X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=967e8e4be3fc714d822fed1b36f591d3aa1f15e0;hb=c5c7502f435e1413c19e373dab1dfebcaa67588d;hp=a60c51468519eb4acaf570657ee083fcf58b9756;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index a60c514..967e8e4 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -7,6 +7,40 @@ objects = { /* Begin PBXBuildFile section */ + 370B88070F8A4EE4005AB382 /* getoturepcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 370B88060F8A4EE4005AB382 /* getoturepcommand.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 */; }; + 3731C1F30F8CFC0A0065A2AD /* treegroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3731C1F20F8CFC0A0065A2AD /* treegroupscommand.cpp */; }; + 374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374610770F40645300460C57 /* unifracweightedcommand.cpp */; }; + 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 */; }; + 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 */; }; + 375873E70F7D63E90040F377 /* coverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873E50F7D63E90040F377 /* coverage.cpp */; }; + 375873EC0F7D64520040F377 /* fullmatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873EB0F7D64520040F377 /* fullmatrix.cpp */; }; + 375873EF0F7D646F0040F377 /* heatmap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873EE0F7D646F0040F377 /* heatmap.cpp */; }; + 375873F20F7D64800040F377 /* heatmapcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873F00F7D64800040F377 /* heatmapcommand.cpp */; }; + 375873F50F7D648F0040F377 /* libshuffcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873F30F7D648F0040F377 /* libshuffcommand.cpp */; }; + 375873F80F7D649C0040F377 /* nocommands.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873F60F7D649C0040F377 /* nocommands.cpp */; }; + 375873FD0F7D64DA0040F377 /* sharedbraycurtis.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */; }; + 375874040F7D64EF0040F377 /* sharedkulczynski.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */; }; + 375874050F7D64EF0040F377 /* sharedlennon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873FF0F7D64EF0040F377 /* sharedlennon.cpp */; }; + 375874060F7D64EF0040F377 /* sharedkulczynskicody.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */; }; + 3758740C0F7D64FC0040F377 /* sharedmorisitahorn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */; }; + 3758740D0F7D64FC0040F377 /* sharedochiai.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3758740B0F7D64FC0040F377 /* sharedochiai.cpp */; }; + 379293C30F2DE73400B9034A /* treemap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379293C20F2DE73400B9034A /* treemap.cpp */; }; + 379294700F2E191800B9034A /* parsimonycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3792946F0F2E191800B9034A /* parsimonycommand.cpp */; }; + 3792948A0F2E258500B9034A /* parsimony.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379294890F2E258500B9034A /* parsimony.cpp */; }; + 37AD4CE40F28AEA300AA2D49 /* sharedlistvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */; }; + 37AD4DBB0F28E2FE00AA2D49 /* tree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */; }; + 37AD4DCA0F28F3DD00AA2D49 /* readtree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */; }; + 37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */; }; + 37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B28F670F27590100808A62 /* deconvolutecommand.cpp */; }; + 37C1D9730F86506E0059E3F0 /* binsequencecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */; }; + 37C7F3A90F8E90AD00E91C2B /* sharedutilities.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37C7F3A80F8E90AD00E91C2B /* sharedutilities.cpp */; }; 37D928550F21331F001D4494 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927B80F21331F001D4494 /* ace.cpp */; }; 37D928560F21331F001D4494 /* averagelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BA0F21331F001D4494 /* averagelinkage.cpp */; }; 37D928570F21331F001D4494 /* bootstrap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BB0F21331F001D4494 /* bootstrap.cpp */; }; @@ -17,7 +51,6 @@ 37D9285C0F21331F001D4494 /* collect.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C50F21331F001D4494 /* collect.cpp */; }; 37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C70F21331F001D4494 /* collectcommand.cpp */; }; 37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */; }; - 37D9285F0F21331F001D4494 /* commandfactory.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927CE0F21331F001D4494 /* commandfactory.cpp */; }; 37D928600F21331F001D4494 /* commandoptionparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D00F21331F001D4494 /* commandoptionparser.cpp */; }; 37D928610F21331F001D4494 /* completelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D20F21331F001D4494 /* completelinkage.cpp */; }; 37D928620F21331F001D4494 /* database.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D30F21331F001D4494 /* database.cpp */; }; @@ -35,7 +68,6 @@ 37D9286E0F21331F001D4494 /* listvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927ED0F21331F001D4494 /* listvector.cpp */; }; 37D9286F0F21331F001D4494 /* mothur.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927EF0F21331F001D4494 /* mothur.cpp */; }; 37D928700F21331F001D4494 /* nameassignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F00F21331F001D4494 /* nameassignment.cpp */; }; - 37D928710F21331F001D4494 /* nocommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F20F21331F001D4494 /* nocommand.cpp */; }; 37D928720F21331F001D4494 /* npshannon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F40F21331F001D4494 /* npshannon.cpp */; }; 37D928730F21331F001D4494 /* ordervector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F70F21331F001D4494 /* ordervector.cpp */; }; 37D928740F21331F001D4494 /* parselistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F90F21331F001D4494 /* parselistcommand.cpp */; }; @@ -47,13 +79,7 @@ 37D9287A0F21331F001D4494 /* rarefact.