moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / formatmatrix.h

diff --git a/formatmatrix.h b/formatmatrix.h
deleted file mode 100644 (file)
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
-