public void Evaluation_BasicExample_WithDelta()
{
Global.Nucleotids = new List <Nucleotid>()
{
new Nucleotid()
{
Sequence = "GCATT"
},
new Nucleotid()
{
Sequence = "ATTGC"
},
new Nucleotid()
{
Sequence = "TGGCC"
},
new Nucleotid()
{
Sequence = "GGCCA"
},
new Nucleotid()
{
Sequence = "GCCAA"
},
new Nucleotid()
{
Sequence = "CAATT"
},
new Nucleotid()
{
Sequence = "ATTTG"
}
};
Global.MaxLength = 8;
Global.ErrorToleration = 1;
Result res = new Result()
{
SequenceIndexes = new int[] { 1, 2, 3, 4, 5, 6, 7 }
};
var result = EvaluationLogic.Evaluate(res);
Assert.AreEqual(4, result);
}
public void Evaluation_BasicExample5()
{
Global.Nucleotids = new List <Nucleotid>()
{
new Nucleotid()
{
Sequence = "GGTTT"
},
new Nucleotid()
{
Sequence = "TTAAC"
},
new Nucleotid()
{
Sequence = "TAACG"
},
new Nucleotid()
{
Sequence = "GATCA"
},
new Nucleotid()
{
Sequence = "CAGGG"
}
};
Global.MaxLength = 8;
Global.ErrorToleration = 0;
Result res = new Result()
{
SequenceIndexes = new int[] { 3, 4, 5, 1, 2 }
};
var result = EvaluationLogic.Evaluate(res);
Assert.AreEqual(2, result);
}
private static void Main(string[] args)
{
int iterations = 10000;
int repetitionsPerFile = 3;
int instanceSize = 200;
int populationSize = 50;
//float maxMutationPercentage = 0.85f;
float mutationPercentage = 0.5f;
int mutationsPlusCrossing = instanceSize - populationSize;
int mutations = (int)(mutationsPlusCrossing * mutationPercentage);
var streamWriter = new StreamWriter("output.csv");
var directoryInfo = new DirectoryInfo(Environment.CurrentDirectory += "\\Data");
var textFiles = directoryInfo.GetFiles("*.txt");
int fileCount = 0;
foreach (var textFile in textFiles)
{
Regex rgx = new Regex("^([0-9]{1,2}).([0-9]{3})");
MatchCollection matches = rgx.Matches(textFile.Name);
int windowLength = int.Parse(matches[0].Groups[2].ToString()) + 9;
InitData(textFile.FullName, windowLength);
//var streamWriter = new StreamWriter("output.txt");
double[] results = new double[iterations];
var dateBefore = DateTime.Now;
for (int i = 0; i < repetitionsPerFile; i++)
{
Result[] population = new Result[instanceSize];
for (int j = 0; j < instanceSize; j++)
{
population[j] = RandomSolutionLogic.GenerateRandomSolution();
}
for (int j = 0; j < iterations; j++)
{
//if (j == 800)
// population[25] = RandomSolutionLogic.GenerateGreedySolution();
Parallel.For(populationSize, populationSize + mutations, k =>
{
population[k] = MutationLogic.GreedMutate(population[StaticRandom.Rand(populationSize - 1)]);
});
Parallel.For(populationSize + mutations, instanceSize, k =>
{
if (StaticRandom.Rand() % 2 == 0)
{
population[k] = CrossingLogic.Cross(population[StaticRandom.Rand(populationSize - 1)], population[StaticRandom.Rand(populationSize - 1)]);
}
else
{
population[k] = CrossingLogic.Cross2Points(population[StaticRandom.Rand(populationSize - 1)], population[StaticRandom.Rand(populationSize - 1)]);
}
});
Parallel.For(0, instanceSize, k =>
{
population[k].EvaluationPoints = EvaluationLogic.Evaluate(population[k]);
population[k].TotalLength = EvaluationLogic.GetTotalLength(population[k]);
});
TournamentLogic.Execute(ref population, population.Length);
var item = population.Where(p => p.EvaluationPoints == population.Max(x => x.EvaluationPoints)).First();
System.Console.WriteLine(String.Format("File {0}/{1} Iteration: {2}, Max: {3}/{4}, MinLength: {5}, BadGuys: {6}", fileCount, textFiles.Count(), j, population.Max(p => p.EvaluationPoints), Global.MaxLength, population.Min(p => p.TotalLength), EvaluationLogic.GetWeakConnectedNucleotidIndexes(item).Count));
results[j] += population.Max(p => p.EvaluationPoints);
}
}
fileCount++;
TimeSpan duration = new TimeSpan((DateTime.Now - dateBefore).Ticks / 5);
streamWriter.WriteLine(textFile.FullName);
for (int i = 0; i < iterations; i++)
{
streamWriter.Write(i.ToString() + ";");
}
streamWriter.WriteLine();
for (int i = 0; i < iterations; i++)
{
streamWriter.Write((results[i] / repetitionsPerFile).ToString() + ";");
}
streamWriter.WriteLine();
streamWriter.WriteLine(String.Format("{0}:{1}:{2}", duration.Minutes, duration.Seconds, duration.Milliseconds));
streamWriter.Flush();
//streamWriter.WriteLine("************ Result ************");
//WriteResult(streamWriter, population[0]);
}
streamWriter.Close();
}
