core/affectanalyser.{h,cpp}: De-templatization of KmerAffectAnalyser

As KmerAffectAnalyser is only used with KmerAffect, we do not need to keep the templates.
The code should be easier to read for C++ newbies such as the author of this commit.

algo/core/affectanalyser.cpp

@@ -10,3 +10,323 @@ bool operator==(const affect_infos &ai1, const affect_infos &ai2) {
   && ai1.nb_after_left == ai2.nb_after_left
   && ai1.max_found == ai2.max_found;
 }
+
+
+
+
+KmerAffectAnalyser::KmerAffectAnalyser(IKmerStore<KmerAffect> &kms, 
+                                       const string &seq)
+  :kms(kms), seq(seq) {
+  assert(seq.length() >=  (size_t)kms.getS());
+  affectations = kms.getResults(seq, true);
+}
+
+
+KmerAffectAnalyser::KmerAffectAnalyser(IKmerStore<KmerAffect> &kms,
+                                          const string &seq,
+                                          vector <KmerAffect> a):
+kms(kms), seq(seq), affectations(a){}
+
+
+KmerAffectAnalyser::~KmerAffectAnalyser(){}
+
+
+int KmerAffectAnalyser::count() const{
+  return affectations.size();
+}
+
+
+int KmerAffectAnalyser::count(const KmerAffect &affect) const{
+  int count = 0;
+  for (vector<KmerAffect>::const_iterator it = affectations.begin(); 
+       it < affectations.end(); it++) {
+    if (*it == affect)
+      count++;
+  }
+  return count;
+}
+
+
+const KmerAffect&KmerAffectAnalyser::getAffectation(int i) const{
+  assert(i >= 0 && i < count());
+  return affectations[i];
+}
+
+
+vector<KmerAffect> KmerAffectAnalyser::getAllAffectations(affect_options_t options) const{
+  if (options == AO_NONE)
+    return affectations;
+  vector<KmerAffect> result;
+  KmerAffect previous = affectations[0];
+  result.push_back(previous);
+  for (size_t i = 1; i < affectations.size(); i++) {
+    if (! (previous == affectations[i])) {
+      result.push_back(affectations[i]);
+      previous = affectations[i];
+    }
+  }
+  return result;
+}
+
+
+set<KmerAffect> KmerAffectAnalyser::getDistinctAffectations() const{
+  set<KmerAffect> result;
+  for (size_t i = 0; i < affectations.size(); i++) {    
+    result.insert(affectations[i]);
+  }
+  return result;
+}
+
+
+affect_infos KmerAffectAnalyser::getMaximum(const KmerAffect &before, 
+                                               const KmerAffect &after, 
+                                               float ratioMin,
+                                               int maxOverlap) const {
+  /* currentValue is the  { affectations[t] == before | t \in 1..i  } - | { affectations[i] == after | t \in 1..i }  */
+  int currentValue;
+  int span = kms.getS();
+  int length = count();
+  affect_infos results;
+
+  if (maxOverlap > span)
+    maxOverlap = span;
+
+  /* Initialize results */
+  results.max_found = false;
+  results.max_value = 0;
+  results.first_pos_max = results.last_pos_max = -1;
+  results.nb_before_left = results.nb_before_right = results.nb_after_right = results.nb_after_left = 0;
+  currentValue = 0;
+
+  for (int i = 0; i < min(length,span - maxOverlap); i++) {
+    if (affectations[i] == after) {
+      currentValue--;
+      results.nb_after_right++;
+    }
+  }
+
+  for (int i = span - maxOverlap; i < length; i++) {
+    /* i - span + maxOverlap, to avoir overlapping k-mers */
+
+
+    /* Read the current affectations, and store them both in currentValue and at the right of the previous maximum.
+       The affectation of 'before' is interpreted relatively to span and maxOverlap */
+
+    if (affectations[i - span + maxOverlap] == before) {
+      currentValue++;
+      results.nb_before_right++;
+    } 
+    if (affectations[i] == after) {
+      currentValue--;
+      results.nb_after_right++;
+    }
+
+    /* Now currentValue = | { affectations[t - span + maxOverlap] == 'before' | t \in span-maxOverlap..i } | - | { affectations[i] == 'after' | t \in 0..i } | */
+
+    /* If we raise above the max, or if we continue a previous maximum (even from a distant position), store in results */
+    if (currentValue >= results.max_value) {
+      if (currentValue > results.max_value)
+        results.first_pos_max = i;
+      results.max_value = currentValue;
+      results.last_pos_max = i;
+
+      /* What was at the right of the previous maximum is now at the left of the current maximum */
+      results.nb_after_left += results.nb_after_right;
+      results.nb_before_left += results.nb_before_right;
+      results.nb_after_right = 0;
+      results.nb_before_right = 0;
+    }
+  }
+  for (int i = length - span + maxOverlap; i < length && i >= 0; i++) {
+    if (affectations[i] == before)
+      results.nb_before_right++;
+  }
+
+  /* Main test: 
+     1) do we have enough affectations in good positions ('before' at the left and 'after' at the right) ?
+     We tolerate some of them in bad positions, but there must be 'ratioMin' more in good positions
+     2) there should be at least one 'before' and one 'after' (? CHECK ?)
+  */
+
+  if (results.nb_after_right >= results.nb_before_right*ratioMin
