]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
added out.hierarchy command
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index fda0adcb25e16f7388a8aad0dd67cf8b37373e03..a44e1f3d7e3e824a58e4b5c0eaa4d9c960b1deb8 100644 (file)
@@ -72,7 +72,6 @@
                379293C30F2DE73400B9034A /* treemap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379293C20F2DE73400B9034A /* treemap.cpp */; };
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+               A7027F2810DFF86D00BF45FE /* preclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7027F2710DFF86D00BF45FE /* preclustercommand.cpp */; };
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+               A70DECD91063D8B40057C03C /* secondarystructurecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */; };
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                A7283FF81056CAE100D0CC69 /* chimeracheckrdp.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */; };
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+               A7B0450D106CEEC90046FC83 /* slayer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slayer.cpp; sourceTree = SOURCE_ROOT; };
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                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 = SOURCE_ROOT; };
                EB1216870F619B83004A865F /* bergerparker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bergerparker.cpp; sourceTree = SOURCE_ROOT; };
                        isa = PBXFrameworksBuildPhase;
                        buildActionMask = 2147483647;
                        files = (
+                               A7F5759710CEBC0600E20E47 /* libreadline.a in Frameworks */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
                                373C68DB0FC1C38D00137ACD /* blastalign.cpp */,
                                37D928A60F2133C0001D4494 /* calculators */,
                                374F2FE81006346600E97C66 /* chimera */,
+                               A787811210A073F40086103D /* classifiers */,
                                37D927C20F21331F001D4494 /* cluster.hpp */,
                                37D927C10F21331F001D4494 /* cluster.cpp */,
                                37D928A90F2133E5001D4494 /* commands */,
                                37D927DF0F21331F001D4494 /* globaldata.cpp */,
                                373C68BB0FC1C1A600137ACD /* gotohoverlap.hpp */,
                                373C68BA0FC1C1A600137ACD /* gotohoverlap.cpp */,
+                               A729ACE210849BBE00139801 /* hcluster.h */,
+                               A729ACE310849BBE00139801 /* hcluster.cpp */,
                                375873ED0F7D646F0040F377 /* heatmap.h */,
                                375873EE0F7D646F0040F377 /* heatmap.cpp */,
                                378598720FDD4C1500EF9D03 /* heatmapsim.h */,
                                7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */,
                                37E3ED800F4D9D0D00B5DF02 /* mothur.h */,
                                37D927EF0F21331F001D4494 /* mothur.cpp */,
-                               37D927F10F21331F001D4494 /* nameassignment.hpp */,
-                               37D927F00F21331F001D4494 /* nameassignment.cpp */,
                                373C691E0FC1C98600137ACD /* nast.hpp */,
                                373C691D0FC1C98600137ACD /* nast.cpp */,
                                373C692A0FC1C9EB00137ACD /* nastreport.hpp */,
                                37D928490F21331F001D4494 /* summarydisplay.h */,
                                37519AB30F810FAE00FED5E8 /* venn.h */,
                                37519AB40F810FAE00FED5E8 /* venn.cpp */,
+                               A7F5759610CEBC0600E20E47 /* libreadline.a */,
                        );
                        name = Source;
                        sourceTree = "<group>";
                                A75B887B104C16860083C454 /* ccode.cpp */,
                                A7283FF61056CAE100D0CC69 /* chimeracheckrdp.h */,
                                A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */,
+                               A7B04491106CC3E60046FC83 /* chimeraslayer.h */,
+                               A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */,
                                372A55531017922B00C5194B /* decalc.h */,
                                372A55541017922B00C5194B /* decalc.cpp */,
+                               A7E4A822106A9AD700688F62 /* maligner.h */,
+                               A7E4A823106A9AD700688F62 /* maligner.cpp */,
                                374F301110063B6F00E97C66 /* pintail.h */,
                                374F301210063B6F00E97C66 /* pintail.cpp */,
+                               A7B0450C106CEEC90046FC83 /* slayer.h */,
+                               A7B0450D106CEEC90046FC83 /* slayer.cpp */,
                        );
                        name = chimera;
                        sourceTree = "<group>";
