org.fhcrc.cpl.viewer.feature.extraction
Class DefaultFeatureScorer

java.lang.Object
  org.fhcrc.cpl.viewer.feature.extraction.DefaultFeatureScorer

All Implemented Interfaces:

FeatureScorer

public class DefaultFeatureScorer
extends java.lang.Object
implements FeatureScorer

Default feature scorer. If we ever implement another one, maybe some machinery can be moved up into a base class* Has side effects on scored features: adjusts m/z, and sets kl, etc.

Field Summary

protected int	_maxPeaksPerFeature
protected double	_maxResampledDistanceBetweenFeatures
protected int	_resamplingFrequency
static int	DEFAULT_MAX_PEAKS_PER_FEATURE
protected boolean	keepStatistics
static float	SUMSQUARES_MZ_WEIGHT
static float	SUMSQUARES_SCALED_INTENSITY_WEIGHT
protected java.util.List<java.lang.Float>	unscaledIntensityDistances
protected java.util.List<java.lang.Float>	unscaledMzDistances

Constructor Summary

DefaultFeatureScorer()

Method Summary

float	calcSumSquaresDistance2D(Feature f, float[] scaledIntensityDistribution, Spectrum.Peak[] peptidePeaks) Assign a score to a particular feature, given a scaled representation of its peak intensities and the peaks themselves.
protected int	findClosestPeak(Spectrum.Peak[] peaks, float x, int start)
int	getMaxPeaksPerFeature()
int	getResamplingFrequency()
boolean	isKeepStatistics()
void	plotStatistics()
float	scoreFeature(Feature f, Spectrum.Peak[] peaks) score a candidate feature f, and set the list of peaks that it's comprised of Expecting charge=0 features and peaks TODO: document this better
void	setKeepStatistics(boolean keepStatistics)
void	setMaxPeaksPerFeature(int maxPeaksPerFeature)
void	setMaxResampledDistanceBetweenFeatures(double newValue)
void	setResamplingFrequency(int resamplingFrequency)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

_resamplingFrequency

protected int _resamplingFrequency

_maxResampledDistanceBetweenFeatures

protected double _maxResampledDistanceBetweenFeatures

DEFAULT_MAX_PEAKS_PER_FEATURE

public static final int DEFAULT_MAX_PEAKS_PER_FEATURE

See Also:

Constant Field Values

_maxPeaksPerFeature

protected int _maxPeaksPerFeature

SUMSQUARES_MZ_WEIGHT

public static final float SUMSQUARES_MZ_WEIGHT

See Also:

Constant Field Values

SUMSQUARES_SCALED_INTENSITY_WEIGHT

public static final float SUMSQUARES_SCALED_INTENSITY_WEIGHT

See Also:

Constant Field Values

keepStatistics

protected boolean keepStatistics

unscaledMzDistances

protected java.util.List<java.lang.Float> unscaledMzDistances

unscaledIntensityDistances

protected java.util.List<java.lang.Float> unscaledIntensityDistances

Constructor Detail

DefaultFeatureScorer

public DefaultFeatureScorer()

Method Detail

scoreFeature

public float scoreFeature(Feature f,
                          Spectrum.Peak[] peaks)

score a candidate feature f, and set the list of peaks that it's comprised of

Expecting charge=0 features and peaks TODO: document this better

Specified by:

scoreFeature in interface FeatureScorer

Parameters:

f -

peaks -

calcSumSquaresDistance2D

public float calcSumSquaresDistance2D(Feature f,
                                      float[] scaledIntensityDistribution,
                                      Spectrum.Peak[] peptidePeaks)

Assign a score to a particular feature, given a scaled representation of its peak intensities and the peaks themselves. This is kind of a 2-dimensional sum-squares distance measure. Lower is better

Parameters:

f -

scaledIntensityDistribution -

peptidePeaks -

Returns:

findClosestPeak

protected int findClosestPeak(Spectrum.Peak[] peaks,
                              float x,
                              int start)

getResamplingFrequency

public int getResamplingFrequency()

setResamplingFrequency

public void setResamplingFrequency(int resamplingFrequency)

setMaxResampledDistanceBetweenFeatures

public void setMaxResampledDistanceBetweenFeatures(double newValue)

getMaxPeaksPerFeature

public int getMaxPeaksPerFeature()

setMaxPeaksPerFeature

public void setMaxPeaksPerFeature(int maxPeaksPerFeature)

isKeepStatistics

public boolean isKeepStatistics()

setKeepStatistics

public void setKeepStatistics(boolean keepStatistics)

plotStatistics

public void plotStatistics()