X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=511f0d65a1dcee18fc9b76a6b345845cf8e23417;hb=c8419b3c5f3c9381f4360f1fbdd95e6749827ff7;hp=7a32b803547870fb6ad5c2f96f8a7835504fd1b7;hpb=ffe79bafe77e733e3a8751114f0726b90058fbce;p=mothur.git diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 7a32b80..511f0d6 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -7,8 +7,16 @@ objects = { /* Begin PBXBuildFile section */ + 7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */; }; 8DD76FB00486AB0100D96B5E /* mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6A0FF2C0290799A04C91782 /* mothur.1 */; }; A70332B712D3A13400761E33 /* makefile in Sources */ = {isa = PBXBuildFile; fileRef = A70332B512D3A13400761E33 /* makefile */; }; + A713EBAC12DC7613000092AC /* readphylipvector.cpp in 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parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = ""; }; - A7E9B78712D37EC400DA6239 /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = ""; }; - A7E9B78812D37EC400DA6239 /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = ""; }; + A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcoacommand.cpp; sourceTree = ""; }; + A7E9B78812D37EC400DA6239 /* pcoacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcoacommand.h; sourceTree = ""; }; A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversity.cpp; sourceTree = ""; }; A7E9B78A12D37EC400DA6239 /* phylodiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversity.h; sourceTree = ""; }; A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversitycommand.cpp; sourceTree = ""; }; @@ -860,6 +888,12 @@ A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weightedlinkage.cpp; sourceTree = SOURCE_ROOT; }; A7E9B87F12D37EC400DA6239 /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = ""; }; A7E9B88012D37EC400DA6239 /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = ""; }; + A7FA10001302E096003860FE /* 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pcacommand.cpp; sourceTree = ""; }; C6A0FF2C0290799A04C91782 /* mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = mothur.1; sourceTree = ""; }; /* End PBXFileReference section */ @@ -887,6 +921,7 @@ 08FB7795FE84155DC02AAC07 /* Source */ = { isa = PBXGroup; children = ( + A7A61F1A130035C800E05B6B /* LICENSE */, A70332B512D3A13400761E33 /* makefile */, A7E9B65912D37EC300DA6239 /* averagelinkage.cpp */, A7E9BA4F12D398D700DA6239 /* clearcut */, @@ -930,11 +965,19 @@ A7E9B72D12D37EC400DA6239 /* inputdata.cpp */, A7E9B73912D37EC400DA6239 /* libshuff.cpp */, A7E9B73A12D37EC400DA6239 /* libshuff.h */, + A7FC480C12D788F20055BC5C /* linearalgebra.h */, + A7FC480D12D788F20055BC5C /* linearalgebra.cpp */, A7E9BA5612D39BD800DA6239 /* metastats */, A7E9B75B12D37EC400DA6239 /* mothur.cpp */, 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 */, @@ -951,13 +994,9 @@ 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 */, @@ -994,6 +1033,8 @@ A7E9B6AE12D37EC400DA6239 /* command.hpp */, A7E9B65112D37EC300DA6239 /* aligncommand.cpp */, A7E9B65212D37EC300DA6239 /* aligncommand.h */, + A7A61F2B130062E000E05B6B /* amovacommand.h */, + A7A61F2C130062E000E05B6B /* amovacommand.cpp */, A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */, A7E9B66112D37EC300DA6239 /* binsequencecommand.h */, A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */, @@ -1080,18 +1121,26 @@ 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 */, @@ -1100,6 +1149,8 @@ A7E9B76912D37EC400DA6239 /* nocommands.cpp */, A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */, A7E9B76C12D37EC400DA6239 /* normalizesharedcommand.h */, + A713EBEB12DC7C5E000092AC /* nmdscommand.h */, + A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */, A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */, A7E9B77A12D37EC400DA6239 /* otuhierarchycommand.h */, A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */, @@ -1110,8 +1161,10 @@ A7E9B78212D37EC400DA6239 /* parselistscommand.h */, A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */, A7E9B78612D37EC400DA6239 /* parsimonycommand.h */, - A7E9B78712D37EC400DA6239 /* pcacommand.cpp */, - A7E9B78812D37EC400DA6239 /* pcacommand.h */, + A7FC486512D795D60055BC5C /* pcacommand.h */, + A7FC486612D795D60055BC5C /* pcacommand.cpp */, + A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */, + A7E9B78812D37EC400DA6239 /* pcoacommand.h */, A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */, A7E9B78C12D37EC400DA6239 /* phylodiversitycommand.h */, A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */, @@ -1138,6 +1191,8 @@ A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */, A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */, A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */, + A727864212E9E28C00F86ABA /* removerarecommand.h */, + A727864312E9E28C00F86ABA /* removerarecommand.cpp */, A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */, A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */, A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */, @@ -1440,8 +1495,8 @@ 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 */, @@ -1511,6 +1566,8 @@ A7E9B7BE12D37EC400DA6239 /* readphylip.h */, A7E9B7BF12D37EC400DA6239 /* readtree.cpp */, A7E9B7C012D37EC400DA6239 /* readtree.h */, + A713EBAA12DC7613000092AC /* readphylipvector.h */, + A713EBAB12DC7613000092AC /* readphylipvector.cpp */, A7E9B84312D37EC400DA6239 /* splitmatrix.cpp */, A7E9B84412D37EC400DA6239 /* splitmatrix.h */, ); @@ -1560,7 +1617,10 @@ /* 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; @@ -1732,7 +1792,7 @@ A7E9B91212D37EC400DA6239 /* parselistscommand.cpp in Sources */, A7E9B91312D37EC400DA6239 /* parsimony.cpp in Sources */, A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */, - A7E9B91512D37EC400DA6239 /* pcacommand.cpp in Sources */, + A7E9B91512D37EC400DA6239 /* pcoacommand.cpp in Sources */, A7E9B91612D37EC400DA6239 /* phylodiversity.cpp in Sources */, A7E9B91712D37EC400DA6239 /* phylodiversitycommand.cpp in Sources */, A7E9B91812D37EC400DA6239 /* phylosummary.cpp in Sources */, @@ -1856,6 +1916,17 @@ A7E9B98E12D37EC400DA6239 /* weightedlinkage.cpp in Sources */, A7E9B98F12D37EC400DA6239 /* whittaker.cpp in Sources */, A70332B712D3A13400761E33 /* makefile in Sources */, + A7FC480E12D788F20055BC5C /* linearalgebra.cpp in Sources */, + 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 */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -1895,15 +1966,17 @@ ARCHS = "$(ARCHS_STANDARD_32_64_BIT)"; DEPLOYMENT_LOCATION = NO; GCC_C_LANGUAGE_STANDARD = gnu99; - GCC_OPTIMIZATION_LEVEL = 0; + GCC_OPTIMIZATION_LEVEL = 3; GCC_PREPROCESSOR_DEFINITIONS = ( "MOTHUR_FILES=\"\\\"../release\\\"\"", - "VERSION=\"\\\"1.15.0\\\"\"", - "RELEASE_DATE=\"\\\"12/10/2010\\\"\"", + "VERSION=\"\\\"1.16.0\\\"\"", + "RELEASE_DATE=\"\\\"2/7/2011\\\"\"", ); + GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_UNUSED_VARIABLE = YES; INSTALL_PATH = ""; + MACH_O_TYPE = mh_execute; ONLY_ACTIVE_ARCH = YES; OTHER_CPLUSPLUSFLAGS = ( "-DUSE_READLINE", @@ -1925,6 +1998,9 @@ ARCHS = "$(ARCHS_STANDARD_32_64_BIT)"; 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\\\"\"", @@ -1939,6 +2015,7 @@ GCC_WARN_UNUSED_VALUE = YES; GCC_WARN_UNUSED_VARIABLE = YES; INSTALL_PATH = ""; + MACH_O_TYPE = mh_execute; OTHER_CPLUSPLUSFLAGS = ( "-DUSE_READLINE", "-DBIT_VERSION", @@ -1965,7 +2042,7 @@ defaultConfigurationIsVisible = 0; defaultConfigurationName = Release; }; - 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */ = { + 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = { isa = XCConfigurationList; buildConfigurations = ( 1DEB928A08733DD80010E9CD /* Debug */,