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... | |
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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... | |
Additional Inherited Members | |
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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... | |
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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 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
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virtual |
destructor
void getModel | ( | HiddenMarkovModel & | model | ) |
generates the model and writes it into model
PILISModelGenerator& operator= | ( | const PILISModelGenerator & | mode | ) |
assignment operator
OpenMS / TOPP release 2.0.0 | Documentation generated on Tue Aug 25 2015 05:54:05 using doxygen 1.8.9.1 |