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928050F21331F001D4494 /* rarefact.cpp */; }; 37D9287B0F21331F001D4494 /* rarefactcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928070F21331F001D4494 /* rarefactcommand.cpp */; }; 37D9287C0F21331F001D4494 /* rarefactsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */; }; - 37D9287D0F21331F001D4494 /* readdistcolumnfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9280C0F21331F001D4494 /* readdistcolumnfilecommand.cpp */; }; - 37D9287E0F21331F001D4494 /* readdistphylipfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9280E0F21331F001D4494 /* readdistphylipfilecommand.cpp */; }; - 37D9287F0F21331F001D4494 /* readlistfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928100F21331F001D4494 /* readlistfilecommand.cpp */; }; 37D928800F21331F001D4494 /* readmatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928120F21331F001D4494 /* readmatrix.cpp */; }; - 37D928810F21331F001D4494 /* readrabundfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928140F21331F001D4494 /* readrabundfilecommand.cpp */; }; - 37D928820F21331F001D4494 /* readsabundfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928160F21331F001D4494 /* readsabundfilecommand.cpp */; }; - 37D928830F21331F001D4494 /* readsharedfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928180F21331F001D4494 /* readsharedfilecommand.cpp */; }; 37D928840F21331F001D4494 /* sabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281A0F21331F001D4494 /* sabundvector.cpp */; }; 37D928850F21331F001D4494 /* sequence.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281C0F21331F001D4494 /* sequence.cpp */; }; 37D928860F21331F001D4494 /* shannon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281E0F21331F001D4494 /* shannon.cpp */; }; @@ -82,7 +108,19 @@ 37D9289D0F21331F001D4494 /* validcalculator.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9284F0F21331F001D4494 /* validcalculator.cpp */; }; 37D9289E0F21331F001D4494 /* validcommands.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928510F21331F001D4494 /* validcommands.cpp */; }; 37D9289F0F21331F001D4494 /* validparameter.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928530F21331F001D4494 /* validparameter.cpp */; }; + 37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37E5F3E20F29FD4200F8D827 /* treenode.cpp */; }; + 37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */; }; 8DD76F6A0486A84900D96B5E /* Mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6859E8B029090EE04C91782 /* Mothur.1 */; }; + A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */; }; + A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */; }; + A70B53AC0F4CD7AD0064797E /* getlinecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */; }; + EB1216880F619B83004A865F /* bergerparker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1216870F619B83004A865F /* bergerparker.cpp */; }; + EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1216E40F61ACFB004A865F /* bstick.cpp */; }; + EB1217230F61C9AC004A865F /* sharedkstest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1217220F61C9AC004A865F /* sharedkstest.cpp */; }; + EB6E68190F5F1C780044E17B /* qstat.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB6E68180F5F1C780044E17B /* qstat.cpp */; }; + EB6F015B0F6AC1670048081A /* sharedbdiversity.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */; }; + EB9303EB0F534D9400E8EF26 /* logsd.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB9303EA0F534D9400E8EF26 /* logsd.cpp */; }; + EB9303F90F53517300E8EF26 /* geom.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB9303F80F53517300E8EF26 /* geom.cpp */; }; /* End PBXBuildFile section */ /* Begin PBXCopyFilesBuildPhase section */ @@ -99,6 +137,76 @@ /* End PBXCopyFilesBuildPhase section */ /* Begin PBXFileReference section */ + 370B88050F8A4EE4005AB382 /* getoturepcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getoturepcommand.h; sourceTree = ""; }; + 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getoturepcommand.cpp; sourceTree = ""; }; + 372E126E0F26365B0095CF7E /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = ""; }; + 372E126F0F26365B0095CF7E /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = ""; }; + 372E12940F263D5A0095CF7E /* readdistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcommand.h; sourceTree = ""; }; + 372E12950F263D5A0095CF7E /* readdistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistcommand.cpp; sourceTree = ""; }; + 372E12EC0F264D320095CF7E /* commandfactory.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandfactory.cpp; sourceTree = ""; }; + 3731C1F10F8CFC0A0065A2AD /* treegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treegroupscommand.h; sourceTree = ""; }; + 3731C1F20F8CFC0A0065A2AD /* treegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treegroupscommand.cpp; sourceTree = ""; }; + 374610760F40645300460C57 /* unifracweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracweightedcommand.h; sourceTree = ""; }; + 374610770F40645300460C57 /* unifracweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracweightedcommand.cpp; sourceTree = ""; }; + 3746107C0F4064D100460C57 /* weighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = weighted.h; sourceTree = ""; }; + 3746107D0F4064D100460C57 /* weighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weighted.cpp; sourceTree = ""; }; + 374610810F40652400460C57 /* unweighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unweighted.h; sourceTree = ""; }; + 374610820F40652400460C57 /* unweighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unweighted.cpp; sourceTree = ""; }; + 3746109B0F40657600460C57 /* unifracunweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracunweightedcommand.h; sourceTree = ""; }; + 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracunweightedcommand.cpp; sourceTree = ""; }; + 37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderbergs.h; sourceTree = ""; }; + 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedanderbergs.cpp; sourceTree = ""; }; + 37519A9F0F810D0200FED5E8 /* venncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venncommand.h; sourceTree = ""; }; + 37519AA00F810D0200FED5E8 /* venncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = venncommand.cpp; sourceTree = ""; }; + 37519AB30F810FAE00FED5E8 /* venn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venn.h; sourceTree = ""; }; + 37519AB40F810FAE00FED5E8 /* venn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = venn.cpp; sourceTree = ""; }; + 375873E50F7D63E90040F377 /* coverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = coverage.cpp; sourceTree = ""; }; + 375873E60F7D63E90040F377 /* coverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = coverage.h; sourceTree = ""; }; + 375873EA0F7D64520040F377 /* fullmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fullmatrix.h; sourceTree = ""; }; + 375873EB0F7D64520040F377 /* fullmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fullmatrix.cpp; sourceTree = ""; }; + 375873ED0F7D646F0040F377 /* heatmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmap.h; sourceTree = ""; }; + 375873EE0F7D646F0040F377 /* heatmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmap.cpp; sourceTree = ""; }; + 375873F00F7D64800040F377 /* heatmapcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapcommand.cpp; sourceTree = ""; }; + 375873F10F7D64800040F377 /* heatmapcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapcommand.h; sourceTree = ""; }; + 375873F30F7D648F0040F377 /* libshuffcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuffcommand.cpp; sourceTree = ""; }; + 375873F40F7D648F0040F377 /* libshuffcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuffcommand.h; sourceTree = ""; }; + 375873F60F7D649C0040F377 /* nocommands.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nocommands.cpp; sourceTree = ""; }; + 375873F70F7D649C0040F377 /* nocommands.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nocommands.h; sourceTree = ""; }; + 375873F90F7D64AB0040F377 /* nseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nseqs.h; sourceTree = ""; }; + 375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedbraycurtis.h; sourceTree = ""; }; + 375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbraycurtis.cpp; sourceTree = ""; }; + 375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkulczynski.cpp; sourceTree = ""; }; + 375873FF0F7D64EF0040F377 /* sharedlennon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlennon.cpp; sourceTree = ""; }; + 375874000F7D64EF0040F377 /* sharedkulczynski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkulczynski.h; sourceTree = ""; }; + 375874010F7D64EF0040F377 /* sharedlennon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlennon.h; sourceTree = ""; }; + 375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkulczynskicody.cpp; sourceTree = ""; }; + 375874030F7D64EF0040F377 /* sharedkulczynskicody.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkulczynskicody.h; sourceTree = ""; }; + 375874070F7D64FC0040F377 /* sharedmorisitahorn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedmorisitahorn.h; sourceTree = ""; }; + 375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedmorisitahorn.cpp; sourceTree = ""; }; + 375874090F7D64FC0040F377 /* sharedochiai.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedochiai.h; sourceTree = ""; }; + 3758740A0F7D64FC0040F377 /* sharednseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharednseqs.h; sourceTree = ""; }; + 3758740B0F7D64FC0040F377 /* sharedochiai.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedochiai.cpp; sourceTree = ""; }; + 379293C10F2DE73400B9034A /* treemap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treemap.h; sourceTree = ""; }; + 379293C20F2DE73400B9034A /* treemap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treemap.cpp; sourceTree = ""; }; + 3792946E0F2E191800B9034A /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = ""; }; + 3792946F0F2E191800B9034A /* parsimonycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimonycommand.cpp; sourceTree = ""; }; + 379294880F2E258500B9034A /* parsimony.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimony.h; sourceTree = ""; }; + 379294890F2E258500B9034A /* parsimony.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimony.cpp; sourceTree = ""; }; + 3792948D0F2E271100B9034A /* treecalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treecalculator.h; sourceTree = ""; }; + 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlistvector.h; sourceTree = ""; }; + 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlistvector.cpp; sourceTree = ""; }; + 37AD4DB90F28E2FE00AA2D49 /* tree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tree.h; sourceTree = ""; }; + 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = tree.cpp; sourceTree = ""; }; + 37AD4DC80F28F3DD00AA2D49 /* readtree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtree.h; sourceTree = ""; }; + 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtree.cpp; sourceTree = ""; }; + 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobscollectsummary.h; sourceTree = ""; }; + 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobscollectsummary.cpp; sourceTree = ""; }; + 37B28F660F27590100808A62 /* deconvolutecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deconvolutecommand.h; sourceTree = ""; }; + 37B28F670F27590100808A62 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = ""; }; + 37C1D9710F86506E0059E3F0 /* binsequencecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = binsequencecommand.h; sourceTree = ""; }; + 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = binsequencecommand.cpp; sourceTree = ""; }; + 37C7F3A70F8E90AD00E91C2B /* sharedutilities.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedutilities.h; sourceTree = ""; }; + 37C7F3A80F8E90AD00E91C2B /* sharedutilities.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedutilities.cpp; sourceTree = ""; }; 37D927B80F21331F001D4494 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = ""; }; 37D927B90F21331F001D4494 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = ""; }; 37D927BA0F21331F001D4494 /* averagelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = averagelinkage.cpp; sourceTree = ""; }; @@ -121,7 +229,6 @@ 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectsharedcommand.cpp; sourceTree = ""; }; 37D927CC0F21331F001D4494 /* collectsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectsharedcommand.h; sourceTree = ""; }; 37D927CD0F21331F001D4494 /* command.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = command.hpp; sourceTree = ""; }; - 37D927CE0F21331F001D4494 /* commandfactory.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandfactory.cpp; sourceTree = ""; }; 37D927CF0F21331F001D4494 /* commandfactory.