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annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/bloom/KCountArray6MT.java @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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jpayne@68 1 package bloom;
jpayne@68 2
jpayne@68 3 import java.util.Arrays;
jpayne@68 4 import java.util.Random;
jpayne@68 5 import java.util.concurrent.ArrayBlockingQueue;
jpayne@68 6
jpayne@68 7 import shared.Shared;
jpayne@68 8 import shared.Timer;
jpayne@68 9 import structures.ByteBuilder;
jpayne@68 10
jpayne@68 11
jpayne@68 12 /**
jpayne@68 13 *
jpayne@68 14 * Uses hashing rather than direct-mapping to support longer kmers.
jpayne@68 15 *
jpayne@68 16 * @author Brian Bushnell
jpayne@68 17 * @date Aug 17, 2012
jpayne@68 18 *
jpayne@68 19 */
jpayne@68 20 public class KCountArray6MT extends KCountArray {
jpayne@68 21
jpayne@68 22 /**
jpayne@68 23 *
jpayne@68 24 */
jpayne@68 25 private static final long serialVersionUID = -1524266549200637631L;
jpayne@68 26
jpayne@68 27 public static void main(String[] args){
jpayne@68 28 long cells=Long.parseLong(args[0]);
jpayne@68 29 int bits=Integer.parseInt(args[1]);
jpayne@68 30 int gap=Integer.parseInt(args[2]);
jpayne@68 31 int hashes=Integer.parseInt(args[3]);
jpayne@68 32
jpayne@68 33 verbose=false;
jpayne@68 34
jpayne@68 35 KCountArray6MT kca=new KCountArray6MT(cells, bits, gap, hashes);
jpayne@68 36
jpayne@68 37 System.out.println(kca.read(0));
jpayne@68 38 kca.increment(0);
jpayne@68 39 System.out.println(kca.read(0));
jpayne@68 40 kca.increment(0);
jpayne@68 41 System.out.println(kca.read(0));
jpayne@68 42 System.out.println();
jpayne@68 43
jpayne@68 44 System.out.println(kca.read(1));
jpayne@68 45 kca.increment(1);
jpayne@68 46 System.out.println(kca.read(1));
jpayne@68 47 kca.increment(1);
jpayne@68 48 System.out.println(kca.read(1));
jpayne@68 49 System.out.println();
jpayne@68 50
jpayne@68 51 System.out.println(kca.read(100));
jpayne@68 52 kca.increment(100);
jpayne@68 53 System.out.println(kca.read(100));
jpayne@68 54 kca.increment(100);
jpayne@68 55 System.out.println(kca.read(100));
jpayne@68 56 kca.increment(100);
jpayne@68 57 System.out.println(kca.read(100));
jpayne@68 58 System.out.println();
jpayne@68 59
jpayne@68 60
jpayne@68 61 System.out.println(kca.read(150));
jpayne@68 62 kca.increment(150);
jpayne@68 63 System.out.println(kca.read(150));
jpayne@68 64 System.out.println();
jpayne@68 65
jpayne@68 66 }
jpayne@68 67
jpayne@68 68 public KCountArray6MT(long cells_, int bits_, int gap_, int hashes_){
jpayne@68 69 super(cells_, bits_);
jpayne@68 70 // verbose=false;
jpayne@68 71 long words=cells/cellsPerWord;
jpayne@68 72 assert(words/numArrays<=Integer.MAX_VALUE);
jpayne@68 73 wordsPerArray=(int)(words/numArrays);
jpayne@68 74 cellsPerArray=cells/numArrays;
jpayne@68 75 cellMod=cellsPerArray-1;
jpayne@68 76 hashes=hashes_;
jpayne@68 77 // System.out.println("cells="+cells+", words="+words+", wordsPerArray="+wordsPerArray+", numArrays="+numArrays+", hashes="+hashes);
jpayne@68 78 // assert(false);
jpayne@68 79 matrix=new int[numArrays][];
jpayne@68 80 assert(hashes>0 && hashes<=hashMasks.length);
jpayne@68 81 }
jpayne@68 82
jpayne@68 83 @Override
jpayne@68 84 public int read(final long rawKey){
jpayne@68 85 assert(finished);
jpayne@68 86 if(verbose){System.err.println("Reading raw key "+rawKey);}
jpayne@68 87
jpayne@68 88 long key1=hash(rawKey, 3);
jpayne@68 89 int arrayNum=(int)(key1&arrayMask);
jpayne@68 90 long key2=hash(rawKey, 0);
