objects = {
/* Begin PBXBuildFile section */
+ 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 */; };
+ 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 */; };
+ 37AFC7A30F44703E005F492D /* readsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AFC7A20F44703E005F492D /* readsharedcommand.cpp */; };
+ 37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B28F670F27590100808A62 /* deconvolutecommand.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 */; };
37D9285C0F21331F001D4494 /* collect.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C50F21331F001D4494 /* collect.cpp */; };
37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927C70F21331F001D4494 /* collectcommand.cpp */; };
37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */; };
- 37D9285F0F21331F001D4494 /* commandfactory.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927CE0F21331F001D4494 /* commandfactory.cpp */; };
37D928600F21331F001D4494 /* commandoptionparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D00F21331F001D4494 /* commandoptionparser.cpp */; };
37D928610F21331F001D4494 /* completelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D20F21331F001D4494 /* completelinkage.cpp */; };
37D928620F21331F001D4494 /* database.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927D30F21331F001D4494 /* database.cpp */; };
37D9287A0F21331F001D4494 /* rarefact.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928050F21331F001D4494 /* rarefact.cpp */; };
37D9287B0F21331F001D4494 /* rarefactcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928070F21331F001D4494 /* rarefactcommand.cpp */; };
37D9287C0F21331F001D4494 /* rarefactsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */; };
- 37D9287D0F21331F001D4494 /* readdistcolumnfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9280C0F21331F001D4494 /* readdistcolumnfilecommand.cpp */; };
- 37D9287E0F21331F001D4494 /* readdistphylipfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9280E0F21331F001D4494 /* readdistphylipfilecommand.cpp */; };
- 37D9287F0F21331F001D4494 /* readlistfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928100F21331F001D4494 /* readlistfilecommand.cpp */; };
37D928800F21331F001D4494 /* readmatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928120F21331F001D4494 /* readmatrix.cpp */; };
- 37D928810F21331F001D4494 /* readrabundfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928140F21331F001D4494 /* readrabundfilecommand.cpp */; };
- 37D928820F21331F001D4494 /* readsabundfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928160F21331F001D4494 /* readsabundfilecommand.cpp */; };
- 37D928830F21331F001D4494 /* readsharedfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928180F21331F001D4494 /* readsharedfilecommand.cpp */; };
37D928840F21331F001D4494 /* sabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281A0F21331F001D4494 /* sabundvector.cpp */; };
37D928850F21331F001D4494 /* sequence.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281C0F21331F001D4494 /* sequence.cpp */; };
37D928860F21331F001D4494 /* shannon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281E0F21331F001D4494 /* shannon.cpp */; };
37D9289D0F21331F001D4494 /* validcalculator.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9284F0F21331F001D4494 /* validcalculator.cpp */; };
37D9289E0F21331F001D4494 /* validcommands.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928510F21331F001D4494 /* validcommands.cpp */; };
37D9289F0F21331F001D4494 /* validparameter.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928530F21331F001D4494 /* validparameter.cpp */; };
+ 37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37E5F3E20F29FD4200F8D827 /* treenode.cpp */; };
+ 37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */; };
8DD76F6A0486A84900D96B5E /* Mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6859E8B029090EE04C91782 /* Mothur.1 */; };
/* End PBXBuildFile section */
/* End PBXCopyFilesBuildPhase section */
/* Begin PBXFileReference section */
+ 372E126E0F26365B0095CF7E /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = "<group>"; };
+ 372E126F0F26365B0095CF7E /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = "<group>"; };
+ 372E12940F263D5A0095CF7E /* readdistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcommand.h; sourceTree = "<group>"; };
+ 372E12950F263D5A0095CF7E /* readdistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistcommand.cpp; sourceTree = "<group>"; };
+ 372E12EC0F264D320095CF7E /* commandfactory.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandfactory.cpp; sourceTree = "<group>"; };
+ 374610760F40645300460C57 /* unifracweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracweightedcommand.h; sourceTree = "<group>"; };
+ 374610770F40645300460C57 /* unifracweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracweightedcommand.cpp; sourceTree = "<group>"; };
+ 3746107C0F4064D100460C57 /* weighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = weighted.h; sourceTree = "<group>"; };
+ 3746107D0F4064D100460C57 /* weighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weighted.cpp; sourceTree = "<group>"; };
+ 374610810F40652400460C57 /* unweighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unweighted.h; sourceTree = "<group>"; };
+ 374610820F40652400460C57 /* unweighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unweighted.cpp; sourceTree = "<group>"; };
+ 3746109B0F40657600460C57 /* unifracunweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracunweightedcommand.h; sourceTree = "<group>"; };
+ 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracunweightedcommand.cpp; sourceTree = "<group>"; };
+ 379293C10F2DE73400B9034A /* treemap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treemap.h; sourceTree = "<group>"; };
+ 379293C20F2DE73400B9034A /* treemap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treemap.cpp; sourceTree = "<group>"; };
+ 3792946E0F2E191800B9034A /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = "<group>"; };
+ 3792946F0F2E191800B9034A /* parsimonycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimonycommand.cpp; sourceTree = "<group>"; };
+ 379294880F2E258500B9034A /* parsimony.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimony.h; sourceTree = "<group>"; };
+ 379294890F2E258500B9034A /* parsimony.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimony.cpp; sourceTree = "<group>"; };
+ 3792948D0F2E271100B9034A /* treecalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treecalculator.h; sourceTree = "<group>"; };
+ 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlistvector.h; sourceTree = "<group>"; };
+ 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlistvector.cpp; sourceTree = "<group>"; };
+ 37AD4DB90F28E2FE00AA2D49 /* tree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tree.h; sourceTree = "<group>"; };