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandfactory.hpp; sourceTree = ""; }; 37D927D00F21331F001D4494 /* commandoptionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandoptionparser.cpp; sourceTree = ""; }; 37D927D10F21331F001D4494 /* commandoptionparser.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandoptionparser.hpp; sourceTree = ""; }; @@ -157,8 +264,6 @@ 37D927EF0F21331F001D4494 /* mothur.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothur.cpp; sourceTree = ""; }; 37D927F00F21331F001D4494 /* nameassignment.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nameassignment.cpp; sourceTree = ""; }; 37D927F10F21331F001D4494 /* nameassignment.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nameassignment.hpp; sourceTree = ""; }; - 37D927F20F21331F001D4494 /* nocommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nocommand.cpp; sourceTree = ""; }; - 37D927F30F21331F001D4494 /* nocommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nocommand.h; sourceTree = ""; }; 37D927F40F21331F001D4494 /* npshannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = npshannon.cpp; sourceTree = ""; }; 37D927F50F21331F001D4494 /* npshannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = npshannon.h; sourceTree = ""; }; 37D927F60F21331F001D4494 /* observable.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = observable.h; sourceTree = ""; }; @@ -183,20 +288,8 @@ 37D928090F21331F001D4494 /* rarefactioncurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactioncurvedata.h; sourceTree = ""; }; 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactsharedcommand.cpp; sourceTree = ""; }; 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactsharedcommand.h; sourceTree = ""; }; - 37D9280C0F21331F001D4494 /* readdistcolumnfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistcolumnfilecommand.cpp; sourceTree = ""; }; - 37D9280D0F21331F001D4494 /* readdistcolumnfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcolumnfilecommand.h; sourceTree = ""; }; - 37D9280E0F21331F001D4494 /* readdistphylipfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistphylipfilecommand.cpp; sourceTree = ""; }; - 37D9280F0F21331F001D4494 /* readdistphylipfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistphylipfilecommand.h; sourceTree = ""; }; - 37D928100F21331F001D4494 /* readlistfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readlistfilecommand.cpp; sourceTree = ""; }; - 37D928110F21331F001D4494 /* readlistfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readlistfilecommand.h; sourceTree = ""; }; 37D928120F21331F001D4494 /* readmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readmatrix.cpp; sourceTree = ""; }; 37D928130F21331F001D4494 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = ""; }; - 37D928140F21331F001D4494 /* readrabundfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readrabundfilecommand.cpp; sourceTree = ""; }; - 37D928150F21331F001D4494 /* readrabundfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readrabundfilecommand.h; sourceTree = ""; }; - 37D928160F21331F001D4494 /* readsabundfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readsabundfilecommand.cpp; sourceTree = ""; }; - 37D928170F21331F001D4494 /* readsabundfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readsabundfilecommand.h; sourceTree = ""; }; - 37D928180F21331F001D4494 /* readsharedfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readsharedfilecommand.cpp; sourceTree = ""; }; - 37D928190F21331F001D4494 /* readsharedfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readsharedfilecommand.h; sourceTree = ""; }; 37D9281A0F21331F001D4494 /* sabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sabundvector.cpp; sourceTree = ""; }; 37D9281B0F21331F001D4494 /* sabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sabundvector.hpp; sourceTree = ""; }; 37D9281C0F21331F001D4494 /* sequence.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequence.cpp; sourceTree = ""; }; @@ -247,7 +340,6 @@ 37D928490F21331F001D4494 /* summarydisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarydisplay.h; sourceTree = ""; }; 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarysharedcommand.cpp; sourceTree = ""; }; 37D9284B0F21331F001D4494 /* summarysharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarysharedcommand.h; sourceTree = ""; }; - 37D9284C0F21331F001D4494 /* utilities.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = utilities.hpp; sourceTree = ""; }; 37D9284D0F21331F001D4494 /* uvest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = uvest.cpp; sourceTree = ""; }; 37D9284E0F21331F001D4494 /* uvest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = uvest.h; sourceTree = ""; }; 37D9284F0F21331F001D4494 /* validcalculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validcalculator.cpp; sourceTree = ""; }; @@ -256,8 +348,33 @@ 37D928520F21331F001D4494 /* validcommands.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validcommands.h; sourceTree = ""; }; 37D928530F21331F001D4494 /* validparameter.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validparameter.cpp; sourceTree = ""; }; 37D928540F21331F001D4494 /* validparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validparameter.h; sourceTree = ""; }; - 8DD76F6C0486A84900D96B5E /* Mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = Mothur; sourceTree = BUILT_PRODUCTS_DIR; }; + 37E3ED800F4D9D0D00B5DF02 /* mothur.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothur.h; sourceTree = ""; }; + 37E5F3E10F29FD4200F8D827 /* treenode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treenode.h; sourceTree = ""; }; + 37E5F3E20F29FD4200F8D827 /* treenode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treenode.cpp; sourceTree = ""; }; + 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = ""; }; + 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = ""; }; + 8DD76F6C0486A84900D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; }; + A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getgroupcommand.cpp; sourceTree = ""; }; + A70B53A50F4CD7AD0064797E /* getgroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupcommand.h; sourceTree = ""; }; + A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlabelcommand.cpp; sourceTree = ""; }; + A70B53A70F4CD7AD0064797E /* getlabelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlabelcommand.h; sourceTree = ""; }; + A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlinecommand.cpp; sourceTree = ""; }; + A70B53A90F4CD7AD0064797E /* getlinecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlinecommand.h; sourceTree = ""; }; C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = ""; }; + EB1216860F619B83004A865F /* bergerparker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bergerparker.h; sourceTree = ""; }; + EB1216870F619B83004A865F /* bergerparker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bergerparker.cpp; sourceTree = ""; }; + EB1216E30F61ACFB004A865F /* bstick.