changes to filter.seqs

[mothur.git] / Mothur.xcodeproj / project.pbxproj

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 21dbf8dfbb074de24a0b70e523bd95e56d414695..89ddb28bfee495e7145be65740f860460bae44d6 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -164,6 +164,8 @@
                A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */; };
                A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */; };
                A70DECD91063D8B40057C03C /* secondarystructurecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */; };
+               A70F3FD01136E391004FDC52 /* mothurout.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70F3FCF1136E391004FDC52 /* mothurout.cpp */; };
+               A71CB8A311354B9F00848EF7 /* parselistscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A71CB8A211354B9F00848EF7 /* parselistscommand.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 */; };
@@ -188,6 +190,7 @@
                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 */; };
+               A7E8A22F1125939F0011D39C /* chimerarealigner.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E8A22E1125939F0011D39C /* chimerarealigner.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 */; };
@@ -544,6 +547,10 @@
                A70B53A70F4CD7AD0064797E /* getlabelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlabelcommand.h; sourceTree = SOURCE_ROOT; };
                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; };
+               A70F3FCE1136E391004FDC52 /* mothurout.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothurout.h; sourceTree = SOURCE_ROOT; };
+               A70F3FCF1136E391004FDC52 /* mothurout.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothurout.cpp; sourceTree = SOURCE_ROOT; };
+               A71CB8A111354B9F00848EF7 /* parselistscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parselistscommand.h; sourceTree = SOURCE_ROOT; };
+               A71CB8A211354B9F00848EF7 /* parselistscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parselistscommand.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; };
@@ -593,6 +600,8 @@
                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; };
+               A7E8A22D1125939F0011D39C /* chimerarealigner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerarealigner.h; sourceTree = SOURCE_ROOT; };
+               A7E8A22E1125939F0011D39C /* chimerarealigner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerarealigner.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; };
@@ -679,6 +688,8 @@
                                7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */,
                                37E3ED800F4D9D0D00B5DF02 /* mothur.h */,
                                37D927EF0F21331F001D4494 /* mothur.cpp */,
+                               A70F3FCE1136E391004FDC52 /* mothurout.h */,
+                               A70F3FCF1136E391004FDC52 /* mothurout.cpp */,
                                373C691E0FC1C98600137ACD /* nast.hpp */,
                                373C691D0FC1C98600137ACD /* nast.cpp */,
                                373C692A0FC1C9EB00137ACD /* nastreport.hpp */,
@@ -733,6 +744,8 @@
                                A75B887B104C16860083C454 /* ccode.cpp */,
                                A7283FF61056CAE100D0CC69 /* chimeracheckrdp.h */,
                                A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */,
+                               A7E8A22D1125939F0011D39C /* chimerarealigner.h */,
+                               A7E8A22E1125939F0011D39C /* chimerarealigner.cpp */,
                                A7B04491106CC3E60046FC83 /* chimeraslayer.h */,
                                A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */,
                                372A55531017922B00C5194B /* decalc.h */,
@@ -951,6 +964,8 @@
                                375873F60F7D649C0040F377 /* nocommands.cpp */,
                                A704E8A11106045D00870157 /* otuhierarchycommand.h */,
                                A704E8A21106045D00870157 /* otuhierarchycommand.cpp */,
+                               A71CB8A111354B9F00848EF7 /* parselistscommand.h */,
+                               A71CB8A211354B9F00848EF7 /* parselistscommand.cpp */,
                                3792946E0F2E191800B9034A /* parsimonycommand.h */,
                                3792946F0F2E191800B9034A /* parsimonycommand.cpp */,
                                A7D176CD10F2558500159497 /* pcacommand.h */,
@@ -1337,6 +1352,9 @@
                                A704E8A31106045D00870157 /* otuhierarchycommand.cpp in Sources */,
                                A70B00C8110885EB002F453A /* setdircommand.cpp in Sources */,
                                A794201111107897003AECCD /* distancedb.cpp in Sources */,
+                               A7E8A22F1125939F0011D39C /* chimerarealigner.cpp in Sources */,
+                               A71CB8A311354B9F00848EF7 /* parselistscommand.cpp in Sources */,
+                               A70F3FD01136E391004FDC52 /* mothurout.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
@@ -1413,6 +1431,8 @@
                                GCC_WARN_UNUSED_PARAMETER = NO;
                                GCC_WARN_UNUSED_VALUE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
+                               LD_MAP_FILE_PATH = "$(TARGET_TEMP_DIR)/$(PRODUCT_NAME)-LinkMap-$(CURRENT_VARIANT)-$(CURRENT_ARCH).txt";
+                               LINK_WITH_STANDARD_LIBRARIES = YES;
                                OTHER_CPLUSPLUSFLAGS = (
                                        "-ansi",
                                        "-pedantic",
@@ -1420,6 +1440,7 @@
                                        "-lreadline",
                                        "-DUSE_READLINE",
                                );
+                               OTHER_LDFLAGS = "";
                                PREBINDING = NO;
                                SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
                                SYMROOT = /Users/johnwestcott/Desktop;