jpayne@68 91
jpayne@68 92 int min=readHashed(key2, arrayNum);
jpayne@68 93 for(int i=1; i<hashes && min>0; i++){
jpayne@68 94 if(verbose){System.err.println("Reading. i="+i+", key2="+key2);}
jpayne@68 95 key2=Long.rotateRight(key2, hashBits);
jpayne@68 96 key2=hash(key2, i);
jpayne@68 97 if(verbose){System.err.println("Rot/hash. i="+i+", key2="+key2);}
jpayne@68 98 min=min(min, readHashed(key2, arrayNum));
jpayne@68 99 }
jpayne@68 100 return min;
jpayne@68 101 }
jpayne@68 102
jpayne@68 103 int readHashed(long key, int arrayNum){
jpayne@68 104 if(verbose){System.err.print("Reading hashed key "+key);}
jpayne@68 105 // System.out.println("key="+key);
jpayne@68 106 // int arrayNum=(int)(key&arrayMask);
jpayne@68 107 key=(key&Long.MAX_VALUE)%(cellMod);
jpayne@68 108 // key=(key>>>(arrayBits+1))%(cellMod);
jpayne@68 109 // System.out.println("array="+arrayNum);
jpayne@68 110 // System.out.println("key2="+key);
jpayne@68 111 int[] array=matrix[arrayNum];
jpayne@68 112 int index=(int)(key>>>indexShift);
jpayne@68 113 // assert(false) : indexShift;
jpayne@68 114 // System.out.println("index="+index);
jpayne@68 115 int word=array[index];
jpayne@68 116 // System.out.println("word="+Integer.toHexString(word));
jpayne@68 117 assert(word>>>(cellBits*key) == word>>>(cellBits*(key&cellMask)));
jpayne@68 118 // int cellShift=(int)(cellBits*(key&cellMask));
jpayne@68 119 int cellShift=(int)(cellBits*key);
jpayne@68 120 if(verbose){System.err.println(", array="+arrayNum+", index="+index+", cellShift="+(cellShift%32)+", value="+((int)((word>>>cellShift)&valueMask)));}
jpayne@68 121 // System.out.println("cellShift="+cellShift);
jpayne@68 122 return (int)((word>>>cellShift)&valueMask);
jpayne@68 123 }
jpayne@68 124
jpayne@68 125 @Override
jpayne@68 126 public void write(final long key, int value){
jpayne@68 127 throw new RuntimeException("Not allowed for this class.");
jpayne@68 128 }
jpayne@68 129
jpayne@68 130 //Slow
jpayne@68 131 @Override
jpayne@68 132 public void increment(final long rawKey, int amt){
jpayne@68 133 for(int i=0; i<amt; i++){increment0(rawKey);}
jpayne@68 134 }
jpayne@68 135
jpayne@68 136 public void increment0(final long rawKey){
jpayne@68 137 if(verbose){System.err.println("\n*** Incrementing raw key "+rawKey+" ***");}
jpayne@68 138
jpayne@68 139 long key1=hash(rawKey, 3);
jpayne@68 140
jpayne@68 141 if(verbose){System.err.println("key2="+key1+", value="+read(rawKey));}
jpayne@68 142
jpayne@68 143 int bnum=(int)(key1&arrayMask);
jpayne@68 144 long[] array=buffers[bnum];
jpayne@68 145 int loc=bufferlen[bnum];
jpayne@68 146
jpayne@68 147 // key2=Long.rotateRight(key2, hashBits);
jpayne@68 148 // array[loc]=key2;
jpayne@68 149
jpayne@68 150 array[loc]=rawKey;
jpayne@68 151 bufferlen[bnum]++;
jpayne@68 152 if(verbose){System.err.println("bufferlen["+bnum+"] = "+bufferlen[bnum]);}
jpayne@68 153 if(bufferlen[bnum]>=array.length){
jpayne@68 154
jpayne@68 155 if(verbose){System.err.println("Moving array.");}
jpayne@68 156 bufferlen[bnum]=0;
jpayne@68 157 buffers[bnum]=new long[array.length];
jpayne@68 158
jpayne@68 159 writers[bnum].add(array);
jpayne@68 160 if(verbose){System.err.println("Moved.");}
jpayne@68 161 }
jpayne@68 162 }
jpayne@68 163
jpayne@68 164 /** Returns unincremented value */
jpayne@68 165 @Override
jpayne@68 166 public int incrementAndReturnUnincremented(long key, int incr){
jpayne@68 167 throw new RuntimeException("Operation not supported.");
jpayne@68 168 }
jpayne@68 169
jpayne@68 170 @Override
