Une MAJ de sécurité est nécessaire sur notre version actuelle. Elle sera effectuée lundi 02/08 entre 12h30 et 13h. L'interruption de service devrait durer quelques minutes (probablement moins de 5 minutes).

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 { ...@@ -381,7 +381,7 @@ KmerAffectAnalyser *KmerSegmenter::getKmerAffectAnalyser() const {
return kaa; return kaa;
} }
int KmerSegmenter::getSegmentationStatus() const { int Segmenter::getSegmentationStatus() const {
return because; return because;
} }
...@@ -521,6 +521,7 @@ string format_del(int deletions) ...@@ -521,6 +521,7 @@ string format_del(int deletions)
FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c) FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c)
{ {
because = 0 ;
segmented_germline = germline ; segmented_germline = germline ;
info_extra = "" ; info_extra = "" ;
label = seq.label ; label = seq.label ;
......
...@@ -48,6 +48,7 @@ protected: ...@@ -48,6 +48,7 @@ protected:
int Dstart, Dend; int Dstart, Dend;
int CDR3start, CDR3end; int CDR3start, CDR3end;
bool reversed, segmented, dSegmented; bool reversed, segmented, dSegmented;
int because;
string removeChevauchement(); string removeChevauchement();
bool finishSegmentation(); bool finishSegmentation();
...@@ -122,6 +123,15 @@ protected: ...@@ -122,6 +123,15 @@ protected:
*/ */
bool isDSegmented() const; 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); friend ostream &operator<<(ostream &out, const Segmenter &s);
}; };
...@@ -136,7 +146,6 @@ class KmerSegmenter : public Segmenter ...@@ -136,7 +146,6 @@ class KmerSegmenter : public Segmenter
{ {
private: private:
int detected; int detected;
int because;
KmerAffectAnalyser *kaa; KmerAffectAnalyser *kaa;
protected: protected:
string affects; string affects;
...@@ -162,14 +171,6 @@ class KmerSegmenter : public Segmenter ...@@ -162,14 +171,6 @@ class KmerSegmenter : public Segmenter
*/ */
KmerAffectAnalyser *getKmerAffectAnalyser() const; 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: private:
void computeSegmentation(int strand, KmerAffect left, KmerAffect right); void computeSegmentation(int strand, KmerAffect left, KmerAffect right);
}; };
...@@ -192,7 +193,6 @@ class KmerMultiSegmenter ...@@ -192,7 +193,6 @@ class KmerMultiSegmenter
class FineSegmenter : public Segmenter class FineSegmenter : public Segmenter
{ {
public: public:
int because;
vector<pair<int, int> > score_V; vector<pair<int, int> > score_V;
vector<pair<int, int> > score_D; vector<pair<int, int> > score_D;
vector<pair<int, int> > score_J; vector<pair<int, int> > score_J;
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment