moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / filters.h

diff --git a/filters.h b/filters.h
deleted file mode 100644 (file)
index 21bc8bb..0000000
--- a/filters.h
+++ /dev/null
@@ -1,112 +0,0 @@
-#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
-