changing command name classify.shared to classifyrf.shared

[mothur.git] / homovacommand.h

diff --git a/homovacommand.h b/homovacommand.h
index 55e4eac7b1a1efc7bac263186fd827bd72d19ad6..22741e979ec9b0847ca660f5ab41eab49fe715d5 100644 (file)
--- a/homovacommand.h
+++ b/homovacommand.h
@@ -12,56 +12,43 @@
 
 
 #include "command.hpp"
-#include "inputdata.h"
-#include "sharedrabundvector.h"
-#include "validcalculator.h"
-#include "readphylipvector.h"
 
-class GlobalData;
+//class GlobalData;
+class GroupMap;
 
 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 getOutputPattern(string);   
+       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:
-       struct linePair {
-               int start;
-               int num;
-               linePair(int i, int j) : start(i), num(j) {}
-       };
-       vector<linePair> lines;
-       
-       GlobalData* globaldata;
+       double runHOMOVA(ofstream& , map<string, vector<int> >, double);
+       double calcSigleSSWithin(vector<int>);
+       double calcBValue(map<string, vector<int> >, vector<double>&);
+       map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
+
+       bool abort;
+       vector<string> outputNames, Sets;
+
+       string outputDir, inputDir, designFileName, phylipFileName;
        GroupMap* designMap;
-       map<string, vector<string> > outputTypes;
-       
-       vector< vector<double> > matrix;
-       bool abort, allLines, pickedGroups;
-       set<string> labels; //holds labels to be used
-       string format, groups, label, outputDir, inputDir, designfile, sets, phylipfile, calc, sharedfile;
-       vector<string> Groups, outputNames, Sets;
-       vector< vector<string> > namesOfGroupCombos;
-       int iters, processors;
-       vector<Calculator*> calculators;
-       
-       int driver(int, int, vector<SharedRAbundVector*>, string);
-       int driver(int, int, vector<string>, string, vector< vector<double> >&);
-       int process(vector<SharedRAbundVector*>);
-       int calcHomova(ofstream&, int, vector<string>);
-       map<string, double> calcWithinEach(vector< vector<double> >&, int, vector<string>, map<string, int>&);
-       double calcWithin(vector< vector<double> >&, int, vector<string>);
-       double calcTotal(int);
+       vector< vector<double> > distanceMatrix;
+       int iters;
+       double experimentwiseAlpha;
 };
 
 #endif
-
-