source code
/* The Computer Language Benchmarks Game
http://benchmarksgame.alioth.debian.org/
contributed by James Wendel
*/
import 'dart:io';
import 'dart:typed_data';
const String ALU =
"GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG"
"GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA"
"CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT"
"ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA"
"GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG"
"AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC"
"AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
final Frequency IUB = new Frequency(
['a', 'c', 'g', 't',
'B', 'D', 'H', 'K',
'M', 'N', 'R', 'S',
'V', 'W', 'Y'],
[0.27, 0.12, 0.12, 0.27,
0.02, 0.02, 0.02, 0.02,
0.02, 0.02, 0.02, 0.02,
0.02, 0.02, 0.02,]);
final Frequency HOMO_SAPIENS = new Frequency(
[ 'a',
'c',
'g',
't'],
[ 0.3029549426680,
0.1979883004921,
0.1975473066391,
0.3015094502008]);
const int IM = 139968;
const int IA = 3877;
const int IC = 29573;
const int LINE_LENGTH = 60;
const int BUFFER_SIZE = (LINE_LENGTH + 1)*1024;
const double oneOverIM = (1.0/ IM);
class Frequency {
Uint8List chars;
Float64List probs;
int last;
double random(double max) {
last = (last * IA + IC) % IM;
return max * last * oneOverIM;
}
Frequency(List<String> charList, List<double> probList) {
chars = new Uint8List(charList.length);
for (int i=0; i < chars.length; i++) {
chars[i] = charList[i].codeUnitAt(0);
}
probs = new Float64List(probList.length);
for (int i=0; i < probList.length; i++) {
probs[i] = probList[i];
}
makeCumulative();
}
void makeCumulative() {
double cp = 0.0;
for (int i = 0; i < probs.length; i++) {
cp += probs[i];
probs[i] = cp;
}
}
int selectRandomIntoBuffer(Uint8List buffer, int bufferIndex, int nRandom) {
final int len = probs.length;
outer:
for (int rIndex = 0; rIndex < nRandom; rIndex++) {
double r = random(1.0);
for (int i = 0; i < len; i++) {
if (r < probs[i]) {
buffer[bufferIndex++] = chars[i];
continue outer;
}
}
buffer[bufferIndex++] = chars[len-1];
}
return bufferIndex;
}
}
makeRepeatFasta(String id, String desc, String alu, int _nChars, IOSink writer) {
writer.write(">${id} ${desc}\n");
int aluIndex = 0;
final List<int> aluCode = alu.codeUnits;
final int aluLength = aluCode.length;
Uint8List buffer = new Uint8List(BUFFER_SIZE);
int bufferIndex = 0;
int nChars = _nChars;
while (nChars > 0) {
final int chunkSize = nChars >= LINE_LENGTH ? LINE_LENGTH : nChars;
if (bufferIndex == BUFFER_SIZE) {
writer.add(new Uint8List.view(buffer.buffer, 0, bufferIndex));
buffer = new Uint8List(BUFFER_SIZE);
bufferIndex = 0;
}
if (aluIndex + chunkSize < aluLength) {
buffer.setRange(bufferIndex, bufferIndex+chunkSize, aluCode, aluIndex);
bufferIndex += chunkSize;
aluIndex += chunkSize;
} else {
int len = aluLength - aluIndex;
buffer.setRange(bufferIndex, bufferIndex+len, aluCode, aluIndex);
bufferIndex += len;
aluIndex = 0;
len = chunkSize - len;
buffer.setRange(bufferIndex, bufferIndex+len, aluCode, aluIndex);
bufferIndex += len;
aluIndex += len;
}
buffer[bufferIndex++] = 10;
nChars -= chunkSize;
}
writer.add(new Uint8List.view(buffer.buffer, 0, bufferIndex));
}
void makeRandomFasta(String id, String desc, Frequency fpf, int nChars, IOSink writer) {
writer.write(">${id} ${desc}\n");
Uint8List buffer = new Uint8List(BUFFER_SIZE);
int bufferIndex = 0;
while (nChars > 0) {
final int chunkSize = nChars >= LINE_LENGTH ? LINE_LENGTH : nChars;
if (bufferIndex == BUFFER_SIZE) {
writer.add(new Uint8List.view(buffer.buffer, 0, bufferIndex));
buffer = new Uint8List(BUFFER_SIZE);
bufferIndex = 0;
}
bufferIndex = fpf.selectRandomIntoBuffer(buffer, bufferIndex, chunkSize);
buffer[bufferIndex++] = 10;
nChars -= chunkSize;
}
writer.add(new Uint8List.view(buffer.buffer, 0, bufferIndex));
}
main(args) {
IOSink writer = stdout;
int n = args.length > 0 ? int.parse(args[0]) : 250;
makeRepeatFasta("ONE", "Homo sapiens alu", ALU, n * 2, writer);
IUB.last = 42;
makeRandomFasta("TWO", "IUB ambiguity codes", IUB, n * 3, writer);
HOMO_SAPIENS.last = IUB.last;
makeRandomFasta("THREE", "Homo sapiens frequency", HOMO_SAPIENS, n * 5, writer);
}