src/test/bench/shootout-fasta-redux.rs

   1 // The Computer Language Benchmarks Game
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   5
   6 // Copyright (c) 2013-2014 The Rust Project Developers
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  40
  41 use std::cmp::min;
  42 use std::env;
  43 use std::io;
  44 use std::io::prelude::*;
  45 use std::iter::repeat;
  46
  47 const LINE_LEN: usize = 60;
  48 const LOOKUP_SIZE: usize = 4 * 1024;
  49 const LOOKUP_SCALE: f32 = (LOOKUP_SIZE - 1) as f32;
  50
  51 // Random number generator constants
  52 const IM: u32 = 139968;
  53 const IA: u32 = 3877;
  54 const IC: u32 = 29573;
  55
  56 const ALU: &'static str = "GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTG\
  57                             GGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGA\
  58                             GACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAA\
  59                             AATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAAT\
  60                             CCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAAC\
  61                             CCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTG\
  62                             CACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
  63
  64 const NULL_AMINO_ACID: AminoAcid = AminoAcid { c: ' ' as u8, p: 0.0 };
  65
  66 static IUB: [AminoAcid;15] = [
  67     AminoAcid { c: 'a' as u8, p: 0.27 },
  68     AminoAcid { c: 'c' as u8, p: 0.12 },
  69     AminoAcid { c: 'g' as u8, p: 0.12 },
  70     AminoAcid { c: 't' as u8, p: 0.27 },
  71     AminoAcid { c: 'B' as u8, p: 0.02 },
  72     AminoAcid { c: 'D' as u8, p: 0.02 },
  73     AminoAcid { c: 'H' as u8, p: 0.02 },
  74     AminoAcid { c: 'K' as u8, p: 0.02 },
  75     AminoAcid { c: 'M' as u8, p: 0.02 },
  76     AminoAcid { c: 'N' as u8, p: 0.02 },
  77     AminoAcid { c: 'R' as u8, p: 0.02 },
  78     AminoAcid { c: 'S' as u8, p: 0.02 },
  79     AminoAcid { c: 'V' as u8, p: 0.02 },
  80     AminoAcid { c: 'W' as u8, p: 0.02 },
  81     AminoAcid { c: 'Y' as u8, p: 0.02 },
  82 ];
  83
  84 static HOMO_SAPIENS: [AminoAcid;4] = [
  85     AminoAcid { c: 'a' as u8, p: 0.3029549426680 },
  86     AminoAcid { c: 'c' as u8, p: 0.1979883004921 },
  87     AminoAcid { c: 'g' as u8, p: 0.1975473066391 },
  88     AminoAcid { c: 't' as u8, p: 0.3015094502008 },
  89 ];
  90
  91 // FIXME: Use map().
  92 fn sum_and_scale(a: &'static [AminoAcid]) -> Vec<AminoAcid> {
  93     let mut result = Vec::new();
  94     let mut p = 0f32;
  95     for a_i in a {
  96         let mut a_i = *a_i;
  97         p += a_i.p;
  98         a_i.p = p * LOOKUP_SCALE;
  99         result.push(a_i);
 100     }
 101     let result_len = result.len();
 102     result[result_len - 1].p = LOOKUP_SCALE;
 103     result
 104 }
 105
 106 #[derive(Copy, Clone)]
 107 struct AminoAcid {
 108     c: u8,
 109     p: f32,
 110 }
 111
 112 struct RepeatFasta<'a, W:'a> {
 113     alu: &'static str,
 114     out: &'a mut W
 115 }
 116
 117 impl<'a, W: Write> RepeatFasta<'a, W> {
 118     fn new(alu: &'static str, w: &'a mut W) -> RepeatFasta<'a, W> {
 119         RepeatFasta { alu: alu, out: w }
 120     }
 121
 122     fn make(&mut self, n: usize) -> io::Result<()> {
 123         let alu_len = self.alu.len();
 124         let mut buf = repeat(0).take(alu_len + LINE_LEN).collect::<Vec<_>>();
 125         let alu: &[u8] = self.alu.as_bytes();
 126
