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

Class UnambiguousExactProteinComparator

java.lang.Object

psidev.psi.mi.jami.utils.comparator.interactor.ProteinComparator

psidev.psi.mi.jami.utils.comparator.interactor.UnambiguousExactProteinComparator

All Implemented Interfaces:

Comparator<Protein>

public class UnambiguousExactProteinComparator
extends ProteinComparator

Unambiguous exact proteins comparator. It will first use UnambiguousExactPolymerComparator to compare the basic interactor properties If the basic interactor properties are the same, It will look for uniprotkb identifier (The interactor with non null uniprot id will always come first). If the uniprotkb identifiers are identical, it will look at the Refseq identifiers (The interactor with non null refseq id will always come first). If the Refseq and uniport identifiers are not set, it will look at the rogids (The interactor with non null rogid will always come first). If the rogids are identical, it will look at the gene names (The interactor with non null gene name will always come first).

Since:

17/01/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
UnambiguousExactProteinComparator()	Creates a new DefaultExactProteinComparator.

Method Summary

Modifier and Type	Method	Description
static boolean	areEquals(Protein protein1, Protein protein2)	Use DefaultExactProteinComparator to know if two proteins are equals.
int	compare(Protein protein1, Protein protein2)	It will first use UnambiguousPolymerComparator to compare the basic interactor properties If the basic interactor properties are the same, It will look for uniprotkb identifier (The interactor with non null uniprot id will always come first).
UnambiguousExactPolymerComparator	getInteractorComparator()	Getter for the field interactorComparator.

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

UnambiguousExactProteinComparator

public UnambiguousExactProteinComparator()

Creates a new DefaultExactProteinComparator. It will uses a DefaultExactPolymerComparator to compare interactor properties and a OrganismTaxIdComparator to compares organism.

Method Detail

compare

public int compare(Protein protein1,
                   Protein protein2)

Description copied from class: ProteinComparator

It will first use UnambiguousPolymerComparator to compare the basic interactor properties If the basic interactor properties are the same, It will look for uniprotkb identifier (The interactor with non null uniprot id will always come first). If the uniprotkb identifiers are identical, it will look at the Refseq identifiers (The interactor with non null refseq id will always come first). If the Refseq and uniport identifiers are not set, it will look at the rogids (The interactor with non null rogid will always come first). If the rogids are identical, it will look at the gene names (The interactor with non null gene name will always come first).

Specified by:

compare in interface Comparator<Protein>

Overrides:

compare in class ProteinComparator

Parameters:

protein1 - a Protein object.

protein2 - a Protein object.

Returns:

a int.

getInteractorComparator

public UnambiguousExactPolymerComparator getInteractorComparator()

Getter for the field interactorComparator.

Overrides:

getInteractorComparator in class ProteinComparator

Returns:

a PolymerComparator object.

areEquals

public static boolean areEquals(Protein protein1,
                                Protein protein2)

Use DefaultExactProteinComparator to know if two proteins are equals.

Parameters:

protein1 - a Protein object.

protein2 - a Protein object.

Returns:

true if the two proteins are equal