X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=qualityscores.h;h=500d3e98db79b934effee830b65f54afb0023af3;hp=dee5917208ed19992ffa9d2c7c6cb7ddaba6f85a;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=fe5bbb79f9434df947347881c47b430112f4253e

diff --git a/qualityscores.h b/qualityscores.h
index dee5917..500d3e9 100644
--- a/qualityscores.h
+++ b/qualityscores.h
@@ -10,6 +10,8 @@
  *
  */
 
+//DataStructure for a quality file.
+
 
 #include "mothur.h"
 #include "mothurout.h"
@@ -20,8 +22,10 @@
 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();
@@ -30,6 +34,12 @@ public:
 	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); 
+    void setScores(vector<int> qs) { qScores = qs; seqLength = qScores.size(); }
+    vector<int> getScores() { return qScores; }
+	
 private:
 	
 	double calculateAverage();
@@ -38,6 +48,8 @@ private:
 	
 	string seqName;
 	int seqLength;
+    
+    string getSequenceName(ifstream&);
 };
 	
 /**************************************************************************************************/