X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.h;fp=qualityscores.h;h=49034b8ecb2a2b937901c9cfda132c00bcd5c4c4;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;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.
+ *
+ */
+
+//DataStructure for a quality file.
+
+
+#include "mothur.h"
+#include "mothurout.h"
+#include "sequence.hpp"
+
+/**************************************************************************************************/
+
+class QualityScores {
+public:
+	QualityScores();
+	QualityScores(ifstream&);
+	string getName();
+	
+	vector<int> getQualityScores() { return qScores; }
+	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);
+	void updateQScoreErrorMap(map<char, vector<int> >&, string, int, int, int);
+	void updateForwardMap(vector<vector<int> >&, int, int, int);
+	void updateReverseMap(vector<vector<int> >&, int, int, int);
+    void setName(string n) { seqName = n; }
+    void setScores(vector<int> qs) { qScores = qs; seqLength = qScores.size(); }
+    
+	
+private:
+	
+	double calculateAverage();
+	MothurOut* m;
+	vector<int> qScores;
+	
+	string seqName;
+	int seqLength;
+};
+	
+/**************************************************************************************************/
+
+#endif