--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/bloom/KCountArray4.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,376 @@
+package bloom;
+
+import java.util.Random;
+
+import shared.Shared;
+import shared.Timer;
+
+
+/**
+ * 
+ * Uses hashing rather than direct-mapping to support longer kmers.
+ * 
+ * @author Brian Bushnell
+ * @date Aug 17, 2012
+ *
+ */
+public class KCountArray4 extends KCountArray {
+	
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -1418539960644885681L;
+
+	public static void main(String[] args){
+		long cells=Long.parseLong(args[0]);
+		int bits=Integer.parseInt(args[1]);
+		int gap=Integer.parseInt(args[2]);
+		int hashes=Integer.parseInt(args[3]);
+		
+		verbose=false;
+		
+		KCountArray4 kca=new KCountArray4(cells, bits, gap, hashes);
+		
+		System.out.println(kca.read(0));
+		kca.increment(0);
+		System.out.println(kca.read(0));
+		kca.increment(0);
+		System.out.println(kca.read(0));
+		System.out.println();
+		
+		System.out.println(kca.read(1));
+		kca.increment(1);
+		System.out.println(kca.read(1));
+		kca.increment(1);
+		System.out.println(kca.read(1));
+		System.out.println();
+		
+		System.out.println(kca.read(100));
+		kca.increment(100);
+		System.out.println(kca.read(100));
+		kca.increment(100);
+		System.out.println(kca.read(100));
+		kca.increment(100);
+		System.out.println(kca.read(100));
+		System.out.println();
+		
+
+		System.out.println(kca.read(150));
+		kca.increment(150);
+		System.out.println(kca.read(150));
+		System.out.println();
+		
+	}
+		
+	public KCountArray4(long cells_, int bits_, int gap_, int hashes_){
+		super(cells_, bits_);
+		long words=cells/cellsPerWord;
+		assert(words/numArrays<=Integer.MAX_VALUE);
+		int wordsPerArray=(int)(words/numArrays);
+		hashes=hashes_;
+//		System.out.println("cells="+cells+", words="+words+", wordsPerArray="+wordsPerArray+", numArrays="+numArrays+", hashes="+hashes);
+//		assert(false);
+		matrix=new int[numArrays][wordsPerArray];
+		assert(hashes>0 && hashes<=hashMasks.length);
+	}
+	
+	@Override
+	public int read(final long rawKey){
+		if(verbose){System.err.println("Reading raw key "+rawKey);}
+		long key2=hash(rawKey, 0);
+		int min=readHashed(key2);
+		for(int i=1; i<hashes && min>0; i++){
+			if(verbose){System.err.println("Reading. i="+i+", key2="+key2);}
+			key2=Long.rotateRight(key2, hashBits);
+			key2=hash(key2, i);
+			if(verbose){System.err.println("Rot/hash. i="+i+", key2="+key2);}
+			min=min(min, readHashed(key2));
+		}
+		return min;
+	}
+	
+	private int readHashed(long key){
+		if(verbose){System.err.print("Reading hashed key "+key);}
+		key=((key&Long.MAX_VALUE)%(cells-1));
+//		System.out.println("key="+key);
+		int arrayNum=(int)(key&arrayMask);
+//		System.out.println("array="+arrayNum);
+		key>>>=arrayBits;
+//		System.out.println("key2="+key);
+		int[] array=matrix[arrayNum];
+		int index=(int)(key>>>indexShift);
+//		assert(false) : indexShift;
+//		System.out.println("index="+index);
+		int word=array[index];
+//		System.out.println("word="+Integer.toHexString(word));
+		assert(word>>>(cellBits*key) == word>>>(cellBits*(key&cellMask)));
+//		int cellShift=(int)(cellBits*(key&cellMask));
+		int cellShift=(int)(cellBits*key);
+		if(verbose){System.err.println(", array="+arrayNum+", index="+index+", cellShift="+(cellShift%32)+", value="+((int)((word>>>cellShift)&valueMask)));}
+//		System.out.println("cellShift="+cellShift);
+		return (int)((word>>>cellShift)&valueMask);
+	}
+	
+	@Override
+	public void write(final long key, int value){
+		throw new RuntimeException("Not allowed for this class.");
+	}
+	
+	@Override
+	public void increment(final long rawKey, int incr){
+//		verbose=(rawKey==32662670693L);
+		if(verbose){System.err.println("\n*** Incrementing raw key "+rawKey+" ***");}
+//		verbose=true;
+		assert(incr>0);
+		
