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DigestSimulation Class Reference

Simulates protein digestion. More...

#include <OpenMS/SIMULATION/DigestSimulation.h>

Inheritance diagram for DigestSimulation:
DefaultParamHandler

Public Member Functions

DigestSimulationoperator= (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 DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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< Stringsubsections_
 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

Default constructor.

DigestSimulation ( const DigestSimulation source)

Copy constructor.

virtual ~DigestSimulation ( )
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_mapInput FeatureMap containing the proteins that should be digested as ProteinIdentification
DigestSimulation& operator= ( const DigestSimulation source)

Assignment operator.

void setDefaultParams_ ( )
private

set defaults


OpenMS / TOPP release 2.0.0 Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11