moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / qualityscores.h

diff --git a/qualityscores.h b/qualityscores.h
deleted file mode 100644 (file)
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