PolymorphismSequenceContainerTools.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef _POLYMORPHISMSEQUENCECONTAINERTOOL_H_
#define _POLYMORPHISMSEQUENCECONTAINERTOOL_H_
 
#include <Bpp/Numeric/Random/RandomTools.h>
#include <Bpp/Text/StringTokenizer.h>
 
// from bpp-seq
#include <Bpp/Seq/Alphabet/CodonAlphabet.h>
#include <Bpp/Seq/Io/Mase.h>
#include <Bpp/Seq/Io/MaseTools.h>
#include <Bpp/Seq/Container/SiteContainerIterator.h>
#include <Bpp/Seq/Container/SequenceContainerTools.h>
#include <Bpp/Seq/Container/VectorSiteContainer.h>
#include <Bpp/Seq/SiteTools.h>
 
// from STL
#include <string>
 
// From Local
#include "PolymorphismSequenceContainer.h"
#include "GeneralExceptions.h"
 
namespace bpp
{
using SimpleSiteContainerIterator = SimpleTemplateSiteContainerIterator<Site, Sequence, std::string>;
using CompleteSiteContainerIterator = CompleteTemplateSiteContainerIterator<Site, Sequence, std::string>;
using NoGapSiteContainerIterator = NoGapTemplateSiteContainerIterator<Site, Sequence, std::string>;
 
class PolymorphismSequenceContainerTools
{
public:
  // Class destructor:
  virtual ~PolymorphismSequenceContainerTools();
 
  /*******************************************************************************/
 
public:
  static std::unique_ptr<PolymorphismSequenceContainer> read(
      const std::string& path,
      std::shared_ptr<const Alphabet> alpha);
 
  static std::unique_ptr<PolymorphismSequenceContainer> extractIngroup(
      const PolymorphismSequenceContainer& psc);
 
  static std::unique_ptr<PolymorphismSequenceContainer> extractOutgroup(
      const PolymorphismSequenceContainer& psc);
 
  static std::unique_ptr<PolymorphismSequenceContainer> extractGroup(
      const PolymorphismSequenceContainer& psc,
      size_t groupId);
 
  static std::unique_ptr<PolymorphismSequenceContainer> getSelectedSequences(
      const PolymorphismSequenceContainer& psc,
      const SequenceSelection& ss);
 
  static std::unique_ptr<PolymorphismSequenceContainer> sample(
      const PolymorphismSequenceContainer& psc,
      size_t n,
      bool replace = true);
 
  static std::unique_ptr<PolymorphismSequenceContainer> getSitesWithoutGaps(
      const PolymorphismSequenceContainer& psc);
 
  static size_t getNumberOfNonGapSites(
      const PolymorphismSequenceContainer& psc,
      bool ingroup);
 
  static size_t getNumberOfCompleteSites(
      const PolymorphismSequenceContainer& psc,
      bool ingroup);
 
 
  static std::unique_ptr<PolymorphismSequenceContainer> getCompleteSites(
      const PolymorphismSequenceContainer& psc);
 
 
  static std::unique_ptr<PolymorphismSequenceContainer> excludeFlankingGap(
      const PolymorphismSequenceContainer& psc);
 
  static std::unique_ptr<PolymorphismSequenceContainer> getSelectedSites(
      const PolymorphismSequenceContainer& psc,
      const std::string& setName, bool phase);
 
  static std::unique_ptr<PolymorphismSequenceContainer> getNonCodingSites(
      const PolymorphismSequenceContainer& psc,
      const std::string& setName);
 
  static std::unique_ptr<PolymorphismSequenceContainer> getOnePosition(
      const PolymorphismSequenceContainer& psc,
      const std::string& setName,
      size_t pos);
 
  static std::unique_ptr<PolymorphismSequenceContainer> getIntrons(
      const PolymorphismSequenceContainer& psc,
      const std::string& setName,
      const GeneticCode& gCode);
 
  static std::unique_ptr<PolymorphismSequenceContainer> get5Prime(
      const PolymorphismSequenceContainer& psc,
      const std::string& setName);
 
  static std::unique_ptr<PolymorphismSequenceContainer> get3Prime(
      const PolymorphismSequenceContainer& psc,
      const std::string& setName,
      const GeneticCode& gCode);
 
  static std::string getIngroupSpeciesName(const PolymorphismSequenceContainer& psc);
 
  static std::unique_ptr<PolymorphismSequenceContainer> getSynonymousSites(
      const PolymorphismSequenceContainer& psc,
      const GeneticCode& gCode);
 
  static std::unique_ptr<PolymorphismSequenceContainer> getNonSynonymousSites(
      const PolymorphismSequenceContainer& psc,
      const GeneticCode& gCode);
};
} // end of namespace bpp;
 
#endif // _POLYMORPHISMSEQUENCECONTAINERTOOL_H_