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lastKnownFileType = sourcecode.cpp.cpp; path = geom.cpp; sourceTree = ""; }; + EBC564170F81479000A5AC46 /* sharedjackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjackknife.h; sourceTree = ""; }; + EBC564180F81479000A5AC46 /* sharedjackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjackknife.cpp; sourceTree = ""; }; /* End PBXFileReference section */ /* Begin PBXFrameworksBuildPhase section */ @@ -388,8 +412,8 @@ 37D927DD0F21331F001D4494 /* fileoutput.cpp */, 37D927E00F21331F001D4494 /* globaldata.hpp */, 37D927DF0F21331F001D4494 /* globaldata.cpp */, - 3765B5440F7A62A000C3EDC5 /* heatmap.h */, - 3765B5450F7A62A000C3EDC5 /* heatmap.cpp */, + 375873ED0F7D646F0040F377 /* heatmap.h */, + 375873EE0F7D646F0040F377 /* heatmap.cpp */, 37D927E60F21331F001D4494 /* inputdata.h */, 37D927E50F21331F001D4494 /* inputdata.cpp */, 37D927EA0F21331F001D4494 /* kmer.hpp */, @@ -417,6 +441,8 @@ 37D928210F21331F001D4494 /* shared.h */, 37D928200F21331F001D4494 /* shared.cpp */, 37D928420F21331F001D4494 /* singlelinkage.cpp */, + 37D928450F21331F001D4494 /* sparsematrix.hpp */, + 37D928440F21331F001D4494 /* sparsematrix.cpp */, 37D928480F21331F001D4494 /* summarydata.h */, 37D928490F21331F001D4494 /* summarydisplay.h */, 37D9284C0F21331F001D4494 /* utilities.hpp */, @@ -440,17 +466,27 @@ 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 */, - 374CD6EF0F65A4C100D90B4A /* coverage.h */, - 374CD6F00F65A4C100D90B4A /* coverage.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 */, - 370936DE0F6E7A4A00EB4C2C /* nseqs.h */, 379294880F2E258500B9034A /* parsimony.h */, 379294890F2E258500B9034A /* parsimony.cpp */, 37D928020F21331F001D4494 /* rarecalc.h */, @@ -459,29 +495,35 @@ 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 */, + 375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */, + 375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */, + EB6F01590F6AC1670048081A /* sharedbdiversity.h */, + EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */, 37D928250F21331F001D4494 /* sharedchao1.h */, 37D928240F21331F001D4494 /* sharedchao1.cpp */, 37D928290F21331F001D4494 /* sharedjabund.h */, 37D928280F21331F001D4494 /* sharedjabund.cpp */, + EBC564170F81479000A5AC46 /* sharedjackknife.h */, + EBC564180F81479000A5AC46 /* 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 */, + 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 */, @@ -527,14 +569,14 @@ A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */, A70B53A90F4CD7AD0064797E /* getlinecommand.h */, A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */, - 3765B5360F7A5A9E00C3EDC5 /* heatmapcommand.h */, - 3765B5370F7A5A9E00C3EDC5 /* heatmapcommand.cpp */, + 375873F00F7D64800040F377 /* heatmapcommand.cpp */, + 375873F10F7D64800040F377 /* heatmapcommand.h */, 37D927E40F21331F001D4494 /* helpcommand.h */, 37D927E30F21331F001D4494 /* helpcommand.cpp */, - 374CD63D0F65832000D90B4A /* libshuffcommand.h */, - 374CD63E0F65832000D90B4A /* libshuffcommand.cpp */, - 3765B4790F77D15900C3EDC5 /* nocommands.h */, - 3765B4780F77D15900C3EDC5 /* nocommands.cpp */, + 375873F30F7D648F0040F377 /* libshuffcommand.cpp */, + 375873F40F7D648F0040F377 /* libshuffcommand.h */, + 375873F60F7D649C0040F377 /* nocommands.cpp */, + 375873F70F7D649C0040F377 /* nocommands.h */, 37D927FA0F21331F001D4494 /* parselistcommand.h */, 37D927F90F21331F001D4494 /* parselistcommand.cpp */, 3792946E0F2E191800B9034A /* parsimonycommand.h */, @@ -571,8 +613,8 @@ 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 */, 37D927EE0F21331F001D4494 /* listvector.hpp */, @@ -591,8 +633,6 @@ 37D928300F21331F001D4494 /* sharedrabundvector.cpp */, 37D928330F21331F001D4494 /* sharedsabundvector.h */, 37D928320F21331F001D4494 /* sharedsabundvector.cpp */, - 37D928450F21331F001D4494 /* sparsematrix.hpp */, - 37D928440F21331F001D4494 /* sparsematrix.cpp */, 37AD4DB90F28E2FE00AA2D49 /* tree.h */, 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */, 379293C10F2DE73400B9034A /* treemap.h */, @@ -756,19 +796,27 @@ 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 */, + 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 */, + 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 */, + 37519A6B0F80E6EB00FED5E8 /* sharedanderbergs.cpp in Sources */, + EBC564190F81479000A5AC46 /* sharedjackknife.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -782,7 +830,7 @@ GCC_DYNAMIC_NO_PIC = NO; GCC_ENABLE_FIX_AND_CONTINUE = YES; GCC_MODEL_TUNING = G5; - GCC_OPTIMIZATION_LEVEL = 3; + GCC_OPTIMIZATION_LEVEL = 0; GCC_PREPROCESSOR_DEFINITIONS = ( "_GLIBCXX_DEBUG=1", "_GLIBCXX_DEBUG_PEDANTIC=1", @@ -798,7 +846,6 @@ buildSettings = { DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym"; GCC_MODEL_TUNING = G5; - GCC_OPTIMIZATION_LEVEL = 3; INSTALL_PATH = /usr/local/bin; PRODUCT_NAME = mothur; }; @@ -810,7 +857,6 @@ 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 = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk"; }; @@ -826,7 +872,6 @@ GCC_OPTIMIZATION_LEVEL = 0; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_UNUSED_VARIABLE = YES; - INSTALL_MODE_FLAG = "a-w,a+rX"; PREBINDING = NO; SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk"; };