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Source file test/bench/shootout/reverse-complement.go

     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	 */
    35	
    36	package main
    37	
    38	import (
    39		"bufio"
    40		"os"
    41	)
    42	
    43	const lineSize = 60
    44	
    45	var complement = [256]uint8{
    46		'A': 'T', 'a': 'T',
    47		'C': 'G', 'c': 'G',
    48		'G': 'C', 'g': 'C',
    49		'T': 'A', 't': 'A',
    50		'U': 'A', 'u': 'A',
    51		'M': 'K', 'm': 'K',
    52		'R': 'Y', 'r': 'Y',
    53		'W': 'W', 'w': 'W',
    54		'S': 'S', 's': 'S',
    55		'Y': 'R', 'y': 'R',
    56		'K': 'M', 'k': 'M',
    57		'V': 'B', 'v': 'B',
    58		'H': 'D', 'h': 'D',
    59		'D': 'H', 'd': 'H',
    60		'B': 'V', 'b': 'V',
    61		'N': 'N', 'n': 'N',
    62	}
    63	
    64	func main() {
    65		in := bufio.NewReader(os.Stdin)
    66		buf := make([]byte, 1024*1024)
    67		line, err := in.ReadSlice('\n')
    68		for err == nil {
    69			os.Stdout.Write(line)
    70	
    71			// Accumulate reversed complement in buf[w:]
    72			nchar := 0
    73			w := len(buf)
    74			for {
    75				line, err = in.ReadSlice('\n')
    76				if err != nil || line[0] == '>' {
    77					break
    78				}
    79				line = line[0 : len(line)-1]
    80				nchar += len(line)
    81				if len(line)+nchar/60+128 >= w {
    82					nbuf := make([]byte, len(buf)*5)
    83					copy(nbuf[len(nbuf)-len(buf):], buf)
    84					w += len(nbuf) - len(buf)
    85					buf = nbuf
    86				}
    87	
    88				// This loop is the bottleneck.
    89				for _, c := range line {
    90					w--
    91					buf[w] = complement[c]
    92				}
    93			}
    94	
    95			// Copy down to beginning of buffer, inserting newlines.
    96			// The loop left room for the newlines and 128 bytes of padding.
    97			i := 0
    98			for j := w; j < len(buf); j += 60 {
    99				n := copy(buf[i:i+60], buf[j:])
   100				buf[i+n] = '\n'
   101				i += n + 1
   102			}
   103			os.Stdout.Write(buf[0:i])
   104		}
   105	}

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