org.fhcrc.cpl.viewer.feature
Class FeatureStrategyUsingWindow

java.lang.Object
  org.fhcrc.cpl.viewer.feature.FeatureExtractor
      org.fhcrc.cpl.viewer.feature.FeatureStrategyUsingWindow

Direct Known Subclasses:

FeatureStrategyCentroided, FeatureStrategyCombined, FeatureStrategyGrossFeatures, FeatureStrategyPeakClustersOld, FeatureStrategyPeaks, FeatureStrategyUsingWindow2D, FeatureStrategyWavelet

public class FeatureStrategyUsingWindow
extends FeatureExtractor

User: mbellew Date: Sep 7, 2004 Time: 12:10:06 PM

Nested Class Summary

Nested classes/interfaces inherited from class org.fhcrc.cpl.viewer.feature.FeatureExtractor

FeatureExtractor.StatusListener

Field Summary

protected double

_noise

Fields inherited from class org.fhcrc.cpl.viewer.feature.FeatureExtractor

_dumpWindowSize, _maxCharge, _mzRange, _run, _scanCount, _sn, _startScan, _status, DEFAULT_EXTRACTOR_PROPERTYNAME, TYPE_1D, TYPE_2D

Constructor Summary

FeatureStrategyUsingWindow(MSRun run, int scan, int count, int maxCharge, FloatRange range, double sn)

Method Summary

Feature[]	_analyze()
protected static void	_logDebug(java.lang.String s)
protected Spectrum.Peak[]	_pickPeaks(Scan scan)
protected float[]	_smooth(float[] s)
protected java.util.Collection<Feature>	analyze1D(Scan scan)
protected java.util.ArrayList<Feature>	ExtractPeptideFeatures(MSRun run, Spectrum.Peak[] peaksIN) For each single-peak feature: Consider all features in a small window around it If multiple have the same m/z, take the one with the lower scan, discard the others Toss out anything < 1/10 the intensity of the highest-intense peak Consider all possible charge states: For each peak, determine the mass distance from the highest-intense peak If within tolerance, create a new multi-peak feature, make sure it contains the highest-intensity peak, score it (a complicated process), add it to a list of candidates Pick the best charge state and create a feature
void	ScoreFeature(Feature f, Spectrum.Peak[] peaks) score a candidate feature f Expecting charge=0 features and peaks TODO: document this better

Methods inherited from class org.fhcrc.cpl.viewer.feature.FeatureExtractor

analyze, analyze2D, analyzeScanAtATime, analyzeWindow, CombineScans, getAccurateMassAdjustmentScans, getDefault, getDefaultClass, getDumpWindowSize, getMzExtractionRange, getMzExtractionRange, getScans, getType, setAccurateMassAdjustmentScans, setDefault, setDumpWindowSize, setStatusListener

Methods inherited from class java.lang.Object

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

Field Detail

_noise

protected double _noise

Constructor Detail

FeatureStrategyUsingWindow

public FeatureStrategyUsingWindow(MSRun run,
                                  int scan,
                                  int count,
                                  int maxCharge,
                                  FloatRange range,
                                  double sn)

Method Detail

_analyze

public Feature[] _analyze()
                   throws java.lang.InterruptedException

Specified by:

_analyze in class FeatureExtractor

Throws:

java.lang.InterruptedException

_smooth

protected float[] _smooth(float[] s)

analyze1D

protected java.util.Collection<Feature> analyze1D(Scan scan)

Overrides:

analyze1D in class FeatureExtractor

_pickPeaks

protected Spectrum.Peak[] _pickPeaks(Scan scan)

ExtractPeptideFeatures

protected java.util.ArrayList<Feature> ExtractPeptideFeatures(MSRun run,
                                                              Spectrum.Peak[] peaksIN)

For each single-peak feature: Consider all features in a small window around it If multiple have the same m/z, take the one with the lower scan, discard the others Toss out anything < 1/10 the intensity of the highest-intense peak Consider all possible charge states: For each peak, determine the mass distance from the highest-intense peak If within tolerance, create a new multi-peak feature, make sure it contains the highest-intensity peak, score it (a complicated process), add it to a list of candidates Pick the best charge state and create a feature

Parameters:

run -

peaksIN -

Returns:

ScoreFeature

public void ScoreFeature(Feature f,
                         Spectrum.Peak[] peaks)

score a candidate feature f

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

Parameters:

f -

peaks -

_logDebug

protected static void _logDebug(java.lang.String s)