X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=80b05db9c02288a1c91fb0085c13426774d06fc7;hp=b09bab447e3307bc279189d5e5b5dae30a677e7a;hb=d1faab5efe1c28700890bdec5b4d8e817fa1dab2;hpb=372fb21ea66ced432b109225851a1b80ef0491a3 diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index b09bab4..80b05db 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -9,6 +9,8 @@ /* Begin PBXBuildFile section */ 219C1DE01552C4BD004209F9 /* newcommandtemplate.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 219C1DDF1552C4BD004209F9 /* newcommandtemplate.cpp */; }; 219C1DE41559BCCF004209F9 /* getcoremicrobiomecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */; }; + 483C952E188F0CAD0035E7B7 /* sharedrjsd.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 483C952D188F0CAD0035E7B7 /* sharedrjsd.cpp */; }; + 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Sources */ = {isa = PBXBuildFile; fileRef = A7128B1C16B7002600723BE4 /* getdistscommand.cpp */; }; + A7132EB3184E792700AAA402 /* communitytype.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7132EB2184E792700AAA402 /* communitytype.cpp */; }; A713EBAC12DC7613000092AC /* readphylipvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBAB12DC7613000092AC /* readphylipvector.cpp */; }; A713EBED12DC7C5E000092AC /* nmdscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */; }; A7190B221768E0DF00A9AFA6 /* lefsecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7190B201768E0DF00A9AFA6 /* lefsecommand.cpp */; }; @@ -29,9 +32,9 @@ A721AB71161C572A009860A1 /* kmernode.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A721AB6D161C572A009860A1 /* kmernode.cpp */; }; A721AB72161C572A009860A1 /* kmertree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A721AB6F161C572A009860A1 /* kmertree.cpp */; }; A721AB77161C573B009860A1 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/* heatmapcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapcommand.cpp; sourceTree = ""; }; @@ -1093,6 +1118,8 @@ A7E9B88012D37EC400DA6239 /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = ""; }; A7EEB0F414F29BFD00344B83 /* classifytreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifytreecommand.cpp; sourceTree = ""; }; A7EEB0F714F29C1B00344B83 /* classifytreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifytreecommand.h; sourceTree = ""; }; + A7F24FC117EA365F0021DC9A /* classifyrfsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifyrfsharedcommand.cpp; sourceTree = ""; }; + A7F24FC217EA365F0021DC9A /* classifyrfsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifyrfsharedcommand.h; sourceTree = ""; }; A7F9F5CD141A5E500032F693 /* sequenceparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sequenceparser.h; sourceTree = ""; }; A7F9F5CE141A5E500032F693 /* sequenceparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequenceparser.cpp; sourceTree = ""; }; A7FA10001302E096003860FE /* mantelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mantelcommand.h; sourceTree = ""; }; @@ -1172,6 +1199,7 @@ A7E9B6B112D37EC400DA6239 /* commandoptionparser.cpp */, A7E9B6B212D37EC400DA6239 /* commandoptionparser.hpp */, A7DAAFA3133A254E003956EB /* commandparameter.h */, + A7D395C1184FA34300A350D7 /* communitytype */, A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */, A7E9BA4212D3960D00DA6239 /* containers */, A7E9B6B612D37EC400DA6239 /* consensus.h */, @@ -1199,6 +1227,8 @@ A7E9B73A12D37EC400DA6239 /* libshuff.h */, A7FC480C12D788F20055BC5C /* linearalgebra.h */, A7FC480D12D788F20055BC5C /* linearalgebra.cpp */, + A7D9378B17B15215001E90B0 /* wilcox.h */, + A7D9378917B146B5001E90B0 /* wilcox.cpp */, A7E9BA5612D39BD800DA6239 /* metastats */, A7E9B75B12D37EC400DA6239 /* mothur.cpp */, A7E9B75C12D37EC400DA6239 /* mothur.h */, @@ -1221,8 +1251,6 @@ A7E9B77C12D37EC400DA6239 /* overlap.hpp */, A7E9B79B12D37EC400DA6239 /* progress.cpp */, A7E9B79C12D37EC400DA6239 /* progress.hpp */, - A7548FAF171440ED00B1F05A /* qFinderDMM.h */, - A7548FAE171440EC00B1F05A /* qFinderDMM.cpp */, A77B7187173D4041002163C2 /* randomnumber.h */, A77B7186173D4041002163C2 /* randomnumber.cpp */, A7E9B7A512D37EC400DA6239 /* rarecalc.cpp */, @@ -1310,6 +1338,21 @@ name = fortran; sourceTree = ""; }; + A7D395C1184FA34300A350D7 /* communitytype */ = { + isa = PBXGroup; + children = ( + A7132EAE184E76EB00AAA402 /* communitytype.h */, + A7132EB2184E792700AAA402 /* communitytype.cpp */, + A7D395C2184FA39300A350D7 /* kmeans.h */, + A7D395C3184FA3A200A350D7 /* kmeans.cpp */, + A7B093BE18579EF600843CD1 /* pam.h */, + A7B093BF18579F0400843CD1 /* pam.cpp */, + A7548FAF171440ED00B1F05A /* qFinderDMM.h */, + A7548FAE171440EC00B1F05A /* qFinderDMM.cpp */, + ); + name = communitytype; + sourceTree = ""; + }; A7E9BA3812D3956100DA6239 /* commands */ = { isa = PBXGroup; children = ( @@ -1346,8 +1389,8 @@ A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */, A7E9B69312D37EC400DA6239 /* classifyseqscommand.h */, A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */, - A7386C221619CCE600651424 /* classifysharedcommand.h */, - A7386C211619CCE600651424 /* classifysharedcommand.cpp */, + A7F24FC217EA365F0021DC9A /* classifyrfsharedcommand.h */, + A7F24FC117EA365F0021DC9A /* classifyrfsharedcommand.cpp */, A7EEB0F714F29C1B00344B83 /* classifytreecommand.h */, A7EEB0F414F29BFD00344B83 /* classifytreecommand.cpp */, A7E9B69712D37EC400DA6239 /* clearcutcommand.h */, @@ -1472,6 +1515,8 @@ A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */, A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */, A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */, + 48E981CD189C38E60042BE9D /* mergesfffilecommand.h */, + 48E981CE189C38FB0042BE9D /* mergesfffilecommand.cpp */, A799314816CBD0BC0017E888 /* mergetaxsummarycommand.h */, A799314A16CBD0CD0017E888 /* mergetaxsummarycommand.cpp */, A7E9B75812D37EC400DA6239 /* metastatscommand.h */, @@ -1570,6 +1615,8 @@ A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */, A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */, A7E9B84112D37EC400DA6239 /* splitgroupscommand.cpp */, + A747EC6F181EA0E500345732 /* sracommand.h */, + A747EC70181EA0F900345732 /* sracommand.cpp */, A7E9B85012D37EC400DA6239 /* subsamplecommand.h */, A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */, A7E9B85812D37EC400DA6239 /* summarycommand.h */, @@ -1673,7 +1720,10 @@ A7E9B7E612D37EC400DA6239 /* shannon.h */, A7E9B7E712D37EC400DA6239 /* shannoneven.cpp */, A7E9B7E812D37EC400DA6239 /* shannoneven.h */, + A7A09B0E18773BF700FAA081 /* shannonrange.h */, + A7A09B0F18773C0E00FAA081 /* shannonrange.cpp */, A7E9B7E912D37EC400DA6239 /* sharedace.cpp */, + A7E9B7F412D37EC400DA6239 /* sharedjabund.cpp */, A7E9B7EA12D37EC400DA6239 /* sharedace.h */, A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */, A7E9B7ED12D37EC400DA6239 /* sharedanderbergs.h */, @@ -1681,7 +1731,6 @@ A7E9B7EF12D37EC400DA6239 /* sharedbraycurtis.h */, A7E9B7F012D37EC400DA6239 /* sharedchao1.cpp */, A7E9B7F112D37EC400DA6239 /* sharedchao1.h */, - A7E9B7F412D37EC400DA6239 /* sharedjabund.cpp */, A7E9B7F512D37EC400DA6239 /* sharedjabund.h */, A7E9B7F612D37EC400DA6239 /* sharedjackknife.cpp */, A7E9B7F712D37EC400DA6239 /* sharedjackknife.h */, @@ -1689,6 +1738,10 @@ A7E9B7F912D37EC400DA6239 /* sharedjclass.h */, A7E9B7FA12D37EC400DA6239 /* sharedjest.cpp */, A7E9B7FB12D37EC400DA6239 /* sharedjest.h */, + A7222D711856276C0055A993 /* sharedjsd.h */, + A7222D721856277C0055A993 /* sharedjsd.cpp */, + 483C952C188F0C960035E7B7 /* sharedrjsd.h */, + 483C952D188F0CAD0035E7B7 /* sharedrjsd.cpp */, A7E9B7FC12D37EC400DA6239 /* sharedkstest.cpp */, A7E9B7FD12D37EC400DA6239 /* sharedkstest.h */, A7E9B7FE12D37EC400DA6239 /* sharedkulczynski.cpp */, @@ -2054,6 +2107,7 @@ A7E9B89712D37EC400DA6239 /* chimerabellerophoncommand.cpp in Sources */, A7E9B89812D37EC400DA6239 /* chimeraccodecommand.cpp in Sources */, A7E9B89912D37EC400DA6239 /* chimeracheckcommand.cpp in Sources */, + 48E981CF189C38FB0042BE9D /* mergesfffilecommand.cpp in Sources */, A7E9B89A12D37EC400DA6239 /* chimeracheckrdp.cpp in Sources */, A7E9B89B12D37EC400DA6239 /* chimerapintailcommand.cpp in Sources */, A7E9B89C12D37EC400DA6239 /* chimerarealigner.cpp in Sources */, @@ -2215,6 +2269,7 @@ A7E9B94112D37EC400DA6239 /* setlogfilecommand.cpp in Sources */, A7E9B94212D37EC400DA6239 /* sffinfocommand.cpp in Sources */, A7E9B94312D37EC400DA6239 /* shannon.cpp in Sources */, + 483C952E188F0CAD0035E7B7 /* sharedrjsd.cpp in Sources */, A7E9B94412D37EC400DA6239 /* shannoneven.cpp in Sources */, A7E9B94512D37EC400DA6239 /* sharedace.cpp in Sources */, A7E9B94612D37EC400DA6239 /* sharedanderbergs.cpp in Sources */, @@ -2359,7 +2414,6 @@ A7E0243D15B4520A00A5F046 /* sparsedistancematrix.cpp in Sources */, A741FAD215D1688E0067BCC5 /* sequencecountparser.cpp in Sources */, A7C7DAB915DA758B0059B0CF /* sffmultiplecommand.cpp in Sources */, - A7386C231619CCE600651424 /* classifysharedcommand.cpp in Sources */, A7386C251619E52300651424 /* abstractdecisiontree.cpp in Sources */, A7386C29161A110800651424 /* decisiontree.cpp in Sources */, A77E1938161B201E00DB1A2A /* randomforest.cpp in Sources */, @@ -2388,6 +2442,14 @@ A741744C175CD9B1007DF49B /* makelefsecommand.cpp in Sources */, A7190B221768E0DF00A9AFA6 /* lefsecommand.cpp in Sources */, A77916E8176F7F7600EEFE18 /* designmap.cpp in Sources */, + A7D9378A17B146B5001E90B0 /* wilcox.cpp in Sources */, + A7F24FC317EA36600021DC9A /* classifyrfsharedcommand.cpp in Sources */, + A747EC71181EA0F900345732 /* sracommand.cpp in Sources */, + A7132EB3184E792700AAA402 /* communitytype.cpp in Sources */, + A7D395C4184FA3A200A350D7 /* kmeans.cpp in Sources */, + A7222D731856277C0055A993 /* sharedjsd.cpp in Sources */, + A7B093C018579F0400843CD1 /* pam.cpp in Sources */, + A7A09B1018773C0E00FAA081 /* shannonrange.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -2404,10 +2466,10 @@ "DSTROOT[sdk=*]" = TARGET_BUILD_DIR; GCC_DYNAMIC_NO_PIC = NO; GCC_MODEL_TUNING = G5; - GCC_OPTIMIZATION_LEVEL = 3; + GCC_OPTIMIZATION_LEVEL = 0; "INSTALL_PATH[sdk=*]" = TARGET_BUILD_DIR; PRODUCT_NAME = mothur; - SDKROOT = macosx10.8; + SDKROOT = macosx; SKIP_INSTALL = NO; }; name = Debug; @@ -2420,7 +2482,7 @@ DEPLOYMENT_LOCATION = YES; DSTROOT = TARGET_BUILD_DIR; GCC_MODEL_TUNING = G5; - GCC_OPTIMIZATION_LEVEL = 3; + GCC_OPTIMIZATION_LEVEL = 0; GCC_WARN_UNUSED_VALUE = YES; PRODUCT_NAME = mothur; SDKROOT = macosx; @@ -2437,12 +2499,13 @@ GCC_ENABLE_SSE3_EXTENSIONS = NO; GCC_ENABLE_SSE41_EXTENSIONS = NO; GCC_ENABLE_SSE42_EXTENSIONS = NO; - GCC_OPTIMIZATION_LEVEL = s; + GCC_OPTIMIZATION_LEVEL = 3; GCC_PREPROCESSOR_DEFINITIONS = ( - "MOTHUR_FILES=\"\\\"../../release\\\"\"", - "VERSION=\"\\\"1.31.0\\\"\"", - "RELEASE_DATE=\"\\\"5/24/2013\\\"\"", + "MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"", + "VERSION=\"\\\"1.33.0\\\"\"", + "RELEASE_DATE=\"\\\"2/7/2014\\\"\"", ); + GCC_VERSION = ""; "GCC_VERSION[arch=*]" = ""; GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; @@ -2460,7 +2523,7 @@ "-lncurses", "-lreadline", ); - SDKROOT = macosx; + SDKROOT = macosx10.8; SKIP_INSTALL = NO; USER_HEADER_SEARCH_PATHS = ""; }; @@ -2474,11 +2537,12 @@ GCC_C_LANGUAGE_STANDARD = gnu99; GCC_GENERATE_DEBUGGING_SYMBOLS = NO; GCC_MODEL_TUNING = ""; - GCC_OPTIMIZATION_LEVEL = s; + GCC_OPTIMIZATION_LEVEL = 3; GCC_PREPROCESSOR_DEFINITIONS = ( - "VERSION=\"\\\"1.31.0\\\"\"", - "RELEASE_DATE=\"\\\"5/24/2013\\\"\"", + "VERSION=\"\\\"1.32.1\\\"\"", + "RELEASE_DATE=\"\\\"10/16/2013\\\"\"", ); + GCC_VERSION = ""; GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; GCC_WARN_MISSING_PARENTHESES = YES; @@ -2498,7 +2562,7 @@ "-lncurses", "-lreadline", ); - SDKROOT = macosx; + SDKROOT = macosx10.8; SKIP_INSTALL = NO; }; name = Release;