package org.seqcode.deepseq;

/**

* <tt>ReadHit</tt> represents the stranded coordinates of a mapped alignment hit

* Read and ReadHit are only used as a convenient way to represent multiply mapping reads when reading from certain file formats.

* <u>Note</u>: <br>

* 1) For a single read, we can have multiple (read) hits <br>

* 2) The <tt>start < end</tt> of the <tt>ReadHit</tt> ALWAYS <br>

* strand <tt>str</tt> is used to indicate whether the read is

* forward or reverse.

* @author mahony

*

*/

public class ReadHit{

protected String chrom;

protected int start, end;

protected char strand;

protected float weight;

public ReadHit(String c, int s, int e, char str){this(c,s,e,str, 1);}

public ReadHit(String c, int s, int e, char str, float w){

chrom = c;

start = s;

end = e;

strand = str;

weight = w;

}

//Accessors

public String getChrom(){return chrom;}

public int getStart(){return start;}

public int getEnd(){return end;}

public int getFivePrime(){return(strand=='+' ? start :end);}

public char getStrand(){return strand;}

public float getWeight(){return(weight);}

public void setWeight(float w){weight=w;}

public double getReadLength(){return(this.getEnd()-this.getStart()+1);}

public String toString(){return chrom+":"+getFivePrime()+":"+strand;}

}