X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=qualityscores.h;h=49034b8ecb2a2b937901c9cfda132c00bcd5c4c4;hb=731d19a6eaf81768ed35e4be25fbac5686a2a7a0;hp=8f2105a1d095bfe94502d28ae387b89e8da9ed7c;hpb=bdb5d82e2a73829b4e1fa42656ad9bcb57e3e948;p=mothur.git

diff --git a/qualityscores.h b/qualityscores.h
index 8f2105a..49034b8 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();
+	
+	vector<int> getQualityScores() { return qScores; }
 	void printQScores(ofstream&);
 	void trimQScores(int, int);
 	void flipQScores();
@@ -32,6 +36,9 @@ public:
 	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: