X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=8a540e6c4e8c4d975245f357fa86a3a206b6fafa;hb=9946a1b4b50969d08ce059b248bdeecafbf989ac;hp=f07824e75ecdba89c37fddc31316861b23d958d8;hpb=30c1fd8c45b6f0d66c17f2714dbb58b8ddccdce2;p=mothur.git diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index f07824e..8a540e6 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -7,6 +7,42 @@ objects = { /* Begin PBXFileReference section */ + 7EC61A0911BEA6AF00F668D9 /* weightedlinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weightedlinkage.cpp; sourceTree = ""; }; + A703FE931194645F002C397E /* makegroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makegroupcommand.h; sourceTree = SOURCE_ROOT; }; + A703FE941194645F002C397E /* makegroupcommand.cpp */ = {isa = PBXFileReference; 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alignment.hpp */, A7DA1FF6113FECD400BF472F /* averagelinkage.cpp */, @@ -534,6 +573,8 @@ A7DA20B0113FECD400BF472F /* nseqs.h */, A7DA20B2113FECD400BF472F /* onegapdist.h */, A7DA20B3113FECD400BF472F /* onegapignore.h */, + A72B3A7B118B4D1B004B9F8D /* phylodiversity.h */, + A72B3A7C118B4D1B004B9F8D /* phylodiversity.cpp */, A7DA20BE113FECD400BF472F /* parsimony.cpp */, A7DA20BF113FECD400BF472F /* parsimony.h */, A7DA20CE113FECD400BF472F /* qstat.cpp */, @@ -600,6 +641,7 @@ A7DA2170113FECD400BF472F /* uvest.h */, A7DA2179113FECD400BF472F /* weighted.cpp */, A7DA217A113FECD400BF472F /* weighted.h */, + 7EC61A0911BEA6AF00F668D9 /* weightedlinkage.cpp */, A7DA217B113FECD400BF472F /* whittaker.cpp */, A7DA217C113FECD400BF472F /* whittaker.h */, ); @@ -612,16 +654,36 @@ A7DA202B113FECD400BF472F /* command.hpp */, A7DA1FEF113FECD400BF472F /* aligncommand.h */, A7DA1FEE113FECD400BF472F /* aligncommand.cpp */, - A7DA1FFD113FECD400BF472F /* binsequencecommand.cpp */, A7DA1FFE113FECD400BF472F /* 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A747E81D116365E000FB9042 /* chimeraslayercommand.cpp */, + A73953DA11987ED100B0B160 /* chopseqscommand.h */, + A73953DB11987ED100B0B160 /* chopseqscommand.cpp */, A7DA201E113FECD400BF472F /* classifyseqscommand.h */, + A7DA201D113FECD400BF472F /* classifyseqscommand.cpp */, + A7BBDA7B11B5694E006E6551 /* classifyotucommand.h */, + A7BBDA7C11B5694E006E6551 /* classifyotucommand.cpp */, + A7D215C811996C6E00F13F13 /* clearcutcommand.h */, + A7D215C911996C6E00F13F13 /* clearcutcommand.cpp */, A7DA2021113FECD400BF472F /* clustercommand.cpp */, A7DA2022113FECD400BF472F /* clustercommand.h */, + A71D924311AEB42400D00CBC /* clustersplitcommand.h */, + A71D924211AEB42400D00CBC /* clustersplitcommand.cpp */, A7DA2025113FECD400BF472F /* collectcommand.cpp */, A7DA2026113FECD400BF472F /* collectcommand.h */, A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */, @@ -638,16 +700,16 @@ A7DA205B113FECD400BF472F /* getgroupcommand.h */, A7DA205C113FECD400BF472F /* getlabelcommand.cpp */, A7DA205D113FECD400BF472F /* getlabelcommand.h */, - A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */, A7DA205F113FECD400BF472F /* getlistcountcommand.h */, - A7DA2060113FECD400BF472F /* getoturepcommand.cpp */, + A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */, A7DA2061113FECD400BF472F /* getoturepcommand.h */, + A7DA2060113FECD400BF472F /* getoturepcommand.cpp */, A7DA2062113FECD400BF472F /* getrabundcommand.cpp */, A7DA2063113FECD400BF472F /* getrabundcommand.h */, A7DA2064113FECD400BF472F /* getsabundcommand.cpp */, A7DA2065113FECD400BF472F /* getsabundcommand.h */, - A7DA2066113FECD400BF472F /* getseqscommand.cpp */, A7DA2067113FECD400BF472F /* getseqscommand.h */, + A7DA2066113FECD400BF472F /* getseqscommand.cpp */, A7DA2068113FECD400BF472F /* getsharedotucommand.cpp */, A7DA2069113FECD400BF472F /* getsharedotucommand.h */, A7DA2074113FECD400BF472F /* hclustercommand.cpp */, @@ -660,8 +722,10 @@ A7DA207F113FECD400BF472F /* helpcommand.h */, A7DA208D113FECD400BF472F /* libshuffcommand.cpp */, A7DA208E113FECD400BF472F /* libshuffcommand.h */, - A7DA208F113FECD400BF472F /* listseqscommand.cpp */, A7DA2090113FECD400BF472F /* listseqscommand.h */, + A7DA208F113FECD400BF472F /* listseqscommand.cpp */, + A703FE931194645F002C397E /* makegroupcommand.h */, + A703FE941194645F002C397E /* makegroupcommand.cpp */, A7DA2098113FECD400BF472F /* matrixoutputcommand.cpp */, A7DA2099113FECD400BF472F /* matrixoutputcommand.h */, A7DA209A113FECD400BF472F /* mergefilecommand.cpp */, @@ -674,56 +738,64 @@ A7DA20B9113FECD400BF472F /* otuhierarchycommand.h */, A7DA20BC113FECD400BF472F /* parselistscommand.cpp */, A7DA20BD113FECD400BF472F /* parselistscommand.h */, + A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */, + A7E8338C115BBDAA00739EC4 /* parsesffcommand.h */, A7DA20C0113FECD400BF472F /* parsimonycommand.cpp */, A7DA20C1113FECD400BF472F /* parsimonycommand.h */, - A7DA20C2113FECD400BF472F /* pcacommand.cpp */, A7DA20C3113FECD400BF472F /* pcacommand.h */, - 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rarefactsharedcommand.cpp */, A7DA20E6113FECD400BF472F /* readdistcommand.h */, - A7DA20EA113FECD400BF472F /* readotucommand.cpp */, + A7DA20E5113FECD400BF472F /* readdistcommand.cpp */, A7DA20EB113FECD400BF472F /* readotucommand.h */, - A7DA20F0113FECD400BF472F /* readtreecommand.cpp */, + A7DA20EA113FECD400BF472F /* readotucommand.cpp */, A7DA20F1113FECD400BF472F /* readtreecommand.h */, - A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */, + A7DA20F0113FECD400BF472F /* readtreecommand.cpp */, A7DA20F3113FECD400BF472F /* removeseqscommand.h */, - A7DA20F4113FECD400BF472F /* reversecommand.cpp */, + A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */, A7DA20F5113FECD400BF472F /* reversecommand.h */, - A7DA20F8113FECD400BF472F /* screenseqscommand.cpp */, + A7DA20F4113FECD400BF472F /* reversecommand.cpp */, A7DA20F9113FECD400BF472F /* screenseqscommand.h */, - A7DA20FA113FECD400BF472F /* secondarystructurecommand.cpp */, + A7DA20F8113FECD400BF472F /* screenseqscommand.cpp */, A7DA20FB113FECD400BF472F /* secondarystructurecommand.h */, - A7DA20FC113FECD400BF472F /* seqsummarycommand.cpp */, + A7DA20FA113FECD400BF472F /* secondarystructurecommand.cpp */, A7DA20FD113FECD400BF472F /* seqsummarycommand.h */, - A7DA2102113FECD400BF472F /* setdircommand.cpp */, + A7DA20FC113FECD400BF472F /* seqsummarycommand.cpp */, A7DA2103113FECD400BF472F /* setdircommand.h */, - A7DA210F113FECD400BF472F /* sharedcommand.cpp */, + A7DA2102113FECD400BF472F /* setdircommand.cpp */, + A76C4A1011876BAF0009460B /* setlogfilecommand.h */, + A76C4A1111876BAF0009460B /* setlogfilecommand.cpp */, A7DA2110113FECD400BF472F /* sharedcommand.h */, - A7DA2154113FECD400BF472F /* summarycommand.cpp */, + A7DA210F113FECD400BF472F /* sharedcommand.cpp */, + A71D924511AEB42400D00CBC /* splitabundcommand.h */, + A71D924411AEB42400D00CBC /* splitabundcommand.cpp */, A7DA2155113FECD400BF472F /* summarycommand.h */, - A7DA2158113FECD400BF472F /* summarysharedcommand.cpp */, + A7DA2154113FECD400BF472F /* summarycommand.cpp */, A7DA2159113FECD400BF472F /* summarysharedcommand.h */, - A7DA215A113FECD400BF472F /* systemcommand.cpp */, + A7DA2158113FECD400BF472F /* summarysharedcommand.cpp */, A7DA215B113FECD400BF472F /* systemcommand.h */, - A7DA2161113FECD400BF472F /* treegroupscommand.cpp */, + A7DA215A113FECD400BF472F /* systemcommand.cpp */, A7DA2162113FECD400BF472F /* treegroupscommand.h */, - A7DA2167113FECD400BF472F /* trimseqscommand.cpp */, + A7DA2161113FECD400BF472F /* treegroupscommand.cpp */, A7DA2168113FECD400BF472F /* trimseqscommand.h */, - A7DA2169113FECD400BF472F /* unifracunweightedcommand.cpp */, + A7DA2167113FECD400BF472F /* trimseqscommand.cpp */, A7DA216A113FECD400BF472F /* unifracunweightedcommand.h */, - A7DA216B113FECD400BF472F /* unifracweightedcommand.cpp */, + A7DA2169113FECD400BF472F /* unifracunweightedcommand.cpp */, A7DA216C113FECD400BF472F /* unifracweightedcommand.h */, - A7DA2177113FECD400BF472F /* venncommand.cpp */, + A7DA216B113FECD400BF472F /* unifracweightedcommand.cpp */, A7DA2178113FECD400BF472F /* venncommand.h */, + A7DA2177113FECD400BF472F /* venncommand.cpp */, ); name = commands; sourceTree = ""; @@ -803,6 +875,8 @@ A7DA208A113FECD400BF472F /* knn.h */, A7DA20C4113FECD400BF472F /* phylotree.cpp */, A7DA20C5113FECD400BF472F /* phylotree.h */, + A76AAD02117F322B003D8DA1 /* phylosummary.h */, + A76AAD03117F322B003D8DA1 /* phylosummary.cpp */, A7DA215C113FECD400BF472F /* taxonomyequalizer.cpp */, A7DA215D113FECD400BF472F /* taxonomyequalizer.h */, ); @@ -857,6 +931,8 @@ A7DA20ED113FECD400BF472F /* readphylip.h */, A7DA20EE113FECD400BF472F /* readtree.cpp */, A7DA20EF113FECD400BF472F /* readtree.h */, + A71D924711AEB42400D00CBC /* splitmatrix.h */, + A71D924611AEB42400D00CBC /* splitmatrix.cpp */, ); name = read; sourceTree = ""; @@ -882,6 +958,10 @@ /* Begin PBXProject section */ 08FB7793FE84155DC02AAC07 /* Project object */ = { isa = PBXProject; + attributes = { + BuildIndependentTargetsInParallel = YES; + ORGANIZATIONNAME = "Schloss Lab"; + }; buildConfigurationList = 1DEB919308733D9F0010E9CD /* Build configuration list for PBXProject "Mothur" */; compatibilityVersion = "Xcode 3.0"; hasScannedForEncodings = 1; @@ -895,23 +975,6 @@ /* End PBXProject section */ /* Begin XCBuildConfiguration section */ - 1DEB919008733D9F0010E9CD /* Debug */ = { - isa = XCBuildConfiguration; - buildSettings = { - COPY_PHASE_STRIP = NO; - DEBUGGING_SYMBOLS = YES; - GCC_DYNAMIC_NO_PIC = NO; - GCC_ENABLE_FIX_AND_CONTINUE = YES; - GCC_GENERATE_DEBUGGING_SYMBOLS = YES; - GCC_OPTIMIZATION_LEVEL = 0; - OPTIMIZATION_CFLAGS = "-O0"; - OTHER_CFLAGS = ""; - OTHER_LDFLAGS = ""; - PRODUCT_NAME = mothur; - ZERO_LINK = YES; - }; - name = Debug; - }; 1DEB919108733D9F0010E9CD /* Release */ = { isa = XCBuildConfiguration; buildSettings = { @@ -924,16 +987,6 @@ }; name = Release; }; - 1DEB919408733D9F0010E9CD /* Debug */ = { - isa = XCBuildConfiguration; - buildSettings = { - GCC_WARN_ABOUT_RETURN_TYPE = YES; - 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