/*
 * 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.
 */

/*
 * GenomeType.java
 *
 * Created on November 8, 2007, 4:20 PM
 *
 * To change this template, choose Tools | Template Manager
 * and open the template in the editor.
 */
package org.broad.igv.feature;

import java.io.IOException;
import java.io.InputStream;

/**
 * @author eflakes
 */
public abstract class GenomeDescriptor {

    private String name;
    private int version;
    private boolean chrNamesAltered;
    private String id;
    protected String cytoBandFileName;
    protected String geneFileName;
    private String geneTrackName;
    private String sequenceLocation;
    private boolean chromosomesAreOrdered = false;

    public GenomeDescriptor(String name,
                            int version,
                            boolean chrNamesAltered,
                            String id,
                            String cytoBandFileName,
                            String geneFileName,
                            String geneTrackName,
                            String sequenceLocation,
                            boolean chromosomesAreOrdered) {
        this.version = version;
        this.chrNamesAltered = chrNamesAltered;
        this.name = name;
        this.id = id;
        this.cytoBandFileName = cytoBandFileName;
        this.geneFileName = geneFileName;
        this.geneTrackName = geneTrackName;
        this.sequenceLocation = sequenceLocation;
        this.chromosomesAreOrdered = chromosomesAreOrdered;
    }

    public String getName() {
        return name;
    }

    public String getId() {
        return id;
    }

    // Used to determine feature file type, really only extension is needed
    public String getGeneFileName() {
        return geneFileName;
    }

    public String getGeneTrackName() {
        return geneTrackName;
    }

    public abstract InputStream getCytoBandStream()
            throws IOException;

    public boolean isCytoBandFileGZipFormat() {
        return isFileGZipFormat(cytoBandFileName);
    }

    public abstract InputStream getGeneStream()
            throws IOException;

    public boolean isGeneFileGZipFormat() {
        String fileName = getGeneFileName();
        return isFileGZipFormat(fileName);
    }

    public void setSequenceLocation(String sequenceLocation) {
        this.sequenceLocation = sequenceLocation;
    }

    public String getSequenceLocation() {
        return sequenceLocation;
    }

    public abstract boolean isUserDefined();

    @Override
    public String toString() {
        return name;
    }

    private boolean isFileGZipFormat(String fileName) {

        if (fileName == null) {
            return false;
        }

        if (fileName.toLowerCase().endsWith(".gz")) {
            return true;
        } else {
            return false;
        }
    }

    /**
     * @return the version
     */
    public int getVersion() {
        return version;
    }

    /**
     * @param version the version to set
     */
    public void setVersion(int version) {
        this.version = version;
    }

    public boolean isChromosomesAreOrdered() {
        return chromosomesAreOrdered;
    }

    public boolean isChrNamesAltered() {
        return chrNamesAltered;
    }
}
