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 jgi;
import java.util.Arrays;
import java.util.Locale;
import shared.Tools;
/**
* @author Brian Bushnell
* @date Sep 19, 2012
*
*/
public final class Info {
public static void main(String[] args){
if(args.length>0){
if(args.length==2 && Tools.isDigit(args[1].charAt(0))){
byte[] s=args[0].getBytes();
int b=Integer.parseInt(args[1]);
int len=prefixForInfoBits(s, b);
if(len<0){
System.out.println("Input string only contains "+String.format(Locale.ROOT, "%.2f",infoInBitsDouble(s, 0, s.length))+" bits.");
}else{
System.out.println("Prefix needed for "+b+" bits is length "+len+": "+args[0].substring(0, len));
// assert(false) : "TODO: This is clearly broken.";
}
}else{
for(String s : args){
printInfo(s);
System.out.println();
}
}
System.exit(0);
}
System.out.println();
printInfo("");
System.out.println();
printInfo("A");
System.out.println();
printInfo("AG");
System.out.println();
printInfo("AGT");
System.out.println();
printInfo("AANAA");
System.out.println();
printInfo("GGGGGGGCGGG");
System.out.println();
printInfo("CGGGGGGGGGG");
System.out.println();
printInfo("AGTCAGTCCTAGNGTACGT");
System.out.println();
printInfo("AGTCAGTCAGTCAGTC");
System.out.println();
printInfo("GCGCGCGCGCGCGCGC");
System.out.println();
String[] s=new String[] {"A", "G", "C", "T", ""};
for(int i=0; i<40; i++){
System.out.println();
s[4]=s[4]+s[i%4];
printInfo(s[4]);
}
System.out.println("PrefixForBits for AAAATATATGAAATGCATGCAATATGTTATGAAA");
for(int i=0; i<60; i+=2){
System.out.println(i+"\t"+prefixForInfoBits("AAAATATATGAAATGCATGCAATATGTTATGAAA".getBytes(), i));
}
System.out.println("PrefixForBits for GCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGC");
for(int i=0; i<60; i+=2){
System.out.println(i+"\t"+prefixForInfoBits("GCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGC".getBytes(), i));
}
System.out.println("PrefixForBits for ACGTACGTACGTACGTACGTACGTACGTACGTAC");
for(int i=0; i<63; i+=2){
System.out.println(i+"\t"+prefixForInfoBits("ACGTACGTACGTACGTACGTACGTACGTACGTAC".getBytes(), i));
}
}
public static void printInfo(String s){
long r=info(s);
double bits=Math.log(r)/Math.log(2);
System.out.println(s+"\nlen="+s.length()+" \tinfo = "+String.format(Locale.ROOT, "%.2f", bits)+" bits. \t("+r+")");
}
public static long info(String s){
return info(s.getBytes(), 0, s.length());
}
public static int infoInBits(final byte[] array, final int from, final int len){return 63-Long.numberOfLeadingZeros(info(array, from, len));}
public static double infoInBitsDouble(final byte[] array, final int from, final int len){return Math.log(info(array, from, len))*invlog2;}
public static long info(final byte[] array){return info(array, 0, array.length);}
public static long info(final byte[] array, final int from, final int len){
short[] counts=new short[4];
long r=1;
int used=0;
for(int i=from, lim=min(from+len, array.length); i<lim; i++){
// System.out.print(((char)array[i])+" -> ");
byte num=baseToNumber[array[i]];
// System.out.println(num);
if(num>=0){
counts[num]++;
used++;
if(used>32 && used>MAX/r){//overflow
// System.out.println("***");
return MAX;
}
r=r*used;
/* alternate method */
// long temp=r*used;
// if(used>32 && temp/used!=r){//overflow
// return MAX;
// }
// r=temp;
r=r/counts[num];
}
}
return r;
}
public static int prefixForInfoBits(final byte[] array, final int bits){assert(bits>=0 && bits<63);return prefixForInfo(array, 1L<<bits, 0);}
public static int prefixForInfoBits(final byte[] array, final int bits, final int from){assert(bits>=0 && bits<63);return prefixForInfo(array, 1L<<bits, from);}
public static int prefixForInfo(final byte[] array, final long info){return prefixForInfo(array, info, 0);}
public static int prefixForInfo(final byte[] array, final long info, final int from){
assert(info>=0);
short[] counts=new short[4];
long r=1;
int used=0;
int i=from;
for(; i<array.length && r<info; i++){
// System.out.print(((char)array[i])+" -> ");
byte num=baseToNumber[array[i]];
// System.out.println(num);
if(num>=0){
counts[num]++;
used++;
if(used>32 && used>MAX/r){//overflow
// System.out.println("***");
return i;
}
r=r*used;
/* alternate method */
// long temp=r*used;
// if(used>32 && temp/used!=r){//overflow
// return MAX;
// }
// r=temp;
r=r/counts[num];
//
// {
// String s=new String(array).substring(0, i+1);
// System.out.println("\n"+s);
// System.out.println("For len "+i+": r="+r+", bits="+(63-Long.numberOfLeadingZeros(r))+"\t->\t"+(Math.log(r)*invlog2));
// System.out.println(infoInBitsDouble(s.getBytes(), 0, i+1));
// System.out.println(info(s.getBytes(), 0, i+1));
// }
}
}
return r<info ? -1 : i;
}
private static final byte[] numberToBase={
'A','C','G','T','N'
};
/** Element i is: 0 for 'A', 1 for 'C', 2 for 'G', 3 for 'T', -1 otherwise */
public static final byte[] baseToNumber=new byte[128];
static{
Arrays.fill(baseToNumber, (byte)-1);
for(int i=0; i<numberToBase.length; i++){
char x=(char)numberToBase[i];
if(x=='A' || x=='C' || x=='G' || x=='T'){
baseToNumber[x]=(byte)i;
baseToNumber[Tools.toLowerCase(x)]=(byte)i;
}
}
baseToNumber['U']=3;
baseToNumber['u']=3;
}
private static final int min(int x, int y){return x<y ? x : y;}
private static final int max(int x, int y){return x>y ? x : y;}
private static final long MAX=Long.MAX_VALUE;
private static final double invlog2=1.0/Math.log(2);
}
|
