changes while testing

[mothur.git] / anosimcommand.h

diff --git a/anosimcommand.h b/anosimcommand.h
index 0b145639d8b0f8551988e67d29ee4a2612efa809..6e5aba0e65980914e6c25e6e0e55fadc4b0136b9 100644 (file)
--- a/anosimcommand.h
+++ b/anosimcommand.h
@@ -12,53 +12,45 @@
 
 
 #include "command.hpp"
-#include "inputdata.h"
-#include "sharedrabundvector.h"
-#include "validcalculator.h"
-#include "readphylipvector.h"
 
-class GlobalData;
+class GroupMap;
 
 class AnosimCommand : public Command {
        
 public:
        AnosimCommand(string);
        AnosimCommand();
-       ~AnosimCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       ~AnosimCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "anosim";                                      }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+    
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "Clarke, K. R. (1993). Non-parametric multivariate analysis of changes in community structure. _Australian Journal of Ecology_ 18, 117-143.\nhttp://www.mothur.org/wiki/Anosim"; }
+       string getDescription()         { return "analysis of similarity"; }
+       
        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;
+       bool abort;
        GroupMap* designMap;
-       map<string, vector<string> > outputTypes;
+       string outputDir, inputDir, designFileName, phylipFileName;
        
-       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<double> > convertToRanks(vector<vector<double> >);
+       double calcR(vector<vector<double> >, map<string, vector<int> >);
+       map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
+       double runANOSIM(ofstream&, vector<vector<double> >, map<string, vector<int> >, double);
+       
+       vector< vector<double> > distanceMatrix;
+       vector<string> outputNames;
+       int iters;
+       double experimentwiseAlpha;
        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 calcAnosim(ofstream&, int, vector<string>);
-       double calcWithinBetween(vector<seqDist>&, vector<string>, double&);
-       vector<seqDist> convertToRanks();
+       
 };
 
 #endif