X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=qualityscores.h;h=500d3e98db79b934effee830b65f54afb0023af3;hp=5db43113f1b4aedea7761cd4ad7bcc3575542919;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=e0fbf58358a72f20352cf2a43922ab6b5bdf0cf8 diff --git a/qualityscores.h b/qualityscores.h index 5db4311..500d3e9 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(); + int getLength(){ return (int)qScores.size(); } + vector getQualityScores() { return qScores; } void printQScores(ofstream&); void trimQScores(int, int); void flipQScores(); @@ -29,6 +33,13 @@ public: bool stripQualRollingAverage(Sequence&, double); bool stripQualWindowAverage(Sequence&, int, int, double); bool cullQualAverage(Sequence&, double); + void updateQScoreErrorMap(map >&, string, int, int, int); + void updateForwardMap(vector >&, int, int, int); + void updateReverseMap(vector >&, int, int, int); + void setName(string n); + void setScores(vector qs) { qScores = qs; seqLength = qScores.size(); } + vector getScores() { return qScores; } + private: double calculateAverage(); @@ -37,6 +48,8 @@ private: string seqName; int seqLength; + + string getSequenceName(ifstream&); }; /**************************************************************************************************/