// 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); }