X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=formatmatrix.h;h=859b78ab2b72569344ccf7c9485de76333ca5ae3;hp=a02ef6cc27ac634eda25ec0c5b7cbc81b13c121a;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=e1cf60b82a48d4d96e3a696a2d221c56cfb0b298

diff --git a/formatmatrix.h b/formatmatrix.h
index a02ef6c..859b78a 100644
--- a/formatmatrix.h
+++ b/formatmatrix.h
@@ -13,17 +13,56 @@
 #include "mothur.h"
 #include "listvector.hpp"
 #include "nameassignment.hpp"
+#include "counttable.h"
 
 
+//**********************************************************************************************************************
+//  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(){	}
+	FormatMatrix(){	m = MothurOut::getInstance(); }
 	virtual ~FormatMatrix() {}
 	
-	virtual void read(NameAssignment*){};
+	virtual int read(NameAssignment*){ return 1; }
+    virtual int read(CountTable*){ return 1; }
 	
 	void setCutoff(float c)			{	cutoff = c;			}
 	ListVector* getListVector()		{	return list;		}
@@ -35,6 +74,7 @@ protected:
 	float cutoff;
 	string distFile;
 	vector<int> rowPos;
+	MothurOut* m;
 };
 
 //**********************************************************************************************************************