added count parameter to chimera.slayer command

[mothur.git] / classifyotucommand.h

diff --git a/classifyotucommand.h b/classifyotucommand.h
index 7f15c71c1847421abb88c3202d96e8ca7015837a..b924775cf5b30436c1783714a758281cf072c32f 100644 (file)
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -25,7 +25,10 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "classify.otu";                }
        string getCommandCategory()             { return "Phylotype Analysis";  }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
+       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()); }  
@@ -42,10 +45,8 @@ private:
        map<string, string> nameMap;
        map<string, string> taxMap;
 
-       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