Commit e522c813 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

core/segment.{h,cpp}: moves 'because' from KmerSegmenter to Segmenter

parent b5ef83fc
......@@ -381,7 +381,7 @@ KmerAffectAnalyser *KmerSegmenter::getKmerAffectAnalyser() const {
return kaa;
}
int KmerSegmenter::getSegmentationStatus() const {
int Segmenter::getSegmentationStatus() const {
return because;
}
......@@ -521,6 +521,7 @@ string format_del(int deletions)
FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c)
{
because = 0 ;
segmented_germline = germline ;
info_extra = "" ;
label = seq.label ;
......
......@@ -48,6 +48,7 @@ protected:
int Dstart, Dend;
int CDR3start, CDR3end;
bool reversed, segmented, dSegmented;
int because;
string removeChevauchement();
bool finishSegmentation();
......@@ -122,6 +123,15 @@ protected:
*/
bool isDSegmented() const;
/**
* @return the status of the segmentation. Tells if the Sequence has been segmented
* of if it has not, what the reason is.
* @assert getSegmentationStatus() == SEG_PLUS || getSegmentationStatus() == SEG_MINUS
* <==> isSegmented()
*/
int getSegmentationStatus() const;
string getInfoLine() const;
friend ostream &operator<<(ostream &out, const Segmenter &s);
};
......@@ -136,7 +146,6 @@ class KmerSegmenter : public Segmenter
{
private:
int detected;
int because;
KmerAffectAnalyser *kaa;
protected:
string affects;
......@@ -162,14 +171,6 @@ class KmerSegmenter : public Segmenter
*/
KmerAffectAnalyser *getKmerAffectAnalyser() const;
/**
* @return the status of the segmentation. Tells if the Sequence has been segmented
* of if it has not, what the reason is.
* @assert getSegmentationStatus() == SEG_PLUS || getSegmentationStatus() == SEG_MINUS
* <==> isSegmented()
*/
int getSegmentationStatus() const;
private:
void computeSegmentation(int strand, KmerAffect left, KmerAffect right);
};
......@@ -192,7 +193,6 @@ class KmerMultiSegmenter
class FineSegmenter : public Segmenter
{
public:
int because;
vector<pair<int, int> > score_V;
vector<pair<int, int> > score_D;
vector<pair<int, int> > score_J;
......
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