Simulates ms2 spectra with support vector machines. More...

#include <OpenMS/CHEMISTRY/SvmTheoreticalSpectrumGenerator.h>

Inheritance diagram for SvmTheoreticalSpectrumGenerator:

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 (RichPeakSpectrum &spectrum, const AASequence &peptide, const gsl_rng *rng, Size precursor_charge)
	Generate the MS/MS according to the given probabilistic model.
void	load ()
	Load a trained Svm and Prob. models.
const std::vector< IonType > &	getIonTypes ()
	return the set of ion types that are modeled by the loaded SVMs
Constructors and Destructors

	SvmTheoreticalSpectrumGenerator ()
	Default constructor.
	SvmTheoreticalSpectrumGenerator (const SvmTheoreticalSpectrumGenerator &source)
	Copy constructor.
SvmTheoreticalSpectrumGenerator &	operator= (const SvmTheoreticalSpectrumGenerator &tsg)
	Assignment operator.
virtual	~SvmTheoreticalSpectrumGenerator ()
	Destructor.
Protected Types
typedef std::map< IonType, DoubleReal >	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 intervall [lower,max] given the maximal and minimal entries for a feature
void	scaleDescriptorSet_ (DescriptorSet &desc, double lower, double upper)
	scale value to the intervall [lower,max] given the maximal and minimal entries for a feature
Size	generateDescriptorSet_ (AASequence peptide, Size position, IonType type, Size precursor_charge, DescriptorSet &desc_set)
	generate the desciptors for an input peptide and a given fragmentation position
String	ResidueTypeToString_ (Residue::ResidueType type)
	Returns the ResidueType (e.g. AIon, BIon) as string for peak annotation.
void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method.
Static Protected Member Functions
static void	initializeMaps_ ()
	initialized the maps
Protected Attributes
Size	precursor_charge_
	charge of the precursors used for training
SvmModelParameterSet	mp_
	set of model parameters read from model file
std::map< IonType, bool >	hide_type_
	whether ion types are hidden or not
Static Protected Attributes
static std::map< String, Size >	aa_to_index_
	map AA to integers
static std::map< String, DoubleReal >	hydrophobicity_
	hydrophobicity values for each AA
static std::map< String, DoubleReal >	helicity_
	helicity values for each AA
static std::map< String, DoubleReal >	basicity_
	basicity values for each AA
static bool	initializedMaps_
	flag to indicate if the hydrophobicity, helicity, and basicity maps were already initialized
Friends
class	SvmTheoreticalSpectrumGeneratorTrainer

Detailed Description

Simulates ms2 spectra with support vector machines.

The models are generated with the SvmTheoreticalSpectrumGeneratorTrainer.
Two modes are supported:

Only a prediction of abundant/missing is performed and for abundant peaks are generated with user defined intensity.
The intensity is predicted using SVM-regression (only for the primary ion types b and y). For the secondary types a Bayesian model is used.

Currently, only a test model is shipped with OpenMS.
Please find trained models at: http://sourceforge.net/projects/open-ms/files/Supplementary/Simulation/.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
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

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Member Typedef Documentation

typedef std::map<IonType, DoubleReal> IntensityMap [protected]

Constructor & Destructor Documentation

SvmTheoreticalSpectrumGenerator ( )

Default constructor.

SvmTheoreticalSpectrumGenerator ( const SvmTheoreticalSpectrumGenerator & source )

Copy constructor.

virtual ~SvmTheoreticalSpectrumGenerator ( ) [virtual]

Destructor.

Member Function Documentation

Size generateDescriptorSet_	(	AASequence	peptide,
		Size	position,
		IonType	type,
		Size	precursor_charge,
		DescriptorSet &	desc_set
	)			`[protected]`

generate the desciptors for an input peptide and a given fragmentation position

const std::vector<IonType>& getIonTypes ( ) [inline]

return the set of ion types that are modeled by the loaded SVMs

static void initializeMaps_ ( ) [static, protected]

initialized the maps

void load ( )

Load a trained Svm and Prob. models.

SvmTheoreticalSpectrumGenerator& operator= ( const SvmTheoreticalSpectrumGenerator & tsg )

Assignment operator.

String ResidueTypeToString_ ( Residue::ResidueType type ) [protected]

Returns the ResidueType (e.g. AIon, BIon) as string for peak annotation.

void scaleDescriptorSet_	(	DescriptorSet &	desc,
		double	lower,
		double	upper
	)			`[protected]`

scale value to the intervall [lower,max] given the maximal and minimal entries for a feature

void scaleSingleFeature_	(	double &	value,
		double	feature_min,
		double	feature_max,
		double	lower = `-1.0`,
		double	upper = `1.0`
	)			`[inline, protected]`

scale value to the intervall [lower,max] given the maximal and minimal entries for a feature

void simulate	(	RichPeakSpectrum &	spectrum,
		const AASequence &	peptide,
		const gsl_rng *	rng,
		Size	precursor_charge
	)

Generate the MS/MS according to the given probabilistic model.

void updateMembers_ ( ) [protected, virtual]

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.

Friends And Related Function Documentation

friend class SvmTheoreticalSpectrumGeneratorTrainer [friend]

Member Data Documentation

std::map<String, Size> aa_to_index_ [static, protected]

map AA to integers

std::map<String, DoubleReal> basicity_ [static, protected]

basicity values for each AA

std::map<String, DoubleReal> helicity_ [static, protected]

helicity values for each AA

std::map<IonType, bool> hide_type_ [protected]

whether ion types are hidden or not

std::map<String, DoubleReal> hydrophobicity_ [static, protected]

hydrophobicity values for each AA

bool initializedMaps_ [static, protected]

flag to indicate if the hydrophobicity, helicity, and basicity maps were already initialized

SvmModelParameterSet mp_ [protected]

set of model parameters read from model file

Size precursor_charge_ [protected]

charge of the precursors used for training

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:50 using doxygen 1.7.1

SvmTheoreticalSpectrumGenerator Class Reference [Chemistry]

Classes

Public Member Functions

Protected Types

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Static Protected Attributes