/// <summary>
/// Create UTR regions for this transcript
/// </summary>
public List <UTR> CreateUTRs()
{
if (CodingDomainSequences.Count == 0)
{
return(UTRs);
}
List <Interval> missing = Exons.OfType <Interval>().ToList();
foreach (Interval interval in UTRs.Concat(CodingDomainSequences.OfType <Interval>().ToList()))
{
missing = missing.SelectMany(i => i.Minus(interval)).ToList();
}
long codingMin = CodingDomainSequences.Select(c => c.OneBasedStart).Min();
long codingMax = CodingDomainSequences.Select(c => c.OneBasedEnd).Max();
foreach (Interval interval in missing)
{
Exon x = FindExon(interval);
if (x == null)
{
throw new ArgumentException("Cannot find exon for UTR: " + interval.ToString());
}
UTR toAdd = null;
if (IsStrandPlus())
{
if (interval.OneBasedEnd <= codingMin)
{
toAdd = new UTR5Prime(x, x.ChromosomeID, x.Source, x.Strand, interval.OneBasedStart, interval.OneBasedEnd);
}
else if (interval.OneBasedStart >= codingMax)
{
toAdd = new UTR3Prime(x, x.ChromosomeID, x.Source, x.Strand, interval.OneBasedStart, interval.OneBasedEnd);
}
}
else
{
if (interval.OneBasedStart >= codingMax)
{
toAdd = new UTR5Prime(x, x.ChromosomeID, x.Source, x.Strand, interval.OneBasedStart, interval.OneBasedEnd);
}
else if (interval.OneBasedEnd <= codingMin)
{
toAdd = new UTR3Prime(x, x.ChromosomeID, x.Source, x.Strand, interval.OneBasedStart, interval.OneBasedEnd);
}
}
// OK?
if (toAdd != null)
{
UTRs.Add(toAdd);
}
}
return(UTRs);
}
protected UTR(UTR utr)
: base(utr)
{
}