+		long key2=rawKey;
+		if(hashes==1){
+			key2=hash(key2, 0);
+			int x=incrementHashedIfAtMost(key2, incr, maxValue-1);
+			assert(x>=incr) : "original=?, new should be >="+(incr)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
+			//return x;
+		}
+		
+		final int min=read(rawKey);
+		if(min>=maxValue){return /*maxValue*/;}
+		
+		assert(key2==rawKey);
+		for(int i=0; i<hashes; i++){
+			key2=hash(key2, i);
+			if(verbose){System.err.println("key2="+key2+", value="+readHashed(key2));}
+			int x=incrementHashedIfAtMost(key2, incr, min);
+			assert(x>=min+incr) : "i="+i+", original="+min+", new should be <="+(min+incr)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
+			if(verbose){System.err.println("postIncr value="+readHashed(key2));}
+//			assert(read(rawKey)<=min+incr) : "i="+i+", original="+min+", new should be <="+(min+incr)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
+//			assert(readHashed(key2)>=min+incr) : "i="+i+", original="+min+", new should be <="+(min+incr)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
+			key2=Long.rotateRight(key2, hashBits);
+		}
+//		assert(read(rawKey)==min+incr) : "original="+min+", new should be "+(min+incr)+", new="+read(rawKey)+", max="+maxValue;
+//		assert(false);
+		//return min(min+incr, maxValue);
+	}
+	
+	/** Returns unincremented value */
+	@Override
+	public int incrementAndReturnUnincremented(long rawKey, int incr){
+//		verbose=(rawKey==32662670693L);
+		if(verbose){System.err.println("\n*** Incrementing raw key "+rawKey+" ***");}
+//		verbose=true;
+		assert(incr>0);
+		
+		long key2=rawKey;
+		if(hashes==1){
+			key2=hash(key2, 0);
+			int x=incrementHashedIfAtMost(key2, incr, maxValue-1);
+			assert(x>=incr) : "original=?, new should be >="+(incr)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
+			return x;
+		}
+		
+		final int min=read(rawKey);
+		if(min>=maxValue){return maxValue;}
+		
+		assert(key2==rawKey);
+		for(int i=0; i<hashes; i++){
+			key2=hash(key2, i);
+			if(verbose){System.err.println("key2="+key2+", value="+readHashed(key2));}
+			int x=incrementHashedIfAtMost(key2, incr, min);
+			assert(x>=min+incr) : "i="+i+", original="+min+", new should be <="+(min+incr)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
+			if(verbose){System.err.println("postIncr value="+readHashed(key2));}
+//			assert(read(rawKey)<=min+incr) : "i="+i+", original="+min+", new should be <="+(min+incr)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
+//			assert(readHashed(key2)>=min+incr) : "i="+i+", original="+min+", new should be <="+(min+incr)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
+			key2=Long.rotateRight(key2, hashBits);
+		}
+//		assert(read(rawKey)==min+incr) : "original="+min+", new should be "+(min+incr)+", new="+read(rawKey)+", max="+maxValue;
+//		assert(false);
+		return min;
+	}
+	
+	private int incrementHashedIfAtMost(long key, int incr, int lim){
+		if(verbose){System.err.print("incrementing hashed key "+key);}
+		key=((key&Long.MAX_VALUE)%(cells-1));
+		int arrayNum=(int)(key&arrayMask);
+		key>>>=arrayBits;
+		int[] array=matrix[arrayNum];
+		int index=(int)(key>>>indexShift);
+		int word=array[index];
+		int cellShift=(int)(cellBits*key);
+		int value=((word>>>cellShift)&valueMask);
+		if(verbose){System.err.println(", array="+arrayNum+", index="+index+", cellShift="+(cellShift%32)+", value="+value+", limit="+lim);}
+		if(value>lim){return value;}
+		if(value==0 && incr>0){cellsUsed++;}
+		value=min(value+incr, maxValue);
+		word=(value<<cellShift)|(word&~((valueMask)<<cellShift));
+		array[index]=word;
+		return value;
+	}
+	
+	private int incrementHashed(long key, int incr){
+		assert(incr>0);
+		int arrayNum=(int)(key&arrayMask);
+		key>>>=arrayBits;
+		int[] array=matrix[arrayNum];
+		int index=(int)(key>>>indexShift);
+		int word=array[index];
