X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=d4625478f17442e3bea270a80df246df2193baa8;hb=725a3d4ff2442c79bfde0a75ed3e0904edcf03b7;hp=e9fbcfe29dd007362506740951d414752a1a9fb9;hpb=197c6d3303439582502840980d6a85cf3aab2314;p=mothur.git diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index e9fbcfe..d462547 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -6,902 +6,990 @@ objectVersion = 44; 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 */; }; - 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 */; }; - 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 */; }; - 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 */; }; - 37D928580F21331F001D4494 /* calculator.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BD0F21331F001D4494 /* calculator.cpp */; }; - 37D928590F21331F001D4494 /* chao1.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BF0F21331F001D4494 /* chao1.cpp */; }; - 37D9285A0F21331F001D4494 /* cluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C10F21331F001D4494 /* cluster.cpp */; }; - 37D9285B0F21331F001D4494 /* clustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C30F21331F001D4494 /* clustercommand.cpp */; }; - 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 */; }; - 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 */; }; - 37D928630F21331F001D4494 /* engine.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D70F21331F001D4494 /* engine.cpp */; }; - 37D928640F21331F001D4494 /* errorchecking.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D90F21331F001D4494 /* errorchecking.cpp */; }; - 37D928650F21331F001D4494 /* fastamap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927DB0F21331F001D4494 /* fastamap.cpp */; }; - 37D928660F21331F001D4494 /* fileoutput.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927DD0F21331F001D4494 /* fileoutput.cpp */; }; - 37D928670F21331F001D4494 /* globaldata.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927DF0F21331F001D4494 /* globaldata.cpp */; }; - 37D928680F21331F001D4494 /* groupmap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E10F21331F001D4494 /* groupmap.cpp */; }; - 37D928690F21331F001D4494 /* helpcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E30F21331F001D4494 /* helpcommand.cpp */; }; - 37D9286A0F21331F001D4494 /* inputdata.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E50F21331F001D4494 /* inputdata.cpp */; }; - 37D9286B0F21331F001D4494 /* jackknife.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E70F21331F001D4494 /* jackknife.cpp */; }; - 37D9286C0F21331F001D4494 /* kmer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927E90F21331F001D4494 /* kmer.cpp */; }; - 37D9286D0F21331F001D4494 /* kmerdb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927EB0F21331F001D4494 /* kmerdb.cpp */; }; - 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 */; }; - 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 */; }; - 37D928750F21331F001D4494 /* progress.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FB0F21331F001D4494 /* progress.cpp */; }; - 37D928760F21331F001D4494 /* quitcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FD0F21331F001D4494 /* quitcommand.cpp */; }; - 37D928770F21331F001D4494 /* rabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FF0F21331F001D4494 /* rabundvector.cpp */; }; - 37D928780F21331F001D4494 /* rarecalc.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928010F21331F001D4494 /* rarecalc.cpp */; }; - 37D928790F21331F001D4494 /* raredisplay.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928030F21331F001D4494 /* raredisplay.cpp */; }; - 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 */; }; - 37D928800F21331F001D4494 /* readmatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928120F21331F001D4494 /* readmatrix.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 */; }; - 37D928870F21331F001D4494 /* shared.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928200F21331F001D4494 /* shared.cpp */; }; - 37D928880F21331F001D4494 /* sharedace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928220F21331F001D4494 /* sharedace.cpp */; }; - 37D928890F21331F001D4494 /* sharedchao1.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928240F21331F001D4494 /* sharedchao1.cpp */; }; - 37D9288A0F21331F001D4494 /* sharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928260F21331F001D4494 /* sharedcommand.cpp */; }; - 37D9288B0F21331F001D4494 /* sharedjabund.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928280F21331F001D4494 /* sharedjabund.cpp */; }; - 37D9288C0F21331F001D4494 /* sharedjclass.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9282A0F21331F001D4494 /* sharedjclass.cpp */; }; - 37D9288D0F21331F001D4494 /* sharedjest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9282C0F21331F001D4494 /* sharedjest.cpp */; }; - 37D9288E0F21331F001D4494 /* sharedordervector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9282E0F21331F001D4494 /* sharedordervector.cpp */; }; - 37D9288F0F21331F001D4494 /* sharedrabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928300F21331F001D4494 /* sharedrabundvector.cpp */; }; - 37D928900F21331F001D4494 /* sharedsabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928320F21331F001D4494 /* sharedsabundvector.cpp */; }; - 37D928910F21331F001D4494 /* sharedsobs.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928340F21331F001D4494 /* sharedsobs.cpp */; }; - 37D928920F21331F001D4494 /* sharedsorabund.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928360F21331F001D4494 /* sharedsorabund.cpp */; }; - 37D928930F21331F001D4494 /* sharedsorclass.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928380F21331F001D4494 /* sharedsorclass.cpp */; }; - 37D928940F21331F001D4494 /* sharedsorest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9283A0F21331F001D4494 /* sharedsorest.cpp */; }; - 37D928950F21331F001D4494 /* sharedthetan.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9283C0F21331F001D4494 /* sharedthetan.cpp */; }; - 37D928960F21331F001D4494 /* sharedthetayc.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */; }; - 37D928970F21331F001D4494 /* simpson.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928400F21331F001D4494 /* simpson.cpp */; }; - 37D928980F21331F001D4494 /* singlelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928420F21331F001D4494 /* singlelinkage.cpp */; }; - 37D928990F21331F001D4494 /* sparsematrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928440F21331F001D4494 /* sparsematrix.cpp */; }; - 37D9289A0F21331F001D4494 /* summarycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928460F21331F001D4494 /* summarycommand.cpp */; }; - 37D9289B0F21331F001D4494 /* summarysharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */; }; - 37D9289C0F21331F001D4494 /* uvest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9284D0F21331F001D4494 /* uvest.cpp */; }; - 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 */; }; - 7E412F490F8D21B600381DD0 /* slibshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E412F480F8D21B600381DD0 /* slibshuff.cpp */; }; - 7E412FEA0F8D3E2C00381DD0 /* libshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */; }; - 7E4130F80F8E58FA00381DD0 /* dlibshuff.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E4130F60F8E58FA00381DD0 /* dlibshuff.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 */ - 8DD76F690486A84900D96B5E /* CopyFiles */ = { - isa = PBXCopyFilesBuildPhase; - buildActionMask = 8; - dstPath = /usr/share/man/man1/; - dstSubfolderSpec = 0; - files = ( - 8DD76F6A0486A84900D96B5E /* Mothur.1 in CopyFiles */, - ); - runOnlyForDeploymentPostprocessing = 1; - }; -/* 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 = ""; }; - 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 = ""; }; - 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 = ""; }; - 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 = ""; }; - 37D927BB0F21331F001D4494 /* bootstrap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bootstrap.cpp; sourceTree = ""; }; - 37D927BC0F21331F001D4494 /* bootstrap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrap.h; sourceTree = ""; }; - 37D927BD0F21331F001D4494 /* calculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = calculator.cpp; sourceTree = ""; }; - 37D927BE0F21331F001D4494 /* calculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = calculator.h; sourceTree = ""; }; - 37D927BF0F21331F001D4494 /* chao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chao1.cpp; sourceTree = ""; }; - 37D927C00F21331F001D4494 /* chao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chao1.h; sourceTree = ""; }; - 37D927C10F21331F001D4494 /* cluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cluster.cpp; sourceTree = ""; }; - 37D927C20F21331F001D4494 /* cluster.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = cluster.hpp; sourceTree = ""; }; - 37D927C30F21331F001D4494 /* clustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clustercommand.cpp; sourceTree = ""; }; - 37D927C40F21331F001D4494 /* clustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clustercommand.h; sourceTree = ""; }; - 37D927C50F21331F001D4494 /* collect.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collect.cpp; sourceTree = ""; }; - 37D927C60F21331F001D4494 /* collect.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collect.h; sourceTree = ""; }; - 37D927C70F21331F001D4494 /* collectcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectcommand.cpp; sourceTree = ""; }; - 37D927C80F21331F001D4494 /* collectcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectcommand.h; sourceTree = ""; }; - 37D927C90F21331F001D4494 /* collectdisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectdisplay.h; sourceTree = ""; }; - 37D927CA0F21331F001D4494 /* collectorscurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectorscurvedata.h; sourceTree = ""; }; - 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 = ""; }; - 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 = ""; }; - 37D927D20F21331F001D4494 /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = completelinkage.cpp; sourceTree = ""; }; - 37D927D30F21331F001D4494 /* database.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = database.cpp; sourceTree = ""; }; - 37D927D40F21331F001D4494 /* database.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = database.hpp; sourceTree = ""; }; - 37D927D50F21331F001D4494 /* datavector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = datavector.hpp; sourceTree = ""; }; - 37D927D60F21331F001D4494 /* display.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = display.h; sourceTree = ""; }; - 37D927D70F21331F001D4494 /* engine.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = engine.cpp; sourceTree = ""; }; - 37D927D80F21331F001D4494 /* engine.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = engine.hpp; sourceTree = ""; }; - 37D927D90F21331F001D4494 /* errorchecking.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = errorchecking.cpp; sourceTree = ""; }; - 37D927DA0F21331F001D4494 /* errorchecking.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = errorchecking.h; sourceTree = ""; }; - 37D927DB0F21331F001D4494 /* fastamap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fastamap.cpp; sourceTree = ""; }; - 37D927DC0F21331F001D4494 /* fastamap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fastamap.h; sourceTree = ""; }; - 37D927DD0F21331F001D4494 /* fileoutput.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fileoutput.cpp; sourceTree = ""; }; - 37D927DE0F21331F001D4494 /* fileoutput.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fileoutput.h; sourceTree = ""; }; - 37D927DF0F21331F001D4494 /* globaldata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = globaldata.cpp; sourceTree = ""; }; - 37D927E00F21331F001D4494 /* globaldata.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = globaldata.hpp; sourceTree = ""; }; - 37D927E10F21331F001D4494 /* groupmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = groupmap.cpp; sourceTree = ""; }; - 37D927E20F21331F001D4494 /* groupmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = groupmap.h; sourceTree = ""; }; - 37D927E30F21331F001D4494 /* helpcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = helpcommand.cpp; sourceTree = ""; }; - 37D927E40F21331F001D4494 /* helpcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = helpcommand.h; sourceTree = ""; }; - 37D927E50F21331F001D4494 /* inputdata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = inputdata.cpp; sourceTree = ""; }; - 37D927E60F21331F001D4494 /* inputdata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = inputdata.h; sourceTree = ""; }; - 37D927E70F21331F001D4494 /* jackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = jackknife.cpp; sourceTree = ""; }; - 37D927E80F21331F001D4494 /* jackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = jackknife.h; sourceTree = ""; }; - 37D927E90F21331F001D4494 /* kmer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmer.cpp; sourceTree = ""; }; - 37D927EA0F21331F001D4494 /* kmer.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmer.hpp; sourceTree = ""; }; - 37D927EB0F21331F001D4494 /* kmerdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmerdb.cpp; sourceTree = ""; }; - 37D927EC0F21331F001D4494 /* kmerdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmerdb.hpp; sourceTree = ""; }; - 37D927ED0F21331F001D4494 /* listvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listvector.cpp; sourceTree = ""; }; - 37D927EE0F21331F001D4494 /* listvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = listvector.hpp; sourceTree = ""; }; - 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 = ""; }; - 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 = ""; }; - 37D927F70F21331F001D4494 /* ordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ordervector.cpp; sourceTree = ""; }; - 37D927F80F21331F001D4494 /* ordervector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = ordervector.hpp; sourceTree = ""; }; - 37D927F90F21331F001D4494 /* parselistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parselistcommand.cpp; sourceTree = ""; }; - 37D927FA0F21331F001D4494 /* parselistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parselistcommand.h; sourceTree = ""; }; - 37D927FB0F21331F001D4494 /* progress.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = progress.cpp; sourceTree = ""; }; - 37D927FC0F21331F001D4494 /* progress.