X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=77cfb8c6cd50b9ec16746ef64d16f142be6fb8dc;hp=d7474058b9a98dc706b1af88db7303d84dc0a074;hb=ef4c1b4dfeecc17a0ad5c1c114c748a0443a88ac;hpb=40eaf5045c389e9e3d1930807ae10b4e77b4dd0d

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index d747405..77cfb8c 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -32,7 +32,6 @@
 		A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727864312E9E28C00F86ABA /* removerarecommand.cpp */; };
 		A7386C231619CCE600651424 /* classifysharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7386C211619CCE600651424 /* classifysharedcommand.cpp */; };
 		A7386C251619E52300651424 /* abstractdecisiontree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7386C241619E52200651424 /* abstractdecisiontree.cpp */; };
-		A7386C27161A0F9D00651424 /* abstractrandomforest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7386C26161A0F9C00651424 /* abstractrandomforest.cpp */; };
 		A7386C29161A110800651424 /* decisiontree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7386C28161A110700651424 /* decisiontree.cpp */; };
 		A73901081588C40900ED2ED6 /* loadlogfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73901071588C40900ED2ED6 /* loadlogfilecommand.cpp */; };
 		A73DDBBA13C4A0D1006AAE38 /* clearmemorycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73DDBB913C4A0D1006AAE38 /* clearmemorycommand.cpp */; };
@@ -77,6 +76,7 @@
 		A7C3DC0B14FE457500FE1924 /* cooccurrencecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7C3DC0914FE457500FE1924 /* cooccurrencecommand.cpp */; };
 		A7C3DC0F14FE469500FE1924 /* trialSwap2.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7C3DC0D14FE469500FE1924 /* trialSwap2.cpp */; };
 		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 */; };
 		A7E0243D15B4520A00A5F046 /* sparsedistancematrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E0243C15B4520A00A5F046 /* sparsedistancematrix.cpp */; };
 		A7E6F69E17427D06006775E2 /* makelookupcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E6F69D17427D06006775E2 /* makelookupcommand.cpp */; };
@@ -438,7 +438,6 @@
 		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>"; };
 		A7386C1B1619CACB00651424 /* abstractdecisiontree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = abstractdecisiontree.hpp; sourceTree = "<group>"; };
-		A7386C1C1619CACB00651424 /* abstractrandomforest.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = abstractrandomforest.hpp; sourceTree = "<group>"; };
 		A7386C1D1619CACB00651424 /* decisiontree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = decisiontree.hpp; sourceTree = "<group>"; };
 		A7386C1E1619CACB00651424 /* macros.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = macros.h; sourceTree = "<group>"; };
 		A7386C1F1619CACB00651424 /* randomforest.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = randomforest.hpp; sourceTree = "<group>"; };
@@ -446,7 +445,6 @@
 		A7386C211619CCE600651424 /* classifysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifysharedcommand.cpp; sourceTree = "<group>"; };
 		A7386C221619CCE600651424 /* classifysharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifysharedcommand.h; sourceTree = "<group>"; };
 		A7386C241619E52200651424 /* abstractdecisiontree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = abstractdecisiontree.cpp; sourceTree = "<group>"; };
-		A7386C26161A0F9C00651424 /* abstractrandomforest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = abstractrandomforest.cpp; sourceTree = "<group>"; };
 		A7386C28161A110700651424 /* decisiontree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = decisiontree.cpp; sourceTree = "<group>"; };
 		A73901051588C3EF00ED2ED6 /* loadlogfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = loadlogfilecommand.h; sourceTree = "<group>"; };
