]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
added rename.seqs command.
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index 284bb592f407196ae05100feb4f0c45160e68027..77cfb8c6cd50b9ec16746ef64d16f142be6fb8dc 100644 (file)
@@ -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 */; };
@@ -54,6 +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 */; };
                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 */; };
                A727864212E9E28C00F86ABA /* removerarecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removerarecommand.h; sourceTree = "<group>"; };
                A727864312E9E28C00F86ABA /* removerarecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removerarecommand.cpp; sourceTree = "<group>"; };
                A7386C1B1619CACB00651424 /* abstractdecisiontree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = abstractdecisiontree.hpp; sourceTree = "<group>"; };
-               A7386C1C1619CACB00651424 /* abstractrandomforest.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = abstractrandomforest.hpp; sourceTree = "<group>"; };
                A7386C1D1619CACB00651424 /* decisiontree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = decisiontree.hpp; sourceTree = "<group>"; };
                A7386C1E1619CACB00651424 /* macros.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = macros.h; sourceTree = "<group>"; };
                A7386C1F1619CACB00651424 /* randomforest.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = randomforest.hpp; sourceTree = "<group>"; };
                A7386C211619CCE600651424 /* classifysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifysharedcommand.cpp; sourceTree = "<group>"; };
                A7386C221619CCE600651424 /* classifysharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifysharedcommand.h; sourceTree = "<group>"; };
                A7386C241619E52200651424 /* abstractdecisiontree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = abstractdecisiontree.cpp; sourceTree = "<group>"; };
-               A7386C26161A0F9C00651424 /* abstractrandomforest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = abstractrandomforest.cpp; sourceTree = "<group>"; };
                A7386C28161A110700651424 /* decisiontree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = decisiontree.cpp; sourceTree = "<group>"; };
                A73901051588C3EF00ED2ED6 /* loadlogfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = loadlogfilecommand.h; sourceTree = "<group>"; };
                A73901071588C40900ED2ED6 /* loadlogfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = loadlogfilecommand.cpp; sourceTree = "<group>"; };
                A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getcommandinfocommand.cpp; sourceTree = "<group>"; };
                A77A221D139001B600B0BE70 /* deuniquetreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deuniquetreecommand.h; sourceTree = "<group>"; };
                A77A221E139001B600B0BE70 /* deuniquetreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deuniquetreecommand.cpp; sourceTree = "<group>"; };
+               A77B7183173D222F002163C2 /* sparcccommand.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; path = sparcccommand.h; sourceTree = "<group>"; };
+               A77B7184173D2240002163C2 /* sparcccommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sparcccommand.cpp; sourceTree = "<group>"; };
+               A77B7186173D4041002163C2 /* randomnumber.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = randomnumber.cpp; sourceTree = "<group>"; };
+               A77B7187173D4041002163C2 /* randomnumber.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = randomnumber.h; sourceTree = "<group>"; };
+               A77B7189173D40E4002163C2 /* calcsparcc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = calcsparcc.cpp; sourceTree = "<group>"; };
+               A77B718A173D40E4002163C2 /* calcsparcc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = calcsparcc.h; sourceTree = "<group>"; };
                A77E1937161B201E00DB1A2A /* randomforest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = randomforest.cpp; sourceTree = "<group>"; };
                A77E193A161B289600DB1A2A /* rftreenode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rftreenode.cpp; sourceTree = "<group>"; };
                A77EBD2C1523707F00ED407C /* createdatabasecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = createdatabasecommand.h; sourceTree = "<group>"; };
                A7C3DC0E14FE469500FE1924 /* trialswap2.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = trialswap2.h; sourceTree = "<group>"; };
                A7C7DAB615DA75760059B0CF /* sffmultiplecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sffmultiplecommand.h; sourceTree = "<group>"; };
                A7C7DAB815DA758B0059B0CF /* sffmultiplecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sffmultiplecommand.cpp; sourceTree = "<group>"; };
+               A7CFA42F1755400500D9ED4D /* renameseqscommand.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; path = renameseqscommand.h; sourceTree = "<group>"; };
+               A7CFA4301755401800D9ED4D /* renameseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = renameseqscommand.cpp; sourceTree = "<group>"; };
                A7D755D71535F665009BF21A /* treereader.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treereader.h; sourceTree = "<group>"; };
                A7D755D91535F679009BF21A /* treereader.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treereader.cpp; sourceTree = "<group>"; };
