/*
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * All Rights Reserved.
 *
 * This software is licensed under the terms of the GNU Lesser General Public License (LGPL), Version 2.1 which
 * is available at http://www.opensource.org/licenses/lgpl-2.1.php.
 *
 * THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR WARRANTIES OF
 * ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT
 * OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE.  IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR
 * RESPECTIVE TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES OF
 * ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES, ECONOMIC
 * DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER THE BROAD OR MIT SHALL
 * BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE
 * FOREGOING.
 */
package org.broad.igv.feature;

//~--- non-JDK imports --------------------------------------------------------

import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.session.ViewContext;

import java.util.HashMap;
import java.util.List;
import java.util.Map;

/**
 * This is a placeholder class for a true "feature database" wrapper.  Its purpose
 * is to return a feature given a name.  Used to support the "search" box.
 *
 * @author jrobinso
 */
public class FeatureDB {

    private static Logger log = Logger.getLogger(FeatureDB.class);
    /**
     * Map for all features other than genes.
     */
    private static Map<String, Feature> featureMap = new HashMap(10000);

    public static void addFeature(Feature feature) {

        if (Globals.isHeadless()) {
            return;
        }

        Genome currentGenome = ViewContext.getInstance().getGenome();
        if (currentGenome == null) {
            return;
        }
        if (currentGenome.getChromosome(feature.getChr()) != null) {

            if (feature.getName() != null && feature.getName().length() > 0) {
                featureMap.put(feature.getName().trim().toUpperCase(), feature);
            }
            if (feature.getIdentifier() != null && feature.getIdentifier().length() > 0) {
                featureMap.put(feature.getIdentifier().trim().toUpperCase(), feature);
            }
        }
    }

    private FeatureDB() {
        // This class can't be instantiated
    }

    /**
     * Method description
     *
     * @param features
     */
    public static void addFeatures(List<Feature> features) {
        for (Feature feature : features) {
            addFeature(feature);
        }
    }

    /**
     * Method description
     */
    public static void clearFeatures() {
        featureMap.clear();
    }

    /**
     * Return the feature, if any, with the given name.  Genes are given
     * precedence.

     */
    public static Feature getFeature(String nm) {

        String name = nm.trim().toUpperCase();


        // First search genes for current genome.  This obviously needs some refactoring.
        String currentGenome = ViewContext.getInstance().getGenomeId();
        GeneManager gm = GeneManager.getGeneManager(currentGenome);
        Feature gene = null;
        if (gm != null) {
            gene = gm.getGene(name);
            if (gene != null) {
                return gene;
            }
        }
        return featureMap.get(name);

    }
}
