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fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = geom.cpp; sourceTree = ""; }; /* End PBXFileReference section */ /* Begin PBXFrameworksBuildPhase section */ @@ -315,21 +445,51 @@ 37D927D60F21331F001D4494 /* display.h */, 37D927D80F21331F001D4494 /* engine.hpp */, 37D927D70F21331F001D4494 /* engine.cpp */, - 7E44EBD00F32358B00B0D45D /* makefile */, 37D928B10F213472001D4494 /* errorcheckor */, 37D927DE0F21331F001D4494 /* fileoutput.h */, 37D927DD0F21331F001D4494 /* fileoutput.cpp */, 37D927E00F21331F001D4494 /* globaldata.hpp */, 37D927DF0F21331F001D4494 /* globaldata.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 */, + 37E3ED800F4D9D0D00B5DF02 /* mothur.h */, 37D927EF0F21331F001D4494 /* mothur.cpp */, 37D927F10F21331F001D4494 /* nameassignment.hpp */, 37D927F00F21331F001D4494 /* nameassignment.cpp */, + 3758738B0F7D61240040F377 /* coverage.cpp */, + 3758738C0F7D61240040F377 /* coverage.h */, + 3758738D0F7D61240040F377 /* fullmatrix.cpp */, + 3758738E0F7D61240040F377 /* fullmatrix.h */, + 3758738F0F7D61240040F377 /* heatmap.cpp */, + 375873900F7D61240040F377 /* heatmap.h */, + 375873910F7D61240040F377 /* heatmapcommand.cpp */, + 375873920F7D61240040F377 /* heatmapcommand.h */, + 375873930F7D61240040F377 /* libshuffcommand.cpp */, + 375873940F7D61240040F377 /* libshuffcommand.h */, + 375873950F7D61240040F377 /* nocommands.cpp */, + 375873960F7D61240040F377 /* nocommands.h */, + 375873970F7D61240040F377 /* nseqs.h */, + 375873980F7D61240040F377 /* sharedanderberg.cpp */, + 375873990F7D61240040F377 /* sharedanderberg.h */, + 3758739A0F7D61240040F377 /* sharedbraycurtis.cpp */, + 3758739B0F7D61240040F377 /* sharedbraycurtis.h */, + 3758739C0F7D61240040F377 /* sharedkulczynski.cpp */, + 3758739D0F7D61240040F377 /* sharedkulczynski.h */, + 3758739E0F7D61240040F377 /* sharedkulczynskicody.cpp */, + 3758739F0F7D61240040F377 /* sharedkulczynskicody.h */, + 375873A00F7D61240040F377 /* sharedlennon.cpp */, + 375873A10F7D61240040F377 /* sharedlennon.h */, + 375873A20F7D61240040F377 /* sharedmorisitahorn.cpp */, + 375873A30F7D61240040F377 /* sharedmorisitahorn.h */, + 375873A40F7D61240040F377 /* sharednseqs.h */, + 375873A50F7D61240040F377 /* sharedochiai.cpp */, + 375873A60F7D61240040F377 /* sharedochiai.h */, 37D927F60F21331F001D4494 /* observable.h */, 37D927FC0F21331F001D4494 /* progress.hpp */, 37D927FB0F21331F001D4494 /* progress.cpp */, @@ -354,7 +514,7 @@ 37D9284C0F21331F001D4494 /* utilities.hpp */, ); name = Source; - sourceTree = SOURCE_ROOT; + sourceTree = ""; }; 1AB674ADFE9D54B511CA2CBB /* Products */ = { isa = PBXGroup; @@ -368,23 +528,45 @@ isa = PBXGroup; children = ( 37D927BE0F21331F001D4494 /* calculator.h */, + 3792948D0F2E271100B9034A /* treecalculator.h */, 37D927BD0F21331F001D4494 /* calculator.cpp */, 37D927B90F21331F001D4494 /* ace.h */, 37D927B80F21331F001D4494 /* ace.cpp */, + EB1216860F619B83004A865F /* bergerparker.h */, + EB1216870F619B83004A865F /* bergerparker.cpp */, 37D927BC0F21331F001D4494 /* bootstrap.h */, 37D927BB0F21331F001D4494 /* bootstrap.cpp */, + EB1216E30F61ACFB004A865F /* bstick.h */, + EB1216E40F61ACFB004A865F /* bstick.cpp */, 37D927C00F21331F001D4494 /* chao1.h */, 37D927BF0F21331F001D4494 /* chao1.cpp */, + 375873E60F7D63E90040F377 /* coverage.h */, + 375873E50F7D63E90040F377 /* coverage.cpp */, + EB9303F70F53517300E8EF26 /* geom.h */, + EB9303F80F53517300E8EF26 /* geom.cpp */, + EB9303E90F534D9400E8EF26 /* logsd.h */, + EB9303EA0F534D9400E8EF26 /* logsd.cpp */, + EB6E68170F5F1C780044E17B /* qstat.h */, + EB6E68180F5F1C780044E17B /* qstat.cpp */, 37D927E80F21331F001D4494 /* jackknife.h */, 37D927E70F21331F001D4494 /* jackknife.cpp */, + 375873F90F7D64AB0040F377 /* nseqs.h */, 37D927F50F21331F001D4494 /* npshannon.h */, 37D927F40F21331F001D4494 /* npshannon.cpp */, + 379294880F2E258500B9034A /* parsimony.h */, + 379294890F2E258500B9034A /* parsimony.cpp */, 37D928020F21331F001D4494 /* rarecalc.h */, 37D928010F21331F001D4494 /* rarecalc.cpp */, 37D9281F0F21331F001D4494 /* shannon.h */, 37D9281E0F21331F001D4494 /* shannon.cpp */, 37D928230F21331F001D4494 /* sharedace.h */, 37D928220F21331F001D4494 /* sharedace.cpp */, + 375873FA0F7D64D20040F377 /* sharedanderberg.h */, + 375873E20F7D63B50040F377 /* sharedanderberg.cpp */, + 375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */, + 375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */, + EB6F01590F6AC1670048081A /* sharedbdiversity.h */, + EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */, 37D928250F21331F001D4494 /* sharedchao1.h */, 37D928240F21331F001D4494 /* sharedchao1.cpp */, 37D928290F21331F001D4494 /* sharedjabund.h */, @@ -393,26 +575,45 @@ 37D9282A0F21331F001D4494 /* sharedjclass.cpp */, 37D9282D0F21331F001D4494 /* sharedjest.h */, 37D9282C0F21331F001D4494 /* sharedjest.cpp */, + EB1217210F61C9AC004A865F /* sharedkstest.h */, + EB1217220F61C9AC004A865F /* sharedkstest.cpp */, + 375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */, + 375873FF0F7D64EF0040F377 /* sharedlennon.cpp */, + 375874000F7D64EF0040F377 /* sharedkulczynski.h */, + 375874010F7D64EF0040F377 /* sharedlennon.h */, + 375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */, + 375874030F7D64EF0040F377 /* sharedkulczynskicody.h */, + 375874070F7D64FC0040F377 /* sharedmorisitahorn.h */, + 375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */, + 375874090F7D64FC0040F377 /* sharedochiai.h */, + 3758740A0F7D64FC0040F377 /* sharednseqs.h */, + 3758740B0F7D64FC0040F377 /* sharedochiai.cpp */, 37D928350F21331F001D4494 /* sharedsobs.h */, 37D928340F21331F001D4494 /* sharedsobs.cpp */, + 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */, + 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */, 37D928370F21331F001D4494 /* sharedsorabund.h */, 37D928360F21331F001D4494 /* sharedsorabund.cpp */, 37D928390F21331F001D4494 /* sharedsorclass.h */, 37D928380F21331F001D4494 /* sharedsorclass.cpp */, 37D9283B0F21331F001D4494 /* sharedsorest.h */, 37D9283A0F21331F001D4494 /* sharedsorest.cpp */, - 37D9283C0F21331F001D4494 /* sharedthetan.cpp */, 37D9283D0F21331F001D4494 /* sharedthetan.h */, + 37D9283C0F21331F001D4494 /* sharedthetan.cpp */, 37D9283F0F21331F001D4494 /* sharedthetayc.h */, 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */, 37D928410F21331F001D4494 /* simpson.h */, 37D928400F21331F001D4494 /* simpson.cpp */, 37D928430F21331F001D4494 /* sobs.h */, + 374610810F40652400460C57 /* unweighted.h */, + 374610820F40652400460C57 /* unweighted.cpp */, 37D9284E0F21331F001D4494 /* uvest.h */, 37D9284D0F21331F001D4494 /* uvest.cpp */, + 3746107C0F4064D100460C57 /* weighted.h */, + 3746107D0F4064D100460C57 /* weighted.cpp */, ); name = calculators; - sourceTree = SOURCE_ROOT; + sourceTree = ""; }; 37D928A90F2133E5001D4494 /* commands */ = { isa = PBXGroup; @@ -426,12 +627,26 @@ 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */, 37B28F660F27590100808A62 /* deconvolutecommand.h */, 37B28F670F27590100808A62 /* deconvolutecommand.cpp */, + A70B53A50F4CD7AD0064797E /* getgroupcommand.h */, + A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */, + A70B53A70F4CD7AD0064797E /* getlabelcommand.h */, + A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */, + A70B53A90F4CD7AD0064797E /* getlinecommand.h */, + A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */, + 375873F00F7D64800040F377 /* heatmapcommand.cpp */, + 375873F10F7D64800040F377 /* heatmapcommand.h */, 37D927E40F21331F001D4494 /* helpcommand.h */, 37D927E30F21331F001D4494 /* helpcommand.cpp */, - 37D927F20F21331F001D4494 /* nocommand.cpp */, - 37D927F30F21331F001D4494 /* nocommand.h */, + 375873F30F7D648F0040F377 /* libshuffcommand.cpp */, + 375873F40F7D648F0040F377 /* libshuffcommand.h */, + 375873F60F7D649C0040F377 /* nocommands.cpp */, + 375873F70F7D649C0040F377 /* nocommands.h */, 37D927FA0F21331F001D4494 /* parselistcommand.h */, 37D927F90F21331F001D4494 /* parselistcommand.cpp */, + 3792946E0F2E191800B9034A /* parsimonycommand.h */, + 3792946F0F2E191800B9034A /* parsimonycommand.cpp */, + 37D927FE0F21331F001D4494 /* quitcommand.h */, + 37D927FD0F21331F001D4494 /* quitcommand.cpp */, 37D928080F21331F001D4494 /* rarefactcommand.h */, 37D928070F21331F001D4494 /* rarefactcommand.cpp */, 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */, @@ -448,11 +663,13 @@ 37D928460F21331F001D4494 /* summarycommand.cpp */, 37D9284B0F21331F001D4494 /* summarysharedcommand.h */, 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */, - 37D927FE0F21331F001D4494 /* quitcommand.h */, - 37D927FD0F21331F001D4494 /* quitcommand.cpp */, + 3746109B0F40657600460C57 /* unifracunweightedcommand.h */, + 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */, + 374610760F40645300460C57 /* unifracweightedcommand.h */, + 374610770F40645300460C57 /* unifracweightedcommand.cpp */, ); name = commands; - sourceTree = SOURCE_ROOT; + sourceTree = ""; }; 37D928AC0F213420001D4494 /* containers */ = { isa = PBXGroup; @@ -460,6 +677,8 @@ 37D927D50F21331F001D4494 /* datavector.hpp */, 37D927DC0F21331F001D4494 /* fastamap.h */, 37D927DB0F21331F001D4494 /* fastamap.cpp */, + 375873EA0F7D64520040F377 /* fullmatrix.h */, + 375873EB0F7D64520040F377 /* fullmatrix.cpp */, 37D927E20F21331F001D4494 /* groupmap.h */, 37D927E10F21331F001D4494 /* groupmap.cpp */, 37D927EE0F21331F001D4494 /* listvector.hpp */, @@ -486,7 +705,7 @@ 37E5F3E20F29FD4200F8D827 /* treenode.cpp */, ); name = containers; - sourceTree = SOURCE_ROOT; + sourceTree = ""; }; 37D928B10F213472001D4494 /* errorcheckor */ = { isa = PBXGroup; @@ -501,7 +720,7 @@ 37D928530F21331F001D4494 /* validparameter.cpp */, ); name = errorcheckor; - sourceTree = SOURCE_ROOT; + sourceTree = ""; }; C6859E8C029090F304C91782 /* Documentation */ = { isa = PBXGroup; @@ -581,7 +800,6 @@ 37D9286E0F21331F001D4494 /* listvector.cpp in Sources */, 37D9286F0F21331F001D4494 /* mothur.cpp in Sources */, 37D928700F21331F001D4494 /* nameassignment.cpp in Sources */, - 37D928710F21331F001D4494 /* nocommand.cpp