/// <summary>
/// This method performs the BurrowsWheelerTransform algorithm on the input SuffixArray.
/// </summary>
/// <returns></returns>
public BurrowsWheelerTransformAsc(SuffixArrayAsc suffixArray)
{
textLength = suffixArray.InputText.Length;
List<string> bwtTemp =
(suffixArray.Suffixes.Select(
i => new { i, lenSuffix = i.Length }).Select(
@t => @t.i + suffixArray.InputText.Substring(0, textLength - @t.lenSuffix)
)
).ToList();
bwtTemp.Sort();
List<char> F = new List<char>();
List<char> L = new List<char>();
for (int i = 0; i < bwtTemp.Count; i++) {
F.Add(bwtTemp[i][0]);
L.Add(bwtTemp[i][bwtTemp[i].Length - 1]);
}
waveletTree = new WaveletTreeAsc(new string(L.ToArray()));
WaveletTreeAsc waveletTreeF = new WaveletTreeAsc(new string(F.ToArray()));
char[] distinctChars = F.Distinct().ToArray();
C = new Dictionary<char, int>(distinctChars.Length);
foreach (char c in distinctChars) {
C.Add(c, waveletTreeF.Select(c, 1));
}
}
public void TestAsciiFiles()
{
var gen = new Random();
var files = Directory.EnumerateFiles(DirectoryString + @"\GenFiles\", "*").Where(u => !u.Contains(@"GenFiles\B_"));
foreach (var file in files) {
var ob = new StatObj { FileName = file };
var commandLineInterpreter = new CommandInterpreter() { Encoding = Encoding.ASCII, Path = ob.FileName };
var fileReader = new AsciiFileReader(commandLineInterpreter);
var sa = new SuffixArrayAsc(fileReader.Data);
var bwt = new BurrowsWheelerTransformAsc(sa);
int bwtWins = 0;
int bfWins = 0;
for (var i = 1; i < Math.Min(2, ob.FileSize / 2); i++) {
ob.PatternSize = i;
commandLineInterpreter.QueryString = fileReader.Data.Substring(
(int)(
(ob.FileSize - ob.PatternSize) * gen.NextDouble()
), ob.PatternSize
);
Console.WriteLine(commandLineInterpreter.QueryString);
// Settings and timers
//===============================================================
int times = 1000;
Stopwatch sw;
//===============================================================
// BWT
//===============================================================
StatObj bwtStat = ob;
bwtStat.EndTimeTicks = 0;
bwtStat.Results = 0;
bwtStat.RuntimeTicks = 0;
bwtStat.StartTimeTicks = 0;
sw = Stopwatch.StartNew();
for (int t = 0; t < times; t++) {
bwtStat.Results = bwt.CountOccurrences(commandLineInterpreter.QueryString);
}
sw.Stop();
bwtStat.RuntimeTicks = sw.ElapsedMilliseconds; //(ulong)sw.ElapsedTicks;
//===============================================================
// BF
//===============================================================
StatObj bfStat = ob;
bfStat.EndTimeTicks = 0;
bfStat.Results = 0;
bfStat.RuntimeTicks = 0;
bfStat.StartTimeTicks = 0;
sw = Stopwatch.StartNew();
for (int t = 0; t < times; t++) {
bfStat.Results = BruteForce.Run(fileReader.Data, commandLineInterpreter.QueryString);
}
sw.Stop();
bfStat.RuntimeTicks = sw.ElapsedMilliseconds; //(ulong)sw.ElapsedTicks;
//===============================================================
// Print Results
//===============================================================
//Console.WriteLine("BWT,{0},{1},{2},{3},{4},{5}", ob.RuntimeTicks, ob.PatternSize, ob.FileSize, ob.AlphabetSize, ob.Results, Encoding.ASCII);
//Console.WriteLine("BruteForce,{0},{1},{2},{3},{4},{5}", ob.RuntimeTicks, ob.PatternSize, ob.FileSize, ob.AlphabetSize, ob.Results, Encoding.ASCII);
//Console.WriteLine("BWT: {0}", bwtStat.RuntimeTicks);
//Console.WriteLine(" BF: {0}", bfStat.RuntimeTicks);
if (bwtStat.Results != bfStat.Results) {
Console.WriteLine("\nBWT FAILED US!\n");
}
if (bfStat.RuntimeTicks >= bwtStat.RuntimeTicks)
bwtWins++;
else
bfWins++;
//===============================================================
}
Console.WriteLine(ob.FileName + "\nBWT Wins: " + bwtWins + "\nBF Wins: " + bfWins + "\n");
}
}
public void TestBinaryFiles()
{
var gen = new Random();
var files = Directory.EnumerateFiles(DirectoryString + @"\GenFiles\", "B_*");
foreach (var file in files) {
var ob = new StatObj { FileName = file };
var commandLineInterpreter = new CommandInterpreter() { Encoding = Encoding.UTF8, Path = ob.FileName };
var fileReader = new AsciiFileReader(commandLineInterpreter);
var sa = new SuffixArrayAsc(fileReader.Data);
var bwt = new BurrowsWheelerTransformAsc(sa);
for (var i = 1; i < Math.Min(20, ob.FileSize / 2); i++) {
ob.PatternSize = i;
commandLineInterpreter.QueryString = fileReader.Data.Substring(
(int)(
(ob.FileSize - ob.PatternSize) * gen.NextDouble()
