IKmerStore: smallestAnalysableLength()

Method which returns how many nucleotides at each time we can get.
Useful to know what is the expected length of a getResults().

algo/core/automaton.h

@@ -64,6 +64,10 @@ public:
    */
   virtual void *next(void *state, char c) = 0;
 
+  /**
+   * @inherited from IKmerStore
+   */
+  size_t smallestAnalysableLength() const;
 
 };
 

algo/core/automaton.hpp

@@ -30,6 +30,10 @@ void *AbstractACAutomaton<Info>::goto_state(const string &seq, void *starting_st
   return current_state;
 }
 
+template<class Info>
+size_t AbstractACAutomaton<Info>::smallestAnalysableLength() const {
+  return 1;
+}
 ///////////////////////
 
 template <class Info>

algo/core/kmerstore.h

@@ -135,11 +135,18 @@ public:
    * @param seq: a sequence
    * @param no_revcomp: force not to revcomp the sequence, even if
    *                    the index was built with revcomp.
-   * @return a vector of length seq.length() - getK() + 1 containing
-   * for each k-mer the corresponding value in the index.
+   * @return a vector of length seq.length() - smallestAnalysableLength() + 1
+   * containing for each position the corresponding value in the index.
    */
   virtual vector<T> getResults(const seqtype &seq, bool no_revcomp=false, string seed="") = 0;
 
+  /**
+   * @return the smallest analysable sequence length by the index. For an
+   * index just storing k-mers it will obviously be getK(). But for more
+   * sophisticated data structures it could be 1 for instance.
+   */
+  size_t smallestAnalysableLength() const;
+
   /**
    * @return true iff the revcomp is indexed
    */
@@ -424,6 +431,11 @@ bool IKmerStore<T>::isRevcomp() const {
   return revcomp_indexed;
 }
 
+template<class T>
+size_t IKmerStore<T>::smallestAnalysableLength() const {
+  return getK();
+}
+
 // MapKmerStore
 
 template <class T>