jpayne@68 171 public long[] transformToFrequency(){
jpayne@68 172 return transformToFrequency(matrix);
jpayne@68 173 }
jpayne@68 174
jpayne@68 175 @Override
jpayne@68 176 public ByteBuilder toContentsString(){
jpayne@68 177 ByteBuilder sb=new ByteBuilder();
jpayne@68 178 sb.append('[');
jpayne@68 179 String comma="";
jpayne@68 180 for(int[] array : matrix){
jpayne@68 181 for(int i=0; i<array.length; i++){
jpayne@68 182 int word=array[i];
jpayne@68 183 for(int j=0; j<cellsPerWord; j++){
jpayne@68 184 int x=word&valueMask;
jpayne@68 185 sb.append(comma);
jpayne@68 186 sb.append(x);
jpayne@68 187 word>>>=cellBits;
jpayne@68 188 comma=", ";
jpayne@68 189 }
jpayne@68 190 }
jpayne@68 191 }
jpayne@68 192 sb.append(']');
jpayne@68 193 return sb;
jpayne@68 194 }
jpayne@68 195
jpayne@68 196 @Override
jpayne@68 197 public double usedFraction(){return cellsUsed/(double)cells;}
jpayne@68 198
jpayne@68 199 @Override
jpayne@68 200 public double usedFraction(int mindepth){return cellsUsed(mindepth)/(double)cells;}
jpayne@68 201
jpayne@68 202 @Override
jpayne@68 203 public long cellsUsed(int mindepth){
jpayne@68 204 long count=0;
jpayne@68 205 for(int[] array : matrix){
jpayne@68 206 if(array!=null){
jpayne@68 207 for(int word : array){
jpayne@68 208 while(word>0){
jpayne@68 209 int x=word&valueMask;
jpayne@68 210 if(x>=mindepth){count++;}
jpayne@68 211 word>>>=cellBits;
jpayne@68 212 }
jpayne@68 213 }
jpayne@68 214 }
jpayne@68 215 }
jpayne@68 216 return count;
jpayne@68 217 }
jpayne@68 218
jpayne@68 219
jpayne@68 220 @Override
jpayne@68 221 final long hash(long key, int row){
jpayne@68 222 int cell=(int)((Long.MAX_VALUE&key)%(hashArrayLength-1));
jpayne@68 223 // int cell=(int)(hashCellMask&(key));
jpayne@68 224
jpayne@68 225 if(row==0){//Doublehash only first time
jpayne@68 226 key=key^hashMasks[(row+4)%hashMasks.length][cell];
jpayne@68 227 cell=(int)(hashCellMask&(key>>4));
jpayne@68 228 // cell=(int)(hashCellMask&(key>>hashBits));
jpayne@68 229 // cell=(int)((Long.MAX_VALUE&key)%(hashArrayLength-1));
jpayne@68 230 }
jpayne@68 231
jpayne@68 232 return key^hashMasks[row][cell];
jpayne@68 233 }
jpayne@68 234
jpayne@68 235 /**
jpayne@68 236 * @param i
jpayne@68 237 * @param j
jpayne@68 238 * @return
jpayne@68 239 */
jpayne@68 240 private static long[][] makeMasks(int rows, int cols) {
jpayne@68 241
jpayne@68 242 long seed;
jpayne@68 243 synchronized(KCountArray6MT.class){
jpayne@68 244 seed=counter;
jpayne@68 245 counter++;
jpayne@68 246 }
jpayne@68 247
jpayne@68 248 Timer t=new Timer();
jpayne@68 249 long[][] r=new long[rows][cols];
jpayne@68 250 Random randy=Shared.threadLocalRandom(seed);
jpayne@68 251 for(int i=0; i<r.length; i++){
jpayne@68 252 fillMasks(r[i], randy);
jpayne@68 253 }
jpayne@68 254 t.stop();
jpayne@68 255 if(t.elapsed>200000000L){System.out.println("Mask-creation time: "+t);}
jpayne@68 256 return r;
jpayne@68 257 }
jpayne@68 258
jpayne@68 259 private static void fillMasks(long[] r, Random randy) {
jpayne@68 260 // for(int i=0; i<r.length; i++){
jpayne@68 261 // long x=0;
jpayne@68 262 // while(Long.bitCount(x&0xFFFFFFFF)!=16){
jpayne@68 263 // x=randy.nextLong();
jpayne@68 264 // }
jpayne@68 265 // r[i]=(x&Long.MAX_VALUE);
jpayne@68 266 // }
jpayne@68 267
jpayne@68 268 final int hlen=(1<<hashBits);
jpayne@68 269 assert(r.length==hlen);
jpayne@68 270 int[] count1=new int[hlen];
jpayne@68 271 int[] count2=new int[hlen];
jpayne@68 272 final long mask=hlen-1;
jpayne@68 273
jpayne@68 274 for(int i=0; i<r.length; i++){