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = progress.hpp; sourceTree = ""; }; - 37D927FD0F21331F001D4494 /* quitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = quitcommand.cpp; sourceTree = ""; }; - 37D927FE0F21331F001D4494 /* quitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = quitcommand.h; sourceTree = ""; }; - 37D927FF0F21331F001D4494 /* rabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rabundvector.cpp; sourceTree = ""; }; - 37D928000F21331F001D4494 /* rabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = rabundvector.hpp; sourceTree = ""; }; - 37D928010F21331F001D4494 /* rarecalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarecalc.cpp; sourceTree = ""; }; - 37D928020F21331F001D4494 /* rarecalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarecalc.h; sourceTree = ""; }; - 37D928030F21331F001D4494 /* raredisplay.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = raredisplay.cpp; sourceTree = ""; }; - 37D928040F21331F001D4494 /* raredisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = raredisplay.h; sourceTree = ""; }; - 37D928050F21331F001D4494 /* rarefact.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefact.cpp; sourceTree = ""; }; - 37D928060F21331F001D4494 /* rarefact.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefact.h; sourceTree = ""; }; - 37D928070F21331F001D4494 /* rarefactcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactcommand.cpp; sourceTree = ""; }; - 37D928080F21331F001D4494 /* rarefactcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactcommand.h; sourceTree = ""; }; - 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 = ""; }; - 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 = ""; }; - 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 = ""; }; - 37D9281D0F21331F001D4494 /* sequence.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sequence.hpp; sourceTree = ""; }; - 37D9281E0F21331F001D4494 /* shannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannon.cpp; sourceTree = ""; }; - 37D9281F0F21331F001D4494 /* shannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannon.h; sourceTree = ""; }; - 37D928200F21331F001D4494 /* shared.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shared.cpp; sourceTree = ""; }; - 37D928210F21331F001D4494 /* shared.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shared.h; sourceTree = ""; }; - 37D928220F21331F001D4494 /* sharedace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedace.cpp; sourceTree = ""; }; - 37D928230F21331F001D4494 /* sharedace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedace.h; sourceTree = ""; }; - 37D928240F21331F001D4494 /* sharedchao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedchao1.cpp; sourceTree = ""; }; - 37D928250F21331F001D4494 /* sharedchao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedchao1.h; sourceTree = ""; }; - 37D928260F21331F001D4494 /* sharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedcommand.cpp; sourceTree = ""; }; - 37D928270F21331F001D4494 /* sharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedcommand.h; sourceTree = ""; }; - 37D928280F21331F001D4494 /* sharedjabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjabund.cpp; sourceTree = ""; }; - 37D928290F21331F001D4494 /* sharedjabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjabund.h; sourceTree = ""; }; - 37D9282A0F21331F001D4494 /* sharedjclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjclass.cpp; sourceTree = ""; }; - 37D9282B0F21331F001D4494 /* sharedjclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjclass.h; sourceTree = ""; }; - 37D9282C0F21331F001D4494 /* sharedjest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjest.cpp; sourceTree = ""; }; - 37D9282D0F21331F001D4494 /* sharedjest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjest.h; sourceTree = ""; }; - 37D9282E0F21331F001D4494 /* sharedordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedordervector.cpp; sourceTree = ""; }; - 37D9282F0F21331F001D4494 /* sharedordervector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedordervector.h; sourceTree = ""; }; - 37D928300F21331F001D4494 /* sharedrabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrabundvector.cpp; sourceTree = ""; }; - 37D928310F21331F001D4494 /* sharedrabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundvector.h; sourceTree = ""; }; - 37D928320F21331F001D4494 /* sharedsabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsabundvector.cpp; sourceTree = ""; }; - 37D928330F21331F001D4494 /* sharedsabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsabundvector.h; sourceTree = ""; }; - 37D928340F21331F001D4494 /* sharedsobs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobs.cpp; sourceTree = ""; }; - 37D928350F21331F001D4494 /* sharedsobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobs.h; sourceTree = ""; }; - 37D928360F21331F001D4494 /* sharedsorabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorabund.cpp; sourceTree = ""; }; - 37D928370F21331F001D4494 /* sharedsorabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorabund.h; sourceTree = ""; }; - 37D928380F21331F001D4494 /* sharedsorclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorclass.cpp; sourceTree = ""; }; - 37D928390F21331F001D4494 /* sharedsorclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorclass.h; sourceTree = ""; }; - 37D9283A0F21331F001D4494 /* sharedsorest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorest.cpp; sourceTree = ""; }; - 37D9283B0F21331F001D4494 /* sharedsorest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorest.h; sourceTree = ""; }; - 37D9283C0F21331F001D4494 /* sharedthetan.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetan.cpp; sourceTree = ""; }; - 37D9283D0F21331F001D4494 /* sharedthetan.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetan.h; sourceTree = ""; }; - 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetayc.cpp; sourceTree = ""; }; - 37D9283F0F21331F001D4494 /* sharedthetayc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetayc.h; sourceTree = ""; }; - 37D928400F21331F001D4494 /* simpson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = simpson.cpp; sourceTree = ""; }; - 37D928410F21331F001D4494 /* simpson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = simpson.h; sourceTree = ""; }; - 37D928420F21331F001D4494 /* singlelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = singlelinkage.cpp; sourceTree = ""; }; - 37D928430F21331F001D4494 /* sobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sobs.h; sourceTree = ""; }; - 37D928440F21331F001D4494 /* sparsematrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sparsematrix.cpp; sourceTree = ""; }; - 37D928450F21331F001D4494 /* sparsematrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sparsematrix.hpp; sourceTree = ""; }; - 37D928460F21331F001D4494 /* summarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarycommand.cpp; sourceTree = ""; }; - 37D928470F21331F001D4494 /* summarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarycommand.h; sourceTree = ""; }; - 37D928480F21331F001D4494 /* summarydata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarydata.h; sourceTree = ""; }; - 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 = ""; }; - 37D928500F21331F001D4494 /* validcalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validcalculator.h; sourceTree = ""; }; - 37D928510F21331F001D4494 /* validcommands.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validcommands.cpp; sourceTree = ""; }; - 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 = ""; }; - 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 = ""; }; - 7E412F420F8D213C00381DD0 /* libshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuff.h; sourceTree = ""; }; - 7E412F470F8D21B600381DD0 /* slibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slibshuff.h; sourceTree = ""; }; - 7E412F480F8D21B600381DD0 /* slibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slibshuff.cpp; sourceTree = ""; }; - 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuff.cpp; sourceTree = ""; }; - 7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = dlibshuff.cpp; sourceTree = ""; }; - 7E4130F70F8E58FA00381DD0 /* dlibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dlibshuff.h; 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 = ""; }; + A703FE931194645F002C397E /* makegroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makegroupcommand.h; sourceTree = SOURCE_ROOT; }; + A703FE941194645F002C397E /* makegroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makegroupcommand.cpp; sourceTree = SOURCE_ROOT; }; + A72B3A62118B37FD004B9F8D /* phylodiversitycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversitycommand.h; sourceTree = ""; }; + A72B3A63118B37FD004B9F8D /* phylodiversitycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversitycommand.cpp; sourceTree = ""; }; + A72B3A7B118B4D1B004B9F8D /* phylodiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversity.h; sourceTree = ""; }; + A72B3A7C118B4D1B004B9F8D /* phylodiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversity.cpp; sourceTree = ""; }; + A730977D11A417BE00117C95 /* splitmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = splitmatrix.h; sourceTree = SOURCE_ROOT; }; + A730977E11A417BE00117C95 /* splitmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitmatrix.cpp; sourceTree = SOURCE_ROOT; }; + A73097B911A43E1300117C95 /* clustersplitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clustersplitcommand.h; sourceTree = ""; }; + A73097BA11A43E1300117C95 /* clustersplitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clustersplitcommand.cpp; sourceTree = ""; }; + A73953DA11987ED100B0B160 /* chopseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chopseqscommand.h; sourceTree = ""; }; + A73953DB11987ED100B0B160 /* chopseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chopseqscommand.cpp; sourceTree = ""; }; + A73F163411A1951D0087CA57 /* splitabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = splitabundcommand.h; sourceTree = ""; }; + A73F163511A1951D0087CA57 /* splitabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitabundcommand.cpp; sourceTree = ""; }; + A747E79B1163442A00FB9042 /* chimeracheckcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeracheckcommand.h; sourceTree = ""; }; + A747E79C1163442A00FB9042 /* chimeracheckcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeracheckcommand.cpp; sourceTree = ""; }; + A747E81C116365E000FB9042 /* chimeraslayercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraslayercommand.h; sourceTree = ""; }; + A747E81D116365E000FB9042 /* chimeraslayercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraslayercommand.cpp; sourceTree = ""; }; + A7639F8D1175DF35008F5578 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = ""; }; + A76AAD02117F322B003D8DA1 /* phylosummary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylosummary.h; sourceTree = ""; }; + A76AAD03117F322B003D8DA1 /* phylosummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylosummary.cpp; sourceTree = ""; }; + A76C4A1011876BAF0009460B /* setlogfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setlogfilecommand.h; sourceTree = SOURCE_ROOT; }; + A76C4A1111876BAF0009460B /* setlogfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setlogfilecommand.cpp; sourceTree = SOURCE_ROOT; }; + A78254461164D7790002E2DD /* chimerapintailcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerapintailcommand.h; sourceTree = ""; }; + A78254471164D7790002E2DD /* chimerapintailcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerapintailcommand.cpp; sourceTree = ""; }; + A7825502116519F70002E2DD /* chimerabellerophoncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerabellerophoncommand.h; sourceTree = ""; }; + A7825503116519F70002E2DD /* chimerabellerophoncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerabellerophoncommand.cpp; sourceTree = ""; }; + A78434881162224F00100BE0 /* chimeraccodecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraccodecommand.h; sourceTree = ""; }; + A78434891162224F00100BE0 /* chimeraccodecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraccodecommand.cpp; sourceTree = ""; }; + A7D215C811996C6E00F13F13 /* clearcutcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clearcutcommand.h; sourceTree = ""; }; + A7D215C911996C6E00F13F13 /* clearcutcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clearcutcommand.cpp; sourceTree = ""; }; + A7D216061199C47F00F13F13 /* catchallcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = catchallcommand.h; sourceTree = ""; }; + A7D216071199C47F00F13F13 /* catchallcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = catchallcommand.cpp; sourceTree = ""; }; + A7DA1FEC113FECD400BF472F /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = ""; }; + A7DA1FED113FECD400BF472F /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = ""; }; + A7DA1FEE113FECD400BF472F /* aligncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = aligncommand.cpp; sourceTree = ""; }; + A7DA1FEF113FECD400BF472F /* aligncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = aligncommand.h; sourceTree = ""; }; + A7DA1FF0113FECD400BF472F /* alignment.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignment.cpp; sourceTree = ""; }; + A7DA1FF1113FECD400BF472F /* alignment.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = alignment.hpp; sourceTree = ""; }; + A7DA1FF2113FECD400BF472F /* alignmentcell.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignmentcell.cpp; sourceTree = ""; }; + A7DA1FF3113FECD400BF472F /* alignmentcell.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = alignmentcell.hpp; sourceTree = ""; }; + A7DA1FF4113FECD400BF472F /* alignmentdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignmentdb.cpp; sourceTree = ""; }; + A7DA1FF5113FECD400BF472F /* alignmentdb.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = alignmentdb.h; sourceTree = ""; }; + A7DA1FF6113FECD400BF472F /* averagelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = averagelinkage.cpp; sourceTree = ""; }; + A7DA1FF7113FECD400BF472F /* bayesian.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bayesian.cpp; sourceTree = ""; }; + A7DA1FF8113FECD400BF472F /* bayesian.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bayesian.h; sourceTree = ""; }; + A7DA1FF9113FECD400BF472F /* bellerophon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bellerophon.cpp; sourceTree = ""; }; + A7DA1FFA113FECD400BF472F /* bellerophon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bellerophon.h; sourceTree = ""; }; + A7DA1FFB113FECD400BF472F /* bergerparker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bergerparker.cpp; sourceTree = ""; }; + A7DA1FFC113FECD400BF472F /* bergerparker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bergerparker.h; sourceTree = ""; }; + A7DA1FFD113FECD400BF472F /* binsequencecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = binsequencecommand.cpp; sourceTree = ""; }; + A7DA1FFE113FECD400BF472F /* binsequencecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = binsequencecommand.h; sourceTree = ""; }; + A7DA1FFF113FECD400BF472F /* blastalign.