working on current change

[mothur.git] / classifyotucommand.h

diff --git a/classifyotucommand.h b/classifyotucommand.h
index e81c246201f36b7904d26b702748e1ba653dff66..f6bf78dfacb99509ada0d5a87d948f9ffe3aacb2 100644 (file)
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -20,13 +20,17 @@ class ClassifyOtuCommand : public Command {
 public:
        ClassifyOtuCommand(string);
        ClassifyOtuCommand();
-       ~ClassifyOtuCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~ClassifyOtuCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "classify.otu";                }
+       string getCommandCategory()             { return "Phylotype Analysis";  }
+       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"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
 
 private:
 
@@ -39,7 +43,6 @@ private:
        vector<string> outputNames;
        map<string, string> nameMap;
        map<string, string> taxMap;
-       map<string, vector<string> > outputTypes;
 
        int readNamesFile();
        int readTaxonomyFile();