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PeptideIdentification Class Reference
[Metadata]

#include <OpenMS/METADATA/PeptideIdentification.h>

Inheritance diagram for PeptideIdentification:

MetaInfoInterface

List of all members.


Detailed Description

Represents the peptide hits for a spectrum.

This class is closely related to Identification, which stores the protein hits and the general information about the ProteinIdentification run.

When loading PeptideHit instances from a File, the retention time and mass-to-charge ratio of the precursor spectrum is stored in the MetaInfoInterface using the names 'MZ' and 'RT'. This information can be used to map the PeptideHits to a MSExperiment or a FeatureMap using IDSpectrumMapper or IDFeatureMapper.

Public Types

typedef PeptideHit HitType
 Hit type definition.

Public Member Functions

const std::vector< PeptideHit > & getHits () const
 returns the peptide hits
void insertHit (const PeptideHit &hit)
 Appends a peptide hit.
void setHits (const std::vector< PeptideHit > &hits)
 Sets the peptide hits.
Real getSignificanceThreshold () const
 returns the peptide significance threshold value
void setSignificanceThreshold (Real value)
 setting of the peptide significance threshold value
String getScoreType () const
 returns the peptide score type
void setScoreType (const String &type)
 sets the peptide score type
bool isHigherScoreBetter () const
 returns the peptide score orientation
void setHigherScoreBetter (bool value)
 sets the peptide score orientation
const StringgetIdentifier () const
 returns the identifier
void setIdentifier (const String &id)
 sets the indentifier
void assignRanks ()
 Sorts the hits by score and assigns ranks coording to the scores.
void sort ()
 Sorts the hits by score.
bool empty () const
 Returns if this ProteinIdentification result is empty.
constructors,destructors,assignment operator
 PeptideIdentification ()
 default constructor
virtual ~PeptideIdentification ()
 destructor
 PeptideIdentification (const PeptideIdentification &source)
 copy constructor
PeptideIdentificationoperator= (const PeptideIdentification &source)
 assignment operator
bool operator== (const PeptideIdentification &rhs) const
 Equality operator.
bool operator!= (const PeptideIdentification &rhs) const
 Inequality operator.
Methods for linking peptide and protein hits
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 Attributes

String id_
 Identifier by which ProteinIdentification and PeptideIdentification are matched.
std::vector< PeptideHithits_
 A list containing the peptide hits.
Real significance_threshold_
 the peptide significance threshold
String score_type_
 The score type (Mascot, Sequest, e-value, p-value).
bool higher_score_better_
 The score orientation.


Member Typedef Documentation

typedef PeptideHit HitType

Hit type definition.


Constructor & Destructor Documentation

PeptideIdentification (  ) 

default constructor

virtual ~PeptideIdentification (  )  [virtual]

destructor

PeptideIdentification ( const PeptideIdentification source  ) 

copy constructor


Member Function Documentation

PeptideIdentification& operator= ( const PeptideIdentification source  ) 

assignment operator

bool operator== ( const PeptideIdentification rhs  )  const

Equality operator.

bool operator!= ( const PeptideIdentification rhs  )  const

Inequality operator.

const std::vector<PeptideHit>& getHits (  )  const

returns the peptide hits

void insertHit ( const PeptideHit hit  ) 

Appends a peptide hit.

void setHits ( const std::vector< PeptideHit > &  hits  ) 

Sets the peptide hits.

Real getSignificanceThreshold (  )  const

returns the peptide significance threshold value

void setSignificanceThreshold ( Real  value  ) 

setting of the peptide significance threshold value

String getScoreType (  )  const

returns the peptide score type

void setScoreType ( const String type  ) 

sets the peptide score type

bool isHigherScoreBetter (  )  const

returns the peptide score orientation

void setHigherScoreBetter ( bool  value  ) 

sets the peptide score orientation

const String& getIdentifier (  )  const

returns the identifier

void setIdentifier ( const String id  ) 

sets the indentifier

void assignRanks (  ) 

Sorts the hits by score and assigns ranks coording to the scores.

void sort (  ) 

Sorts the hits by score.

bool empty (  )  const

Returns if this ProteinIdentification result is empty.

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


Member Data Documentation

String id_ [protected]

Identifier by which ProteinIdentification and PeptideIdentification are matched.

std::vector<PeptideHit> hits_ [protected]

A list containing the peptide hits.

Real significance_threshold_ [protected]

the peptide significance threshold

String score_type_ [protected]

The score type (Mascot, Sequest, e-value, p-value).

bool higher_score_better_ [protected]

The score orientation.


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:46 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1