modified calculators to use doubles, added numotu and fontsize parameters to heatmap...

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

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 1609df908abaa8a95559d009f2351d616049872b..b081984feced8b3ae7d88646b56e100b39cd450d 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -7,9 +7,19 @@
        objects = {
 
 /* Begin PBXFileReference section */
+               7E84528511EF4BEB00564975 /* seqerrorcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqerrorcommand.h; sourceTree = "<group>"; };
+               7E84528611EF4BEB00564975 /* seqerrorcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqerrorcommand.cpp; sourceTree = "<group>"; };
+               7E85BD1C11EB5E9B00FD37C0 /* qualityscores.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qualityscores.h; sourceTree = "<group>"; };
+               7E85BD1D11EB5E9B00FD37C0 /* qualityscores.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qualityscores.cpp; sourceTree = "<group>"; };
+               7EA299BA11E384940022D8D3 /* sensspeccommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sensspeccommand.h; sourceTree = "<group>"; };
+               7EA299BB11E384940022D8D3 /* sensspeccommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sensspeccommand.cpp; sourceTree = "<group>"; };
                7EC61A0911BEA6AF00F668D9 /* weightedlinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weightedlinkage.cpp; sourceTree = "<group>"; };
                A703FE931194645F002C397E /* makegroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makegroupcommand.h; sourceTree = SOURCE_ROOT; };
                A703FE941194645F002C397E /* makegroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makegroupcommand.cpp; sourceTree = SOURCE_ROOT; };
+               A7118EE511CFCAC000CFDE03 /* degapseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = degapseqscommand.h; sourceTree = "<group>"; };
+               A7118EE611CFCAC000CFDE03 /* degapseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = degapseqscommand.cpp; sourceTree = "<group>"; };
+               A7118F0F11CFD5DC00CFDE03 /* getrelabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getrelabundcommand.h; sourceTree = "<group>"; };
+               A7118F1011CFD5DC00CFDE03 /* getrelabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getrelabundcommand.cpp; sourceTree = "<group>"; };
                A71D924211AEB42400D00CBC /* clustersplitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clustersplitcommand.cpp; sourceTree = "<group>"; };
                A71D924311AEB42400D00CBC /* clustersplitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clustersplitcommand.h; sourceTree = "<group>"; };
                A71D924411AEB42400D00CBC /* splitabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitabundcommand.cpp; sourceTree = "<group>"; };
@@ -20,6 +30,8 @@
                A72B3A63118B37FD004B9F8D /* phylodiversitycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversitycommand.cpp; sourceTree = "<group>"; };
                A72B3A7B118B4D1B004B9F8D /* phylodiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversity.h; sourceTree = "<group>"; };
                A72B3A7C118B4D1B004B9F8D /* phylodiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversity.cpp; sourceTree = "<group>"; };
+               A732505E11E49EF100484B90 /* sffinfocommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sffinfocommand.h; sourceTree = "<group>"; };
+               A732505F11E49EF100484B90 /* sffinfocommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sffinfocommand.cpp; sourceTree = "<group>"; };
                A73953DA11987ED100B0B160 /* chopseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chopseqscommand.h; sourceTree = "<group>"; };
                A73953DB11987ED100B0B160 /* chopseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chopseqscommand.cpp; sourceTree = "<group>"; };
                A747E79B1163442A00FB9042 /* chimeracheckcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeracheckcommand.h; sourceTree = "<group>"; };
@@ -31,12 +43,15 @@
                A76AAD03117F322B003D8DA1 /* phylosummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylosummary.cpp; sourceTree = "<group>"; };
                A76C4A1011876BAF0009460B /* setlogfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setlogfilecommand.h; sourceTree = SOURCE_ROOT; };
                A76C4A1111876BAF0009460B /* setlogfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setlogfilecommand.cpp; sourceTree = SOURCE_ROOT; };
+               A780E6CB11E7745D00BB5718 /* endiannessmacros.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = endiannessmacros.h; sourceTree = "<group>"; };
                A78254461164D7790002E2DD /* chimerapintailcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerapintailcommand.h; sourceTree = "<group>"; };
                A78254471164D7790002E2DD /* chimerapintailcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerapintailcommand.cpp; sourceTree = "<group>"; };
                A7825502116519F70002E2DD /* chimerabellerophoncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerabellerophoncommand.h; sourceTree = "<group>"; };
                A7825503116519F70002E2DD /* chimerabellerophoncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerabellerophoncommand.cpp; sourceTree = "<group>"; };
                A78434881162224F00100BE0 /* chimeraccodecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraccodecommand.h; sourceTree = "<group>"; };
                A78434891162224F00100BE0 /* chimeraccodecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraccodecommand.cpp; sourceTree = "<group>"; };
+               A7AE6302121C3408001DE6FC /* sharedrabundfloatvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundfloatvector.h; sourceTree = "<group>"; };
