Simulates protein digestion. More...
#include <OpenMS/SIMULATION/DigestSimulation.h>
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... | |
![]() | |
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 | |
![]() | |
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... | |
![]() | |
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... | |
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.
DigestSimulation | ( | ) |
Default constructor.
DigestSimulation | ( | const DigestSimulation & | source | ) |
Copy constructor.
|
virtual |
Destructor.
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.
feature_map | Input FeatureMap containing the proteins that should be digested as ProteinIdentification |
DigestSimulation& operator= | ( | const DigestSimulation & | source | ) |
Assignment operator.
|
private |
set defaults
OpenMS / TOPP release 2.0.0 | Documentation generated on Wed Mar 30 2016 12:49:27 using doxygen 1.8.11 |