OpenMS  2.7.0
Classes | Static Public Attributes | List of all members
ProteinHit Class Reference

Representation of a protein hit. More...

#include <OpenMS/METADATA/ProteinHit.h>

Inheritance diagram for ProteinHit:
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Collaboration diagram for ProteinHit:
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Classes

class  ProteinHitAccessionHash
 Hash of a ProteinHit based on its accession only! More...
 
class  ProteinHitPtrAccessionHash
 
class  ScoreLess
 Lesser predicate for scores of hits. More...
 
class  ScoreMore
 Greater predicate for scores of hits. More...
 

Public Member Functions

Constructors and Destructor
 ProteinHit ()
 Default constructor. More...
 
 ProteinHit (double score, UInt rank, String accession, String sequence)
 Values constructor. More...
 
 ProteinHit (const ProteinHit &)=default
 Copy constructor. More...
 
 ProteinHit (ProteinHit &&)=default
 Move constructor. More...
 
ProteinHitoperator= (const ProteinHit &)=default
 Assignment operator. More...
 
ProteinHitoperator= (ProteinHit &&)=default
 Move assignment operator. More...
 
ProteinHitoperator= (const MetaInfoInterface &source)
 Assignment for MetaInfo. More...
 
bool operator== (const ProteinHit &rhs) const
 Equality operator. More...
 
bool operator!= (const ProteinHit &rhs) const
 Inequality operator. More...
 
- Public Member Functions inherited from MetaInfoInterface
 MetaInfoInterface ()
 Constructor. More...
 
 MetaInfoInterface (const MetaInfoInterface &rhs)
 Copy constructor. More...
 
 MetaInfoInterface (MetaInfoInterface &&) noexcept
 Move constructor. More...
 
 ~MetaInfoInterface ()
 Destructor. More...
 
MetaInfoInterfaceoperator= (const MetaInfoInterface &rhs)
 Assignment operator. More...
 
MetaInfoInterfaceoperator= (MetaInfoInterface &&) noexcept
 Move assignment operator. More...
 
bool operator== (const MetaInfoInterface &rhs) const
 Equality operator. More...
 
bool operator!= (const MetaInfoInterface &rhs) const
 Equality operator. More...
 
const DataValuegetMetaValue (const String &name, const DataValue &default_value=DataValue::EMPTY) const
 Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not found. More...
 
const DataValuegetMetaValue (UInt index, const DataValue &default_value=DataValue::EMPTY) const
 Returns the value corresponding to an index, or a default value (default: DataValue::EMPTY) if not found. More...
 
bool metaValueExists (const String &name) const
 Returns whether an entry with the given name exists. More...
 
bool metaValueExists (UInt index) const
 Returns whether an entry with the given index exists. More...
 
void setMetaValue (const String &name, const DataValue &value)
 Sets the DataValue corresponding to a name. More...
 
void setMetaValue (UInt index, const DataValue &value)
 Sets the DataValue corresponding to an index. More...
 
void removeMetaValue (const String &name)
 Removes the DataValue corresponding to name if it exists. More...
 
void removeMetaValue (UInt index)
 Removes the DataValue corresponding to index if it exists. More...
 
void addMetaValues (const MetaInfoInterface &from)
 function to copy all meta values from one object to this one More...
 
void getKeys (std::vector< String > &keys) const
 Fills the given vector with a list of all keys for which a value is set. More...
 
void getKeys (std::vector< UInt > &keys) const
 Fills the given vector with a list of all keys for which a value is set. More...
 
bool isMetaEmpty () const
 Returns if the MetaInfo is empty. More...
 
void clearMetaInfo ()
 Removes all meta values. More...
 

Static Public Attributes

static const double COVERAGE_UNKNOWN
 

Accessors

double score_
 the score of the protein hit More...
 
UInt rank_
 the position(rank) where the hit appeared in the hit list More...
 
String accession_
 the protein identifier More...
 
String sequence_
 the amino acid sequence of the protein hit More...
 
double coverage_
 coverage of the protein based upon the matched peptide sequences More...
 
std::set< std::pair< Size, ResidueModification > > modifications_
 modified positions in a protein More...
 
double getScore () const
 returns the score of the protein hit More...
 
UInt getRank () const
 returns the rank of the protein hit More...
 
const StringgetSequence () const
 returns the protein sequence More...
 
const StringgetAccession () const
 returns the accession of the protein More...
 
