X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=a44e1f3d7e3e824a58e4b5c0eaa4d9c960b1deb8;hb=ee4dd201fa4f2c4ede5b2e525c82cce0a37de363;hp=5dc0ea90e1cc5d932d128d2ec885505ffb5d47b7;hpb=12a28e2ea55790a27a39be09934015320f2419ee;p=mothur.git

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 5dc0ea9..a44e1f3 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -158,10 +158,13 @@
 		7EC3D4550FA0FFF900338DA5 /* coverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7EC3D4500FA0FFF900338DA5 /* coverage.cpp */; };
 		7EC3D4560FA0FFF900338DA5 /* whittaker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */; };
 		8DD76F6A0486A84900D96B5E /* Mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6859E8B029090EE04C91782 /* Mothur.1 */; };
+		A7027F2810DFF86D00BF45FE /* preclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7027F2710DFF86D00BF45FE /* preclustercommand.cpp */; };
+		A704E8A31106045D00870157 /* otuhierarchycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A704E8A21106045D00870157 /* otuhierarchycommand.cpp */; };
 		A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */; };
 		A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */; };
 		A70B53AC0F4CD7AD0064797E /* getlinecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */; };
 		A70DECD91063D8B40057C03C /* secondarystructurecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */; };
+		A727E84A10D14568001A8432 /* readblast.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727E84910D14568001A8432 /* readblast.cpp */; };
 		A7283FF81056CAE100D0CC69 /* chimeracheckrdp.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */; };
 		A729ACD010848E6100139801 /* hclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A729ACCF10848E6100139801 /* hclustercommand.cpp */; };
 		A729ACE410849BBE00139801 /* hcluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A729ACE310849BBE00139801 /* hcluster.cpp */; };
@@ -178,8 +181,13 @@
 		A787844510A1EBDD0086103D /* knn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A787844410A1EBDD0086103D /* knn.cpp */; };
 		A7B04493106CC3E60046FC83 /* chimeraslayer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */; };
 		A7B0450E106CEEC90046FC83 /* slayer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7B0450D106CEEC90046FC83 /* slayer.cpp */; };
+		A7D176CF10F2558500159497 /* pcacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D176CE10F2558500159497 /* pcacommand.cpp */; };
+		A7D86C7D10FE09AB00865661 /* formatcolumn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D86C7C10FE09AB00865661 /* formatcolumn.cpp */; };
+		A7D86C8C10FE09FE00865661 /* formatphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D86C8B10FE09FE00865661 /* formatphylip.cpp */; };
+		A7E0AAB610D2886D00CF407B /* mgclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E0AAB510D2886D00CF407B /* mgclustercommand.cpp */; };
 		A7E4A783106913F900688F62 /* getsharedotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E4A782106913F900688F62 /* getsharedotucommand.cpp */; };
 		A7E4A824106A9AD700688F62 /* maligner.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E4A823106A9AD700688F62 /* maligner.cpp */; };
+		A7F5759710CEBC0600E20E47 /* libreadline.a in Frameworks */ = {isa = PBXBuildFile; fileRef = A7F5759610CEBC0600E20E47 /* libreadline.a */; };
 		EB1216880F619B83004A865F /* bergerparker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1216870F619B83004A865F /* bergerparker.cpp */; };
 		EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1216E40F61ACFB004A865F /* bstick.cpp */; };
 		EB1217230F61C9AC004A865F /* sharedkstest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = EB1217220F61C9AC004A865F /* sharedkstest.cpp */; };
@@ -523,6 +531,10 @@
 		7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = SOURCE_ROOT; };
 		7EC3D4540FA0FFF900338DA5 /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = SOURCE_ROOT; };
 		8DD76F6C0486A84900D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; };
+		A7027F2610DFF86D00BF45FE /* preclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = preclustercommand.h; sourceTree = SOURCE_ROOT; };
+		A7027F2710DFF86D00BF45FE /* preclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = preclustercommand.cpp; sourceTree = SOURCE_ROOT; };
+		A704E8A11106045D00870157 /* otuhierarchycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = otuhierarchycommand.h; sourceTree = SOURCE_ROOT; };
