X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=3ee1d81bc1944bdb301d2930b82b03cb51e2be63;hb=84f93a9e670eb7f7e69e0468b9be4c53890c07f2;hp=e30c0d4acd457fb66f0a21b289853eb7578b310a;hpb=99c986582ae659c205411639a8e9fa88fb680cd0;p=mothur.git

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index e30c0d4..3ee1d81 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -7,6 +7,21 @@
 	objects = {
 
 /* Begin PBXFileReference section */
+		A747E79B1163442A00FB9042 /* chimeracheckcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeracheckcommand.h; sourceTree = "<group>"; };
+		A747E79C1163442A00FB9042 /* chimeracheckcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeracheckcommand.cpp; sourceTree = "<group>"; };
+		A747E81C116365E000FB9042 /* chimeraslayercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraslayercommand.h; sourceTree = "<group>"; };
+		A747E81D116365E000FB9042 /* chimeraslayercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraslayercommand.cpp; sourceTree = "<group>"; };
+		A7639F8D1175DF35008F5578 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = "<group>"; };
+		A76AAD02117F322B003D8DA1 /* phylosummary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylosummary.h; sourceTree = "<group>"; };
+		A76AAD03117F322B003D8DA1 /* phylosummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylosummary.cpp; sourceTree = "<group>"; };
+		A76C4A1011876BAF0009460B /* setlogfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setlogfilecommand.h; sourceTree = SOURCE_ROOT; };
+		A76C4A1111876BAF0009460B /* setlogfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setlogfilecommand.cpp; sourceTree = SOURCE_ROOT; };
+		A78254461164D7790002E2DD /* chimerapintailcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerapintailcommand.h; sourceTree = "<group>"; };
+		A78254471164D7790002E2DD /* chimerapintailcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerapintailcommand.cpp; sourceTree = "<group>"; };
+		A7825502116519F70002E2DD /* chimerabellerophoncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerabellerophoncommand.h; sourceTree = "<group>"; };
+		A7825503116519F70002E2DD /* chimerabellerophoncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerabellerophoncommand.cpp; sourceTree = "<group>"; };
+		A78434881162224F00100BE0 /* chimeraccodecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraccodecommand.h; sourceTree = "<group>"; };
+		A78434891162224F00100BE0 /* chimeraccodecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraccodecommand.cpp; sourceTree = "<group>"; };
 		A7DA1FEC113FECD400BF472F /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = "<group>"; };
 		A7DA1FED113FECD400BF472F /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = "<group>"; };
 		A7DA1FEE113FECD400BF472F /* aligncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = aligncommand.cpp; sourceTree = "<group>"; };
@@ -405,12 +420,15 @@
 		A7DA217A113FECD400BF472F /* weighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = weighted.h; sourceTree = "<group>"; };
 		A7DA217B113FECD400BF472F /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = "<group>"; };
 		A7DA217C113FECD400BF472F /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = "<group>"; };
+		A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsesffcommand.cpp; sourceTree = "<group>"; };
+		A7E8338C115BBDAA00739EC4 /* parsesffcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsesffcommand.h; sourceTree = "<group>"; };
 /* End PBXFileReference section */
 
