]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
added the Calculators Thomas made in the fall. Added parameter and command error...
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index a403f35250d8e910f63798ac2ae26e46798b810c..b34805bab97accaebdd0b539420c7f0dfd4ca03d 100644 (file)
@@ -14,7 +14,6 @@
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@@ -50,7 +49,6 @@
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                                37D928200F21331F001D4494 /* shared.cpp */,
                                37D928420F21331F001D4494 /* singlelinkage.cpp */,
+                               37D928450F21331F001D4494 /* sparsematrix.hpp */,
+                               37D928440F21331F001D4494 /* sparsematrix.cpp */,
                                37D928480F21331F001D4494 /* summarydata.h */,
                                37D928490F21331F001D4494 /* summarydisplay.h */,
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                                37D927BF0F21331F001D4494 /* chao1.cpp */,
+                               EB9303F70F53517300E8EF26 /* geom.h */,
+                               EB9303F80F53517300E8EF26 /* geom.cpp */,
+                               EB6E68170F5F1C780044E17B /* qstat.h */,
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+                               EB9303E90F534D9400E8EF26 /* logsd.h */,
+                               EB9303EA0F534D9400E8EF26 /* logsd.cpp */,
+                               EB1216860F619B83004A865F /* bergerparker.h */,
+                               EB1216870F619B83004A865F /* bergerparker.cpp */,
+                               EB1216E30F61ACFB004A865F /* bstick.h */,
+                               EB1216E40F61ACFB004A865F /* bstick.cpp */,
+                               EB1217210F61C9AC004A865F /* sharedkstest.h */,
+                               EB1217220F61C9AC004A865F /* sharedkstest.cpp */,
+                               EB6F01590F6AC1670048081A /* sharedbdiversity.h */,
+                               EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */,
+                               EBE2A41C0F7D5C5C00A54BF8 /* jackknife2.h */,
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                                37D927E70F21331F001D4494 /* jackknife.cpp */,
                                37D927F50F21331F001D4494 /* npshannon.h */,
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                                37D928300F21331F001D4494 /* sharedrabundvector.cpp */,
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                                37D928320F21331F001D4494 /* sharedsabundvector.cpp */,
-                               37D928450F21331F001D4494 /* sparsematrix.hpp */,
-                               37D928440F21331F001D4494 /* sparsematrix.cpp */,
                                37AD4DB90F28E2FE00AA2D49 /* tree.h */,
                                37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */,
                                379293C10F2DE73400B9034A /* treemap.h */,
                                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 */,
                                A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */,
                                A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */,
                                A70B53AC0F4CD7AD0064797E /* getlinecommand.cpp in Sources */,
-                               3782163D0F616079008E1F6D /* fullmatrix.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 */,
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                        );
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-                               GCC_OPTIMIZATION_LEVEL = 3;
+                               GCC_OPTIMIZATION_LEVEL = 0;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "_GLIBCXX_DEBUG=1",
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                                GCC_MODEL_TUNING = G5;
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                                INSTALL_PATH = /usr/local/bin;
                                PRODUCT_NAME = mothur;
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                                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 = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
                        };
                                GCC_OPTIMIZATION_LEVEL = 0;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
-                               INSTALL_MODE_FLAG = "a-w,a+rX";
                                PREBINDING = NO;
                                SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
                        };