Mercurial > repos > rliterman > csp2

annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/kmer/HashBuffer.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 kmer;
jpayne@68 2
jpayne@68 3 import java.util.concurrent.atomic.AtomicLong;
jpayne@68 4
jpayne@68 5 import fileIO.ByteStreamWriter;
jpayne@68 6 import fileIO.TextStreamWriter;
jpayne@68 7 import structures.ByteBuilder;
jpayne@68 8 import structures.SuperLongList;
jpayne@68 9
jpayne@68 10 /**
jpayne@68 11 * @author Brian Bushnell
jpayne@68 12 * @date Nov 22, 2013
jpayne@68 13 *
jpayne@68 14 */
jpayne@68 15 public class HashBuffer extends AbstractKmerTable {
jpayne@68 16
jpayne@68 17 /*--------------------------------------------------------------*/
jpayne@68 18 /*---------------- Initialization ----------------*/
jpayne@68 19 /*--------------------------------------------------------------*/
jpayne@68 20
jpayne@68 21 public HashBuffer(AbstractKmerTable[] tables_, int buflen_, int k_, boolean initValues, boolean setIfNotPresent_){
jpayne@68 22 tables=tables_;
jpayne@68 23 buflen=buflen_;
jpayne@68 24 halflen=(int)Math.ceil(buflen*0.5);
jpayne@68 25 ways=tables.length;
jpayne@68 26 buffers=new KmerBuffer[ways];
jpayne@68 27 setIfNotPresent=setIfNotPresent_;
jpayne@68 28 useValues=initValues;
jpayne@68 29 coreMask=(AbstractKmerTableSet.MASK_CORE ? ~(((-1L)<<(2*(k_-1)))|3) : -1L);
jpayne@68 30 for(int i=0; i<ways; i++){
jpayne@68 31 buffers[i]=new KmerBuffer(buflen, k_, useValues);
jpayne@68 32 }
jpayne@68 33 }
jpayne@68 34
jpayne@68 35 /*--------------------------------------------------------------*/
jpayne@68 36 /*---------------- Public Methods ----------------*/
jpayne@68 37 /*--------------------------------------------------------------*/
jpayne@68 38
jpayne@68 39 public final int kmerToWay(final long kmer){
jpayne@68 40 final int way=(int)((kmer&coreMask)%ways);
jpayne@68 41 return way;
jpayne@68 42 }
jpayne@68 43
jpayne@68 44 @Override
jpayne@68 45 public int incrementAndReturnNumCreated(final long kmer, final int incr) {
jpayne@68 46 assert(incr==1); //I could just add the kmer multiple times if not true, with addMulti
jpayne@68 47 final int way=kmerToWay(kmer);
jpayne@68 48 KmerBuffer buffer=buffers[way];
jpayne@68 49 // final int size=buffer.addMulti(kmer, incr);
jpayne@68 50 final int size=buffer.add(kmer);
jpayne@68 51 if(size>=halflen && (size>=buflen || (size&SIZEMASK)==0)){
jpayne@68 52 return dumpBuffer(way, size>=buflen);
jpayne@68 53 }
jpayne@68 54 return 0;
jpayne@68 55 }
jpayne@68 56
jpayne@68 57 @Override
jpayne@68 58 public final long flush(){
jpayne@68 59 long added=0;
jpayne@68 60 for(int i=0; i<ways; i++){added+=dumpBuffer(i, true);}
jpayne@68 61 return added;
jpayne@68 62 }
jpayne@68 63
jpayne@68 64 @Override
jpayne@68 65 public int set(long kmer, int value) {
jpayne@68 66 final int way=kmerToWay(kmer);
jpayne@68 67 KmerBuffer buffer=buffers[way];
jpayne@68 68 final int size=buffer.add(kmer, value);
jpayne@68 69 if(size>=halflen && (size>=buflen || (size&SIZEMASK)==0)){
jpayne@68 70 return dumpBuffer(way, size>=buflen);
jpayne@68 71 }
jpayne@68 72 return 0;
jpayne@68 73 }
jpayne@68 74
jpayne@68 75 @Override
jpayne@68 76 public int set(long kmer, int[] vals, int vlen) {
jpayne@68 77 throw new RuntimeException("Unimplemented method; this class lacks value buffers");
jpayne@68 78 }
jpayne@68 79
jpayne@68 80 @Override
