OpenMS
2.4.0
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Simulates MS2 spectra with support vector machines. More...
#include <OpenMS/CHEMISTRY/SvmTheoreticalSpectrumGenerator.h>
Classes | |
struct | DescriptorSet |
A set of descriptors for a single training row. More... | |
struct | IonType |
nested class More... | |
struct | SvmModelParameterSet |
Simple container storing the model parameters required for simulation. More... | |
Public Member Functions | |
void | simulate (PeakSpectrum &spectrum, const AASequence &peptide, boost::random::mt19937_64 &rng, Size precursor_charge) |
Generate the MS/MS according to the given probabilistic model. More... | |
void | load () |
Load a trained Svm and Prob. models. More... | |
const std::vector< IonType > & | getIonTypes () |
return the set of ion types that are modeled by the loaded SVMs More... | |
Constructors and Destructors | |
SvmTheoreticalSpectrumGenerator () | |
Default constructor. More... | |
SvmTheoreticalSpectrumGenerator (const SvmTheoreticalSpectrumGenerator &source) | |
Copy constructor. More... | |
SvmTheoreticalSpectrumGenerator & | operator= (const SvmTheoreticalSpectrumGenerator &tsg) |
Assignment operator. More... | |
~SvmTheoreticalSpectrumGenerator () override | |
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 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 Types | |
typedef std::map< IonType, double > | IntensityMap |
Protected Member Functions | |
void | scaleSingleFeature_ (double &value, double feature_min, double feature_max, double lower=-1.0, double upper=1.0) |
scale value to the interval [lower,max] given the maximal and minimal entries for a feature More... | |
void | scaleDescriptorSet_ (DescriptorSet &desc, double lower, double upper) |
scale value to the interval [lower,max] given the maximal and minimal entries for a feature More... | |
Size | generateDescriptorSet_ (AASequence peptide, Size position, IonType type, Size precursor_charge, DescriptorSet &desc_set) |
generate the descriptors for an input peptide and a given fragmentation position More... | |
String | ResidueTypeToString_ (Residue::ResidueType type) |
Returns the ResidueType (e.g. AIon, BIon) as string for peak annotation. More... | |
void | updateMembers_ () override |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
Protected Member Functions inherited from DefaultParamHandler | |
void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Static Protected Member Functions | |
static void | initializeMaps_ () |
initialized the maps More... | |
Protected Attributes | |
Size | precursor_charge_ |
charge of the precursors used for training More... | |
SvmModelParameterSet | mp_ |
set of model parameters read from model file More... | |
std::map< IonType, bool > | hide_type_ |
whether ion types are hidden or not 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< 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... | |
Static Protected Attributes | |
static std::map< String, Size > | aa_to_index_ |
map AA to integers More... | |
static std::map< String, double > | hydrophobicity_ |
hydrophobicity values for each AA More... | |
static std::map< String, double > | helicity_ |
helicity values for each AA More... | |
static std::map< String, double > | basicity_ |
basicity values for each AA More... | |
static bool | initializedMaps_ |
flag to indicate if the hydrophobicity, helicity, and basicity maps were already initialized More... | |
Friends | |
class | SvmTheoreticalSpectrumGeneratorTrainer |
Simulates MS2 spectra with support vector machines.
The models are generated with the SvmTheoreticalSpectrumGeneratorTrainer.
Two modes are supported:
Currently, only a test model is shipped with OpenMS.
Please find trained models at: http://sourceforge.net/projects/open-ms/files/Supplementary/Simulation/.
Name | Type | Default | Restrictions | Description |
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svm_mode | int | 1 | whether to predict abundant/missing using SVC (0) or predict intensities using SVR (1) | |
model_file_name | string | examples/simulation/SvmMSim.model | Name of the probabilistic Model file | |
add_isotopes | string | false | true, false | If set to 1 isotope peaks of the product ion peaks are added |
max_isotope | int | 2 | Defines the maximal isotopic peak which is added, add_isotopes must be set to 1 | |
add_metainfo | string | false | true, false | Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++ |
add_first_prefix_ion | string | false | true, false | If set to true e.g. b1 ions are added |
hide_y_ions | string | false | true, false | Add peaks of y-ions to the spectrum |
hide_y2_ions | string | false | true, false | Add peaks of y-ions to the spectrum |
hide_b_ions | string | false | true, false | Add peaks of b-ions to the spectrum |
hide_b2_ions | string | false | true, false | Add peaks of b-ions to the spectrum |
hide_a_ions | string | false | true, false | Add peaks of a-ions to the spectrum |
hide_c_ions | string | false | true, false | Add peaks of c-ions to the spectrum |
hide_x_ions | string | false | true, false | Add peaks of x-ions to the spectrum |
hide_z_ions | string | false | true, false | Add peaks of z-ions to the spectrum |
hide_losses | string | false | true, false | Adds common losses to those ion expect to have them, only water and ammonia loss is considered |
y_intensity | float | 1 | Intensity of the y-ions | |
b_intensity | float | 1 | Intensity of the b-ions | |
a_intensity | float | 1 | Intensity of the a-ions | |
c_intensity | float | 1 | Intensity of the c-ions | |
x_intensity | float | 1 | Intensity of the x-ions | |
z_intensity | float | 1 | Intensity of the z-ions | |
relative_loss_intensity | float | 0.1 | Intensity of loss ions, in relation to the intact ion intensity |
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protected |
Default constructor.
SvmTheoreticalSpectrumGenerator | ( | const SvmTheoreticalSpectrumGenerator & | source | ) |
Copy constructor.
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override |
Destructor.
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protected |
generate the descriptors for an input peptide and a given fragmentation position
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inline |
return the set of ion types that are modeled by the loaded SVMs
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staticprotected |
initialized the maps
void load | ( | ) |
Load a trained Svm and Prob. models.
SvmTheoreticalSpectrumGenerator& operator= | ( | const SvmTheoreticalSpectrumGenerator & | tsg | ) |
Assignment operator.
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protected |
Returns the ResidueType (e.g. AIon, BIon) as string for peak annotation.
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scale value to the interval [lower,max] given the maximal and minimal entries for a feature
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inlineprotected |
scale value to the interval [lower,max] given the maximal and minimal entries for a feature
void simulate | ( | PeakSpectrum & | spectrum, |
const AASequence & | peptide, | ||
boost::random::mt19937_64 & | rng, | ||
Size | precursor_charge | ||
) |
Generate the MS/MS according to the given probabilistic model.
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overrideprotectedvirtual |
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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whether ion types are hidden or not
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staticprotected |
flag to indicate if the hydrophobicity, helicity, and basicity maps were already initialized
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set of model parameters read from model file
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protected |
charge of the precursors used for training