This class implements the simulation of the spectra from PILIS. More...
#include <OpenMS/ANALYSIS/ID/PILISNeutralLossModel.h>
Public Member Functions | |
PILISNeutralLossModel & | operator= (const PILISNeutralLossModel &mode) |
assignment operator More... | |
Constructors and destructors | |
PILISNeutralLossModel () | |
default constructor More... | |
PILISNeutralLossModel (const PILISNeutralLossModel &model) | |
copy constructor More... | |
virtual | ~PILISNeutralLossModel () |
destructor More... | |
Accessors | |
double | train (const RichPeakSpectrum &spec, const AASequence &peptide, double ion_weight, UInt charge, double peptide_weight) |
performs a training step; needs as parameters a spectrum with annotated sequence and charge; returns the intensity sum of the matched peaks More... | |
void | getIons (std::vector< RichPeak1D > &peaks, const AASequence &peptide, double initial_prob) |
given a peptide (a ion) the model returns the peaks with intensities relative to initial_prob More... | |
void | setHMM (const HiddenMarkovModel &model) |
sets the hidden markov model More... | |
const HiddenMarkovModel & | getHMM () const |
writes the HMM to the given file in the GraphML format. A detailed description of the GraphML format can be found under http://graphml.graphdrawing.org/ More... | |
void | generateModel () |
generates the models More... | |
void | evaluate () |
this method evaluates the model after training; it should be called after all training steps with train 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... | |
Protected Member Functions | |
double | getIntensitiesFromSpectrum_ (const RichPeakSpectrum &train_spec, Map< String, double > &pre_ints, double ion_weight, const AASequence &peptide, UInt charge) |
extracts the precursor and related intensities of a training spectrum More... | |
void | trainIons_ (double initial_probability, const Map< String, double > &intensities, const AASequence &peptide) |
trains precursor and related peaks More... | |
void | getIons_ (Map< String, double > &intensities, double initial_probability, const AASequence &precursor) |
estimates the precursor intensities More... | |
void | enableIonStates_ (const AASequence &peptide) |
enables the states needed for precursor training/simulation More... | |
void | updateMembers_ () |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
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void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Protected Attributes | |
HiddenMarkovModel | hmm_precursor_ |
precursor model used More... | |
UInt | num_explicit_ |
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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... | |
Friends | |
class | PILISNeutralLossModelGenerator |
This class implements the simulation of the spectra from PILIS.
PILIS uses a HMM based structure to model the population of fragment ions from a peptide. The spectrum generator can be accessed via the getSpectrum method.
default constructor
PILISNeutralLossModel | ( | const PILISNeutralLossModel & | model | ) |
copy constructor
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virtual |
destructor
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protected |
enables the states needed for precursor training/simulation
void evaluate | ( | ) |
this method evaluates the model after training; it should be called after all training steps with train
void generateModel | ( | ) |
generates the models
const HiddenMarkovModel& getHMM | ( | ) | const |
writes the HMM to the given file in the GraphML format. A detailed description of the GraphML format can be found under http://graphml.graphdrawing.org/
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protected |
extracts the precursor and related intensities of a training spectrum
void getIons | ( | std::vector< RichPeak1D > & | peaks, |
const AASequence & | peptide, | ||
double | initial_prob | ||
) |
given a peptide (a ion) the model returns the peaks with intensities relative to initial_prob
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protected |
estimates the precursor intensities
PILISNeutralLossModel& operator= | ( | const PILISNeutralLossModel & | mode | ) |
assignment operator
void setHMM | ( | const HiddenMarkovModel & | model | ) |
sets the hidden markov model
double train | ( | const RichPeakSpectrum & | spec, |
const AASequence & | peptide, | ||
double | ion_weight, | ||
UInt | charge, | ||
double | peptide_weight | ||
) |
performs a training step; needs as parameters a spectrum with annotated sequence and charge; returns the intensity sum of the matched peaks
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protected |
trains precursor and related peaks
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protectedvirtual |
This method is used to update extra member variables at the end of the setParameters() method.
Also call it at the end of the derived classes' copy constructor and assignment operator.
The default implementation is empty.
Reimplemented from DefaultParamHandler.
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friend |
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protected |
precursor model used
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protected |
OpenMS / TOPP release 2.0.0 | Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11 |