in Sources */, 37D928720F21331F001D4494 /* npshannon.cpp in Sources */, 37D928730F21331F001D4494 /* ordervector.cpp in Sources */, 37D928740F21331F001D4494 /* parselistcommand.cpp in Sources */, @@ -632,7 +850,49 @@ 37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */, 37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */, 379293C30F2DE73400B9034A /* treemap.cpp in Sources */, - 7E44EBD10F3235D900B0D45D /* makefile in Sources */, + 379294700F2E191800B9034A /* parsimonycommand.cpp in Sources */, + 3792948A0F2E258500B9034A /* parsimony.cpp in Sources */, + 374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */, + 3746107E0F4064D100460C57 /* weighted.cpp in Sources */, + 374610830F40652400460C57 /* unweighted.cpp in Sources */, + 3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */, + 37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */, + A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */, + A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */, + A70B53AC0F4CD7AD0064797E /* getlinecommand.cpp in Sources */, + EB9303EB0F534D9400E8EF26 /* logsd.cpp in Sources */, + EB9303F90F53517300E8EF26 /* geom.cpp in Sources */, + EB6E68190F5F1C780044E17B /* qstat.cpp in Sources */, + EB1216880F619B83004A865F /* bergerparker.cpp in Sources */, + EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */, + EB1217230F61C9AC004A865F /* sharedkstest.cpp in Sources */, + EB6F015B0F6AC1670048081A /* sharedbdiversity.cpp in Sources */, + 375873A70F7D61240040F377 /* coverage.cpp in Sources */, + 375873A80F7D61240040F377 /* fullmatrix.cpp in Sources */, + 375873A90F7D61240040F377 /* heatmap.cpp in Sources */, + 375873AA0F7D61240040F377 /* heatmapcommand.cpp in Sources */, + 375873AB0F7D61240040F377 /* libshuffcommand.cpp in Sources */, + 375873AC0F7D61240040F377 /* nocommands.cpp in Sources */, + 375873AD0F7D61240040F377 /* sharedanderberg.cpp in Sources */, + 375873AE0F7D61240040F377 /* sharedbraycurtis.cpp in Sources */, + 375873AF0F7D61240040F377 /* sharedkulczynski.cpp in Sources */, + 375873B00F7D61240040F377 /* sharedkulczynskicody.cpp in Sources */, + 375873B10F7D61240040F377 /* sharedlennon.cpp in Sources */, + 375873B20F7D61240040F377 /* sharedmorisitahorn.cpp in Sources */, + 375873B30F7D61240040F377 /* sharedochiai.cpp in Sources */, + 375873E30F7D63B50040F377 /* sharedanderberg.cpp in Sources */, + 375873E70F7D63E90040F377 /* coverage.cpp in Sources */, + 375873EC0F7D64520040F377 /* fullmatrix.cpp in Sources */, + 375873EF0F7D646F0040F377 /* heatmap.cpp in Sources */, + 375873F20F7D64800040F377 /* heatmapcommand.cpp in Sources */, + 375873F50F7D648F0040F377 /* libshuffcommand.cpp in Sources */, + 375873F80F7D649C0040F377 /* nocommands.cpp in Sources */, + 375873FD0F7D64DA0040F377 /* sharedbraycurtis.cpp in Sources */, + 375874040F7D64EF0040F377 /* sharedkulczynski.cpp in Sources */, + 375874050F7D64EF0040F377 /* sharedlennon.cpp in Sources */, + 375874060F7D64EF0040F377 /* sharedkulczynskicody.cpp in Sources */, + 3758740C0F7D64FC0040F377 /* sharedmorisitahorn.cpp in Sources */, + 3758740D0F7D64FC0040F377 /* sharedochiai.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -685,7 +945,7 @@ ppc, i386, ); - GCC_OPTIMIZATION_LEVEL = 3; + GCC_OPTIMIZATION_LEVEL = 0; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_UNUSED_VARIABLE = YES; PREBINDING = NO;