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package prok;
import java.util.Comparator;
import structures.Feature;
/**
* Represents a genomic feature such as a gene, with start, stop, and strand.
* @author Brian Bushnell
* @date Sep 24, 2018
*
*/
abstract class PFeature extends ProkObject implements Comparable<PFeature>, Feature {
/*--------------------------------------------------------------*/
/*---------------- Constructor ----------------*/
/*--------------------------------------------------------------*/
public PFeature(String scafName_, int start_, int stop_, int strand_, int scaflen_){
scafName=scafName_;
start=start_;
stop=stop_;
strand=strand_;
scaflen=scaflen_;
}
/*--------------------------------------------------------------*/
/*---------------- Methods ----------------*/
/*--------------------------------------------------------------*/
public final void flip(){
int a=scaflen-start-1;
int b=scaflen-stop-1;
start=b;
stop=a;
flipped=flipped^1;
}
public final int currentStrand(){
return strand^flipped;
}
public final int length(){
return stop-start+1;
}
@Override
public final int compareTo(PFeature f) {
int x=scafName.compareTo(f.scafName);
if(x!=0){return x;}
if(stop!=f.stop){return stop-f.stop;}
return start-f.start;
}
public final int flipped(){return flipped;}
public abstract float score();
@Override
public final int start() {return start;}
@Override
public final int stop() {return stop;}
@Override
public final int strand() {return strand;}
@Override
public final String name() {return null;}
@Override
public final String seqid() {return scafName;}
/*--------------------------------------------------------------*/
/*---------------- Fields ----------------*/
/*--------------------------------------------------------------*/
public final String scafName;
public final int strand;
public final int scaflen;
/** 0-based position of first base of feature **/
public int start;
/** 0-based position of last base of feature **/
public int stop;
private int flipped=0;
/*--------------------------------------------------------------*/
/*---------------- Nested Classes ----------------*/
/*--------------------------------------------------------------*/
@SuppressWarnings("synthetic-access")
public static final FeatureComparatorScore featureComparatorScore=new FeatureComparatorScore();
//Sorts so that high scores are first.
private static class FeatureComparatorScore implements Comparator<PFeature> {
private FeatureComparatorScore(){}
@Override
public int compare(PFeature a, PFeature b) {
float sa=a.score(), sb=b.score();
if(sa<sb){return 1;}
if(sb<sa){return -1;}
return a.compareTo(b);
}
}
}
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