added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / classifyotucommand.h

diff --git a/classifyotucommand.h b/classifyotucommand.h
index c38a7c97111b4bd842fb7038a6faaf2acedc5d53..a0baf1849d92935fec3ca360a135805d3c41ddbc 100644 (file)
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -26,8 +26,8 @@ public:
        string getCommandName()                 { return "classify.otu";                }
        string getCommandCategory()             { return "Phylotype Analysis";  }
        string getHelpString(); 
-       string getCitation() { return "http://www.mothur.org/wiki/Classify.otu"; }
-
+       string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Classify.otu"; }
+       string getDescription()         { return "find the concensus taxonomy for each OTU"; }
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
@@ -46,8 +46,8 @@ private:
 
        int readNamesFile();
        int readTaxonomyFile();
-       void removeConfidences(string&);
        int process(ListVector*);
+       string addUnclassifieds(string, int);
        vector<string> findConsensusTaxonomy(int, ListVector*, int&, string&);  // returns the name of the "representative" taxonomy of given bin