Mercurial > repos > rliterman > csp2

annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/bloom/KCountArray5MT.java @ 68:5028fdace37b

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
parents
children
rev   line source
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
jpayne@68 10
jpayne@68 11 /**
jpayne@68 12 *
jpayne@68 13 * Uses hashing rather than direct-mapping to support longer kmers.
jpayne@68 14 *
jpayne@68 15 * @author Brian Bushnell
jpayne@68 16 * @date Aug 17, 2012
jpayne@68 17 *
jpayne@68 18 */
jpayne@68 19 public class KCountArray5MT extends KCountArray {
jpayne@68 20
jpayne@68 21 /**
jpayne@68 22 *
jpayne@68 23 */
jpayne@68 24 private static final long serialVersionUID = -5456926900022701212L;
jpayne@68 25
jpayne@68 26 public static void main(String[] args){
jpayne@68 27 long cells=Long.parseLong(args[0]);
jpayne@68 28 int bits=Integer.parseInt(args[1]);
jpayne@68 29 int gap=Integer.parseInt(args[2]);
jpayne@68 30 int hashes=Integer.parseInt(args[3]);
jpayne@68 31
jpayne@68 32 verbose=false;
jpayne@68 33
jpayne@68 34 KCountArray5MT kca=new KCountArray5MT(cells, bits, gap, hashes);
jpayne@68 35
jpayne@68 36 System.out.println(kca.read(0));
jpayne@68 37 kca.increment(0);
jpayne@68 38 System.out.println(kca.read(0));
jpayne@68 39 kca.increment(0);
jpayne@68 40 System.out.println(kca.read(0));
jpayne@68 41 System.out.println();
jpayne@68 42
jpayne@68 43 System.out.println(kca.read(1));
jpayne@68 44 kca.increment(1);
jpayne@68 45 System.out.println(kca.read(1));
jpayne@68 46 kca.increment(1);
jpayne@68 47 System.out.println(kca.read(1));
jpayne@68 48 System.out.println();
jpayne@68 49
jpayne@68 50 System.out.println(kca.read(100));
jpayne@68 51 kca.increment(100);
jpayne@68 52 System.out.println(kca.read(100));
jpayne@68 53 kca.increment(100);
jpayne@68 54 System.out.println(kca.read(100));
jpayne@68 55 kca.increment(100);
jpayne@68 56 System.out.println(kca.read(100));
jpayne@68 57 System.out.println();
jpayne@68 58
jpayne@68 59
jpayne@68 60 System.out.println(kca.read(150));
jpayne@68 61 kca.increment(150);
jpayne@68 62 System.out.println(kca.read(150));
jpayne@68 63 System.out.println();
jpayne@68 64
jpayne@68 65 }
jpayne@68 66
jpayne@68 67 public KCountArray5MT(long cells_, int bits_, int gap_, int hashes_){
jpayne@68 68 super(cells_, bits_);
jpayne@68 69 // verbose=false;
jpayne@68 70 long words=cells/cellsPerWord;
jpayne@68 71 assert(words/numArrays<=Integer.MAX_VALUE);
jpayne@68 72 wordsPerArray=(int)(words/numArrays);
jpayne@68 73 cellsPerArray=cells/numArrays;
jpayne@68 74 cellMod=cellsPerArray-1;
jpayne@68 75 hashes=hashes_;
jpayne@68 76 // System.out.println("cells="+cells+", words="+words+", wordsPerArray="+wordsPerArray+", numArrays="+numArrays+", hashes="+hashes);
jpayne@68 77 // assert(false);
jpayne@68 78 matrix=new int[numArrays][];
jpayne@68 79 assert(hashes>0 && hashes<=hashMasks.length);
jpayne@68 80 }
jpayne@68 81
jpayne@68 82 @Override
jpayne@68 83 public int read(final long rawKey){
jpayne@68 84 assert(finished);
jpayne@68 85 if(verbose){System.err.println("Reading raw key "+rawKey);}
jpayne@68 86 long key2=hash(rawKey, 0);
jpayne@68 87 int min=readHashed(key2);
jpayne@68 88 for(int i=1; i<hashes && min>0; i++){
jpayne@68 89 if(verbose){System.err.println("Reading. i="+i+", key2="+key2);}
jpayne@68 90 key2=Long.rotateRight(key2, hashBits);
