X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=77cfb8c6cd50b9ec16746ef64d16f142be6fb8dc;hp=3c14d55163ab260db87b7a35c271e664b7584945;hb=ef4c1b4dfeecc17a0ad5c1c114c748a0443a88ac;hpb=7439a3c94e96c9e0e78ca53f0356415a879f8b80 diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 3c14d55..77cfb8c 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -32,7 +32,6 @@ A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727864312E9E28C00F86ABA /* removerarecommand.cpp */; }; A7386C231619CCE600651424 /* classifysharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7386C211619CCE600651424 /* classifysharedcommand.cpp */; }; A7386C251619E52300651424 /* abstractdecisiontree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7386C241619E52200651424 /* abstractdecisiontree.cpp */; }; - A7386C27161A0F9D00651424 /* abstractrandomforest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7386C26161A0F9C00651424 /* abstractrandomforest.cpp */; }; A7386C29161A110800651424 /* decisiontree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7386C28161A110700651424 /* decisiontree.cpp */; }; A73901081588C40900ED2ED6 /* loadlogfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73901071588C40900ED2ED6 /* loadlogfilecommand.cpp */; }; A73DDBBA13C4A0D1006AAE38 /* clearmemorycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73DDBB913C4A0D1006AAE38 /* clearmemorycommand.cpp */; }; @@ -44,6 +43,8 @@ A74D36B8137DAFAA00332B0C /* 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 */; }; + A7548FAD17142EBC00B1F05A /* getmetacommunitycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7548FAC17142EBC00B1F05A /* getmetacommunitycommand.cpp */; }; + A7548FB0171440ED00B1F05A /* qFinderDMM.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7548FAE171440EC00B1F05A /* qFinderDMM.cpp */; }; A75790591301749D00A30DAB /* homovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A75790581301749D00A30DAB /* homovacommand.cpp */; }; A76CDD821510F143004C8458 /* prcseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A76CDD811510F143004C8458 /* prcseqscommand.cpp */; }; A7730EFF13967241007433A3 /* countseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7730EFE13967241007433A3 /* countseqscommand.cpp */; }; @@ -52,6 +53,9 @@ A77410F614697C300098E6AC /* seqnoise.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A77410F414697C300098E6AC /* seqnoise.cpp */; }; A778FE6B134CA6CA00C0BA33 /* getcommandinfocommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */; }; A77A221F139001B600B0BE70 /* deuniquetreecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A77A221E139001B600B0BE70 /* deuniquetreecommand.cpp */; }; + A77B7185173D2240002163C2 /* sparcccommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A77B7184173D2240002163C2 /* sparcccommand.cpp */; }; + A77B7188173D4042002163C2 /* randomnumber.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A77B7186173D4041002163C2 /* randomnumber.cpp */; }; + A77B718B173D40E5002163C2 /* calcsparcc.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A77B7189173D40E4002163C2 /* calcsparcc.cpp */; }; A77E1938161B201E00DB1A2A /* randomforest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A77E1937161B201E00DB1A2A /* randomforest.cpp */; }; A77E193B161B289600DB1A2A /* rftreenode.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A77E193A161B289600DB1A2A /* rftreenode.cpp */; }; A77EBD2F1523709100ED407C /* createdatabasecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A77EBD2E1523709100ED407C /* createdatabasecommand.cpp */; }; @@ -72,8 +76,10 @@ A7C3DC0B14FE457500FE1924 /* cooccurrencecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7C3DC0914FE457500FE1924 /* cooccurrencecommand.cpp */; }; A7C3DC0F14FE469500FE1924 /* trialSwap2.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7C3DC0D14FE469500FE1924 /* trialSwap2.cpp */; }; A7C7DAB915DA758B0059B0CF /* sffmultiplecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7C7DAB815DA758B0059B0CF /* sffmultiplecommand.cpp */; }; + A7CFA4311755401800D9ED4D /* renameseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7CFA4301755401800D9ED4D /* renameseqscommand.cpp */; }; A7D755DA1535F679009BF21A /* treereader.