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+#ifndef FORMATMATRIX_H
+#define FORMATMATRIX_H
+
+/*
+ *  formatmatrix.h
+ *  Mothur
+ *
+ *  Created by westcott on 1/13/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mothur.h"
+#include "listvector.hpp"
+#include "nameassignment.hpp"
+
+
+//**********************************************************************************************************************
+//  This class takes a distance matrix file and converts it to a file where each row contains all distances below the cutoff
+//  for a given sequence.
+
+//  Example:
+	/*	5
+		A  
+		B  0.01 
+		C  0.015 0.03 
+		D  0.03 0.02 0.02  
+		E  0.04 0.05 0.03 0.02   
+		
+		becomes 
+		
+		0	4	1	0.01	2	0.015	3	0.03	4	0.04	
+		1	4	0	0.01	2	0.03	3	0.02	4	0.05	
+		2	4	0	0.015	1	0.03	3	0.02	4	0.03	
+		3	4	0	0.03	1	0.02	2	0.02	4	0.02	
+		4	4	0	0.04	1	0.05	2	0.03	3	0.02
+		
+		column 1 - sequence name converted to row number
+		column 2 - numDists under cutoff
+		rest of line - sequence row -> distance, sequence row -> distance
+		
+		if you had a cutoff of 0.03 then the file would look like,
+		
+		0	3	1	0.01	2	0.015	3	0.03	
+		1	3	0	0.01	2	0.03	3	0.02	
+		2	4	0	0.015	1	0.03	3	0.02	4	0.03	
+		3	4	0	0.03	1	0.02	2	0.02	4	0.02	
+		4	2	2	0.03	3	0.02	
+		
+		This class also creates a vector of ints, rowPos.
+		
+		rowPos[0] = position in the file of distances related to sequence 0.
+		If a sequence is excluded by the cutoff, it's rowPos = -1.
+*/
+//**********************************************************************************************************************
+
+class FormatMatrix {
+
+public:
+	FormatMatrix(){	m = MothurOut::getInstance(); }
+	virtual ~FormatMatrix() {}
+	
+	virtual int read(NameAssignment*){ return 1; }
+	
+	void setCutoff(float c)			{	cutoff = c;			}
+	ListVector* getListVector()		{	return list;		}
+	string getFormattedFileName()	{	return distFile;	}
+	vector<int> getRowPositions()	{	return rowPos;		}
+	
+protected:
+	ListVector* list;
+	float cutoff;
+	string distFile;
+	vector<int> rowPos;
+	MothurOut* m;
+};
+
+//**********************************************************************************************************************
+
+#endif
+