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PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bergerparker.h; sourceTree = SOURCE_ROOT; }; + EB1216870F619B83004A865F /* bergerparker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bergerparker.cpp; sourceTree = SOURCE_ROOT; }; + EB1216E30F61ACFB004A865F /* bstick.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bstick.h; sourceTree = SOURCE_ROOT; }; + EB1216E40F61ACFB004A865F /* bstick.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bstick.cpp; sourceTree = SOURCE_ROOT; }; + EB1217210F61C9AC004A865F /* sharedkstest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkstest.h; sourceTree = SOURCE_ROOT; }; + EB1217220F61C9AC004A865F /* sharedkstest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkstest.cpp; 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sourcecode.cpp.cpp; path = logsd.cpp; sourceTree = SOURCE_ROOT; }; + EB9303F70F53517300E8EF26 /* geom.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = geom.h; sourceTree = SOURCE_ROOT; }; + EB9303F80F53517300E8EF26 /* geom.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = geom.cpp; sourceTree = SOURCE_ROOT; }; /* End PBXFileReference section */ /* Begin PBXFrameworksBuildPhase section */ @@ -344,6 +600,7 @@ isa = PBXFrameworksBuildPhase; buildActionMask = 2147483647; files = ( + A7F5759710CEBC0600E20E47 /* libreadline.a in Frameworks */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -364,7 +621,11 @@ isa = PBXGroup; children = ( 37D927BA0F21331F001D4494 /* averagelinkage.cpp */, + 373C68DC0FC1C38D00137ACD /* blastalign.hpp */, + 373C68DB0FC1C38D00137ACD /* blastalign.cpp */, 37D928A60F2133C0001D4494 /* calculators */, + 374F2FE81006346600E97C66 /* chimera */, + A787811210A073F40086103D /* classifiers */, 37D927C20F21331F001D4494 /* cluster.hpp */, 37D927C10F21331F001D4494 /* cluster.cpp */, 37D928A90F2133E5001D4494 /* commands */, @@ -378,8 +639,8 @@ 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 */, @@ -388,19 +649,33 @@ 37D927DD0F21331F001D4494 /* fileoutput.cpp */, 37D927E00F21331F001D4494 /* globaldata.hpp */, 37D927DF0F21331F001D4494 /* globaldata.cpp */, - 3765B5440F7A62A000C3EDC5 /* heatmap.h */, - 3765B5450F7A62A000C3EDC5 /* heatmap.cpp */, + 373C68BB0FC1C1A600137ACD /* gotohoverlap.hpp */, + 373C68BA0FC1C1A600137ACD /* gotohoverlap.cpp */, 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nastreport.cpp */, + 373C68CE0FC1C2D900137ACD /* needlemanoverlap.hpp */, + 373C68CD0FC1C2D900137ACD /* needlemanoverlap.cpp */, + 373C68E40FC1C4A500137ACD /* noalign.hpp */, + 373C68E30FC1C4A500137ACD /* noalign.cpp */, 37D927F60F21331F001D4494 /* observable.h */, + 3785990E0FDD7E8E00EF9D03 /* optionparser.h */, + 3785990F0FDD7E8E00EF9D03 /* optionparser.cpp */, + 373C68C40FC1C25F00137ACD /* overlap.hpp */, + 373C68C30FC1C25F00137ACD /* overlap.cpp */, 37D927FC0F21331F001D4494 /* progress.hpp */, 37D927FB0F21331F001D4494 /* progress.cpp */, 37D928040F21331F001D4494 /* raredisplay.h */, @@ -408,18 +683,17 @@ 37D928060F21331F001D4494 /* rarefact.h */, 37D928050F21331F001D4494 /* rarefact.cpp */, 37D928090F21331F001D4494 /* rarefactioncurvedata.h */, - 37D928130F21331F001D4494 /* readmatrix.hpp */, - 37D928120F21331F001D4494 /* readmatrix.cpp */, - 37AD4DC80F28F3DD00AA2D49 /* readtree.h */, - 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */, - 37D9281D0F21331F001D4494 /* sequence.hpp */, - 37D9281C0F21331F001D4494 /* sequence.cpp */, - 37D928210F21331F001D4494 /* shared.h */, - 37D928200F21331F001D4494 /* shared.cpp */, + 3796441D0FB9B9650081FDB6 /* read */, + 211C38310F961DD400FEE541 /* sharedutilities.h */, + 211C38300F961DD400FEE541 /* sharedutilities.cpp */, 37D928420F21331F001D4494 /* singlelinkage.cpp */, + 7E412F470F8D21B600381DD0 /* slibshuff.h */, + 7E412F480F8D21B600381DD0 /* slibshuff.cpp */, 37D928480F21331F001D4494 /* summarydata.h */, 37D928490F21331F001D4494 /* summarydisplay.h */, - 37D9284C0F21331F001D4494 /* utilities.hpp */, + 37519AB30F810FAE00FED5E8 /* venn.h */, + 37519AB40F810FAE00FED5E8 /* venn.cpp */, + A7F5759610CEBC0600E20E47 /* libreadline.a */, ); name = Source; sourceTree = ""; @@ -432,56 +706,131 @@ name = Products; sourceTree = ""; }; + 374F2FE81006346600E97C66 /* chimera */ = { + isa = PBXGroup; + children = ( + 374F2FD51006320200E97C66 /* chimera.h */, + 372095C1103196D70004D347 /* chimera.cpp */, + 374F2FE9100634B600E97C66 /* bellerophon.h */, + 374F2FEA100634B600E97C66 /* bellerophon.cpp */, + A75B887C104C16860083C454 /* ccode.h */, + A75B887B104C16860083C454 /* ccode.cpp */, + A7283FF61056CAE100D0CC69 /* chimeracheckrdp.h */, + A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */, + A7B04491106CC3E60046FC83 /* chimeraslayer.h */, + A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */, + 372A55531017922B00C5194B /* decalc.h */, + 372A55541017922B00C5194B /* decalc.cpp */, + A7E4A822106A9AD700688F62 /* maligner.h */, + A7E4A823106A9AD700688F62 /* maligner.cpp */, + 374F301110063B6F00E97C66 /* pintail.h */, + 374F301210063B6F00E97C66 /* pintail.cpp */, + A7B0450C106CEEC90046FC83 /* slayer.h */, + A7B0450D106CEEC90046FC83 /* slayer.cpp */, + ); + name = chimera; + sourceTree = ""; + }; + 3796441D0FB9B9650081FDB6 /* read */ = { + isa = PBXGroup; + children = ( + A727E84810D14568001A8432 /* readblast.h */, + A727E84910D14568001A8432 /* readblast.cpp */, + A751ACE81098B283003D0911 /* readcluster.h */, + A751ACE91098B283003D0911 /* readcluster.cpp */, + 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 */, + ); + name = read; + sourceTree = ""; + }; 37D928A60F2133C0001D4494 /* calculators */ = { isa = PBXGroup; children = ( 37D927BE0F21331F001D4494 /* calculator.h */, - 3792948D0F2E271100B9034A /* treecalculator.h */, 37D927BD0F21331F001D4494 /* calculator.cpp */, + 3792948D0F2E271100B9034A /* treecalculator.h */, 37D927B90F21331F001D4494 /* ace.h */, 37D927B80F21331F001D4494 /* ace.cpp */, + EB1216860F619B83004A865F /* bergerparker.h */, + EB1216870F619B83004A865F /* bergerparker.cpp */, + 373C69950FC1E63600137ACD /* boneh.h */, + 373C69940FC1E63600137ACD /* boneh.cpp */, 37D927BC0F21331F001D4494 /* bootstrap.h */, 37D927BB0F21331F001D4494 /* bootstrap.cpp */, + EB1216E30F61ACFB004A865F /* bstick.h */, + EB1216E40F61ACFB004A865F /* bstick.cpp */, 37D927C00F21331F001D4494 /* chao1.h */, 37D927BF0F21331F001D4494 /* chao1.cpp */, - 374CD6EF0F65A4C100D90B4A /* coverage.h */, - 374CD6F00F65A4C100D90B4A /* coverage.cpp */, + 7EC3D4510FA0FFF900338DA5 /* coverage.h */, + 7EC3D4500FA0FFF900338DA5 /* coverage.cpp */, + 37C753DF0FB3492400DBD02E /* dist.h */, + 37C753F00FB34AE800DBD02E /* eachgapdist.h */, + 37C753F40FB34C0300DBD02E /* eachgapignore.h */, + 373C69960FC1E63600137ACD /* efron.cpp */, + 373C69970FC1E63600137ACD /* efron.h */, + 379D3D6B0FF917F40068C1C0 /* filters.h */, + EB9303F70F53517300E8EF26 /* geom.h */, + EB9303F80F53517300E8EF26 /* geom.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 */, - 370936DE0F6E7A4A00EB4C2C /* nseqs.h */, + 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 */, 37D9281E0F21331F001D4494 /* shannon.cpp */, 37D928230F21331F001D4494 /* sharedace.h */, 37D928220F21331F001D4494 /* sharedace.cpp */, - 3765B5140F780A7F00C3EDC5 /* sharedanderberg.h */, - 3765B5150F780A7F00C3EDC5 /* sharedanderberg.cpp */, - 2175956F0F792A33001CC3C6 /* sharedbraycurtis.h */, - 217595700F792A33001CC3C6 /* sharedbraycurtis.cpp */, + 37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */, + 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */, + 7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */, + 375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */, + 375873FC0F7D64DA0040F377 /* sharedbraycurtis.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 */, 37D9282C0F21331F001D4494 /* sharedjest.cpp */, - 217595310F791EEE001CC3C6 /* sharedkulczynski.h */, - 217595320F791EEE001CC3C6 /* sharedkulczynski.cpp */, - 2175953D0F792111001CC3C6 /* sharedkulczynskicody.h */, - 2175953E0F792111001CC3C6 /* sharedkulczynskicody.cpp */, - 217595570F792490001CC3C6 /* sharedlennon.h */, - 217595580F792490001CC3C6 /* sharedlennon.cpp */, - 217595620F7927BB001CC3C6 /* sharedmorisitahorn.h */, - 217595630F7927BB001CC3C6 /* sharedmorisitahorn.cpp */, - 3709370A0F6E7FC100EB4C2C /* sharednseqs.h */, - 3765B4E00F78055000C3EDC5 /* sharedochiai.h */, - 3765B4E10F78055000C3EDC5 /* sharedochiai.cpp */, + EB1217210F61C9AC004A865F /* sharedkstest.h */, + EB1217220F61C9AC004A865F /* sharedkstest.cpp */, + 375874000F7D64EF0040F377 /* sharedkulczynski.h */, + 375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */, + 375874030F7D64EF0040F377 /* sharedkulczynskicody.h */, + 375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */, + 375874010F7D64EF0040F377 /* sharedlennon.h */, + 375873FF0F7D64EF0040F377 /* sharedlennon.cpp */, + 378C1B020FB0644D004D63F5 /* sharedmarczewski.h */, + 378C1B010FB0644D004D63F5 /* sharedmarczewski.cpp */, + 375874070F7D64FC0040F377 /* sharedmorisitahorn.h */, + 375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */, + 375874090F7D64FC0040F377 /* sharedochiai.h */, + 3758740B0F7D64FC0040F377 /* sharedochiai.cpp */, + 3758740A0F7D64FC0040F377 /* sharednseqs.h */, 37D928350F21331F001D4494 /* sharedsobs.h */, 37D928340F21331F001D4494 /* sharedsobs.cpp */, 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */, @@ -496,15 +845,21 @@ 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 = ""; @@ -513,32 +868,74 @@ isa = PBXGroup; children = ( 37D927CD0F21331F001D4494 /* command.hpp */, + 378DC5CD0FBDE1C8003B8607 /* aligncommand.h */, + 378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */, + 37C1D9710F86506E0059E3F0 /* binsequencecommand.h */, + 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */, + 21DDC0190F97A8FE0060691C /* bootstrapsharedcommand.h */, + 21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */, 37D927C40F21331F001D4494 /* clustercommand.h */, 37D927C30F21331F001D4494 /* clustercommand.cpp */, 37D927C80F21331F001D4494 /* collectcommand.h */, 37D927C70F21331F001D4494 /* collectcommand.cpp */, 37D927CC0F21331F001D4494 /* collectsharedcommand.h */, 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */, + 377326640FAF16E0007ABB8B /* consensuscommand.h */, + 377326630FAF16E0007ABB8B /* consensuscommand.cpp */, + 379D3D4F0FF90E090068C1C0 /* chimeraseqscommand.h */, + 379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */, + A7861476109F5FA00010AAAF /* classifyseqscommand.h */, + A7861477109F5FA00010AAAF /* classifyseqscommand.