]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
added rename.seqs command.
[mothur.git] / Mothur.xcodeproj / project.pbxproj
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                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>"; };
                A73DDC3713C4BF64006AAE38 /* mothurmetastats.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothurmetastats.cpp; sourceTree = "<group>"; };
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+               A7496D2C167B531B00CC7D7C /* kruskalwalliscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kruskalwalliscommand.cpp; sourceTree = "<group>"; };
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                A74D36B6137DAFAA00332B0C /* chimerauchimecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerauchimecommand.h; sourceTree = "<group>"; };
                A74D36B7137DAFAA00332B0C /* chimerauchimecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerauchimecommand.cpp; sourceTree = "<group>"; };
                A74D59A3159A1E2000043046 /* counttable.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = counttable.cpp; sourceTree = "<group>"; };
                A74D59A6159A1E3600043046 /* counttable.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = counttable.h; sourceTree = "<group>"; };
                A754149514840CF7005850D1 /* summaryqualcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summaryqualcommand.h; sourceTree = "<group>"; };
                A754149614840CF7005850D1 /* summaryqualcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summaryqualcommand.cpp; sourceTree = "<group>"; };
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+               A7548FAE171440EC00B1F05A /* qFinderDMM.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qFinderDMM.cpp; sourceTree = "<group>"; };
+               A7548FAF171440ED00B1F05A /* qFinderDMM.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qFinderDMM.h; sourceTree = "<group>"; };
                A75790571301749D00A30DAB /* homovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = homovacommand.h; sourceTree = "<group>"; };
                A75790581301749D00A30DAB /* homovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = homovacommand.cpp; sourceTree = "<group>"; };
                A76CDD7F1510F09A004C8458 /* pcrseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcrseqscommand.h; 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>"; };
                A79234D613C74BF6002B08E2 /* mothurfisher.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothurfisher.cpp; sourceTree = "<group>"; };
                A795840B13F13CD900F201D5 /* countgroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = countgroupscommand.h; sourceTree = "<group>"; };
                A795840C13F13CD900F201D5 /* countgroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = countgroupscommand.cpp; sourceTree = "<group>"; };
+               A799314816CBD0BC0017E888 /* mergetaxsummarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergetaxsummarycommand.h; sourceTree = "<group>"; };
+               A799314A16CBD0CD0017E888 /* mergetaxsummarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergetaxsummarycommand.cpp; sourceTree = "<group>"; };
                A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makefastqcommand.h; sourceTree = "<group>"; };
                A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makefastqcommand.cpp; sourceTree = "<group>"; };
+               A79EEF8516971D4A0006DEC1 /* filtersharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = filtersharedcommand.cpp; sourceTree = "<group>"; };
+               A79EEF8816971D640006DEC1 /* filtersharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filtersharedcommand.h; sourceTree = "<group>"; };
                A7A067191562946F0095C8C5 /* listotulabelscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listotulabelscommand.cpp; sourceTree = "<group>"; };
                A7A0671C156294810095C8C5 /* listotulabelscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = listotulabelscommand.h; sourceTree = "<group>"; };
                A7A0671D1562AC230095C8C5 /* makecontigscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makecontigscommand.h; sourceTree = "<group>"; };
                A7A61F2B130062E000E05B6B /* amovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = amovacommand.h; sourceTree = "<group>"; };
                A7A61F2C130062E000E05B6B /* amovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = amovacommand.cpp; sourceTree = "<group>"; };
                A7AACFBA132FE008003D6C4D /* currentfile.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = currentfile.h; sourceTree = "<group>"; };
+               A7B0231416B8244B006BA09E /* removedistscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removedistscommand.cpp; sourceTree = "<group>"; };
+               A7B0231716B8245D006BA09E /* removedistscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removedistscommand.h; sourceTree = "<group>"; };
                A7BF221214587886000AD524 /* myPerseus.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = myPerseus.cpp; sourceTree = "<group>"; };
                A7BF221314587886000AD524 /* myPerseus.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = myPerseus.h; sourceTree = "<group>"; };
                A7BF2230145879B2000AD524 /* chimeraperseuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraperseuscommand.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 */,
