jpayne@68: package bloom;
jpayne@68: 
jpayne@68: import java.util.Arrays;
jpayne@68: import java.util.Random;
jpayne@68: import java.util.concurrent.ArrayBlockingQueue;
jpayne@68: 
jpayne@68: import shared.Shared;
jpayne@68: import shared.Timer;
jpayne@68: import structures.ByteBuilder;
jpayne@68: 
jpayne@68: 
jpayne@68: /**
jpayne@68:  * 
jpayne@68:  * Uses hashing rather than direct-mapping to support longer kmers.
jpayne@68:  * 
jpayne@68:  * @author Brian Bushnell
jpayne@68:  * @date Aug 17, 2012
jpayne@68:  *
jpayne@68:  */
jpayne@68: public class KCountArray6MT extends KCountArray {
jpayne@68: 	
jpayne@68: 	/**
jpayne@68: 	 * 
jpayne@68: 	 */
jpayne@68: 	private static final long serialVersionUID = -1524266549200637631L;
jpayne@68: 
jpayne@68: 	public static void main(String[] args){
jpayne@68: 		long cells=Long.parseLong(args[0]);
jpayne@68: 		int bits=Integer.parseInt(args[1]);
jpayne@68: 		int gap=Integer.parseInt(args[2]);
jpayne@68: 		int hashes=Integer.parseInt(args[3]);
jpayne@68: 		
jpayne@68: 		verbose=false;
jpayne@68: 		
jpayne@68: 		KCountArray6MT kca=new KCountArray6MT(cells, bits, gap, hashes);
jpayne@68: 		
jpayne@68: 		System.out.println(kca.read(0));
jpayne@68: 		kca.increment(0);
jpayne@68: 		System.out.println(kca.read(0));
jpayne@68: 		kca.increment(0);
jpayne@68: 		System.out.println(kca.read(0));
jpayne@68: 		System.out.println();
jpayne@68: 		
jpayne@68: 		System.out.println(kca.read(1));
jpayne@68: 		kca.increment(1);
jpayne@68: 		System.out.println(kca.read(1));
jpayne@68: 		kca.increment(1);
jpayne@68: 		System.out.println(kca.read(1));
jpayne@68: 		System.out.println();
jpayne@68: 		
jpayne@68: 		System.out.println(kca.read(100));
jpayne@68: 		kca.increment(100);
jpayne@68: 		System.out.println(kca.read(100));
jpayne@68: 		kca.increment(100);
jpayne@68: 		System.out.println(kca.read(100));
jpayne@68: 		kca.increment(100);
jpayne@68: 		System.out.println(kca.read(100));
jpayne@68: 		System.out.println();
jpayne@68: 		
jpayne@68: 
jpayne@68: 		System.out.println(kca.read(150));
jpayne@68: 		kca.increment(150);
jpayne@68: 		System.out.println(kca.read(150));
jpayne@68: 		System.out.println();
jpayne@68: 		
jpayne@68: 	}
jpayne@68: 		
jpayne@68: 	public KCountArray6MT(long cells_, int bits_, int gap_, int hashes_){
jpayne@68: 		super(cells_, bits_);
jpayne@68: //		verbose=false;
jpayne@68: 		long words=cells/cellsPerWord;
jpayne@68: 		assert(words/numArrays<=Integer.MAX_VALUE);
jpayne@68: 		wordsPerArray=(int)(words/numArrays);
jpayne@68: 		cellsPerArray=cells/numArrays;
jpayne@68: 		cellMod=cellsPerArray-1;
jpayne@68: 		hashes=hashes_;
jpayne@68: //		System.out.println("cells="+cells+", words="+words+", wordsPerArray="+wordsPerArray+", numArrays="+numArrays+", hashes="+hashes);
jpayne@68: //		assert(false);
jpayne@68: 		matrix=new int[numArrays][];
jpayne@68: 		assert(hashes>0 && hashes<=hashMasks.length);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public int read(final long rawKey){
jpayne@68: 		assert(finished);
jpayne@68: 		if(verbose){System.err.println("Reading raw key "+rawKey);}
jpayne@68: 
jpayne@68: 		long key1=hash(rawKey, 3);
jpayne@68: 		int arrayNum=(int)(key1&arrayMask);
jpayne@68: 		long key2=hash(rawKey, 0);
jpayne@68: 		
jpayne@68: 		int min=readHashed(key2, arrayNum);
jpayne@68: 		for(int i=1; i<hashes && min>0; i++){
jpayne@68: 			if(verbose){System.err.println("Reading. i="+i+", key2="+key2);}