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = blastalign.cpp; sourceTree = ""; }; + A7DA2000113FECD400BF472F /* blastalign.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = blastalign.hpp; sourceTree = ""; }; + A7DA2001113FECD400BF472F /* blastdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = blastdb.cpp; sourceTree = ""; }; + A7DA2002113FECD400BF472F /* blastdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = blastdb.hpp; sourceTree = ""; }; + A7DA2003113FECD400BF472F /* boneh.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = boneh.cpp; sourceTree = ""; }; + A7DA2004113FECD400BF472F /* boneh.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = boneh.h; sourceTree = ""; }; + A7DA2005113FECD400BF472F /* bootstrap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bootstrap.cpp; sourceTree = ""; }; + A7DA2006113FECD400BF472F /* bootstrap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrap.h; sourceTree = ""; }; + A7DA2007113FECD400BF472F /* bootstrapsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bootstrapsharedcommand.cpp; sourceTree = ""; }; + A7DA2008113FECD400BF472F /* bootstrapsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrapsharedcommand.h; sourceTree = ""; }; + A7DA2009113FECD400BF472F /* bstick.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bstick.cpp; sourceTree = ""; }; + A7DA200A113FECD400BF472F /* bstick.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bstick.h; sourceTree = ""; }; + A7DA200B113FECD400BF472F /* calculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = calculator.cpp; sourceTree = ""; }; + A7DA200C113FECD400BF472F /* calculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = calculator.h; sourceTree = ""; }; + A7DA200D113FECD400BF472F /* ccode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ccode.cpp; sourceTree = ""; }; + A7DA200E113FECD400BF472F /* ccode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ccode.h; sourceTree = ""; }; + A7DA200F113FECD400BF472F /* chao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chao1.cpp; sourceTree = ""; }; + A7DA2010113FECD400BF472F /* chao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chao1.h; sourceTree = ""; }; + A7DA2011113FECD400BF472F /* chimera.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimera.cpp; sourceTree = ""; }; + A7DA2012113FECD400BF472F /* chimera.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimera.h; sourceTree = ""; }; + A7DA2013113FECD400BF472F /* chimeracheckrdp.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeracheckrdp.cpp; sourceTree = ""; }; + A7DA2014113FECD400BF472F /* chimeracheckrdp.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeracheckrdp.h; sourceTree = ""; }; + A7DA2015113FECD400BF472F /* chimerarealigner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerarealigner.cpp; sourceTree = ""; }; + A7DA2016113FECD400BF472F /* chimerarealigner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerarealigner.h; sourceTree = ""; }; + A7DA2017113FECD400BF472F /* chimeraseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraseqscommand.cpp; sourceTree = ""; }; + A7DA2018113FECD400BF472F /* chimeraseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraseqscommand.h; sourceTree = ""; }; + A7DA2019113FECD400BF472F /* chimeraslayer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraslayer.cpp; sourceTree = ""; }; + A7DA201A113FECD400BF472F /* chimeraslayer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraslayer.h; sourceTree = ""; }; + A7DA201B113FECD400BF472F /* classify.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classify.cpp; sourceTree = ""; }; + A7DA201C113FECD400BF472F /* classify.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classify.h; sourceTree = ""; }; + A7DA201D113FECD400BF472F /* classifyseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifyseqscommand.cpp; sourceTree = ""; }; + A7DA201E113FECD400BF472F /* classifyseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifyseqscommand.h; sourceTree = ""; }; + A7DA201F113FECD400BF472F /* cluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cluster.cpp; sourceTree = ""; }; + A7DA2020113FECD400BF472F /* cluster.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = cluster.hpp; sourceTree = ""; }; + A7DA2021113FECD400BF472F /* clustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clustercommand.cpp; sourceTree = ""; }; + A7DA2022113FECD400BF472F /* clustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clustercommand.h; sourceTree = ""; }; + A7DA2023113FECD400BF472F /* collect.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collect.cpp; sourceTree = ""; }; + A7DA2024113FECD400BF472F /* collect.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collect.h; sourceTree = ""; }; + A7DA2025113FECD400BF472F /* collectcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectcommand.cpp; sourceTree = ""; }; + A7DA2026113FECD400BF472F /* collectcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectcommand.h; sourceTree = ""; }; + A7DA2027113FECD400BF472F /* collectdisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectdisplay.h; sourceTree = ""; }; + A7DA2028113FECD400BF472F /* collectorscurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectorscurvedata.h; sourceTree = ""; }; + A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectsharedcommand.cpp; sourceTree = ""; }; + A7DA202A113FECD400BF472F /* collectsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectsharedcommand.h; sourceTree = ""; }; + A7DA202B113FECD400BF472F /* command.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = command.hpp; sourceTree = ""; }; + A7DA202C113FECD400BF472F /* commandfactory.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandfactory.cpp; sourceTree = ""; }; + A7DA202D113FECD400BF472F /* commandfactory.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandfactory.hpp; sourceTree = ""; }; + A7DA202E113FECD400BF472F /* commandoptionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandoptionparser.cpp; sourceTree = ""; }; + A7DA202F113FECD400BF472F /* commandoptionparser.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandoptionparser.hpp; sourceTree = ""; }; + A7DA2030113FECD400BF472F /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = completelinkage.cpp; sourceTree = ""; }; + A7DA2031113FECD400BF472F /* consensuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensuscommand.cpp; sourceTree = ""; }; + A7DA2032113FECD400BF472F /* consensuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensuscommand.h; sourceTree = ""; }; + A7DA2033113FECD400BF472F /* coverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = coverage.cpp; sourceTree = ""; }; + A7DA2034113FECD400BF472F /* coverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = coverage.h; sourceTree = ""; }; + A7DA2035113FECD400BF472F /* database.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = database.cpp; sourceTree = ""; }; + A7DA2036113FECD400BF472F /* database.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = database.hpp; sourceTree = ""; }; + A7DA2037113FECD400BF472F /* datavector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = datavector.hpp; sourceTree = ""; }; + A7DA2038113FECD400BF472F /* decalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = decalc.cpp; sourceTree = ""; }; + A7DA2039113FECD400BF472F /* decalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = decalc.h; sourceTree = ""; }; + A7DA203A113FECD400BF472F /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = ""; }; + A7DA203B113FECD400BF472F /* deconvolutecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deconvolutecommand.h; sourceTree = ""; }; + A7DA203C113FECD400BF472F /* display.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = display.h; sourceTree = ""; }; + A7DA203D113FECD400BF472F /* dist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dist.h; sourceTree = ""; }; + A7DA203E113FECD400BF472F /* distancecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancecommand.cpp; sourceTree = ""; }; + A7DA203F113FECD400BF472F /* distancecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distancecommand.h; sourceTree = ""; }; + A7DA2040113FECD400BF472F /* distancedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancedb.cpp; sourceTree = ""; }; + A7DA2041113FECD400BF472F /* distancedb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = distancedb.hpp; sourceTree = ""; }; + A7DA2042113FECD400BF472F /* dlibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = dlibshuff.cpp; sourceTree = ""; }; + A7DA2043113FECD400BF472F /* dlibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dlibshuff.h; sourceTree = ""; }; + A7DA2044113FECD400BF472F /* eachgapdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdist.h; sourceTree = ""; }; + A7DA2045113FECD400BF472F /* eachgapignore.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapignore.h; sourceTree = ""; }; + A7DA2046113FECD400BF472F /* efron.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = efron.cpp; sourceTree = ""; }; + A7DA2047113FECD400BF472F /* efron.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = efron.h; sourceTree = ""; }; + A7DA2048113FECD400BF472F /* engine.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = engine.cpp; sourceTree = ""; }; + A7DA2049113FECD400BF472F /* engine.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = engine.hpp; sourceTree = ""; }; + A7DA204A113FECD400BF472F /* fastamap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fastamap.cpp; sourceTree = ""; }; + A7DA204B113FECD400BF472F /* fastamap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fastamap.h; sourceTree = ""; }; + A7DA204C113FECD400BF472F /* fileoutput.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fileoutput.cpp; sourceTree = ""; }; + A7DA204D113FECD400BF472F /* fileoutput.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fileoutput.h; sourceTree = ""; }; + A7DA204E113FECD400BF472F /* filters.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filters.h; sourceTree = ""; }; + A7DA204F113FECD400BF472F /* filterseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = filterseqscommand.cpp; sourceTree = ""; }; + A7DA2050113FECD400BF472F /* filterseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filterseqscommand.h; sourceTree = ""; }; + A7DA2051113FECD400BF472F /* formatcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = formatcolumn.cpp; sourceTree = ""; }; + A7DA2052113FECD400BF472F /* formatcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatcolumn.h; sourceTree = ""; }; + A7DA2053113FECD400BF472F /* formatmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatmatrix.h; sourceTree = ""; }; + A7DA2054113FECD400BF472F /* formatphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = formatphylip.cpp; sourceTree = ""; }; + A7DA2055113FECD400BF472F /* formatphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatphylip.h; sourceTree = ""; }; + A7DA2056113FECD400BF472F /* fullmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fullmatrix.cpp; sourceTree = ""; }; + A7DA2057113FECD400BF472F /* fullmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fullmatrix.h; sourceTree = ""; }; + A7DA2058113FECD400BF472F /* geom.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = geom.cpp; sourceTree = ""; }; + A7DA2059113FECD400BF472F /* geom.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = geom.h; sourceTree = ""; }; + A7DA205A113FECD400BF472F /* getgroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getgroupcommand.cpp; sourceTree = ""; }; + A7DA205B113FECD400BF472F /* getgroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupcommand.h; sourceTree = ""; }; + A7DA205C113FECD400BF472F /* getlabelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlabelcommand.cpp; sourceTree = ""; }; + A7DA205D113FECD400BF472F /* getlabelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlabelcommand.h; sourceTree = ""; }; + A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlistcountcommand.cpp; sourceTree = ""; }; + A7DA205F113FECD400BF472F /* getlistcountcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlistcountcommand.h; sourceTree = ""; }; + A7DA2060113FECD400BF472F /* getoturepcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getoturepcommand.cpp; sourceTree = ""; }; + A7DA2061113FECD400BF472F /* getoturepcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getoturepcommand.h; sourceTree = ""; }; + A7DA2062113FECD400BF472F /* getrabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getrabundcommand.cpp; sourceTree = ""; }; + A7DA2063113FECD400BF472F /* getrabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getrabundcommand.h; sourceTree = ""; }; + A7DA2064113FECD400BF472F /* getsabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsabundcommand.cpp; sourceTree = ""; }; + A7DA2065113FECD400BF472F /* getsabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsabundcommand.h; sourceTree = ""; }; + A7DA2066113FECD400BF472F /* getseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getseqscommand.cpp; sourceTree = ""; }; + A7DA2067113FECD400BF472F /* getseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getseqscommand.h; sourceTree = ""; }; + A7DA2068113FECD400BF472F /* getsharedotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsharedotucommand.cpp; sourceTree = ""; }; + A7DA2069113FECD400BF472F /* getsharedotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsharedotucommand.h; sourceTree = ""; }; + A7DA206A113FECD400BF472F /* globaldata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = globaldata.cpp; sourceTree = ""; }; + A7DA206B113FECD400BF472F /* globaldata.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = globaldata.hpp; sourceTree = ""; }; + A7DA206C113FECD400BF472F /* goodscoverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = goodscoverage.cpp; sourceTree = ""; }; + A7DA206D113FECD400BF472F /* goodscoverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = goodscoverage.h; sourceTree = ""; }; + A7DA206E113FECD400BF472F /* gotohoverlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = gotohoverlap.cpp; sourceTree = ""; }; + A7DA206F113FECD400BF472F /* gotohoverlap.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = gotohoverlap.hpp; sourceTree = ""; }; + A7DA2070113FECD400BF472F /* groupmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = groupmap.cpp; sourceTree = ""; }; + A7DA2071113FECD400BF472F /* groupmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = groupmap.h; sourceTree = ""; }; + A7DA2072113FECD400BF472F /* hcluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hcluster.cpp; sourceTree = ""; }; + A7DA2073113FECD400BF472F /* hcluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hcluster.h; sourceTree = ""; }; + A7DA2074113FECD400BF472F /* hclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hclustercommand.cpp; sourceTree = ""; }; + A7DA2075113FECD400BF472F /* hclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hclustercommand.h; sourceTree = ""; }; + A7DA2076113FECD400BF472F /* heatmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmap.cpp; sourceTree = ""; }; + A7DA2077113FECD400BF472F /* heatmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmap.h; sourceTree = ""; }; + A7DA2078113FECD400BF472F /* heatmapcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapcommand.cpp; sourceTree = ""; }; + A7DA2079113FECD400BF472F /* heatmapcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapcommand.h; sourceTree = ""; }; + A7DA207A113FECD400BF472F /* heatmapsim.