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ProteinHit Class Reference

Representation of a protein hit. More...

#include <OpenMS/METADATA/ProteinHit.h>

Inheritance diagram for ProteinHit:
MetaInfoInterface

Classes

class  ScoreLess
 Lesser predicate for scores of hits. More...
 
class  ScoreMore
 Greater predicate for scores of hits. More...
 

Public Member Functions

ProteinHitoperator= (const ProteinHit &source)
 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...
 
Constructors and Destructor
 ProteinHit ()
 default constructor More...
 
 ProteinHit (double score, UInt rank, String accession, String sequence)
 values constructor More...
 
 ProteinHit (const ProteinHit &source)
 copy constructor More...
 
virtual ~ProteinHit ()
 destructor More...
 
Accessors
float 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...
 
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 setCoverage (const double coverage)
 sets the coverage (in percent) of the protein hit based upon matched peptides More...
 
- Public Member Functions inherited from MetaInfoInterface
 MetaInfoInterface ()
 constructor More...
 
 MetaInfoInterface (const MetaInfoInterface &rhs)
 copy constructor More...
 
 ~MetaInfoInterface ()
 destructor More...
 
MetaInfoInterfaceoperator= (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 DataValuegetMetaValue (const String &name) const
 returns the value corresponding to a string More...
 
const DataValuegetMetaValue (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

float 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...
 
- Protected Attributes inherited from MetaInfoInterface
MetaInfometa_
 pointer to the MetaInfo object. 0 by default 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...
 

Detailed Description

Representation of a protein hit.

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

Constructor & Destructor Documentation

default constructor

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

values constructor

ProteinHit ( const ProteinHit source)

copy constructor

virtual ~ProteinHit ( )
virtual

destructor

Member Function Documentation

const String& getAccession ( ) const

returns the accession of the protein

double getCoverage ( ) const

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

UInt getRank ( ) const

returns the rank of the protein hit

float getScore ( ) const

returns the score of the protein hit

const String& getSequence ( ) const

returns the protein sequence

bool operator!= ( const ProteinHit rhs) const

Inequality operator.

ProteinHit& operator= ( const ProteinHit source)

assignment operator

ProteinHit& operator= ( const MetaInfoInterface source)

assignment for MetaInfo

bool operator== ( const ProteinHit rhs) const

Equality operator.

void setAccession ( const String accession)

sets the accession of the protein

void setCoverage ( const double  coverage)

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

void setRank ( UInt  newrank)

sets the rank

void setScore ( const double  score)

sets the score of the protein hit

void setSequence ( const String sequence)

sets the protein sequence

Member Data Documentation

String accession_
protected

the protein identifier

double coverage_
protected

coverage of the protein based upon the matched peptide sequences

UInt rank_
protected

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

float score_
protected

the score of the protein hit

String sequence_
protected

the amino acid sequence of the protein hit


OpenMS / TOPP release 2.0.0 Documentation generated on Sat May 16 2015 16:14:03 using doxygen 1.8.9.1