jpayne@68: package aligner;
jpayne@68: 
jpayne@68: import prok.GeneCaller;
jpayne@68: import stream.Read;
jpayne@68: 
jpayne@68: public class Alignment implements Comparable<Alignment>{
jpayne@68: 	
jpayne@68: 	public Alignment(Read r_){
jpayne@68: 		r=r_;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public int compareTo(Alignment o) {
jpayne@68: 		return id>o.id ? 1 : id<o.id ? -1 : r.length()>o.r.length() ? 1 : r.length()<o.r.length() ? -1 : 0;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public float align(byte[] ref){
jpayne@68: 		id=align(r, ref);
jpayne@68: 		match=r.match;
jpayne@68: 		start=r.start;
jpayne@68: 		stop=r.stop;
jpayne@68: 		return id;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public static float align(Read r, byte[] ref){
jpayne@68: 		SingleStateAlignerFlat2 ssa=GeneCaller.getSSA();
jpayne@68: 		final int a=0, b=ref.length-1;
jpayne@68: 		int[] max=ssa.fillUnlimited(r.bases, ref, a, b, 0);
jpayne@68: 		if(max==null){return 0;}
jpayne@68: 		
jpayne@68: 		final int rows=max[0];
jpayne@68: 		final int maxCol=max[1];
jpayne@68: 		final int maxState=max[2];
jpayne@68: 		
jpayne@68: 		//returns {score, bestRefStart, bestRefStop} 
jpayne@68: 		//padded: {score, bestRefStart, bestRefStop, padLeft, padRight};
jpayne@68: 		int[] score=ssa.score(r.bases, ref, a, b, rows, maxCol, maxState);
jpayne@68: 		int rstart=score[1];
jpayne@68: 		int rstop=score[2];
jpayne@68: 		r.start=rstart;
jpayne@68: 		r.stop=rstop;
jpayne@68: 		
jpayne@68: 		byte[] match=ssa.traceback(r.bases, ref, a, b, rows, maxCol, maxState);
jpayne@68: 		float id=Read.identity(match);
jpayne@68: 		return id;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public final Read r;
jpayne@68: 	public float id=-1;
jpayne@68: 	public byte[] match;
jpayne@68: 	public int start;
jpayne@68: 	public int stop;
jpayne@68: 	
jpayne@68: }