X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=112cf3c7fdc7305c62bce17667f81232492860f6;hb=fa08e82ec2dd48f73d051c210dad54a403308949;hp=1b87a4f360376eb978f94c7a1e846ec2a18ffb7c;hpb=d04f948b1a2a1a2984fc4a45d04403b8c121c5bc;p=mothur.git

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 1b87a4f..112cf3c 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -7,10 +7,13 @@
 	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 */; };
+		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 */; };
@@ -300,12 +303,18 @@
 /* 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>"; };
+		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>"; };
@@ -1005,6 +1014,8 @@
 		A7E9BA3812D3956100DA6239 /* commands */ = {
 			isa = PBXGroup;
 			children = (
+				7E6BE10812F710D8007ADDBE /* refchimeratest.h */,
+				7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */,
 				A7E9B6AE12D37EC400DA6239 /* command.hpp */,
 				A7E9B65112D37EC300DA6239 /* aligncommand.cpp */,
 				A7E9B65212D37EC300DA6239 /* aligncommand.h */,
@@ -1106,6 +1117,8 @@
 				A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */,
 				A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */,
 				A7E9B75412D37EC400DA6239 /* mergefilecommand.h */,
+				A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */,
+				A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */,
 				A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */,
 				A7E9B75812D37EC400DA6239 /* metastatscommand.h */,
 				A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */,
@@ -1156,6 +1169,8 @@
 				A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */,
 				A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */,
 				A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */,
+				A727864212E9E28C00F86ABA /* removerarecommand.h */,
+				A727864312E9E28C00F86ABA /* removerarecommand.cpp */,
 				A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */,
 				A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */,
 				A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */,
@@ -1580,7 +1595,10 @@
 /* Begin PBXProject section */
 		08FB7793FE84155DC02AAC07 /* Project object */ = {
 			isa = PBXProject;
-			buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */;
+			attributes = {
+				ORGANIZATIONNAME = "Schloss Lab";
+			};
+			buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */;
 			compatibilityVersion = "Xcode 3.1";
 			developmentRegion = English;
 			hasScannedForEncodings = 1;
@@ -1880,6 +1898,9 @@
 				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 */,
+				7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */,
 			);
 			runOnlyForDeploymentPostprocessing = 0;
 		};
@@ -1919,15 +1940,17 @@
 				ARCHS = "$(ARCHS_STANDARD_32_64_BIT)";
 				DEPLOYMENT_LOCATION = NO;
 				GCC_C_LANGUAGE_STANDARD = gnu99;
-				GCC_OPTIMIZATION_LEVEL = 0;
+				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_PREPROCESSOR_DEFINITIONS = (
 					"MOTHUR_FILES=\"\\\"../release\\\"\"",
-					"VERSION=\"\\\"1.15.0\\\"\"",
-					"RELEASE_DATE=\"\\\"12/10/2010\\\"\"",
+					"VERSION=\"\\\"1.16.0\\\"\"",
+					"RELEASE_DATE=\"\\\"1/26/2010\\\"\"",
 				);
+				GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
 				GCC_WARN_ABOUT_RETURN_TYPE = YES;
 				GCC_WARN_UNUSED_VARIABLE = YES;
 				INSTALL_PATH = "";
+				MACH_O_TYPE = mh_execute;
 				ONLY_ACTIVE_ARCH = YES;
 				OTHER_CPLUSPLUSFLAGS = (
 					"-DUSE_READLINE",
@@ -1949,6 +1972,9 @@
 				ARCHS = "$(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\\\"\"",
@@ -1963,6 +1989,7 @@
 				GCC_WARN_UNUSED_VALUE = YES;
 				GCC_WARN_UNUSED_VARIABLE = YES;
 				INSTALL_PATH = "";
+				MACH_O_TYPE = mh_execute;
 				OTHER_CPLUSPLUSFLAGS = (
 					"-DUSE_READLINE",
 					"-DBIT_VERSION",
@@ -1989,7 +2016,7 @@
 			defaultConfigurationIsVisible = 0;
 			defaultConfigurationName = Release;
 		};
-		1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */ = {
+		1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
 			isa = XCConfigurationList;
 			buildConfigurations = (
 				1DEB928A08733DD80010E9CD /* Debug */,