Merge remote-tracking branch 'origin'

[mothur.git] / Mothur.xcodeproj / project.pbxproj

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 0b945f5e899372cc6e5cbe16ce8ef4abaa96d738..8304f072147391d834a1a82f002ee60a697c04fe 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -81,6 +81,7 @@
                A7C7DAB915DA758B0059B0CF /* sffmultiplecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7C7DAB815DA758B0059B0CF /* sffmultiplecommand.cpp */; };
                A7CFA4311755401800D9ED4D /* renameseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7CFA4301755401800D9ED4D /* renameseqscommand.cpp */; };
                A7D755DA1535F679009BF21A /* treereader.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D755D91535F679009BF21A /* treereader.cpp */; };
+               A7D9378A17B146B5001E90B0 /* wilcox.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D9378917B146B5001E90B0 /* wilcox.cpp */; };
                A7E0243D15B4520A00A5F046 /* sparsedistancematrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E0243C15B4520A00A5F046 /* sparsedistancematrix.cpp */; };
                A7E6F69E17427D06006775E2 /* makelookupcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E6F69D17427D06006775E2 /* makelookupcommand.cpp */; };
                A7E9B88112D37EC400DA6239 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B64F12D37EC300DA6239 /* ace.cpp */; };
@@ -545,6 +546,8 @@
                A7CFA4301755401800D9ED4D /* renameseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = renameseqscommand.cpp; sourceTree = "<group>"; };
                A7D755D71535F665009BF21A /* treereader.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treereader.h; sourceTree = "<group>"; };
                A7D755D91535F679009BF21A /* treereader.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treereader.cpp; sourceTree = "<group>"; };
+               A7D9378917B146B5001E90B0 /* wilcox.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = wilcox.cpp; sourceTree = "<group>"; };
+               A7D9378B17B15215001E90B0 /* wilcox.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; path = wilcox.h; sourceTree = "<group>"; };
                A7DAAFA3133A254E003956EB /* commandparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = commandparameter.h; sourceTree = "<group>"; };
                A7E0243C15B4520A00A5F046 /* sparsedistancematrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sparsedistancematrix.cpp; sourceTree = "<group>"; };
                A7E0243F15B4522000A5F046 /* sparsedistancematrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sparsedistancematrix.h; sourceTree = "<group>"; };
@@ -586,20 +589,20 @@
                A7E9B67212D37EC400DA6239 /* catchallcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = catchallcommand.cpp; sourceTree = "<group>"; };
                A7E9B67312D37EC400DA6239 /* catchallcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = catchallcommand.h; sourceTree = "<group>"; };
                A7E9B67412D37EC400DA6239 /* ccode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ccode.cpp; sourceTree = "<group>"; };
-               A7E9B67512D37EC400DA6239 /* ccode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ccode.h; sourceTree = "<group>"; };
+               A7E9B67512D37EC400DA6239 /* ccode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; lineEnding = 0; path = ccode.h; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.objcpp; };
                A7E9B67612D37EC400DA6239 /* chao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chao1.cpp; sourceTree = "<group>"; };
                A7E9B67712D37EC400DA6239 /* chao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chao1.h; sourceTree = "<group>"; };
                A7E9B67812D37EC400DA6239 /* chimera.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimera.cpp; sourceTree = "<group>"; };
                A7E9B67912D37EC400DA6239 /* chimera.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimera.h; sourceTree = "<group>"; };
                A7E9B67A12D37EC400DA6239 /* chimerabellerophoncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerabellerophoncommand.cpp; sourceTree = "<group>"; };
                A7E9B67B12D37EC400DA6239 /* chimerabellerophoncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerabellerophoncommand.h; sourceTree = "<group>"; };
-               A7E9B67C12D37EC400DA6239 /* chimeraccodecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraccodecommand.cpp; sourceTree = "<group>"; };
+               A7E9B67C12D37EC400DA6239 /* chimeraccodecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; path = chimeraccodecommand.cpp; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
                A7E9B67D12D37EC400DA6239 /* chimeraccodecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraccodecommand.h; sourceTree = "<group>"; };
-               A7E9B67E12D37EC400DA6239 /* chimeracheckcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeracheckcommand.cpp; sourceTree = "<group>"; };
+               A7E9B67E12D37EC400DA6239 /* chimeracheckcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; path = chimeracheckcommand.cpp; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
                A7E9B67F12D37EC400DA6239 /* chimeracheckcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeracheckcommand.h; sourceTree = "<group>"; };
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-               A7E9B68112D37EC400DA6239 /* chimeracheckrdp.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeracheckrdp.h; sourceTree = "<group>"; };
-               A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerapintailcommand.cpp; sourceTree = "<group>"; };
+               A7E9B68112D37EC400DA6239 /* chimeracheckrdp.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; lineEnding = 0; path = chimeracheckrdp.h; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.objcpp; };
+               A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; path = chimerapintailcommand.cpp; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
                A7E9B68312D37EC400DA6239 /* chimerapintailcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerapintailcommand.h; sourceTree = "<group>"; };
                A7E9B68412D37EC400DA6239 /* chimerarealigner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerarealigner.cpp; sourceTree = "<group>"; };
                A7E9B68512D37EC400DA6239 /* chimerarealigner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerarealigner.h; sourceTree = "<group>"; };
@@ -624,12 +627,12 @@
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                A7E9B69B12D37EC400DA6239 /* clusterclassic.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clusterclassic.h; sourceTree = "<group>"; };
                A7E9B69C12D37EC400DA6239 /* clustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clustercommand.cpp; sourceTree = "<group>"; };
-               A7E9B69D12D37EC400DA6239 /* clustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clustercommand.h; sourceTree = "<group>"; };
