fixes while testing 1.33.0

[mothur.git] / amovacommand.h

diff --git a/amovacommand.h b/amovacommand.h
index d9fe1e6fe7e941c89ed65ffafce0f0ad2cc72c61..98d19ddfc249d550c5d6d5b7c33cf036642393a0 100644 (file)
--- a/amovacommand.h
+++ b/amovacommand.h
@@ -11,25 +11,26 @@
  */
 
 #include "command.hpp"
-#include "inputdata.h"
-#include "sharedrabundvector.h"
-#include "validcalculator.h"
-#include "readphylipvector.h"
-
-class GlobalData;
+class GroupMap;
 
 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);
@@ -37,34 +38,14 @@ private:
        double calcSSTotal(map<string, vector<int> >&);
        map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
 
-       
        bool abort;
-       GlobalData* globaldata;
-       map<string, vector<string> > outputTypes;
-       vector<string> outputNames;
+       vector<string> outputNames, Sets;
 
        string outputDir, inputDir, designFileName, phylipFileName;
        GroupMap* designMap;
        vector< vector<double> > distanceMatrix;
        int iters;
        double experimentwiseAlpha;
-       
-//     struct linePair {
-//             int start;
-//             int num;
-//             linePair(int i, int j) : start(i), num(j) {}
-//     };
-//     vector<linePair> lines;
-//
-//     vector< vector<string> > namesOfGroupCombos;
-//     vector<string> Groups, outputNames, Sets;
-//     int processors;
-//     string groups, sets, calc, sharedfile, label, allLines, pickedGroups;
-//     vector<Calculator*> calculators;
-//     set<string> labels; //holds labels to be used
-//     int driver(int, int, vector<SharedRAbundVector*>, string);
-//     int driver(int, int, vector<string>, string, vector< vector<double> >&);
-//     int process(vector<SharedRAbundVector*>);       
 };
 
 #endif