X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=d72922c68689a444662447f4964f9abcec521993;hb=9ca2caadbeac83bb84b3330d9204b1b659d62941;hp=d678294bcf11674e75ccdc40dd068df8300c7750;hpb=44c1323a88b2a697c7047df1b3bb8c59eadd15b1;p=mothur.git

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index d678294..d72922c 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -14,6 +14,9 @@
 		3746107E0F4064D100460C57 /* weighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746107D0F4064D100460C57 /* weighted.cpp */; };
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 		3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */; };
+		374CD63F0F65832000D90B4A /* libshuffcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374CD63E0F65832000D90B4A /* libshuffcommand.cpp */; };
+		374CD6F10F65A4C100D90B4A /* coverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374CD6F00F65A4C100D90B4A /* coverage.cpp */; };
+		3782163D0F616079008E1F6D /* fullmatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3782163C0F616079008E1F6D /* fullmatrix.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 */; };
@@ -93,6 +96,9 @@
 		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 */; };
+		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 */; };
 /* End PBXBuildFile section */
 
 /* Begin PBXCopyFilesBuildPhase section */
@@ -109,6 +115,8 @@
 /* End PBXCopyFilesBuildPhase section */
 
 /* Begin PBXFileReference section */
+		370936DE0F6E7A4A00EB4C2C /* nseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nseqs.h; sourceTree = "<group>"; };
+		3709370A0F6E7FC100EB4C2C /* sharednseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharednseqs.h; sourceTree = "<group>"; };
 		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>"; };
@@ -122,6 +130,12 @@
 		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>"; };
+		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>"; };
+		374CD6EF0F65A4C100D90B4A /* coverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = coverage.h; sourceTree = "<group>"; };
+		374CD6F00F65A4C100D90B4A /* coverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = coverage.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>"; };
 		3792946E0F2E191800B9034A /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = "<group>"; };
@@ -283,11 +297,18 @@
 		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>"; };
+		37E3ED800F4D9D0D00B5DF02 /* mothur.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothur.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; };
+		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>"; };
+		A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlabelcommand.cpp; sourceTree = "<group>"; };
+		A70B53A70F4CD7AD0064797E /* getlabelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlabelcommand.h; sourceTree = "<group>"; };
+		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>"; };
 /* End PBXFileReference section */
 
