def __init__(self,id,strand=None):
if(type(id)!=EssexNode): # not an EssexNode
self.transcriptId=id
self.strand=strand
self.exons=[]
self.UTR=[]
self.rawExons=None
self.stopCodons={"TAG":1,"TGA":1,"TAA":1}
self.startCodon=None
self.extraFields=None
else: # EssexNode
essex=id
self.transcriptId=essex.getAttribute("ID")
self.strand=essex.getAttribute("strand")
self.source=essex.getAttribute("source")
self.begin=essex.getAttribute("begin")
self.end=essex.getAttribute("end")
self.geneId=essex.getAttribute("gene")
self.substrate=essex.getAttribute("substrate")
self.exons=[]
self.UTR=[]
self.rawExons=None
self.startCodon=None
self.extraFields=None
self.stopCodons={"TAG":1,"TGA":1,"TAA":1}
exons=self.exons
UTR=self.UTR
exonsElem=essex.findChild("exons")
if(exonsElem):
n=exonsElem.numElements()
for i in range(0,n):
exon=exonsElem.getIthElem(i)
begin=int(exon.getIthElem(0))
end=int(exon.getIthElem(1))
exon=Exon(begin,end,self)
exons.append(exon)
utrElem=essex.findChild("UTR")
if(utrElem):
n=utrElem.numElements()
for i in range(0,n):
exon=utrElem.getIthElem(i)
begin=int(exon.getIthElem(0))
end=int(exon.getIthElem(1))
exon=Exon(begin,end,self)
UTR.append(exon)
