MaseTools.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_IO_MASETOOLS_H
#define BPP_SEQ_IO_MASETOOLS_H
 
#include <Bpp/Exceptions.h>
 
#include "../Container/SequenceContainer.h"
#include "../Container/SequenceContainerTools.h"
#include "../Container/SiteContainer.h"
#include "../Container/SiteContainerTools.h"
 
namespace bpp
{
class MaseTools
{
public:
  static SiteSelection getSiteSet(const Comments& maseFileHeader, const std::string& setName);
 
  static SequenceSelection getSequenceSet(const Comments& maseFileHeader, const std::string& setName);
 
  template<class SiteType, class SequenceType>
  static std::unique_ptr< TemplateVectorSiteContainer<SiteType, SequenceType>>
  getSelectedSites(
      const TemplateSiteContainerInterface<SiteType, SequenceType, std::string>& sequences,
      const std::string& setName)
  {
    SiteSelection ss = getSiteSet(sequences.getComments(), setName);
    return SiteContainerTools::getSelectedPositions<SiteType, SequenceType>(sequences, ss);
  }
 
 
  template<class SequenceType, class HashType>
  static std::unique_ptr< TemplateSequenceContainerInterface<SequenceType, HashType>>
  getSelectedSequences(
      const TemplateSequenceContainerInterface<SequenceType, HashType>& sequences,
      const std::string& setName)
  {
    SequenceSelection ss = getSequenceSet(sequences.getGeneralComments(), setName);
    return SequenceContainerTools::getSelectedSequences<SequenceType, HashType>(sequences, ss);
  }
 
 
  static std::map<std::string, size_t> getAvailableSiteSelections(const Comments& maseHeader);
 
  static std::map<std::string, size_t> getAvailableSequenceSelections(const Comments& maseHeader);
 
  static size_t getPhase(const Comments& maseFileHeader, const std::string& setName);
};
} // end of namespace bpp.
#endif // BPP_SEQ_IO_MASETOOLS_H