]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
added merge.groups command
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index 1e52e09f149fff725e5b5914e74b44f07525c52a..24187d82fd0bff1934e3faeb458bb062fba6548b 100644 (file)
@@ -9,6 +9,10 @@
 /* Begin PBXBuildFile section */
                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 */; };
+               A71FE12C12EDF72400963CA7 /* mergegroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */; };
+               A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727864312E9E28C00F86ABA /* removerarecommand.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 */; };
                A7E9B91212D37EC400DA6239 /* parselistscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78112D37EC400DA6239 /* parselistscommand.cpp */; };
                A7E9B91312D37EC400DA6239 /* parsimony.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78312D37EC400DA6239 /* parsimony.cpp */; };
                A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */; };
-               A7E9B91512D37EC400DA6239 /* pcacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78712D37EC400DA6239 /* pcacommand.cpp */; };
+               A7E9B91512D37EC400DA6239 /* pcoacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */; };
                A7E9B91612D37EC400DA6239 /* phylodiversity.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */; };
                A7E9B91712D37EC400DA6239 /* phylodiversitycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */; };
                A7E9B91812D37EC400DA6239 /* phylosummary.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78D12D37EC400DA6239 /* phylosummary.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 */; };
+               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 */
 
 /* Begin PBXCopyFilesBuildPhase section */
 /* End PBXCopyFilesBuildPhase section */
 
 /* Begin PBXFileReference section */
-               8DD76FB20486AB0100D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; };
+               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>"; };
+               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>"; };
                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>"; };
                A7E9B78412D37EC400DA6239 /* parsimony.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimony.h; sourceTree = "<group>"; };
                A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimonycommand.cpp; sourceTree = "<group>"; };
                A7E9B78612D37EC400DA6239 /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = "<group>"; };
-               A7E9B78712D37EC400DA6239 /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = "<group>"; };
-               A7E9B78812D37EC400DA6239 /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = "<group>"; };
+               A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcoacommand.cpp; sourceTree = "<group>"; };
+               A7E9B78812D37EC400DA6239 /* pcoacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcoacommand.h; sourceTree = "<group>"; };
                A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversity.cpp; sourceTree = "<group>"; };
                A7E9B78A12D37EC400DA6239 /* phylodiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversity.h; sourceTree = "<group>"; };
                A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversitycommand.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>"; };
+               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>"; };
+               A7FC486612D795D60055BC5C /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = "<group>"; };
                C6A0FF2C0290799A04C91782 /* mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = mothur.1; sourceTree = "<group>"; };
 /* End PBXFileReference section */
 
                                A7E9B72D12D37EC400DA6239 /* inputdata.cpp */,
                                A7E9B73912D37EC400DA6239 /* libshuff.cpp */,
                                A7E9B73A12D37EC400DA6239 /* libshuff.h */,
+                               A7FC480C12D788F20055BC5C /* linearalgebra.h */,
+                               A7FC480D12D788F20055BC5C /* linearalgebra.cpp */,
                                A7E9BA5612D39BD800DA6239 /* metastats */,
                                A7E9B75B12D37EC400DA6239 /* mothur.cpp */,
                                A7E9B75C12D37EC400DA6239 /* mothur.h */,
                1AB674ADFE9D54B511CA2CBB /* Products */ = {
                        isa = PBXGroup;
                        children = (
-                               8DD76FB20486AB0100D96B5E /* mothur */,
+                               8DD76FB20486AB0100D96B5E /* Mothur */,
                        );
                        name = Products;
                        sourceTree = "<group>";
                                A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */,
                                A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */,
                                A7E9B75412D37EC400DA6239 /* mergefilecommand.h */,
+                               A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */,
+                               A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */,
                                A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */,
                                A7E9B75812D37EC400DA6239 /* metastatscommand.h */,
                                A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */,
                                A7E9B76912D37EC400DA6239 /* nocommands.cpp */,
                                A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */,
                                A7E9B76C12D37EC400DA6239 /* normalizesharedcommand.h */,
+                               A713EBEB12DC7C5E000092AC /* nmdscommand.h */,
+                               A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */,
                                A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */,
                                A7E9B77A12D37EC400DA6239 /* otuhierarchycommand.h */,
                                A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */,
                                A7E9B78212D37EC400DA6239 /* parselistscommand.h */,
                                A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */,
                                A7E9B78612D37EC400DA6239 /* parsimonycommand.h */,
-                               A7E9B78712D37EC400DA6239 /* pcacommand.cpp */,
-                               A7E9B78812D37EC400DA6239 /* pcacommand.h */,
+                               A7FC486512D795D60055BC5C /* pcacommand.h */,
+                               A7FC486612D795D60055BC5C /* pcacommand.cpp */,
+                               A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */,
+                               A7E9B78812D37EC400DA6239 /* pcoacommand.h */,
                                A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */,
                                A7E9B78C12D37EC400DA6239 /* phylodiversitycommand.h */,
                                A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */,
                                A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */,
                                A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */,
                                A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */,
+                               A727864212E9E28C00F86ABA /* removerarecommand.h */,
+                               A727864312E9E28C00F86ABA /* removerarecommand.cpp */,
                                A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */,
                                A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */,
                                A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */,
                                A7E9B7BE12D37EC400DA6239 /* readphylip.h */,
                                A7E9B7BF12D37EC400DA6239 /* readtree.cpp */,
                                A7E9B7C012D37EC400DA6239 /* readtree.h */,
+                               A713EBAA12DC7613000092AC /* readphylipvector.h */,
+                               A713EBAB12DC7613000092AC /* readphylipvector.cpp */,
                                A7E9B84312D37EC400DA6239 /* splitmatrix.cpp */,
                                A7E9B84412D37EC400DA6239 /* splitmatrix.h */,
                        );
 /* End PBXGroup section */
 