jpayne@68 81 public int setIfNotPresent(long kmer, int value) {
jpayne@68 82 throw new RuntimeException("Unimplemented method; this class lacks value buffers");
jpayne@68 83 }
jpayne@68 84
jpayne@68 85 @Override
jpayne@68 86 public int getValue(long kmer) {
jpayne@68 87 final int way=kmerToWay(kmer);
jpayne@68 88 return tables[way].getValue(kmer);
jpayne@68 89 }
jpayne@68 90
jpayne@68 91 @Override
jpayne@68 92 public int[] getValues(long kmer, int[] singleton){
jpayne@68 93 final int way=kmerToWay(kmer);
jpayne@68 94 return tables[way].getValues(kmer, singleton);
jpayne@68 95 }
jpayne@68 96
jpayne@68 97 @Override
jpayne@68 98 public boolean contains(long kmer) {
jpayne@68 99 final int way=kmerToWay(kmer);
jpayne@68 100 return tables[way].contains(kmer);
jpayne@68 101 }
jpayne@68 102
jpayne@68 103
jpayne@68 104
jpayne@68 105 /*--------------------------------------------------------------*/
jpayne@68 106 /*---------------- Ownership ----------------*/
jpayne@68 107 /*--------------------------------------------------------------*/
jpayne@68 108
jpayne@68 109 @Override
jpayne@68 110 public final void initializeOwnership(){
jpayne@68 111 for(AbstractKmerTable t : tables){t.initializeOwnership();}
jpayne@68 112 }
jpayne@68 113
jpayne@68 114 @Override
jpayne@68 115 public final void clearOwnership(){
jpayne@68 116 for(AbstractKmerTable t : tables){t.clearOwnership();}
jpayne@68 117 }
jpayne@68 118
jpayne@68 119 @Override
jpayne@68 120 public final int setOwner(final long kmer, final int newOwner){
jpayne@68 121 final int way=kmerToWay(kmer);
jpayne@68 122 return tables[way].setOwner(kmer, newOwner);
jpayne@68 123 }
jpayne@68 124
jpayne@68 125 @Override
jpayne@68 126 public final boolean clearOwner(final long kmer, final int owner){
jpayne@68 127 final int way=kmerToWay(kmer);
jpayne@68 128 return tables[way].clearOwner(kmer, owner);
jpayne@68 129 }
jpayne@68 130
jpayne@68 131 @Override
jpayne@68 132 public final int getOwner(final long kmer){
jpayne@68 133 final int way=kmerToWay(kmer);
jpayne@68 134 return tables[way].getOwner(kmer);
jpayne@68 135 }
jpayne@68 136
jpayne@68 137 /*--------------------------------------------------------------*/
jpayne@68 138 /*---------------- Nonpublic Methods ----------------*/
jpayne@68 139 /*--------------------------------------------------------------*/
jpayne@68 140
jpayne@68 141 @Override
jpayne@68 142 Object get(long kmer) {
jpayne@68 143 final int way=kmerToWay(kmer);
jpayne@68 144 return tables[way].get(kmer);
jpayne@68 145 }
jpayne@68 146
jpayne@68 147 /*--------------------------------------------------------------*/
jpayne@68 148 /*---------------- Private Methods ----------------*/
jpayne@68 149 /*--------------------------------------------------------------*/
jpayne@68 150
jpayne@68 151 private int dumpBuffer(final int way, boolean force){
jpayne@68 152 final KmerBuffer buffer=buffers[way];
jpayne@68 153 final AbstractKmerTable table=tables[way];
jpayne@68 154 final int lim=buffer.size();
jpayne@68 155 if(lim<0){return 0;}
jpayne@68 156
jpayne@68 157 if(force){table.lock();}
jpayne@68 158 else if(!table.tryLock()){return 0;}
jpayne@68 159
jpayne@68 160 if(SORT_BUFFERS && buffer.values==null){//Can go before or after lock; neither helps much
jpayne@68 161 buffer.kmers.sortSerial();
jpayne@68 162 }
jpayne@68 163
jpayne@68 164 final int x=dumpBuffer_inner(way);
