X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=e80c7330c4b9b7b9dccacaf6d6a9bfc481a437f2;hb=a150db3c2bfd7b76420048a1e94ebe397f2c6045;hp=00f51b2fa99b508e95e6a038b2ebe98245c6768e;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17;p=mothur.git diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 00f51b2..e80c733 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -15,6 +15,29 @@ A71CB160130B04A2001E7287 /* anosimcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A71CB15E130B04A2001E7287 /* anosimcommand.cpp */; }; A71FE12C12EDF72400963CA7 /* mergegroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */; }; A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727864312E9E28C00F86ABA /* removerarecommand.cpp */; }; + A74D3687137DAB8300332B0C /* addtargets2.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3655137DAB8300332B0C /* addtargets2.cpp */; }; + A74D3688137DAB8400332B0C /* alignchime.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3656137DAB8300332B0C /* alignchime.cpp */; }; + A74D3689137DAB8400332B0C /* alignchimel.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3657137DAB8300332B0C /* alignchimel.cpp */; }; + A74D368A137DAB8400332B0C /* alnparams.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D365A137DAB8300332B0C /* alnparams.cpp */; }; + A74D368B137DAB8400332B0C /* alpha.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D365C137DAB8300332B0C /* alpha.cpp */; }; + A74D368C137DAB8400332B0C /* alpha2.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D365E137DAB8300332B0C /* alpha2.cpp */; }; + A74D368D137DAB8400332B0C /* fractid.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3664137DAB8300332B0C /* fractid.cpp */; }; + A74D368E137DAB8400332B0C /* getparents.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3665137DAB8300332B0C /* getparents.cpp */; }; + A74D368F137DAB8400332B0C /* globalalign2.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3666137DAB8300332B0C /* globalalign2.cpp */; }; + A74D3690137DAB8400332B0C /* make3way.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D366A137DAB8300332B0C /* make3way.cpp */; }; + A74D3691137DAB8400332B0C /* mx.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D366B137DAB8300332B0C /* mx.cpp */; }; + A74D3692137DAB8400332B0C /* myutils.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D366E137DAB8300332B0C /* myutils.cpp */; }; + A74D3693137DAB8400332B0C /* path.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3672137DAB8300332B0C /* path.cpp */; }; + A74D3694137DAB8400332B0C /* searchchime.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3674137DAB8300332B0C /* searchchime.cpp */; }; + A74D3695137DAB8400332B0C /* seqdb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3676137DAB8300332B0C /* seqdb.cpp */; }; + A74D3696137DAB8400332B0C /* setnucmx.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3678137DAB8300332B0C /* setnucmx.cpp */; }; + A74D3697137DAB8400332B0C /* sfasta.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3679137DAB8300332B0C /* sfasta.cpp */; }; + A74D3698137DAB8400332B0C /* tracebackbit.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D367F137DAB8300332B0C /* tracebackbit.cpp */; }; + A74D3699137DAB8400332B0C /* uchime_main.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3681137DAB8300332B0C /* uchime_main.cpp */; }; + A74D369A137DAB8400332B0C /* usort.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3683137DAB8300332B0C /* usort.cpp */; }; + A74D369B137DAB8400332B0C /* viterbifast.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3684137DAB8300332B0C /* viterbifast.cpp */; }; + A74D369C137DAB8400332B0C /* writechhit.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3686137DAB8300332B0C /* writechhit.cpp */; }; + A74D36B8137DAFAA00332B0C /* chimerauchimecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D36B7137DAFAA00332B0C /* chimerauchimecommand.cpp */; }; A75790591301749D00A30DAB /* homovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A75790581301749D00A30DAB /* homovacommand.cpp */; }; A778FE6B134CA6CA00C0BA33 /* getcommandinfocommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */; }; A799F5B91309A3E000AEEFA0 /* makefastqcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */; }; @@ -107,7 +130,6 @@ A7E9B8D712D37EC400DA6239 /* getsabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */; }; A7E9B8D812D37EC400DA6239 /* getseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70812D37EC400DA6239 /* getseqscommand.cpp */; }; A7E9B8D912D37EC400DA6239 /* getsharedotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */; }; - A7E9B8DA12D37EC400DA6239 /* globaldata.