SequenceWithQualityTools.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_SEQUENCEWITHQUALITYTOOLS_H
#define BPP_SEQ_SEQUENCEWITHQUALITYTOOLS_H
 
 
#include "SequenceTools.h"
#include "SequenceWithQuality.h"
 
namespace bpp
{
class SequenceWithQualityTools
{
private:
  static DNA DNA_;
  static RNA RNA_;
  static NucleicAcidsReplication DNARep_;
  static NucleicAcidsReplication RNARep_;
  static NucleicAcidsReplication transc_;
 
public:
  static void subseq(const SequenceWithQuality& sequence, size_t begin, size_t end, SequenceWithQuality& output)
  {
    if (end < begin || end >= sequence.size())
      throw Exception("SequenceWithQualityTools::subseq. Invalid coordinates begin=" + TextTools::toString(begin) + ", end=" + TextTools::toString(end) + " for a sequence of size " + TextTools::toString(sequence.size()) + ".");
    std::vector<int> content(end - begin + 1);
    std::vector<int> scores(end - begin + 1);
    for (size_t i = 0; i <= end - begin; ++i)
    {
      content[i] = sequence[begin + i];
      scores[i] = sequence.getQuality(begin + i);
    }
    output.append(content, scores);
  }
 
  static std::unique_ptr<SequenceWithQuality> subseq(const SequenceWithQuality& sequence, size_t begin, size_t end)
  {
    auto alphaPtr = sequence.getAlphabet();
    auto seq = std::make_unique<SequenceWithQuality>(alphaPtr);
    seq->setName(sequence.getName());
    seq->setComments(sequence.getComments());
    subseq(sequence, begin, end, *seq);
    return seq;
  }
 
 
  static std::unique_ptr<SequenceWithQuality> concatenate(
      const SequenceWithQuality& seqwq1,
      const SequenceWithQuality& seqwq2);
 
  static std::unique_ptr<SequenceWithQuality> complement(
      const SequenceWithQuality& sequence);
 
  static std::unique_ptr<SequenceWithQuality> transcript(
      const SequenceWithQuality& sequence);
 
  static std::unique_ptr<SequenceWithQuality> reverseTranscript(
      const SequenceWithQuality& sequence);
 
  static std::unique_ptr<SequenceWithQuality> invert(
      const SequenceWithQuality& sequence);
 
  static std::unique_ptr<SequenceWithQuality> removeGaps(const SequenceWithQuality& seq);
};
}
#endif // BPP_SEQ_SEQUENCEWITHQUALITYTOOLS_H