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 #include "counttable.h"
  17
  18
  19 //**********************************************************************************************************************
  20 //  This class takes a distance matrix file and converts it to a file where each row contains all distances below the cutoff
  21 //  for a given sequence.
  22
  23 //  Example:
  24         /*      5
  25                 A
  26                 B  0.01
  27                 C  0.015 0.03
  28                 D  0.03 0.02 0.02
  29                 E  0.04 0.05 0.03 0.02
  30
  31                 becomes
  32
  33                 0       4       1       0.01    2       0.015   3       0.03    4       0.04
  34                 1       4       0       0.01    2       0.03    3       0.02    4       0.05
  35                 2       4       0       0.015   1       0.03    3       0.02    4       0.03
  36                 3       4       0       0.03    1       0.02    2       0.02    4       0.02
  37                 4       4       0       0.04    1       0.05    2       0.03    3       0.02
  38
  39                 column 1 - sequence name converted to row number
  40                 column 2 - numDists under cutoff
  41                 rest of line - sequence row -> distance, sequence row -> distance
  42
  43                 if you had a cutoff of 0.03 then the file would look like,
  44
  45                 0       3       1       0.01    2       0.015   3       0.03
  46                 1       3       0       0.01    2       0.03    3       0.02
  47                 2       4       0       0.015   1       0.03    3       0.02    4       0.03
  48                 3       4       0       0.03    1       0.02    2       0.02    4       0.02
  49                 4       2       2       0.03    3       0.02
  50
  51                 This class also creates a vector of ints, rowPos.
  52
  53                 rowPos[0] = position in the file of distances related to sequence 0.
  54                 If a sequence is excluded by the cutoff, it's rowPos = -1.
  55 */
  56 //**********************************************************************************************************************
  57
  58 class FormatMatrix {
  59
  60 public:
  61         FormatMatrix(){ m = MothurOut::getInstance(); }
  62         virtual ~FormatMatrix() {}
  63
  64         virtual int read(NameAssignment*){ return 1; }
  65     virtual int read(CountTable*){ return 1; }
  66
  67         void setCutoff(float c)                 {       cutoff = c;                     }
  68         ListVector* getListVector()             {       return list;            }
  69         string getFormattedFileName()   {       return distFile;        }
  70         vector<int> getRowPositions()   {       return rowPos;          }
  71
  72 protected:
  73         ListVector* list;
  74         float cutoff;
  75         string distFile;
  76         vector<int> rowPos;
  77         MothurOut* m;
  78 };
  79
  80 //**********************************************************************************************************************
  81
  82 #endif
  83