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fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mantelcommand.h; sourceTree = ""; }; A7FA10011302E096003860FE /* mantelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mantelcommand.cpp; sourceTree = ""; }; + A7FA2ABC14A0E881007C09A6 /* bsplvb.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = bsplvb.f; sourceTree = ""; }; + A7FA2ABD14A0E881007C09A6 /* bsplvd.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = bsplvd.f; sourceTree = ""; }; + A7FA2ABE14A0E881007C09A6 /* bvalue.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = bvalue.f; sourceTree = ""; }; + A7FA2ABF14A0E881007C09A6 /* daxpy.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = daxpy.f; sourceTree = ""; }; + A7FA2AC014A0E881007C09A6 /* ddot.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = ddot.f; sourceTree = ""; }; + A7FA2AC114A0E881007C09A6 /* dpbfa.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = dpbfa.f; sourceTree = ""; }; + A7FA2AC214A0E881007C09A6 /* dpbsl.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = dpbsl.f; sourceTree = ""; }; + A7FA2AC314A0E881007C09A6 /* interv.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = interv.f; sourceTree = ""; }; + A7FA2AC414A0E881007C09A6 /* sgram.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = sgram.f; sourceTree = ""; }; + A7FA2AC514A0E881007C09A6 /* sinerp.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = sinerp.f; sourceTree = ""; }; + A7FA2AC614A0E881007C09A6 /* stxwx.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = stxwx.f; sourceTree = ""; }; + A7FA2B1514A0EBEA007C09A6 /* sslvrg.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = sslvrg.f; sourceTree = ""; }; + A7FA2B5A14A0F0C2007C09A6 /* intrv.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = intrv.f; sourceTree = ""; }; A7FC480C12D788F20055BC5C /* linearalgebra.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = linearalgebra.h; sourceTree = ""; }; A7FC480D12D788F20055BC5C /* linearalgebra.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = linearalgebra.cpp; sourceTree = ""; }; A7FC486512D795D60055BC5C /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = ""; }; @@ -899,6 +1072,10 @@ A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getcurrentcommand.cpp; sourceTree = ""; }; A7FE7E6B13311EA400F7B327 /* setcurrentcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setcurrentcommand.h; sourceTree = ""; }; A7FE7E6C13311EA400F7B327 /* setcurrentcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setcurrentcommand.cpp; sourceTree = ""; }; + A7FF19F0140FFDA500AD216D /* trimoligos.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = trimoligos.h; sourceTree = ""; }; + A7FF19F1140FFDA500AD216D /* trimoligos.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = trimoligos.cpp; sourceTree = ""; }; + A7FFB556142CA02C004884F2 /* summarytaxcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarytaxcommand.h; sourceTree = ""; }; + A7FFB557142CA02C004884F2 /* summarytaxcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarytaxcommand.cpp; sourceTree = ""; }; C6A0FF2C0290799A04C91782 /* mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = mothur.1; sourceTree = ""; }; /* End PBXFileReference section */ @@ -977,6 +1154,8 @@ A7E9B75C12D37EC400DA6239 /* mothur.h */, A7E9B75D12D37EC400DA6239 /* mothurout.cpp */, A7E9B75E12D37EC400DA6239 /* mothurout.h */, + A774104714696F320098E6AC /* myseqdist.h */, + A774104614696F320098E6AC /* myseqdist.cpp */, A7E9B76112D37EC400DA6239 /* nast.cpp */, A7E9B76212D37EC400DA6239 /* nast.hpp */, A7E9B76312D37EC400DA6239 /* nastreport.cpp */, @@ -1001,18 +1180,18 @@ A7E9B7AD12D37EC400DA6239 /* rarefactioncurvedata.h */, 7E6BE10812F710D8007ADDBE /* refchimeratest.h */, 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */, + A77410F514697C300098E6AC /* seqnoise.h */, + A77410F414697C300098E6AC /* seqnoise.cpp */, A7E9BA5312D39A5E00DA6239 /* read */, A7E9B82312D37EC400DA6239 /* sharedutilities.cpp */, A7E9B82412D37EC400DA6239 /* sharedutilities.h */, A7E9B82D12D37EC400DA6239 /* singlelinkage.cpp */, A7E9B83012D37EC400DA6239 /* slibshuff.cpp */, - A7E9B85112D37EC400DA6239 /* suffixdb.cpp */, A7E9B83112D37EC400DA6239 /* slibshuff.h */, - A7E9B85212D37EC400DA6239 /* suffixdb.hpp */, - A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */, - A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */, - A7E9B85512D37EC400DA6239 /* suffixtree.cpp */, - A7E9B85612D37EC400DA6239 /* suffixtree.hpp */, + A7C3DC0E14FE469500FE1924 /* trialswap2.h */, + A7C3DC0D14FE469500FE1924 /* trialSwap2.cpp */, + A7FF19F0140FFDA500AD216D /* trimoligos.h */, + A7FF19F1140FFDA500AD216D /* trimoligos.cpp */, A7E9B87412D37EC400DA6239 /* validcalculator.cpp */, A7E9B87512D37EC400DA6239 /* validcalculator.h */, A7E9B87612D37EC400DA6239 /* validparameter.cpp */, @@ -1032,6 +1211,83 @@ name = Products; sourceTree = ""; }; + A74D3644137DA7CE00332B0C /* uchime */ = { + isa = PBXGroup; + children = ( + A74D3655137DAB8300332B0C /* addtargets2.cpp */, + A74D3656137DAB8300332B0C /* alignchime.cpp */, + A74D3657137DAB8300332B0C /* alignchimel.cpp */, + A74D3658137DAB8300332B0C /* allocs.h */, + A74D3659137DAB8300332B0C /* alnheuristics.h */, + A74D365A137DAB8300332B0C /* alnparams.cpp */, + A74D365B137DAB8300332B0C /* alnparams.h */, + A74D365C137DAB8300332B0C /* alpha.cpp */, + A74D365D137DAB8300332B0C /* alpha.h */, + A74D365E137DAB8300332B0C /* alpha2.cpp */, + A74D365F137DAB8300332B0C /* chainer.h */, + A74D3660137DAB8300332B0C /* chime.h */, + A74D3661137DAB8300332B0C /* diagbox.h */, + A74D3662137DAB8300332B0C /* dp.h */, + A74D3663137DAB8300332B0C /* evalue.h */, + A74D3664137DAB8300332B0C /* fractid.cpp */, + A74D3665137DAB8300332B0C /* getparents.cpp */, + A74D3666137DAB8300332B0C /* globalalign2.cpp */, + A74D3667137DAB8300332B0C /* help.h */, + A74D3668137DAB8300332B0C /* hsp.h */, + A74D3669137DAB8300332B0C /* hspfinder.h */, + A74D366A137DAB8300332B0C /* make3way.cpp */, + A74D366B137DAB8300332B0C /* mx.cpp */, + A74D366C137DAB8300332B0C /* mx.h */, + A74D366D137DAB8300332B0C /* myopts.h */, + A74D366E137DAB8300332B0C /* myutils.cpp */, + A74D366F137DAB8300332B0C /* myutils.h */, + A74D3670137DAB8300332B0C /* orf.h */, + A74D3671137DAB8300332B0C /* out.h */, + A74D3672137DAB8300332B0C /* path.cpp */, + A74D3673137DAB8300332B0C /* path.h */, + A74D3674137DAB8300332B0C /* searchchime.cpp */, + A74D3675137DAB8300332B0C /* seq.h */, + A74D3676137DAB8300332B0C /* seqdb.cpp */, + A74D3677137DAB8300332B0C /* seqdb.h */, + A74D3678137DAB8300332B0C /* setnucmx.cpp */, + A74D3679137DAB8300332B0C /* sfasta.cpp */, + A74D367A137DAB8300332B0C /* sfasta.h */, + A74D367B137DAB8300332B0C /* svnmods.h */, + A74D367C137DAB8300332B0C /* svnversion.h */, + A74D367D137DAB8300332B0C /* timers.h */, + A74D367E137DAB8300332B0C /* timing.h */, + A74D367F137DAB8300332B0C /* tracebackbit.cpp */, + A74D3680137DAB8300332B0C /* uc.h */, + A74D3681137DAB8300332B0C /* uchime_main.cpp */, + A74D3682137DAB8300332B0C /* ultra.h */, + A74D3683137DAB8300332B0C /* usort.cpp */, + A74D3684137DAB8300332B0C /* viterbifast.cpp */, + A74D3685137DAB8300332B0C /* windex.h */, + A74D3686137DAB8300332B0C /* writechhit.cpp */, + ); + name = uchime; + sourceTree = ""; + }; + A7D161E7149F7F50000523E8 /* fortran */ = { + isa = PBXGroup; + children = ( + A7FA2B5A14A0F0C2007C09A6 /* intrv.f */, + A7FA2B1514A0EBEA007C09A6 /* sslvrg.f */, + A7FA2ABC14A0E881007C09A6 /* bsplvb.f */, + A7FA2ABD14A0E881007C09A6 /* bsplvd.f */, + A7FA2ABE14A0E881007C09A6 /* bvalue.f */, + A7FA2ABF14A0E881007C09A6 /* daxpy.f */, + A7FA2AC014A0E881007C09A6 /* ddot.f */, + A7FA2AC114A0E881007C09A6 /* dpbfa.f */, + A7FA2AC214A0E881007C09A6 /* dpbsl.f */, + A7FA2AC314A0E881007C09A6 /* interv.f */, + A7FA2AC414A0E881007C09A6 /* sgram.f */, + A7FA2AC514A0E881007C09A6 /* sinerp.f */, + A7FA2AC614A0E881007C09A6 /* stxwx.f */, + ); + name = fortran; + sourceTree = ""; + }; A7E9BA3812D3956100DA6239 /* commands */ = { isa = PBXGroup; children = ( @@ -1056,16 +1312,24 @@ A7E9B67E12D37EC400DA6239 /* chimeracheckcommand.cpp */, A7E9B68312D37EC400DA6239 /* chimerapintailcommand.h */, A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */, + A7BF2230145879B2000AD524 /* chimeraperseuscommand.h */, + A7BF2231145879B2000AD524 /* chimeraperseuscommand.cpp */, A7E9B68B12D37EC400DA6239 /* chimeraslayercommand.h */, A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */, + A74D36B6137DAFAA00332B0C /* chimerauchimecommand.h */, + A74D36B7137DAFAA00332B0C /* chimerauchimecommand.cpp */, A7E9B68D12D37EC400DA6239 /* chopseqscommand.h */, A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */, A7E9B69112D37EC400DA6239 /* classifyotucommand.h */, A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */, A7E9B69312D37EC400DA6239 /* classifyseqscommand.h */, A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */, + A7EEB0F714F29C1B00344B83 /* classifytreecommand.h */, + A7EEB0F414F29BFD00344B83 /* classifytreecommand.cpp */, A7E9B69712D37EC400DA6239 /* clearcutcommand.h */, A7E9B69612D37EC400DA6239 /* clearcutcommand.cpp */, + A73DDBB813C4A0D1006AAE38 /* clearmemorycommand.h */, + A73DDBB913C4A0D1006AAE38 /* clearmemorycommand.cpp */, A7E9B69D12D37EC400DA6239 /* clustercommand.h */, A7E9B69C12D37EC400DA6239 /* clustercommand.cpp */, A7E9B69F12D37EC400DA6239 /* clusterdoturcommand.h */, @@ -1082,14 +1346,22 @@ A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */, A7E9B6B812D37EC400DA6239 /* consensusseqscommand.h */, A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */, + A7C3DC0A14FE457500FE1924 /* cooccurrencecommand.h */, + A7C3DC0914FE457500FE1924 /* cooccurrencecommand.cpp */, A7E9B6BA12D37EC400DA6239 /* corraxescommand.h */, A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */, + A795840B13F13CD900F201D5 /* countgroupscommand.h */, + A795840C13F13CD900F201D5 /* countgroupscommand.cpp */, + A7730EFD13967241007433A3 /* countseqscommand.h */, + A7730EFE13967241007433A3 /* countseqscommand.cpp */, A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */, A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */, A7E9B6C612D37EC400DA6239 /* degapseqscommand.h */, A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */, A7E9B6C812D37EC400DA6239 /* deuniqueseqscommand.h */, A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */, + A77A221D139001B600B0BE70 /* deuniquetreecommand.h */, + A77A221E139001B600B0BE70 /* deuniquetreecommand.cpp */, A7E9B6CC12D37EC400DA6239 /* distancecommand.h */, A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */, A7E9B6E412D37EC400DA6239 /* filterseqscommand.h */, @@ -1160,6 +1432,8 @@ A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */, A713EBEB12DC7C5E000092AC /* nmdscommand.h */, A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */, + A7A3C8C814D041AD00B1BFBE /* otuassociationcommand.h */, + A7A3C8C714D041AD00B1BFBE /* otuassociationcommand.cpp */, A7E9B77A12D37EC400DA6239 /* otuhierarchycommand.h */, A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */, A7E9B77E12D37EC400DA6239 /* pairwiseseqscommand.h */, @@ -1174,6 +1448,8 @@ A7FC486612D795D60055BC5C /* pcacommand.cpp */, A7E9B78812D37EC400DA6239 /* pcoacommand.h */, A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */, + A76CDD7F1510F09A004C8458 /* pcrseqscommand.h */, + A76CDD811510F143004C8458 /* prcseqscommand.cpp */, A7E9B78C12D37EC400DA6239 /* phylodiversitycommand.h */, A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */, A7E9B79212D37EC400DA6239 /* phylotypecommand.h */, @@ -1228,6 +1504,10 @@ A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */, A7E9B82812D37EC400DA6239 /* shhhercommand.h */, A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */, + A774101214695AF60098E6AC /* shhhseqscommand.h */, + A774101314695AF60098E6AC /* shhhseqscommand.cpp */, + A7A32DAC14DC43D10001D2E5 /* sortseqscommand.h */, + A7A32DA914DC43B00001D2E5 /* sortseqscommand.cpp */, A7E9B84012D37EC400DA6239 /* splitabundcommand.h */, A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */, A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */, @@ -1236,8 +1516,12 @@ A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */, A7E9B85812D37EC400DA6239 /* summarycommand.h */, A7E9B85712D37EC400DA6239 /* summarycommand.cpp */, + A754149514840CF7005850D1 /* summaryqualcommand.h */, + A754149614840CF7005850D1 /* summaryqualcommand.cpp */, A7E9B85A12D37EC400DA6239 /* summarysharedcommand.h */, A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */, + A7FFB556142CA02C004884F2 /* summarytaxcommand.h */, + A7FFB557142CA02C004884F2 /* summarytaxcommand.cpp */, A7E9B85C12D37EC400DA6239 /* systemcommand.h */, A7E9B85B12D37EC400DA6239 /* systemcommand.cpp */, A7E9B86312D37EC400DA6239 /* treegroupscommand.h */, @@ -1259,6 +1543,7 @@ A7E9BA3F12D395F700DA6239 /* calculators */ = { isa = PBXGroup; children = ( + 7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */, A7E9B64F12D37EC300DA6239 /* ace.cpp */, A7E9B65012D37EC300DA6239 /* ace.h */, A7E9B65E12D37EC300DA6239 /* bergerparker.cpp */, @@ -1286,8 +1571,6 @@ A7E9B6D712D37EC400DA6239 /* efron.cpp */, A7E9B6D812D37EC400DA6239 /* efron.h */, A7E9B6E212D37EC400DA6239 /* filters.h */, - A7E9B6E512D37EC400DA6239 /* fisher2.c */, - A7E9B6E612D37EC400DA6239 /* fisher2.h */, A7E9B6F012D37EC400DA6239 /* geom.cpp */, A7E9B6F112D37EC400DA6239 /* geom.h */, A7E9B70E12D37EC400DA6239 /* goodscoverage.cpp */, @@ -1336,7 +1619,6 @@ A7E9B7E812D37EC400DA6239 /* shannoneven.h */, A7E9B7E912D37EC400DA6239 /* sharedace.cpp */, A7E9B7EA12D37EC400DA6239 /* sharedace.h */, - A7E9B7EB12D37EC400DA6239 /* sharedanderberg.h */, A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */, A7E9B7ED12D37EC400DA6239 /* sharedanderbergs.h */, A7E9B7EE12D37EC400DA6239 /* sharedbraycurtis.cpp */, @@ -1460,6 +1742,8 @@ A7E9B7A012D37EC400DA6239 /* qualityscores.h */, A7E9B7A312D37EC400DA6239 /* rabundvector.cpp */, A7E9B7A412D37EC400DA6239 /* rabundvector.hpp */, + A721765513BB9F7D0014DAAE /* referencedb.h */, + A721765613BB9F7D0014DAAE /* referencedb.cpp */, A7E9B7CB12D37EC400DA6239 /* reportfile.cpp */, A7E9B7CC12D37EC400DA6239 /* reportfile.h */, A7E9B7CF12D37EC400DA6239 /* sabundvector.cpp */, @@ -1468,18 +1752,26 @@ A7E9B7DC12D37EC400DA6239 /* sequence.hpp */, A7E9B7DD12D37EC400DA6239 /* sequencedb.cpp */, A7E9B7DE12D37EC400DA6239 /* sequencedb.h */, + A7F9F5CD141A5E500032F693 /* sequenceparser.h */, + A7F9F5CE141A5E500032F693 /* sequenceparser.cpp */, A7E9B80412D37EC400DA6239 /* sharedlistvector.cpp */, A7E9B80512D37EC400DA6239 /* sharedlistvector.h */, A7E9B80E12D37EC400DA6239 /* sharedordervector.h */, A7E9B80D12D37EC400DA6239 /* sharedordervector.cpp */, - A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */, A7E9B81012D37EC400DA6239 /* sharedrabundfloatvector.h */, + A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */, A7E9B81112D37EC400DA6239 /* sharedrabundvector.cpp */, A7E9B81212D37EC400DA6239 /* sharedrabundvector.h */, A7E9B81312D37EC400DA6239 /* sharedsabundvector.cpp */, A7E9B81412D37EC400DA6239 /* sharedsabundvector.h */, A7E9B83912D37EC400DA6239 /* sparsematrix.cpp */, A7E9B83A12D37EC400DA6239 /* sparsematrix.hpp */, + A7E9B85112D37EC400DA6239 /* suffixdb.cpp */, + A7E9B85212D37EC400DA6239 /* suffixdb.hpp */, + A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */, + A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */, + A7E9B85512D37EC400DA6239 /* suffixtree.cpp */, + A7E9B85612D37EC400DA6239 /* suffixtree.hpp */, A7E9B85F12D37EC400DA6239 /* tree.cpp */, A7E9B86012D37EC400DA6239 /* tree.h */, A7E9B86412D37EC400DA6239 /* treemap.cpp */, @@ -1493,6 +1785,7 @@ A7E9BA4512D3965600DA6239 /* chimera */ = { isa = PBXGroup; children = ( + A74D3644137DA7CE00332B0C /* uchime */, A7E9B65C12D37EC300DA6239 /* bellerophon.cpp */, A7E9B65D12D37EC300DA6239 /* bellerophon.h */, A7E9B67412D37EC400DA6239 /* ccode.cpp */, @@ -1503,12 +1796,14 @@ A7E9B68112D37EC400DA6239 /* chimeracheckrdp.h */, A7E9B68412D37EC400DA6239 /* chimerarealigner.cpp */, A7E9B68512D37EC400DA6239 /* chimerarealigner.h */, + A7E9B6C212D37EC400DA6239 /* decalc.h */, + A7E9B6C112D37EC400DA6239 /* decalc.cpp */, A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */, A7E9B68912D37EC400DA6239 /* chimeraslayer.h */, - A7E9B6C112D37EC400DA6239 /* decalc.cpp */, A7E9B74612D37EC400DA6239 /* maligner.h */, - A7E9B6C212D37EC400DA6239 /* decalc.h */, A7E9B74512D37EC400DA6239 /* maligner.cpp */, + A7BF221314587886000AD524 /* myPerseus.h */, + A7BF221214587886000AD524 /* myPerseus.cpp */, A7E9B79312D37EC400DA6239 /* pintail.cpp */, A7E9B79412D37EC400DA6239 /* pintail.h */, A7E9B82E12D37EC400DA6239 /* slayer.cpp */, @@ -1586,8 +1881,13 @@ A7E9BA5612D39BD800DA6239 /* metastats */ = { isa = PBXGroup; children = ( - A7E9B75512D37EC400DA6239 /* metastats.h */, - A7E9B75612D37EC400DA6239 /* metastats2.c */, + A7D161E7149F7F50000523E8 /* fortran */, + A79234D513C74BF6002B08E2 /* mothurfisher.h */, + A79234D613C74BF6002B08E2 /* mothurfisher.cpp */, + A73DDC3613C4BF64006AAE38 /* mothurmetastats.h */, + A73DDC3713C4BF64006AAE38 /* mothurmetastats.cpp */, + A74A9A9D148E881E00AB5E3E /* spline.h */, + A74A9A9E148E881E00AB5E3E /* spline.cpp */, ); name = metastats; sourceTree = ""; @@ -1612,6 +1912,7 @@ 8DD76FAF0486AB0100D96B5E /* CopyFiles */, ); buildRules = ( + A7D162CB149F96CA000523E8 /* PBXBuildRule */, ); dependencies = ( ); @@ -1722,7 +2023,6 @@ A7E9B8C412D37EC400DA6239 /* fastamap.cpp in Sources */, A7E9B8C512D37EC400DA6239 /* fileoutput.cpp in Sources */, A7E9B8C612D37EC400DA6239 /* filterseqscommand.cpp in Sources */, - A7E9B8C712D37EC400DA6239 /* fisher2.c in Sources */, A7E9B8C812D37EC400DA6239 /* flowdata.cpp in Sources */, A7E9B8C912D37EC400DA6239 /* formatcolumn.cpp in Sources */, A7E9B8CA12D37EC400DA6239 /* formatphylip.cpp in Sources */, @@ -1776,7 +2076,6 @@ A7E9B8FB12D37EC400DA6239 /* memeuclidean.cpp in Sources */, A7E9B8FC12D37EC400DA6239 /* mempearson.cpp in Sources */, A7E9B8FD12D37EC400DA6239 /* mergefilecommand.cpp in Sources */, - A7E9B8FE12D37EC400DA6239 /* metastats2.c in Sources */, A7E9B8FF12D37EC400DA6239 /* metastatscommand.cpp in Sources */, A7E9B90012D37EC400DA6239 /* mgclustercommand.cpp in Sources */, A7E9B90112D37EC400DA6239 /* mothur.cpp in Sources */, @@ -1937,6 +2236,65 @@ A7FE7C401330EA1000F7B327 /* getcurrentcommand.cpp in Sources */, A7FE7E6D13311EA400F7B327 /* setcurrentcommand.cpp in Sources */, A778FE6B134CA6CA00C0BA33 /* getcommandinfocommand.cpp in Sources */, + A74D3687137DAB8300332B0C /* addtargets2.cpp in Sources */, + A74D3688137DAB8400332B0C /* alignchime.cpp in Sources */, + A74D3689137DAB8400332B0C /* alignchimel.cpp in Sources */, + A74D368A137DAB8400332B0C /* alnparams.cpp in Sources */, + A74D368B137DAB8400332B0C /* alpha.cpp in Sources */, + A74D368C137DAB8400332B0C /* alpha2.cpp in Sources */, + A74D368D137DAB8400332B0C /* fractid.cpp in Sources */, + A74D368E137DAB8400332B0C /* getparents.cpp in Sources */, + A74D368F137DAB8400332B0C /* globalalign2.cpp in Sources */, + A74D3690137DAB8400332B0C /* make3way.cpp in Sources */, + A74D3691137DAB8400332B0C /* mx.cpp in Sources */, + A74D3692137DAB8400332B0C /* myutils.cpp in Sources */, + A74D3693137DAB8400332B0C /* path.cpp in Sources */, + A74D3694137DAB8400332B0C /* searchchime.cpp in Sources */, + A74D3695137DAB8400332B0C /* seqdb.cpp in Sources */, + A74D3696137DAB8400332B0C /* setnucmx.cpp in Sources */, + A74D3697137DAB8400332B0C /* sfasta.cpp in Sources */, + A74D3698137DAB8400332B0C /* tracebackbit.cpp in Sources */, + A74D3699137DAB8400332B0C /* uchime_main.cpp in Sources */, + A74D369A137DAB8400332B0C /* usort.cpp in Sources */, + A74D369B137DAB8400332B0C /* viterbifast.cpp in Sources */, + A74D369C137DAB8400332B0C /* writechhit.cpp in Sources */, + A74D36B8137DAFAA00332B0C /* chimerauchimecommand.cpp in Sources */, + A77A221F139001B600B0BE70 /* deuniquetreecommand.cpp in Sources */, + A7730EFF13967241007433A3 /* countseqscommand.cpp in Sources */, + A721765713BB9F7D0014DAAE /* referencedb.cpp in Sources */, + A73DDBBA13C4A0D1006AAE38 /* clearmemorycommand.cpp in Sources */, + A73DDC3813C4BF64006AAE38 /* mothurmetastats.cpp in Sources */, + A79234D713C74BF6002B08E2 /* mothurfisher.cpp in Sources */, + A795840D13F13CD900F201D5 /* countgroupscommand.cpp in Sources */, + A7FF19F2140FFDA500AD216D /* trimoligos.cpp in Sources */, + A7F9F5CF141A5E500032F693 /* sequenceparser.cpp in Sources */, + A7FFB558142CA02C004884F2 /* summarytaxcommand.cpp in Sources */, + A7BF221414587886000AD524 /* myPerseus.cpp in Sources */, + A7BF2232145879B2000AD524 /* chimeraperseuscommand.cpp in Sources */, + A774101414695AF60098E6AC /* shhhseqscommand.cpp in Sources */, + A774104814696F320098E6AC /* myseqdist.cpp in Sources */, + A77410F614697C300098E6AC /* seqnoise.cpp in Sources */, + A754149714840CF7005850D1 /* summaryqualcommand.cpp in Sources */, + A74A9A9F148E881E00AB5E3E /* spline.cpp in Sources */, + A7FA2AC714A0E881007C09A6 /* bsplvb.f in Sources */, + A7FA2AC814A0E881007C09A6 /* bsplvd.f in Sources */, + A7FA2AC914A0E881007C09A6 /* bvalue.f in Sources */, + A7FA2ACA14A0E881007C09A6 /* daxpy.f in Sources */, + A7FA2ACB14A0E881007C09A6 /* ddot.f in Sources */, + A7FA2ACC14A0E881007C09A6 /* dpbfa.f in Sources */, + A7FA2ACD14A0E881007C09A6 /* dpbsl.f in Sources */, + A7FA2ACE14A0E881007C09A6 /* interv.f in Sources */, + A7FA2ACF14A0E881007C09A6 /* sgram.f in Sources */, + A7FA2AD014A0E881007C09A6 /* sinerp.f in Sources */, + A7FA2AD114A0E881007C09A6 /* stxwx.f in Sources */, + A7FA2B1614A0EBEA007C09A6 /* sslvrg.f in Sources */, + A7FA2B5B14A0F0C2007C09A6 /* intrv.f in Sources */, + A7A3C8C914D041AD00B1BFBE /* otuassociationcommand.cpp in Sources */, + A7A32DAA14DC43B00001D2E5 /* sortseqscommand.cpp in Sources */, + A7EEB0F514F29BFE00344B83 /* classifytreecommand.cpp in Sources */, + A7C3DC0B14FE457500FE1924 /* cooccurrencecommand.cpp in Sources */, + A7C3DC0F14FE469500FE1924 /* trialSwap2.cpp in Sources */, + A76CDD821510F143004C8458 /* prcseqscommand.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -1977,15 +2335,20 @@ ARCHS = "$(ARCHS_STANDARD_64_BIT)"; DEPLOYMENT_LOCATION = NO; GCC_C_LANGUAGE_STANDARD = gnu99; - GCC_OPTIMIZATION_LEVEL = 3; + GCC_ENABLE_SSE3_EXTENSIONS = NO; + GCC_ENABLE_SSE41_EXTENSIONS = NO; + GCC_ENABLE_SSE42_EXTENSIONS = NO; + GCC_OPTIMIZATION_LEVEL = 0; GCC_PREPROCESSOR_DEFINITIONS = ( "MOTHUR_FILES=\"\\\"../release\\\"\"", - "VERSION=\"\\\"1.18.1\\\"\"", - "RELEASE_DATE=\"\\\"4/15/2011\\\"\"", + "VERSION=\"\\\"1.24.0\\\"\"", + "RELEASE_DATE=\"\\\"3/12/2012\\\"\"", ); + "GCC_VERSION[arch=*]" = ""; GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_UNUSED_VARIABLE = YES; + HEADER_SEARCH_PATHS = ""; INSTALL_PATH = ""; MACH_O_TYPE = mh_execute; ONLY_ACTIVE_ARCH = YES; @@ -2000,6 +2363,7 @@ ); PREBINDING = NO; SDKROOT = macosx10.6; + USER_HEADER_SEARCH_PATHS = ""; }; name = Debug; }; @@ -2011,10 +2375,10 @@ GCC_C_LANGUAGE_STANDARD = gnu99; GCC_GENERATE_DEBUGGING_SYMBOLS = NO; GCC_MODEL_TUNING = ""; - GCC_OPTIMIZATION_LEVEL = 3; + GCC_OPTIMIZATION_LEVEL = 0; GCC_PREPROCESSOR_DEFINITIONS = ( - "VERSION=\"\\\"1.18.1\\\"\"", - "RELEASE_DATE=\"\\\"4/15/2011\\\"\"", + "VERSION=\"\\\"1.24.0\\\"\"", + "RELEASE_DATE=\"\\\"3/12/2012\\\"\"", ); GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES;