Interval.java

package jannovar.interval;

import jannovar.exception.JannovarException;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;

/**
 * This class implements an interval on a numberline with a lowpoint
 * and a highpoint (where lowpoint <= highpoint). The Interval is intended
 * to contain some other kind of data (clients of this templated class will
 * need to initialize the template variable T to the corresponding datatype). The
 * intervals are intended to be used with the
 * {@link jannovar.interval.IntervalTree IntervallTree}.
 * @param <T>
 * @see "jannovar.interval.IntervalTree"
 * @author Christopher Dommaschenz, Radostina Misirkova, Nadine Taube, Gizem Top
 * @version 0.03 (22 May, 2013)
 */
public class Interval<T> implements java.io.Serializable { 
    private static final Log LOG = LogFactory.getLog(Interval.class);
    /** The object that we are putting into the interval tree (such as a 
     * {@link jannovar.reference.TranscriptModel TranscriptModel} object).*/
    private T value;
    /** The smaller end point of the interval */
    private int lowpoint;
    /** The larger end point of the interval */
    private int highpoint;
     /** Class version (for serialization).*/
    public static final long serialVersionUID = 1L;

    /**
     * @param lpoint The lower end of the Interval
     */
    public void setLow(int lpoint) {
    	this.lowpoint = lpoint;
    }

    /**
     * @return the lower end of the interval.
     */
    public int getLow() {
        return lowpoint;
    }

    /**
     * @param hpoint The upper end of the Interval
     */
    public void setHigh(int hpoint) {
        this.highpoint = hpoint;
    }

    /**
     * @return the upper end of the interval.
     */
    public int getHigh() {
    	return highpoint;
    }

    /**
     * @param val The object that is to be represented by the interval
     */
    public void setValue(T val) {
        this.value = val;
    }

    /**
     *	@return The object that is represented by this interval
     */
    public T getValue() {
        return value;
    }

    /**
     * Interval constructor.
     * @param low lower endpoint of the interval (cannot be higher than the upper endpoint or exception is thrown)
     * @param high upper endpoint of the interval
     * @param value The object represented by the interval.
     */
    public Interval(int low, int high, T value) throws JannovarException {
        if (low <= high) {
	    this.lowpoint = low;
	    this.highpoint = high;
	    this.value = value;
	} else {
	    String s = ("Error, low endpoint higher than upper endpoint for interval");
	    s += ("Recheck the format of the input data, low end of interval must be less than high end");
	    s += (String.format("lo:%d-high:%d ()",this.lowpoint,this.highpoint));
	    LOG.error(s);
            throw new JannovarException(s);
	}
    }

    

	

    /* returns a string that represents the interval */
    @Override
    public String toString() {
	return "[" + lowpoint + "," + highpoint + "," + value + "]";
    }

}