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

[mothur.git] / pairwiseseqscommand.h

diff --git a/pairwiseseqscommand.h b/pairwiseseqscommand.h
index 0e749d5c7e252ceb7c777de1e8878084f61b0a4d..33fcfca0b6d0207ed1f282a36061893805745203 100644 (file)
--- a/pairwiseseqscommand.h
+++ b/pairwiseseqscommand.h
@@ -40,8 +40,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "pairwise.seqs";               }
        string getCommandCategory()             { return "Sequence Processing"; }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "Needleman SB, Wunsch CD (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-53. [ for needleman ]\nGotoh O (1982). An improved algorithm for matching biological sequences. J Mol Biol 162: 705-8. [ for gotoh ] \nhttp://www.mothur.org/wiki/Pairwise.seqs"; }
        string getDescription()         { return "calculates pairwise distances from an unaligned fasta file"; }