X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=dbe9347e33ebe48637d991f4b31bff75091dfc98;hb=643cdf74ccd4fc2d565168716fb5645917dee834;hp=1e52e09f149fff725e5b5914e74b44f07525c52a;hpb=3cebc384d8b267156aef2d09ce578a66cd36f98e;p=mothur.git diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 1e52e09..dbe9347 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -7,8 +7,18 @@ objects = { /* Begin PBXBuildFile section */ + 7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */; }; 8DD76FB00486AB0100D96B5E /* mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6A0FF2C0290799A04C91782 /* mothur.1 */; }; A70332B712D3A13400761E33 /* makefile in Sources */ = {isa = PBXBuildFile; fileRef = A70332B512D3A13400761E33 /* makefile */; }; + A713EBAC12DC7613000092AC /* readphylipvector.cpp in 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/* chimeraslayercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraslayercommand.cpp; sourceTree = ""; }; @@ -610,8 +645,8 @@ A7E9B78412D37EC400DA6239 /* parsimony.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimony.h; sourceTree = ""; }; A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimonycommand.cpp; sourceTree = ""; }; A7E9B78612D37EC400DA6239 /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = ""; }; - A7E9B78712D37EC400DA6239 /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = ""; }; - A7E9B78812D37EC400DA6239 /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = ""; }; + A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcoacommand.cpp; sourceTree = ""; }; + A7E9B78812D37EC400DA6239 /* pcoacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcoacommand.h; sourceTree = ""; }; A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversity.cpp; sourceTree = ""; }; A7E9B78A12D37EC400DA6239 /* phylodiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversity.h; sourceTree = ""; }; A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversitycommand.cpp; sourceTree = ""; }; @@ -860,6 +895,16 @@ 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commandparameter.h */, A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */, A7E9BA4212D3960D00DA6239 /* containers */, + A7AACFBA132FE008003D6C4D /* currentfile.h */, A7E9B6C912D37EC400DA6239 /* display.h */, A7E9B6D112D37EC400DA6239 /* dlibshuff.cpp */, A7E9B6D212D37EC400DA6239 /* dlibshuff.h */, @@ -930,11 +978,19 @@ A7E9B72D12D37EC400DA6239 /* inputdata.cpp */, A7E9B73912D37EC400DA6239 /* libshuff.cpp */, A7E9B73A12D37EC400DA6239 /* libshuff.h */, + A7FC480C12D788F20055BC5C /* linearalgebra.h */, + A7FC480D12D788F20055BC5C /* linearalgebra.cpp */, A7E9BA5612D39BD800DA6239 /* metastats */, A7E9B75B12D37EC400DA6239 /* mothur.cpp */, A7E9B75C12D37EC400DA6239 /* mothur.h */, A7E9B75D12D37EC400DA6239 /* mothurout.cpp */, A7E9B75E12D37EC400DA6239 /* mothurout.h */, + A7E9B76112D37EC400DA6239 /* nast.cpp */, + A7E9B76212D37EC400DA6239 /* nast.hpp */, + A7E9B76312D37EC400DA6239 /* nastreport.cpp */, + A7E9B76412D37EC400DA6239 /* nastreport.hpp */, + A7E9B76712D37EC400DA6239 /* noalign.cpp */, + A7E9B76812D37EC400DA6239 /* noalign.hpp */, A7E9B76512D37EC400DA6239 /* needlemanoverlap.cpp */, A7E9B76612D37EC400DA6239 /* needlemanoverlap.hpp */, A7E9B77012D37EC400DA6239 /* observable.h */, @@ -951,19 +1007,15 @@ A7E9B7A912D37EC400DA6239 /* rarefact.cpp */, A7E9B7AA12D37EC400DA6239 /* rarefact.h */, A7E9B7AD12D37EC400DA6239 /* rarefactioncurvedata.h */, + 7E6BE10812F710D8007ADDBE /* refchimeratest.h */, + 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */, A7E9BA5312D39A5E00DA6239 /* read */, - A7E9B76112D37EC400DA6239 /* nast.cpp */, - A7E9B76212D37EC400DA6239 /* nast.hpp */, - A7E9B76312D37EC400DA6239 /* nastreport.cpp */, - A7E9B76412D37EC400DA6239 /* nastreport.hpp */, - A7E9B76712D37EC400DA6239 /* noalign.cpp */, - A7E9B76812D37EC400DA6239 /* noalign.hpp */, A7E9B82312D37EC400DA6239 /* sharedutilities.cpp */, A7E9B82412D37EC400DA6239 /* sharedutilities.h */, A7E9B82D12D37EC400DA6239 /* singlelinkage.cpp */, A7E9B83012D37EC400DA6239 /* slibshuff.cpp */, - A7E9B83112D37EC400DA6239 /* slibshuff.h */, A7E9B85112D37EC400DA6239 /* suffixdb.cpp */, + A7E9B83112D37EC400DA6239 /* slibshuff.h */, A7E9B85212D37EC400DA6239 /* suffixdb.hpp */, A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */, A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */, @@ -983,7 +1035,7 @@ 1AB674ADFE9D54B511CA2CBB /* Products */ = { isa = PBXGroup; children = ( - 8DD76FB20486AB0100D96B5E /* mothur */, + 8DD76FB20486AB0100D96B5E /* Mothur */, ); name = Products; sourceTree = ""; @@ -992,200 +1044,222 @@ isa = PBXGroup; children = ( A7E9B6AE12D37EC400DA6239 /* command.hpp */, - A7E9B65112D37EC300DA6239 /* aligncommand.cpp */, A7E9B65212D37EC300DA6239 /* aligncommand.h */, - A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */, + A7E9B65112D37EC300DA6239 /* aligncommand.cpp */, + A7A61F2B130062E000E05B6B /* amovacommand.h */, + A7A61F2C130062E000E05B6B /* amovacommand.cpp */, + A71CB15F130B04A2001E7287 /* anosimcommand.h */, + A71CB15E130B04A2001E7287 /* anosimcommand.cpp */, A7E9B66112D37EC300DA6239 /* binsequencecommand.h */, - A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */, + A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */, A7E9B66B12D37EC400DA6239 /* bootstrapsharedcommand.h */, - A7E9B67212D37EC400DA6239 /* catchallcommand.cpp */, + A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */, A7E9B67312D37EC400DA6239 /* catchallcommand.h */, - A7E9B67A12D37EC400DA6239 /* chimerabellerophoncommand.cpp */, + A7E9B67212D37EC400DA6239 /* catchallcommand.cpp */, A7E9B67B12D37EC400DA6239 /* chimerabellerophoncommand.h */, - A7E9B67C12D37EC400DA6239 /* chimeraccodecommand.cpp */, + A7E9B67A12D37EC400DA6239 /* chimerabellerophoncommand.cpp */, A7E9B67D12D37EC400DA6239 /* chimeraccodecommand.h */, - A7E9B67E12D37EC400DA6239 /* chimeracheckcommand.cpp */, + A7E9B67C12D37EC400DA6239 /* chimeraccodecommand.cpp */, A7E9B67F12D37EC400DA6239 /* chimeracheckcommand.h */, - A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */, + A7E9B67E12D37EC400DA6239 /* chimeracheckcommand.cpp */, A7E9B68312D37EC400DA6239 /* chimerapintailcommand.h */, - A7E9B68612D37EC400DA6239 /* chimeraseqscommand.cpp */, - A7E9B68712D37EC400DA6239 /* chimeraseqscommand.h */, - A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */, + A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */, A7E9B68B12D37EC400DA6239 /* chimeraslayercommand.h */, - A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */, + A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */, A7E9B68D12D37EC400DA6239 /* chopseqscommand.h */, - A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */, + A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */, A7E9B69112D37EC400DA6239 /* classifyotucommand.h */, - A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */, + A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */, A7E9B69312D37EC400DA6239 /* classifyseqscommand.h */, - A7E9B69612D37EC400DA6239 /* clearcutcommand.cpp */, + A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */, A7E9B69712D37EC400DA6239 /* clearcutcommand.h */, - A7E9B69C12D37EC400DA6239 /* clustercommand.cpp */, + A7E9B69612D37EC400DA6239 /* clearcutcommand.cpp */, A7E9B69D12D37EC400DA6239 /* clustercommand.h */, - A7E9B69E12D37EC400DA6239 /* clusterdoturcommand.cpp */, + A7E9B69C12D37EC400DA6239 /* clustercommand.cpp */, A7E9B69F12D37EC400DA6239 /* clusterdoturcommand.h */, - A7E9B6A012D37EC400DA6239 /* clusterfragmentscommand.cpp */, + A7E9B69E12D37EC400DA6239 /* clusterdoturcommand.cpp */, A7E9B6A112D37EC400DA6239 /* clusterfragmentscommand.h */, - A7E9B6A212D37EC400DA6239 /* clustersplitcommand.cpp */, + A7E9B6A012D37EC400DA6239 /* clusterfragmentscommand.cpp */, A7E9B6A312D37EC400DA6239 /* clustersplitcommand.h */, - A7E9B6A812D37EC400DA6239 /* collectcommand.cpp */, + A7E9B6A212D37EC400DA6239 /* clustersplitcommand.cpp */, A7E9B6A912D37EC400DA6239 /* collectcommand.h */, - A7E9B6AC12D37EC400DA6239 /* collectsharedcommand.cpp */, + A7E9B6A812D37EC400DA6239 /* collectcommand.cpp */, A7E9B6AD12D37EC400DA6239 /* collectsharedcommand.h */, - A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */, + A7E9B6AC12D37EC400DA6239 /* collectsharedcommand.cpp */, A7E9B6B612D37EC400DA6239 /* consensuscommand.h */, - A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */, + A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */, A7E9B6B812D37EC400DA6239 /* consensusseqscommand.h */, - A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */, + A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */, A7E9B6BA12D37EC400DA6239 /* corraxescommand.h */, - A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */, + A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */, A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */, - A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */, + A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */, A7E9B6C612D37EC400DA6239 /* degapseqscommand.h */, - A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */, + A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */, A7E9B6C812D37EC400DA6239 /* deuniqueseqscommand.h */, - A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */, + A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */, A7E9B6CC12D37EC400DA6239 /* distancecommand.h */, - A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */, + A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */, A7E9B6E412D37EC400DA6239 /* filterseqscommand.h */, - A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */, + A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */, + A778FE69134CA6CA00C0BA33 /* getcommandinfocommand.h */, + A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */, + A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */, + A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */, A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */, - A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */, + A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */, A7E9B6F512D37EC400DA6239 /* getgroupscommand.h */, - A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */, + A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */, A7E9B6F712D37EC400DA6239 /* getlabelcommand.h */, - A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */, + A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */, A7E9B6F912D37EC400DA6239 /* getlineagecommand.h */, - A7E9B6FA12D37EC400DA6239 /* getlistcountcommand.cpp */, + A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */, A7E9B6FB12D37EC400DA6239 /* getlistcountcommand.h */, - A7E9B6FE12D37EC400DA6239 /* getoturepcommand.cpp */, + A7E9B6FA12D37EC400DA6239 /* getlistcountcommand.cpp */, A7E9B6FF12D37EC400DA6239 /* getoturepcommand.h */, - A7E9B70012D37EC400DA6239 /* getotuscommand.cpp */, + A7E9B6FE12D37EC400DA6239 /* getoturepcommand.cpp */, A7E9B70112D37EC400DA6239 /* getotuscommand.h */, - A7E9B70212D37EC400DA6239 /* getrabundcommand.cpp */, + A7E9B70012D37EC400DA6239 /* getotuscommand.cpp */, A7E9B70312D37EC400DA6239 /* getrabundcommand.h */, - A7E9B70412D37EC400DA6239 /* getrelabundcommand.cpp */, + A7E9B70212D37EC400DA6239 /* getrabundcommand.cpp */, A7E9B70512D37EC400DA6239 /* getrelabundcommand.h */, - A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */, + A7E9B70412D37EC400DA6239 /* getrelabundcommand.cpp */, A7E9B70712D37EC400DA6239 /* getsabundcommand.h */, - A7E9B70812D37EC400DA6239 /* getseqscommand.cpp */, + A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */, A7E9B70912D37EC400DA6239 /* getseqscommand.h */, - A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */, + A7E9B70812D37EC400DA6239 /* getseqscommand.cpp */, A7E9B70B12D37EC400DA6239 /* getsharedotucommand.h */, - A7E9B71A12D37EC400DA6239 /* hclustercommand.cpp */, + A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */, A7E9B71B12D37EC400DA6239 /* hclustercommand.h */, - A7E9B71E12D37EC400DA6239 /* heatmapcommand.cpp */, + A7E9B71A12D37EC400DA6239 /* hclustercommand.cpp */, A7E9B71F12D37EC400DA6239 /* heatmapcommand.h */, - A7E9B72212D37EC400DA6239 /* heatmapsimcommand.cpp */, + A7E9B71E12D37EC400DA6239 /* heatmapcommand.cpp */, A7E9B72312D37EC400DA6239 /* heatmapsimcommand.h */, - A7E9B72812D37EC400DA6239 /* helpcommand.cpp */, + A7E9B72212D37EC400DA6239 /* heatmapsimcommand.cpp */, A7E9B72912D37EC400DA6239 /* helpcommand.h */, - A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */, + A7E9B72812D37EC400DA6239 /* helpcommand.cpp */, + A75790571301749D00A30DAB /* homovacommand.h */, + A75790581301749D00A30DAB /* homovacommand.cpp */, A7E9B72C12D37EC400DA6239 /* indicatorcommand.h */, - A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */, + A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */, A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */, - A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */, + A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */, A7E9B73E12D37EC400DA6239 /* listseqscommand.h */, - A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */, + A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */, + A7FA10001302E096003860FE /* mantelcommand.h */, + A7FA10011302E096003860FE /* mantelcommand.cpp */, + A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */, + A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */, A7E9B74412D37EC400DA6239 /* makegroupcommand.h */, - A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */, + A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */, A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */, - A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */, + A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */, A7E9B75412D37EC400DA6239 /* mergefilecommand.h */, - A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */, + A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */, + A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */, + A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */, A7E9B75812D37EC400DA6239 /* metastatscommand.h */, - A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */, + A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */, A7E9B75A12D37EC400DA6239 /* mgclustercommand.h */, + A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */, A7E9B76A12D37EC400DA6239 /* nocommands.h */, A7E9B76912D37EC400DA6239 /* nocommands.cpp */, - A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */, A7E9B76C12D37EC400DA6239 /* normalizesharedcommand.h */, - A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */, + A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */, + A713EBEB12DC7C5E000092AC /* nmdscommand.h */, + A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */, A7E9B77A12D37EC400DA6239 /* otuhierarchycommand.h */, - A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */, + A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */, A7E9B77E12D37EC400DA6239 /* pairwiseseqscommand.h */, - A7E9B77F12D37EC400DA6239 /* parsefastaqcommand.cpp */, + A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */, A7E9B78012D37EC400DA6239 /* parsefastaqcommand.h */, - A7E9B78112D37EC400DA6239 /* parselistscommand.cpp */, + A7E9B77F12D37EC400DA6239 /* parsefastaqcommand.cpp */, A7E9B78212D37EC400DA6239 /* parselistscommand.h */, - A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */, + A7E9B78112D37EC400DA6239 /* parselistscommand.cpp */, A7E9B78612D37EC400DA6239 /* parsimonycommand.h */, - A7E9B78712D37EC400DA6239 /* pcacommand.cpp */, - A7E9B78812D37EC400DA6239 /* pcacommand.h */, - A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */, + A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */, + A7FC486512D795D60055BC5C /* pcacommand.h */, + A7FC486612D795D60055BC5C /* pcacommand.cpp */, + A7E9B78812D37EC400DA6239 /* pcoacommand.h */, + A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */, A7E9B78C12D37EC400DA6239 /* phylodiversitycommand.h */, - A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */, + A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */, A7E9B79212D37EC400DA6239 /* phylotypecommand.h */, - A7E9B79512D37EC400DA6239 /* pipelinepdscommand.cpp */, + A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */, A7E9B79612D37EC400DA6239 /* pipelinepdscommand.h */, - A7E9B79712D37EC400DA6239 /* preclustercommand.cpp */, + A7E9B79512D37EC400DA6239 /* pipelinepdscommand.cpp */, A7E9B79812D37EC400DA6239 /* preclustercommand.h */, - A7E9B7A112D37EC400DA6239 /* quitcommand.cpp */, + A7E9B79712D37EC400DA6239 /* preclustercommand.cpp */, A7E9B7A212D37EC400DA6239 /* quitcommand.h */, - A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */, + A7E9B7A112D37EC400DA6239 /* quitcommand.cpp */, A7E9B7AC12D37EC400DA6239 /* rarefactcommand.h */, - A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */, + A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */, A7E9B7AF12D37EC400DA6239 /* rarefactsharedcommand.h */, - A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */, + A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */, A7E9B7B712D37EC400DA6239 /* readdistcommand.h */, - A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */, + A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */, A7E9B7BC12D37EC400DA6239 /* readotucommand.h */, - A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */, + A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */, A7E9B7C212D37EC400DA6239 /* readtreecommand.h */, - A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */, + A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */, A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */, - A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */, + A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */, A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */, - A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */, + A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */, A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */, - A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */, + A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */, + A727864212E9E28C00F86ABA /* removerarecommand.h */, + A727864312E9E28C00F86ABA /* removerarecommand.cpp */, A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */, - A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */, + A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */, A7E9B7CE12D37EC400DA6239 /* reversecommand.h */, - A7E9B7D112D37EC400DA6239 /* screenseqscommand.cpp */, + A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */, A7E9B7D212D37EC400DA6239 /* screenseqscommand.h */, - A7E9B7D312D37EC400DA6239 /* secondarystructurecommand.cpp */, + A7E9B7D112D37EC400DA6239 /* screenseqscommand.cpp */, A7E9B7D412D37EC400DA6239 /* secondarystructurecommand.h */, - A7E9B7D512D37EC400DA6239 /* sensspeccommand.cpp */, + A7E9B7D312D37EC400DA6239 /* secondarystructurecommand.cpp */, A7E9B7D612D37EC400DA6239 /* sensspeccommand.h */, - A7E9B7D712D37EC400DA6239 /* seqerrorcommand.cpp */, + A7E9B7D512D37EC400DA6239 /* sensspeccommand.cpp */, A7E9B7D812D37EC400DA6239 /* seqerrorcommand.h */, - A7E9B7D912D37EC400DA6239 /* seqsummarycommand.cpp */, + A7E9B7D712D37EC400DA6239 /* seqerrorcommand.cpp */, A7E9B7DA12D37EC400DA6239 /* seqsummarycommand.h */, - A7E9B7DF12D37EC400DA6239 /* setdircommand.cpp */, + A7E9B7D912D37EC400DA6239 /* seqsummarycommand.cpp */, + A7FE7E6B13311EA400F7B327 /* setcurrentcommand.h */, + A7FE7E6C13311EA400F7B327 /* setcurrentcommand.cpp */, A7E9B7E012D37EC400DA6239 /* setdircommand.h */, - A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */, + A7E9B7DF12D37EC400DA6239 /* setdircommand.cpp */, A7E9B7E212D37EC400DA6239 /* setlogfilecommand.h */, - A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */, + A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */, A7E9B7E412D37EC400DA6239 /* sffinfocommand.h */, - A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */, + A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */, A7E9B7F312D37EC400DA6239 /* sharedcommand.h */, - A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */, + A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */, A7E9B82812D37EC400DA6239 /* shhhercommand.h */, - A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */, + A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */, A7E9B84012D37EC400DA6239 /* splitabundcommand.h */, - A7E9B84112D37EC400DA6239 /* splitgroupscommand.cpp */, + A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */, A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */, - A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */, + A7E9B84112D37EC400DA6239 /* splitgroupscommand.cpp */, A7E9B85012D37EC400DA6239 /* subsamplecommand.h */, - A7E9B85712D37EC400DA6239 /* summarycommand.cpp */, + A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */, A7E9B85812D37EC400DA6239 /* summarycommand.h */, - A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */, + A7E9B85712D37EC400DA6239 /* summarycommand.cpp */, A7E9B85A12D37EC400DA6239 /* summarysharedcommand.h */, - A7E9B85B12D37EC400DA6239 /* systemcommand.cpp */, + A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */, A7E9B85C12D37EC400DA6239 /* systemcommand.h */, - A7E9B86212D37EC400DA6239 /* treegroupscommand.cpp */, + A7E9B85B12D37EC400DA6239 /* systemcommand.cpp */, A7E9B86312D37EC400DA6239 /* treegroupscommand.h */, - A7E9B86812D37EC400DA6239 /* trimflowscommand.cpp */, + A7E9B86212D37EC400DA6239 /* treegroupscommand.cpp */, A7E9B86912D37EC400DA6239 /* trimflowscommand.h */, - A7E9B86A12D37EC400DA6239 /* trimseqscommand.cpp */, + A7E9B86812D37EC400DA6239 /* trimflowscommand.cpp */, A7E9B86B12D37EC400DA6239 /* trimseqscommand.h */, - A7E9B86C12D37EC400DA6239 /* unifracunweightedcommand.cpp */, + A7E9B86A12D37EC400DA6239 /* trimseqscommand.cpp */, A7E9B86D12D37EC400DA6239 /* unifracunweightedcommand.h */, - A7E9B86E12D37EC400DA6239 /* unifracweightedcommand.cpp */, + A7E9B86C12D37EC400DA6239 /* unifracunweightedcommand.cpp */, A7E9B86F12D37EC400DA6239 /* unifracweightedcommand.h */, - A7E9B87A12D37EC400DA6239 /* venncommand.cpp */, + A7E9B86E12D37EC400DA6239 /* unifracweightedcommand.cpp */, A7E9B87B12D37EC400DA6239 /* venncommand.h */, + A7E9B87A12D37EC400DA6239 /* venncommand.cpp */, ); name = commands; sourceTree = ""; @@ -1342,12 +1416,12 @@ A7E9B84D12D37EC400DA6239 /* structpearson.cpp */, A7E9B84E12D37EC400DA6239 /* structpearson.h */, A7E9B86112D37EC400DA6239 /* treecalculator.h */, - A7E9B87012D37EC400DA6239 /* unweighted.cpp */, A7E9B87112D37EC400DA6239 /* unweighted.h */, + A7E9B87012D37EC400DA6239 /* unweighted.cpp */, A7E9B87212D37EC400DA6239 /* uvest.cpp */, A7E9B87312D37EC400DA6239 /* uvest.h */, - A7E9B87C12D37EC400DA6239 /* weighted.cpp */, A7E9B87D12D37EC400DA6239 /* weighted.h */, + A7E9B87C12D37EC400DA6239 /* weighted.cpp */, A7E9B87F12D37EC400DA6239 /* whittaker.cpp */, A7E9B88012D37EC400DA6239 /* whittaker.h */, ); @@ -1404,8 +1478,8 @@ A7E9B7DE12D37EC400DA6239 /* sequencedb.h */, A7E9B80412D37EC400DA6239 /* sharedlistvector.cpp */, A7E9B80512D37EC400DA6239 /* sharedlistvector.h */, - A7E9B80D12D37EC400DA6239 /* sharedordervector.cpp */, A7E9B80E12D37EC400DA6239 /* sharedordervector.h */, + A7E9B80D12D37EC400DA6239 /* sharedordervector.cpp */, A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */, A7E9B81012D37EC400DA6239 /* sharedrabundfloatvector.h */, A7E9B81112D37EC400DA6239 /* sharedrabundvector.cpp */, @@ -1440,8 +1514,8 @@ A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */, A7E9B68912D37EC400DA6239 /* chimeraslayer.h */, A7E9B6C112D37EC400DA6239 /* decalc.cpp */, - A7E9B6C212D37EC400DA6239 /* decalc.h */, A7E9B74612D37EC400DA6239 /* maligner.h */, + A7E9B6C212D37EC400DA6239 /* decalc.h */, A7E9B74512D37EC400DA6239 /* maligner.cpp */, A7E9B79312D37EC400DA6239 /* pintail.cpp */, A7E9B79412D37EC400DA6239 /* pintail.h */, @@ -1505,12 +1579,14 @@ A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */, A7E9B7B512D37EC400DA6239 /* readcolumn.h */, A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */, - A7E9B7B912D37EC400DA6239 /* readotu.cpp */, A7E9B7BA12D37EC400DA6239 /* readotu.h */, + A7E9B7B912D37EC400DA6239 /* readotu.cpp */, A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */, A7E9B7BE12D37EC400DA6239 /* readphylip.h */, A7E9B7BF12D37EC400DA6239 /* readtree.cpp */, A7E9B7C012D37EC400DA6239 /* readtree.h */, + A713EBAA12DC7613000092AC /* readphylipvector.h */, + A713EBAB12DC7613000092AC /* readphylipvector.cpp */, A7E9B84312D37EC400DA6239 /* splitmatrix.cpp */, A7E9B84412D37EC400DA6239 /* splitmatrix.h */, ); @@ -1537,9 +1613,9 @@ /* End PBXGroup section */ /* Begin PBXNativeTarget section */ - 8DD76FA90486AB0100D96B5E /* mothur */ = { + 8DD76FA90486AB0100D96B5E /* Mothur */ = { isa = PBXNativeTarget; - buildConfigurationList = 1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "mothur" */; + buildConfigurationList = 1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */; buildPhases = ( 8DD76FAB0486AB0100D96B5E /* Sources */, 8DD76FAD0486AB0100D96B5E /* Frameworks */, @@ -1549,10 +1625,10 @@ ); dependencies = ( ); - name = mothur; + name = Mothur; productInstallPath = "$(HOME)/bin"; productName = mothur; - productReference = 8DD76FB20486AB0100D96B5E /* mothur */; + productReference = 8DD76FB20486AB0100D96B5E /* Mothur */; productType = "com.apple.product-type.tool"; }; /* End PBXNativeTarget section */ @@ -1560,7 +1636,10 @@ /* Begin PBXProject section */ 08FB7793FE84155DC02AAC07 /* Project object */ = { isa = PBXProject; - buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */; + attributes = { + ORGANIZATIONNAME = "Schloss Lab"; + }; + buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */; compatibilityVersion = "Xcode 3.1"; developmentRegion = English; hasScannedForEncodings = 1; @@ -1574,7 +1653,7 @@ projectDirPath = ""; projectRoot = ""; targets = ( - 8DD76FA90486AB0100D96B5E /* mothur */, + 8DD76FA90486AB0100D96B5E /* Mothur */, ); }; /* End PBXProject section */ @@ -1612,7 +1691,6 @@ A7E9B89A12D37EC400DA6239 /* chimeracheckrdp.cpp in Sources */, A7E9B89B12D37EC400DA6239 /* chimerapintailcommand.cpp in Sources */, A7E9B89C12D37EC400DA6239 /* chimerarealigner.cpp in Sources */, - A7E9B89D12D37EC400DA6239 /* chimeraseqscommand.cpp in Sources */, A7E9B89E12D37EC400DA6239 /* chimeraslayer.cpp in Sources */, A7E9B89F12D37EC400DA6239 /* chimeraslayercommand.cpp in Sources */, A7E9B8A012D37EC400DA6239 /* chopseqscommand.cpp in Sources */, @@ -1732,7 +1810,7 @@ A7E9B91212D37EC400DA6239 /* parselistscommand.cpp in Sources */, A7E9B91312D37EC400DA6239 /* parsimony.cpp in Sources */, A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */, - A7E9B91512D37EC400DA6239 /* pcacommand.cpp in Sources */, + A7E9B91512D37EC400DA6239 /* pcoacommand.cpp in Sources */, A7E9B91612D37EC400DA6239 /* phylodiversity.cpp in Sources */, A7E9B91712D37EC400DA6239 /* phylodiversitycommand.cpp in Sources */, A7E9B91812D37EC400DA6239 /* phylosummary.cpp in Sources */, @@ -1856,6 +1934,21 @@ A7E9B98E12D37EC400DA6239 /* weightedlinkage.cpp in Sources */, A7E9B98F12D37EC400DA6239 /* whittaker.cpp in Sources */, A70332B712D3A13400761E33 /* makefile in Sources */, + A7FC480E12D788F20055BC5C /* linearalgebra.cpp in Sources */, + A7FC486712D795D60055BC5C /* pcacommand.cpp in Sources */, + A713EBAC12DC7613000092AC /* readphylipvector.cpp in Sources */, + A713EBED12DC7C5E000092AC /* nmdscommand.cpp in Sources */, + A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */, + A71FE12C12EDF72400963CA7 /* mergegroupscommand.cpp in Sources */, + 7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */, + A7A61F2D130062E000E05B6B /* amovacommand.cpp in Sources */, + A75790591301749D00A30DAB /* homovacommand.cpp in Sources */, + A7FA10021302E097003860FE /* mantelcommand.cpp in Sources */, + A799F5B91309A3E000AEEFA0 /* makefastqcommand.cpp in Sources */, + A71CB160130B04A2001E7287 /* anosimcommand.cpp in Sources */, + A7FE7C401330EA1000F7B327 /* getcurrentcommand.cpp in Sources */, + A7FE7E6D13311EA400F7B327 /* setcurrentcommand.cpp in Sources */, + A778FE6B134CA6CA00C0BA33 /* getcommandinfocommand.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -1872,7 +1965,8 @@ GCC_MODEL_TUNING = G5; GCC_OPTIMIZATION_LEVEL = 0; INSTALL_PATH = /usr/local/bin; - PRODUCT_NAME = mothur; + PRODUCT_NAME = Mothur; + SDKROOT = macosx10.6; }; name = Debug; }; @@ -1885,29 +1979,31 @@ GCC_MODEL_TUNING = G5; GCC_WARN_UNUSED_VALUE = YES; INSTALL_PATH = ./; - PRODUCT_NAME = mothur; + PRODUCT_NAME = Mothur; }; name = Release; }; 1DEB928A08733DD80010E9CD /* Debug */ = { isa = XCBuildConfiguration; buildSettings = { - ARCHS = "$(ARCHS_STANDARD_32_64_BIT)"; + ARCHS = "$(ARCHS_STANDARD_64_BIT)"; DEPLOYMENT_LOCATION = NO; GCC_C_LANGUAGE_STANDARD = gnu99; - GCC_OPTIMIZATION_LEVEL = 0; + GCC_OPTIMIZATION_LEVEL = 3; GCC_PREPROCESSOR_DEFINITIONS = ( "MOTHUR_FILES=\"\\\"../release\\\"\"", - "VERSION=\"\\\"1.15.0\\\"\"", - "RELEASE_DATE=\"\\\"12/10/2010\\\"\"", + "VERSION=\"\\\"1.18.0\\\"\"", + "RELEASE_DATE=\"\\\"4/11/2011\\\"\"", ); + GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_UNUSED_VARIABLE = YES; INSTALL_PATH = ""; + MACH_O_TYPE = mh_execute; ONLY_ACTIVE_ARCH = YES; OTHER_CPLUSPLUSFLAGS = ( - "-DUSE_READLINE", "-DBIT_VERSION", + "-DUSE_READLINE", "$(OTHER_CFLAGS)", ); OTHER_LDFLAGS = ( @@ -1915,20 +2011,22 @@ "-lreadline", ); PREBINDING = NO; - SDKROOT = macosx10.5; + SDKROOT = macosx10.6; }; name = Debug; }; 1DEB928B08733DD80010E9CD /* Release */ = { isa = XCBuildConfiguration; buildSettings = { - ARCHS = "$(ARCHS_STANDARD_32_64_BIT)"; + ARCHS = "$(ARCHS_STANDARD_64_BIT)"; DEPLOYMENT_LOCATION = NO; GCC_C_LANGUAGE_STANDARD = gnu99; + GCC_GENERATE_DEBUGGING_SYMBOLS = NO; + GCC_MODEL_TUNING = ""; + GCC_OPTIMIZATION_LEVEL = 3; GCC_PREPROCESSOR_DEFINITIONS = ( - "MOTHUR_FILES=\"\\\"../release\\\"\"", - "VERSION=\"\\\"1.15.0\\\"\"", - "RELEASE_DATE=\"\\\"12/10/2010\\\"\"", + "VERSION=\"\\\"1.18.0\\\"\"", + "RELEASE_DATE=\"\\\"4/11/2011\\\"\"", ); GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; @@ -1939,6 +2037,7 @@ GCC_WARN_UNUSED_VALUE = YES; GCC_WARN_UNUSED_VARIABLE = YES; INSTALL_PATH = ""; + MACH_O_TYPE = mh_execute; OTHER_CPLUSPLUSFLAGS = ( "-DUSE_READLINE", "-DBIT_VERSION", @@ -1956,7 +2055,7 @@ /* End XCBuildConfiguration section */ /* Begin XCConfigurationList section */ - 1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "mothur" */ = { + 1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */ = { isa = XCConfigurationList; buildConfigurations = ( 1DEB928608733DD80010E9CD /* Debug */, @@ -1965,7 +2064,7 @@ defaultConfigurationIsVisible = 0; defaultConfigurationName = Release; }; - 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */ = { + 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = { isa = XCConfigurationList; buildConfigurations = ( 1DEB928A08733DD80010E9CD /* Debug */,