                A7DAAFA3133A254E003956EB /* commandparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = commandparameter.h; sourceTree = "<group>"; };
                A7E0243C15B4520A00A5F046 /* sparsedistancematrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sparsedistancematrix.cpp; sourceTree = "<group>"; };
                A7E0243F15B4522000A5F046 /* sparsedistancematrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sparsedistancematrix.h; sourceTree = "<group>"; };
+               A7E6F69C17427CF2006775E2 /* makelookupcommand.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; path = makelookupcommand.h; sourceTree = "<group>"; };
+               A7E6F69D17427D06006775E2 /* makelookupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makelookupcommand.cpp; sourceTree = "<group>"; };
                A7E9B64F12D37EC300DA6239 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = "<group>"; };
                A7E9B65012D37EC300DA6239 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = "<group>"; };
                A7E9B65112D37EC300DA6239 /* aligncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = aligncommand.cpp; sourceTree = "<group>"; };
                                A7A61F1A130035C800E05B6B /* LICENSE */,
                                A70332B512D3A13400761E33 /* makefile */,
                                A7E9B65912D37EC300DA6239 /* averagelinkage.cpp */,
+                               A77B718A173D40E4002163C2 /* calcsparcc.h */,
+                               A77B7189173D40E4002163C2 /* calcsparcc.cpp */,
                                A7E9BA4F12D398D700DA6239 /* clearcut */,
                                A7E9B69812D37EC400DA6239 /* cluster.cpp */,
                                A7E9B69912D37EC400DA6239 /* cluster.hpp */,
                                A7E9B79C12D37EC400DA6239 /* progress.hpp */,
                                A7548FAF171440ED00B1F05A /* qFinderDMM.h */,
                                A7548FAE171440EC00B1F05A /* qFinderDMM.cpp */,
+                               A77B7187173D4041002163C2 /* randomnumber.h */,
+                               A77B7186173D4041002163C2 /* randomnumber.cpp */,
                                A7E9B7A512D37EC400DA6239 /* rarecalc.cpp */,
                                A7386C191619C9FB00651424 /* randomforest */,
                                A7E9B7A612D37EC400DA6239 /* rarecalc.h */,
                        children = (
                                A7386C1B1619CACB00651424 /* abstractdecisiontree.hpp */,
                                A7386C241619E52200651424 /* abstractdecisiontree.cpp */,
-                               A7386C1C1619CACB00651424 /* abstractrandomforest.hpp */,
-                               A7386C26161A0F9C00651424 /* abstractrandomforest.cpp */,
                                A7386C1D1619CACB00651424 /* decisiontree.hpp */,
                                A7386C28161A110700651424 /* decisiontree.cpp */,
                                A7386C1E1619CACB00651424 /* macros.h */,
                                A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */,
                                A7E9B74412D37EC400DA6239 /* makegroupcommand.h */,
                                A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */,
+                               A7E6F69C17427CF2006775E2 /* makelookupcommand.h */,
+                               A7E6F69D17427D06006775E2 /* makelookupcommand.cpp */,
                                A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */,
                                A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */,
                                A7E9B75412D37EC400DA6239 /* mergefilecommand.h */,
                                A727864312E9E28C00F86ABA /* removerarecommand.cpp */,
                                A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */,
                                A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */,
+                               A7CFA42F1755400500D9ED4D /* renameseqscommand.h */,
+                               A7CFA4301755401800D9ED4D /* renameseqscommand.cpp */,
                                A7E9B7CE12D37EC400DA6239 /* reversecommand.h */,
                                A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */,
                                A7E9B7D212D37EC400DA6239 /* screenseqscommand.h */,
                                A774101314695AF60098E6AC /* shhhseqscommand.cpp */,
                                A7A32DAC14DC43D10001D2E5 /* sortseqscommand.h */,
                                A7A32DA914DC43B00001D2E5 /* sortseqscommand.cpp */,
+                               A77B7183173D222F002163C2 /* sparcccommand.h */,
+                               A77B7184173D2240002163C2 /* sparcccommand.cpp */,
                                A7E9B84012D37EC400DA6239 /* splitabundcommand.h */,
                                A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */,
                                A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */,
                                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 */,
                                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;
                };
                                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;
                                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=\"\\\"1.30.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"4/01/2013\\\"\"",
+                                       "VERSION=\"\\\"1.31.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"5/24/2013\\\"\"",
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;