filters.h

   1 #ifndef FILTERS_H
   2 #define FILTERS_H
   3
   4 /*
   5  *  filters.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 6/29/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14 #include "sequence.hpp"
  15
  16
  17 /***********************************************************************/
  18
  19 class Filters {
  20
  21 public:
  22         Filters() { m = MothurOut::getInstance(); };
  23         ~Filters(){};
  24
  25         string getFilter()                      {       return filter;          }
  26         void setFilter(string s)        {  filter = s;                  }
  27         void setLength(int l)           { alignmentLength = l;  }
  28         void setSoft(float s)           {               soft = s;               }
  29         void setTrump(float t)          {               trump = t;              }
  30         void setNumSeqs(int num)        {       numSeqs = num;          }
  31         vector<int> a, t, g, c, gap;
  32
  33
  34         void initialize() {
  35                 a.assign(alignmentLength, 0);
  36                 t.assign(alignmentLength, 0);
  37                 g.assign(alignmentLength, 0);
  38                 c.assign(alignmentLength, 0);
  39                 gap.assign(alignmentLength, 0);
  40         }
  41
  42         void doSoft() {
  43                 int threshold = int (soft * numSeqs);
  44
  45                 for(int i=0;i<alignmentLength;i++){
  46                         if(a[i] < threshold && t[i] < threshold && g[i] < threshold && c[i] < threshold){       filter[i] = 0;  }
  47                 }
  48         }
  49
  50         void mergeFilter(string newFilter){
  51                 for(int i=0;i<alignmentLength;i++){
  52                         if(newFilter[i] == '0'){
  53                                 filter[i] = 0;
  54                         }
  55                 }
  56         }
  57
  58         void doVertical() {
  59
  60                 for(int i=0;i<alignmentLength;i++){
  61                         if(gap[i] == numSeqs)   {       filter[i] = '0';        }
  62                 }
  63
  64         }
  65
  66         void doTrump(Sequence seq) {
  67
  68                 string curAligned = seq.getAligned();
  69
  70                 for(int j = 0; j < alignmentLength; j++) {
  71                         if(curAligned[j] == trump){
  72                                 filter[j] = '0';
  73                         }
  74                 }
  75
  76         }
  77
  78         void doHard(string hard) {
  79                 ifstream fileHandle;
  80                 m->openInputFile(hard, fileHandle);
  81
  82                 fileHandle >> filter;
  83
  84                 fileHandle.close();
  85
  86         if (filter.length() != alignmentLength) {  m->mothurOut("[ERROR]: Sequences are not all the same length as the filter, please correct.\n");  m->control_pressed = true; }
  87         }
  88
  89         void getFreqs(Sequence seq) {
  90
  91                 string curAligned = seq.getAligned();
  92
  93                 for(int j=0;j<alignmentLength;j++){
  94                         if(toupper(curAligned[j]) == 'A')                                                                               {       a[j]++;         }
  95                         else if(toupper(curAligned[j]) == 'T' || toupper(curAligned[j]) == 'U') {       t[j]++;         }
  96                         else if(toupper(curAligned[j]) == 'G')                                                                  {       g[j]++;         }
  97                         else if(toupper(curAligned[j]) == 'C')                                                                  {       c[j]++;         }
  98                         else if(curAligned[j] == '-' || curAligned[j] == '.')                                   {       gap[j]++;       }
  99                 }
 100         }
 101
 102 protected:
 103         string filter;
 104         int alignmentLength, numSeqs;
 105         float soft;
 106         char trump;
 107         MothurOut* m;
 108
 109 };
 110
 111 /***********************************************************************/
 112
 113 #endif
 114