X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=amovacommand.h;h=98d19ddfc249d550c5d6d5b7c33cf036642393a0;hp=3b90b967437df2c0ad360675fc89537976dce989;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=ea34218a94af7cb96d4a1b44e444a87c7ab7456c

diff --git a/amovacommand.h b/amovacommand.h
index 3b90b96..98d19dd 100644
--- a/amovacommand.h
+++ b/amovacommand.h
@@ -11,53 +11,41 @@
  */
 
 #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; }
-	int execute();
-	void help();
+	~AmovaCommand() {}
 	
-private:
-	struct linePair {
-		int start;
-		int num;
-		linePair(int i, int j) : start(i), num(j) {}
-	};
-	vector<linePair> lines;
+	vector<string> setParameters();
+	string getCommandName()			{ return "amova";					}
+	string getCommandCategory()		{ return "Hypothesis Testing";		}
 	
-	GlobalData* globaldata;
-	GroupMap* designMap;
-	map<string, vector<string> > outputTypes;
+	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"; }
 	
-	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 execute();
+	void help() { m->mothurOut(getHelpString()); }
 	
-	int driver(int, int, vector<SharedRAbundVector*>, string);
-	int driver(int, int, vector<string>, string, vector< vector<double> >&);
-	int process(vector<SharedRAbundVector*>);
-	int calcAmova(ofstream&, int, vector<string>);
-	double calcWithin(vector< vector<double> >&, int, vector<string>);
-	double calcTotal(int);
+private:
+	double runAMOVA(ofstream&, map<string, vector<int> >, double);
+	double calcSSWithin(map<string, vector<int> >&);
+	double calcSSTotal(map<string, vector<int> >&);
+	map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
+
+	bool abort;
+	vector<string> outputNames, Sets;
+
+	string outputDir, inputDir, designFileName, phylipFileName;
+	GroupMap* designMap;
+	vector< vector<double> > distanceMatrix;
+	int iters;
+	double experimentwiseAlpha;
 };
 
 #endif