1.19.0

[mothur.git] / classifyotucommand.h

diff --git a/classifyotucommand.h b/classifyotucommand.h
index 1077781e59b998892d699bf09b34c897a0a15375..7f15c71c1847421abb88c3202d96e8ca7015837a 100644 (file)
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -19,15 +19,22 @@ class ClassifyOtuCommand : public Command {
 
 public:
        ClassifyOtuCommand(string);
-       ~ClassifyOtuCommand();
-       int execute();
-       void help();
+       ClassifyOtuCommand();
+       ~ClassifyOtuCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "classify.otu";                }
+       string getCommandCategory()             { return "Phylotype Analysis";  }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
 
 private:
 
        ListVector* list;
        InputData* input;
-       string listfile, namefile, taxfile, label, outputDir;
+       string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis;
        bool abort, allLines, probs;
        int cutoff;
        set<string> labels; //holds labels to be used
@@ -39,7 +46,7 @@ private:
        int readTaxonomyFile();
        void removeConfidences(string&);
        int process(ListVector*);
-       string findConsensusTaxonomy(int, ListVector*, int&);   // returns the name of the "representative" taxonomy of given bin
+       vector<string> findConsensusTaxonomy(int, ListVector*, int&, string&);  // returns the name of the "representative" taxonomy of given bin
        
                                                                                                
 };