fixed classify.seqs output file name - had issue if reference taxonomy file did not...

[mothur.git] / homovacommand.h

diff --git a/homovacommand.h b/homovacommand.h
index 11f3c07fcebb96ddfe7a473aac8ccb0f234e167d..4afaeb8e3120b42558f5e555c9237474b27a510e 100644 (file)
--- a/homovacommand.h
+++ b/homovacommand.h
@@ -21,13 +21,17 @@ 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(); 
+       string getCitation() { return "Stewart CN, Excoffier L (1996). Assessing population genetic structure and variability with RAPD data: Application to Vaccinium macrocarpon (American Cranberry). J Evol Biol 9: 153-71. \nhttp://www.mothur.org/wiki/Homova"; }
+       string getDescription()         { return "homova"; }
+
        int execute();
-       void help();
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        double runHOMOVA(ofstream& , map<string, vector<int> >, double);
@@ -36,7 +40,6 @@ 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;