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