| OpenMS 2.5.0

Classes | Public Member Functions | Static Public Attributes | Protected Attributes | List of all members
ProteinHit Class Reference
Metadata

Representation of a protein hit. More...

`#include <OpenMS/METADATA/ProteinHit.h>`

Inheritance diagram for ProteinHit:

## 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

ProteinHit & | operator= (const ProteinHit &)=default
| Assignment operator. More...
ProteinHit & | operator= (ProteinHit &&)=default
| Move assignment operator. More...
ProteinHit & | operator= (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...
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...
Accessors
double | getScore () const
| returns the score of the protein hit More...
UInt | getRank () const
| returns the rank of the protein hit More...
const String & | getSequence () const
| returns the protein sequence More...
const String & | getAccession () 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...
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...
MetaInfoInterface & | operator= (const MetaInfoInterface &rhs)
| Assignment operator. More...
MetaInfoInterface & | operator= (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 DataValue & | getMetaValue (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 DataValue & | getMetaValue (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 | 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

## Protected Attributes

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...
Protected Attributes inherited from MetaInfoInterface
MetaInfo * | meta_
| Pointer to the MetaInfo object (0 by default) More...

## Additional Inherited Members

Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry & | metaRegistry ()
| 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...

## 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]

ProteinHit | ( |  | ) |

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

returns the accession of the protein

Referenced by ConsensusMapMergerAlgorithm::accessionEqual_(), IDMergerAlgorithm::accessionEqual_(), ConsensusMapMergerAlgorithm::accessionHash_(), IDMergerAlgorithm::accessionHash_(), ProteinHit::ProteinHitAccessionHash::operator()(), ProteinHit::ProteinHitPtrAccessionHash::operator()(), IDBoostGraph::LabelVisitor::operator()(), PercolatorFeatureSetHelper::lq_ProteinHit::operator()(), IDBoostGraph::PrintAddressVisitor< CharT >::operator()(), IDFilter::HasMatchingAccessionUnordered< HitType >::operator()(), and IDFilter::HasMatchingAccession< HitType >::operator()().

## ◆ 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 ProteinHit & |  | ) |

default

Assignment operator.

## ◆ operator=() [2/3]

ProteinHit& operator= | ( | ProteinHit && |  | ) |

default

Move assignment operator.

## ◆ operator=() [3/3]

ProteinHit& operator= | ( | const MetaInfoInterface & | source | ) |

Assignment for MetaInfo.

## ◆ 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