Kmer: provide getLength(), isNull() and isUnknown()

Those functions are not really used with Kmer but they are there for
the compatibility with KmerAffect.

algo/core/kmerstore.cpp

@@ -42,14 +42,22 @@ Kmer &Kmer::operator+=(const Kmer &kmer) {
   return *this;
 }
 
+size_t Kmer::getLength() const{
+  return 10;
+}
+
 bool Kmer::hasRevcompSymetry() {
   return true;
 }
 
-bool Kmer::isNull() {
+bool Kmer::isNull() const{
   return count == 0;
 }
 
+bool Kmer::isUnknown() const{
+  return false;
+}
+
 ostream &operator<<(ostream &os, const Kmer &kmer) {
   os << kmer.count << ",";
   return os;

algo/core/kmerstore.h

@@ -25,6 +25,11 @@ public:
 
   Kmer &operator+=(const Kmer &);
 
+  /**
+   * @return the length of the kmer (only there for compatibility with KmerAffect)
+   */
+  size_t getLength() const;
+
   /**
    * When indexing revcomp, should the value be the same or not?
    * In other words, does the information stored by the class is strand-dependent?
@@ -34,7 +39,13 @@ public:
   /**
    * @return true if the element is the same as when initialised with default constructor.
    */
-  bool isNull();
+  bool isNull() const;
+
+  /**
+   * @return true iff the kmer is unknown (which doesn't make sense here but
+   * it only there for a reason of compatibility with KmerAffect)
+   */
+  bool isUnknown() const;
 } ;
 ostream &operator<<(ostream &os, const Kmer &kmer);
 

[Mathieu Giraud]

:-)

Voir #3727

[Mikaël Salson]

On utilise des KmerAffect ;)