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);
}
public override void AddFileElement(string ele_name, int start, int end)
{
if (end - start > 0)
{
GeneElement ele;
int cnt = 0;
switch (ele_name)
{
case "five_prime_UTR":
ele = new UTR5(start, end, this.Sense);
if (!Elements.ContainsKey("five_prime_UTR"))
{
Elements.Add("five_prime_UTR", new List <GeneElement> ());
}
Elements ["five_prime_UTR"].Add(ele);
break;
case "three_prime_UTR":
ele = new UTR3(start, end, this.Sense);
if (!Elements.ContainsKey("three_prime_UTR"))
{
Elements.Add("three_prime_UTR", new List <GeneElement> ());
}
Elements ["three_prime_UTR"].Add(ele);
break;
case "exon":
if (!Elements.ContainsKey("exon"))
{
Elements.Add("exon", new List <GeneElement> ());
}
cnt = Elements ["exon"].Count + 1;
ele = new Exon(cnt, start, end, this.Sense);
Elements ["exon"].Add(ele);
break;
case "CDS":
if (!Elements.ContainsKey("CDS"))
{
Elements.Add("CDS", new List <GeneElement> ());
}
cnt = Elements ["CDS"].Count + 1;
ele = new CDS(cnt, start, end, this.Sense);
Elements ["CDS"].Add(ele);
break;
default:
if (ele_name.Contains("promoter"))
{
ele = new Promoter(ele_name, start, end, this.Sense);
if (!Elements.ContainsKey(ele_name))
{
Elements.Add(ele_name, new List <GeneElement> ());
}
Elements [ele_name].Add(ele);
}
else
{
if (!Elements.ContainsKey(ele_name))
{
Elements.Add(ele_name, new List <GeneElement> ());
}
ele = new MiscElement(ele_name, start, end, this.Sense);
Elements [ele_name].Add(ele);
}
break;
}
}
}
