Representation of a peptide hit. More...
#include <OpenMS/METADATA/PeptideHit.h>
Classes | |
class | ScoreLess |
Lesser predicate for scores of hits. More... | |
class | ScoreMore |
Greater predicate for scores of hits. More... | |
Public Member Functions | |
PeptideHit & | operator= (const PeptideHit &source) |
assignment operator More... | |
bool | operator== (const PeptideHit &rhs) const |
Equality operator. More... | |
bool | operator!= (const PeptideHit &rhs) const |
Inequality operator. More... | |
Constructors and Destructor | |
PeptideHit () | |
default constructor More... | |
PeptideHit (DoubleReal score, UInt rank, Int charge, const AASequence &sequence) | |
values constructor More... | |
PeptideHit (const PeptideHit &source) | |
copy constructor More... | |
virtual | ~PeptideHit () |
destructor More... | |
Accessors | |
DoubleReal | getScore () const |
returns the score of the peptide hit More... | |
UInt | getRank () const |
returns the rank of the peptide hit More... | |
const AASequence & | getSequence () const |
returns the peptide sequence without trailing or following spaces More... | |
Int | getCharge () const |
returns the carge of the peptide More... | |
const std::vector< String > & | getProteinAccessions () const |
returns the corresponding protein accessions More... | |
void | setProteinAccessions (const std::vector< String > &accessions) |
sets the corresponding protein accessions More... | |
void | setScore (DoubleReal score) |
sets the score of the peptide hit More... | |
void | setRank (UInt newrank) |
sets the rank More... | |
void | setSequence (const AASequence &sequence) |
sets the peptide sequence More... | |
void | setCharge (Int charge) |
sets the charge of the peptide More... | |
void | addProteinAccession (const String &accession) |
adds an accession of a protein which contains this peptide hit More... | |
void | setAABefore (char acid) |
sets the amino acid before the sequence More... | |
char | getAABefore () const |
returns the amino acid before the sequence More... | |
void | setAAAfter (char acid) |
sets the amino acid after the sequence More... | |
char | getAAAfter () const |
returns the amino acid after the sequence More... | |
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MetaInfoInterface () | |
constructor More... | |
MetaInfoInterface (const MetaInfoInterface &rhs) | |
copy constructor More... | |
~MetaInfoInterface () | |
destructor More... | |
MetaInfoInterface & | operator= (const MetaInfoInterface &rhs) |
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 |
returns the value corresponding to a string More... | |
const DataValue & | getMetaValue (UInt index) const |
returns the value corresponding to an index More... | |
bool | metaValueExists (const String &name) const |
returns if this MetaInfo is set More... | |
bool | metaValueExists (UInt index) const |
returns if this MetaInfo is set 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... | |
Protected Attributes | |
DoubleReal | score_ |
the score of the peptide hit More... | |
UInt | rank_ |
the position(rank) where the hit appeared in the hit list More... | |
Int | charge_ |
the charge of the peptide More... | |
AASequence | sequence_ |
the amino acid sequence of the peptide hit More... | |
char | aa_before_ |
Amino acid before the sequence. More... | |
char | aa_after_ |
Amino acid after the sequence. More... | |
std::vector< String > | corresponding_protein_accessions_ |
the accessions of the corresponding proteins More... | |
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MetaInfo * | meta_ |
pointer to the MetaInfo object. 0 by default More... | |
Additional Inherited Members | |
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static MetaInfoRegistry & | metaRegistry () |
retuns a reference to the MetaInfoRegistry More... | |
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void | createIfNotExists_ () |
creates the MetaInfo object if it does not exist More... | |
Representation of a peptide hit.
It contains the fields score, score_type, rank, and sequence.
PeptideHit | ( | ) |
default constructor
PeptideHit | ( | DoubleReal | score, |
UInt | rank, | ||
Int | charge, | ||
const AASequence & | sequence | ||
) |
values constructor
PeptideHit | ( | const PeptideHit & | source | ) |
copy constructor
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virtual |
destructor
void addProteinAccession | ( | const String & | accession | ) |
adds an accession of a protein which contains this peptide hit
Referenced by MRMFeatureFinderScoring::scorePeakgroups_().
char getAAAfter | ( | ) | const |
returns the amino acid after the sequence
char getAABefore | ( | ) | const |
returns the amino acid before the sequence
Int getCharge | ( | ) | const |
returns the carge of the peptide
const std::vector<String>& getProteinAccessions | ( | ) | const |
returns the corresponding protein accessions
UInt getRank | ( | ) | const |
returns the rank of the peptide hit
DoubleReal getScore | ( | ) | const |
returns the score of the peptide hit
const AASequence& getSequence | ( | ) | const |
returns the peptide sequence without trailing or following spaces
bool operator!= | ( | const PeptideHit & | rhs | ) | const |
Inequality operator.
PeptideHit& operator= | ( | const PeptideHit & | source | ) |
assignment operator
bool operator== | ( | const PeptideHit & | rhs | ) | const |
Equality operator.
void setAAAfter | ( | char | acid | ) |
sets the amino acid after the sequence
Referenced by DBAdapter::loadSpectrum().
void setAABefore | ( | char | acid | ) |
sets the amino acid before the sequence
Referenced by DBAdapter::loadSpectrum().
void setCharge | ( | Int | charge | ) |
sets the charge of the peptide
Referenced by DBAdapter::loadSpectrum(), and MRMFeatureFinderScoring::scorePeakgroups_().
void setProteinAccessions | ( | const std::vector< String > & | accessions | ) |
sets the corresponding protein accessions
void setRank | ( | UInt | newrank | ) |
sets the rank
void setScore | ( | DoubleReal | score | ) |
sets the score of the peptide hit
Referenced by DBAdapter::loadSpectrum(), and MRMFeatureFinderScoring::scorePeakgroups_().
void setSequence | ( | const AASequence & | sequence | ) |
sets the peptide sequence
Referenced by DBAdapter::loadSpectrum(), and MRMFeatureFinderScoring::scorePeakgroups_().
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protected |
Amino acid after the sequence.
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protected |
Amino acid before the sequence.
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protected |
the charge of the peptide
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protected |
the accessions of the corresponding proteins
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protected |
the position(rank) where the hit appeared in the hit list
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protected |
the score of the peptide hit
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protected |
the amino acid sequence of the peptide hit
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:33 using doxygen 1.8.5 |