core/representative.{h,cpp}: remove unused setters/getters

algo/core/representative.cpp

@@ -16,24 +16,6 @@ Sequence RepresentativeComputer::getRepresentative() const{
   return representative;
 }
 
-string RepresentativeComputer::getRequiredSequence() const {
-  return required;
-}
-
-list<Sequence>& RepresentativeComputer::getSequenceList() const{
-  return sequences;
-}
-
-size_t RepresentativeComputer::getMinCover() const {
-  return min_cover;
-}
-float RepresentativeComputer::getPercentCoverage() const {
-  return percent_cover;
-}
-bool RepresentativeComputer::getRevcomp() const {
-  return revcomp;
-}
-
 bool RepresentativeComputer::hasRepresentative() const{
   return is_computed;
 }
@@ -71,14 +53,6 @@ string KmerRepresentativeComputer::getSeed() const{
   return seed;
 }
 
-void KmerRepresentativeComputer::setSeed(string seed) {
-  this->seed = seed;
-}
-
-int KmerRepresentativeComputer::getStabilityLimit() const {
-  return stability_limit;
-}
-
 void KmerRepresentativeComputer::setStabilityLimit(int limit) {
   stability_limit = limit;
 }

algo/core/representative.h

@@ -34,21 +34,6 @@ public:
    */
   Sequence getRepresentative() const;
 
-  /**
-   * @return the sequence that must be contained in the representative sequence 
-   *         ie. getRepresentative().find(getRequiredSequence()) != string::npos
-   */
-  string getRequiredSequence() const;
-
-  /**
-   * @return the input sequences we are working on
-   */
-  list<Sequence>& getSequenceList() const;
-
-  size_t getMinCover() const;
-  float getPercentCoverage() const;
-  bool getRevcomp() const;
-
   /**
    * @return true iff compute() has been called and the criteria have been met.
    */
@@ -111,13 +96,6 @@ public:
   // Getters, setters
   string getSeed() const;
 
-  /**
-   * Sets the length of the k-mer used for computing the representative
-   */
-  void setSeed(string seed);
-
-  int getStabilityLimit() const;
-
   /**
    * @param limit: maximal number of iterations to be performed before reaching 
    *               stability. If after limit number of iterations, the length