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// Licensed to the .NET Foundation under one or more agreements.
// The .NET Foundation licenses this file to you under the MIT license.
// See the LICENSE file in the project root for more information.
/* The Computer Language Benchmarks Game
http://benchmarksgame.alioth.debian.org/
*
* contributed by Jimmy Tang
*
* modified for use with xunit-performance
*/
using Microsoft.Xunit.Performance;
using System;
using System.Collections.Generic;
using System.Diagnostics;
using System.IO;
using System.Linq;
using System.Text.RegularExpressions;
using System.Threading;
[assembly: OptimizeForBenchmarks]
[assembly: MeasureInstructionsRetired]
namespace BenchmarksGame
{
public static class Regexdna
{
#if DEBUG
const bool Verbose = true;
const int Iterations = 1;
const string InputFile = "regexdna-input25.txt";
#else
const bool Verbose = false;
const int Iterations = 6;
const string InputFile = "regexdna-input25000.txt";
#endif
static string FindInput(string s)
{
string CoreRoot = System.Environment.GetEnvironmentVariable("CORE_ROOT");
if (CoreRoot == null)
{
Console.WriteLine("This benchmark requries CORE_ROOT to be set");
return null;
}
string inputFile = s ?? InputFile;
// Normal testing -- input file will end up next to the assembly
// and CoreRoot points at the test overlay dir
string[] pathPartsNormal = new string[] {
CoreRoot, "..", "..", "JIT", "Performance",
"CodeQuality", "BenchmarksGame", "regexdna", "regexdna", inputFile
};
string inputPathNormal = Path.Combine(pathPartsNormal);
// Perf testing -- input file will end up next to the assembly
// and CoreRoot points at this directory
string[] pathPartsPerf = new string[] { CoreRoot, inputFile };
string inputPathPerf = Path.Combine(pathPartsPerf);
string inputPath = null;
if (File.Exists(inputPathNormal))
{
inputPath = inputPathNormal;
}
else if (File.Exists(inputPathPerf))
{
inputPath = inputPathPerf;
}
if (inputPath != null)
{
Console.WriteLine("Using input file {0}", inputPath);
}
else
{
Console.WriteLine("Unable to find input file {0}", inputFile);
}
return inputPath;
}
public static int Main(string[] args)
{
string inputFile = InputFile;
int iterations = Iterations;
bool verbose = Verbose;
for (int i = 0; i < args.Length; i++)
{
if (args[i] == "-v")
{
verbose = true;
}
else if (args[i] == "-q")
{
verbose = false;
}
else if (args[i] == "-i")
{
i++;
if (i < args.Length)
{
Int32.TryParse(args[i], out iterations);
}
}
else
{
inputFile = args[i];
}
}
string fullInputFile = FindInput(inputFile);
if (fullInputFile == null)
{
Console.WriteLine("unable to find input");
return -1;
}
if (iterations != Iterations)
{
Console.WriteLine("Running {0} iterations", iterations);
}
using (var r = File.OpenText(fullInputFile))
{
string sequence = r.ReadToEnd();
// Warmup
BenchInner(verbose, sequence);
Stopwatch sw = Stopwatch.StartNew();
for (int j = 0; j < iterations; j++)
{
BenchInner(verbose, sequence);
}
sw.Stop();
Console.WriteLine("regexdna [{0} iters]: {1}ms", iterations, sw.ElapsedMilliseconds);
}
return 100;
}
static void BenchInner(bool verbose, string sequence)
{
int initialLength = sequence.Length;
sequence = Regex.Replace(sequence, ">.*\n|\n", "");
int codeLength = sequence.Length;
string[] variants = {
"agggtaaa|tttaccct"
,"[cgt]gggtaaa|tttaccc[acg]"
,"a[act]ggtaaa|tttacc[agt]t"
,"ag[act]gtaaa|tttac[agt]ct"
,"agg[act]taaa|ttta[agt]cct"
,"aggg[acg]aaa|ttt[cgt]ccct"
,"agggt[cgt]aa|tt[acg]accct"
,"agggta[cgt]a|t[acg]taccct"
,"agggtaa[cgt]|[acg]ttaccct"
};
var flags = variants.Select((v, i) => {
var flag = new ManualResetEvent(false);
ThreadPool.QueueUserWorkItem(x => {
variants[i] += " " + Regex.Matches(sequence, v).Count;
flag.Set();
});
return flag;
});
WaitHandle.WaitAll(flags.ToArray());
if (verbose)
{
Console.WriteLine(string.Join("\n", variants));
}
var dict = new Dictionary<string, string> {
{"B", "(c|g|t)"}, {"D", "(a|g|t)"}, {"H", "(a|c|t)"}, {"K", "(g|t)"},
{"M", "(a|c)"}, {"N", "(a|c|g|t)"}, {"R", "(a|g)"}, {"S", "(c|g)"},
{"V", "(a|c|g)"}, {"W", "(a|t)"}, {"Y", "(c|t)"}
};
sequence = new Regex("[WYKMSRBDVHN]").Replace(sequence, m => dict[m.Value]);
if (verbose)
{
Console.WriteLine("\n{0}\n{1}\n{2}", initialLength, codeLength, sequence.Length);
}
}
[Benchmark]
public static void Bench()
{
string fullInputFile = FindInput(InputFile);
if (fullInputFile == null)
{
throw new Exception("unable to find input");
}
using (var r = File.OpenText(fullInputFile))
{
string sequence = r.ReadToEnd();
foreach (var iteration in Benchmark.Iterations)
{
using (iteration.StartMeasurement())
{
for (int i = 0; i < Iterations; i++)
{
BenchInner(false, sequence);
}
}
}
}
}
}
}
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