]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
added code to format fast files for uchime. started work on sff.multiple command
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index ff18d5890cef43d65aabd4f444cef07b6bf2b0fe..4c2e330a280e84434f269e5ee08d133a8fd8c2a4 100644 (file)
@@ -7,8 +7,12 @@
        objects = {
 
 /* Begin PBXBuildFile section */
+               219C1DE01552C4BD004209F9 /* newcommandtemplate.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 219C1DDF1552C4BD004209F9 /* newcommandtemplate.cpp */; };
+               219C1DE41559BCCF004209F9 /* getcoremicrobiomecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */; };
                7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */; };
                8DD76FB00486AB0100D96B5E /* mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6A0FF2C0290799A04C91782 /* mothur.1 */; };
+               A70056E6156A93D000924A2D /* getotulabelscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70056E5156A93D000924A2D /* getotulabelscommand.cpp */; };
+               A70056EB156AB6E500924A2D /* removeotulabelscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70056EA156AB6E500924A2D /* removeotulabelscommand.cpp */; };
                A70332B712D3A13400761E33 /* makefile in Sources */ = {isa = PBXBuildFile; fileRef = A70332B512D3A13400761E33 /* makefile */; };
                A713EBAC12DC7613000092AC /* readphylipvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBAB12DC7613000092AC /* readphylipvector.cpp */; };
                A713EBED12DC7C5E000092AC /* nmdscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */; };
                A721765713BB9F7D0014DAAE /* referencedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A721765613BB9F7D0014DAAE /* referencedb.cpp */; };
                A724D2B7153C8628000A826F /* makebiomcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A724D2B6153C8628000A826F /* makebiomcommand.cpp */; };
                A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727864312E9E28C00F86ABA /* removerarecommand.cpp */; };
+               A73901081588C40900ED2ED6 /* loadlogfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73901071588C40900ED2ED6 /* loadlogfilecommand.cpp */; };
                A73DDBBA13C4A0D1006AAE38 /* clearmemorycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73DDBB913C4A0D1006AAE38 /* clearmemorycommand.cpp */; };
                A73DDC3813C4BF64006AAE38 /* mothurmetastats.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73DDC3713C4BF64006AAE38 /* mothurmetastats.cpp */; };
+               A741FAD215D1688E0067BCC5 /* sequencecountparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A741FAD115D1688E0067BCC5 /* sequencecountparser.cpp */; };
                A74A9A9F148E881E00AB5E3E /* spline.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74A9A9E148E881E00AB5E3E /* spline.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 */; };
+               A74D59A4159A1E2000043046 /* counttable.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D59A3159A1E2000043046 /* counttable.cpp */; };
                A754149714840CF7005850D1 /* summaryqualcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A754149614840CF7005850D1 /* summaryqualcommand.cpp */; };
                A75790591301749D00A30DAB /* homovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A75790581301749D00A30DAB /* homovacommand.cpp */; };
                A76CDD821510F143004C8458 /* prcseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A76CDD811510F143004C8458 /* prcseqscommand.cpp */; };
@@ -57,6 +42,8 @@
                A79234D713C74BF6002B08E2 /* mothurfisher.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A79234D613C74BF6002B08E2 /* mothurfisher.cpp */; };
                A795840D13F13CD900F201D5 /* countgroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A795840C13F13CD900F201D5 /* countgroupscommand.cpp */; };
                A799F5B91309A3E000AEEFA0 /* makefastqcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */; };
+               A7A0671A1562946F0095C8C5 /* listotulabelscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A067191562946F0095C8C5 /* listotulabelscommand.cpp */; };
+               A7A0671F1562AC3E0095C8C5 /* makecontigscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A0671E1562AC3E0095C8C5 /* makecontigscommand.cpp */; };
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@@ -64,7 +51,9 @@
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+               A7C7DAB915DA758B0059B0CF /* sffmultiplecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7C7DAB815DA758B0059B0CF /* sffmultiplecommand.cpp */; };
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+               A7E0243D15B4520A00A5F046 /* sparsedistancematrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E0243C15B4520A00A5F046 /* sparsedistancematrix.cpp */; };
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                A7E9B92F12D37EC400DA6239 /* readphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */; };
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                A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readcolumn.cpp; sourceTree = "<group>"; };
                A7E9B7B512D37EC400DA6239 /* readcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcolumn.h; sourceTree = "<group>"; };
-               A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistcommand.cpp; sourceTree = "<group>"; };
-               A7E9B7B712D37EC400DA6239 /* readdistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcommand.h; sourceTree = "<group>"; };
                A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = "<group>"; };
