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 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... | |
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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 DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
Assignment operator. More... | |
virtual bool | operator== (const DefaultParamHandler &rhs) const |
Equality operator. More... | |
void | setParameters (const Param ¶m) |
Sets the parameters. More... | |
const Param & | getParameters () const |
Non-mutable access to the parameters. More... | |
const Param & | getDefaults () const |
Non-mutable access to the default parameters. More... | |
const String & | getName () 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... | |
PILISModel * | getPILISModel_ () |
returns the model pointer More... | |
void | updateMembers_ () |
update members method from DefaultParamHandler to update the members More... | |
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void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Protected Attributes | |
PILISModel * | hmm_model_ |
returns the sequence database pointer More... | |
Map< char, double > | aa_weight_ |
amino acids weights for the simple spectra generator More... | |
PeakSpectrumCompareFunctor * | pre_scorer_ |
scorer for pre comparison More... | |
PeakSpectrumCompareFunctor * | scorer_ |
scorer for spectra comparison More... | |
RichPeak1D | p_ |
a peaks, just to not instantiate it over and over again More... | |
std::vector< RichPeakSpectrum > | sim_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... | |
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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< String > | subsections_ |
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... | |
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 |
default constructor
PILISIdentification | ( | const PILISIdentification & | source | ) |
copy constructor
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virtual |
destructor
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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
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protected |
returns the model pointer
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protected |
performs a pre-scoring of the given spec with very simple spectra from the candidate peptides
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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
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protectedvirtual |
update members method from DefaultParamHandler to update the members
Reimplemented from DefaultParamHandler.
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protected |
returns the sequence database pointer
the sequence database for the candidate peptides the model for spectra simulation
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protected |
flag whether the instance has a internal model
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protected |
flag whether the instance has a internal sequence db
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protected |
a peaks, just to not instantiate it over and over again
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protected |
scorer for pre comparison
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protected |
scorer for spectra comparison
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protected |
OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 16:18:44 using doxygen 1.8.5 |