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package sort;
import dna.Data;
import ml.CellNet;
import ml.CellNetParser;
import ml.ScoreSequence;
import shared.Parse;
import stream.Read;
import structures.SeqCountM;
/**
* @author Brian Bushnell
* @date Oct 27, 2014
*
*/
public class ReadComparatorCrispr extends ReadComparator{
private ReadComparatorCrispr(){}
@Override
public int compare(Read r1, Read r2) {
return ascending*compare(r1, r2, true);
}
private SeqCountM getSCM(Read r) {
if(r.obj!=null) {return (SeqCountM)r.obj;}
String id=r.id;
int x=id.indexOf("count=");
int count=(x>=0 ? Parse.parseInt(id, x+6) : 0);
int y=id.indexOf("score=");
float score=(y>=0 ? Parse.parseFloat(id, y+6) : -1);
if((y<0 || score==-1) && net!=null) {//TODO
synchronized(ReadComparatorCrispr.class) {
score=ScoreSequence.score(r.bases, vec, 0, net);
}
}
SeqCountM scm=new SeqCountM(r.bases);
scm.count=count;
scm.score=score;
r.obj=scm;
return scm;
}
public int compare(Read r1, Read r2, boolean compareMates) {
SeqCountM s1=getSCM(r1);
SeqCountM s2=getSCM(r2);
int x=s1.compareTo(s2);
if(x!=0) {return x;}
// if(r1.numericID!=r2.numericID){return r1.numericID>r2.numericID ? 1 : -1;}
return r1.id.compareTo(r2.id);
}
@Override
public void setAscending(boolean asc) {
ascending=(asc ? 1 : -1);
}
public static synchronized void loadNet() {
if(net!=null) {return;}
setNet(CellNetParser.load(netFile));
}
public static synchronized void setNet(CellNet net_) {
if(net_==null) {
net=null;
vec=null;
return;
}
net=net_.copy(false);
vec=new float[net.numInputs()];
}
private static String netFile=Data.findPath("?crispr.bbnet.gz", false);
public static final ReadComparatorCrispr comparator=new ReadComparatorCrispr();
private static CellNet net=null;
private static float[] vec=null;
int ascending=1;
}
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