]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
working on windows paralellization, added trimOligos class to be used by trim.flows...
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index 2e6f5a8244aead5d33354fd4d765e183ee2092c2..3ccc0b91d1f48140d421358f3a2983c13b3cb9aa 100644 (file)
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+               A74D3677137DAB8300332B0C /* seqdb.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqdb.h; sourceTree = "<group>"; };
+               A74D3678137DAB8300332B0C /* setnucmx.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setnucmx.cpp; sourceTree = "<group>"; };
+               A74D3679137DAB8300332B0C /* sfasta.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sfasta.cpp; sourceTree = "<group>"; };
+               A74D367A137DAB8300332B0C /* sfasta.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sfasta.h; sourceTree = "<group>"; };
+               A74D367B137DAB8300332B0C /* svnmods.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = svnmods.h; sourceTree = "<group>"; };
+               A74D367C137DAB8300332B0C /* svnversion.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = svnversion.h; sourceTree = "<group>"; };
+               A74D367D137DAB8300332B0C /* timers.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = timers.h; sourceTree = "<group>"; };
+               A74D367E137DAB8300332B0C /* timing.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = timing.h; sourceTree = "<group>"; };
+               A74D367F137DAB8300332B0C /* tracebackbit.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = tracebackbit.cpp; sourceTree = "<group>"; };
+               A74D3680137DAB8300332B0C /* uc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = uc.h; sourceTree = "<group>"; };
+               A74D3681137DAB8300332B0C /* uchime_main.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = uchime_main.cpp; sourceTree = "<group>"; };
+               A74D3682137DAB8300332B0C /* ultra.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ultra.h; sourceTree = "<group>"; };
+               A74D3683137DAB8300332B0C /* usort.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = usort.cpp; sourceTree = "<group>"; };
+               A74D3684137DAB8300332B0C /* viterbifast.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = viterbifast.cpp; sourceTree = "<group>"; };
+               A74D3685137DAB8300332B0C /* windex.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = windex.h; sourceTree = "<group>"; };
+               A74D3686137DAB8300332B0C /* writechhit.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = writechhit.cpp; sourceTree = "<group>"; };
+               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>"; };
                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>"; };
+               A7730EFD13967241007433A3 /* countseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = countseqscommand.h; sourceTree = "<group>"; };
+               A7730EFE13967241007433A3 /* countseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = countseqscommand.cpp; sourceTree = "<group>"; };
                A778FE69134CA6CA00C0BA33 /* getcommandinfocommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getcommandinfocommand.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>"; };
+               A79234D513C74BF6002B08E2 /* mothurfisher.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothurfisher.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>"; };
                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>"; };
                A7A61F1A130035C800E05B6B /* LICENSE */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = LICENSE; sourceTree = "<group>"; };
                A7E9B7E812D37EC400DA6239 /* shannoneven.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannoneven.h; sourceTree = "<group>"; };
                A7E9B7E912D37EC400DA6239 /* sharedace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedace.cpp; sourceTree = "<group>"; };
                A7E9B7EA12D37EC400DA6239 /* sharedace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedace.h; sourceTree = "<group>"; };
-               A7E9B7EB12D37EC400DA6239 /* sharedanderberg.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderberg.h; sourceTree = "<group>"; };
                A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedanderbergs.cpp; sourceTree = "<group>"; };
                A7E9B7ED12D37EC400DA6239 /* sharedanderbergs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderbergs.h; sourceTree = "<group>"; };
                A7E9B7EE12D37EC400DA6239 /* sharedbraycurtis.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbraycurtis.cpp; sourceTree = "<group>"; };
                A7E9B84E12D37EC400DA6239 /* structpearson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = structpearson.h; sourceTree = "<group>"; };
                A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = subsamplecommand.cpp; sourceTree = "<group>"; };
                A7E9B85012D37EC400DA6239 /* subsamplecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = subsamplecommand.h; sourceTree = "<group>"; };
-               A7E9B85112D37EC400DA6239 /* suffixdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixdb.cpp; sourceTree = SOURCE_ROOT; };
-               A7E9B85212D37EC400DA6239 /* suffixdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixdb.hpp; sourceTree = SOURCE_ROOT; };