+      && (results.nb_after_right > 0 || results.nb_before_right == 0)
+      && currentValue < results.max_value
+      && results.max_value > 0) {
+    results.max_found = true;
+    return results;
+  }
+  return results;
+}
+
+
+const string &KmerAffectAnalyser::getSequence() const{
+  return seq;
+}
+
+
+int KmerAffectAnalyser::first(const KmerAffect &affect) const{
+  for (size_t i = 0; i < affectations.size(); i++) 
+    if (affect == affectations[i])
+      return i;
+  return (int) string::npos;
+}
+
+
+int KmerAffectAnalyser::last(const KmerAffect &affect) const{
+  for (size_t i = affectations.size(); i > 0;  i--) 
+    if (affect == affectations[i-1])
+      return i-1;
+  return (int) string::npos;
+}
+
+
+string KmerAffectAnalyser::toString() const{
+  string kmer;
+  for (size_t i = 0; i < affectations.size(); i++) {
+    kmer += affectations[i].toString();
+#ifdef DEBUG_KMERS
+    kmer += ": "+spaced(seq.substr(i,kms.getS()), kms.getSeed())+"\n";
+#endif
+  }
+  return kmer;
+}
+
+/* CountKmerAffectAnalyser */
+
+
+CountKmerAffectAnalyser::CountKmerAffectAnalyser(IKmerStore<KmerAffect> &kms, const string &seq): KmerAffectAnalyser(kms, seq) {
+  buildCounts();
+  overlap=0;
+}
+
+
+CountKmerAffectAnalyser::~CountKmerAffectAnalyser() {
+  set<KmerAffect> affects = this->getDistinctAffectations();
+
+  /* Initialize each key with a 0-integer array */
+  for (set<KmerAffect>::iterator it = affects.begin(); 
+       it != affects.end(); it++) {
+    delete [] counts[*it];
+  }  
+}
+
+
+int CountKmerAffectAnalyser::count() const {
+  return KmerAffectAnalyser::count();
+}
+
+
+int CountKmerAffectAnalyser::count(const KmerAffect &affect) const {
+  if (counts.count(affect) == 0)
+    return 0;
+
+  return counts.find(affect)->second[KmerAffectAnalyser::count() - 1];
+}
+
+
+KmerAffect CountKmerAffectAnalyser::max(const set<KmerAffect> forbidden) const {
+  map<KmerAffect, int* >::const_iterator it = counts.begin();
+  KmerAffect max_affect = KmerAffect::getUnknown();
+  int max_count = -1;
+
+  for (; it != counts.end(); it++) {
+    if (forbidden.count(it->first) == 0) {
+      int current_count = count(it->first);
+      if (current_count > max_count) {
+        max_affect = it->first;
+        max_count = current_count;
+      }
+    }
+  }
+
+  return max_affect;
+}
+
+
+int CountKmerAffectAnalyser::countBefore(const KmerAffect&affect, int pos) const {
+  if (pos == 0 || counts.count(affect) == 0)
+    return 0;
+  return counts.find(affect)->second[pos-1];
+}
+
+
+int CountKmerAffectAnalyser::countAfter(const KmerAffect&affect, int pos) const {
+  if (counts.count(affect) == 0)
+    return 0;
+  int length = KmerAffectAnalyser::count();
+  map<KmerAffect, int*>::const_iterator it = counts.find(affect);
+  return it->second[length-1] - it->second[pos];
+}  
+
+
+int CountKmerAffectAnalyser::firstMax(const KmerAffect&before, const KmerAffect&after, 
+                                         int start, int min) const {
+  return searchMax(before, after, start, KmerAffectAnalyser::count()-1,1, min);
+}
+
+
+int CountKmerAffectAnalyser::lastMax(const KmerAffect&before, const KmerAffect&after, 
+                                        int end, int min) const {
+  if (end == -1)
+    end = KmerAffectAnalyser::count()-1;
+  return searchMax(before, after, end, 0, -1, min);
+}
+
+
+int CountKmerAffectAnalyser::getAllowedOverlap() {
+  return overlap;
+}
+
+
+void CountKmerAffectAnalyser::setAllowedOverlap(int overlap) {
+  this->overlap = overlap;
+}
+
+
+int CountKmerAffectAnalyser::searchMax(const KmerAffect&before, const KmerAffect& after,
+                                          int start, int end, int iter, int min) const {
+  if (count(before) == 0 || count(after) == 0)
+    return -1;
+  int first_pos_max = -1;
+  int max_value = min;
+  int shift = KmerAffectAnalyser::kms.getS() - overlap - 1;
+  int shiftedStart = start, shiftedEnd = end;
+  if (iter == 1)
+    shiftedStart += shift;
+  else
+    shiftedEnd += shift;
+  for (int i = shiftedStart; (i)*iter <= iter*shiftedEnd; i+=iter) {
+    int valueBefore = countBefore(before, i - shift);
+    int valueAfter = countAfter(after, i);
+    if (valueAfter + valueBefore > max_value 
+        && valueAfter > 0 && valueBefore > 0) {
+      max_value = valueAfter + valueBefore;
+      first_pos_max = i;
+    }
+  }
+  return first_pos_max;
+}
+
+
+void CountKmerAffectAnalyser::buildCounts() {
+  int length = KmerAffectAnalyser::count();
+  set<KmerAffect> affects = this->getDistinctAffectations();
+
+  for (set<KmerAffect>::iterator it = affects.begin(); 
+       it != affects.end(); it++) {
+    int *array = new int[length];
+    /* Initialize each key with a 0-integer array */
+    array[0] = (this->getAffectation(0) == *it) ? 1 : 0;
+
+    /* Fill the array with actual values */
+    for (int i = 1; i < length; i++) {
+      KmerAffect current = this->getAffectation(i);
+      int value = (current == *it) ? 1 : 0;
+
+      array[i] = array[i-1]+value;
+    }
+    counts[*it] = array;
+  }
+
+}
+

