changes while testing

[mothur.git] / mantelcommand.h

diff --git a/mantelcommand.h b/mantelcommand.h
index 0646b294c0a53bd327aca2a256a4eaa9ba45735b..33fa3ea21e91fa2663994947720080933fad3d61 100644 (file)
--- a/mantelcommand.h
+++ b/mantelcommand.h
@@ -17,13 +17,19 @@ class MantelCommand : public Command {
 public:
        MantelCommand(string);
        MantelCommand();
-       ~MantelCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       ~MantelCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "mantel";                                      }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR. \nLegendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York. \nhttp://www.mothur.org/wiki/Mantel"; }
+       string getDescription()         { return "Mantel’s test for correlation between matrices"; }
+
        int execute();
-       void help();
+       void help() { m->mothurOut(getHelpString()); }
        
 private:
        
@@ -32,7 +38,6 @@ private:
        int iters;
        
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
 };