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*/ = {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; }; @@ -560,8 +750,6 @@ A7E9B75212D37EC400DA6239 /* mempearson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mempearson.h; sourceTree = ""; }; A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergefilecommand.cpp; sourceTree = ""; }; A7E9B75412D37EC400DA6239 /* mergefilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergefilecommand.h; sourceTree = ""; }; - A7E9B75512D37EC400DA6239 /* metastats.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = metastats.h; sourceTree = ""; }; - A7E9B75612D37EC400DA6239 /* metastats2.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; path = metastats2.c; sourceTree = ""; }; A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = metastatscommand.cpp; sourceTree = ""; }; A7E9B75812D37EC400DA6239 /* metastatscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = metastatscommand.h; sourceTree = ""; }; A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mgclustercommand.cpp; sourceTree = ""; }; @@ -660,8 +848,6 @@ 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 = ""; }; @@ -710,7 +896,6 @@ 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 = ""; }; @@ -812,12 +997,12 @@ A7E9B84E12D37EC400DA6239 /* structpearson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = structpearson.h; sourceTree = ""; }; A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = subsamplecommand.cpp; sourceTree = ""; }; A7E9B85012D37EC400DA6239 /* subsamplecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = subsamplecommand.h; sourceTree = ""; }; - 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 = ""; }; + A7E9B85212D37EC400DA6239 /* suffixdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixdb.hpp; sourceTree = ""; }; + A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixnodes.cpp; sourceTree = ""; }; + A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixnodes.hpp; sourceTree = ""; }; + A7E9B85512D37EC400DA6239 /* suffixtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixtree.cpp; sourceTree = ""; }; + A7E9B85612D37EC400DA6239 /* suffixtree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixtree.hpp; sourceTree = ""; }; A7E9B85712D37EC400DA6239 /* summarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarycommand.cpp; sourceTree = ""; }; A7E9B85812D37EC400DA6239 /* summarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarycommand.h; sourceTree = ""; }; A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarysharedcommand.cpp; sourceTree = ""; }; @@ -860,6 +1045,37 @@ 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 = ""; }; A7E9B88012D37EC400DA6239 /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = ""; }; + A7EEB0F414F29BFD00344B83 /* classifytreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifytreecommand.cpp; sourceTree = ""; }; + A7EEB0F714F29C1B00344B83 /* classifytreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifytreecommand.h; sourceTree = ""; }; + A7F9F5CD141A5E500032F693 /* sequenceparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sequenceparser.h; sourceTree = ""; }; + A7F9F5CE141A5E500032F693 /* sequenceparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequenceparser.cpp; sourceTree = ""; }; + A7FA10001302E096003860FE /* mantelcommand.h */ = {isa = PBXFileReference; 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 = ""; }; + A7FC486612D795D60055BC5C /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = ""; }; + A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getcurrentcommand.h; sourceTree = ""; }; + 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 */ @@ -887,6 +1103,7 @@ 08FB7795FE84155DC02AAC07 /* Source */ = { isa = PBXGroup; children = ( + A7A61F1A130035C800E05B6B /* LICENSE */, A70332B512D3A13400761E33 /* makefile */, A7E9B65912D37EC300DA6239 /* averagelinkage.cpp */, A7E9BA4F12D398D700DA6239 /* clearcut */, @@ -906,8 +1123,10 @@ A7E9B6B012D37EC400DA6239 /* commandfactory.hpp */, A7E9B6B112D37EC400DA6239 /* commandoptionparser.cpp */, A7E9B6B212D37EC400DA6239 /* commandoptionparser.hpp */, + A7DAAFA3133A254E003956EB /* commandparameter.h */, A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */, A7E9BA4212D3960D00DA6239 /* containers */, + A7AACFBA132FE008003D6C4D /* currentfile.h */, A7E9B6C912D37EC400DA6239 /* display.h */, A7E9B6D112D37EC400DA6239 /* dlibshuff.cpp */, A7E9B6D212D37EC400DA6239 /* dlibshuff.h */, @@ -916,8 +1135,6 @@ A7E9B6DB12D37EC400DA6239 /* engine.hpp */, A7E9B6E012D37EC400DA6239 /* fileoutput.cpp */, A7E9B6E112D37EC400DA6239 /* fileoutput.h */, - A7E9B70C12D37EC400DA6239 /* globaldata.cpp */, - A7E9B70D12D37EC400DA6239 /* globaldata.hpp */, A7E9B71112D37EC400DA6239 /* gotohoverlap.hpp */, A7E9B71012D37EC400DA6239 /* gotohoverlap.cpp */, A7E9B71812D37EC400DA6239 /* hcluster.cpp */, @@ -930,11 +1147,21 @@ A7E9B72D12D37EC400DA6239 /* inputdata.cpp */, A7E9B73912D37EC400DA6239 /* libshuff.cpp */, A7E9B73A12D37EC400DA6239 /* libshuff.h */, + A7FC480C12D788F20055BC5C /* linearalgebra.h */, + A7FC480D12D788F20055BC5C /* linearalgebra.cpp */, A7E9BA5612D39BD800DA6239 /* metastats */, A7E9B75B12D37EC400DA6239 /* mothur.cpp */, A7E9B75C12D37EC400DA6239 /* mothur.h */, A7E9B75D12D37EC400DA6239 /* mothurout.cpp */, A7E9B75E12D37EC400DA6239 /* mothurout.h */, + A774104714696F320098E6AC /* myseqdist.h */, + A774104614696F320098E6AC /* myseqdist.cpp */, + A7E9B76112D37EC400DA6239 /* nast.cpp */, + A7E9B76212D37EC400DA6239 /* nast.hpp */, + A7E9B76312D37EC400DA6239 /* nastreport.cpp */, + A7E9B76412D37EC400DA6239 /* nastreport.hpp */, + A7E9B76712D37EC400DA6239 /* noalign.cpp */, + A7E9B76812D37EC400DA6239 /* noalign.hpp */, A7E9B76512D37EC400DA6239 /* needlemanoverlap.cpp */, A7E9B76612D37EC400DA6239 /* needlemanoverlap.hpp */, A7E9B77012D37EC400DA6239 /* observable.h */, @@ -951,24 +1178,20 @@ A7E9B7A912D37EC400DA6239 /* rarefact.cpp */, A7E9B7AA12D37EC400DA6239 /* rarefact.h */, A7E9B7AD12D37EC400DA6239 /* rarefactioncurvedata.h */, + 7E6BE10812F710D8007ADDBE /* refchimeratest.h */, + 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */, + A77410F514697C300098E6AC /* seqnoise.h */, + A77410F414697C300098E6AC /* seqnoise.cpp */, A7E9BA5312D39A5E00DA6239 /* read */, - A7E9B76112D37EC400DA6239 /* nast.cpp */, - A7E9B76212D37EC400DA6239 /* nast.hpp */, - A7E9B76312D37EC400DA6239 /* nastreport.cpp */, - A7E9B76412D37EC400DA6239 /* nastreport.hpp */, - A7E9B76712D37EC400DA6239 /* noalign.cpp */, - A7E9B76812D37EC400DA6239 /* noalign.hpp */, A7E9B82312D37EC400DA6239 /* sharedutilities.cpp */, A7E9B82412D37EC400DA6239 /* sharedutilities.h */, A7E9B82D12D37EC400DA6239 /* singlelinkage.cpp */, A7E9B83012D37EC400DA6239 /* slibshuff.cpp */, A7E9B83112D37EC400DA6239 /* slibshuff.h */, - A7E9B85112D37EC400DA6239 /* suffixdb.cpp */, - 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 */, @@ -988,204 +1211,331 @@ 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 = ( A7E9B6AE12D37EC400DA6239 /* command.hpp */, - A7E9B65112D37EC300DA6239 /* aligncommand.cpp */, A7E9B65212D37EC300DA6239 /* aligncommand.h */, - A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */, + A7E9B65112D37EC300DA6239 /* aligncommand.cpp */, + A7A61F2B130062E000E05B6B /* amovacommand.h */, + A7A61F2C130062E000E05B6B /* amovacommand.cpp */, + A71CB15F130B04A2001E7287 /* anosimcommand.h */, + A71CB15E130B04A2001E7287 /* anosimcommand.cpp */, A7E9B66112D37EC300DA6239 /* binsequencecommand.h */, - A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */, + A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */, A7E9B66B12D37EC400DA6239 /* bootstrapsharedcommand.h */, - A7E9B67212D37EC400DA6239 /* catchallcommand.cpp */, + A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */, A7E9B67312D37EC400DA6239 /* catchallcommand.h */, - A7E9B67A12D37EC400DA6239 /* chimerabellerophoncommand.cpp */, + A7E9B67212D37EC400DA6239 /* catchallcommand.cpp */, A7E9B67B12D37EC400DA6239 /* chimerabellerophoncommand.h */, - A7E9B67C12D37EC400DA6239 /* chimeraccodecommand.cpp */, + A7E9B67A12D37EC400DA6239 /* chimerabellerophoncommand.cpp */, A7E9B67D12D37EC400DA6239 /* chimeraccodecommand.h */, - A7E9B67E12D37EC400DA6239 /* chimeracheckcommand.cpp */, + A7E9B67C12D37EC400DA6239 /* chimeraccodecommand.cpp */, A7E9B67F12D37EC400DA6239 /* chimeracheckcommand.h */, - A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */, + A7E9B67E12D37EC400DA6239 /* chimeracheckcommand.cpp */, A7E9B68312D37EC400DA6239 /* chimerapintailcommand.h */, - A7E9B68612D37EC400DA6239 /* chimeraseqscommand.cpp */, - A7E9B68712D37EC400DA6239 /* chimeraseqscommand.h */, - A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */, + A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */, + A7BF2230145879B2000AD524 /* chimeraperseuscommand.h */, + A7BF2231145879B2000AD524 /* chimeraperseuscommand.cpp */, A7E9B68B12D37EC400DA6239 /* chimeraslayercommand.h */, - A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */, + A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */, + A74D36B6137DAFAA00332B0C /* chimerauchimecommand.h */, + A74D36B7137DAFAA00332B0C /* chimerauchimecommand.cpp */, A7E9B68D12D37EC400DA6239 /* chopseqscommand.h */, - A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */, + A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */, A7E9B69112D37EC400DA6239 /* classifyotucommand.h */, - A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */, + A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */, A7E9B69312D37EC400DA6239 /* classifyseqscommand.h */, - A7E9B69612D37EC400DA6239 /* clearcutcommand.cpp */, + A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */, + A7EEB0F714F29C1B00344B83 /* classifytreecommand.h */, + A7EEB0F414F29BFD00344B83 /* classifytreecommand.cpp */, A7E9B69712D37EC400DA6239 /* clearcutcommand.h */, - A7E9B69C12D37EC400DA6239 /* clustercommand.cpp */, + A7E9B69612D37EC400DA6239 /* clearcutcommand.cpp */, + A73DDBB813C4A0D1006AAE38 /* clearmemorycommand.h */, + A73DDBB913C4A0D1006AAE38 /* clearmemorycommand.cpp */, A7E9B69D12D37EC400DA6239 /* clustercommand.h */, - A7E9B69E12D37EC400DA6239 /* clusterdoturcommand.cpp */, + A7E9B69C12D37EC400DA6239 /* clustercommand.cpp */, A7E9B69F12D37EC400DA6239 /* clusterdoturcommand.h */, - A7E9B6A012D37EC400DA6239 /* clusterfragmentscommand.cpp */, + A7E9B69E12D37EC400DA6239 /* clusterdoturcommand.cpp */, A7E9B6A112D37EC400DA6239 /* clusterfragmentscommand.h */, - A7E9B6A212D37EC400DA6239 /* clustersplitcommand.cpp */, + A7E9B6A012D37EC400DA6239 /* clusterfragmentscommand.cpp */, A7E9B6A312D37EC400DA6239 /* clustersplitcommand.h */, - A7E9B6A812D37EC400DA6239 /* collectcommand.cpp */, + A7E9B6A212D37EC400DA6239 /* clustersplitcommand.cpp */, A7E9B6A912D37EC400DA6239 /* collectcommand.h */, - A7E9B6AC12D37EC400DA6239 /* collectsharedcommand.cpp */, + A7E9B6A812D37EC400DA6239 /* collectcommand.cpp */, A7E9B6AD12D37EC400DA6239 /* collectsharedcommand.h */, - A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */, + A7E9B6AC12D37EC400DA6239 /* collectsharedcommand.cpp */, A7E9B6B612D37EC400DA6239 /* consensuscommand.h */, - A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */, + A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */, A7E9B6B812D37EC400DA6239 /* consensusseqscommand.h */, - A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */, + A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */, + A7C3DC0A14FE457500FE1924 /* cooccurrencecommand.h */, + A7C3DC0914FE457500FE1924 /* cooccurrencecommand.cpp */, A7E9B6BA12D37EC400DA6239 /* corraxescommand.h */, - A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */, + A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */, + A795840B13F13CD900F201D5 /* countgroupscommand.h */, + A795840C13F13CD900F201D5 /* countgroupscommand.cpp */, + A7730EFD13967241007433A3 /* countseqscommand.h */, + A7730EFE13967241007433A3 /* countseqscommand.cpp */, A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */, - A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */, + A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */, A7E9B6C612D37EC400DA6239 /* degapseqscommand.h */, - A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */, + A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */, A7E9B6C812D37EC400DA6239 /* deuniqueseqscommand.h */, - A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */, + A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */, + A77A221D139001B600B0BE70 /* deuniquetreecommand.h */, + A77A221E139001B600B0BE70 /* deuniquetreecommand.cpp */, A7E9B6CC12D37EC400DA6239 /* distancecommand.h */, - A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */, + A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */, A7E9B6E412D37EC400DA6239 /* filterseqscommand.h */, - A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */, + A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */, + A778FE69134CA6CA00C0BA33 /* getcommandinfocommand.h */, + A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */, + A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */, + A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */, A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */, - A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */, + A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */, A7E9B6F512D37EC400DA6239 /* getgroupscommand.h */, - A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */, + A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */, A7E9B6F712D37EC400DA6239 /* getlabelcommand.h */, - A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */, + A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */, A7E9B6F912D37EC400DA6239 /* getlineagecommand.h */, - A7E9B6FA12D37EC400DA6239 /* getlistcountcommand.cpp */, + A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */, A7E9B6FB12D37EC400DA6239 /* getlistcountcommand.h */, - A7E9B6FE12D37EC400DA6239 /* getoturepcommand.cpp */, + A7E9B6FA12D37EC400DA6239 /* getlistcountcommand.cpp */, A7E9B6FF12D37EC400DA6239 /* getoturepcommand.h */, - A7E9B70012D37EC400DA6239 /* getotuscommand.cpp */, + A7E9B6FE12D37EC400DA6239 /* getoturepcommand.cpp */, A7E9B70112D37EC400DA6239 /* getotuscommand.h */, - A7E9B70212D37EC400DA6239 /* getrabundcommand.cpp */, + A7E9B70012D37EC400DA6239 /* getotuscommand.cpp */, A7E9B70312D37EC400DA6239 /* getrabundcommand.h */, - A7E9B70412D37EC400DA6239 /* getrelabundcommand.cpp */, + A7E9B70212D37EC400DA6239 /* getrabundcommand.cpp */, A7E9B70512D37EC400DA6239 /* getrelabundcommand.h */, - A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */, + A7E9B70412D37EC400DA6239 /* getrelabundcommand.cpp */, A7E9B70712D37EC400DA6239 /* getsabundcommand.h */, - A7E9B70812D37EC400DA6239 /* getseqscommand.cpp */, + A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */, A7E9B70912D37EC400DA6239 /* getseqscommand.h */, - A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */, + A7E9B70812D37EC400DA6239 /* getseqscommand.cpp */, A7E9B70B12D37EC400DA6239 /* getsharedotucommand.h */, - A7E9B71A12D37EC400DA6239 /* hclustercommand.cpp */, + A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */, A7E9B71B12D37EC400DA6239 /* hclustercommand.h */, - A7E9B71E12D37EC400DA6239 /* heatmapcommand.cpp */, + A7E9B71A12D37EC400DA6239 /* hclustercommand.cpp */, A7E9B71F12D37EC400DA6239 /* heatmapcommand.h */, - A7E9B72212D37EC400DA6239 /* heatmapsimcommand.cpp */, + A7E9B71E12D37EC400DA6239 /* heatmapcommand.cpp */, A7E9B72312D37EC400DA6239 /* heatmapsimcommand.h */, - A7E9B72812D37EC400DA6239 /* helpcommand.cpp */, + A7E9B72212D37EC400DA6239 /* heatmapsimcommand.cpp */, A7E9B72912D37EC400DA6239 /* helpcommand.h */, - A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */, + A7E9B72812D37EC400DA6239 /* helpcommand.cpp */, + A75790571301749D00A30DAB /* homovacommand.h */, + A75790581301749D00A30DAB /* homovacommand.cpp */, A7E9B72C12D37EC400DA6239 /* indicatorcommand.h */, - A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */, + A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */, A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */, - A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */, + A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */, A7E9B73E12D37EC400DA6239 /* listseqscommand.h */, - A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */, + A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */, + A7FA10001302E096003860FE /* mantelcommand.h */, + A7FA10011302E096003860FE /* mantelcommand.cpp */, + A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */, + A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */, A7E9B74412D37EC400DA6239 /* makegroupcommand.h */, - A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */, + A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */, A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */, - A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */, + A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */, A7E9B75412D37EC400DA6239 /* mergefilecommand.h */, - A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */, + A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */, + A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */, + A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */, A7E9B75812D37EC400DA6239 /* metastatscommand.h */, - A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */, + A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */, A7E9B75A12D37EC400DA6239 /* mgclustercommand.h */, + A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */, A7E9B76A12D37EC400DA6239 /* nocommands.h */, A7E9B76912D37EC400DA6239 /* nocommands.cpp */, - A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */, A7E9B76C12D37EC400DA6239 /* normalizesharedcommand.h */, - A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */, + A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */, + A713EBEB12DC7C5E000092AC /* nmdscommand.h */, + A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */, + A7A3C8C814D041AD00B1BFBE /* otuassociationcommand.h */, + A7A3C8C714D041AD00B1BFBE /* otuassociationcommand.cpp */, A7E9B77A12D37EC400DA6239 /* otuhierarchycommand.h */, - A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */, + A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */, A7E9B77E12D37EC400DA6239 /* pairwiseseqscommand.h */, - A7E9B77F12D37EC400DA6239 /* parsefastaqcommand.cpp */, + A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */, A7E9B78012D37EC400DA6239 /* parsefastaqcommand.h */, - A7E9B78112D37EC400DA6239 /* parselistscommand.cpp */, + A7E9B77F12D37EC400DA6239 /* parsefastaqcommand.cpp */, A7E9B78212D37EC400DA6239 /* parselistscommand.h */, - A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */, + A7E9B78112D37EC400DA6239 /* parselistscommand.cpp */, A7E9B78612D37EC400DA6239 /* parsimonycommand.h */, - A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */, + A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */, + A7FC486512D795D60055BC5C /* pcacommand.h */, + A7FC486612D795D60055BC5C /* pcacommand.cpp */, A7E9B78812D37EC400DA6239 /* pcoacommand.h */, - A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */, + A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */, + A76CDD7F1510F09A004C8458 /* pcrseqscommand.h */, + A76CDD811510F143004C8458 /* prcseqscommand.cpp */, A7E9B78C12D37EC400DA6239 /* phylodiversitycommand.h */, - A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */, + A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */, A7E9B79212D37EC400DA6239 /* phylotypecommand.h */, - A7E9B79512D37EC400DA6239 /* pipelinepdscommand.cpp */, + A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */, A7E9B79612D37EC400DA6239 /* pipelinepdscommand.h */, - A7E9B79712D37EC400DA6239 /* preclustercommand.cpp */, + A7E9B79512D37EC400DA6239 /* pipelinepdscommand.cpp */, A7E9B79812D37EC400DA6239 /* preclustercommand.h */, - A7E9B7A112D37EC400DA6239 /* quitcommand.cpp */, + A7E9B79712D37EC400DA6239 /* preclustercommand.cpp */, A7E9B7A212D37EC400DA6239 /* quitcommand.h */, - A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */, + A7E9B7A112D37EC400DA6239 /* quitcommand.cpp */, A7E9B7AC12D37EC400DA6239 /* rarefactcommand.h */, - A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */, + A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */, A7E9B7AF12D37EC400DA6239 /* rarefactsharedcommand.h */, - A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */, + A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */, A7E9B7B712D37EC400DA6239 /* readdistcommand.h */, - A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */, + A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */, A7E9B7BC12D37EC400DA6239 /* readotucommand.h */, - A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */, + A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */, A7E9B7C212D37EC400DA6239 /* readtreecommand.h */, - A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */, + A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */, A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */, - A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */, + A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */, A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */, - A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */, + A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */, A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */, - A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */, + A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */, + A727864212E9E28C00F86ABA /* removerarecommand.h */, + A727864312E9E28C00F86ABA /* removerarecommand.cpp */, A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */, - A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */, + A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */, A7E9B7CE12D37EC400DA6239 /* reversecommand.h */, - A7E9B7D112D37EC400DA6239 /* screenseqscommand.cpp */, + A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */, A7E9B7D212D37EC400DA6239 /* screenseqscommand.h */, - A7E9B7D312D37EC400DA6239 /* secondarystructurecommand.cpp */, + A7E9B7D112D37EC400DA6239 /* screenseqscommand.cpp */, A7E9B7D412D37EC400DA6239 /* secondarystructurecommand.h */, - A7E9B7D512D37EC400DA6239 /* sensspeccommand.cpp */, + A7E9B7D312D37EC400DA6239 /* secondarystructurecommand.cpp */, A7E9B7D612D37EC400DA6239 /* sensspeccommand.h */, - A7E9B7D712D37EC400DA6239 /* seqerrorcommand.cpp */, + A7E9B7D512D37EC400DA6239 /* sensspeccommand.cpp */, A7E9B7D812D37EC400DA6239 /* seqerrorcommand.h */, - A7E9B7D912D37EC400DA6239 /* seqsummarycommand.cpp */, + A7E9B7D712D37EC400DA6239 /* seqerrorcommand.cpp */, A7E9B7DA12D37EC400DA6239 /* seqsummarycommand.h */, - A7E9B7DF12D37EC400DA6239 /* setdircommand.cpp */, + A7E9B7D912D37EC400DA6239 /* seqsummarycommand.cpp */, + A7FE7E6B13311EA400F7B327 /* setcurrentcommand.h */, + A7FE7E6C13311EA400F7B327 /* setcurrentcommand.cpp */, A7E9B7E012D37EC400DA6239 /* setdircommand.h */, - A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */, + A7E9B7DF12D37EC400DA6239 /* setdircommand.cpp */, A7E9B7E212D37EC400DA6239 /* setlogfilecommand.h */, - A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */, + A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */, A7E9B7E412D37EC400DA6239 /* sffinfocommand.h */, - A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */, + A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */, A7E9B7F312D37EC400DA6239 /* sharedcommand.h */, - A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */, + A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */, A7E9B82812D37EC400DA6239 /* shhhercommand.h */, - A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */, + A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */, + A774101214695AF60098E6AC /* shhhseqscommand.h */, + A774101314695AF60098E6AC /* shhhseqscommand.cpp */, + A7A32DAC14DC43D10001D2E5 /* sortseqscommand.h */, + A7A32DA914DC43B00001D2E5 /* sortseqscommand.cpp */, A7E9B84012D37EC400DA6239 /* splitabundcommand.h */, - A7E9B84112D37EC400DA6239 /* splitgroupscommand.cpp */, + A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */, A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */, - A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */, + A7E9B84112D37EC400DA6239 /* splitgroupscommand.cpp */, A7E9B85012D37EC400DA6239 /* subsamplecommand.h */, - A7E9B85712D37EC400DA6239 /* summarycommand.cpp */, + A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */, A7E9B85812D37EC400DA6239 /* summarycommand.h */, - A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */, + A7E9B85712D37EC400DA6239 /* summarycommand.cpp */, + A754149514840CF7005850D1 /* summaryqualcommand.h */, + A754149614840CF7005850D1 /* summaryqualcommand.cpp */, A7E9B85A12D37EC400DA6239 /* summarysharedcommand.h */, - A7E9B85B12D37EC400DA6239 /* systemcommand.cpp */, + A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */, + A7FFB556142CA02C004884F2 /* summarytaxcommand.h */, + A7FFB557142CA02C004884F2 /* summarytaxcommand.cpp */, A7E9B85C12D37EC400DA6239 /* systemcommand.h */, - A7E9B86212D37EC400DA6239 /* treegroupscommand.cpp */, + A7E9B85B12D37EC400DA6239 /* systemcommand.cpp */, A7E9B86312D37EC400DA6239 /* treegroupscommand.h */, - A7E9B86812D37EC400DA6239 /* trimflowscommand.cpp */, + A7E9B86212D37EC400DA6239 /* treegroupscommand.cpp */, A7E9B86912D37EC400DA6239 /* trimflowscommand.h */, - A7E9B86A12D37EC400DA6239 /* trimseqscommand.cpp */, + A7E9B86812D37EC400DA6239 /* trimflowscommand.cpp */, A7E9B86B12D37EC400DA6239 /* trimseqscommand.h */, - A7E9B86C12D37EC400DA6239 /* unifracunweightedcommand.cpp */, + A7E9B86A12D37EC400DA6239 /* trimseqscommand.cpp */, A7E9B86D12D37EC400DA6239 /* unifracunweightedcommand.h */, - A7E9B86E12D37EC400DA6239 /* unifracweightedcommand.cpp */, + A7E9B86C12D37EC400DA6239 /* unifracunweightedcommand.cpp */, A7E9B86F12D37EC400DA6239 /* unifracweightedcommand.h */, - A7E9B87A12D37EC400DA6239 /* venncommand.cpp */, + A7E9B86E12D37EC400DA6239 /* unifracweightedcommand.cpp */, A7E9B87B12D37EC400DA6239 /* venncommand.h */, + A7E9B87A12D37EC400DA6239 /* venncommand.cpp */, ); name = commands; sourceTree = ""; @@ -1193,6 +1543,7 @@ A7E9BA3F12D395F700DA6239 /* calculators */ = { isa = PBXGroup; children = ( + 7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */, A7E9B64F12D37EC300DA6239 /* ace.cpp */, A7E9B65012D37EC300DA6239 /* ace.h */, A7E9B65E12D37EC300DA6239 /* bergerparker.cpp */, @@ -1220,8 +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 */, @@ -1270,7 +1619,6 @@ A7E9B7E812D37EC400DA6239 /* shannoneven.h */, A7E9B7E912D37EC400DA6239 /* sharedace.cpp */, A7E9B7EA12D37EC400DA6239 /* sharedace.h */, - A7E9B7EB12D37EC400DA6239 /* sharedanderberg.h */, A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */, A7E9B7ED12D37EC400DA6239 /* sharedanderbergs.h */, A7E9B7EE12D37EC400DA6239 /* sharedbraycurtis.cpp */, @@ -1342,12 +1690,12 @@ A7E9B84D12D37EC400DA6239 /* structpearson.cpp */, A7E9B84E12D37EC400DA6239 /* structpearson.h */, A7E9B86112D37EC400DA6239 /* treecalculator.h */, - A7E9B87012D37EC400DA6239 /* unweighted.cpp */, A7E9B87112D37EC400DA6239 /* unweighted.h */, + A7E9B87012D37EC400DA6239 /* unweighted.cpp */, A7E9B87212D37EC400DA6239 /* uvest.cpp */, A7E9B87312D37EC400DA6239 /* uvest.h */, - A7E9B87C12D37EC400DA6239 /* weighted.cpp */, A7E9B87D12D37EC400DA6239 /* weighted.h */, + A7E9B87C12D37EC400DA6239 /* weighted.cpp */, A7E9B87F12D37EC400DA6239 /* whittaker.cpp */, A7E9B88012D37EC400DA6239 /* whittaker.h */, ); @@ -1394,6 +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 */, @@ -1402,18 +1752,26 @@ A7E9B7DC12D37EC400DA6239 /* sequence.hpp */, A7E9B7DD12D37EC400DA6239 /* sequencedb.cpp */, A7E9B7DE12D37EC400DA6239 /* sequencedb.h */, + A7F9F5CD141A5E500032F693 /* sequenceparser.h */, + A7F9F5CE141A5E500032F693 /* sequenceparser.cpp */, A7E9B80412D37EC400DA6239 /* sharedlistvector.cpp */, A7E9B80512D37EC400DA6239 /* sharedlistvector.h */, - A7E9B80D12D37EC400DA6239 /* sharedordervector.cpp */, A7E9B80E12D37EC400DA6239 /* sharedordervector.h */, - A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */, + A7E9B80D12D37EC400DA6239 /* sharedordervector.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 */, @@ -1427,6 +1785,7 @@ A7E9BA4512D3965600DA6239 /* chimera */ = { isa = PBXGroup; children = ( + A74D3644137DA7CE00332B0C /* uchime */, A7E9B65C12D37EC300DA6239 /* bellerophon.cpp */, A7E9B65D12D37EC300DA6239 /* bellerophon.h */, A7E9B67412D37EC400DA6239 /* ccode.cpp */, @@ -1437,12 +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 */, - A7E9B6C212D37EC400DA6239 /* decalc.h */, A7E9B74612D37EC400DA6239 /* maligner.h */, A7E9B74512D37EC400DA6239 /* maligner.cpp */, + A7BF221314587886000AD524 /* myPerseus.h */, + A7BF221214587886000AD524 /* myPerseus.cpp */, A7E9B79312D37EC400DA6239 /* pintail.cpp */, A7E9B79412D37EC400DA6239 /* pintail.h */, A7E9B82E12D37EC400DA6239 /* slayer.cpp */, @@ -1505,12 +1866,12 @@ A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */, A7E9B7B512D37EC400DA6239 /* readcolumn.h */, A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */, - A7E9B7B912D37EC400DA6239 /* readotu.cpp */, - A7E9B7BA12D37EC400DA6239 /* readotu.h */, A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */, A7E9B7BE12D37EC400DA6239 /* readphylip.h */, A7E9B7BF12D37EC400DA6239 /* readtree.cpp */, A7E9B7C012D37EC400DA6239 /* readtree.h */, + A713EBAA12DC7613000092AC /* readphylipvector.h */, + A713EBAB12DC7613000092AC /* readphylipvector.cpp */, A7E9B84312D37EC400DA6239 /* splitmatrix.cpp */, A7E9B84412D37EC400DA6239 /* splitmatrix.h */, ); @@ -1520,8 +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 = ""; @@ -1546,6 +1912,7 @@ 8DD76FAF0486AB0100D96B5E /* CopyFiles */, ); buildRules = ( + A7D162CB149F96CA000523E8 /* PBXBuildRule */, ); dependencies = ( ); @@ -1560,7 +1927,10 @@ /* Begin PBXProject section */ 08FB7793FE84155DC02AAC07 /* Project object */ = { isa = PBXProject; - buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */; + attributes = { + ORGANIZATIONNAME = "Schloss Lab"; + }; + buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */; compatibilityVersion = "Xcode 3.1"; developmentRegion = English; hasScannedForEncodings = 1; @@ -1612,7 +1982,6 @@ A7E9B89A12D37EC400DA6239 /* chimeracheckrdp.cpp in Sources */, A7E9B89B12D37EC400DA6239 /* chimerapintailcommand.cpp in Sources */, A7E9B89C12D37EC400DA6239 /* chimerarealigner.cpp in Sources */, - A7E9B89D12D37EC400DA6239 /* chimeraseqscommand.cpp in Sources */, A7E9B89E12D37EC400DA6239 /* chimeraslayer.cpp in Sources */, A7E9B89F12D37EC400DA6239 /* chimeraslayercommand.cpp in Sources */, A7E9B8A012D37EC400DA6239 /* chopseqscommand.cpp in Sources */, @@ -1654,7 +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 */, @@ -1673,7 +2041,6 @@ 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 */, @@ -1709,7 +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 */, @@ -1756,7 +2122,6 @@ 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 */, @@ -1856,6 +2221,80 @@ A7E9B98E12D37EC400DA6239 /* weightedlinkage.cpp in Sources */, A7E9B98F12D37EC400DA6239 /* whittaker.cpp in Sources */, A70332B712D3A13400761E33 /* makefile in Sources */, + A7FC480E12D788F20055BC5C /* linearalgebra.cpp in Sources */, + A7FC486712D795D60055BC5C /* pcacommand.cpp in Sources */, + A713EBAC12DC7613000092AC /* readphylipvector.cpp in Sources */, + A713EBED12DC7C5E000092AC /* nmdscommand.cpp in Sources */, + A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */, + A71FE12C12EDF72400963CA7 /* mergegroupscommand.cpp in Sources */, + 7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */, + A7A61F2D130062E000E05B6B /* amovacommand.cpp in Sources */, + A75790591301749D00A30DAB /* homovacommand.cpp in Sources */, + A7FA10021302E097003860FE /* mantelcommand.cpp in Sources */, + A799F5B91309A3E000AEEFA0 /* makefastqcommand.cpp in Sources */, + A71CB160130B04A2001E7287 /* anosimcommand.cpp in Sources */, + 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; }; @@ -1873,6 +2312,7 @@ GCC_OPTIMIZATION_LEVEL = 0; INSTALL_PATH = /usr/local/bin; PRODUCT_NAME = Mothur; + SDKROOT = macosx10.6; }; name = Debug; }; @@ -1892,22 +2332,29 @@ 1DEB928A08733DD80010E9CD /* Debug */ = { isa = XCBuildConfiguration; buildSettings = { - ARCHS = "$(ARCHS_STANDARD_32_64_BIT)"; + ARCHS = "$(ARCHS_STANDARD_64_BIT)"; DEPLOYMENT_LOCATION = NO; GCC_C_LANGUAGE_STANDARD = gnu99; + 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=\"\\\"1.15.0\\\"\"", - "RELEASE_DATE=\"\\\"12/10/2010\\\"\"", + "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; OTHER_CPLUSPLUSFLAGS = ( - "-DUSE_READLINE", "-DBIT_VERSION", + "-DUSE_READLINE", "$(OTHER_CFLAGS)", ); OTHER_LDFLAGS = ( @@ -1915,20 +2362,23 @@ "-lreadline", ); PREBINDING = NO; - SDKROOT = macosx10.5; + SDKROOT = macosx10.6; + USER_HEADER_SEARCH_PATHS = ""; }; name = Debug; }; 1DEB928B08733DD80010E9CD /* Release */ = { isa = XCBuildConfiguration; buildSettings = { - ARCHS = "$(ARCHS_STANDARD_32_64_BIT)"; + ARCHS = "$(ARCHS_STANDARD_64_BIT)"; DEPLOYMENT_LOCATION = NO; GCC_C_LANGUAGE_STANDARD = gnu99; + GCC_GENERATE_DEBUGGING_SYMBOLS = NO; + GCC_MODEL_TUNING = ""; + GCC_OPTIMIZATION_LEVEL = 0; GCC_PREPROCESSOR_DEFINITIONS = ( - "MOTHUR_FILES=\"\\\"../release\\\"\"", - "VERSION=\"\\\"1.15.0\\\"\"", - "RELEASE_DATE=\"\\\"12/10/2010\\\"\"", + "VERSION=\"\\\"1.24.0\\\"\"", + "RELEASE_DATE=\"\\\"3/12/2012\\\"\"", ); GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; @@ -1939,6 +2389,7 @@ GCC_WARN_UNUSED_VALUE = YES; GCC_WARN_UNUSED_VARIABLE = YES; INSTALL_PATH = ""; + MACH_O_TYPE = mh_execute; OTHER_CPLUSPLUSFLAGS = ( "-DUSE_READLINE", "-DBIT_VERSION", @@ -1949,7 +2400,7 @@ "-lreadline", ); PREBINDING = NO; - SDKROOT = macosx10.5; + SDKROOT = macosx10.6; }; name = Release; }; @@ -1965,7 +2416,7 @@ defaultConfigurationIsVisible = 0; defaultConfigurationName = Release; }; - 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */ = { + 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = { isa = XCConfigurationList; buildConfigurations = ( 1DEB928A08733DD80010E9CD /* Debug */,