X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=b34805bab97accaebdd0b539420c7f0dfd4ca03d;hb=eb1c88346fb246e95a6b38935b103f95e38b82ca;hp=e9446df8c629b83c5c065f84b2a768414fe372e8;hpb=8fd4a602269974e6548f4a387dddd6bd80a999ab;p=mothur.git

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index e9446df..b34805b 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -14,8 +14,6 @@
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-		3782163D0F616079008E1F6D /* fullmatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3782163C0F616079008E1F6D /* fullmatrix.cpp */; };
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 		3792948A0F2E258500B9034A /* parsimony.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379294890F2E258500B9034A /* parsimony.cpp */; };
@@ -51,7 +49,6 @@
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 		37D9286F0F21331F001D4494 /* mothur.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927EF0F21331F001D4494 /* mothur.cpp */; };
 		37D928700F21331F001D4494 /* nameassignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F00F21331F001D4494 /* nameassignment.cpp */; };
-		37D928710F21331F001D4494 /* nocommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F20F21331F001D4494 /* nocommand.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 */; };
@@ -98,6 +95,14 @@
 		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 */; };
+		EBE2A41E0F7D5C6100A54BF8 /* jackknife2.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EBE2A41D0F7D5C6100A54BF8 /* jackknife2.cpp */; };
 /* End PBXBuildFile section */
 
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@@ -127,10 +132,6 @@
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-		374CD63D0F65832000D90B4A /* libshuffcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuffcommand.h; sourceTree = "<group>"; };
-		374CD63E0F65832000D90B4A /* libshuffcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuffcommand.cpp; sourceTree = "<group>"; };
-		3782163B0F616079008E1F6D /* fullmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fullmatrix.h; sourceTree = "<group>"; };
-		3782163C0F616079008E1F6D /* fullmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fullmatrix.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>"; };
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@@ -205,8 +206,6 @@
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 		37D927F00F21331F001D4494 /* nameassignment.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nameassignment.cpp; sourceTree = "<group>"; };
 		37D927F10F21331F001D4494 /* nameassignment.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nameassignment.hpp; sourceTree = "<group>"; };
-		37D927F20F21331F001D4494 /* nocommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nocommand.cpp; sourceTree = "<group>"; };
-		37D927F30F21331F001D4494 /* nocommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nocommand.h; sourceTree = "<group>"; };
 		37D927F40F21331F001D4494 /* npshannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = npshannon.cpp; sourceTree = "<group>"; };
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 		37D927F60F21331F001D4494 /* observable.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = observable.h; sourceTree = "<group>"; };
@@ -305,6 +304,22 @@
 		A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlinecommand.cpp; sourceTree = "<group>"; };
 		A70B53A90F4CD7AD0064797E /* getlinecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlinecommand.h; sourceTree = "<group>"; };
 		C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = "<group>"; };
