--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/bloom/KCountArray5MT.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,515 @@
+package bloom;
+
+import java.util.Arrays;
+import java.util.Random;
+import java.util.concurrent.ArrayBlockingQueue;
+
+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 KCountArray5MT extends KCountArray {
+	
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -5456926900022701212L;
+
+	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;
+		
+		KCountArray5MT kca=new KCountArray5MT(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 KCountArray5MT(long cells_, int bits_, int gap_, int hashes_){
+		super(cells_, bits_);
+//		verbose=false;
+		long words=cells/cellsPerWord;
+		assert(words/numArrays<=Integer.MAX_VALUE);
+		wordsPerArray=(int)(words/numArrays);
+		cellsPerArray=cells/numArrays;
+		cellMod=cellsPerArray-1;
+		hashes=hashes_;
+//		System.out.println("cells="+cells+", words="+words+", wordsPerArray="+wordsPerArray+", numArrays="+numArrays+", hashes="+hashes);
+//		assert(false);
+		matrix=new int[numArrays][];
+		assert(hashes>0 && hashes<=hashMasks.length);
+	}
+	
+	@Override
+	public int read(final long rawKey){
+		assert(finished);
+		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;
+	}
+	
+	int readHashed(long key){
+		assert(finished);
+		if(verbose){System.err.print("Reading hashed key "+key);}
+//		System.out.println("key="+key);
+		int arrayNum=(int)(key&arrayMask);
+		key=(key>>>arrayBits)%(cellMod);
+//		System.out.println("array="+arrayNum);
+//		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.");
+	}
+	
+	//Slow
+	@Override
+	public void increment(final long rawKey, int amt){
+		for(int i=0; i<amt; i++){increment0(rawKey);}
+	}
+	
+	public void increment0(final long rawKey){
+		if(verbose){System.err.println("\n*** Incrementing raw key "+rawKey+" ***");}
+
+		buffer[bufferlen]=hash(rawKey, 0);
+		bufferlen++;
+
+		if(bufferlen>=buffer.length){
+
+			if(verbose){System.err.println("Moving array.");}
+
+			for(int w=0; w<writers.length; w++){
+				writers[w].add(buffer);
+			}
+			bufferlen=0;
+			buffer=new long[buffer.length];
+			if(verbose){System.err.println("Moved.");}
+		}
+
+	}
+	
+
+	@Override
+	public synchronized void increment(long[] keys){
+		for(int i=0; i<keys.length; i++){
+			keys[i]=hash(keys[i],0);
+		}
+		for(int w=0; w<writers.length; w++){
+			writers[w].add(keys);
+		}
+	}
+	
+	/** Returns unincremented value */
+	@Override
+	public int incrementAndReturnUnincremented(long key, int incr){
+		throw new RuntimeException("Operation not supported.");
+	}
+	
+	@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(KCountArray5MT.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]++;
+		}
+		
+	}
+	
+	
+	@Override
+	public void initialize(){
+		for(int i=0; i<writers.length; i++){
+			writers[i]=new WriteThread(i);
+			writers[i].start();
+
+			while(!writers[i].isAlive()){
+				System.out.print(".");
+			}
+		}
+	}
+	
+	@Override
+	public void shutdown(){
+		if(finished){return;}
+		synchronized(this){
+			if(finished){return;}
+			
+			//Clear buffer
+			if(bufferlen<buffer.length){
+				buffer=Arrays.copyOf(buffer, bufferlen);
+			}
+			
+			if(buffer.length>0){
+				for(int i=0; i<writers.length; i++)
+				writers[i].add(buffer);
+			}
+			buffer=null;
+			bufferlen=0;
+			
+			
+			//Add poison
+			for(WriteThread wt : writers){
+				wt.add(poison);
+			}
+			
+			//Wait for termination
+			for(WriteThread wt : writers){
+//				System.out.println("wt"+wt.num+" is alive: "+wt.isAlive());
+				while(wt.isAlive()){
+//					System.out.println("wt"+wt.num+" is alive: "+wt.isAlive());
+					try {
+						wt.join(10000);
+					} catch (InterruptedException e) {
+						// TODO Auto-generated catch block
+						e.printStackTrace();
+					}
+					if(wt.isAlive()){System.err.println(wt.getClass().getCanonicalName()+" is taking a long time to die.");}
+				}
+				cellsUsed+=wt.cellsUsedPersonal;
+//				System.out.println("cellsUsed="+cellsUsed);
+			}
+			
+			assert(!finished);
+			finished=true;
+		}
+	}
+	
+	private class WriteThread extends Thread{
+		
+		public WriteThread(int tnum){
+			num=tnum;
+		}
+		
+		@Override
+		public void run(){
+			assert(matrix[num]==null);
+			array=new int[wordsPerArray]; //Makes NUMA systems use local memory.
