]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
fixed bug with trim.flows that was adding flow files names to the .flow.files file...
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index 49de82685f9d1a43325306eb1854b7011eee86b7..ff6df12d115aecca886d2498ce36a8df54908ecb 100644 (file)
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 /* End PBXFileReference section */
 
                                A7E9B75C12D37EC400DA6239 /* mothur.h */,
                                A7E9B75D12D37EC400DA6239 /* mothurout.cpp */,
                                A7E9B75E12D37EC400DA6239 /* mothurout.h */,
+                               A774104714696F320098E6AC /* myseqdist.h */,
+                               A774104614696F320098E6AC /* myseqdist.cpp */,
                                A7E9B76112D37EC400DA6239 /* nast.cpp */,
                                A7E9B76212D37EC400DA6239 /* nast.hpp */,
                                A7E9B76312D37EC400DA6239 /* nastreport.cpp */,
                                A7E9B7AD12D37EC400DA6239 /* rarefactioncurvedata.h */,
                                7E6BE10812F710D8007ADDBE /* refchimeratest.h */,
                                7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */,
+                               A77410F514697C300098E6AC /* seqnoise.h */,
+                               A77410F414697C300098E6AC /* seqnoise.cpp */,
                                A7E9BA5312D39A5E00DA6239 /* read */,
                                A7E9B82312D37EC400DA6239 /* sharedutilities.cpp */,
                                A7E9B82412D37EC400DA6239 /* sharedutilities.h */,
                                A7E9B82D12D37EC400DA6239 /* singlelinkage.cpp */,
                                A7E9B83012D37EC400DA6239 /* slibshuff.cpp */,
-                               A7E9B85112D37EC400DA6239 /* suffixdb.cpp */,
                                A7E9B83112D37EC400DA6239 /* slibshuff.h */,
-                               A7E9B85212D37EC400DA6239 /* suffixdb.hpp */,
-                               A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */,
-                               A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */,
-                               A7E9B85512D37EC400DA6239 /* suffixtree.cpp */,
-                               A7E9B85612D37EC400DA6239 /* suffixtree.hpp */,
+                               A7FF19F0140FFDA500AD216D /* trimoligos.h */,
+                               A7FF19F1140FFDA500AD216D /* trimoligos.cpp */,
                                A7E9B87412D37EC400DA6239 /* validcalculator.cpp */,
                                A7E9B87512D37EC400DA6239 /* validcalculator.h */,
                                A7E9B87612D37EC400DA6239 /* validparameter.cpp */,
                                A7E9B67E12D37EC400DA6239 /* chimeracheckcommand.cpp */,
                                A7E9B68312D37EC400DA6239 /* chimerapintailcommand.h */,
                                A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */,
+                               A7BF2230145879B2000AD524 /* chimeraperseuscommand.h */,
+                               A7BF2231145879B2000AD524 /* chimeraperseuscommand.cpp */,
                                A7E9B68B12D37EC400DA6239 /* chimeraslayercommand.h */,
                                A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */,
                                A74D36B6137DAFAA00332B0C /* chimerauchimecommand.h */,
                                A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */,
                                A7E9B6BA12D37EC400DA6239 /* corraxescommand.h */,
                                A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */,
+                               A795840B13F13CD900F201D5 /* countgroupscommand.h */,
+                               A795840C13F13CD900F201D5 /* countgroupscommand.cpp */,
                                A7730EFD13967241007433A3 /* countseqscommand.h */,
                                A7730EFE13967241007433A3 /* countseqscommand.cpp */,
                                A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */,
                                A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */,
                                A7E9B82812D37EC400DA6239 /* shhhercommand.h */,
                                A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */,
+                               A774101214695AF60098E6AC /* shhhseqscommand.h */,
+                               A774101314695AF60098E6AC /* shhhseqscommand.cpp */,
                                A7E9B84012D37EC400DA6239 /* splitabundcommand.h */,
                                A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */,
                                A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */,
                                A7E9B85712D37EC400DA6239 /* summarycommand.cpp */,
                                A7E9B85A12D37EC400DA6239 /* summarysharedcommand.h */,
                                A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */,
+                               A7FFB556142CA02C004884F2 /* summarytaxcommand.h */,
+                               A7FFB557142CA02C004884F2 /* summarytaxcommand.cpp */,
