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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 BenchmarkRevcomp25M(b *testing.B) {
        b.SetBytes(int64(len(fasta25m)))
        for i := 0; i < b.N; i++ {
                revcomp(fasta25m)
        }
}