]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
broke apart read matrix file
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index 57af531c164b323c10eef636b574d969a7c7ee48..1c8df765aba58235fdb4c557be80834880aa1da0 100644 (file)
@@ -7,6 +7,10 @@
        objects = {
 
 /* Begin PBXBuildFile section */
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                372E12700F26365B0095CF7E /* readotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E126F0F26365B0095CF7E /* readotucommand.cpp */; };
                372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E12950F263D5A0095CF7E /* readdistcommand.cpp */; };
                372E12ED0F264D320095CF7E /* commandfactory.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 372E12EC0F264D320095CF7E /* commandfactory.cpp */; };
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+               37519AB50F810FAE00FED5E8 /* venn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519AB40F810FAE00FED5E8 /* venn.cpp */; };
+               375873EC0F7D64520040F377 /* fullmatrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873EB0F7D64520040F377 /* fullmatrix.cpp */; };
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+               375873F50F7D648F0040F377 /* libshuffcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873F30F7D648F0040F377 /* libshuffcommand.cpp */; };
+               375873F80F7D649C0040F377 /* nocommands.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375873F60F7D649C0040F377 /* nocommands.cpp */; };
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+               375874060F7D64EF0040F377 /* sharedkulczynskicody.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */; };
+               3758740C0F7D64FC0040F377 /* sharedmorisitahorn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */; };
+               3758740D0F7D64FC0040F377 /* sharedochiai.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3758740B0F7D64FC0040F377 /* sharedochiai.cpp */; };
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@@ -26,6 +43,7 @@
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                37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */; };
                37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B28F670F27590100808A62 /* deconvolutecommand.cpp */; };
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@@ -64,7 +82,6 @@
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 /* End PBXFileReference section */
 
 /* Begin PBXFrameworksBuildPhase section */
                08FB7795FE84155DC02AAC07 /* Source */ = {
                        isa = PBXGroup;
                        children = (
+                               7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */,
+                               7E4130F70F8E58FA00381DD0 /* dlibshuff.h */,
                                37D927BA0F21331F001D4494 /* averagelinkage.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 */,
                                37D927DD0F21331F001D4494 /* fileoutput.cpp */,
                                37D927E00F21331F001D4494 /* globaldata.hpp */,
                                37D927DF0F21331F001D4494 /* globaldata.cpp */,
+                               375873ED0F7D646F0040F377 /* heatmap.h */,
+                               375873EE0F7D646F0040F377 /* heatmap.cpp */,
                                37D927E60F21331F001D4494 /* inputdata.h */,
                                37D927E50F21331F001D4494 /* inputdata.cpp */,
                                37D927EA0F21331F001D4494 /* kmer.hpp */,
                                37D928060F21331F001D4494 /* rarefact.h */,
                                37D928050F21331F001D4494 /* rarefact.cpp */,
                                37D928090F21331F001D4494 /* rarefactioncurvedata.h */,
+                               375AA1340F9E433D008EF9B8 /* readcolumn.h */,
+                               375AA1330F9E433D008EF9B8 /* readcolumn.cpp */,
                                37D928130F21331F001D4494 /* readmatrix.hpp */,
-                               37D928120F21331F001D4494 /* readmatrix.cpp */,
+                               375AA1360F9E433D008EF9B8 /* readotu.h */,
+                               375AA1350F9E433D008EF9B8 /* readotu.cpp */,
+                               375AA1380F9E433D008EF9B8 /* readphylip.h */,
+                               375AA1370F9E433D008EF9B8 /* readphylip.cpp */,
                                37AD4DC80F28F3DD00AA2D49 /* readtree.h */,
                                37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */,
                                37D9281D0F21331F001D4494 /* sequence.hpp */,
                                37D9281C0F21331F001D4494 /* sequence.cpp */,
                                37D928210F21331F001D4494 /* shared.h */,
                                37D928200F21331F001D4494 /* shared.cpp */,
+                               211C38310F961DD400FEE541 /* sharedutilities.h */,
+                               211C38300F961DD400FEE541 /* sharedutilities.cpp */,
                                37D928420F21331F001D4494 /* singlelinkage.cpp */,
                                37D928480F21331F001D4494 /* summarydata.h */,
                                37D928490F21331F001D4494 /* summarydisplay.h */,
-                               37D9284C0F21331F001D4494 /* utilities.hpp */,
+                               37519AB30F810FAE00FED5E8 /* venn.h */,
+                               37519AB40F810FAE00FED5E8 /* venn.cpp */,
                        );
                        name = Source;
                        sourceTree = "<group>";
                                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 */,
+                               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 */,
                                37D9281E0F21331F001D4494 /* shannon.cpp */,
                                37D928230F21331F001D4494 /* sharedace.h */,
                                37D928220F21331F001D4494 /* sharedace.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 */,
                                37D9282A0F21331F001D4494 /* sharedjclass.cpp */,
