org.fhcrc.cpl.toolbox.proteomics.feature.matching
Class Window2DFeatureSetMatcher

java.lang.Object
  org.fhcrc.cpl.toolbox.proteomics.feature.matching.Window2DFeatureSetMatcher

public class Window2DFeatureSetMatcher
extends java.lang.Object

Attempts to match one feature set against another using a window of minimum and maximum mass and elution time differences, not necessarily centered at 0.

Field Summary

static int	DEFAULT_ELUTION_MODE
static int	ELUTION_MODE_HYDROPHOBICITY
static int	ELUTION_MODE_SCAN
static int	ELUTION_MODE_TIME
static int	ELUTION_RANGE_MODE_POINT
static int	ELUTION_RANGE_MODE_RANGE
protected int	elutionMode
protected int	elutionRangeMode
protected int	massDiffType
protected boolean	matchWithinChargeOnly
protected float	maxElutionDiff
protected float	maxMassDiff
protected float	minElutionDiff
protected float	minMassDiff

Constructor Summary

Window2DFeatureSetMatcher()

Method Summary

protected float	calcElutionDiff(Feature feature1, Feature feature2)
java.util.List<Feature>	findMatchingFeatures(Feature[] slaveFeatures, Feature masterFeature, java.util.Comparator<Feature> featureComparator) Find the single slave features that most closely match this Master feature
int	getElutionMode()
int	getElutionRangeMode()
int	getMassDiffType()
float	getMaxElutionDiff()
protected double	getMaxElutionRangeValue(Feature feature) switch on elutionMode to return the appropriate elution value for this feature
float	getMaxMassDiff()
float	getMinElutionDiff()
protected double	getMinElutionRangeValue(Feature feature) switch on elutionMode to return the appropriate elution value for this feature
float	getMinMassDiff()
protected double	getPointElutionValue(Feature feature) switch on elutionMode to return the appropriate elution value for this feature
boolean	isMatchWithinChargeOnly()
FeatureSetMatcher.FeatureMatchingResult	matchFeatures(FeatureSet masterFeatures, FeatureSet slaveFeatures) Match the features in ms2Features against ms1Features.
void	setElutionMode(int elutionMode)
void	setElutionRangeMode(int elutionRangeMode)
void	setMassDiffType(int massDiffType)
void	setMatchingParameters(float minMassDiff, float maxMassDiff, float minElutionDiff, float maxElutionDiff, int massDiffType) Convenience method to set a bunch of parameters at once
void	setMatchWithinChargeOnly(boolean matchWithinChargeOnly)
void	setMaxElutionDiff(float maxElutionDiff)
void	setMaxMassDiff(float maxMassDiff)
void	setMinElutionDiff(float minElutionDiff)
void	setMinMassDiff(float minMassDiff)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

minMassDiff

protected float minMassDiff

maxMassDiff

protected float maxMassDiff

minElutionDiff

protected float minElutionDiff

maxElutionDiff

protected float maxElutionDiff

massDiffType

protected int massDiffType

ELUTION_MODE_HYDROPHOBICITY

public static final int ELUTION_MODE_HYDROPHOBICITY

See Also:

Constant Field Values

ELUTION_MODE_TIME

public static final int ELUTION_MODE_TIME

See Also:

Constant Field Values

ELUTION_MODE_SCAN

public static final int ELUTION_MODE_SCAN

See Also:

Constant Field Values

DEFAULT_ELUTION_MODE

public static final int DEFAULT_ELUTION_MODE

See Also:

Constant Field Values

elutionMode

protected int elutionMode

ELUTION_RANGE_MODE_POINT

public static final int ELUTION_RANGE_MODE_POINT

See Also:

Constant Field Values

ELUTION_RANGE_MODE_RANGE

public static final int ELUTION_RANGE_MODE_RANGE

See Also:

Constant Field Values

elutionRangeMode

protected int elutionRangeMode

matchWithinChargeOnly

protected boolean matchWithinChargeOnly

Constructor Detail

Window2DFeatureSetMatcher

public Window2DFeatureSetMatcher()

Method Detail

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

setMatchingParameters

public void setMatchingParameters(float minMassDiff,
                                  float maxMassDiff,
                                  float minElutionDiff,
                                  float maxElutionDiff,
                                  int massDiffType)

Convenience method to set a bunch of parameters at once

matchFeatures

public FeatureSetMatcher.FeatureMatchingResult matchFeatures(FeatureSet masterFeatures,
                                                             FeatureSet slaveFeatures)

Match the features in ms2Features against ms1Features. Populate the passed-in unmatchedMS2Features ArrayList with all unmatched features. Can also be used to match ms1 features against other ms1 features

Returns:

findMatchingFeatures

public java.util.List<Feature> findMatchingFeatures(Feature[] slaveFeatures,
                                                    Feature masterFeature,
                                                    java.util.Comparator<Feature> featureComparator)

Find the single slave features that most closely match this Master feature

Returns:

the index of the nearest feature, or -1 if none found in the range

calcElutionDiff

protected float calcElutionDiff(Feature feature1,
                                Feature feature2)

getMinElutionRangeValue

protected double getMinElutionRangeValue(Feature feature)

switch on elutionMode to return the appropriate elution value for this feature

Parameters:

feature -

Returns:

getMaxElutionRangeValue

protected double getMaxElutionRangeValue(Feature feature)

switch on elutionMode to return the appropriate elution value for this feature

Parameters:

feature -

Returns:

getPointElutionValue

protected double getPointElutionValue(Feature feature)

switch on elutionMode to return the appropriate elution value for this feature

Parameters:

feature -

Returns:

getMinMassDiff

public float getMinMassDiff()

setMinMassDiff

public void setMinMassDiff(float minMassDiff)

getMaxMassDiff

public float getMaxMassDiff()

setMaxMassDiff

public void setMaxMassDiff(float maxMassDiff)

getMinElutionDiff

public float getMinElutionDiff()

setMinElutionDiff

public void setMinElutionDiff(float minElutionDiff)

getMaxElutionDiff

public float getMaxElutionDiff()

setMaxElutionDiff

public void setMaxElutionDiff(float maxElutionDiff)

getMassDiffType

public int getMassDiffType()

setMassDiffType

public void setMassDiffType(int massDiffType)

getElutionRangeMode

public int getElutionRangeMode()

setElutionRangeMode

public void setElutionRangeMode(int elutionRangeMode)

getElutionMode

public int getElutionMode()

setElutionMode

public void setElutionMode(int elutionMode)

isMatchWithinChargeOnly

public boolean isMatchWithinChargeOnly()

setMatchWithinChargeOnly

public void setMatchWithinChargeOnly(boolean matchWithinChargeOnly)