Exon.java

/* Copyright (c)  2016   The Salk Institute for Biological Studies.
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*/
/**
 * Defines a span of overlapping reads.
 * @author Maxim Shokhirev (C) 2015-2018
 *
 */
public class Exon implements Comparable<Exon>, Filterable
{
	int start, end;
	float count = 0;
	boolean plus;
	
	public Exon(int start, int end,boolean plus, float count)
	{
		this.start = start; this.end = end; this.plus = plus;this.count = count;
	}

	public double getDensity()
	{
		return (1.0*count)/Math.max(1,(end-start));
	}
	
	public int getScore()
	{
		return (int) Math.max(1,Math.min(1000,getDensity()*1000));
	}

	@Override
	public int compareTo(Exon o) {
		if(plus)
		{
			if(start < o.start)
			{
				if(end < o.start)
					return -2;   //start is less and not overlapping
				else
					return -1;   //start is less but still overlapping
			}
			else if(start > o.start)
			{
				if(start > o.end)
					return 2;  //start is greater and not overlapping
				else return 1;  //start is greater but still overlapping
			}
			else  //start the same
			{
				if(end < o.end)  //this one is shorter so it should go first
					return -1;
				else if(end > o.end)return 1;  
				else return 0;
			}
		}
		else
		{
			if(end < o.end)
			{
				if(end >= o.start)
					return 2;   //no overlap
				else
					return 1;   //overlap
			}
			else if(end > o.end) 
			{
				if(start > o.end)
					return -2;  //no overlap
				else return -1;  //overlap
			}
			else  //end the same
			{
				if(start > o.start)  //this one is shorter so it should go first
					return -1;
				else if(start < o.start)return 1;  
				else return 0;  //exactly the same exon
			}
		}
	}

	@Override
	public boolean filter() {
		if(Math.abs(end-start) >= 5 && count > 1)
			return false;
		return true;
	}
	@Override
	public String toString()
	{
		if(plus)
			return start+"-"+end+" + "+count;
		else return start+"-"+end+" - "+count;
	}
	
	public boolean overlaps(int start2, int end2, int ext)
	{
		double x = Math.min(end2, end);
		double y = Math.max(start2,start);
		if(x-y < -ext) return false;
		else return true;
	}
	
	
	public boolean overlaps(int start2, int end2)
	{
		double x = Math.min(end2, end);
		double y = Math.max(start2,start);
		if(x-y < 0) return false;
		else return true;
	}

	public double computeOverlapSize(Exon e) {
		double x = Math.min(e.end, end);
		double y = Math.max(e.start,start);
		if(x-y < 0) return 0;
		else return x-y;
	}
	
}