+		EB1216860F619B83004A865F /* bergerparker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bergerparker.h; sourceTree = "<group>"; };
+		EB1216870F619B83004A865F /* bergerparker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bergerparker.cpp; sourceTree = "<group>"; };
+		EB1216E30F61ACFB004A865F /* bstick.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bstick.h; sourceTree = "<group>"; };
+		EB1216E40F61ACFB004A865F /* bstick.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bstick.cpp; sourceTree = "<group>"; };
+		EB1217210F61C9AC004A865F /* sharedkstest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkstest.h; sourceTree = "<group>"; };
+		EB1217220F61C9AC004A865F /* sharedkstest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkstest.cpp; sourceTree = "<group>"; };
+		EB6E68170F5F1C780044E17B /* qstat.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qstat.h; sourceTree = "<group>"; };
+		EB6E68180F5F1C780044E17B /* qstat.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qstat.cpp; sourceTree = "<group>"; };
+		EB6F01590F6AC1670048081A /* sharedbdiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedbdiversity.h; sourceTree = "<group>"; };
+		EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbdiversity.cpp; sourceTree = "<group>"; };
+		EB9303E90F534D9400E8EF26 /* logsd.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = logsd.h; sourceTree = "<group>"; };
+		EB9303EA0F534D9400E8EF26 /* logsd.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = logsd.cpp; sourceTree = "<group>"; };
+		EB9303F70F53517300E8EF26 /* geom.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = geom.h; sourceTree = "<group>"; };
+		EB9303F80F53517300E8EF26 /* geom.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = geom.cpp; sourceTree = "<group>"; };
+		EBE2A41C0F7D5C5C00A54BF8 /* jackknife2.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = jackknife2.h; path = ../jackknife2.h; sourceTree = SOURCE_ROOT; };
+		EBE2A41D0F7D5C6100A54BF8 /* jackknife2.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = jackknife2.cpp; path = ../jackknife2.cpp; sourceTree = SOURCE_ROOT; };
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 /* Begin PBXFrameworksBuildPhase section */
@@ -383,6 +398,8 @@
 				37D928210F21331F001D4494 /* shared.h */,
 				37D928200F21331F001D4494 /* shared.cpp */,
 				37D928420F21331F001D4494 /* singlelinkage.cpp */,
+				37D928450F21331F001D4494 /* sparsematrix.hpp */,
+				37D928440F21331F001D4494 /* sparsematrix.cpp */,
 				37D928480F21331F001D4494 /* summarydata.h */,
 				37D928490F21331F001D4494 /* summarydisplay.h */,
 				37D9284C0F21331F001D4494 /* utilities.hpp */,
@@ -410,6 +427,22 @@
 				37D927BB0F21331F001D4494 /* bootstrap.cpp */,
 				37D927C00F21331F001D4494 /* chao1.h */,
 				37D927BF0F21331F001D4494 /* chao1.cpp */,
+				EB9303F70F53517300E8EF26 /* geom.h */,
+				EB9303F80F53517300E8EF26 /* geom.cpp */,
+				EB6E68170F5F1C780044E17B /* qstat.h */,
+				EB6E68180F5F1C780044E17B /* qstat.cpp */,
+				EB9303E90F534D9400E8EF26 /* logsd.h */,
+				EB9303EA0F534D9400E8EF26 /* logsd.cpp */,
+				EB1216860F619B83004A865F /* bergerparker.h */,
+				EB1216870F619B83004A865F /* bergerparker.cpp */,
+				EB1216E30F61ACFB004A865F /* bstick.h */,
+				EB1216E40F61ACFB004A865F /* bstick.cpp */,
+				EB1217210F61C9AC004A865F /* sharedkstest.h */,
+				EB1217220F61C9AC004A865F /* sharedkstest.cpp */,
+				EB6F01590F6AC1670048081A /* sharedbdiversity.h */,
+				EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */,
+				EBE2A41C0F7D5C5C00A54BF8 /* jackknife2.h */,
+				EBE2A41D0F7D5C6100A54BF8 /* jackknife2.cpp */,
