]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
added bootstrap.shared command and fixed some bugs with heatmap
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index b63f1088509f56feac3399ebf925a6f095d69af3..aaeab8d13b86103bf0b25ab11624342f2bd3433d 100644 (file)
@@ -7,6 +7,9 @@
        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 */; };
+               21DDC01B0F97A8FE0060691C /* bootstrapsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */; };
                370B88070F8A4EE4005AB382 /* getoturepcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */; };
                372E12700F26365B0095CF7E /* readotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E126F0F26365B0095CF7E /* readotucommand.cpp */; };
                372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E12950F263D5A0095CF7E /* readdistcommand.cpp */; };
@@ -18,7 +21,6 @@
                37519A6B0F80E6EB00FED5E8 /* sharedanderbergs.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */; };
                37519AA10F810D0200FED5E8 /* venncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519AA00F810D0200FED5E8 /* venncommand.cpp */; };
                37519AB50F810FAE00FED5E8 /* venn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519AB40F810FAE00FED5E8 /* venn.cpp */; };
-               375873E70F7D63E90040F377 /* coverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873E50F7D63E90040F377 /* coverage.cpp */; };
                375873EC0F7D64520040F377 /* fullmatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873EB0F7D64520040F377 /* fullmatrix.cpp */; };
                375873EF0F7D646F0040F377 /* heatmap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873EE0F7D646F0040F377 /* heatmap.cpp */; };
                375873F20F7D64800040F377 /* heatmapcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873F00F7D64800040F377 /* heatmapcommand.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 */; };
+               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 */; };
                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 */; };
 /* End PBXCopyFilesBuildPhase section */
 
 /* Begin PBXFileReference section */
+               211C38300F961DD400FEE541 /* sharedutilities.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedutilities.cpp; sourceTree = "<group>"; };
+               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>"; };
                372E126E0F26365B0095CF7E /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = "<group>"; };
                37519AA00F810D0200FED5E8 /* venncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = venncommand.cpp; sourceTree = "<group>"; };
                37519AB30F810FAE00FED5E8 /* venn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venn.h; sourceTree = "<group>"; };
                37519AB40F810FAE00FED5E8 /* venn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = venn.cpp; sourceTree = "<group>"; };
-               375873E50F7D63E90040F377 /* coverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = coverage.cpp; sourceTree = "<group>"; };
-               375873E60F7D63E90040F377 /* coverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = coverage.h; sourceTree = "<group>"; };
                375873EA0F7D64520040F377 /* fullmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fullmatrix.h; sourceTree = "<group>"; };
                375873EB0F7D64520040F377 /* fullmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fullmatrix.cpp; sourceTree = "<group>"; };
                375873ED0F7D646F0040F377 /* heatmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmap.h; sourceTree = "<group>"; };
                37D928490F21331F001D4494 /* summarydisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarydisplay.h; sourceTree = "<group>"; };
                37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarysharedcommand.cpp; sourceTree = "<group>"; };
                37D9284B0F21331F001D4494 /* summarysharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarysharedcommand.h; sourceTree = "<group>"; };
-               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>"; };
                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>"; };
+               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>"; };
                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 */,
                                37D9281C0F21331F001D4494 /* sequence.cpp */,
                                37D928210F21331F001D4494 /* shared.h */,
                                37D928200F21331F001D4494 /* shared.cpp */,
+                               211C38310F961DD400FEE541 /* sharedutilities.h */,
+                               211C38300F961DD400FEE541 /* sharedutilities.cpp */,
                                37D928420F21331F001D4494 /* singlelinkage.cpp */,
                                37D928480F21331F001D4494 /* summarydata.h */,
                                37D928490F21331F001D4494 /* summarydisplay.h */,
-                               37D9284C0F21331F001D4494 /* utilities.hpp */,
                                37519AB30F810FAE00FED5E8 /* venn.h */,
                                37519AB40F810FAE00FED5E8 /* venn.cpp */,
                        );
                                EB1216E40F61ACFB004A865F /* bstick.cpp */,
                                37D927C00F21331F001D4494 /* chao1.h */,
                                37D927BF0F21331F001D4494 /* chao1.cpp */,
-                               375873E60F7D63E90040F377 /* coverage.h */,
-                               375873E50F7D63E90040F377 /* coverage.cpp */,
                                EB9303F70F53517300E8EF26 /* geom.h */,
                                EB9303F80F53517300E8EF26 /* geom.cpp */,
                                EB9303E90F534D9400E8EF26 /* logsd.h */,
                                37D927CD0F21331F001D4494 /* command.hpp */,
                                37C1D9710F86506E0059E3F0 /* binsequencecommand.h */,
                                37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */,
+                               21DDC0190F97A8FE0060691C /* bootstrapsharedcommand.h */,
+                               21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */,
                                37D927C40F21331F001D4494 /* clustercommand.h */,
                                37D927C30F21331F001D4494 /* clustercommand.cpp */,
                                37D927C80F21331F001D4494 /* collectcommand.h */,
                                37D928460F21331F001D4494 /* summarycommand.cpp */,
                                37D9284B0F21331F001D4494 /* summarysharedcommand.h */,
                                37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
+                               211C38370F961E1F00FEE541 /* treegroupscommand.h */,
+                               211C38360F961E1F00FEE541 /* treegroupscommand.cpp */,
                                3746109B0F40657600460C57 /* unifracunweightedcommand.h */,
                                3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */,
                                374610760F40645300460C57 /* unifracweightedcommand.h */,
                                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 */,
                                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 */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
                                        ppc,
                                        i386,
                                );
-                               GCC_OPTIMIZATION_LEVEL = 0;
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
                                PREBINDING = NO;