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsim.cpp; sourceTree = ""; }; + A7DA207B113FECD400BF472F /* heatmapsim.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsim.h; sourceTree = ""; }; + A7DA207C113FECD400BF472F /* heatmapsimcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsimcommand.cpp; sourceTree = ""; }; + A7DA207D113FECD400BF472F /* heatmapsimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsimcommand.h; sourceTree = ""; }; + A7DA207E113FECD400BF472F /* helpcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = helpcommand.cpp; sourceTree = ""; }; + A7DA207F113FECD400BF472F /* helpcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = helpcommand.h; sourceTree = ""; }; + A7DA2080113FECD400BF472F /* ignoregaps.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ignoregaps.h; sourceTree = ""; }; + A7DA2081113FECD400BF472F /* inputdata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = inputdata.cpp; sourceTree = ""; }; + A7DA2082113FECD400BF472F /* inputdata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = inputdata.h; sourceTree = ""; }; + A7DA2083113FECD400BF472F /* jackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = jackknife.cpp; sourceTree = ""; }; + A7DA2084113FECD400BF472F /* jackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = jackknife.h; sourceTree = ""; }; + A7DA2085113FECD400BF472F /* kmer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmer.cpp; sourceTree = ""; }; + A7DA2086113FECD400BF472F /* kmer.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmer.hpp; sourceTree = ""; }; + A7DA2087113FECD400BF472F /* kmerdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmerdb.cpp; sourceTree = ""; }; + A7DA2088113FECD400BF472F /* kmerdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmerdb.hpp; sourceTree = ""; }; + A7DA2089113FECD400BF472F /* knn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = knn.cpp; sourceTree = ""; }; + A7DA208A113FECD400BF472F /* knn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = knn.h; sourceTree = ""; }; + A7DA208B113FECD400BF472F /* libshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuff.cpp; sourceTree = ""; }; + A7DA208C113FECD400BF472F /* libshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuff.h; sourceTree = ""; }; + A7DA208D113FECD400BF472F /* libshuffcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuffcommand.cpp; sourceTree = ""; }; + A7DA208E113FECD400BF472F /* libshuffcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuffcommand.h; sourceTree = ""; }; + A7DA208F113FECD400BF472F /* listseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listseqscommand.cpp; sourceTree = ""; }; + A7DA2090113FECD400BF472F /* listseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = listseqscommand.h; sourceTree = ""; }; + A7DA2091113FECD400BF472F /* listvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listvector.cpp; sourceTree = ""; }; + A7DA2092113FECD400BF472F /* listvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = listvector.hpp; sourceTree = ""; }; + A7DA2093113FECD400BF472F /* logsd.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = logsd.cpp; sourceTree = ""; }; + A7DA2094113FECD400BF472F /* logsd.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = logsd.h; sourceTree = ""; }; + A7DA2095113FECD400BF472F /* maligner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = maligner.cpp; sourceTree = ""; }; + A7DA2096113FECD400BF472F /* maligner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = maligner.h; sourceTree = ""; }; + A7DA2098113FECD400BF472F /* matrixoutputcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = matrixoutputcommand.cpp; sourceTree = ""; }; + A7DA2099113FECD400BF472F /* matrixoutputcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = matrixoutputcommand.h; sourceTree = ""; }; + A7DA209A113FECD400BF472F /* mergefilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergefilecommand.cpp; sourceTree = ""; }; + A7DA209B113FECD400BF472F /* mergefilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergefilecommand.h; sourceTree = ""; }; + A7DA209C113FECD400BF472F /* mgclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mgclustercommand.cpp; sourceTree = ""; }; + A7DA209D113FECD400BF472F /* mgclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mgclustercommand.h; sourceTree = ""; }; + A7DA209E113FECD400BF472F /* mothur.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothur.cpp; sourceTree = ""; }; + A7DA209F113FECD400BF472F /* mothur.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothur.h; sourceTree = ""; }; + A7DA20A0113FECD400BF472F /* mothurout.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothurout.cpp; sourceTree = ""; }; + A7DA20A1113FECD400BF472F /* mothurout.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothurout.h; sourceTree = ""; }; + A7DA20A2113FECD400BF472F /* nameassignment.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nameassignment.cpp; sourceTree = ""; }; + A7DA20A3113FECD400BF472F /* nameassignment.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nameassignment.hpp; sourceTree = ""; }; + A7DA20A4113FECD400BF472F /* nast.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nast.cpp; sourceTree = ""; }; + A7DA20A5113FECD400BF472F /* nast.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nast.hpp; sourceTree = ""; }; + A7DA20A6113FECD400BF472F /* nastreport.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nastreport.cpp; sourceTree = ""; }; + A7DA20A7113FECD400BF472F /* nastreport.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nastreport.hpp; sourceTree = ""; }; + A7DA20A8113FECD400BF472F /* needlemanoverlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = needlemanoverlap.cpp; sourceTree = ""; }; + A7DA20A9113FECD400BF472F /* needlemanoverlap.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = needlemanoverlap.hpp; sourceTree = ""; }; + A7DA20AA113FECD400BF472F /* noalign.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = noalign.cpp; sourceTree = ""; }; + A7DA20AB113FECD400BF472F /* noalign.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = noalign.hpp; sourceTree = ""; }; + A7DA20AC113FECD400BF472F /* nocommands.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nocommands.cpp; sourceTree = ""; }; + A7DA20AD113FECD400BF472F /* nocommands.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nocommands.h; sourceTree = ""; }; + A7DA20AE113FECD400BF472F /* npshannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = npshannon.cpp; sourceTree = ""; }; + A7DA20AF113FECD400BF472F /* npshannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = npshannon.h; sourceTree = ""; }; + A7DA20B0113FECD400BF472F /* nseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nseqs.h; sourceTree = ""; }; + A7DA20B1113FECD400BF472F /* observable.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = observable.h; sourceTree = ""; }; + A7DA20B2113FECD400BF472F /* onegapdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = onegapdist.h; sourceTree = ""; }; + A7DA20B3113FECD400BF472F /* onegapignore.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = onegapignore.h; sourceTree = ""; }; + A7DA20B4113FECD400BF472F /* optionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = optionparser.cpp; sourceTree = ""; }; + A7DA20B5113FECD400BF472F /* optionparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = optionparser.h; sourceTree = ""; }; + A7DA20B6113FECD400BF472F /* ordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ordervector.cpp; sourceTree = ""; }; + A7DA20B7113FECD400BF472F /* ordervector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = ordervector.hpp; sourceTree = ""; }; + A7DA20B8113FECD400BF472F /* otuhierarchycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = otuhierarchycommand.cpp; sourceTree = ""; }; + A7DA20B9113FECD400BF472F /* otuhierarchycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = otuhierarchycommand.h; sourceTree = ""; }; + A7DA20BA113FECD400BF472F /* overlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = overlap.cpp; sourceTree = ""; }; + A7DA20BB113FECD400BF472F /* overlap.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = overlap.hpp; sourceTree = ""; }; + A7DA20BC113FECD400BF472F /* parselistscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parselistscommand.cpp; sourceTree = ""; }; + A7DA20BD113FECD400BF472F /* parselistscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parselistscommand.h; sourceTree = ""; }; + A7DA20BE113FECD400BF472F /* parsimony.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimony.cpp; sourceTree = ""; }; + A7DA20BF113FECD400BF472F /* parsimony.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimony.h; sourceTree = ""; }; + A7DA20C0113FECD400BF472F /* parsimonycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimonycommand.cpp; sourceTree = ""; }; + A7DA20C1113FECD400BF472F /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = ""; }; + A7DA20C2113FECD400BF472F /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = ""; }; + A7DA20C3113FECD400BF472F /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = ""; }; + A7DA20C4113FECD400BF472F /* phylotree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylotree.cpp; sourceTree = ""; }; + A7DA20C5113FECD400BF472F /* phylotree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylotree.h; sourceTree = ""; }; + A7DA20C6113FECD400BF472F /* phylotypecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylotypecommand.cpp; sourceTree = ""; }; + A7DA20C7113FECD400BF472F /* phylotypecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylotypecommand.h; sourceTree = ""; }; + A7DA20C8113FECD400BF472F /* pintail.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pintail.cpp; sourceTree = ""; }; + A7DA20C9113FECD400BF472F /* pintail.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pintail.h; sourceTree = ""; }; + A7DA20CA113FECD400BF472F /* preclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = preclustercommand.cpp; sourceTree = ""; }; + A7DA20CB113FECD400BF472F /* preclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = preclustercommand.h; sourceTree = ""; }; + A7DA20CC113FECD400BF472F /* progress.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = progress.cpp; sourceTree = ""; }; + A7DA20CD113FECD400BF472F /* progress.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = progress.hpp; sourceTree = ""; }; + A7DA20CE113FECD400BF472F /* qstat.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qstat.cpp; sourceTree = ""; }; + A7DA20CF113FECD400BF472F /* qstat.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qstat.h; sourceTree = ""; }; + A7DA20D0113FECD400BF472F /* quitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = quitcommand.cpp; sourceTree = ""; }; + A7DA20D1113FECD400BF472F /* quitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = quitcommand.h; sourceTree = ""; }; + A7DA20D2113FECD400BF472F /* rabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rabundvector.cpp; sourceTree = ""; }; + A7DA20D3113FECD400BF472F /* rabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = rabundvector.hpp; sourceTree = ""; }; + A7DA20D4113FECD400BF472F /* rarecalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarecalc.cpp; sourceTree = ""; }; + A7DA20D5113FECD400BF472F /* rarecalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarecalc.h; sourceTree = ""; }; + A7DA20D6113FECD400BF472F /* raredisplay.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = raredisplay.cpp; sourceTree = ""; }; + A7DA20D7113FECD400BF472F /* raredisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = raredisplay.h; sourceTree = ""; }; + A7DA20D8113FECD400BF472F /* rarefact.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefact.cpp; sourceTree = ""; }; + A7DA20D9113FECD400BF472F /* rarefact.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefact.h; sourceTree = ""; }; + A7DA20DA113FECD400BF472F /* rarefactcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactcommand.cpp; sourceTree = ""; }; + A7DA20DB113FECD400BF472F /* rarefactcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactcommand.h; sourceTree = ""; }; + A7DA20DC113FECD400BF472F /* rarefactioncurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactioncurvedata.h; sourceTree = ""; }; + A7DA20DD113FECD400BF472F /* rarefactsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactsharedcommand.cpp; sourceTree = ""; }; + A7DA20DE113FECD400BF472F /* rarefactsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactsharedcommand.h; sourceTree = ""; }; + A7DA20DF113FECD400BF472F /* readblast.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readblast.cpp; sourceTree = ""; }; + A7DA20E0113FECD400BF472F /* readblast.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readblast.h; sourceTree = ""; }; + A7DA20E1113FECD400BF472F /* readcluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readcluster.cpp; sourceTree = ""; }; + A7DA20E2113FECD400BF472F /* readcluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcluster.h; sourceTree = ""; }; + A7DA20E3113FECD400BF472F /* readcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readcolumn.cpp; sourceTree = ""; }; + A7DA20E4113FECD400BF472F /* readcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcolumn.h; sourceTree = ""; }; + A7DA20E5113FECD400BF472F /* readdistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistcommand.cpp; sourceTree = ""; }; + A7DA20E6113FECD400BF472F /* readdistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcommand.h; sourceTree = ""; }; + A7DA20E7113FECD400BF472F /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = ""; }; + A7DA20E8113FECD400BF472F /* readotu.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotu.cpp; sourceTree = ""; }; + A7DA20E9113FECD400BF472F /* readotu.