/**
* \brief Registers the created species to the simulation speciesManager
*
* <p>Registers the created species to the simulation speciesManager
*
* @param aSimulator The simulator object being used to create the conditions specified in the
* protocol file
* @param aSpRoot XML markup for the species being created. Taken from the protocol file
*/
public void register(Simulator aSimulator, XMLParser aSpRoot) {
currentSimulator = aSimulator;
speciesName = aSpRoot.getName();
speciesIndex = aSimulator.speciesList.size();
aSimulator.speciesList.add(this);
domain = aSimulator.world.getDomain(aSpRoot.getAttribute("computationDomain"));
}
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 Used in 'one-time' attachment scenarios, where clones of the progenitor are created in
* the birth area of the substratum.
*
* @param spRoot The XML mark-up group for a particular species being created.
*/
public void createPop(XMLParser spRoot) {
int howMany = spRoot.getAttributeInt("number");
if (howMany <= 0) return;
// Define the birth area - this is taken from the coordinates tags in the protocol file
// (Nov13) OR if an initial area is not declared, this is the whole Y and Z of the domain with a
// height of 1.
ContinuousVector[] _initArea = defineSquareArea(spRoot);
// Create all the required agents
ContinuousVector cc = new ContinuousVector();
for (int i = 0; i < howMany; i++)
if (_progenitor instanceof LocatedAgent) {
// Set coordinates within the birth area - randomly
if (!Simulator.isChemostat) shuffleCoordinates(cc, _initArea);
// Create the agent at these coordinates
((LocatedAgent) _progenitor).createNewAgent(cc);
} else _progenitor.createNewAgent();
LogFile.writeLog(
howMany
+ " agents of species "
+ speciesName
+ " for one-time attachment successfully created");
}
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);
}
}
/**
* \brief Defines a region of the computation domain where a new species may be created, using
* restrictions in the protocol file
*
* <p>Defines a region of the computation domain where a new species may be created, using
* restrictions in the protocol file. These restrictions for a particular species are specified in
* 'coordinates' tags. There should be two such tags where this is used - one to start the
* restriction and one to end it. Example of use: \<coordinates x="0" y="0" z="0"/\> \<coordinates
* x="1" y="264" z="0"/\>. This method will read these in and create an array that represents this
* area
*
* @param spRoot The information within the 'initArea' tags of the protocol file
* @return A continuous vector representing the area of the domain specified in these tags
*/
public ContinuousVector[] defineSquareArea(XMLParser spRoot) {
List<XMLParser> area = spRoot.getChildrenParsers("coordinates");
ContinuousVector[] initArea = new ContinuousVector[2];
initArea[0] = new ContinuousVector();
initArea[1] = new ContinuousVector();
// KA NOV 13 - CHANGED THIS, AS WE'RE GOING TO LET THE USER NOT DECLARE AN INITIAL AREA IF THEY
// WANT THE CELLS SPREAD ACROSS
// THE WHOLE DOMAIN. THUS THIS NEEDS CHECKING AND FIXING
if (area.size() > 0) {
// First Coordinate Tag
ContinuousVector cc1 = new ContinuousVector(area.get(0));
// Second Coordinate Tag
ContinuousVector cc2 = new ContinuousVector(area.get(1));
// Set each point
initArea[0].x = Math.min(cc1.x, cc2.x);
initArea[1].x = Math.max(cc1.x, cc2.x);
initArea[0].y = Math.min(cc1.y, cc2.y);
initArea[1].y = Math.max(cc1.y, cc2.y);
// In the case of 2D simulation, the agent's z-coordinate is 0.
if (domain.is3D) {
initArea[0].z = Math.min(cc1.z, cc2.z);
initArea[1].z = Math.max(cc1.z, cc2.z);
} else {
initArea[0].z = initArea[1].z = 0.0;
}
} else {
// NO INITIAL AREA HAS BEEN DECLARED, USE THE WHOLE SUBSTRATUM. NOTE THAT THE X (HEIGHT)
// COORDINATE IS SET TO 1 SO THE
// CELLS ARE PLACED NEAR THE SUBSTRATUM
// Set each point
initArea[0].x = 0.0;
initArea[0].y = 0.0;
initArea[0].z = 0.0;
initArea[1].x = 1.0;
initArea[1].y = domain.length_Y;
initArea[1].z = domain.length_Z;
}
return initArea;
}
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);
}
}
/**
* \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));
}
public static void main(String[] args) throws Exception {
// Modeler is either LDA or mallet
XMLParser parser = new XMLParser();
parser.processPosts(args[0], args[1]);
}