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Variant annotation and effect prediction package.
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/*
 * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard.  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
 * WARRANTES 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.bbfile;

/**
 * Created by IntelliJ IDEA.
 * User: martind
 * Date: Jan 6, 2010
 * Time: 4:29:53 PM
 * To change this template use File | Settings | File Templates.
 */
/*
*   RPTreeNodeItem interface for storage of R+ tree node item information.
*
*   Note: The bounding 1D rectangle defined by:
*       (mStartBase mChromosome, mStartBase base) to (mEndBase mChromosome, mEndBase base)
*    is used as a key for insertion and searches on the R+ tree.
*
* */

interface RPTreeNodeItem  {


    // returns the chromosome boundary for the item
    public RPChromosomeRegion getChromosomeBounds();

    // Note: compareRegions returns the following values:
     //   -2 indicates chromosome region is completely below node region
     //   -1 indicates that chromosome region intersect node region from below
     //  0 means that chromosome region is inclusive to node region
     //  1 indicates chromosome region intersects node region from above
     //  2 indicates that this region is completely above that region
    public int compareRegions(RPChromosomeRegion chromosomeRegion);

    // Prints the tree node item.
    void print();
}