-               A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixnodes.cpp; sourceTree = SOURCE_ROOT; };
-               A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixnodes.hpp; sourceTree = SOURCE_ROOT; };
-               A7E9B85512D37EC400DA6239 /* suffixtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixtree.cpp; sourceTree = SOURCE_ROOT; };
-               A7E9B85612D37EC400DA6239 /* suffixtree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixtree.hpp; sourceTree = SOURCE_ROOT; };
+               A7E9B85112D37EC400DA6239 /* suffixdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixdb.cpp; sourceTree = "<group>"; };
+               A7E9B85212D37EC400DA6239 /* suffixdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixdb.hpp; sourceTree = "<group>"; };
+               A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixnodes.cpp; sourceTree = "<group>"; };
+               A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixnodes.hpp; sourceTree = "<group>"; };
+               A7E9B85512D37EC400DA6239 /* suffixtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixtree.cpp; sourceTree = "<group>"; };
+               A7E9B85612D37EC400DA6239 /* suffixtree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixtree.hpp; sourceTree = "<group>"; };
                A7E9B85712D37EC400DA6239 /* summarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarycommand.cpp; sourceTree = "<group>"; };
                A7E9B85812D37EC400DA6239 /* summarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarycommand.h; sourceTree = "<group>"; };
                A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarysharedcommand.cpp; sourceTree = "<group>"; };
                A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weightedlinkage.cpp; sourceTree = SOURCE_ROOT; };
                A7E9B87F12D37EC400DA6239 /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = "<group>"; };
                A7E9B88012D37EC400DA6239 /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = "<group>"; };
+               A7F9F5CD141A5E500032F693 /* sequenceparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sequenceparser.h; sourceTree = "<group>"; };
+               A7F9F5CE141A5E500032F693 /* sequenceparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequenceparser.cpp; sourceTree = "<group>"; };
                A7FA10001302E096003860FE /* mantelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mantelcommand.h; sourceTree = "<group>"; };
                A7FA10011302E096003860FE /* mantelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mantelcommand.cpp; sourceTree = "<group>"; };
                A7FC480C12D788F20055BC5C /* linearalgebra.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = linearalgebra.h; sourceTree = "<group>"; };
                A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getcurrentcommand.cpp; sourceTree = "<group>"; };
                A7FE7E6B13311EA400F7B327 /* setcurrentcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setcurrentcommand.h; sourceTree = "<group>"; };
                A7FE7E6C13311EA400F7B327 /* setcurrentcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setcurrentcommand.cpp; sourceTree = "<group>"; };
+               A7FF19F0140FFDA500AD216D /* trimoligos.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = trimoligos.h; sourceTree = "<group>"; };
+               A7FF19F1140FFDA500AD216D /* trimoligos.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = trimoligos.cpp; sourceTree = "<group>"; };
                C6A0FF2C0290799A04C91782 /* mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = mothur.1; sourceTree = "<group>"; };
 /* End PBXFileReference section */
 
                                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 */,
+                               A7FF19F0140FFDA500AD216D /* trimoligos.h */,
+                               A7FF19F1140FFDA500AD216D /* trimoligos.cpp */,
                                A7E9B87412D37EC400DA6239 /* validcalculator.cpp */,
                                A7E9B87512D37EC400DA6239 /* validcalculator.h */,
                                A7E9B87612D37EC400DA6239 /* validparameter.cpp */,
                        name = Products;
                        sourceTree = "<group>";
                };
+               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 = "<group>";
+               };
                A7E9BA3812D3956100DA6239 /* commands */ = {
                        isa = PBXGroup;
                        children = (
                                A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */,
                                A7E9B68B12D37EC400DA6239 /* chimeraslayercommand.h */,
                                A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */,
+                               A74D36B6137DAFAA00332B0C /* chimerauchimecommand.h */,
+                               A74D36B7137DAFAA00332B0C /* chimerauchimecommand.cpp */,
                                A7E9B68D12D37EC400DA6239 /* chopseqscommand.h */,
                                A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */,
                                A7E9B69112D37EC400DA6239 /* classifyotucommand.h */,
                                A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */,
