]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
fixed bugs for 1.8
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index efe0beb43d14d80310535868942a7f4ba1321626..21dbf8dfbb074de24a0b70e523bd95e56d414695 100644 (file)
                7EC3D4550FA0FFF900338DA5 /* coverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7EC3D4500FA0FFF900338DA5 /* coverage.cpp */; };
                7EC3D4560FA0FFF900338DA5 /* whittaker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */; };
                8DD76F6A0486A84900D96B5E /* Mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6859E8B029090EE04C91782 /* Mothur.1 */; };
+               A7027F2810DFF86D00BF45FE /* preclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7027F2710DFF86D00BF45FE /* preclustercommand.cpp */; };
+               A704E8A31106045D00870157 /* otuhierarchycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A704E8A21106045D00870157 /* otuhierarchycommand.cpp */; };
+               A70B00C8110885EB002F453A /* setdircommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B00C7110885EB002F453A /* setdircommand.cpp */; };
                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 */; };
                A70DECD91063D8B40057C03C /* secondarystructurecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */; };
+               A727E84A10D14568001A8432 /* readblast.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727E84910D14568001A8432 /* readblast.cpp */; };
                A7283FF81056CAE100D0CC69 /* chimeracheckrdp.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */; };
                A729ACD010848E6100139801 /* hclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A729ACCF10848E6100139801 /* hclustercommand.cpp */; };
                A729ACE410849BBE00139801 /* hcluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A729ACE310849BBE00139801 /* hcluster.cpp */; };
                A787821110A0AAE70086103D /* bayesian.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A787821010A0AAE70086103D /* bayesian.cpp */; };
                A78782AB10A1B1CB0086103D /* alignmentdb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A78782AA10A1B1CB0086103D /* alignmentdb.cpp */; };
                A787844510A1EBDD0086103D /* knn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A787844410A1EBDD0086103D /* knn.cpp */; };
+               A794201111107897003AECCD /* distancedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A794200F11107897003AECCD /* distancedb.cpp */; };
                A7B04493106CC3E60046FC83 /* chimeraslayer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */; };
                A7B0450E106CEEC90046FC83 /* slayer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7B0450D106CEEC90046FC83 /* slayer.cpp */; };
+               A7D176CF10F2558500159497 /* pcacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D176CE10F2558500159497 /* pcacommand.cpp */; };
+               A7D86C7D10FE09AB00865661 /* formatcolumn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D86C7C10FE09AB00865661 /* formatcolumn.cpp */; };
+               A7D86C8C10FE09FE00865661 /* formatphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D86C8B10FE09FE00865661 /* formatphylip.cpp */; };
+               A7E0AAB610D2886D00CF407B /* mgclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E0AAB510D2886D00CF407B /* mgclustercommand.cpp */; };
                A7E4A783106913F900688F62 /* getsharedotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E4A782106913F900688F62 /* getsharedotucommand.cpp */; };
                A7E4A824106A9AD700688F62 /* maligner.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E4A823106A9AD700688F62 /* maligner.cpp */; };
                A7F5759710CEBC0600E20E47 /* libreadline.a in Frameworks */ = {isa = PBXBuildFile; fileRef = A7F5759610CEBC0600E20E47 /* libreadline.a */; };
                7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = SOURCE_ROOT; };
                7EC3D4540FA0FFF900338DA5 /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = SOURCE_ROOT; };
                8DD76F6C0486A84900D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; };
+               A7027F2610DFF86D00BF45FE /* preclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = preclustercommand.h; sourceTree = SOURCE_ROOT; };
+               A7027F2710DFF86D00BF45FE /* preclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = preclustercommand.cpp; sourceTree = SOURCE_ROOT; };
+               A704E8A11106045D00870157 /* otuhierarchycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = otuhierarchycommand.h; sourceTree = SOURCE_ROOT; };
+               A704E8A21106045D00870157 /* otuhierarchycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = otuhierarchycommand.cpp; sourceTree = SOURCE_ROOT; };
+               A70B00C6110885EB002F453A /* setdircommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setdircommand.h; sourceTree = SOURCE_ROOT; };
+               A70B00C7110885EB002F453A /* setdircommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setdircommand.cpp; sourceTree = SOURCE_ROOT; };
                A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getgroupcommand.cpp; sourceTree = SOURCE_ROOT; };
                A70B53A50F4CD7AD0064797E /* getgroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupcommand.h; sourceTree = SOURCE_ROOT; };
                A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlabelcommand.cpp; sourceTree = SOURCE_ROOT; };
                A70B53A70F4CD7AD0064797E /* getlabelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlabelcommand.h; sourceTree = SOURCE_ROOT; };
-               A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlinecommand.cpp; sourceTree = SOURCE_ROOT; };
