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}; + 378C1AF30FB0644D004D63F5 /* readclustal.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readclustal.h; sourceTree = ""; }; + 378C1AF40FB0644D004D63F5 /* readfasta.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readfasta.cpp; sourceTree = ""; }; + 378C1AF50FB0644D004D63F5 /* readfasta.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readfasta.h; sourceTree = ""; }; + 378C1AF60FB0644D004D63F5 /* readnexus.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readnexus.cpp; sourceTree = ""; }; + 378C1AF70FB0644D004D63F5 /* readnexus.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readnexus.h; sourceTree = ""; }; + 378C1AF80FB0644D004D63F5 /* readnexusal.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readnexusal.h; 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lastKnownFileType = sourcecode.c.h; path = sharedjackknife.h; sourceTree = ""; }; + 378C1B010FB0644D004D63F5 /* sharedmarczewski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedmarczewski.cpp; sourceTree = ""; }; + 378C1B020FB0644D004D63F5 /* sharedmarczewski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedmarczewski.h; sourceTree = ""; }; + 378DC5CD0FBDE1C8003B8607 /* aligncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = aligncommand.h; sourceTree = ""; }; + 378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = aligncommand.cpp; sourceTree = ""; }; 379293C10F2DE73400B9034A /* treemap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treemap.h; sourceTree = ""; }; 379293C20F2DE73400B9034A /* treemap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treemap.cpp; sourceTree = ""; }; 3792946E0F2E191800B9034A /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = ""; }; @@ -206,6 +298,8 @@ 379294880F2E258500B9034A /* parsimony.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimony.h; sourceTree = ""; }; 379294890F2E258500B9034A /* parsimony.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimony.cpp; sourceTree = ""; }; 3792948D0F2E271100B9034A /* treecalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treecalculator.h; sourceTree = ""; }; + 379643EB0FB9B5A80081FDB6 /* readseqs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readseqs.cpp; sourceTree = ""; }; + 379643EC0FB9B5A80081FDB6 /* readseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readseqs.h; sourceTree = ""; }; 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlistvector.h; sourceTree = ""; }; 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlistvector.cpp; sourceTree = ""; }; 37AD4DB90F28E2FE00AA2D49 /* tree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tree.h; sourceTree = ""; }; @@ -218,6 +312,14 @@ 37B28F670F27590100808A62 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = ""; }; 37C1D9710F86506E0059E3F0 /* binsequencecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = binsequencecommand.h; sourceTree = ""; }; 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = binsequencecommand.cpp; sourceTree = ""; }; + 37C753CC0FB3415200DBD02E /* distancecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distancecommand.h; sourceTree = ""; }; + 37C753CD0FB3415200DBD02E /* distancecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancecommand.cpp; sourceTree = ""; }; + 37C753DF0FB3492400DBD02E /* dist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dist.h; sourceTree = ""; }; + 37C753ED0FB34A5700DBD02E /* ignoregaps.