added oligos class. added check orient parameter to trim.flows, sffinfo, fastq.info...

[mothur.git] / qualityscores.h

diff --git a/qualityscores.h b/qualityscores.h
index 87699739d34ad012b121a295be53f976b122a5b7..756b36ffce2cd217f46a6ca4c31060b897a02439 100644 (file)
--- a/qualityscores.h
+++ b/qualityscores.h
@@ -22,6 +22,7 @@
 class QualityScores {
 public:
        QualityScores();
+    QualityScores(string n, vector<int> qs);
        QualityScores(ifstream&);
        string getName();
        int getLength(){    return (int)qScores.size();  }
@@ -30,19 +31,19 @@ public:
        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;