core/kmeraffect.{h,cpp}: remove KmerStringAffect

KmerStringAffect is no more used in the code.
If one day we would like to "store more things" in the affectations,
we could still extend KmerAffect with a pointer to something else.

algo/core/kmeraffect.cpp

@@ -166,109 +166,3 @@ ostream &operator<<(ostream &os, const KmerAffect &kmer) {
   return os;
 }
 
-//////////////////////////////////////////////////
-
-KmerStringAffect::KmerStringAffect() {
-  label = "";
-  strand = 0;
-}
-
-KmerStringAffect::KmerStringAffect(const KmerStringAffect &ksa):
-  label(ksa.label),strand(ksa.strand){}
-
-
-KmerStringAffect::KmerStringAffect(const string &label,
-                                   int strand) {
-  this->label = label;
-  this->strand = strand;
-}
-
-KmerStringAffect &KmerStringAffect::operator+=(const KmerStringAffect &kmer) {
-  if (*this != kmer) {
-    if (*this == KSA_UNKNOWN) 
-      // Not defined yet
-      *this = kmer;
-    else if (*this != KSA_AMBIGUOUS) {
-      if (this->label == kmer.label)
-        // Different strand but same label, put ambiguous
-        *this = KSA_AMBIGUOUS;
-      else
-        // Ambiguous: different labels
-        *this = KSA_AMBIGUOUS;
-    } // else we are already ambiguous, stay as is.
-  }
-  return *this;
-}
-
-KmerStringAffect &KmerStringAffect::operator=(const KmerStringAffect &ka) {
-  label = ka.label;
-  strand = ka.strand;
-  return *this;
-}
-
-KmerStringAffect KmerStringAffect::getAmbiguous() {
-  return KSA_AMBIGUOUS;
-}
-
-int KmerStringAffect::getStrand() const {
-  return (isUnknown() || isAmbiguous()) ? 0 : strand;
-}
-
-string KmerStringAffect::getLabel() const {
-  return label;
-}
-
-KmerStringAffect KmerStringAffect::getUnknown() {
-  return KSA_UNKNOWN;
-}
-
-bool KmerStringAffect::isAmbiguous() const {
-  return *this == KSA_AMBIGUOUS;
-}
-
-bool KmerStringAffect::isUnknown() const {
-  return *this == KSA_UNKNOWN;
-}
-
-string KmerStringAffect::toString() const {
-  if (isUnknown()) {
-    return " _";
-  }
-  
-  switch(strand) {
-  case 1:
-    return "+"+label;
-  case -1:
-    return "-"+label;
-  default:
-    return " ?";
-  }
-}
-
-bool operator==(const KmerStringAffect &k1, const KmerStringAffect &k2) {
-  return k1.strand == k2.strand && (k1.label == k2.label || k1.strand == 0);
-}
-bool operator!=(const KmerStringAffect &k1, const KmerStringAffect &k2) {
-  return ! (k1 == k2);
-}
-bool operator<(const KmerStringAffect &k1, const KmerStringAffect &k2) {
-  return k1.label < k2.label || (k1.label == k2.label && k1.strand < k2.strand);
-}
-bool operator>(const KmerStringAffect &k1, const KmerStringAffect &k2) {
-  return k1.label > k2.label || (k1.label == k2.label && k1.strand > k2.strand);
-}
-bool operator<=(const KmerStringAffect &k1, const KmerStringAffect &k2) {
-  return ! (k1 > k2);
-}
-bool operator>=(const KmerStringAffect &k1, const KmerStringAffect &k2) {
-  return ! (k1 < k2);
-}
-
-ostream &operator<<(ostream &os, const KmerStringAffect &kmer) {
-  os << kmer.toString();
-  return os;
-}
-
-bool KmerStringAffect::hasRevcompSymetry() {
-  return false;
-}

algo/core/kmeraffect.h

@@ -160,94 +160,4 @@ const KmerAffect AFFECT_J_BWD = KmerAffect("J", -1);
 
 ////////////////////////////////////////////////////////////////////////////////////////////////////
 
-/**
- * This class represents the affectation with a string for the label.  Two
- * constants are defined representing affectation that are either unknown
- * (KSA_UNKNOWN) or ambiguous (KSA_AMBIGUOUS).
- */
-class KmerStringAffect {
-public:
-  string label;
-  int strand;
-
-  /**
-   * Construct an unknown affectation.
-   * @post isUnknown()
-   */
-  KmerStringAffect();
-  KmerStringAffect(const KmerStringAffect &);
-  /**
-   * Construct an affectation as stated by the parameters
-   * @post affect_strand(affect) == strand AND affect_char(affect) == kmer[0]
-   */
-  KmerStringAffect(const string &label, int strand=1);
-  /**
-   * Add another affectation to the current one.
-   * @post The current affectation is not modified if the parameter is the same
-   *       affectation as the current one.
-   *       If the current affectation is unknown, the affectation is set to the
-   *       parameter.
-   *       If the label is the same but the strand is different, the strand is
-   *       arbitrarily put to forward.
-   *       In the other cases, the affectation is set to ambiguous.
-   */
-  KmerStringAffect &operator+=(const KmerStringAffect &);
-
-  /**
-   * Affectation
-   */
-  KmerStringAffect &operator=(const KmerStringAffect &ka);
-
-  /**
-   * @return the ambiguous affectation
-   */
-  static KmerStringAffect getAmbiguous();
-
-  /**
-   * @return the strand of the affectation
-   *         -1 for backward
-   *          1 for forward
-   *          0 for unknown or ambiguous
-   */
-  int getStrand() const;
-
-  /**
-   * @return the label of the affectation.
-   */
-  string getLabel() const;
-
-  /**
-   * @return the unknown affectation
-   */
-  static KmerStringAffect getUnknown();
-
-  /**
-   * @return true iff the class does not take care of the strand
-   *         (false in our case).
-   */
-  static bool hasRevcompSymetry();
-
-  /**
-   * @return true iff the affectation should be considered as ambiguous.
-   */
-  bool isAmbiguous() const;
-
-  /**
-   * @return true iff the affectation is unkwown yet.
-   */
-  bool isUnknown() const;
-
-  string toString() const;
-};
-bool operator!=(const KmerStringAffect &k1, const KmerStringAffect &k2);
-bool operator==(const KmerStringAffect &k1, const KmerStringAffect &k2);
-bool operator<(const KmerStringAffect &k1, const KmerStringAffect &k2);
-bool operator>(const KmerStringAffect &k1, const KmerStringAffect &k2);
-bool operator<=(const KmerStringAffect &k1, const KmerStringAffect &k2);
-bool operator>=(const KmerStringAffect &k1, const KmerStringAffect &k2);
-ostream &operator<<(ostream &os, const KmerStringAffect &kmer);
-
-const KmerStringAffect KSA_UNKNOWN = KmerStringAffect();
-const KmerStringAffect KSA_AMBIGUOUS = KmerStringAffect("", 2);
-
 #endif