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 | getMS2Identifications (std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides) const |
Access the simulated MS2 identifications (proteins and peptides) 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... | |
virtual | ~MSSim () |
Destructor. More... | |
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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... | |
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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... | |
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_ () |
Synchronize members with param class. More... | |
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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 | |
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enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
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static String | logTypeToFactoryName_ (LogType type) |
Return the name of the factory product used for this log type. More... | |
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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... | |
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LogType | type_ |
time_t | last_invoke_ |
ProgressLoggerImpl * | current_logger_ |
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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.
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virtual |
Destructor.
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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.
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 |
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protectedvirtual |
Synchronize members with param class.
Reimplemented from DefaultParamHandler.
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private |
Holds consensus ground-truth about the charge associations.
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private |
Holds the ground-truth on generated contaminants.
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private |
Holds the simulated data.
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private |
Holds the ground-truth on generated features.
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private |
Labeling functionality.
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private |
Holds the ground-truth on generated peaks positions and intensities.
OpenMS / TOPP release 2.0.0 | Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11 |