC1242299300299875 /* metastatsource */ = { + isa = PBXGroup; + children = ( + A7F6C8E2124229F900299875 /* fisher2.h */, + A7F6C8E1124229F900299875 /* fisher2.c */, + A7F6C9D512425D4600299875 /* metastats.h */, + A7F6C8E3124229F900299875 /* metastats2.c */, + ); + name = metastatsource; + sourceTree = ""; + }; /* End PBXGroup section */ /* Begin PBXLegacyTarget section */