org.snpeff.interval.Interval Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of SnpEff Show documentation
Variant annotation and effect prediction package.
The newest version!
package org.snpeff.interval;

import java.io.Serializable;

/**
 * A genomic interval.
 * 
 * Note: Intervals are assumed to be zero-based and inclusive
 *       i.e. an interval including the first base up to base X would
 *       be [0,X] NOT [1,X]
 *
 * @author pcingola
 */
public class Interval implements Comparable, Serializable, Cloneable {

	private static final long serialVersionUID = -3547434510230920403L;

	protected int start, end;
	protected boolean strandMinus;
	protected String id = ""; // Interval's ID (e.g. gene name, transcript ID)
	protected String chromosomeNameOri; // Original chromosome name (e.g. literal form a file)
	protected Interval parent;

	protected Interval() {
		start = -1;
		end = -1;
		id = null;
		strandMinus = false;
		parent = null;
	}

	public Interval(Interval parent, int start, int end, boolean strandMinus, String id) {
		this.start = start;
		this.end = end;
		this.id = id;
		this.strandMinus = strandMinus;
		this.parent = parent;
	}

	@Override
	public Interval clone() {
		try {
			return (Interval) super.clone();
		} catch (CloneNotSupportedException e) {
			throw new RuntimeException(e);
		}
	}

	/**
	 * Compare by start and end
	 */
	@Override
	public int compareTo(Interval i2) {
		// Start
		if (start > i2.start) return 1;
		if (start < i2.start) return -1;

		// End
		if (end > i2.end) return 1;
		if (end < i2.end) return -1;

		return 0;
	}

	public boolean equals(Interval interval) {
		return compareTo(interval) == 0;
	}

	/**
	 * Go up (parent) until we find an instance of 'clazz'
	 */
	@SuppressWarnings("rawtypes")
	public Interval findParent(Class clazz) {
		if (this.getClass().equals(clazz)) return this;
		if ((parent != null) && (parent instanceof Marker)) return ((Marker) parent).findParent(clazz);
		return null;
	}

	public Chromosome getChromosome() {
		return (Chromosome) findParent(Chromosome.class);
	}

	/**
	 * Find chromosome name
	 */
	public String getChromosomeName() {
		Chromosome chromo = getChromosome();
		if (chromo != null) return chromo.getId();
		return "";
	}

	public String getChromosomeNameOri() {
		return chromosomeNameOri;
	}

	/**
	 * Find chromosome and return it's number
	 *
	 * @return Chromosome number if found, -1 otherwise
	 */
	public double getChromosomeNum() {
		Chromosome chromo = (Chromosome) findParent(Chromosome.class);
		if (chromo != null) return chromo.chromosomeNum;
		return -1;
	}

	public int getEnd() {
		return end;
	}

	/**
	 * Find genome
	 */
	public Genome getGenome() {
		return (Genome) findParent(Genome.class);
	}

	/**
	 * Find genome name
	 */
	public String getGenomeName() {
		Genome genome = (Genome) findParent(Genome.class);
		if (genome != null) return genome.getId();
		return "";
	}

	public String getId() {
		return id;
	}

	public Interval getParent() {
		return parent;
	}

	public int getStart() {
		return start;
	}

	public String getStrand() {
		return strandMinus ? "-" : "+";
	}

	@Override
	public int hashCode() {
		int hashCode = getChromosomeName().hashCode();
		hashCode = hashCode * 31 + start;
		hashCode = hashCode * 31 + end;
		hashCode = hashCode * 31 + (strandMinus ? -1 : 1);
		if (id != null) hashCode = hashCode * 31 + id.hashCode();
		return hashCode;
	}

	/**
	 * Return true if this intersects '[iStart, iEnd]'
	 */
	public boolean intersects(int iStart, int iEnd) {
		return (iEnd >= start) && (iStart <= end);
	}

	/**
	 * Return true if this intersects 'interval'
	 */
	public boolean intersects(Interval interval) {
		return (interval.getEnd() >= start) && (interval.getStart() <= end);
	}

	/**
	 * @return  true if this interval contains point (inclusive)
	 */
	public boolean intersects(long point) {
		return (start <= point) && (point <= end);
	}

	/**
	 * Do the intervals intersect?
	 * @return  return true if this intersects 'interval'
	 */
	public boolean intersects(Marker interval) {
		if (!interval.getChromosomeName().equals(getChromosomeName())) return false;
		return (interval.getEnd() >= start) && (interval.getStart() <= end);
	}

	/**
	 * How much do intervals intersect?
	 * @return  number of bases these intervals intersect
	 */
	public int intersectSize(Marker interval) {
		if (!interval.getChromosomeName().equals(getChromosomeName())) return 0;

		int start = Math.max(this.start, interval.getStart());
		int end = Math.min(this.end, interval.getEnd());

		if (end < start) return 0;
		return (end - start) + 1;
	}

	/**
	 * Is this interval part of a circular chromosome and it spans
	 * the 'chromosome zero / chromosome end' line?
	 */
	public boolean isCircular() {
		Chromosome chr = getChromosome();
		return start < 0 // Negative coordinates?
				|| (start > end) // Start before end?
				|| (end > chr.getEnd()) // Ends after chromosome end?
		;
	}

	public boolean isSameChromo(Marker interval) {
		return interval.getChromosomeName().equals(getChromosomeName());
	}

	public boolean isStrandMinus() {
		return strandMinus;
	}

	public boolean isStrandPlus() {
		return !strandMinus;
	}

	public boolean isValid() {
		return start <= end;
	}

	public void setChromosomeNameOri(String chromosomeNameOri) {
		this.chromosomeNameOri = chromosomeNameOri;
	}

	public void setEnd(int end) {
		if (end < start) throw new RuntimeException("Trying to set end before start:\n\tstart: " + start + "\n\tend : " + end + "\n\t" + this);
		this.end = end;
	}

	public void setId(String id) {
		this.id = id;
	}

	public void setParent(Interval parent) {
		this.parent = parent;
	}

	public void setStart(int start) {
		this.start = start;
	}

	public void setStrandMinus(boolean strand) {
		strandMinus = strand;
	}

	public void shiftCoordinates(int shift) {
		start += shift;
		end += shift;
	}

	public int size() {
		return end - start + 1;
	}

	/**
	 * To string as a simple "chr:start-end" format
	 */
	public String toStr() {
		return getClass().getSimpleName() //
				+ "_" + getChromosomeName() //
				+ ":" + (start + 1) //
				+ "-" + (end + 1) //
		;
	}

	@Override
	public String toString() {
		return start + "-" + end //
				+ ((id != null) && (id.length() > 0) ? " '" + id + "'" : "");
	}

	/**
	 * Show it as an ASCII art
	 */
	public String toStringAsciiArt(int maxLen) {
		StringBuilder sb = new StringBuilder();

		for (int i = 0; i < maxLen; i++) {
			if ((i >= start) && (i <= end)) sb.append('-');
			else sb.append(' ');
		}

		return sb.toString();
	}

}