jpayne@68 165 table.unlock();
jpayne@68 166 return x;
jpayne@68 167 }
jpayne@68 168
jpayne@68 169 private int dumpBuffer_inner(final int way){
jpayne@68 170 if(verbose){System.err.println("Dumping buffer for way "+way+" of "+ways);}
jpayne@68 171 final KmerBuffer buffer=buffers[way];
jpayne@68 172 final int lim=buffer.size();
jpayne@68 173 if(lim<1){return 0;}
jpayne@68 174 final long[] kmers=buffer.kmers.array;
jpayne@68 175 final int[] values=(buffer.values==null ? null : buffer.values.array);
jpayne@68 176 if(lim<1){return 0;}
jpayne@68 177 int added=0;
jpayne@68 178 final AbstractKmerTable table=tables[way];
jpayne@68 179 // synchronized(table){
jpayne@68 180 if(values==null){
jpayne@68 181 // Arrays.sort(kmers, 0, lim); //Makes it slower
jpayne@68 182 if(SORT_BUFFERS){
jpayne@68 183 long prev=-1;
jpayne@68 184 int sum=0;
jpayne@68 185 for(int i=0; i<lim; i++){
jpayne@68 186 final long kmer=kmers[i];
jpayne@68 187 if(kmer==prev){
jpayne@68 188 sum++;
jpayne@68 189 }else{
jpayne@68 190 if(sum>0){added+=table.incrementAndReturnNumCreated(prev, sum);}
jpayne@68 191 prev=kmer;
jpayne@68 192 sum=1;
jpayne@68 193 }
jpayne@68 194 }
jpayne@68 195 if(sum>0){added+=table.incrementAndReturnNumCreated(prev, sum);}
jpayne@68 196 }else{
jpayne@68 197 for(int i=0; i<lim; i++){
jpayne@68 198 final long kmer=kmers[i];
jpayne@68 199 added+=table.incrementAndReturnNumCreated(kmer, 1);
jpayne@68 200 }
jpayne@68 201 }
jpayne@68 202 }else{
jpayne@68 203 if(setIfNotPresent){
jpayne@68 204 for(int i=0; i<lim; i++){
jpayne@68 205 final long kmer=kmers[i];
jpayne@68 206 final int value=values[i];
jpayne@68 207 added+=table.setIfNotPresent(kmer, value);
jpayne@68 208 }
jpayne@68 209 }else{
jpayne@68 210 for(int i=0; i<lim; i++){
jpayne@68 211 final long kmer=kmers[i];
jpayne@68 212 final int value=values[i];
jpayne@68 213 added+=table.set(kmer, value);
jpayne@68 214 // System.err.println("B: "+kmer+", "+Arrays.toString(((HashArrayHybrid)table).getValues(kmer, new int[1])));
jpayne@68 215 }
jpayne@68 216 }
jpayne@68 217 }
jpayne@68 218 // }
jpayne@68 219 buffer.clear();
jpayne@68 220 uniqueAdded+=added;
jpayne@68 221 return added;
jpayne@68 222 }
jpayne@68 223
jpayne@68 224 /*--------------------------------------------------------------*/
jpayne@68 225 /*---------------- Resizing and Rebalancing ----------------*/
jpayne@68 226 /*--------------------------------------------------------------*/
jpayne@68 227
jpayne@68 228 @Override
jpayne@68 229 final boolean canResize() {return false;}
jpayne@68 230
jpayne@68 231 @Override
jpayne@68 232 public final boolean canRebalance() {return false;}
jpayne@68 233
jpayne@68 234 @Deprecated
jpayne@68 235 @Override
jpayne@68 236 public long size() {
jpayne@68 237 throw new RuntimeException("Unimplemented.");
jpayne@68 238 }
jpayne@68 239
jpayne@68 240 @Deprecated
jpayne@68 241 @Override
jpayne@68 242 public int arrayLength() {
jpayne@68 243 throw new RuntimeException("Unimplemented.");
jpayne@68 244 }
jpayne@68 245
jpayne@68 246 @Deprecated
jpayne@68 247 @Override
jpayne@68 248 void resize() {
jpayne@68 249 throw new RuntimeException("Unimplemented.");
jpayne@68 250 }
jpayne@68 251
jpayne@68 252 @Deprecated
jpayne@68 253 @Override
jpayne@68 254 public void rebalance() {
jpayne@68 255 throw new RuntimeException("Unimplemented.");
jpayne@68 256 }
jpayne@68 257