jpayne@68: 			key2=Long.rotateRight(key2, hashBits);
jpayne@68: 			key2=hash(key2, i);
jpayne@68: 			if(verbose){System.err.println("Rot/hash. i="+i+", key2="+key2);}
jpayne@68: 			min=min(min, readHashed(key2, arrayNum));
jpayne@68: 		}
jpayne@68: 		return min;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	int readHashed(long key, int arrayNum){
jpayne@68: 		if(verbose){System.err.print("Reading hashed key "+key);}
jpayne@68: //		System.out.println("key="+key);
jpayne@68: //		int arrayNum=(int)(key&arrayMask);
jpayne@68: 		key=(key&Long.MAX_VALUE)%(cellMod);
jpayne@68: //		key=(key>>>(arrayBits+1))%(cellMod);
jpayne@68: //		System.out.println("array="+arrayNum);
jpayne@68: //		System.out.println("key2="+key);
jpayne@68: 		int[] array=matrix[arrayNum];
jpayne@68: 		int index=(int)(key>>>indexShift);
jpayne@68: //		assert(false) : indexShift;
jpayne@68: //		System.out.println("index="+index);
jpayne@68: 		int word=array[index];
jpayne@68: //		System.out.println("word="+Integer.toHexString(word));
jpayne@68: 		assert(word>>>(cellBits*key) == word>>>(cellBits*(key&cellMask)));
jpayne@68: //		int cellShift=(int)(cellBits*(key&cellMask));
jpayne@68: 		int cellShift=(int)(cellBits*key);
jpayne@68: 		if(verbose){System.err.println(", array="+arrayNum+", index="+index+", cellShift="+(cellShift%32)+", value="+((int)((word>>>cellShift)&valueMask)));}
jpayne@68: //		System.out.println("cellShift="+cellShift);
jpayne@68: 		return (int)((word>>>cellShift)&valueMask);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public void write(final long key, int value){
jpayne@68: 		throw new RuntimeException("Not allowed for this class.");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	//Slow
jpayne@68: 	@Override
jpayne@68: 	public void increment(final long rawKey, int amt){
jpayne@68: 		for(int i=0; i<amt; i++){increment0(rawKey);}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	public void increment0(final long rawKey){
jpayne@68: 		if(verbose){System.err.println("\n*** Incrementing raw key "+rawKey+" ***");}
jpayne@68: 
jpayne@68: 		long key1=hash(rawKey, 3);
jpayne@68: 
jpayne@68: 		if(verbose){System.err.println("key2="+key1+", value="+read(rawKey));}
jpayne@68: 
jpayne@68: 		int bnum=(int)(key1&arrayMask);
jpayne@68: 		long[] array=buffers[bnum];
jpayne@68: 		int loc=bufferlen[bnum];
jpayne@68: 		
jpayne@68: //		key2=Long.rotateRight(key2, hashBits);
jpayne@68: //		array[loc]=key2;
jpayne@68: 		
jpayne@68: 		array[loc]=rawKey;
jpayne@68: 		bufferlen[bnum]++;
jpayne@68: 		if(verbose){System.err.println("bufferlen["+bnum+"] = "+bufferlen[bnum]);}
jpayne@68: 		if(bufferlen[bnum]>=array.length){
jpayne@68: 
jpayne@68: 			if(verbose){System.err.println("Moving array.");}
jpayne@68: 			bufferlen[bnum]=0;
jpayne@68: 			buffers[bnum]=new long[array.length];
jpayne@68: 
jpayne@68: 			writers[bnum].add(array);
jpayne@68: 			if(verbose){System.err.println("Moved.");}
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Returns unincremented value */
jpayne@68: 	@Override
jpayne@68: 	public int incrementAndReturnUnincremented(long key, int incr){
jpayne@68: 		throw new RuntimeException("Operation not supported.");
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public long[] transformToFrequency(){
jpayne@68: 		return transformToFrequency(matrix);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public ByteBuilder toContentsString(){