), ob.PatternSize
);
ob.StartTimeTicks = (ulong)DateTime.Now.Ticks;
/* try
{*/
ob.Results = bwt.CountOccurrences(commandLineInterpreter.QueryString);
/*}
catch
{
}*/
ob.EndTimeTicks = (ulong)DateTime.Now.Ticks;
Console.WriteLine("BWT,{0},{1},{2},{3},{4},{5}", ob.RuntimeTicks, ob.PatternSize, ob.FileSize, ob.AlphabetSize, ob.Results, Encoding.UTF8);
ob.StartTimeTicks = (ulong)DateTime.Now.Ticks; /*try
{*/
ob.Results = BruteForce.Run(fileReader.Data, commandLineInterpreter.QueryString);
/*}
catch
{
}*/
ob.EndTimeTicks = (ulong)DateTime.Now.Ticks;
Console.WriteLine("BruteForce,{0},{1},{2},{3},{4},{5}", ob.RuntimeTicks, ob.PatternSize, ob.FileSize, ob.AlphabetSize, ob.Results, Encoding.UTF8);
}
}
}
public static void RunAsciiTestFiles()
{
const string DirectoryString = @"..\..";
var gen = new Random();
var files = Directory.EnumerateFiles(DirectoryString + @"\GenFiles\", "*").Where(u => !u.Contains(@"GenFiles\B_"));
StringBuilder output = new StringBuilder();
int fileNum = 0;
foreach (var file in files) {
var ob = new StatObj { FileName = file };
var commandLineInterpreter = new CommandInterpreter() { Encoding = Encoding.ASCII, Path = ob.FileName };
var fileReader = new AsciiFileReader(commandLineInterpreter);
var sa = new SuffixArrayAsc(fileReader.Data);
var bwt = new BurrowsWheelerTransformAsc(sa);
for (var i = 1; i < Math.Min(20, ob.FileSize / 2); i++) {
ob.PatternSize = i;
commandLineInterpreter.QueryString = fileReader.Data.Substring(
(int)(
(ob.FileSize - ob.PatternSize) * gen.NextDouble()
), ob.PatternSize
);
// Settings and timers
//===============================================================
int times = 1000;
Stopwatch sw;
//===============================================================
// BWT
//===============================================================
StatObj bwtStat = ob;
bwtStat.EndTimeTicks = 0;
bwtStat.Results = 0;
bwtStat.RuntimeTicks = 0;
bwtStat.StartTimeTicks = 0;
sw = Stopwatch.StartNew();
for (int t = 0; t < times; t++) {
bwtStat.Results = bwt.CountOccurrences(commandLineInterpreter.QueryString);
}
sw.Stop();
bwtStat.RuntimeTicks = sw.ElapsedMilliseconds;
//===============================================================
// BF
//===============================================================
StatObj bfStat = ob;
bfStat.EndTimeTicks = 0;
bfStat.Results = 0;
bfStat.RuntimeTicks = 0;
bfStat.StartTimeTicks = 0;
sw = Stopwatch.StartNew();
for (int t = 0; t < times; t++) {
bfStat.Results = BruteForce.Run(fileReader.Data, commandLineInterpreter.QueryString);
}
sw.Stop();
bfStat.RuntimeTicks = sw.ElapsedMilliseconds;
//===============================================================
// Print Results
//===============================================================
int m = ob.PatternSize;
int n = ob.FileSize;
int ep = ob.AlphabetSize;
output.AppendLine(String.Format("BWT,{0},{1},{2},{3},{4},{5}", bwtStat.RuntimeTicks, m, n, ep, bwtStat.Results, Encoding.ASCII));
output.AppendLine(String.Format("BruteForce,{0},{1},{2},{3},{4},{5}", bfStat.RuntimeTicks, m, n, ep, bfStat.Results, Encoding.ASCII));
//===============================================================
}
fileNum++;
Console.WriteLine(((((double)fileNum) / files.ToArray<string>().Length) * 100).ToString() + " %");
}
using (StreamWriter writer = new StreamWriter(DirectoryString + @"\GenFiles\AsciiResults.csv")) {
writer.Write(output.ToString());
}
}
public static void RunAsciiTestOnce(string text, string pattern, int times = 10000)
{
Console.WriteLine("T: " + text);
Console.WriteLine("P: " + pattern);
Console.WriteLine();
SuffixArrayAsc sa = new SuffixArrayAsc(text);
BurrowsWheelerTransformAsc bwt = new BurrowsWheelerTransformAsc(sa);
int answer = 0;
// BWT
Stopwatch sw = Stopwatch.StartNew();
for (int i = 0; i < times; i++) {
answer = bwt.CountOccurrences(pattern);
}
double time = ((double)sw.ElapsedMilliseconds) / times;
Console.WriteLine("BWT:\n====");
Console.WriteLine(" Time: " + time + " ms");
Console.WriteLine(" Matches: " + answer.ToString());
Console.WriteLine();
// Brute Force
Stopwatch sw2 = Stopwatch.StartNew();
for (int i = 0; i < times; i++) {
answer = BruteForce.Run(text, pattern);
}
double time2 = ((double)sw2.ElapsedMilliseconds) / times;
Console.WriteLine("BF:\n====");
Console.WriteLine(" Time: " + time2 + " ms");
Console.WriteLine(" Matches: " + answer.ToString());
Console.WriteLine();
}