-               A70B53A90F4CD7AD0064797E /* getlinecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlinecommand.h; sourceTree = SOURCE_ROOT; };
                A70DECD71063D8B40057C03C /* secondarystructurecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = secondarystructurecommand.h; sourceTree = SOURCE_ROOT; };
                A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = secondarystructurecommand.cpp; sourceTree = SOURCE_ROOT; };
+               A727E84810D14568001A8432 /* readblast.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readblast.h; sourceTree = SOURCE_ROOT; };
+               A727E84910D14568001A8432 /* readblast.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readblast.cpp; sourceTree = SOURCE_ROOT; };
                A7283FF61056CAE100D0CC69 /* chimeracheckrdp.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeracheckrdp.h; sourceTree = SOURCE_ROOT; };
                A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeracheckrdp.cpp; sourceTree = SOURCE_ROOT; };
                A729ACCE10848E6100139801 /* hclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hclustercommand.h; sourceTree = SOURCE_ROOT; };
                A78782AA10A1B1CB0086103D /* alignmentdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignmentdb.cpp; sourceTree = SOURCE_ROOT; };
                A787844310A1EBDD0086103D /* knn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = knn.h; sourceTree = SOURCE_ROOT; };
                A787844410A1EBDD0086103D /* knn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = knn.cpp; sourceTree = SOURCE_ROOT; };
+               A794200F11107897003AECCD /* distancedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancedb.cpp; sourceTree = SOURCE_ROOT; };
+               A794201011107897003AECCD /* distancedb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = distancedb.hpp; sourceTree = SOURCE_ROOT; };
                A7B04491106CC3E60046FC83 /* chimeraslayer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraslayer.h; sourceTree = SOURCE_ROOT; };
                A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraslayer.cpp; sourceTree = SOURCE_ROOT; };
                A7B0450C106CEEC90046FC83 /* slayer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slayer.h; sourceTree = SOURCE_ROOT; };
                A7B0450D106CEEC90046FC83 /* slayer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slayer.cpp; sourceTree = SOURCE_ROOT; };
+               A7D176CD10F2558500159497 /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = SOURCE_ROOT; };
+               A7D176CE10F2558500159497 /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = SOURCE_ROOT; };
+               A7D86C6A10FE084300865661 /* formatmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatmatrix.h; sourceTree = SOURCE_ROOT; };
+               A7D86C7B10FE09AB00865661 /* formatcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatcolumn.h; sourceTree = SOURCE_ROOT; };
+               A7D86C7C10FE09AB00865661 /* formatcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = formatcolumn.cpp; sourceTree = SOURCE_ROOT; };
+               A7D86C8A10FE09FE00865661 /* formatphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatphylip.h; sourceTree = SOURCE_ROOT; };
+               A7D86C8B10FE09FE00865661 /* formatphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = formatphylip.cpp; sourceTree = SOURCE_ROOT; };
+               A7E0AAB410D2886D00CF407B /* mgclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mgclustercommand.h; sourceTree = SOURCE_ROOT; };
+               A7E0AAB510D2886D00CF407B /* mgclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mgclustercommand.cpp; sourceTree = SOURCE_ROOT; };
                A7E4A781106913F900688F62 /* getsharedotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsharedotucommand.h; sourceTree = SOURCE_ROOT; };
                A7E4A782106913F900688F62 /* getsharedotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsharedotucommand.cpp; sourceTree = SOURCE_ROOT; };
                A7E4A822106A9AD700688F62 /* maligner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = maligner.h; sourceTree = SOURCE_ROOT; };
                3796441D0FB9B9650081FDB6 /* read */ = {
                        isa = PBXGroup;
                        children = (
+                               A7D86C6A10FE084300865661 /* formatmatrix.h */,
+                               A7D86C7B10FE09AB00865661 /* formatcolumn.h */,
+                               A7D86C7C10FE09AB00865661 /* formatcolumn.cpp */,
+                               A7D86C8A10FE09FE00865661 /* formatphylip.h */,
+                               A7D86C8B10FE09FE00865661 /* formatphylip.cpp */,
+                               A727E84810D14568001A8432 /* readblast.h */,
+                               A727E84910D14568001A8432 /* readblast.cpp */,
                                A751ACE81098B283003D0911 /* readcluster.h */,
                                A751ACE91098B283003D0911 /* readcluster.cpp */,
                                375AA1340F9E433D008EF9B8 /* readcolumn.h */,
                                A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */,
                                A70B53A70F4CD7AD0064797E /* getlabelcommand.h */,
                                A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */,
-                               A70B53A90F4CD7AD0064797E /* getlinecommand.h */,
-                               A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */,
                                A73329CD1083B3B3003B10C5 /* getlistcountcommand.h */,
                                A73329CE1083B3B3003B10C5 /* getlistcountcommand.cpp */,
                                370B88050F8A4EE4005AB382 /* getoturepcommand.h */,