-               A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = "<group>"; };
-               A7E9B7BC12D37EC400DA6239 /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = "<group>"; };
                A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = "<group>"; };
                A7E9B7BE12D37EC400DA6239 /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = "<group>"; };
                A7E9B7BF12D37EC400DA6239 /* readtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtree.cpp; sourceTree = "<group>"; };
                A7E9B7C012D37EC400DA6239 /* readtree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtree.h; sourceTree = "<group>"; };
-               A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = "<group>"; };
-               A7E9B7C212D37EC400DA6239 /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = "<group>"; };
                A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removegroupscommand.cpp; sourceTree = "<group>"; };
                A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removegroupscommand.h; sourceTree = "<group>"; };
                A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removelineagecommand.cpp; sourceTree = "<group>"; };
                1AB674ADFE9D54B511CA2CBB /* Products */ = {
                        isa = PBXGroup;
                        children = (
-                               8DD76FB20486AB0100D96B5E /* Mothur */,
+                               8DD76FB20486AB0100D96B5E /* mothur */,
                        );
                        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>";
-               };
                A7D161E7149F7F50000523E8 /* fortran */ = {
                        isa = PBXGroup;
                        children = (
                        isa = PBXGroup;
                        children = (
                                A7E9B6AE12D37EC400DA6239 /* command.hpp */,
+                               219C1DE11552C508004209F9 /* newcommandtemplate.h */,
+                               219C1DDF1552C4BD004209F9 /* newcommandtemplate.cpp */,
                                A7E9B65212D37EC300DA6239 /* aligncommand.h */,
                                A7E9B65112D37EC300DA6239 /* aligncommand.cpp */,
                                A7A61F2B130062E000E05B6B /* amovacommand.h */,
                                A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */,
                                A778FE69134CA6CA00C0BA33 /* getcommandinfocommand.h */,
                                A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */,
+                               219C1DE51559BCF2004209F9 /* getcoremicrobiomecommand.h */,
+                               219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */,
                                A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */,
                                A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */,
                                A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */,
                                A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */,
                                A7E9B6F712D37EC400DA6239 /* getlabelcommand.h */,
                                A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */,
+                               A70056E8156A93E300924A2D /* getotulabelscommand.h */,
+                               A70056E5156A93D000924A2D /* getotulabelscommand.cpp */,
                                A7E9B6F912D37EC400DA6239 /* getlineagecommand.h */,
                                A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */,
                                A7E9B6FB12D37EC400DA6239 /* getlistcountcommand.h */,
                                A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */,
                                A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */,
                                A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */,
+                               A7A0671C156294810095C8C5 /* listotulabelscommand.h */,
+                               A7A067191562946F0095C8C5 /* listotulabelscommand.cpp */,
                                A7E9B73E12D37EC400DA6239 /* listseqscommand.h */,
                                A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */,
+                               A73901051588C3EF00ED2ED6 /* loadlogfilecommand.h */,
+                               A73901071588C40900ED2ED6 /* loadlogfilecommand.cpp */,
                                A7FA10001302E096003860FE /* mantelcommand.h */,
                                A7FA10011302E096003860FE /* mantelcommand.cpp */,
                                A724D2B4153C8600000A826F /* makebiomcommand.h */,
                                A724D2B6153C8628000A826F /* makebiomcommand.cpp */,
+                               A7A0671D1562AC230095C8C5 /* makecontigscommand.h */,
+                               A7A0671E1562AC3E0095C8C5 /* makecontigscommand.cpp */,
                                A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */,
                                A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */,
                                A7E9B74412D37EC400DA6239 /* makegroupcommand.h */,
                                A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */,
                                A7E9B7AF12D37EC400DA6239 /* rarefactsharedcommand.h */,
                                A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */,
-                               A7E9B7B712D37EC400DA6239 /* readdistcommand.h */,