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bstick.h; sourceTree = ""; }; + EB1216E40F61ACFB004A865F /* bstick.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bstick.cpp; sourceTree = ""; }; + EB1217210F61C9AC004A865F /* sharedkstest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkstest.h; sourceTree = ""; }; + EB1217220F61C9AC004A865F /* sharedkstest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkstest.cpp; sourceTree = ""; }; + EB6E68170F5F1C780044E17B /* qstat.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qstat.h; sourceTree = ""; }; + EB6E68180F5F1C780044E17B /* qstat.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qstat.cpp; sourceTree = ""; }; + EB6F01590F6AC1670048081A /* sharedbdiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedbdiversity.h; sourceTree = ""; }; + EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbdiversity.cpp; sourceTree = ""; }; + EB9303E90F534D9400E8EF26 /* logsd.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = logsd.h; sourceTree = ""; }; + EB9303EA0F534D9400E8EF26 /* logsd.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = logsd.cpp; sourceTree = ""; }; + EB9303F70F53517300E8EF26 /* geom.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = geom.h; sourceTree = ""; }; + EB9303F80F53517300E8EF26 /* geom.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = geom.cpp; sourceTree = ""; }; /* End PBXFileReference section */ /* Begin PBXFrameworksBuildPhase section */ @@ -286,58 +403,64 @@ children = ( 37D927BA0F21331F001D4494 /* averagelinkage.cpp */, 37D928A60F2133C0001D4494 /* calculators */, - 37D927C10F21331F001D4494 /* cluster.cpp */, 37D927C20F21331F001D4494 /* cluster.hpp */, + 37D927C10F21331F001D4494 /* cluster.cpp */, 37D928A90F2133E5001D4494 /* commands */, - 37D927C50F21331F001D4494 /* collect.cpp */, 37D927C60F21331F001D4494 /* collect.h */, + 37D927C50F21331F001D4494 /* collect.cpp */, 37D927C90F21331F001D4494 /* collectdisplay.h */, 37D928AC0F213420001D4494 /* containers */, 37D927CA0F21331F001D4494 /* collectorscurvedata.h */, - 37D927CE0F21331F001D4494 /* commandfactory.cpp */, 37D927CF0F21331F001D4494 /* commandfactory.hpp */, - 37D927D00F21331F001D4494 /* commandoptionparser.cpp */, + 372E12EC0F264D320095CF7E /* commandfactory.cpp */, 37D927D10F21331F001D4494 /* commandoptionparser.hpp */, + 37D927D00F21331F001D4494 /* commandoptionparser.cpp */, 37D927D20F21331F001D4494 /* completelinkage.cpp */, - 37D927D30F21331F001D4494 /* database.cpp */, 37D927D40F21331F001D4494 /* database.hpp */, + 37D927D30F21331F001D4494 /* database.cpp */, 37D927D60F21331F001D4494 /* display.h */, - 37D927D70F21331F001D4494 /* engine.cpp */, 37D927D80F21331F001D4494 /* engine.hpp */, + 37D927D70F21331F001D4494 /* engine.cpp */, 37D928B10F213472001D4494 /* errorcheckor */, - 37D927DD0F21331F001D4494 /* fileoutput.cpp */, 37D927DE0F21331F001D4494 /* fileoutput.h */, - 37D927DF0F21331F001D4494 /* globaldata.cpp */, + 37D927DD0F21331F001D4494 /* fileoutput.cpp */, 37D927E00F21331F001D4494 /* globaldata.hpp */, - 37D927E50F21331F001D4494 /* inputdata.cpp */, + 37D927DF0F21331F001D4494 /* globaldata.cpp */, + 375873ED0F7D646F0040F377 /* heatmap.h */, + 375873EE0F7D646F0040F377 /* heatmap.cpp */, 37D927E60F21331F001D4494 /* inputdata.h */, - 37D927E90F21331F001D4494 /* kmer.cpp */, + 37D927E50F21331F001D4494 /* inputdata.cpp */, 37D927EA0F21331F001D4494 /* kmer.hpp */, - 37D927EB0F21331F001D4494 /* kmerdb.cpp */, + 37D927E90F21331F001D4494 /* kmer.cpp */, 37D927EC0F21331F001D4494 /* kmerdb.hpp */, + 37D927EB0F21331F001D4494 /* kmerdb.cpp */, + 37E3ED800F4D9D0D00B5DF02 /* mothur.h */, 37D927EF0F21331F001D4494 /* mothur.cpp */, - 37D927F00F21331F001D4494 /* nameassignment.cpp */, 37D927F10F21331F001D4494 /* nameassignment.hpp */, + 37D927F00F21331F001D4494 /* nameassignment.cpp */, 37D927F60F21331F001D4494 /* observable.h */, - 37D927FB0F21331F001D4494 /* progress.cpp */, 37D927FC0F21331F001D4494 /* progress.hpp */, - 37D928030F21331F001D4494 /* raredisplay.cpp */, + 37D927FB0F21331F001D4494 /* progress.cpp */, 37D928040F21331F001D4494 /* raredisplay.h */, - 37D928050F21331F001D4494 /* rarefact.cpp */, + 37D928030F21331F001D4494 /* raredisplay.cpp */, 37D928060F21331F001D4494 /* rarefact.h */, + 37D928050F21331F001D4494 /* rarefact.cpp */, 37D928090F21331F001D4494 /* rarefactioncurvedata.h */, - 37D928120F21331F001D4494 /* readmatrix.cpp */, 37D928130F21331F001D4494 /* readmatrix.hpp */, - 37D9281C0F21331F001D4494 /* sequence.cpp */, + 37D928120F21331F001D4494 /* readmatrix.cpp */, + 37AD4DC80F28F3DD00AA2D49 /* readtree.h */, + 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */, 37D9281D0F21331F001D4494 /* sequence.hpp */, - 37D928200F21331F001D4494 /* shared.cpp */, + 37D9281C0F21331F001D4494 /* sequence.cpp */, 37D928210F21331F001D4494 /* shared.h */, + 37D928200F21331F001D4494 /* shared.cpp */, + 37C7F3A70F8E90AD00E91C2B /* sharedutilities.h */, + 37C7F3A80F8E90AD00E91C2B /* sharedutilities.cpp */, 37D928420F21331F001D4494 /* singlelinkage.cpp */, - 37D928440F21331F001D4494 /* sparsematrix.cpp */, - 37D928450F21331F001D4494 /* sparsematrix.hpp */, 37D928480F21331F001D4494 /* summarydata.h */, 37D928490F21331F001D4494 /* summarydisplay.h */, - 37D9284C0F21331F001D4494 /* utilities.hpp */, + 37519AB30F810FAE00FED5E8 /* venn.h */, + 37519AB40F810FAE00FED5E8 /* venn.cpp */, ); name = Source; sourceTree = ""; @@ -345,7 +468,7 @@ 1AB674ADFE9D54B511CA2CBB /* Products */ = { isa = PBXGroup; children = ( - 8DD76F6C0486A84900D96B5E /* Mothur */, + 8DD76F6C0486A84900D96B5E /* mothur */, ); name = Products; sourceTree = ""; @@ -354,48 +477,89 @@ isa = PBXGroup; children = ( 37D927BE0F21331F001D4494 /* calculator.h */, + 3792948D0F2E271100B9034A /* treecalculator.h */, 37D927BD0F21331F001D4494 /* calculator.cpp */, 37D927B90F21331F001D4494 /* ace.h */, 37D927B80F21331F001D4494 /* ace.cpp */, + EB1216860F619B83004A865F /* bergerparker.h */, + EB1216870F619B83004A865F /* bergerparker.cpp */, 37D927BC0F21331F001D4494 /* bootstrap.h */, 37D927BB0F21331F001D4494 /* bootstrap.cpp */, + EB1216E30F61ACFB004A865F /* bstick.h */, + EB1216E40F61ACFB004A865F /* bstick.cpp */, 37D927C00F21331F001D4494 /* chao1.h */, 37D927BF0F21331F001D4494 /* chao1.cpp */, - 37D927E70F21331F001D4494 /* jackknife.cpp */, + 375873E60F7D63E90040F377 /* coverage.h */, + 375873E50F7D63E90040F377 /* coverage.cpp */, + EB9303F70F53517300E8EF26 /* geom.h */, + EB9303F80F53517300E8EF26 /* geom.cpp */, + EB9303E90F534D9400E8EF26 /* logsd.h */, + EB9303EA0F534D9400E8EF26 /* logsd.cpp */, + EB6E68170F5F1C780044E17B /* qstat.h */, + EB6E68180F5F1C780044E17B /* qstat.cpp */, 37D927E80F21331F001D4494 /* jackknife.h */, - 37D927F40F21331F001D4494 /* npshannon.cpp */, + 37D927E70F21331F001D4494 /* jackknife.cpp */, + 375873F90F7D64AB0040F377 /* nseqs.h */, 37D927F50F21331F001D4494 /* npshannon.h */, - 37D928010F21331F001D4494 /* rarecalc.cpp */, + 37D927F40F21331F001D4494 /* npshannon.cpp */, + 379294880F2E258500B9034A /* parsimony.h */, + 379294890F2E258500B9034A /* parsimony.cpp */, 37D928020F21331F001D4494 /* rarecalc.h */, - 37D9281E0F21331F001D4494 /* shannon.cpp */, + 37D928010F21331F001D4494 /* rarecalc.cpp */, 37D9281F0F21331F001D4494 /* shannon.h */, - 37D928220F21331F001D4494 /* sharedace.cpp */, + 37D9281E0F21331F001D4494 /* shannon.cpp */, 37D928230F21331F001D4494 /* sharedace.h */, - 37D928240F21331F001D4494 /* sharedchao1.cpp */, + 37D928220F21331F001D4494 /* sharedace.cpp */, + 37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */, + 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */, + 375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */, + 375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */, + EB6F01590F6AC1670048081A /* sharedbdiversity.h */, + EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */, 37D928250F21331F001D4494 /* sharedchao1.h */, - 37D928280F21331F001D4494 /* sharedjabund.cpp */, + 37D928240F21331F001D4494 /* sharedchao1.cpp */, 37D928290F21331F001D4494 /* sharedjabund.h */, - 37D9282A0F21331F001D4494 /* sharedjclass.cpp */, + 37D928280F21331F001D4494 /* sharedjabund.cpp */, 37D9282B0F21331F001D4494 /* sharedjclass.h */, - 37D9282C0F21331F001D4494 /* sharedjest.cpp */, + 37D9282A0F21331F001D4494 /* sharedjclass.cpp */, 37D9282D0F21331F001D4494 /* sharedjest.h */, - 37D928340F21331F001D4494 /* sharedsobs.cpp */, + 37D9282C0F21331F001D4494 /* sharedjest.cpp */, + EB1217210F61C9AC004A865F /* sharedkstest.h */, + EB1217220F61C9AC004A865F /* sharedkstest.cpp */, + 375874000F7D64EF0040F377 /* sharedkulczynski.h */, + 375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */, + 375874030F7D64EF0040F377 /* sharedkulczynskicody.h */, + 375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */, + 375874010F7D64EF0040F377 /* sharedlennon.h */, + 375873FF0F7D64EF0040F377 /* sharedlennon.cpp */, + 375874070F7D64FC0040F377 /* sharedmorisitahorn.h */, + 375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */, + 375874090F7D64FC0040F377 /* sharedochiai.h */, + 3758740B0F7D64FC0040F377 /* sharedochiai.cpp */, + 3758740A0F7D64FC0040F377 /* sharednseqs.h */, 37D928350F21331F001D4494 /* sharedsobs.h */, - 37D928360F21331F001D4494 /* sharedsorabund.cpp */, + 37D928340F21331F001D4494 /* sharedsobs.cpp */, + 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */, + 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */, 37D928370F21331F001D4494 /* sharedsorabund.h */, - 37D928380F21331F001D4494 /* sharedsorclass.cpp */, + 37D928360F21331F001D4494 /* sharedsorabund.cpp */, 37D928390F21331F001D4494 /* sharedsorclass.h */, - 37D9283A0F21331F001D4494 /* sharedsorest.cpp */, + 37D928380F21331F001D4494 /* sharedsorclass.cpp */, 37D9283B0F21331F001D4494 /* sharedsorest.h */, - 37D9283C0F21331F001D4494 /* sharedthetan.cpp */, + 37D9283A0F21331F001D4494 /* sharedsorest.cpp */, 37D9283D0F21331F001D4494 /* sharedthetan.h */, - 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */, + 37D9283C0F21331F001D4494 /* sharedthetan.cpp */, 37D9283F0F21331F001D4494 /* sharedthetayc.h */, - 37D928400F21331F001D4494 /* simpson.cpp */, + 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */, 37D928410F21331F001D4494 /* simpson.h */, + 37D928400F21331F001D4494 /* simpson.cpp */, 37D928430F21331F001D4494 /* sobs.h */, - 37D9284D0F21331F001D4494 /* uvest.cpp */, + 374610810F40652400460C57 /* unweighted.h */, + 374610820F40652400460C57 /* unweighted.cpp */, 37D9284E0F21331F001D4494 /* uvest.h */, + 37D9284D0F21331F001D4494 /* uvest.cpp */, + 3746107C0F4064D100460C57 /* weighted.h */, + 3746107D0F4064D100460C57 /* weighted.cpp */, ); name = calculators; sourceTree = ""; @@ -404,42 +568,62 @@ isa = PBXGroup; children = ( 37D927CD0F21331F001D4494 /* command.hpp */, + 37C1D9710F86506E0059E3F0 /* binsequencecommand.h */, + 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */, 37D927C40F21331F001D4494 /* clustercommand.h */, 37D927C30F21331F001D4494 /* clustercommand.cpp */, 37D927C80F21331F001D4494 /* collectcommand.h */, 37D927C70F21331F001D4494 /* collectcommand.cpp */, - 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */, 37D927CC0F21331F001D4494 /* collectsharedcommand.h */, - 37D927E30F21331F001D4494 /* helpcommand.cpp */, + 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */, + 37B28F660F27590100808A62 /* deconvolutecommand.h */, + 37B28F670F27590100808A62 /* deconvolutecommand.cpp */, + A70B53A50F4CD7AD0064797E /* getgroupcommand.h */, + A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */, + A70B53A70F4CD7AD0064797E /* getlabelcommand.h */, + A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */, + A70B53A90F4CD7AD0064797E /* getlinecommand.h */, + A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */, + 370B88050F8A4EE4005AB382 /* getoturepcommand.h */, + 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */, + 375873F10F7D64800040F377 /* heatmapcommand.h */, + 375873F00F7D64800040F377 /* heatmapcommand.cpp */, 37D927E40F21331F001D4494 /* helpcommand.h */, - 37D927F20F21331F001D4494 /* nocommand.cpp */, - 37D927F30F21331F001D4494 /* nocommand.h */, - 37D927F90F21331F001D4494 /* parselistcommand.cpp */, + 37D927E30F21331F001D4494 /* helpcommand.cpp */, + 375873F40F7D648F0040F377 /* libshuffcommand.h */, + 375873F30F7D648F0040F377 /* libshuffcommand.cpp */, + 375873F60F7D649C0040F377 /* nocommands.cpp */, + 375873F70F7D649C0040F377 /* nocommands.h */, 37D927FA0F21331F001D4494 /* parselistcommand.h */, - 37D927FD0F21331F001D4494 /* quitcommand.cpp */, + 37D927F90F21331F001D4494 /* parselistcommand.cpp */, + 3792946E0F2E191800B9034A /* parsimonycommand.h */, + 3792946F0F2E191800B9034A /* parsimonycommand.cpp */, 37D927FE0F21331F001D4494 /* quitcommand.h */, - 37D928070F21331F001D4494 /* rarefactcommand.cpp */, + 37D927FD0F21331F001D4494 /* quitcommand.cpp */, 37D928080F21331F001D4494 /* rarefactcommand.h */, - 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */, + 37D928070F21331F001D4494 /* rarefactcommand.cpp */, 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */, - 37D9280C0F21331F001D4494 /* readdistcolumnfilecommand.cpp */, - 37D9280D0F21331F001D4494 /* readdistcolumnfilecommand.h */, - 37D9280E0F21331F001D4494 /* readdistphylipfilecommand.cpp */, - 37D9280F0F21331F001D4494 /* readdistphylipfilecommand.h */, - 37D928100F21331F001D4494 /* readlistfilecommand.cpp */, - 37D928110F21331F001D4494 /* readlistfilecommand.h */, - 37D928140F21331F001D4494 /* readrabundfilecommand.cpp */, - 37D928150F21331F001D4494 /* readrabundfilecommand.h */, - 37D928160F21331F001D4494 /* readsabundfilecommand.cpp */, - 37D928170F21331F001D4494 /* readsabundfilecommand.h */, - 37D928180F21331F001D4494 /* readsharedfilecommand.cpp */, - 37D928190F21331F001D4494 /* readsharedfilecommand.h */, - 37D928260F21331F001D4494 /* sharedcommand.cpp */, + 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */, + 372E12940F263D5A0095CF7E /* readdistcommand.h */, + 372E12950F263D5A0095CF7E /* readdistcommand.cpp */, + 372E126E0F26365B0095CF7E /* readotucommand.h */, + 372E126F0F26365B0095CF7E /* readotucommand.cpp */, + 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */, + 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */, 37D928270F21331F001D4494 /* sharedcommand.h */, - 37D928460F21331F001D4494 /* summarycommand.cpp */, + 37D928260F21331F001D4494 /* sharedcommand.cpp */, 37D928470F21331F001D4494 /* summarycommand.h */, - 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */, + 37D928460F21331F001D4494 /* summarycommand.cpp */, 37D9284B0F21331F001D4494 /* summarysharedcommand.h */, + 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */, + 3731C1F10F8CFC0A0065A2AD /* treegroupscommand.h */, + 3731C1F20F8CFC0A0065A2AD /* treegroupscommand.cpp */, + 3746109B0F40657600460C57 /* unifracunweightedcommand.h */, + 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */, + 374610760F40645300460C57 /* unifracweightedcommand.h */, + 374610770F40645300460C57 /* unifracweightedcommand.cpp */, + 37519A9F0F810D0200FED5E8 /* venncommand.h */, + 37519AA00F810D0200FED5E8 /* venncommand.cpp */, ); name = commands; sourceTree = ""; @@ -448,24 +632,36 @@ isa = PBXGroup; children = ( 37D927D50F21331F001D4494 /* datavector.hpp */, - 37D927DB0F21331F001D4494 /* fastamap.cpp */, 37D927DC0F21331F001D4494 /* fastamap.h */, - 37D927E10F21331F001D4494 /* groupmap.cpp */, + 37D927DB0F21331F001D4494 /* fastamap.cpp */, + 375873EA0F7D64520040F377 /* fullmatrix.h */, + 375873EB0F7D64520040F377 /* fullmatrix.cpp */, 37D927E20F21331F001D4494 /* groupmap.h */, - 37D927ED0F21331F001D4494 /* listvector.cpp */, + 37D927E10F21331F001D4494 /* groupmap.cpp */, 37D927EE0F21331F001D4494 /* listvector.hpp */, - 37D927F70F21331F001D4494 /* ordervector.cpp */, + 37D927ED0F21331F001D4494 /* listvector.cpp */, 37D927F80F21331F001D4494 /* ordervector.hpp */, - 37D927FF0F21331F001D4494 /* rabundvector.cpp */, + 37D927F70F21331F001D4494 /* ordervector.cpp */, 37D928000F21331F001D4494 /* rabundvector.hpp */, - 37D9281A0F21331F001D4494 /* sabundvector.cpp */, + 37D927FF0F21331F001D4494 /* rabundvector.cpp */, 37D9281B0F21331F001D4494 /* sabundvector.hpp */, - 37D9282E0F21331F001D4494 /* sharedordervector.cpp */, + 37D9281A0F21331F001D4494 /* sabundvector.cpp */, + 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */, + 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */, 37D9282F0F21331F001D4494 /* sharedordervector.h */, - 37D928300F21331F001D4494 /* sharedrabundvector.cpp */, + 37D9282E0F21331F001D4494 /* sharedordervector.cpp */, 37D928310F21331F001D4494 /* sharedrabundvector.h */, - 37D928320F21331F001D4494 /* sharedsabundvector.cpp */, + 37D928300F21331F001D4494 /* sharedrabundvector.cpp */, 37D928330F21331F001D4494 /* sharedsabundvector.h */, + 37D928320F21331F001D4494 /* sharedsabundvector.cpp */, + 37D928450F21331F001D4494 /* sparsematrix.hpp */, + 37D928440F21331F001D4494 /* sparsematrix.cpp */, + 37AD4DB90F28E2FE00AA2D49 /* tree.h */, + 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */, + 379293C10F2DE73400B9034A /* treemap.h */, + 379293C20F2DE73400B9034A /* treemap.cpp */, + 37E5F3E10F29FD4200F8D827 /* treenode.h */, + 37E5F3E20F29FD4200F8D827 /* treenode.cpp */, ); name = containers; sourceTree = ""; @@ -473,14 +669,14 @@ 37D928B10F213472001D4494 /* errorcheckor */ = { isa = PBXGroup; children = ( - 37D927D90F21331F001D4494 /* errorchecking.cpp */, 37D927DA0F21331F001D4494 /* errorchecking.h */, - 37D9284F0F21331F001D4494 /* validcalculator.cpp */, + 37D927D90F21331F001D4494 /* errorchecking.cpp */, 37D928500F21331F001D4494 /* validcalculator.h */, - 37D928510F21331F001D4494 /* validcommands.cpp */, + 37D9284F0F21331F001D4494 /* validcalculator.cpp */, 37D928520F21331F001D4494 /* validcommands.h */, - 37D928530F21331F001D4494 /* validparameter.cpp */, + 37D928510F21331F001D4494 /* validcommands.cpp */, 37D928540F21331F001D4494 /* validparameter.h */, + 37D928530F21331F001D4494 /* validparameter.cpp */, ); name = errorcheckor; sourceTree = ""; @@ -496,9 +692,9 @@ /* End PBXGroup section */ /* Begin PBXNativeTarget section */ - 8DD76F620486A84900D96B5E /* Mothur */ = { + 8DD76F620486A84900D96B5E /* mothur */ = { isa = PBXNativeTarget; - buildConfigurationList = 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */; + buildConfigurationList = 