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LmaIsotopeModel Class Reference

Isotope distribution approximated using linear interpolation. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/LmaIsotopeModel.h>

Inheritance diagram for LmaIsotopeModel:
InterpolationModel BaseModel< 1 > DefaultParamHandler

Public Types

enum  Averagines {
  C = 0, H, N, O,
  S, AVERAGINE_NUM
}
 
typedef
InterpolationModel::CoordinateType 
CoordinateType
 
typedef
InterpolationModel::CoordinateType 
IntensityType
 
- Public Types inherited from InterpolationModel
typedef DoubleReal IntensityType
 
typedef DPosition< 1 > PositionType
 
typedef DoubleReal CoordinateType
 
typedef
Math::LinearInterpolation
< DoubleReal
LinearInterpolation
 
- Public Types inherited from BaseModel< 1 >
typedef DoubleReal IntensityType
 
typedef DoubleReal CoordinateType
 
typedef DPosition< D > PositionType
 
typedef DPeak< D >::Type PeakType
 
typedef std::vector< PeakTypeSamplesType
 

Public Member Functions

 LmaIsotopeModel ()
 Default constructor. More...
 
 LmaIsotopeModel (const LmaIsotopeModel &source)
 copy constructor More...
 
virtual ~LmaIsotopeModel ()
 destructor More...
 
virtual LmaIsotopeModeloperator= (const LmaIsotopeModel &source)
 assignment operator More...
 
UInt getCharge ()
 returns the charge More...
 
void setOffset (CoordinateType offset)
 set the offset of the model More...
 
CoordinateType getOffset ()
 returns the offset More...
 
void setSamples ()
 set sample/supporting points of interpolation More...
 
CoordinateType getCenter () const
 get the monoisotopic mass of the Isotope model This is a m/z-value not necessarily the monoisotopic mass. More...
 
- Public Member Functions inherited from InterpolationModel
 InterpolationModel ()
 Default constructor. More...
 
 InterpolationModel (const InterpolationModel &source)
 copy constructor More...
 
virtual ~InterpolationModel ()
 destructor More...
 
virtual InterpolationModeloperator= (const InterpolationModel &source)
 assignment operator More...
 
IntensityType getIntensity (const PositionType &pos) const
 access model predicted intensity at position pos More...
 
IntensityType getIntensity (CoordinateType coord) const
 access model predicted intensity at position pos More...
 
const LinearInterpolationgetInterpolation () const
 Returns the interpolation class. More...
 
CoordinateType getScalingFactor () const
 get the scaling for the model More...
 
void getSamples (SamplesType &cont) const
 get reasonable set of samples from the model (i.e. for printing) More...
 
void setInterpolationStep (CoordinateType interpolation_step)
 Set the interpolation step for the linear interpolation of the model. More...
 
void setScalingFactor (CoordinateType scaling)
 
- Public Member Functions inherited from BaseModel< 1 >
 BaseModel ()
 Default constructor. More...
 
 BaseModel (const BaseModel &source)
 copy constructor More...
 
virtual ~BaseModel ()
 Destructor. More...
 
virtual BaseModeloperator= (const BaseModel &source)
 assignment operator More...
 
virtual IntensityType getIntensity (const PositionType &pos) const =0
 access model predicted intensity at position pos More...
 
virtual bool isContained (const PositionType &pos) const
 check if position pos is part of the model regarding the models cut-off. More...
 
void fillIntensity (PeakType &peak) const
 Convenience function to set the intensity of a peak to the predicted intensity at its current position, calling virtual void getIntensity(). More...
 
void fillIntensities (PeakIterator begin, PeakIterator end) const
 Convenience function that applies fillIntensity() to an iterator range. More...
 
virtual IntensityType getCutOff () const
 get cutoff value More...
 
virtual void setCutOff (IntensityType cut_off)
 set cutoff value More...
 
virtual void getSamples (std::ostream &os)
 fill stream with reasonable set of samples from the model (i.e. for printing) 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 DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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...
 

Static Public Member Functions

static BaseModel< 1 > * create ()
 create new LmaIsotopeModel object (needed by Factory) More...
 
static const String getProductName ()
 name of the model (needed by Factory) More...
 
- Static Public Member Functions inherited from BaseModel< 1 >
static void registerChildren ()
 register all derived classes here (implemented in file BaseModel_impl.h) More...
 

Protected Member Functions

void updateMembers_ ()
 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...
 