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotu.h; sourceTree = ""; }; + A7DA20EA113FECD400BF472F /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = ""; }; + A7DA20EB113FECD400BF472F /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = ""; }; + A7DA20EC113FECD400BF472F /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = ""; }; + A7DA20ED113FECD400BF472F /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = ""; }; + A7DA20EE113FECD400BF472F /* readtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtree.cpp; sourceTree = ""; }; + A7DA20EF113FECD400BF472F /* readtree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtree.h; sourceTree = ""; }; + A7DA20F0113FECD400BF472F /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = ""; }; + A7DA20F1113FECD400BF472F /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = ""; }; + A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeseqscommand.cpp; sourceTree = ""; }; + A7DA20F3113FECD400BF472F /* removeseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeseqscommand.h; sourceTree = ""; }; + A7DA20F4113FECD400BF472F /* reversecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = reversecommand.cpp; sourceTree = ""; }; + A7DA20F5113FECD400BF472F /* reversecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = reversecommand.h; sourceTree = ""; }; + A7DA20F6113FECD400BF472F /* sabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sabundvector.cpp; sourceTree = ""; }; + A7DA20F7113FECD400BF472F /* sabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sabundvector.hpp; sourceTree = ""; }; + A7DA20F8113FECD400BF472F /* screenseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = screenseqscommand.cpp; sourceTree = ""; }; + A7DA20F9113FECD400BF472F /* screenseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = screenseqscommand.h; sourceTree = ""; }; + A7DA20FA113FECD400BF472F /* secondarystructurecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = secondarystructurecommand.cpp; sourceTree = ""; }; + A7DA20FB113FECD400BF472F /* secondarystructurecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = secondarystructurecommand.h; sourceTree = ""; }; + A7DA20FC113FECD400BF472F /* seqsummarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqsummarycommand.cpp; sourceTree = ""; }; + A7DA20FD113FECD400BF472F /* seqsummarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqsummarycommand.h; sourceTree = ""; }; + A7DA20FE113FECD400BF472F /* sequence.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequence.cpp; sourceTree = ""; }; + A7DA20FF113FECD400BF472F /* sequence.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sequence.hpp; sourceTree = ""; }; + A7DA2100113FECD400BF472F /* sequencedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequencedb.cpp; sourceTree = ""; }; + A7DA2101113FECD400BF472F /* sequencedb.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sequencedb.h; sourceTree = ""; }; + A7DA2102113FECD400BF472F /* setdircommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setdircommand.cpp; sourceTree = ""; }; + A7DA2103113FECD400BF472F /* setdircommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setdircommand.h; sourceTree = ""; }; + A7DA2104113FECD400BF472F /* shannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannon.cpp; sourceTree = ""; }; + A7DA2105113FECD400BF472F /* shannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannon.h; sourceTree = ""; }; + A7DA2106113FECD400BF472F /* sharedace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedace.cpp; sourceTree = ""; }; + A7DA2107113FECD400BF472F /* sharedace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedace.h; sourceTree = ""; }; + A7DA2108113FECD400BF472F /* sharedanderberg.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderberg.h; sourceTree = ""; }; + A7DA2109113FECD400BF472F /* sharedanderbergs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedanderbergs.cpp; sourceTree = ""; }; + A7DA210A113FECD400BF472F /* sharedanderbergs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderbergs.h; sourceTree = ""; }; + A7DA210B113FECD400BF472F /* sharedbraycurtis.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbraycurtis.cpp; sourceTree = ""; }; + A7DA210C113FECD400BF472F /* sharedbraycurtis.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedbraycurtis.h; sourceTree = ""; }; + A7DA210D113FECD400BF472F /* sharedchao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedchao1.cpp; sourceTree = ""; }; + A7DA210E113FECD400BF472F /* sharedchao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedchao1.h; sourceTree = ""; }; + A7DA210F113FECD400BF472F /* sharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedcommand.cpp; sourceTree = ""; }; + A7DA2110113FECD400BF472F /* sharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedcommand.h; sourceTree = ""; }; + A7DA2111113FECD400BF472F /* sharedjabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjabund.cpp; sourceTree = ""; }; + A7DA2112113FECD400BF472F /* sharedjabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjabund.h; sourceTree = ""; }; + A7DA2113113FECD400BF472F /* sharedjackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjackknife.cpp; sourceTree = ""; }; + A7DA2114113FECD400BF472F /* sharedjackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjackknife.h; sourceTree = ""; }; + A7DA2115113FECD400BF472F /* sharedjclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjclass.cpp; sourceTree = ""; }; + A7DA2116113FECD400BF472F /* sharedjclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjclass.h; sourceTree = ""; }; + A7DA2117113FECD400BF472F /* sharedjest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjest.cpp; sourceTree = ""; }; + A7DA2118113FECD400BF472F /* sharedjest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjest.h; sourceTree = ""; }; + A7DA2119113FECD400BF472F /* sharedkstest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkstest.cpp; sourceTree = ""; }; + A7DA211A113FECD400BF472F /* sharedkstest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkstest.h; sourceTree = ""; }; + A7DA211B113FECD400BF472F /* sharedkulczynski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkulczynski.cpp; sourceTree = ""; }; + A7DA211C113FECD400BF472F /* sharedkulczynski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkulczynski.h; sourceTree = ""; }; + A7DA211D113FECD400BF472F /* sharedkulczynskicody.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkulczynskicody.cpp; sourceTree = ""; }; + A7DA211E113FECD400BF472F /* sharedkulczynskicody.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkulczynskicody.h; sourceTree = ""; }; + A7DA211F113FECD400BF472F /* sharedlennon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlennon.cpp; sourceTree = ""; }; + A7DA2120113FECD400BF472F /* sharedlennon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlennon.h; sourceTree = ""; }; + A7DA2121113FECD400BF472F /* sharedlistvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlistvector.cpp; sourceTree = ""; }; + A7DA2122113FECD400BF472F /* sharedlistvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlistvector.h; sourceTree = ""; }; + A7DA2123113FECD400BF472F /* sharedmarczewski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedmarczewski.cpp; sourceTree = ""; }; + A7DA2124113FECD400BF472F /* sharedmarczewski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedmarczewski.h; sourceTree = ""; }; + A7DA2125113FECD400BF472F /* sharedmorisitahorn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedmorisitahorn.cpp; sourceTree = ""; }; + A7DA2126113FECD400BF472F /* sharedmorisitahorn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedmorisitahorn.h; sourceTree = ""; }; + A7DA2127113FECD400BF472F /* sharednseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharednseqs.h; sourceTree = ""; }; + A7DA2128113FECD400BF472F /* sharedochiai.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedochiai.cpp; sourceTree = ""; }; + A7DA2129113FECD400BF472F /* sharedochiai.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedochiai.h; sourceTree = ""; }; + A7DA212A113FECD400BF472F /* sharedordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedordervector.cpp; sourceTree = ""; }; + A7DA212B113FECD400BF472F /* sharedordervector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedordervector.h; sourceTree = ""; }; + A7DA212C113FECD400BF472F /* sharedrabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrabundvector.cpp; sourceTree = ""; }; + A7DA212D113FECD400BF472F /* sharedrabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundvector.h; sourceTree = ""; }; + A7DA212E113FECD400BF472F /* sharedsabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsabundvector.cpp; sourceTree = ""; }; + A7DA212F113FECD400BF472F /* sharedsabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsabundvector.h; sourceTree = ""; }; + A7DA2130113FECD400BF472F /* sharedsobs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobs.cpp; sourceTree = ""; }; + A7DA2131113FECD400BF472F /* sharedsobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobs.h; sourceTree = ""; }; + A7DA2132113FECD400BF472F /* sharedsobscollectsummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobscollectsummary.cpp; sourceTree = ""; }; + A7DA2133113FECD400BF472F /* sharedsobscollectsummary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobscollectsummary.h; sourceTree = ""; }; + A7DA2134113FECD400BF472F /* sharedsorabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorabund.cpp; sourceTree = ""; }; + A7DA2135113FECD400BF472F /* sharedsorabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorabund.h; sourceTree = ""; }; + A7DA2136113FECD400BF472F /* sharedsorclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorclass.cpp; sourceTree = ""; }; + A7DA2137113FECD400BF472F /* sharedsorclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorclass.h; sourceTree = ""; }; + A7DA2138113FECD400BF472F /* sharedsorest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorest.cpp; sourceTree = ""; }; + A7DA2139113FECD400BF472F /* sharedsorest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorest.h; sourceTree = ""; }; + A7DA213A113FECD400BF472F /* sharedthetan.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetan.cpp; sourceTree = ""; }; + A7DA213B113FECD400BF472F /* sharedthetan.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetan.h; sourceTree = ""; }; + A7DA213C113FECD400BF472F /* sharedthetayc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetayc.cpp; sourceTree = ""; }; + A7DA213D113FECD400BF472F /* sharedthetayc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetayc.h; sourceTree = ""; }; + A7DA213E113FECD400BF472F /* sharedutilities.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedutilities.cpp; sourceTree = ""; }; + A7DA213F113FECD400BF472F /* sharedutilities.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedutilities.h; sourceTree = ""; }; + A7DA2140113FECD400BF472F /* shen.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shen.cpp; sourceTree = ""; }; + A7DA2141113FECD400BF472F /* shen.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shen.h; sourceTree = ""; }; + A7DA2142113FECD400BF472F /* simpson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = simpson.cpp; sourceTree = ""; }; + A7DA2143113FECD400BF472F /* simpson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = simpson.h; sourceTree = ""; }; + A7DA2144113FECD400BF472F /* singlelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = singlelinkage.cpp; sourceTree = ""; }; + A7DA2145113FECD400BF472F /* slayer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slayer.cpp; sourceTree = ""; }; + A7DA2146113FECD400BF472F /* slayer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slayer.h; sourceTree = ""; }; + A7DA2147113FECD400BF472F /* slibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slibshuff.cpp; sourceTree = ""; }; + A7DA2148113FECD400BF472F /* slibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slibshuff.h; sourceTree = ""; }; + A7DA2149113FECD400BF472F /* sobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sobs.h; sourceTree = ""; }; + A7DA214A113FECD400BF472F /* solow.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = solow.cpp; sourceTree = ""; }; + A7DA214B113FECD400BF472F /* solow.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = solow.h; sourceTree = ""; }; + A7DA214C113FECD400BF472F /* sparsematrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sparsematrix.cpp; sourceTree = ""; }; + A7DA214D113FECD400BF472F /* sparsematrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sparsematrix.hpp; sourceTree = ""; }; + A7DA214E113FECD400BF472F /* suffixdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixdb.cpp; sourceTree = ""; }; + A7DA214F113FECD400BF472F /* suffixdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixdb.hpp; sourceTree = ""; }; + A7DA2150113FECD400BF472F /* suffixnodes.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixnodes.cpp; sourceTree = ""; }; + A7DA2151113FECD400BF472F /* suffixnodes.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixnodes.hpp; sourceTree = ""; }; + A7DA2152113FECD400BF472F /* suffixtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixtree.cpp; sourceTree = ""; }; + A7DA2153113FECD400BF472F /* suffixtree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixtree.hpp; sourceTree = ""; }; + A7DA2154113FECD400BF472F /* summarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarycommand.cpp; sourceTree = ""; }; + A7DA2155113FECD400BF472F /* summarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarycommand.h; sourceTree = ""; }; + A7DA2158113FECD400BF472F /* summarysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarysharedcommand.cpp; sourceTree = ""; }; + A7DA2159113FECD400BF472F /* summarysharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarysharedcommand.h; sourceTree = ""; }; + A7DA215A113FECD400BF472F /* systemcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = systemcommand.cpp; sourceTree = ""; }; + A7DA215B113FECD400BF472F /* systemcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = systemcommand.h; sourceTree = ""; }; + A7DA215C113FECD400BF472F /* taxonomyequalizer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = taxonomyequalizer.cpp; sourceTree = ""; }; + A7DA215D113FECD400BF472F /* taxonomyequalizer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = taxonomyequalizer.h; sourceTree = ""; }; + A7DA215E113FECD400BF472F /* tree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = tree.cpp; sourceTree = ""; }; + A7DA215F113FECD400BF472F /* tree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tree.h; sourceTree = ""; }; + A7DA2160113FECD400BF472F /* treecalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treecalculator.h; sourceTree = ""; }; + A7DA2161113FECD400BF472F /* treegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treegroupscommand.cpp; sourceTree = ""; }; + A7DA2162113FECD400BF472F /* treegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treegroupscommand.h; sourceTree = ""; }; + A7DA2163113FECD400BF472F /* treemap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treemap.cpp; sourceTree = ""; }; + A7DA2164113FECD400BF472F /* treemap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treemap.h; sourceTree = ""; }; + A7DA2165113FECD400BF472F /* treenode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treenode.cpp; sourceTree = ""; }; + A7DA2166113FECD400BF472F /* treenode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treenode.h; sourceTree = ""; }; + A7DA2167113FECD400BF472F /* trimseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = trimseqscommand.cpp; sourceTree = ""; }; + A7DA2168113FECD400BF472F /* trimseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = trimseqscommand.h; sourceTree = ""; }; + A7DA2169113FECD400BF472F /* unifracunweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracunweightedcommand.cpp; sourceTree = ""; }; + A7DA216A113FECD400BF472F /* unifracunweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracunweightedcommand.h; sourceTree = ""; }; + A7DA216B113FECD400BF472F /* unifracweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracweightedcommand.cpp; sourceTree = ""; }; + A7DA216C113FECD400BF472F /* unifracweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracweightedcommand.h; sourceTree = ""; }; + A7DA216D113FECD400BF472F /* unweighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unweighted.cpp; sourceTree = ""; }; + A7DA216E113FECD400BF472F /* unweighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unweighted.h; sourceTree = ""; }; + A7DA216F113FECD400BF472F /* uvest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = uvest.cpp; sourceTree = ""; }; + A7DA2170113FECD400BF472F /* uvest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = uvest.h; sourceTree = ""; }; + A7DA2171113FECD400BF472F /* validcalculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validcalculator.cpp; sourceTree = ""; }; + A7DA2172113FECD400BF472F /* validcalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validcalculator.h; sourceTree = ""; }; + A7DA2173113FECD400BF472F /* validparameter.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validparameter.cpp; sourceTree = ""; }; + A7DA2174113FECD400BF472F /* validparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validparameter.h; sourceTree = ""; }; + A7DA2175113FECD400BF472F /* venn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = venn.cpp; sourceTree = ""; }; + A7DA2176113FECD400BF472F /* venn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venn.h; sourceTree = ""; }; + A7DA2177113FECD400BF472F /* venncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = venncommand.cpp; sourceTree = ""; }; + A7DA2178113FECD400BF472F /* venncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venncommand.h; sourceTree = ""; }; + A7DA2179113FECD400BF472F /* weighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weighted.cpp; sourceTree = ""; }; + A7DA217A113FECD400BF472F /* weighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = weighted.h; sourceTree = ""; }; + A7DA217B113FECD400BF472F /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = ""; }; + A7DA217C113FECD400BF472F /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = ""; }; + A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsesffcommand.cpp; sourceTree = ""; }; + A7E8338C115BBDAA00739EC4 /* parsesffcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsesffcommand.h; sourceTree = ""; }; /* End PBXFileReference section */ -/* Begin PBXFrameworksBuildPhase section */ - 8DD76F660486A84900D96B5E /* Frameworks */ = { - isa = PBXFrameworksBuildPhase; - buildActionMask = 2147483647; - files = ( - ); - runOnlyForDeploymentPostprocessing = 0; - }; -/* End PBXFrameworksBuildPhase section */ - /* Begin PBXGroup section */ - 08FB7794FE84155DC02AAC07 /* Mothur */ = { + 08FB7794FE84155DC02AAC07 /* mothur */ = { isa = PBXGroup; children = ( - 08FB7795FE84155DC02AAC07 /* Source */, - C6859E8C029090F304C91782 /* Documentation */, - 1AB674ADFE9D54B511CA2CBB /* Products */, + A7639F8D1175DF35008F5578 /* makefile */, + A7DA1FF0113FECD400BF472F /* alignment.cpp */, + A7DA1FF1113FECD400BF472F /* alignment.hpp */, + A7DA1FF6113FECD400BF472F /* averagelinkage.cpp */, + A7DA2000113FECD400BF472F /* blastalign.hpp */, + A7DA1FFF113FECD400BF472F /* blastalign.cpp */, + A7DA201F113FECD400BF472F /* cluster.cpp */, + A7DA2020113FECD400BF472F /* cluster.hpp */, + A7CB593B11402EF90010EB83 /* calculators */, + A7CB594A11402FB40010EB83 /* chimeras */, + A7CB594511402F6E0010EB83 /* classifers */, + A7CB593E11402F110010EB83 /* commands */, + A7CB594211402F430010EB83 /* containers */, + A7DA2023113FECD400BF472F /* collect.cpp */, + A7DA2024113FECD400BF472F /* collect.h */, + A7DA2027113FECD400BF472F /* collectdisplay.h */, + A7DA2028113FECD400BF472F /* collectorscurvedata.h */, + A7DA202C113FECD400BF472F /* commandfactory.cpp */, + A7DA202D113FECD400BF472F /* commandfactory.hpp */, + A7DA202E113FECD400BF472F /* commandoptionparser.cpp */, + A7DA202F113FECD400BF472F /* commandoptionparser.hpp */, + A7DA2030113FECD400BF472F /* completelinkage.cpp */, + A7DA203C113FECD400BF472F /* display.h */, + A7DA2042113FECD400BF472F /* dlibshuff.cpp */, + A7DA2043113FECD400BF472F /* dlibshuff.h */, + A7DA2048113FECD400BF472F /* engine.cpp */, + A7DA2049113FECD400BF472F /* engine.hpp */, + A7DA204C113FECD400BF472F /* fileoutput.cpp */, + A7DA204D113FECD400BF472F /* fileoutput.h */, + A7DA206A113FECD400BF472F /* globaldata.cpp */, + A7DA206B113FECD400BF472F /* globaldata.hpp */, + A7DA206E113FECD400BF472F /* gotohoverlap.cpp */, + A7DA206F113FECD400BF472F /* gotohoverlap.hpp */, + A7DA2072113FECD400BF472F /* hcluster.cpp */, + A7DA2073113FECD400BF472F /* hcluster.h */, + A7DA2076113FECD400BF472F /* heatmap.cpp */, + A7DA2077113FECD400BF472F /* heatmap.h */, + A7DA207A113FECD400BF472F /* heatmapsim.cpp */, + A7DA207B113FECD400BF472F /* heatmapsim.h */, + A7DA2081113FECD400BF472F /* inputdata.cpp */, + A7DA2082113FECD400BF472F /* inputdata.h */, + A7DA208B113FECD400BF472F /* libshuff.cpp */, + A7DA208C113FECD400BF472F /* libshuff.h */, + A7DA209E113FECD400BF472F /* mothur.cpp */, + A7DA209F113FECD400BF472F /* mothur.h */, + A7DA20A0113FECD400BF472F /* mothurout.cpp */, + A7DA20A1113FECD400BF472F /* mothurout.h */, + A7DA20A4113FECD400BF472F /* nast.cpp */, + A7DA20A5113FECD400BF472F /* nast.hpp */, + A7DA20A6113FECD400BF472F /* nastreport.cpp */, + A7DA20A7113FECD400BF472F /* nastreport.hpp */, + A7DA20A8113FECD400BF472F /* needlemanoverlap.cpp */, + A7DA20A9113FECD400BF472F /* needlemanoverlap.hpp */, + A7DA20AA113FECD400BF472F /* noalign.cpp */, + A7DA20AB113FECD400BF472F /* noalign.hpp */, + A7DA20B1113FECD400BF472F /* observable.h */, + A7DA20B4113FECD400BF472F /* optionparser.cpp */, + A7DA20B5113FECD400BF472F /* optionparser.h */, + A7DA20BA113FECD400BF472F /* overlap.cpp */, + A7DA20BB113FECD400BF472F /* overlap.hpp */, + A7DA20CC113FECD400BF472F /* progress.cpp */, + A7DA20CD113FECD400BF472F /* progress.hpp */, + A7DA20D4113FECD400BF472F /* rarecalc.cpp */, + A7DA20D5113FECD400BF472F /* rarecalc.h */, + A7DA20D6113FECD400BF472F /* raredisplay.cpp */, + A7DA20D7113FECD400BF472F /* raredisplay.h */, + A7DA20D8113FECD400BF472F /* rarefact.cpp */, + A7DA20D9113FECD400BF472F /* rarefact.h */, + A7DA20DC113FECD400BF472F /* rarefactioncurvedata.h */, + A7CB5953114033220010EB83 /* read */, + A7DA213E113FECD400BF472F /* sharedutilities.cpp */, + A7DA213F113FECD400BF472F /* sharedutilities.h */, + A7DA2144113FECD400BF472F /* singlelinkage.cpp */, + A7DA2147113FECD400BF472F /* slibshuff.cpp */, + A7DA2148113FECD400BF472F /* slibshuff.h */, + A7DA2171113FECD400BF472F /* validcalculator.cpp */, + A7DA2172113FECD400BF472F /* validcalculator.h */, + A7DA2173113FECD400BF472F /* validparameter.cpp */, + A7DA2174113FECD400BF472F /* validparameter.h */, + A7DA2175113FECD400BF472F /* venn.cpp */, + A7DA2176113FECD400BF472F /* venn.h */, ); - name = Mothur; - sourceTree = ""; - }; - 08FB7795FE84155DC02AAC07 /* Source */ = { - isa = PBXGroup; - children = ( - 7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */, - 7E4130F70F8E58FA00381DD0 /* dlibshuff.h */, - 37D927BA0F21331F001D4494 /* averagelinkage.cpp */, - 37D928A60F2133C0001D4494 /* calculators */, - 37D927C20F21331F001D4494 /* cluster.hpp */, - 37D927C10F21331F001D4494 /* cluster.cpp */, - 7E412F470F8D21B600381DD0 /* slibshuff.h */, - 7E412F480F8D21B600381DD0 /* slibshuff.cpp */, - 7E412F420F8D213C00381DD0 /* libshuff.h */, - 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */, - 37D928A90F2133E5001D4494 /* commands */, - 37D927C60F21331F001D4494 /* collect.h */, - 37D927C50F21331F001D4494 /* collect.cpp */, - 37D927C90F21331F001D4494 /* collectdisplay.h */, - 37D928AC0F213420001D4494 /* containers */, - 37D927CA0F21331F001D4494 /* collectorscurvedata.h */, - 37D927CF0F21331F001D4494 /* commandfactory.hpp */, - 372E12EC0F264D320095CF7E /* commandfactory.cpp */, - 37D927D10F21331F001D4494 /* commandoptionparser.hpp */, - 37D927D00F21331F001D4494 /* commandoptionparser.cpp */, - 37D927D20F21331F001D4494 /* completelinkage.cpp */, - 37D927D40F21331F001D4494 /* database.hpp */, - 37D927D30F21331F001D4494 /* database.cpp */, - 37D927D60F21331F001D4494 /* display.h */, - 37D927D80F21331F001D4494 /* engine.hpp */, - 37D927D70F21331F001D4494 /* engine.cpp */, - 37D928B10F213472001D4494 /* errorcheckor */, - 37D927DE0F21331F001D4494 /* fileoutput.h */, - 37D927DD0F21331F001D4494 /* fileoutput.cpp */, - 37D927E00F21331F001D4494 /* globaldata.hpp */, - 37D927DF0F21331F001D4494 /* globaldata.cpp */, - 375873ED0F7D646F0040F377 /* heatmap.h */, - 375873EE0F7D646F0040F377 /* heatmap.cpp */, - 37D927E60F21331F001D4494 /* inputdata.h */, - 37D927E50F21331F001D4494 /* inputdata.cpp */, - 37D927EA0F21331F001D4494 /* kmer.hpp */, - 37D927E90F21331F001D4494 /* kmer.cpp */, - 37D927EC0F21331F001D4494 /* kmerdb.hpp */, - 37D927EB0F21331F001D4494 /* kmerdb.cpp */, - 37E3ED800F4D9D0D00B5DF02 /* mothur.h */, - 37D927EF0F21331F001D4494 /* mothur.cpp */, - 37D927F10F21331F001D4494 /* nameassignment.hpp */, - 37D927F00F21331F001D4494 /* nameassignment.cpp */, - 37D927F60F21331F001D4494 /* observable.h */, - 37D927FC0F21331F001D4494 /* progress.hpp */, - 37D927FB0F21331F001D4494 /* progress.cpp */, - 37D928040F21331F001D4494 /* raredisplay.h */, - 37D928030F21331F001D4494 /* raredisplay.cpp */, - 37D928060F21331F001D4494 /* rarefact.h */, - 37D928050F21331F001D4494 /* rarefact.cpp */, - 37D928090F21331F001D4494 /* rarefactioncurvedata.h */, - 37D928130F21331F001D4494 /* readmatrix.hpp */, - 37D928120F21331F001D4494 /* readmatrix.cpp */, - 37AD4DC80F28F3DD00AA2D49 /* readtree.h */, - 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */, - 37D9281D0F21331F001D4494 /* sequence.hpp */, - 37D9281C0F21331F001D4494 /* sequence.cpp */, - 37D928210F21331F001D4494 /* shared.h */, - 37D928200F21331F001D4494 /* shared.cpp */, - 37D928420F21331F001D4494 /* singlelinkage.cpp */, - 37D928480F21331F001D4494 /* summarydata.h */, - 37D928490F21331F001D4494 /* summarydisplay.h */, - 37D9284C0F21331F001D4494 /* utilities.hpp */, - 37519AB30F810FAE00FED5E8 /* venn.h */, - 37519AB40F810FAE00FED5E8 /* venn.cpp */, - ); - name = Source; + name = mothur; sourceTree = ""; }; - 1AB674ADFE9D54B511CA2CBB /* Products */ = { + A7CB593B11402EF90010EB83 /* calculators */ = { isa = PBXGroup; children = ( - 8DD76F6C0486A84900D96B5E /* mothur */, + A7DA200B113FECD400BF472F /* calculator.cpp */, + A7DA200C113FECD400BF472F /* calculator.h */, + A7DA1FED113FECD400BF472F /* ace.h */, + A7DA1FEC113FECD400BF472F /* ace.cpp */, + A7DA1FFB113FECD400BF472F /* bergerparker.cpp */, + A7DA1FFC113FECD400BF472F /* bergerparker.h */, + A7DA2003113FECD400BF472F /* boneh.cpp */, + A7DA2004113FECD400BF472F /* boneh.h */, + A7DA2005113FECD400BF472F /* bootstrap.cpp */, + A7DA2006113FECD400BF472F /* bootstrap.h */, + A7DA2009113FECD400BF472F /* bstick.cpp */, + A7DA200A113FECD400BF472F /* bstick.h */, + A7DA200F113FECD400BF472F /* chao1.cpp */, + A7DA2010113FECD400BF472F /* chao1.h */, + A7DA2033113FECD400BF472F /* coverage.cpp */, + A7DA2034113FECD400BF472F /* coverage.h */, + A7DA203D113FECD400BF472F /* dist.h */, + A7DA2044113FECD400BF472F /* eachgapdist.h */, + A7DA2045113FECD400BF472F /* eachgapignore.h */, + A7DA2046113FECD400BF472F /* efron.cpp */, + A7DA2047113FECD400BF472F /* efron.h */, + A7DA204E113FECD400BF472F /* filters.h */, + A7DA2058113FECD400BF472F /* geom.cpp */, + A7DA2059113FECD400BF472F /* geom.h */, + A7DA206C113FECD400BF472F /* goodscoverage.cpp */, + A7DA206D113FECD400BF472F /* goodscoverage.h */, + A7DA2080113FECD400BF472F /* ignoregaps.h */, + A7DA2083113FECD400BF472F /* jackknife.cpp */, + A7DA2084113FECD400BF472F /* jackknife.h */, + A7DA2093113FECD400BF472F /* logsd.cpp */, + A7DA2094113FECD400BF472F /* logsd.h */, + A7DA20AE113FECD400BF472F /* npshannon.cpp */, + A7DA20AF113FECD400BF472F /* npshannon.h */, + A7DA20B0113FECD400BF472F /* nseqs.h */, + A7DA20B2113FECD400BF472F /* onegapdist.h */, + A7DA20B3113FECD400BF472F /* onegapignore.h */, + A72B3A7B118B4D1B004B9F8D /* phylodiversity.h */, + A72B3A7C118B4D1B004B9F8D /* phylodiversity.cpp */, + A7DA20BE113FECD400BF472F /* parsimony.cpp */, + A7DA20BF113FECD400BF472F /* parsimony.h */, + A7DA20CE113FECD400BF472F /* qstat.cpp */, + A7DA20CF113FECD400BF472F /* qstat.h */, + A7DA2104113FECD400BF472F /* shannon.cpp */, + A7DA2105113FECD400BF472F /* shannon.h */, + A7DA2106113FECD400BF472F /* sharedace.cpp */, + A7DA2107113FECD400BF472F /* sharedace.h */, + A7DA2108113FECD400BF472F /* sharedanderberg.h */, + A7DA2109113FECD400BF472F /* sharedanderbergs.cpp */, + A7DA210A113FECD400BF472F /* sharedanderbergs.h */, + A7DA210B113FECD400BF472F /* sharedbraycurtis.cpp */, + A7DA210C113FECD400BF472F /* sharedbraycurtis.h */, + A7DA210D113FECD400BF472F /* sharedchao1.cpp */, + A7DA210E113FECD400BF472F /* sharedchao1.h */, + A7DA2111113FECD400BF472F /* sharedjabund.cpp */, + A7DA2112113FECD400BF472F /* sharedjabund.h */, + A7DA2113113FECD400BF472F /* sharedjackknife.cpp */, + A7DA2114113FECD400BF472F /* sharedjackknife.h */, + A7DA2115113FECD400BF472F /* sharedjclass.cpp */, + A7DA2116113FECD400BF472F /* sharedjclass.h */, + A7DA2117113FECD400BF472F /* sharedjest.cpp */, + A7DA2118113FECD400BF472F /* sharedjest.h */, + A7DA2119113FECD400BF472F /* sharedkstest.cpp */, + A7DA211A113FECD400BF472F /* sharedkstest.h */, + A7DA211B113FECD400BF472F /* sharedkulczynski.cpp */, + A7DA211C113FECD400BF472F /* sharedkulczynski.h */, + A7DA211D113FECD400BF472F /* sharedkulczynskicody.cpp */, + A7DA211E113FECD400BF472F /* sharedkulczynskicody.h */, + A7DA211F113FECD400BF472F /* sharedlennon.cpp */, + A7DA2120113FECD400BF472F /* sharedlennon.h */, + A7DA2123113FECD400BF472F /* sharedmarczewski.cpp */, + A7DA2124113FECD400BF472F /* sharedmarczewski.h */, + A7DA2125113FECD400BF472F /* sharedmorisitahorn.cpp */, + A7DA2126113FECD400BF472F /* sharedmorisitahorn.h */, + A7DA2127113FECD400BF472F /* sharednseqs.h */, + A7DA2128113FECD400BF472F /* sharedochiai.cpp */, + A7DA2129113FECD400BF472F /* sharedochiai.h */, + A7DA2130113FECD400BF472F /* sharedsobs.cpp */, + A7DA2131113FECD400BF472F /* sharedsobs.h */, + A7DA2132113FECD400BF472F /* sharedsobscollectsummary.cpp */, + A7DA2133113FECD400BF472F /* sharedsobscollectsummary.h */, + A7DA2134113FECD400BF472F /* sharedsorabund.cpp */, + A7DA2135113FECD400BF472F /* sharedsorabund.h */, + A7DA2136113FECD400BF472F /* sharedsorclass.cpp */, + A7DA2137113FECD400BF472F /* sharedsorclass.h */, + A7DA2138113FECD400BF472F /* sharedsorest.cpp */, + A7DA2139113FECD400BF472F /* sharedsorest.h */, + A7DA213A113FECD400BF472F /* sharedthetan.cpp */, + A7DA213B113FECD400BF472F /* sharedthetan.h */, + A7DA213C113FECD400BF472F /* sharedthetayc.cpp */, + A7DA213D113FECD400BF472F /* sharedthetayc.h */, + A7DA2140113FECD400BF472F /* shen.cpp */, + A7DA2141113FECD400BF472F /* shen.h */, + A7DA2142113FECD400BF472F /* simpson.cpp */, + A7DA2143113FECD400BF472F /* simpson.h */, + A7DA2149113FECD400BF472F /* sobs.h */, + A7DA214A113FECD400BF472F /* solow.cpp */, + A7DA214B113FECD400BF472F /* solow.h */, + A7DA2160113FECD400BF472F /* treecalculator.h */, + A7DA216D113FECD400BF472F /* unweighted.cpp */, + A7DA216E113FECD400BF472F /* unweighted.h */, + A7DA216F113FECD400BF472F /* uvest.cpp */, + A7DA2170113FECD400BF472F /* uvest.h */, + A7DA2179113FECD400BF472F /* weighted.cpp */, + A7DA217A113FECD400BF472F /* weighted.h */, + A7DA217B113FECD400BF472F /* whittaker.cpp */, + A7DA217C113FECD400BF472F /* whittaker.h */, ); - name = Products; + name = calculators; sourceTree = ""; }; - 37D928A60F2133C0001D4494 /* calculators */ = { + A7CB593E11402F110010EB83 /* commands */ = { 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 */, - EB9303F70F53517300E8EF26 /* geom.h */, - EB9303F80F53517300E8EF26 /* geom.cpp */, - EB9303E90F534D9400E8EF26 /* logsd.h */, - EB9303EA0F534D9400E8EF26 /* logsd.cpp */, - EB6E68170F5F1C780044E17B /* qstat.h */, - EB6E68180F5F1C780044E17B /* qstat.cpp */, - 37D927E80F21331F001D4494 /* jackknife.h */, - 37D927E70F21331F001D4494 /* jackknife.cpp */, - 375873F90F7D64AB0040F377 /* nseqs.h */, - 37D927F50F21331F001D4494 /* npshannon.h */, - 37D927F40F21331F001D4494 /* npshannon.cpp */, - 379294880F2E258500B9034A /* parsimony.h */, - 379294890F2E258500B9034A /* parsimony.cpp */, - 37D928020F21331F001D4494 /* rarecalc.h */, - 37D928010F21331F001D4494 /* rarecalc.cpp */, - 37D9281F0F21331F001D4494 /* shannon.h */, - 37D9281E0F21331F001D4494 /* shannon.cpp */, - 37D928230F21331F001D4494 /* sharedace.h */, - 37D928220F21331F001D4494 /* sharedace.cpp */, - 37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */, - 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */, - 375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */, - 375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */, - EB6F01590F6AC1670048081A /* sharedbdiversity.h */, - EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */, - 37D928250F21331F001D4494 /* sharedchao1.h */, - 37D928240F21331F001D4494 /* sharedchao1.cpp */, - 37D928290F21331F001D4494 /* sharedjabund.h */, - 37D928280F21331F001D4494 /* sharedjabund.cpp */, - 37D9282B0F21331F001D4494 /* sharedjclass.h */, - 37D9282A0F21331F001D4494 /* sharedjclass.cpp */, - 37D9282D0F21331F001D4494 /* sharedjest.h */, - 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 */, - 37D928340F21331F001D4494 /* sharedsobs.cpp */, - 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */, - 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */, - 37D928370F21331F001D4494 /* sharedsorabund.h */, - 37D928360F21331F001D4494 /* sharedsorabund.cpp */, - 37D928390F21331F001D4494 /* sharedsorclass.h */, - 37D928380F21331F001D4494 /* sharedsorclass.cpp */, - 37D9283B0F21331F001D4494 /* sharedsorest.h */, - 37D9283A0F21331F001D4494 /* sharedsorest.cpp */, - 37D9283D0F21331F001D4494 /* sharedthetan.h */, - 37D9283C0F21331F001D4494 /* sharedthetan.cpp */, - 37D9283F0F21331F001D4494 /* sharedthetayc.h */, - 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */, - 37D928410F21331F001D4494 /* simpson.h */, - 37D928400F21331F001D4494 /* simpson.cpp */, - 37D928430F21331F001D4494 /* sobs.h */, - 374610810F40652400460C57 /* unweighted.h */, - 374610820F40652400460C57 /* unweighted.cpp */, - 37D9284E0F21331F001D4494 /* uvest.h */, - 37D9284D0F21331F001D4494 /* uvest.cpp */, - 3746107C0F4064D100460C57 /* weighted.h */, - 3746107D0F4064D100460C57 /* weighted.cpp */, + A7DA202B113FECD400BF472F /* command.hpp */, + A7DA1FEF113FECD400BF472F /* aligncommand.h */, + A7DA1FEE113FECD400BF472F /* aligncommand.cpp */, + A7DA1FFD113FECD400BF472F /* binsequencecommand.cpp */, + A7DA1FFE113FECD400BF472F /* binsequencecommand.h */, + A7DA2007113FECD400BF472F /* bootstrapsharedcommand.cpp */, + A7DA2008113FECD400BF472F /* bootstrapsharedcommand.h */, + A7D216061199C47F00F13F13 /* catchallcommand.h */, + A7D216071199C47F00F13F13 /* catchallcommand.cpp */, + A7DA2017113FECD400BF472F /* chimeraseqscommand.cpp */, + A78434881162224F00100BE0 /* chimeraccodecommand.h */, + A7DA2018113FECD400BF472F /* chimeraseqscommand.h */, + A7825502116519F70002E2DD /* chimerabellerophoncommand.h */, + A7825503116519F70002E2DD /* chimerabellerophoncommand.cpp */, + A747E79B1163442A00FB9042 /* chimeracheckcommand.h */, + A747E79C1163442A00FB9042 /* chimeracheckcommand.cpp */, + A78434891162224F00100BE0 /* chimeraccodecommand.cpp */, + A78254461164D7790002E2DD /* chimerapintailcommand.h */, + A78254471164D7790002E2DD /* chimerapintailcommand.cpp */, + A747E81C116365E000FB9042 /* chimeraslayercommand.h */, + A747E81D116365E000FB9042 /* chimeraslayercommand.cpp */, + A73953DA11987ED100B0B160 /* chopseqscommand.h */, + A73953DB11987ED100B0B160 /* chopseqscommand.cpp */, + A7DA201E113FECD400BF472F /* classifyseqscommand.h */, + A7DA201D113FECD400BF472F /* classifyseqscommand.cpp */, + A7D215C811996C6E00F13F13 /* clearcutcommand.h */, + A7D215C911996C6E00F13F13 /* clearcutcommand.cpp */, + A7DA2022113FECD400BF472F /* clustercommand.h */, + A7DA2021113FECD400BF472F /* clustercommand.cpp */, + A73097B911A43E1300117C95 /* clustersplitcommand.h */, + A73097BA11A43E1300117C95 /* clustersplitcommand.cpp */, + A7DA2025113FECD400BF472F /* collectcommand.cpp */, + A7DA2026113FECD400BF472F /* collectcommand.h */, + A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */, + A7DA202A113FECD400BF472F /* collectsharedcommand.h */, + A7DA2031113FECD400BF472F /* consensuscommand.cpp */, + A7DA2032113FECD400BF472F /* consensuscommand.h */, + A7DA203A113FECD400BF472F /* deconvolutecommand.cpp */, + A7DA203B113FECD400BF472F /* deconvolutecommand.h */, + A7DA203E113FECD400BF472F /* distancecommand.cpp */, + A7DA203F113FECD400BF472F /* distancecommand.h */, + A7DA204F113FECD400BF472F /* filterseqscommand.cpp */, + A7DA2050113FECD400BF472F /* filterseqscommand.h */, + A7DA205A113FECD400BF472F /* getgroupcommand.cpp */, + A7DA205B113FECD400BF472F /* getgroupcommand.h */, + A7DA205C113FECD400BF472F /* getlabelcommand.cpp */, + A7DA205D113FECD400BF472F /* getlabelcommand.h */, + A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */, + A7DA205F113FECD400BF472F /* getlistcountcommand.h */, + A7DA2060113FECD400BF472F /* getoturepcommand.cpp */, + A7DA2061113FECD400BF472F /* getoturepcommand.h */, + A7DA2062113FECD400BF472F /* getrabundcommand.cpp */, + A7DA2063113FECD400BF472F /* getrabundcommand.h */, + A7DA2064113FECD400BF472F /* getsabundcommand.cpp */, + A7DA2065113FECD400BF472F /* getsabundcommand.h */, + A7DA2067113FECD400BF472F /* getseqscommand.h */, + A7DA2066113FECD400BF472F /* getseqscommand.cpp */, + A7DA2068113FECD400BF472F /* getsharedotucommand.cpp */, + A7DA2069113FECD400BF472F /* getsharedotucommand.h */, + A7DA2074113FECD400BF472F /* hclustercommand.cpp */, + A7DA2075113FECD400BF472F /* hclustercommand.h */, + A7DA2078113FECD400BF472F /* heatmapcommand.cpp */, + A7DA2079113FECD400BF472F /* heatmapcommand.h */, + A7DA207C113FECD400BF472F /* heatmapsimcommand.cpp */, + A7DA207D113FECD400BF472F /* heatmapsimcommand.h */, + A7DA207E113FECD400BF472F /* helpcommand.cpp */, + A7DA207F113FECD400BF472F /* helpcommand.h */, + A7DA208D113FECD400BF472F /* libshuffcommand.cpp */, + A7DA208E113FECD400BF472F /* libshuffcommand.h */, + A7DA2090113FECD400BF472F /* listseqscommand.h */, + A7DA208F113FECD400BF472F /* listseqscommand.cpp */, + A703FE931194645F002C397E /* makegroupcommand.h */, + A703FE941194645F002C397E /* makegroupcommand.cpp */, + A7DA2098113FECD400BF472F /* matrixoutputcommand.cpp */, + A7DA2099113FECD400BF472F /* matrixoutputcommand.h */, + A7DA209A113FECD400BF472F /* mergefilecommand.cpp */, + A7DA209B113FECD400BF472F /* mergefilecommand.h */, + A7DA209C113FECD400BF472F /* mgclustercommand.cpp */, + A7DA209D113FECD400BF472F /* mgclustercommand.h */, + A7DA20AC113FECD400BF472F /* nocommands.cpp */, + A7DA20AD113FECD400BF472F /* nocommands.h */, + A7DA20B8113FECD400BF472F /* otuhierarchycommand.cpp */, + A7DA20B9113FECD400BF472F /* otuhierarchycommand.h */, + A7DA20BC113FECD400BF472F /* parselistscommand.cpp */, + A7DA20BD113FECD400BF472F /* parselistscommand.h */, + A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */, + A7E8338C115BBDAA00739EC4 /* parsesffcommand.h */, + A7DA20C0113FECD400BF472F /* parsimonycommand.cpp */, + A7DA20C1113FECD400BF472F /* parsimonycommand.h */, + A7DA20C3113FECD400BF472F /* pcacommand.h */, + A7DA20C2113FECD400BF472F /* pcacommand.cpp */, + A72B3A62118B37FD004B9F8D /* phylodiversitycommand.h */, + A72B3A63118B37FD004B9F8D /* phylodiversitycommand.cpp */, + A7DA20C7113FECD400BF472F /* phylotypecommand.h */, + A7DA20C6113FECD400BF472F /* phylotypecommand.cpp */, + A7DA20CB113FECD400BF472F /* preclustercommand.h */, + A7DA20CA113FECD400BF472F /* preclustercommand.cpp */, + A7DA20D1113FECD400BF472F /* quitcommand.h */, + A7DA20D0113FECD400BF472F /* quitcommand.cpp */, + A7DA20DB113FECD400BF472F /* rarefactcommand.h */, + A7DA20DA113FECD400BF472F /* rarefactcommand.cpp */, + A7DA20DE113FECD400BF472F /* rarefactsharedcommand.h */, + A7DA20DD113FECD400BF472F /* rarefactsharedcommand.cpp */, + A7DA20E6113FECD400BF472F /* readdistcommand.h */, + A7DA20E5113FECD400BF472F /* readdistcommand.cpp */, + A7DA20EB113FECD400BF472F /* readotucommand.h */, + A7DA20EA113FECD400BF472F /* readotucommand.cpp */, + A7DA20F1113FECD400BF472F /* readtreecommand.h */, + A7DA20F0113FECD400BF472F /* readtreecommand.cpp */, + A7DA20F3113FECD400BF472F /* removeseqscommand.h */, + A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */, + A7DA20F5113FECD400BF472F /* reversecommand.h */, + A7DA20F4113FECD400BF472F /* reversecommand.cpp */, + A7DA20F9113FECD400BF472F /* screenseqscommand.h */, + A7DA20F8113FECD400BF472F /* screenseqscommand.cpp */, + A7DA20FB113FECD400BF472F /* secondarystructurecommand.h */, + A7DA20FA113FECD400BF472F /* secondarystructurecommand.cpp */, + A7DA20FD113FECD400BF472F /* seqsummarycommand.h */, + A7DA20FC113FECD400BF472F /* seqsummarycommand.cpp */, + A7DA2103113FECD400BF472F /* setdircommand.h */, + A7DA2102113FECD400BF472F /* setdircommand.cpp */, + A76C4A1011876BAF0009460B /* setlogfilecommand.h */, + A76C4A1111876BAF0009460B /* setlogfilecommand.cpp */, + A7DA2110113FECD400BF472F /* sharedcommand.h */, + A7DA210F113FECD400BF472F /* sharedcommand.cpp */, + A73F163411A1951D0087CA57 /* splitabundcommand.h */, + A73F163511A1951D0087CA57 /* splitabundcommand.cpp */, + A7DA2155113FECD400BF472F /* summarycommand.h */, + A7DA2154113FECD400BF472F /* summarycommand.cpp */, + A7DA2159113FECD400BF472F /* summarysharedcommand.h */, + A7DA2158113FECD400BF472F /* summarysharedcommand.cpp */, + A7DA215B113FECD400BF472F /* systemcommand.h */, + A7DA215A113FECD400BF472F /* systemcommand.cpp */, + A7DA2162113FECD400BF472F /* treegroupscommand.h */, + A7DA2161113FECD400BF472F /* treegroupscommand.cpp */, + A7DA2168113FECD400BF472F /* trimseqscommand.h */, + A7DA2167113FECD400BF472F /* trimseqscommand.cpp */, + A7DA216A113FECD400BF472F /* unifracunweightedcommand.h */, + A7DA2169113FECD400BF472F /* unifracunweightedcommand.cpp */, + A7DA216C113FECD400BF472F /* unifracweightedcommand.h */, + A7DA216B113FECD400BF472F /* unifracweightedcommand.cpp */, + A7DA2178113FECD400BF472F /* venncommand.h */, + A7DA2177113FECD400BF472F /* venncommand.cpp */, ); - name = calculators; + name = commands; sourceTree = ""; }; - 37D928A90F2133E5001D4494 /* commands */ = { + A7CB594211402F430010EB83 /* containers */ = { isa = PBXGroup; children = ( - 37D927CD0F21331F001D4494 /* command.hpp */, - 37C1D9710F86506E0059E3F0 /* binsequencecommand.h */, - 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */, - 37D927C40F21331F001D4494 /* clustercommand.h */, - 37D927C30F21331F001D4494 /* clustercommand.cpp */, - 37D927C80F21331F001D4494 /* collectcommand.h */, - 37D927C70F21331F001D4494 /* collectcommand.cpp */, - 37D927CC0F21331F001D4494 /* collectsharedcommand.h */, - 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 */, - 37D927E30F21331F001D4494 /* helpcommand.cpp */, - 375873F40F7D648F0040F377 /* libshuffcommand.h */, - 375873F30F7D648F0040F377 /* libshuffcommand.cpp */, - 375873F60F7D649C0040F377 /* nocommands.cpp */, - 375873F70F7D649C0040F377 /* nocommands.h */, - 37D927FA0F21331F001D4494 /* parselistcommand.h */, - 37D927F90F21331F001D4494 /* parselistcommand.cpp */, - 3792946E0F2E191800B9034A /* parsimonycommand.h */, - 3792946F0F2E191800B9034A /* parsimonycommand.cpp */, - 37D927FE0F21331F001D4494 /* quitcommand.h */, - 37D927FD0F21331F001D4494 /* quitcommand.cpp */, - 37D928080F21331F001D4494 /* rarefactcommand.h */, - 37D928070F21331F001D4494 /* rarefactcommand.cpp */, - 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */, - 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */, - 372E12940F263D5A0095CF7E /* readdistcommand.h */, - 372E12950F263D5A0095CF7E /* readdistcommand.cpp */, - 372E126E0F26365B0095CF7E /* readotucommand.h */, - 372E126F0F26365B0095CF7E /* readotucommand.cpp */, - 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */, - 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */, - 37D928270F21331F001D4494 /* sharedcommand.h */, - 37D928260F21331F001D4494 /* sharedcommand.cpp */, - 37D928470F21331F001D4494 /* summarycommand.h */, - 37D928460F21331F001D4494 /* summarycommand.cpp */, - 37D9284B0F21331F001D4494 /* summarysharedcommand.h */, - 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */, - 3746109B0F40657600460C57 /* unifracunweightedcommand.h */, - 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */, - 374610760F40645300460C57 /* unifracweightedcommand.h */, - 374610770F40645300460C57 /* unifracweightedcommand.cpp */, - 37519A9F0F810D0200FED5E8 /* venncommand.h */, - 37519AA00F810D0200FED5E8 /* venncommand.cpp */, + A7DA1FF3113FECD400BF472F /* alignmentcell.hpp */, + A7DA1FF2113FECD400BF472F /* alignmentcell.cpp */, + A7DA1FF4113FECD400BF472F /* alignmentdb.cpp */, + A7DA1FF5113FECD400BF472F /* alignmentdb.h */, + A7DA2001113FECD400BF472F /* blastdb.cpp */, + A7DA2002113FECD400BF472F /* blastdb.hpp */, + A7DA2035113FECD400BF472F /* database.cpp */, + A7DA2036113FECD400BF472F /* database.hpp */, + A7DA2037113FECD400BF472F /* datavector.hpp */, + A7DA2040113FECD400BF472F /* distancedb.cpp */, + A7DA2041113FECD400BF472F /* distancedb.hpp */, + A7DA204A113FECD400BF472F /* fastamap.cpp */, + A7DA204B113FECD400BF472F /* fastamap.h */, + A7DA2056113FECD400BF472F /* fullmatrix.cpp */, + A7DA2057113FECD400BF472F /* fullmatrix.h */, + A7DA2070113FECD400BF472F /* groupmap.cpp */, + A7DA2071113FECD400BF472F /* groupmap.h */, + A7DA2085113FECD400BF472F /* kmer.cpp */, + A7DA2086113FECD400BF472F /* kmer.hpp */, + A7DA2087113FECD400BF472F /* kmerdb.cpp */, + A7DA2088113FECD400BF472F /* kmerdb.hpp */, + A7DA2091113FECD400BF472F /* listvector.cpp */, + A7DA2092113FECD400BF472F /* listvector.hpp */, + A7DA20A2113FECD400BF472F /* nameassignment.cpp */, + A7DA20A3113FECD400BF472F /* nameassignment.hpp */, + A7DA20B6113FECD400BF472F /* ordervector.cpp */, + A7DA20B7113FECD400BF472F /* ordervector.hpp */, + A7DA20D2113FECD400BF472F /* rabundvector.cpp */, + A7DA20D3113FECD400BF472F /* rabundvector.hpp */, + A7DA20F6113FECD400BF472F /* sabundvector.cpp */, + A7DA20F7113FECD400BF472F /* sabundvector.hpp */, + A7DA20FE113FECD400BF472F /* sequence.cpp */, + A7DA20FF113FECD400BF472F /* sequence.hpp */, + A7DA2100113FECD400BF472F /* sequencedb.cpp */, + A7DA2101113FECD400BF472F /* sequencedb.h */, + A7DA2121113FECD400BF472F /* sharedlistvector.cpp */, + A7DA2122113FECD400BF472F /* sharedlistvector.h */, + A7DA212A113FECD400BF472F /* sharedordervector.cpp */, + A7DA212B113FECD400BF472F /* sharedordervector.h */, + A7DA212C113FECD400BF472F /* sharedrabundvector.cpp */, + A7DA212D113FECD400BF472F /* sharedrabundvector.h */, + A7DA212E113FECD400BF472F /* sharedsabundvector.cpp */, + A7DA212F113FECD400BF472F /* sharedsabundvector.h */, + A7DA214C113FECD400BF472F /* sparsematrix.cpp */, + A7DA214D113FECD400BF472F /* sparsematrix.hpp */, + A7DA214E113FECD400BF472F /* suffixdb.cpp */, + A7DA214F113FECD400BF472F /* suffixdb.hpp */, + A7DA2150113FECD400BF472F /* suffixnodes.cpp */, + A7DA2151113FECD400BF472F /* suffixnodes.hpp */, + A7DA2152113FECD400BF472F /* suffixtree.cpp */, + A7DA2153113FECD400BF472F /* suffixtree.hpp */, + A7DA215E113FECD400BF472F /* tree.cpp */, + A7DA215F113FECD400BF472F /* tree.h */, + A7DA2163113FECD400BF472F /* treemap.cpp */, + A7DA2164113FECD400BF472F /* treemap.h */, + A7DA2165113FECD400BF472F /* treenode.cpp */, + A7DA2166113FECD400BF472F /* treenode.h */, ); - name = commands; + name = containers; sourceTree = ""; }; - 37D928AC0F213420001D4494 /* containers */ = { + A7CB594511402F6E0010EB83 /* classifers */ = { isa = PBXGroup; children = ( - 37D927D50F21331F001D4494 /* datavector.hpp */, - 37D927DC0F21331F001D4494 /* fastamap.h */, - 37D927DB0F21331F001D4494 /* fastamap.cpp */, - 375873EA0F7D64520040F377 /* fullmatrix.h */, - 375873EB0F7D64520040F377 /* fullmatrix.cpp */, - 37D927E20F21331F001D4494 /* groupmap.h */, - 37D927E10F21331F001D4494 /* groupmap.cpp */, - 37D927EE0F21331F001D4494 /* listvector.hpp */, - 37D927ED0F21331F001D4494 /* listvector.cpp */, - 37D927F80F21331F001D4494 /* ordervector.hpp */, - 37D927F70F21331F001D4494 /* ordervector.cpp */, - 37D928000F21331F001D4494 /* rabundvector.hpp */, - 37D927FF0F21331F001D4494 /* rabundvector.cpp */, - 37D9281B0F21331F001D4494 /* sabundvector.hpp */, - 37D9281A0F21331F001D4494 /* sabundvector.cpp */, - 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */, - 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */, - 37D9282F0F21331F001D4494 /* sharedordervector.h */, - 37D9282E0F21331F001D4494 /* sharedordervector.cpp */, - 37D928310F21331F001D4494 /* sharedrabundvector.h */, - 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 */, + A7DA201B113FECD400BF472F /* classify.cpp */, + A7DA201C113FECD400BF472F /* classify.h */, + A7DA1FF7113FECD400BF472F /* bayesian.cpp */, + A7DA1FF8113FECD400BF472F /* bayesian.h */, + A7DA2089113FECD400BF472F /* knn.cpp */, + A7DA208A113FECD400BF472F /* knn.h */, + A7DA20C4113FECD400BF472F /* phylotree.cpp */, + A7DA20C5113FECD400BF472F /* phylotree.h */, + A76AAD02117F322B003D8DA1 /* phylosummary.h */, + A76AAD03117F322B003D8DA1 /* phylosummary.cpp */, + A7DA215C113FECD400BF472F /* taxonomyequalizer.cpp */, + A7DA215D113FECD400BF472F /* taxonomyequalizer.h */, ); - name = containers; + name = classifers; sourceTree = ""; }; - 37D928B10F213472001D4494 /* errorcheckor */ = { + A7CB594A11402FB40010EB83 /* chimeras */ = { 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 */, + A7DA2011113FECD400BF472F /* chimera.cpp */, + A7DA2012113FECD400BF472F /* chimera.h */, + A7DA1FF9113FECD400BF472F /* bellerophon.cpp */, + A7DA1FFA113FECD400BF472F /* bellerophon.h */, + A7DA200D113FECD400BF472F /* ccode.cpp */, + A7DA200E113FECD400BF472F /* ccode.h */, + A7DA2013113FECD400BF472F /* chimeracheckrdp.cpp */, + A7DA2014113FECD400BF472F /* chimeracheckrdp.h */, + A7DA2015113FECD400BF472F /* chimerarealigner.cpp */, + A7DA2016113FECD400BF472F /* chimerarealigner.h */, + A7DA2019113FECD400BF472F /* chimeraslayer.cpp */, + A7DA201A113FECD400BF472F /* chimeraslayer.h */, + A7DA2038113FECD400BF472F /* decalc.cpp */, + A7DA2039113FECD400BF472F /* decalc.h */, + A7DA2095113FECD400BF472F /* maligner.cpp */, + A7DA2096113FECD400BF472F /* maligner.h */, + A7DA20C8113FECD400BF472F /* pintail.cpp */, + A7DA20C9113FECD400BF472F /* pintail.h */, + A7DA2145113FECD400BF472F /* slayer.cpp */, + A7DA2146113FECD400BF472F /* slayer.h */, ); - name = errorcheckor; + name = chimeras; sourceTree = ""; }; - C6859E8C029090F304C91782 /* Documentation */ = { + A7CB5953114033220010EB83 /* read */ = { isa = PBXGroup; children = ( - C6859E8B029090EE04C91782 /* Mothur.1 */, + A7DA2051113FECD400BF472F /* formatcolumn.cpp */, + A7DA2052113FECD400BF472F /* formatcolumn.h */, + A7DA2053113FECD400BF472F /* formatmatrix.h */, + A7DA2054113FECD400BF472F /* formatphylip.cpp */, + A7DA2055113FECD400BF472F /* formatphylip.h */, + A7DA20DF113FECD400BF472F /* readblast.cpp */, + A7DA20E0113FECD400BF472F /* readblast.h */, + A7DA20E1113FECD400BF472F /* readcluster.cpp */, + A7DA20E2113FECD400BF472F /* readcluster.h */, + A7DA20E3113FECD400BF472F /* readcolumn.cpp */, + A7DA20E4113FECD400BF472F /* readcolumn.h */, + A7DA20E7113FECD400BF472F /* readmatrix.hpp */, + A7DA20E8113FECD400BF472F /* readotu.cpp */, + A7DA20E9113FECD400BF472F /* readotu.h */, + A7DA20EC113FECD400BF472F /* readphylip.cpp */, + A7DA20ED113FECD400BF472F /* readphylip.h */, + A7DA20EE113FECD400BF472F /* readtree.cpp */, + A7DA20EF113FECD400BF472F /* readtree.h */, + A730977D11A417BE00117C95 /* splitmatrix.h */, + A730977E11A417BE00117C95 /* splitmatrix.cpp */, ); - name = Documentation; + name = read; sourceTree = ""; }; /* End PBXGroup section */ -/* Begin PBXNativeTarget section */ - 8DD76F620486A84900D96B5E /* mothur */ = { - isa = PBXNativeTarget; - buildConfigurationList = 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */; +/* Begin PBXLegacyTarget section */ + D28A88AD04BDD90700651E21 /* mothur */ = { + isa = PBXLegacyTarget; + buildArgumentsString = "$(ACTION)"; + buildConfigurationList = 1DEB918F08733D9F0010E9CD /* Build configuration list for PBXLegacyTarget "mothur" */; buildPhases = ( - 8DD76F640486A84900D96B5E /* Sources */, - 8DD76F660486A84900D96B5E /* Frameworks */, - 8DD76F690486A84900D96B5E /* CopyFiles */, - ); - buildRules = ( ); + buildToolPath = /usr/bin/make; dependencies = ( ); name = mothur; - productInstallPath = "$(HOME)/bin"; - productName = Mothur; - productReference = 8DD76F6C0486A84900D96B5E /* mothur */; - productType = "com.apple.product-type.tool"; + passBuildSettingsInEnvironment = 1; + productName = mothur; }; -/* End PBXNativeTarget section */ +/* End PBXLegacyTarget section */ /* Begin PBXProject section */ 08FB7793FE84155DC02AAC07 /* Project object */ = { isa = PBXProject; - buildConfigurationList = 1DEB923508733DC60010E9CD /* Build configuration list for PBXProject "Mothur" */; + attributes = { + BuildIndependentTargetsInParallel = YES; + }; + buildConfigurationList = 1DEB919308733D9F0010E9CD /* Build configuration list for PBXProject "Mothur" */; compatibilityVersion = "Xcode 3.0"; hasScannedForEncodings = 1; - mainGroup = 08FB7794FE84155DC02AAC07 /* Mothur */; + mainGroup = 08FB7794FE84155DC02AAC07 /* mothur */; projectDirPath = ""; projectRoot = ""; targets = ( - 8DD76F620486A84900D96B5E /* mothur */, + D28A88AD04BDD90700651E21 /* mothur */, ); }; /* End PBXProject section */ -/* Begin PBXSourcesBuildPhase section */ - 8DD76F640486A84900D96B5E /* Sources */ = { - isa = PBXSourcesBuildPhase; - buildActionMask = 2147483647; - files = ( - 37D928550F21331F001D4494 /* ace.cpp in Sources */, - 37D928560F21331F001D4494 /* averagelinkage.cpp in Sources */, - 37D928570F21331F001D4494 /* bootstrap.cpp in Sources */, - 37D928580F21331F001D4494 /* calculator.cpp in Sources */, - 37D928590F21331F001D4494 /* chao1.cpp in Sources */, - 37D9285A0F21331F001D4494 /* cluster.cpp in Sources */, - 37D9285B0F21331F001D4494 /* clustercommand.cpp in Sources */, - 37D9285C0F21331F001D4494 /* collect.cpp in Sources */, - 37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */, - 37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */, - 37D928600F21331F001D4494 /* commandoptionparser.cpp in Sources */, - 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 */, - 37D928680F21331F001D4494 /* groupmap.cpp in Sources */, - 37D928690F21331F001D4494 /* helpcommand.cpp in Sources */, - 37D9286A0F21331F001D4494 /* inputdata.cpp in Sources */, - 37D9286B0F21331F001D4494 /* jackknife.cpp in Sources */, - 37D9286C0F21331F001D4494 /* kmer.cpp in Sources */, - 37D9286D0F21331F001D4494 /* kmerdb.cpp in Sources */, - 37D9286E0F21331F001D4494 /* listvector.cpp in Sources */, - 37D9286F0F21331F001D4494 /* mothur.cpp in Sources */, - 37D928700F21331F001D4494 /* nameassignment.cpp in Sources */, - 37D928720F21331F001D4494 /* npshannon.cpp in Sources */, - 37D928730F21331F001D4494 /* ordervector.cpp in Sources */, - 37D928740F21331F001D4494 /* parselistcommand.cpp in Sources */, - 37D928750F21331F001D4494 /* progress.cpp in Sources */, - 37D928760F21331F001D4494 /* quitcommand.cpp in Sources */, - 37D928770F21331F001D4494 /* rabundvector.cpp in Sources */, - 37D928780F21331F001D4494 /* rarecalc.cpp in Sources */, - 37D928790F21331F001D4494 /* raredisplay.cpp in Sources */, - 37D9287A0F21331F001D4494 /* rarefact.cpp in Sources */, - 37D9287B0F21331F001D4494 /* rarefactcommand.cpp in Sources */, - 37D9287C0F21331F001D4494 /* rarefactsharedcommand.cpp in Sources */, - 37D928800F21331F001D4494 /* readmatrix.cpp in Sources */, - 37D928840F21331F001D4494 /* sabundvector.cpp in Sources */, - 37D928850F21331F001D4494 /* sequence.cpp in Sources */, - 37D928860F21331F001D4494 /* shannon.cpp in Sources */, - 37D928870F21331F001D4494 /* shared.cpp in Sources */, - 37D928880F21331F001D4494 /* sharedace.cpp in Sources */, - 37D928890F21331F001D4494 /* sharedchao1.cpp in Sources */, - 37D9288A0F21331F001D4494 /* sharedcommand.cpp in Sources */, - 37D9288B0F21331F001D4494 /* sharedjabund.cpp in Sources */, - 37D9288C0F21331F001D4494 /* sharedjclass.cpp in Sources */, - 37D9288D0F21331F001D4494 /* sharedjest.cpp in Sources */, - 37D9288E0F21331F001D4494 /* sharedordervector.cpp in Sources */, - 37D9288F0F21331F001D4494 /* sharedrabundvector.cpp in Sources */, - 37D928900F21331F001D4494 /* sharedsabundvector.cpp in Sources */, - 37D928910F21331F001D4494 /* sharedsobs.cpp in Sources */, - 37D928920F21331F001D4494 /* sharedsorabund.cpp in Sources */, - 37D928930F21331F001D4494 /* sharedsorclass.cpp in Sources */, - 37D928940F21331F001D4494 /* sharedsorest.cpp in Sources */, - 37D928950F21331F001D4494 /* sharedthetan.cpp in Sources */, - 37D928960F21331F001D4494 /* sharedthetayc.cpp in Sources */, - 37D928970F21331F001D4494 /* simpson.cpp in Sources */, - 37D928980F21331F001D4494 /* singlelinkage.cpp in Sources */, - 37D928990F21331F001D4494 /* sparsematrix.cpp in Sources */, - 37D9289A0F21331F001D4494 /* summarycommand.cpp in Sources */, - 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 */, - 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 */, - 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 */, - 7E412F490F8D21B600381DD0 /* slibshuff.cpp in Sources */, - 7E412FEA0F8D3E2C00381DD0 /* libshuff.cpp in Sources */, - 7E4130F80F8E58FA00381DD0 /* dlibshuff.cpp in Sources */, - ); - runOnlyForDeploymentPostprocessing = 0; - }; -/* End PBXSourcesBuildPhase section */ - /* Begin XCBuildConfiguration section */ - 1DEB923208733DC60010E9CD /* Debug */ = { + 1DEB919108733D9F0010E9CD /* Release */ = { isa = XCBuildConfiguration; buildSettings = { - COPY_PHASE_STRIP = NO; - GCC_DYNAMIC_NO_PIC = NO; - GCC_ENABLE_FIX_AND_CONTINUE = YES; - GCC_MODEL_TUNING = G5; - GCC_OPTIMIZATION_LEVEL = 0; - GCC_PREPROCESSOR_DEFINITIONS = ( - "_GLIBCXX_DEBUG=1", - "_GLIBCXX_DEBUG_PEDANTIC=1", - ); - INSTALL_PATH = /usr/local/bin; - PRODUCT_NAME = mothur; - ZERO_LINK = YES; - }; - name = Debug; - }; - 1DEB923308733DC60010E9CD /* Release */ = { - isa = XCBuildConfiguration; - buildSettings = { - DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym"; - GCC_MODEL_TUNING = G5; - INSTALL_PATH = /usr/local/bin; + COPY_PHASE_STRIP = YES; + GCC_ENABLE_FIX_AND_CONTINUE = NO; + OTHER_CFLAGS = ""; + OTHER_LDFLAGS = ""; PRODUCT_NAME = mothur; + ZERO_LINK = NO; }; name = Release; }; - 1DEB923608733DC60010E9CD /* Debug */ = { - isa = XCBuildConfiguration; - buildSettings = { - GCC_OPTIMIZATION_LEVEL = 3; - GCC_WARN_ABOUT_RETURN_TYPE = YES; - GCC_WARN_UNUSED_VARIABLE = YES; - PREBINDING = NO; - SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk"; - }; - name = Debug; - }; - 1DEB923708733DC60010E9CD /* Release */ = { + 1DEB919508733D9F0010E9CD /* Release */ = { isa = XCBuildConfiguration; buildSettings = { ARCHS = ( ppc, i386, ); - GCC_OPTIMIZATION_LEVEL = 3; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_UNUSED_VARIABLE = YES; + LINK_WITH_STANDARD_LIBRARIES = YES; PREBINDING = NO; SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk"; }; @@ -910,20 +998,18 @@ /* End XCBuildConfiguration section */ /* Begin XCConfigurationList section */ - 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */ = { + 1DEB918F08733D9F0010E9CD /* Build configuration list for PBXLegacyTarget "mothur" */ = { isa = XCConfigurationList; buildConfigurations = ( - 1DEB923208733DC60010E9CD /* Debug */, - 1DEB923308733DC60010E9CD /* Release */, + 1DEB919108733D9F0010E9CD /* Release */, ); defaultConfigurationIsVisible = 0; defaultConfigurationName = Release; }; - 1DEB923508733DC60010E9CD /* Build configuration list for PBXProject "Mothur" */ = { + 1DEB919308733D9F0010E9CD /* Build configuration list for PBXProject "Mothur" */ = { isa = XCConfigurationList; buildConfigurations = ( - 1DEB923608733DC60010E9CD /* Debug */, - 1DEB923708733DC60010E9CD /* Release */, + 1DEB919508733D9F0010E9CD /* Release */, ); defaultConfigurationIsVisible = 0; defaultConfigurationName = Release;