X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=b04bf2a564483a942f68eda44fe2412bc5cfc83e;hb=29c0d3ec01be5372807eb86261100d77de253787;hp=8b890ae6b59a2088be0ac1b385d30620ef2a65ab;hpb=de2dc9fb831f569b823031d0730f5a0d739e8290;p=mothur.git

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 8b890ae..b04bf2a 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -105,7 +105,6 @@
 		37D928700F21331F001D4494 /* nameassignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F00F21331F001D4494 /* nameassignment.cpp */; };
 		37D928720F21331F001D4494 /* npshannon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F40F21331F001D4494 /* npshannon.cpp */; };
 		37D928730F21331F001D4494 /* ordervector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F70F21331F001D4494 /* ordervector.cpp */; };
-		37D928740F21331F001D4494 /* parselistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F90F21331F001D4494 /* parselistcommand.cpp */; };
 		37D928750F21331F001D4494 /* progress.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FB0F21331F001D4494 /* progress.cpp */; };
 		37D928760F21331F001D4494 /* quitcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FD0F21331F001D4494 /* quitcommand.cpp */; };
 		37D928770F21331F001D4494 /* rabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FF0F21331F001D4494 /* rabundvector.cpp */; };
@@ -117,7 +116,6 @@
 		37D928840F21331F001D4494 /* sabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281A0F21331F001D4494 /* sabundvector.cpp */; };
 		37D928850F21331F001D4494 /* sequence.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281C0F21331F001D4494 /* sequence.cpp */; };
 		37D928860F21331F001D4494 /* shannon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D9281E0F21331F001D4494 /* shannon.cpp */; };
-		37D928870F21331F001D4494 /* shared.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928200F21331F001D4494 /* shared.cpp */; };
 		37D928880F21331F001D4494 /* sharedace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928220F21331F001D4494 /* sharedace.cpp */; };
 		37D928890F21331F001D4494 /* sharedchao1.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928240F21331F001D4494 /* sharedchao1.cpp */; };
 		37D9288A0F21331F001D4494 /* sharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D928260F21331F001D4494 /* sharedcommand.cpp */; };
@@ -277,12 +275,12 @@
 		375AA1380F9E433D008EF9B8 /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = SOURCE_ROOT; };
 		377326630FAF16E0007ABB8B /* concensuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = concensuscommand.cpp; sourceTree = SOURCE_ROOT; };
 		377326640FAF16E0007ABB8B /* concensuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = concensuscommand.h; sourceTree = SOURCE_ROOT; };
-		378598640FDD497000EF9D03 /* heatmapsimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsimcommand.h; sourceTree = "<group>"; };
-		378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsimcommand.cpp; sourceTree = "<group>"; };
-		378598720FDD4C1500EF9D03 /* heatmapsim.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsim.h; sourceTree = "<group>"; };
-		378598730FDD4C1500EF9D03 /* heatmapsim.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsim.cpp; sourceTree = "<group>"; };
-		3785990E0FDD7E8E00EF9D03 /* optionparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = optionparser.h; sourceTree = "<group>"; };
-		3785990F0FDD7E8E00EF9D03 /* optionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = optionparser.cpp; sourceTree = "<group>"; };
+		378598640FDD497000EF9D03 /* heatmapsimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsimcommand.h; sourceTree = SOURCE_ROOT; };
+		378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsimcommand.cpp; sourceTree = SOURCE_ROOT; };
+		378598720FDD4C1500EF9D03 /* heatmapsim.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsim.h; sourceTree = SOURCE_ROOT; };
+		378598730FDD4C1500EF9D03 /* heatmapsim.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsim.cpp; sourceTree = SOURCE_ROOT; };
+		3785990E0FDD7E8E00EF9D03 /* optionparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = optionparser.h; sourceTree = SOURCE_ROOT; };
+		3785990F0FDD7E8E00EF9D03 /* optionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = optionparser.cpp; sourceTree = SOURCE_ROOT; };
 		378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = filterseqscommand.cpp; sourceTree = SOURCE_ROOT; };
 		378C1AEF0FB0644D004D63F5 /* filterseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filterseqscommand.h; sourceTree = SOURCE_ROOT; };
 		378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = goodscoverage.cpp; sourceTree = SOURCE_ROOT; };
@@ -386,8 +384,6 @@
 		37D927F60F21331F001D4494 /* observable.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = observable.h; sourceTree = SOURCE_ROOT; };
 		37D927F70F21331F001D4494 /* ordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ordervector.cpp; sourceTree = SOURCE_ROOT; };
 		37D927F80F21331F001D4494 /* ordervector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = ordervector.hpp; sourceTree = SOURCE_ROOT; };
-		37D927F90F21331F001D4494 /* parselistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parselistcommand.cpp; sourceTree = SOURCE_ROOT; };
-		37D927FA0F21331F001D4494 /* parselistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parselistcommand.h; sourceTree = SOURCE_ROOT; };
 		37D927FB0F21331F001D4494 /* progress.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = progress.cpp; sourceTree = SOURCE_ROOT; };
 		37D927FC0F21331F001D4494 /* progress.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = progress.hpp; sourceTree = SOURCE_ROOT; };