Protected Attributes

CoordinateType total_intensity_
 total intensity (area under curve) More...
 
CoordinateType min_
 
CoordinateType max_
 
CoordinateType isotope_stdev_
 
UInt charge_
 
CoordinateType mean_
 
CoordinateType monoisotopic_mz_
 
DoubleReal averagine_ [AVERAGINE_NUM]
 
Int max_isotope_
 
DoubleReal trim_right_cutoff_
 
DoubleReal isotope_distance_
 
- Protected Attributes inherited from InterpolationModel
LinearInterpolation interpolation_
 
CoordinateType interpolation_step_
 
CoordinateType scaling_
 
- Protected Attributes inherited from BaseModel< 1 >
IntensityType cut_off_
 
- 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< Stringsubsections_
 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...
 

Detailed Description

Isotope distribution approximated using linear interpolation.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
cutoff float0  Low intensity cutoff of the model. Peaks below this intensity are not considered part of the model.
interpolation_step float0.1  Sampling rate for the interpolation of the model function
intensity_scaling float1  Scaling factor used to adjust the model distribution to the intensities of the data
charge int1  Charge state of the model.
total_intensity float100  Total intensity under isotope curve.
monoisotopic_mz float0  Position (mz) of the monoisotopic peak.
averagines:C float0.0444398894906044  Number of C atoms per Dalton of mass.
averagines:H float0.0698157176375389  Number of H atoms per Dalton of mass.
averagines:N float0.0122177302837372  Number of N atoms per Dalton of mass.
averagines:O float0.0132939899340272  Number of O atoms per Dalton of mass.
averagines:S float0.000375250005163252  Number of S atoms per Dalton of mass.
isotope:trim_right_cutoff float0.001  Cutoff in averagine distribution, trailing isotopes below this relative intensity are not considered.
isotope:maximum int100  Maximum isotopic rank to be considered.
isotope:distance float1.000495  Distance between consecutive isotopic peaks.
isotope:stdev float0.1  Standard deviation of gaussian applied to the averagine isotopic pattern to simulate the inaccuracy of the mass spectrometer.
statistics:mean float0  Centroid m/z (as opposed to monoisotopic m/z).
bounding_box:min float0  Lower end of bounding box enclosing the data used to fit the model.
bounding_box:max float1  Upper end of bounding box enclosing the data used to fit the model.

Note:

Member Typedef Documentation

Member Enumeration Documentation

enum Averagines
Enumerator
C 
H 
N 
O 
S 
AVERAGINE_NUM 

Constructor & Destructor Documentation

Default constructor.

LmaIsotopeModel ( const LmaIsotopeModel source)

copy constructor

virtual ~LmaIsotopeModel ( )
virtual

destructor

Member Function Documentation

static BaseModel<1>* create ( )
inlinestatic

create new LmaIsotopeModel object (needed by Factory)

CoordinateType getCenter ( ) const
virtual

get the monoisotopic mass of the Isotope model This is a m/z-value not necessarily the monoisotopic mass.

Reimplemented from InterpolationModel.

UInt getCharge ( )

returns the charge

CoordinateType getOffset ( )

returns the offset

static const String getProductName ( )
inlinestatic

name of the model (needed by Factory)

virtual LmaIsotopeModel& operator= ( const LmaIsotopeModel source)
virtual

assignment operator

void setOffset ( CoordinateType  offset)
virtual

set the offset of the model

The whole model will be shifted to the new offset without being computing all over. This leaves a discrepancy which is minor in small shifts (i.e. shifting by one or two standard deviations) but can get significant otherwise. In that case use setParameters() which enforces a recomputation of the model.

Reimplemented from InterpolationModel.

void setSamples ( )
virtual

set sample/supporting points of interpolation

Reimplemented from InterpolationModel.

void updateMembers_ ( )
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 InterpolationModel.

Member Data Documentation

DoubleReal averagine_[AVERAGINE_NUM]
protected
UInt charge_
protected
DoubleReal isotope_distance_
protected
CoordinateType isotope_stdev_
protected
CoordinateType max_
protected
Int max_isotope_
protected
CoordinateType mean_
protected
CoordinateType min_
protected
CoordinateType monoisotopic_mz_
protected
CoordinateType total_intensity_
protected

total intensity (area under curve)

DoubleReal trim_right_cutoff_
protected

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:34 using doxygen 1.8.5