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70C12D37EC400DA6239 /* globaldata.cpp */; }; A7E9B8DB12D37EC400DA6239 /* goodscoverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70E12D37EC400DA6239 /* goodscoverage.cpp */; }; A7E9B8DC12D37EC400DA6239 /* gotohoverlap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B71012D37EC400DA6239 /* gotohoverlap.cpp */; }; A7E9B8DD12D37EC400DA6239 /* gower.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B71212D37EC400DA6239 /* gower.cpp */; }; @@ -190,7 +212,6 @@ A7E9B92A12D37EC400DA6239 /* readcluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B212D37EC400DA6239 /* readcluster.cpp */; }; A7E9B92B12D37EC400DA6239 /* readcolumn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */; }; A7E9B92C12D37EC400DA6239 /* readdistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */; }; - A7E9B92D12D37EC400DA6239 /* readotu.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B912D37EC400DA6239 /* readotu.cpp */; }; A7E9B92E12D37EC400DA6239 /* readotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */; }; A7E9B92F12D37EC400DA6239 /* readphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */; }; A7E9B93012D37EC400DA6239 /* readtree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7BF12D37EC400DA6239 /* readtree.cpp */; }; @@ -312,6 +333,7 @@ /* Begin PBXFileReference section */ 7E6BE10812F710D8007ADDBE /* refchimeratest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = refchimeratest.h; sourceTree = ""; }; 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = refchimeratest.cpp; sourceTree = ""; }; + 7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdistignorens.h; sourceTree = ""; }; 8DD76FB20486AB0100D96B5E /* Mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = Mothur; sourceTree = BUILT_PRODUCTS_DIR; }; A70332B512D3A13400761E33 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = ""; }; A713EBAA12DC7613000092AC /* readphylipvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylipvector.h; sourceTree = ""; }; @@ -324,6 +346,58 @@ A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergegroupscommand.cpp; sourceTree = ""; }; A727864212E9E28C00F86ABA /* removerarecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removerarecommand.h; sourceTree = ""; }; A727864312E9E28C00F86ABA /* removerarecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removerarecommand.cpp; sourceTree = ""; }; + A74D3655137DAB8300332B0C /* addtargets2.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = addtargets2.cpp; sourceTree = ""; }; + A74D3656137DAB8300332B0C /* alignchime.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignchime.cpp; sourceTree = ""; }; + A74D3657137DAB8300332B0C /* alignchimel.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignchimel.cpp; sourceTree = ""; }; + A74D3658137DAB8300332B0C /* allocs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = allocs.h; sourceTree = ""; }; + A74D3659137DAB8300332B0C /* alnheuristics.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = alnheuristics.h; sourceTree = ""; }; + A74D365A137DAB8300332B0C /* alnparams.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alnparams.cpp; sourceTree = ""; }; + A74D365B137DAB8300332B0C /* alnparams.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = alnparams.h; sourceTree = ""; }; + A74D365C137DAB8300332B0C /* alpha.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alpha.cpp; sourceTree = ""; }; + A74D365D137DAB8300332B0C /* alpha.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = alpha.h; sourceTree = ""; }; + A74D365E137DAB8300332B0C /* alpha2.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alpha2.cpp; sourceTree = ""; }; + A74D365F137DAB8300332B0C /* chainer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chainer.h; sourceTree = ""; }; + A74D3660137DAB8300332B0C /* chime.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chime.h; sourceTree = ""; }; + A74D3661137DAB8300332B0C /* diagbox.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = diagbox.h; sourceTree = ""; }; + A74D3662137DAB8300332B0C /* dp.