 				37D927E80F21331F001D4494 /* jackknife.h */,
 				37D927E70F21331F001D4494 /* jackknife.cpp */,
 				37D927F50F21331F001D4494 /* npshannon.h */,
@@ -477,10 +510,6 @@
 				A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */,
 				37D927E40F21331F001D4494 /* helpcommand.h */,
 				37D927E30F21331F001D4494 /* helpcommand.cpp */,
-				374CD63D0F65832000D90B4A /* libshuffcommand.h */,
-				374CD63E0F65832000D90B4A /* libshuffcommand.cpp */,
-				37D927F30F21331F001D4494 /* nocommand.h */,
-				37D927F20F21331F001D4494 /* nocommand.cpp */,
 				37D927FA0F21331F001D4494 /* parselistcommand.h */,
 				37D927F90F21331F001D4494 /* parselistcommand.cpp */,
 				3792946E0F2E191800B9034A /* parsimonycommand.h */,
@@ -517,8 +546,6 @@
 				37D927D50F21331F001D4494 /* datavector.hpp */,
 				37D927DC0F21331F001D4494 /* fastamap.h */,
 				37D927DB0F21331F001D4494 /* fastamap.cpp */,
-				3782163B0F616079008E1F6D /* fullmatrix.h */,
-				3782163C0F616079008E1F6D /* fullmatrix.cpp */,
 				37D927E20F21331F001D4494 /* groupmap.h */,
 				37D927E10F21331F001D4494 /* groupmap.cpp */,
 				37D927EE0F21331F001D4494 /* listvector.hpp */,
@@ -537,8 +564,6 @@
 				37D928300F21331F001D4494 /* sharedrabundvector.cpp */,
 				37D928330F21331F001D4494 /* sharedsabundvector.h */,
 				37D928320F21331F001D4494 /* sharedsabundvector.cpp */,
-				37D928450F21331F001D4494 /* sparsematrix.hpp */,
-				37D928440F21331F001D4494 /* sparsematrix.cpp */,
 				37AD4DB90F28E2FE00AA2D49 /* tree.h */,
 				37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */,
 				379293C10F2DE73400B9034A /* treemap.h */,
@@ -642,7 +667,6 @@
 				37D9286E0F21331F001D4494 /* listvector.cpp in Sources */,
 				37D9286F0F21331F001D4494 /* mothur.cpp in Sources */,
 				37D928700F21331F001D4494 /* nameassignment.cpp in Sources */,
-				37D928710F21331F001D4494 /* nocommand.cpp in Sources */,
 				37D928720F21331F001D4494 /* npshannon.cpp in Sources */,
 				37D928730F21331F001D4494 /* ordervector.cpp in Sources */,
 				37D928740F21331F001D4494 /* parselistcommand.cpp in Sources */,
@@ -703,8 +727,14 @@
 				A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */,
 				A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */,
 				A70B53AC0F4CD7AD0064797E /* getlinecommand.cpp in Sources */,
-				3782163D0F616079008E1F6D /* fullmatrix.cpp in Sources */,
-				374CD63F0F65832000D90B4A /* libshuffcommand.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 */,
+				EBE2A41E0F7D5C6100A54BF8 /* jackknife2.cpp in Sources */,
 			);
 			runOnlyForDeploymentPostprocessing = 0;
 		};
@@ -718,7 +748,7 @@
 				GCC_DYNAMIC_NO_PIC = NO;
 				GCC_ENABLE_FIX_AND_CONTINUE = YES;
 				GCC_MODEL_TUNING = G5;
-				GCC_OPTIMIZATION_LEVEL = 3;
+				GCC_OPTIMIZATION_LEVEL = 0;
 				GCC_PREPROCESSOR_DEFINITIONS = (
 					"_GLIBCXX_DEBUG=1",
 					"_GLIBCXX_DEBUG_PEDANTIC=1",
@@ -734,7 +764,6 @@
 			buildSettings = {
 				DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
 				GCC_MODEL_TUNING = G5;
-				GCC_OPTIMIZATION_LEVEL = 3;
 				INSTALL_PATH = /usr/local/bin;
 				PRODUCT_NAME = mothur;
 			};
@@ -746,7 +775,6 @@
 				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_WARN_ABOUT_RETURN_TYPE = YES;
 				GCC_WARN_UNUSED_VARIABLE = YES;
-				INSTALL_MODE_FLAG = "a-w,a+rX";
 				PREBINDING = NO;
 				SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
 			};
@@ -762,7 +790,6 @@
 				GCC_OPTIMIZATION_LEVEL = 0;
 				GCC_WARN_ABOUT_RETURN_TYPE = YES;
 				GCC_WARN_UNUSED_VARIABLE = YES;
-				INSTALL_MODE_FLAG = "a-w,a+rX";
 				PREBINDING = NO;
 				SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
 			};