PeptideIdentification.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Nico Pfeifer $
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#ifndef OPENMS_METADATA_PEPTIDEIDENTIFICATION_H
#define OPENMS_METADATA_PEPTIDEIDENTIFICATION_H

#include <OpenMS/METADATA/PeptideHit.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>
#include <OpenMS/METADATA/ProteinHit.h>

#include <string>
#include <map>

namespace OpenMS
{
  class OPENMS_DLLAPI PeptideIdentification :
    public MetaInfoInterface
  {
public:

    typedef PeptideHit HitType;



    PeptideIdentification();
    virtual ~PeptideIdentification();
    PeptideIdentification(const PeptideIdentification & source);
    PeptideIdentification & operator=(const PeptideIdentification & source);
    bool operator==(const PeptideIdentification & rhs) const;
    bool operator!=(const PeptideIdentification & rhs) const;

    const std::vector<PeptideHit> & getHits() const;
    void insertHit(const PeptideHit & hit);
    void setHits(const std::vector<PeptideHit> & hits);

    DoubleReal getSignificanceThreshold() const;
    void setSignificanceThreshold(DoubleReal value);

    String getScoreType() const;
    void setScoreType(const String & type);

    bool isHigherScoreBetter() const;
    void setHigherScoreBetter(bool value);

    const String & getIdentifier() const;
    void setIdentifier(const String & id);

    void assignRanks();

    void sort();

    bool empty() const;



    void getReferencingHits(const String & protein_accession, std::vector<PeptideHit> & peptide_hits) const;

    void getReferencingHits(const std::vector<String> & accessions, std::vector<PeptideHit> & peptide_hits) const;

    void getReferencingHits(const std::vector<ProteinHit> & protein_hits, std::vector<PeptideHit> & peptide_hits) const;

    void getNonReferencingHits(const String & protein_accession, std::vector<PeptideHit> & peptide_hits) const;
    void getNonReferencingHits(const std::vector<String> & accessions, std::vector<PeptideHit> & peptide_hits) const;
    void getNonReferencingHits(const std::vector<ProteinHit> & protein_hits, std::vector<PeptideHit> & peptide_hits) const;

protected:
    String id_;                                                          
    std::vector<PeptideHit> hits_;               
    DoubleReal significance_threshold_;              
    String score_type_;                                      
    bool higher_score_better_;                       
  };

} //namespace OpenMS
#endif // OPENMS_METADATA_PEPTIDEIDENTIFICATION_H