/// <summary>
/// The slices.
/// </summary>
public MitochondrialAssemblyPlotMaker(MitochondrialAssembly assembly)
{
this.Assembly = assembly;
slices = new List <GenomeSlice>(assembly.AllNodesInGraph.Select(x => new GenomeSlice(x)));
if (this.Assembly.SuccessfulAssembly)
{
foreach (var s in slices)
{
if (Assembly.NodesInCompleteAssembly.Contains(s.Node))
{
s.InMainAssembly = true;
}
}
if (Assembly.GreedyPathAssembly.Sequence.Count > StaticResources.CRS_LENGTH)
{
assemblyAligner = new NucMerQueryable(Assembly.GreedyPathAssembly.Sequence);
}
else
{
assemblyAligner = new NucMerQueryable(ReferenceGenome.ReferenceSequence);
}
assignLeftRightPositionsToSlices();
assignHeightPositionsToSlices();
arrows = Assembly.AllNodesInGraph.SelectMany(x => x.GetAllEdges()).Where(z => !z.IsInferiorEdge).Select(x => new Arrow(x)).ToList();
}
}
static ReferenceGenome()
{
ReferenceSequence = new Sequence(NoGapDnaAlphabet.Instance, rCRS, false);
nucmer = new NucMerQueryable(ReferenceSequence);
}
