sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / qualityscores.h

diff --git a/qualityscores.h b/qualityscores.h
index 8f2105a1d095bfe94502d28ae387b89e8da9ed7c..500d3e98db79b934effee830b65f54afb0023af3 100644 (file)
--- 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();
@@ -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); 
+    void setScores(vector<int> qs) { qScores = qs; seqLength = qScores.size(); }
+    vector<int> getScores() { return qScores; }
        
 private:
        
@@ -41,6 +48,8 @@ private:
        
        string seqName;
        int seqLength;
+    
+    string getSequenceName(ifstream&);
 };
        
 /**************************************************************************************************/