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fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treenode.h; sourceTree = ""; }; + 37E5F3E20F29FD4200F8D827 /* treenode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treenode.cpp; sourceTree = ""; }; + 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = ""; }; + 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = ""; }; 8DD76F6C0486A84900D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; }; C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = ""; }; /* End PBXFileReference section */ @@ -286,55 +320,57 @@ children = ( 37D927BA0F21331F001D4494 /* averagelinkage.cpp */, 37D928A60F2133C0001D4494 /* calculators */, - 37D927C10F21331F001D4494 /* cluster.cpp */, 37D927C20F21331F001D4494 /* cluster.hpp */, + 37D927C10F21331F001D4494 /* cluster.cpp */, 37D928A90F2133E5001D4494 /* commands */, - 37D927C50F21331F001D4494 /* collect.cpp */, 37D927C60F21331F001D4494 /* collect.h */, + 37D927C50F21331F001D4494 /* collect.cpp */, 37D927C90F21331F001D4494 /* collectdisplay.h */, 37D928AC0F213420001D4494 /* containers */, 37D927CA0F21331F001D4494 /* collectorscurvedata.h */, - 37D927CE0F21331F001D4494 /* commandfactory.cpp */, 37D927CF0F21331F001D4494 /* commandfactory.hpp */, - 37D927D00F21331F001D4494 /* commandoptionparser.cpp */, + 372E12EC0F264D320095CF7E /* commandfactory.cpp */, 37D927D10F21331F001D4494 /* commandoptionparser.hpp */, + 37D927D00F21331F001D4494 /* commandoptionparser.cpp */, 37D927D20F21331F001D4494 /* completelinkage.cpp */, - 37D927D30F21331F001D4494 /* database.cpp */, 37D927D40F21331F001D4494 /* database.hpp */, + 37D927D30F21331F001D4494 /* database.cpp */, 37D927D60F21331F001D4494 /* display.h */, - 37D927D70F21331F001D4494 /* engine.cpp */, 37D927D80F21331F001D4494 /* engine.hpp */, + 37D927D70F21331F001D4494 /* engine.cpp */, 37D928B10F213472001D4494 /* errorcheckor */, - 37D927DD0F21331F001D4494 /* fileoutput.cpp */, 37D927DE0F21331F001D4494 /* fileoutput.h */, - 37D927DF0F21331F001D4494 /* globaldata.cpp */, + 37D927DD0F21331F001D4494 /* fileoutput.cpp */, 37D927E00F21331F001D4494 /* globaldata.hpp */, - 37D927E50F21331F001D4494 /* inputdata.cpp */, + 37D927DF0F21331F001D4494 /* globaldata.cpp */, 37D927E60F21331F001D4494 /* inputdata.h */, - 37D927E90F21331F001D4494 /* kmer.cpp */, + 37D927E50F21331F001D4494 /* inputdata.cpp */, 37D927EA0F21331F001D4494 /* kmer.hpp */, - 37D927EB0F21331F001D4494 /* kmerdb.cpp */, + 37D927E90F21331F001D4494 /* kmer.cpp */, 37D927EC0F21331F001D4494 /* kmerdb.hpp */, + 37D927EB0F21331F001D4494 /* kmerdb.cpp */, 37D927EF0F21331F001D4494 /* mothur.cpp */, - 37D927F00F21331F001D4494 /* nameassignment.cpp */, 37D927F10F21331F001D4494 /* nameassignment.hpp */, + 37D927F00F21331F001D4494 /* nameassignment.cpp */, 37D927F60F21331F001D4494 /* observable.h */, - 37D927FB0F21331F001D4494 /* progress.cpp */, 37D927FC0F21331F001D4494 /* progress.hpp */, - 37D928030F21331F001D4494 /* raredisplay.cpp */, + 37D927FB0F21331F001D4494 /* progress.cpp */, 37D928040F21331F001D4494 /* raredisplay.h */, - 37D928050F21331F001D4494 /* rarefact.cpp */, + 37D928030F21331F001D4494 /* raredisplay.cpp */, 37D928060F21331F001D4494 /* rarefact.h */, + 37D928050F21331F001D4494 /* rarefact.cpp */, 37D928090F21331F001D4494 /* rarefactioncurvedata.h */, - 37D928120F21331F001D4494 /* readmatrix.cpp */, 37D928130F21331F001D4494 /* readmatrix.hpp */, - 37D9281C0F21331F001D4494 /* sequence.cpp */, + 37D928120F21331F001D4494 /* readmatrix.cpp */, + 37AD4DC80F28F3DD00AA2D49 /* readtree.h */, + 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */, 37D9281D0F21331F001D4494 /* sequence.hpp */, - 37D928200F21331F001D4494 /* shared.cpp */, + 37D9281C0F21331F001D4494 /* sequence.cpp */, 37D928210F21331F001D4494 /* shared.h */, + 37D928200F21331F001D4494 /* shared.cpp */, 37D928420F21331F001D4494 /* singlelinkage.cpp */, - 37D928440F21331F001D4494 /* sparsematrix.cpp */, 37D928450F21331F001D4494 /* sparsematrix.hpp */, + 37D928440F21331F001D4494 /* sparsematrix.cpp */, 37D928480F21331F001D4494 /* summarydata.h */, 37D928490F21331F001D4494 /* summarydisplay.h */, 37D9284C0F21331F001D4494 /* utilities.hpp */, @@ -354,6 +390,7 @@ isa = PBXGroup; children = ( 37D927BE0F21331F001D4494 /* calculator.h */, + 3792948D0F2E271100B9034A /* treecalculator.h */, 37D927BD0F21331F001D4494 /* calculator.cpp */, 37D927B90F21331F001D4494 /* ace.h */, 37D927B80F21331F001D4494 /* ace.cpp */, @@ -361,41 +398,49 @@ 37D927BB0F21331F001D4494 /* bootstrap.cpp */, 37D927C00F21331F001D4494 /* chao1.h */, 37D927BF0F21331F001D4494 /* chao1.cpp */, - 37D927E70F21331F001D4494 /* jackknife.cpp */, 37D927E80F21331F001D4494 /* jackknife.h */, - 37D927F40F21331F001D4494 /* npshannon.cpp */, + 37D927E70F21331F001D4494 /* jackknife.cpp */, 37D927F50F21331F001D4494 /* npshannon.h */, - 37D928010F21331F001D4494 /* rarecalc.cpp */, + 37D927F40F21331F001D4494 /* npshannon.cpp */, + 379294880F2E258500B9034A /* parsimony.h */, + 379294890F2E258500B9034A /* parsimony.cpp */, 37D928020F21331F001D4494 /* rarecalc.h */, - 37D9281E0F21331F001D4494 /* shannon.cpp */, + 37D928010F21331F001D4494 /* rarecalc.cpp */, 37D9281F0F21331F001D4494 /* shannon.h */, - 37D928220F21331F001D4494 /* sharedace.cpp */, + 37D9281E0F21331F001D4494 /* shannon.cpp */, 37D928230F21331F001D4494 /* sharedace.h */, - 37D928240F21331F001D4494 /* sharedchao1.cpp */, + 37D928220F21331F001D4494 /* sharedace.cpp */, 37D928250F21331F001D4494 /* sharedchao1.h */, - 37D928280F21331F001D4494 /* sharedjabund.cpp */, + 37D928240F21331F001D4494 /* sharedchao1.cpp */, 37D928290F21331F001D4494 /* sharedjabund.h */, - 37D9282A0F21331F001D4494 /* sharedjclass.cpp */, + 37D928280F21331F001D4494 /* sharedjabund.cpp */, 37D9282B0F21331F001D4494 /* sharedjclass.h */, - 37D9282C0F21331F001D4494 /* sharedjest.cpp */, + 37D9282A0F21331F001D4494 /* sharedjclass.cpp */, 37D9282D0F21331F001D4494 /* sharedjest.h */, - 37D928340F21331F001D4494 /* sharedsobs.cpp */, + 37D9282C0F21331F001D4494 /* sharedjest.cpp */, 37D928350F21331F001D4494 /* sharedsobs.h */, - 