// Creates a subsequence from a source sequence given the settings provided
private ISequence CreateSubsequence(SimulatorSettings settings, int index)
{
double err = (double)settings.ErrorFrequency;
// Set the length using the appropriate random number distribution type
int subLength = settings.SequenceLength;
if (settings.DistributionType == (int)Distribution.Uniform)
{
subLength += random.Next(settings.LengthVariation * 2) - settings.LengthVariation;
}
else if (settings.DistributionType == (int)Distribution.Normal)
{
subLength = (int)MBF.Util.Helper.GetNormalRandom((double)settings.SequenceLength,
(double)settings.LengthVariation);
}
// Quick sanity checks on the length of the subsequence
if (subLength <= 0)
{
subLength = 1;
}
if (subLength > Sequence.Count)
{
subLength = Sequence.Count;
}
// Set the start position
int startPosition = random.Next(Sequence.Count - subLength);
Sequence result = new Sequence(Sequence.Alphabet);
result.IsReadOnly = false;
List <ISequenceItem> errorSource = Sequence.Alphabet.LookupAll(true, false, settings.AllowAmbiguities, false);
for (int i = 0; i < subLength; i++)
{
// Apply Errors if applicable
if (random.NextDouble() < err)
{
result.Add(errorSource[random.Next(errorSource.Count - 1)]);
}
else
{
result.Add(Sequence[startPosition + i]);
}
}
result.ID = Sequence.ID + " (Split " + (index + 1) + ", " + result.Count + "bp)";
// Reverse Sequence if applicable
if (settings.ReverseHalf && random.NextDouble() < 0.5f)
{
return(result.Reverse);
}
return(result);
}
/// <summary>
/// Does the logic behind the sequence simulation
/// </summary>
internal void DoSimulation(SimulatorWindow window, string outputFileName, SimulatorSettings settings)
{
FileInfo file = new FileInfo(outputFileName);
if (!file.Directory.Exists)
{
throw new ArgumentException("Could not write to the output directory for " + outputFileName);
}
if (settings.OutputSequenceCount <= 0)
{
throw new ArgumentException("'Max Output Sequences Per File' should be greater than zero.");
}
if (settings.SequenceLength <= 0)
{
throw new ArgumentException("'Mean Output Length' should be greater than zero.");
}
string filePrefix;
if (String.IsNullOrEmpty(file.Extension))
{
filePrefix = file.FullName;
}
else
{
filePrefix = file.FullName.Substring(0, file.FullName.IndexOf(file.Extension));
}
string filePostfix = "_{0}.fa";
int seqCount = (settings.DepthOfCoverage * Sequence.Count) / settings.SequenceLength;
int fileCount = seqCount / settings.OutputSequenceCount;
if (seqCount % settings.OutputSequenceCount != 0)
{
fileCount++;
}
window.UpdateSimulationStats(seqCount, fileCount);
if (results == null)
{
results = new List <ISequence>();
}
else
{
results.Clear();
}
int fileIndex = 1;
FastaFormatter formatter = new FastaFormatter();
for (int i = 0; i < seqCount; i++)
{
results.Add(CreateSubsequence(settings, i));
if (results.Count >= settings.OutputSequenceCount)
{
FileInfo outFile = new FileInfo(filePrefix + string.Format(filePostfix, fileIndex++));
formatter.Format(results, outFile.FullName);
results.Clear();
}
}
if (results.Count > 0)
{
FileInfo outFile = new FileInfo(filePrefix + string.Format(filePostfix, fileIndex++));
formatter.Format(results, outFile.FullName);
}
window.NotifySimulationComplete();
}
