X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.h;h=756b36ffce2cd217f46a6ca4c31060b897a02439;hb=HEAD;hp=77c3ee0d52beefad645e7ecd87ff19327b137c2d;hpb=23f4ffb61f28ec1e6b837633f77f7c6a81c46352;p=mothur.git

diff --git a/qualityscores.h b/qualityscores.h
index 77c3ee0..756b36f 100644
--- a/qualityscores.h
+++ b/qualityscores.h
@@ -22,6 +22,7 @@
 class QualityScores {
 public:
 	QualityScores();
+    QualityScores(string n, vector<int> qs);
 	QualityScores(ifstream&);
 	string getName();
 	int getLength(){    return (int)qScores.size();  }
@@ -30,24 +31,26 @@ public:
 	void trimQScores(int, int);
 	void flipQScores();
 	bool stripQualThreshold(Sequence&, double);
-	bool stripQualRollingAverage(Sequence&, double);
-	bool stripQualWindowAverage(Sequence&, int, int, double);
-	bool cullQualAverage(Sequence&, double);
+	bool stripQualRollingAverage(Sequence&, double, bool);
+	bool stripQualWindowAverage(Sequence&, int, int, double, bool);
+	bool cullQualAverage(Sequence&, double, bool);
 	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 setName(string n); 
     void setScores(vector<int> qs) { qScores = qs; seqLength = qScores.size(); }
-    
+    vector<int> getScores() { return qScores; }
 	
 private:
 	
-	double calculateAverage();
+	double calculateAverage(bool);
 	MothurOut* m;
 	vector<int> qScores;
 	
 	string seqName;
 	int seqLength;
+    
+    string getSequenceName(ifstream&);
 };
 	
 /**************************************************************************************************/