                                21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */,
                                7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */,
                                7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */,
+                               A7E0AAB410D2886D00CF407B /* mgclustercommand.h */,
+                               A7E0AAB510D2886D00CF407B /* mgclustercommand.cpp */,
                                375873F70F7D649C0040F377 /* nocommands.h */,
                                375873F60F7D649C0040F377 /* nocommands.cpp */,
+                               A704E8A11106045D00870157 /* otuhierarchycommand.h */,
+                               A704E8A21106045D00870157 /* otuhierarchycommand.cpp */,
                                3792946E0F2E191800B9034A /* parsimonycommand.h */,
                                3792946F0F2E191800B9034A /* parsimonycommand.cpp */,
+                               A7D176CD10F2558500159497 /* pcacommand.h */,
+                               A7D176CE10F2558500159497 /* pcacommand.cpp */,
                                A773808E10B6EFD1002A6A61 /* phylotypecommand.h */,
                                A773808F10B6EFD1002A6A61 /* phylotypecommand.cpp */,
+                               A7027F2610DFF86D00BF45FE /* preclustercommand.h */,
+                               A7027F2710DFF86D00BF45FE /* preclustercommand.cpp */,
                                37D927FE0F21331F001D4494 /* quitcommand.h */,
                                37D927FD0F21331F001D4494 /* quitcommand.cpp */,
                                37D928080F21331F001D4494 /* rarefactcommand.h */,
                                371B30B20FD7EE67000414CA /* screenseqscommand.cpp */,
                                3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */,
                                3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */,
+                               A70B00C6110885EB002F453A /* setdircommand.h */,
+                               A70B00C7110885EB002F453A /* setdircommand.cpp */,
                                37D928270F21331F001D4494 /* sharedcommand.h */,
                                37D928260F21331F001D4494 /* sharedcommand.cpp */,
                                37D928470F21331F001D4494 /* summarycommand.h */,
                                37D927D40F21331F001D4494 /* database.hpp */,
                                37D927D30F21331F001D4494 /* database.cpp */,
                                37D927D50F21331F001D4494 /* datavector.hpp */,
+                               A794201011107897003AECCD /* distancedb.hpp */,
+                               A794200F11107897003AECCD /* distancedb.cpp */,
                                37D927DC0F21331F001D4494 /* fastamap.h */,
                                37D927DB0F21331F001D4494 /* fastamap.cpp */,
                                375873EA0F7D64520040F377 /* fullmatrix.h */,
                                37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */,
                                A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */,
                                A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */,
-                               A70B53AC0F4CD7AD0064797E /* getlinecommand.cpp in Sources */,
                                EB9303EB0F534D9400E8EF26 /* logsd.cpp in Sources */,
                                EB9303F90F53517300E8EF26 /* geom.cpp in Sources */,
                                EB6E68190F5F1C780044E17B /* qstat.cpp in Sources */,
                                A787844510A1EBDD0086103D /* knn.cpp in Sources */,
                                A773805F10B6D6FC002A6A61 /* taxonomyequalizer.cpp in Sources */,
                                A773809010B6EFD1002A6A61 /* phylotypecommand.cpp in Sources */,
+                               A727E84A10D14568001A8432 /* readblast.cpp in Sources */,
+                               A7E0AAB610D2886D00CF407B /* mgclustercommand.cpp in Sources */,
+                               A7027F2810DFF86D00BF45FE /* preclustercommand.cpp in Sources */,
+                               A7D176CF10F2558500159497 /* pcacommand.cpp in Sources */,
+                               A7D86C7D10FE09AB00865661 /* formatcolumn.cpp in Sources */,
+                               A7D86C8C10FE09FE00865661 /* formatphylip.cpp in Sources */,
+                               A704E8A31106045D00870157 /* otuhierarchycommand.cpp in Sources */,
+                               A70B00C8110885EB002F453A /* setdircommand.cpp in Sources */,
+                               A794201111107897003AECCD /* distancedb.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
                1DEB923608733DC60010E9CD /* Debug */ = {
                        isa = XCBuildConfiguration;
                        buildSettings = {
+                               ARCHS = "$(ARCHS_STANDARD_64_BIT_PRE_XCODE_3_1)";
+                               ARCHS_STANDARD_64_BIT_PRE_XCODE_3_1 = x86_64;
                                GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                1DEB923708733DC60010E9CD /* Release */ = {
                        isa = XCBuildConfiguration;
                        buildSettings = {
-                               ARCHS = (
-                                       ppc,
-                                       i386,
-                               );
+                               ARCHS = "$(ARCHS_STANDARD_64_BIT_PRE_XCODE_3_1)";
+                               ARCHS_STANDARD_64_BIT_PRE_XCODE_3_1 = x86_64;
                                GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_MISSING_PROTOTYPES = YES;