+++ /dev/null
-#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
-