jpayne@68 275 long x=0;
jpayne@68 276 int y=0;
jpayne@68 277 int z=0;
jpayne@68 278 while(Long.bitCount(x&0xFFFFFFFFL)!=16){
jpayne@68 279 x=randy.nextLong();
jpayne@68 280 while(Long.bitCount(x&0xFFFFFFFFL)<16){
jpayne@68 281 x|=(1L<<randy.nextInt(32));
jpayne@68 282 }
jpayne@68 283 while(Long.bitCount(x&0xFFFFFFFFL)>16){
jpayne@68 284 x&=(~(1L<<randy.nextInt(32)));
jpayne@68 285 }
jpayne@68 286 while(Long.bitCount(x&0xFFFFFFFF00000000L)<16){
jpayne@68 287 x|=(1L<<(randy.nextInt(32)+32));
jpayne@68 288 }
jpayne@68 289 while(Long.bitCount(x&0xFFFFFFFF00000000L)>16){
jpayne@68 290 x&=(~(1L<<(randy.nextInt(32)+32)));
jpayne@68 291 }
jpayne@68 292
jpayne@68 293 // System.out.print(".");
jpayne@68 294 // y=(((int)(x&mask))^i);
jpayne@68 295 y=(((int)(x&mask)));
jpayne@68 296 z=(int)((x>>hashBits)&mask);
jpayne@68 297 if(count1[y]>0 || count2[z]>0){
jpayne@68 298 x=0;
jpayne@68 299 }
jpayne@68 300 }
jpayne@68 301 // System.out.println(Long.toBinaryString(x));
jpayne@68 302 r[i]=(x&Long.MAX_VALUE);
jpayne@68 303 count1[y]++;
jpayne@68 304 count2[z]++;
jpayne@68 305 }
jpayne@68 306
jpayne@68 307 }
jpayne@68 308
jpayne@68 309
jpayne@68 310 @Override
jpayne@68 311 public void initialize(){
jpayne@68 312 for(int i=0; i<writers.length; i++){
jpayne@68 313 writers[i]=new WriteThread(i);
jpayne@68 314 writers[i].start();
jpayne@68 315
jpayne@68 316 // while(!writers[i].isAlive()){
jpayne@68 317 // System.out.print(".");
jpayne@68 318 // }
jpayne@68 319 }
jpayne@68 320 }
jpayne@68 321
jpayne@68 322 @Override
jpayne@68 323 public void shutdown(){
jpayne@68 324 if(finished){return;}
jpayne@68 325 synchronized(this){
jpayne@68 326 if(finished){return;}
jpayne@68 327
jpayne@68 328 //Clear buffers
jpayne@68 329 for(int i=0; i<numArrays; i++){
jpayne@68 330 long[] array=buffers[i];
jpayne@68 331 int len=bufferlen[i];
jpayne@68 332 buffers[i]=null;
jpayne@68 333 bufferlen[i]=0;
jpayne@68 334
jpayne@68 335 if(len<array.length){
jpayne@68 336 array=Arrays.copyOf(array, len);
jpayne@68 337 }
jpayne@68 338
jpayne@68 339 if(array.length>0){
jpayne@68 340 writers[i].add(array);
jpayne@68 341 }
jpayne@68 342 }
jpayne@68 343
jpayne@68 344 //Add poison
jpayne@68 345 for(WriteThread wt : writers){
jpayne@68 346 wt.add(poison);
jpayne@68 347 }
jpayne@68 348
jpayne@68 349 //Wait for termination
jpayne@68 350 for(WriteThread wt : writers){
jpayne@68 351 // System.out.println("wt"+wt.num+" is alive: "+wt.isAlive());
jpayne@68 352 while(wt.isAlive()){
jpayne@68 353 // System.out.println("wt"+wt.num+" is alive: "+wt.isAlive());
jpayne@68 354 try {
jpayne@68 355 wt.join(10000);
jpayne@68 356 } catch (InterruptedException e) {
jpayne@68 357 // TODO Auto-generated catch block
jpayne@68 358 e.printStackTrace();
jpayne@68 359 }
jpayne@68 360 if(wt.isAlive()){System.err.println(wt.getClass().getCanonicalName()+" is taking a long time to die.");}
jpayne@68 361 }
jpayne@68 362 cellsUsed+=wt.cellsUsedPersonal;
jpayne@68 363 // System.out.println("cellsUsed="+cellsUsed);
jpayne@68 364 }
jpayne@68 365
jpayne@68 366 assert(!finished);
jpayne@68 367 finished=true;
jpayne@68 368 }
jpayne@68 369 }
jpayne@68 370
jpayne@68 371 private class WriteThread extends Thread{
jpayne@68 372
jpayne@68 373 public WriteThread(int tnum){
jpayne@68 374 num=tnum;
jpayne@68 375 }
jpayne@68 376
jpayne@68 377 @Override
jpayne@68 378 public void run(){
jpayne@68 379 assert(matrix[num]==null);
jpayne@68 380 array=new int[wordsPerArray]; //Makes NUMA systems use local memory.
