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

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

public class AccurateMassAdjuster
extends java.lang.Object

For adjusting the masses of features found in a resampled space, to take advantage of the higher mass accuracy to be found in the unresampled space

Field Summary

protected int	_resamplingFrequency
protected int	_scanWindowSize
static int	DEFAULT_RESAMPLING_FREQUENCY
static int	DEFAULT_SCAN_WINDOW_SIZE

Constructor Summary

AccurateMassAdjuster()

Method Summary

void	adjustAllMasses(MSRun run, Feature[] features)
float	calculateAccurateMass(MSRun run, Feature f) Switch on whether the run is in centroid mode and do the appropriate thing
float	calculateAccurateMassCentroid(MSRun run, Feature f)
float	calculateAccurateMassProfile(MSRun run, Feature f) adjustment of profile-mode mass; average results from some number of adjacent scans
protected float	calculateAccurateMassProfileCenter(org.fhcrc.cpl.toolbox.proteomics.Scan scan, Feature f) adjustment of profile-mode mass using center of mass
protected float	calculateAccurateMassProfileMax(org.fhcrc.cpl.toolbox.proteomics.Scan scan, Feature f) adjustment of profile-mode mass using max peak
int	getResamplingFrequency()
int	getScanWindowSize()
void	setResamplingFrequency(int resamplingFrequency)
void	setScanWindowSize(int scanWindowSize)

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_RESAMPLING_FREQUENCY

public static final int DEFAULT_RESAMPLING_FREQUENCY

See Also:

Constant Field Values

DEFAULT_SCAN_WINDOW_SIZE

public static final int DEFAULT_SCAN_WINDOW_SIZE

See Also:

Constant Field Values

_resamplingFrequency

protected int _resamplingFrequency

_scanWindowSize

protected int _scanWindowSize

Constructor Detail

AccurateMassAdjuster

public AccurateMassAdjuster()

Method Detail

adjustAllMasses

public void adjustAllMasses(MSRun run,
                            Feature[] features)
                     throws java.lang.InterruptedException

Throws:

java.lang.InterruptedException

calculateAccurateMass

public float calculateAccurateMass(MSRun run,
                                   Feature f)

Switch on whether the run is in centroid mode and do the appropriate thing

Parameters:

run -

f -

Returns:

calculateAccurateMassCentroid

public float calculateAccurateMassCentroid(MSRun run,
                                           Feature f)

calculateAccurateMassProfile

public float calculateAccurateMassProfile(MSRun run,
                                          Feature f)

adjustment of profile-mode mass; average results from some number of adjacent scans

calculateAccurateMassProfileMax

protected float calculateAccurateMassProfileMax(org.fhcrc.cpl.toolbox.proteomics.Scan scan,
                                                Feature f)

adjustment of profile-mode mass using max peak

calculateAccurateMassProfileCenter

protected float calculateAccurateMassProfileCenter(org.fhcrc.cpl.toolbox.proteomics.Scan scan,
                                                   Feature f)

adjustment of profile-mode mass using center of mass

Parameters:

scan -

f -

Returns:

getResamplingFrequency

public int getResamplingFrequency()

setResamplingFrequency

public void setResamplingFrequency(int resamplingFrequency)

getScanWindowSize

public int getScanWindowSize()

setScanWindowSize

public void setScanWindowSize(int scanWindowSize)