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      1 /*
      2 Redistribution and use in source and binary forms, with or without
      3 modification, are permitted provided that the following conditions are met:
      4 
      5     * Redistributions of source code must retain the above copyright
      6     notice, this list of conditions and the following disclaimer.
      7 
      8     * Redistributions in binary form must reproduce the above copyright
      9     notice, this list of conditions and the following disclaimer in the
     10     documentation and/or other materials provided with the distribution.
     11 
     12     * Neither the name of "The Computer Language Benchmarks Game" nor the
     13     name of "The Computer Language Shootout Benchmarks" nor the names of
     14     its contributors may be used to endorse or promote products derived
     15     from this software without specific prior written permission.
     16 
     17 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
     18 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
     19 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
     20 ARE DISCLAIMED.  IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
     21 LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
     22 CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
     23 SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
     24 INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
     25 CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
     26 ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
     27 POSSIBILITY OF SUCH DAMAGE.
     28 */
     29 
     30 /* The Computer Language Benchmarks Game
     31  * http://shootout.alioth.debian.org/
     32  *
     33  * contributed by The Go Authors.
     34  * Based on C program by by Petr Prokhorenkov.
     35  */
     36 
     37 package main
     38 
     39 import (
     40 	"flag"
     41 	"os"
     42 )
     43 
     44 var out = make(buffer, 0, 32768)
     45 
     46 var n = flag.Int("n", 1000, "length of result")
     47 
     48 const Line = 60
     49 
     50 func Repeat(alu []byte, n int) {
     51 	buf := append(alu, alu...)
     52 	off := 0
     53 	for n > 0 {
     54 		m := n
     55 		if m > Line {
     56 			m = Line
     57 		}
     58 		buf1 := out.NextWrite(m + 1)
     59 		copy(buf1, buf[off:])
     60 		buf1[m] = '\n'
     61 		if off += m; off >= len(alu) {
     62 			off -= len(alu)
     63 		}
     64 		n -= m
     65 	}
     66 }
     67 
     68 const (
     69 	IM = 139968
     70 	IA = 3877
     71 	IC = 29573
     72 
     73 	LookupSize          = 4096
     74 	LookupScale float64 = LookupSize - 1
     75 )
     76 
     77 var rand uint32 = 42
     78 
     79 type Acid struct {
     80 	sym   byte
     81 	prob  float64
     82 	cprob float64
     83 	next  *Acid
     84 }
     85 
     86 func computeLookup(acid []Acid) *[LookupSize]*Acid {
     87 	var lookup [LookupSize]*Acid
     88 	var p float64
     89 	for i := range acid {
     90 		p += acid[i].prob
     91 		acid[i].cprob = p * LookupScale
     92 		if i > 0 {
     93 			acid[i-1].next = &acid[i]
     94 		}
     95 	}
     96 	acid[len(acid)-1].cprob = 1.0 * LookupScale
     97 
     98 	j := 0
     99 	for i := range lookup {
    100 		for acid[j].cprob < float64(i) {
    101 			j++
    102 		}
    103 		lookup[i] = &acid[j]
    104 	}
    105 
    106 	return &lookup
    107 }
    108 
    109 func Random(acid []Acid, n int) {
    110 	lookup := computeLookup(acid)
    111 	for n > 0 {
    112 		m := n
    113 		if m > Line {
    114 			m = Line
    115 		}
    116 		buf := out.NextWrite(m + 1)
    117 		f := LookupScale / IM
    118 		myrand := rand
    119 		for i := 0; i < m; i++ {
    120 			myrand = (myrand*IA + IC) % IM
    121 			r := float64(int(myrand)) * f
    122 			a := lookup[int(r)]
    123 			for a.cprob < r {
    124 				a = a.next
    125 			}
    126 			buf[i] = a.sym
    127 		}
    128 		rand = myrand
    129 		buf[m] = '\n'
    130 		n -= m
    131 	}
    132 }
    133 
    134 func main() {
    135 	defer out.Flush()
    136 
    137 	flag.Parse()
    138 
    139 	iub := []Acid{
    140 		{prob: 0.27, sym: 'a'},
    141 		{prob: 0.12, sym: 'c'},
    142 		{prob: 0.12, sym: 'g'},
    143 		{prob: 0.27, sym: 't'},
    144 		{prob: 0.02, sym: 'B'},
    145 		{prob: 0.02, sym: 'D'},
    146 		{prob: 0.02, sym: 'H'},
    147 		{prob: 0.02, sym: 'K'},
    148 		{prob: 0.02, sym: 'M'},
    149 		{prob: 0.02, sym: 'N'},
    150 		{prob: 0.02, sym: 'R'},
    151 		{prob: 0.02, sym: 'S'},
    152 		{prob: 0.02, sym: 'V'},
    153 		{prob: 0.02, sym: 'W'},
    154 		{prob: 0.02, sym: 'Y'},
    155 	}
    156 
    157 	homosapiens := []Acid{
    158 		{prob: 0.3029549426680, sym: 'a'},
    159 		{prob: 0.1979883004921, sym: 'c'},
    160 		{prob: 0.1975473066391, sym: 'g'},
    161 		{prob: 0.3015094502008, sym: 't'},
    162 	}
    163 
    164 	alu := []byte(
    165 		"GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGG" +
    166 			"GAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGA" +
    167 			"CCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAAT" +
    168 			"ACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCA" +
    169 			"GCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGG" +
    170 			"AGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCC" +
    171 			"AGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA")
    172 
    173 	out.WriteString(">ONE Homo sapiens alu\n")
    174 	Repeat(alu, 2**n)
    175 	out.WriteString(">TWO IUB ambiguity codes\n")
    176 	Random(iub, 3**n)
    177 	out.WriteString(">THREE Homo sapiens frequency\n")
    178 	Random(homosapiens, 5**n)
    179 }
    180 
    181 type buffer []byte
    182 
    183 func (b *buffer) Flush() {
    184 	p := *b
    185 	if len(p) > 0 {
    186 		os.Stdout.Write(p)
    187 	}
    188 	*b = p[0:0]
    189 }
    190 
    191 func (b *buffer) WriteString(s string) {
    192 	p := b.NextWrite(len(s))
    193 	copy(p, s)
    194 }
    195 
    196 func (b *buffer) NextWrite(n int) []byte {
    197 	p := *b
    198 	if len(p)+n > cap(p) {
    199 		b.Flush()
    200 		p = *b
    201 	}
    202 	out := p[len(p) : len(p)+n]
    203 	*b = p[:len(p)+n]
    204 	return out
    205 }
    206