37D928360F21331F001D4494 /* sharedsorabund.cpp */, + 37D928340F21331F001D4494 /* sharedsobs.cpp */, + 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */, + 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */, 37D928370F21331F001D4494 /* sharedsorabund.h */, - 37D928380F21331F001D4494 /* sharedsorclass.cpp */, + 37D928360F21331F001D4494 /* sharedsorabund.cpp */, 37D928390F21331F001D4494 /* sharedsorclass.h */, - 37D9283A0F21331F001D4494 /* sharedsorest.cpp */, + 37D928380F21331F001D4494 /* sharedsorclass.cpp */, 37D9283B0F21331F001D4494 /* sharedsorest.h */, + 37D9283A0F21331F001D4494 /* sharedsorest.cpp */, 37D9283C0F21331F001D4494 /* sharedthetan.cpp */, 37D9283D0F21331F001D4494 /* sharedthetan.h */, - 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */, 37D9283F0F21331F001D4494 /* sharedthetayc.h */, - 37D928400F21331F001D4494 /* simpson.cpp */, + 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */, 37D928410F21331F001D4494 /* simpson.h */, + 37D928400F21331F001D4494 /* simpson.cpp */, 37D928430F21331F001D4494 /* sobs.h */, - 37D9284D0F21331F001D4494 /* uvest.cpp */, + 374610810F40652400460C57 /* unweighted.h */, + 374610820F40652400460C57 /* unweighted.cpp */, 37D9284E0F21331F001D4494 /* uvest.h */, + 37D9284D0F21331F001D4494 /* uvest.cpp */, + 3746107C0F4064D100460C57 /* weighted.h */, + 3746107D0F4064D100460C57 /* weighted.cpp */, ); name = calculators; sourceTree = ""; @@ -408,38 +453,42 @@ 37D927C30F21331F001D4494 /* clustercommand.cpp */, 37D927C80F21331F001D4494 /* collectcommand.h */, 37D927C70F21331F001D4494 /* collectcommand.cpp */, - 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */, 37D927CC0F21331F001D4494 /* collectsharedcommand.h */, - 37D927E30F21331F001D4494 /* helpcommand.cpp */, + 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */, + 37B28F660F27590100808A62 /* deconvolutecommand.h */, + 37B28F670F27590100808A62 /* deconvolutecommand.cpp */, 37D927E40F21331F001D4494 /* helpcommand.h */, + 37D927E30F21331F001D4494 /* helpcommand.cpp */, 37D927F20F21331F001D4494 /* nocommand.cpp */, 37D927F30F21331F001D4494 /* nocommand.h */, - 37D927F90F21331F001D4494 /* parselistcommand.cpp */, 37D927FA0F21331F001D4494 /* parselistcommand.h */, - 37D927FD0F21331F001D4494 /* quitcommand.cpp */, + 37D927F90F21331F001D4494 /* parselistcommand.cpp */, + 3792946E0F2E191800B9034A /* parsimonycommand.h */, + 3792946F0F2E191800B9034A /* parsimonycommand.cpp */, 37D927FE0F21331F001D4494 /* quitcommand.h */, - 37D928070F21331F001D4494 /* rarefactcommand.cpp */, + 37D927FD0F21331F001D4494 /* quitcommand.cpp */, 37D928080F21331F001D4494 /* rarefactcommand.h */, - 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */, + 37D928070F21331F001D4494 /* rarefactcommand.cpp */, 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */, - 37D9280C0F21331F001D4494 /* readdistcolumnfilecommand.cpp */, - 37D9280D0F21331F001D4494 /* readdistcolumnfilecommand.h */, - 37D9280E0F21331F001D4494 /* readdistphylipfilecommand.cpp */, - 37D9280F0F21331F001D4494 /* readdistphylipfilecommand.h */, - 37D928100F21331F001D4494 /* readlistfilecommand.cpp */, - 37D928110F21331F001D4494 /* readlistfilecommand.h */, - 37D928140F21331F001D4494 /* readrabundfilecommand.cpp */, - 37D928150F21331F001D4494 /* readrabundfilecommand.h */, - 37D928160F21331F001D4494 /* readsabundfilecommand.cpp */, - 37D928170F21331F001D4494 /* readsabundfilecommand.h */, - 37D928180F21331F001D4494 /* readsharedfilecommand.cpp */, - 37D928190F21331F001D4494 /* readsharedfilecommand.h */, - 37D928260F21331F001D4494 /* sharedcommand.cpp */, + 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */, + 372E12940F263D5A0095CF7E /* readdistcommand.h */, + 372E12950F263D5A0095CF7E /* readdistcommand.cpp */, + 372E126E0F26365B0095CF7E /* readotucommand.h */, + 372E126F0F26365B0095CF7E /* readotucommand.cpp */, + 37AFC7A10F44703E005F492D /* readsharedcommand.h */, + 37AFC7A20F44703E005F492D /* readsharedcommand.cpp */, + 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */, + 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */, 37D928270F21331F001D4494 /* sharedcommand.h */, - 37D928460F21331F001D4494 /* summarycommand.cpp */, + 37D928260F21331F001D4494 /* sharedcommand.cpp */, 37D928470F21331F001D4494 /* summarycommand.h */, - 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */, + 37D928460F21331F001D4494 /* summarycommand.cpp */, 37D9284B0F21331F001D4494 /* summarysharedcommand.h */, + 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */, + 3746109B0F40657600460C57 /* unifracunweightedcommand.h */, + 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */, + 374610760F40645300460C57 /* unifracweightedcommand.h */, + 374610770F40645300460C57 /* unifracweightedcommand.cpp */, ); name = commands; sourceTree = ""; @@ -448,24 +497,32 @@ isa = PBXGroup; children = ( 37D927D50F21331F001D4494 /* datavector.hpp */, - 37D927DB0F21331F001D4494 /* fastamap.cpp */, 37D927DC0F21331F001D4494 /* fastamap.h */, - 37D927E10F21331F001D4494 /* groupmap.cpp */, + 37D927DB0F21331F001D4494 /* fastamap.cpp */, 37D927E20F21331F001D4494 /* groupmap.h */, - 37D927ED0F21331F001D4494 /* listvector.cpp */, + 37D927E10F21331F001D4494 /* groupmap.cpp */, 37D927EE0F21331F001D4494 /* listvector.hpp */, - 37D927F70F21331F001D4494 /* ordervector.cpp */, + 37D927ED0F21331F001D4494 /* listvector.cpp */, 37D927F80F21331F001D4494 /* ordervector.hpp */, - 37D927FF0F21331F001D4494 /* rabundvector.cpp */, + 37D927F70F21331F001D4494 /* ordervector.cpp */, 37D928000F21331F001D4494 /* rabundvector.hpp */, - 37D9281A0F21331F001D4494 /* sabundvector.cpp */, + 37D927FF0F21331F001D4494 /* rabundvector.cpp */, 37D9281B0F21331F001D4494 /* sabundvector.hpp */, - 37D9282E0F21331F001D4494 /* sharedordervector.cpp */, + 37D9281A0F21331F001D4494 /* sabundvector.cpp */, + 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */, + 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */, 37D9282F0F21331F001D4494 /* sharedordervector.h */, - 37D928300F21331F001D4494 /* sharedrabundvector.cpp */, + 37D9282E0F21331F001D4494 /* sharedordervector.cpp */, 