double CCopasiSpringLayout::potSpeciesSpecies(const CLMetabGlyph & a, const CLMetabGlyph & b) const
{
double tmp;
tmp = bound_distance(a.getX() + a.getWidth() / 2, a.getY() + a.getHeight() / 2,
b.getX() + b.getWidth() / 2, b.getY() + b.getHeight() / 2, 200);
if (tmp < 1) tmp = 1;
return /*a.charge*b.charge*/ 1 / tmp; //TODO: reintroduce the charge
}
/*
return ret;
}
*/
double CCopasiSpringLayout::potSpeciesCompartment(const CLMetabGlyph & s, const CLCompartmentGlyph & c) const
{
double tmp = 0;
double dist = fabs((s.getX() + 0.5 * s.getWidth()) - (c.getX() + 0.5 * c.getWidth()));
if (dist > (0.5 * c.getWidth() - 50))
tmp += pow(dist - 0.5 * c.getWidth() + 50, 2);
dist = fabs((s.getY() + 0.5 * s.getHeight()) - (c.getY() + 0.5 * c.getHeight()));
if (dist > (0.5 * c.getHeight() - 50))
tmp += pow(dist - 0.5 * c.getHeight() + 50, 2);
return tmp /**s.charge*/; //TODO reintroduce charge
}