This class implements the simulation of the spectra from PILIS. More...
#include <OpenMS/ANALYSIS/ID/PILISModelGenerator.h>
Public Member Functions | |
| PILISModelGenerator & | operator= (const PILISModelGenerator &mode) |
| assignment operator More... | |
Constructors and destructors | |
| PILISModelGenerator () | |
| default constructor More... | |
| PILISModelGenerator (const PILISModelGenerator &model) | |
| copy constructor More... | |
| virtual | ~PILISModelGenerator () |
| destructor More... | |
Accessors | |
| void | getModel (HiddenMarkovModel &model) |
| generates the model and writes it into model 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 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... | |
Additional Inherited Members | |
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< 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 implements the simulation of the spectra from PILIS.
PILIS uses a HMM based structure to model the population of fragment ions from a peptide. The spectrum generator can be accessed via the getSpectrum method.
Parameters of this class are:| Name | Type | Default | Restrictions | Description |
|---|---|---|---|---|
| model_depth | int | 4 | The number of explicitly modeled backbone cleavages from N-terminus and C-terminus, would be 9 for the default value | |
| visible_model_depth | int | 30 | The maximal possible size of a peptide to be modeled | |
| variable_modifications | string list | [Oxidation (M), Carbamidomethyl (C)] | Modifications which should be included in the model, represented by PSI-MOD accessions. | |
| fixed_modifications | string list | [] | Modifications which should replace the unmodified amino acid, represented by PSI-MOD accessions. |
default constructor
| PILISModelGenerator | ( | const PILISModelGenerator & | model | ) |
copy constructor
|
virtual |
destructor
| void getModel | ( | HiddenMarkovModel & | model | ) |
generates the model and writes it into model
| PILISModelGenerator& operator= | ( | const PILISModelGenerator & | mode | ) |
assignment operator
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5 |