htsjdk.tribble.index.interval.Interval Maven / Gradle / Ivy
/*
* 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 htsjdk.tribble.index.interval;
import htsjdk.tribble.index.Block;
/**
* Quick and dirty interval class
* Describes a genomic interval and where in a file information for that
* interval can be obtained
*/
public class Interval implements Comparable {
/**
* Start of the interval in genomic coordinates -- this is exposed on purpose, getters have a significant
* performance penalty for this field.
*/
final int start;
/**
* End of the interval in genomic coordinates -- this is exposed on purpose, getters have a significant
* performance penalty for this field.
*/
final int end;
/**
* File block (position, size) containing the data for this interval
*/
private Block block;
public Interval(int start, int end) {
assert start <= end;
this.start = start;
this.end = end;
}
public Interval(int start, int end, Block block) {
assert start <= end;
this.start = start;
this.end = end;
this.block = block;
}
public boolean equals(Object other) {
if (this == other)
return true;
if (this.getClass().equals(other.getClass())) {
Interval otherInterval = (Interval) other;
return (this.start == otherInterval.start &&
this.end == otherInterval.end);
}
return false;
}
public int hashCode() {
return start;
}
@Override
public int compareTo(Object o) {
Interval other = (Interval) o;
if (this.start < other.start)
return -1;
if (this.start > other.start)
return 1;
if (this.end < other.end)
return -1;
if (this.end > other.end)
return 1;
return 0;
}
public String toString() {
return "Interval[" + this.start + ", " + this.end + "]";
}
/**
* @return whether this interval overlaps the other.
*/
public boolean overlaps(Interval other) {
return (this.start <= other.end &&
other.start <= this.end);
}
/**
* @return The file block for this interval
*/
public Block getBlock() {
return block;
}
}