X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filters.h;fp=filters.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=21bc8bb5eec729d7b3f59d06d2a6cc6aff09080a;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/filters.h b/filters.h
deleted file mode 100644
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
-