X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filters.h;fp=filters.h;h=21bc8bb5eec729d7b3f59d06d2a6cc6aff09080a;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/filters.h b/filters.h
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+#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
+