X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.h;fp=qualityscores.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=49034b8ecb2a2b937901c9cfda132c00bcd5c4c4;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/qualityscores.h b/qualityscores.h
deleted file mode 100644
index 49034b8..0000000
--- a/qualityscores.h
+++ /dev/null
@@ -1,55 +0,0 @@
-#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