+               A7AE6303121C3408001DE6FC /* sharedrabundfloatvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrabundfloatvector.cpp; sourceTree = "<group>"; };
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                A7BBDA7C11B5694E006E6551 /* classifyotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifyotucommand.cpp; sourceTree = "<group>"; };
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@@ -474,6 +489,7 @@
                                A7DA203C113FECD400BF472F /* display.h */,
                                A7DA2042113FECD400BF472F /* dlibshuff.cpp */,
                                A7DA2043113FECD400BF472F /* dlibshuff.h */,
+                               A780E6CB11E7745D00BB5718 /* endiannessmacros.h */,
                                A7DA2048113FECD400BF472F /* engine.cpp */,
                                A7DA2049113FECD400BF472F /* engine.hpp */,
                                A7DA204C113FECD400BF472F /* fileoutput.cpp */,
@@ -690,6 +706,8 @@
                                A7DA202A113FECD400BF472F /* collectsharedcommand.h */,
                                A7DA2031113FECD400BF472F /* consensuscommand.cpp */,
                                A7DA2032113FECD400BF472F /* consensuscommand.h */,
+                               A7118EE511CFCAC000CFDE03 /* degapseqscommand.h */,
+                               A7118EE611CFCAC000CFDE03 /* degapseqscommand.cpp */,
                                A7DA203A113FECD400BF472F /* deconvolutecommand.cpp */,
                                A7DA203B113FECD400BF472F /* deconvolutecommand.h */,
                                A7DA203E113FECD400BF472F /* distancecommand.cpp */,
@@ -706,6 +724,8 @@
                                A7DA2060113FECD400BF472F /* getoturepcommand.cpp */,
                                A7DA2062113FECD400BF472F /* getrabundcommand.cpp */,
                                A7DA2063113FECD400BF472F /* getrabundcommand.h */,
+                               A7118F0F11CFD5DC00CFDE03 /* getrelabundcommand.h */,
+                               A7118F1011CFD5DC00CFDE03 /* getrelabundcommand.cpp */,
                                A7DA2064113FECD400BF472F /* getsabundcommand.cpp */,
                                A7DA2065113FECD400BF472F /* getsabundcommand.h */,
                                A7DA2067113FECD400BF472F /* getseqscommand.h */,
@@ -770,12 +790,18 @@
                                A7DA20F8113FECD400BF472F /* screenseqscommand.cpp */,
                                A7DA20FB113FECD400BF472F /* secondarystructurecommand.h */,
                                A7DA20FA113FECD400BF472F /* secondarystructurecommand.cpp */,
+                               7EA299BA11E384940022D8D3 /* sensspeccommand.h */,
+                               7EA299BB11E384940022D8D3 /* sensspeccommand.cpp */,
+                               7E84528511EF4BEB00564975 /* seqerrorcommand.h */,
+                               7E84528611EF4BEB00564975 /* seqerrorcommand.cpp */,
                                A7DA20FD113FECD400BF472F /* seqsummarycommand.h */,
                                A7DA20FC113FECD400BF472F /* seqsummarycommand.cpp */,
                                A7DA2103113FECD400BF472F /* setdircommand.h */,
                                A7DA2102113FECD400BF472F /* setdircommand.cpp */,
                                A76C4A1011876BAF0009460B /* setlogfilecommand.h */,
                                A76C4A1111876BAF0009460B /* setlogfilecommand.cpp */,
+                               A732505E11E49EF100484B90 /* sffinfocommand.h */,
+                               A732505F11E49EF100484B90 /* sffinfocommand.cpp */,
                                A7DA2110113FECD400BF472F /* sharedcommand.h */,
                                A7DA210F113FECD400BF472F /* sharedcommand.cpp */,
                                A71D924511AEB42400D00CBC /* splitabundcommand.h */,
@@ -830,8 +856,10 @@
                                A7DA20A3113FECD400BF472F /* nameassignment.hpp */,
                                A7DA20B6113FECD400BF472F /* ordervector.cpp */,
                                A7DA20B7113FECD400BF472F /* ordervector.hpp */,
-                               A7DA20D2113FECD400BF472F /* rabundvector.cpp */,
+                               7E85BD1C11EB5E9B00FD37C0 /* qualityscores.h */,
+                               7E85BD1D11EB5E9B00FD37C0 /* qualityscores.cpp */,
                                A7DA20D3113FECD400BF472F /* rabundvector.hpp */,
+                               A7DA20D2113FECD400BF472F /* rabundvector.cpp */,
                                A7DA20F6113FECD400BF472F /* sabundvector.cpp */,
                                A7DA20F7113FECD400BF472F /* sabundvector.hpp */,
                                A7DA20FE113FECD400BF472F /* sequence.cpp */,
@@ -844,8 +872,10 @@
                                A7DA212B113FECD400BF472F /* sharedordervector.h */,
                                A7DA212C113FECD400BF472F /* sharedrabundvector.cpp */,
                                A7DA212D113FECD400BF472F /* sharedrabundvector.h */,
-                               A7DA212E113FECD400BF472F /* sharedsabundvector.cpp */,
+                               A7AE6302121C3408001DE6FC /* sharedrabundfloatvector.h */,
+                               A7AE6303121C3408001DE6FC /* sharedrabundfloatvector.cpp */,
                                A7DA212F113FECD400BF472F /* sharedsabundvector.h */,
+                               A7DA212E113FECD400BF472F /* sharedsabundvector.cpp */,
                                A7DA214C113FECD400BF472F /* sparsematrix.cpp */,
                                A7DA214D113FECD400BF472F /* sparsematrix.hpp */,
                                A7DA214E113FECD400BF472F /* suffixdb.cpp */,