camberra fix

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

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 00bcf9abb0d7eb68be32387532647584da236157..769e33999b25da3d3751b2249476e7c53fab7a6a 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -46,6 +46,7 @@
                A778FE6B134CA6CA00C0BA33 /* getcommandinfocommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */; };
                A77A221F139001B600B0BE70 /* deuniquetreecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A77A221E139001B600B0BE70 /* deuniquetreecommand.cpp */; };
                A79234D713C74BF6002B08E2 /* mothurfisher.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A79234D613C74BF6002B08E2 /* mothurfisher.cpp */; };
+               A795840D13F13CD900F201D5 /* countgroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A795840C13F13CD900F201D5 /* countgroupscommand.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 */; };
@@ -316,11 +317,14 @@
                A7E9B98D12D37EC400DA6239 /* weighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87C12D37EC400DA6239 /* weighted.cpp */; };
                A7E9B98E12D37EC400DA6239 /* weightedlinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */; };
                A7E9B98F12D37EC400DA6239 /* whittaker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87F12D37EC400DA6239 /* whittaker.cpp */; };
+               A7F9F5CF141A5E500032F693 /* sequenceparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7F9F5CE141A5E500032F693 /* sequenceparser.cpp */; };
                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 */; };
+               A7FF19F2140FFDA500AD216D /* trimoligos.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FF19F1140FFDA500AD216D /* trimoligos.cpp */; };
+               A7FFB558142CA02C004884F2 /* summarytaxcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FFB557142CA02C004884F2 /* summarytaxcommand.cpp */; };
 /* End PBXBuildFile section */
 
 /* Begin PBXCopyFilesBuildPhase section */
@@ -420,6 +424,8 @@
                A77A221E139001B600B0BE70 /* deuniquetreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deuniquetreecommand.cpp; sourceTree = "<group>"; };
                A79234D513C74BF6002B08E2 /* mothurfisher.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothurfisher.h; sourceTree = "<group>"; };
                A79234D613C74BF6002B08E2 /* mothurfisher.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothurfisher.cpp; sourceTree = "<group>"; };
+               A795840B13F13CD900F201D5 /* countgroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = countgroupscommand.h; sourceTree = "<group>"; };
+               A795840C13F13CD900F201D5 /* countgroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = countgroupscommand.cpp; sourceTree = "<group>"; };
                A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makefastqcommand.h; sourceTree = "<group>"; };
                A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makefastqcommand.cpp; sourceTree = "<group>"; };
                A7A61F1A130035C800E05B6B /* LICENSE */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = LICENSE; sourceTree = "<group>"; };
@@ -934,12 +940,12 @@
                A7E9B84E12D37EC400DA6239 /* structpearson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = structpearson.h; sourceTree = "<group>"; };
                A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = subsamplecommand.cpp; sourceTree = "<group>"; };
                A7E9B85012D37EC400DA6239 /* subsamplecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = subsamplecommand.h; sourceTree = "<group>"; };
-               A7E9B85112D37EC400DA6239 /* suffixdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixdb.cpp; sourceTree = SOURCE_ROOT; };
-               A7E9B85212D37EC400DA6239 /* suffixdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixdb.hpp; sourceTree = SOURCE_ROOT; };
-               A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixnodes.cpp; sourceTree = SOURCE_ROOT; };
-               A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixnodes.hpp; sourceTree = SOURCE_ROOT; };
-               A7E9B85512D37EC400DA6239 /* suffixtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixtree.cpp; sourceTree = SOURCE_ROOT; };
-               A7E9B85612D37EC400DA6239 /* suffixtree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixtree.hpp; sourceTree = SOURCE_ROOT; };
+               A7E9B85112D37EC400DA6239 /* suffixdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixdb.cpp; sourceTree = "<group>"; };
+               A7E9B85212D37EC400DA6239 /* suffixdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixdb.hpp; sourceTree = "<group>"; };
+               A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixnodes.cpp; sourceTree = "<group>"; };
