This class actually implements a complete ProteinIdentification run with PILIS. More...
#include <OpenMS/ANALYSIS/ID/PILISIdentification.h>
Public Member Functions | |
| PILISIdentification & | operator= (const PILISIdentification &source) |
constructors and destructors | |
| PILISIdentification () | |
| default constructor | |
| PILISIdentification (const PILISIdentification &source) | |
| copy constructor | |
| virtual | ~PILISIdentification () |
| destructor | |
Accessors | |
| void | setModel (PILISModel *hmm_model) |
| sets the sequence DB to be used for the ProteinIdentification runs | |
| void | getIdentifications (const std::vector< std::map< String, UInt > > &candidates, std::vector< PeptideIdentification > &ids, const RichPeakMap &exp) |
| performs an ProteinIdentification run on a RichPeakMap | |
| void | getIdentification (const std::map< String, UInt > &candidates, PeptideIdentification &id, const RichPeakSpectrum &spectrum) |
| performs an ProteinIdentification run on a PeakSpectrum | |
Protected Member Functions | |
| void | getSpectrum_ (RichPeakSpectrum &spec, const String &sequence, int charge) |
| fast method to create spectra for pre-scoring | |
| 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 | |
| void | getFinalIdentification_ (PeptideIdentification &id, const RichPeakSpectrum &spec, const PeptideIdentification &pre_id) |
| performs a ProteinIdentification via spectra comparison with the PILISModel spectrum generator | |
| PILISModel * | getPILISModel_ () |
| returns the model pointer | |
| void | updateMembers_ () |
| update members method from DefaultParamHandler to update the members | |
Protected Attributes | |
| PILISModel * | hmm_model_ |
| returns the sequence database pointer | |
| Map< char, double > | aa_weight_ |
| amino acids weights for the simple spectra generator | |
| PeakSpectrumCompareFunctor * | pre_scorer_ |
| scorer for pre comparison | |
| PeakSpectrumCompareFunctor * | scorer_ |
| scorer for spectra comparison | |
| RichPeak1D | p_ |
| a peaks, just to not instantiate it over and over again | |
| std::vector< RichPeakSpectrum > | sim_specs_ |
| bool | own_sequence_db_ |
| flag whether the istance has a internal sequence db | |
| bool | own_model_ |
| flag whether the istance has a internal model | |
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.
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| precursor_mass_tolerance | float | 3 | Precursor mass tolerance which is used to query the peptide database for peptides | |
| peak_mass_tolerance | float | 0.3 | Peak mass tolerance to align the simulated and experimental spectra | |
| max_candidates | int | 200 | Number of candidates which are kept at the end of the identification | |
| pre_score_name | string | ZhangSimilarityScore | The prescoring which is used | |
| score_name | string | ZhangSimilarityScore | The scoring for the comparison of simulated and experimental spectrum | |
| use_evalue_scoring | int | 1 | If set to 1 EValue scoring as described in PILISScoring is used, otherwise similarity scores are directly reported | |
| fixed_modifications | string | fixed modifications to used in the format 57.001@@C |
Note:
- If a section name is documented, the documentation is displayed as tooltip.
- Advanced parameter names are italic.
Constructor & Destructor Documentation
default constructor
| PILISIdentification | ( | const PILISIdentification & | source | ) |
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_ | ( | ) | [protected, virtual] |
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 istance has a internal model
bool own_sequence_db_ [protected] |
flag whether the istance 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 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:49 using doxygen 1.7.1 |