algo/core/affectanalyser.h

+
 #ifndef AFFECT_ANALYSER_H
 #define AFFECT_ANALYSER_H
 
 #include "kmerstore.h"
+#include "kmeraffect.h"
 #include <set>
 #include <vector>
 #include <cassert>
@@ -41,7 +43,7 @@ bool operator==(const affect_infos &ai1, const affect_infos &ai2);
  * Input: Index that constitutes the k-mer sequence repertoire
  * Input: Sequence whose k-mers must be affected
  */
-template<class T>
+
 class AffectAnalyser {
  public:
 
@@ -58,14 +60,14 @@ class AffectAnalyser {
    * @param affect: An affectation
    * @return the number of times this affectation has been given in the read.
    */
-  virtual int count(const T &affect) const = 0;
+  virtual int count(const KmerAffect &affect) const = 0;
 
   /**
    * @param i: the position to consider
    * @pre i >= 0 && i < count()
    * @return the affectation of the k-mer at position i.
    */
-  virtual const T&getAffectation(int i)  const = 0;
+  virtual const KmerAffect &getAffectation(int i)  const = 0;
 
   /**
    * @param options: options can either be AO_NONE or AO_NO_CONSECUTIVE 
@@ -74,12 +76,12 @@ class AffectAnalyser {
    *                                     will be different (we remove consecutive
    *                                     duplicates)
    */
-  virtual vector<T> getAllAffectations(affect_options_t options) const = 0;
+  virtual vector<KmerAffect> getAllAffectations(affect_options_t options) const = 0;
 
   /**
    * @return the distinct affectations
    */
-  virtual set<T> getDistinctAffectations() const = 0;
+  virtual set<KmerAffect> getDistinctAffectations() const = 0;
 
   /**
    * @return the sequence we are analysing
@@ -93,7 +95,7 @@ class AffectAnalyser {
    * @post getAffectation(first(affect)) == affect 
    * ==>  getAffectation(1...first(affect)-1) != affect
    */
-  virtual int first(const T &affect) const  = 0;
+  virtual int first(const KmerAffect &affect) const  = 0;
 
