X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=d678294bcf11674e75ccdc40dd068df8300c7750;hb=44c1323a88b2a697c7047df1b3bb8c59eadd15b1;hp=e8d32aa4a491d48e11ae83d223138908708d34ab;hpb=4761e165b4a196fefa57755d3176d9ced19df6b1;p=mothur.git

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index e8d32aa..d678294 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -10,9 +10,17 @@
 		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 */; };
 		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 */; };
@@ -82,6 +90,8 @@
 		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 */
 
@@ -104,12 +114,29 @@
 		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>"; };
 		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>"; };
@@ -256,6 +283,10 @@
 		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 */
@@ -356,6 +387,7 @@
 			isa = PBXGroup;
 			children = (
 				37D927BE0F21331F001D4494 /* calculator.h */,
+				3792948D0F2E271100B9034A /* treecalculator.h */,
 				37D927BD0F21331F001D4494 /* calculator.cpp */,
 				37D927B90F21331F001D4494 /* ace.h */,
 				37D927B80F21331F001D4494 /* ace.cpp */,
@@ -367,6 +399,8 @@
 				37D927E70F21331F001D4494 /* jackknife.cpp */,
 				37D927F50F21331F001D4494 /* npshannon.h */,
 				37D927F40F21331F001D4494 /* npshannon.cpp */,
+				379294880F2E258500B9034A /* parsimony.h */,
+				379294890F2E258500B9034A /* parsimony.cpp */,
 				37D928020F21331F001D4494 /* rarecalc.h */,
 				37D928010F21331F001D4494 /* rarecalc.cpp */,
 				37D9281F0F21331F001D4494 /* shannon.h */,
@@ -383,6 +417,8 @@
 				37D9282C0F21331F001D4494 /* sharedjest.cpp */,
 				37D928350F21331F001D4494 /* sharedsobs.h */,
 				37D928340F21331F001D4494 /* sharedsobs.cpp */,
+				37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */,
+				37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */,
 				37D928370F21331F001D4494 /* sharedsorabund.h */,
 				37D928360F21331F001D4494 /* sharedsorabund.cpp */,
 				37D928390F21331F001D4494 /* sharedsorclass.h */,
@@ -396,8 +432,12 @@
 				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 */,
 			);
 			name = calculators;
 			sourceTree = "<group>";
@@ -420,6 +460,8 @@
 				37D927F30F21331F001D4494 /* nocommand.h */,
 				37D927FA0F21331F001D4494 /* parselistcommand.h */,
 				37D927F90F21331F001D4494 /* parselistcommand.cpp */,
+				3792946E0F2E191800B9034A /* parsimonycommand.h */,
+				3792946F0F2E191800B9034A /* parsimonycommand.cpp */,
 				37D927FE0F21331F001D4494 /* quitcommand.h */,
 				37D927FD0F21331F001D4494 /* quitcommand.cpp */,
 				37D928080F21331F001D4494 /* rarefactcommand.h */,
@@ -430,12 +472,18 @@
 				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 */,
 			);
 			name = commands;
 			sourceTree = "<group>";
@@ -466,6 +514,10 @@
 				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>";
@@ -611,6 +663,16 @@
 				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 */,
 			);
 			runOnlyForDeploymentPostprocessing = 0;
 		};
@@ -663,7 +725,7 @@
 					ppc,
 					i386,
 				);
-				GCC_OPTIMIZATION_LEVEL = 3;
+				GCC_OPTIMIZATION_LEVEL = 0;
 				GCC_WARN_ABOUT_RETURN_TYPE = YES;
 				GCC_WARN_UNUSED_VARIABLE = YES;
 				PREBINDING = NO;