Commit 4fda3ca5 authored by Mathieu Giraud's avatar Mathieu Giraud

core/segment.{h,cpp}: do not store 'detected' field, update comment

The test for pseudo-germline MAX12 is useless since we have the e-value.
parent ae1ac525
......@@ -79,10 +79,6 @@ bool Segmenter::isDSegmented() const {
return dSegmented;
}
bool KmerSegmenter::isDetected() const {
return detected;
}
// Chevauchement
string Segmenter::removeChevauchement()
......@@ -197,7 +193,6 @@ KmerSegmenter::KmerSegmenter(Sequence seq, Germline *germline, double threshold,
sequence = seq.sequence ;
info = "" ;
info_extra = "seed";
detected = false ;
segmented = false;
segmented_germline = germline ;
reversed = false;
......@@ -256,9 +251,6 @@ KmerSegmenter::KmerSegmenter(Sequence seq, Germline *germline, double threshold,
strand = nb_strand[0] > nb_strand[1] ? -1 : 1 ;
computeSegmentation(strand, max12.first, max12.second, threshold, multiplier);
if (!detected)
because = UNSEG_TOO_FEW_ZERO ;
// The pseudo-germline should never take precedence over the regular germlines
evalue = 1.0 ;
}
......@@ -439,7 +431,7 @@ void KmerSegmenter::computeSegmentation(int strand, KmerAffect before, KmerAffec
//
// We labeled it detected if there were both enough affect_5 and enough affect_3
detected = (max.nb_before_left + max.nb_before_right >= DETECT_THRESHOLD)
bool detected = (max.nb_before_left + max.nb_before_right >= DETECT_THRESHOLD)
&& (max.nb_after_left + max.nb_after_right >= DETECT_THRESHOLD);
if (! max.max_found) {
......
......@@ -21,10 +21,8 @@
segment to a given strand */
#define DETECT_THRESHOLD 5 /* If the number of both V and J affectations
is above this threshold, then the sequence
will be labeled as 'detected', and, if it
not segmented, the remaining germlines will
not be tested */
is above this threshold, then the sequence,
if it not segmented, will be marked as AMBIGUOUS */
#define JSON_REMEMBER_BEST 4 /* The number of V/D/J predictions to keep */
......@@ -168,13 +166,11 @@ ostream &operator<<(ostream &out, const Segmenter &s);
class KmerSegmenter : public Segmenter
{
private:
int detected;
KmerAffectAnalyser *kaa;
protected:
string affects;
public:
bool isDetected() const;
int score;
int pvalue_left;
int pvalue_right;
......
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