// constructor
public TQuery(String[] args) {
try {
long startTime = System.currentTimeMillis();
processArgs(args);
queryIndex = new QueryIndex(this);
queryLoader = new QueryLoader(this);
// print some stats on building the engine
String diffTime =
Num.formatNumberOneFraction(((double) (System.currentTimeMillis() - startTime)) / 1000);
int numFiles = vcfDataFiles.length + bedDataFiles.length + mafDataFiles.length;
System.err.println("\n" + diffTime + " Sec to build using " + IO.memory() + " of RAM");
System.err.println("\t" + numFiles + "\tData sources loaded");
System.err.println("\t" + dataSources.getRecordsLoaded() + "\tRecords indexed");
System.err.println("\t" + dataSources.getRecordsSkipped() + "\tRecords skipped\n");
// print summary of available filters
System.err.println(dataSources.fetchSummary());
queryFilesFromCmdLine();
// release file handles
queryLoader.closeTabixReaders();
} catch (Exception e) {
e.printStackTrace();
System.err.println("\nProblem with executing the TQuery!");
}
}
@Override
public void open(int run_id) throws SiriusException {
success = false;
if (1 != scenario.numEnsemble) logger.warn("scenario.numEnsembles != 1");
if (null == db_scenario) throw new SiriusException("Scenario was not loaded from the database");
logger.info("Initializing simulation run");
Connection conn = null;
try {
conn = Transaction.begin();
DataSources db_ds = new DataSources();
db_ds.setId(DataSourcesPeer.nextId(DataSourcesPeer.ID, conn));
db_ds.save(conn);
Criteria crit = new Criteria();
crit.add(ScenariosPeer.ID, db_scenario.getId());
com.workingdogs.village.Value max_runnum =
SimulationRunsPeer.maxColumnValue(SimulationRunsPeer.RUN_NUMBER, crit, conn);
final long run_number = null == max_runnum ? 1 : max_runnum.asLong() + 1;
logger.info("Run number: " + run_number);
db_simulation_run = new com.relteq.sirius.om.SimulationRuns();
db_simulation_run.setDataSources(db_ds);
db_simulation_run.setScenarios(db_scenario);
db_simulation_run.setRunNumber(run_number);
db_simulation_run.setVersion(com.relteq.sirius.Version.get().getEngineVersion());
db_simulation_run.setBuild("");
db_simulation_run.setSimulationStartTime(BigDecimal.valueOf(scenario.getTimeStart()));
db_simulation_run.setSimulationDuration(
BigDecimal.valueOf(scenario.getTimeEnd() - scenario.getTimeStart()));
db_simulation_run.setSimulationDt(BigDecimal.valueOf(scenario.getSimDtInSeconds()));
db_simulation_run.setOutputDt(BigDecimal.valueOf(scenario.getOutputDt()));
db_simulation_run.setExecutionStartTime(Calendar.getInstance().getTime());
db_simulation_run.setStatus(-1);
db_simulation_run.save(conn);
Transaction.commit(conn);
conn = null;
success = true;
} catch (TorqueException exc) {
throw new SiriusException(exc);
} catch (DataSetException exc) {
throw new SiriusException(exc);
} finally {
if (null != conn) {
Transaction.safeRollback(conn);
db_simulation_run = null;
}
}
ts = Calendar.getInstance();
ts.set(Calendar.MILLISECOND, 0);
}
public void setDataResources(@NonNull DataSources dataResources) {
if (dataResources == null) {
throw new NullPointerException("DataSources can not be null");
}
this.mDataResources = dataResources;
this.setAdapter(mDataResources.getDataListAdapter());
}
public void testOneSeriePlot() throws Exception {
Workbook wb = new XSSFWorkbook();
Sheet sheet = new SheetBuilder(wb, plotData).build();
Drawing drawing = sheet.createDrawingPatriarch();
ClientAnchor anchor = drawing.createAnchor(0, 0, 0, 0, 1, 1, 10, 30);
Chart chart = drawing.createChart(anchor);
ChartAxis bottomAxis = chart.getChartAxisFactory().createValueAxis(AxisPosition.BOTTOM);
ChartAxis leftAxis = chart.getChartAxisFactory().createValueAxis(AxisPosition.LEFT);
ScatterChartData scatterChartData = chart.getChartDataFactory().createScatterChartData();
ChartDataSource<String> xs =
DataSources.fromStringCellRange(sheet, CellRangeAddress.valueOf("A1:J1"));
ChartDataSource<Number> ys =
DataSources.fromNumericCellRange(sheet, CellRangeAddress.valueOf("A2:J2"));
ScatterChartSerie serie = scatterChartData.addSerie(xs, ys);
assertNotNull(serie);
assertEquals(1, scatterChartData.getSeries().size());
assertTrue(scatterChartData.getSeries().contains(serie));
chart.plot(scatterChartData, bottomAxis, leftAxis);
}
