/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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package org.broad.igv.bbfile;
import org.apache.log4j.Logger;
/**
* 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.
*
* */
abstract class RPTreeNodeItem {
private static Logger log = Logger.getLogger(RPTreeNodeItem.class);
protected RPChromosomeRegion chromosomeBounds; // chromosome bounds for item
public RPTreeNodeItem(RPChromosomeRegion chromosomeBounds) {
this.chromosomeBounds = chromosomeBounds;
}
public RPChromosomeRegion getChromosomeBounds() {
return chromosomeBounds;
}
// 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) {
return chromosomeBounds.compareRegions(chromosomeRegion);
}
public void print() {
log.debug("Child node item :\n");
log.debug(" StartChromID = " + chromosomeBounds.getStartChromID() + "\n");
log.debug(" StartBase = " + chromosomeBounds.getStartBase() + "\n");
log.debug(" EndChromID = " + chromosomeBounds.getEndChromID() + "\n");
log.debug(" EndBase = " + chromosomeBounds.getEndBase() + "\n");
}
}