SequenceWithAnnotationTools.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_SEQUENCEWITHANNOTATIONTOOLS_H
#define BPP_SEQ_SEQUENCEWITHANNOTATIONTOOLS_H
 
#include <Bpp/Numeric/VectorTools.h>
#include <cstddef>
 
#include "SequenceTools.h"
#include "SequenceWithAnnotation.h"
 
namespace bpp
{
class SequenceMask :
  public virtual SequenceAnnotation
{
private:
  bool removable_;
  std::vector<bool> mask_;
 
public:
  static const std::string MASK;
 
public:
  SequenceMask(size_t size = 0, bool removable = true) :
    removable_(removable),
    mask_(size, false)
  {}
 
 
  SequenceMask(const std::vector<bool>& mask, bool removable = true) :
    removable_(removable),
    mask_(mask)
  {}
 
  virtual ~SequenceMask() {}
  SequenceMask* clone() const override { return new SequenceMask(*this); }
public:
  void init(const Sequence& seq) override
  {
    mask_.resize(seq.size());
    std::fill(mask_.begin(), mask_.end(), false);
  }
 
  const std::string& getType() const override { return MASK; }
 
  bool isValidWith(const SequenceWithAnnotation& sequence, bool throwException = true) const override
  {
    if (throwException && mask_.size() != sequence.size()) throw Exception("SequenceMask. The mask size must match the sequence size.");
    return mask_.size() == sequence.size();
  }
 
  bool isRemovable() const override { return removable_; }
  bool isShared() const override { return false; }
  void beforeSequenceChanged(const IntSymbolListEditionEvent& event) override {}
  void afterSequenceChanged(const IntSymbolListEditionEvent& event) override;
  void beforeSequenceInserted(const IntSymbolListInsertionEvent& event) override {}
  void afterSequenceInserted(const IntSymbolListInsertionEvent& event) override;
  void beforeSequenceDeleted(const IntSymbolListDeletionEvent& event) override {}
  void afterSequenceDeleted(const IntSymbolListDeletionEvent& event) override;
  void beforeSequenceSubstituted(const IntSymbolListSubstitutionEvent& event) override {}
  void afterSequenceSubstituted(const IntSymbolListSubstitutionEvent& event) override {}
 
  size_t getSize() const { return mask_.size(); }
 
  const bool operator[](size_t i) const { return mask_[i]; }
 
  void setMask(const std::vector<bool>& mask)
  {
    if (mask.size() != mask_.size())
      throw DimensionException("SequenceMask::setMask. Trying to replace mask by a vector with different length.", mask.size(), mask_.size());
    mask_ = mask;
  }
 
  const std::vector<bool>& getMask() const { return mask_; }
 
  void setMask(size_t pos, bool mask)
  {
    if (pos >= mask_.size())
      throw Exception("SequenceMask::setMask. Vector overflow. Scores number: " + TextTools::toString(mask_.size()) + ", but trying to insert mask at position " + TextTools::toString(pos) + ".");
    mask_[pos] = mask;
  }
 
  void setMask(size_t pos, const std::vector<bool>& mask)
  {
    if (pos + mask.size() > mask_.size())
      throw Exception("SequenceMask::setMask. Vector overflow. Scores number: " + TextTools::toString(mask_.size()) + ", but trying to insert " + TextTools::toString(mask.size()) + " scores at position " + TextTools::toString(pos) + ".");
    std::copy(mask.begin(), mask.end(), mask_.begin() + static_cast<ptrdiff_t>(pos));
  }
 
  bool merge(const SequenceAnnotation& anno) override
  {
    try
    {
      const SequenceMask* mask = &dynamic_cast<const SequenceMask&>(anno);
      VectorTools::append(mask_, mask->getMask());
      return true;
    }
    catch (std::exception& e)
    {
      return false;
    }
  }
 
  std::unique_ptr<SequenceAnnotation> getPartAnnotation(size_t pos, size_t len) const override
  {
    return std::unique_ptr<SequenceAnnotation>(new SequenceMask(std::vector<bool>(mask_.begin() + static_cast<ptrdiff_t>(pos), mask_.begin() + static_cast<ptrdiff_t>(pos + len)), removable_));
  }
};
 
class SequenceWithAnnotationTools
{
public:
  std::unique_ptr<SequenceWithAnnotation> createMaskAnnotation(const Sequence& seq);
};
}
#endif // BPP_SEQ_SEQUENCEWITHANNOTATIONTOOLS_H