void CChemEq::addElement(CCopasiVector < CChemEqElement > & structure,
const CChemEqElement & element,
CChemEq::MetaboliteRole role)
{
unsigned C_INT32 i;
std::string key = element.getMetaboliteKey();
if (key == "")
return; // don�t add empty element
for (i = 0; i < structure.size(); i++)
if (key == structure[i]->getMetaboliteKey())
break;
if (i >= structure.size())
{
CChemEqElement * Element = new CChemEqElement(element);
if (role == CChemEq::SUBSTRATE)
Element->setMultiplicity(- Element->getMultiplicity());
structure.add(Element, true);
}
else if (role == CChemEq::SUBSTRATE)
structure[i]->addToMultiplicity(- element.getMultiplicity());
else
structure[i]->addToMultiplicity(element.getMultiplicity());
}
// calculates the clustering coefficient of gene g
C_FLOAT64 cluster(CCopasiVector < CGene > &gene, C_INT32 g)
{
C_INT32 i, j, k, m, n, edges;
CCopasiVector <CGene> neighbors;
CGene *ptG;
// create the neighborhood
n = gene[g]->getModifierNumber();
if (n <= 1)
return 0.0;
for (i = 0; i < n; i++)
neighbors.add(gene[g]->getModifier(i));
// count the number of links within the neighborhood
for (edges = i = 0; i < n; i++)
{// one neighbor at a time
m = neighbors[i]->getModifierNumber();
for (j = 0; j < m; j++)
{// one modifier at a time
ptG = neighbors[i]->getModifier(j);
// increment if this modifier is in the neighborhood
// but it is not itself
if (ptG != neighbors[i])
for (k = 0; k < n; k++)
if (ptG == neighbors[k])
edges++;
}
}
return (C_FLOAT64) edges / (C_FLOAT64) (n*(n - 1));
}