                                A7E9B85C12D37EC400DA6239 /* systemcommand.h */,
                                A7E9B85B12D37EC400DA6239 /* systemcommand.cpp */,
                                A7E9B86312D37EC400DA6239 /* treegroupscommand.h */,
                                A7E9B7DC12D37EC400DA6239 /* sequence.hpp */,
                                A7E9B7DD12D37EC400DA6239 /* sequencedb.cpp */,
                                A7E9B7DE12D37EC400DA6239 /* sequencedb.h */,
+                               A7F9F5CD141A5E500032F693 /* sequenceparser.h */,
+                               A7F9F5CE141A5E500032F693 /* sequenceparser.cpp */,
                                A7E9B80412D37EC400DA6239 /* sharedlistvector.cpp */,
                                A7E9B80512D37EC400DA6239 /* sharedlistvector.h */,
                                A7E9B80E12D37EC400DA6239 /* sharedordervector.h */,
                                A7E9B80D12D37EC400DA6239 /* sharedordervector.cpp */,
-                               A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */,
                                A7E9B81012D37EC400DA6239 /* sharedrabundfloatvector.h */,
+                               A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */,
                                A7E9B81112D37EC400DA6239 /* sharedrabundvector.cpp */,
                                A7E9B81212D37EC400DA6239 /* sharedrabundvector.h */,
                                A7E9B81312D37EC400DA6239 /* sharedsabundvector.cpp */,
                                A7E9B81412D37EC400DA6239 /* sharedsabundvector.h */,
                                A7E9B83912D37EC400DA6239 /* sparsematrix.cpp */,
                                A7E9B83A12D37EC400DA6239 /* sparsematrix.hpp */,
+                               A7E9B85112D37EC400DA6239 /* suffixdb.cpp */,
+                               A7E9B85212D37EC400DA6239 /* suffixdb.hpp */,
+                               A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */,
+                               A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */,
+                               A7E9B85512D37EC400DA6239 /* suffixtree.cpp */,
+                               A7E9B85612D37EC400DA6239 /* suffixtree.hpp */,
                                A7E9B85F12D37EC400DA6239 /* tree.cpp */,
                                A7E9B86012D37EC400DA6239 /* tree.h */,
                                A7E9B86412D37EC400DA6239 /* treemap.cpp */,
                                A7E9B68912D37EC400DA6239 /* chimeraslayer.h */,
                                A7E9B74612D37EC400DA6239 /* maligner.h */,
                                A7E9B74512D37EC400DA6239 /* maligner.cpp */,
+                               A7BF221314587886000AD524 /* myPerseus.h */,
+                               A7BF221214587886000AD524 /* myPerseus.cpp */,
                                A7E9B79312D37EC400DA6239 /* pintail.cpp */,
                                A7E9B79412D37EC400DA6239 /* pintail.h */,
                                A7E9B82E12D37EC400DA6239 /* slayer.cpp */,
                                A73DDBBA13C4A0D1006AAE38 /* clearmemorycommand.cpp in Sources */,
                                A73DDC3813C4BF64006AAE38 /* mothurmetastats.cpp in Sources */,
                                A79234D713C74BF6002B08E2 /* mothurfisher.cpp in Sources */,
+                               A795840D13F13CD900F201D5 /* countgroupscommand.cpp in Sources */,
+                               A7FF19F2140FFDA500AD216D /* trimoligos.cpp in Sources */,
+                               A7F9F5CF141A5E500032F693 /* sequenceparser.cpp in Sources */,
+                               A7FFB558142CA02C004884F2 /* summarytaxcommand.cpp in Sources */,
+                               A7BF221414587886000AD524 /* myPerseus.cpp in Sources */,
+                               A7BF2232145879B2000AD524 /* chimeraperseuscommand.cpp in Sources */,
+                               A774101414695AF60098E6AC /* shhhseqscommand.cpp in Sources */,
+                               A774104814696F320098E6AC /* myseqdist.cpp in Sources */,
+                               A77410F614697C300098E6AC /* seqnoise.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
                                GCC_ENABLE_SSE3_EXTENSIONS = NO;
                                GCC_ENABLE_SSE41_EXTENSIONS = NO;
                                GCC_ENABLE_SSE42_EXTENSIONS = NO;
-                               GCC_OPTIMIZATION_LEVEL = 0;
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "MOTHUR_FILES=\"\\\"../release\\\"\"",
-                                       "VERSION=\"\\\"1.21.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"7/25/2011\\\"\"",
+                                       "VERSION=\"\\\"1.22.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"10/12/2011\\\"\"",
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_C_LANGUAGE_STANDARD = gnu99;
                                GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
                                GCC_MODEL_TUNING = "";
-                               GCC_OPTIMIZATION_LEVEL = 0;
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "VERSION=\"\\\"1.19.0\\\"\"",
                                        "RELEASE_DATE=\"\\\"5/9/2011\\\"\"",