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

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

All Implemented Interfaces:

FeatureStrategy

Direct Known Subclasses:

FeatureStrategyWindow

public abstract class BaseFeatureStrategy
extends java.lang.Object
implements FeatureStrategy

Nested Class Summary

static interface

BaseFeatureStrategy.StatusListener

Field Summary

protected int	_dumpWindowSize
protected int	_endScan
protected boolean	_keepStatistics
protected int	_maxCharge
protected org.fhcrc.cpl.toolbox.FloatRange	_mzRange
protected static int	_resamplingFrequency
protected MSRun	_run
protected int	_scanCount
protected double	_sn
protected int	_startScan
protected BaseFeatureStrategy.StatusListener	_status
protected org.fhcrc.cpl.toolbox.CPUTimer	timerResample

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

DEFAULT_RESAMPLING_FREQUENCY

Constructor Summary

BaseFeatureStrategy()

Method Summary

int	getDumpWindowSize()
static FeatureStrategy	getInstance(MSRun run, int startScan, int scanCount, int maxCharge, org.fhcrc.cpl.toolbox.FloatRange mzRange, java.lang.Class<? extends FeatureStrategy> featureStrategyClass, boolean plotStatistics) This is what we use to instantiate FeatureStrategy objects.
int	getResamplingFrequency()
void	init(MSRun run, int startScan, int scanCount, int maxCharge, org.fhcrc.cpl.toolbox.FloatRange mzRange, boolean plotStatistics) pass all of the interesting stuff to the FeatureStrategy so that the findPeptides() method doesn't need any additional parameters
boolean	isKeepStatistics()
void	plotStatistics() Can be overridden
protected float[][]	resampleSpectra(org.fhcrc.cpl.toolbox.proteomics.Scan[] scans) Utility method to resample spectra onto a standard grid
void	setDumpWindowSize(int dumpWindowSize)
void	setKeepStatistics(boolean keepStatistics)
void	setResamplingFrequency(int resamplingFrequency)
void	setStatusListener(BaseFeatureStrategy.StatusListener status)

Methods inherited from class java.lang.Object

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

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

findPeptides, isPeakRidgeWalkSmoothed, setPeakRidgeWalkSmoothed

Field Detail

_run

protected MSRun _run

_maxCharge

protected int _maxCharge

_mzRange

protected org.fhcrc.cpl.toolbox.FloatRange _mzRange

_sn

protected double _sn

_startScan

protected int _startScan

_endScan

protected int _endScan

_scanCount

protected int _scanCount

_status

protected BaseFeatureStrategy.StatusListener _status

_dumpWindowSize

protected int _dumpWindowSize

_resamplingFrequency

protected static int _resamplingFrequency

timerResample

protected org.fhcrc.cpl.toolbox.CPUTimer timerResample

_keepStatistics

protected boolean _keepStatistics

Constructor Detail

BaseFeatureStrategy

public BaseFeatureStrategy()

Method Detail

init

public void init(MSRun run,
                 int startScan,
                 int scanCount,
                 int maxCharge,
                 org.fhcrc.cpl.toolbox.FloatRange mzRange,
                 boolean plotStatistics)

Description copied from interface: FeatureStrategy

pass all of the interesting stuff to the FeatureStrategy so that the findPeptides() method doesn't need any additional parameters

Specified by:

init in interface FeatureStrategy

getInstance

public static FeatureStrategy getInstance(MSRun run,
                                          int startScan,
                                          int scanCount,
                                          int maxCharge,
                                          org.fhcrc.cpl.toolbox.FloatRange mzRange,
                                          java.lang.Class<? extends FeatureStrategy> featureStrategyClass,
                                          boolean plotStatistics)

This is what we use to instantiate FeatureStrategy objects. It's a bit crude. Could reimplement

Parameters:

run -

startScan -

scanCount -

maxCharge -

mzRange -

featureStrategyClass -

Returns:

resampleSpectra

protected float[][] resampleSpectra(org.fhcrc.cpl.toolbox.proteomics.Scan[] scans)
                             throws java.lang.InterruptedException

Utility method to resample spectra onto a standard grid

Parameters:

scans -

Returns:

Throws:

java.lang.InterruptedException

setDumpWindowSize

public void setDumpWindowSize(int dumpWindowSize)

Specified by:

setDumpWindowSize in interface FeatureStrategy

getDumpWindowSize

public int getDumpWindowSize()

Specified by:

getDumpWindowSize in interface FeatureStrategy

setResamplingFrequency

public void setResamplingFrequency(int resamplingFrequency)

getResamplingFrequency

public int getResamplingFrequency()

setStatusListener

public void setStatusListener(BaseFeatureStrategy.StatusListener status)

Specified by:

setStatusListener in interface FeatureStrategy

isKeepStatistics

public boolean isKeepStatistics()

Specified by:

isKeepStatistics in interface FeatureStrategy

setKeepStatistics

public void setKeepStatistics(boolean keepStatistics)

Specified by:

setKeepStatistics in interface FeatureStrategy

plotStatistics

public void plotStatistics()

Can be overridden

Specified by:

plotStatistics in interface FeatureStrategy