/**
 * Copyright (C) 2010-2015 The Roslin Institute <contact andy.law@roslin.ed.ac.uk>
 *
 * This file is part of JEnsembl: a Java API to Ensembl data sources developed by the
 * Bioinformatics Group at The Roslin Institute, The Royal (Dick) School of
 * Veterinary Studies, University of Edinburgh.
 *
 * Project hosted at: http://jensembl.sourceforge.net
 *
 * This is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License (version 3) as published by
 * the Free Software Foundation.
 *
 * This software is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * in this software distribution. If not, see: http://opensource.org/licenses/gpl-3.0.html
 */
package uk.ac.roslin.ensembl.datasourceaware;

import java.util.TreeSet;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import uk.ac.roslin.ensembl.config.EnsemblCoreObjectType;
import uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory;
import uk.ac.roslin.ensembl.exception.DAOException;
import uk.ac.roslin.ensembl.model.Evidence;
import uk.ac.roslin.ensembl.model.ExternalDB;
import uk.ac.roslin.ensembl.model.ObjectType;
import uk.ac.roslin.ensembl.model.XRef;

/**
 *
 * @author tpaterso
 */
public class DAXRef extends DAObject implements XRef {

    private ExternalDB dB = null ;
    protected String version = null ;
    private String description = null ;
    private String infoType = null;
    private String info = null;
    private String displayID = null ;
    private String primaryAccession = null ;
    protected boolean initialized = false;
    private TreeSet<String> synonyms = null;
    final static Logger LOGGER = LoggerFactory.getLogger(DAXRef.class);
    private Evidence evidence = null;

    @Override
    public DAOCoreFactory getDaoFactory() {
        return (daoFactory!=null && daoFactory instanceof DAOCoreFactory)?(DAOCoreFactory) daoFactory:null;
    }
    
    @Override
    public ExternalDB getDB() {
        if (dB==null) {
            this.reinitialize();
        }
        return dB;
    }

    public void setDB(ExternalDB dB) {
        this.dB = dB;
    }

    @Override
    public String getDescription() {
        if (description==null) {
            this.reinitialize();
        }
        return description;
    }

    public void setDescription(String description) {
        this.description = description;
    }

    @Override
    public String getDisplayID() {
        if (displayID==null) {
            this.reinitialize();
        }
        return displayID;
    }

    public void setDisplayID(String displayID) {
        this.displayID = displayID;
    }

    @Override
    public String getInfo() {
        if (info==null) {
            this.reinitialize();
        }
        return info;
    }

    public void setInfo(String info) {
        this.info = info;
    }

    @Override
    public String getInfoType() {
        if (infoType==null) {
            this.reinitialize();
        }
        return infoType;
    }

    public void setInfoType(String infoType) {
        this.infoType = infoType;
    }

    @Override
    public String getVersion() {
        if (version==null) {
            this.reinitialize();
        }
        return version;
    }

    public void setVersion(String version) {
        this.version = version;
    }

    @Override 
    public String getDBDisplayName() {
            return (this.getDB()!=null)?dB.getDBDisplayName():"";
    }

    @Override
    public ObjectType getType() {
        return EnsemblCoreObjectType.xref;
    }

    @Override
    public String getPrimaryAccession() {
        if (primaryAccession==null) {
            this.reinitialize();
        }
        return primaryAccession;
    }

    public void setPrimaryAccession(String primaryAccession) {
        this.primaryAccession = primaryAccession;
    }

    
    private void reinitialize()  {
        if (this.isInitialized()) {
            return;
        }
        try {
            //nb getDaoFactory() will try and make a factory if we have at least species and ensembl version
            this.getDaoFactory().getXRefDAO().reInitialize(this);
                       
        } catch (Exception ex) {
            LOGGER.info("Failed to reinitialize the XRef from the Database (using its xref_id: "
                    +this.getId()+").", ex);
        } finally {
            //always set this so dont try again
            this.setInitialized(true);
        }        
        
    }

    public boolean isInitialized() {
        return initialized;
    }
    
    public void setInitialized(boolean init) {
        this.initialized = init;
    }
    
    @Override
    public TreeSet<String> getSynonyms() {

        if (synonyms!=null) {
            return synonyms;
        }
        this.reinitialize();
        if (this.getDaoFactory() != null) {
            try {
                synonyms = this.getDaoFactory().getXRefDAO().getSynonyms(this);
            } catch (DAOException ex) {
                LOGGER.debug("Failed to getSynonyms for an XRef", ex);
            }
        }
        if (synonyms==null) {
            synonyms = new TreeSet<String>();
        }
        return synonyms;
    }    

    @Override
    public Evidence getEvidence() {
        if (this.evidence==null) {
            this.reinitialize();
        }
        return this.evidence;
    }
    
    public void setEvidence(Evidence evidence) {
        this.evidence = evidence;
    }
}