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D755D91535F679009BF21A /* treereader.cpp */; }; A7E0243D15B4520A00A5F046 /* sparsedistancematrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E0243C15B4520A00A5F046 /* sparsedistancematrix.cpp */; }; + A7E6F69E17427D06006775E2 /* makelookupcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E6F69D17427D06006775E2 /* makelookupcommand.cpp */; }; A7E9B88112D37EC400DA6239 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B64F12D37EC300DA6239 /* ace.cpp */; }; A7E9B88212D37EC400DA6239 /* aligncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65112D37EC300DA6239 /* aligncommand.cpp */; }; A7E9B88312D37EC400DA6239 /* alignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65312D37EC300DA6239 /* alignment.cpp */; }; @@ -432,7 +438,6 @@ A727864212E9E28C00F86ABA /* removerarecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removerarecommand.h; sourceTree = ""; }; A727864312E9E28C00F86ABA /* removerarecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removerarecommand.cpp; sourceTree = ""; }; A7386C1B1619CACB00651424 /* abstractdecisiontree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = abstractdecisiontree.hpp; sourceTree = ""; }; - A7386C1C1619CACB00651424 /* abstractrandomforest.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = abstractrandomforest.hpp; sourceTree = ""; }; A7386C1D1619CACB00651424 /* decisiontree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = decisiontree.hpp; sourceTree = ""; }; A7386C1E1619CACB00651424 /* macros.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = macros.h; sourceTree = ""; }; A7386C1F1619CACB00651424 /* randomforest.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = randomforest.hpp; sourceTree = ""; }; @@ -440,7 +445,6 @@ A7386C211619CCE600651424 /* classifysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifysharedcommand.cpp; 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sourceTree = ""; }; + A7548FAE171440EC00B1F05A /* qFinderDMM.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qFinderDMM.cpp; sourceTree = ""; }; + A7548FAF171440ED00B1F05A /* qFinderDMM.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qFinderDMM.h; sourceTree = ""; }; A75790571301749D00A30DAB /* homovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = homovacommand.h; sourceTree = ""; }; A75790581301749D00A30DAB /* homovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = homovacommand.cpp; sourceTree = ""; }; A76CDD7F1510F09A004C8458 /* pcrseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcrseqscommand.h; sourceTree = ""; }; @@ -478,6 +486,12 @@ A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; 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fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = randomnumber.h; sourceTree = ""; }; + A77B7189173D40E4002163C2 /* calcsparcc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = calcsparcc.cpp; sourceTree = ""; }; + A77B718A173D40E4002163C2 /* calcsparcc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = calcsparcc.h; sourceTree = ""; }; A77E1937161B201E00DB1A2A /* randomforest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = randomforest.cpp; sourceTree = ""; }; A77E193A161B289600DB1A2A /* rftreenode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rftreenode.cpp; sourceTree = ""; }; A77EBD2C1523707F00ED407C /* createdatabasecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = createdatabasecommand.h; sourceTree = ""; }; @@ -518,11 +532,15 @@ A7C3DC0E14FE469500FE1924 /* trialswap2.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = trialswap2.h; sourceTree = ""; }; A7C7DAB615DA75760059B0CF /* sffmultiplecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sffmultiplecommand.h; sourceTree = ""; }; A7C7DAB815DA758B0059B0CF /* sffmultiplecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sffmultiplecommand.cpp; sourceTree = ""; }; + A7CFA42F1755400500D9ED4D /* renameseqscommand.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; path = renameseqscommand.h; sourceTree = ""; }; + A7CFA4301755401800D9ED4D /* renameseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = renameseqscommand.cpp; sourceTree = ""; }; A7D755D71535F665009BF21A /* treereader.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treereader.h; sourceTree = ""; }; A7D755D91535F679009BF21A /* treereader.cpp */ = {isa = PBXFileReference; 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}; A7E9B64F12D37EC300DA6239 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = ""; }; A7E9B65012D37EC300DA6239 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = ""; }; A7E9B65112D37EC300DA6239 /* aligncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = aligncommand.cpp; sourceTree = ""; }; @@ -1125,6 +1143,8 @@ A7A61F1A130035C800E05B6B /* LICENSE */, A70332B512D3A13400761E33 /* makefile */, A7E9B65912D37EC300DA6239 /* averagelinkage.cpp */, + A77B718A173D40E4002163C2 /* calcsparcc.h */, + A77B7189173D40E4002163C2 /* calcsparcc.cpp */, A7E9BA4F12D398D700DA6239 /* clearcut */, A7E9B69812D37EC400DA6239 /* cluster.cpp */, A7E9B69912D37EC400DA6239 /* cluster.hpp */, @@ -1192,6 +1212,10 @@ A7E9B77C12D37EC400DA6239 /* overlap.hpp */, A7E9B79B12D37EC400DA6239 /* progress.cpp */, A7E9B79C12D37EC400DA6239 /* progress.hpp */, + A7548FAF171440ED00B1F05A /* qFinderDMM.h */, + A7548FAE171440EC00B1F05A /* qFinderDMM.cpp */, + A77B7187173D4041002163C2 /* randomnumber.h */, + A77B7186173D4041002163C2 /* randomnumber.cpp */, A7E9B7A512D37EC400DA6239 /* rarecalc.cpp */, A7386C191619C9FB00651424 /* randomforest */, A7E9B7A612D37EC400DA6239 /* rarecalc.h */, @@ -1240,8 +1264,6 @@ children = ( A7386C1B1619CACB00651424 /* abstractdecisiontree.hpp */, A7386C241619E52200651424 /* abstractdecisiontree.cpp */, - A7386C1C1619CACB00651424 /* abstractrandomforest.hpp */, - A7386C26161A0F9C00651424 /* abstractrandomforest.cpp */, A7386C1D1619CACB00651424 /* decisiontree.hpp */, A7386C28161A110700651424 /* decisiontree.cpp */, A7386C1E1619CACB00651424 /* macros.h */, @@ -1375,6 +1397,8 @@ A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */, A7E9B6F712D37EC400DA6239 /* getlabelcommand.h */, A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */, + A7548FAB17142EA500B1F05A /* getmetacommunitycommand.h */, + A7548FAC17142EBC00B1F05A /* getmetacommunitycommand.cpp */, A70056E8156A93E300924A2D /* getotulabelscommand.h */, A70056E5156A93D000924A2D /* getotulabelscommand.cpp */, A7E9B6F912D37EC400DA6239 /* getlineagecommand.h */, @@ -1427,6 +1451,8 @@ A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */, A7E9B74412D37EC400DA6239 /* makegroupcommand.h */, A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */, + A7E6F69C17427CF2006775E2 /* makelookupcommand.h */, + A7E6F69D17427D06006775E2 /* makelookupcommand.cpp */, A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */, A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */, A7E9B75412D37EC400DA6239 /* mergefilecommand.h */, @@ -1493,6 +1519,8 @@ A727864312E9E28C00F86ABA /* removerarecommand.cpp */, A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */, A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */, + A7CFA42F1755400500D9ED4D /* renameseqscommand.h */, + A7CFA4301755401800D9ED4D /* renameseqscommand.cpp */, A7E9B7CE12D37EC400DA6239 /* reversecommand.h */, A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */, A7E9B7D212D37EC400DA6239 /* screenseqscommand.h */, @@ -1523,6 +1551,8 @@ A774101314695AF60098E6AC /* shhhseqscommand.cpp */, A7A32DAC14DC43D10001D2E5 /* sortseqscommand.h */, A7A32DA914DC43B00001D2E5 /* sortseqscommand.cpp */, + A77B7183173D222F002163C2 /* sparcccommand.h */, + A77B7184173D2240002163C2 /* sparcccommand.cpp */, A7E9B84012D37EC400DA6239 /* splitabundcommand.h */, A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */, A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */, @@ -2316,7 +2346,6 @@ A7C7DAB915DA758B0059B0CF /* sffmultiplecommand.cpp in Sources */, A7386C231619CCE600651424 /* classifysharedcommand.cpp in Sources */, A7386C251619E52300651424 /* abstractdecisiontree.cpp in Sources */, - A7386C27161A0F9D00651424 /* abstractrandomforest.cpp in Sources */, A7386C29161A110800651424 /* decisiontree.cpp in Sources */, A77E1938161B201E00DB1A2A /* randomforest.cpp in Sources */, A77E193B161B289600DB1A2A /* rftreenode.cpp in Sources */, @@ -2334,6 +2363,13 @@ A7128B1D16B7002A00723BE4 /* getdistscommand.cpp in Sources */, A7B0231516B8244C006BA09E /* removedistscommand.cpp in Sources */, A799314B16CBD0CD0017E888 /* mergetaxsummarycommand.cpp in Sources */, + A7548FAD17142EBC00B1F05A /* getmetacommunitycommand.cpp in Sources */, + A7548FB0171440ED00B1F05A /* qFinderDMM.cpp in Sources */, + A77B7185173D2240002163C2 /* sparcccommand.cpp in Sources */, + A77B7188173D4042002163C2 /* randomnumber.cpp in Sources */, + A77B718B173D40E5002163C2 /* calcsparcc.cpp in Sources */, + A7E6F69E17427D06006775E2 /* makelookupcommand.cpp in Sources */, + A7CFA4311755401800D9ED4D /* renameseqscommand.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -2353,7 +2389,6 @@ GCC_OPTIMIZATION_LEVEL = 3; "INSTALL_PATH[sdk=*]" = TARGET_BUILD_DIR; PRODUCT_NAME = mothur; - SDKROOT = macosx; SDKROOT = macosx10.8; SKIP_INSTALL = NO; }; @@ -2384,11 +2419,11 @@ GCC_ENABLE_SSE3_EXTENSIONS = NO; GCC_ENABLE_SSE41_EXTENSIONS = NO; GCC_ENABLE_SSE42_EXTENSIONS = NO; - GCC_OPTIMIZATION_LEVEL = 3; + GCC_OPTIMIZATION_LEVEL = s; GCC_PREPROCESSOR_DEFINITIONS = ( "MOTHUR_FILES=\"\\\"../../release\\\"\"", - "VERSION=\"\\\"1.29.2\\\"\"", - "RELEASE_DATE=\"\\\"2/12/2013\\\"\"", + "VERSION=\"\\\"1.31.0\\\"\"", + "RELEASE_DATE=\"\\\"5/24/2013\\\"\"", ); "GCC_VERSION[arch=*]" = ""; GCC_WARN_ABOUT_MISSING_NEWLINE = YES; @@ -2421,10 +2456,10 @@ GCC_C_LANGUAGE_STANDARD = gnu99; GCC_GENERATE_DEBUGGING_SYMBOLS = NO; GCC_MODEL_TUNING = ""; - GCC_OPTIMIZATION_LEVEL = 3; + GCC_OPTIMIZATION_LEVEL = s; GCC_PREPROCESSOR_DEFINITIONS = ( - "VERSION=\"\\\"1.29.2\\\"\"", - "RELEASE_DATE=\"\\\"2/12/2013\\\"\"", + "VERSION=\"\\\"1.31.0\\\"\"", + "RELEASE_DATE=\"\\\"5/24/2013\\\"\"", ); GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES;