/**
* Called during the division of an EpiBac ; apply the segregation of plasmids, modify the number
* for the plasmid calling the method and sends the number for the other one.
*
* @param aPlasmid Episome
*/
public void segregation(Episome aPlasmid) {
if (ExtraMath.getUniRandDbl() > getSpeciesParam().lossProbability) {
_nCopy = 1;
aPlasmid._nCopy = 1;
} else {
_nCopy =
0; // jan: this introduces a bias, the 'old' cell always looses the plasmid. If the two
// daughter cells are not equal, then this is poor
aPlasmid._nCopy = 1;
}
}
@Override
public void makeKid() throws CloneNotSupportedException {
/*
* Clone the plasmid.
*/
Episome baby = this.sendNewAgent();
/*
* Register the plasmid (species population).
*/
baby.registerBirth();
}
@Override
public void createNewAgent() {
try {
// Clone the plasmid
Episome baby = this.sendNewAgent();
// Register the plasmid (species population)
baby.registerBirth();
} catch (CloneNotSupportedException e) {
LogFile.writeError(e, "Episome.createNewAgent()");
}
}
@Override
@SuppressWarnings("unchecked")
public Object clone() throws CloneNotSupportedException {
Episome o = (Episome) super.clone();
o._host = this._host;
o._speciesParam = _speciesParam;
o.reactionActive = (ArrayList<Integer>) this.reactionActive.clone();
o.lastExchange = this.lastExchange;
o.lastReception = this.lastReception;
return o;
}
public Boolean isCompatible(Episome aPlasmid) {
return aPlasmid.getSpeciesParam().compatibilityMarker
!= this.getSpeciesParam().compatibilityMarker;
}
/** You are doing a conjugation! Update your lag variables. */
public void updateConjugationTime(Episome baby) {
lastExchange = SimTimer.getCurrentTime();
baby.lastReception = SimTimer.getCurrentTime();
}
@Override
public Episome sendNewAgent() throws CloneNotSupportedException {
Episome baby = (Episome) this.clone();
baby.init();
return baby;
}