   /**
    * @param affect: an affectation
@@ -102,7 +104,7 @@ class AffectAnalyser {
    * @post getAffectation(last(affect)) == affect 
    * ==> getAffectation(last(affect)+1 ... count() -1) != affect
    */
-  virtual int last(const T &affect) const  = 0;
+  virtual int last(const KmerAffect &affect) const  = 0;
 
   /**
    * @return a string representation of the object
@@ -110,19 +112,19 @@ class AffectAnalyser {
   virtual string toString() const  = 0;
 };
 
-template <class T>
-class KmerAffectAnalyser: public AffectAnalyser<T> {
+
+class KmerAffectAnalyser: public AffectAnalyser {
  protected:
-  IKmerStore<T> &kms;
+  IKmerStore<KmerAffect> &kms;
   const string &seq;
-  vector<T> affectations;
+  vector<KmerAffect> affectations;
  public:
   /**
    * @param kms: the index storing the affectation for the k-mers
    *             (parameter is not copied)
    * @param seq: the sequence to analyse (parameter is not copied)
    */
-  KmerAffectAnalyser(IKmerStore<T> &kms, const string &seq);
+  KmerAffectAnalyser(IKmerStore<KmerAffect> &kms, const string &seq);
 
   /**
    * This constructor must be seen as a “toy” constructor, used for 
@@ -133,19 +135,19 @@ class KmerAffectAnalyser: public AffectAnalyser<T> {
    * @param seq: basically not used in the class
    * @param a: the affectation we must use.
    */
-  KmerAffectAnalyser(IKmerStore<T> &kms, const string &seq, vector<T> a);
+  KmerAffectAnalyser(IKmerStore<KmerAffect> &kms, const string &seq, vector<KmerAffect> a);
 
   ~KmerAffectAnalyser();
 
   int count() const;
 
-  int count(const T &affect) const;
+  int count(const KmerAffect &affect) const;
 
-  const T&getAffectation(int i) const;
+  const KmerAffect &getAffectation(int i) const;
 
-  vector<T> getAllAffectations(affect_options_t options) const;
+  vector<KmerAffect> getAllAffectations(affect_options_t options) const;
 
-  set<T> getDistinctAffectations() const;
+  set<KmerAffect> getDistinctAffectations() const;
 
   /**
    * @param maxOverlap: if greater than kms.getS(), it is automatically set
@@ -162,15 +164,15 @@ class KmerAffectAnalyser: public AffectAnalyser<T> {
    *
    * @complexity time: linear in count(), space: constant
    */
-  affect_infos getMaximum(const T &before, const T &after, 
+  affect_infos getMaximum(const KmerAffect &before, const KmerAffect &after, 
                           float ratioMin=2., 
                           int maxOverlap=1) const;
 
   const string &getSequence() const;
 
-  int first(const T &affect) const;
+  int first(const KmerAffect &affect) const;
 
-  int last(const T &affect) const ;
+  int last(const KmerAffect &affect) const ;
 
   string toString() const;
 };
@@ -179,14 +181,14 @@ class KmerAffectAnalyser: public AffectAnalyser<T> {
  * Class that allows to count in constant time the number of affectations
  * before or after a given point.
  */
-template <class T>
-class CountKmerAffectAnalyser: public KmerAffectAnalyser<T> {
+
+class CountKmerAffectAnalyser: public KmerAffectAnalyser {
  private:
-  map<T, int* >counts;
+  map<KmerAffect, int* >counts;
   int overlap;
  public:
 
-  CountKmerAffectAnalyser(IKmerStore<T> &kms, const string &seq);
+  CountKmerAffectAnalyser(IKmerStore<KmerAffect> &kms, const string &seq);
   ~CountKmerAffectAnalyser();
 
   int count() const;
@@ -194,19 +196,19 @@ class CountKmerAffectAnalyser: public KmerAffectAnalyser<T> {
   /**
    * @complexity constant time
    */
-  int count(const T &affect) const;
+  int count(const KmerAffect &affect) const;
 
   /**
    * Count the number of an affectation before (strictly) than a position
    * @complexity constant time
    */
-  int countBefore(const T&affect, int pos) const;
+  int countBefore(const KmerAffect &affect, int pos) const;
 
   /**
    * Count the number of an affectation after (strictly) than a position)
    * @complexity constant time
    */
-  int countAfter(const T&affect, int pos) const;
+  int countAfter(const KmerAffect &affect, int pos) const;
 
