protected GeneElement MakeSideEle(string comp, int buff, int st, int ed)
{
GeneElement ele = null;
if (comp == "promoter")
{
ele = new Promoter(buff, st, ed, this.Sense);
}
else if (comp == "flank3")
{
ele = new Flank3(st, ed, this.Sense);
}
return(ele);
}
protected bool GenerateSideElement(string comp, bool from5Prime, int size, int buff, int scaffLen, out GeneElement result)
{
result = null;
if (this.Sense == Sense.Sense)
{
if (from5Prime)
{
if (this.Start - buff - size > 0)
{
result = MakeSideEle(comp, buff, this.Start - buff - size, this.Start - buff);
}
}
else
{
if (this.End + buff + size < scaffLen)
{
result = MakeSideEle(comp, buff, this.End + buff, this.End + buff + size);
}
}
}
else if (this.Sense != Sense.Sense)
{
if (from5Prime)
{
if (this.End + buff + size < scaffLen)
{
result = MakeSideEle(comp, buff, this.End + buff, this.End + buff + size);
}
}
else
{
if (this.Start - buff - size < 0)
{
result = MakeSideEle(comp, buff, this.Start - buff - size, this.Start - buff);
}
}
}
if (result == null)
{
return(false);
}
else
{
return(true);
}
}
