]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
fixed some bugs and added mgcluster command
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index 9427eec004a889ab0481a0da9e7d47431367e046..5ae6f336987553e85d2841145f2f151008351554 100644 (file)
@@ -13,6 +13,8 @@
                21E859D80FC4632E005E1A48 /* matrixoutputcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */; };
                370B88070F8A4EE4005AB382 /* getoturepcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */; };
                371B30B40FD7EE67000414CA /* screenseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */; };
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+               372A55551017922B00C5194B /* decalc.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372A55541017922B00C5194B /* decalc.cpp */; };
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@@ -70,7 +72,6 @@
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                                374F2FE81006346600E97C66 /* chimera */,
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                                373C68BA0FC1C1A600137ACD /* gotohoverlap.cpp */,
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                                374F2FE9100634B600E97C66 /* bellerophon.h */,
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                        isa = PBXGroup;
                        children = (
+                               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 */,
                                3792946E0F2E191800B9034A /* parsimonycommand.h */,
                                3792946F0F2E191800B9034A /* parsimonycommand.cpp */,
+                               A773808E10B6EFD1002A6A61 /* phylotypecommand.h */,
+                               A773808F10B6EFD1002A6A61 /* phylotypecommand.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 */,
-                               3799A9500FD6A58C00E33EDE /* distancedb.cpp in Sources */,
                                3799A9510FD6A58C00E33EDE /* seqsummarycommand.cpp in Sources */,
                                371B30B40FD7EE67000414CA /* screenseqscommand.cpp in Sources */,
                                7E09C5140FDA79C5002ECAE5 /* reversecommand.cpp in Sources */,
                                37B73CCF1004F5E0008C4B41 /* systemcommand.cpp in Sources */,
                                374F2FEB100634B600E97C66 /* bellerophon.cpp in Sources */,
                                374F301310063B6F00E97C66 /* pintail.cpp in Sources */,
+                               372A55551017922B00C5194B /* decalc.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 */,
                        );
                        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;
                                        "-ansi",
                                        "-pedantic",
                                        "-wall",
+                                       "-lreadline",
+                                       "-DUSE_READLINE",
                                );
                                PREBINDING = NO;
                                SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
+                               SYMROOT = /Users/johnwestcott/Desktop;
                                WARNING_CFLAGS = "";
                        };
                        name = Release;