![]() |
OpenMS
2.4.0
|
Central class for simulation of mass spectrometry experiments. More...
#include <OpenMS/SIMULATION/MSSim.h>
Public Member Functions | |
void | simulate (SimTypes::MutableSimRandomNumberGeneratorPtr rnd_gen, SimTypes::SampleChannels &peptides) |
General purpose function to simulate a mass spectrometry run. More... | |
const SimTypes::MSSimExperiment & | getExperiment () const |
Access the simulated experiment. More... | |
const SimTypes::FeatureMapSim & | getSimulatedFeatures () const |
Access the simulated features. More... | |
ConsensusMap & | getChargeConsensus () |
Access the charge consensus map of simulated features. More... | |
const SimTypes::FeatureMapSim & | getContaminants () const |
Access the contaminants feature map of simulated features. More... | |
ConsensusMap & | getLabelingConsensus () |
Access the labeling consensus map of simulated features. More... | |
const SimTypes::MSSimExperiment & | getPeakMap () const |
Access the picked (centroided) experiment. More... | |
void | getIdentifications (std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides) const |
Access the simulated identifications (proteins and peptides) More... | |
void | getMS2Identifications (std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides) const |
Access the simulated MS2 identifications (proteins and peptides) More... | |
void | getFeatureIdentifications (std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides) const |
Access the simulated identifications (proteins and peptides) from feature annotations. More... | |
Param | getParameters () const |
Returns the default parameters for simulation including the labeling technique with name labeling_name . More... | |
Constructors and Destructors | |
MSSim () | |
Default constructor. More... | |
~MSSim () override | |
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... | |
![]() | |
ProgressLogger () | |
Constructor. More... | |
~ProgressLogger () | |
Destructor. More... | |
ProgressLogger (const ProgressLogger &other) | |
Copy constructor. More... | |
ProgressLogger & | operator= (const ProgressLogger &other) |
Assignment Operator. More... | |
void | setLogType (LogType type) const |
Sets the progress log that should be used. The default type is NONE! More... | |
LogType | getLogType () const |
Returns the type of progress log being used. More... | |
void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
Initializes the progress display. More... | |
void | setProgress (SignedSize value) const |
Sets the current progress. More... | |
void | endProgress () const |
Ends the progress display. More... | |
void | nextProgress () const |
increment progress by 1 (according to range begin-end) More... | |
Protected Member Functions | |
void | syncParams_ (Param &p, bool to_outer) |
handle global params More... | |
void | createFeatureMap_ (const SimTypes::SampleProteins &peptides, SimTypes::FeatureMapSim &features, Size map_index) |
Convert a list of peptides with given abundance values into a FeatureMap. More... | |
void | updateMembers_ () override |
Synchronize members with param class. More... | |
![]() | |
void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Private Attributes | |
SimTypes::MSSimExperiment | experiment_ |
Holds the simulated data. More... | |
SimTypes::MSSimExperiment | peak_map_ |
Holds the ground-truth on generated peaks positions and intensities. More... | |
SimTypes::FeatureMapSimVector | feature_maps_ |
Holds the ground-truth on generated features. More... | |
ConsensusMap | consensus_map_ |
Holds consensus ground-truth about the charge associations. More... | |
SimTypes::FeatureMapSim | contaminants_map_ |
Holds the ground-truth on generated contaminants. More... | |
BaseLabeler * | labeler_ |
Labeling functionality. More... | |
Additional Inherited Members | |
![]() | |
enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
![]() | |
static String | logTypeToFactoryName_ (LogType type) |
Return the name of the factory product used for this log type. 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... | |
![]() | |
LogType | type_ |
time_t | last_invoke_ |
ProgressLoggerImpl * | current_logger_ |
![]() | |
static int | recursion_depth_ |
Central class for simulation of mass spectrometry experiments.
This implementation is an extended and rewritten version of the concepts and ideas presented in:
Ole Schulz-Trieglaff, Nico Pfeifer, Clemens Gropl, Oliver Kohlbacher, and Knut Reinert.
LC-MSsim - A simulation software for liquid chromatography mass spectrometry data.
BMC Bioinformatics 9:423, 2008.
MSSim | ( | ) |
Default constructor.
|
override |
Destructor.
|
protected |
Convert a list of peptides with given abundance values into a FeatureMap.
ConsensusMap& getChargeConsensus | ( | ) |
Access the charge consensus map of simulated features.
const SimTypes::FeatureMapSim& getContaminants | ( | ) | const |
Access the contaminants feature map of simulated features.
const SimTypes::MSSimExperiment& getExperiment | ( | ) | const |
Access the simulated experiment.
void getFeatureIdentifications | ( | std::vector< ProteinIdentification > & | proteins, |
std::vector< PeptideIdentification > & | peptides | ||
) | const |
Access the simulated identifications (proteins and peptides) from feature annotations.
proteins | Will be filled with a single ProteinIdentification holding all ProteinHits. |
peptides | Will be filled with PeptideIdentifications for all simulated features. |
void getIdentifications | ( | std::vector< ProteinIdentification > & | proteins, |
std::vector< PeptideIdentification > & | peptides | ||
) | const |
Access the simulated identifications (proteins and peptides)
If an MS2 signal has been simulated, identifications are generated based on their corresponding MS2 spectra. If MS2 simulation has been disabled, peptide IDs are generated from feature annotations. Otherwise, the -out_id idXML file would be empty if MS2 simulation is disabled (which is the default).
proteins | Will be filled with a single ProteinIdentification holding all ProteinHits. |
peptides | Will be filled with PeptideIdentifications. |
ConsensusMap& getLabelingConsensus | ( | ) |
Access the labeling consensus map of simulated features.
void getMS2Identifications | ( | std::vector< ProteinIdentification > & | proteins, |
std::vector< PeptideIdentification > & | peptides | ||
) | const |
Access the simulated MS2 identifications (proteins and peptides)
proteins | Will be filled with a single ProteinIdentification holding all ProteinHits used in the simulated MS2 spectra. |
peptides | Will be filled with PeptideIdentifications for each simulated MS2 spectra holding all contributing peptides scored by their intensity contribution. |
Param getParameters | ( | ) | const |
Returns the default parameters for simulation including the labeling technique with name labeling_name
.
const SimTypes::MSSimExperiment& getPeakMap | ( | ) | const |
Access the picked (centroided) experiment.
const SimTypes::FeatureMapSim& getSimulatedFeatures | ( | ) | const |
Access the simulated features.
void simulate | ( | SimTypes::MutableSimRandomNumberGeneratorPtr | rnd_gen, |
SimTypes::SampleChannels & | peptides | ||
) |
General purpose function to simulate a mass spectrometry run.
rnd_gen | random number generator which will be passed to the different classes |
peptides | List of peptides and abundances that will be simulated |
|
protected |
handle global params
|
overrideprotectedvirtual |
Synchronize members with param class.
Reimplemented from DefaultParamHandler.
|
private |
Holds consensus ground-truth about the charge associations.
|
private |
Holds the ground-truth on generated contaminants.
|
private |
Holds the simulated data.
|
private |
Holds the ground-truth on generated features.
|
private |
Labeling functionality.
|
private |
Holds the ground-truth on generated peaks positions and intensities.