Transliterator.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include <memory>
 
using namespace std;
 
#include "Transliterator.h"
 
using namespace bpp;
 
unique_ptr<Sequence> AbstractTransliterator::translate(const SequenceInterface& sequence) const
{
  if (sequence.alphabet().getAlphabetType() != sourceAlphabet().getAlphabetType())
    throw AlphabetMismatchException("AbstractTransliterator::translate", getSourceAlphabet(), getTargetAlphabet());
  auto alphaPtr = getTargetAlphabet();
  auto tSeq = make_unique<Sequence>(sequence.getName(), "", sequence.getComments(), alphaPtr);
  int gap = sequence.getAlphabet()->getGapCharacterCode();
  for (size_t i = 0; i < sequence.size(); ++i)
  {
    int state = sequence.getValue(i);
    if (state == gap)
      tSeq->addElement(gap);
    else
      tSeq->addElement(translate(state));
  }
  return tSeq;
}
 
unique_ptr<Sequence> AbstractReverseTransliterator::reverse(const SequenceInterface& sequence) const
{
  if (sequence.alphabet().getAlphabetType() != targetAlphabet().getAlphabetType())
    throw AlphabetMismatchException("AbstractReverseTransliterator::reverse", getSourceAlphabet(), getTargetAlphabet());
  auto alphaPtr = getSourceAlphabet();
  auto rSeq = make_unique<Sequence>(sequence.getName(), "", sequence.getComments(), alphaPtr);
  for (size_t i = 0; i < sequence.size(); ++i)
  {
    rSeq->addElement(reverse(sequence.getValue(i)));
  }
  return rSeq;
}