added count file to cluster.classic and cluster.split. modified splitting classes...

[mothur.git] / qualityscores.h

diff --git a/qualityscores.h b/qualityscores.h
index dee5917208ed19992ffa9d2c7c6cb7ddaba6f85a..49034b8ecb2a2b937901c9cfda132c00bcd5c4c4 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();
+       
+       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) { seqName = n; }
+    void setScores(vector<int> qs) { qScores = qs; seqLength = qScores.size(); }
+    
+       
 private:
        
        double calculateAverage();