]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
working on anosim command
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index ade49c9e90545eaeaa8e121555dff073c54308e4..e4797253008a0057cc5562ddef17f0c4b4a8efa2 100644 (file)
@@ -7,11 +7,17 @@
        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 Sources */ = {isa = PBXBuildFile; fileRef = A713EBAB12DC7613000092AC /* readphylipvector.cpp */; };
                A713EBED12DC7C5E000092AC /* nmdscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */; };
+               A71CB160130B04A2001E7287 /* anosimcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A71CB15E130B04A2001E7287 /* anosimcommand.cpp */; };
+               A71FE12C12EDF72400963CA7 /* mergegroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */; };
                A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727864312E9E28C00F86ABA /* removerarecommand.cpp */; };
+               A75790591301749D00A30DAB /* homovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A75790581301749D00A30DAB /* homovacommand.cpp */; };
+               A799F5B91309A3E000AEEFA0 /* makefastqcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */; };
+               A7A61F2D130062E000E05B6B /* amovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A61F2C130062E000E05B6B /* amovacommand.cpp */; };
                A7E9B88112D37EC400DA6239 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B64F12D37EC300DA6239 /* ace.cpp */; };
                A7E9B88212D37EC400DA6239 /* aligncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65112D37EC300DA6239 /* aligncommand.cpp */; };
                A7E9B88312D37EC400DA6239 /* alignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65312D37EC300DA6239 /* alignment.cpp */; };
                A7E9B98D12D37EC400DA6239 /* weighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87C12D37EC400DA6239 /* weighted.cpp */; };
                A7E9B98E12D37EC400DA6239 /* weightedlinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */; };
                A7E9B98F12D37EC400DA6239 /* whittaker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87F12D37EC400DA6239 /* whittaker.cpp */; };
+               A7FA10021302E097003860FE /* mantelcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FA10011302E096003860FE /* mantelcommand.cpp */; };
                A7FC480E12D788F20055BC5C /* linearalgebra.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FC480D12D788F20055BC5C /* linearalgebra.cpp */; };
                A7FC486712D795D60055BC5C /* pcacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FC486612D795D60055BC5C /* pcacommand.cpp */; };
 /* End PBXBuildFile section */
 /* End PBXCopyFilesBuildPhase section */
 
 /* Begin PBXFileReference section */
+               7E6BE10812F710D8007ADDBE /* refchimeratest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = refchimeratest.h; sourceTree = "<group>"; };
+               7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = refchimeratest.cpp; sourceTree = "<group>"; };
                8DD76FB20486AB0100D96B5E /* Mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = Mothur; sourceTree = BUILT_PRODUCTS_DIR; };
                A70332B512D3A13400761E33 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = "<group>"; };
                A713EBAA12DC7613000092AC /* readphylipvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylipvector.h; sourceTree = "<group>"; };
                A713EBAB12DC7613000092AC /* readphylipvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylipvector.cpp; sourceTree = "<group>"; };
                A713EBEB12DC7C5E000092AC /* nmdscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nmdscommand.h; sourceTree = "<group>"; };
                A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nmdscommand.cpp; sourceTree = "<group>"; };
+               A71CB15E130B04A2001E7287 /* anosimcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = anosimcommand.cpp; sourceTree = "<group>"; };
+               A71CB15F130B04A2001E7287 /* anosimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = anosimcommand.h; sourceTree = "<group>"; };
+               A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergegroupscommand.h; sourceTree = "<group>"; };
+               A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergegroupscommand.cpp; sourceTree = "<group>"; };
                A727864212E9E28C00F86ABA /* removerarecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removerarecommand.h; sourceTree = "<group>"; };
                A727864312E9E28C00F86ABA /* removerarecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removerarecommand.cpp; sourceTree = "<group>"; };
+               A75790571301749D00A30DAB /* homovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = homovacommand.h; sourceTree = "<group>"; };
+               A75790581301749D00A30DAB /* homovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = homovacommand.cpp; sourceTree = "<group>"; };
+               A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makefastqcommand.h; sourceTree = "<group>"; };
+               A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makefastqcommand.cpp; sourceTree = "<group>"; };
+               A7A61F1A130035C800E05B6B /* LICENSE */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = LICENSE; sourceTree = "<group>"; };
+               A7A61F2B130062E000E05B6B /* amovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = amovacommand.h; sourceTree = "<group>"; };
+               A7A61F2C130062E000E05B6B /* amovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = amovacommand.cpp; sourceTree = "<group>"; };
                A7E9B64F12D37EC300DA6239 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = "<group>"; };
                A7E9B65012D37EC300DA6239 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = "<group>"; };
                A7E9B65112D37EC300DA6239 /* aligncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = aligncommand.cpp; sourceTree = "<group>"; };
                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 = "<group>"; };
                A7E9B88012D37EC400DA6239 /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = "<group>"; };
+               A7FA10001302E096003860FE /* mantelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mantelcommand.h; sourceTree = "<group>"; };
+               A7FA10011302E096003860FE /* mantelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mantelcommand.cpp; sourceTree = "<group>"; };
                A7FC480C12D788F20055BC5C /* linearalgebra.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = linearalgebra.h; sourceTree = "<group>"; };
                A7FC480D12D788F20055BC5C /* linearalgebra.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = linearalgebra.cpp; sourceTree = "<group>"; };
                A7FC486512D795D60055BC5C /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = "<group>"; };
                08FB7795FE84155DC02AAC07 /* Source */ = {
                        isa = PBXGroup;
                        children = (
+                               A7A61F1A130035C800E05B6B /* LICENSE */,
                                A70332B512D3A13400761E33 /* makefile */,
                                A7E9B65912D37EC300DA6239 /* averagelinkage.cpp */,
                                A7E9BA4F12D398D700DA6239 /* clearcut */,
                                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 */,
                                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 */,
                                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 */,
                                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 */,
                                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 */,
                                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 */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
                                ARCHS = "$(ARCHS_STANDARD_32_64_BIT)";
                                DEPLOYMENT_LOCATION = NO;
                                GCC_C_LANGUAGE_STANDARD = gnu99;
-                               GCC_OPTIMIZATION_LEVEL = 0;
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "MOTHUR_FILES=\"\\\"../release\\\"\"",
-                                       "VERSION=\"\\\"1.15.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"12/10/2010\\\"\"",
+                                       "VERSION=\"\\\"1.16.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"2/7/2011\\\"\"",
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
                                INSTALL_PATH = "";
+                               MACH_O_TYPE = mh_execute;
                                ONLY_ACTIVE_ARCH = YES;
                                OTHER_CPLUSPLUSFLAGS = (
                                        "-DUSE_READLINE",
                                ARCHS = "$(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\\\"\"",
                                GCC_WARN_UNUSED_VALUE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
                                INSTALL_PATH = "";
+                               MACH_O_TYPE = mh_execute;
                                OTHER_CPLUSPLUSFLAGS = (
                                        "-DUSE_READLINE",
                                        "-DBIT_VERSION",