uk.ac.ebi.bioinvindex.model.HasReferences.java Source code

Introduction

Here is the source code for uk.ac.ebi.bioinvindex.model.HasReferences.java

Source

package uk.ac.ebi.bioinvindex.model;

/*
 * __________
 * CREDITS
 * __________
 *
 * Team page: http://isatab.sf.net/
 * - Marco Brandizi (software engineer: ISAvalidator, ISAconverter, BII data management utility, BII model)
 * - Eamonn Maguire (software engineer: ISAcreator, ISAcreator configurator, ISAvalidator, ISAconverter,  BII data management utility, BII web)
 * - Nataliya Sklyar (software engineer: BII web application, BII model,  BII data management utility)
 * - Philippe Rocca-Serra (technical coordinator: user requirements and standards compliance for ISA software, ISA-tab format specification, BII model, ISAcreator wizard, ontology)
 * - Susanna-Assunta Sansone (coordinator: ISA infrastructure design, standards compliance, ISA-tab format specification, BII model, funds raising)
 *
 * Contributors:
 * - Manon Delahaye (ISA team trainee:  BII web services)
 * - Richard Evans (ISA team trainee: rISAtab)
 *
 *
 * ______________________
 * Contacts and Feedback:
 * ______________________
 *
 * Project overview: http://isatab.sourceforge.net/
 *
 * To follow general discussion: isatab-devel@list.sourceforge.net
 * To contact the developers: isatools@googlegroups.com
 *
 * To report bugs: http://sourceforge.net/tracker/?group_id=215183&atid=1032649
 * To request enhancements:  http://sourceforge.net/tracker/?group_id=215183&atid=1032652
 *
 *
 * __________
 * License:
 * __________
 *
 * This work is licenced under the Creative Commons Attribution-Share Alike 2.0 UK: England & Wales License. To view a copy of this licence, visit http://creativecommons.org/licenses/by-sa/2.0/uk/ or send a letter to Creative Commons, 171 Second Street, Suite 300, San Francisco, California 94105, USA.
 *
 * __________
 * Sponsors
 * __________
 * This work has been funded mainly by the EU Carcinogenomics (http://www.carcinogenomics.eu) [PL 037712] and in part by the
 * EU NuGO [NoE 503630](http://www.nugo.org/everyone) projects and in part by EMBL-EBI.
 */

import org.apache.commons.collections.CollectionUtils;
import org.apache.commons.collections.Predicate;
import org.apache.commons.lang.StringUtils;

import uk.ac.ebi.bioinvindex.model.xref.ReferenceSource;
import uk.ac.ebi.bioinvindex.model.xref.Xref;

import javax.persistence.MappedSuperclass;
import javax.persistence.Transient;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;

/**
 * A superclass for classes with may have references to external data sources (e.g. DB, ontology)
 *
 * @author brandizi
 */
@MappedSuperclass
public abstract class HasReferences extends Accessible {

    private Collection<Xref> refs = new ArrayList<Xref>();

    @Transient
    public Collection<Xref> getXrefs() {
        return this.refs;
    }

    public void addXref(Xref ref) {
        this.refs.add(ref);
    }

    protected void setXrefs(Collection<Xref> refs) {
        this.refs = refs;
    }

    public boolean removeXref(Xref xref) {
        return this.refs.remove(xref);
    }

    /**
     * @return the xrefs having a source with a given accession. An empty list if none available.
     */
    @SuppressWarnings("unchecked")
    public List<Xref> getXrefs(final String sourceAcc) {
        return (List<Xref>) CollectionUtils.select(refs, new Predicate() {
            public boolean evaluate(Object xref) {
                ReferenceSource source = ((Xref) xref).getSource();
                if (source == null)
                    return false;
                if (sourceAcc == null)
                    return source.getAcc() == null;
                return sourceAcc.equals(source.getAcc());
            }
        });
    }

    /** @return the first element in {@link #getXrefs(String)} or null if it doesn't exist.
     */
    public Xref getSingleXref(final String sourceAcc) {
        List<Xref> xrefs = getXrefs(sourceAcc);
        return xrefs.size() == 0 ? null : xrefs.get(0);
    }

    /**
     * It's like {@link #getXrefs(String)}, but uses a containment criterion
     * 
     */
    @SuppressWarnings("unchecked")
    public List<Xref> getXrefsContaining(final String sourceAcc) {
        return (List<Xref>) CollectionUtils.select(refs, new Predicate() {
            public boolean evaluate(Object xref) {
                ReferenceSource source = ((Xref) xref).getSource();
                if (source == null)
                    return false;
                if (sourceAcc == null)
                    return source.getAcc() == null;
                return StringUtils.containsIgnoreCase(source.getAcc(), sourceAcc);
            }
        });
    }

    /** @return the first element in {@link #getXrefs(String)} or null if it doesn't exist.
     */
    public Xref getSingleXrefContaining(final String sourceAcc) {
        List<Xref> xrefs = getXrefsContaining(sourceAcc);
        return xrefs.size() == 0 ? null : xrefs.get(0);
    }

}