 		37D927FD0F21331F001D4494 /* quitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = quitcommand.cpp; sourceTree = SOURCE_ROOT; };
@@ -412,8 +408,6 @@
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 		37D9281E0F21331F001D4494 /* shannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannon.cpp; sourceTree = SOURCE_ROOT; };
 		37D9281F0F21331F001D4494 /* shannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannon.h; sourceTree = SOURCE_ROOT; };
-		37D928200F21331F001D4494 /* shared.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shared.cpp; sourceTree = SOURCE_ROOT; };
-		37D928210F21331F001D4494 /* shared.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shared.h; sourceTree = SOURCE_ROOT; };
 		37D928220F21331F001D4494 /* sharedace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedace.cpp; sourceTree = SOURCE_ROOT; };
 		37D928230F21331F001D4494 /* sharedace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedace.h; sourceTree = SOURCE_ROOT; };
 		37D928240F21331F001D4494 /* sharedchao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedchao1.cpp; sourceTree = SOURCE_ROOT; };
@@ -477,8 +471,8 @@
 		7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuff.cpp; sourceTree = SOURCE_ROOT; };
 		7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = dlibshuff.cpp; sourceTree = SOURCE_ROOT; };
 		7E4130F70F8E58FA00381DD0 /* dlibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dlibshuff.h; sourceTree = SOURCE_ROOT; };
-		7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergefilecommand.h; sourceTree = "<group>"; };
-		7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergefilecommand.cpp; sourceTree = "<group>"; };
+		7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergefilecommand.h; sourceTree = SOURCE_ROOT; };
+		7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergefilecommand.cpp; sourceTree = SOURCE_ROOT; };
 		7EC3D4500FA0FFF900338DA5 /* coverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = coverage.cpp; sourceTree = SOURCE_ROOT; };
 		7EC3D4510FA0FFF900338DA5 /* coverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = coverage.h; sourceTree = SOURCE_ROOT; };
 		7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderberg.h; sourceTree = SOURCE_ROOT; };
@@ -594,8 +588,6 @@
 				37D928050F21331F001D4494 /* rarefact.cpp */,
 				37D928090F21331F001D4494 /* rarefactioncurvedata.h */,
 				3796441D0FB9B9650081FDB6 /* read */,
-				37D928210F21331F001D4494 /* shared.h */,
-				37D928200F21331F001D4494 /* shared.cpp */,
 				211C38310F961DD400FEE541 /* sharedutilities.h */,
 				211C38300F961DD400FEE541 /* sharedutilities.cpp */,
 				37D928420F21331F001D4494 /* singlelinkage.cpp */,
@@ -748,8 +740,6 @@
 		37D928A90F2133E5001D4494 /* commands */ = {
 			isa = PBXGroup;
 			children = (
-				7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */,
-				7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */,
 				37D927CD0F21331F001D4494 /* command.hpp */,
 				378DC5CD0FBDE1C8003B8607 /* aligncommand.h */,
 				378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */,
@@ -793,10 +783,10 @@
 				375873F30F7D648F0040F377 /* libshuffcommand.cpp */,
 				21E859D60FC4632E005E1A48 /* matrixoutputcommand.h */,
 				21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */,
+				7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */,
+				7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */,
 				375873F70F7D649C0040F377 /* nocommands.h */,
 				375873F60F7D649C0040F377 /* nocommands.cpp */,
-				37D927FA0F21331F001D4494 /* parselistcommand.h */,
-				37D927F90F21331F001D4494 /* parselistcommand.cpp */,
 				3792946E0F2E191800B9034A /* parsimonycommand.h */,
 				3792946F0F2E191800B9034A /* parsimonycommand.cpp */,
 				37D927FE0F21331F001D4494 /* quitcommand.h */,
@@ -989,7 +979,6 @@
 				37D928700F21331F001D4494 /* nameassignment.cpp in Sources */,
 				37D928720F21331F001D4494 /* npshannon.cpp in Sources */,
 				37D928730F21331F001D4494 /* ordervector.cpp in Sources */,
-				37D928740F21331F001D4494 /* parselistcommand.cpp in Sources */,
 				37D928750F21331F001D4494 /* progress.cpp in Sources */,
 				37D928760F21331F001D4494 /* quitcommand.cpp in Sources */,
 				37D928770F21331F001D4494 /* rabundvector.cpp in Sources */,
@@ -1001,7 +990,6 @@
 				37D928840F21331F001D4494 /* sabundvector.cpp in Sources */,
 				37D928850F21331F001D4494 /* sequence.cpp in Sources */,
 				37D928860F21331F001D4494 /* shannon.cpp in Sources */,
-				37D928870F21331F001D4494 /* shared.cpp in Sources */,
 				37D928880F21331F001D4494 /* sharedace.cpp in Sources */,
 				37D928890F21331F001D4494 /* sharedchao1.cpp in Sources */,
 				37D9288A0F21331F001D4494 /* sharedcommand.cpp in Sources */,
@@ -1153,10 +1141,15 @@
 			isa = XCBuildConfiguration;
 			buildSettings = {
 				GCC_OPTIMIZATION_LEVEL = 3;
+				GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
 				GCC_WARN_ABOUT_RETURN_TYPE = YES;
+				GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO;
+				GCC_WARN_PEDANTIC = NO;
 				GCC_WARN_UNUSED_VARIABLE = YES;
+				OTHER_CPLUSPLUSFLAGS = "";
 				PREBINDING = NO;
 				SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
+				WARNING_CFLAGS = "";
 			};
 			name = Debug;
 		};
@@ -1168,10 +1161,15 @@
 					i386,
 				);
 				GCC_OPTIMIZATION_LEVEL = 3;
+				GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
 				GCC_WARN_ABOUT_RETURN_TYPE = YES;
+				GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO;
+				GCC_WARN_PEDANTIC = NO;
 				GCC_WARN_UNUSED_VARIABLE = YES;
+				OTHER_CPLUSPLUSFLAGS = "";
 				PREBINDING = NO;
 				SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
+				WARNING_CFLAGS = "";
 			};
 			name = Release;
 		};