org.fhcrc.cpl.viewer.feature
Class FeatureExtractor

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

Direct Known Subclasses:

FeatureStrategySpectrumFit, FeatureStrategyUsingWindow

public abstract class FeatureExtractor
extends java.lang.Object

User: mbellew Date: Sep 7, 2004 Time: 12:08:54 PM

Nested Class Summary

static interface

FeatureExtractor.StatusListener

Field Summary

protected int	_dumpWindowSize
protected int	_maxCharge
protected FloatRange	_mzRange
protected MSRun	_run
protected int	_scanCount
protected double	_sn
protected int	_startScan
protected FeatureExtractor.StatusListener	_status
static java.lang.String	DEFAULT_EXTRACTOR_PROPERTYNAME
static int	TYPE_1D
static int	TYPE_2D

Constructor Summary

protected

FeatureExtractor(MSRun run, int startScan, int scanCount, int maxCharge, FloatRange mzRange, double sn)

Method Summary

protected abstract Feature[]	_analyze()
protected static void	_logDebug(java.lang.String s)
FeatureSet	analyze()
protected java.util.Collection<Feature>	analyze1D(Scan scan)
protected java.util.Collection<Feature>	analyze2D(Scan[] scans)
protected Feature[]	analyzeScanAtATime(Scan[] scans) Helper function for one scan at a time analyzer (TYPE_1D)
protected Feature[]	analyzeWindow(Scan[] scans, int windowWidth, int windowMargin) Helper function for window analyzer (TYPE_2D)
protected float[][]	CombineScans(Scan[] scans, FloatRange range, int resample_freq)
protected int	getAccurateMassAdjustmentScans()
static FeatureExtractor	getDefault(MSRun run, int scan, int count, int maxCharge, FloatRange range, double sn) Instantiate the default FeatureExtractor
static java.lang.Class	getDefaultClass()
protected int	getDumpWindowSize()
static FloatRange	getMzExtractionRange(MSRun.MSScan scan) Return the mz range for the given scan.
static FloatRange	getMzExtractionRange(MSRun run) Return the mz range for the given run.
protected Scan[]	getScans(MSRun run, int start, int count)
int	getType()
void	setAccurateMassAdjustmentScans(int accurateMassAdjustmentScans)
static void	setDefault(java.lang.Class c)
void	setDumpWindowSize(int dumpWindowSize)
void	setStatusListener(FeatureExtractor.StatusListener status)

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_EXTRACTOR_PROPERTYNAME

public static final java.lang.String DEFAULT_EXTRACTOR_PROPERTYNAME

TYPE_1D

public static final int TYPE_1D

See Also:

Constant Field Values

TYPE_2D

public static final int TYPE_2D

See Also:

Constant Field Values

_run

protected MSRun _run

_maxCharge

protected int _maxCharge

_mzRange

protected FloatRange _mzRange

_sn

protected double _sn

_status

protected FeatureExtractor.StatusListener _status

_startScan

protected int _startScan

_scanCount

protected int _scanCount

_dumpWindowSize

protected int _dumpWindowSize

Constructor Detail

FeatureExtractor

protected FeatureExtractor(MSRun run,
                           int startScan,
                           int scanCount,
                           int maxCharge,
                           FloatRange mzRange,
                           double sn)

Method Detail

setDefault

public static void setDefault(java.lang.Class c)

getDefaultClass

public static java.lang.Class getDefaultClass()

getDefault

public static FeatureExtractor getDefault(MSRun run,
                                          int scan,
                                          int count,
                                          int maxCharge,
                                          FloatRange range,
                                          double sn)

Instantiate the default FeatureExtractor

Parameters:

run -

scan -

count -

maxCharge -

range -

sn -

Returns:

getMzExtractionRange

public static FloatRange getMzExtractionRange(MSRun.MSScan scan)

Return the mz range for the given scan. If computed lowMz and highMz were supplied, use those; otherwise try startMz and endMz.

getMzExtractionRange

public static FloatRange getMzExtractionRange(MSRun run)

Return the mz range for the given run. First, check scan zero. If range is no good, use the mzRange computed when the run was read.

setStatusListener

public void setStatusListener(FeatureExtractor.StatusListener status)

setDumpWindowSize

public void setDumpWindowSize(int dumpWindowSize)

getDumpWindowSize

protected int getDumpWindowSize()

setAccurateMassAdjustmentScans

public void setAccurateMassAdjustmentScans(int accurateMassAdjustmentScans)

getAccurateMassAdjustmentScans

protected int getAccurateMassAdjustmentScans()

getScans

protected Scan[] getScans(MSRun run,
                          int start,
                          int count)

CombineScans

protected float[][] CombineScans(Scan[] scans,
                                 FloatRange range,
                                 int resample_freq)

analyzeScanAtATime

protected Feature[] analyzeScanAtATime(Scan[] scans)
                                throws java.lang.InterruptedException

Helper function for one scan at a time analyzer (TYPE_1D)

Parameters:

scans -

Returns:

Throws:

java.lang.InterruptedException

analyzeWindow

protected Feature[] analyzeWindow(Scan[] scans,
                                  int windowWidth,
                                  int windowMargin)
                           throws java.lang.InterruptedException

Helper function for window analyzer (TYPE_2D)

Parameters:

scans -

Returns:

Throws:

java.lang.InterruptedException

analyze1D

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

Throws:

java.lang.InterruptedException

analyze2D

protected java.util.Collection<Feature> analyze2D(Scan[] scans)
                                           throws java.lang.InterruptedException

Throws:

java.lang.InterruptedException

getType

public int getType()

_logDebug

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

_analyze

protected abstract Feature[] _analyze()
                               throws java.lang.InterruptedException

Throws:

java.lang.InterruptedException

analyze

public FeatureSet analyze()
                   throws java.lang.InterruptedException

Throws:

java.lang.InterruptedException