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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.
// Adapted from k-nucleotide C# .NET Core program
// http://benchmarksgame.alioth.debian.org/u64q/program.php?test=knucleotide&lang=csharpcore&id=1
// aka (as of 2017-09-01) rev 1.2 of https://alioth.debian.org/scm/viewvc.php/benchmarksgame/bench/knucleotide/knucleotide.csharp?root=benchmarksgame&view=log
// Best-scoring single-threaded C# .NET Core version as of 2017-09-01
/* The Computer Language Benchmarks Game
http://benchmarksgame.alioth.debian.org/
*
* byte processing version using C# *3.0 idioms by Robert F. Tobler
*/
using System;
using System.IO;
using System.Collections.Generic;
using System.Text;
using Microsoft.Xunit.Performance;
using Xunit;
[assembly: OptimizeForBenchmarks]
[assembly: MeasureGCCounts]
namespace BenchmarksGame
{
public struct ByteString : IEquatable<ByteString>
{
public byte[] Array;
public int Start;
public int Length;
public ByteString(byte[] array, int start, int length)
{
Array = array; Start = start; Length = length;
}
public ByteString(string text)
{
Start = 0; Length = text.Length;
Array = Encoding.ASCII.GetBytes(text);
}
public override int GetHashCode()
{
if (Length < 1) return 0;
int hc = Length ^ (Array[Start] << 24); if (Length < 2) return hc;
hc ^= Array[Start + Length - 1] << 20; if (Length < 3) return hc;
for (int c = Length - 2; c > 0; c--)
hc ^= Array[Start + c] << (c & 0xf);
return hc;
}
public bool Equals(ByteString other)
{
if (Length != other.Length) return false;
for (int i = 0; i < Length; i++)
if (Array[Start + i] != other.Array[other.Start + i]) return false;
return true;
}
public override string ToString()
{
return Encoding.ASCII.GetString(Array, Start, Length);
}
}
public static class Extensions
{
public static byte[] GetBytes(this List<string> input)
{
int count = 0;
for (int i = 0; i < input.Count; i++) count += input[i].Length;
var byteArray = new byte[count];
count = 0;
for (int i = 0; i < input.Count; i++)
{
string line = input[i];
Encoding.ASCII.GetBytes(line, 0, line.Length, byteArray, count);
count += line.Length;
}
return byteArray;
}
}
public class KNucleotide_1
{
public static int Main(string[] args)
{
var helpers = new TestHarnessHelpers(bigInput: false);
using (var inputStream = helpers.GetInputStream())
{
if (!Bench(inputStream, helpers, true))
{
return -1;
}
}
return 100;
}
[Benchmark(InnerIterationCount = 3)]
public static void RunBench()
{
var helpers = new TestHarnessHelpers(bigInput: true);
bool ok = true;
Benchmark.Iterate(() =>
{
using (var inputStream = helpers.GetInputStream())
{
ok &= Bench(inputStream, helpers, false);
}
});
Assert.True(ok);
}
static bool Bench(Stream inputStream, TestHarnessHelpers helpers, bool verbose)
{
string line;
StreamReader source = new StreamReader(inputStream);
var input = new List<string>();
while ((line = source.ReadLine()) != null)
if (line[0] == '>' && line.Substring(1, 5) == "THREE")
break;
while ((line = source.ReadLine()) != null)
{
char c = line[0];
if (c == '>') break;
if (c != ';') input.Add(line.ToUpper());
}
KNucleotide kn = new KNucleotide(input.GetBytes());
input = null;
bool ok = true;
for (int f = 1; f < 3; f++)
ok &= kn.WriteFrequencies(f, helpers.expectedFrequencies[f - 1], verbose);
int i = 0;
foreach (var seq in
new[] { "GGT", "GGTA", "GGTATT", "GGTATTTTAATT",
"GGTATTTTAATTTATAGT"})
ok &= kn.WriteCount(seq, helpers.expectedCountFragments[i++], verbose);
return ok;
}
}
public class KNucleotide
{
private class Count
{
public int V;
public Count(int v) { V = v; }
}
private Dictionary<ByteString, Count> frequencies
= new Dictionary<ByteString, Count>();
private byte[] sequence;
public KNucleotide(byte[] s) { sequence = s; }
public bool WriteFrequencies(int length, int[] expectedCounts, bool verbose)
{
GenerateFrequencies(length);
var items = new List<KeyValuePair<ByteString, Count>>(frequencies);
items.Sort(SortByFrequencyAndCode);
double percent = 100.0 / (sequence.Length - length + 1);
bool ok = true;
int i = 0;
foreach (var item in items)
{
ok &= (item.Value.V == expectedCounts[i++]);
if (verbose)
{
Console.WriteLine("{0} {1:f3}",
item.Key.ToString(), item.Value.V * percent);
}
}
if (verbose) Console.WriteLine();
return ok;
}
public bool WriteCount(string fragment, int expectedCount, bool verbose)
{
GenerateFrequencies(fragment.Length);
Count count;
if (!frequencies.TryGetValue(new ByteString(fragment), out count))
count = new Count(0);
if (verbose) Console.WriteLine("{0}\t{1}", count.V, fragment);
return (count.V == expectedCount);
}
private void GenerateFrequencies(int length)
{
frequencies.Clear();
for (int frame = 0; frame < length; frame++)
KFrequency(frame, length);
}
private void KFrequency(int frame, int k)
{
int n = sequence.Length - k + 1;
for (int i = frame; i < n; i += k)
{
var key = new ByteString(sequence, i, k);
Count count;
if (frequencies.TryGetValue(key, out count))
count.V++;
else
frequencies[key] = new Count(1);
}
}
int SortByFrequencyAndCode(
KeyValuePair<ByteString, Count> i0,
KeyValuePair<ByteString, Count> i1)
{
int order = i1.Value.V.CompareTo(i0.Value.V);
if (order != 0) return order;
return i0.Key.ToString().CompareTo(i1.Key.ToString());
}
}
}
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