jpayne@68: package bloom;
jpayne@68: 
jpayne@68: import java.util.Random;
jpayne@68: 
jpayne@68: import shared.Shared;
jpayne@68: import shared.Timer;
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 KCountArray4 extends KCountArray {
jpayne@68: 	
jpayne@68: 	/**
jpayne@68: 	 * 
jpayne@68: 	 */
jpayne@68: 	private static final long serialVersionUID = -1418539960644885681L;
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: 		KCountArray4 kca=new KCountArray4(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 KCountArray4(long cells_, int bits_, int gap_, int hashes_){
jpayne@68: 		super(cells_, bits_);
jpayne@68: 		long words=cells/cellsPerWord;
jpayne@68: 		assert(words/numArrays<=Integer.MAX_VALUE);
jpayne@68: 		int wordsPerArray=(int)(words/numArrays);
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][wordsPerArray];
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: 		if(verbose){System.err.println("Reading raw key "+rawKey);}
jpayne@68: 		long key2=hash(rawKey, 0);
jpayne@68: 		int min=readHashed(key2);
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));
jpayne@68: 		}
jpayne@68: 		return min;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private int readHashed(long key){
jpayne@68: 		if(verbose){System.err.print("Reading hashed key "+key);}
jpayne@68: 		key=((key&Long.MAX_VALUE)%(cells-1));
jpayne@68: //		System.out.println("key="+key);
jpayne@68: 		int arrayNum=(int)(key&arrayMask);
jpayne@68: //		System.out.println("array="+arrayNum);
jpayne@68: 		key>>>=arrayBits;
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: 	@Override
jpayne@68: 	public void increment(final long rawKey, int incr){
jpayne@68: //		verbose=(rawKey==32662670693L);
jpayne@68: 		if(verbose){System.err.println("\n*** Incrementing raw key "+rawKey+" ***");}
jpayne@68: //		verbose=true;
jpayne@68: 		assert(incr>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, incr, maxValue-1);
jpayne@68: 			assert(x>=incr) : "original=?, new should be >="+(incr)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
jpayne@68: 			//return x;
jpayne@68: 		}
jpayne@68: 		
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));}
jpayne@68: 			int x=incrementHashedIfAtMost(key2, incr, min);
jpayne@68: 			assert(x>=min+incr) : "i="+i+", original="+min+", new should be <="+(min+incr)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
jpayne@68: 			if(verbose){System.err.println("postIncr value="+readHashed(key2));}
jpayne@68: //			assert(read(rawKey)<=min+incr) : "i="+i+", original="+min+", new should be <="+(min+incr)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
jpayne@68: //			assert(readHashed(key2)>=min+incr) : "i="+i+", original="+min+", new should be <="+(min+incr)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
jpayne@68: 			key2=Long.rotateRight(key2, hashBits);
jpayne@68: 		}
jpayne@68: //		assert(read(rawKey)==min+incr) : "original="+min+", new should be "+(min+incr)+", new="+read(rawKey)+", max="+maxValue;
jpayne@68: //		assert(false);
jpayne@68: 		//return min(min+incr, maxValue);
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	/** Returns unincremented value */
jpayne@68: 	@Override
jpayne@68: 	public int incrementAndReturnUnincremented(long rawKey, int incr){
jpayne@68: //		verbose=(rawKey==32662670693L);
jpayne@68: 		if(verbose){System.err.println("\n*** Incrementing raw key "+rawKey+" ***");}
jpayne@68: //		verbose=true;
jpayne@68: 		assert(incr>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, incr, maxValue-1);
jpayne@68: 			assert(x>=incr) : "original=?, new should be >="+(incr)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
jpayne@68: 			return x;
jpayne@68: 		}
jpayne@68: 		
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));}
jpayne@68: 			int x=incrementHashedIfAtMost(key2, incr, min);
jpayne@68: 			assert(x>=min+incr) : "i="+i+", original="+min+", new should be <="+(min+incr)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
jpayne@68: 			if(verbose){System.err.println("postIncr value="+readHashed(key2));}
jpayne@68: //			assert(read(rawKey)<=min+incr) : "i="+i+", original="+min+", new should be <="+(min+incr)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
jpayne@68: //			assert(readHashed(key2)>=min+incr) : "i="+i+", original="+min+", new should be <="+(min+incr)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
jpayne@68: 			key2=Long.rotateRight(key2, hashBits);
jpayne@68: 		}
jpayne@68: //		assert(read(rawKey)==min+incr) : "original="+min+", new should be "+(min+incr)+", new="+read(rawKey)+", max="+maxValue;
jpayne@68: //		assert(false);
jpayne@68: 		return min;
jpayne@68: 	}
jpayne@68: 	
jpayne@68: 	private int incrementHashedIfAtMost(long key, int incr, int lim){
jpayne@68: 		if(verbose){System.err.print("incrementing hashed key "+key);}
jpayne@68: 		key=((key&Long.MAX_VALUE)%(cells-1));
jpayne@68: 		int arrayNum=(int)(key&arrayMask);
jpayne@68: 		key>>>=arrayBits;
jpayne@68: 		int[] array=matrix[arrayNum];
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(verbose){System.err.println(", array="+arrayNum+", index="+index+", cellShift="+(cellShift%32)+", value="+value+", limit="+lim);}
jpayne@68: 		if(value>lim){return value;}
jpayne@68: 		if(value==0 && incr>0){cellsUsed++;}
jpayne@68: 		value=min(value+incr, 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 incrementHashed(long key, int incr){
jpayne@68: 		assert(incr>0);
jpayne@68: 		int arrayNum=(int)(key&arrayMask);
jpayne@68: 		key>>>=arrayBits;
jpayne@68: 		int[] array=matrix[arrayNum];
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 && incr>0){cellsUsed++;}
jpayne@68: 		value=min(value+incr, maxValue);
jpayne@68: 		word=(value<<cellShift)|(word&~((valueMask)<<cellShift));
jpayne@68: 		array[index]=word;
jpayne@68: 		return value;
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 String toContentsString(){
jpayne@68: 		StringBuilder sb=new StringBuilder();
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.toString();
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(KCountArray4.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: 	public long cellsUsed(){return cellsUsed;}
jpayne@68: 
jpayne@68: 	private long cellsUsed;
jpayne@68: 	private final int[][] matrix;
jpayne@68: 	private final int hashes;
jpayne@68: 	
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: 	private final long[][] hashMasks=makeMasks(8, hashArrayLength);
jpayne@68: 	
jpayne@68: 	private static long counter=0;
jpayne@68: 	
jpayne@68: }