-                               A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */,
-                               A7E9B7BC12D37EC400DA6239 /* readotucommand.h */,
-                               A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */,
-                               A7E9B7C212D37EC400DA6239 /* readtreecommand.h */,
-                               A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */,
                                A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */,
                                A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */,
                                A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */,
                                A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */,
                                A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */,
                                A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */,
+                               A70056E9156AB6D400924A2D /* removeotulabelscommand.h */,
+                               A70056EA156AB6E500924A2D /* removeotulabelscommand.cpp */,
                                A727864212E9E28C00F86ABA /* removerarecommand.h */,
                                A727864312E9E28C00F86ABA /* removerarecommand.cpp */,
                                A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */,
                                A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */,
                                A7E9B7E412D37EC400DA6239 /* sffinfocommand.h */,
                                A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */,
+                               A7C7DAB615DA75760059B0CF /* sffmultiplecommand.h */,
+                               A7C7DAB815DA758B0059B0CF /* sffmultiplecommand.cpp */,
                                A7E9B7F312D37EC400DA6239 /* sharedcommand.h */,
                                A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */,
                                A7E9B82812D37EC400DA6239 /* shhhercommand.h */,
                                A7E9B66312D37EC400DA6239 /* blastalign.hpp */,
                                A7E9B66412D37EC400DA6239 /* blastdb.cpp */,
                                A7E9B66512D37EC400DA6239 /* blastdb.hpp */,
+                               A74D59A6159A1E3600043046 /* counttable.h */,
+                               A74D59A3159A1E2000043046 /* counttable.cpp */,
+                               A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */,
                                A7E9B6BD12D37EC400DA6239 /* database.cpp */,
                                A7E9B6BE12D37EC400DA6239 /* database.hpp */,
                                A7E9B6BF12D37EC400DA6239 /* datavector.hpp */,
-                               A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */,
                                A7E9B6CE12D37EC400DA6239 /* distancedb.hpp */,
                                A7E9B6DE12D37EC400DA6239 /* fastamap.cpp */,
                                A7E9B6DF12D37EC400DA6239 /* fastamap.h */,
                                A7E9B7D012D37EC400DA6239 /* sabundvector.hpp */,
                                A7E9B7DB12D37EC400DA6239 /* sequence.cpp */,
                                A7E9B7DC12D37EC400DA6239 /* sequence.hpp */,
+                               A741FAD415D168A00067BCC5 /* sequencecountparser.h */,
+                               A741FAD115D1688E0067BCC5 /* sequencecountparser.cpp */,
                                A7E9B7DD12D37EC400DA6239 /* sequencedb.cpp */,
                                A7E9B7DE12D37EC400DA6239 /* sequencedb.h */,
                                A7F9F5CD141A5E500032F693 /* sequenceparser.h */,
                                A7E9B81412D37EC400DA6239 /* sharedsabundvector.h */,
                                A7E9B83912D37EC400DA6239 /* sparsematrix.cpp */,
                                A7E9B83A12D37EC400DA6239 /* sparsematrix.hpp */,
+                               A7E0243F15B4522000A5F046 /* sparsedistancematrix.h */,
+                               A7E0243C15B4520A00A5F046 /* sparsedistancematrix.cpp */,
                                A7E9B85112D37EC400DA6239 /* suffixdb.cpp */,
                                A7E9B85212D37EC400DA6239 /* suffixdb.hpp */,
                                A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */,
                A7E9BA4512D3965600DA6239 /* chimera */ = {
                        isa = PBXGroup;
                        children = (
-                               A74D3644137DA7CE00332B0C /* uchime */,
                                A7E9B65C12D37EC300DA6239 /* bellerophon.cpp */,
                                A7E9B65D12D37EC300DA6239 /* bellerophon.h */,
                                A7E9B67412D37EC400DA6239 /* ccode.cpp */,
                        name = Mothur;
                        productInstallPath = "$(HOME)/bin";
                        productName = mothur;
-                       productReference = 8DD76FB20486AB0100D96B5E /* Mothur */;
+                       productReference = 8DD76FB20486AB0100D96B5E /* mothur */;
                        productType = "com.apple.product-type.tool";
                };
 /* End PBXNativeTarget section */
                                A7E9B92912D37EC400DA6239 /* readblast.cpp in Sources */,
                                A7E9B92A12D37EC400DA6239 /* readcluster.cpp in Sources */,
                                A7E9B92B12D37EC400DA6239 /* readcolumn.cpp in Sources */,
-                               A7E9B92C12D37EC400DA6239 /* readdistcommand.cpp in Sources */,