jpayne@68 381
jpayne@68 382 matrix[num]=array;
jpayne@68 383
jpayne@68 384 long[] keys=null;
jpayne@68 385 while(!shutdown){
jpayne@68 386
jpayne@68 387 if(verbose){System.err.println(" - Reading keys for wt"+num+".");}
jpayne@68 388 while(keys==null){
jpayne@68 389 try {
jpayne@68 390 keys=writeQueue.take();
jpayne@68 391 } catch (InterruptedException e) {
jpayne@68 392 // TODO Auto-generated catch block
jpayne@68 393 e.printStackTrace();
jpayne@68 394 }
jpayne@68 395 }
jpayne@68 396 if(keys==poison){
jpayne@68 397 // assert(false);
jpayne@68 398 shutdown=true;
jpayne@68 399 }else{
jpayne@68 400 for(long key : keys){
jpayne@68 401 incrementRawLocal(key);
jpayne@68 402 }
jpayne@68 403 }
jpayne@68 404 // System.out.println(" -- Read keys for wt"+num+". poison="+(keys==poison)+", len="+keys.length);
jpayne@68 405 if(verbose){System.err.println(" -- Read keys for wt"+num+". (success)");}
jpayne@68 406 keys=null;
jpayne@68 407 if(verbose){System.err.println("shutdown="+shutdown);}
jpayne@68 408 }
jpayne@68 409
jpayne@68 410 // System.out.println(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I died: "+shutdown+", "+(keys==null)+".");
jpayne@68 411 // assert(false) : ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I died: "+shutdown+", "+(keys==null)+".";
jpayne@68 412
jpayne@68 413 array=null;
jpayne@68 414 }
jpayne@68 415
jpayne@68 416 void add(long[] keys){
jpayne@68 417 // assert(isAlive());
jpayne@68 418 assert(!shutdown);
jpayne@68 419 if(shutdown){return;}
jpayne@68 420 // assert(keys!=poison);
jpayne@68 421 if(verbose){System.err.println(" + Adding keys to wt"+num+".");}
jpayne@68 422 boolean success=false;
jpayne@68 423 while(!success){
jpayne@68 424 try {
jpayne@68 425 writeQueue.put(keys);
jpayne@68 426 success=true;
jpayne@68 427 } catch (InterruptedException e) {
jpayne@68 428 // TODO Auto-generated catch block
jpayne@68 429 e.printStackTrace();
jpayne@68 430 }
jpayne@68 431 }
jpayne@68 432 if(verbose){System.err.println(" ++ Added keys to wt"+num+". (success)");}
jpayne@68 433 }
jpayne@68 434
jpayne@68 435 private int incrementRawLocal(long rawKey){
jpayne@68 436 // verbose=(rawKey==32662670693L);
jpayne@68 437 if(verbose){System.err.println("\n*** Incrementing raw key "+rawKey+" ***");}
jpayne@68 438 // verbose=true;
jpayne@68 439 assert(1>0);
jpayne@68 440
jpayne@68 441 long key2=rawKey;
jpayne@68 442 if(hashes==1){
jpayne@68 443 key2=hash(key2, 0);
jpayne@68 444 // int x=incrementHashedIfAtMost(key2, 1, maxValue-1);
jpayne@68 445 int x=incrementHashedLocal(key2);
jpayne@68 446 assert(x>=1) : "original=?, new should be >="+(1)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
jpayne@68 447 return x;
jpayne@68 448 }
jpayne@68 449
jpayne@68 450 int min=0;
jpayne@68 451 // final int min=read(rawKey);
jpayne@68 452 // if(min>=maxValue){return maxValue;}
jpayne@68 453
jpayne@68 454 assert(key2==rawKey);
jpayne@68 455 for(int i=0; i<hashes; i++){
jpayne@68 456 key2=hash(key2, i);
jpayne@68 457 if(verbose){System.err.println("key2="+key2+", value="+readHashed(key2, num));}