+ 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = tree.cpp; sourceTree = "<group>"; };
+ 37AD4DC80F28F3DD00AA2D49 /* readtree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtree.h; sourceTree = "<group>"; };
+ 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtree.cpp; sourceTree = "<group>"; };
+ 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobscollectsummary.h; sourceTree = "<group>"; };
+ 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobscollectsummary.cpp; sourceTree = "<group>"; };
+ 37AFC7A10F44703E005F492D /* readsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readsharedcommand.h; sourceTree = "<group>"; };
+ 37AFC7A20F44703E005F492D /* readsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readsharedcommand.cpp; sourceTree = "<group>"; };
+ 37B28F660F27590100808A62 /* deconvolutecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deconvolutecommand.h; sourceTree = "<group>"; };
+ 37B28F670F27590100808A62 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = "<group>"; };
37D927B80F21331F001D4494 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = "<group>"; };
37D927B90F21331F001D4494 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = "<group>"; };
37D927BA0F21331F001D4494 /* averagelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = averagelinkage.cpp; sourceTree = "<group>"; };
37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectsharedcommand.cpp; sourceTree = "<group>"; };
37D927CC0F21331F001D4494 /* collectsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectsharedcommand.h; sourceTree = "<group>"; };
37D927CD0F21331F001D4494 /* command.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = command.hpp; sourceTree = "<group>"; };
- 37D927CE0F21331F001D4494 /* commandfactory.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandfactory.cpp; sourceTree = "<group>"; };
37D927CF0F21331F001D4494 /* commandfactory.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandfactory.hpp; sourceTree = "<group>"; };
37D927D00F21331F001D4494 /* commandoptionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandoptionparser.cpp; sourceTree = "<group>"; };
37D927D10F21331F001D4494 /* commandoptionparser.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandoptionparser.hpp; sourceTree = "<group>"; };
37D928090F21331F001D4494 /* rarefactioncurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactioncurvedata.h; sourceTree = "<group>"; };
37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactsharedcommand.cpp; sourceTree = "<group>"; };
37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactsharedcommand.h; sourceTree = "<group>"; };
- 37D9280C0F21331F001D4494 /* readdistcolumnfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistcolumnfilecommand.cpp; sourceTree = "<group>"; };
- 37D9280D0F21331F001D4494 /* readdistcolumnfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcolumnfilecommand.h; sourceTree = "<group>"; };
- 37D9280E0F21331F001D4494 /* readdistphylipfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistphylipfilecommand.cpp; sourceTree = "<group>"; };
- 37D9280F0F21331F001D4494 /* readdistphylipfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistphylipfilecommand.h; sourceTree = "<group>"; };
- 37D928100F21331F001D4494 /* readlistfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readlistfilecommand.cpp; sourceTree = "<group>"; };
- 37D928110F21331F001D4494 /* readlistfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readlistfilecommand.h; sourceTree = "<group>"; };
37D928120F21331F001D4494 /* readmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readmatrix.cpp; sourceTree = "<group>"; };
37D928130F21331F001D4494 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = "<group>"; };
- 37D928140F21331F001D4494 /* readrabundfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readrabundfilecommand.cpp; sourceTree = "<group>"; };
- 37D928150F21331F001D4494 /* readrabundfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readrabundfilecommand.h; sourceTree = "<group>"; };
- 37D928160F21331F001D4494 /* readsabundfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readsabundfilecommand.cpp; sourceTree = "<group>"; };
- 37D928170F21331F001D4494 /* readsabundfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readsabundfilecommand.h; sourceTree = "<group>"; };
- 37D928180F21331F001D4494 /* readsharedfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readsharedfilecommand.cpp; sourceTree = "<group>"; };
- 37D928190F21331F001D4494 /* readsharedfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readsharedfilecommand.h; sourceTree = "<group>"; };
37D9281A0F21331F001D4494 /* sabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sabundvector.cpp; sourceTree = "<group>"; };
37D9281B0F21331F001D4494 /* sabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sabundvector.hpp; sourceTree = "<group>"; };
37D9281C0F21331F001D4494 /* sequence.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequence.cpp; sourceTree = "<group>"; };
37D928520F21331F001D4494 /* validcommands.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validcommands.h; sourceTree = "<group>"; };
37D928530F21331F001D4494 /* validparameter.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validparameter.cpp; sourceTree = "<group>"; };
37D928540F21331F001D4494 /* validparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validparameter.h; sourceTree = "<group>"; };
+ 37E5F3E10F29FD4200F8D827 /* treenode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treenode.h; sourceTree = "<group>"; };
+ 37E5F3E20F29FD4200F8D827 /* treenode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treenode.cpp; sourceTree = "<group>"; };
+ 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = "<group>"; };
+ 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = "<group>"; };
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 = "<group>"; };
/* End PBXFileReference section */
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 */,
isa = PBXGroup;
children = (
37D927BE0F21331F001D4494 /* calculator.h */,
+ 3792948D0F2E271100B9034A /* treecalculator.h */,
37D927BD0F21331F001D4494 /* calculator.cpp */,
37D927B90F21331F001D4494 /* ace.h */,
37D927B80F21331F001D4494 /* ace.cpp */,
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 = "<group>";
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 = "<group>";
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 = "<group>";
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 = "<group>";
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 */,
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 */,
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;
};
ppc,
i386,
);
- GCC_OPTIMIZATION_LEVEL = 3;
+ GCC_OPTIMIZATION_LEVEL = 0;
GCC_WARN_ABOUT_RETURN_TYPE = YES;
GCC_WARN_UNUSED_VARIABLE = YES;
PREBINDING = NO;
projects / mothur.git / blobdiff