 /* Begin PBXNativeTarget section */
-               8DD76FA90486AB0100D96B5E /* mothur */ = {
+               8DD76FA90486AB0100D96B5E /* Mothur */ = {
                        isa = PBXNativeTarget;
-                       buildConfigurationList = 1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "mothur" */;
+                       buildConfigurationList = 1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */;
                        buildPhases = (
                                8DD76FAB0486AB0100D96B5E /* Sources */,
                                8DD76FAD0486AB0100D96B5E /* Frameworks */,
                        );
                        dependencies = (
                        );
-                       name = mothur;
+                       name = Mothur;
                        productInstallPath = "$(HOME)/bin";
                        productName = mothur;
-                       productReference = 8DD76FB20486AB0100D96B5E /* mothur */;
+                       productReference = 8DD76FB20486AB0100D96B5E /* Mothur */;
                        productType = "com.apple.product-type.tool";
                };
 /* End PBXNativeTarget section */
 /* Begin PBXProject section */
                08FB7793FE84155DC02AAC07 /* Project object */ = {
                        isa = PBXProject;
+                       attributes = {
+                               ORGANIZATIONNAME = "Schloss Lab";
+                       };
                        buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */;
                        compatibilityVersion = "Xcode 3.1";
                        developmentRegion = English;
                        projectDirPath = "";
                        projectRoot = "";
                        targets = (
-                               8DD76FA90486AB0100D96B5E /* mothur */,
+                               8DD76FA90486AB0100D96B5E /* Mothur */,
                        );
                };
 /* End PBXProject section */
                                A7E9B91212D37EC400DA6239 /* parselistscommand.cpp in Sources */,
                                A7E9B91312D37EC400DA6239 /* parsimony.cpp in Sources */,
                                A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */,
-                               A7E9B91512D37EC400DA6239 /* pcacommand.cpp in Sources */,
+                               A7E9B91512D37EC400DA6239 /* pcoacommand.cpp in Sources */,
                                A7E9B91612D37EC400DA6239 /* phylodiversity.cpp in Sources */,
                                A7E9B91712D37EC400DA6239 /* phylodiversitycommand.cpp in Sources */,
                                A7E9B91812D37EC400DA6239 /* phylosummary.cpp in Sources */,
                                A7E9B98E12D37EC400DA6239 /* weightedlinkage.cpp in Sources */,
                                A7E9B98F12D37EC400DA6239 /* whittaker.cpp in Sources */,
                                A70332B712D3A13400761E33 /* makefile in Sources */,
+                               A7FC480E12D788F20055BC5C /* linearalgebra.cpp in Sources */,
+                               A7FC486712D795D60055BC5C /* pcacommand.cpp in Sources */,
+                               A713EBAC12DC7613000092AC /* readphylipvector.cpp in Sources */,
+                               A713EBED12DC7C5E000092AC /* nmdscommand.cpp in Sources */,
+                               A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */,
+                               A71FE12C12EDF72400963CA7 /* mergegroupscommand.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
                                GCC_MODEL_TUNING = G5;
                                GCC_OPTIMIZATION_LEVEL = 0;
                                INSTALL_PATH = /usr/local/bin;
-                               PRODUCT_NAME = mothur;
+                               PRODUCT_NAME = Mothur;
                        };
                        name = Debug;
                };
                                GCC_MODEL_TUNING = G5;
                                GCC_WARN_UNUSED_VALUE = YES;
                                INSTALL_PATH = ./;
-                               PRODUCT_NAME = mothur;
+                               PRODUCT_NAME = Mothur;
                        };
                        name = Release;
                };
                                        "VERSION=\"\\\"1.15.0\\\"\"",
                                        "RELEASE_DATE=\"\\\"12/10/2010\\\"\"",
                                );
+                               GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
                                INSTALL_PATH = "";
 /* End XCBuildConfiguration section */
 
 /* Begin XCConfigurationList section */
-               1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "mothur" */ = {
+               1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */ = {
                        isa = XCConfigurationList;
                        buildConfigurations = (
                                1DEB928608733DD80010E9CD /* Debug */,