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annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/kmer/KmerNode2D.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.Arrays;
jpayne@68 4 import java.util.concurrent.atomic.AtomicLong;
jpayne@68 5
jpayne@68 6 import fileIO.ByteStreamWriter;
jpayne@68 7 import shared.KillSwitch;
jpayne@68 8 import shared.Shared;
jpayne@68 9 import shared.Tools;
jpayne@68 10 import structures.ByteBuilder;
jpayne@68 11
jpayne@68 12 /**
jpayne@68 13 * Allows multiple values per kmer.
jpayne@68 14 * @author Brian Bushnell
jpayne@68 15 * @date Nov 7, 2014
jpayne@68 16 *
jpayne@68 17 */
jpayne@68 18 public class KmerNode2D extends KmerNode {
jpayne@68 19
jpayne@68 20 /*--------------------------------------------------------------*/
jpayne@68 21 /*---------------- Initialization ----------------*/
jpayne@68 22 /*--------------------------------------------------------------*/
jpayne@68 23
jpayne@68 24 public KmerNode2D(long pivot_){
jpayne@68 25 super(pivot_);
jpayne@68 26 }
jpayne@68 27
jpayne@68 28 public KmerNode2D(long pivot_, int value_){
jpayne@68 29 super(pivot_);
jpayne@68 30 assert(value_>=0 || value_==-1);
jpayne@68 31 values=new int[] {value_, -1};
jpayne@68 32 numValues=1;
jpayne@68 33 }
jpayne@68 34
jpayne@68 35 public KmerNode2D(long pivot_, int[] vals_, int vlen){
jpayne@68 36 super(pivot_);
jpayne@68 37 values=vals_;
jpayne@68 38 numValues=vlen;
jpayne@68 39 assert(values!=null || vlen==0);
jpayne@68 40 assert(values==null || (vlen<=values.length && vlen>=0));
jpayne@68 41 // assert(countValues(values)==vlen) : countValues(values)+", "+vlen; //TODO: Slow assertion //123
jpayne@68 42 }
jpayne@68 43
jpayne@68 44 @Override
jpayne@68 45 public final KmerNode makeNode(long pivot_, int value_){
jpayne@68 46 return new KmerNode2D(pivot_, value_);
jpayne@68 47 }
jpayne@68 48
jpayne@68 49 @Override
jpayne@68 50 public final KmerNode makeNode(long pivot_, int[] values_, int vlen){
jpayne@68 51 return new KmerNode2D(pivot_, values_, vlen);
jpayne@68 52 }
jpayne@68 53
jpayne@68 54 /*--------------------------------------------------------------*/
jpayne@68 55 /*---------------- Public Methods ----------------*/
jpayne@68 56 /*--------------------------------------------------------------*/
jpayne@68 57
jpayne@68 58 // public final int set_Test(final long kmer, final int v[]){
jpayne@68 59 // assert(TESTMODE);
jpayne@68 60 // final int x;
jpayne@68 61 // if(TWOD()){
jpayne@68 62 // int[] old=getValues(kmer, null);
jpayne@68 63 // assert(old==null || contains(kmer, old));
jpayne@68 64 // x=set0(kmer, v);
jpayne@68 65 // assert(old==null || contains(kmer, old));
jpayne@68 66 // assert(contains(kmer, v));
jpayne@68 67 // }else{
jpayne@68 68 // int old=getValue(kmer);
jpayne@68 69 // assert(old==0 || old==-1 || contains(kmer, old));
jpayne@68 70 // x=set0(kmer, v);
jpayne@68 71 // assert(contains(kmer, v)) : "old="+old+", v="+v+", kmer="+kmer+", get(kmer)="+getValue(kmer);
jpayne@68 72 // assert(v[0]==old || !contains(kmer, old));
jpayne@68 73 // }
jpayne@68 74 // return x;
jpayne@68 75 // }
jpayne@68 76
jpayne@68 77 /** Returns number of nodes added */
