Mercurial > repos > rliterman > csp2

annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/bloom/KCountArray3.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 /**
jpayne@68 4 * @author Brian Bushnell
jpayne@68 5 * @date Aug 17, 2012
jpayne@68 6 *
jpayne@68 7 */
jpayne@68 8 public class KCountArray3 extends KCountArray {
jpayne@68 9
jpayne@68 10 /**
jpayne@68 11 *
jpayne@68 12 */
jpayne@68 13 private static final long serialVersionUID = -5466091642729698944L;
jpayne@68 14
jpayne@68 15 public KCountArray3(long cells_, int bits_){
jpayne@68 16 super(cells_, bits_);
jpayne@68 17 long words=cells/cellsPerWord;
jpayne@68 18 int wordsPerArray=(int)(words/numArrays);
jpayne@68 19 matrix=new int[numArrays][wordsPerArray];
jpayne@68 20 }
jpayne@68 21
jpayne@68 22 @Override
jpayne@68 23 public int read(long key){
jpayne@68 24 if(verbose){System.err.println("Reading "+key);}
jpayne@68 25 // System.out.println("key="+key);
jpayne@68 26 int arrayNum=(int)(key&arrayMask);
jpayne@68 27 // System.out.println("array="+arrayNum);
jpayne@68 28 key>>>=arrayBits;
jpayne@68 29 // System.out.println("key2="+key);
jpayne@68 30 int[] array=matrix[arrayNum];
jpayne@68 31 int index=(int)(key>>>indexShift);
jpayne@68 32 // System.out.println("index="+index);
jpayne@68 33 int word=array[index];
jpayne@68 34 // System.out.println("word="+Integer.toHexString(word));
jpayne@68 35 int cellShift=(int)(cellBits*key);
jpayne@68 36 // System.out.println("cellShift="+cellShift);
jpayne@68 37 int value=(int)((word>>>cellShift)&valueMask);
jpayne@68 38 if(verbose){System.err.println("Read "+value);}
jpayne@68 39 return value;
jpayne@68 40 }
jpayne@68 41
jpayne@68 42 @Override
jpayne@68 43 public void write(long key, int value){
jpayne@68 44 if(verbose){System.err.println("Writing "+key+", "+value);}
jpayne@68 45 int arrayNum=(int)(key&arrayMask);
jpayne@68 46 key>>>=arrayBits;
jpayne@68 47 int[] array=matrix[arrayNum];
jpayne@68 48 int index=(int)(key>>>indexShift);
jpayne@68 49 int word=array[index];
jpayne@68 50 int cellShift=(int)(cellBits*key);
jpayne@68 51 word=(value<<cellShift)|(word&~((valueMask)<<cellShift));
jpayne@68 52 array[index]=word;
jpayne@68 53 }
jpayne@68 54
jpayne@68 55 // static int count138=0;
jpayne@68 56 @Override
jpayne@68 57 public void increment(long key, int incr){
jpayne@68 58 if(verbose){System.err.println("*** Incrementing "+key);}
jpayne@68 59 // if(key==138){
jpayne@68 60 // assert(count138==0) : count138;
jpayne@68 61 // count138++;
jpayne@68 62 // }
jpayne@68 63 int arrayNum=(int)(key&arrayMask);
jpayne@68 64 key>>>=arrayBits;
jpayne@68 65 int[] array=matrix[arrayNum];
jpayne@68 66 int index=(int)(key>>>indexShift);
jpayne@68 67 int word=array[index];
jpayne@68 68 int cellShift=(int)(cellBits*key);
jpayne@68 69 int value=((word>>>cellShift)&valueMask);
jpayne@68 70 if(value==0 && incr>0){cellsUsed++;}
jpayne@68 71 else if(incr<0 && value+incr==0){cellsUsed--;}
jpayne@68 72 value=min(value+incr, maxValue);
jpayne@68 73 word=(value<<cellShift)|(word&~((valueMask)<<cellShift));
jpayne@68 74 array[index]=word;
jpayne@68 75 if(verbose){System.err.println("Returning "+value);}
jpayne@68 76 //return (int)value;
jpayne@68 77 }
jpayne@68 78
jpayne@68 79 /** Returns unincremented value */
jpayne@68 80 @Override
jpayne@68 81 public int incrementAndReturnUnincremented(long key, int incr){
jpayne@68 82 if(verbose){System.err.println("Incrementing2 "+key);}
jpayne@68 83 int arrayNum=(int)(key&arrayMask);
jpayne@68 84 key>>>=arrayBits;
jpayne@68 85 int[] array=matrix[arrayNum];
jpayne@68 86 int index=(int)(key>>>indexShift);
jpayne@68 87 int word=array[index];
jpayne@68 88 int cellShift=(int)(cellBits*key);
jpayne@68 89 final int value=((word>>>cellShift)&valueMask);
jpayne@68 90 final int value2=min(value+incr, maxValue);
jpayne@68 91 word=(value2<<cellShift)|(word&~((valueMask)<<cellShift));
jpayne@68 92 array[index]=word;
jpayne@68 93 if(verbose){System.err.println("Returning "+value);}
jpayne@68 94 return value;
jpayne@68 95 }
jpayne@68 96
jpayne@68 97 @Override
jpayne@68 98 public long[] transformToFrequency(){
jpayne@68 99 return transformToFrequency(matrix);
jpayne@68 100 }
jpayne@68 101
jpayne@68 102 @Override
jpayne@68 103 public String toContentsString(){
jpayne@68 104 StringBuilder sb=new StringBuilder();
jpayne@68 105 sb.append("[");
jpayne@68 106 String comma="";
jpayne@68 107 for(int[] array : matrix){
jpayne@68 108 for(int i=0; i<array.length; i++){
jpayne@68 109 int word=array[i];
jpayne@68 110 for(int j=0; j<cellsPerWord; j++){
jpayne@68 111 int x=word&valueMask;
jpayne@68 112 sb.append(comma);
jpayne@68 113 sb.append(x);
jpayne@68 114 word>>>=cellBits;
jpayne@68 115 comma=", ";
jpayne@68 116 }
jpayne@68 117 }
jpayne@68 118 }
jpayne@68 119 sb.append("]");
jpayne@68 120 return sb.toString();
jpayne@68 121 }
jpayne@68 122
jpayne@68 123 @Override
jpayne@68 124 public double usedFraction(){return cellsUsed/(double)cells;}
jpayne@68 125
jpayne@68 126 @Override
jpayne@68 127 public double usedFraction(int mindepth){return cellsUsed(mindepth)/(double)cells;}
jpayne@68 128
jpayne@68 129 @Override
jpayne@68 130 public long cellsUsed(int mindepth){
jpayne@68 131 long count=0;
jpayne@68 132 for(int[] array : matrix){
jpayne@68 133 if(array!=null){
jpayne@68 134 for(int word : array){
jpayne@68 135 while(word>0){
jpayne@68 136 int x=word&valueMask;
jpayne@68 137 if(x>=mindepth){count++;}
jpayne@68 138 word>>>=cellBits;
jpayne@68 139 }
jpayne@68 140 }
jpayne@68 141 }
jpayne@68 142 }
jpayne@68 143 return count;
jpayne@68 144 }
jpayne@68 145
jpayne@68 146 @Override
jpayne@68 147 long hash(long x, int y) {
jpayne@68 148 assert(false) : "Unsupported.";
jpayne@68 149 return x;
jpayne@68 150 }
jpayne@68 151
jpayne@68 152 private long cellsUsed;
jpayne@68 153 private final int[][] matrix;
jpayne@68 154
jpayne@68 155 }