jpayne@68 91 key2=hash(key2, i);
jpayne@68 92 if(verbose){System.err.println("Rot/hash. i="+i+", key2="+key2);}
jpayne@68 93 min=min(min, readHashed(key2));
jpayne@68 94 }
jpayne@68 95 return min;
jpayne@68 96 }
jpayne@68 97
jpayne@68 98 int readHashed(long key){
jpayne@68 99 assert(finished);
jpayne@68 100 if(verbose){System.err.print("Reading hashed key "+key);}
jpayne@68 101 // System.out.println("key="+key);
jpayne@68 102 int arrayNum=(int)(key&arrayMask);
jpayne@68 103 key=(key>>>arrayBits)%(cellMod);
jpayne@68 104 // System.out.println("array="+arrayNum);
jpayne@68 105 // System.out.println("key2="+key);
jpayne@68 106 int[] array=matrix[arrayNum];
jpayne@68 107 int index=(int)(key>>>indexShift);
jpayne@68 108 // assert(false) : indexShift;
jpayne@68 109 // System.out.println("index="+index);
jpayne@68 110 int word=array[index];
jpayne@68 111 // System.out.println("word="+Integer.toHexString(word));
jpayne@68 112 assert(word>>>(cellBits*key) == word>>>(cellBits*(key&cellMask)));
jpayne@68 113 // int cellShift=(int)(cellBits*(key&cellMask));
jpayne@68 114 int cellShift=(int)(cellBits*key);
jpayne@68 115 if(verbose){System.err.println(", array="+arrayNum+", index="+index+", cellShift="+(cellShift%32)+", value="+((int)((word>>>cellShift)&valueMask)));}
jpayne@68 116 // System.out.println("cellShift="+cellShift);
jpayne@68 117 return (int)((word>>>cellShift)&valueMask);
jpayne@68 118 }
jpayne@68 119
jpayne@68 120 @Override
jpayne@68 121 public void write(final long key, int value){
jpayne@68 122 throw new RuntimeException("Not allowed for this class.");
jpayne@68 123 }
jpayne@68 124
jpayne@68 125 //Slow
jpayne@68 126 @Override
jpayne@68 127 public void increment(final long rawKey, int amt){
jpayne@68 128 for(int i=0; i<amt; i++){increment0(rawKey);}
jpayne@68 129 }
jpayne@68 130
jpayne@68 131 public void increment0(final long rawKey){
jpayne@68 132 if(verbose){System.err.println("\n*** Incrementing raw key "+rawKey+" ***");}
jpayne@68 133
jpayne@68 134 buffer[bufferlen]=hash(rawKey, 0);
jpayne@68 135 bufferlen++;
jpayne@68 136
jpayne@68 137 if(bufferlen>=buffer.length){
jpayne@68 138
jpayne@68 139 if(verbose){System.err.println("Moving array.");}
jpayne@68 140
jpayne@68 141 for(int w=0; w<writers.length; w++){
jpayne@68 142 writers[w].add(buffer);
jpayne@68 143 }
jpayne@68 144 bufferlen=0;
jpayne@68 145 buffer=new long[buffer.length];
jpayne@68 146 if(verbose){System.err.println("Moved.");}
jpayne@68 147 }
jpayne@68 148
jpayne@68 149 }
jpayne@68 150
jpayne@68 151
jpayne@68 152 @Override
jpayne@68 153 public synchronized void increment(long[] keys){
jpayne@68 154 for(int i=0; i<keys.length; i++){
jpayne@68 155 keys[i]=hash(keys[i],0);
jpayne@68 156 }
jpayne@68 157 for(int w=0; w<writers.length; w++){
jpayne@68 158 writers[w].add(keys);
jpayne@68 159 }
jpayne@68 160 }
jpayne@68 161
jpayne@68 162 /** Returns unincremented value */
jpayne@68 163 @Override
jpayne@68 164 public int incrementAndReturnUnincremented(long key, int incr){
jpayne@68 165 throw new RuntimeException("Operation not supported.");
jpayne@68 166 }
jpayne@68 167
jpayne@68 168 @Override
jpayne@68 169 public long[] transformToFrequency(){
jpayne@68 170 return transformToFrequency(matrix);
jpayne@68 171 }
jpayne@68 172
jpayne@68 173 @Override
jpayne@68 174 public String toContentsString(){