                                37D9282D0F21331F001D4494 /* sharedjest.h */,
                                37D9282C0F21331F001D4494 /* sharedjest.cpp */,
-                               3709370A0F6E7FC100EB4C2C /* sharednseqs.h */,
+                               EB1217210F61C9AC004A865F /* sharedkstest.h */,
+                               EB1217220F61C9AC004A865F /* sharedkstest.cpp */,
+                               375874000F7D64EF0040F377 /* sharedkulczynski.h */,
+                               375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */,
+                               375874030F7D64EF0040F377 /* sharedkulczynskicody.h */,
+                               375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */,
+                               375874010F7D64EF0040F377 /* sharedlennon.h */,
+                               375873FF0F7D64EF0040F377 /* sharedlennon.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 */,
                        isa = PBXGroup;
                        children = (
                                37D927CD0F21331F001D4494 /* command.hpp */,
+                               37C1D9710F86506E0059E3F0 /* binsequencecommand.h */,
+                               37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */,
+                               21DDC0190F97A8FE0060691C /* bootstrapsharedcommand.h */,
+                               21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */,
                                37D927C40F21331F001D4494 /* clustercommand.h */,
                                37D927C30F21331F001D4494 /* clustercommand.cpp */,
                                37D927C80F21331F001D4494 /* collectcommand.h */,
                                A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */,
                                A70B53A90F4CD7AD0064797E /* getlinecommand.h */,
                                A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */,
+                               370B88050F8A4EE4005AB382 /* getoturepcommand.h */,
+                               370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */,
+                               375873F10F7D64800040F377 /* heatmapcommand.h */,
+                               375873F00F7D64800040F377 /* heatmapcommand.cpp */,
                                37D927E40F21331F001D4494 /* helpcommand.h */,
                                37D927E30F21331F001D4494 /* helpcommand.cpp */,
-                               374CD63D0F65832000D90B4A /* libshuffcommand.h */,
-                               374CD63E0F65832000D90B4A /* libshuffcommand.cpp */,
-                               3765B4790F77D15900C3EDC5 /* nocommands.h */,
-                               3765B4780F77D15900C3EDC5 /* nocommands.cpp */,
+                               375873F40F7D648F0040F377 /* libshuffcommand.h */,
+                               375873F30F7D648F0040F377 /* libshuffcommand.cpp */,
+                               375873F60F7D649C0040F377 /* nocommands.cpp */,
+                               375873F70F7D649C0040F377 /* nocommands.h */,
                                37D927FA0F21331F001D4494 /* parselistcommand.h */,
                                37D927F90F21331F001D4494 /* parselistcommand.cpp */,
                                3792946E0F2E191800B9034A /* parsimonycommand.h */,
                                37D928460F21331F001D4494 /* summarycommand.cpp */,
                                37D9284B0F21331F001D4494 /* summarysharedcommand.h */,
                                37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
+                               211C38370F961E1F00FEE541 /* treegroupscommand.h */,
+                               211C38360F961E1F00FEE541 /* treegroupscommand.cpp */,
                                3746109B0F40657600460C57 /* unifracunweightedcommand.h */,
                                3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */,
                                374610760F40645300460C57 /* unifracweightedcommand.h */,
                                374610770F40645300460C57 /* unifracweightedcommand.cpp */,
+                               37519A9F0F810D0200FED5E8 /* venncommand.h */,
+                               37519AA00F810D0200FED5E8 /* venncommand.cpp */,
                        );
                        name = commands;
                        sourceTree = "<group>";
                                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 */,
                                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 */,
                                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 */,
+                               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 */,
+                               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 */,
+                               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 */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
                                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",
                        buildSettings = {
                                DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
                                GCC_MODEL_TUNING = G5;
-                               GCC_OPTIMIZATION_LEVEL = 3;
                                INSTALL_PATH = /usr/local/bin;
                                PRODUCT_NAME = mothur;
                        };
                                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 = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
                        };
                                        ppc,
                                        i386,
                                );
-                               GCC_OPTIMIZATION_LEVEL = 0;
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
-                               INSTALL_MODE_FLAG = "a-w,a+rX";
                                PREBINDING = NO;
                                SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
                        };