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fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupcommand.h; sourceTree = ""; }; + A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlabelcommand.cpp; sourceTree = ""; }; + A70B53A70F4CD7AD0064797E /* getlabelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlabelcommand.h; sourceTree = ""; }; + A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlinecommand.cpp; sourceTree = ""; }; + A70B53A90F4CD7AD0064797E /* getlinecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlinecommand.h; sourceTree = ""; }; C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = ""; }; /* End PBXFileReference section */ @@ -318,12 +388,15 @@ 37D927DD0F21331F001D4494 /* fileoutput.cpp */, 37D927E00F21331F001D4494 /* globaldata.hpp */, 37D927DF0F21331F001D4494 /* globaldata.cpp */, + 3765B5440F7A62A000C3EDC5 /* heatmap.h */, + 3765B5450F7A62A000C3EDC5 /* 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 */, @@ -344,8 +417,6 @@ 37D928210F21331F001D4494 /* shared.h */, 37D928200F21331F001D4494 /* shared.cpp */, 37D928420F21331F001D4494 /* singlelinkage.cpp */, - 37D928450F21331F001D4494 /* sparsematrix.hpp */, - 37D928440F21331F001D4494 /* sparsematrix.cpp */, 37D928480F21331F001D4494 /* summarydata.h */, 37D928490F21331F001D4494 /* summarydisplay.h */, 37D9284C0F21331F001D4494 /* utilities.hpp */, @@ -365,6 +436,7 @@ isa = PBXGroup; children = ( 37D927BE0F21331F001D4494 /* calculator.h */, + 3792948D0F2E271100B9034A /* treecalculator.h */, 37D927BD0F21331F001D4494 /* calculator.cpp */, 37D927B90F21331F001D4494 /* ace.h */, 37D927B80F21331F001D4494 /* ace.cpp */, @@ -372,16 +444,25 @@ 37D927BB0F21331F001D4494 /* bootstrap.cpp */, 37D927C00F21331F001D4494 /* chao1.h */, 37D927BF0F21331F001D4494 /* chao1.cpp */, + 374CD6EF0F65A4C100D90B4A /* coverage.h */, + 374CD6F00F65A4C100D90B4A /* coverage.cpp */, 37D927E80F21331F001D4494 /* jackknife.h */, 37D927E70F21331F001D4494 /* jackknife.cpp */, 37D927F50F21331F001D4494 /* npshannon.h */, 37D927F40F21331F001D4494 /* npshannon.cpp */, + 370936DE0F6E7A4A00EB4C2C /* nseqs.h */, + 379294880F2E258500B9034A /* parsimony.h */, + 379294890F2E258500B9034A /* parsimony.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 */, 37D928250F21331F001D4494 /* sharedchao1.h */, 37D928240F21331F001D4494 /* sharedchao1.cpp */, 37D928290F21331F001D4494 /* sharedjabund.h */, @@ -390,23 +471,40 @@ 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 */, 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 = ""; @@ -423,12 +521,24 @@ 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 */, + 3765B5360F7A5A9E00C3EDC5 /* heatmapcommand.h */, + 3765B5370F7A5A9E00C3EDC5 /* heatmapcommand.cpp */, 37D927E40F21331F001D4494 /* helpcommand.h */, 37D927E30F21331F001D4494 /* helpcommand.cpp */, - 37D927F20F21331F001D4494 /* nocommand.cpp */, - 37D927F30F21331F001D4494 /* nocommand.h */, + 374CD63D0F65832000D90B4A /* libshuffcommand.h */, + 374CD63E0F65832000D90B4A /* libshuffcommand.cpp */, + 3765B4790F77D15900C3EDC5 /* nocommands.h */, + 3765B4780F77D15900C3EDC5 /* nocommands.cpp */, 37D927FA0F21331F001D4494 /* parselistcommand.h */, 37D927F90F21331F001D4494 /* parselistcommand.cpp */, + 3792946E0F2E191800B9034A /* parsimonycommand.h */, + 3792946F0F2E191800B9034A /* parsimonycommand.cpp */, 37D927FE0F21331F001D4494 /* quitcommand.h */, 37D927FD0F21331F001D4494 /* quitcommand.cpp */, 37D928080F21331F001D4494 /* rarefactcommand.h */, @@ -447,6 +557,10 @@ 37D928460F21331F001D4494 /* summarycommand.cpp */, 37D9284B0F21331F001D4494 /* summarysharedcommand.h */, 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */, + 3746109B0F40657600460C57 /* unifracunweightedcommand.h */, + 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */, + 374610760F40645300460C57 /* unifracweightedcommand.h */, + 374610770F40645300460C57 /* unifracweightedcommand.cpp */, ); name = commands; sourceTree = ""; @@ -457,6 +571,8 @@ 37D927D50F21331F001D4494 /* datavector.hpp */, 37D927DC0F21331F001D4494 /* fastamap.h */, 37D927DB0F21331F001D4494 /* fastamap.cpp */, + 3782163B0F616079008E1F6D /* fullmatrix.h */, + 3782163C0F616079008E1F6D /* fullmatrix.cpp */, 37D927E20F21331F001D4494 /* groupmap.h */, 37D927E10F21331F001D4494 /* groupmap.cpp */, 37D927EE0F21331F001D4494 /* listvector.hpp */, @@ -475,6 +591,8 @@ 37D928300F21331F001D4494 /* sharedrabundvector.cpp */, 37D928330F21331F001D4494 /* sharedsabundvector.h */, 37D928320F21331F001D4494 /* sharedsabundvector.cpp */, + 37D928450F21331F001D4494 /* sparsematrix.hpp */, + 37D928440F21331F001D4494 /* sparsematrix.cpp */, 37AD4DB90F28E2FE00AA2D49 /* tree.h */, 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */, 379293C10F2DE73400B9034A /* treemap.h */, @@ -578,7 +696,6 @@ 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 */, @@ -629,6 +746,29 @@ 37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */, 37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */, 379293C30F2DE73400B9034A /* treemap.cpp 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 */, + 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 */, + 217595640F7927BB001CC3C6 /* sharedmorisitahorn.cpp in Sources */, + 217595710F792A33001CC3C6 /* sharedbraycurtis.cpp in Sources */, + 3765B5380F7A5A9E00C3EDC5 /* heatmapcommand.cpp in Sources */, + 3765B5460F7A62A000C3EDC5 /* heatmap.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -642,7 +782,7 @@ GCC_DYNAMIC_NO_PIC = NO; GCC_ENABLE_FIX_AND_CONTINUE = YES; GCC_MODEL_TUNING = G5; - GCC_OPTIMIZATION_LEVEL = 0; + GCC_OPTIMIZATION_LEVEL = 3; GCC_PREPROCESSOR_DEFINITIONS = ( "_GLIBCXX_DEBUG=1", "_GLIBCXX_DEBUG_PEDANTIC=1", @@ -658,6 +798,7 @@ buildSettings = { DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym"; GCC_MODEL_TUNING = G5; + GCC_OPTIMIZATION_LEVEL = 3; INSTALL_PATH = /usr/local/bin; PRODUCT_NAME = mothur; }; @@ -669,6 +810,7 @@ GCC_OPTIMIZATION_LEVEL = 3; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_UNUSED_VARIABLE = YES; + INSTALL_MODE_FLAG = "a-w,a+rX"; PREBINDING = NO; SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk"; }; @@ -681,9 +823,10 @@ ppc, i386, ); - GCC_OPTIMIZATION_LEVEL = 3; + GCC_OPTIMIZATION_LEVEL = 0; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_UNUSED_VARIABLE = YES; + INSTALL_MODE_FLAG = "a-w,a+rX"; PREBINDING = NO; SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk"; };