added SequenceCountParser class to parse the count table by group. added count parame...

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

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 6db66c6184bc3798ee4d8ba2fc7247a9feb6acb4..104c6d5c12c6e4185823e2d5e833760134f8c16a 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -24,8 +24,10 @@
                A73901081588C40900ED2ED6 /* loadlogfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73901071588C40900ED2ED6 /* loadlogfilecommand.cpp */; };
                A73DDBBA13C4A0D1006AAE38 /* clearmemorycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73DDBB913C4A0D1006AAE38 /* clearmemorycommand.cpp */; };
                A73DDC3813C4BF64006AAE38 /* mothurmetastats.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73DDC3713C4BF64006AAE38 /* mothurmetastats.cpp */; };
+               A741FAD215D1688E0067BCC5 /* sequencecountparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A741FAD115D1688E0067BCC5 /* sequencecountparser.cpp */; };
                A74A9A9F148E881E00AB5E3E /* spline.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74A9A9E148E881E00AB5E3E /* spline.cpp */; };
                A74D36B8137DAFAA00332B0C /* chimerauchimecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D36B7137DAFAA00332B0C /* chimerauchimecommand.cpp */; };
+               A74D59A4159A1E2000043046 /* counttable.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D59A3159A1E2000043046 /* counttable.cpp */; };
                A754149714840CF7005850D1 /* summaryqualcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A754149614840CF7005850D1 /* summaryqualcommand.cpp */; };
                A75790591301749D00A30DAB /* homovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A75790581301749D00A30DAB /* homovacommand.cpp */; };
                A76CDD821510F143004C8458 /* prcseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A76CDD811510F143004C8458 /* prcseqscommand.cpp */; };
@@ -50,6 +52,7 @@
                A7C3DC0B14FE457500FE1924 /* cooccurrencecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7C3DC0914FE457500FE1924 /* cooccurrencecommand.cpp */; };
                A7C3DC0F14FE469500FE1924 /* trialSwap2.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7C3DC0D14FE469500FE1924 /* trialSwap2.cpp */; };
                A7D755DA1535F679009BF21A /* treereader.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D755D91535F679009BF21A /* treereader.cpp */; };
+               A7E0243D15B4520A00A5F046 /* sparsedistancematrix.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E0243C15B4520A00A5F046 /* sparsedistancematrix.cpp */; };
                A7E9B88112D37EC400DA6239 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B64F12D37EC300DA6239 /* ace.cpp */; };
                A7E9B88212D37EC400DA6239 /* aligncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65112D37EC300DA6239 /* aligncommand.cpp */; };
                A7E9B88312D37EC400DA6239 /* alignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65312D37EC300DA6239 /* alignment.cpp */; };
@@ -395,10 +398,14 @@
                A73DDBB913C4A0D1006AAE38 /* clearmemorycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clearmemorycommand.cpp; sourceTree = "<group>"; };
                A73DDC3613C4BF64006AAE38 /* mothurmetastats.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothurmetastats.h; sourceTree = "<group>"; };
                A73DDC3713C4BF64006AAE38 /* mothurmetastats.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothurmetastats.cpp; sourceTree = "<group>"; };
+               A741FAD115D1688E0067BCC5 /* sequencecountparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequencecountparser.cpp; sourceTree = "<group>"; };
+               A741FAD415D168A00067BCC5 /* sequencecountparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sequencecountparser.h; sourceTree = "<group>"; };
                A74A9A9D148E881E00AB5E3E /* spline.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = spline.h; sourceTree = "<group>"; };
                A74A9A9E148E881E00AB5E3E /* spline.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = spline.cpp; sourceTree = "<group>"; };
                A74D36B6137DAFAA00332B0C /* chimerauchimecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerauchimecommand.h; sourceTree = "<group>"; };
                A74D36B7137DAFAA00332B0C /* chimerauchimecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerauchimecommand.cpp; sourceTree = "<group>"; };
+               A74D59A3159A1E2000043046 /* counttable.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = counttable.cpp; sourceTree = "<group>"; };
+               A74D59A6159A1E3600043046 /* counttable.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = counttable.h; sourceTree = "<group>"; };
                A754149514840CF7005850D1 /* summaryqualcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summaryqualcommand.h; sourceTree = "<group>"; };
                A754149614840CF7005850D1 /* summaryqualcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summaryqualcommand.cpp; sourceTree = "<group>"; };
