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PILISIdentification Class Reference

This class actually implements a complete ProteinIdentification run with PILIS. More...

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

Inheritance diagram for PILISIdentification:
DefaultParamHandler

Public Member Functions

PILISIdentificationoperator= (const PILISIdentification &source)
 
constructors and destructors
 PILISIdentification ()
 default constructor More...
 
 PILISIdentification (const PILISIdentification &source)
 copy constructor More...
 
virtual ~PILISIdentification ()
 destructor More...
 
Accessors
void setModel (PILISModel *hmm_model)
 sets the sequence DB to be used for the ProteinIdentification runs More...
 
void getIdentifications (const std::vector< std::map< String, UInt > > &candidates, std::vector< PeptideIdentification > &ids, const RichPeakMap &exp)
 performs an ProteinIdentification run on a RichPeakMap More...
 
void getIdentification (const std::map< String, UInt > &candidates, PeptideIdentification &id, const RichPeakSpectrum &spectrum)
 performs an ProteinIdentification run on a PeakSpectrum 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...
 

Protected Member Functions

void getSpectrum_ (RichPeakSpectrum &spec, const String &sequence, int charge)
 fast method to create spectra for pre-scoring More...
 
void getPreIdentification_ (PeptideIdentification &id, const RichPeakSpectrum &spec, const std::map< String, UInt > &cand_peptides)
 performs a pre-scoring of the given spec with very simple spectra from the candidate peptides More...
 
void getFinalIdentification_ (PeptideIdentification &id, const RichPeakSpectrum &spec, const PeptideIdentification &pre_id)
 performs a ProteinIdentification via spectra comparison with the PILISModel spectrum generator More...
 
PILISModelgetPILISModel_ ()
 returns the model pointer More...
 
void updateMembers_ ()
 update members method from DefaultParamHandler to update the members More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 

Protected Attributes

PILISModelhmm_model_
 returns the sequence database pointer More...
 
Map< char, doubleaa_weight_
 amino acids weights for the simple spectra generator More...
 
PeakSpectrumCompareFunctorpre_scorer_
 scorer for pre comparison More...
 
PeakSpectrumCompareFunctorscorer_
 scorer for spectra comparison More...
 
RichPeak1D p_
 a peaks, just to not instantiate it over and over again More...
 
std::vector< RichPeakSpectrumsim_specs_
 
bool own_sequence_db_
 flag whether the instance has a internal sequence db More...
 
bool own_model_
 flag whether the instance has a internal model 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

This class actually implements a complete ProteinIdentification run with PILIS.

The PILISIdentification class needs a PILISModel and a PILISSequenceDB to generate identifications. Simply call getIdentifications with a RichPeakMap.

Constructor & Destructor Documentation

default constructor

copy constructor

virtual ~PILISIdentification ( )
virtual

destructor

Member Function Documentation

void getFinalIdentification_ ( PeptideIdentification id,
const RichPeakSpectrum spec,
const PeptideIdentification pre_id 
)
protected

performs a ProteinIdentification via spectra comparison with the PILISModel spectrum generator

void getIdentification ( const std::map< String, UInt > &  candidates,
PeptideIdentification id,
const RichPeakSpectrum spectrum 
)

performs an ProteinIdentification run on a PeakSpectrum

void getIdentifications ( const std::vector< std::map< String, UInt > > &  candidates,
std::vector< PeptideIdentification > &  ids,
const RichPeakMap exp 
)

performs an ProteinIdentification run on a RichPeakMap

PILISModel* getPILISModel_ ( )
protected

returns the model pointer

void getPreIdentification_ ( PeptideIdentification id,
const RichPeakSpectrum spec,
const std::map< String, UInt > &  cand_peptides 
)
protected

performs a pre-scoring of the given spec with very simple spectra from the candidate peptides

void getSpectrum_ ( RichPeakSpectrum spec,
const String sequence,
int  charge 
)
protected

fast method to create spectra for pre-scoring

PILISIdentification& operator= ( const PILISIdentification source)
void setModel ( PILISModel hmm_model)

sets the sequence DB to be used for the ProteinIdentification runs

sets the model to be used for the ProteinIdentification run

void updateMembers_ ( )
protectedvirtual

update members method from DefaultParamHandler to update the members

Reimplemented from DefaultParamHandler.

Member Data Documentation

Map<char, double> aa_weight_
protected

amino acids weights for the simple spectra generator

PILISModel* hmm_model_
protected

returns the sequence database pointer

the sequence database for the candidate peptides the model for spectra simulation

bool own_model_
protected

flag whether the instance has a internal model

bool own_sequence_db_
protected

flag whether the instance has a internal sequence db

RichPeak1D p_
protected

a peaks, just to not instantiate it over and over again

PeakSpectrumCompareFunctor* pre_scorer_
protected

scorer for pre comparison

PeakSpectrumCompareFunctor* scorer_
protected

scorer for spectra comparison

std::vector<RichPeakSpectrum> sim_specs_
protected

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11