Simulates protein digestion. More...
#include <OpenMS/SIMULATION/DigestSimulation.h>
Inheritance diagram for DigestSimulation:
Public Member Functions | |
| DigestSimulation & | operator= (const DigestSimulation &source) |
| Assignment operator. More... | |
| void | digest (SimTypes::FeatureMapSim &feature_map) |
| Digest a set of proteins into peptides. More... | |
Constructors and Destructors | |
| DigestSimulation () | |
| Default constructor. More... | |
| DigestSimulation (const DigestSimulation &source) | |
| Copy constructor. More... | |
| virtual | ~DigestSimulation () |
| Destructor. 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... | |
Private Member Functions | |
| void | setDefaultParams_ () |
| set defaults 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... | |
Detailed Description
Simulates protein digestion.
Supports all enzymes supported by EnzymaticDigestion.h and additionally incorporates abundance values, which are distributed evenly among digestion products of each protein.
Constructor & Destructor Documentation
| DigestSimulation | ( | ) |
Default constructor.
| DigestSimulation | ( | const DigestSimulation & | source | ) |
Copy constructor.
|
virtual |
Destructor.
Member Function Documentation
| void digest | ( | SimTypes::FeatureMapSim & | feature_map | ) |
Digest a set of proteins into peptides.
Digest proteins to peptides, with protein abundance distributes equally among created sibling peptides (this also applies for peptides with missed cleavages). Should a peptide be non-unique the abundances of its instances from proteins are summed up.
- Parameters
-
feature_map Input FeatureMap containing the proteins that should be digested as ProteinIdentification
| DigestSimulation& operator= | ( | const DigestSimulation & | source | ) |
Assignment operator.
|
private |
set defaults