formatmatrix.h

   1 #ifndef FORMATMATRIX_H
   2 #define FORMATMATRIX_H
   3
   4 /*
   5  *  formatmatrix.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 1/13/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14 #include "listvector.hpp"
  15 #include "nameassignment.hpp"
  16
  17
  18 //**********************************************************************************************************************
  19 //  This class takes a distance matrix file and converts it to a file where each row contains all distances below the cutoff
  20 //  for a given sequence.
  21
  22 //  Example:
  23         /*      5
  24                 A
  25                 B  0.01
  26                 C  0.015 0.03
  27                 D  0.03 0.02 0.02
  28                 E  0.04 0.05 0.03 0.02
  29
  30                 becomes
  31
  32                 0       4       1       0.01    2       0.015   3       0.03    4       0.04
  33                 1       4       0       0.01    2       0.03    3       0.02    4       0.05
  34                 2       4       0       0.015   1       0.03    3       0.02    4       0.03
  35                 3       4       0       0.03    1       0.02    2       0.02    4       0.02
  36                 4       4       0       0.04    1       0.05    2       0.03    3       0.02
  37
  38                 column 1 - sequence name converted to row number
  39                 column 2 - numDists under cutoff
  40                 rest of line - sequence row -> distance, sequence row -> distance
  41
  42                 if you had a cutoff of 0.03 then the file would look like,
  43
  44                 0       3       1       0.01    2       0.015   3       0.03
  45                 1       3       0       0.01    2       0.03    3       0.02
  46                 2       4       0       0.015   1       0.03    3       0.02    4       0.03
  47                 3       4       0       0.03    1       0.02    2       0.02    4       0.02
  48                 4       2       2       0.03    3       0.02
  49
  50                 This class also creates a vector of ints, rowPos.
  51
  52                 rowPos[0] = position in the file of distances related to sequence 0.
  53                 If a sequence is excluded by the cutoff, it's rowPos = -1.
  54 */
  55 //**********************************************************************************************************************
  56
  57 class FormatMatrix {
  58
  59 public:
  60         FormatMatrix(){ m = MothurOut::getInstance(); }
  61         virtual ~FormatMatrix() {}
  62
  63         virtual int read(NameAssignment*){ return 1; }
  64
  65         void setCutoff(float c)                 {       cutoff = c;                     }
  66         ListVector* getListVector()             {       return list;            }
  67         string getFormattedFileName()   {       return distFile;        }
  68         vector<int> getRowPositions()   {       return rowPos;          }
  69
  70 protected:
  71         ListVector* list;
  72         float cutoff;
  73         string distFile;
  74         vector<int> rowPos;
  75         MothurOut* m;
  76 };
  77
  78 //**********************************************************************************************************************
  79
  80 #endif
  81