SequenceWithQuality.cpp

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#include <Bpp/Numeric/VectorTools.h>
 
#include "SequenceWithQuality.h"
 
using namespace bpp;
 
#include <string>
#include <iostream>
 
using namespace std;
 
const string SequenceQuality::QUALITY_SCORE = "Quality score";
const int SequenceQuality::DEFAULT_QUALITY_VALUE = 20;
 
/******************************************************************************/
 
void SequenceQuality::afterSequenceChanged(const IntSymbolListEditionEvent& event)
{
  qualScores_.clear();
  qualScores_.insert(qualScores_.begin(), event.getCoreSymbolList()->size(), DEFAULT_QUALITY_VALUE);
}
 
/******************************************************************************/
 
void SequenceQuality::afterSequenceInserted(const IntSymbolListInsertionEvent& event)
{
  qualScores_.insert(
      qualScores_.begin() + static_cast<ptrdiff_t>(event.getPosition()),
      event.getLength(), DEFAULT_QUALITY_VALUE);
}
 
/******************************************************************************/
 
void SequenceQuality::afterSequenceDeleted(const IntSymbolListDeletionEvent& event)
{
  qualScores_.erase(
      qualScores_.begin() + static_cast<ptrdiff_t>(event.getPosition()),
      qualScores_.begin() + static_cast<ptrdiff_t>(event.getPosition() + event.getLength()));
}
 
/******************************************************************************/