/*
* @see org.primordion.xholon.app.IApplication#initialize(java.lang.String)
*/
public void initialize(String configFileName) throws XholonConfigurationException {
super.initialize(configFileName);
// Monitoring with plotting of the monitored data.
if (getUseDataPlotter()) {
// Monitor these values as the BloodPlasma and contained Erythrocyte circulate in the
// CirculatorySystem.
IXholon monitorContext =
getXPath().evaluate("./descendant::Heart/LeftVentricle/BloodPlasma[2]", root);
xhMonitored[0] = getXPath().evaluate("ExtraCellularSolution/Glucose", monitorContext);
xhMonitored[1] = getXPath().evaluate("ExtraCellularSolution/Oxygen", monitorContext);
xhMonitored[2] = getXPath().evaluate("ExtraCellularSolution/CarbonDioxide", monitorContext);
xhMonitored[3] = getXPath().evaluate("Erythrocyte[1]/descendant::Glucose", monitorContext);
xhMonitored[4] = getXPath().evaluate("Erythrocyte[1]/descendant::Oxygen", monitorContext);
xhMonitored[5] =
getXPath().evaluate("Erythrocyte[1]/descendant::CarbonDioxide", monitorContext);
}
// write an SBML level 2 file
// if (writeSbml) {
// IXholon sbmlContext = xpath.evaluate("./descendant::Eye/descendant::Cone/TerminalButtons",
// root);
// if (sbmlContext != null) {
// Cellontro2Sbml cellontro2sbml = new Cellontro2Sbml("./sbml/LifeModel.xml", "LifeModel",
// sbmlContext);
// cellontro2sbml.writeAll();
// }
// }
}
/*
* @see org.primordion.xholon.app.IApplication#wrapup()
*/
public void wrapup() {
root.preAct();
if (getUseDataPlotter()) {
chartViewer.capture(timeStep);
}
super.wrapup();
}
public void initialize(String configFileName) throws XholonConfigurationException {
super.initialize(configFileName);
if (getUseInteractions()) {
// include complete class name on sequence diagrams, rather than truncating long names
interaction.setMaxNameLen(100);
interaction.setMaxDataLen(6);
IPortInterface providedRequiredInterface = new PortInterface();
providedRequiredInterface.setInterface(Xhmodel04.getSignalIDs());
providedRequiredInterface.setInterfaceNames(Xhmodel04.getSignalNames());
interaction.setProvidedRequiredInterface(providedRequiredInterface);
}
}
public void wrapup() {
root.preAct();
if (getUseDataPlotter()) {
chartViewer.capture(getTimeStep());
}
if (getUseGridViewer()) {
for (int vIx = 0; vIx < gridViewers.size(); vIx++) {
GridViewerDetails gvd = (GridViewerDetails) gridViewers.get(vIx);
if (gvd.useGridViewer) {
// gvd.gridFrame.setInfoLabel("Time step: " + timeStep);
// gvd.gridPanel.paintComponent(gvd.gridPanel.getGraphics());
}
}
}
super.wrapup();
}
/*
* @see org.primordion.xholon.app.Application#wrapup()
*/
public void wrapup() {
root.cleanup(); // cancel timers
super.wrapup();
}