String getDescription () const
 returns the description of the protein More...
 
double getCoverage () const
 returns the coverage (in percent) of the protein hit based upon matched peptides More...
 
void setScore (const double score)
 sets the score of the protein hit More...
 
void setRank (UInt newrank)
 sets the rank More...
 
void setSequence (const String &sequence)
 sets the protein sequence More...
 
void setAccession (const String &accession)
 sets the accession of the protein More...
 
void setDescription (const String &description)
 sets the description of the protein More...
 
void setCoverage (const double coverage)
 sets the coverage (in percent) of the protein hit based upon matched peptides More...
 
const std::set< std::pair< Size, ResidueModification > > & getModifications () const
 returns the set of modified protein positions More...
 
void setModifications (std::set< std::pair< Size, ResidueModification > > &mods)
 sets the set of modified protein positions More...
 

Additional Inherited Members

- Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistrymetaRegistry ()
 Returns a reference to the MetaInfoRegistry. More...
 
- Protected Member Functions inherited from MetaInfoInterface
void createIfNotExists_ ()
 Creates the MetaInfo object if it does not exist. More...
 
- Protected Attributes inherited from MetaInfoInterface
MetaInfometa_
 Pointer to the MetaInfo object (0 by default) More...
 

Detailed Description

Representation of a protein hit.

It contains the fields score, score_type, rank, accession, sequence and coverage.

Constructor & Destructor Documentation

◆ ProteinHit() [1/4]

Default constructor.

◆ ProteinHit() [2/4]

ProteinHit ( double  score,
UInt  rank,
String  accession,
String  sequence 
)

Values constructor.

◆ ProteinHit() [3/4]

ProteinHit ( const ProteinHit )
default

Copy constructor.

◆ ProteinHit() [4/4]

ProteinHit ( ProteinHit &&  )
default

Move constructor.

Member Function Documentation

◆ getAccession()

const String& getAccession ( ) const

◆ getCoverage()

double getCoverage ( ) const

returns the coverage (in percent) of the protein hit based upon matched peptides

◆ getDescription()

String getDescription ( ) const

returns the description of the protein

◆ getModifications()

const std::set<std::pair<Size, ResidueModification> >& getModifications ( ) const

returns the set of modified protein positions

◆ getRank()

UInt getRank ( ) const

returns the rank of the protein hit

◆ getScore()

double getScore ( ) const

returns the score of the protein hit

Referenced by IDScoreGetterSetter::getScores_(), and IDBoostGraph::GetPosteriorVisitor::operator()().

◆ getSequence()

const String& getSequence ( ) const

returns the protein sequence

◆ operator!=()

bool operator!= ( const ProteinHit rhs) const

Inequality operator.

◆ operator=() [1/3]

ProteinHit& operator= ( const MetaInfoInterface source)

Assignment for MetaInfo.

◆ operator=() [2/3]

ProteinHit& operator= ( const ProteinHit )
default

Assignment operator.

◆ operator=() [3/3]

ProteinHit& operator= ( ProteinHit &&  )
default

Move assignment operator.

◆ operator==()

bool operator== ( const ProteinHit rhs) const

Equality operator.

◆ setAccession()

void setAccession ( const String accession)

sets the accession of the protein

Referenced by PeptideIndexing::run().

◆ setCoverage()

void setCoverage ( const double  coverage)

sets the coverage (in percent) of the protein hit based upon matched peptides

◆ setDescription()

void setDescription ( const String description)

sets the description of the protein

Referenced by PeptideIndexing::run().

◆ setModifications()

void setModifications ( std::set< std::pair< Size, ResidueModification > > &  mods)

sets the set of modified protein positions

◆ setRank()

void setRank ( UInt  newrank)

sets the rank

◆ setScore()

void setScore ( const double  score)

sets the score of the protein hit

Referenced by IDBoostGraph::SetPosteriorVisitor::operator()().

◆ setSequence()

void setSequence ( const String sequence)

sets the protein sequence

Referenced by PeptideIndexing::run().

Member Data Documentation

◆ accession_

String accession_
protected

the protein identifier

◆ coverage_

double coverage_
protected

coverage of the protein based upon the matched peptide sequences

◆ COVERAGE_UNKNOWN

const double COVERAGE_UNKNOWN
static

◆ modifications_

std::set<std::pair<Size, ResidueModification> > modifications_
protected

modified positions in a protein

◆ rank_

UInt rank_
protected

the position(rank) where the hit appeared in the hit list

◆ score_

double score_
protected

the score of the protein hit

◆ sequence_

String sequence_
protected

the amino acid sequence of the protein hit