jpayne@68 458 // int x=incrementHashedIfAtMost(key2, 1, min);
jpayne@68 459 int x=incrementHashedLocal(key2);
jpayne@68 460 assert(x>=min+1) : "i="+i+", original="+min+", new should be <="+(min+1)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
jpayne@68 461 if(verbose){System.err.println("postIncr value="+readHashed(key2, num));}
jpayne@68 462 // assert(read(rawKey)<=min+1) : "i="+i+", original="+min+", new should be <="+(min+1)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
jpayne@68 463 // assert(readHashed(key2)>=min+1) : "i="+i+", original="+min+", new should be <="+(min+1)+", new="+read(rawKey)+", max="+maxValue+", key="+rawKey;
jpayne@68 464 key2=Long.rotateRight(key2, hashBits);
jpayne@68 465 }
jpayne@68 466 // assert(read(rawKey)==min+1) : "original="+min+", new should be "+(min+1)+", new="+read(rawKey)+", max="+maxValue;
jpayne@68 467 // assert(false);
jpayne@68 468 return min(min+1, maxValue);
jpayne@68 469 }
jpayne@68 470
jpayne@68 471 private int incrementHashedLocal(long key){
jpayne@68 472 // assert((key&arrayMask)==num);
jpayne@68 473 key=(key&Long.MAX_VALUE)%(cellMod);
jpayne@68 474 // key=(key>>>(arrayBits+1))%(cellMod);
jpayne@68 475 int index=(int)(key>>>indexShift);
jpayne@68 476 int word=array[index];
jpayne@68 477 int cellShift=(int)(cellBits*key);
jpayne@68 478 int value=((word>>>cellShift)&valueMask);
jpayne@68 479 if(value==0){cellsUsedPersonal++;}
jpayne@68 480 value=min(value+1, maxValue);
jpayne@68 481 word=(value<<cellShift)|(word&~((valueMask)<<cellShift));
jpayne@68 482 array[index]=word;
jpayne@68 483 return value;
jpayne@68 484 }
jpayne@68 485
jpayne@68 486 private int[] array;
jpayne@68 487 private final int num;
jpayne@68 488 public long cellsUsedPersonal=0;
jpayne@68 489
jpayne@68 490 public ArrayBlockingQueue<long[]> writeQueue=new ArrayBlockingQueue<long[]>(16);
jpayne@68 491 public boolean shutdown=false;
jpayne@68 492
jpayne@68 493 }
jpayne@68 494
jpayne@68 495
jpayne@68 496 public long cellsUsed(){return cellsUsed;}
jpayne@68 497
jpayne@68 498 private boolean finished=false;
jpayne@68 499
jpayne@68 500 private long cellsUsed;
jpayne@68 501 final int[][] matrix;
jpayne@68 502 private final WriteThread[] writers=new WriteThread[numArrays];
jpayne@68 503 final int hashes;
jpayne@68 504 final int wordsPerArray;
jpayne@68 505 private final long cellsPerArray;
jpayne@68 506 final long cellMod;
jpayne@68 507 private final long[][] hashMasks=makeMasks(8, hashArrayLength);
jpayne@68 508
jpayne@68 509 private final long[][] buffers=new long[numArrays][1000];
jpayne@68 510 private final int[] bufferlen=new int[numArrays];
jpayne@68 511
jpayne@68 512 private static final int hashBits=6;
jpayne@68 513 private static final int hashArrayLength=1<<hashBits;
jpayne@68 514 private static final int hashCellMask=hashArrayLength-1;
jpayne@68 515 static final long[] poison=new long[0];
jpayne@68 516
jpayne@68 517 private static long counter=0;
jpayne@68 518
jpayne@68 519 }