X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=25e6296c919929232721518d587ba9da02c421c4;hb=753dc84cf289b1d5dc0ca5b0c043640927aa951a;hp=245ed5535ecc449999a20ae363a09cd4d90b6037;hpb=5b7ac70116137b52dd7884b76c5bca660a5fea38;p=mothur.git diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 245ed55..25e6296 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -12,6 +12,7 @@ 21DDC01B0F97A8FE0060691C /* bootstrapsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */; }; 21E859D80FC4632E005E1A48 /* matrixoutputcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */; }; 370B88070F8A4EE4005AB382 /* getoturepcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */; }; + 371B30B40FD7EE67000414CA /* screenseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */; }; 372E12700F26365B0095CF7E /* readotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E126F0F26365B0095CF7E /* readotucommand.cpp */; }; 372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E12950F263D5A0095CF7E /* readdistcommand.cpp */; }; 372E12ED0F264D320095CF7E /* commandfactory.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E12EC0F264D320095CF7E /* commandfactory.cpp */; }; @@ -35,6 +36,8 @@ 3746107E0F4064D100460C57 /* weighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746107D0F4064D100460C57 /* weighted.cpp */; }; 374610830F40652400460C57 /* unweighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374610820F40652400460C57 /* unweighted.cpp */; }; 3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */; }; + 3749271D0FD58C840031C06B /* getsabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3749271C0FD58C840031C06B /* getsabundcommand.cpp */; }; + 3749273F0FD5956B0031C06B /* getrabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3749273E0FD5956B0031C06B /* getrabundcommand.cpp */; }; 37519A6B0F80E6EB00FED5E8 /* sharedanderbergs.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */; }; 37519AA10F810D0200FED5E8 /* venncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519AA00F810D0200FED5E8 /* venncommand.cpp */; }; 37519AB50F810FAE00FED5E8 /* venn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519AB40F810FAE00FED5E8 /* venn.cpp */; }; @@ -53,12 +56,11 @@ 375AA13A0F9E433D008EF9B8 /* readotu.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375AA1350F9E433D008EF9B8 /* readotu.cpp */; }; 375AA13B0F9E433D008EF9B8 /* readphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375AA1370F9E433D008EF9B8 /* readphylip.cpp */; }; 377326650FAF16E0007ABB8B /* concensuscommand.cpp in Sources */ = {isa = PBXBuildFile; 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}; @@ -454,8 +460,6 @@ 37D9284E0F21331F001D4494 /* uvest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = uvest.h; sourceTree = SOURCE_ROOT; }; 37D9284F0F21331F001D4494 /* validcalculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validcalculator.cpp; sourceTree = SOURCE_ROOT; }; 37D928500F21331F001D4494 /* validcalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validcalculator.h; sourceTree = SOURCE_ROOT; }; - 37D928510F21331F001D4494 /* validcommands.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validcommands.cpp; sourceTree = SOURCE_ROOT; }; - 37D928520F21331F001D4494 /* validcommands.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validcommands.h; sourceTree = SOURCE_ROOT; }; 37D928530F21331F001D4494 /* validparameter.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validparameter.cpp; sourceTree = SOURCE_ROOT; }; 37D928540F21331F001D4494 /* validparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validparameter.h; sourceTree = SOURCE_ROOT; }; 37E3ED800F4D9D0D00B5DF02 /* mothur.