@@ -346,6 +367,7 @@
 				37D927E90F21331F001D4494 /* kmer.cpp */,
 				37D927EC0F21331F001D4494 /* kmerdb.hpp */,
 				37D927EB0F21331F001D4494 /* kmerdb.cpp */,
+				37E3ED800F4D9D0D00B5DF02 /* mothur.h */,
 				37D927EF0F21331F001D4494 /* mothur.cpp */,
 				37D927F10F21331F001D4494 /* nameassignment.hpp */,
 				37D927F00F21331F001D4494 /* nameassignment.cpp */,
@@ -366,8 +388,6 @@
 				37D928210F21331F001D4494 /* shared.h */,
 				37D928200F21331F001D4494 /* shared.cpp */,
 				37D928420F21331F001D4494 /* singlelinkage.cpp */,
-				37D928450F21331F001D4494 /* sparsematrix.hpp */,
-				37D928440F21331F001D4494 /* sparsematrix.cpp */,
 				37D928480F21331F001D4494 /* summarydata.h */,
 				37D928490F21331F001D4494 /* summarydisplay.h */,
 				37D9284C0F21331F001D4494 /* utilities.hpp */,
@@ -395,10 +415,13 @@
 				37D927BB0F21331F001D4494 /* bootstrap.cpp */,
 				37D927C00F21331F001D4494 /* chao1.h */,
 				37D927BF0F21331F001D4494 /* chao1.cpp */,
+				374CD6EF0F65A4C100D90B4A /* coverage.h */,
+				374CD6F00F65A4C100D90B4A /* coverage.cpp */,
 				37D927E80F21331F001D4494 /* jackknife.h */,
 				37D927E70F21331F001D4494 /* jackknife.cpp */,
 				37D927F50F21331F001D4494 /* npshannon.h */,
 				37D927F40F21331F001D4494 /* npshannon.cpp */,
+				370936DE0F6E7A4A00EB4C2C /* nseqs.h */,
 				379294880F2E258500B9034A /* parsimony.h */,
 				379294890F2E258500B9034A /* parsimony.cpp */,
 				37D928020F21331F001D4494 /* rarecalc.h */,
@@ -415,6 +438,7 @@
 				37D9282A0F21331F001D4494 /* sharedjclass.cpp */,
 				37D9282D0F21331F001D4494 /* sharedjest.h */,
 				37D9282C0F21331F001D4494 /* sharedjest.cpp */,
+				3709370A0F6E7FC100EB4C2C /* sharednseqs.h */,
 				37D928350F21331F001D4494 /* sharedsobs.h */,
 				37D928340F21331F001D4494 /* sharedsobs.cpp */,
 				37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */,
@@ -425,8 +449,8 @@
 				37D928380F21331F001D4494 /* sharedsorclass.cpp */,
 				37D9283B0F21331F001D4494 /* sharedsorest.h */,
 				37D9283A0F21331F001D4494 /* sharedsorest.cpp */,
-				37D9283C0F21331F001D4494 /* sharedthetan.cpp */,
 				37D9283D0F21331F001D4494 /* sharedthetan.h */,
+				37D9283C0F21331F001D4494 /* sharedthetan.cpp */,
 				37D9283F0F21331F001D4494 /* sharedthetayc.h */,
 				37D9283E0F21331F001D4494 /* sharedthetayc.cpp */,
 				37D928410F21331F001D4494 /* simpson.h */,
@@ -454,10 +478,18 @@
 				37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */,
 				37B28F660F27590100808A62 /* deconvolutecommand.h */,
 				37B28F670F27590100808A62 /* deconvolutecommand.cpp */,
+				A70B53A50F4CD7AD0064797E /* getgroupcommand.h */,
+				A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */,
+				A70B53A70F4CD7AD0064797E /* getlabelcommand.h */,
+				A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */,
+				A70B53A90F4CD7AD0064797E /* getlinecommand.h */,
+				A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */,
 				37D927E40F21331F001D4494 /* helpcommand.h */,
 				37D927E30F21331F001D4494 /* helpcommand.cpp */,
-				37D927F20F21331F001D4494 /* nocommand.cpp */,
+				374CD63D0F65832000D90B4A /* libshuffcommand.h */,
+				374CD63E0F65832000D90B4A /* libshuffcommand.cpp */,
 				37D927F30F21331F001D4494 /* nocommand.h */,
+				37D927F20F21331F001D4494 /* nocommand.cpp */,
 				37D927FA0F21331F001D4494 /* parselistcommand.h */,
 				37D927F90F21331F001D4494 /* parselistcommand.cpp */,
 				3792946E0F2E191800B9034A /* parsimonycommand.h */,
@@ -494,6 +526,8 @@
 				37D927D50F21331F001D4494 /* datavector.hpp */,
 				37D927DC0F21331F001D4494 /* fastamap.h */,
 				37D927DB0F21331F001D4494 /* fastamap.cpp */,
+				3782163B0F616079008E1F6D /* fullmatrix.h */,
+				3782163C0F616079008E1F6D /* fullmatrix.cpp */,
 				37D927E20F21331F001D4494 /* groupmap.h */,
 				37D927E10F21331F001D4494 /* groupmap.cpp */,
 				37D927EE0F21331F001D4494 /* listvector.hpp */,
@@ -512,6 +546,8 @@
 				37D928300F21331F001D4494 /* sharedrabundvector.cpp */,
 				37D928330F21331F001D4494 /* sharedsabundvector.h */,
 				37D928320F21331F001D4494 /* sharedsabundvector.cpp */,
+				37D928450F21331F001D4494 /* sparsematrix.hpp */,
+				37D928440F21331F001D4494 /* sparsematrix.cpp */,
 				37AD4DB90F28E2FE00AA2D49 /* tree.h */,
 				37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */,
 				379293C10F2DE73400B9034A /* treemap.h */,
@@ -673,6 +709,12 @@
 				374610830F40652400460C57 /* unweighted.cpp in Sources */,
 				3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */,
 				37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */,
+				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 */,
+				374CD6F10F65A4C100D90B4A /* coverage.cpp in Sources */,
 			);
 			runOnlyForDeploymentPostprocessing = 0;
 		};
@@ -686,7 +728,7 @@
 				GCC_DYNAMIC_NO_PIC = NO;
 				GCC_ENABLE_FIX_AND_CONTINUE = YES;
 				GCC_MODEL_TUNING = G5;
-				GCC_OPTIMIZATION_LEVEL = 0;
+				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_PREPROCESSOR_DEFINITIONS = (
 					"_GLIBCXX_DEBUG=1",
 					"_GLIBCXX_DEBUG_PEDANTIC=1",
@@ -702,6 +744,7 @@
 			buildSettings = {
 				DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
 				GCC_MODEL_TUNING = G5;
+				GCC_OPTIMIZATION_LEVEL = 3;
 				INSTALL_PATH = /usr/local/bin;
 				PRODUCT_NAME = mothur;
 			};
@@ -713,6 +756,7 @@
 				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 = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
 			};
@@ -728,6 +772,7 @@
 				GCC_OPTIMIZATION_LEVEL = 0;
 				GCC_WARN_ABOUT_RETURN_TYPE = YES;
 				GCC_WARN_UNUSED_VARIABLE = YES;
+				INSTALL_MODE_FLAG = "a-w,a+rX";
 				PREBINDING = NO;
 				SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
 			};