// option. This file may not be copied, modified, or distributed
// except according to those terms.
-#[feature(managed_boxes)];
-
/* -*- mode: rust; indent-tabs-mode: nil -*-
* Implementation of 'fasta' benchmark from
* Computer Language Benchmarks Game
* http://shootout.alioth.debian.org/
*/
-extern mod extra;
-use std::int;
use std::io;
+use std::io::buffered::BufferedWriter;
use std::io::File;
+use std::num::min;
use std::os;
-use std::rand::Rng;
-use std::rand;
-use std::str;
-static LINE_LENGTH: uint = 60u;
+static LINE_LENGTH: uint = 60;
+static IM: u32 = 139968;
struct MyRandom {
last: u32
}
-
-fn myrandom_next(r: @mut MyRandom, mx: u32) -> u32 {
- r.last = (r.last * 3877u32 + 29573u32) % 139968u32;
- mx * r.last / 139968u32
-}
-
-#[deriving(Clone)]
-struct AminoAcids {
- ch: char,
- prob: u32
-}
-
-fn make_cumulative(aa: ~[AminoAcids]) -> ~[AminoAcids] {
- let mut cp: u32 = 0u32;
- let mut ans: ~[AminoAcids] = ~[];
- for a in aa.iter() {
- cp += a.prob;
- ans.push(AminoAcids {ch: a.ch, prob: cp});
+impl MyRandom {
+ fn new() -> MyRandom { MyRandom { last: 42 } }
+ fn normalize(p: f32) -> u32 {(p * IM as f32).floor() as u32}
+ fn gen(&mut self) -> u32 {
+ self.last = (self.last * 3877 + 29573) % IM;
+ self.last
}
- ans
}
-fn select_random(r: u32, genelist: ~[AminoAcids]) -> char {
- if r < genelist[0].prob { return genelist[0].ch; }
- fn bisect(v: ~[AminoAcids], lo: uint, hi: uint, target: u32) -> char {
- if hi > lo + 1u {
- let mid: uint = lo + (hi - lo) / 2u;
- if target < v[mid].prob {
- return bisect(v, lo, mid, target);
- } else {
- return bisect(v, mid, hi, target);
- }
- } else {
- return v[hi].ch;
- }
+struct AAGen<'a> {
+ rng: &'a mut MyRandom,
+ data: ~[(u32, u8)]
+}
+impl<'a> AAGen<'a> {
+ fn new<'b>(rng: &'b mut MyRandom, aa: &[(char, f32)]) -> AAGen<'b> {
+ let mut cum = 0.;
+ let data = aa.iter()
+ .map(|&(ch, p)| { cum += p; (MyRandom::normalize(cum), ch as u8) })
+ .collect();
+ AAGen { rng: rng, data: data }
}
- bisect(genelist.clone(), 0, genelist.len() - 1, r)
}
-
-fn make_random_fasta(wr: @mut io::Writer,
- id: ~str,
- desc: ~str,
- genelist: ~[AminoAcids],
- n: int) {
- writeln!(wr, ">{} {}", id, desc);
- let mut rng = rand::rng();
- let rng = @mut MyRandom {
- last: rng.gen()
- };
- let mut op: ~str = ~"";
- for _ in range(0u, n as uint) {
- op.push_char(select_random(myrandom_next(rng, 100u32),
- genelist.clone()));
- if op.len() >= LINE_LENGTH {
- writeln!(wr, "{}", op);
- op = ~"";
- }
+impl<'a> Iterator<u8> for AAGen<'a> {
+ fn next(&mut self) -> Option<u8> {
+ let r = self.rng.gen();
+ self.data.iter()
+ .skip_while(|pc| pc.n0() < r)
+ .map(|&(_, c)| c)
+ .next()
}
- if op.len() > 0u { writeln!(wr, "{}", op); }
}
-fn make_repeat_fasta(wr: @mut io::Writer, id: ~str, desc: ~str, s: ~str, n: int) {
- writeln!(wr, ">{} {}", id, desc);
- let mut op = str::with_capacity( LINE_LENGTH );
- let sl = s.len();
- for i in range(0u, n as uint) {
- if (op.len() >= LINE_LENGTH) {
- writeln!(wr, "{}", op);
- op = str::with_capacity( LINE_LENGTH );
+fn make_fasta<W: Writer, I: Iterator<u8>>(
+ wr: &mut W, header: &str, mut it: I, mut n: uint)
+{
+ wr.write(header.as_bytes());
+ let mut line = [0u8, .. LINE_LENGTH + 1];
+ while n > 0 {
+ let nb = min(LINE_LENGTH, n);
+ for i in range(0, nb) {
+ line[i] = it.next().unwrap();
}
