org.fhcrc.cpl.viewer.align
Class Aligner.MassOrMzFeaturePairSelector

java.lang.Object
  org.fhcrc.cpl.viewer.align.Aligner.MassOrMzFeaturePairSelector

All Implemented Interfaces:

Aligner.FeaturePairSelector

Direct Known Subclasses:

Aligner.MassFeaturePairSelector, Aligner.MzFeaturePairSelector

Enclosing class:

Aligner

public static class Aligner.MassOrMzFeaturePairSelector
extends java.lang.Object
implements Aligner.FeaturePairSelector

This class selects pairs of features purely based on m/z -- it pairs up features that are within a given m/z tolerance. This emulates the old behavior, which was implemented in R

Field Summary

static float	DEFAULT_DELTA_MASS_OR_MZ
static int	DEFAULT_DELTA_MASS_TYPE
static float	DEFAULT_MIN_INTENSITY
protected float	deltaMassOrMz
protected int	deltaMassType
protected int	massOrMzMode
protected float	minIntensity
static int	MODE_MASS
static int	MODE_MZ
protected int	topN

Constructor Summary

Aligner.MassOrMzFeaturePairSelector()

Method Summary

float	getDeltaMassOrMz()
int	getDeltaMassType()
int	getMassOrMzMode()
float	getMinIntensity()
int	getTopN()
org.fhcrc.cpl.toolbox.Pair<Feature,Feature>[]	selectPairs(FeatureSet sourceFeatureSet, FeatureSet destFeatureSet) Select pairs based on m/z or
void	setDeltaMassOrMz(float deltaMz)
void	setDeltaMassType(int deltaMassType)
void	setMassOrMzMode(int massOrMzMode)
void	setMinIntensity(float minIntensity)
void	setTopN(int newTopN)
protected FeatureSet	stripAllButTopNFeaturesByIntensity(FeatureSet featureSet) This will return more than N entries when more than one entry shares the _exact_ value of the boundry element; we do this to avoid making random exclusions of "equivalent" values.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_DELTA_MASS_OR_MZ

public static final float DEFAULT_DELTA_MASS_OR_MZ

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Constant Field Values

DEFAULT_MIN_INTENSITY

public static final float DEFAULT_MIN_INTENSITY

See Also:

Constant Field Values

topN

protected int topN

deltaMassOrMz

protected float deltaMassOrMz

minIntensity

protected float minIntensity

MODE_MASS

public static final int MODE_MASS

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Constant Field Values

MODE_MZ

public static final int MODE_MZ

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Constant Field Values

massOrMzMode

protected int massOrMzMode

deltaMassType

protected int deltaMassType

DEFAULT_DELTA_MASS_TYPE

public static final int DEFAULT_DELTA_MASS_TYPE

See Also:

Constant Field Values

Constructor Detail

Aligner.MassOrMzFeaturePairSelector

public Aligner.MassOrMzFeaturePairSelector()

Method Detail

setTopN

public void setTopN(int newTopN)

getTopN

public int getTopN()

getDeltaMassOrMz

public float getDeltaMassOrMz()

setDeltaMassOrMz

public void setDeltaMassOrMz(float deltaMz)

getMinIntensity

public float getMinIntensity()

setMinIntensity

public void setMinIntensity(float minIntensity)

stripAllButTopNFeaturesByIntensity

protected FeatureSet stripAllButTopNFeaturesByIntensity(FeatureSet featureSet)

This will return more than N entries when more than one entry shares the _exact_ value of the boundry element; we do this to avoid making random exclusions of "equivalent" values. Note that, in the degenerate case, this will return all features if all members of the input list have the same value.

selectPairs

public org.fhcrc.cpl.toolbox.Pair<Feature,Feature>[] selectPairs(FeatureSet sourceFeatureSet,
                                                                 FeatureSet destFeatureSet)

Select pairs based on m/z or

Specified by:

selectPairs in interface Aligner.FeaturePairSelector

Returns:

getMassOrMzMode

public int getMassOrMzMode()

setMassOrMzMode

public void setMassOrMzMode(int massOrMzMode)

getDeltaMassType

public int getDeltaMassType()

setDeltaMassType

public void setDeltaMassType(int deltaMassType)