package org.seqcode.deepseq;

import java.util.ArrayList;

import java.util.List;

/**

* Read represents the sequence tag which is generated by a short read sequencer. <br>

* Each <tt>Read</tt> can map to different locations (<tt>ReadHits</tt>) on

* the genome (if non-unique hits are supported)

*

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

* @author mahony

*

*/

public class Read {

protected List<ReadHit> hits = new ArrayList<ReadHit>();

protected float numHits=0; //have to store this separately because we can't always trust the size of the hits list

public Read(){

}

//Accessor

public double getNumHits(){return (double)hits.size();}

public void setNumHits(float n){

numHits=n;

float w = 1/numHits;

for(ReadHit x : hits){

x.setWeight(w);

}

}

public void addHit(ReadHit h){addHit(h, true);}

public void addHit(ReadHit h, boolean updateWeight){

//First add the hit

hits.add(h);

numHits++;

if(updateWeight){

//Now propagate the effect of adding the hit to the read weights

float w = 1/numHits;

for(ReadHit x : hits){

x.setWeight(w);

}

}

}

public List<ReadHit> getHits(){return hits;}

}