Range.h

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//
// File: Range.h
// Created by: Julien Dutheil
// Created on: Mon Nov 21 15:52 2011
//

/*
   Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)

   This software is a computer program whose purpose is to provide classes
   for numerical calculus.

   This software is governed by the CeCILL  license under French law and
   abiding by the rules of distribution of free software.  You can  use,
   modify and/ or redistribute the software under the terms of the CeCILL
   license as circulated by CEA, CNRS and INRIA at the following URL
   "http://www.cecill.info".

   As a counterpart to the access to the source code and  rights to copy,
   modify and redistribute granted by the license, users are provided only
   with a limited warranty  and the software's author,  the holder of the
   economic rights,  and the successive licensors  have only  limited
   liability.

   In this respect, the user's attention is drawn to the risks associated
   with loading,  using,  modifying and/or developing or reproducing the
   software by the user in light of its specific status of free software,
   that may mean  that it is complicated to manipulate,  and  that  also
   therefore means  that it is reserved for developers  and  experienced
   professionals having in-depth computer knowledge. Users are therefore
   encouraged to load and test the software's suitability as regards their
   requirements in conditions enabling the security of their systems and/or
   data to be ensured and,  more generally, to use and operate it in the
   same conditions as regards security.

   The fact that you are presently reading this means that you have had
   knowledge of the CeCILL license and that you accept its terms.
 */

#ifndef _RANGE_H_
#define _RANGE_H_

#include "../Text/TextTools.h"
#include "../Clonable.h"

//From the STL:
#include <string>
#include <set>
#include <algorithm>
#include <iostream>
#include <cstddef>

namespace bpp {

template<class T> class Range:
  public virtual Clonable
{
  private:
    T begin_;
    T end_;

  public:
    Range(const T& a = 0, const T& b = 0):
      begin_(std::min(a, b)),
      end_(std::max(a, b))
    {}

    Range(const Range<T>& range): begin_(range.begin_), end_(range.end_) {}
    
    Range<T>& operator=(const Range<T>& range) {
      begin_ = range.begin_;
      end_   = range.end_;
      return *this;
    }

    Range<T>* clone() const { return new Range<T>(*this); }

    virtual ~Range() {}

  public:
    bool operator==(const Range<T>& r) const {
      return begin_ == r.begin_ && end_ == r.end_;
    }
    bool operator!=(const Range<T>& r) const {
      return begin_ != r.begin_ || end_ != r.end_;
    }
    bool operator<(const Range<T>& r) const {
      return begin_ < r.begin_ || end_ < r.end_;
    }
    virtual Range& operator+=(const T& val) {
      begin_ += val;
      end_ += val;
      return *this;
    }
    virtual Range operator+(const T& val) {
      return Range<T>(*this) += val;
    }
    virtual Range& operator-=(const T& val) {
      begin_ -= val;
      end_ -= val;
      return *this;
    }
    virtual Range operator-(const T& val) {
      return Range<T>(*this) -= val;
    }

    T begin() const { return begin_; }
    
    T end() const { return end_; }
    
    T length() const { return end_ - begin_; }

    bool overlap(const Range& r) const
    {
      return (r.begin_ < end_ && r.end_ > begin_);
    }

    bool isContiguous(const Range& r) const
    {
      return (r.begin_ == end_ || r.end_ == begin_);
    }

    bool contains(const Range& r) const
    {
      return (r.begin_ >= begin_ && r.end_ <= end_);
    }

    void expandWith(const Range& r)
    {
      if (r.begin_ < begin_ && r.end_ >= begin_)
        begin_ = r.begin_;
      if (r.end_ > end_ && r.begin_ <= end_)
        end_ = r.end_;
    }

    void sliceWith(const Range& r)
    {
      if (!overlap(r)) {
        begin_ = 0;
        end_   = 0;
      } else {
        if (r.begin_ > begin_ && r.begin_ <= end_)
          begin_ = r.begin_;
        if (r.end_ < end_ && r.end_ >= begin_)
          end_ = r.end_;
      }
    }

    bool isEmpty() const { return begin_ == end_; }

    std::string toString() const {
      return ("[" + TextTools::toString(begin_) + "," + TextTools::toString(end_) + "[");
    }

};

template<class T> class RangeCollection {
  public:
    virtual ~RangeCollection() {}
    virtual void addRange(const Range<T>& r) = 0;

    virtual void restrictTo(const Range<T>& r) = 0;

    virtual void filterWithin(const Range<T>& r) = 0;

    virtual std::string toString() const = 0;

    virtual bool isEmpty() const = 0;

    virtual size_t size() const = 0;

    virtual const Range<T>& getRange(size_t i) const = 0;

    virtual void clear() = 0;
};

template<class T> class rangeComp_ {
  public:
    bool operator() (const Range<T>* a, const Range<T>* b) const {
      return ((*a) < (*b));
    }
};

template<class T> class RangeSet:
  public RangeCollection<T>
{
  public:

  private:
    std::set< Range<T>*, rangeComp_<T> > ranges_;

  public:
    RangeSet(): ranges_() {}

    RangeSet(const RangeSet<T>& set): ranges_()
    {
      for (typename std::set< Range<T>* >::iterator it = set.ranges_.begin(); it != set.ranges_.end(); ++it) {
        ranges_.insert(ranges_.end(), (**it).clone());
      }
    }

