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
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
|
package structures;
import java.util.concurrent.atomic.AtomicIntegerArray;
import shared.KillSwitch;
import shared.Tools;
/**
* Atomic version
* @author Brian Bushnell
* @date Sep 20, 2014
*
*/
public class CoverageArray2A extends CoverageArray {
/**
*
*/
private static final long serialVersionUID = 98483952072098494L;
public static void main(String[] args){
//TODO
}
public CoverageArray2A(int chrom, int len){
super(chrom, len);
int intLen=intIdx(len)+1;
array=KillSwitch.allocAtomicInt(intLen);
minIndex=0;
maxIndex=len-1;
}
private static final int intIdx(int idx) {
return (idx+1)/2;
}
/**
* @param loc
*/
@Override
public void increment(int loc){
increment(loc, 1);
}
@Override
public void increment(final int loc, final int amt) {
assert(amt>=0) : "This does not currently allow negative increments.";
final int intIdx=intIdx(loc);
boolean overflow=((loc&1)==1 ? incrementUpper(intIdx, amt) : incrementLower(intIdx, amt));
if(overflow && !OVERFLOWED){
System.err.println("Note: Coverage capped at "+0xFFFF);
OVERFLOWED=true;
}
}
private boolean incrementLower(final int intIdx, final int amt) {
boolean overflow=false;
for(int oldVal=0, actual=amt; oldVal!=actual; ) {
oldVal=array.get(intIdx);
int lower=oldVal&lowerMask, upper=oldVal&upperMask;
int charVal=lower;
int charVal2=Tools.min(0xFFFF, charVal+amt);
overflow=(charVal2>=0xFFFF);
int newVal=(charVal2)|upper;
actual=array.compareAndExchange(intIdx, oldVal, newVal);
}
return overflow;
}
private boolean incrementUpper(int intIdx, int amt) {
boolean overflow=false;
for(int oldVal=0, actual=amt; oldVal!=actual; ) {
oldVal=array.get(intIdx);
int lower=oldVal&lowerMask, upper=oldVal&upperMask;
int charVal=upper>>>16;
int charVal2=Tools.min(0xFFFF, charVal+amt);
overflow=(charVal2>=0xFFFF);
int newVal=(charVal2<<16)|lower;
actual=array.compareAndExchange(intIdx, oldVal, newVal);
}
return overflow;
}
@Override
public void incrementRangeSynchronized(int min, int max, int amt) {
incrementRange(min, max, amt);//Synchronized is not needed
}
public void incrementRangeSlow(int min, int max, int amt){
if(min<0){min=0;}
if(max>maxIndex){max=maxIndex;}
for(int loc=min; loc<=max; loc++){
increment(loc, amt);
}
}
@Override
public void incrementRange(int min, int max, int amt){
if(amt>0xFFF || true) {
incrementRangeSlow(min, max, amt);
return;
}
//TODO: This should be 2x as fast, but currently gives slightly wrong results.
//Off by ~1% so probably a boundary issue
//Try printing range and aborting
if(max>maxIndex){max=maxIndex;}
if((min&1)==1) {increment(min, amt);}
if((max&1)==0) {increment(max, amt);}
int minIdx=intIdx(min+1);
int maxIdx=intIdx(max-1);
for(int i=minIdx; i<=maxIdx; i++) {
for(int oldVal=0, actual=amt; oldVal!=actual; ) {
oldVal=array.get(i);
int lower=oldVal&lowerMask, upper=(oldVal&upperMask)>>16;
int lower2=Tools.min(0xFFFF, lower+amt);
int upper2=Tools.min(0xFFFF, upper+amt);
int newVal=lower2|(upper2<<16);
actual=array.compareAndExchange(i, oldVal, newVal);
}
}
}
@Override
public void set(int loc, int val0){
assert(val0>=0) : "This does not currently allow negative values.";
final int intIdx=intIdx(loc);
final int val=Tools.min(val0, 0xFFFF);
boolean overflow=((loc&1)==1 ? setUpper(intIdx, val) : setLower(intIdx, val));
if(val0!=val && !OVERFLOWED){
System.err.println("Note: Coverage capped at "+0xFFFF);
OVERFLOWED=true;
}
}
private boolean setLower(final int intIdx, final int amt) {
for(int oldVal=0, actual=amt; oldVal!=actual; ) {
oldVal=array.get(intIdx);
int lower=amt, upper=oldVal&upperMask;
int newVal=lower|upper;
actual=array.compareAndExchange(intIdx, oldVal, newVal);
}
return false;
}
private boolean setUpper(int intIdx, int amt) {
for(int oldVal=0, actual=amt; oldVal!=actual; ) {
oldVal=array.get(intIdx);
int lower=oldVal&lowerMask, upper=amt<<16;
int newVal=lower|upper;
actual=array.compareAndExchange(intIdx, oldVal, newVal);
}
return false;
}
@Override
public int get(int loc){
final int intIdx=intIdx(loc);
final int intVal=intIdx<0 || intIdx>=array.length() ? 0 : array.get(intIdx);
return (loc&1)==1 ? (intVal>>>16) : (intVal&lowerMask);
}
@Override
public void resize(int newlen){
throw new RuntimeException("Resize: Unsupported.");
}
@Override
public String toString(){
StringBuilder sb=new StringBuilder();
sb.append('[');
for(int i=0; i<=length(); i++){
if(i>0){sb.append(", ");}
sb.append(get(i));
}
sb.append(']');
return sb.toString();
}
@Override
public char[] toArray() {
char[] array2=new char[length()];
for(int i=0; i<array2.length; i++) {
array2[i]=(char)get(i);
}
return array2;
}
public final AtomicIntegerArray array;
// @Override
// public int length(){return maxIndex-minIndex+1;}
@Override
public int arrayLength(){return array.length();}
private static boolean OVERFLOWED=false;
private static final int lowerMask=0x0000FFFF;
private static final int upperMask=0xFFFF0000;
}
|