jpayne@68 175 StringBuilder sb=new StringBuilder();
jpayne@68 176 sb.append("[");
jpayne@68 177 String comma="";
jpayne@68 178 for(int[] array : matrix){
jpayne@68 179 for(int i=0; i<array.length; i++){
jpayne@68 180 int word=array[i];
jpayne@68 181 for(int j=0; j<cellsPerWord; j++){
jpayne@68 182 int x=word&valueMask;
jpayne@68 183 sb.append(comma);
jpayne@68 184 sb.append(x);
jpayne@68 185 word>>>=cellBits;
jpayne@68 186 comma=", ";
jpayne@68 187 }
jpayne@68 188 }
jpayne@68 189 }
jpayne@68 190 sb.append("]");
jpayne@68 191 return sb.toString();
jpayne@68 192 }
jpayne@68 193
jpayne@68 194 @Override
jpayne@68 195 public double usedFraction(){return cellsUsed/(double)cells;}
jpayne@68 196
jpayne@68 197 @Override
jpayne@68 198 public double usedFraction(int mindepth){return cellsUsed(mindepth)/(double)cells;}
jpayne@68 199
jpayne@68 200 @Override
jpayne@68 201 public long cellsUsed(int mindepth){
jpayne@68 202 long count=0;
jpayne@68 203 for(int[] array : matrix){
jpayne@68 204 if(array!=null){
jpayne@68 205 for(int word : array){
jpayne@68 206 while(word>0){
jpayne@68 207 int x=word&valueMask;
jpayne@68 208 if(x>=mindepth){count++;}
jpayne@68 209 word>>>=cellBits;
jpayne@68 210 }
jpayne@68 211 }
jpayne@68 212 }
jpayne@68 213 }
jpayne@68 214 return count;
jpayne@68 215 }
jpayne@68 216
jpayne@68 217
jpayne@68 218 @Override
jpayne@68 219 final long hash(long key, int row){
jpayne@68 220 int cell=(int)((Long.MAX_VALUE&key)%(hashArrayLength-1));
jpayne@68 221 // int cell=(int)(hashCellMask&(key));
jpayne@68 222
jpayne@68 223 if(row==0){//Doublehash only first time
jpayne@68 224 key=key^hashMasks[(row+4)%hashMasks.length][cell];
jpayne@68 225 cell=(int)(hashCellMask&(key>>4));
jpayne@68 226 // cell=(int)(hashCellMask&(key>>hashBits));
jpayne@68 227 // cell=(int)((Long.MAX_VALUE&key)%(hashArrayLength-1));
jpayne@68 228 }
jpayne@68 229
jpayne@68 230 return key^hashMasks[row][cell];
jpayne@68 231 }
jpayne@68 232
jpayne@68 233 /**
jpayne@68 234 * @param i
jpayne@68 235 * @param j
jpayne@68 236 * @return
jpayne@68 237 */
jpayne@68 238 private static long[][] makeMasks(int rows, int cols) {
jpayne@68 239
jpayne@68 240 long seed;
jpayne@68 241 synchronized(KCountArray5MT.class){
jpayne@68 242 seed=counter;
jpayne@68 243 counter++;
jpayne@68 244 }
jpayne@68 245
jpayne@68 246 Timer t=new Timer();
jpayne@68 247 long[][] r=new long[rows][cols];
jpayne@68 248 Random randy=Shared.threadLocalRandom(seed);
jpayne@68 249 for(int i=0; i<r.length; i++){
jpayne@68 250 fillMasks(r[i], randy);
jpayne@68 251 }
jpayne@68 252 t.stop();
jpayne@68 253 if(t.elapsed>200000000L){System.out.println("Mask-creation time: "+t);}
jpayne@68 254 return r;
jpayne@68 255 }
jpayne@68 256
jpayne@68 257 private static void fillMasks(long[] r, Random randy) {
jpayne@68 258 // for(int i=0; i<r.length; i++){
jpayne@68 259 // long x=0;
jpayne@68 260 // while(Long.bitCount(x&0xFFFFFFFF)!=16){
jpayne@68 261 // x=randy.nextLong();
jpayne@68 262 // }
jpayne@68 263 // r[i]=(x&Long.MAX_VALUE);
jpayne@68 264 // }
jpayne@68 265
jpayne@68 266 final int hlen=(1<<hashBits);
jpayne@68 267 assert(r.length==hlen);
jpayne@68 268 int[] count1=new int[hlen];
jpayne@68 269 int[] count2=new int[hlen];
jpayne@68 270 final long mask=hlen-1;
jpayne@68 271
jpayne@68 272 for(int i=0; i<r.length; i++){
jpayne@68 273 long x=0;
jpayne@68 274 int y=0;
jpayne@68 275 int z=0;
jpayne@68 276 while(Long.bitCount(x&0xFFFFFFFFL)!=16){
jpayne@68 277 x=randy.nextLong();
jpayne@68 278 while(Long.bitCount(x&0xFFFFFFFFL)<16){
jpayne@68 279 x|=(1L<<randy.nextInt(32));
jpayne@68 280 }
jpayne@68 281 while(Long.bitCount(x&0xFFFFFFFFL)>16){
jpayne@68 282 x&=(~(1L<<randy.nextInt(32)));
jpayne@68 283 }
jpayne@68 284 while(Long.bitCount(x&0xFFFFFFFF00000000L)<16){
jpayne@68 285 x|=(1L<<(randy.nextInt(32)+32));
jpayne@68 286 }
jpayne@68 287 while(Long.bitCount(x&0xFFFFFFFF00000000L)>16){
jpayne@68 288 x&=(~(1L<<(randy.nextInt(32)+32)));
jpayne@68 289 }
jpayne@68 290
jpayne@68 291 // System.out.print(".");
jpayne@68 292 // y=(((int)(x&mask))^i);
jpayne@68 293 y=(((int)(x&mask)));
jpayne@68 294 z=(int)((x>>hashBits)&mask);
jpayne@68 295 if(count1[y]>0 || count2[z]>0){
jpayne@68 296 x=0;
jpayne@68 297 }
jpayne@68 298 }
jpayne@68 299 // System.out.println(Long.toBinaryString(x));
jpayne@68 300 r[i]=(x&Long.MAX_VALUE);
jpayne@68 301 count1[y]++;
jpayne@68 302 count2[z]++;
jpayne@68 303 }
jpayne@68 304
jpayne@68 305 }
jpayne@68 306
jpayne@68 307
jpayne@68 308 @Override
jpayne@68 309 public void initialize(){
jpayne@68 310 for(int i=0; i<writers.length; i++){
jpayne@68 311 writers[i]=new WriteThread(i);
jpayne@68 312 writers[i].start();
jpayne@68 313
jpayne@68 314 while(!writers[i].isAlive()){
jpayne@68 315 System.out.print(".");
jpayne@68 316 }
jpayne@68 317 }
jpayne@68 318 }
jpayne@68 319
jpayne@68 320 @Override
jpayne@68 321 public void shutdown(){
jpayne@68 322 if(finished){return;}
jpayne@68 323 synchronized(this){
jpayne@68 324 if(finished){return;}
jpayne@68 325
jpayne@68 326 //Clear buffer
jpayne@68 327 if(bufferlen<buffer.length){
jpayne@68 328 buffer=Arrays.copyOf(buffer, bufferlen);
jpayne@68 329 }
jpayne@68 330
jpayne@68 331 if(buffer.length>0){
jpayne@68 332 for(int i=0; i<writers.length; i++)
jpayne@68 333 writers[i].add(buffer);
jpayne@68 334 }
jpayne@68 335 buffer=null;
jpayne@68 336 bufferlen=0;
jpayne@68 337
jpayne@68 338
jpayne@68 339 //Add poison
jpayne@68 340 for(WriteThread wt : writers){
jpayne@68 341 wt.add(poison);
jpayne@68 342 }
jpayne@68 343
jpayne@68 344 //Wait for termination
jpayne@68 345 for(WriteThread wt : writers){
jpayne@68 346 // System.out.println("wt"+wt.num+" is alive: "+wt.isAlive());
jpayne@68 347 while(wt.isAlive()){
jpayne@68 348 // System.out.println("wt"+wt.num+" is alive: "+wt.isAlive());
jpayne@68 349 try {
jpayne@68 350 wt.join(10000);
jpayne@68 351 } catch (InterruptedException e) {
jpayne@68 352 // TODO Auto-generated catch block
jpayne@68 353 e.printStackTrace();
jpayne@68 354 }
jpayne@68 355 if(wt.isAlive()){System.err.println(wt.getClass().getCanonicalName()+" is taking a long time to die.");}
jpayne@68 356 }
jpayne@68 357 cellsUsed+=wt.cellsUsedPersonal;
jpayne@68 358 // System.out.println("cellsUsed="+cellsUsed);
jpayne@68 359 }
jpayne@68 360
jpayne@68 361 assert(!finished);
jpayne@68 362 finished=true;
jpayne@68 363 }
jpayne@68 364 }
jpayne@68 365
jpayne@68 366 private class WriteThread extends Thread{
jpayne@68 367
jpayne@68 368 public WriteThread(int tnum){
jpayne@68 369 num=tnum;
jpayne@68 370 }
jpayne@68 371
jpayne@68 372 @Override
jpayne@68 373 public void run(){
jpayne@68 374 assert(matrix[num]==null);
jpayne@68 375 array=new int[wordsPerArray]; //Makes NUMA systems use local memory.
