--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/sketch/CompareBuffer.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,241 @@
+package sketch;
+
+import shared.Tools;
+import structures.AbstractBitSet;
+
+public class CompareBuffer extends SketchObject{
+	
+	public CompareBuffer(boolean makeBS){
+		if(makeBS){
+			cbs=AbstractBitSet.make(0, bitSetBits);
+		}else{
+			cbs=null;
+		}
+	}
+	
+	void set(final int hits_, final int multiHits_, final int unique2_, final int unique3_, final int noHits_,
+			final int contamHits_, final int contam2Hits_, final int multiContamHits_,
+			final int queryDivisor_, final int refDivisor_, final int querySize_, final int refSize_, 
+			final long depthSum_, final double depthSum2_, final long refHitSum_,
+			final int k1hits_, final int k1seenQ_, final int k1seenR_){
+		hits=hits_;
+		multiHits=multiHits_;
+		unique2=unique2_;
+		unique3=unique3_;
+		noHits=noHits_;
+		
+		contamHits=contamHits_;
+		contam2Hits=contam2Hits_;
+		multiContamHits=multiContamHits_;
+		
+		queryDivisor=queryDivisor_;
+		refDivisor=refDivisor_;
+		
+		querySize=querySize_;
+		refSize=refSize_;
+
+		depthSum=depthSum_;
+		depthSum2=(float)depthSum2_;
+		refHitSum=refHitSum_;
+
+		hits1=k1hits_;
+		qSeen1=k1seenQ_;
+		rSeen1=k1seenR_;
+	}
+	
+	void clear(){
+		hits=multiHits=0;
+		unique2=unique3=noHits=0;
+		contamHits=contam2Hits=multiContamHits=0;
+		refDivisor=queryDivisor=0;
+		refSize=querySize=0;
+		depthSum=0;
+		depthSum2=0;
+		refHitSum=0;
+		hits1=qSeen1=rSeen1=0;
+	}
+	
+	float depth(){
+		return depthSum<1 ? 0 : depthSum/Tools.max(1.0f, hits);
+	}
+	
+	float depth2(){
+		return depthSum2<=0 ? 0 : depthSum2/Tools.max(1.0f, hits);
+	}
+	
+	float avgRefHits(){
+		return refHitSum<1 ? 0 : refHitSum/Tools.max(1.0f, hits);
+	}
+	
+	/*--------------------------------------------------------------*/
+	
+	@Override
+	public String toString(){
+		return "hits="+hits+", refDivisor="+refDivisor+", queryDivisor="+queryDivisor+", refSize="+refSize+", querySize="+querySize+
+				", contamHits="+contamHits+", contam2Hits="+contam2Hits+", multiContamHits="+multiContamHits+", depthSum="+depthSum+", depthSum2="+depthSum2+
+				", hits="+hits+", multiHits="+multiHits+", unique2="+unique2+", unique3="+unique3+", noHits="+noHits;
+	}
+	
+	/*--------------------------------------------------------------*/
+	
+	final float wkid(){
+		final int div=minDivisor();
+		return hits/(float)div;
+	}
+	final float kid(){
+		final int div=maxDivisor();
+		return hits/(float)div;
+	}
+	final float aniOld(){
+		float wkid=wkid();
+		final float ani=wkidToAni(wkid);
+		return ani;
+	}
+	final float ani(){
+		final float ani;
+		if(k2>0 && useToValue2){
+			float ani1=ani1();
+			float ani2=ani2();
+//			ani=0.5f*(ani1+ani2);
+			ani=0.5f*(Tools.max(0.9f*ani2, ani1)+Tools.max(0.8f*ani1, ani2));
+//			return (ani1*qSeen1+ani2*qSeen2())/queryDivisor;
+		}else{
+			ani=aniOld();
+		}
+		
+//		System.err.println("ani="+ani+"aniOld="+aniOld()+", ani1="+ani1()+", ani2="+ani2()+", anid="+(float)aniDual()+"\n"
+////				+"gf="+(float)gf+", wkid1="+wkid1+", wkid2="+wkid2+"\n"
+//						+ "k1f="+k1Fraction()+", hits="+hits+", hits1="+hits1+", hits2="+hits2()+", qSeen1()="+qSeen1()+", rSeen1()="+rSeen1()+"\n"
+//								+ "qSeen2()="+qSeen2()+", rSeen2()="+rSeen2()+", minDivisor1()="+minDivisor1()+", minDivisor2()="+minDivisor2()+"\n");
+		return ani;
+	}
+
+	final float wkid1(){
+		final int div=minDivisor1();
+		return hits1()/(float)div;
+	}
+	final float kid1(){
+		final int div=maxDivisor1();
+		return hits1()/(float)div;
