X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=Mothur.xcodeproj%2Fproject.pbxproj;h=1c8df765aba58235fdb4c557be80834880aa1da0;hb=e4827e0945cbda536064e5a345996b2a7dfcbb81;hp=619737b080a84c6175b6d9ac7628ee467495b175;hpb=f18d75f9c996cb619a5051a7664620c0c5ae05fb;p=mothur.git

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 619737b..1c8df76 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -7,6 +7,10 @@
 	objects = {
 
 /* Begin PBXBuildFile section */
+		211C38320F961DD400FEE541 /* sharedutilities.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 211C38300F961DD400FEE541 /* sharedutilities.cpp */; };
+		211C38380F961E1F00FEE541 /* treegroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 211C38360F961E1F00FEE541 /* treegroupscommand.cpp */; };
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+		370B88070F8A4EE4005AB382 /* getoturepcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */; };
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@@ -17,7 +21,6 @@
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@@ -29,6 +32,9 @@
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 		3758740D0F7D64FC0040F377 /* sharedochiai.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3758740B0F7D64FC0040F377 /* sharedochiai.cpp */; };
+		375AA1390F9E433D008EF9B8 /* readcolumn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375AA1330F9E433D008EF9B8 /* readcolumn.cpp */; };
+		375AA13A0F9E433D008EF9B8 /* readotu.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375AA1350F9E433D008EF9B8 /* readotu.cpp */; };
+		375AA13B0F9E433D008EF9B8 /* readphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375AA1370F9E433D008EF9B8 /* readphylip.cpp */; };
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@@ -76,7 +82,6 @@
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@@ -107,6 +112,9 @@
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+		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 */; };
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@@ -134,6 +142,14 @@
 /* End PBXCopyFilesBuildPhase section */
 
 /* Begin PBXFileReference section */
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+		211C38310F961DD400FEE541 /* sharedutilities.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedutilities.h; sourceTree = "<group>"; };
+		211C38360F961E1F00FEE541 /* treegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treegroupscommand.cpp; sourceTree = "<group>"; };
+		211C38370F961E1F00FEE541 /* treegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treegroupscommand.h; sourceTree = "<group>"; };
+		21DDC0190F97A8FE0060691C /* bootstrapsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrapsharedcommand.h; sourceTree = "<group>"; };
+		21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bootstrapsharedcommand.cpp; sourceTree = "<group>"; };
+		370B88050F8A4EE4005AB382 /* getoturepcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getoturepcommand.h; sourceTree = "<group>"; };
+		370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getoturepcommand.cpp; sourceTree = "<group>"; };
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@@ -153,8 +169,6 @@
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-		375873E60F7D63E90040F377 /* coverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = coverage.h; sourceTree = "<group>"; };
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@@ -179,6 +193,12 @@
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+		375AA1330F9E433D008EF9B8 /* readcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readcolumn.cpp; sourceTree = "<group>"; };
+		375AA1340F9E433D008EF9B8 /* readcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcolumn.h; sourceTree = "<group>"; };
+		375AA1350F9E433D008EF9B8 /* readotu.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotu.cpp; sourceTree = "<group>"; };
+		375AA1360F9E433D008EF9B8 /* readotu.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotu.h; sourceTree = "<group>"; };
+		375AA1370F9E433D008EF9B8 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = "<group>"; };
+		375AA1380F9E433D008EF9B8 /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = "<group>"; };
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@@ -279,7 +299,6 @@
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-		37D928120F21331F001D4494 /* readmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readmatrix.cpp; sourceTree = "<group>"; };
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@@ -331,7 +350,6 @@
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-		37D9284C0F21331F001D4494 /* utilities.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = utilities.hpp; sourceTree = "<group>"; };
 		37D9284D0F21331F001D4494 /* uvest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = uvest.cpp; sourceTree = "<group>"; };
 		37D9284E0F21331F001D4494 /* uvest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = uvest.h; sourceTree = "<group>"; };
 		37D9284F0F21331F001D4494 /* validcalculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validcalculator.cpp; sourceTree = "<group>"; };
@@ -345,6 +363,12 @@
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 		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>"; };
+		7E412F420F8D213C00381DD0 /* libshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuff.h; sourceTree = "<group>"; };
+		7E412F470F8D21B600381DD0 /* slibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slibshuff.h; sourceTree = "<group>"; };
+		7E412F480F8D21B600381DD0 /* slibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slibshuff.cpp; sourceTree = "<group>"; };
+		7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuff.cpp; sourceTree = "<group>"; };
+		7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = dlibshuff.cpp; sourceTree = "<group>"; };
+		7E4130F70F8E58FA00381DD0 /* dlibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dlibshuff.h; sourceTree = "<group>"; };
 		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 = "<group>"; };
 		A70B53A50F4CD7AD0064797E /* getgroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupcommand.h; sourceTree = "<group>"; };
@@ -393,10 +417,16 @@
 		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 */,
@@ -438,18 +468,24 @@
 				37D928060F21331F001D4494 /* rarefact.h */,
 				37D928050F21331F001D4494 /* rarefact.cpp */,
 				37D928090F21331F001D4494 /* rarefactioncurvedata.h */,
+				375AA1340F9E433D008EF9B8 /* readcolumn.h */,
+				375AA1330F9E433D008EF9B8 /* readcolumn.cpp */,
 				37D928130F21331F001D4494 /* readmatrix.hpp */,
-				37D928120F21331F001D4494 /* readmatrix.cpp */,
+				375AA1360F9E433D008EF9B8 /* readotu.h */,
+				375AA1350F9E433D008EF9B8 /* readotu.cpp */,
+				375AA1380F9E433D008EF9B8 /* readphylip.h */,
+				375AA1370F9E433D008EF9B8 /* readphylip.cpp */,
 				37AD4DC80F28F3DD00AA2D49 /* readtree.h */,
 				37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */,
 				37D9281D0F21331F001D4494 /* sequence.hpp */,
 				37D9281C0F21331F001D4494 /* sequence.cpp */,
 				37D928210F21331F001D4494 /* shared.h */,
 				37D928200F21331F001D4494 /* shared.cpp */,
+				211C38310F961DD400FEE541 /* sharedutilities.h */,
+				211C38300F961DD400FEE541 /* sharedutilities.cpp */,
 				37D928420F21331F001D4494 /* singlelinkage.cpp */,
 				37D928480F21331F001D4494 /* summarydata.h */,
 				37D928490F21331F001D4494 /* summarydisplay.h */,
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 			);
@@ -480,8 +516,6 @@
 				EB1216E40F61ACFB004A865F /* bstick.cpp */,
 				37D927C00F21331F001D4494 /* chao1.h */,
 				37D927BF0F21331F001D4494 /* chao1.cpp */,
-				375873E60F7D63E90040F377 /* coverage.h */,
-				375873E50F7D63E90040F377 /* coverage.cpp */,
 				EB9303F70F53517300E8EF26 /* geom.h */,
 				EB9303F80F53517300E8EF26 /* geom.cpp */,
 				EB9303E90F534D9400E8EF26 /* logsd.h */,
@@ -561,6 +595,8 @@
 				37D927CD0F21331F001D4494 /* command.hpp */,
 				37C1D9710F86506E0059E3F0 /* binsequencecommand.h */,
 				37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */,
+				21DDC0190F97A8FE0060691C /* bootstrapsharedcommand.h */,
+				21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */,
 				37D927C40F21331F001D4494 /* clustercommand.h */,
 				37D927C30F21331F001D4494 /* clustercommand.cpp */,
 				37D927C80F21331F001D4494 /* collectcommand.h */,
@@ -575,6 +611,8 @@
 				A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */,
 				A70B53A90F4CD7AD0064797E /* getlinecommand.h */,
 				A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */,
+				370B88050F8A4EE4005AB382 /* getoturepcommand.h */,
+				370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */,
 				375873F10F7D64800040F377 /* heatmapcommand.h */,
 				375873F00F7D64800040F377 /* heatmapcommand.cpp */,
 				37D927E40F21331F001D4494 /* helpcommand.h */,
@@ -605,6 +643,8 @@
 				37D928460F21331F001D4494 /* summarycommand.cpp */,
 				37D9284B0F21331F001D4494 /* summarysharedcommand.h */,
 				37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
+				211C38370F961E1F00FEE541 /* treegroupscommand.h */,
+				211C38360F961E1F00FEE541 /* treegroupscommand.cpp */,
 				3746109B0F40657600460C57 /* unifracunweightedcommand.h */,
 				3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */,
 				374610760F40645300460C57 /* unifracweightedcommand.h */,
@@ -757,7 +797,6 @@
 				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 */,
@@ -813,7 +852,6 @@
 				EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */,
 				EB1217230F61C9AC004A865F /* sharedkstest.cpp in Sources */,
 				EB6F015B0F6AC1670048081A /* sharedbdiversity.cpp in Sources */,
-				375873E70F7D63E90040F377 /* coverage.cpp in Sources */,
 				375873EC0F7D64520040F377 /* fullmatrix.cpp in Sources */,
 				375873EF0F7D646F0040F377 /* heatmap.cpp in Sources */,
 				375873F20F7D64800040F377 /* heatmapcommand.cpp in Sources */,
@@ -829,6 +867,16 @@
 				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 */,
+				211C38320F961DD400FEE541 /* sharedutilities.cpp in Sources */,
+				211C38380F961E1F00FEE541 /* treegroupscommand.cpp in Sources */,
+				21DDC01B0F97A8FE0060691C /* bootstrapsharedcommand.cpp in Sources */,
+				375AA1390F9E433D008EF9B8 /* readcolumn.cpp in Sources */,
+				375AA13A0F9E433D008EF9B8 /* readotu.cpp in Sources */,
+				375AA13B0F9E433D008EF9B8 /* readphylip.cpp in Sources */,
 			);
 			runOnlyForDeploymentPostprocessing = 0;
 		};
@@ -881,7 +929,7 @@
 					ppc,
 					i386,
 				);
-				GCC_OPTIMIZATION_LEVEL = 0;
+				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_WARN_ABOUT_RETURN_TYPE = YES;
 				GCC_WARN_UNUSED_VARIABLE = YES;
 				PREBINDING = NO;