X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=formatmatrix.h;fp=formatmatrix.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=7e7a99c1dbcf4bf495ad7b1a7c7caec49bef3e90;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/formatmatrix.h b/formatmatrix.h
deleted file mode 100644
index 7e7a99c..0000000
--- a/formatmatrix.h
+++ /dev/null
@@ -1,81 +0,0 @@
-#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
-