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ignoregaps.h; sourceTree = ""; }; + 37C753F00FB34AE800DBD02E /* eachgapdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdist.h; sourceTree = ""; }; + 37C753F10FB34B4700DBD02E /* onegapdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = onegapdist.h; sourceTree = ""; }; + 37C753F30FB34BBF00DBD02E /* onegapignore.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = onegapignore.h; sourceTree = ""; }; + 37C753F40FB34C0300DBD02E /* eachgapignore.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapignore.h; sourceTree = ""; }; 37D927B80F21331F001D4494 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = ""; }; 37D927B90F21331F001D4494 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = ""; }; 37D927BA0F21331F001D4494 /* averagelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = averagelinkage.cpp; sourceTree = ""; }; @@ -369,6 +471,11 @@ 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuff.cpp; sourceTree = ""; }; 7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = dlibshuff.cpp; sourceTree = ""; }; 7E4130F70F8E58FA00381DD0 /* dlibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dlibshuff.h; sourceTree = ""; }; + 7EC3D4500FA0FFF900338DA5 /* coverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = coverage.cpp; sourceTree = ""; }; + 7EC3D4510FA0FFF900338DA5 /* coverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = coverage.h; sourceTree = ""; }; + 7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderberg.h; sourceTree = ""; }; + 7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = ""; }; + 7EC3D4540FA0FFF900338DA5 /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = ""; }; 8DD76F6C0486A84900D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; }; A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getgroupcommand.cpp; sourceTree = ""; }; A70B53A50F4CD7AD0064797E /* getgroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupcommand.h; sourceTree = ""; }; @@ -385,8 +492,8 @@ EB1217220F61C9AC004A865F /* sharedkstest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkstest.cpp; sourceTree = ""; }; EB6E68170F5F1C780044E17B /* qstat.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qstat.h; sourceTree = ""; }; EB6E68180F5F1C780044E17B /* qstat.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qstat.cpp; sourceTree = ""; }; - EB6F01590F6AC1670048081A /* sharedbdiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedbdiversity.h; sourceTree = ""; }; - EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbdiversity.cpp; sourceTree = ""; }; + EB72FE240FC1F5CA0051AC11 /* shen.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shen.cpp; sourceTree = ""; }; + EB72FE250FC1F5CA0051AC11 /* shen.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shen.h; sourceTree = ""; }; EB9303E90F534D9400E8EF26 /* logsd.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = logsd.h; sourceTree = ""; }; EB9303EA0F534D9400E8EF26 /* logsd.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = logsd.cpp; sourceTree = ""; }; EB9303F70F53517300E8EF26 /* geom.