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

algo/core/segment.cpp

@@ -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;
 }
 

algo/core/segment.h

@@ -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