public TestSample(string sampleID, Haplogroup predefiniedHaplogroup, Sample sample, SampleRange sampleRange, string state)
{
this.testSampleID = sampleID;
this.sample = sample;
this.predefiniedHaplogroup = predefiniedHaplogroup;
this.sampleRange = sampleRange;
this.state = state;
}
private void exportResults(string outFilename)
{
StringBuilder result = new StringBuilder();
var sampleCollection = session.CurrentSampleFile.TestSamples;
sampleCollection.Sort();
result.Append("SampleID\tRange\tHaplogroup\tQuality\tPolymorphisms\n");
if (sampleCollection != null)
{
foreach (TestSample sample in sampleCollection)
{
result.Append(sample.SampleID + "\t");
SampleRange range = sample.SampleRanges;
var startRange = range.Starts;
var endRange = range.Ends;
string resultRange = "";
for (int i = 0; i < startRange.Count; i++)
{
if (startRange[i] == endRange[i])
{
resultRange = resultRange + startRange[i] + ";";
}
else
{
resultRange = resultRange + startRange[i] + "-" + endRange[i] + ";";
}
}
result.Append(resultRange + "\t");
result.Append(sample.RecognizedHaplogroup + "\t");
result.Append(sample.ResultQuality + "\t");
getPolysUsed(result, session.getClassificationResults(sample.SampleID));
getPolysNotUsed(result, session.getClassificationResults(sample.SampleID));
getPolysUnused(result, session.getClassificationResults(sample.SampleID));
result.Append("\n");
}
}
StreamWriter fileWriter = new StreamWriter(outFilename);
fileWriter.Write(result.ToString());
fileWriter.Close();
}
public TestSample(string currentLine)
{
string[] tokens = currentLine.Split(new char[] { '\t' }, StringSplitOptions.RemoveEmptyEntries);
if (tokens.Length < 4)
{
throw new HaploGrepException("Not enough columns in .hsd file");
}
this.testSampleID = tokens[0].Trim();
if (tokens[1].Length == 0)
{
throw new ArgumentException("No range specified, range given was: " + tokens[1]);
}
tokens[1] = tokens[1].Replace("\"", "");
this.sampleRange = new SampleRange(tokens[1]);
if ((tokens[2].Equals("?")) || (tokens[2].Equals("SEQ")))
{
this.predefiniedHaplogroup = new Haplogroup("");
}
else
{
this.predefiniedHaplogroup = new Haplogroup(tokens[2]);
}
StringBuilder sampleString = new StringBuilder();
for (int i = 3; i < tokens.Length; i++)
{
sampleString.Append(tokens[i] + " ");
}
try
{
this.sample = new Sample(sampleString.ToString(), 0);
}
catch (Exception e)
{
throw e;
}
}
public SampleRange(SampleRange rangeToCopy)
{
this.starts.AddRange(rangeToCopy.starts);
this.ends.AddRange(rangeToCopy.ends);
}