--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/prok/Feature.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,93 @@
+package prok;
+
+import java.util.Comparator;
+
+/**
+ * Represents a genomic feature such as a gene, with start, stop, and strand.
+ * @author Brian Bushnell
+ * @date Sep 24, 2018
+ *
+ */
+abstract class Feature extends ProkObject implements Comparable<Feature>{
+	
+	/*--------------------------------------------------------------*/
+	/*----------------         Constructor          ----------------*/
+	/*--------------------------------------------------------------*/
+
+	public Feature(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(Feature 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();
+	
+	/*--------------------------------------------------------------*/
+	/*----------------            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<Feature> {
+
+		private FeatureComparatorScore(){}
+		
+		@Override
+		public int compare(Feature a, Feature b) {
+			float sa=a.score(), sb=b.score();
+			if(sa<sb){return 1;}
+			if(sb<sa){return -1;}
+			return a.compareTo(b);
+		}
+		
+	}
+	
+}