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
  32         void initialize() {
  33                 a.assign(alignmentLength, 0);
  34                 t.assign(alignmentLength, 0);
  35                 g.assign(alignmentLength, 0);
  36                 c.assign(alignmentLength, 0);
  37                 gap.assign(alignmentLength, 0);
  38         }
  39
  40         void doSoft() {
  41                 int threshold = int (soft * numSeqs);
  42
  43                 for(int i=0;i<alignmentLength;i++){
  44                         if(a[i] < threshold && t[i] < threshold && g[i] < threshold && c[i] < threshold){       filter[i] = 0;  }
  45                 }
  46         }
  47
  48         void doVertical() {
  49
  50                 for(int i=0;i<alignmentLength;i++){
  51                         if(gap[i] == numSeqs)   {       filter[i] = '0';        }
  52                 }
  53
  54         }
  55
  56         void doTrump(Sequence seq) {
  57
  58                 string curAligned = seq.getAligned();
  59
  60                 for(int j = 0; j < alignmentLength; j++) {
  61                         if(curAligned[j] == trump){
  62                                 filter[j] = '0';
  63                         }
  64                 }
  65
  66         }
  67
  68         void doHard(string hard) {
  69                 ifstream fileHandle;
  70                 openInputFile(hard, fileHandle);
  71
  72                 fileHandle >> filter;
  73
  74                 fileHandle.close();
  75         }
  76
  77         void getFreqs(Sequence seq) {
  78
  79                 string curAligned = seq.getAligned();
  80
  81                 for(int j=0;j<alignmentLength;j++){
  82                         if(toupper(curAligned[j]) == 'A')                                                                               {       a[j]++;         }
  83                         else if(toupper(curAligned[j]) == 'T' || toupper(curAligned[j]) == 'U') {       t[j]++;         }
  84                         else if(toupper(curAligned[j]) == 'G')                                                                  {       g[j]++;         }
  85                         else if(toupper(curAligned[j]) == 'C')                                                                  {       c[j]++;         }
  86                         else if(curAligned[j] == '-' || curAligned[j] == '.')                                   {       gap[j]++;       }
  87                 }
  88         }
  89
  90 protected:
  91         string filter;
  92         vector<int> a, t, g, c, gap;
  93         int alignmentLength, numSeqs;
  94         float soft;
  95         char trump;
  96
  97 };
  98
  99 /***********************************************************************/
 100
 101 #endif
 102