added set.current and get.current commands and modified existing commands to update...

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

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index e4797253008a0057cc5562ddef17f0c4b4a8efa2..4bc5960998187c10304d8ea3d6874250d2120f1e 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -292,6 +292,8 @@
                A7FA10021302E097003860FE /* mantelcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FA10011302E096003860FE /* mantelcommand.cpp */; };
                A7FC480E12D788F20055BC5C /* linearalgebra.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FC480D12D788F20055BC5C /* linearalgebra.cpp */; };
                A7FC486712D795D60055BC5C /* pcacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FC486612D795D60055BC5C /* pcacommand.cpp */; };
+               A7FE7C401330EA1000F7B327 /* getcurrentcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */; };
+               A7FE7E6D13311EA400F7B327 /* setcurrentcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FE7E6C13311EA400F7B327 /* setcurrentcommand.cpp */; };
 /* End PBXBuildFile section */
 
 /* Begin PBXCopyFilesBuildPhase section */
@@ -329,6 +331,7 @@
                A7A61F1A130035C800E05B6B /* LICENSE */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = LICENSE; sourceTree = "<group>"; };
                A7A61F2B130062E000E05B6B /* amovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = amovacommand.h; sourceTree = "<group>"; };
                A7A61F2C130062E000E05B6B /* amovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = amovacommand.cpp; sourceTree = "<group>"; };
+               A7AACFBA132FE008003D6C4D /* currentfile.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = currentfile.h; sourceTree = "<group>"; };
                A7E9B64F12D37EC300DA6239 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = "<group>"; };
                A7E9B65012D37EC300DA6239 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = "<group>"; };
                A7E9B65112D37EC300DA6239 /* aligncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = aligncommand.cpp; sourceTree = "<group>"; };
@@ -897,6 +900,10 @@
                A7FC480D12D788F20055BC5C /* linearalgebra.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = linearalgebra.cpp; sourceTree = "<group>"; };
                A7FC486512D795D60055BC5C /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = "<group>"; };
                A7FC486612D795D60055BC5C /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = "<group>"; };
+               A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getcurrentcommand.h; sourceTree = "<group>"; };
+               A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getcurrentcommand.cpp; sourceTree = "<group>"; };
+               A7FE7E6B13311EA400F7B327 /* setcurrentcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setcurrentcommand.h; sourceTree = "<group>"; };
+               A7FE7E6C13311EA400F7B327 /* setcurrentcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setcurrentcommand.cpp; sourceTree = "<group>"; };
                C6A0FF2C0290799A04C91782 /* mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = mothur.1; sourceTree = "<group>"; };
 /* End PBXFileReference section */
 
