public Element(string name, string type, Element src, Element tgt)
{
this.name = name;
this.type = type;
this.src = src;
this.tgt = tgt;
}
private static Element GenerateTerminationSequence(List<Element> elements, Element prevNode)
{
Element[] n = new Element[24 * 2];
// CCCACT
n[0*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[0*2+1] = new Element(getNodeName(), CYTOSIN);
n[1*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[1*2+1] = new Element(getNodeName(), CYTOSIN);
n[2*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[2*2+1] = new Element(getNodeName(), CYTOSIN);
n[3*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[3*2+1] = new Element(getNodeName(), ADENIN);
n[4*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[4*2+1] = new Element(getNodeName(), CYTOSIN);
n[5*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[5*2+1] = new Element(getNodeName(), THYMIN);
// ......
n[6*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[6*2+1] = new Element(getNodeName(), drawAminoAcid());
n[7*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[7*2+1] = new Element(getNodeName(), drawAminoAcid());
n[8*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[8*2+1] = new Element(getNodeName(), drawAminoAcid());
n[9*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[9*2+1] = new Element(getNodeName(), drawAminoAcid());
n[10*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[10*2+1] = new Element(getNodeName(), drawAminoAcid());
n[11*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[11*2+1] = new Element(getNodeName(), drawAminoAcid());
// AGTGGG = invers und gespiegelt zu CCCACT
n[12*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[12*2+1] = new Element(getNodeName(), ADENIN);
n[13*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[13*2+1] = new Element(getNodeName(), GUANIN);
n[14*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[14*2+1] = new Element(getNodeName(), THYMIN);
n[15*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[15*2+1] = new Element(getNodeName(), GUANIN);
n[16*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[16*2+1] = new Element(getNodeName(), GUANIN);
n[17*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[17*2+1] = new Element(getNodeName(), GUANIN);
// AAAAAA
n[18*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[18*2+1] = new Element(getNodeName(), ADENIN);
n[19*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[19*2+1] = new Element(getNodeName(), ADENIN);
n[20*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[20*2+1] = new Element(getNodeName(), ADENIN);
n[21*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[21*2+1] = new Element(getNodeName(), ADENIN);
n[22*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[22*2+1] = new Element(getNodeName(), ADENIN);
n[23*2] = new Element(getNodeName(), DESOXYRIBOSE);
n[23*2+1] = new Element(getNodeName(), ADENIN);
for (int i = 0; i < 24*2; ++i)
{
elements.Add(n[i]);
}
Element currNode = null;
Element nucleotideNode = null;
for (int i = 0; i < 24*2; i+=2)
{
currNode = n[i];
nucleotideNode = n[i+1];
elements.Add(new Element(getEdgeName(), BINDING, currNode, nucleotideNode));
if (prevNode != null) elements.Add(new Element(getEdgeName(), PHOSPHATE_GROUP, prevNode, currNode));
prevNode = currNode;
}
return currNode;
}
private static Element GenerateDNAChain(List<Element> elements,
int length, Element prevNode, string comment)
{
Element currNode = null;
Element currNucleotideNode = null;
Element prevNucleotideNode = null;
for (int i = 1; i <= length; ++i)
{
currNode = new Element(getNodeName(), DESOXYRIBOSE);
currNucleotideNode = new Element(getNodeName(), drawAminoAcid());
while(currNucleotideNode.type==ADENIN && prevNucleotideNode!=null && prevNucleotideNode.type==THYMIN)
currNucleotideNode.type = drawAminoAcid();
if(i==1) currNode.comment = currNucleotideNode.comment = comment + "/first of " + length.ToString();
if(i==length) currNode.comment = currNucleotideNode.comment = comment + "/last of " + length.ToString();
elements.Add(currNode);
elements.Add(currNucleotideNode);
elements.Add(new Element(getEdgeName(), BINDING, currNode, currNucleotideNode));
if (prevNode != null) elements.Add(new Element(getEdgeName(), PHOSPHATE_GROUP, prevNode, currNode));
prevNode = currNode;
prevNucleotideNode = currNucleotideNode;
}
return currNode;
}
private static Element GenerateCorruptDNAChain(List<Element> elements,
int length, Element prevNode)
{
Element currNode = null;
Element currNucleotideNode = null;
Element prevNucleotideNode = null;
bool isCorrupt = false;
for(int i = 1; i <= length; ++i)
{
currNode = new Element(getNodeName(), DESOXYRIBOSE);
currNucleotideNode = new Element(getNodeName(), drawMaybeCorruptAminoAcid());
while(currNucleotideNode.type==ADENIN && prevNucleotideNode!=null && prevNucleotideNode.type==THYMIN)
currNucleotideNode.type = drawAminoAcid();
if (currNucleotideNode.type == URACIL || currNucleotideNode.type == HYDROXYGUANIN) isCorrupt = true;
if(i==length && !isCorrupt) currNucleotideNode.type = URACIL;
elements.Add(currNode);
elements.Add(currNucleotideNode);
elements.Add(new Element(getEdgeName(), BINDING, currNode, currNucleotideNode));
if (prevNode != null) elements.Add(new Element(getEdgeName(), PHOSPHATE_GROUP, prevNode, currNode));
prevNode = currNode;
prevNucleotideNode = currNucleotideNode;
}
return currNode;
}
private static Element GenerateTATABox(List<Element> elements, Element prevNode)
{
Element[] n = new Element[6*2];
// TATAAA
n[0] = new Element(getNodeName(), DESOXYRIBOSE);
n[0 + 1] = new Element(getNodeName(), THYMIN);
n[2] = new Element(getNodeName(), DESOXYRIBOSE);
n[2 + 1] = new Element(getNodeName(), ADENIN);
n[4] = new Element(getNodeName(), DESOXYRIBOSE);
n[4 + 1] = new Element(getNodeName(), THYMIN);
n[6] = new Element(getNodeName(), DESOXYRIBOSE);
n[6 + 1] = new Element(getNodeName(), ADENIN);
n[8] = new Element(getNodeName(), DESOXYRIBOSE);
n[8 + 1] = new Element(getNodeName(), ADENIN);
n[10] = new Element(getNodeName(), DESOXYRIBOSE);
n[10 + 1] = new Element(getNodeName(), ADENIN);
for (int i = 0; i < 6*2; ++i)
{
elements.Add(n[i]);
}
Element currNode = null;
Element nucleotideNode = null;
for (int i = 0; i < 6*2; i+=2)
{
currNode = n[i];
nucleotideNode = n[i+1];
elements.Add(new Element(getEdgeName(), BINDING, currNode, nucleotideNode));
if (prevNode != null) elements.Add(new Element(getEdgeName(), PHOSPHATE_GROUP, prevNode, currNode));
prevNode = currNode;
}
return currNode;
}