X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=amovacommand.h;h=51a420064fc0e560cebb291035b1d9245febce5c;hb=4f9a6e14a608172f8a97f0297a3b8e6ea267c518;hp=3b90b967437df2c0ad360675fc89537976dce989;hpb=ea34218a94af7cb96d4a1b44e444a87c7ab7456c;p=mothur.git

diff --git a/amovacommand.h b/amovacommand.h
index 3b90b96..51a4200 100644
--- a/amovacommand.h
+++ b/amovacommand.h
@@ -11,12 +11,9 @@
  */
 
 #include "command.hpp"
-#include "inputdata.h"
-#include "sharedrabundvector.h"
-#include "validcalculator.h"
-#include "readphylipvector.h"
 
-class GlobalData;
+//class GlobalData;
+class GroupMap;
 
 class AmovaCommand : public Command {
 	
@@ -32,32 +29,21 @@ public:
 	void help();
 	
 private:
-	struct linePair {
-		int start;
-		int num;
-		linePair(int i, int j) : start(i), num(j) {}
-	};
-	vector<linePair> lines;
+	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> >);
+
 	
-	GlobalData* globaldata;
-	GroupMap* designMap;
+	bool abort;
 	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 calcAmova(ofstream&, int, vector<string>);
-	double calcWithin(vector< vector<double> >&, int, vector<string>);
-	double calcTotal(int);
+	vector<string> outputNames;
+
+	string outputDir, inputDir, designFileName, phylipFileName;
+	GroupMap* designMap;
+	vector< vector<double> > distanceMatrix;
+	int iters;
+	double experimentwiseAlpha;
 };
 
 #endif