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */; buildPhases = ( 8DD76F640486A84900D96B5E /* Sources */, 8DD76F660486A84900D96B5E /* Frameworks */, @@ -508,10 +704,10 @@ ); dependencies = ( ); - name = Mothur; + name = mothur; productInstallPath = "$(HOME)/bin"; productName = Mothur; - productReference = 8DD76F6C0486A84900D96B5E /* Mothur */; + productReference = 8DD76F6C0486A84900D96B5E /* mothur */; productType = "com.apple.product-type.tool"; }; /* End PBXNativeTarget section */ @@ -526,7 +722,7 @@ projectDirPath = ""; projectRoot = ""; targets = ( - 8DD76F620486A84900D96B5E /* Mothur */, + 8DD76F620486A84900D96B5E /* mothur */, ); }; /* End PBXProject section */ @@ -546,7 +742,6 @@ 37D9285C0F21331F001D4494 /* collect.cpp in Sources */, 37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */, 37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */, - 37D9285F0F21331F001D4494 /* commandfactory.cpp in Sources */, 37D928600F21331F001D4494 /* commandoptionparser.cpp in Sources */, 37D928610F21331F001D4494 /* completelinkage.cpp in Sources */, 37D928620F21331F001D4494 /* database.cpp in Sources */, @@ -564,7 +759,6 @@ 37D9286E0F21331F001D4494 /* listvector.cpp in Sources */, 37D9286F0F21331F001D4494 /* mothur.cpp in Sources */, 37D928700F21331F001D4494 /* nameassignment.cpp in Sources */, - 37D928710F21331F001D4494 /* nocommand.cpp in Sources */, 37D928720F21331F001D4494 /* npshannon.cpp in Sources */, 37D928730F21331F001D4494 /* ordervector.cpp in Sources */, 37D928740F21331F001D4494 /* parselistcommand.cpp in Sources */, @@ -576,13 +770,7 @@ 37D9287A0F21331F001D4494 /* rarefact.cpp in Sources */, 37D9287B0F21331F001D4494 /* rarefactcommand.cpp in Sources */, 37D9287C0F21331F001D4494 /* rarefactsharedcommand.cpp in Sources */, - 37D9287D0F21331F001D4494 /* readdistcolumnfilecommand.cpp in Sources */, - 37D9287E0F21331F001D4494 /* readdistphylipfilecommand.cpp in Sources */, - 37D9287F0F21331F001D4494 /* readlistfilecommand.cpp in Sources */, 37D928800F21331F001D4494 /* readmatrix.cpp in Sources */, - 37D928810F21331F001D4494 /* readrabundfilecommand.cpp in Sources */, - 37D928820F21331F001D4494 /* readsabundfilecommand.cpp in Sources */, - 37D928830F21331F001D4494 /* readsharedfilecommand.cpp in Sources */, 37D928840F21331F001D4494 /* sabundvector.cpp in Sources */, 37D928850F21331F001D4494 /* sequence.cpp in Sources */, 37D928860F21331F001D4494 /* shannon.cpp in Sources */, @@ -611,6 +799,52 @@ 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 */, + 372E12ED0F264D320095CF7E /* commandfactory.cpp in Sources */, + 37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */, + 37AD4CE40F28AEA300AA2D49 /* sharedlistvector.cpp in Sources */, + 37AD4DBB0F28E2FE00AA2D49 /* tree.cpp in Sources */, + 37AD4DCA0F28F3DD00AA2D49 /* readtree.cpp in Sources */, + 37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */, + 37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */, + 379293C30F2DE73400B9034A /* treemap.cpp in Sources */, + 379294700F2E191800B9034A /* parsimonycommand.cpp in Sources */, + 3792948A0F2E258500B9034A /* parsimony.cpp in Sources */, + 374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */, + 3746107E0F4064D100460C57 /* weighted.cpp in Sources */, + 374610830F40652400460C57 /* unweighted.cpp in Sources */, + 3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */, + 37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */, + A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */, + A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */, + A70B53AC0F4CD7AD0064797E /* getlinecommand.cpp in Sources */, + EB9303EB0F534D9400E8EF26 /* logsd.cpp in Sources */, + EB9303F90F53517300E8EF26 /* geom.cpp in Sources */, + EB6E68190F5F1C780044E17B /* qstat.cpp in Sources */, + EB1216880F619B83004A865F /* bergerparker.cpp in Sources */, + EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */, + EB1217230F61C9AC004A865F /* sharedkstest.cpp in Sources */, + EB6F015B0F6AC1670048081A /* sharedbdiversity.cpp in Sources */, + 375873E70F7D63E90040F377 /* coverage.cpp in Sources */, + 375873EC0F7D64520040F377 /* fullmatrix.cpp in Sources */, + 375873EF0F7D646F0040F377 /* heatmap.cpp in Sources */, + 375873F20F7D64800040F377 /* heatmapcommand.cpp in Sources */, + 375873F50F7D648F0040F377 /* libshuffcommand.cpp in Sources */, + 375873F80F7D649C0040F377 /* nocommands.cpp in Sources */, + 375873FD0F7D64DA0040F377 /* sharedbraycurtis.cpp in Sources */, + 375874040F7D64EF0040F377 /* sharedkulczynski.cpp in Sources */, + 375874050F7D64EF0040F377 /* sharedlennon.cpp in Sources */, + 375874060F7D64EF0040F377 /* sharedkulczynskicody.cpp in Sources */, + 3758740C0F7D64FC0040F377 /* sharedmorisitahorn.cpp in Sources */, + 3758740D0F7D64FC0040F377 /* sharedochiai.cpp in Sources */, + 37519A6B0F80E6EB00FED5E8 /* sharedanderbergs.cpp in Sources */, + 37519AA10F810D0200FED5E8 /* venncommand.cpp in Sources */, + 37519AB50F810FAE00FED5E8 /* venn.cpp in Sources */, + 37C1D9730F86506E0059E3F0 /* binsequencecommand.cpp in Sources */, + 370B88070F8A4EE4005AB382 /* getoturepcommand.cpp in Sources */, + 3731C1F30F8CFC0A0065A2AD /* treegroupscommand.cpp in Sources */, + 37C7F3A90F8E90AD00E91C2B /* sharedutilities.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -630,7 +864,7 @@ "_GLIBCXX_DEBUG_PEDANTIC=1", ); INSTALL_PATH = /usr/local/bin; - PRODUCT_NAME = Mothur; + PRODUCT_NAME = mothur; ZERO_LINK = YES; }; name = Debug; @@ -641,13 +875,14 @@ DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym"; GCC_MODEL_TUNING = G5; INSTALL_PATH = /usr/local/bin; - PRODUCT_NAME = Mothur; + PRODUCT_NAME = mothur; }; name = Release; }; 1DEB923608733DC60010E9CD /* Debug */ = { isa = XCBuildConfiguration; buildSettings = { + GCC_OPTIMIZATION_LEVEL = 3; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_UNUSED_VARIABLE = YES; PREBINDING = NO; @@ -662,6 +897,7 @@ ppc, i386, ); + GCC_OPTIMIZATION_LEVEL = 0; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_UNUSED_VARIABLE = YES; PREBINDING = NO; @@ -672,7 +908,7 @@ /* End XCBuildConfiguration section */ /* Begin XCConfigurationList section */ - 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */ = { + 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */ = { isa = XCConfigurationList; buildConfigurations = ( 1DEB923208733DC60010E9CD /* Debug */,