jpayne@68: 		ByteBuilder sb=new ByteBuilder();
jpayne@68: 		sb.append('[');
jpayne@68: 		String comma="";
jpayne@68: 		for(int[] array : matrix){
jpayne@68: 			for(int i=0; i<array.length; i++){
jpayne@68: 				int word=array[i];
jpayne@68: 				for(int j=0; j<cellsPerWord; j++){
jpayne@68: 					int x=word&valueMask;
jpayne@68: 					sb.append(comma);
jpayne@68: 					sb.append(x);
jpayne@68: 					word>>>=cellBits;
jpayne@68: 					comma=", ";
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		sb.append(']');
jpayne@68: 		return sb;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public double usedFraction(){return cellsUsed/(double)cells;}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public double usedFraction(int mindepth){return cellsUsed(mindepth)/(double)cells;}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public long cellsUsed(int mindepth){
jpayne@68: 		long count=0;
jpayne@68: 		for(int[] array : matrix){
jpayne@68: 			if(array!=null){
jpayne@68: 				for(int word : array){
jpayne@68: 					while(word>0){
jpayne@68: 						int x=word&valueMask;
jpayne@68: 						if(x>=mindepth){count++;}
jpayne@68: 						word>>>=cellBits;
jpayne@68: 					}
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 		}
jpayne@68: 		return count;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	final long hash(long key, int row){
jpayne@68: 		int cell=(int)((Long.MAX_VALUE&key)%(hashArrayLength-1));
jpayne@68: //		int cell=(int)(hashCellMask&(key));
jpayne@68: 		
jpayne@68: 		if(row==0){//Doublehash only first time
jpayne@68: 			key=key^hashMasks[(row+4)%hashMasks.length][cell];
jpayne@68: 			cell=(int)(hashCellMask&(key>>4));
jpayne@68: //			cell=(int)(hashCellMask&(key>>hashBits));
jpayne@68: //			cell=(int)((Long.MAX_VALUE&key)%(hashArrayLength-1));
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		return key^hashMasks[row][cell];
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/**
jpayne@68: 	 * @param i
jpayne@68: 	 * @param j
jpayne@68: 	 * @return
jpayne@68: 	 */
jpayne@68: 	private static long[][] makeMasks(int rows, int cols) {
jpayne@68: 		
jpayne@68: 		long seed;
jpayne@68: 		synchronized(KCountArray6MT.class){
jpayne@68: 			seed=counter;
jpayne@68: 			counter++;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		Timer t=new Timer();
jpayne@68: 		long[][] r=new long[rows][cols];
jpayne@68: 		Random randy=Shared.threadLocalRandom(seed);
jpayne@68: 		for(int i=0; i<r.length; i++){
jpayne@68: 			fillMasks(r[i], randy);
jpayne@68: 		}
jpayne@68: 		t.stop();
jpayne@68: 		if(t.elapsed>200000000L){System.out.println("Mask-creation time: "+t);}
jpayne@68: 		return r;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private static void fillMasks(long[] r, Random randy) {
jpayne@68: //		for(int i=0; i<r.length; i++){
jpayne@68: //			long x=0;
jpayne@68: //			while(Long.bitCount(x&0xFFFFFFFF)!=16){
jpayne@68: //				x=randy.nextLong();
jpayne@68: //			}
jpayne@68: //			r[i]=(x&Long.MAX_VALUE);
jpayne@68: //		}
jpayne@68: 		
jpayne@68: 		final int hlen=(1<<hashBits);
jpayne@68: 		assert(r.length==hlen);
jpayne@68: 		int[] count1=new int[hlen];
jpayne@68: 		int[] count2=new int[hlen];
jpayne@68: 		final long mask=hlen-1;
jpayne@68: 
jpayne@68: 		for(int i=0; i<r.length; i++){
jpayne@68: 			long x=0;
jpayne@68: 			int y=0;
jpayne@68: 			int z=0;
jpayne@68: 			while(Long.bitCount(x&0xFFFFFFFFL)!=16){
