org.fhcrc.cpl.viewer.amt
Class BaseAmtFeatureSetMatcherImpl

java.lang.Object
  org.fhcrc.cpl.viewer.amt.BaseAmtFeatureSetMatcherImpl

All Implemented Interfaces:

AmtFeatureSetMatcher

Direct Known Subclasses:

ClusteringFeatureSetMatcher, RecursiveFeatureSetMatcher

public abstract class BaseAmtFeatureSetMatcherImpl
extends java.lang.Object
implements AmtFeatureSetMatcher

Base implementing class for FeatureSetMatcher classes. FeatureSetMatchers don't have to extend from this class, it just provides some helpful methods. In particular, it makes it easy for implementing classes to order the feature matches, and to use different elution modes (scan, time, hydrophobicity)

Nested Class Summary

protected class

BaseAmtFeatureSetMatcherImpl.FeatureElutionClosenessToBaseFeatureComparatorDesc Compare features based on closeness in hydrophobicity to a base feature

Nested classes/interfaces inherited from interface org.fhcrc.cpl.viewer.amt.AmtFeatureSetMatcher

AmtFeatureSetMatcher.FeatureMatchingResult

Field Summary

static int	DEFAULT_ELUTION_MODE
protected float	deltaElution
protected float	deltaMass
protected int	deltaMassType
static int	ELUTION_MODE_HYDROPHOBICITY
static int	ELUTION_MODE_SCAN
static int	ELUTION_MODE_TIME
protected int	elutionMode
static int	ORDER_BY_ELUTION_CLOSENESS_TO_MASTER_MODE
static int	ORDER_BY_FEATURE_QUALITY_MODE
protected int	slaveSetOrderingMode

Fields inherited from interface org.fhcrc.cpl.viewer.amt.AmtFeatureSetMatcher

DEFAULT_DELTA_HYDROPHOBICITY, DEFAULT_DELTA_MASS_ABSOLUTE, DEFAULT_DELTA_MASS_PPM, DEFAULT_DELTA_MASS_TYPE, DEFAULT_DELTA_SCAN, DEFAULT_DELTA_TIME, DELTA_MASS_TYPE_ABSOLUTE, DELTA_MASS_TYPE_PPM

Constructor Summary

BaseAmtFeatureSetMatcherImpl()

Method Summary

float	getDeltaElution()
float	getDeltaMass()
int	getDeltaMassType()
int	getElutionMode()
protected double	getElutionValue(Feature feature) switch on elutionMode to return the appropriate elution value for this feature
int	getSlaveSetOrderingMode()
void	init(float deltaMass, int deltaMassType, float deltaHydrophobicity) Set the parameters that are common to all FeatureSetMatchers
protected java.util.List<Feature>	orderSlaveSetFeatures(java.util.List<Feature> slaveSetFeatures, Feature masterSetFeature) Order the slave set features appropriately, in descending order of "goodness"
void	setDeltaElution(float deltaElution)
void	setDeltaMass(float deltaMass)
void	setDeltaMassType(int deltaMassType)
void	setElutionMode(int elutionMode)
void	setSlaveSetOrderingMode(int slaveSetOrderingMode)

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.amt.AmtFeatureSetMatcher

matchFeatures

Field Detail

ORDER_BY_FEATURE_QUALITY_MODE

public static final int ORDER_BY_FEATURE_QUALITY_MODE

See Also:

Constant Field Values

ORDER_BY_ELUTION_CLOSENESS_TO_MASTER_MODE

public static final int ORDER_BY_ELUTION_CLOSENESS_TO_MASTER_MODE

See Also:

Constant Field Values

slaveSetOrderingMode

protected int slaveSetOrderingMode

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

deltaMass

protected float deltaMass

deltaMassType

protected int deltaMassType

deltaElution

protected float deltaElution

Constructor Detail

BaseAmtFeatureSetMatcherImpl

public BaseAmtFeatureSetMatcherImpl()

Method Detail

init

public void init(float deltaMass,
                 int deltaMassType,
                 float deltaHydrophobicity)

Set the parameters that are common to all FeatureSetMatchers

Specified by:

init in interface AmtFeatureSetMatcher

Parameters:

deltaMass -

deltaMassType -

deltaHydrophobicity -

orderSlaveSetFeatures

protected java.util.List<Feature> orderSlaveSetFeatures(java.util.List<Feature> slaveSetFeatures,
                                                        Feature masterSetFeature)

Order the slave set features appropriately, in descending order of "goodness"

Parameters:

slaveSetFeatures -

masterSetFeature -

Returns:

a DISTINCT LIST from the input list, ordered

getElutionValue

protected double getElutionValue(Feature feature)

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

Parameters:

feature -

Returns:

getDeltaMass

public float getDeltaMass()

setDeltaMass

public void setDeltaMass(float deltaMass)

getDeltaMassType

public int getDeltaMassType()

setDeltaMassType

public void setDeltaMassType(int deltaMassType)

getDeltaElution

public float getDeltaElution()

setDeltaElution

public void setDeltaElution(float deltaElution)

getSlaveSetOrderingMode

public int getSlaveSetOrderingMode()

setSlaveSetOrderingMode

public void setSlaveSetOrderingMode(int slaveSetOrderingMode)

setElutionMode

public void setElutionMode(int elutionMode)

getElutionMode

public int getElutionMode()