37D928310F21331F001D4494 /* sharedrabundvector.h */, - 37D928320F21331F001D4494 /* sharedsabundvector.cpp */, + 37D928300F21331F001D4494 /* sharedrabundvector.cpp */, 37D928330F21331F001D4494 /* sharedsabundvector.h */, + 37D928320F21331F001D4494 /* sharedsabundvector.cpp */, + 37AD4DB90F28E2FE00AA2D49 /* tree.h */, + 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */, + 379293C10F2DE73400B9034A /* treemap.h */, + 379293C20F2DE73400B9034A /* treemap.cpp */, + 37E5F3E10F29FD4200F8D827 /* treenode.h */, + 37E5F3E20F29FD4200F8D827 /* treenode.cpp */, ); name = containers; sourceTree = ""; @@ -473,14 +530,14 @@ 37D928B10F213472001D4494 /* errorcheckor */ = { isa = PBXGroup; children = ( - 37D927D90F21331F001D4494 /* errorchecking.cpp */, 37D927DA0F21331F001D4494 /* errorchecking.h */, - 37D9284F0F21331F001D4494 /* validcalculator.cpp */, + 37D927D90F21331F001D4494 /* errorchecking.cpp */, 37D928500F21331F001D4494 /* validcalculator.h */, - 37D928510F21331F001D4494 /* validcommands.cpp */, + 37D9284F0F21331F001D4494 /* validcalculator.cpp */, 37D928520F21331F001D4494 /* validcommands.h */, - 37D928530F21331F001D4494 /* validparameter.cpp */, + 37D928510F21331F001D4494 /* validcommands.cpp */, 37D928540F21331F001D4494 /* validparameter.h */, + 37D928530F21331F001D4494 /* validparameter.cpp */, ); name = errorcheckor; sourceTree = ""; @@ -546,7 +603,6 @@ 37D9285C0F21331F001D4494 /* collect.cpp in Sources */, 37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */, 37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */, - 37D9285F0F21331F001D4494 /* commandfactory.cpp in Sources */, 37D928600F21331F001D4494 /* commandoptionparser.cpp in Sources */, 37D928610F21331F001D4494 /* completelinkage.cpp in Sources */, 37D928620F21331F001D4494 /* database.cpp in Sources */, @@ -576,13 +632,7 @@ 37D9287A0F21331F001D4494 /* rarefact.cpp in Sources */, 37D9287B0F21331F001D4494 /* rarefactcommand.cpp in Sources */, 37D9287C0F21331F001D4494 /* rarefactsharedcommand.cpp in Sources */, - 37D9287D0F21331F001D4494 /* readdistcolumnfilecommand.cpp in Sources */, - 37D9287E0F21331F001D4494 /* readdistphylipfilecommand.cpp in Sources */, - 37D9287F0F21331F001D4494 /* readlistfilecommand.cpp in Sources */, 37D928800F21331F001D4494 /* readmatrix.cpp in Sources */, - 37D928810F21331F001D4494 /* readrabundfilecommand.cpp in Sources */, - 37D928820F21331F001D4494 /* readsabundfilecommand.cpp in Sources */, - 37D928830F21331F001D4494 /* readsharedfilecommand.cpp in Sources */, 37D928840F21331F001D4494 /* sabundvector.cpp in Sources */, 37D928850F21331F001D4494 /* sequence.cpp in Sources */, 37D928860F21331F001D4494 /* shannon.cpp in Sources */, @@ -611,6 +661,24 @@ 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 */, + 37AFC7A30F44703E005F492D /* readsharedcommand.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -663,7 +731,7 @@ ppc, i386, ); - GCC_OPTIMIZATION_LEVEL = 3; + GCC_OPTIMIZATION_LEVEL = 0; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_UNUSED_VARIABLE = YES; PREBINDING = NO;