jpayne@68: 				x=randy.nextLong();
jpayne@68: 				while(Long.bitCount(x&0xFFFFFFFFL)<16){
jpayne@68: 					x|=(1L<<randy.nextInt(32));
jpayne@68: 				}
jpayne@68: 				while(Long.bitCount(x&0xFFFFFFFFL)>16){
jpayne@68: 					x&=(~(1L<<randy.nextInt(32)));
jpayne@68: 				}
jpayne@68: 				while(Long.bitCount(x&0xFFFFFFFF00000000L)<16){
jpayne@68: 					x|=(1L<<(randy.nextInt(32)+32));
jpayne@68: 				}
jpayne@68: 				while(Long.bitCount(x&0xFFFFFFFF00000000L)>16){
jpayne@68: 					x&=(~(1L<<(randy.nextInt(32)+32)));
jpayne@68: 				}
jpayne@68: 				
jpayne@68: //				System.out.print(".");
jpayne@68: //				y=(((int)(x&mask))^i);
jpayne@68: 				y=(((int)(x&mask)));
jpayne@68: 				z=(int)((x>>hashBits)&mask);
jpayne@68: 				if(count1[y]>0 || count2[z]>0){
jpayne@68: 					x=0;
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: //			System.out.println(Long.toBinaryString(x));
jpayne@68: 			r[i]=(x&Long.MAX_VALUE);
jpayne@68: 			count1[y]++;
jpayne@68: 			count2[z]++;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public void initialize(){
jpayne@68: 		for(int i=0; i<writers.length; i++){
jpayne@68: 			writers[i]=new WriteThread(i);
jpayne@68: 			writers[i].start();
jpayne@68: 
jpayne@68: //			while(!writers[i].isAlive()){
jpayne@68: //				System.out.print(".");
jpayne@68: //			}
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	@Override
jpayne@68: 	public void shutdown(){
jpayne@68: 		if(finished){return;}
jpayne@68: 		synchronized(this){
jpayne@68: 			if(finished){return;}
jpayne@68: 			
jpayne@68: 			//Clear buffers
jpayne@68: 			for(int i=0; i<numArrays; i++){
jpayne@68: 				long[] array=buffers[i];
jpayne@68: 				int len=bufferlen[i];
jpayne@68: 				buffers[i]=null;
jpayne@68: 				bufferlen[i]=0;
jpayne@68: 				
jpayne@68: 				if(len<array.length){
jpayne@68: 					array=Arrays.copyOf(array, len);
jpayne@68: 				}
jpayne@68: 				
jpayne@68: 				if(array.length>0){
jpayne@68: 					writers[i].add(array);
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 			
jpayne@68: 			//Add poison
jpayne@68: 			for(WriteThread wt : writers){
jpayne@68: 				wt.add(poison);
jpayne@68: 			}
jpayne@68: 			
jpayne@68: 			//Wait for termination
jpayne@68: 			for(WriteThread wt : writers){
jpayne@68: //				System.out.println("wt"+wt.num+" is alive: "+wt.isAlive());
jpayne@68: 				while(wt.isAlive()){
jpayne@68: //					System.out.println("wt"+wt.num+" is alive: "+wt.isAlive());
jpayne@68: 					try {
jpayne@68: 						wt.join(10000);
jpayne@68: 					} catch (InterruptedException e) {
jpayne@68: 						// TODO Auto-generated catch block
jpayne@68: 						e.printStackTrace();
jpayne@68: 					}
jpayne@68: 					if(wt.isAlive()){System.err.println(wt.getClass().getCanonicalName()+" is taking a long time to die.");}
jpayne@68: 				}
jpayne@68: 				cellsUsed+=wt.cellsUsedPersonal;
jpayne@68: //				System.out.println("cellsUsed="+cellsUsed);
jpayne@68: 			}
jpayne@68: 			
jpayne@68: 			assert(!finished);
jpayne@68: 			finished=true;
jpayne@68: 		}
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private class WriteThread extends Thread{
jpayne@68: 		
jpayne@68: 		public WriteThread(int tnum){
jpayne@68: 			num=tnum;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		@Override
jpayne@68: 		public void run(){
jpayne@68: 			assert(matrix[num]==null);
jpayne@68: 			array=new int[wordsPerArray]; //Makes NUMA systems use local memory.
