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/* LICENSE */, A70332B512D3A13400761E33 /* makefile */, A7E9B65912D37EC300DA6239 /* averagelinkage.cpp */, A7E9BA4F12D398D700DA6239 /* clearcut */, @@ -920,6 +953,7 @@ A7E9B6B212D37EC400DA6239 /* commandoptionparser.hpp */, A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */, A7E9BA4212D3960D00DA6239 /* containers */, + A7AACFBA132FE008003D6C4D /* currentfile.h */, A7E9B6C912D37EC400DA6239 /* display.h */, A7E9B6D112D37EC400DA6239 /* dlibshuff.cpp */, A7E9B6D212D37EC400DA6239 /* dlibshuff.h */, @@ -949,6 +983,12 @@ 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 */, @@ -965,13 +1005,9 @@ 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 */, @@ -1008,6 +1044,10 @@ 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 */, @@ -1062,6 +1102,8 @@ A7E9B6CC12D37EC400DA6239 /* distancecommand.h */, A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */, A7E9B6E412D37EC400DA6239 /* filterseqscommand.h */, + A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */, + A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */, A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */, A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */, A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */, @@ -1094,18 +1136,26 @@ 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 */, A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */, A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */, A7E9B75412D37EC400DA6239 /* mergefilecommand.h */, + A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */, + A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */, A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */, A7E9B75812D37EC400DA6239 /* metastatscommand.h */, A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */, @@ -1156,6 +1206,8 @@ A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */, A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */, A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */, + A727864212E9E28C00F86ABA /* removerarecommand.h */, + A727864312E9E28C00F86ABA /* removerarecommand.cpp */, A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */, A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */, A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */, @@ -1170,6 +1222,8 @@ A7E9B7D812D37EC400DA6239 /* seqerrorcommand.h */, A7E9B7D912D37EC400DA6239 /* seqsummarycommand.cpp */, A7E9B7DA12D37EC400DA6239 /* seqsummarycommand.h */, + A7FE7E6B13311EA400F7B327 /* setcurrentcommand.h */, + A7FE7E6C13311EA400F7B327 /* setcurrentcommand.cpp */, A7E9B7DF12D37EC400DA6239 /* setdircommand.cpp */, A7E9B7E012D37EC400DA6239 /* setdircommand.h */, A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */, @@ -1458,8 +1512,8 @@ 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 */, @@ -1580,7 +1634,10 @@ /* Begin PBXProject section */ 08FB7793FE84155DC02AAC07 /* Project object */ = { isa = PBXProject; - buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */; + attributes = { + ORGANIZATIONNAME = "Schloss Lab"; + }; + buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */; compatibilityVersion = "Xcode 3.1"; developmentRegion = English; hasScannedForEncodings = 1; @@ -1880,6 +1937,16 @@ A7FC486712D795D60055BC5C /* pcacommand.cpp in Sources */, A713EBAC12DC7613000092AC /* readphylipvector.cpp in Sources */, A713EBED12DC7C5E000092AC /* nmdscommand.cpp in Sources */, + A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */, + A71FE12C12EDF72400963CA7 /* mergegroupscommand.cpp in Sources */, + 7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */, + A7A61F2D130062E000E05B6B /* amovacommand.cpp in Sources */, + A75790591301749D00A30DAB /* homovacommand.cpp in Sources */, + A7FA10021302E097003860FE /* mantelcommand.cpp in Sources */, + A799F5B91309A3E000AEEFA0 /* makefastqcommand.cpp in Sources */, + A71CB160130B04A2001E7287 /* anosimcommand.cpp in Sources */, + A7FE7C401330EA1000F7B327 /* getcurrentcommand.cpp in Sources */, + A7FE7E6D13311EA400F7B327 /* setcurrentcommand.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -1897,6 +1964,7 @@ GCC_OPTIMIZATION_LEVEL = 0; INSTALL_PATH = /usr/local/bin; PRODUCT_NAME = Mothur; + SDKROOT = macosx10.6; }; name = Debug; }; @@ -1916,22 +1984,24 @@ 1DEB928A08733DD80010E9CD /* Debug */ = { isa = XCBuildConfiguration; buildSettings = { - ARCHS = "$(ARCHS_STANDARD_32_64_BIT)"; + ARCHS = "$(ARCHS_STANDARD_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=\"\\\"1.15.0\\\"\"", - "RELEASE_DATE=\"\\\"12/10/2010\\\"\"", + "VERSION=\"\\\"1.17.3\\\"\"", + "RELEASE_DATE=\"\\\"3/07/2011\\\"\"", ); + 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", "-DBIT_VERSION", + "-DUSE_READLINE", "$(OTHER_CFLAGS)", ); OTHER_LDFLAGS = ( @@ -1939,16 +2009,19 @@ "-lreadline", ); PREBINDING = NO; - SDKROOT = macosx10.5; + SDKROOT = macosx10.6; }; name = Debug; }; 1DEB928B08733DD80010E9CD /* Release */ = { isa = XCBuildConfiguration; buildSettings = { - ARCHS = "$(ARCHS_STANDARD_32_64_BIT)"; + ARCHS = "$(NATIVE_ARCH_ACTUAL)"; DEPLOYMENT_LOCATION = NO; GCC_C_LANGUAGE_STANDARD = gnu99; + GCC_GENERATE_DEBUGGING_SYMBOLS = NO; + GCC_MODEL_TUNING = ""; + GCC_OPTIMIZATION_LEVEL = 3; GCC_PREPROCESSOR_DEFINITIONS = ( "MOTHUR_FILES=\"\\\"../release\\\"\"", "VERSION=\"\\\"1.15.0\\\"\"", @@ -1963,6 +2036,7 @@ GCC_WARN_UNUSED_VALUE = YES; GCC_WARN_UNUSED_VARIABLE = YES; INSTALL_PATH = ""; + MACH_O_TYPE = mh_execute; OTHER_CPLUSPLUSFLAGS = ( "-DUSE_READLINE", "-DBIT_VERSION", @@ -1973,7 +2047,7 @@ "-lreadline", ); PREBINDING = NO; - SDKROOT = macosx10.5; + SDKROOT = ""; }; name = Release; }; @@ -1989,7 +2063,7 @@ defaultConfigurationIsVisible = 0; defaultConfigurationName = Release; }; - 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */ = { + 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = { isa = XCConfigurationList; buildConfigurations = ( 1DEB928A08733DD80010E9CD /* Debug */,