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

Class ProteinComparator

  • All Implemented Interfaces:
    Comparator<Protein>
    Direct Known Subclasses:
    UnambiguousExactProteinComparator, UnambiguousProteinComparator
    public class ProteinComparator
extends Object
implements Comparator<Protein>
    proteins comparator. 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).
    Since:
    15/01/13
    Version:
    $Id$
    Author:
    Marine Dumousseau (marine@ebi.ac.uk)

    • Constructor Detail

      • ProteinComparator

        public ProteinComparator​(PolymerComparator polymerComparator)
        Creates a new UnambiguousProteinComparator. It will uses a UnambiguousPolymerComparator to compare interactor properties and a OrganismTaxIdComparator to compares organism.
        Parameters:
        polymerComparator - a PolymerComparator object.

    • Method Detail

      • compare

        public 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). 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>
        Parameters:
        protein1 - a Protein object.
        protein2 - a Protein object.
        Returns:
        a int.