+	}
+	final float ani1(){
+		float wkid=wkid1();
+		final float ani=wkidToAniExact(wkid, k);
+		return ani;
+	}
+
+	final float wkid2(){
+		final int div=minDivisor2();
+		return hits2()/(float)div;
+	}
+	final float kid2(){
+		final int div=maxDivisor2();
+		return hits2()/(float)div;
+	}
+	final float ani2(){
+		assert(k2>0);
+		float wkid=wkid2();
+		final float ani=wkidToAniExact(wkid, k2);
+		return ani;
+	}
+	
+	final float aniDual(){
+		assert(k2>0);
+		float wkid1=wkid1();
+		float wkid2=wkid2();
+		float ratio=(wkid1/wkid2);
+		float exp=1f/(k-k2);//TODO - make this initialized
+		double ani=Math.pow(ratio, exp);
+		double gf=wkid2/Math.pow(ani, k2);
+		
+//		System.err.println("ani="+ani()+"aniOld="+aniOld()+", ani1="+ani1()+", ani2="+ani2()+", anid="+(float)ani+"\n"
+//				+"gf="+(float)gf+", wkid1="+wkid1+", wkid2="+wkid2+"\n"
+//						+ "k1f="+k1Fraction()+", hits="+hits+", hits1="+hits1+", hits2="+hits2()+", qSeen1()="+qSeen1()+", rSeen1()="+rSeen1()+"\n"
+//								+ "qSeen2()="+qSeen2()+", rSeen2()="+rSeen2()+", minDivisor1()="+minDivisor1()+", minDivisor2()="+minDivisor2()+"\n");
+		
+		return (float)ani;
+	}
+	
+	/*--------------------------------------------------------------*/
+	
+	int hits(){return hits;}
+	int multiHits(){return multiHits;}
+	int noHits(){return noHits;}
+	int unique2(){return unique2;}
+	int unique3(){return unique3;}
+
+	int contamHits(){return contamHits;}
+	int contam2Hits(){return contam2Hits;}
+	int multiContamHits(){return multiContamHits;}
+	
+	int queryDivisor(){return queryDivisor;}
+	int refDivisor(){return refDivisor;}
+	
+	int querySize(){return querySize;}
+	int refSize(){return refSize;}
+
+	long depthSum(){return depthSum;}
+	float depthSum2(){return depthSum2;}
+	long refHitSum(){return refHitSum;}
+	
+	/*--------------------------------------------------------------*/
+
+	int hits1(){return hits1;}
+	int qSeen1(){return qSeen1;}
+	int rSeen1(){return rSeen1;}
+	int minDivisor1(){return Tools.max(1, Tools.min(qSeen1, rSeen1));}
+	int maxDivisor1(){return Tools.max(1, qSeen1, rSeen1);}
+
+	int hits2(){return hits-hits1;}
+	int qSeen2(){return queryDivisor-qSeen1;}
+	int rSeen2(){return refDivisor-rSeen1;}
+	int minDivisor2(){return Tools.max(1, Tools.min(qSeen2(), rSeen2()));}
+	int maxDivisor2(){return Tools.max(1, qSeen2(), rSeen2());}
+	
+	/*--------------------------------------------------------------*/
+
+	//For WKID
+	int minDivisor(){return Tools.max(1, Tools.min(queryDivisor, refDivisor));}
+	//For KID
+	int maxDivisor(){return Tools.max(1, queryDivisor, refDivisor);}
+	int minSize(){return Tools.max(1, Tools.min(querySize, refSize));}
+	int maxSize(){return Tools.max(1, querySize, refSize);}
+
+	int uniqueHits(){return hits-multiHits;}
+	int uniqueContamHits(){return contamHits-multiContamHits;}
+	
+	float k1Fraction(){
+		return qSeen1/Tools.max(queryDivisor, 1f);
+	}
+	
+	/*--------------------------------------------------------------*/
+	
+	private int hits;
+	private int multiHits;
+	private int noHits;
+	private int unique2;
+	private int unique3;
+
+	private int contamHits;
+	private int contam2Hits;
+	private int multiContamHits;
+	
+	private int queryDivisor;
+	private int refDivisor;
+	
+	private int querySize;
+	private int refSize;
+
+	private long depthSum;
+	private float depthSum2;
+	private long refHitSum;
+
+	private int hits1;
+	private int qSeen1;
+	private int rSeen1;
+	
+	/*--------------------------------------------------------------*/
+
+	public final AbstractBitSet cbs; //Only for comparisons, not index
+	
+}