jpayne@68 78 @Override
jpayne@68 79 public int set(long kmer, int vals[], int vlen){
jpayne@68 80 if(pivot<0){pivot=kmer; insertValue(vals, vlen); return 1;} //Allows initializing empty nodes to -1
jpayne@68 81 if(kmer<pivot){
jpayne@68 82 if(left==null){left=new KmerNode2D(kmer, vals, vlen); return 1;}
jpayne@68 83 return left.set(kmer, vals, vlen);
jpayne@68 84 }else if(kmer>pivot){
jpayne@68 85 if(right==null){right=new KmerNode2D(kmer, vals, vlen); return 1;}
jpayne@68 86 return right.set(kmer, vals, vlen);
jpayne@68 87 }else{
jpayne@68 88 insertValue(vals, vlen);
jpayne@68 89 }
jpayne@68 90 return 0;
jpayne@68 91 }
jpayne@68 92
jpayne@68 93 /*--------------------------------------------------------------*/
jpayne@68 94 /*---------------- Nonpublic Methods ----------------*/
jpayne@68 95 /*--------------------------------------------------------------*/
jpayne@68 96
jpayne@68 97 @Override
jpayne@68 98 protected int value(){return values==null ? 0 : values[0];}
jpayne@68 99
jpayne@68 100 @Override
jpayne@68 101 protected int[] values(int[] singleton){
jpayne@68 102 return values;
jpayne@68 103 }
jpayne@68 104
jpayne@68 105 @Override
jpayne@68 106 public int set(int value_){
jpayne@68 107 insertValue(value_);
jpayne@68 108 return value_;
jpayne@68 109 }
jpayne@68 110
jpayne@68 111 @Override
jpayne@68 112 protected int set(int[] values_, int vlen){
jpayne@68 113 int ret=(values==null ? 1 : 0);
jpayne@68 114 insertValue(values_, vlen);
jpayne@68 115 return ret;
jpayne@68 116 }
jpayne@68 117
jpayne@68 118 @Override
jpayne@68 119 int numValues(){
jpayne@68 120 // assert(countValues(values)==numValues) : countValues(values)+", "+numValues; //TODO: Slow assertion //123
jpayne@68 121 return numValues;
jpayne@68 122 // asdf
jpayne@68 123 // if(values==null){return 0;}
jpayne@68 124 // for(int i=0; i<values.length; i++){
jpayne@68 125 // if(values[i]==-1){return i;}
jpayne@68 126 // }
jpayne@68 127 // return values.length;
jpayne@68 128 }
jpayne@68 129
jpayne@68 130 /*--------------------------------------------------------------*/
jpayne@68 131 /*---------------- Private Methods ----------------*/
jpayne@68 132 /*--------------------------------------------------------------*/
jpayne@68 133
jpayne@68 134 /** Returns number of values added */
jpayne@68 135 private int insertValue(int v){
jpayne@68 136 return insertIntoList(v);
jpayne@68 137 }
jpayne@68 138
jpayne@68 139 /** Returns number of values added */
jpayne@68 140 private int insertValue(int[] vals, int vlen){
jpayne@68 141 // assert(countValues(vals)==vlen) : countValues(vals)+", "+vlen; //TODO: Slow assertion //123
jpayne@68 142 assert(vals!=null || vlen==0);
jpayne@68 143 assert(vals==null || (vlen<=vals.length && vlen>=0));
jpayne@68 144 if(values==null){
jpayne@68 145 values=vals;
jpayne@68 146 numValues=vlen;
jpayne@68 147 return 1;
jpayne@68 148 }
jpayne@68 149 for(int v : vals){
jpayne@68 150 if(v<0){break;}
jpayne@68 151 insertIntoList(v);
jpayne@68 152 }
jpayne@68 153 return 0;
jpayne@68 154 }
jpayne@68 155
jpayne@68 156 private final int countValues(int[] vals){
jpayne@68 157 if(vals==null) {return 0;}
