OpenMS  2.6.0
Public Member Functions | Private Member Functions | List of all members
IDRipper Class Reference

Ripping protein/peptide identification according their file origin. More...

#include <OpenMS/ANALYSIS/ID/IDRipper.h>

Inheritance diagram for IDRipper:
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Collaboration diagram for IDRipper:
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Public Member Functions

 IDRipper ()
 Default constructor. More...
 
 ~IDRipper () override
 Destructor. More...
 
void rip (std::map< String, std::pair< std::vector< ProteinIdentification >, std::vector< PeptideIdentification > > > &ripped, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides)
 Ripping protein/peptide identification according their file origin. More...
 
- Public Member Functions inherited from DefaultParamHandler
 DefaultParamHandler (const String &name)
 Constructor with name that is displayed in error messages. More...
 
 DefaultParamHandler (const DefaultParamHandler &rhs)
 Copy constructor. More...
 
virtual ~DefaultParamHandler ()
 Destructor. More...
 
virtual DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () const
 Non-mutable access to the name. More...
 
void setName (const String &name)
 Mutable access to the name. More...
 
const std::vector< String > & getSubsections () const
 Non-mutable access to the registered subsections. More...
 

Private Member Functions

 IDRipper (const IDRipper &rhs)
 Copy constructor. More...
 
IDRipperoperator= (const IDRipper &rhs)
 Assignment. More...
 
void getProteinHits_ (std::vector< ProteinHit > &result, const std::vector< ProteinHit > &protein_hits, const std::vector< String > &protein_accessions)
 helper function, extracts all protein hits that match the protein accession More...
 
void getProteinAccessions_ (std::vector< String > &result, const std::vector< PeptideHit > &peptide_hits)
 helper function, returns the string representation of the peptide hit accession More...
 
void getProteinIdentification_ (ProteinIdentification &result, PeptideIdentification pep_ident, std::vector< ProteinIdentification > &prot_idents)
 helper function, returns the protein identification for the given peptide identification based on the same identifier More...
 

Additional Inherited Members

- Static Public Member Functions inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &prefix="")
 Writes all parameters to meta values. More...
 
- Protected Member Functions inherited from DefaultParamHandler
virtual void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 
- Protected Attributes inherited from DefaultParamHandler
Param param_
 Container for current parameters. More...
 
Param defaults_
 Container for default parameters. This member should be filled in the constructor of derived classes! More...
 
std::vector< Stringsubsections_
 Container for registered subsections. This member should be filled in the constructor of derived classes! More...
 
String error_name_
 Name that is displayed in error messages during the parameter checking. More...
 
bool check_defaults_
 If this member is set to false no checking if parameters in done;. More...
 
bool warn_empty_defaults_
 If this member is set to false no warning is emitted when defaults are empty;. More...
 

Detailed Description

Ripping protein/peptide identification according their file origin.

Helper class, which is used by ProteinQuantifier. See there for further documentation.

Constructor & Destructor Documentation

◆ IDRipper() [1/2]

IDRipper ( )

Default constructor.

◆ ~IDRipper()

~IDRipper ( )
override

Destructor.

◆ IDRipper() [2/2]

IDRipper ( const IDRipper rhs)
private

Copy constructor.

Member Function Documentation

◆ getProteinAccessions_()

void getProteinAccessions_ ( std::vector< String > &  result,
const std::vector< PeptideHit > &  peptide_hits 
)
private

helper function, returns the string representation of the peptide hit accession

◆ getProteinHits_()

void getProteinHits_ ( std::vector< ProteinHit > &  result,
const std::vector< ProteinHit > &  protein_hits,
const std::vector< String > &  protein_accessions 
)
private

helper function, extracts all protein hits that match the protein accession

◆ getProteinIdentification_()

void getProteinIdentification_ ( ProteinIdentification result,
PeptideIdentification  pep_ident,
std::vector< ProteinIdentification > &  prot_idents 
)
private

helper function, returns the protein identification for the given peptide identification based on the same identifier

◆ operator=()

IDRipper& operator= ( const IDRipper rhs)
private

Assignment.

◆ rip()

void rip ( std::map< String, std::pair< std::vector< ProteinIdentification >, std::vector< PeptideIdentification > > > &  ripped,
std::vector< ProteinIdentification > &  proteins,
std::vector< PeptideIdentification > &  peptides 
)

Ripping protein/peptide identification according their file origin.

Iteration over all PeptideIdentification. For each annotated file origin create a map entry and store the respective PeptideIdentification and ProteinIdentification.

Parameters
rippedContains the protein identification and peptide identification for each file origin annotated in proteins and peptides
proteinsPeptide identification annotated with file origin
peptidesProtein identification