]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
added rename.seqs command.
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index f510cfe15c1449b9878439aff18eb85cef333ec4..77cfb8c6cd50b9ec16746ef64d16f142be6fb8dc 100644 (file)
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                A7E9B70312D37EC400DA6239 /* getrabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getrabundcommand.h; sourceTree = "<group>"; };
                A7E9B70412D37EC400DA6239 /* getrelabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getrelabundcommand.cpp; sourceTree = "<group>"; };
                A7E9B70512D37EC400DA6239 /* getrelabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getrelabundcommand.h; sourceTree = "<group>"; };
-               A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsabundcommand.cpp; sourceTree = "<group>"; };
+               A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; path = getsabundcommand.cpp; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
                A7E9B70712D37EC400DA6239 /* getsabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsabundcommand.h; sourceTree = "<group>"; };
                A7E9B70812D37EC400DA6239 /* getseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getseqscommand.cpp; sourceTree = "<group>"; };
                A7E9B70912D37EC400DA6239 /* getseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getseqscommand.h; sourceTree = "<group>"; };
                A7E9B73A12D37EC400DA6239 /* libshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuff.h; sourceTree = SOURCE_ROOT; };
                A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuffcommand.cpp; sourceTree = "<group>"; };
                A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuffcommand.h; sourceTree = "<group>"; };
-               A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listseqscommand.cpp; sourceTree = "<group>"; };
+               A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; path = listseqscommand.cpp; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
                A7E9B73E12D37EC400DA6239 /* listseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = listseqscommand.h; sourceTree = "<group>"; };
                A7E9B73F12D37EC400DA6239 /* listvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listvector.cpp; sourceTree = "<group>"; };
                A7E9B74012D37EC400DA6239 /* listvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = listvector.hpp; sourceTree = "<group>"; };
                A7E9B74112D37EC400DA6239 /* logsd.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = logsd.cpp; sourceTree = "<group>"; };
                A7E9B74212D37EC400DA6239 /* logsd.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = logsd.h; sourceTree = "<group>"; };
-               A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makegroupcommand.cpp; sourceTree = "<group>"; };
+               A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; path = makegroupcommand.cpp; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
                A7E9B74412D37EC400DA6239 /* makegroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makegroupcommand.h; sourceTree = "<group>"; };
                A7E9B74512D37EC400DA6239 /* maligner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = maligner.cpp; sourceTree = "<group>"; };
                A7E9B74612D37EC400DA6239 /* maligner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = maligner.h; sourceTree = "<group>"; };
                A7E9B7B312D37EC400DA6239 /* readcluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcluster.h; sourceTree = "<group>"; };
                A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readcolumn.cpp; sourceTree = "<group>"; };
                A7E9B7B512D37EC400DA6239 /* readcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcolumn.h; sourceTree = "<group>"; };
-               A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistcommand.cpp; sourceTree = "<group>"; };
-               A7E9B7B712D37EC400DA6239 /* readdistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcommand.h; sourceTree = "<group>"; };
                A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = "<group>"; };
-               A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = "<group>"; };
-               A7E9B7BC12D37EC400DA6239 /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = "<group>"; };
                A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = "<group>"; };
                A7E9B7BE12D37EC400DA6239 /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = "<group>"; };
                A7E9B7BF12D37EC400DA6239 /* readtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtree.cpp; sourceTree = "<group>"; };
                A7E9B7C012D37EC400DA6239 /* readtree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtree.h; sourceTree = "<group>"; };
-               A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = "<group>"; };
-               A7E9B7C212D37EC400DA6239 /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = "<group>"; };
                A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removegroupscommand.cpp; sourceTree = "<group>"; };
                A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removegroupscommand.h; sourceTree = "<group>"; };
                A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removelineagecommand.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 */,
                                A7E9B7A712D37EC400DA6239 /* raredisplay.cpp */,
                                A7E9B7A812D37EC400DA6239 /* raredisplay.h */,
                1AB674ADFE9D54B511CA2CBB /* Products */ = {
                        isa = PBXGroup;