jpayne@68 258 @Override
jpayne@68 259 public long regenerate(final int limit){
jpayne@68 260 long sum=0;
jpayne@68 261 for(AbstractKmerTable table : tables){
jpayne@68 262 sum+=table.regenerate(limit);
jpayne@68 263 }
jpayne@68 264 return sum;
jpayne@68 265 }
jpayne@68 266
jpayne@68 267 /*--------------------------------------------------------------*/
jpayne@68 268 /*---------------- Info Dumping ----------------*/
jpayne@68 269 /*--------------------------------------------------------------*/
jpayne@68 270
jpayne@68 271 @Override
jpayne@68 272 public boolean dumpKmersAsText(TextStreamWriter tsw, int k, int mincount, int maxcount){
jpayne@68 273 for(AbstractKmerTable table : tables){
jpayne@68 274 table.dumpKmersAsText(tsw, k, mincount, maxcount);
jpayne@68 275 }
jpayne@68 276 return true;
jpayne@68 277 }
jpayne@68 278
jpayne@68 279 @Override
jpayne@68 280 public boolean dumpKmersAsBytes(ByteStreamWriter bsw, int k, int mincount, int maxcount, AtomicLong remaining){
jpayne@68 281 for(AbstractKmerTable table : tables){
jpayne@68 282 table.dumpKmersAsBytes(bsw, k, mincount, maxcount, remaining);
jpayne@68 283 }
jpayne@68 284 return true;
jpayne@68 285 }
jpayne@68 286
jpayne@68 287 @Override
jpayne@68 288 @Deprecated
jpayne@68 289 public boolean dumpKmersAsBytes_MT(final ByteStreamWriter bsw, final ByteBuilder bb, final int k, final int mincount, int maxcount, AtomicLong remaining){
jpayne@68 290 throw new RuntimeException("Unsupported.");
jpayne@68 291 }
jpayne@68 292
jpayne@68 293 @Override
jpayne@68 294 @Deprecated
jpayne@68 295 public void fillHistogram(long[] ca, int max){
jpayne@68 296 throw new RuntimeException("Unsupported.");
jpayne@68 297 }
jpayne@68 298
jpayne@68 299 @Override
jpayne@68 300 @Deprecated
jpayne@68 301 public void fillHistogram(SuperLongList sll){
jpayne@68 302 throw new RuntimeException("Unsupported.");
jpayne@68 303 }
jpayne@68 304
jpayne@68 305 @Override
jpayne@68 306 public void countGC(long[] gcCounts, int max){
jpayne@68 307 for(AbstractKmerTable table : tables){
jpayne@68 308 table.countGC(gcCounts, max);
jpayne@68 309 }
jpayne@68 310 }
jpayne@68 311
jpayne@68 312 /*--------------------------------------------------------------*/
jpayne@68 313 /*---------------- Invalid Methods ----------------*/
jpayne@68 314 /*--------------------------------------------------------------*/
jpayne@68 315
jpayne@68 316 @Override
jpayne@68 317 public int increment(final long kmer, final int incr) {
jpayne@68 318 throw new RuntimeException("Unsupported");
jpayne@68 319 }
jpayne@68 320
jpayne@68 321 /*--------------------------------------------------------------*/
jpayne@68 322 /*---------------- Fields ----------------*/
jpayne@68 323 /*--------------------------------------------------------------*/
jpayne@68 324
jpayne@68 325 private final AbstractKmerTable[] tables;
jpayne@68 326 private final int buflen;
jpayne@68 327 private final int halflen;
jpayne@68 328 private final int ways;
jpayne@68 329 private final boolean useValues;
jpayne@68 330 private final KmerBuffer[] buffers;
jpayne@68 331 private final long coreMask;
jpayne@68 332 public long uniqueAdded=0;
jpayne@68 333
jpayne@68 334 private static final int SIZEMASK=15;
jpayne@68 335 private final boolean setIfNotPresent;
jpayne@68 336
jpayne@68 337 public static boolean SORT_BUFFERS=false;
jpayne@68 338
jpayne@68 339 }