                                A7E9B69712D37EC400DA6239 /* clearcutcommand.h */,
                                A7E9B69612D37EC400DA6239 /* clearcutcommand.cpp */,
+                               A73DDBB813C4A0D1006AAE38 /* clearmemorycommand.h */,
+                               A73DDBB913C4A0D1006AAE38 /* clearmemorycommand.cpp */,
                                A7E9B69D12D37EC400DA6239 /* clustercommand.h */,
                                A7E9B69C12D37EC400DA6239 /* clustercommand.cpp */,
                                A7E9B69F12D37EC400DA6239 /* clusterdoturcommand.h */,
                                A7E9B6B712D37EC400DA6239 /* consensusseqscommand.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 */,
                                A7E9B7E412D37EC400DA6239 /* sffinfocommand.h */,
                                A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */,
                                A7E9B7F312D37EC400DA6239 /* sharedcommand.h */,
-                               A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */,
                                A7E9B82812D37EC400DA6239 /* shhhercommand.h */,
                                A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */,
+                               A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */,
                                A7E9B84012D37EC400DA6239 /* splitabundcommand.h */,
                                A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */,
                                A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */,
                                A7E9B6D712D37EC400DA6239 /* efron.cpp */,
                                A7E9B6D812D37EC400DA6239 /* efron.h */,
                                A7E9B6E212D37EC400DA6239 /* filters.h */,
-                               A7E9B6E512D37EC400DA6239 /* fisher2.c */,
-                               A7E9B6E612D37EC400DA6239 /* fisher2.h */,
                                A7E9B6F012D37EC400DA6239 /* geom.cpp */,
                                A7E9B6F112D37EC400DA6239 /* geom.h */,
                                A7E9B70E12D37EC400DA6239 /* goodscoverage.cpp */,
                                A7E9B7E812D37EC400DA6239 /* shannoneven.h */,
                                A7E9B7E912D37EC400DA6239 /* sharedace.cpp */,
                                A7E9B7EA12D37EC400DA6239 /* sharedace.h */,
-                               A7E9B7EB12D37EC400DA6239 /* sharedanderberg.h */,
                                A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */,
                                A7E9B7ED12D37EC400DA6239 /* sharedanderbergs.h */,
                                A7E9B7EE12D37EC400DA6239 /* sharedbraycurtis.cpp */,
                                A7E9B7A012D37EC400DA6239 /* qualityscores.h */,
                                A7E9B7A312D37EC400DA6239 /* rabundvector.cpp */,
                                A7E9B7A412D37EC400DA6239 /* rabundvector.hpp */,
+                               A721765513BB9F7D0014DAAE /* referencedb.h */,
+                               A721765613BB9F7D0014DAAE /* referencedb.cpp */,
                                A7E9B7CB12D37EC400DA6239 /* reportfile.cpp */,
                                A7E9B7CC12D37EC400DA6239 /* reportfile.h */,
                                A7E9B7CF12D37EC400DA6239 /* sabundvector.cpp */,
                                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 */,
                A7E9BA4512D3965600DA6239 /* chimera */ = {
                        isa = PBXGroup;
                        children = (
+                               A74D3644137DA7CE00332B0C /* uchime */,
                                A7E9B65C12D37EC300DA6239 /* bellerophon.cpp */,
                                A7E9B65D12D37EC300DA6239 /* bellerophon.h */,
                                A7E9B67412D37EC400DA6239 /* ccode.cpp */,
                A7E9BA5612D39BD800DA6239 /* metastats */ = {
                        isa = PBXGroup;
                        children = (
+                               A7E9B6E512D37EC400DA6239 /* fisher2.c */,
+                               A7E9B6E612D37EC400DA6239 /* fisher2.h */,
                                A7E9B75512D37EC400DA6239 /* metastats.h */,
                                A7E9B75612D37EC400DA6239 /* metastats2.c */,
+                               A79234D513C74BF6002B08E2 /* mothurfisher.h */,
+                               A79234D613C74BF6002B08E2 /* mothurfisher.cpp */,
+                               A73DDC3613C4BF64006AAE38 /* mothurmetastats.h */,
+                               A73DDC3713C4BF64006AAE38 /* mothurmetastats.cpp */,
                        );
                        name = metastats;
                        sourceTree = "<group>";
                                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 */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
                                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=\"\\\"1.21.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"7/25/2011\\\"\"",
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                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=\"\\\"1.19.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"5/9/2011\\\"\"",
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;