                        children = (
-                               8DD76FB20486AB0100D96B5E /* Mothur */,
+                               8DD76FB20486AB0100D96B5E /* mothur */,
                        );
                        name = Products;
                        sourceTree = "<group>";
                };
+               A7386C191619C9FB00651424 /* randomforest */ = {
+                       isa = PBXGroup;
+                       children = (
+                               A7386C1B1619CACB00651424 /* abstractdecisiontree.hpp */,
+                               A7386C241619E52200651424 /* abstractdecisiontree.cpp */,
+                               A7386C1D1619CACB00651424 /* decisiontree.hpp */,
+                               A7386C28161A110700651424 /* decisiontree.cpp */,
+                               A7386C1E1619CACB00651424 /* macros.h */,
+                               A7386C1F1619CACB00651424 /* randomforest.hpp */,
+                               A77E1937161B201E00DB1A2A /* randomforest.cpp */,
+                               A7386C201619CACB00651424 /* rftreenode.hpp */,
+                               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>";
+               };
                A7D161E7149F7F50000523E8 /* fortran */ = {
                        isa = PBXGroup;
                        children = (
                                A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */,
                                A7E9B69312D37EC400DA6239 /* classifyseqscommand.h */,
                                A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */,
+                               A7386C221619CCE600651424 /* classifysharedcommand.h */,
+                               A7386C211619CCE600651424 /* classifysharedcommand.cpp */,
                                A7EEB0F714F29C1B00344B83 /* classifytreecommand.h */,
                                A7EEB0F414F29BFD00344B83 /* classifytreecommand.cpp */,
                                A7E9B69712D37EC400DA6239 /* clearcutcommand.h */,
                                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 */,
                                A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */,
                                A7E9B6FB12D37EC400DA6239 /* getlistcountcommand.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 */,
+                               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 */,
                                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 */,
-                               A7E9B7B712D37EC400DA6239 /* readdistcommand.h */,
-                               A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */,
-                               A7E9B7BC12D37EC400DA6239 /* readotucommand.h */,
-                               A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */,
-                               A7E9B7C212D37EC400DA6239 /* readtreecommand.h */,
-                               A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */,
+                               A7B0231716B8245D006BA09E /* removedistscommand.h */,
+                               A7B0231416B8244B006BA09E /* removedistscommand.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 */,
                                A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */,
+                               A7CFA42F1755400500D9ED4D /* renameseqscommand.h */,
+                               A7CFA4301755401800D9ED4D /* renameseqscommand.cpp */,
                                A7E9B7CE12D37EC400DA6239 /* reversecommand.h */,
                                A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */,
                                A7E9B7D212D37EC400DA6239 /* screenseqscommand.h */,
                                A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */,
                                A7E9B7E412D37EC400DA6239 /* sffinfocommand.h */,
                                A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */,
+                               A7C7DAB615DA75760059B0CF /* sffmultiplecommand.h */,
+                               A7C7DAB815DA758B0059B0CF /* sffmultiplecommand.cpp */,
                                A7E9B7F312D37EC400DA6239 /* sharedcommand.h */,
                                A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */,
                                A7E9B82812D37EC400DA6239 /* shhhercommand.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 */,
                                A7E9B67112D37EC400DA6239 /* canberra.h */,
                                A7E9B67612D37EC400DA6239 /* chao1.cpp */,
                                A7E9B67712D37EC400DA6239 /* chao1.h */,
-                               A7E9B6A412D37EC400DA6239 /* cmdargs.cpp */,
-                               A7E9B6A512D37EC400DA6239 /* cmdargs.h */,
                                A7E9B6BB12D37EC400DA6239 /* coverage.cpp */,
                                A7E9B6BC12D37EC400DA6239 /* coverage.h */,
                                A7E9B6CA12D37EC400DA6239 /* dist.h */,
                                A7E9B66312D37EC400DA6239 /* blastalign.hpp */,
                                A7E9B66412D37EC400DA6239 /* blastdb.cpp */,
                                A7E9B66512D37EC400DA6239 /* blastdb.hpp */,
+                               A74D59A6159A1E3600043046 /* counttable.h */,
+                               A74D59A3159A1E2000043046 /* counttable.cpp */,
                                A7E9B6BD12D37EC400DA6239 /* database.cpp */,
                                A7E9B6BE12D37EC400DA6239 /* database.hpp */,
                                A7E9B6BF12D37EC400DA6239 /* datavector.hpp */,
-                               A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */,