                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 */,
                                375AA1330F9E433D008EF9B8 /* readcolumn.cpp */,
                                37D928130F21331F001D4494 /* readmatrix.hpp */,
                                377326630FAF16E0007ABB8B /* consensuscommand.cpp */,
                                379D3D4F0FF90E090068C1C0 /* chimeraseqscommand.h */,
                                379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */,
+                               A7861476109F5FA00010AAAF /* classifyseqscommand.h */,
+                               A7861477109F5FA00010AAAF /* classifyseqscommand.cpp */,
                                37B28F660F27590100808A62 /* deconvolutecommand.h */,
                                37B28F670F27590100808A62 /* deconvolutecommand.cpp */,
                                37C753CC0FB3415200DBD02E /* distancecommand.h */,
                                A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */,
                                A70B53A90F4CD7AD0064797E /* getlinecommand.h */,
                                A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */,
+                               A73329CD1083B3B3003B10C5 /* getlistcountcommand.h */,
+                               A73329CE1083B3B3003B10C5 /* getlistcountcommand.cpp */,
                                370B88050F8A4EE4005AB382 /* getoturepcommand.h */,
                                370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */,
                                3749273D0FD5956B0031C06B /* getrabundcommand.h */,
                                3749271C0FD58C840031C06B /* getsabundcommand.cpp */,
                                37B73CA41004D89A008C4B41 /* getseqscommand.h */,
                                37B73CA51004D89A008C4B41 /* getseqscommand.cpp */,
+                               A7E4A781106913F900688F62 /* getsharedotucommand.h */,
+                               A7E4A782106913F900688F62 /* getsharedotucommand.cpp */,
+                               A729ACCE10848E6100139801 /* hclustercommand.h */,
+                               A729ACCF10848E6100139801 /* hclustercommand.cpp */,
                                375873F10F7D64800040F377 /* heatmapcommand.h */,
                                375873F00F7D64800040F377 /* heatmapcommand.cpp */,
                                378598640FDD497000EF9D03 /* heatmapsimcommand.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 */,
                                37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */,
                                7E09C5120FDA79C5002ECAE5 /* reversecommand.h */,
                                7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */,
+                               A70DECD71063D8B40057C03C /* secondarystructurecommand.h */,
+                               A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */,
                                371B30B30FD7EE67000414CA /* screenseqscommand.h */,
                                371B30B20FD7EE67000414CA /* screenseqscommand.cpp */,
                                3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */,
                                373C68A00FC1C07D00137ACD /* alignment.cpp */,
                                373C68A30FC1C07D00137ACD /* alignmentcell.hpp */,
                                373C68A20FC1C07D00137ACD /* alignmentcell.cpp */,
+                               A78782A910A1B1CB0086103D /* alignmentdb.h */,
+                               A78782AA10A1B1CB0086103D /* alignmentdb.cpp */,
                                373C69170FC1C8AF00137ACD /* blastdb.hpp */,
                                373C69160FC1C8AF00137ACD /* blastdb.cpp */,
                                37D927D40F21331F001D4494 /* database.hpp */,
                                37D927D30F21331F001D4494 /* database.cpp */,
                                37D927D50F21331F001D4494 /* datavector.hpp */,
-                               3799A94D0FD6A58C00E33EDE /* distancedb.hpp */,
-                               3799A94C0FD6A58C00E33EDE /* distancedb.cpp */,
                                37D927DC0F21331F001D4494 /* fastamap.h */,
                                37D927DB0F21331F001D4494 /* fastamap.cpp */,
                                375873EA0F7D64520040F377 /* fullmatrix.h */,
                                37D927EB0F21331F001D4494 /* kmerdb.cpp */,
                                37D927EE0F21331F001D4494 /* listvector.hpp */,
                                37D927ED0F21331F001D4494 /* listvector.cpp */,
+                               37D927F10F21331F001D4494 /* nameassignment.hpp */,
+                               37D927F00F21331F001D4494 /* nameassignment.cpp */,
                                37D927F80F21331F001D4494 /* ordervector.hpp */,
                                37D927F70F21331F001D4494 /* ordervector.cpp */,
                                37D928000F21331F001D4494 /* rabundvector.hpp */,
                        name = errorcheckor;
                        sourceTree = "<group>";
