List of usage examples for java.io BufferedWriter newLine
public void newLine() throws IOException
From source file:Evaluator.PerQueryRelDocs.java
public void storeRunQid(String fileName) throws IOException, Exception { FileReader fr = new FileReader(new File(runFileList)); BufferedReader br = new BufferedReader(fr); String line = br.readLine();/*from w ww . j av a 2s .c om*/ ArrayList<String> runlist = new ArrayList<>(); while (line != null) { runlist.add(line); line = br.readLine(); } br.close(); HashMap<String, HashMap<Integer, Double>> runQidApMap = new HashMap<>(); HashMap<String, Double> qidCosineMap = new HashMap<>(); for (int pos = startQid; pos <= endQid; pos++) { Integer qidValue = pos; InferredApKDE iapk = new InferredApKDE(qidValue.toString(), 5, "", this, reader, .30, h, sigma, cosineFolderPath, lambda, relRcds.perQueryRels.get(qidValue.toString()).searcher); System.out.println(pos); qidCosineMap = iapk.reldocList.perQuerydocCosineSim; HashMap<String, Double> docRankMap = null; if (kdeMode.equals("2")) { docRankMap = computeAvgRank(runlist, pos, iapk.sampledData); } for (int j = 0; j < runlist.size(); j++) { retRcds.resFile = runFileFolderPath + "/" + runlist.get(j); retRcds.allRetMap = new TreeMap<>(); retRcds.load(); Set<String> rel = new HashSet<String>(); Iterator it = iapk.sampledData.iterator(); HashMap<String, Integer> rankMap = new HashMap<>(); while (it.hasNext()) { String st = (String) it.next(); if (iapk.reldoc.contains(st)) { rel.add(st); } } iapk.retriveList = this.retRcds.allRetMap.get(qidValue.toString()); iapk.processRetrievedResult(); iapk.computeprob(iapk.retriveList.pool); double g = iapk.evaluateAP(); // System.out.println("kk" + g); HashMap<Integer, Double> qidApMap = runQidApMap.get(runlist.get(j)); if (qidApMap == null) { qidApMap = new HashMap<>(); } qidApMap.put(qidValue, g); runQidApMap.put(runlist.get(j), qidApMap); } } FileWriter fw = new FileWriter(new File(fileName)); BufferedWriter bw = new BufferedWriter(fw); for (int j = 0; j < runlist.size(); j++) { HashMap<Integer, Double> values = runQidApMap.get(runlist.get(j)); double sum = 0; for (int i = startQid; i <= endQid; i++) { sum += values.get(i); } bw.write(runlist.get(j) + " " + sum / (endQid - startQid + 1)); bw.newLine(); // System.out.println(sum / (endQid - startQid + 1)); } bw.close(); }
From source file:chibi.gemmaanalysis.OutlierDetectionTestCli.java
/*** Write results to the output file; file name must be given as argument ***/ private void writeResultsToFileByMedian(BufferedWriter bw, ExpressionExperiment ee, OutlierDetectionTestDetails testDetails) { NumberFormat nf = NumberFormat.getInstance(); nf.setMaximumFractionDigits(4);//from w w w . ja v a 2 s .co m try { // Get information about the experiment: ee = this.eeService.thawLite(ee); System.out.println("Writing results to file for " + ee.getShortName()); bw.write(ee.getShortName()); bw.write("\t" + getPlatforms(ee)); bw.write("\t" + testDetails.getNumExpFactors()); if (useRegression) { bw.write("\t" + testDetails.getNumSigFactors()); } bw.write("\t" + ee.getBioAssays().size()); bw.write("\t" + testDetails.getNumOutliers()); // Get information about each of the outliers (should be in sorted order since outliers is a sorted list): for (OutlierDetails outlier : testDetails.getOutliers()) { bw.write("\t" + outlier.getBioAssay().getName()); bw.write("\t" + nf.format(outlier.getFirstQuartile()) + "/" + nf.format(outlier.getMedianCorrelation()) + "/" + nf.format(outlier.getThirdQuartile())); } if (useRegression) { for (ExperimentalFactor factor : testDetails.getSignificantFactors()) { bw.write("\t" + factor.getName()); } } bw.newLine(); } catch (IOException e) { throw new RuntimeException(e); } }