 		A73901071588C40900ED2ED6 /* loadlogfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = loadlogfilecommand.cpp; sourceTree = "<group>"; };
@@ -534,6 +532,8 @@
 		A7C3DC0E14FE469500FE1924 /* trialswap2.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = trialswap2.h; sourceTree = "<group>"; };
 		A7C7DAB615DA75760059B0CF /* sffmultiplecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sffmultiplecommand.h; sourceTree = "<group>"; };
 		A7C7DAB815DA758B0059B0CF /* sffmultiplecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sffmultiplecommand.cpp; sourceTree = "<group>"; };
+		A7CFA42F1755400500D9ED4D /* renameseqscommand.h */ = {isa = PBXFileReference; lastKnownFileType = sourcecode.c.h; path = renameseqscommand.h; sourceTree = "<group>"; };
+		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>"; };
 		A7DAAFA3133A254E003956EB /* commandparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = commandparameter.h; sourceTree = "<group>"; };
@@ -1264,8 +1264,6 @@
 			children = (
 				A7386C1B1619CACB00651424 /* abstractdecisiontree.hpp */,
 				A7386C241619E52200651424 /* abstractdecisiontree.cpp */,
-				A7386C1C1619CACB00651424 /* abstractrandomforest.hpp */,
-				A7386C26161A0F9C00651424 /* abstractrandomforest.cpp */,
 				A7386C1D1619CACB00651424 /* decisiontree.hpp */,
 				A7386C28161A110700651424 /* decisiontree.cpp */,
 				A7386C1E1619CACB00651424 /* macros.h */,
@@ -1521,6 +1519,8 @@
 				A727864312E9E28C00F86ABA /* removerarecommand.cpp */,
 				A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */,
 				A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */,
+				A7CFA42F1755400500D9ED4D /* renameseqscommand.h */,
+				A7CFA4301755401800D9ED4D /* renameseqscommand.cpp */,
 				A7E9B7CE12D37EC400DA6239 /* reversecommand.h */,
 				A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */,
 				A7E9B7D212D37EC400DA6239 /* screenseqscommand.h */,
@@ -2346,7 +2346,6 @@
 				A7C7DAB915DA758B0059B0CF /* sffmultiplecommand.cpp in Sources */,
 				A7386C231619CCE600651424 /* classifysharedcommand.cpp in Sources */,
 				A7386C251619E52300651424 /* abstractdecisiontree.cpp in Sources */,
-				A7386C27161A0F9D00651424 /* abstractrandomforest.cpp in Sources */,
 				A7386C29161A110800651424 /* decisiontree.cpp in Sources */,
 				A77E1938161B201E00DB1A2A /* randomforest.cpp in Sources */,
 				A77E193B161B289600DB1A2A /* rftreenode.cpp in Sources */,
@@ -2370,6 +2369,7 @@
 				A77B7188173D4042002163C2 /* randomnumber.cpp in Sources */,
 				A77B718B173D40E5002163C2 /* calcsparcc.cpp in Sources */,
 				A7E6F69E17427D06006775E2 /* makelookupcommand.cpp in Sources */,
+				A7CFA4311755401800D9ED4D /* renameseqscommand.cpp in Sources */,
 			);
 			runOnlyForDeploymentPostprocessing = 0;
 		};
@@ -2419,11 +2419,11 @@
 				GCC_ENABLE_SSE3_EXTENSIONS = NO;
 				GCC_ENABLE_SSE41_EXTENSIONS = NO;
 				GCC_ENABLE_SSE42_EXTENSIONS = NO;
-				GCC_OPTIMIZATION_LEVEL = 3;
+				GCC_OPTIMIZATION_LEVEL = s;
 				GCC_PREPROCESSOR_DEFINITIONS = (
 					"MOTHUR_FILES=\"\\\"../../release\\\"\"",
-					"VERSION=\"\\\"1.29.2\\\"\"",
-					"RELEASE_DATE=\"\\\"2/12/2013\\\"\"",
+					"VERSION=\"\\\"1.31.0\\\"\"",
+					"RELEASE_DATE=\"\\\"5/24/2013\\\"\"",
 				);
 				"GCC_VERSION[arch=*]" = "";
 				GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
@@ -2456,10 +2456,10 @@
 				GCC_C_LANGUAGE_STANDARD = gnu99;
 				GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
 				GCC_MODEL_TUNING = "";
-				GCC_OPTIMIZATION_LEVEL = 3;
+				GCC_OPTIMIZATION_LEVEL = s;
 				GCC_PREPROCESSOR_DEFINITIONS = (
-					"VERSION=\"\\\"1.30.0\\\"\"",
-					"RELEASE_DATE=\"\\\"4/01/2013\\\"\"",
+					"VERSION=\"\\\"1.31.0\\\"\"",
+					"RELEASE_DATE=\"\\\"5/24/2013\\\"\"",
 				);
 				GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
 				GCC_WARN_ABOUT_RETURN_TYPE = YES;