Revert to previous commit

[mothur.git] / filters.h

diff --git a/filters.h b/filters.h
new file mode 100644 (file)
index 0000000..21bc8bb
--- /dev/null
+++ b/filters.h
@@ -0,0 +1,112 @@
+#ifndef FILTERS_H
+#define FILTERS_H
+
+/*
+ *  filters.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 6/29/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "mothur.h"
+#include "sequence.hpp"
+
+
+/***********************************************************************/
+
+class Filters {
+
+public:
+       Filters() { m = MothurOut::getInstance(); };
+       ~Filters(){};
+               
+       string getFilter()                      {       return filter;          }
+       void setFilter(string s)        {  filter = s;                  }
+       void setLength(int l)           { alignmentLength = l;  }
+       void setSoft(float s)           {               soft = s;               }
+       void setTrump(float t)          {               trump = t;              }
+       void setNumSeqs(int num)        {       numSeqs = num;          }
+       vector<int> a, t, g, c, gap;
+       
+       
+       void initialize() {
+               a.assign(alignmentLength, 0);
+               t.assign(alignmentLength, 0);
+               g.assign(alignmentLength, 0);
+               c.assign(alignmentLength, 0);
+               gap.assign(alignmentLength, 0);
+       }
+
+       void doSoft() { 
+               int threshold = int (soft * numSeqs);
+       
+               for(int i=0;i<alignmentLength;i++){
+                       if(a[i] < threshold && t[i] < threshold && g[i] < threshold && c[i] < threshold){       filter[i] = 0;  }
+               }
+       }
+
+       void mergeFilter(string newFilter){
+               for(int i=0;i<alignmentLength;i++){
+                       if(newFilter[i] == '0'){
+                               filter[i] = 0;
+                       }
+               }
+       }
+       
+       void doVertical() {
+
+               for(int i=0;i<alignmentLength;i++){
+                       if(gap[i] == numSeqs)   {       filter[i] = '0';        }
+               }
+       
+       }
+       
+       void doTrump(Sequence seq) {
+       
+               string curAligned = seq.getAligned();
+
+               for(int j = 0; j < alignmentLength; j++) {
+                       if(curAligned[j] == trump){
+                               filter[j] = '0';
+                       }
+               }
+
+       }
+
+       void doHard(string hard) {
+               ifstream fileHandle;
+               m->openInputFile(hard, fileHandle);
+       
+               fileHandle >> filter;
+       
+               fileHandle.close();
+       }
+
+       void getFreqs(Sequence seq) {
+       
+               string curAligned = seq.getAligned();
+       
+               for(int j=0;j<alignmentLength;j++){
+                       if(toupper(curAligned[j]) == 'A')                                                                               {       a[j]++;         }
+                       else if(toupper(curAligned[j]) == 'T' || toupper(curAligned[j]) == 'U') {       t[j]++;         }
+                       else if(toupper(curAligned[j]) == 'G')                                                                  {       g[j]++;         }
+                       else if(toupper(curAligned[j]) == 'C')                                                                  {       c[j]++;         }
+                       else if(curAligned[j] == '-' || curAligned[j] == '.')                                   {       gap[j]++;       }
+               }
+       }
+               
+protected:
+       string filter;
+       int alignmentLength, numSeqs;
+       float soft;
+       char trump;
+       MothurOut* m;
+
+};
+
+/***********************************************************************/
+
+#endif
+