+               A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixnodes.hpp; sourceTree = "<group>"; };
+               A7E9B85512D37EC400DA6239 /* suffixtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixtree.cpp; sourceTree = "<group>"; };
+               A7E9B85612D37EC400DA6239 /* suffixtree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixtree.hpp; sourceTree = "<group>"; };
                A7E9B85712D37EC400DA6239 /* summarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarycommand.cpp; sourceTree = "<group>"; };
                A7E9B85812D37EC400DA6239 /* summarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarycommand.h; sourceTree = "<group>"; };
                A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarysharedcommand.cpp; sourceTree = "<group>"; };
@@ -982,6 +988,8 @@
                A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weightedlinkage.cpp; sourceTree = SOURCE_ROOT; };
                A7E9B87F12D37EC400DA6239 /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = "<group>"; };
                A7E9B88012D37EC400DA6239 /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = "<group>"; };
+               A7F9F5CD141A5E500032F693 /* sequenceparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sequenceparser.h; sourceTree = "<group>"; };
+               A7F9F5CE141A5E500032F693 /* sequenceparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequenceparser.cpp; sourceTree = "<group>"; };
                A7FA10001302E096003860FE /* mantelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mantelcommand.h; sourceTree = "<group>"; };
                A7FA10011302E096003860FE /* mantelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mantelcommand.cpp; sourceTree = "<group>"; };
                A7FC480C12D788F20055BC5C /* linearalgebra.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = linearalgebra.h; sourceTree = "<group>"; };
@@ -992,6 +1000,10 @@
                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>"; };
+               A7FF19F0140FFDA500AD216D /* trimoligos.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = trimoligos.h; sourceTree = "<group>"; };
+               A7FF19F1140FFDA500AD216D /* trimoligos.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = trimoligos.cpp; sourceTree = "<group>"; };
+               A7FFB556142CA02C004884F2 /* summarytaxcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarytaxcommand.h; sourceTree = "<group>"; };
+               A7FFB557142CA02C004884F2 /* summarytaxcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarytaxcommand.cpp; sourceTree = "<group>"; };
                C6A0FF2C0290799A04C91782 /* mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = mothur.1; sourceTree = "<group>"; };
 /* End PBXFileReference section */
 
@@ -1099,13 +1111,9 @@
                                A7E9B82412D37EC400DA6239 /* sharedutilities.h */,
                                A7E9B82D12D37EC400DA6239 /* singlelinkage.cpp */,
                                A7E9B83012D37EC400DA6239 /* slibshuff.cpp */,
-                               A7E9B85112D37EC400DA6239 /* suffixdb.cpp */,
                                A7E9B83112D37EC400DA6239 /* slibshuff.h */,
-                               A7E9B85212D37EC400DA6239 /* suffixdb.hpp */,
-                               A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */,
-                               A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */,
-                               A7E9B85512D37EC400DA6239 /* suffixtree.cpp */,
-                               A7E9B85612D37EC400DA6239 /* suffixtree.hpp */,
+                               A7FF19F0140FFDA500AD216D /* trimoligos.h */,
+                               A7FF19F1140FFDA500AD216D /* trimoligos.cpp */,
                                A7E9B87412D37EC400DA6239 /* validcalculator.cpp */,
                                A7E9B87512D37EC400DA6239 /* validcalculator.h */,
                                A7E9B87612D37EC400DA6239 /* validparameter.cpp */,
@@ -1238,6 +1246,8 @@
                                A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */,
                                A7E9B6BA12D37EC400DA6239 /* corraxescommand.h */,
                                A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */,
+                               A795840B13F13CD900F201D5 /* countgroupscommand.h */,
+                               A795840C13F13CD900F201D5 /* countgroupscommand.cpp */,
                                A7730EFD13967241007433A3 /* countseqscommand.h */,
                                A7730EFE13967241007433A3 /* countseqscommand.cpp */,
                                A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */,
@@ -1396,6 +1406,8 @@
