core/segment.{h,cpp}: Revert "clean, remove 'detected' field"

This reverts 6815ffb5.
With '-x', we need to have some check, even when there is no e-value check.

algo/core/segment.cpp

@@ -79,6 +79,10 @@ bool Segmenter::isDSegmented() const {
   return dSegmented;
 }
 
+bool KmerSegmenter::isDetected() const {
+  return detected;
+}
+
 // Chevauchement
 
 string Segmenter::removeChevauchement()
@@ -431,12 +435,10 @@ void KmerSegmenter::computeSegmentation(int strand, KmerAffect before, KmerAffec
   max = kaa->getMaximum(before, after); 
 
       // We labeled it detected if there were both enough affect_5 and enough affect_3
-       bool detected = (max.nb_before_left + max.nb_before_right >= DETECT_THRESHOLD)
+      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) {
-        // ----------------------------
-        // This code is only here to set the UNSEG cause. It could be streamlined.
         if ((strand == 1 && max.nb_before_left == 0)
             || (strand == -1 && max.nb_after_right == 0)) 
           because = detected ? UNSEG_AMBIGUOUS : UNSEG_TOO_FEW_V ;
@@ -446,7 +448,6 @@ void KmerSegmenter::computeSegmentation(int strand, KmerAffect before, KmerAffec
 	  because = detected ? UNSEG_AMBIGUOUS : UNSEG_TOO_FEW_J ;
 	} else 
           because = UNSEG_AMBIGUOUS; 
-        // ----------------------------
       } else {
         Vend = max.first_pos_max;
         Jstart = max.last_pos_max + 1;

algo/core/segment.h

@@ -169,6 +169,7 @@ class KmerSegmenter : public Segmenter
   string affects;
 
  public:
+  bool isDetected() const;
   int score;
 
   KmerSegmenter();