/*
* This method is called to wind down the simulation.
*/
public void finish() {
super.finish();
System.out.println("Terminating the simulation");
/*
* write CSV and XML output from simulation
*/
File csvDataFile =
new File(resultFilePath + "/" + description + "/" + runFilePath + "/simOutputData.csv");
System.out.println("Output written to " + csvDataFile);
// File xmlDataFile = new File(resultFilePath + "/" + description + "/Results/" + runFilePath +
// "/simOutputData.xml");
PrintWriter dataOutput;
try {
dataOutput = new PrintWriter(csvDataFile);
dataOutput.print(dataStore.compileTableToString());
dataOutput.close();
// dataStore.compileXMLOutput(xmlDataFile);
} catch (Exception e) {
e.printStackTrace();
}
System.out.println("Run took " + (System.currentTimeMillis() - startTime) + " milliseconds");
}
/**
* This method is called to start the simulation. the run parameters are copied to the results
* output directory. The run output file is created ready for writing.
*/
public void start() {
super.start(); // call supertype's start method.
// System.out.println("In main on CBSimulation class");
// need to read the parameter file
readParameters(true);
// And I want to write the random number seed used for this run - for record keeping
PrintWriter dataOutput;
new File(resultFilePath + "/" + description + "/" + runFilePath).mkdirs();
File runSeedFile =
new File(resultFilePath + "/" + description + "/" + runFilePath + "/simRunSeed");
System.out.println("Creating output file " + runSeedFile.getName());
String paramCopyFile =
resultFilePath + "/" + description + "/" + runFilePath + "/" + paramCopyName;
copyFile(xmlFileLocation, paramCopyFile);
try {
dataOutput = new PrintWriter(runSeedFile);
dataOutput.print(seed);
dataOutput.close();
} catch (Exception e) {
e.printStackTrace();
}
// I'll need to instantiate the data store here
// I'll schedule it from the constructor...
dataStore = new DataStore(this);
// System.out.println("Created DataStore object " + dataStore);
}
public void readParameters(boolean ic) {
try {
// open the xmlFileLocation to read input
DocumentBuilderFactory docBuilderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder docBuilder = docBuilderFactory.newDocumentBuilder();
Document doc = docBuilder.parse(new File(xmlFileLocation));
Element setupComponent = (Element) doc.getElementsByTagName("simulation_setup").item(0);
processSetupParams(setupComponent);
// locate the <cistromes> tag
Element cistromesComponent = (Element) doc.getElementsByTagName("cistromes").item(0);
// process this into details of individual cistromes
processCistromesComponent(cistromesComponent);
// we'll pass the Cistrome components on to the Cell Object to make sense of...
// if(instantiateCell)
// {
// We'll set up a Cell object to hold our Cistrome(s)
// System.out.println("Cistrome data sources are " + sources);
cell = new Cell(sources, this);
// System.out.println("Created cell object " + cell);
// }
// System.out.println("Fetching cistrome data from " + cell);
ArrayList<Cistrome> cistromeList = cell.getCistromeList();
for (int c = 0; c < cistromeList.size(); c++) {
Cistrome thisCistrome = ((Cistrome) cistromeList.get(c));
// System.out.println("Cistrome " + c);
thisCistrome.setName(names.get(c));
// System.out.println("Name: " + names.get(c));
thisCistrome.setBranchingRate(branchingRates.get(c));
// System.out.println("Branching rate: " + branchingRates.get(c));
thisCistrome.setInitialReds(numsInitialReds.get(c));
// System.out.println("Initial reds: " + numsInitialReds.get(c));
}
} catch (Exception e) {
e.printStackTrace();
}
}