SequenceWithAnnotationTools.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include "Alphabet/CaseMaskedAlphabet.h"
#include "SequenceWithAnnotationTools.h"
 
using namespace bpp;
using namespace std;
 
const string SequenceMask::MASK = "Boolean mask";
 
/******************************************************************************/
 
void SequenceMask::afterSequenceChanged(const IntSymbolListEditionEvent& event)
{
  mask_.clear();
  mask_.insert(mask_.begin(), event.getCoreSymbolList()->size(), false);
}
 
/******************************************************************************/
 
void SequenceMask::afterSequenceInserted(const IntSymbolListInsertionEvent& event)
{
  mask_.insert(mask_.begin() + static_cast<ptrdiff_t>(event.getPosition()),
      event.getLength(), false);
}
 
/******************************************************************************/
 
void SequenceMask::afterSequenceDeleted(const IntSymbolListDeletionEvent& event)
{
  mask_.erase(mask_.begin() + static_cast<ptrdiff_t>(event.getPosition()),
      mask_.begin() + static_cast<ptrdiff_t>(event.getPosition() + event.getLength()));
}
 
/******************************************************************************/
 
unique_ptr<SequenceWithAnnotation> SequenceWithAnnotationTools::createMaskAnnotation(const Sequence& seq)
{
  auto cma = dynamic_pointer_cast<const CaseMaskedAlphabet>(seq.getAlphabet());
  if (cma)
  {
    auto alphaPtr = seq.getAlphabet();
    auto seqa = make_unique<SequenceWithAnnotation>(seq.getName(), seq.toString(), seq.getComments(), alphaPtr);
    vector<bool> mask(seq.size());
    for (size_t i = 0; i < seq.size(); ++i)
    {
      mask[i] = cma->isMasked(seq[i]);
    }
    seqa->addAnnotation(make_shared<SequenceMask>(mask));
    return seqa;
  }
  else
  {
    throw AlphabetException("SequenceWithAnnotationTools::createMaskAnnotation. Alphabet should be a CaseMaskedAlphabet.", seq.getAlphabet());
  }
}
 
/******************************************************************************/