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = geom.h; sourceTree = ""; }; @@ -417,16 +524,12 @@ 08FB7795FE84155DC02AAC07 /* Source */ = { isa = PBXGroup; children = ( - 7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */, - 7E4130F70F8E58FA00381DD0 /* dlibshuff.h */, 37D927BA0F21331F001D4494 /* averagelinkage.cpp */, + 373C68DC0FC1C38D00137ACD /* blastalign.hpp */, + 373C68DB0FC1C38D00137ACD /* blastalign.cpp */, 37D928A60F2133C0001D4494 /* calculators */, 37D927C20F21331F001D4494 /* cluster.hpp */, 37D927C10F21331F001D4494 /* cluster.cpp */, - 7E412F470F8D21B600381DD0 /* slibshuff.h */, - 7E412F480F8D21B600381DD0 /* slibshuff.cpp */, - 7E412F420F8D213C00381DD0 /* libshuff.h */, - 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */, 37D928A90F2133E5001D4494 /* commands */, 37D927C60F21331F001D4494 /* collect.h */, 37D927C50F21331F001D4494 /* collect.cpp */, @@ -438,8 +541,8 @@ 37D927D10F21331F001D4494 /* commandoptionparser.hpp */, 37D927D00F21331F001D4494 /* commandoptionparser.cpp */, 37D927D20F21331F001D4494 /* completelinkage.cpp */, - 37D927D40F21331F001D4494 /* database.hpp */, - 37D927D30F21331F001D4494 /* database.cpp */, + 7E4130F70F8E58FA00381DD0 /* dlibshuff.h */, + 7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */, 37D927D60F21331F001D4494 /* display.h */, 37D927D80F21331F001D4494 /* engine.hpp */, 37D927D70F21331F001D4494 /* engine.cpp */, @@ -448,19 +551,29 @@ 37D927DD0F21331F001D4494 /* fileoutput.cpp */, 37D927E00F21331F001D4494 /* globaldata.hpp */, 37D927DF0F21331F001D4494 /* globaldata.cpp */, + 373C68BB0FC1C1A600137ACD /* gotohoverlap.hpp */, + 373C68BA0FC1C1A600137ACD /* gotohoverlap.cpp */, 375873ED0F7D646F0040F377 /* heatmap.h */, 375873EE0F7D646F0040F377 /* heatmap.cpp */, 37D927E60F21331F001D4494 /* inputdata.h */, 37D927E50F21331F001D4494 /* inputdata.cpp */, - 37D927EA0F21331F001D4494 /* kmer.hpp */, - 37D927E90F21331F001D4494 /* kmer.cpp */, - 37D927EC0F21331F001D4494 /* kmerdb.hpp */, - 37D927EB0F21331F001D4494 /* kmerdb.cpp */, + 7E412F420F8D213C00381DD0 /* libshuff.h */, + 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */, 37E3ED800F4D9D0D00B5DF02 /* mothur.h */, 37D927EF0F21331F001D4494 /* mothur.cpp */, 37D927F10F21331F001D4494 /* nameassignment.hpp */, 37D927F00F21331F001D4494 /* nameassignment.cpp */, + 373C691E0FC1C98600137ACD /* nast.hpp */, + 373C691D0FC1C98600137ACD /* nast.cpp */, + 373C692A0FC1C9EB00137ACD /* nastreport.hpp */, + 373C69290FC1C9EB00137ACD /* nastreport.cpp */, + 373C68CE0FC1C2D900137ACD /* needlemanoverlap.hpp */, + 373C68CD0FC1C2D900137ACD /* needlemanoverlap.cpp */, + 373C68E40FC1C4A500137ACD /* noalign.hpp */, + 373C68E30FC1C4A500137ACD /* noalign.cpp */, 37D927F60F21331F001D4494 /* observable.h */, + 373C68C40FC1C25F00137ACD /* overlap.hpp */, + 373C68C30FC1C25F00137ACD /* overlap.cpp */, 37D927FC0F21331F001D4494 /* progress.hpp */, 37D927FB0F21331F001D4494 /* progress.cpp */, 37D928040F21331F001D4494 /* raredisplay.h */, @@ -468,22 +581,14 @@ 37D928060F21331F001D4494 /* rarefact.h */, 37D928050F21331F001D4494 /* rarefact.cpp */, 37D928090F21331F001D4494 /* rarefactioncurvedata.h */, - 375AA1340F9E433D008EF9B8 /* readcolumn.h */, - 375AA1330F9E433D008EF9B8 /* readcolumn.cpp */, - 37D928130F21331F001D4494 /* readmatrix.hpp */, - 375AA1360F9E433D008EF9B8 /* readotu.h */, - 375AA1350F9E433D008EF9B8 /* readotu.cpp */, - 375AA1380F9E433D008EF9B8 /* readphylip.h */, - 375AA1370F9E433D008EF9B8 /* readphylip.cpp */, - 37AD4DC80F28F3DD00AA2D49 /* readtree.h */, - 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */, - 37D9281D0F21331F001D4494 /* sequence.hpp */, - 37D9281C0F21331F001D4494 /* sequence.cpp */, + 3796441D0FB9B9650081FDB6 /* read */, 37D928210F21331F001D4494 /* shared.h */, 37D928200F21331F001D4494 /* shared.cpp */, 211C38310F961DD400FEE541 /* sharedutilities.h */, 211C38300F961DD400FEE541 /* sharedutilities.cpp */, 37D928420F21331F001D4494 /* singlelinkage.cpp */, + 7E412F470F8D21B600381DD0 /* slibshuff.h */, + 7E412F480F8D21B600381DD0 /* slibshuff.cpp */, 37D928480F21331F001D4494 /* summarydata.h */, 37D928490F21331F001D4494 /* summarydisplay.h */, 37519AB30F810FAE00FED5E8 /* venn.h */, @@ -500,10 +605,39 @@ name = Products; sourceTree = ""; }; + 3796441D0FB9B9650081FDB6 /* read */ = { + isa = PBXGroup; + children = ( + 378C1AF30FB0644D004D63F5 /* readclustal.h */, + 378C1AF20FB0644D004D63F5 /* readclustal.cpp */, + 375AA1340F9E433D008EF9B8 /* readcolumn.h */, + 375AA1330F9E433D008EF9B8 /* readcolumn.cpp */, + 378C1AF50FB0644D004D63F5 /* readfasta.h */, + 378C1AF40FB0644D004D63F5 /* readfasta.cpp */, + 37D928130F21331F001D4494 /* readmatrix.hpp */, + 378C1AF70FB0644D004D63F5 /* readnexus.h */, + 378C1AF60FB0644D004D63F5 /* readnexus.cpp */, + 378C1AF80FB0644D004D63F5 /* readnexusal.h */, + 375AA1360F9E433D008EF9B8 /* readotu.h */, + 375AA1350F9E433D008EF9B8 /* readotu.cpp */, + 375AA1380F9E433D008EF9B8 /* readphylip.h */, + 375AA1370F9E433D008EF9B8 /* readphylip.cpp */, + 378C1AFC0FB0644D004D63F5 /* readseqsphylip.h */, + 378C1AFB0FB0644D004D63F5 /* readseqsphylip.cpp */, + 379643EB0FB9B5A80081FDB6 /* readseqs.cpp */, + 379643EC0FB9B5A80081FDB6 /* readseqs.h */, + 37AD4DC80F28F3DD00AA2D49 /* readtree.h */, + 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */, + ); + name = read; + sourceTree = ""; + }; 37D928A60F2133C0001D4494 /* calculators */ = { isa = PBXGroup; children = ( 37D927BE0F21331F001D4494 /* calculator.h */, + 373C69950FC1E63600137ACD /* boneh.h */, + 373C69940FC1E63600137ACD /* boneh.cpp */, 3792948D0F2E271100B9034A /* treecalculator.h */, 37D927BD0F21331F001D4494 /* calculator.cpp */, 37D927B90F21331F001D4494 /* ace.h */, @@ -516,19 +650,31 @@ EB1216E40F61ACFB004A865F /* bstick.cpp */, 37D927C00F21331F001D4494 /* chao1.h */, 37D927BF0F21331F001D4494 /* chao1.cpp */, + 7EC3D4510FA0FFF900338DA5 /* coverage.h */, + 7EC3D4500FA0FFF900338DA5 /* coverage.cpp */, + 37C753DF0FB3492400DBD02E /* dist.h */, + 37C753F00FB34AE800DBD02E /* eachgapdist.h */, + 37C753F40FB34C0300DBD02E /* eachgapignore.h */, + 373C69960FC1E63600137ACD /* efron.cpp */, + 373C69970FC1E63600137ACD /* efron.h */, EB9303F70F53517300E8EF26 /* geom.h */, EB9303F80F53517300E8EF26 /* geom.cpp */, - EB9303E90F534D9400E8EF26 /* logsd.h */, - EB9303EA0F534D9400E8EF26 /* logsd.cpp */, - EB6E68170F5F1C780044E17B /* qstat.h */, - EB6E68180F5F1C780044E17B /* qstat.cpp */, + 378C1AF10FB0644D004D63F5 /* goodscoverage.h */, + 378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */, + 37C753ED0FB34A5700DBD02E /* ignoregaps.h */, 37D927E80F21331F001D4494 /* jackknife.h */, 37D927E70F21331F001D4494 /* jackknife.cpp */, + EB9303E90F534D9400E8EF26 /* logsd.h */, + EB9303EA0F534D9400E8EF26 /* logsd.cpp */, 375873F90F7D64AB0040F377 /* nseqs.h */, 37D927F50F21331F001D4494 /* npshannon.h */, 37D927F40F21331F001D4494 /* npshannon.cpp */, + 37C753F10FB34B4700DBD02E /* onegapdist.h */, + 37C753F30FB34BBF00DBD02E /* onegapignore.h */, 379294880F2E258500B9034A /* parsimony.h */, 379294890F2E258500B9034A /* parsimony.cpp */, + EB6E68170F5F1C780044E17B /* qstat.h */, + EB6E68180F5F1C780044E17B /* qstat.cpp */, 37D928020F21331F001D4494 /* rarecalc.h */, 37D928010F21331F001D4494 /* rarecalc.cpp */, 37D9281F0F21331F001D4494 /* shannon.h */, @@ -537,14 +683,15 @@ 37D928220F21331F001D4494 /* sharedace.cpp */, 37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */, 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */, + 7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */, 375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */, 375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */, - EB6F01590F6AC1670048081A /* sharedbdiversity.h */, - EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */, 37D928250F21331F001D4494 /* sharedchao1.h */, 37D928240F21331F001D4494 /* sharedchao1.cpp */, 37D928290F21331F001D4494 /* sharedjabund.h */, 37D928280F21331F001D4494 /* sharedjabund.cpp */, + 378C1B000FB0644D004D63F5 /* sharedjackknife.h */, + 378C1AFF0FB0644D004D63F5 /* sharedjackknife.cpp */, 37D9282B0F21331F001D4494 /* sharedjclass.h */, 37D9282A0F21331F001D4494 /* sharedjclass.cpp */, 37D9282D0F21331F001D4494 /* sharedjest.h */, @@ -557,6 +704,8 @@ 375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */, 375874010F7D64EF0040F377 /* sharedlennon.h */, 375873FF0F7D64EF0040F377 /* sharedlennon.cpp */, + 378C1B020FB0644D004D63F5 /* sharedmarczewski.h */, + 378C1B010FB0644D004D63F5 /* sharedmarczewski.cpp */, 375874070F7D64FC0040F377 /* sharedmorisitahorn.h */, 375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */, 375874090F7D64FC0040F377 /* sharedochiai.h */, @@ -576,15 +725,21 @@ 37D9283C0F21331F001D4494 /* sharedthetan.cpp */, 37D9283F0F21331F001D4494 /* sharedthetayc.h */, 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */, + EB72FE250FC1F5CA0051AC11 /* shen.h */, + EB72FE240FC1F5CA0051AC11 /* shen.cpp */, 37D928410F21331F001D4494 /* simpson.h */, 37D928400F21331F001D4494 /* simpson.cpp */, 37D928430F21331F001D4494 /* sobs.h */, + 373C69980FC1E63600137ACD /* solow.cpp */, + 373C69990FC1E63600137ACD /* solow.h */, 374610810F40652400460C57 /* unweighted.h */, 374610820F40652400460C57 /* unweighted.cpp */, 37D9284E0F21331F001D4494 /* uvest.h */, 37D9284D0F21331F001D4494 /* uvest.cpp */, 3746107C0F4064D100460C57 /* weighted.h */, 3746107D0F4064D100460C57 /* weighted.cpp */, + 7EC3D4540FA0FFF900338DA5 /* whittaker.h */, + 7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */, ); name = calculators; sourceTree = ""; @@ -593,6 +748,8 @@ isa = PBXGroup; children = ( 37D927CD0F21331F001D4494 /* command.hpp */, + 378DC5CD0FBDE1C8003B8607 /* aligncommand.h */, + 378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */, 37C1D9710F86506E0059E3F0 /* binsequencecommand.h */, 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */, 21DDC0190F97A8FE0060691C /* bootstrapsharedcommand.h */, @@ -603,8 +760,14 @@ 