                                A7E9B85712D37EC400DA6239 /* summarycommand.cpp */,
                                A7E9B85A12D37EC400DA6239 /* summarysharedcommand.h */,
                                A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */,
+                               A7FFB556142CA02C004884F2 /* summarytaxcommand.h */,
+                               A7FFB557142CA02C004884F2 /* summarytaxcommand.cpp */,
                                A7E9B85C12D37EC400DA6239 /* systemcommand.h */,
                                A7E9B85B12D37EC400DA6239 /* systemcommand.cpp */,
                                A7E9B86312D37EC400DA6239 /* treegroupscommand.h */,
@@ -1626,18 +1638,26 @@
                                A7E9B7DC12D37EC400DA6239 /* sequence.hpp */,
                                A7E9B7DD12D37EC400DA6239 /* sequencedb.cpp */,
                                A7E9B7DE12D37EC400DA6239 /* sequencedb.h */,
+                               A7F9F5CD141A5E500032F693 /* sequenceparser.h */,
+                               A7F9F5CE141A5E500032F693 /* sequenceparser.cpp */,
                                A7E9B80412D37EC400DA6239 /* sharedlistvector.cpp */,
                                A7E9B80512D37EC400DA6239 /* sharedlistvector.h */,
                                A7E9B80E12D37EC400DA6239 /* sharedordervector.h */,
                                A7E9B80D12D37EC400DA6239 /* sharedordervector.cpp */,
-                               A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */,
                                A7E9B81012D37EC400DA6239 /* sharedrabundfloatvector.h */,
+                               A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */,
                                A7E9B81112D37EC400DA6239 /* sharedrabundvector.cpp */,
                                A7E9B81212D37EC400DA6239 /* sharedrabundvector.h */,
                                A7E9B81312D37EC400DA6239 /* sharedsabundvector.cpp */,
                                A7E9B81412D37EC400DA6239 /* sharedsabundvector.h */,
                                A7E9B83912D37EC400DA6239 /* sparsematrix.cpp */,
                                A7E9B83A12D37EC400DA6239 /* sparsematrix.hpp */,
+                               A7E9B85112D37EC400DA6239 /* suffixdb.cpp */,
+                               A7E9B85212D37EC400DA6239 /* suffixdb.hpp */,
+                               A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */,
+                               A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */,
+                               A7E9B85512D37EC400DA6239 /* suffixtree.cpp */,
+                               A7E9B85612D37EC400DA6239 /* suffixtree.hpp */,
                                A7E9B85F12D37EC400DA6239 /* tree.cpp */,
                                A7E9B86012D37EC400DA6239 /* tree.h */,
                                A7E9B86412D37EC400DA6239 /* treemap.cpp */,
@@ -2131,6 +2151,10 @@
                                A73DDBBA13C4A0D1006AAE38 /* clearmemorycommand.cpp in Sources */,
                                A73DDC3813C4BF64006AAE38 /* mothurmetastats.cpp in Sources */,
                                A79234D713C74BF6002B08E2 /* mothurfisher.cpp in Sources */,
+                               A795840D13F13CD900F201D5 /* countgroupscommand.cpp in Sources */,
+                               A7FF19F2140FFDA500AD216D /* trimoligos.cpp in Sources */,
+                               A7F9F5CF141A5E500032F693 /* sequenceparser.cpp in Sources */,
+                               A7FFB558142CA02C004884F2 /* summarytaxcommand.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
@@ -2174,11 +2198,11 @@
                                GCC_ENABLE_SSE3_EXTENSIONS = NO;
                                GCC_ENABLE_SSE41_EXTENSIONS = NO;
                                GCC_ENABLE_SSE42_EXTENSIONS = NO;
-                               GCC_OPTIMIZATION_LEVEL = 0;
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "MOTHUR_FILES=\"\\\"../release\\\"\"",
-                                       "VERSION=\"\\\"1.20.2\\\"\"",
-                                       "RELEASE_DATE=\"\\\"7/05/2011\\\"\"",
+                                       "VERSION=\"\\\"1.21.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"7/25/2011\\\"\"",
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
@@ -2208,7 +2232,7 @@
                                GCC_C_LANGUAGE_STANDARD = gnu99;
                                GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
                                GCC_MODEL_TUNING = "";
-                               GCC_OPTIMIZATION_LEVEL = 0;
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "VERSION=\"\\\"1.19.0\\\"\"",
                                        "RELEASE_DATE=\"\\\"5/9/2011\\\"\"",