 /* Begin PBXGroup section */
 		08FB7794FE84155DC02AAC07 /* mothur */ = {
 			isa = PBXGroup;
 			children = (
+				A7639F8D1175DF35008F5578 /* makefile */,
 				A7DA1FF0113FECD400BF472F /* alignment.cpp */,
 				A7DA1FF1113FECD400BF472F /* alignment.hpp */,
 				A7DA1FF6113FECD400BF472F /* averagelinkage.cpp */,
@@ -618,6 +636,16 @@
 				A7DA2008113FECD400BF472F /* bootstrapsharedcommand.h */,
 				A7DA2017113FECD400BF472F /* chimeraseqscommand.cpp */,
 				A7DA2018113FECD400BF472F /* chimeraseqscommand.h */,
+				A7825502116519F70002E2DD /* chimerabellerophoncommand.h */,
+				A7825503116519F70002E2DD /* chimerabellerophoncommand.cpp */,
+				A747E79B1163442A00FB9042 /* chimeracheckcommand.h */,
+				A747E79C1163442A00FB9042 /* chimeracheckcommand.cpp */,
+				A78434881162224F00100BE0 /* chimeraccodecommand.h */,
+				A78434891162224F00100BE0 /* chimeraccodecommand.cpp */,
+				A78254461164D7790002E2DD /* chimerapintailcommand.h */,
+				A78254471164D7790002E2DD /* chimerapintailcommand.cpp */,
+				A747E81C116365E000FB9042 /* chimeraslayercommand.h */,
+				A747E81D116365E000FB9042 /* chimeraslayercommand.cpp */,
 				A7DA201D113FECD400BF472F /* classifyseqscommand.cpp */,
 				A7DA201E113FECD400BF472F /* classifyseqscommand.h */,
 				A7DA2021113FECD400BF472F /* clustercommand.cpp */,
@@ -674,6 +702,8 @@
 				A7DA20B9113FECD400BF472F /* otuhierarchycommand.h */,
 				A7DA20BC113FECD400BF472F /* parselistscommand.cpp */,
 				A7DA20BD113FECD400BF472F /* parselistscommand.h */,
+				A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */,
+				A7E8338C115BBDAA00739EC4 /* parsesffcommand.h */,
 				A7DA20C0113FECD400BF472F /* parsimonycommand.cpp */,
 				A7DA20C1113FECD400BF472F /* parsimonycommand.h */,
 				A7DA20C2113FECD400BF472F /* pcacommand.cpp */,
@@ -706,6 +736,8 @@
 				A7DA20FD113FECD400BF472F /* seqsummarycommand.h */,
 				A7DA2102113FECD400BF472F /* setdircommand.cpp */,
 				A7DA2103113FECD400BF472F /* setdircommand.h */,
+				A76C4A1011876BAF0009460B /* setlogfilecommand.h */,
+				A76C4A1111876BAF0009460B /* setlogfilecommand.cpp */,
 				A7DA210F113FECD400BF472F /* sharedcommand.cpp */,
 				A7DA2110113FECD400BF472F /* sharedcommand.h */,
 				A7DA2154113FECD400BF472F /* summarycommand.cpp */,
@@ -803,6 +835,8 @@
 				A7DA208A113FECD400BF472F /* knn.h */,
 				A7DA20C4113FECD400BF472F /* phylotree.cpp */,
 				A7DA20C5113FECD400BF472F /* phylotree.h */,
+				A76AAD02117F322B003D8DA1 /* phylosummary.h */,
+				A76AAD03117F322B003D8DA1 /* phylosummary.cpp */,
 				A7DA215C113FECD400BF472F /* taxonomyequalizer.cpp */,
 				A7DA215D113FECD400BF472F /* taxonomyequalizer.h */,
 			);
@@ -882,6 +916,9 @@
 /* Begin PBXProject section */
 		08FB7793FE84155DC02AAC07 /* Project object */ = {
 			isa = PBXProject;
+			attributes = {
+				BuildIndependentTargetsInParallel = YES;
+			};
 			buildConfigurationList = 1DEB919308733D9F0010E9CD /* Build configuration list for PBXProject "Mothur" */;
 			compatibilityVersion = "Xcode 3.0";
 			hasScannedForEncodings = 1;
@@ -895,23 +932,6 @@
 /* End PBXProject section */
 
 /* Begin XCBuildConfiguration section */
-		1DEB919008733D9F0010E9CD /* Debug */ = {
-			isa = XCBuildConfiguration;
-			buildSettings = {
-				COPY_PHASE_STRIP = NO;
-				DEBUGGING_SYMBOLS = YES;
-				GCC_DYNAMIC_NO_PIC = NO;
-				GCC_ENABLE_FIX_AND_CONTINUE = YES;
-				GCC_GENERATE_DEBUGGING_SYMBOLS = YES;
-				GCC_OPTIMIZATION_LEVEL = 0;
-				OPTIMIZATION_CFLAGS = "-O0";
-				OTHER_CFLAGS = "";
-				OTHER_LDFLAGS = "";
-				PRODUCT_NAME = mothur;
-				ZERO_LINK = YES;
-			};
-			name = Debug;
-		};
 		1DEB919108733D9F0010E9CD /* Release */ = {
 			isa = XCBuildConfiguration;
 			buildSettings = {
@@ -924,16 +944,6 @@
 			};
 			name = Release;
 		};
-		1DEB919408733D9F0010E9CD /* Debug */ = {
-			isa = XCBuildConfiguration;
-			buildSettings = {
-				GCC_WARN_ABOUT_RETURN_TYPE = YES;
-				GCC_WARN_UNUSED_VARIABLE = YES;
-				PREBINDING = NO;
-				SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
-			};
-			name = Debug;
-		};
 		1DEB919508733D9F0010E9CD /* Release */ = {
 			isa = XCBuildConfiguration;
 			buildSettings = {
@@ -943,6 +953,7 @@
 				);
 				GCC_WARN_ABOUT_RETURN_TYPE = YES;
 				GCC_WARN_UNUSED_VARIABLE = YES;
+				LINK_WITH_STANDARD_LIBRARIES = YES;
 				PREBINDING = NO;
 				SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
 			};
@@ -954,7 +965,6 @@
 		1DEB918F08733D9F0010E9CD /* Build configuration list for PBXLegacyTarget "mothur" */ = {
 			isa = XCConfigurationList;
 			buildConfigurations = (
-				1DEB919008733D9F0010E9CD /* Debug */,
 				1DEB919108733D9F0010E9CD /* Release */,
 			);
 			defaultConfigurationIsVisible = 0;
@@ -963,7 +973,6 @@
 		1DEB919308733D9F0010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
 			isa = XCConfigurationList;
 			buildConfigurations = (
-				1DEB919408733D9F0010E9CD /* Debug */,
 				1DEB919508733D9F0010E9CD /* Release */,
 			);
 			defaultConfigurationIsVisible = 0;