public bool containsSuperhaplogroup(Haplogroup haplogroup)
{
if (haplogroup.isSuperHaplogroup(Cluster[0].Haplogroup))
{
return(true);
}
return(false);
}
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;
}
public SearchResult(string haplogroup, Sample polysInTestSample)
{
this.haplogroup = new Haplogroup(haplogroup);
this.usedPolysInSample = polysInTestSample;
this.unusedPolys.AddRange(polysInTestSample.Polymorphismn);
foreach (Polymorphism currentPoly in polysInTestSample.Polymorphismn)
{
this.usedWeightPolys += currentPoly.getMutationRate();
}
}
public virtual PhyloTreePath getPhyloTreePath(Haplogroup haplogroup)
{
foreach (SearchResult currentResult in this.cluster)
{
if (currentResult.Haplogroup.Equals(haplogroup))
{
return(currentResult.UsedPath);
}
}
return(null);
}
public void changePoly(Haplogroup hg, Polymorphism polyOld, Polymorphism polyNew)
{
var e = getPolysOfHg(hg);
foreach (XmlNode ce in e)
{
if (ce.InnerText.Equals(polyOld.ToString()))
{
ce.InnerText = polyNew.ToString();
return;
}
}
throw new HaploGrepException("Polymorphism does not exit");
}
public override bool Equals(object haplogroup)
{
if (!(haplogroup is Haplogroup))
{
return(false);
}
Haplogroup c = (Haplogroup)haplogroup;
if (!this.id.Equals(c.id))
{
return(false);
}
return(true);
}
public bool isSuperHaplogroup(Haplogroup hgToCheck)
{
if (!(hgToCheck is Haplogroup))
{
return(false);
}
Haplogroup c = hgToCheck;
if (!c.id.Contains(this.id))
{
return(false);
}
return(true);
}
public SearchResult(string newHaplogroup, SearchResult resultToCopy)
{
this.haplogroup = new Haplogroup(newHaplogroup);
this.usedPolysInSample = resultToCopy.usedPolysInSample;
this.allCheckedPolys.AddRange(resultToCopy.allCheckedPolys);
this.correctPolys.AddRange(resultToCopy.correctPolys);
this.unusedPolys.AddRange(resultToCopy.unusedPolys);
this.correctedBackmutations.AddRange(resultToCopy.correctedBackmutations);
this.unusedPolysNotInRange.AddRange(resultToCopy.unusedPolysNotInRange);
this.missingPolysOutOfRange.AddRange(resultToCopy.missingPolysOutOfRange);
this.usedPath = new PhyloTreePath(resultToCopy.usedPath);
this.usedWeightPolys = resultToCopy.usedWeightPolys;
this.correctWeightPolys = resultToCopy.correctWeightPolys;
this.expectedWeightPolys = resultToCopy.expectedWeightPolys;
this.missingWeightPolys = resultToCopy.missingWeightPolys;
}
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 XmlNodeList getPolysOfHg(Haplogroup hg)
{
var titleNode = xmlDoc.SelectSingleNode("//haplogroup[@name=\"" + hg.ToString() + "\"]/details");
return(titleNode.SelectNodes("poly"));
}
public static List <ClusteredSearchResult> createClusteredSearchResult(List <SearchResult> unclusteredResults, Haplogroup hg)
{
List <ClusteredSearchResult> clusteredSearchResult = new List <ClusteredSearchResult>();
//sort the results by top hit
unclusteredResults.Sort();
int i = 0;
double currentRank = -1.0D;
bool foundPredefinedHG = false;
foreach (SearchResult currentResult in unclusteredResults)
{
if (i == 50)
{
break;
}
if (currentRank != currentResult.Rank)
{
clusteredSearchResult.Add(new ClusteredSearchResult(i + 1));
i++;
currentRank = currentResult.Rank;
}
clusteredSearchResult[i - 1].Cluster.Add(currentResult);
if (currentResult.Haplogroup.Equals(hg))
{
foundPredefinedHG = true;
}
}
if ((!foundPredefinedHG) && (!hg.ToString().Equals("")))
{
int pos = 1;
foreach (SearchResult currentResult in unclusteredResults)
{
if (currentResult.Haplogroup.Equals(hg))
{
clusteredSearchResult.Add(new ClusteredSearchResult(pos));
clusteredSearchResult[i].Cluster.Add(currentResult);
break;
}
pos++;
}
}
return(clusteredSearchResult);
}
public PhyloTreeNode(Haplogroup haplogroup)
{
this.haplogroup = haplogroup;
}