--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/edu/unc/genomics/nucleosomes/NucleosomeCall.java	Mon Feb 13 22:12:06 2012 -0500
@@ -0,0 +1,174 @@
+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;
+			}
+		}
+		
+	}
+
+}