jpayne@68: 			
jpayne@68: 			matrix[num]=array;
jpayne@68: 			
jpayne@68: 			long[] keys=null;
jpayne@68: 			while(!shutdown){
jpayne@68: 
jpayne@68: 				if(verbose){System.err.println(" - Reading keys for wt"+num+".");}
jpayne@68: 				while(keys==null){
jpayne@68: 					try {
jpayne@68: 						keys=writeQueue.take();
jpayne@68: 					} catch (InterruptedException e) {
jpayne@68: 						// TODO Auto-generated catch block
jpayne@68: 						e.printStackTrace();
jpayne@68: 					}
jpayne@68: 				}
jpayne@68: 				if(keys==poison){
jpayne@68: //					assert(false);
jpayne@68: 					shutdown=true;
jpayne@68: 				}else{
jpayne@68: 					for(long key : keys){
jpayne@68: 						incrementRawLocal(key);
jpayne@68: 					}
jpayne@68: 				}
jpayne@68: //				System.out.println(" -- Read keys for   wt"+num+". poison="+(keys==poison)+", len="+keys.length);
jpayne@68: 				if(verbose){System.err.println(" -- Read keys for   wt"+num+". (success)");}
jpayne@68: 				keys=null;
jpayne@68: 				if(verbose){System.err.println("shutdown="+shutdown);}
jpayne@68: 			}
jpayne@68: 
jpayne@68: //			System.out.println(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I died: "+shutdown+", "+(keys==null)+".");
jpayne@68: //			assert(false) : ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I died: "+shutdown+", "+(keys==null)+".";
jpayne@68: 			
jpayne@68: 			array=null;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		void add(long[] keys){
jpayne@68: //			assert(isAlive());
jpayne@68: 			assert(!shutdown);
jpayne@68: 			if(shutdown){return;}
jpayne@68: //			assert(keys!=poison);
jpayne@68: 			if(verbose){System.err.println(" + Adding keys to wt"+num+".");}
jpayne@68: 			boolean success=false;
jpayne@68: 			while(!success){
jpayne@68: 				try {
jpayne@68: 					writeQueue.put(keys);
jpayne@68: 					success=true;
jpayne@68: 				} catch (InterruptedException e) {
jpayne@68: 					// TODO Auto-generated catch block
jpayne@68: 					e.printStackTrace();
jpayne@68: 				}
jpayne@68: 			}
jpayne@68: 			if(verbose){System.err.println(" ++ Added keys to wt"+num+". (success)");}
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		private int incrementRawLocal(long rawKey){
jpayne@68: //			verbose=(rawKey==32662670693L);
jpayne@68: 			if(verbose){System.err.println("\n*** Incrementing raw key "+rawKey+" ***");}
jpayne@68: //			verbose=true;
jpayne@68: 			assert(1>0);
jpayne@68: 			
jpayne@68: 			long key2=rawKey;
jpayne@68: 			if(hashes==1){
jpayne@68: 				key2=hash(key2, 0);
jpayne@68: //				int x=incrementHashedIfAtMost(key2, 1, maxValue-1);
jpayne@68: 				int x=incrementHashedLocal(key2);
jpayne@68: 				assert(x>=1) : "original=?, new should be >="+(1)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
jpayne@68: 				return x;
jpayne@68: 			}
jpayne@68: 			
jpayne@68: 			int min=0;
jpayne@68: //			final int min=read(rawKey);
jpayne@68: //			if(min>=maxValue){return maxValue;}
jpayne@68: 			
jpayne@68: 			assert(key2==rawKey);
jpayne@68: 			for(int i=0; i<hashes; i++){
jpayne@68: 				key2=hash(key2, i);
