go/test/bench/k-nucleotide-parallel.go

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    * Redistributions of source code must retain the above copyright
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    * 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.

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*/

/* The Computer Language Benchmarks Game
 * http://shootout.alioth.debian.org/
 *
 * contributed by The Go Authors.
 */

package main

import (
	"bufio"
	"bytes"
	"fmt"
	"io/ioutil"
	"os"
	"sort"
)

func count(data string, n int) map[string]int {
	counts := make(map[string]int)
	top := len(data) - n
	for i := 0; i <= top; i++ {
		s := data[i : i+n]
		counts[s]++
	}
	return counts
}

func countOne(data string, s string) int {
	return count(data, len(s))[s]
}

type kNuc struct {
	name  string
	count int
}

type kNucArray []kNuc

func (kn kNucArray) Len() int      { return len(kn) }
func (kn kNucArray) Swap(i, j int) { kn[i], kn[j] = kn[j], kn[i] }
func (kn kNucArray) Less(i, j int) bool {
	if kn[i].count == kn[j].count {
		return kn[i].name > kn[j].name // sort down
	}
	return kn[i].count > kn[j].count
}

func sortedArray(m map[string]int) kNucArray {
	kn := make(kNucArray, len(m))
	i := 0
	for k, v := range m {
		kn[i] = kNuc{k, v}
		i++
	}
	sort.Sort(kn)
	return kn
}

func printKnucs(a kNucArray) {
	sum := 0
	for _, kn := range a {
		sum += kn.count
	}
	for _, kn := range a {
		fmt.Printf("%s %.3f\n", kn.name, 100*float64(kn.count)/float64(sum))
	}
	fmt.Print("\n")
}

func main() {
	in := bufio.NewReader(os.Stdin)
	three := []byte(">THREE ")
	for {
		line, err := in.ReadSlice('\n')
		if err != nil {
			fmt.Fprintln(os.Stderr, "ReadLine err:", err)
			os.Exit(2)
		}
		if line[0] == '>' && bytes.Equal(line[0:len(three)], three) {
			break
		}
	}
	data, err := ioutil.ReadAll(in)
	if err != nil {
		fmt.Fprintln(os.Stderr, "ReadAll err:", err)
		os.Exit(2)
	}
	// delete the newlines and convert to upper case
	j := 0
	for i := 0; i < len(data); i++ {
		if data[i] != '\n' {
			data[j] = data[i] &^ ' ' // upper case
			j++
		}
	}
	str := string(data[0:j])

	var arr1, arr2 kNucArray
	countsdone := make(chan bool)
	go func() {
		arr1 = sortedArray(count(str, 1))
		countsdone <- true
	}()
	go func() {
		arr2 = sortedArray(count(str, 2))
		countsdone <- true
	}()

	interests := []string{"GGT", "GGTA", "GGTATT", "GGTATTTTAATT", "GGTATTTTAATTTATAGT"}
	results := make([]chan string, len(interests))
	for i, s := range interests {
		ch := make(chan string)
		results[i] = ch
		go func(result chan string, ss string) {
			result <- fmt.Sprintf("%d %s\n", countOne(str, ss), ss)
		}(ch, s)
	}
	<-countsdone
	<-countsdone
	printKnucs(arr1)
	printKnucs(arr2)
	for _, rc := range results {
		fmt.Print(<-rc)
	}

}