                                A7E9B6CE12D37EC400DA6239 /* distancedb.hpp */,
+                               A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */,
                                A7E9B6DE12D37EC400DA6239 /* fastamap.cpp */,
                                A7E9B6DF12D37EC400DA6239 /* fastamap.h */,
                                A7E9B6E812D37EC400DA6239 /* flowdata.h */,
                                A7E9B7D012D37EC400DA6239 /* sabundvector.hpp */,
                                A7E9B7DB12D37EC400DA6239 /* sequence.cpp */,
                                A7E9B7DC12D37EC400DA6239 /* sequence.hpp */,
+                               A741FAD415D168A00067BCC5 /* sequencecountparser.h */,
+                               A741FAD115D1688E0067BCC5 /* sequencecountparser.cpp */,
                                A7E9B7DD12D37EC400DA6239 /* sequencedb.cpp */,
                                A7E9B7DE12D37EC400DA6239 /* sequencedb.h */,
                                A7F9F5CD141A5E500032F693 /* sequenceparser.h */,
                                A7E9B81412D37EC400DA6239 /* sharedsabundvector.h */,
                                A7E9B83912D37EC400DA6239 /* sparsematrix.cpp */,
                                A7E9B83A12D37EC400DA6239 /* sparsematrix.hpp */,
+                               A7E0243F15B4522000A5F046 /* sparsedistancematrix.h */,
+                               A7E0243C15B4520A00A5F046 /* sparsedistancematrix.cpp */,
                                A7E9B85112D37EC400DA6239 /* suffixdb.cpp */,
                                A7E9B85212D37EC400DA6239 /* suffixdb.hpp */,
                                A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */,
                A7E9BA4B12D3966900DA6239 /* classifier */ = {
                        isa = PBXGroup;
                        children = (
-                               A7E9B65A12D37EC300DA6239 /* bayesian.cpp */,
+                               A721AB67161C570F009860A1 /* alignnode.h */,
+                               A721AB66161C570F009860A1 /* alignnode.cpp */,
+                               A721AB69161C570F009860A1 /* aligntree.h */,
+                               A721AB68161C570F009860A1 /* aligntree.cpp */,
                                A7E9B65B12D37EC300DA6239 /* bayesian.h */,
+                               A7E9B65A12D37EC300DA6239 /* bayesian.cpp */,
                                A7E9B68E12D37EC400DA6239 /* classify.cpp */,
                                A7E9B68F12D37EC400DA6239 /* classify.h */,
+                               A721AB6E161C572A009860A1 /* kmernode.h */,
+                               A721AB6D161C572A009860A1 /* kmernode.cpp */,
+                               A721AB70161C572A009860A1 /* kmertree.h */,
+                               A721AB6F161C572A009860A1 /* kmertree.cpp */,
                                A7E9B73812D37EC400DA6239 /* knn.h */,
                                A7E9B73712D37EC400DA6239 /* knn.cpp */,
                                A7E9B78D12D37EC400DA6239 /* phylosummary.cpp */,
                                A7E9B79012D37EC400DA6239 /* phylotree.h */,
                                A7E9B85D12D37EC400DA6239 /* taxonomyequalizer.cpp */,
                                A7E9B85E12D37EC400DA6239 /* taxonomyequalizer.h */,
+                               A721AB74161C573B009860A1 /* taxonomynode.h */,
+                               A721AB73161C573B009860A1 /* taxonomynode.cpp */,
                        );
                        name = classifier;
                        sourceTree = "<group>";
                        children = (
                                A7E9B69412D37EC400DA6239 /* clearcut.cpp */,
                                A7E9B69512D37EC400DA6239 /* clearcut.h */,
+                               A7E9B6A412D37EC400DA6239 /* cmdargs.cpp */,
+                               A7E9B6A512D37EC400DA6239 /* cmdargs.h */,
                                A7E9B6B312D37EC400DA6239 /* common.h */,
                                A7E9B6CF12D37EC400DA6239 /* distclearcut.cpp */,
                                A7E9B6D012D37EC400DA6239 /* distclearcut.h */,
                        name = Mothur;
                        productInstallPath = "$(HOME)/bin";
                        productName = mothur;
-                       productReference = 8DD76FB20486AB0100D96B5E /* Mothur */;
+                       productReference = 8DD76FB20486AB0100D96B5E /* mothur */;
                        productType = "com.apple.product-type.tool";
                };
 /* End PBXNativeTarget section */
                08FB7793FE84155DC02AAC07 /* Project object */ = {
                        isa = PBXProject;
                        attributes = {
-                               LastUpgradeCheck = 0420;
+                               LastUpgradeCheck = 0460;
                                ORGANIZATIONNAME = "Schloss Lab";
                        };
                        buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */;
                                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 */,
                                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 */,
+                               A741FAD215D1688E0067BCC5 /* sequencecountparser.cpp in Sources */,
+                               A7C7DAB915DA758B0059B0CF /* sffmultiplecommand.cpp in Sources */,
+                               A7386C231619CCE600651424 /* classifysharedcommand.cpp in Sources */,
+                               A7386C251619E52300651424 /* abstractdecisiontree.cpp in Sources */,
+                               A7386C29161A110800651424 /* decisiontree.cpp in Sources */,
+                               A77E1938161B201E00DB1A2A /* randomforest.cpp in Sources */,