   /**
    * @return the first position pos in the sequence such that 
@@ -217,7 +219,7 @@ class CountKmerAffectAnalyser: public KmerAffectAnalyser<T> {
    *         Where s is kms.getS() - getAllowedOverlap() - 1.
    * @complexity linear in getSequence().size() 
    */
-  int firstMax(const T&before, const T&after, int start=0, int min=-1) const;
+  int firstMax(const KmerAffect &before, const KmerAffect &after, int start=0, int min=-1) const;
 
   /**
    * @return the last position pos in the sequence such that
@@ -228,7 +230,7 @@ class CountKmerAffectAnalyser: public KmerAffectAnalyser<T> {
    *         Where s is kms.getS() - getAllowedOverlap() - 1.
    * @complexity linear in getSequence().size()
    */
-  int lastMax(const T&before, const T&after, int end=-1, int min=-1) const;
+  int lastMax(const KmerAffect &before, const KmerAffect &after, int end=-1, int min=-1) const;
 
   /**
    * @return the allowed overlap between two k-mers with distinct affectations
@@ -245,7 +247,7 @@ class CountKmerAffectAnalyser: public KmerAffectAnalyser<T> {
    *         taken apart the forbidden ones.
    * @complexity Time: linear on the number of distinct affectations
    */
-  T max(const set<T> forbidden = set<T>()) const;
+  KmerAffect max(const set<KmerAffect> forbidden = set<KmerAffect>()) const;
 
   /**
    * Set the overlap allowed between two k-mers with two different affectations,
@@ -264,325 +266,8 @@ class CountKmerAffectAnalyser: public KmerAffectAnalyser<T> {
    * Search the maximum. Used by firstMax and lastMax.
    * @param iter: should be either 1 or -1
    */
-  int searchMax(const T&before, const T &after,
+  int searchMax(const KmerAffect &before, const KmerAffect &after,
                 int start, int end, int iter, int min) const;
 };
 
-template <class T>
-KmerAffectAnalyser<T>::KmerAffectAnalyser(IKmerStore<T> &kms, 
-                                       const string &seq)
-  :kms(kms), seq(seq) {
-  assert(seq.length() >=  (size_t)kms.getS());
-  affectations = kms.getResults(seq, true);
-}
-
-template <class T>
-KmerAffectAnalyser<T>::KmerAffectAnalyser(IKmerStore<T> &kms,
-                                          const string &seq,
-                                          vector <T> a):
-kms(kms), seq(seq), affectations(a){}
-
-template <class T>
-KmerAffectAnalyser<T>::~KmerAffectAnalyser(){}
-
-template <class T>
-int KmerAffectAnalyser<T>::count() const{
-  return affectations.size();
-}
-
-template <class T>
-int KmerAffectAnalyser<T>::count(const T &affect) const{
-  int count = 0;
-  for (typename vector<T>::const_iterator it = affectations.begin(); 
-       it < affectations.end(); it++) {
-    if (*it == affect)
-      count++;
-  }
-  return count;
-}
-
-template <class T>
-const T&KmerAffectAnalyser<T>::getAffectation(int i) const{
-  assert(i >= 0 && i < count());
-  return affectations[i];
-}
-
-template <class T>
-vector<T> KmerAffectAnalyser<T>::getAllAffectations(affect_options_t options) const{
-  if (options == AO_NONE)
-    return affectations;
-  vector<T> result;
-  T previous = affectations[0];
-  result.push_back(previous);
-  for (size_t i = 1; i < affectations.size(); i++) {
-    if (! (previous == affectations[i])) {
-      result.push_back(affectations[i]);
-      previous = affectations[i];
-    }
-  }
-  return result;
-}
-
-template <class T>
-set<T> KmerAffectAnalyser<T>::getDistinctAffectations() const{
-  set<T> result;
-  for (size_t i = 0; i < affectations.size(); i++) {    
-    result.insert(affectations[i]);
-  }
-  return result;
-}
-
-template <class T>
-affect_infos KmerAffectAnalyser<T>::getMaximum(const T &before, 
-                                               const T &after, 
-                                               float ratioMin,
-                                               int maxOverlap) const {
-  /* currentValue is the  { affectations[t] == before | t \in 1..i  } - | { affectations[i] == after | t \in 1..i }  */
-  int currentValue;
-  int span = kms.getS();
-  int length = count();
-  affect_infos results;
-
-  if (maxOverlap > span)
-    maxOverlap = span;
-