X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=24187d82fd0bff1934e3faeb458bb062fba6548b;hb=f598bd8389840cf030d61f5da7d0b2c3e37c06ba;hp=e7e81830d7733593c273015e4d4d4a938b5752c6;hpb=4956d362c5bc6a47cf7a6290258f0e763e3a406e;p=mothur.git

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index e7e8183..24187d8 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -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 */; };
@@ -280,6 +284,8 @@
 		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 */
@@ -298,6 +304,14 @@
 /* Begin PBXFileReference section */
 		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>"; };
@@ -860,6 +874,10 @@
 		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 */
 
@@ -930,6 +948,8 @@
 				A7E9B72D12D37EC400DA6239 /* inputdata.cpp */,
 				A7E9B73912D37EC400DA6239 /* libshuff.cpp */,
 				A7E9B73A12D37EC400DA6239 /* libshuff.h */,
+				A7FC480C12D788F20055BC5C /* linearalgebra.h */,
+				A7FC480D12D788F20055BC5C /* linearalgebra.cpp */,
 				A7E9BA5612D39BD800DA6239 /* metastats */,
 				A7E9B75B12D37EC400DA6239 /* mothur.cpp */,
 				A7E9B75C12D37EC400DA6239 /* mothur.h */,
@@ -1092,6 +1112,8 @@
 				A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */,
 				A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */,
 				A7E9B75412D37EC400DA6239 /* mergefilecommand.h */,
+				A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */,
+				A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */,
 				A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */,
 				A7E9B75812D37EC400DA6239 /* metastatscommand.h */,
 				A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */,
@@ -1100,6 +1122,8 @@
 				A7E9B76912D37EC400DA6239 /* nocommands.cpp */,
 				A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */,
 				A7E9B76C12D37EC400DA6239 /* normalizesharedcommand.h */,
+				A713EBEB12DC7C5E000092AC /* nmdscommand.h */,
+				A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */,
 				A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */,
 				A7E9B77A12D37EC400DA6239 /* otuhierarchycommand.h */,
 				A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */,
@@ -1110,6 +1134,8 @@
 				A7E9B78212D37EC400DA6239 /* parselistscommand.h */,
 				A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */,
 				A7E9B78612D37EC400DA6239 /* parsimonycommand.h */,
+				A7FC486512D795D60055BC5C /* pcacommand.h */,
+				A7FC486612D795D60055BC5C /* pcacommand.cpp */,
 				A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */,
 				A7E9B78812D37EC400DA6239 /* pcoacommand.h */,
 				A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */,
@@ -1138,6 +1164,8 @@
 				A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */,
 				A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */,
 				A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */,
+				A727864212E9E28C00F86ABA /* removerarecommand.h */,
+				A727864312E9E28C00F86ABA /* removerarecommand.cpp */,
 				A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */,
 				A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */,
 				A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */,
@@ -1511,6 +1539,8 @@
 				A7E9B7BE12D37EC400DA6239 /* readphylip.h */,
 				A7E9B7BF12D37EC400DA6239 /* readtree.cpp */,
 				A7E9B7C012D37EC400DA6239 /* readtree.h */,
+				A713EBAA12DC7613000092AC /* readphylipvector.h */,
+				A713EBAB12DC7613000092AC /* readphylipvector.cpp */,
 				A7E9B84312D37EC400DA6239 /* splitmatrix.cpp */,
 				A7E9B84412D37EC400DA6239 /* splitmatrix.h */,
 			);
@@ -1560,6 +1590,9 @@
 /* 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;
@@ -1856,6 +1889,12 @@
 				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;
 		};
@@ -1901,6 +1940,7 @@
 					"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 = "";