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

java.lang.Object
  org.fhcrc.cpl.toolbox.proteomics.feature.matching.BaseFeatureSetMatcherImpl
      org.fhcrc.cpl.toolbox.proteomics.feature.matching.ClusteringFeatureSetMatcher

All Implemented Interfaces:

FeatureSetMatcher

public class ClusteringFeatureSetMatcher
extends BaseFeatureSetMatcherImpl
implements FeatureSetMatcher

Attempts to match one feature set against another using clustering

Nested Class Summary

Nested classes/interfaces inherited from class org.fhcrc.cpl.toolbox.proteomics.feature.matching.BaseFeatureSetMatcherImpl

BaseFeatureSetMatcherImpl.FeatureElutionClosenessToBaseFeatureComparatorDesc

Nested classes/interfaces inherited from interface org.fhcrc.cpl.toolbox.proteomics.feature.matching.FeatureSetMatcher

FeatureSetMatcher.FeatureMatchingResult

Field Summary

protected static double	ABSOLUTE_MASS_BUCKET_INCREMENT
protected double	bestElutionBucketSize
protected double	bestMassBucketSize
static double	DEFAULT_HYDRO_ELUTION_BUCKET_INCREMENT
protected double	elutionBucketIncrement
protected double	massBucketIncrement
protected int	numElutionBuckets
protected int	numMassBuckets
protected static double	PPM_MASS_BUCKET_INCREMENT
protected boolean	useMassInsteadOfMz

Fields inherited from class org.fhcrc.cpl.toolbox.proteomics.feature.matching.BaseFeatureSetMatcherImpl

DEFAULT_ELUTION_MODE, deltaElution, deltaMass, deltaMassType, ELUTION_MODE_HYDROPHOBICITY, ELUTION_MODE_SCAN, ELUTION_MODE_TIME, elutionMode, ORDER_BY_ELUTION_CLOSENESS_TO_MASTER_MODE, ORDER_BY_FEATURE_QUALITY_MODE, slaveSetOrderingMode

Fields inherited from interface org.fhcrc.cpl.toolbox.proteomics.feature.matching.FeatureSetMatcher

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

ClusteringFeatureSetMatcher()

ClusteringFeatureSetMatcher(float deltaMass, int deltaMassType, float deltaElution)

Method Summary

protected double[]	calculateBuckets(int numBuckets, double bucketIncrement, double maxBucketSize) Calculate the buckets to use for either mass or hydro clustering
double	getBestElutionBucketSize()
double	getBestMassBucketSize()
double	getElutionBucketIncrement()
protected java.util.List<Feature>	getFeatureListForClusterableList(java.util.List<Clusterer2D.Clusterable> clusterableList) Convert a list of Clusterables, assumed to be FeatureMassHydroClusterables, to a list of Features
double	getMassBucketIncrement()
int	getNumElutionBuckets()
int	getNumMassBuckets()
void	init(float deltaMass, int deltaMassType, float deltaElution) Set the parameters that are common to all FeatureSetMatchers
FeatureSetMatcher.FeatureMatchingResult	matchFeatures(FeatureSet featureSet1, FeatureSet featureSet2) Match two feature sets using clustering
protected Feature	pickClosestByMass(Feature baseFeature, java.util.List<Feature> featuresToMatch) Pick the closest feature to a given feature by mass, from a list.
void	setBestElutionBucketSize(double bestElutionBucketSize)
void	setBestMassBucketSize(double bestMassBucketSize)
void	setElutionBucketIncrement(double elutionBucketIncrement)
void	setMassBucketIncrement(double massBucketIncrement)
void	setNumElutionBuckets(int numElutionBuckets)
void	setNumMassBuckets(int numMassBuckets)
void	setUseMassInsteadOfMz(boolean value)
java.lang.String	toString()

