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lastKnownFileType = archive.ar; name = libreadline.a; path = "../readline-6.0/libreadline.a"; sourceTree = SOURCE_ROOT; }; C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = ""; }; 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; }; @@ -541,6 +613,7 @@ isa = PBXFrameworksBuildPhase; buildActionMask = 2147483647; files = ( + A7F5759710CEBC0600E20E47 /* libreadline.a in Frameworks */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -565,6 +638,7 @@ 373C68DB0FC1C38D00137ACD /* blastalign.cpp */, 37D928A60F2133C0001D4494 /* calculators */, 374F2FE81006346600E97C66 /* chimera */, + A787811210A073F40086103D /* classifiers */, 37D927C20F21331F001D4494 /* cluster.hpp */, 37D927C10F21331F001D4494 /* cluster.cpp */, 37D928A90F2133E5001D4494 /* commands */, @@ -590,6 +664,8 @@ 37D927DF0F21331F001D4494 /* globaldata.cpp */, 373C68BB0FC1C1A600137ACD /* gotohoverlap.hpp */, 373C68BA0FC1C1A600137ACD /* gotohoverlap.cpp */, + A729ACE210849BBE00139801 /* hcluster.h */, + A729ACE310849BBE00139801 /* hcluster.cpp */, 375873ED0F7D646F0040F377 /* heatmap.h */, 375873EE0F7D646F0040F377 /* heatmap.cpp */, 378598720FDD4C1500EF9D03 /* heatmapsim.h */, @@ -600,8 +676,6 @@ 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */, 37E3ED800F4D9D0D00B5DF02 /* mothur.h */, 37D927EF0F21331F001D4494 /* mothur.cpp */, - 37D927F10F21331F001D4494 /* nameassignment.hpp */, - 37D927F00F21331F001D4494 /* nameassignment.cpp */, 373C691E0FC1C98600137ACD /* nast.hpp */, 373C691D0FC1C98600137ACD /* nast.cpp */, 373C692A0FC1C9EB00137ACD /* nastreport.hpp */, @@ -632,6 +706,7 @@ 37D928490F21331F001D4494 /* summarydisplay.h */, 37519AB30F810FAE00FED5E8 /* venn.h */, 37519AB40F810FAE00FED5E8 /* venn.cpp */, + A7F5759610CEBC0600E20E47 /* libreadline.a */, ); name = Source; sourceTree = ""; @@ -655,10 +730,16 @@ 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 = ""; @@ -666,6 +747,15 @@ 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 */, @@ -812,6 +902,8 @@ 377326630FAF16E0007ABB8B /* consensuscommand.cpp */, 379D3D4F0FF90E090068C1C0 /* chimeraseqscommand.h */, 379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */, + A7861476109F5FA00010AAAF /* classifyseqscommand.h */, + A7861477109F5FA00010AAAF /* classifyseqscommand.cpp */, 37B28F660F27590100808A62 /* deconvolutecommand.h */, 37B28F670F27590100808A62 /* deconvolutecommand.cpp */, 37C753CC0FB3415200DBD02E /* distancecommand.h */, @@ -824,6 +916,8 @@ A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */, A70B53A90F4CD7AD0064797E /* getlinecommand.h */, A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */, + A73329CD1083B3B3003B10C5 /* getlistcountcommand.h */, + A73329CE1083B3B3003B10C5 /* getlistcountcommand.cpp */, 370B88050F8A4EE4005AB382 /* getoturepcommand.h */, 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */, 3749273D0FD5956B0031C06B /* getrabundcommand.h */, @@ -832,6 +926,10 @@ 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 */, @@ -846,10 +944,20 @@ 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 */, @@ -866,6 +974,8 @@ 37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */, 7E09C5120FDA79C5002ECAE5 /* reversecommand.h */, 7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */, + A70DECD71063D8B40057C03C /* secondarystructurecommand.h */, + A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */, 371B30B30FD7EE67000414CA /* screenseqscommand.h */, 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */, 3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */, @@ -899,13 +1009,13 @@ 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 */, @@ -918,6 +1028,8 @@ 37D927EB0F21331F001D4494 /* kmerdb.cpp */, 37D927EE0F21331F001D4494 /* listvector.hpp */, 37D927ED0F21331F001D4494 /* listvector.cpp */, + 37D927F10F21331F001D4494 /* nameassignment.hpp */, + 37D927F00F21331F001D4494 /* nameassignment.cpp */, 37D927F80F21331F001D4494 /* ordervector.hpp */, 37D927F70F21331F001D4494 /* ordervector.cpp */, 37D928000F21331F001D4494 /* rabundvector.hpp */, @@ -965,6 +1077,23 @@ name = errorcheckor; sourceTree = ""; }; + 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 = ""; + }; C6859E8C029090F304C91782 /* Documentation */ = { isa = PBXGroup; children = ( @@ -1159,7 +1288,6 @@ 21E859D80FC4632E005E1A48 /* matrixoutputcommand.cpp in Sources */, 3749271D0FD58C840031C06B /* getsabundcommand.cpp in Sources */, 3749273F0FD5956B0031C06B /* getrabundcommand.cpp in Sources */, - 3799A9500FD6A58C00E33EDE /* distancedb.cpp in Sources */, 3799A9510FD6A58C00E33EDE /* seqsummarycommand.cpp in Sources */, 371B30B40FD7EE67000414CA /* screenseqscommand.cpp in Sources */, 7E09C5140FDA79C5002ECAE5 /* reversecommand.cpp in Sources */, @@ -1179,6 +1307,30 @@ 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; }; @@ -1198,6 +1350,10 @@ "_GLIBCXX_DEBUG_PEDANTIC=1", ); INSTALL_PATH = /usr/local/bin; + LIBRARY_SEARCH_PATHS = ( + "$(inherited)", + "\"$(SRCROOT)/../readline-6.0\"", + ); PRODUCT_NAME = mothur; ZERO_LINK = YES; }; @@ -1209,6 +1365,10 @@ 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; @@ -1216,6 +1376,8 @@ 1DEB923608733DC60010E9CD /* Debug */ = { isa = XCBuildConfiguration; buildSettings = { + ARCHS = "$(ARCHS_STANDARD_64_BIT_PRE_XCODE_3_1)"; + ARCHS_STANDARD_64_BIT_PRE_XCODE_3_1 = x86_64; GCC_OPTIMIZATION_LEVEL = 3; GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; @@ -1232,10 +1394,8 @@ 1DEB923708733DC60010E9CD /* Release */ = { isa = XCBuildConfiguration; buildSettings = { - ARCHS = ( - ppc, - i386, - ); + ARCHS = "$(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; @@ -1251,6 +1411,8 @@ "-ansi", "-pedantic", "-wall", + "-lreadline", + "-DUSE_READLINE", ); PREBINDING = NO; SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";