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 |