X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.h;fp=qualityscores.h;h=710200a8db096239d873083c9fa7fce7a9cbc6f8;hb=0fb6d165c8dc8dc7153a101513a05f457431d0bc;hp=0000000000000000000000000000000000000000;hpb=956cdff34f2d609a7736838b1631cd7957580b8b;p=mothur.git

diff --git a/qualityscores.h b/qualityscores.h
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+#ifndef QUALITYSCORES
+#define QUALITYSCORES
+
+/*
+ *  qualityscores.h
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 7/12/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "mothur.h"
+#include "mothurout.h"
+#include "sequence.hpp"
+
+/**************************************************************************************************/
+
+class QualityScores {
+public:
+	QualityScores();
+	QualityScores(ifstream&);
+	string getName();
+	void printQScores(ofstream&);
+	void trimQScores(int, int);
+	void flipQScores();
+	bool stripQualThreshold(Sequence&, double);
+	bool stripQualRollingAverage(Sequence&, double);
+	bool stripQualWindowAverage(Sequence&, int, int, double);
+	bool cullQualAverage(Sequence&, double);
+private:
+	
+	double calculateAverage();
+	MothurOut* m;
+	vector<int> qScores;
+	
+	string seqName;
+	int seqLength;
+};
+	
+/**************************************************************************************************/
+
+#endif