Commit 90cab056 authored by Mikaël Salson's avatar Mikaël Salson

Segment: Use KmerAffectAnalyser instead of CountKmerAffectAnalyser.

While CountKmerAffectAnalyser is more flexible, the heuristic implemented
in KmerAffectAnalyser is more efficient, that's why we use it in the KmerSegmenter
parent d10bcf90
......@@ -181,7 +181,7 @@ KmerSegmenter::KmerSegmenter(Sequence seq, IKmerStore<KmerAffect> *index,
return ;
}
kaa = new CountKmerAffectAnalyser<KmerAffect>(*index, sequence);
kaa = new KmerAffectAnalyser<KmerAffect>(*index, sequence);
// Check strand consistency among the affectations.
int strand;
......@@ -304,7 +304,7 @@ void KmerSegmenter::computeSegmentation(int strand, int delta_min, int delta_max
segmented = false;
}
CountKmerAffectAnalyser<KmerAffect> *KmerSegmenter::getKmerAffectAnalyser() const {
KmerAffectAnalyser<KmerAffect> *KmerSegmenter::getKmerAffectAnalyser() const {
return kaa;
}
......
......@@ -127,7 +127,7 @@ class KmerSegmenter : public Segmenter
{
private:
int because;
CountKmerAffectAnalyser<KmerAffect> *kaa;
KmerAffectAnalyser<KmerAffect> *kaa;
protected:
string affects;
......@@ -151,7 +151,7 @@ class KmerSegmenter : public Segmenter
/**
* @return the KmerAffectAnalyser of the current sequence.
*/
CountKmerAffectAnalyser<KmerAffect> *getKmerAffectAnalyser() const;
KmerAffectAnalyser<KmerAffect> *getKmerAffectAnalyser() const;
/**
* @return the status of the segmentation. Tells if the Sequence has been segmented
......
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