StringSequenceTools.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_STRINGSEQUENCETOOLS_H
#define BPP_SEQ_STRINGSEQUENCETOOLS_H
 
#include <Bpp/Exceptions.h>
 
#include "Alphabet/Alphabet.h"
#include "Alphabet/AlphabetExceptions.h"
#include "SequenceExceptions.h"
 
// From the STL:
#include <string>
#include <vector>
 
namespace bpp
{
class StringSequenceTools
{
public:
  StringSequenceTools() {}
  ~StringSequenceTools() {}
 
public:
  static std::string subseq(const std::string& sequence, size_t begin, size_t end);
 
  static std::string setToSizeR(const std::string& sequence, size_t size);
 
  static std::string setToSizeL(const std::string& sequence, size_t size);
 
  static std::string deleteChar(const std::string& sequence, char chars);
 
  static std::string deleteChar(const std::string& sequence, std::string chars);
 
  static std::string* reverse(const std::string& sequence);
 
  static std::string* complement(const std::string& sequence);
 
  static double getGCcontent(const std::string& sequence, size_t pos, size_t window);
 
  static std::vector<int> codeSequence(const std::string& sequence, std::shared_ptr<const Alphabet>& alphabet);
 
  static std::string decodeSequence(const std::vector<int>& sequence, std::shared_ptr<const Alphabet>& alphabet);
 
  static std::shared_ptr<const Alphabet> getAlphabetFromSequence(const std::string& sequence);
};
} // end of namespace bpp.
#endif // BPP_SEQ_STRINGSEQUENCETOOLS_H