jpayne@68: 				if(verbose){System.err.println("key2="+key2+", value="+readHashed(key2, num));}
jpayne@68: //				int x=incrementHashedIfAtMost(key2, 1, min);
jpayne@68: 				int x=incrementHashedLocal(key2);
jpayne@68: 				assert(x>=min+1) : "i="+i+", original="+min+", new should be <="+(min+1)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
jpayne@68: 				if(verbose){System.err.println("postIncr value="+readHashed(key2, num));}
jpayne@68: //				assert(read(rawKey)<=min+1) : "i="+i+", original="+min+", new should be <="+(min+1)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
jpayne@68: //				assert(readHashed(key2)>=min+1) : "i="+i+", original="+min+", new should be <="+(min+1)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
jpayne@68: 				key2=Long.rotateRight(key2, hashBits);
jpayne@68: 			}
jpayne@68: //			assert(read(rawKey)==min+1) : "original="+min+", new should be "+(min+1)+", new="+read(rawKey)+", max="+maxValue;
jpayne@68: //			assert(false);
jpayne@68: 			return min(min+1, maxValue);
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		private int incrementHashedLocal(long key){
jpayne@68: //			assert((key&arrayMask)==num);
jpayne@68: 			key=(key&Long.MAX_VALUE)%(cellMod);
jpayne@68: //			key=(key>>>(arrayBits+1))%(cellMod);
jpayne@68: 			int index=(int)(key>>>indexShift);
jpayne@68: 			int word=array[index];
jpayne@68: 			int cellShift=(int)(cellBits*key);
jpayne@68: 			int value=((word>>>cellShift)&valueMask);
jpayne@68: 			if(value==0){cellsUsedPersonal++;}
jpayne@68: 			value=min(value+1, maxValue);
jpayne@68: 			word=(value<<cellShift)|(word&~((valueMask)<<cellShift));
jpayne@68: 			array[index]=word;
jpayne@68: 			return value;
jpayne@68: 		}
jpayne@68: 		
jpayne@68: 		private int[] array;
jpayne@68: 		private final int num;
jpayne@68: 		public long cellsUsedPersonal=0;
jpayne@68: 		
jpayne@68: 		public ArrayBlockingQueue<long[]> writeQueue=new ArrayBlockingQueue<long[]>(16);
jpayne@68: 		public boolean shutdown=false;
jpayne@68: 		
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	
jpayne@68: 	public long cellsUsed(){return cellsUsed;}
jpayne@68: 	
jpayne@68: 	private boolean finished=false;
jpayne@68: 	
jpayne@68: 	private long cellsUsed;
jpayne@68: 	final int[][] matrix;
jpayne@68: 	private final WriteThread[] writers=new WriteThread[numArrays];
jpayne@68: 	final int hashes;
jpayne@68: 	final int wordsPerArray;
jpayne@68: 	private final long cellsPerArray;
jpayne@68: 	final long cellMod;
jpayne@68: 	private final long[][] hashMasks=makeMasks(8, hashArrayLength);
jpayne@68: 	
jpayne@68: 	private final long[][] buffers=new long[numArrays][1000];
jpayne@68: 	private final int[] bufferlen=new int[numArrays];
jpayne@68: 	
jpayne@68: 	private static final int hashBits=6;
jpayne@68: 	private static final int hashArrayLength=1<<hashBits;
jpayne@68: 	private static final int hashCellMask=hashArrayLength-1;
jpayne@68: 	static final long[] poison=new long[0];
jpayne@68: 	
jpayne@68: 	private static long counter=0;
jpayne@68: 	
jpayne@68: }