jpayne@68 376 // assert(false);
jpayne@68 377 matrix[num]=array;
jpayne@68 378
jpayne@68 379 // assert(num==1);
jpayne@68 380
jpayne@68 381 long[] keys=null;
jpayne@68 382 while(!shutdown){
jpayne@68 383 // assert(false);
jpayne@68 384
jpayne@68 385 if(verbose){System.err.println(" - Reading keys for wt"+num+".");}
jpayne@68 386 while(keys==null){
jpayne@68 387 // System.out.println("Searching for keys.");
jpayne@68 388 try {
jpayne@68 389 keys=writeQueue.take();
jpayne@68 390 } catch (InterruptedException e) {
jpayne@68 391 // TODO Auto-generated catch block
jpayne@68 392 e.printStackTrace();
jpayne@68 393 }
jpayne@68 394 // System.out.println("*******************************************Found keys: "+keys.length);
jpayne@68 395 // assert(false);
jpayne@68 396 }
jpayne@68 397 if(keys==poison){
jpayne@68 398 // assert(false) : " ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~0 ";
jpayne@68 399 shutdown=true;
jpayne@68 400 }else{
jpayne@68 401 // assert(false) : " ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~1 ";
jpayne@68 402 for(long rawKey : keys){
jpayne@68 403 // assert(false) : " ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~2 ";
jpayne@68 404 if(verbose){System.err.println("Writer "+num+" considering raw key "+rawKey);}
jpayne@68 405 long key2=rawKey;
jpayne@68 406 // int y=read(rawKey);
jpayne@68 407 if((key2&arrayMask)==num){
jpayne@68 408 int x=incrementHashedLocal(key2);
jpayne@68 409 assert(x>=0) : "i="+0+", original=?, new should be >=0, new="+readHashed(key2)+", max="+maxValue+", key="+rawKey;
jpayne@68 410 if(verbose){System.err.println("postIncr value="+readHashed(key2));}
jpayne@68 411
jpayne@68 412 // assert(false) : " ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~4 ";
jpayne@68 413 }
jpayne@68 414
jpayne@68 415 for(int i=1; i<hashes; i++){
jpayne@68 416 key2=Long.rotateRight(key2, hashBits);
jpayne@68 417 key2=hash(key2, i);
jpayne@68 418 // assert(false) : " ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~3 ";
jpayne@68 419 if(verbose){System.err.println("rawKey="+rawKey+", i="+i+", key2="+key2+", value="+readHashed(key2));}
jpayne@68 420 if((key2&arrayMask)==num){
jpayne@68 421 int x=incrementHashedLocal(key2);
jpayne@68 422 assert(x>=0) : "i="+i+", original=?, new should be >=0, new="+readHashed(key2)+", max="+maxValue+", key="+rawKey;
jpayne@68 423 if(verbose){System.err.println("postIncr value="+readHashed(key2));}
jpayne@68 424
jpayne@68 425 // assert(false) : " ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~4 ";
jpayne@68 426 }
jpayne@68 427
jpayne@68 428 // assert(false) : " ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~5 ";
jpayne@68 429 }
jpayne@68 430 // int z=read(rawKey);
jpayne@68 431 // assert(hashes!=1 || !b || z==maxValue || z==y+1) : "b="+b+", y="+y+", z="+z+", rawKey="+rawKey+", num="+num;
jpayne@68 432 }
jpayne@68 433 }
jpayne@68 434 // System.out.println(" -- Read keys for wt"+num+". poison="+(keys==poison)+", len="+keys.length);
jpayne@68 435 if(verbose){System.err.println(" -- Read keys for wt"+num+". (success)");}
jpayne@68 436 keys=null;
jpayne@68 437 if(verbose){System.err.println("shutdown="+shutdown);}
jpayne@68 438 }
