X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.h;h=a802636fd364071ab15aa84c148ebb38fead14b4;hb=0c5f99d1282405e20458e2822aa1a54774d2fa83;hp=5db43113f1b4aedea7761cd4ad7bcc3575542919;hpb=e0fbf58358a72f20352cf2a43922ab6b5bdf0cf8;p=mothur.git

diff --git a/qualityscores.h b/qualityscores.h
index 5db4311..a802636 100644
--- a/qualityscores.h
+++ b/qualityscores.h
@@ -10,6 +10,8 @@
  *
  */
 
+//DataStructure for a quality file.
+
 
 #include "mothur.h"
 #include "mothurout.h"
@@ -20,23 +22,34 @@
 class QualityScores {
 public:
 	QualityScores();
-	QualityScores(ifstream&, int);
+	QualityScores(ifstream&);
 	string getName();
+	int getLength(){    return (int)qScores.size();  }
+	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);
+	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); 
+    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&);
 };
 	
 /**************************************************************************************************/