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dp.h; sourceTree = ""; }; + A74D3663137DAB8300332B0C /* evalue.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = evalue.h; sourceTree = ""; }; + A74D3664137DAB8300332B0C /* fractid.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fractid.cpp; sourceTree = ""; }; + A74D3665137DAB8300332B0C /* getparents.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getparents.cpp; sourceTree = ""; }; + A74D3666137DAB8300332B0C /* globalalign2.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = globalalign2.cpp; sourceTree = ""; }; + A74D3667137DAB8300332B0C /* help.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = help.h; sourceTree = ""; }; + A74D3668137DAB8300332B0C /* hsp.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hsp.h; sourceTree = ""; }; + A74D3669137DAB8300332B0C /* hspfinder.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hspfinder.h; sourceTree = ""; }; + A74D366A137DAB8300332B0C /* make3way.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = make3way.cpp; sourceTree = ""; }; + A74D366B137DAB8300332B0C /* mx.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mx.cpp; sourceTree = ""; }; + A74D366C137DAB8300332B0C /* mx.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mx.h; sourceTree = ""; }; + A74D366D137DAB8300332B0C /* myopts.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = myopts.h; sourceTree = ""; }; + A74D366E137DAB8300332B0C /* myutils.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = myutils.cpp; sourceTree = ""; }; + A74D366F137DAB8300332B0C /* myutils.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = myutils.h; sourceTree = ""; }; + A74D3670137DAB8300332B0C /* orf.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = orf.h; sourceTree = ""; }; + A74D3671137DAB8300332B0C /* out.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = out.h; sourceTree = ""; }; + A74D3672137DAB8300332B0C /* path.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = path.cpp; sourceTree = ""; }; + A74D3673137DAB8300332B0C /* path.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = path.h; sourceTree = ""; }; + A74D3674137DAB8300332B0C /* searchchime.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = searchchime.cpp; sourceTree = ""; }; + A74D3675137DAB8300332B0C /* seq.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seq.h; sourceTree = ""; }; + A74D3676137DAB8300332B0C /* seqdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqdb.cpp; sourceTree = ""; }; + A74D3677137DAB8300332B0C /* seqdb.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqdb.h; sourceTree = ""; }; + A74D3678137DAB8300332B0C /* setnucmx.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setnucmx.cpp; sourceTree = ""; }; + A74D3679137DAB8300332B0C /* sfasta.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sfasta.cpp; sourceTree = ""; }; + A74D367A137DAB8300332B0C /* sfasta.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sfasta.h; sourceTree = ""; }; + A74D367B137DAB8300332B0C /* svnmods.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = svnmods.h; sourceTree = ""; }; + A74D367C137DAB8300332B0C /* svnversion.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = svnversion.h; sourceTree = ""; }; + A74D367D137DAB8300332B0C /* timers.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = timers.h; sourceTree = ""; }; + A74D367E137DAB8300332B0C /* timing.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = timing.h; sourceTree = ""; }; + A74D367F137DAB8300332B0C /* tracebackbit.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = tracebackbit.cpp; sourceTree = ""; }; + A74D3680137DAB8300332B0C /* uc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = uc.h; sourceTree = ""; }; + A74D3681137DAB8300332B0C /* uchime_main.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = uchime_main.cpp; sourceTree = ""; }; + A74D3682137DAB8300332B0C /* ultra.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ultra.h; sourceTree = ""; }; + A74D3683137DAB8300332B0C /* usort.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = usort.cpp; sourceTree = ""; }; + A74D3684137DAB8300332B0C /* viterbifast.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = viterbifast.cpp; sourceTree = ""; }; + A74D3685137DAB8300332B0C /* windex.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = windex.h; sourceTree = ""; }; + A74D3686137DAB8300332B0C /* writechhit.