org.fhcrc.cpl.viewer.feature.extraction.strategy
Class BaseFeatureStrategyModular

java.lang.Object
  org.fhcrc.cpl.viewer.feature.extraction.strategy.BaseFeatureStrategy
      org.fhcrc.cpl.viewer.feature.extraction.strategy.FeatureStrategyWindow
          org.fhcrc.cpl.viewer.feature.extraction.strategy.BaseFeatureStrategyModular

All Implemented Interfaces:

FeatureStrategy

Direct Known Subclasses:

FeatureStrategyPeakClusters, FeatureStrategySmallMolecule

public class BaseFeatureStrategyModular
extends FeatureStrategyWindow

Base class for a modular feature strategy that contains well-defined components

Nested Class Summary

Nested classes/interfaces inherited from class org.fhcrc.cpl.viewer.feature.extraction.strategy.BaseFeatureStrategy

BaseFeatureStrategy.StatusListener

Field Summary

protected static int	_resamplingFrequency
protected PeakCombiner	peakCombiner
protected PeakExtractor	peakExtractor
protected boolean	peakRidgeWalkSmoothed
protected CPUTimer	timerAnalyze
protected CPUTimer	timerExtractPeaks
protected CPUTimer	timerExtractPeptides
protected static int	WINDOW_MARGIN

Fields inherited from class org.fhcrc.cpl.viewer.feature.extraction.strategy.FeatureStrategyWindow

_endScanNum, _scans, _startScanNum, _WindowMargin, _windowWidth, DEFAULT_WINDOW_WIDTH

Fields inherited from class org.fhcrc.cpl.viewer.feature.extraction.strategy.BaseFeatureStrategy

_dumpWindowSize, _endScan, _keepStatistics, _maxCharge, _mzRange, _run, _scanCount, _sn, _startScan, _status, timerResample

Fields inherited from interface org.fhcrc.cpl.viewer.feature.extraction.strategy.FeatureStrategy

DEFAULT_RESAMPLING_FREQUENCY

Constructor Summary

BaseFeatureStrategyModular()

Method Summary

protected java.util.Collection<Feature>	findPeptidesIn2DWindow(float[][] spectra, Scan[] scans) THIS IS THE MAIN FEATURE FINDING ROUTINE Structure: Extract peaks -- wavelet decomposition, FeatureStrategyUsingWindow.ExtractPeptideFeatures(), to tie features together Change scan numbers, which are currently indexes, to the actual scan numbers If centroided, call AccurateMassCentroid() to fix mass
PeakCombiner	getPeakCombiner()
PeakExtractor	getPeakExtractor()
boolean	isPeakRidgeWalkSmoothed()
void	setPeakCombiner(PeakCombiner peakCombiner)
void	setPeakExtractor(PeakExtractor peakExtractor)
void	setPeakRidgeWalkSmoothed(boolean peakRidgeWalkSmoothed)

Methods inherited from class org.fhcrc.cpl.viewer.feature.extraction.strategy.FeatureStrategyWindow

analyzeWindow, dumpWindow, findPeptides, getWindowWidth, init, setWindowWidth

Methods inherited from class org.fhcrc.cpl.viewer.feature.extraction.strategy.BaseFeatureStrategy

getDumpWindowSize, getInstance, getResamplingFrequency, isKeepStatistics, plotStatistics, resampleSpectra, setDumpWindowSize, setKeepStatistics, setResamplingFrequency, setStatusListener

Methods inherited from class java.lang.Object

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

Field Detail

WINDOW_MARGIN

protected static final int WINDOW_MARGIN

See Also:

Constant Field Values

timerAnalyze

protected CPUTimer timerAnalyze

timerExtractPeaks

protected CPUTimer timerExtractPeaks

timerExtractPeptides

protected CPUTimer timerExtractPeptides

_resamplingFrequency

protected static int _resamplingFrequency

peakExtractor

protected PeakExtractor peakExtractor

peakCombiner

protected PeakCombiner peakCombiner

peakRidgeWalkSmoothed

protected boolean peakRidgeWalkSmoothed

Constructor Detail

BaseFeatureStrategyModular

public BaseFeatureStrategyModular()

Method Detail

findPeptidesIn2DWindow

protected java.util.Collection<Feature> findPeptidesIn2DWindow(float[][] spectra,
                                                               Scan[] scans)
                                                        throws java.lang.InterruptedException

THIS IS THE MAIN FEATURE FINDING ROUTINE Structure: Extract peaks -- wavelet decomposition, FeatureStrategyUsingWindow.ExtractPeptideFeatures(), to tie features together Change scan numbers, which are currently indexes, to the actual scan numbers If centroided, call AccurateMassCentroid() to fix mass

Specified by:

findPeptidesIn2DWindow in class FeatureStrategyWindow

Returns:

Throws:

java.lang.InterruptedException

getPeakExtractor

public PeakExtractor getPeakExtractor()

setPeakExtractor

public void setPeakExtractor(PeakExtractor peakExtractor)

getPeakCombiner

public PeakCombiner getPeakCombiner()

setPeakCombiner

public void setPeakCombiner(PeakCombiner peakCombiner)

isPeakRidgeWalkSmoothed

public boolean isPeakRidgeWalkSmoothed()

setPeakRidgeWalkSmoothed

public void setPeakRidgeWalkSmoothed(boolean peakRidgeWalkSmoothed)