/// <summary>
/// Creates upstream and downstream intervals for this transcript
/// </summary>
/// <param name="chromosomeSequence"></param>
public List <Interval> CreateUpDown(Chromosome chromosomeSequence)
{
long chrMin = 1;
long chrMax = chromosomeSequence.Sequence.Count;
// Create up/down stream intervals and add them to the list
long beforeStart = Math.Max(chrMin - DEFAULT_UP_DOWN_LENGTH, chrMin);
long beforeEnd = Math.Max(chrMin - 1, chrMin);
long afterStart = Math.Min(OneBasedEnd + 1, chrMax);
long afterEnd = Math.Min(OneBasedEnd + DEFAULT_UP_DOWN_LENGTH, chrMax);
if (IsStrandPlus())
{
if (beforeStart < beforeEnd)
{
Upstream = new Upstream(this, chromosomeSequence.ChromosomeID, Source, Strand, beforeStart, beforeEnd);
}
if (afterStart < afterEnd)
{
Downstream = new Downstream(this, chromosomeSequence.ChromosomeID, Source, Strand, afterStart, afterEnd);
}
}
else
{
if (afterStart < afterEnd)
{
Upstream = new Upstream(this, chromosomeSequence.ChromosomeID, Source, Strand, afterStart, afterEnd);
}
if (beforeStart < beforeEnd)
{
Downstream = new Downstream(this, chromosomeSequence.ChromosomeID, Source, Strand, beforeStart, beforeEnd);
}
}
return(new List <Interval> {
Upstream, Downstream
});
}
public Upstream(Downstream downstream)
: base(downstream)
{
}