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 */, A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */, A70B53A90F4CD7AD0064797E /* getlinecommand.h */, A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */, - 3765B5360F7A5A9E00C3EDC5 /* heatmapcommand.h */, - 3765B5370F7A5A9E00C3EDC5 /* heatmapcommand.cpp */, + A73329CD1083B3B3003B10C5 /* getlistcountcommand.h */, + A73329CE1083B3B3003B10C5 /* getlistcountcommand.cpp */, + 370B88050F8A4EE4005AB382 /* getoturepcommand.h */, + 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */, + 3749273D0FD5956B0031C06B /* getrabundcommand.h */, + 3749273E0FD5956B0031C06B /* getrabundcommand.cpp */, + 3749271B0FD58C840031C06B /* getsabundcommand.h */, + 3749271C0FD58C840031C06B /* getsabundcommand.cpp */, + 37B73CA41004D89A008C4B41 /* getseqscommand.h */, + 37B73CA51004D89A008C4B41 /* getseqscommand.cpp */, + A7E4A781106913F900688F62 /* getsharedotucommand.h */, + A7E4A782106913F900688F62 /* getsharedotucommand.cpp */, + A729ACCE10848E6100139801 /* hclustercommand.h */, + A729ACCF10848E6100139801 /* hclustercommand.cpp */, + 375873F10F7D64800040F377 /* heatmapcommand.h */, + 375873F00F7D64800040F377 /* heatmapcommand.cpp */, + 378598640FDD497000EF9D03 /* heatmapsimcommand.h */, + 378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */, 37D927E40F21331F001D4494 /* helpcommand.h */, 37D927E30F21331F001D4494 /* helpcommand.cpp */, - 374CD63D0F65832000D90B4A /* libshuffcommand.h */, - 374CD63E0F65832000D90B4A /* libshuffcommand.cpp */, - 3765B4790F77D15900C3EDC5 /* nocommands.h */, - 3765B4780F77D15900C3EDC5 /* nocommands.cpp */, - 37D927FA0F21331F001D4494 /* parselistcommand.h */, - 37D927F90F21331F001D4494 /* parselistcommand.cpp */, + 375873F40F7D648F0040F377 /* libshuffcommand.h */, + 375873F30F7D648F0040F377 /* libshuffcommand.cpp */, + 37B73C741004BEFD008C4B41 /* listseqscommand.h */, + 37B73C751004BEFD008C4B41 /* listseqscommand.cpp */, + 21E859D60FC4632E005E1A48 /* matrixoutputcommand.h */, + 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */, + 7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */, + 7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */, + A7E0AAB410D2886D00CF407B /* mgclustercommand.h */, + A7E0AAB510D2886D00CF407B /* mgclustercommand.cpp */, + 375873F70F7D649C0040F377 /* nocommands.h */, + 375873F60F7D649C0040F377 /* nocommands.cpp */, 3792946E0F2E191800B9034A /* parsimonycommand.h */, 3792946F0F2E191800B9034A /* parsimonycommand.cpp */, + A773808E10B6EFD1002A6A61 /* phylotypecommand.h */, + A773808F10B6EFD1002A6A61 /* phylotypecommand.cpp */, + A7027F2610DFF86D00BF45FE /* preclustercommand.h */, + A7027F2710DFF86D00BF45FE /* preclustercommand.cpp */, 37D927FE0F21331F001D4494 /* quitcommand.h */, 37D927FD0F21331F001D4494 /* quitcommand.cpp */, 37D928080F21331F001D4494 /* rarefactcommand.h */, @@ -551,16 +948,34 @@ 372E126F0F26365B0095CF7E /* readotucommand.cpp */, 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */, 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */, + 37B73CBE1004EB38008C4B41 /* removeseqscommand.h */, + 37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */, + 7E09C5120FDA79C5002ECAE5 /* reversecommand.h */, + 7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */, + A70DECD71063D8B40057C03C /* secondarystructurecommand.h */, + A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */, + 371B30B30FD7EE67000414CA /* screenseqscommand.h */, + 371B30B20FD7EE67000414CA /* screenseqscommand.cpp */, + 3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */, + 3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */, 37D928270F21331F001D4494 /* sharedcommand.h */, 37D928260F21331F001D4494 /* sharedcommand.cpp */, 37D928470F21331F001D4494 /* summarycommand.h */, 37D928460F21331F001D4494 /* summarycommand.cpp */, 37D9284B0F21331F001D4494 /* summarysharedcommand.h */, 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */, + 37B73CCD1004F5E0008C4B41 /* systemcommand.h */, + 37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */, + 211C38370F961E1F00FEE541 /* treegroupscommand.h */, + 211C38360F961E1F00FEE541 /* treegroupscommand.cpp */, + 7E09C5340FDA7F65002ECAE5 /* trimseqscommand.h */, + 7E09C5350FDA7F65002ECAE5 /* trimseqscommand.cpp */, 3746109B0F40657600460C57 /* unifracunweightedcommand.h */, 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */, 374610760F40645300460C57 /* unifracweightedcommand.h */, 374610770F40645300460C57 /* unifracweightedcommand.cpp */, + 37519A9F0F810D0200FED5E8 /* venncommand.h */, + 37519AA00F810D0200FED5E8 /* venncommand.cpp */, ); name = commands; sourceTree = ""; @@ -568,21 +983,41 @@ 37D928AC0F213420001D4494 /* containers */ = { isa = PBXGroup; children = ( + 373C68A10FC1C07D00137ACD /* alignment.hpp */, + 373C68A00FC1C07D00137ACD /* alignment.cpp */, + 373C68A30FC1C07D00137ACD /* alignmentcell.hpp */, + 373C68A20FC1C07D00137ACD /* alignmentcell.cpp */, + A78782A910A1B1CB0086103D /* alignmentdb.h */, + A78782AA10A1B1CB0086103D /* alignmentdb.cpp */, + 373C69170FC1C8AF00137ACD /* blastdb.hpp */, + 373C69160FC1C8AF00137ACD /* blastdb.cpp */, + 37D927D40F21331F001D4494 /* database.hpp */, + 37D927D30F21331F001D4494 /* database.cpp */, 37D927D50F21331F001D4494 /* datavector.hpp */, 37D927DC0F21331F001D4494 /* fastamap.h */, 37D927DB0F21331F001D4494 /* fastamap.cpp */, - 3782163B0F616079008E1F6D /* fullmatrix.h */, - 3782163C0F616079008E1F6D /* fullmatrix.cpp */, + 375873EA0F7D64520040F377 /* fullmatrix.h */, + 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 */, + 37D927F10F21331F001D4494 /* nameassignment.hpp */, + 37D927F00F21331F001D4494 /* nameassignment.cpp */, 37D927F80F21331F001D4494 /* ordervector.hpp */, 37D927F70F21331F001D4494 /* ordervector.cpp */, 37D928000F21331F001D4494 /* rabundvector.hpp */, 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 */, @@ -593,6 +1028,12 @@ 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 */, @@ -606,18 +1047,31 @@ 37D928B10F213472001D4494 /* errorcheckor */ = { isa = PBXGroup; children = ( - 37D927DA0F21331F001D4494 /* errorchecking.h */, - 37D927D90F21331F001D4494 /* errorchecking.cpp */, 37D928500F21331F001D4494 /* validcalculator.h */, 37D9284F0F21331F001D4494 /* validcalculator.cpp */, - 37D928520F21331F001D4494 /* validcommands.h */, - 37D928510F21331F001D4494 /* validcommands.cpp */, 37D928540F21331F001D4494 /* validparameter.h */, 37D928530F21331F001D4494 /* validparameter.cpp */, ); name = errorcheckor; sourceTree = ""; }; + A787811210A073F40086103D /* classifiers */ = { + isa = PBXGroup; + children = ( + A78780FE10A06B8B0086103D /* classify.h */, + A787810210A06D5D0086103D /* classify.cpp */, + A787820F10A0AAE70086103D /* bayesian.h */, + A787821010A0AAE70086103D /* bayesian.cpp */, + A773805D10B6D6FC002A6A61 /* taxonomyequalizer.h */, + A773805E10B6D6FC002A6A61 /* taxonomyequalizer.cpp */, + A78781B910A0813D0086103D /* phylotree.h */, + A78781B810A0813D0086103D /* phylotree.cpp */, + A787844310A1EBDD0086103D /* knn.h */, + A787844410A1EBDD0086103D /* knn.cpp */, + ); + name = classifiers; + sourceTree = ""; + }; C6859E8C029090F304C91782 /* Documentation */ = { isa = PBXGroup; children = ( @@ -683,7 +1137,6 @@ 37D928610F21331F001D4494 /* completelinkage.cpp in Sources */, 37D928620F21331F001D4494 /* database.cpp in Sources */, 37D928630F21331F001D4494 /* engine.cpp in Sources */, - 37D928640F21331F001D4494 /* errorchecking.cpp in Sources */, 37D928650F21331F001D4494 /* fastamap.cpp in Sources */, 37D928660F21331F001D4494 /* fileoutput.cpp in Sources */, 37D928670F21331F001D4494 /* globaldata.cpp in Sources */, @@ -698,7 +1151,6 @@ 37D928700F21331F001D4494 /* nameassignment.cpp in Sources */, 37D928720F21331F001D4494 /* npshannon.cpp in Sources */, 37D928730F21331F001D4494 /* ordervector.cpp in Sources */, - 37D928740F21331F001D4494 /* parselistcommand.cpp in Sources */, 37D928750F21331F001D4494 /* progress.cpp in Sources */, 37D928760F21331F001D4494 /* quitcommand.cpp in Sources */, 37D928770F21331F001D4494 /* rabundvector.cpp in Sources */, @@ -707,11 +1159,9 @@ 37D9287A0F21331F001D4494 /* rarefact.cpp in Sources */, 37D9287B0F21331F001D4494 /* rarefactcommand.cpp in Sources */, 37D9287C0F21331F001D4494 /* rarefactsharedcommand.cpp in Sources */, - 37D928800F21331F001D4494 /* readmatrix.cpp in Sources */, 37D928840F21331F001D4494 /* sabundvector.cpp in Sources */, 37D928850F21331F001D4494 /* sequence.cpp in Sources */, 37D928860F21331F001D4494 /* shannon.cpp in Sources */, - 37D928870F21331F001D4494 /* shared.cpp in Sources */, 37D928880F21331F001D4494 /* sharedace.cpp in Sources */, 37D928890F21331F001D4494 /* sharedchao1.cpp in Sources */, 37D9288A0F21331F001D4494 /* sharedcommand.cpp in Sources */, @@ -734,7 +1184,6 @@ 37D9289B0F21331F001D4494 /* summarysharedcommand.cpp in Sources */, 37D9289C0F21331F001D4494 /* uvest.cpp in Sources */, 37D9289D0F21331F001D4494 /* validcalculator.cpp in Sources */, - 37D9289E0F21331F001D4494 /* validcommands.cpp in Sources */, 37D9289F0F21331F001D4494 /* validparameter.cpp in Sources */, 372E12700F26365B0095CF7E /* readotucommand.cpp in Sources */, 372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */, @@ -756,19 +1205,106 @@ A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */, A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */, A70B53AC0F4CD7AD0064797E /* getlinecommand.cpp in Sources */, - 3782163D0F616079008E1F6D /* fullmatrix.cpp in Sources */, - 374CD63F0F65832000D90B4A /* libshuffcommand.cpp in Sources */, - 374CD6F10F65A4C100D90B4A /* coverage.cpp in Sources */, - 3765B47A0F77D15900C3EDC5 /* nocommands.cpp in Sources */, - 3765B4E20F78055000C3EDC5 /* sharedochiai.cpp in Sources */, - 3765B5160F780A7F00C3EDC5 /* sharedanderberg.cpp in Sources */, - 217595330F791EEE001CC3C6 /* sharedkulczynski.cpp in Sources */, - 2175953F0F792111001CC3C6 /* sharedkulczynskicody.cpp in