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[mothur.git] / formatmatrix.h

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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
+