                                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 */,
                        children = (
                                A7386C1B1619CACB00651424 /* abstractdecisiontree.hpp */,
                                A7386C241619E52200651424 /* abstractdecisiontree.cpp */,
-                               A7386C1C1619CACB00651424 /* abstractrandomforest.hpp */,
-                               A7386C26161A0F9C00651424 /* abstractrandomforest.cpp */,
                                A7386C1D1619CACB00651424 /* decisiontree.hpp */,
                                A7386C28161A110700651424 /* decisiontree.cpp */,
                                A7386C1E1619CACB00651424 /* macros.h */,
                                A77E193A161B289600DB1A2A /* rftreenode.cpp */,
                                83F25B0A163B031200ABE73D /* forest.cpp */,
                                83F25B0B163B031200ABE73D /* forest.h */,
+                               834D9D561656D7C400E7FAB9 /* regularizedrandomforest.cpp */,
+                               834D9D571656D7C400E7FAB9 /* regularizedrandomforest.h */,
+                               834D9D5A1656DEC700E7FAB9 /* regularizeddecisiontree.cpp */,
+                               834D9D5B1656DEC700E7FAB9 /* regularizeddecisiontree.h */,
                        );
                        name = randomforest;
                        sourceTree = "<group>";
                                A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */,
                                A7E9B6E412D37EC400DA6239 /* filterseqscommand.h */,
                                A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */,
+                               A79EEF8816971D640006DEC1 /* filtersharedcommand.h */,
+                               A79EEF8516971D4A0006DEC1 /* filtersharedcommand.cpp */,
                                A778FE69134CA6CA00C0BA33 /* getcommandinfocommand.h */,
                                A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */,
                                219C1DE51559BCF2004209F9 /* getcoremicrobiomecommand.h */,
                                219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */,
                                A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */,
                                A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */,
+                               A7128B1A16B7001200723BE4 /* getdistscommand.h */,
+                               A7128B1C16B7002600723BE4 /* getdistscommand.cpp */,
                                A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */,
                                A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */,
                                A7E9B6F512D37EC400DA6239 /* getgroupscommand.h */,
                                A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */,
                                A7E9B6F712D37EC400DA6239 /* getlabelcommand.h */,
                                A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */,
+                               A7548FAB17142EA500B1F05A /* getmetacommunitycommand.h */,
+                               A7548FAC17142EBC00B1F05A /* getmetacommunitycommand.cpp */,
                                A70056E8156A93E300924A2D /* getotulabelscommand.h */,
                                A70056E5156A93D000924A2D /* getotulabelscommand.cpp */,
                                A7E9B6F912D37EC400DA6239 /* getlineagecommand.h */,
                                A75790581301749D00A30DAB /* homovacommand.cpp */,
                                A7E9B72C12D37EC400DA6239 /* indicatorcommand.h */,
                                A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */,
+                               A7496D2D167B531B00CC7D7C /* kruskalwalliscommand.h */,
+                               A7496D2C167B531B00CC7D7C /* kruskalwalliscommand.cpp */,
                                A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */,
                                A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */,
                                A7A0671C156294810095C8C5 /* listotulabelscommand.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 */,
                                A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */,
                                A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */,
                                A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */,
+                               A799314816CBD0BC0017E888 /* mergetaxsummarycommand.h */,
+                               A799314A16CBD0CD0017E888 /* mergetaxsummarycommand.cpp */,
                                A7E9B75812D37EC400DA6239 /* metastatscommand.h */,
                                A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */,
                                A7E9B75A12D37EC400DA6239 /* mgclustercommand.h */,
                                A7E9B79512D37EC400DA6239 /* pipelinepdscommand.cpp */,
                                A7E9B79812D37EC400DA6239 /* preclustercommand.h */,
                                A7E9B79712D37EC400DA6239 /* preclustercommand.cpp */,
+                               A74C06E616A9C097008390A3 /* primerdesigncommand.h */,
+                               A74C06E816A9C0A8008390A3 /* primerdesigncommand.cpp */,
                                A7E9B7A212D37EC400DA6239 /* quitcommand.h */,
                                A7E9B7A112D37EC400DA6239 /* quitcommand.cpp */,
                                A7E9B7AC12D37EC400DA6239 /* rarefactcommand.h */,
                                A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */,
                                A7E9B7AF12D37EC400DA6239 /* rarefactsharedcommand.h */,
                                A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */,
+                               A7B0231716B8245D006BA09E /* removedistscommand.h */,
+                               A7B0231416B8244B006BA09E /* removedistscommand.cpp */,
                                A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */,
                                A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */,
                                A7E9B7C612D37EC400DA6239 /* removelineagecommand.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 */,
                                A7E9B66512D37EC400DA6239 /* blastdb.hpp */,
                                A74D59A6159A1E3600043046 /* counttable.h */,
                                A74D59A3159A1E2000043046 /* counttable.cpp */,
-                               A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */,
                                A7E9B6BD12D37EC400DA6239 /* database.cpp */,
                                A7E9B6BE12D37EC400DA6239 /* database.hpp */,
                                A7E9B6BF12D37EC400DA6239 /* datavector.hpp */,
                                A7E9B6CE12D37EC400DA6239 /* distancedb.hpp */,
+                               A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */,
                                A7E9B6DE12D37EC400DA6239 /* fastamap.cpp */,
                                A7E9B6DF12D37EC400DA6239 /* fastamap.h */,
                                A7E9B6E812D37EC400DA6239 /* flowdata.h */,
                08FB7793FE84155DC02AAC07 /* Project object */ = {
                        isa = PBXProject;
                        attributes = {
-                               LastUpgradeCheck = 0420;
+                               LastUpgradeCheck = 0460;
                                ORGANIZATIONNAME = "Schloss Lab";
                        };
                        buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */;
                                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 */,
                                A721AB72161C572A009860A1 /* kmertree.cpp in Sources */,
                                A721AB77161C573B009860A1 /* taxonomynode.cpp in Sources */,
                                83F25B0C163B031200ABE73D /* forest.cpp in Sources */,
+                               834D9D581656D7C400E7FAB9 /* regularizedrandomforest.cpp in Sources */,
+                               834D9D5C1656DEC800E7FAB9 /* regularizeddecisiontree.cpp in Sources */,
+                               A7496D2E167B531B00CC7D7C /* kruskalwalliscommand.cpp in Sources */,
+                               A79EEF8616971D4A0006DEC1 /* filtersharedcommand.cpp in Sources */,
+                               A74C06E916A9C0A9008390A3 /* primerdesigncommand.cpp in Sources */,
+                               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;
                };
                                GCC_OPTIMIZATION_LEVEL = 3;
                                "INSTALL_PATH[sdk=*]" = TARGET_BUILD_DIR;
                                PRODUCT_NAME = mothur;
-                               SDKROOT = macosx10.6;
+                               SDKROOT = macosx10.8;
                                SKIP_INSTALL = NO;
                        };
                        name = Debug;
                                GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_WARN_UNUSED_VALUE = YES;
                                PRODUCT_NAME = mothur;
+                               SDKROOT = macosx;
                                SKIP_INSTALL = NO;
                        };
                        name = Release;
                                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=\"\\\"1.28.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"11/2/2012\\\"\"",
+                                       "MOTHUR_FILES=\"\\\"../../release\\\"\"",
+                                       "VERSION=\"\\\"1.31.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"5/24/2013\\\"\"",
                                );
                                "GCC_VERSION[arch=*]" = "";
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                        "-lncurses",
                                        "-lreadline",
                                );
-                               SDKROOT = macosx10.6;
+                               SDKROOT = macosx;
                                SKIP_INSTALL = NO;
                                USER_HEADER_SEARCH_PATHS = "";
                        };
                                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=\"\\\"1.28.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"11/2/2012\\\"\"",
+                                       "VERSION=\"\\\"1.31.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"5/24/2013\\\"\"",
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                        "-lncurses",
                                        "-lreadline",
                                );
-                               SDKROOT = macosx10.6;
+                               SDKROOT = macosx;
                                SKIP_INSTALL = NO;
                        };
                        name = Release;