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothur.h; sourceTree = SOURCE_ROOT; }; @@ -463,14 +467,18 @@ 37E5F3E20F29FD4200F8D827 /* treenode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treenode.cpp; sourceTree = SOURCE_ROOT; }; 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = SOURCE_ROOT; }; 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = SOURCE_ROOT; }; + 7E09C5120FDA79C5002ECAE5 /* reversecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = reversecommand.h; sourceTree = SOURCE_ROOT; }; + 7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = reversecommand.cpp; sourceTree = SOURCE_ROOT; }; + 7E09C5340FDA7F65002ECAE5 /* trimseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = trimseqscommand.h; sourceTree = SOURCE_ROOT; }; + 7E09C5350FDA7F65002ECAE5 /* trimseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = trimseqscommand.cpp; sourceTree = SOURCE_ROOT; }; 7E412F420F8D213C00381DD0 /* libshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuff.h; sourceTree = SOURCE_ROOT; }; 7E412F470F8D21B600381DD0 /* slibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slibshuff.h; sourceTree = SOURCE_ROOT; }; 7E412F480F8D21B600381DD0 /* slibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slibshuff.cpp; sourceTree = SOURCE_ROOT; }; 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuff.cpp; sourceTree = SOURCE_ROOT; }; 7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = dlibshuff.cpp; sourceTree = SOURCE_ROOT; }; 7E4130F70F8E58FA00381DD0 /* dlibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dlibshuff.h; sourceTree = SOURCE_ROOT; }; - 7E9214800FD2081200699BF3 /* seqsummarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqsummarycommand.h; sourceTree = ""; }; - 7E9214810FD2081200699BF3 /* seqsummarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqsummarycommand.cpp; sourceTree = ""; }; + 7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergefilecommand.h; sourceTree = ""; }; + 7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergefilecommand.cpp; sourceTree = ""; }; 7EC3D4500FA0FFF900338DA5 /* coverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = coverage.cpp; sourceTree = SOURCE_ROOT; }; 7EC3D4510FA0FFF900338DA5 /* coverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = coverage.h; sourceTree = SOURCE_ROOT; }; 7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderberg.h; sourceTree = SOURCE_ROOT; }; @@ -555,6 +563,8 @@ 373C68BA0FC1C1A600137ACD /* gotohoverlap.cpp */, 375873ED0F7D646F0040F377 /* heatmap.h */, 375873EE0F7D646F0040F377 /* heatmap.cpp */, + 378598720FDD4C1500EF9D03 /* heatmapsim.h */, + 378598730FDD4C1500EF9D03 /* heatmapsim.cpp */, 37D927E60F21331F001D4494 /* inputdata.h */, 37D927E50F21331F001D4494 /* inputdata.cpp */, 7E412F420F8D213C00381DD0 /* libshuff.h */, @@ -572,6 +582,8 @@ 373C68E40FC1C4A500137ACD /* noalign.hpp */, 373C68E30FC1C4A500137ACD /* noalign.cpp */, 37D927F60F21331F001D4494 /* observable.h */, + 3785990E0FDD7E8E00EF9D03 /* optionparser.h */, + 3785990F0FDD7E8E00EF9D03 /* optionparser.cpp */, 373C68C40FC1C25F00137ACD /* overlap.hpp */, 373C68C30FC1C25F00137ACD /* overlap.cpp */, 37D927FC0F21331F001D4494 /* progress.hpp */, @@ -608,24 +620,13 @@ 3796441D0FB9B9650081FDB6 /* read */ = { isa = PBXGroup; children = ( - 378C1AF30FB0644D004D63F5 /* readclustal.h */, - 378C1AF20FB0644D004D63F5 /* readclustal.cpp */, 375AA1340F9E433D008EF9B8 /* readcolumn.h */, 375AA1330F9E433D008EF9B8 /* readcolumn.cpp */, - 378C1AF50FB0644D004D63F5 /* readfasta.h */, - 378C1AF40FB0644D004D63F5 /* readfasta.cpp */, 37D928130F21331F001D4494 /* readmatrix.hpp */, - 378C1AF70FB0644D004D63F5 /* readnexus.h */, - 378C1AF60FB0644D004D63F5 /* readnexus.cpp */, - 378C1AF80FB0644D004D63F5 /* readnexusal.h */, 375AA1360F9E433D008EF9B8 /* readotu.h */, 375AA1350F9E433D008EF9B8 /* readotu.cpp */, 375AA1380F9E433D008EF9B8 /* readphylip.h */, 375AA1370F9E433D008EF9B8 /* readphylip.cpp */, - 378C1AFC0FB0644D004D63F5 /* readseqsphylip.h */, - 378C1AFB0FB0644D004D63F5 /* readseqsphylip.cpp */, - 379643EB0FB9B5A80081FDB6 /* readseqs.cpp */, - 379643EC0FB9B5A80081FDB6 /* readseqs.h */, 37AD4DC80F28F3DD00AA2D49 /* readtree.h */, 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */, ); @@ -747,8 +748,6 @@ 37D928A90F2133E5001D4494 /* commands */ = { isa = PBXGroup; children = ( - 7E9214800FD2081200699BF3 /* seqsummarycommand.h */, - 7E9214810FD2081200699BF3 /* seqsummarycommand.cpp */, 37D927CD0F21331F001D4494 /* command.hpp */, 378DC5CD0FBDE1C8003B8607 /* aligncommand.h */, 378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */, @@ -778,16 +777,24 @@ A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */, 370B88050F8A4EE4005AB382 /* getoturepcommand.h */, 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */, + 3749273D0FD5956B0031C06B /* getrabundcommand.h */, + 3749273E0FD5956B0031C06B /* getrabundcommand.cpp */, + 3749271B0FD58C840031C06B /* getsabundcommand.h */, + 3749271C0FD58C840031C06B /* getsabundcommand.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 */, 21E859D60FC4632E005E1A48 /* matrixoutputcommand.h */, 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */, - 375873F60F7D649C0040F377 /* nocommands.cpp */, + 7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */, + 7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */, 375873F70F7D649C0040F377 /* nocommands.h */, + 375873F60F7D649C0040F377 /* nocommands.cpp */, 37D927FA0F21331F001D4494 /* parselistcommand.h */, 37D927F90F21331F001D4494 /* parselistcommand.cpp */, 3792946E0F2E191800B9034A /* parsimonycommand.h */, @@ -804,6 +811,12 @@ 372E126F0F26365B0095CF7E /* readotucommand.cpp */, 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */, 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */, + 7E09C5120FDA79C5002ECAE5 /* reversecommand.h */, + 7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */, + 371B30B30FD7EE67000414CA /* screenseqscommand.h */, + 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */, + 3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */, + 3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */, 37D928270F21331F001D4494 /* sharedcommand.h */, 37D928260F21331F001D4494 /* sharedcommand.cpp */, 37D928470F21331F001D4494 /* summarycommand.h */, @@ -812,6 +825,8 @@ 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */, 211C38370F961E1F00FEE541 /* treegroupscommand.h */, 211C38360F961E1F00FEE541 /* treegroupscommand.cpp */, + 7E09C5340FDA7F65002ECAE5 /* trimseqscommand.h */, + 7E09C5350FDA7F65002ECAE5 /* trimseqscommand.cpp */, 3746109B0F40657600460C57 /* unifracunweightedcommand.h */, 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */, 374610760F40645300460C57 /* unifracweightedcommand.h */, @@ -834,6 +849,8 @@ 37D927D40F21331F001D4494 /* database.hpp */, 37D927D30F21331F001D4494 /* database.cpp */, 37D927D50F21331F001D4494 /* datavector.hpp */, + 3799A94D0FD6A58C00E33EDE /* distancedb.hpp */, + 3799A94C0FD6A58C00E33EDE /* distancedb.cpp */, 37D927DC0F21331F001D4494 /* fastamap.h */, 37D927DB0F21331F001D4494 /* fastamap.cpp */, 375873EA0F7D64520040F377 /* fullmatrix.h */, @@ -885,12 +902,8 @@ 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 */, ); @@ -962,7 +975,6 @@ 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 */, @@ -1012,7 +1024,6 @@ 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 */, @@ -1070,15 +1081,10 @@ 377326650FAF16E0007ABB8B /* concensuscommand.cpp in Sources */, 378C1B030FB0644E004D63F5 /* filterseqscommand.cpp in Sources */, 378C1B040FB0644E004D63F5 /* goodscoverage.cpp in Sources */, - 378C1B050FB0644E004D63F5 /* readclustal.cpp in Sources */, - 378C1B060FB0644E004D63F5 /* readfasta.cpp in Sources */, - 378C1B070FB0644E004D63F5 /* readnexus.cpp in Sources */, - 378C1B090FB0644E004D63F5 /* readseqsphylip.cpp in Sources */, 378C1B0A0FB0644E004D63F5 /* sequencedb.cpp in Sources */, 378C1B0B0FB0644E004D63F5 /* sharedjackknife.cpp in Sources */, 378C1B0C0FB0644E004D63F5 /* sharedmarczewski.cpp in Sources */, 37C753CE0FB3415200DBD02E /* distancecommand.cpp in Sources */, - 379643ED0FB9B5A80081FDB6 /* readseqs.cpp in Sources */, 378DC5CF0FBDE1C8003B8607 /* aligncommand.cpp in Sources */, 373C68A40FC1C07D00137ACD /* alignment.cpp in Sources */, 373C68A50FC1C07D00137ACD /* alignmentcell.cpp in Sources */, @@ -1098,7 +1104,17 @@ 373C699C0FC1E63600137ACD /* solow.cpp in Sources */, EB72FE260FC1F5CA0051AC11 /* shen.cpp in Sources */, 21E859D80FC4632E005E1A48 /* matrixoutputcommand.cpp in Sources */, - 7E9214820FD2081200699BF3 /* seqsummarycommand.cpp in Sources */, + 3749271D0FD58C840031C06B /* getsabundcommand.cpp in Sources */, + 3749273F0FD5956B0031C06B /* getrabundcommand.cpp in Sources */, + 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 */, ); runOnlyForDeploymentPostprocessing = 0; };