+		A704E8A21106045D00870157 /* otuhierarchycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = otuhierarchycommand.cpp; sourceTree = SOURCE_ROOT; };
 		A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getgroupcommand.cpp; sourceTree = SOURCE_ROOT; };
 		A70B53A50F4CD7AD0064797E /* getgroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupcommand.h; sourceTree = SOURCE_ROOT; };
 		A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlabelcommand.cpp; sourceTree = SOURCE_ROOT; };
@@ -531,6 +543,8 @@
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 		A70DECD71063D8B40057C03C /* secondarystructurecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = secondarystructurecommand.h; sourceTree = SOURCE_ROOT; };
 		A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = secondarystructurecommand.cpp; sourceTree = SOURCE_ROOT; };
+		A727E84810D14568001A8432 /* readblast.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readblast.h; sourceTree = SOURCE_ROOT; };
+		A727E84910D14568001A8432 /* readblast.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readblast.cpp; sourceTree = SOURCE_ROOT; };
 		A7283FF61056CAE100D0CC69 /* chimeracheckrdp.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeracheckrdp.h; sourceTree = SOURCE_ROOT; };
 		A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeracheckrdp.cpp; sourceTree = SOURCE_ROOT; };
 		A729ACCE10848E6100139801 /* hclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hclustercommand.h; sourceTree = SOURCE_ROOT; };
@@ -563,10 +577,20 @@
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 		A7B0450C106CEEC90046FC83 /* slayer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slayer.h; sourceTree = SOURCE_ROOT; };
 		A7B0450D106CEEC90046FC83 /* slayer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slayer.cpp; sourceTree = SOURCE_ROOT; };
+		A7D176CD10F2558500159497 /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = SOURCE_ROOT; };
+		A7D176CE10F2558500159497 /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = SOURCE_ROOT; };
+		A7D86C6A10FE084300865661 /* formatmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatmatrix.h; sourceTree = SOURCE_ROOT; };
+		A7D86C7B10FE09AB00865661 /* formatcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatcolumn.h; sourceTree = SOURCE_ROOT; };
+		A7D86C7C10FE09AB00865661 /* formatcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = formatcolumn.cpp; sourceTree = SOURCE_ROOT; };
+		A7D86C8A10FE09FE00865661 /* formatphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatphylip.h; sourceTree = SOURCE_ROOT; };
+		A7D86C8B10FE09FE00865661 /* formatphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = formatphylip.cpp; sourceTree = SOURCE_ROOT; };
+		A7E0AAB410D2886D00CF407B /* mgclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mgclustercommand.h; sourceTree = SOURCE_ROOT; };
+		A7E0AAB510D2886D00CF407B /* mgclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mgclustercommand.cpp; sourceTree = SOURCE_ROOT; };
 		A7E4A781106913F900688F62 /* getsharedotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsharedotucommand.h; sourceTree = SOURCE_ROOT; };
 		A7E4A782106913F900688F62 /* getsharedotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsharedotucommand.cpp; sourceTree = SOURCE_ROOT; };
 		A7E4A822106A9AD700688F62 /* maligner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = maligner.h; sourceTree = SOURCE_ROOT; };
 		A7E4A823106A9AD700688F62 /* maligner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = maligner.cpp; sourceTree = SOURCE_ROOT; };
+		A7F5759610CEBC0600E20E47 /* libreadline.a */ = {isa = PBXFileReference; lastKnownFileType = archive.ar; name = libreadline.a; path = "../readline-6.0/libreadline.a"; sourceTree = SOURCE_ROOT; };
 		C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = "<group>"; };
 		EB1216860F619B83004A865F /* bergerparker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bergerparker.h; sourceTree = SOURCE_ROOT; };
 		EB1216870F619B83004A865F /* bergerparker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bergerparker.cpp; sourceTree = SOURCE_ROOT; };
@@ -589,6 +613,7 @@
 			isa = PBXFrameworksBuildPhase;
 			buildActionMask = 2147483647;
 			files = (
+				A7F5759710CEBC0600E20E47 /* libreadline.a in Frameworks */,