Sources */, - 217595590F792490001CC3C6 /* sharedlennon.cpp in Sources */, 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sharedkulczynski.cpp in Sources */, + 375874050F7D64EF0040F377 /* sharedlennon.cpp in Sources */, + 375874060F7D64EF0040F377 /* sharedkulczynskicody.cpp in Sources */, + 3758740C0F7D64FC0040F377 /* sharedmorisitahorn.cpp in Sources */, + 3758740D0F7D64FC0040F377 /* sharedochiai.cpp in Sources */, + 37519A6B0F80E6EB00FED5E8 /* sharedanderbergs.cpp in Sources */, + 37519AA10F810D0200FED5E8 /* venncommand.cpp in Sources */, + 37519AB50F810FAE00FED5E8 /* venn.cpp in Sources */, + 37C1D9730F86506E0059E3F0 /* binsequencecommand.cpp in Sources */, + 370B88070F8A4EE4005AB382 /* getoturepcommand.cpp in Sources */, + 7E412F490F8D21B600381DD0 /* slibshuff.cpp in Sources */, + 7E412FEA0F8D3E2C00381DD0 /* libshuff.cpp in Sources */, + 7E4130F80F8E58FA00381DD0 /* dlibshuff.cpp in Sources */, + 211C38320F961DD400FEE541 /* sharedutilities.cpp in Sources */, + 211C38380F961E1F00FEE541 /* treegroupscommand.cpp in Sources */, + 21DDC01B0F97A8FE0060691C /* bootstrapsharedcommand.cpp in Sources */, + 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 /* consensuscommand.cpp in Sources */, + 378C1B030FB0644E004D63F5 /* filterseqscommand.cpp in Sources */, + 378C1B040FB0644E004D63F5 /* goodscoverage.cpp in Sources */, + 378C1B0A0FB0644E004D63F5 /* sequencedb.cpp in Sources */, + 378C1B0B0FB0644E004D63F5 /* sharedjackknife.cpp in Sources */, + 378C1B0C0FB0644E004D63F5 /* sharedmarczewski.cpp in Sources */, + 37C753CE0FB3415200DBD02E /* distancecommand.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 */, + 21E859D80FC4632E005E1A48 /* matrixoutputcommand.cpp in Sources */, + 3749271D0FD58C840031C06B /* getsabundcommand.cpp in Sources */, + 3749273F0FD5956B0031C06B /* getrabundcommand.cpp in 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DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym"; GCC_MODEL_TUNING = G5; - GCC_OPTIMIZATION_LEVEL = 3; INSTALL_PATH = /usr/local/bin; + LIBRARY_SEARCH_PATHS = ( + "$(inherited)", + "\"$(SRCROOT)/../readline-6.0\"", + ); PRODUCT_NAME = mothur; }; name = Release; @@ -808,11 +1351,15 @@ isa = XCBuildConfiguration; buildSettings = { GCC_OPTIMIZATION_LEVEL = 3; + GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; + GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO; + GCC_WARN_PEDANTIC = NO; GCC_WARN_UNUSED_VARIABLE = YES; - INSTALL_MODE_FLAG = "a-w,a+rX"; + OTHER_CPLUSPLUSFLAGS = ""; PREBINDING = NO; SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk"; + WARNING_CFLAGS = ""; }; name = Debug; }; @@ -823,12 +1370,28 @@ ppc, i386, ); - GCC_OPTIMIZATION_LEVEL = 0; + GCC_OPTIMIZATION_LEVEL = 3; + GCC_WARN_ABOUT_MISSING_NEWLINE = YES; + GCC_WARN_ABOUT_MISSING_PROTOTYPES = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; + GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO; + GCC_WARN_MISSING_PARENTHESES = YES; + GCC_WARN_PEDANTIC = YES; + GCC_WARN_UNUSED_FUNCTION = YES; + GCC_WARN_UNUSED_PARAMETER = NO; + GCC_WARN_UNUSED_VALUE = YES; GCC_WARN_UNUSED_VARIABLE = YES; - INSTALL_MODE_FLAG = "a-w,a+rX"; + OTHER_CPLUSPLUSFLAGS = ( + "-ansi", + "-pedantic", + "-wall", + "-lreadline", + "-DUSE_READLINE", + ); PREBINDING = NO; SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk"; + SYMROOT = /Users/johnwestcott/Desktop; + WARNING_CFLAGS = ""; }; name = Release; };