added Jensen-Shannon calc. working on get.communitytype command. fixed bug in get...

[mothur.git] / qualityscores.h

diff --git a/qualityscores.h b/qualityscores.h
index 500d3e98db79b934effee830b65f54afb0023af3..a802636fd364071ab15aa84c148ebb38fead14b4 100644 (file)
--- a/qualityscores.h
+++ b/qualityscores.h
@@ -30,9 +30,9 @@ 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);
@@ -42,7 +42,7 @@ public:
        
 private:
        
-       double calculateAverage();
+       double calculateAverage(bool);
        MothurOut* m;
        vector<int> qScores;