/// <summary>
/// Create a new class that compares a sample to a known haplotype
/// </summary>
public HaplotypeComparison(PhyloTreeNodev2 node, SimpleSample sample)
{
this.node = node;
var polysInNode = sample.Filter.FilterPolys(node.Mutations).ToList();
NumberOfPolymorhpismsInHaplotype = (ushort)polysInNode.Count;
haplotypeWeightPoly = polysInNode.Sum(x => x.getMutationRate());
MatchingPolymorphisms = polysInNode.Where(z => sample.Polymorphisms.Contains(z)).ToList();
NumberOfPolymorphismsMissingFromGenotype = (ushort)(polysInNode.Count - MatchingPolymorphisms.Count);
NumberOfPolymorphismsMissingFromHaplotype = (ushort)(sample.Polymorphisms.Count - MatchingPolymorphisms.Count);
matchingWeightPoly = MatchingPolymorphisms.Sum(x => x.getMutationRate());
var CorrectInHaplotypeRatio = haplotypeWeightPoly == 0 ? 1.0 : (matchingWeightPoly / haplotypeWeightPoly);
var CorrectInSampleRatio = sample.TotalSampleWeight == 0 ? 1.0 : (matchingWeightPoly / sample.TotalSampleWeight);
Rank = .5 * CorrectInHaplotypeRatio + .5 * CorrectInSampleRatio;
}
public HaplotypeSearcher()
{
treeRoot = TreeLoader.LoadTree(); //CONSTANTS.TREE_XML_FILE);
var skipped = HaploSearchManager.SetPhylogeneticWeights(); //CONSTANTS.WEIGHT_FILE);
}