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = writechhit.cpp; sourceTree = ""; }; + A74D36B6137DAFAA00332B0C /* chimerauchimecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerauchimecommand.h; sourceTree = ""; }; + A74D36B7137DAFAA00332B0C /* chimerauchimecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerauchimecommand.cpp; sourceTree = ""; }; A75790571301749D00A30DAB /* homovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = homovacommand.h; sourceTree = ""; }; A75790581301749D00A30DAB /* homovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = homovacommand.cpp; sourceTree = ""; }; A778FE69134CA6CA00C0BA33 /* getcommandinfocommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getcommandinfocommand.h; sourceTree = ""; }; @@ -522,8 +596,6 @@ A7E9B70912D37EC400DA6239 /* getseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getseqscommand.h; sourceTree = ""; }; A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsharedotucommand.cpp; sourceTree = ""; }; A7E9B70B12D37EC400DA6239 /* getsharedotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsharedotucommand.h; sourceTree = ""; }; - A7E9B70C12D37EC400DA6239 /* globaldata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = globaldata.cpp; sourceTree = SOURCE_ROOT; }; - A7E9B70D12D37EC400DA6239 /* globaldata.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = globaldata.hpp; sourceTree = SOURCE_ROOT; }; A7E9B70E12D37EC400DA6239 /* goodscoverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = goodscoverage.cpp; sourceTree = ""; }; A7E9B70F12D37EC400DA6239 /* goodscoverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = goodscoverage.h; sourceTree = ""; }; A7E9B71012D37EC400DA6239 /* gotohoverlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = gotohoverlap.cpp; sourceTree = SOURCE_ROOT; }; @@ -695,8 +767,6 @@ A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistcommand.cpp; sourceTree = ""; }; A7E9B7B712D37EC400DA6239 /* readdistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcommand.h; sourceTree = ""; }; A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = ""; }; - A7E9B7B912D37EC400DA6239 /* readotu.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotu.cpp; sourceTree = ""; }; - A7E9B7BA12D37EC400DA6239 /* readotu.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotu.h; sourceTree = ""; }; A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = ""; }; A7E9B7BC12D37EC400DA6239 /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = ""; }; A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = ""; }; @@ -745,7 +815,6 @@ A7E9B7E812D37EC400DA6239 /* shannoneven.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannoneven.h; sourceTree = ""; }; A7E9B7E912D37EC400DA6239 /* sharedace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedace.cpp; sourceTree = ""; }; A7E9B7EA12D37EC400DA6239 /* sharedace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedace.h; sourceTree = ""; }; - A7E9B7EB12D37EC400DA6239 /* sharedanderberg.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderberg.h; sourceTree = ""; }; A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedanderbergs.cpp; sourceTree = ""; }; A7E9B7ED12D37EC400DA6239 /* sharedanderbergs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderbergs.h; sourceTree = ""; }; A7E9B7EE12D37EC400DA6239 /* sharedbraycurtis.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbraycurtis.cpp; sourceTree = ""; }; @@ -964,8 +1033,6 @@ A7E9B6DB12D37EC400DA6239 /* engine.hpp */, A7E9B6E012D37EC400DA6239 /* fileoutput.cpp */, A7E9B6E112D37EC400DA6239 /* fileoutput.h */, - A7E9B70C12D37EC400DA6239 /* globaldata.cpp */, - A7E9B70D12D37EC400DA6239 /* globaldata.hpp */, A7E9B71112D37EC400DA6239 /* gotohoverlap.hpp */, A7E9B71012D37EC400DA6239 /* gotohoverlap.cpp */, A7E9B71812D37EC400DA6239 /* hcluster.cpp */, @@ -1014,8 +1081,8 @@ A7E9B82412D37EC400DA6239 /* sharedutilities.h */, A7E9B82D12D37EC400DA6239 /* singlelinkage.cpp */, A7E9B83012D37EC400DA6239 /* slibshuff.cpp */, - A7E9B83112D37EC400DA6239 /* slibshuff.h */, A7E9B85112D37EC400DA6239 /* suffixdb.cpp */, + A7E9B83112D37EC400DA6239 /* slibshuff.h */, A7E9B85212D37EC400DA6239 /* suffixdb.hpp */, A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */, A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */, @@ -1040,6 +1107,63 @@ 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 = ""; + }; A7E9BA3812D3956100DA6239 /* commands */ = { isa = PBXGroup; children = ( @@ -1066,6 +1190,8 @@ A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */, A7E9B68B12D37EC400DA6239 /* chimeraslayercommand.h */, A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */, + A74D36B6137DAFAA00332B0C /* chimerauchimecommand.h */, + A74D36B7137DAFAA00332B0C /* chimerauchimecommand.cpp */, A7E9B68D12D37EC400DA6239 /* chopseqscommand.h */, A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */, A7E9B69112D37EC400DA6239 /* classifyotucommand.h */, @@ -1267,6 +1393,7 @@ A7E9BA3F12D395F700DA6239 /* calculators */ = { isa = PBXGroup; children = ( + 7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */, A7E9B64F12D37EC300DA6239 /* ace.cpp */, A7E9B65012D37EC300DA6239 /* ace.h */, A7E9B65E12D37EC300DA6239 /* bergerparker.cpp */, @@ -1344,7 +1471,6 @@ A7E9B7E812D37EC400DA6239 /* shannoneven.h */, A7E9B7E912D37EC400DA6239 /* sharedace.cpp */, A7E9B7EA12D37EC400DA6239 /* sharedace.h */, - A7E9B7EB12D37EC400DA6239 /* sharedanderberg.h */, A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */, A7E9B7ED12D37EC400DA6239 /* sharedanderbergs.h */, A7E9B7EE12D37EC400DA6239 /* sharedbraycurtis.cpp */, @@ -1501,6 +1627,7 @@ A7E9BA4512D3965600DA6239 /* chimera */ = { isa = PBXGroup; children = ( + A74D3644137DA7CE00332B0C /* uchime */, A7E9B65C12D37EC300DA6239 /* bellerophon.cpp */, A7E9B65D12D37EC300DA6239 /* bellerophon.h */, A7E9B67412D37EC400DA6239 /* ccode.cpp */, @@ -1511,11 +1638,11 @@ 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 */, A7E9B79312D37EC400DA6239 /* pintail.cpp */, A7E9B79412D37EC400DA6239 /* pintail.h */, @@ -1579,8 +1706,6 @@ A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */, A7E9B7B512D37EC400DA6239 /* readcolumn.h */, A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */, - A7E9B7BA12D37EC400DA6239 /* readotu.h */, - A7E9B7B912D37EC400DA6239 /* readotu.cpp */, A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */, A7E9B7BE12D37EC400DA6239 /* readphylip.h */, A7E9B7BF12D37EC400DA6239 /* readtree.cpp */, @@ -1751,7 +1876,6 @@ A7E9B8D712D37EC400DA6239 /* getsabundcommand.cpp in Sources */, A7E9B8D812D37EC400DA6239 /* getseqscommand.cpp in Sources */, A7E9B8D912D37EC400DA6239 /* getsharedotucommand.cpp in Sources */, - A7E9B8DA12D37EC400DA6239 /* globaldata.cpp in Sources */, A7E9B8DB12D37EC400DA6239 /* goodscoverage.cpp in Sources */, A7E9B8DC12D37EC400DA6239 /* gotohoverlap.cpp in Sources */, A7E9B8DD12D37EC400DA6239 /* gower.cpp in Sources */, @@ -1834,7 +1958,6 @@ A7E9B92A12D37EC400DA6239 /* readcluster.cpp in Sources */, A7E9B92B12D37EC400DA6239 /* readcolumn.cpp in Sources */, A7E9B92C12D37EC400DA6239 /* readdistcommand.cpp in Sources */, - A7E9B92D12D37EC400DA6239 /* readotu.cpp in Sources */, A7E9B92E12D37EC400DA6239 /* readotucommand.cpp in Sources */, A7E9B92F12D37EC400DA6239 /* readphylip.cpp in Sources */, A7E9B93012D37EC400DA6239 /* readtree.cpp in Sources */, @@ -1949,6 +2072,29 @@ 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 */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -1989,11 +2135,14 @@ ARCHS = "$(ARCHS_STANDARD_64_BIT)"; DEPLOYMENT_LOCATION = NO; GCC_C_LANGUAGE_STANDARD = gnu99; - GCC_OPTIMIZATION_LEVEL = 3; + GCC_ENABLE_SSE3_EXTENSIONS = NO; + GCC_ENABLE_SSE41_EXTENSIONS = NO; + GCC_ENABLE_SSE42_EXTENSIONS = NO; + GCC_OPTIMIZATION_LEVEL = 0; GCC_PREPROCESSOR_DEFINITIONS = ( "MOTHUR_FILES=\"\\\"../release\\\"\"", - "VERSION=\"\\\"1.17.3\\\"\"", - "RELEASE_DATE=\"\\\"3/07/2011\\\"\"", + "VERSION=\"\\\"1.19.0\\\"\"", + "RELEASE_DATE=\"\\\"5/9/2011\\\"\"", ); GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; @@ -2018,16 +2167,15 @@ 1DEB928B08733DD80010E9CD /* Release */ = { isa = XCBuildConfiguration; buildSettings = { - ARCHS = "$(NATIVE_ARCH_ACTUAL)"; + ARCHS = "$(ARCHS_STANDARD_64_BIT)"; DEPLOYMENT_LOCATION = NO; GCC_C_LANGUAGE_STANDARD = gnu99; GCC_GENERATE_DEBUGGING_SYMBOLS = NO; GCC_MODEL_TUNING = ""; - GCC_OPTIMIZATION_LEVEL = 3; + GCC_OPTIMIZATION_LEVEL = 0; GCC_PREPROCESSOR_DEFINITIONS = ( - "MOTHUR_FILES=\"\\\"../release\\\"\"", - "VERSION=\"\\\"1.15.0\\\"\"", - "RELEASE_DATE=\"\\\"12/10/2010\\\"\"", + "VERSION=\"\\\"1.19.0\\\"\"", + "RELEASE_DATE=\"\\\"5/9/2011\\\"\"", ); GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; @@ -2049,7 +2197,7 @@ "-lreadline", ); PREBINDING = NO; - SDKROOT = ""; + SDKROOT = macosx10.6; }; name = Release; };