@@ -946,6 +953,7 @@
                                A7E9B6B212D37EC400DA6239 /* commandoptionparser.hpp */,
                                A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */,
                                A7E9BA4212D3960D00DA6239 /* containers */,
+                               A7AACFBA132FE008003D6C4D /* currentfile.h */,
                                A7E9B6C912D37EC400DA6239 /* display.h */,
                                A7E9B6D112D37EC400DA6239 /* dlibshuff.cpp */,
                                A7E9B6D212D37EC400DA6239 /* dlibshuff.h */,
@@ -1094,6 +1102,8 @@
                                A7E9B6CC12D37EC400DA6239 /* distancecommand.h */,
                                A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */,
                                A7E9B6E412D37EC400DA6239 /* filterseqscommand.h */,
+                               A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */,
+                               A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */,
                                A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */,
                                A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */,
                                A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */,
@@ -1212,6 +1222,8 @@
                                A7E9B7D812D37EC400DA6239 /* seqerrorcommand.h */,
                                A7E9B7D912D37EC400DA6239 /* seqsummarycommand.cpp */,
                                A7E9B7DA12D37EC400DA6239 /* seqsummarycommand.h */,
+                               A7FE7E6B13311EA400F7B327 /* setcurrentcommand.h */,
+                               A7FE7E6C13311EA400F7B327 /* setcurrentcommand.cpp */,
                                A7E9B7DF12D37EC400DA6239 /* setdircommand.cpp */,
                                A7E9B7E012D37EC400DA6239 /* setdircommand.h */,
                                A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */,
@@ -1625,7 +1637,7 @@
                        attributes = {
                                ORGANIZATIONNAME = "Schloss Lab";
                        };
-                       buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */;
+                       buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */;
                        compatibilityVersion = "Xcode 3.1";
                        developmentRegion = English;
                        hasScannedForEncodings = 1;
@@ -1933,6 +1945,8 @@
                                A7FA10021302E097003860FE /* mantelcommand.cpp in Sources */,
                                A799F5B91309A3E000AEEFA0 /* makefastqcommand.cpp in Sources */,
                                A71CB160130B04A2001E7287 /* anosimcommand.cpp in Sources */,
+                               A7FE7C401330EA1000F7B327 /* getcurrentcommand.cpp in Sources */,
+                               A7FE7E6D13311EA400F7B327 /* setcurrentcommand.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
@@ -1950,6 +1964,7 @@
                                GCC_OPTIMIZATION_LEVEL = 0;
                                INSTALL_PATH = /usr/local/bin;
                                PRODUCT_NAME = Mothur;
+                               SDKROOT = macosx10.6;
                        };
                        name = Debug;
                };
@@ -1969,14 +1984,14 @@
                1DEB928A08733DD80010E9CD /* Debug */ = {
                        isa = XCBuildConfiguration;
                        buildSettings = {
-                               ARCHS = "$(ARCHS_STANDARD_32_64_BIT)";
+                               ARCHS = "$(ARCHS_STANDARD_64_BIT)";
                                DEPLOYMENT_LOCATION = NO;
                                GCC_C_LANGUAGE_STANDARD = gnu99;
                                GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "MOTHUR_FILES=\"\\\"../release\\\"\"",
-                                       "VERSION=\"\\\"1.16.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"2/7/2011\\\"\"",
+                                       "VERSION=\"\\\"1.17.3\\\"\"",
+                                       "RELEASE_DATE=\"\\\"3/07/2011\\\"\"",
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
@@ -1985,8 +2000,8 @@
                                MACH_O_TYPE = mh_execute;
                                ONLY_ACTIVE_ARCH = YES;
                                OTHER_CPLUSPLUSFLAGS = (
-                                       "-DUSE_READLINE",
                                        "-DBIT_VERSION",
+                                       "-DUSE_READLINE",
                                        "$(OTHER_CFLAGS)",
                                );
                                OTHER_LDFLAGS = (
@@ -1994,14 +2009,14 @@
                                        "-lreadline",
                                );
                                PREBINDING = NO;
-                               SDKROOT = macosx10.5;
+                               SDKROOT = macosx10.6;
                        };
                        name = Debug;
                };
                1DEB928B08733DD80010E9CD /* Release */ = {
                        isa = XCBuildConfiguration;
                        buildSettings = {
-                               ARCHS = "$(ARCHS_STANDARD_32_64_BIT)";
+                               ARCHS = "$(NATIVE_ARCH_ACTUAL)";
                                DEPLOYMENT_LOCATION = NO;
                                GCC_C_LANGUAGE_STANDARD = gnu99;
                                GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
@@ -2032,7 +2047,7 @@
                                        "-lreadline",
                                );
                                PREBINDING = NO;
-                               SDKROOT = macosx10.5;
+                               SDKROOT = "";
                        };
                        name = Release;
                };
@@ -2048,7 +2063,7 @@
                        defaultConfigurationIsVisible = 0;
                        defaultConfigurationName = Release;
                };
-               1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */ = {
+               1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
                        isa = XCConfigurationList;
                        buildConfigurations = (
                                1DEB928A08733DD80010E9CD /* Debug */,