X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=amovacommand.h;h=98d19ddfc249d550c5d6d5b7c33cf036642393a0;hp=d9fe1e6fe7e941c89ed65ffafce0f0ad2cc72c61;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=0486bc2eed084ac387d2f59b6d23d13b2382daf7

diff --git a/amovacommand.h b/amovacommand.h
index d9fe1e6..98d19dd 100644
--- 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