+		int cellShift=(int)(cellBits*key);
+		int value=((word>>>cellShift)&valueMask);
+		if(value==0 && incr>0){cellsUsed++;}
+		value=min(value+incr, maxValue);
+		word=(value<<cellShift)|(word&~((valueMask)<<cellShift));
+		array[index]=word;
+		return value;
+	}
+	
+	@Override
+	public long[] transformToFrequency(){
+		return transformToFrequency(matrix);
+	}
+	
+	@Override
+	public String toContentsString(){
+		StringBuilder sb=new StringBuilder();
+		sb.append("[");
+		String comma="";
+		for(int[] array : matrix){
+			for(int i=0; i<array.length; i++){
+				int word=array[i];
+				for(int j=0; j<cellsPerWord; j++){
+					int x=word&valueMask;
+					sb.append(comma);
+					sb.append(x);
+					word>>>=cellBits;
+					comma=", ";
+				}
+			}
+		}
+		sb.append("]");
+		return sb.toString();
+	}
+	
+	@Override
+	public double usedFraction(){return cellsUsed/(double)cells;}
+	
+	@Override
+	public double usedFraction(int mindepth){return cellsUsed(mindepth)/(double)cells;}
+	
+	@Override
+	public long cellsUsed(int mindepth){
+		long count=0;
+		for(int[] array : matrix){
+			if(array!=null){
+				for(int word : array){
+					while(word>0){
+						int x=word&valueMask;
+						if(x>=mindepth){count++;}
+						word>>>=cellBits;
+					}
+				}
+			}
+		}
+		return count;
+	}
+	
+	
+	@Override
+	final long hash(long key, int row){
+		int cell=(int)((Long.MAX_VALUE&key)%(hashArrayLength-1));
+//		int cell=(int)(hashCellMask&(key));
+		
+		if(row==0){//Doublehash only first time
+			key=key^hashMasks[(row+4)%hashMasks.length][cell];
+			cell=(int)(hashCellMask&(key>>4));
+//			cell=(int)(hashCellMask&(key>>hashBits));
+//			cell=(int)((Long.MAX_VALUE&key)%(hashArrayLength-1));
+		}
+		
+		return key^hashMasks[row][cell];
+	}
+	
+	/**
+	 * @param i
+	 * @param j
+	 * @return
+	 */
+	private static long[][] makeMasks(int rows, int cols) {
+		
+		long seed;
+		synchronized(KCountArray4.class){
+			seed=counter;
+			counter++;
+		}
+		
+		Timer t=new Timer();
+		long[][] r=new long[rows][cols];
+		Random randy=Shared.threadLocalRandom(seed);
+		for(int i=0; i<r.length; i++){
+			fillMasks(r[i], randy);
+		}
+		t.stop();
+		if(t.elapsed>200000000L){System.out.println("Mask-creation time: "+t);}
+		return r;
+	}
+	
+	private static void fillMasks(long[] r, Random randy) {
+//		for(int i=0; i<r.length; i++){
+//			long x=0;
+//			while(Long.bitCount(x&0xFFFFFFFF)!=16){
+//				x=randy.nextLong();
+//			}
+//			r[i]=(x&Long.MAX_VALUE);
+//		}
+		
+		final int hlen=(1<<hashBits);
+		assert(r.length==hlen);
+		int[] count1=new int[hlen];
+		int[] count2=new int[hlen];
+		final long mask=hlen-1;
+
+		for(int i=0; i<r.length; i++){
+			long x=0;
+			int y=0;
+			int z=0;
+			while(Long.bitCount(x&0xFFFFFFFFL)!=16){
+				x=randy.nextLong();
+				while(Long.bitCount(x&0xFFFFFFFFL)<16){
+					x|=(1L<<randy.nextInt(32));
+				}
+				while(Long.bitCount(x&0xFFFFFFFFL)>16){
+					x&=(~(1L<<randy.nextInt(32)));
+				}
+				while(Long.bitCount(x&0xFFFFFFFF00000000L)<16){
+					x|=(1L<<(randy.nextInt(32)+32));
+				}
+				while(Long.bitCount(x&0xFFFFFFFF00000000L)>16){
+					x&=(~(1L<<(randy.nextInt(32)+32)));
+				}
+				
+//				System.out.print(".");
+//				y=(((int)(x&mask))^i);
+				y=(((int)(x&mask)));
+				z=(int)((x>>hashBits)&mask);
+				if(count1[y]>0 || count2[z]>0){
+					x=0;
+				}
+			}
+//			System.out.println(Long.toBinaryString(x));
+			r[i]=(x&Long.MAX_VALUE);
+			count1[y]++;
+			count2[z]++;
+		}
+		
+	}
+	
+	public long cellsUsed(){return cellsUsed;}
+
+	private long cellsUsed;
+	private final int[][] matrix;
+	private final int hashes;
+	
+	
+	private static final int hashBits=6;
+	private static final int hashArrayLength=1<<hashBits;
+	private static final int hashCellMask=hashArrayLength-1;
+	private final long[][] hashMasks=makeMasks(8, hashArrayLength);
+	
+	private static long counter=0;
+	
+}