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// Copyright 2011 The Go Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.
// This benchmark, taken from the shootout, tests array indexing
// and array bounds elimination performance.
package go1
import (
"bufio"
"bytes"
"io/ioutil"
"testing"
)
var revCompTable = [256]uint8{
'A': 'T', 'a': 'T',
'C': 'G', 'c': 'G',
'G': 'C', 'g': 'C',
'T': 'A', 't': 'A',
'U': 'A', 'u': 'A',
'M': 'K', 'm': 'K',
'R': 'Y', 'r': 'Y',
'W': 'W', 'w': 'W',
'S': 'S', 's': 'S',
'Y': 'R', 'y': 'R',
'K': 'M', 'k': 'M',
'V': 'B', 'v': 'B',
'H': 'D', 'h': 'D',
'D': 'H', 'd': 'H',
'B': 'V', 'b': 'V',
'N': 'N', 'n': 'N',
}
func revcomp(data []byte) {
in := bufio.NewReader(bytes.NewBuffer(data))
out := ioutil.Discard
buf := make([]byte, 1024*1024)
line, err := in.ReadSlice('\n')
for err == nil {
out.Write(line)
// Accumulate reversed complement in buf[w:]
nchar := 0
w := len(buf)
for {
line, err = in.ReadSlice('\n')
if err != nil || line[0] == '>' {
break
}
line = line[0 : len(line)-1]
nchar += len(line)
if len(line)+nchar/60+128 >= w {
nbuf := make([]byte, len(buf)*5)
copy(nbuf[len(nbuf)-len(buf):], buf)
w += len(nbuf) - len(buf)
buf = nbuf
}
// This loop is the bottleneck.
for _, c := range line {
w--
buf[w] = revCompTable[c]
}
}
// Copy down to beginning of buffer, inserting newlines.
// The loop left room for the newlines and 128 bytes of padding.
i := 0
for j := w; j < len(buf); j += 60 {
n := copy(buf[i:i+60], buf[j:])
buf[i+n] = '\n'
i += n + 1
}
out.Write(buf[0:i])
}
}
func BenchmarkRevcomp(b *testing.B) {
b.SetBytes(int64(len(fastabytes)))
for i := 0; i < b.N; i++ {
revcomp(fastabytes)
}
}
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