 			);
 			runOnlyForDeploymentPostprocessing = 0;
 		};
@@ -681,6 +706,7 @@
 				37D928490F21331F001D4494 /* summarydisplay.h */,
 				37519AB30F810FAE00FED5E8 /* venn.h */,
 				37519AB40F810FAE00FED5E8 /* venn.cpp */,
+				A7F5759610CEBC0600E20E47 /* libreadline.a */,
 			);
 			name = Source;
 			sourceTree = "<group>";
@@ -721,6 +747,13 @@
 		3796441D0FB9B9650081FDB6 /* read */ = {
 			isa = PBXGroup;
 			children = (
+				A7D86C6A10FE084300865661 /* formatmatrix.h */,
+				A7D86C7B10FE09AB00865661 /* formatcolumn.h */,
+				A7D86C7C10FE09AB00865661 /* formatcolumn.cpp */,
+				A7D86C8A10FE09FE00865661 /* formatphylip.h */,
+				A7D86C8B10FE09FE00865661 /* formatphylip.cpp */,
+				A727E84810D14568001A8432 /* readblast.h */,
+				A727E84910D14568001A8432 /* readblast.cpp */,
 				A751ACE81098B283003D0911 /* readcluster.h */,
 				A751ACE91098B283003D0911 /* readcluster.cpp */,
 				375AA1340F9E433D008EF9B8 /* readcolumn.h */,
@@ -911,12 +944,20 @@
 				21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */,
 				7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */,
 				7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */,
+				A7E0AAB410D2886D00CF407B /* mgclustercommand.h */,
+				A7E0AAB510D2886D00CF407B /* mgclustercommand.cpp */,
 				375873F70F7D649C0040F377 /* nocommands.h */,
 				375873F60F7D649C0040F377 /* nocommands.cpp */,
+				A704E8A11106045D00870157 /* otuhierarchycommand.h */,
+				A704E8A21106045D00870157 /* otuhierarchycommand.cpp */,
 				3792946E0F2E191800B9034A /* parsimonycommand.h */,
 				3792946F0F2E191800B9034A /* parsimonycommand.cpp */,
+				A7D176CD10F2558500159497 /* pcacommand.h */,
+				A7D176CE10F2558500159497 /* pcacommand.cpp */,
 				A773808E10B6EFD1002A6A61 /* phylotypecommand.h */,
 				A773808F10B6EFD1002A6A61 /* phylotypecommand.cpp */,
+				A7027F2610DFF86D00BF45FE /* preclustercommand.h */,
+				A7027F2710DFF86D00BF45FE /* preclustercommand.cpp */,
 				37D927FE0F21331F001D4494 /* quitcommand.h */,
 				37D927FD0F21331F001D4494 /* quitcommand.cpp */,
 				37D928080F21331F001D4494 /* rarefactcommand.h */,
@@ -1283,6 +1324,13 @@
 				A787844510A1EBDD0086103D /* knn.cpp in Sources */,
 				A773805F10B6D6FC002A6A61 /* taxonomyequalizer.cpp in Sources */,
 				A773809010B6EFD1002A6A61 /* phylotypecommand.cpp in Sources */,
+				A727E84A10D14568001A8432 /* readblast.cpp in Sources */,
+				A7E0AAB610D2886D00CF407B /* mgclustercommand.cpp in Sources */,
+				A7027F2810DFF86D00BF45FE /* preclustercommand.cpp in Sources */,
+				A7D176CF10F2558500159497 /* pcacommand.cpp in Sources */,
+				A7D86C7D10FE09AB00865661 /* formatcolumn.cpp in Sources */,
+				A7D86C8C10FE09FE00865661 /* formatphylip.cpp in Sources */,
+				A704E8A31106045D00870157 /* otuhierarchycommand.cpp in Sources */,
 			);
 			runOnlyForDeploymentPostprocessing = 0;
 		};
@@ -1302,6 +1350,10 @@
 					"_GLIBCXX_DEBUG_PEDANTIC=1",
 				);
 				INSTALL_PATH = /usr/local/bin;
+				LIBRARY_SEARCH_PATHS = (
+					"$(inherited)",
+					"\"$(SRCROOT)/../readline-6.0\"",
+				);
 				PRODUCT_NAME = mothur;
 				ZERO_LINK = YES;
 			};
@@ -1313,6 +1365,10 @@
 				DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
 				GCC_MODEL_TUNING = G5;
 				INSTALL_PATH = /usr/local/bin;
+				LIBRARY_SEARCH_PATHS = (
+					"$(inherited)",
+					"\"$(SRCROOT)/../readline-6.0\"",
+				);
 				PRODUCT_NAME = mothur;
 			};
 			name = Release;
@@ -1320,6 +1376,8 @@
 		1DEB923608733DC60010E9CD /* Debug */ = {
 			isa = XCBuildConfiguration;
 			buildSettings = {
+				ARCHS = "$(ARCHS_STANDARD_64_BIT_PRE_XCODE_3_1)";
+				ARCHS_STANDARD_64_BIT_PRE_XCODE_3_1 = x86_64;
 				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
 				GCC_WARN_ABOUT_RETURN_TYPE = YES;
@@ -1336,10 +1394,8 @@
 		1DEB923708733DC60010E9CD /* Release */ = {
 			isa = XCBuildConfiguration;
 			buildSettings = {
-				ARCHS = (
-					ppc,
-					i386,
-				);
+				ARCHS = "$(ARCHS_STANDARD_64_BIT_PRE_XCODE_3_1)";
+				ARCHS_STANDARD_64_BIT_PRE_XCODE_3_1 = x86_64;
 				GCC_OPTIMIZATION_LEVEL = 3;
 				GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
 				GCC_WARN_ABOUT_MISSING_PROTOTYPES = YES;
@@ -1355,6 +1411,8 @@
 					"-ansi",
 					"-pedantic",
 					"-wall",
+					"-lreadline",
+					"-DUSE_READLINE",
 				);
 				PREBINDING = NO;
 				SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";