SeqHit.java

package org.seqcode.data.seqdata;

import org.seqcode.deepseq.StrandedBaseCount;
import org.seqcode.genome.Genome;
import org.seqcode.genome.location.StrandedRegion;

public class SeqHit extends StrandedRegion {

	private double weight = 1.0;

	public SeqHit(Genome g, String chrom, int start, int end, char strand, double weight) {
		super(g,chrom,start,end,strand);
		this.weight = weight;
	}
  
	public SeqHit(Genome g, String chrom, StrandedBaseCount sbc) {
		super(g,chrom,
				sbc.getStrand()=='+' ? sbc.getCoordinate() : sbc.getCoordinate()-1,
				sbc.getStrand()=='+' ? sbc.getCoordinate()+1 : sbc.getCoordinate(),
				sbc.getStrand());
	    this.weight = sbc.getCount();
	}

	public double getWeight() {
		return weight;
	}

	
	public void setWeight(double weight) {
		this.weight = weight;
	}

	public String toString() { 
		return String.format("%s:%c", getLocationString(), getStrand());
	}

	public SeqHit extendHit(int ext) { 
		if(getStrand() == '+') { 
			return new SeqHit(getGenome(), getChrom(), getStart(), getEnd() + ext, getStrand(), weight);
		} else { 
			return new SeqHit(getGenome(), getChrom(), getStart() - ext, getEnd(), getStrand(), weight);
		}
	}
	public SeqHit fivePrime() { 
		if(getStrand() == '+') { 
	      return new SeqHit(getGenome(), getChrom(), getStart(), getStart(), getStrand(), weight);
	    } else { 
	      return new SeqHit(getGenome(), getChrom(), getEnd(), getEnd(), getStrand(), weight);
	    }
	}
  
	public SeqHit shiftExtendHit(int ext, int shift) { 
		if(getStrand() == '+') { 
			return new SeqHit(getGenome(), getChrom(), getStart()+shift-(ext/2), getEnd()+shift+(ext/2), getStrand(), weight);
		} else { 
			return new SeqHit(getGenome(), getChrom(), getStart()-shift-(ext/2), getEnd()-shift+(ext/2), getStrand(), weight);
		}
	}

	public int hashCode() { 
		int code = 17;
		code += super.hashCode(); code *= 37;
		return code; 
	}

	public boolean equals(Object o) { 
		return this == o;
	}  
}