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PeptideEvidence Class Reference

Representation of a MzIdentML PeptideEvidence. More...

#include <OpenMS/METADATA/PeptideEvidence.h>

Inheritance diagram for PeptideEvidence:
MetaInfoInterface

Public Member Functions

PeptideEvidenceoperator= (const PeptideEvidence &source)
 assignment operator More...
 
bool operator== (const PeptideEvidence &rhs) const
 Equality operator. More...
 
bool operator!= (const PeptideEvidence &rhs) const
 Inequality operator. More...
 
Constructors and Destructor
 PeptideEvidence ()
 default constructor More...
 
 PeptideEvidence (DoubleReal score, UInt rank, Int charge, const AASequence &sequence)
 values constructor More...
 
 PeptideEvidence (const PeptideEvidence &source)
 copy constructor More...
 
virtual ~PeptideEvidence ()
 destructor More...
 
Accessors
const StringgetDBSequenceRef () const
 returns the corresponding protein db sequence ref More...
 
void setDBSequenceRef (const String &rhs)
 sets the corresponding protein db sequence ref More...
 
const StringgetTranslationTableRef () const
 returns the translation table reference More...
 
void setTranslationTableRef (const String &rhs)
 sets the translation table reference More...
 
void setStart (Int start)
 start position in the sequence (xsd:int) More...
 
Int getStart () const
 returns the start position in the sequence (xsd:int) More...
 
void setEnd (Int end)
 sets the end position in the sequence More...
 
Int getEnd () const
 returns the end position in the sequence More...
 
void setPre (char rhs)
 sets the amino acid before the sequence, "-" if N-terminal, "?" if not applicable (e.g. de novo) More...
 
char getPre () const
 returns the amino acid before the sequence More...
 
void setPost (char rhs)
 sets the amino acid after the sequence, "-" if C-terminal, "?" if not applicable (e.g. de novo) More...
 
char getPost () const
 returns the amino acid after the sequence More...
 
void setId (const String &id)
 unique id of the file, set of files or repository More...
 
const StringgetId () const
 returns the unqiue id of the instance More...
 
void setName (const String &name)
 sets the potentially ambigous but human readable name More...
 
const StringgetName () const
 returns the human readable name More...
 
void setMissedCleavages (Int rhs)
 sets the number of missed cleavages More...
 
Int getMissedCleavages () const
 returns the number of missed cleavages More...
 
void setIsDecoy (bool is_decoy)
 sets whether the hit is a decoy hit More...
 
bool getIsDecoy () const
 returns the whether the hit is decoy More...
 
void setFrame (Int frame)
 Frame of the DB, e.g. from nucleic acids. More...
 
Int getFrame () const
 returns the frame of the peptide evidence 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

String db_sequence_ref_
 
String translation_table_ref_
 
Int start_
 
Int end_
 
char pre_
 
char post_
 
String id_
 
String name_
 
Int missed_cleavages_
 
bool is_decoy_
 
Int frame_
 
- 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 ()
 retuns 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 MzIdentML PeptideEvidence.

It contains information about the protein the peptide comes from and additional information were it is located in the protein.

Todo:
implement CVParam

Constructor & Destructor Documentation

default constructor

PeptideEvidence ( DoubleReal  score,
UInt  rank,
Int  charge,
const AASequence sequence 
)

values constructor

PeptideEvidence ( const PeptideEvidence source)

copy constructor

virtual ~PeptideEvidence ( )
virtual

destructor

Member Function Documentation

const String& getDBSequenceRef ( ) const

returns the corresponding protein db sequence ref

Int getEnd ( ) const

returns the end position in the sequence

Int getFrame ( ) const

returns the frame of the peptide evidence

const String& getId ( ) const

returns the unqiue id of the instance

bool getIsDecoy ( ) const

returns the whether the hit is decoy

Int getMissedCleavages ( ) const

returns the number of missed cleavages

const String& getName ( ) const

returns the human readable name

char getPost ( ) const

returns the amino acid after the sequence

char getPre ( ) const

returns the amino acid before the sequence

Int getStart ( ) const

returns the start position in the sequence (xsd:int)

const String& getTranslationTableRef ( ) const

returns the translation table reference

bool operator!= ( const PeptideEvidence rhs) const

Inequality operator.

PeptideEvidence& operator= ( const PeptideEvidence source)

assignment operator

bool operator== ( const PeptideEvidence rhs) const

Equality operator.

void setDBSequenceRef ( const String rhs)

sets the corresponding protein db sequence ref

void setEnd ( Int  end)

sets the end position in the sequence

void setFrame ( Int  frame)

Frame of the DB, e.g. from nucleic acids.

void setId ( const String id)

unique id of the file, set of files or repository

void setIsDecoy ( bool  is_decoy)

sets whether the hit is a decoy hit

void setMissedCleavages ( Int  rhs)

sets the number of missed cleavages

void setName ( const String name)

sets the potentially ambigous but human readable name

void setPost ( char  rhs)

sets the amino acid after the sequence, "-" if C-terminal, "?" if not applicable (e.g. de novo)

void setPre ( char  rhs)

sets the amino acid before the sequence, "-" if N-terminal, "?" if not applicable (e.g. de novo)

void setStart ( Int  start)

start position in the sequence (xsd:int)

void setTranslationTableRef ( const String rhs)

sets the translation table reference

Member Data Documentation

String db_sequence_ref_
protected
Int end_
protected
Int frame_
protected
String id_
protected
bool is_decoy_
protected
Int missed_cleavages_
protected
String name_
protected
char post_
protected
char pre_
protected
Int start_
protected
String translation_table_ref_
protected

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:33 using doxygen 1.8.5