From source file:org.openmrs.module.clinicalsummary.web.controller.utils.ExtendedDataEncounterController.java
@RequestMapping(method = RequestMethod.POST) public void processSubmit(final @RequestParam(required = true, value = "data") MultipartFile data, final @RequestParam(required = true, value = "conceptNames") String conceptNames, final HttpServletResponse response) throws IOException { List<Concept> concepts = new ArrayList<Concept>(); for (String conceptName : StringUtils.splitPreserveAllTokens(conceptNames, ",")) { Concept concept = Context.getConceptService().getConcept(conceptName); if (concept != null) concepts.add(concept);//from w w w. j a v a 2s . co m } PatientService patientService = Context.getPatientService(); PatientSetService patientSetService = Context.getPatientSetService(); File identifierData = File.createTempFile(STUDY_DATA, INPUT_PREFIX); OutputStream identifierDataStream = new BufferedOutputStream(new FileOutputStream(identifierData)); FileCopyUtils.copy(data.getInputStream(), identifierDataStream); File extendedData = File.createTempFile(STUDY_DATA, OUTPUT_PREFIX); BufferedWriter writer = new BufferedWriter(new FileWriter(extendedData)); String line; BufferedReader reader = new BufferedReader(new FileReader(identifierData)); while ((line = reader.readLine()) != null) { Patient patient = null; String[] elements = StringUtils.splitPreserveAllTokens(line, ","); try { if (isDigit(StringUtils.trim(elements[1]))) patient = patientService.getPatient(NumberUtils.toInt(elements[1])); else { Cohort cohort = patientSetService.convertPatientIdentifier(Arrays.asList(elements[1])); for (Integer patientId : cohort.getMemberIds()) { Patient cohortPatient = patientService.getPatient(patientId); if (cohortPatient != null && !cohortPatient.isVoided()) patient = cohortPatient; } } } catch (Exception e) { log.error("Unable to resolve patients!", e); } Date referenceDate = WebUtils.parse(elements[2], "MM/dd/yyyy", new Date()); if (patient != null) { ExtendedData extended = new ExtendedData(patient, referenceDate); extended.setEncounters(searchEncounters(patient)); for (Concept concept : concepts) extended.addObservations(concept, searchObservations(patient, concept)); writer.write(extended.generateEncounterData()); writer.newLine(); ResultCacheInstance.getInstance().clearCache(patient); } else { writer.write("Unresolved patient id or patient identifier for " + elements[1]); writer.newLine(); } } reader.close(); writer.close(); InputStream inputStream = new BufferedInputStream(new FileInputStream(extendedData)); response.setHeader("Content-Disposition", "attachment; filename=generated-" + data.getOriginalFilename()); response.setContentType("text/plain"); FileCopyUtils.copy(inputStream, response.getOutputStream()); }
From source file:de.bfs.radon.omsimulation.gui.OMPanelTesting.java
/** * Initialises the interface of the results panel. *//*from ww w. j a v a 2 s .c o m*/ protected void initialize() { setLayout(null); isSimulated = false; lblExportChartTo = new JLabel("Export chart to ..."); lblExportChartTo.setBounds(436, 479, 144, 14); lblExportChartTo.setFont(new Font(Font.SANS_SERIF, Font.PLAIN, 11)); lblExportChartTo.setVisible(false); add(lblExportChartTo); btnCsv = new JButton("CSV"); btnCsv.