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() {};
  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 doVertical() {
  51
  52                 for(int i=0;i<alignmentLength;i++){
  53                         if(gap[i] == numSeqs)   {       filter[i] = '0';        }
  54                 }
  55
  56         }
  57
  58         void doTrump(Sequence seq) {
  59
  60                 string curAligned = seq.getAligned();
  61
  62                 for(int j = 0; j < alignmentLength; j++) {
  63                         if(curAligned[j] == trump){
  64                                 filter[j] = '0';
  65                         }
  66                 }
  67
  68         }
  69
  70         void doHard(string hard) {
  71                 ifstream fileHandle;
  72                 openInputFile(hard, fileHandle);
  73
  74                 fileHandle >> filter;
  75
  76                 fileHandle.close();
  77         }
  78
  79         void getFreqs(Sequence seq) {
  80
  81                 string curAligned = seq.getAligned();
  82
  83                 for(int j=0;j<alignmentLength;j++){
  84                         if(toupper(curAligned[j]) == 'A')                                                                               {       a[j]++;         }
  85                         else if(toupper(curAligned[j]) == 'T' || toupper(curAligned[j]) == 'U') {       t[j]++;         }
  86                         else if(toupper(curAligned[j]) == 'G')                                                                  {       g[j]++;         }
  87                         else if(toupper(curAligned[j]) == 'C')                                                                  {       c[j]++;         }
  88                         else if(curAligned[j] == '-' || curAligned[j] == '.')                                   {       gap[j]++;       }
  89                 }
  90         }
  91
  92 protected:
  93         string filter;
  94         int alignmentLength, numSeqs;
  95         float soft;
  96         char trump;
  97
  98 };
  99
 100 /***********************************************************************/
 101
 102 #endif
 103