jpayne@68 158 int count=0;
jpayne@68 159 for(int v : vals){
jpayne@68 160 if(v>=0){
jpayne@68 161 count++;
jpayne@68 162 }else{
jpayne@68 163 break;
jpayne@68 164 }
jpayne@68 165 }
jpayne@68 166 return count;
jpayne@68 167 }
jpayne@68 168
jpayne@68 169 private final int insertIntoList(final int v){
jpayne@68 170 // assert(countValues(values)==numValues) : countValues(values)+", "+numValues; //TODO: Slow assertion //123
jpayne@68 171 assert(v>=0);
jpayne@68 172
jpayne@68 173 if(values==null){
jpayne@68 174 values=new int[] {v, -1};
jpayne@68 175 numValues=1;
jpayne@68 176 return 1;
jpayne@68 177 }
jpayne@68 178
jpayne@68 179 for(int i=numValues-1, lim=Tools.max(0, numValues-slowAddLimit); i>=lim; i--){//This is the slow bit
jpayne@68 180 if(values[i]==v){return 0;}
jpayne@68 181 if(values[i]<0){
jpayne@68 182 values[i]=v;
jpayne@68 183 numValues++;
jpayne@68 184 return 1;
jpayne@68 185 }
jpayne@68 186 }
jpayne@68 187 //At this point the size is big, or the element was not found
jpayne@68 188
jpayne@68 189 if(numValues>=values.length){//resize
jpayne@68 190 assert(numValues==values.length);
jpayne@68 191 final int oldSize=values.length;
jpayne@68 192 final int newSize=(int)Tools.min(Shared.MAX_ARRAY_LEN, oldSize*2L);
jpayne@68 193 assert(newSize>values.length) : "Overflow.";
jpayne@68 194 values=KillSwitch.copyOf(values, newSize);
jpayne@68 195 Arrays.fill(values, oldSize, newSize, -1);
jpayne@68 196 }
jpayne@68 197
jpayne@68 198 //quick add
jpayne@68 199 assert(values[numValues]<0);
jpayne@68 200 values[numValues]=v;
jpayne@68 201 numValues++;
jpayne@68 202
jpayne@68 203 // assert(countValues(values)==numValues) : countValues(values)+", "+numValues; //TODO: Slow assertion //123
jpayne@68 204 return 1;
jpayne@68 205 }
jpayne@68 206
jpayne@68 207 /*--------------------------------------------------------------*/
jpayne@68 208 /*---------------- Resizing and Rebalancing ----------------*/
jpayne@68 209 /*--------------------------------------------------------------*/
jpayne@68 210
jpayne@68 211 @Override
jpayne@68 212 boolean canResize() {
jpayne@68 213 return false;
jpayne@68 214 }
jpayne@68 215
jpayne@68 216 @Override
jpayne@68 217 public boolean canRebalance() {
jpayne@68 218 return true;
jpayne@68 219 }
jpayne@68 220
jpayne@68 221 @Deprecated
jpayne@68 222 @Override
jpayne@68 223 public int arrayLength() {
jpayne@68 224 throw new RuntimeException("Unsupported.");
jpayne@68 225 }
jpayne@68 226
jpayne@68 227 @Deprecated
jpayne@68 228 @Override
jpayne@68 229 void resize() {
jpayne@68 230 throw new RuntimeException("Unsupported.");
jpayne@68 231 }
jpayne@68 232
jpayne@68 233 @Deprecated
jpayne@68 234 @Override
jpayne@68 235 public void rebalance() {
jpayne@68 236 throw new RuntimeException("Please call rebalance(ArrayList<KmerNode>) instead, with an empty list.");
jpayne@68 237 }
jpayne@68 238
jpayne@68 239 /*--------------------------------------------------------------*/
jpayne@68 240 /*---------------- Info Dumping ----------------*/
jpayne@68 241 /*--------------------------------------------------------------*/
jpayne@68 242
jpayne@68 243 @Override
