X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=4d37747693cceafd0d66ea97075c0ca07cc94ec0;hb=4160a27002f4a3ca436fcd62eca0366b09f8e901;hp=582beaf70ddc256d955b4677911069ab97971d16;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 582beaf..4d37747 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -16,6 +16,7 @@ A71FE12C12EDF72400963CA7 /* mergegroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */; }; A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727864312E9E28C00F86ABA /* removerarecommand.cpp */; }; A75790591301749D00A30DAB /* homovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A75790581301749D00A30DAB /* homovacommand.cpp */; }; + A778FE6B134CA6CA00C0BA33 /* getcommandinfocommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */; }; A799F5B91309A3E000AEEFA0 /* makefastqcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */; }; A7A61F2D130062E000E05B6B /* amovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A61F2C130062E000E05B6B /* amovacommand.cpp */; }; A7E9B88112D37EC400DA6239 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B64F12D37EC300DA6239 /* ace.cpp */; }; @@ -106,7 +107,6 @@ A7E9B8D712D37EC400DA6239 /* getsabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */; }; A7E9B8D812D37EC400DA6239 /* getseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70812D37EC400DA6239 /* getseqscommand.cpp */; }; A7E9B8D912D37EC400DA6239 /* getsharedotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */; }; - A7E9B8DA12D37EC400DA6239 /* globaldata.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70C12D37EC400DA6239 /* globaldata.cpp */; }; A7E9B8DB12D37EC400DA6239 /* goodscoverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70E12D37EC400DA6239 /* goodscoverage.cpp */; }; A7E9B8DC12D37EC400DA6239 /* gotohoverlap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B71012D37EC400DA6239 /* gotohoverlap.cpp */; }; A7E9B8DD12D37EC400DA6239 /* gower.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B71212D37EC400DA6239 /* gower.cpp */; }; @@ -189,7 +189,6 @@ A7E9B92A12D37EC400DA6239 /* readcluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B212D37EC400DA6239 /* readcluster.cpp */; }; A7E9B92B12D37EC400DA6239 /* readcolumn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */; }; A7E9B92C12D37EC400DA6239 /* readdistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */; }; - A7E9B92D12D37EC400DA6239 /* readotu.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B912D37EC400DA6239 /* readotu.cpp */; }; A7E9B92E12D37EC400DA6239 /* readotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */; }; A7E9B92F12D37EC400DA6239 /* readphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */; }; A7E9B93012D37EC400DA6239 /* readtree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7BF12D37EC400DA6239 /* readtree.cpp */; }; @@ -311,6 +310,7 @@ /* Begin PBXFileReference section */ 7E6BE10812F710D8007ADDBE /* refchimeratest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = refchimeratest.h; sourceTree = ""; }; 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = refchimeratest.cpp; sourceTree = ""; }; + 7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdistignorens.h; sourceTree = ""; }; 8DD76FB20486AB0100D96B5E /* Mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = Mothur; sourceTree = BUILT_PRODUCTS_DIR; }; A70332B512D3A13400761E33 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = ""; }; A713EBAA12DC7613000092AC /* readphylipvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylipvector.h; sourceTree = ""; }; @@ -325,6 +325,8 @@ A727864312E9E28C00F86ABA /* removerarecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removerarecommand.cpp; sourceTree = ""; }; A75790571301749D00A30DAB /* homovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = homovacommand.h; sourceTree = ""; }; A75790581301749D00A30DAB /* homovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = homovacommand.cpp; sourceTree = ""; }; + A778FE69134CA6CA00C0BA33 /* getcommandinfocommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getcommandinfocommand.h; sourceTree = ""; }; + A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getcommandinfocommand.cpp; sourceTree = ""; }; A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makefastqcommand.h; sourceTree = ""; }; A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makefastqcommand.cpp; sourceTree = ""; }; A7A61F1A130035C800E05B6B /* LICENSE */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = LICENSE; sourceTree = ""; }; @@ -519,8 +521,6 @@ A7E9B70912D37EC400DA6239 /* getseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getseqscommand.h; sourceTree = ""; }; A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsharedotucommand.cpp; sourceTree = ""; }; A7E9B70B12D37EC400DA6239 /* getsharedotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsharedotucommand.h; sourceTree = ""; }; - A7E9B70C12D37EC400DA6239 /* globaldata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = globaldata.cpp; sourceTree = SOURCE_ROOT; }; - A7E9B70D12D37EC400DA6239 /* globaldata.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = globaldata.hpp; sourceTree = SOURCE_ROOT; }; A7E9B70E12D37EC400DA6239 /* goodscoverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = goodscoverage.cpp; sourceTree = ""; }; A7E9B70F12D37EC400DA6239 /* goodscoverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = goodscoverage.h; sourceTree = ""; }; A7E9B71012D37EC400DA6239 /* gotohoverlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = gotohoverlap.cpp; sourceTree = SOURCE_ROOT; }; @@ -692,8 +692,6 @@ A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistcommand.cpp; sourceTree = ""; }; A7E9B7B712D37EC400DA6239 /* readdistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcommand.h; sourceTree = ""; }; A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = ""; }; - A7E9B7B912D37EC400DA6239 /* readotu.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotu.cpp; sourceTree = ""; }; - A7E9B7BA12D37EC400DA6239 /* readotu.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotu.h; sourceTree = ""; }; A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = ""; }; A7E9B7BC12D37EC400DA6239 /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = ""; }; A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = ""; }; @@ -961,8 +959,6 @@ A7E9B6DB12D37EC400DA6239 /* engine.hpp */, A7E9B6E012D37EC400DA6239 /* fileoutput.cpp */, A7E9B6E112D37EC400DA6239 /* fileoutput.h */, - A7E9B70C12D37EC400DA6239 /* globaldata.cpp */, - A7E9B70D12D37EC400DA6239 /* globaldata.hpp */, A7E9B71112D37EC400DA6239 /* gotohoverlap.hpp */, A7E9B71012D37EC400DA6239 /* gotohoverlap.cpp */, A7E9B71812D37EC400DA6239 /* hcluster.cpp */, @@ -1011,8 +1007,8 @@ A7E9B82412D37EC400DA6239 /* sharedutilities.h */, A7E9B82D12D37EC400DA6239 /* singlelinkage.cpp */, A7E9B83012D37EC400DA6239 /* slibshuff.cpp */, - A7E9B83112D37EC400DA6239 /* slibshuff.h */, A7E9B85112D37EC400DA6239 /* suffixdb.cpp */, + A7E9B83112D37EC400DA6239 /* slibshuff.h */, A7E9B85212D37EC400DA6239 /* suffixdb.hpp */, A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */, A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */, @@ -1099,6 +1095,8 @@ A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */, A7E9B6E412D37EC400DA6239 /* filterseqscommand.h */, A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */, + A778FE69134CA6CA00C0BA33 /* getcommandinfocommand.h */, + A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */, A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */, A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */, A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */, @@ -1262,6 +1260,7 @@ A7E9BA3F12D395F700DA6239 /* calculators */ = { isa = PBXGroup; children = ( + 7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */, A7E9B64F12D37EC300DA6239 /* ace.cpp */, A7E9B65012D37EC300DA6239 /* ace.h */, A7E9B65E12D37EC300DA6239 /* bergerparker.cpp */, @@ -1506,11 +1505,11 @@ A7E9B68112D37EC400DA6239 /* chimeracheckrdp.h */, A7E9B68412D37EC400DA6239 /* chimerarealigner.cpp */, A7E9B68512D37EC400DA6239 /* chimerarealigner.h */, + A7E9B6C212D37EC400DA6239 /* decalc.h */, + A7E9B6C112D37EC400DA6239 /* decalc.cpp */, A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */, A7E9B68912D37EC400DA6239 /* chimeraslayer.h */, - A7E9B6C112D37EC400DA6239 /* decalc.cpp */, A7E9B74612D37EC400DA6239 /* maligner.h */, - A7E9B6C212D37EC400DA6239 /* decalc.h */, A7E9B74512D37EC400DA6239 /* maligner.cpp */, A7E9B79312D37EC400DA6239 /* pintail.cpp */, A7E9B79412D37EC400DA6239 /* pintail.h */, @@ -1574,8 +1573,6 @@ A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */, A7E9B7B512D37EC400DA6239 /* readcolumn.h */, A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */, - A7E9B7BA12D37EC400DA6239 /* readotu.h */, - A7E9B7B912D37EC400DA6239 /* readotu.cpp */, A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */, A7E9B7BE12D37EC400DA6239 /* readphylip.h */, A7E9B7BF12D37EC400DA6239 /* readtree.cpp */, @@ -1746,7 +1743,6 @@ A7E9B8D712D37EC400DA6239 /* getsabundcommand.cpp in Sources */, A7E9B8D812D37EC400DA6239 /* getseqscommand.cpp in Sources */, A7E9B8D912D37EC400DA6239 /* getsharedotucommand.cpp in Sources */, - A7E9B8DA12D37EC400DA6239 /* globaldata.cpp in Sources */, A7E9B8DB12D37EC400DA6239 /* goodscoverage.cpp in Sources */, A7E9B8DC12D37EC400DA6239 /* gotohoverlap.cpp in Sources */, A7E9B8DD12D37EC400DA6239 /* gower.cpp in Sources */, @@ -1829,7 +1825,6 @@ A7E9B92A12D37EC400DA6239 /* readcluster.cpp in Sources */, A7E9B92B12D37EC400DA6239 /* readcolumn.cpp in Sources */, A7E9B92C12D37EC400DA6239 /* readdistcommand.cpp in Sources */, - A7E9B92D12D37EC400DA6239 /* readotu.cpp in Sources */, A7E9B92E12D37EC400DA6239 /* readotucommand.cpp in Sources */, A7E9B92F12D37EC400DA6239 /* readphylip.cpp in Sources */, A7E9B93012D37EC400DA6239 /* readtree.cpp in Sources */, @@ -1943,6 +1938,7 @@ A71CB160130B04A2001E7287 /* anosimcommand.cpp in Sources */, A7FE7C401330EA1000F7B327 /* getcurrentcommand.cpp in Sources */, A7FE7E6D13311EA400F7B327 /* setcurrentcommand.cpp in Sources */, + A778FE6B134CA6CA00C0BA33 /* getcommandinfocommand.cpp in Sources */, ); runOnlyForDeploymentPostprocessing = 0; }; @@ -1983,11 +1979,11 @@ ARCHS = "$(ARCHS_STANDARD_64_BIT)"; DEPLOYMENT_LOCATION = NO; GCC_C_LANGUAGE_STANDARD = gnu99; - GCC_OPTIMIZATION_LEVEL = 3; + GCC_OPTIMIZATION_LEVEL = 0; GCC_PREPROCESSOR_DEFINITIONS = ( "MOTHUR_FILES=\"\\\"../release\\\"\"", - "VERSION=\"\\\"1.17.3\\\"\"", - "RELEASE_DATE=\"\\\"3/07/2011\\\"\"", + "VERSION=\"\\\"1.19.0\\\"\"", + "RELEASE_DATE=\"\\\"5/9/2011\\\"\"", ); GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; @@ -2012,16 +2008,15 @@ 1DEB928B08733DD80010E9CD /* Release */ = { isa = XCBuildConfiguration; buildSettings = { - ARCHS = "$(NATIVE_ARCH_ACTUAL)"; + ARCHS = "$(ARCHS_STANDARD_64_BIT)"; DEPLOYMENT_LOCATION = NO; GCC_C_LANGUAGE_STANDARD = gnu99; GCC_GENERATE_DEBUGGING_SYMBOLS = NO; GCC_MODEL_TUNING = ""; - GCC_OPTIMIZATION_LEVEL = 3; + GCC_OPTIMIZATION_LEVEL = 0; GCC_PREPROCESSOR_DEFINITIONS = ( - "MOTHUR_FILES=\"\\\"../release\\\"\"", - "VERSION=\"\\\"1.15.0\\\"\"", - "RELEASE_DATE=\"\\\"12/10/2010\\\"\"", + "VERSION=\"\\\"1.19.0\\\"\"", + "RELEASE_DATE=\"\\\"5/9/2011\\\"\"", ); GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; @@ -2043,7 +2038,7 @@ "-lreadline", ); PREBINDING = NO; - SDKROOT = ""; + SDKROOT = macosx10.6; }; name = Release; };