-                               A7E9B92E12D37EC400DA6239 /* readotucommand.cpp in Sources */,
                                A7E9B92F12D37EC400DA6239 /* readphylip.cpp in Sources */,
                                A7E9B93012D37EC400DA6239 /* readtree.cpp in Sources */,
-                               A7E9B93112D37EC400DA6239 /* readtreecommand.cpp in Sources */,
                                A7E9B93212D37EC400DA6239 /* removegroupscommand.cpp in Sources */,
                                A7E9B93312D37EC400DA6239 /* removelineagecommand.cpp in Sources */,
                                A7E9B93412D37EC400DA6239 /* removeotuscommand.cpp in Sources */,
                                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 */,
                                A7876A26152A017C00A0AE86 /* subsample.cpp in Sources */,
                                A7D755DA1535F679009BF21A /* treereader.cpp in Sources */,
                                A724D2B7153C8628000A826F /* makebiomcommand.cpp in Sources */,
+                               219C1DE01552C4BD004209F9 /* newcommandtemplate.cpp in Sources */,
+                               219C1DE41559BCCF004209F9 /* getcoremicrobiomecommand.cpp in Sources */,
+                               A7A0671A1562946F0095C8C5 /* listotulabelscommand.cpp in Sources */,
+                               A7A0671F1562AC3E0095C8C5 /* makecontigscommand.cpp in Sources */,
+                               A70056E6156A93D000924A2D /* getotulabelscommand.cpp in Sources */,
+                               A70056EB156AB6E500924A2D /* removeotulabelscommand.cpp in Sources */,
+                               A73901081588C40900ED2ED6 /* loadlogfilecommand.cpp in Sources */,
+                               A74D59A4159A1E2000043046 /* counttable.cpp in Sources */,
+                               A7E0243D15B4520A00A5F046 /* sparsedistancematrix.cpp in Sources */,
+                               A741FAD215D1688E0067BCC5 /* sequencecountparser.cpp in Sources */,
+                               A7C7DAB915DA758B0059B0CF /* sffmultiplecommand.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
                        buildSettings = {
                                ALWAYS_SEARCH_USER_PATHS = NO;
                                COPY_PHASE_STRIP = NO;
+                               DEPLOYMENT_LOCATION = YES;
                                GCC_DYNAMIC_NO_PIC = NO;
                                GCC_MODEL_TUNING = G5;
                                GCC_OPTIMIZATION_LEVEL = 0;
-                               INSTALL_PATH = /usr/local/bin;
-                               PRODUCT_NAME = Mothur;
+                               PRODUCT_NAME = mothur;
                                SDKROOT = macosx10.6;
+                               SKIP_INSTALL = NO;
                        };
                        name = Debug;
                };
                                DEPLOYMENT_LOCATION = YES;
                                GCC_MODEL_TUNING = G5;
                                GCC_WARN_UNUSED_VALUE = YES;
-                               INSTALL_PATH = ./;
-                               PRODUCT_NAME = Mothur;
+                               PRODUCT_NAME = mothur;
+                               SKIP_INSTALL = NO;
                        };
                        name = Release;
                };
                                GCC_OPTIMIZATION_LEVEL = 0;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "MOTHUR_FILES=\"\\\"../release\\\"\"",
-                                       "VERSION=\"\\\"1.24.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"3/12/2012\\\"\"",
+                                       "VERSION=\"\\\"1.26.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"7/9/2012\\\"\"",
                                );
                                "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 = "";
+                               INSTALL_PATH = TARGET_BUILD_DIR;
                                MACH_O_TYPE = mh_execute;
                                ONLY_ACTIVE_ARCH = YES;
                                OTHER_CPLUSPLUSFLAGS = (
                                        "-lreadline",
                                );
                                SDKROOT = macosx10.6;
+                               SKIP_INSTALL = NO;
                                USER_HEADER_SEARCH_PATHS = "";
                        };
                        name = Debug;
                                GCC_MODEL_TUNING = "";
                                GCC_OPTIMIZATION_LEVEL = 0;
                                GCC_PREPROCESSOR_DEFINITIONS = (
-                                       "VERSION=\"\\\"1.25.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"4/30/2012\\\"\"",
+                                       "VERSION=\"\\\"1.26.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"7/9/2012\\\"\"",
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_PARAMETER = YES;
                                GCC_WARN_UNUSED_VALUE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
-                               INSTALL_PATH = "";
+                               INSTALL_PATH = TARGET_BUILD_DIR;
                                MACH_O_TYPE = mh_execute;
                                OTHER_CPLUSPLUSFLAGS = (
                                        "-DUSE_READLINE",
                                        "-lreadline",
                                );
                                SDKROOT = macosx10.6;
+                               SKIP_INSTALL = NO;
                        };
                        name = Release;
                };