Simulates/Predicts retention times for peptides or peptide separation. More...
#include <OpenMS/SIMULATION/RTSimulation.h>
Public Member Functions | |
RTSimulation & | operator= (const RTSimulation &source) |
Assignment operator. More... | |
void | predictRT (SimTypes::FeatureMapSim &features) |
Predict retention times for given peptide features based for HPLC or CE. More... | |
void | predictContaminantsRT (SimTypes::FeatureMapSim &) |
Set retention times randomly for given contaminants. More... | |
bool | isRTColumnOn () const |
Returns true if a RT column was simulated. More... | |
void | wrapSVM (std::vector< AASequence > &peptide_sequences, std::vector< double > &predicted_retention_times) |
Wrapper for the SVM RT Prediction (HPLC) using AASequences. More... | |
SimTypes::SimCoordinateType | getGradientTime () const |
void | createExperiment (SimTypes::MSSimExperiment &experiment) |
Size experiment and assign retention time grid. More... | |
Constructors and Destructors | |
RTSimulation () | |
Default constructor. More... | |
RTSimulation (SimTypes::MutableSimRandomNumberGeneratorPtr random_generator) | |
Constructor taking a random generator. More... | |
RTSimulation (const RTSimulation &source) | |
Copy constructor. More... | |
virtual | ~RTSimulation () |
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... | |
Protected Member Functions | |
void | updateMembers_ () |
Synchronize members with param class. More... | |
![]() | |
void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Protected Attributes | |
SimTypes::MutableSimRandomNumberGeneratorPtr | rnd_gen_ |
Random number generator. 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... | |
Private Member Functions | |
void | setDefaultParams_ () |
Set default parameters. More... | |
void | noRTColumn_ (SimTypes::FeatureMapSim &) |
Simply set all retention times to -1. More... | |
void | smoothRTDistortion_ (SimTypes::MSSimExperiment &experiment) |
smoothes the simulated distortion for the elution profiles with a moving average filter of size 3 More... | |
void | calculateMT_ (SimTypes::FeatureMapSim &features, std::vector< double > &predicted_retention_times) |
void | getChargeContribution_ (Map< String, double > &q_cterm, Map< String, double > &q_nterm, Map< String, double > &q_aa_basic, Map< String, double > &q_aa_acidic) |
Private Attributes | |
OpenMS::String | rt_model_file_ |
SimTypes::SimCoordinateType | total_gradient_time_ |
Total gradient time. More... | |
SimTypes::SimCoordinateType | gradient_min_ |
gradient ranges More... | |
SimTypes::SimCoordinateType | gradient_max_ |
Maximal observed gradient time. More... | |
SimTypes::SimCoordinateType | rt_sampling_rate_ |
bin size in rt dimension More... | |
double | egh_tau_location_ |
EGH tau value. More... | |
double | egh_tau_scale_ |
EGH tau scale parameter of the lorentzian variation. More... | |
double | egh_variance_location_ |
EGH sigma value. More... | |
double | egh_variance_scale_ |
EGH sigma scale parameter of the lorentzian variation. More... | |
Simulates/Predicts retention times for peptides or peptide separation.
The retention times for the different peptides are determined based on a SVM model or are all set to -1 in case of simulations without a HPLC column.
RTSimulation | ( | ) |
Default constructor.
|
explicit |
Constructor taking a random generator.
RTSimulation | ( | const RTSimulation & | source | ) |
Copy constructor.
|
virtual |
Destructor.
|
private |
Wrapper for the Migration time calculation (CE)
features | will get modified with metavalue "RT_CE_width_factor", describing widening of MT shape. |
predicted_retention_times | will contain afterwards the predicted retention times. |
void createExperiment | ( | SimTypes::MSSimExperiment & | experiment | ) |
Size experiment and assign retention time grid.
|
private |
SimTypes::SimCoordinateType getGradientTime | ( | ) | const |
bool isRTColumnOn | ( | ) | const |
Returns true if a RT column was simulated.
|
private |
Simply set all retention times to -1.
RTSimulation& operator= | ( | const RTSimulation & | source | ) |
Assignment operator.
void predictContaminantsRT | ( | SimTypes::FeatureMapSim & | ) |
Set retention times randomly for given contaminants.
void predictRT | ( | SimTypes::FeatureMapSim & | features | ) |
|
private |
Set default parameters.
|
private |
smoothes the simulated distortion for the elution profiles with a moving average filter of size 3
|
protectedvirtual |
Synchronize members with param class.
Reimplemented from DefaultParamHandler.
void wrapSVM | ( | std::vector< AASequence > & | peptide_sequences, |
std::vector< double > & | predicted_retention_times | ||
) |
Wrapper for the SVM RT Prediction (HPLC) using AASequences.
|
private |
EGH tau value.
|
private |
EGH tau scale parameter of the lorentzian variation.
|
private |
EGH sigma value.
|
private |
EGH sigma scale parameter of the lorentzian variation.
|
private |
Maximal observed gradient time.
|
private |
gradient ranges
Minimal observed gradient time
|
protected |
Random number generator.
|
private |
|
private |
bin size in rt dimension
|
private |
Total gradient time.
OpenMS / TOPP release 2.0.0 | Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11 |