public void initFromProtocolFile(Simulator aSim, XMLParser aSpeciesRoot) {
// Initialisation of Bacterium
super.initFromProtocolFile(aSim, aSpeciesRoot);
// Chemotaxis-specific protocol parameters
chemoeffector = aSpeciesRoot.getParam("chemoeffector").trim();
repellent = aSpeciesRoot.getParamBool("repellent");
chem_threshold = aSpeciesRoot.getParamDbl("chem_threshold");
init();
}
/**
* \brief Creates a species object from that specified in the XML protocol file
*
* <p>This method takes an object specified in the SPECIES mark-up and creates a simulation object
* for that species
*
* @param aSimulator The simulation object used to simulate the conditions specified in the
* protocol file
* @param aSpRoot A Species mark-up within the specified protocol file
*/
public Species(Simulator aSimulator, XMLParser aSpRoot, XMLParser speciesDefaults) {
// Name of the species as specified in the protocol file
speciesName = aSpRoot.getName();
// colour is used to distinguish agents in POV-Ray output images - read this from the protocol
// file
String colorName = aSpRoot.getParam("color");
// Set the colour to white if not specified
if (colorName == null) colorName = "white";
// Translate this text string into a colour
color = utils.UnitConverter.getColor(colorName);
// Register this species
// KA 8/3/13 - is this correct - this is storing the number of species in the simulation
speciesIndex = aSimulator.speciesList.size();
// Take a local copy of the current simulation
currentSimulator = aSimulator;
// KA May 2013
// If this is self-attach, useful to store the injection period parameters here, so can
// reference these later
cellInjectionStartHour = aSpRoot.getParamDbl("cellInjectionStartHour");
injectionOnAttachmentFrequency = aSpRoot.getParamDbl("injectionOnAttachmentFrequency");
cellInjectionEndHour = aSpRoot.getParamDbl("cellInjectionEndHour");
injectionOffAttachmentFrequency = aSpRoot.getParamDbl("injectionOffAttachmentFrequency");
// Create the progenitor and tune its speciesParam object
_progenitor = (SpecialisedAgent) aSpRoot.instanceCreator("simulator.agent.zoo");
// Get parameters for this progenitor object from the protocol file if present
_progenitor.getSpeciesParam().init(aSimulator, aSpRoot, speciesDefaults);
_progenitor.setSpecies(this);
// Set the computational domain this species is associated with
// KA Aug 13 - changed as this may be a default
domain =
aSimulator.world.getDomain(
_progenitor
.getSpeciesParam()
.getSpeciesParameterString("computationDomain", aSpRoot, speciesDefaults));
}