Package psidev.psi.mi.jami.utils.comparator.feature

Class FeatureBaseComparator

java.lang.Object

psidev.psi.mi.jami.utils.comparator.feature.FeatureBaseComparator

All Implemented Interfaces:

Comparator<Feature>

Direct Known Subclasses:

UnambiguousFeatureBaseComparator

public class FeatureBaseComparator
extends Object
implements Comparator<Feature>

feature comparator. It will look first at the feature shortnames (case insensitive). Then, it will compare the feature types using a UnambiguousCvTermComparator. If the feature types are the same, it will compare interactionEffect and then interactionDependency using UnambiguousCvTermComparator. Then it will compare interpro identifier and if the features do not have an interpro identifier, it will look for at the identifiers in the feature identifiers using UnambiguousIdentifierComparator. Finally, it will look at the ranges using UnambiguousRangeComparator.

Since:

16/01/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
FeatureBaseComparator(Comparator<CvTerm> cvComparator, Comparator<Xref> identifierComparator, RangeComparator rangeComparator)	Creates a new UnambiguousFeatureBaseComparator.
FeatureBaseComparator(Comparator<CvTerm> cvComparator, CollectionComparator<Xref> identifierComparator, CollectionComparator<Range> rangeComparator)	Constructor for FeatureBaseComparator.

Method Summary

Modifier and Type	Method	Description
int	compare(Feature feature1, Feature feature2)	It will look first at the feature shortnames (case insensitive).
Comparator<CvTerm>	getCvTermComparator()	Getter for the field cvTermComparator.
CollectionComparator<Xref>	getExternalIdentifierCollectionComparator()	Getter for the field externalIdentifierCollectionComparator.
Comparator<Xref>	getIdentifierComparator()	Getter for the field identifierComparator.
CollectionComparator<Range>	getRangeCollectionComparator()	Getter for the field rangeCollectionComparator.

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Comparator

equals, reversed, thenComparing, thenComparing, thenComparing, thenComparingDouble, thenComparingInt, thenComparingLong

Constructor Detail

FeatureBaseComparator

public FeatureBaseComparator(Comparator<CvTerm> cvComparator,
                             Comparator<Xref> identifierComparator,
                             RangeComparator rangeComparator)

Creates a new UnambiguousFeatureBaseComparator. It will use a UnambiguousCvTermComparator to compare feature types and range status, a UnambiguousExternalIdentifierComparator to compare identifiers and a UnambiguousRangeComparator to compare ranges

Parameters:

cvComparator - a Comparator object.

identifierComparator - a Comparator object.

rangeComparator - a RangeComparator object.

FeatureBaseComparator

public FeatureBaseComparator(Comparator<CvTerm> cvComparator,
                             CollectionComparator<Xref> identifierComparator,
                             CollectionComparator<Range> rangeComparator)

Constructor for FeatureBaseComparator.

Parameters:

cvComparator - a Comparator object.

identifierComparator - a CollectionComparator object.

rangeComparator - a CollectionComparator object.

Method Detail

getExternalIdentifierCollectionComparator

public CollectionComparator<Xref> getExternalIdentifierCollectionComparator()

Getter for the field externalIdentifierCollectionComparator.

Returns:

a CollectionComparator object.

compare

public int compare(Feature feature1,
                   Feature feature2)

It will look first at the feature shortnames (case insensitive). Then, it will compare the feature types using a UnambiguousCvTermComparator. If the feature types are the same, it will compare interactionEffect and then interactionDependency using UnambiguousCvTermComparator. Then it will compare interpro identifier and if the features do not have an interpro identifier, it will look for at the identifiers in the feature identifiers using UnambiguousIdentifierComparator. Finally, it will look at the ranges using UnambiguousRangeComparator.

Specified by:

compare in interface Comparator<Feature>

Parameters:

feature1 - a Feature object.

feature2 - a Feature object.

Returns:

a int.

getCvTermComparator

public Comparator<CvTerm> getCvTermComparator()

Getter for the field cvTermComparator.

Returns:

a Comparator object.

getIdentifierComparator

public Comparator<Xref> getIdentifierComparator()

Getter for the field identifierComparator.

Returns:

a Comparator object.

getRangeCollectionComparator

public CollectionComparator<Range> getRangeCollectionComparator()

Getter for the field rangeCollectionComparator.

Returns:

a CollectionComparator object.