Methods inherited from class org.fhcrc.cpl.toolbox.proteomics.feature.matching.BaseFeatureSetMatcherImpl

getDeltaElution, getDeltaMass, getDeltaMassType, getElutionMode, getElutionValue, getSlaveSetOrderingMode, orderSlaveSetFeatures, setDeltaElution, setDeltaMass, setDeltaMassType, setElutionMode, setSlaveSetOrderingMode

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_HYDRO_ELUTION_BUCKET_INCREMENT

public static final double DEFAULT_HYDRO_ELUTION_BUCKET_INCREMENT

See Also:

Constant Field Values

ABSOLUTE_MASS_BUCKET_INCREMENT

protected static final double ABSOLUTE_MASS_BUCKET_INCREMENT

See Also:

Constant Field Values

PPM_MASS_BUCKET_INCREMENT

protected static final double PPM_MASS_BUCKET_INCREMENT

See Also:

Constant Field Values

massBucketIncrement

protected double massBucketIncrement

elutionBucketIncrement

protected double elutionBucketIncrement

numMassBuckets

protected int numMassBuckets

numElutionBuckets

protected int numElutionBuckets

bestMassBucketSize

protected double bestMassBucketSize

bestElutionBucketSize

protected double bestElutionBucketSize

useMassInsteadOfMz

protected boolean useMassInsteadOfMz

Constructor Detail

ClusteringFeatureSetMatcher

public ClusteringFeatureSetMatcher()

ClusteringFeatureSetMatcher

public ClusteringFeatureSetMatcher(float deltaMass,
                                   int deltaMassType,
                                   float deltaElution)

Method Detail

init

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

Description copied from class: BaseFeatureSetMatcherImpl

Set the parameters that are common to all FeatureSetMatchers

Specified by:

init in interface FeatureSetMatcher

Overrides:

init in class BaseFeatureSetMatcherImpl

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

calculateBuckets

protected double[] calculateBuckets(int numBuckets,
                                    double bucketIncrement,
                                    double maxBucketSize)

Calculate the buckets to use for either mass or hydro clustering

Parameters:

numBuckets -

bucketIncrement -

maxBucketSize -

Returns:

matchFeatures

public FeatureSetMatcher.FeatureMatchingResult matchFeatures(FeatureSet featureSet1,
                                                             FeatureSet featureSet2)

Match two feature sets using clustering

Specified by:

matchFeatures in interface FeatureSetMatcher

Parameters:

featureSet1 -

featureSet2 -

Returns:

getFeatureListForClusterableList

protected java.util.List<Feature> getFeatureListForClusterableList(java.util.List<Clusterer2D.Clusterable> clusterableList)

Convert a list of Clusterables, assumed to be FeatureMassHydroClusterables, to a list of Features

Parameters:

clusterableList -

Returns:

pickClosestByMass

protected Feature pickClosestByMass(Feature baseFeature,
                                    java.util.List<Feature> featuresToMatch)

Pick the closest feature to a given feature by mass, from a list.

Parameters:

baseFeature -

featuresToMatch -

Returns:

getBestMassBucketSize

public double getBestMassBucketSize()

setBestMassBucketSize

public void setBestMassBucketSize(double bestMassBucketSize)

getBestElutionBucketSize

public double getBestElutionBucketSize()

setBestElutionBucketSize

public void setBestElutionBucketSize(double bestElutionBucketSize)

getNumMassBuckets

public int getNumMassBuckets()

setNumMassBuckets

public void setNumMassBuckets(int numMassBuckets)

getNumElutionBuckets

public int getNumElutionBuckets()

setNumElutionBuckets

public void setNumElutionBuckets(int numElutionBuckets)

getMassBucketIncrement

public double getMassBucketIncrement()

setMassBucketIncrement

public void setMassBucketIncrement(double massBucketIncrement)

getElutionBucketIncrement

public double getElutionBucketIncrement()

setElutionBucketIncrement

public void setElutionBucketIncrement(double elutionBucketIncrement)

setUseMassInsteadOfMz

public void setUseMassInsteadOfMz(boolean value)