fixed bug in phylo.diversity rooting. added filename patterns and create filename...

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 87d4f51cf78230f6ab301e1d72462a461b9f9da9..a3328d8dcea09eebe63c641e04e1b816fc92fee1 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -43,8 +43,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "classify.seqs";               }
        string getCommandCategory()             { return "Phylotype Analysis";  }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "Wang Q, Garrity GM, Tiedje JM, Cole JR (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-7. [ for Bayesian classifier ] \nAltschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-402. [ for BLAST ] \nDeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-72. [ for kmer ] \nhttp://www.mothur.org/wiki/Classify.seqs"; }
        string getDescription()         { return "classify sequences"; }