jpayne@68 439
jpayne@68 440 // System.out.println(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I died: "+shutdown+", "+(keys==null)+".");
jpayne@68 441 // assert(false) : ">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I died: "+shutdown+", "+(keys==null)+".";
jpayne@68 442
jpayne@68 443 array=null;
jpayne@68 444 }
jpayne@68 445
jpayne@68 446 void add(long[] keys){
jpayne@68 447 // assert(isAlive());
jpayne@68 448
jpayne@68 449 // assert(!shutdown);
jpayne@68 450 // if(shutdown){return;}
jpayne@68 451
jpayne@68 452 if(verbose){System.err.println(" + Adding keys to wt"+num+".");}
jpayne@68 453 boolean success=false;
jpayne@68 454 while(!success){
jpayne@68 455 try {
jpayne@68 456 writeQueue.put(keys);
jpayne@68 457 success=true;
jpayne@68 458 } catch (InterruptedException e) {
jpayne@68 459 // TODO Auto-generated catch block
jpayne@68 460 e.printStackTrace();
jpayne@68 461 }
jpayne@68 462 }
jpayne@68 463 if(verbose){System.err.println(" ++ Added keys to wt"+num+". (success)");}
jpayne@68 464 }
jpayne@68 465
jpayne@68 466 private int incrementHashedLocal(final long key_){
jpayne@68 467 if(verbose){System.err.println("\n*** wt"+num+" incrementing hashed key "+key_+" ***");}
jpayne@68 468 assert((key_&arrayMask)==num);
jpayne@68 469 long key=(key_>>>arrayBits)%(cellMod);
jpayne@68 470 int index=(int)(key>>>indexShift);
jpayne@68 471 int word=array[index];
jpayne@68 472 int cellShift=(int)(cellBits*key);
jpayne@68 473 int value=((word>>>cellShift)&valueMask);
jpayne@68 474 if(value==0){cellsUsedPersonal++;}
jpayne@68 475 value=min(value+1, maxValue);
jpayne@68 476 word=(value<<cellShift)|(word&~((valueMask)<<cellShift));
jpayne@68 477 array[index]=word;
jpayne@68 478 if(verbose){System.err.println("\n*** wt"+num+" Incremented hashed key "+key_+". Value = "+readHashed(key_)+" ***");}
jpayne@68 479 return value;
jpayne@68 480 }
jpayne@68 481
jpayne@68 482 private int[] array;
jpayne@68 483 private final int num;
jpayne@68 484 public long cellsUsedPersonal=0;
jpayne@68 485
jpayne@68 486 public ArrayBlockingQueue<long[]> writeQueue=new ArrayBlockingQueue<long[]>(8);
jpayne@68 487 public boolean shutdown=false;
jpayne@68 488
jpayne@68 489 }
jpayne@68 490
jpayne@68 491
jpayne@68 492 public long cellsUsed(){return cellsUsed;}
jpayne@68 493
jpayne@68 494 private boolean finished=false;
jpayne@68 495
jpayne@68 496 private long cellsUsed;
jpayne@68 497 final int[][] matrix;
jpayne@68 498 private final WriteThread[] writers=new WriteThread[numArrays];
jpayne@68 499 final int hashes;
jpayne@68 500 final int wordsPerArray;
jpayne@68 501 private final long cellsPerArray;
jpayne@68 502 final long cellMod;
jpayne@68 503 private final long[][] hashMasks=makeMasks(8, hashArrayLength);
jpayne@68 504
jpayne@68 505 private long[] buffer=new long[2000];
jpayne@68 506 private int bufferlen=0;
jpayne@68 507
jpayne@68 508 private static final int hashBits=6;
jpayne@68 509 private static final int hashArrayLength=1<<hashBits;
jpayne@68 510 private static final int hashCellMask=hashArrayLength-1;
jpayne@68 511 static final long[] poison=new long[0];
jpayne@68 512
jpayne@68 513 private static long counter=0;
jpayne@68 514
jpayne@68 515 }