                };
+               A787811210A073F40086103D /* classifiers */ = {
+                       isa = PBXGroup;
+                       children = (
+                               A78780FE10A06B8B0086103D /* classify.h */,
+                               A787810210A06D5D0086103D /* classify.cpp */,
+                               A787820F10A0AAE70086103D /* bayesian.h */,
+                               A787821010A0AAE70086103D /* bayesian.cpp */,
+                               A773805D10B6D6FC002A6A61 /* taxonomyequalizer.h */,
+                               A773805E10B6D6FC002A6A61 /* taxonomyequalizer.cpp */,
+                               A78781B910A0813D0086103D /* phylotree.h */,
+                               A78781B810A0813D0086103D /* phylotree.cpp */,
+                               A787844310A1EBDD0086103D /* knn.h */,
+                               A787844410A1EBDD0086103D /* knn.cpp */,
+                       );
+                       name = classifiers;
+                       sourceTree = "<group>";
+               };
                C6859E8C029090F304C91782 /* Documentation */ = {
                        isa = PBXGroup;
                        children = (
                                21E859D80FC4632E005E1A48 /* matrixoutputcommand.cpp in Sources */,
                                3749271D0FD58C840031C06B /* getsabundcommand.cpp in Sources */,
                                3749273F0FD5956B0031C06B /* getrabundcommand.cpp in Sources */,
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                                3799A9510FD6A58C00E33EDE /* seqsummarycommand.cpp in Sources */,
                                371B30B40FD7EE67000414CA /* screenseqscommand.cpp in Sources */,
                                7E09C5140FDA79C5002ECAE5 /* reversecommand.cpp in Sources */,
                                372095C2103196D70004D347 /* chimera.cpp in Sources */,
                                A75B887E104C16860083C454 /* ccode.cpp in Sources */,
                                A7283FF81056CAE100D0CC69 /* chimeracheckrdp.cpp in Sources */,
+                               A70DECD91063D8B40057C03C /* secondarystructurecommand.cpp in Sources */,
+                               A7E4A783106913F900688F62 /* getsharedotucommand.cpp in Sources */,
+                               A7E4A824106A9AD700688F62 /* maligner.cpp in Sources */,
+                               A7B04493106CC3E60046FC83 /* chimeraslayer.cpp in Sources */,
+                               A7B0450E106CEEC90046FC83 /* slayer.cpp in Sources */,
+                               A73329CF1083B3B3003B10C5 /* getlistcountcommand.cpp in Sources */,
+                               A729ACD010848E6100139801 /* hclustercommand.cpp in Sources */,
+                               A729ACE410849BBE00139801 /* hcluster.cpp in Sources */,
+                               A751ACEA1098B283003D0911 /* readcluster.cpp in Sources */,
+                               A7861478109F5FA00010AAAF /* classifyseqscommand.cpp in Sources */,
+                               A787810310A06D5D0086103D /* classify.cpp in Sources */,
+                               A78781BA10A0813E0086103D /* phylotree.cpp in Sources */,
+                               A787821110A0AAE70086103D /* bayesian.cpp in Sources */,
+                               A78782AB10A1B1CB0086103D /* alignmentdb.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 */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
                                        "_GLIBCXX_DEBUG_PEDANTIC=1",
                                );
                                INSTALL_PATH = /usr/local/bin;
+                               LIBRARY_SEARCH_PATHS = (
+                                       "$(inherited)",
+                                       "\"$(SRCROOT)/../readline-6.0\"",
+                               );
                                PRODUCT_NAME = mothur;
                                ZERO_LINK = YES;
                        };
                                DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
                                GCC_MODEL_TUNING = G5;
                                INSTALL_PATH = /usr/local/bin;
+                               LIBRARY_SEARCH_PATHS = (
+                                       "$(inherited)",
+                                       "\"$(SRCROOT)/../readline-6.0\"",
+                               );
                                PRODUCT_NAME = mothur;
                        };
                        name = Release;
                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;
                                        "-ansi",
                                        "-pedantic",
                                        "-wall",
+                                       "-lreadline",
+                                       "-DUSE_READLINE",
                                );
                                PREBINDING = NO;
                                SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";