public void init(Simulator aSim, XMLParser aSpeciesRoot, XMLParser speciesDefaults) {
super.init(aSim, aSpeciesRoot, speciesDefaults);
/*
* Retrieving list of environments to which this species is sensitive
* to and the correspondent probability of dying if under the
* influence of that environment.
*/
String s;
Double p;
for (Element aSpeciesMarkUp : aSpeciesRoot.getChildrenElements("envSensitivity")) {
s = aSpeciesMarkUp.getAttributeValue("name");
envSensitivity.add(s);
p = aSpeciesRoot.getDblAttrOfChildSuchAttribute("envSensitivity", "name", s, "probDie");
envProbDie.put(s, p);
}
}
public void initFromProtocolFile(Simulator aSim, XMLParser xmlMarkUp) {
// Initilaisation of the Located agent
// super.initFromProtocolFile(aSimulator, aSpeciesRoot);
// init();
_nCopy = getSpeciesParam().nCopy;
int reacIndex;
reactionActive = new ArrayList<Integer>();
for (Element aReactionMarkUp : xmlMarkUp.getChildrenElements("reaction")) {
reacIndex = aSim.getReactionIndex(aReactionMarkUp.getAttributeValue("name"));
/*
* Add the reaction to the list of active reactions.
*/
if (aReactionMarkUp.getAttributeValue("status").equals("active"))
reactionActive.add(reacIndex);
}
}