    RangeSet& operator=(const RangeSet<T>& set)
    {
      clear_();
      for (typename std::set< Range<T>* >::iterator it = set.ranges_.begin(); it != set.ranges_.end(); ++it) {
        ranges_.insert(ranges_.end(), (**it).clone());
      }
      return *this;
    }

    virtual ~RangeSet() {
      clear_();
    }

  public:
    void addRange(const Range<T>& r) {
      if (!r.isEmpty())
        ranges_.insert(r.clone());
    }

    void restrictTo(const Range<T>& r) {
      typename std::set< Range<T>* >::iterator it = ranges_.begin();
      while (it != ranges_.end()) {
        (**it).sliceWith(r);
        if ((**it).isEmpty()) {
          typename std::set< Range<T>* >::iterator it2 = it;
          delete *it;
          ++it;
          ranges_.erase(it2);
        } else {
          ++it;
        }
      }
    }

    void filterWithin(const Range<T>& r) {
      typename std::set< Range<T>* >::iterator it = ranges_.begin();
      while (it != ranges_.end()) {
        if (r.contains(**it)) {
          ++it;
        } else {
          typename std::set< Range<T>* >::iterator it2 = it;
          delete *it;
          ++it;
          ranges_.erase(it2);
        }
      }
    }
    
    std::string toString() const {
      std::string s = "{ ";
      for (typename std::set< Range<T>* >::const_iterator it = ranges_.begin(); it != ranges_.end(); ++it) {
        s += (**it).toString() + " ";
      }
      s += "}";
      return s;
    }

    bool isEmpty() const { return ranges_.size() == 0; }
    
    size_t size() const { return ranges_.size(); }

    const Range<T>& getRange(size_t i) const {
      typename std::set< Range<T>* >::const_iterator it = ranges_.begin();
      for (size_t c = 0; c < i; ++c)
        ++it;
        //it = it++;
      return **it;
    }
    
    const std::set< Range<T>*, rangeComp_<T> >& getSet() const { return ranges_; }

    std::set< Range<T>*, rangeComp_<T> >& getSet() { return ranges_; }

    void clear() {
      clear_();
    }

  private:
    void clear_() {
      for (typename std::set< Range<T>* >::const_iterator it = ranges_.begin(); it != ranges_.end(); ++it) {
        delete *it;
      }
      ranges_.clear();
    }
};

template<class T> class MultiRange:
  public RangeCollection<T>
{
  private:
    std::vector<Range<T>*> ranges_;

  public:
    MultiRange(): ranges_() {}

    MultiRange(const MultiRange<T>& mr): ranges_()
    {
      for (size_t i = 0; i < mr.ranges_.size(); ++i)
        ranges_.push_back(mr.ranges_[i]->clone());
    }

    MultiRange& operator=(const MultiRange<T>& mr)
    {
      clear_();
      for (size_t i = 0; i < mr.ranges_.size(); ++i)
        ranges_.push_back(mr.ranges_[i]->clone());
      return *this;
    }

    virtual ~MultiRange() {
      clear_();
    }


  public:
    void addRange(const Range<T>& r) {
      //this is a bit tricky, as many cases can happen. we have to check how many ranges overlap with the new one:
      std::vector<size_t> overlappingPositions;
      for (size_t i = 0; i < ranges_.size(); ++i) {
        if (ranges_[i]->overlap(r))
          overlappingPositions.push_back(i);
      }
      //check if not overlap:
      if (overlappingPositions.size() == 0) {
        //We simply add the new range to the list:
        ranges_.push_back(r.clone());
      } else {
        //We extend the first overlapping element:
        ranges_[overlappingPositions[0]]->expandWith(r);
        //Now we merge all other overlapping ranges, if any:
        for (size_t i = overlappingPositions.size() - 1; i > 0; --i) {
          //Expand first range:
          ranges_[overlappingPositions[0]]->expandWith(*ranges_[overlappingPositions[i]]);
          //Then removes this range:
          delete ranges_[overlappingPositions[i]];
          ranges_.erase(ranges_.begin() + static_cast<ptrdiff_t>(overlappingPositions[i]));
        }
      }
      clean_();
    }

    void restrictTo(const Range<T>& r) {
      for (size_t i = 0; i < ranges_.size(); ++i)
        ranges_[i]->sliceWith(r);
      clean_();
    }

    void filterWithin(const Range<T>& r) {
      typename std::vector< Range<T>* >::iterator it = ranges_.begin();
      while (it != ranges_.end()) {
        if (r.contains(**it)) {
          ++it;
        } else {
          delete *it;
          it = ranges_.erase(it);
        }
      }
    }
 
    std::string toString() const {
      std::string s = "{ ";
      for (size_t i = 0; i < ranges_.size(); ++i)
        s += ranges_[i]->toString() + " ";
      s += "}";
      return s;
    }

    std::vector<T> getBounds() const {
      std::vector<T> bounds;
      for (size_t i = 0; i < ranges_.size(); ++i) {
        bounds.push_back(ranges_[i]->begin());
        bounds.push_back(ranges_[i]->end());
      }
      return bounds;
    }

    bool isEmpty() const { return ranges_.size() == 0; }

    size_t size() const { return ranges_.size(); }

    const Range<T>& getRange(size_t i) const { return *ranges_[i]; }

    void clear() {
      clear_();
    }

  private:
    void clean_() {
      //Reorder
      rangeComp_<T> comp;
      std::sort(ranges_.begin(), ranges_.end(), comp);
      //Remove empty intervals:
      typename std::vector< Range<T>* >::iterator it = ranges_.begin();
      while (it != ranges_.end()) {
        if ((**it).isEmpty()) {
          delete *it;
          it = ranges_.erase(it);
        } else {
          ++it;
        }
      }
    }
  private:
    void clear_() {
      for (size_t i = 0; i < ranges_.size(); ++i) {
        delete ranges_[i];
      }
      ranges_.clear();
    }

};

} //end of namespace bpp

#endif //_RANGE_H_