- op.push_char( s[i % sl] as char );
+ n -= nb;
+ line[nb] = '\n' as u8;
+ wr.write(line.slice_to(nb + 1));
}
- if op.len() > 0 {
- writeln!(wr, "{}", op);
- }
-}
-
-fn acid(ch: char, prob: u32) -> AminoAcids {
- AminoAcids {ch: ch, prob: prob}
}
-fn main() {
+fn run<W: Writer>(writer: &mut W) {
let args = os::args();
- let args = if os::getenv("RUST_BENCH").is_some() {
- // alioth tests k-nucleotide with this data at 25,000,000
- ~[~"", ~"5000000"]
+ let n = if os::getenv("RUST_BENCH").is_some() {
+ 25000000
} else if args.len() <= 1u {
- ~[~"", ~"1000"]
+ 1000
} else {
- args
+ from_str(args[1]).unwrap()
};
- let writer = if os::getenv("RUST_BENCH").is_some() {
- let file = File::create(&Path::new("./shootout-fasta.data"));
- @mut file as @mut io::Writer
- } else {
- @mut io::stdout() as @mut io::Writer
- };
-
- let n = from_str::<int>(args[1]).unwrap();
+ let rng = &mut MyRandom::new();
+ let alu =
+ "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG\
+ GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA\
+ CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT\
+ ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA\
+ GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG\
+ AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC\
+ AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
+ let iub = &[('a', 0.27), ('c', 0.12), ('g', 0.12),
+ ('t', 0.27), ('B', 0.02), ('D', 0.02),
+ ('H', 0.02), ('K', 0.02), ('M', 0.02),
+ ('N', 0.02), ('R', 0.02), ('S', 0.02),
+ ('V', 0.02), ('W', 0.02), ('Y', 0.02)];
+ let homosapiens = &[('a', 0.3029549426680),
+ ('c', 0.1979883004921),
+ ('g', 0.1975473066391),
+ ('t', 0.3015094502008)];
+
+ make_fasta(writer, ">ONE Homo sapiens alu\n",
+ alu.as_bytes().iter().cycle().map(|c| *c), n * 2);
+ make_fasta(writer, ">TWO IUB ambiguity codes\n",
+ AAGen::new(rng, iub), n * 3);
+ make_fasta(writer, ">THREE Homo sapiens frequency\n",
+ AAGen::new(rng, homosapiens), n * 5);
+
+ writer.flush();
+}
- let iub: ~[AminoAcids] =
- make_cumulative(~[acid('a', 27u32), acid('c', 12u32), acid('g', 12u32),
- acid('t', 27u32), acid('B', 2u32), acid('D', 2u32),
- acid('H', 2u32), acid('K', 2u32), acid('M', 2u32),
- acid('N', 2u32), acid('R', 2u32), acid('S', 2u32),
- acid('V', 2u32), acid('W', 2u32), acid('Y', 2u32)]);
- let homosapiens: ~[AminoAcids] =
- make_cumulative(~[acid('a', 30u32), acid('c', 20u32), acid('g', 20u32),
- acid('t', 30u32)]);
- let alu: ~str =
- ~"GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG\
- GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA\
- CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT\
- ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA\
- GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG\
- AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC\
- AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
- make_repeat_fasta(writer, ~"ONE", ~"Homo sapiens alu", alu, n * 2);
- make_random_fasta(writer, ~"TWO", ~"IUB ambiguity codes", iub, n * 3);
- make_random_fasta(writer, ~"THREE",
- ~"Homo sapiens frequency", homosapiens, n * 5);
+fn main() {
+ if os::getenv("RUST_BENCH").is_some() {
+ let mut file = BufferedWriter::new(File::create(&Path::new("./shootout-fasta.data")));
+ run(&mut file);
+ } else {
+ run(&mut BufferedWriter::new(io::stdout()));
+ }
}
projects / rust.git / commitdiff