                A75790571301749D00A30DAB /* homovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = homovacommand.h; sourceTree = "<group>"; };
@@ -450,6 +457,8 @@
                A7D755D71535F665009BF21A /* treereader.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treereader.h; sourceTree = "<group>"; };
                A7D755D91535F679009BF21A /* treereader.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treereader.cpp; sourceTree = "<group>"; };
                A7DAAFA3133A254E003956EB /* commandparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = commandparameter.h; sourceTree = "<group>"; };
+               A7E0243C15B4520A00A5F046 /* sparsedistancematrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sparsedistancematrix.cpp; sourceTree = "<group>"; };
+               A7E0243F15B4522000A5F046 /* sparsedistancematrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sparsedistancematrix.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>"; };
@@ -1616,10 +1625,12 @@
                                A7E9B66312D37EC400DA6239 /* blastalign.hpp */,
                                A7E9B66412D37EC400DA6239 /* blastdb.cpp */,
                                A7E9B66512D37EC400DA6239 /* blastdb.hpp */,
+                               A74D59A6159A1E3600043046 /* counttable.h */,
+                               A74D59A3159A1E2000043046 /* counttable.cpp */,
+                               A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */,
                                A7E9B6BD12D37EC400DA6239 /* database.cpp */,
                                A7E9B6BE12D37EC400DA6239 /* database.hpp */,
                                A7E9B6BF12D37EC400DA6239 /* datavector.hpp */,
-                               A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */,
                                A7E9B6CE12D37EC400DA6239 /* distancedb.hpp */,
                                A7E9B6DE12D37EC400DA6239 /* fastamap.cpp */,
                                A7E9B6DF12D37EC400DA6239 /* fastamap.h */,
@@ -1651,6 +1662,8 @@
                                A7E9B7D012D37EC400DA6239 /* sabundvector.hpp */,
                                A7E9B7DB12D37EC400DA6239 /* sequence.cpp */,
                                A7E9B7DC12D37EC400DA6239 /* sequence.hpp */,
+                               A741FAD415D168A00067BCC5 /* sequencecountparser.h */,
+                               A741FAD115D1688E0067BCC5 /* sequencecountparser.cpp */,
                                A7E9B7DD12D37EC400DA6239 /* sequencedb.cpp */,
                                A7E9B7DE12D37EC400DA6239 /* sequencedb.h */,
                                A7F9F5CD141A5E500032F693 /* sequenceparser.h */,
@@ -1667,6 +1680,8 @@
                                A7E9B81412D37EC400DA6239 /* sharedsabundvector.h */,
                                A7E9B83912D37EC400DA6239 /* sparsematrix.cpp */,
                                A7E9B83A12D37EC400DA6239 /* sparsematrix.hpp */,
+                               A7E0243F15B4522000A5F046 /* sparsedistancematrix.h */,
+                               A7E0243C15B4520A00A5F046 /* sparsedistancematrix.cpp */,
                                A7E9B85112D37EC400DA6239 /* suffixdb.cpp */,
                                A7E9B85212D37EC400DA6239 /* suffixdb.hpp */,
                                A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */,
@@ -2180,6 +2195,9 @@
                                A70056E6156A93D000924A2D /* getotulabelscommand.cpp in Sources */,
                                A70056EB156AB6E500924A2D /* removeotulabelscommand.cpp in Sources */,
                                A73901081588C40900ED2ED6 /* loadlogfilecommand.cpp in Sources */,
+                               A74D59A4159A1E2000043046 /* counttable.cpp in Sources */,
+                               A7E0243D15B4520A00A5F046 /* sparsedistancematrix.cpp in Sources */,
+                               A741FAD215D1688E0067BCC5 /* sequencecountparser.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
@@ -2226,8 +2244,8 @@
                                GCC_OPTIMIZATION_LEVEL = 0;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "MOTHUR_FILES=\"\\\"../release\\\"\"",
-                                       "VERSION=\"\\\"1.25.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"5/01/2012\\\"\"",
+                                       "VERSION=\"\\\"1.26.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"7/9/2012\\\"\"",
                                );
                                "GCC_VERSION[arch=*]" = "";
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
@@ -2262,8 +2280,8 @@
                                GCC_MODEL_TUNING = "";
                                GCC_OPTIMIZATION_LEVEL = 0;
                                GCC_PREPROCESSOR_DEFINITIONS = (
-                                       "VERSION=\"\\\"1.25.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"4/30/2012\\\"\"",
+                                       "VERSION=\"\\\"1.26.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"7/9/2012\\\"\"",
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;