jpayne@68 244 public final boolean dumpKmersAsBytes(ByteStreamWriter bsw, int k, int mincount, int maxcount, AtomicLong remaining){
jpayne@68 245 if(values==null){return true;}
jpayne@68 246 if(remaining!=null && remaining.decrementAndGet()<0){return true;}
jpayne@68 247 bsw.printlnKmer(pivot, values, k);
jpayne@68 248 if(left!=null){left.dumpKmersAsBytes(bsw, k, mincount, maxcount, remaining);}
jpayne@68 249 if(right!=null){right.dumpKmersAsBytes(bsw, k, mincount, maxcount, remaining);}
jpayne@68 250 return true;
jpayne@68 251 }
jpayne@68 252
jpayne@68 253 @Override
jpayne@68 254 public final boolean dumpKmersAsBytes_MT(final ByteStreamWriter bsw, final ByteBuilder bb, final int k, final int mincount, int maxcount, AtomicLong remaining){
jpayne@68 255 if(values==null){return true;}
jpayne@68 256 if(remaining!=null && remaining.decrementAndGet()<0){return true;}
jpayne@68 257 toBytes(pivot, values, k, bb);
jpayne@68 258 bb.nl();
jpayne@68 259 if(bb.length()>=16000){
jpayne@68 260 ByteBuilder bb2=new ByteBuilder(bb);
jpayne@68 261 synchronized(bsw){bsw.addJob(bb2);}
jpayne@68 262 bb.clear();
jpayne@68 263 }
jpayne@68 264 if(left!=null){left.dumpKmersAsBytes_MT(bsw, bb, k, mincount, maxcount, remaining);}
jpayne@68 265 if(right!=null){right.dumpKmersAsBytes_MT(bsw, bb, k, mincount, maxcount, remaining);}
jpayne@68 266 return true;
jpayne@68 267 }
jpayne@68 268
jpayne@68 269 @Override
jpayne@68 270 protected final StringBuilder dumpKmersAsText(StringBuilder sb, int k, int mincount, int maxcount){
jpayne@68 271 if(values==null){return sb;}
jpayne@68 272 if(sb==null){sb=new StringBuilder(32);}
jpayne@68 273 sb.append(AbstractKmerTable.toText(pivot, values, k)).append('\n');
jpayne@68 274 if(left!=null){left.dumpKmersAsText(sb, k, mincount, maxcount);}
jpayne@68 275 if(right!=null){right.dumpKmersAsText(sb, k, mincount, maxcount);}
jpayne@68 276 return sb;
jpayne@68 277 }
jpayne@68 278
jpayne@68 279 @Override
jpayne@68 280 protected final ByteBuilder dumpKmersAsText(ByteBuilder bb, int k, int mincount, int maxcount){
jpayne@68 281 if(values==null){return bb;}
jpayne@68 282 if(bb==null){bb=new ByteBuilder(32);}
jpayne@68 283 bb.append(AbstractKmerTable.toBytes(pivot, values, k)).append('\n');
jpayne@68 284 if(left!=null){left.dumpKmersAsText(bb, k, mincount, maxcount);}
jpayne@68 285 if(right!=null){right.dumpKmersAsText(bb, k, mincount, maxcount);}
jpayne@68 286 return bb;
jpayne@68 287 }
jpayne@68 288
jpayne@68 289 @Override
jpayne@68 290 final boolean TWOD(){return true;}
jpayne@68 291
jpayne@68 292 /*--------------------------------------------------------------*/
jpayne@68 293 /*---------------- Invalid Methods ----------------*/
jpayne@68 294 /*--------------------------------------------------------------*/
jpayne@68 295
jpayne@68 296 /*--------------------------------------------------------------*/
jpayne@68 297 /*---------------- Fields ----------------*/
jpayne@68 298 /*--------------------------------------------------------------*/
jpayne@68 299
jpayne@68 300 int[] values;
jpayne@68 301 private int numValues;
jpayne@68 302 private static final int slowAddLimit=4;
jpayne@68 303
jpayne@68 304 }