/**
* \brief Create an agent using information in a previous state or initialisation file
*
* <p>Create an agent using information in a previous state or initialisation file
*
* @param aSim The simulation object used to simulate the conditions specified in the protocol
* file
* @param singleAgentData Data from the result or initialisation file that is used to recreate
* this agent
*/
public void initFromResultFile(Simulator aSim, String[] singleAgentData) {
// this routine will read data from the end of the singleAgentData array
// and then pass the remaining values onto the super class
// Chemostat "if" added by Sonia 27.10.09
// Rearranged by Rob 10.01.11
// find the position to start at by using length and number of values read
int nValsRead = 5;
int iDataStart = singleAgentData.length - nValsRead;
if (Simulator.isChemostat) {
// Rob: this is necessary for the case when biofilm agents in one simulation
// are transferred into a chemostat for the next.
_location.set(0, 0, 0);
} else {
double newAgentX, newAgentY, newAgentZ;
newAgentX = Double.parseDouble(singleAgentData[iDataStart]);
newAgentY = Double.parseDouble(singleAgentData[iDataStart + 1]);
newAgentZ = Double.parseDouble(singleAgentData[iDataStart + 2]);
_location.set(newAgentX, newAgentY, newAgentZ);
}
// agent size
_radius = Double.parseDouble(singleAgentData[iDataStart + 3]);
_totalRadius = Double.parseDouble(singleAgentData[iDataStart + 4]);
_myDivRadius = getDivRadius();
_myDeathRadius = getDeathRadius();
// now go up the hierarchy with the rest of the data
String[] remainingSingleAgentData = new String[iDataStart];
for (int i = 0; i < iDataStart; i++) remainingSingleAgentData[i] = singleAgentData[i];
super.initFromResultFile(aSim, remainingSingleAgentData);
}
/**
* \brief Mutate inherited agent parameters after agent division.
*
* <p>Mutation Function. If you don't want apply a mutation in a specified class, do not redefine
* this method. If you want, you are free to choose which fields to mutate for each different
* class by a simple redefinition
*/
public void mutateAgent() {
// Mutate parameters inherited
super.mutateAgent();
// Now mutate your parameters
}
/**
* \brief Kills an agent. Called by detachment and starving test
*
* <p>Kills an agent. Called by detachment and starving test
*/
public void die(boolean isStarving) {
super.die(isStarving);
}
/**
* \brief Creates an agent of the specified species and notes the grid in which this is assigned
*
* <p>Creates an agent of the specified species and notes the grid in which this is assigned
*
* @param aSim The simulation object used to simulate the conditions specified in the protocol
* file
* @param xmlMarkUp A species mark-up within the specified protocol file
*/
public void initFromProtocolFile(Simulator aSim, XMLParser xmlMarkUp) {
super.initFromProtocolFile(aSim, xmlMarkUp);
_myDivRadius = getDivRadius();
_myDeathRadius = getDeathRadius();
}
/**
* \brief Registers a created agent into a respective container. Each agent must be referenced by
* one such container.
*
* <p>Registers a created agent into a respective container. Each agent must be referenced by one
* such container. In this case, the species is registered into the agent grid
*/
public void registerBirth() {
// Register on species and reaction guilds
super.registerBirth();
}