+                               A77E193B161B289600DB1A2A /* rftreenode.cpp in Sources */,
+                               A721AB6A161C570F009860A1 /* alignnode.cpp in Sources */,
+                               A721AB6B161C570F009860A1 /* aligntree.cpp in Sources */,
+                               A721AB71161C572A009860A1 /* kmernode.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;
                };
                        isa = XCBuildConfiguration;
                        buildSettings = {
                                ALWAYS_SEARCH_USER_PATHS = NO;
-                               CONFIGURATION_TEMP_DIR = /Users/pschloss/Desktop/mothur;
                                COPY_PHASE_STRIP = NO;
                                DEPLOYMENT_LOCATION = YES;
+                               DSTROOT = TARGET_BUILD_DIR;
+                               "DSTROOT[sdk=*]" = TARGET_BUILD_DIR;
                                GCC_DYNAMIC_NO_PIC = NO;
                                GCC_MODEL_TUNING = G5;
-                               GCC_OPTIMIZATION_LEVEL = 0;
-                               INSTALL_PATH = /Users/pschloss/Desktop/mothur/build/Debug;
-                               OBJROOT = /Users/pschloss/Desktop/mothur;
-                               PRODUCT_NAME = Mothur;
-                               SDKROOT = macosx10.6;
-                               SYMROOT = /Users/pschloss/Desktop/mothur;
+                               GCC_OPTIMIZATION_LEVEL = 3;
+                               "INSTALL_PATH[sdk=*]" = TARGET_BUILD_DIR;
+                               PRODUCT_NAME = mothur;
+                               SDKROOT = macosx10.8;
+                               SKIP_INSTALL = NO;
                        };
                        name = Debug;
                };
                        isa = XCBuildConfiguration;
                        buildSettings = {
                                ALWAYS_SEARCH_USER_PATHS = NO;
-                               CONFIGURATION_TEMP_DIR = /Users/pschloss/Desktop/mothur;
                                DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
                                DEPLOYMENT_LOCATION = YES;
+                               DSTROOT = TARGET_BUILD_DIR;
                                GCC_MODEL_TUNING = G5;
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_WARN_UNUSED_VALUE = YES;
-                               INSTALL_PATH = /Users/pschloss/Desktop/mothur/build/Debug;
-                               OBJROOT = /Users/pschloss/Desktop/mothur;
-                               PRODUCT_NAME = Mothur;
-                               SYMROOT = /Users/pschloss/Desktop/mothur;
+                               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 = 0;
+                               GCC_OPTIMIZATION_LEVEL = s;
                                GCC_PREPROCESSOR_DEFINITIONS = (
-                                       "MOTHUR_FILES=\"\\\"../release\\\"\"",
-                                       "VERSION=\"\\\"1.24.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"3/12/2012\\\"\"",
+                                       "MOTHUR_FILES=\"\\\"../../release\\\"\"",
+                                       "VERSION=\"\\\"1.31.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"5/24/2013\\\"\"",
                                );
                                "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 = (
                                        "-lncurses",
                                        "-lreadline",
                                );
-                               SDKROOT = macosx10.6;
+                               SDKROOT = macosx;
+                               SKIP_INSTALL = NO;
                                USER_HEADER_SEARCH_PATHS = "";
                        };
                        name = Debug;
                                GCC_C_LANGUAGE_STANDARD = gnu99;
                                GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
                                GCC_MODEL_TUNING = "";
-                               GCC_OPTIMIZATION_LEVEL = 0;
+                               GCC_OPTIMIZATION_LEVEL = s;
                                GCC_PREPROCESSOR_DEFINITIONS = (
-                                       "VERSION=\"\\\"1.25.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"4/30/2012\\\"\"",
+                                       "VERSION=\"\\\"1.31.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"5/24/2013\\\"\"",
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                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",
                                        "-lncurses",
                                        "-lreadline",
                                );
-                               SDKROOT = macosx10.6;
+                               SDKROOT = macosx;
+                               SKIP_INSTALL = NO;
                        };
                        name = Release;
                };
                                1DEB928708733DD80010E9CD /* Release */,
                        );
                        defaultConfigurationIsVisible = 0;
-                       defaultConfigurationName = Release;
+                       defaultConfigurationName = Debug;
                };
                1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
                        isa = XCConfigurationList;
                                1DEB928B08733DD80010E9CD /* Release */,
                        );
                        defaultConfigurationIsVisible = 0;
-                       defaultConfigurationName = Release;
+                       defaultConfigurationName = Debug;
                };
 /* End XCConfigurationList section */
        };