fixes while testing 1.33.0

[mothur.git] / amovacommand.h

diff --git a/amovacommand.h b/amovacommand.h
index 51a420064fc0e560cebb291035b1d9245febce5c..98d19ddfc249d550c5d6d5b7c33cf036642393a0 100644 (file)
--- a/amovacommand.h
+++ b/amovacommand.h
@@ -11,8 +11,6 @@
  */
 
 #include "command.hpp"
-
-//class GlobalData;
 class GroupMap;
 
 class AmovaCommand : public Command {
@@ -20,13 +18,19 @@ class AmovaCommand : public Command {
 public:
        AmovaCommand(string);
        AmovaCommand();
-       ~AmovaCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       ~AmovaCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "amova";                                       }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+    string getCitation() { return "Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.\nhttp://www.mothur.org/wiki/Amova"; }
+       string getDescription()         { return "analysis of molecular variance"; }
+       
        int execute();
-       void help();
+       void help() { m->mothurOut(getHelpString()); }
        
 private:
        double runAMOVA(ofstream&, map<string, vector<int> >, double);
@@ -34,10 +38,8 @@ private:
        double calcSSTotal(map<string, vector<int> >&);
        map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
 
-       
        bool abort;
-       map<string, vector<string> > outputTypes;
-       vector<string> outputNames;
+       vector<string> outputNames, Sets;
 
        string outputDir, inputDir, designFileName, phylipFileName;
        GroupMap* designMap;