+//			assert(false);
+			matrix[num]=array;
+			
+//			assert(num==1);
+			
+			long[] keys=null;
+			while(!shutdown){
+//				assert(false);
+
+				if(verbose){System.err.println(" - Reading keys for wt"+num+".");}
+				while(keys==null){
+//					System.out.println("Searching for keys.");
+					try {
+						keys=writeQueue.take();
+					} catch (InterruptedException e) {
+						// TODO Auto-generated catch block
+						e.printStackTrace();
+					}
+//					System.out.println("*******************************************Found keys: "+keys.length);
+//					assert(false);
+				}
+				if(keys==poison){
+//					assert(false) : "  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~0  ";
+					shutdown=true;
+				}else{
+//					assert(false) : "  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~1  ";
+					for(long rawKey : keys){
+//						assert(false) : "  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~2  ";
+						if(verbose){System.err.println("Writer "+num+" considering raw key "+rawKey);}
+						long key2=rawKey;
+//						int y=read(rawKey);
+						if((key2&arrayMask)==num){
+							int x=incrementHashedLocal(key2);
+							assert(x>=0) : "i="+0+", original=?, new should be >=0, new="+readHashed(key2)+", max="+maxValue+", key="+rawKey;
+							if(verbose){System.err.println("postIncr value="+readHashed(key2));}
+
+//							assert(false) : "  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~4  ";
+						}
+						
+						for(int i=1; i<hashes; i++){
+							key2=Long.rotateRight(key2, hashBits);
+							key2=hash(key2, i);
+//							assert(false) : "  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~3  ";
+							if(verbose){System.err.println("rawKey="+rawKey+", i="+i+", key2="+key2+", value="+readHashed(key2));}
+							if((key2&arrayMask)==num){
+								int x=incrementHashedLocal(key2);
+								assert(x>=0) : "i="+i+", original=?, new should be >=0, new="+readHashed(key2)+", max="+maxValue+", key="+rawKey;
+								if(verbose){System.err.println("postIncr value="+readHashed(key2));}
+
+//								assert(false) : "  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~4  ";
+							}
+
+//							assert(false) : "  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~5  ";
+						}
+//						int z=read(rawKey);
+//						assert(hashes!=1 || !b || z==maxValue || z==y+1) : "b="+b+", y="+y+", z="+z+", rawKey="+rawKey+", num="+num;
+					}
+				}
+//				System.out.println(" -- Read keys for   wt"+num+". poison="+(keys==poison)+", len="+keys.length);
+				if(verbose){System.err.println(" -- Read keys for   wt"+num+". (success)");}
+				keys=null;
+				if(verbose){System.err.println("shutdown="+shutdown);}
+			}
+
+//			System.out.println(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I died: "+shutdown+", "+(keys==null)+".");
+//			assert(false) : ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I died: "+shutdown+", "+(keys==null)+".";
+			
+			array=null;
+		}
+		
+		void add(long[] keys){
+//			assert(isAlive());
+			
+//			assert(!shutdown);
+//			if(shutdown){return;}
+			
+			if(verbose){System.err.println(" + Adding keys to wt"+num+".");}
+			boolean success=false;
+			while(!success){
+				try {
+					writeQueue.put(keys);
+					success=true;
+				} catch (InterruptedException e) {
+					// TODO Auto-generated catch block
+					e.printStackTrace();
+				}
+			}
+			if(verbose){System.err.println(" ++ Added keys to wt"+num+". (success)");}
+		}
+		
+		private int incrementHashedLocal(final long key_){
+			if(verbose){System.err.println("\n*** wt"+num+" incrementing hashed key "+key_+" ***");}
+			assert((key_&arrayMask)==num);
+			long key=(key_>>>arrayBits)%(cellMod);
+			int index=(int)(key>>>indexShift);
+			int word=array[index];
+			int cellShift=(int)(cellBits*key);
+			int value=((word>>>cellShift)&valueMask);
+			if(value==0){cellsUsedPersonal++;}
+			value=min(value+1, maxValue);
+			word=(value<<cellShift)|(word&~((valueMask)<<cellShift));
+			array[index]=word;
+			if(verbose){System.err.println("\n*** wt"+num+" Incremented hashed key "+key_+".  Value = "+readHashed(key_)+" ***");}
+			return value;
+		}
+		
+		private int[] array;
+		private final int num;
+		public long cellsUsedPersonal=0;
+		
+		public ArrayBlockingQueue<long[]> writeQueue=new ArrayBlockingQueue<long[]>(8);
+		public boolean shutdown=false;
+		
+	}
+	
+	
+	public long cellsUsed(){return cellsUsed;}
+	
+	private boolean finished=false;
+	
+	private long cellsUsed;
+	final int[][] matrix;
+	private final WriteThread[] writers=new WriteThread[numArrays];
+	final int hashes;
+	final int wordsPerArray;
+	private final long cellsPerArray;
+	final long cellMod;
+	private final long[][] hashMasks=makeMasks(8, hashArrayLength);
+	
+	private long[] buffer=new long[2000];
+	private int bufferlen=0;
+	
+	private static final int hashBits=6;
+	private static final int hashArrayLength=1<<hashBits;
+	private static final int hashCellMask=hashArrayLength-1;
+	static final long[] poison=new long[0];
+	
+	private static long counter=0;
+	
+}