X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=582beaf70ddc256d955b4677911069ab97971d16;hb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;hp=865f078d99ea2504c19c97befe28ead0d6a2254e;hpb=e840ba0e90a2b2be39e0910e4be23dde6a14cbac;p=mothur.git diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 865f078..582beaf 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -46,7 +46,6 @@ A7E9B89A12D37EC400DA6239 /* chimeracheckrdp.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68012D37EC400DA6239 /* chimeracheckrdp.cpp */; }; A7E9B89B12D37EC400DA6239 /* chimerapintailcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */; }; A7E9B89C12D37EC400DA6239 /* chimerarealigner.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68412D37EC400DA6239 /* chimerarealigner.cpp */; }; - A7E9B89D12D37EC400DA6239 /* chimeraseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68612D37EC400DA6239 /* chimeraseqscommand.cpp */; }; A7E9B89E12D37EC400DA6239 /* chimeraslayer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */; }; A7E9B89F12D37EC400DA6239 /* chimeraslayercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */; }; A7E9B8A012D37EC400DA6239 /* chopseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */; }; @@ -292,6 +291,8 @@ A7FA10021302E097003860FE /* mantelcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FA10011302E096003860FE /* mantelcommand.cpp */; }; A7FC480E12D788F20055BC5C /* linearalgebra.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FC480D12D788F20055BC5C /* linearalgebra.cpp */; }; A7FC486712D795D60055BC5C /* pcacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FC486612D795D60055BC5C /* pcacommand.cpp */; }; + A7FE7C401330EA1000F7B327 /* getcurrentcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */; }; + A7FE7E6D13311EA400F7B327 /* setcurrentcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FE7E6C13311EA400F7B327 /* setcurrentcommand.cpp */; }; /* End PBXBuildFile section */ /* Begin PBXCopyFilesBuildPhase section */ @@ -329,6 +330,8 @@ A7A61F1A130035C800E05B6B /* LICENSE */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = LICENSE; sourceTree = ""; }; A7A61F2B130062E000E05B6B /* amovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = amovacommand.h; sourceTree = ""; }; A7A61F2C130062E000E05B6B /* amovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = amovacommand.cpp; sourceTree = ""; }; + A7AACFBA132FE008003D6C4D /* currentfile.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = currentfile.h; sourceTree = ""; }; + A7DAAFA3133A254E003956EB /* commandparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = commandparameter.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 = ""; }; @@ -384,8 +387,6 @@ A7E9B68312D37EC400DA6239 /* chimerapintailcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerapintailcommand.h; sourceTree = ""; }; A7E9B68412D37EC400DA6239 /* chimerarealigner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerarealigner.cpp; sourceTree = ""; }; A7E9B68512D37EC400DA6239 /* chimerarealigner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerarealigner.h; sourceTree = ""; }; - A7E9B68612D37EC400DA6239 /* chimeraseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraseqscommand.cpp; sourceTree = ""; }; - A7E9B68712D37EC400DA6239 /* chimeraseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraseqscommand.h; sourceTree = ""; }; A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraslayer.cpp; sourceTree = ""; }; A7E9B68912D37EC400DA6239 /* chimeraslayer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraslayer.h; sourceTree = ""; }; A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraslayercommand.cpp; sourceTree = ""; }; @@ -897,6 +898,10 @@ A7FC480D12D788F20055BC5C /* linearalgebra.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = linearalgebra.cpp; sourceTree = ""; }; A7FC486512D795D60055BC5C /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = ""; }; A7FC486612D795D60055BC5C /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = ""; }; + A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getcurrentcommand.h; sourceTree = ""; }; + A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getcurrentcommand.cpp; sourceTree = ""; }; + A7FE7E6B13311EA400F7B327 /* setcurrentcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setcurrentcommand.h; sourceTree = ""; }; + A7FE7E6C13311EA400F7B327 /* setcurrentcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setcurrentcommand.cpp; sourceTree = ""; }; C6A0FF2C0290799A04C91782 /* mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = mothur.1; sourceTree = ""; }; /* End PBXFileReference section */ @@ -944,8 +949,10 @@ A7E9B6B012D37EC400DA6239 /* commandfactory.hpp */, A7E9B6B112D37EC400DA6239 /* commandoptionparser.cpp */, A7E9B6B212D37EC400DA6239 /* commandoptionparser.hpp */, + A7DAAFA3133A254E003956EB /* commandparameter.h */, A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */, A7E9BA4212D3960D00DA6239 /* containers */, + A7AACFBA132FE008003D6C4D /* currentfile.h */, A7E9B6C912D37EC400DA6239 /* display.h */, A7E9B6D112D37EC400DA6239 /* dlibshuff.cpp */, A7E9B6D212D37EC400DA6239 /* dlibshuff.h */, @@ -1034,218 +1041,220 @@ isa = PBXGroup; children = ( A7E9B6AE12D37EC400DA6239 /* command.hpp */, - A7E9B65112D37EC300DA6239 /* aligncommand.cpp */, A7E9B65212D37EC300DA6239 /* aligncommand.h */, + A7E9B65112D37EC300DA6239 /* aligncommand.cpp */, A7A61F2B130062E000E05B6B /* amovacommand.h */, A7A61F2C130062E000E05B6B /* amovacommand.cpp */, - A71CB15E130B04A2001E7287 /* anosimcommand.cpp */, A71CB15F130B04A2001E7287 /* anosimcommand.h */, - A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */, + 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 */, + 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 */, + A7E9B72812D37EC400DA6239 /* helpcommand.cpp */, A75790571301749D00A30DAB /* homovacommand.h */, A75790581301749D00A30DAB /* homovacommand.cpp */, - A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */, A7E9B72C12D37EC400DA6239 /* indicatorcommand.h */, - A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */, + A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */, A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */, - A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */, + A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */, A7E9B73E12D37EC400DA6239 /* listseqscommand.h */, + A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */, A7FA10001302E096003860FE /* mantelcommand.h */, A7FA10011302E096003860FE /* mantelcommand.cpp */, A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */, A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */, - A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */, A7E9B74412D37EC400DA6239 /* makegroupcommand.h */, - A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */, + A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */, A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */, - A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */, + A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */, A7E9B75412D37EC400DA6239 /* mergefilecommand.h */, + A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */, A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */, A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */, - A7E9B75712D37EC400DA6239 /* metastatscommand.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 */, + A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */, A713EBEB12DC7C5E000092AC /* nmdscommand.h */, A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */, - A7E9B77912D37EC400DA6239 /* otuhierarchycommand.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 */, + A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */, A7FC486512D795D60055BC5C /* pcacommand.h */, A7FC486612D795D60055BC5C /* pcacommand.cpp */, - A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */, A7E9B78812D37EC400DA6239 /* pcoacommand.h */, - A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */, + 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 */, + A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */, A727864212E9E28C00F86ABA /* removerarecommand.h */, A727864312E9E28C00F86ABA /* removerarecommand.cpp */, - A7E9B7C912D37EC400DA6239 /* removeseqscommand.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 = ""; @@ -1402,12 +1411,12 @@ 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 */, ); @@ -1464,8 +1473,8 @@ 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 */, @@ -1565,8 +1574,8 @@ 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 */, @@ -1625,7 +1634,7 @@ attributes = { ORGANIZATIONNAME = "Schloss Lab"; }; - buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */; + buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */; compatibilityVersion = "Xcode 3.1"; developmentRegion = English; hasScannedForEncodings = 1; @@ -1677,7 +1686,6 @@ 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 */, @@ -1933,6 +1941,8 @@ 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 */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -1976,8 +1986,8 @@ GCC_OPTIMIZATION_LEVEL = 3; GCC_PREPROCESSOR_DEFINITIONS = ( "MOTHUR_FILES=\"\\\"../release\\\"\"", - "VERSION=\"\\\"1.17.2\\\"\"", - "RELEASE_DATE=\"\\\"3/02/2011\\\"\"", + "VERSION=\"\\\"1.17.3\\\"\"", + "RELEASE_DATE=\"\\\"3/07/2011\\\"\"", ); GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; @@ -2049,7 +2059,7 @@ defaultConfigurationIsVisible = 0; defaultConfigurationName = Release; }; - 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */ = { + 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = { isa = XCConfigurationList; buildConfigurations = ( 1DEB928A08733DD80010E9CD /* Debug */,