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/*
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
* Neither the name of "The Computer Language Benchmarks Game" nor the
name of "The Computer Language Shootout Benchmarks" nor the names of
its contributors may be used to endorse or promote products derived
from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
/* The Computer Language Benchmarks Game
* http://shootout.alioth.debian.org/
*
* contributed by The Go Authors.
* Based on C program by by Petr Prokhorenkov.
*/
package main
import (
"bytes"
"flag"
"os"
)
var out = make(buffer, 0, 32768)
var n = flag.Int("n", 1000, "length of result")
const Line = 60
func Repeat(alu []byte, n int) {
buf := bytes.Add(alu, alu)
off := 0
for n > 0 {
m := n
if m > Line {
m = Line
}
buf1 := out.NextWrite(m + 1)
copy(buf1, buf[off:])
buf1[m] = '\n'
if off += m; off >= len(alu) {
off -= len(alu)
}
n -= m
}
}
const (
IM = 139968
IA = 3877
IC = 29573
LookupSize = 4096
LookupScale float64 = LookupSize - 1
)
var rand uint32 = 42
type Acid struct {
sym byte
prob float64
cprob float64
next *Acid
}
func computeLookup(acid []Acid) *[LookupSize]*Acid {
var lookup [LookupSize]*Acid
var p float64
for i := range acid {
p += acid[i].prob
acid[i].cprob = p * LookupScale
if i > 0 {
acid[i-1].next = &acid[i]
}
}
acid[len(acid)-1].cprob = 1.0 * LookupScale
j := 0
for i := range lookup {
for acid[j].cprob < float64(i) {
j++
}
lookup[i] = &acid[j]
}
return &lookup
}
func Random(acid []Acid, n int) {
lookup := computeLookup(acid)
for n > 0 {
m := n
if m > Line {
m = Line
}
buf := out.NextWrite(m + 1)
f := LookupScale / IM
myrand := rand
for i := 0; i < m; i++ {
myrand = (myrand*IA + IC) % IM
r := float64(int(myrand)) * f
a := lookup[int(r)]
for a.cprob < r {
a = a.next
}
buf[i] = a.sym
}
rand = myrand
buf[m] = '\n'
n -= m
}
}
func main() {
defer out.Flush()
flag.Parse()
iub := []Acid{
Acid{prob: 0.27, sym: 'a'},
Acid{prob: 0.12, sym: 'c'},
Acid{prob: 0.12, sym: 'g'},
Acid{prob: 0.27, sym: 't'},
Acid{prob: 0.02, sym: 'B'},
Acid{prob: 0.02, sym: 'D'},
Acid{prob: 0.02, sym: 'H'},
Acid{prob: 0.02, sym: 'K'},
Acid{prob: 0.02, sym: 'M'},
Acid{prob: 0.02, sym: 'N'},
Acid{prob: 0.02, sym: 'R'},
Acid{prob: 0.02, sym: 'S'},
Acid{prob: 0.02, sym: 'V'},
Acid{prob: 0.02, sym: 'W'},
Acid{prob: 0.02, sym: 'Y'},
}
homosapiens := []Acid{
Acid{prob: 0.3029549426680, sym: 'a'},
Acid{prob: 0.1979883004921, sym: 'c'},
Acid{prob: 0.1975473066391, sym: 'g'},
Acid{prob: 0.3015094502008, sym: 't'},
}
alu := []byte(
"GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG" +
"GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA" +
"CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT" +
"ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA" +
"GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG" +
"AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC" +
"AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA")
out.WriteString(">ONE Homo sapiens alu\n")
Repeat(alu, 2**n)
out.WriteString(">TWO IUB ambiguity codes\n")
Random(iub, 3**n)
out.WriteString(">THREE Homo sapiens frequency\n")
Random(homosapiens, 5**n)
}
type buffer []byte
func (b *buffer) Flush() {
p := *b
if len(p) > 0 {
os.Stdout.Write(p)
}
*b = p[0:0]
}
func (b *buffer) WriteString(s string) {
p := b.NextWrite(len(s))
for i := 0; i < len(s); i++ {
p[i] = s[i]
}
}
func (b *buffer) NextWrite(n int) []byte {
p := *b
if len(p)+n > cap(p) {
b.Flush()
p = *b
}
out := p[len(p) : len(p)+n]
*b = p[0 : len(p)+n]
return out
}
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