/*
 * 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;

import java.io.IOException;
import java.io.InputStream;
import java.util.Map;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;


public class GenomeZipDescriptor extends GenomeDescriptor {
    private Map<String, ZipEntry> zipEntries;
    private ZipFile genomeZipFile;
    private boolean userDefined;

    public GenomeZipDescriptor(String name,
                               int version,
                               boolean chrNamesAltered,
                               String id,
                               String cytoBandFileName,
                               String geneFileName,
                               String geneTrackName,
                               String sequenceLocation,
                               ZipFile genomeZipFile,
                               Map<String, ZipEntry> zipEntries,
                               boolean userDefined,
                               boolean chromosomesAreOrdered) {
        super(name, version, chrNamesAltered, id, cytoBandFileName, geneFileName, geneTrackName, sequenceLocation, chromosomesAreOrdered);
        this.zipEntries = zipEntries;
        this.genomeZipFile = genomeZipFile;
        this.userDefined = userDefined;

    }

    public InputStream getCytoBandStream()
            throws IOException {

        String fileName = cytoBandFileName;
        if (fileName == null) {
            return null;
        }
        return genomeZipFile.getInputStream((ZipEntry) zipEntries.get(fileName));
    }

    public InputStream getGeneStream()
            throws IOException {
        if (geneFileName == null) {
            return null;
        }
        return genomeZipFile.getInputStream((ZipEntry) zipEntries.get(geneFileName));
    }

    public boolean isUserDefined() {
        return userDefined;
    }
}
