X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=ff0e35bbb0bac1d955c7629e75eeb872e2cc1d65;hb=0cefb55a2616975bd4a144fc345693695ffc9bb6;hp=6e156df32f8d604dacdc37e9d350b6a6645f8a14;hpb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;p=mothur.git diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 6e156df..ff0e35b 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -7,8 +7,12 @@ objects = { /* Begin PBXBuildFile section */ + 219C1DE01552C4BD004209F9 /* newcommandtemplate.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 219C1DDF1552C4BD004209F9 /* newcommandtemplate.cpp */; }; + 219C1DE41559BCCF004209F9 /* getcoremicrobiomecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */; }; 7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E6BE10912F710D8007ADDBE /* 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/* chimerauchimecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D36B7137DAFAA00332B0C /* chimerauchimecommand.cpp */; }; + A74D59A4159A1E2000043046 /* counttable.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D59A3159A1E2000043046 /* counttable.cpp */; }; A754149714840CF7005850D1 /* summaryqualcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A754149614840CF7005850D1 /* summaryqualcommand.cpp */; }; A75790591301749D00A30DAB /* homovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A75790581301749D00A30DAB /* homovacommand.cpp */; }; A76CDD821510F143004C8458 /* prcseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A76CDD811510F143004C8458 /* prcseqscommand.cpp */; }; @@ -35,6 +41,8 @@ A79234D713C74BF6002B08E2 /* mothurfisher.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A79234D613C74BF6002B08E2 /* mothurfisher.cpp */; }; A795840D13F13CD900F201D5 /* countgroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 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sourcecode.cpp.cpp; path = counttable.cpp; sourceTree = ""; }; + A74D59A6159A1E3600043046 /* counttable.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = counttable.h; sourceTree = ""; }; A754149514840CF7005850D1 /* summaryqualcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summaryqualcommand.h; sourceTree = ""; }; A754149614840CF7005850D1 /* summaryqualcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summaryqualcommand.cpp; sourceTree = ""; }; A75790571301749D00A30DAB /* homovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = homovacommand.h; sourceTree = ""; }; @@ -413,6 +431,10 @@ A795840C13F13CD900F201D5 /* countgroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = countgroupscommand.cpp; sourceTree = ""; }; 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A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = ""; }; - A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = ""; }; - A7E9B7BC12D37EC400DA6239 /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = ""; }; A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = ""; }; A7E9B7BE12D37EC400DA6239 /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = ""; }; A7E9B7BF12D37EC400DA6239 /* readtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; 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{isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removelineagecommand.cpp; sourceTree = ""; }; @@ -1144,7 +1162,7 @@ 1AB674ADFE9D54B511CA2CBB /* Products */ = { isa = PBXGroup; children = ( - 8DD76FB20486AB0100D96B5E /* Mothur */, + 8DD76FB20486AB0100D96B5E /* mothur */, ); name = Products; sourceTree = ""; @@ -1173,6 +1191,8 @@ isa = PBXGroup; children = ( A7E9B6AE12D37EC400DA6239 /* command.hpp */, + 219C1DE11552C508004209F9 /* newcommandtemplate.h */, + 219C1DDF1552C4BD004209F9 /* newcommandtemplate.cpp */, A7E9B65212D37EC300DA6239 /* aligncommand.h */, A7E9B65112D37EC300DA6239 /* aligncommand.cpp */, A7A61F2B130062E000E05B6B /* amovacommand.h */, @@ -1247,6 +1267,8 @@ A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */, A778FE69134CA6CA00C0BA33 /* getcommandinfocommand.h */, A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */, + 219C1DE51559BCF2004209F9 /* getcoremicrobiomecommand.h */, + 219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */, A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */, A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */, A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */, @@ -1255,6 +1277,8 @@ A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */, A7E9B6F712D37EC400DA6239 /* getlabelcommand.h */, A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */, + A70056E8156A93E300924A2D /* getotulabelscommand.h */, + A70056E5156A93D000924A2D /* getotulabelscommand.cpp */, A7E9B6F912D37EC400DA6239 /* getlineagecommand.h */, A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */, A7E9B6FB12D37EC400DA6239 /* getlistcountcommand.h */, @@ -1287,12 +1311,18 @@ A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */, A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */, A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */, + A7A0671C156294810095C8C5 /* listotulabelscommand.h */, + A7A067191562946F0095C8C5 /* listotulabelscommand.cpp */, A7E9B73E12D37EC400DA6239 /* listseqscommand.h */, A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */, + A73901051588C3EF00ED2ED6 /* loadlogfilecommand.h */, + A73901071588C40900ED2ED6 /* loadlogfilecommand.cpp */, A7FA10001302E096003860FE /* mantelcommand.h */, A7FA10011302E096003860FE /* mantelcommand.cpp */, A724D2B4153C8600000A826F /* makebiomcommand.h */, A724D2B6153C8628000A826F /* makebiomcommand.cpp */, + A7A0671D1562AC230095C8C5 /* makecontigscommand.h */, + A7A0671E1562AC3E0095C8C5 /* makecontigscommand.cpp */, A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */, A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */, A7E9B74412D37EC400DA6239 /* makegroupcommand.h */, @@ -1345,18 +1375,14 @@ A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */, A7E9B7AF12D37EC400DA6239 /* rarefactsharedcommand.h */, A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */, - A7E9B7B712D37EC400DA6239 /* readdistcommand.h */, - A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */, - A7E9B7BC12D37EC400DA6239 /* readotucommand.h */, - A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */, - A7E9B7C212D37EC400DA6239 /* readtreecommand.h */, - A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */, A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */, A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */, A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */, A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */, A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */, A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */, + A70056E9156AB6D400924A2D /* removeotulabelscommand.h */, + A70056EA156AB6E500924A2D /* removeotulabelscommand.cpp */, A727864212E9E28C00F86ABA /* removerarecommand.h */, A727864312E9E28C00F86ABA /* removerarecommand.cpp */, A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */, @@ -1596,10 +1622,12 @@ A7E9B66312D37EC400DA6239 /* blastalign.hpp */, A7E9B66412D37EC400DA6239 /* blastdb.cpp */, A7E9B66512D37EC400DA6239 /* blastdb.hpp */, + A74D59A6159A1E3600043046 /* counttable.h */, + A74D59A3159A1E2000043046 /* counttable.cpp */, + A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */, A7E9B6BD12D37EC400DA6239 /* database.cpp */, A7E9B6BE12D37EC400DA6239 /* database.hpp */, A7E9B6BF12D37EC400DA6239 /* datavector.hpp */, - A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */, A7E9B6CE12D37EC400DA6239 /* distancedb.hpp */, A7E9B6DE12D37EC400DA6239 /* fastamap.cpp */, A7E9B6DF12D37EC400DA6239 /* fastamap.h */, @@ -1647,6 +1675,8 @@ A7E9B81412D37EC400DA6239 /* sharedsabundvector.h */, A7E9B83912D37EC400DA6239 /* sparsematrix.cpp */, A7E9B83A12D37EC400DA6239 /* sparsematrix.hpp */, + A7E0243F15B4522000A5F046 /* sparsedistancematrix.h */, + A7E0243C15B4520A00A5F046 /* sparsedistancematrix.cpp */, A7E9B85112D37EC400DA6239 /* suffixdb.cpp */, A7E9B85212D37EC400DA6239 /* suffixdb.hpp */, A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */, @@ -1799,7 +1829,7 @@ name = Mothur; productInstallPath = "$(HOME)/bin"; productName = mothur; - productReference = 8DD76FB20486AB0100D96B5E /* Mothur */; + productReference = 8DD76FB20486AB0100D96B5E /* mothur */; productType = "com.apple.product-type.tool"; }; /* End PBXNativeTarget section */ @@ -2000,11 +2030,8 @@ A7E9B92912D37EC400DA6239 /* readblast.cpp in Sources */, A7E9B92A12D37EC400DA6239 /* readcluster.cpp in Sources */, A7E9B92B12D37EC400DA6239 /* readcolumn.cpp in Sources */, - A7E9B92C12D37EC400DA6239 /* readdistcommand.cpp in Sources */, - A7E9B92E12D37EC400DA6239 /* readotucommand.cpp in Sources */, A7E9B92F12D37EC400DA6239 /* readphylip.cpp in Sources */, A7E9B93012D37EC400DA6239 /* readtree.cpp in Sources */, - A7E9B93112D37EC400DA6239 /* readtreecommand.cpp in Sources */, A7E9B93212D37EC400DA6239 /* removegroupscommand.cpp in Sources */, A7E9B93312D37EC400DA6239 /* removelineagecommand.cpp in Sources */, A7E9B93412D37EC400DA6239 /* removeotuscommand.cpp in Sources */, @@ -2156,6 +2183,15 @@ A7876A26152A017C00A0AE86 /* subsample.cpp in Sources */, A7D755DA1535F679009BF21A /* treereader.cpp in Sources */, A724D2B7153C8628000A826F /* makebiomcommand.cpp in Sources */, + 219C1DE01552C4BD004209F9 /* newcommandtemplate.cpp in Sources */, + 219C1DE41559BCCF004209F9 /* getcoremicrobiomecommand.cpp in Sources */, + A7A0671A1562946F0095C8C5 /* listotulabelscommand.cpp in Sources */, + A7A0671F1562AC3E0095C8C5 /* makecontigscommand.cpp in Sources */, + A70056E6156A93D000924A2D /* getotulabelscommand.cpp in Sources */, + A70056EB156AB6E500924A2D /* removeotulabelscommand.cpp in Sources */, + A73901081588C40900ED2ED6 /* loadlogfilecommand.cpp in Sources */, + A74D59A4159A1E2000043046 /* counttable.cpp in Sources */, + A7E0243D15B4520A00A5F046 /* sparsedistancematrix.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -2167,12 +2203,13 @@ buildSettings = { ALWAYS_SEARCH_USER_PATHS = NO; COPY_PHASE_STRIP = NO; + DEPLOYMENT_LOCATION = YES; GCC_DYNAMIC_NO_PIC = NO; GCC_MODEL_TUNING = G5; GCC_OPTIMIZATION_LEVEL = 0; - INSTALL_PATH = /usr/local/bin; - PRODUCT_NAME = Mothur; + PRODUCT_NAME = mothur; SDKROOT = macosx10.6; + SKIP_INSTALL = NO; }; name = Debug; }; @@ -2184,8 +2221,8 @@ DEPLOYMENT_LOCATION = YES; GCC_MODEL_TUNING = G5; GCC_WARN_UNUSED_VALUE = YES; - INSTALL_PATH = ./; - PRODUCT_NAME = Mothur; + PRODUCT_NAME = mothur; + SKIP_INSTALL = NO; }; name = Release; }; @@ -2201,15 +2238,15 @@ GCC_OPTIMIZATION_LEVEL = 0; GCC_PREPROCESSOR_DEFINITIONS = ( "MOTHUR_FILES=\"\\\"../release\\\"\"", - "VERSION=\"\\\"1.24.0\\\"\"", - "RELEASE_DATE=\"\\\"3/12/2012\\\"\"", + "VERSION=\"\\\"1.26.0\\\"\"", + "RELEASE_DATE=\"\\\"7/9/2012\\\"\"", ); "GCC_VERSION[arch=*]" = ""; GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_UNUSED_VARIABLE = YES; HEADER_SEARCH_PATHS = ""; - INSTALL_PATH = ""; + INSTALL_PATH = TARGET_BUILD_DIR; MACH_O_TYPE = mh_execute; ONLY_ACTIVE_ARCH = YES; OTHER_CPLUSPLUSFLAGS = ( @@ -2222,6 +2259,7 @@ "-lreadline", ); SDKROOT = macosx10.6; + SKIP_INSTALL = NO; USER_HEADER_SEARCH_PATHS = ""; }; name = Debug; @@ -2236,8 +2274,8 @@ GCC_MODEL_TUNING = ""; GCC_OPTIMIZATION_LEVEL = 0; GCC_PREPROCESSOR_DEFINITIONS = ( - "VERSION=\"\\\"1.25.0\\\"\"", - "RELEASE_DATE=\"\\\"4/30/2012\\\"\"", + "VERSION=\"\\\"1.26.0\\\"\"", + "RELEASE_DATE=\"\\\"7/9/2012\\\"\"", ); GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; @@ -2247,7 +2285,7 @@ GCC_WARN_UNUSED_PARAMETER = YES; GCC_WARN_UNUSED_VALUE = YES; GCC_WARN_UNUSED_VARIABLE = YES; - INSTALL_PATH = ""; + INSTALL_PATH = TARGET_BUILD_DIR; MACH_O_TYPE = mh_execute; OTHER_CPLUSPLUSFLAGS = ( "-DUSE_READLINE", @@ -2259,6 +2297,7 @@ "-lreadline", ); SDKROOT = macosx10.6; + SKIP_INSTALL = NO; }; name = Release; };