finished wrapper for catchall

[mothur.git] / classifyotucommand.h

diff --git a/classifyotucommand.h b/classifyotucommand.h
index 0ac0288e5bcf1d8879105295e41ad632fce1bdf1..60bfb29a900dbabedcb49a23523b4b704e98352e 100644 (file)
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -19,7 +19,12 @@ 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();
 
@@ -34,12 +39,13 @@ private:
        vector<string> outputNames;
        map<string, string> nameMap;
        map<string, string> taxMap;
+       map<string, vector<string> > outputTypes;
 
        int readNamesFile();
        int readTaxonomyFile();
        void removeConfidences(string&);
        int process(ListVector*);
-       string findConcensusTaxonomy(int, ListVector*, int&);   // returns the name of the "representative" taxonomy of given bin
+       string findConsensusTaxonomy(int, ListVector*, int&);   // returns the name of the "representative" taxonomy of given bin
        
                                                                                                
 };