 127         for (slot, val) in buf.iter_mut().zip(alu) {
 128             *slot = *val;
 129         }
 130         let buf_len = buf.len();
 131         for (slot, val) in buf[alu_len..buf_len].iter_mut().zip(&alu[..LINE_LEN]) {
 132             *slot = *val;
 133         }
 134
 135         let mut pos = 0;
 136         let mut bytes;
 137         let mut n = n;
 138         while n > 0 {
 139             bytes = min(LINE_LEN, n);
 140             try!(self.out.write_all(&buf[pos..pos + bytes]));
 141             try!(self.out.write_all(&[b'\n']));
 142             pos += bytes;
 143             if pos > alu_len {
 144                 pos -= alu_len;
 145             }
 146             n -= bytes;
 147         }
 148         Ok(())
 149     }
 150 }
 151
 152 fn make_lookup(a: &[AminoAcid]) -> [AminoAcid;LOOKUP_SIZE] {
 153     let mut lookup = [ NULL_AMINO_ACID;LOOKUP_SIZE ];
 154     let mut j = 0;
 155     for (i, slot) in lookup.iter_mut().enumerate() {
 156         while a[j].p < (i as f32) {
 157             j += 1;
 158         }
 159         *slot = a[j];
 160     }
 161     lookup
 162 }
 163
 164 struct RandomFasta<'a, W:'a> {
 165     seed: u32,
 166     lookup: [AminoAcid;LOOKUP_SIZE],
 167     out: &'a mut W,
 168 }
 169
 170 impl<'a, W: Write> RandomFasta<'a, W> {
 171     fn new(w: &'a mut W, a: &[AminoAcid]) -> RandomFasta<'a, W> {
 172         RandomFasta {
 173             seed: 42,
 174             out: w,
 175             lookup: make_lookup(a),
 176         }
 177     }
 178
 179     fn rng(&mut self, max: f32) -> f32 {
 180         self.seed = (self.seed * IA + IC) % IM;
 181         max * (self.seed as f32) / (IM as f32)
 182     }
 183
 184     fn nextc(&mut self) -> u8 {
 185         let r = self.rng(1.0);
 186         for a in &self.lookup[..] {
 187             if a.p >= r {
 188                 return a.c;
 189             }
 190         }
 191         0
 192     }
 193
 194     fn make(&mut self, n: usize) -> io::Result<()> {
 195         let lines = n / LINE_LEN;
 196         let chars_left = n % LINE_LEN;
 197         let mut buf = [0;LINE_LEN + 1];
 198
 199         for _ in 0..lines {
 200             for i in 0..LINE_LEN {
 201                 buf[i] = self.nextc();
 202             }
 203             buf[LINE_LEN] = '\n' as u8;
 204             try!(self.out.write(&buf));
 205         }
 206         for i in 0..chars_left {
 207             buf[i] = self.nextc();
 208         }
 209         self.out.write_all(&buf[..chars_left])
 210     }
 211 }
 212
 213 fn main() {
 214     let mut args = env::args();
 215     let n = if args.len() > 1 {
 216         args.nth(1).unwrap().parse::<usize>().unwrap()
 217     } else {
 218         5
 219     };
 220
 221     let mut out = io::stdout();
 222
 223     out.write_all(b">ONE Homo sapiens alu\n").unwrap();
 224     {
 225         let mut repeat = RepeatFasta::new(ALU, &mut out);
 226         repeat.make(n * 2).unwrap();
 227     }
 228
 229     out.write_all(b">TWO IUB ambiguity codes\n").unwrap();
 230     let iub = sum_and_scale(&IUB);
 231     let mut random = RandomFasta::new(&mut out, &iub);
 232     random.make(n * 3).unwrap();
 233
 234     random.out.write_all(b">THREE Homo sapiens frequency\n").unwrap();
 235     let homo_sapiens = sum_and_scale(&HOMO_SAPIENS);
 236     random.lookup = make_lookup(&homo_sapiens);
 237     random.make(n * 5).unwrap();
 238
 239     random.out.write_all(b"\n").unwrap();
 240 }