+               A7E9B69D12D37EC400DA6239 /* clustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; lineEnding = 0; path = clustercommand.h; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.objcpp; };
                A7E9B69E12D37EC400DA6239 /* clusterdoturcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clusterdoturcommand.cpp; sourceTree = "<group>"; };
                A7E9B69F12D37EC400DA6239 /* clusterdoturcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clusterdoturcommand.h; sourceTree = "<group>"; };
                A7E9B6A012D37EC400DA6239 /* clusterfragmentscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clusterfragmentscommand.cpp; sourceTree = "<group>"; };
                A7E9B6A112D37EC400DA6239 /* clusterfragmentscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clusterfragmentscommand.h; sourceTree = "<group>"; };
-               A7E9B6A212D37EC400DA6239 /* clustersplitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clustersplitcommand.cpp; sourceTree = "<group>"; };
+               A7E9B6A212D37EC400DA6239 /* clustersplitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; path = clustersplitcommand.cpp; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
                A7E9B6A312D37EC400DA6239 /* clustersplitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clustersplitcommand.h; sourceTree = "<group>"; };
                A7E9B6A412D37EC400DA6239 /* cmdargs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cmdargs.cpp; sourceTree = "<group>"; };
                A7E9B6A512D37EC400DA6239 /* cmdargs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cmdargs.h; sourceTree = "<group>"; };
@@ -661,7 +664,7 @@
                A7E9B6BF12D37EC400DA6239 /* datavector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = datavector.hpp; sourceTree = "<group>"; };
                A7E9B6C012D37EC400DA6239 /* dayhoff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dayhoff.h; sourceTree = "<group>"; };
                A7E9B6C112D37EC400DA6239 /* decalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = decalc.cpp; sourceTree = "<group>"; };
-               A7E9B6C212D37EC400DA6239 /* decalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = decalc.h; sourceTree = "<group>"; };
+               A7E9B6C212D37EC400DA6239 /* decalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; lineEnding = 0; path = decalc.h; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.objcpp; };
                A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = "<group>"; };
                A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deconvolutecommand.h; sourceTree = "<group>"; };
                A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; path = degapseqscommand.cpp; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
@@ -746,7 +749,7 @@
                A7E9B71812D37EC400DA6239 /* hcluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hcluster.cpp; sourceTree = SOURCE_ROOT; };
                A7E9B71912D37EC400DA6239 /* hcluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hcluster.h; sourceTree = SOURCE_ROOT; };
                A7E9B71A12D37EC400DA6239 /* hclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hclustercommand.cpp; sourceTree = "<group>"; };
-               A7E9B71B12D37EC400DA6239 /* hclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hclustercommand.h; sourceTree = "<group>"; };
+               A7E9B71B12D37EC400DA6239 /* hclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; lineEnding = 0; path = hclustercommand.h; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.objcpp; };
                A7E9B71C12D37EC400DA6239 /* heatmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmap.cpp; sourceTree = SOURCE_ROOT; };
                A7E9B71D12D37EC400DA6239 /* heatmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmap.h; sourceTree = SOURCE_ROOT; };
                A7E9B71E12D37EC400DA6239 /* heatmapcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapcommand.cpp; sourceTree = "<group>"; };
@@ -1199,6 +1202,8 @@
                                A7E9B73A12D37EC400DA6239 /* libshuff.h */,
                                A7FC480C12D788F20055BC5C /* linearalgebra.h */,
                                A7FC480D12D788F20055BC5C /* linearalgebra.cpp */,
+                               A7D9378B17B15215001E90B0 /* wilcox.h */,
+                               A7D9378917B146B5001E90B0 /* wilcox.cpp */,
                                A7E9BA5612D39BD800DA6239 /* metastats */,
                                A7E9B75B12D37EC400DA6239 /* mothur.cpp */,
                                A7E9B75C12D37EC400DA6239 /* mothur.h */,
@@ -2388,6 +2393,7 @@
                                A741744C175CD9B1007DF49B /* makelefsecommand.cpp in Sources */,
                                A7190B221768E0DF00A9AFA6 /* lefsecommand.cpp in Sources */,
                                A77916E8176F7F7600EEFE18 /* designmap.cpp in Sources */,
+                               A7D9378A17B146B5001E90B0 /* wilcox.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
@@ -2407,7 +2413,7 @@
                                GCC_OPTIMIZATION_LEVEL = 3;
                                "INSTALL_PATH[sdk=*]" = TARGET_BUILD_DIR;
                                PRODUCT_NAME = mothur;
-                               SDKROOT = macosx10.8;
+                               SDKROOT = macosx;
                                SKIP_INSTALL = NO;
                        };
                        name = Debug;
@@ -2443,6 +2449,7 @@
                                        "VERSION=\"\\\"1.31.0\\\"\"",
                                        "RELEASE_DATE=\"\\\"5/24/2013\\\"\"",
                                );
+                               GCC_VERSION = "";
                                "GCC_VERSION[arch=*]" = "";
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
@@ -2460,7 +2467,7 @@
                                        "-lncurses",
                                        "-lreadline",
                                );
-                               SDKROOT = macosx;
+                               SDKROOT = macosx10.8;
                                SKIP_INSTALL = NO;
                                USER_HEADER_SEARCH_PATHS = "";
                        };
@@ -2479,6 +2486,7 @@
                                        "VERSION=\"\\\"1.31.0\\\"\"",
                                        "RELEASE_DATE=\"\\\"5/24/2013\\\"\"",
                                );
+                               GCC_VERSION = "";
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_MISSING_PARENTHESES = YES;
@@ -2498,7 +2506,7 @@
                                        "-lncurses",
                                        "-lreadline",
                                );
-                               SDKROOT = macosx;
+                               SDKROOT = macosx10.8;
                                SKIP_INSTALL = NO;
                        };
                        name = Release;