1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
|
package cardinality;
import shared.Parser;
import shared.Tools;
/**
* @author Brian Bushnell
* @date Feb 20, 2020
*
*/
public final class BBLog_simple extends CardinalityTracker {
/*--------------------------------------------------------------*/
/*---------------- Initialization ----------------*/
/*--------------------------------------------------------------*/
/** Create a LogLog with default parameters */
BBLog_simple(){
this(2048, 31, -1, 0f);
}
/** Create a LogLog with parsed parameters */
BBLog_simple(Parser p){
super(p);
maxArray=new long[buckets];
counts=(trackCounts ? new int[buckets] : null);
}
/**
* Create a LogLog with specified parameters
* @param buckets_ Number of buckets (counters)
* @param k_ Kmer length
* @param seed Random number generator seed; -1 for a random seed
* @param minProb_ Ignore kmers with under this probability of being correct
*/
BBLog_simple(int buckets_, int k_, long seed, float minProb_){
super(buckets_, k_, seed, minProb_);
maxArray=new long[buckets];
counts=(trackCounts ? new int[buckets] : null);
}
/*--------------------------------------------------------------*/
/*---------------- Methods ----------------*/
/*--------------------------------------------------------------*/
@Override
public final long cardinality(){
double difSum=0;
int count=0;
for(int i=0; i<maxArray.length; i++){
long val=maxArray[i];
if(val>0){
long dif=Long.MAX_VALUE-val;
difSum+=dif;
count++;
}
}
final double mean=difSum/Tools.max(count, 1);
final double estimatePerSet=2*(Long.MAX_VALUE/mean);
final double total=estimatePerSet*count*((count+buckets)/(float)(buckets+buckets));
long cardinality=(long)(total);
lastCardinality=cardinality;
return cardinality;
}
@Override
public int[] getCounts(){
return counts;
}
@Override
public final void add(CardinalityTracker log){
assert(log.getClass()==this.getClass());
add((BBLog_simple)log);
}
public void add(BBLog_simple log){
if(maxArray!=log.maxArray){
for(int i=0; i<buckets; i++){
maxArray[i]=Tools.max(maxArray[i], log.maxArray[i]);
}
}
}
@Override
public void hashAndStore(final long number){
// if(number%SKIPMOD!=0){return;}
// final long key=hash(number, tables[((int)number)&numTablesMask]);
final long key=Tools.hash64shift(number);
// if(key<minKey){return;}
final int bucket=(int)(key&bucketMask);
{
maxArray[bucket]=Tools.max(key, maxArray[bucket]);
}
}
@Override
public final float[] compensationFactorLogBucketsArray(){
return null;
}
/*--------------------------------------------------------------*/
/*---------------- Fields ----------------*/
/*--------------------------------------------------------------*/
/** Maintains state. These are the actual buckets. */
private final long[] maxArray;
/** Counts associated with values in the buckets. */
private final int[] counts;
// private static long minKey=(long)(0.75f*Long.MAX_VALUE); //non-atomic 15% faster without this
}
|
