annotate java-genomics-toolkit/src/edu/unc/genomics/nucleosomes/NucleosomeCall.java @ 0:1daf3026d231

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package edu.unc.genomics.nucleosomes;

import java.util.Comparator;

import edu.unc.genomics.ValuedInterval;
import edu.unc.genomics.io.IntervalFileFormatException;

/**
 * @author timpalpant
 *
 */
public class NucleosomeCall extends ValuedInterval implements Comparable<NucleosomeCall> {

	private static final long serialVersionUID = 6522702303121259979L;
	
	private int dyad;
	private double dyadStdev;
	private double dyadMean;
	private double conditionalPosition;
	private int length;
	private double lengthStdev;

	/**
	 * @param chr
	 * @param start
	 * @param stop
	 */
	public NucleosomeCall(String chr, int start, int stop) {
		super(chr, start, stop);
	}
	
	public static NucleosomeCall parse(String line) {
		if (line.startsWith("#")) return null;
		
		String[] entry = line.split("\t");
		if (entry.length < 10) {
			throw new IntervalFileFormatException("Invalid nucleosome call has < 10 columns");
		}
		
		String chr = entry[0];
		int start = Integer.parseInt(entry[1]);
		int stop = Integer.parseInt(entry[2]);
		
		NucleosomeCall call = new NucleosomeCall(chr, start, stop);
		call.setLength(Integer.parseInt(entry[3]));
		call.setLengthStdev(Double.parseDouble(entry[4]));
		call.setDyad(Integer.parseInt(entry[5]));
		call.setDyadStdev(Double.parseDouble(entry[6]));
		call.setConditionalPosition(Double.parseDouble(entry[7]));
		call.setDyadMean(Double.parseDouble(entry[8]));
		call.setValue(Double.parseDouble(entry[9]));
		
		return call;
	}
	
	@Override
	public String toString() {
		return chr+"\t"+start+"\t"+stop+"\t"+length()+"\t"+lengthStdev+"\t"+dyad+"\t"+dyadStdev+"\t"+conditionalPosition+"\t"+dyadMean+"\t"+occupancy();
	}

	/**
	 * @return the dyad
	 */
	public int getDyad() {
		return dyad;
	}

	/**
	 * @param dyad the dyad to set
	 */
	public void setDyad(int dyad) {
		this.dyad = dyad;
	}

	/**
	 * @return the dyadStdev
	 */
	public double getDyadStdev() {
		return dyadStdev;
	}

	/**
	 * @param dyadStdev the dyadStdev to set
	 */
	public void setDyadStdev(double dyadStdev) {
		this.dyadStdev = dyadStdev;
	}

	/**
	 * @return the dyadMean
	 */
	public double getDyadMean() {
		return dyadMean;
	}

	/**
	 * @param dyadMean the dyadMean to set
	 */
	public void setDyadMean(double dyadMean) {
		this.dyadMean = dyadMean;
	}

	/**
	 * @return the conditionalPosition
	 */
	public double getConditionalPosition() {
		return conditionalPosition;
	}

	/**
	 * @param conditionalPosition the conditionalPosition to set
	 */
	public void setConditionalPosition(double conditionalPosition) {
		this.conditionalPosition = conditionalPosition;
	}

	/**
	 * @return the length
	 */
	public int getLength() {
		return length;
	}

	/**
	 * @param length the length to set
	 */
	public void setLength(int length) {
		this.length = length;
	}

	/**
	 * @return the lengthStdev
	 */
	public double getLengthStdev() {
		return lengthStdev;
	}

	/**
	 * @param lengthStdev the lengthStdev to set
	 */
	public void setLengthStdev(double lengthStdev) {
		this.lengthStdev = lengthStdev;
	}
	
	public double occupancy() {
		return value;
	}
	
	public void setOccupancy(double value) {
		this.value = value;
	}
	
	@Override
	public int compareTo(NucleosomeCall o) {
		DyadComparator comparator = new DyadComparator();
		return comparator.compare(this, o);
	}
	
	public static class DyadComparator implements Comparator<NucleosomeCall> {

		@Override
		public int compare(NucleosomeCall o1, NucleosomeCall o2) {
			if (o1.getDyad() == o2.getDyad()) {
				return 0;
			} else if (o1.getDyad() < o2.getDyad()) {
				return -1;
			} else {
				return 1;
			}
		}
		
	}

}