37D927C70F21331F001D4494 /* collectcommand.cpp */, 37D927CC0F21331F001D4494 /* collectsharedcommand.h */, 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */, + 377326640FAF16E0007ABB8B /* concensuscommand.h */, + 377326630FAF16E0007ABB8B /* concensuscommand.cpp */, 37B28F660F27590100808A62 /* deconvolutecommand.h */, 37B28F670F27590100808A62 /* deconvolutecommand.cpp */, + 37C753CC0FB3415200DBD02E /* distancecommand.h */, + 37C753CD0FB3415200DBD02E /* distancecommand.cpp */, + 378C1AEF0FB0644D004D63F5 /* filterseqscommand.h */, + 378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */, A70B53A50F4CD7AD0064797E /* getgroupcommand.h */, A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */, A70B53A70F4CD7AD0064797E /* getlabelcommand.h */, @@ -613,12 +776,16 @@ A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */, 370B88050F8A4EE4005AB382 /* getoturepcommand.h */, 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */, + 211A24E90FC306BC00769A33 /* getrepseqscommand.h */, + 211A24EA0FC306BC00769A33 /* getrepseqscommand.cpp */, 375873F10F7D64800040F377 /* heatmapcommand.h */, 375873F00F7D64800040F377 /* heatmapcommand.cpp */, 37D927E40F21331F001D4494 /* helpcommand.h */, 37D927E30F21331F001D4494 /* helpcommand.cpp */, 375873F40F7D648F0040F377 /* libshuffcommand.h */, 375873F30F7D648F0040F377 /* libshuffcommand.cpp */, + 21E859D60FC4632E005E1A48 /* matrixoutputcommand.h */, + 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */, 375873F60F7D649C0040F377 /* nocommands.cpp */, 375873F70F7D649C0040F377 /* nocommands.h */, 37D927FA0F21331F001D4494 /* parselistcommand.h */, @@ -658,6 +825,14 @@ 37D928AC0F213420001D4494 /* containers */ = { isa = PBXGroup; children = ( + 373C68A10FC1C07D00137ACD /* alignment.hpp */, + 373C68A00FC1C07D00137ACD /* alignment.cpp */, + 373C68A30FC1C07D00137ACD /* alignmentcell.hpp */, + 373C68A20FC1C07D00137ACD /* alignmentcell.cpp */, + 373C69170FC1C8AF00137ACD /* blastdb.hpp */, + 373C69160FC1C8AF00137ACD /* blastdb.cpp */, + 37D927D40F21331F001D4494 /* database.hpp */, + 37D927D30F21331F001D4494 /* database.cpp */, 37D927D50F21331F001D4494 /* datavector.hpp */, 37D927DC0F21331F001D4494 /* fastamap.h */, 37D927DB0F21331F001D4494 /* fastamap.cpp */, @@ -665,6 +840,10 @@ 375873EB0F7D64520040F377 /* fullmatrix.cpp */, 37D927E20F21331F001D4494 /* groupmap.h */, 37D927E10F21331F001D4494 /* groupmap.cpp */, + 37D927EA0F21331F001D4494 /* kmer.hpp */, + 37D927E90F21331F001D4494 /* kmer.cpp */, + 37D927EC0F21331F001D4494 /* kmerdb.hpp */, + 37D927EB0F21331F001D4494 /* kmerdb.cpp */, 37D927EE0F21331F001D4494 /* listvector.hpp */, 37D927ED0F21331F001D4494 /* listvector.cpp */, 37D927F80F21331F001D4494 /* ordervector.hpp */, @@ -673,6 +852,10 @@ 37D927FF0F21331F001D4494 /* rabundvector.cpp */, 37D9281B0F21331F001D4494 /* sabundvector.hpp */, 37D9281A0F21331F001D4494 /* sabundvector.cpp */, + 37D9281D0F21331F001D4494 /* sequence.hpp */, + 37D9281C0F21331F001D4494 /* sequence.cpp */, + 378C1AFE0FB0644D004D63F5 /* sequencedb.h */, + 378C1AFD0FB0644D004D63F5 /* sequencedb.cpp */, 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */, 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */, 37D9282F0F21331F001D4494 /* sharedordervector.h */, @@ -683,6 +866,12 @@ 37D928320F21331F001D4494 /* sharedsabundvector.cpp */, 37D928450F21331F001D4494 /* sparsematrix.hpp */, 37D928440F21331F001D4494 /* sparsematrix.cpp */, + 373C68F40FC1C6A800137ACD /* suffixdb.hpp */, + 373C68F30FC1C6A800137ACD /* suffixdb.cpp */, + 373C68F60FC1C6A800137ACD /* suffixnodes.hpp */, + 373C68F50FC1C6A800137ACD /* suffixnodes.cpp */, + 373C68F80FC1C6A800137ACD /* suffixtree.hpp */, + 373C68F70FC1C6A800137ACD /* suffixtree.cpp */, 37AD4DB90F28E2FE00AA2D49 /* tree.h */, 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */, 379293C10F2DE73400B9034A /* treemap.h */, @@ -851,7 +1040,6 @@ EB1216880F619B83004A865F /* bergerparker.cpp in Sources */, EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */, EB1217230F61C9AC004A865F /* sharedkstest.cpp in Sources */, - EB6F015B0F6AC1670048081A /* sharedbdiversity.cpp in Sources */, 375873EC0F7D64520040F377 /* fullmatrix.cpp in Sources */, 375873EF0F7D646F0040F377 /* heatmap.cpp in Sources */, 375873F20F7D64800040F377 /* heatmapcommand.cpp in Sources */, @@ -877,6 +1065,40 @@ 375AA1390F9E433D008EF9B8 /* readcolumn.cpp in Sources */, 375AA13A0F9E433D008EF9B8 /* readotu.cpp in Sources */, 375AA13B0F9E433D008EF9B8 /* readphylip.cpp in Sources */, + 7EC3D4550FA0FFF900338DA5 /* coverage.cpp in Sources */, + 7EC3D4560FA0FFF900338DA5 /* whittaker.cpp in Sources */, + 377326650FAF16E0007ABB8B /* concensuscommand.cpp in Sources */, + 378C1B030FB0644E004D63F5 /* filterseqscommand.cpp in Sources */, + 378C1B040FB0644E004D63F5 /* goodscoverage.cpp in Sources */, + 378C1B050FB0644E004D63F5 /* readclustal.cpp in Sources */, + 378C1B060FB0644E004D63F5 /* readfasta.cpp in Sources */, + 378C1B070FB0644E004D63F5 /* readnexus.cpp in Sources */, + 378C1B090FB0644E004D63F5 /* readseqsphylip.cpp in Sources */, + 378C1B0A0FB0644E004D63F5 /* sequencedb.cpp in Sources */, + 378C1B0B0FB0644E004D63F5 /* sharedjackknife.cpp in Sources */, + 378C1B0C0FB0644E004D63F5 /* sharedmarczewski.cpp in Sources */, + 37C753CE0FB3415200DBD02E /* distancecommand.cpp in Sources */, + 379643ED0FB9B5A80081FDB6 /* readseqs.cpp in Sources */, + 378DC5CF0FBDE1C8003B8607 /* aligncommand.cpp in Sources */, + 373C68A40FC1C07D00137ACD /* alignment.cpp in Sources */, + 373C68A50FC1C07D00137ACD /* alignmentcell.cpp in Sources */, + 373C68BC0FC1C1A600137ACD /* gotohoverlap.cpp in Sources */, + 373C68C50FC1C25F00137ACD /* overlap.cpp in Sources */, + 373C68CF0FC1C2D900137ACD /* needlemanoverlap.cpp in Sources */, + 373C68DD0FC1C38D00137ACD /* blastalign.cpp in Sources */, + 373C68E50FC1C4A500137ACD /* noalign.cpp in Sources */, + 373C68F90FC1C6A800137ACD /* suffixdb.cpp in Sources */, + 373C68FA0FC1C6A800137ACD /* suffixnodes.cpp in Sources */, + 373C68FB0FC1C6A800137ACD /* suffixtree.cpp in Sources */, + 373C69180FC1C8AF00137ACD /* blastdb.cpp in Sources */, + 373C691F0FC1C98600137ACD /* nast.cpp in Sources */, + 373C692B0FC1C9EB00137ACD /* nastreport.cpp in Sources */, + 373C699A0FC1E63600137ACD /* boneh.cpp in Sources */, + 373C699B0FC1E63600137ACD /* efron.cpp in Sources */, + 373C699C0FC1E63600137ACD /* solow.cpp in Sources */, + EB72FE260FC1F5CA0051AC11 /* shen.cpp in Sources */, + 211A24EB0FC306BC00769A33 /* getrepseqscommand.cpp in Sources */, + 21E859D80FC4632E005E1A48 /* matrixoutputcommand.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; };