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children = ( + A7A61F1A130035C800E05B6B /* LICENSE */, A70332B512D3A13400761E33 /* makefile */, A7E9B65912D37EC300DA6239 /* averagelinkage.cpp */, A7E9BA4F12D398D700DA6239 /* clearcut */, @@ -955,6 +975,12 @@ A7E9B75C12D37EC400DA6239 /* mothur.h */, A7E9B75D12D37EC400DA6239 /* mothurout.cpp */, A7E9B75E12D37EC400DA6239 /* mothurout.h */, + A7E9B76112D37EC400DA6239 /* nast.cpp */, + A7E9B76212D37EC400DA6239 /* nast.hpp */, + A7E9B76312D37EC400DA6239 /* nastreport.cpp */, + A7E9B76412D37EC400DA6239 /* nastreport.hpp */, + A7E9B76712D37EC400DA6239 /* noalign.cpp */, + A7E9B76812D37EC400DA6239 /* noalign.hpp */, A7E9B76512D37EC400DA6239 /* needlemanoverlap.cpp */, A7E9B76612D37EC400DA6239 /* needlemanoverlap.hpp */, A7E9B77012D37EC400DA6239 /* observable.h */, @@ -971,13 +997,9 @@ A7E9B7A912D37EC400DA6239 /* rarefact.cpp */, A7E9B7AA12D37EC400DA6239 /* rarefact.h */, A7E9B7AD12D37EC400DA6239 /* rarefactioncurvedata.h */, + 7E6BE10812F710D8007ADDBE /* refchimeratest.h */, + 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */, A7E9BA5312D39A5E00DA6239 /* read */, - A7E9B76112D37EC400DA6239 /* nast.cpp */, - A7E9B76212D37EC400DA6239 /* nast.hpp */, - A7E9B76312D37EC400DA6239 /* nastreport.cpp */, - A7E9B76412D37EC400DA6239 /* nastreport.hpp */, - A7E9B76712D37EC400DA6239 /* noalign.cpp */, - A7E9B76812D37EC400DA6239 /* noalign.hpp */, A7E9B82312D37EC400DA6239 /* sharedutilities.cpp */, A7E9B82412D37EC400DA6239 /* sharedutilities.h */, A7E9B82D12D37EC400DA6239 /* singlelinkage.cpp */, @@ -1014,6 +1036,10 @@ A7E9B6AE12D37EC400DA6239 /* command.hpp */, A7E9B65112D37EC300DA6239 /* aligncommand.cpp */, A7E9B65212D37EC300DA6239 /* aligncommand.h */, + A7A61F2B130062E000E05B6B /* amovacommand.h */, + A7A61F2C130062E000E05B6B /* amovacommand.cpp */, + A71CB15E130B04A2001E7287 /* anosimcommand.cpp */, + A71CB15F130B04A2001E7287 /* anosimcommand.h */, A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */, A7E9B66112D37EC300DA6239 /* binsequencecommand.h */, A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */, @@ -1100,12 +1126,18 @@ A7E9B72312D37EC400DA6239 /* heatmapsimcommand.h */, A7E9B72812D37EC400DA6239 /* helpcommand.cpp */, A7E9B72912D37EC400DA6239 /* helpcommand.h */, + A75790571301749D00A30DAB /* homovacommand.h */, + A75790581301749D00A30DAB /* homovacommand.cpp */, A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */, A7E9B72C12D37EC400DA6239 /* indicatorcommand.h */, A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */, A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */, A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */, A7E9B73E12D37EC400DA6239 /* listseqscommand.h */, + A7FA10001302E096003860FE /* mantelcommand.h */, + A7FA10011302E096003860FE /* mantelcommand.cpp */, + A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */, + A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */, A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */, A7E9B74412D37EC400DA6239 /* makegroupcommand.h */, A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */, @@ -1468,8 +1500,8 @@ A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */, A7E9B68912D37EC400DA6239 /* chimeraslayer.h */, A7E9B6C112D37EC400DA6239 /* decalc.cpp */, - A7E9B6C212D37EC400DA6239 /* decalc.h */, A7E9B74612D37EC400DA6239 /* maligner.h */, + A7E9B6C212D37EC400DA6239 /* decalc.h */, A7E9B74512D37EC400DA6239 /* maligner.cpp */, A7E9B79312D37EC400DA6239 /* pintail.cpp */, A7E9B79412D37EC400DA6239 /* pintail.h */, @@ -1593,7 +1625,7 @@ attributes = { ORGANIZATIONNAME = "Schloss Lab"; 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INSTALL_PATH = /usr/local/bin; PRODUCT_NAME = Mothur; + SDKROOT = macosx10.6; }; name = Debug; }; @@ -1934,16 +1973,17 @@ ARCHS = "$(ARCHS_STANDARD_32_64_BIT)"; DEPLOYMENT_LOCATION = NO; GCC_C_LANGUAGE_STANDARD = gnu99; - GCC_OPTIMIZATION_LEVEL = 0; + GCC_OPTIMIZATION_LEVEL = 3; GCC_PREPROCESSOR_DEFINITIONS = ( "MOTHUR_FILES=\"\\\"../release\\\"\"", - "VERSION=\"\\\"1.16.0\\\"\"", - "RELEASE_DATE=\"\\\"1/26/2010\\\"\"", + "VERSION=\"\\\"1.17.0\\\"\"", + "RELEASE_DATE=\"\\\"2/25/2011\\\"\"", ); GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_UNUSED_VARIABLE = YES; INSTALL_PATH = ""; + MACH_O_TYPE = mh_execute; ONLY_ACTIVE_ARCH = YES; OTHER_CPLUSPLUSFLAGS = ( "-DUSE_READLINE", @@ -1962,9 +2002,12 @@ 1DEB928B08733DD80010E9CD /* Release */ = { isa = XCBuildConfiguration; buildSettings = { - ARCHS = "$(ARCHS_STANDARD_32_64_BIT)"; + ARCHS = "$(NATIVE_ARCH_ACTUAL)"; DEPLOYMENT_LOCATION = NO; GCC_C_LANGUAGE_STANDARD = gnu99; + GCC_GENERATE_DEBUGGING_SYMBOLS = NO; 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