Isotope distribution approximated using linear interpolation. More...
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/LmaIsotopeModel.h>
Public Types | |
enum | Averagines { C = 0, H, N, O, S, AVERAGINE_NUM } |
typedef InterpolationModel::CoordinateType | CoordinateType |
typedef InterpolationModel::CoordinateType | IntensityType |
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typedef DoubleReal | IntensityType |
typedef DPosition< 1 > | PositionType |
typedef DoubleReal | CoordinateType |
typedef Math::LinearInterpolation < DoubleReal > | LinearInterpolation |
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typedef DoubleReal | IntensityType |
typedef DoubleReal | CoordinateType |
typedef DPosition< D > | PositionType |
typedef DPeak< D >::Type | PeakType |
typedef std::vector< PeakType > | SamplesType |
Public Member Functions | |
LmaIsotopeModel () | |
Default constructor. More... | |
LmaIsotopeModel (const LmaIsotopeModel &source) | |
copy constructor More... | |
virtual | ~LmaIsotopeModel () |
destructor More... | |
virtual LmaIsotopeModel & | operator= (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... | |
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InterpolationModel () | |
Default constructor. More... | |
InterpolationModel (const InterpolationModel &source) | |
copy constructor More... | |
virtual | ~InterpolationModel () |
destructor More... | |
virtual InterpolationModel & | operator= (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 LinearInterpolation & | getInterpolation () 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) |
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BaseModel () | |
Default constructor. More... | |
BaseModel (const BaseModel &source) | |
copy constructor More... | |
virtual | ~BaseModel () |
Destructor. More... | |
virtual BaseModel & | operator= (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... | |
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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... | |
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... | |
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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... | |
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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_ |
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LinearInterpolation | interpolation_ |
CoordinateType | interpolation_step_ |
CoordinateType | scaling_ |
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IntensityType | cut_off_ |
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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... | |
Isotope distribution approximated using linear interpolation.
Parameters of this class are:Name | Type | Default | Restrictions | Description |
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cutoff | float | 0 | Low intensity cutoff of the model. Peaks below this intensity are not considered part of the model. | |
interpolation_step | float | 0.1 | Sampling rate for the interpolation of the model function | |
intensity_scaling | float | 1 | Scaling factor used to adjust the model distribution to the intensities of the data | |
charge | int | 1 | Charge state of the model. | |
total_intensity | float | 100 | Total intensity under isotope curve. | |
monoisotopic_mz | float | 0 | Position (mz) of the monoisotopic peak. | |
averagines:C | float | 0.0444398894906044 | Number of C atoms per Dalton of mass. | |
averagines:H | float | 0.0698157176375389 | Number of H atoms per Dalton of mass. | |
averagines:N | float | 0.0122177302837372 | Number of N atoms per Dalton of mass. | |
averagines:O | float | 0.0132939899340272 | Number of O atoms per Dalton of mass. | |
averagines:S | float | 0.000375250005163252 | Number of S atoms per Dalton of mass. | |
isotope:trim_right_cutoff | float | 0.001 | Cutoff in averagine distribution, trailing isotopes below this relative intensity are not considered. | |
isotope:maximum | int | 100 | Maximum isotopic rank to be considered. | |
isotope:distance | float | 1.000495 | Distance between consecutive isotopic peaks. | |
isotope:stdev | float | 0.1 | Standard deviation of gaussian applied to the averagine isotopic pattern to simulate the inaccuracy of the mass spectrometer. | |
statistics:mean | float | 0 | Centroid m/z (as opposed to monoisotopic m/z). | |
bounding_box:min | float | 0 | Lower end of bounding box enclosing the data used to fit the model. | |
bounding_box:max | float | 1 | Upper end of bounding box enclosing the data used to fit the model. |
enum Averagines |
LmaIsotopeModel | ( | ) |
Default constructor.
LmaIsotopeModel | ( | const LmaIsotopeModel & | source | ) |
copy constructor
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destructor
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inlinestatic |
create new LmaIsotopeModel object (needed by Factory)
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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
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assignment operator
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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.
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set sample/supporting points of interpolation
Reimplemented from InterpolationModel.
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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 InterpolationModel.
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total intensity (area under curve)
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OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:34 using doxygen 1.8.5 |