removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / homovacommand.h

diff --git a/homovacommand.h b/homovacommand.h
index 11f3c07fcebb96ddfe7a473aac8ccb0f234e167d..ec7a793bc25082fe12bf1fc768a72e0209d6b96a 100644 (file)
--- a/homovacommand.h
+++ b/homovacommand.h
@@ -21,13 +21,15 @@ class HomovaCommand : public Command {
 public:
        HomovaCommand(string);
        HomovaCommand();
-       ~HomovaCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       ~HomovaCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "homova";                                      }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+       string getHelpString(); 
+       
        int execute();
-       void help();
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        double runHOMOVA(ofstream& , map<string, vector<int> >, double);
@@ -36,7 +38,6 @@ private:
        map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
 
        bool abort;
-       map<string, vector<string> > outputTypes;
        vector<string> outputNames;
 
        string outputDir, inputDir, designFileName, phylipFileName;