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { JFileChooser fileDialog = new JFileChooser(); fileDialog.setFileFilter(new FileNameExtensionFilter("*.csv", "csv")); fileDialog.showSaveDialog(getParent()); final File file = fileDialog.getSelectedFile(); if (file != null) { String csv; String[] tmpFileName = file.getAbsolutePath().split("\\."); if (tmpFileName[tmpFileName.length - 1].equals("csv")) { csv = ""; } else { csv = ".csv"; } String csvPath = file.getAbsolutePath() + csv; double[] selectedValues; OMRoom[] rooms = new OMRoom[7]; rooms[0] = (OMRoom) comboBoxRoom1.getSelectedItem(); rooms[1] = (OMRoom) comboBoxRoom2.getSelectedItem(); rooms[2] = (OMRoom) comboBoxRoom3.getSelectedItem(); rooms[3] = (OMRoom) comboBoxRoom4.getSelectedItem(); rooms[4] = (OMRoom) comboBoxRoom5.getSelectedItem(); rooms[5] = (OMRoom) comboBoxRoom6.getSelectedItem(); rooms[6] = (OMRoom) comboBoxRoom7.getSelectedItem(); int start = sliderStartTime.getValue(); final int day = 24; File csvFile = new File(csvPath); try { OMCampaign campaign; if (isResult) { campaign = getResultCampaign(); } else { campaign = new OMCampaign(start, rooms, 0); } FileWriter logWriter = new FileWriter(csvFile); BufferedWriter csvOutput = new BufferedWriter(logWriter); csvOutput.write("\"ID\";\"Room\";\"Radon\""); csvOutput.newLine(); selectedValues = campaign.getValueChain(); int x = 0; for (int i = start; i < start + day; i++) { csvOutput.write("\"" + i + "\";\"" + rooms[0].getId() + "\";\"" + (int) selectedValues[x] + "\""); csvOutput.newLine(); x++; } start = start + day; for (int i = start; i < start + day; i++) { csvOutput.write("\"" + i + "\";\"" + rooms[1].getId() + "\";\"" + (int) selectedValues[x] + "\""); csvOutput.newLine(); x++; } start = start + day; for (int i = start; i < start + day; i++) { csvOutput.write("\"" + i + "\";\"" + rooms[2].getId() + "\";\"" + (int) selectedValues[x] + "\""); csvOutput.newLine(); x++; } start = start + day; for (int i = start; i < start + day; i++) { csvOutput.write("\"" + i + "\";\"" + rooms[3].getId() + "\";\"" + (int) selectedValues[x] + "\""); csvOutput.newLine(); x++; } start = start + day; for (int i = start; i < start + day; i++) { csvOutput.write("\"" + i + "\";\"" + rooms[4].getId() + "\";\"" + (int) selectedValues[x] + "\""); csvOutput.newLine(); x++; } start = start + day; for (int i = start; i < start + day; i++) { csvOutput.write("\"" + i + "\";\"" + rooms[5].getId() + "\";\"" + (int) selectedValues[x] + "\""); csvOutput.newLine(); x++; } start = start + day; for (int i = start; i < start + day; i++) { csvOutput.write("\"" + i + "\";\"" + rooms[6].getId() + "\";\"" + (int) selectedValues[x] + "\""); csvOutput.newLine(); x++; } JOptionPane.showMessageDialog(null, "CSV saved successfully!\n" + csvPath, "Success", JOptionPane.INFORMATION_MESSAGE); csvOutput.close(); } catch (IOException ioe) { JOptionPane.showMessageDialog(null, "Failed to write CSV. Please check permissions!\n" + ioe.getMessage(), "Failed", JOptionPane.ERROR_MESSAGE); ioe.printStackTrace(); } } else { JOptionPane.showMessageDialog(null, "Failed to write CSV. Please check the file path!", "Failed", JOptionPane.ERROR_MESSAGE); } } }); btnCsv.setBounds(590, 475, 70, 23); btnCsv.setFont(new Font(Font.SANS_SERIF, Font.PLAIN, 11)); btnCsv.setVisible(false); add(btnCsv); btnPdf = new JButton("PDF"); btnPdf.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { JFileChooser fileDialog = new JFileChooser(); fileDialog.setFileFilter(new FileNameExtensionFilter("*.pdf", "pdf")); fileDialog.showSaveDialog(getParent()); final File file = fileDialog.getSelectedFile(); if (file != null) { String pdf; String[] tmpFileName = file.getAbsolutePath().split("\\."); if (tmpFileName[tmpFileName.length - 1].equals("pdf")) { pdf = ""; } else { pdf = ".pdf"; } String pdfPath = file.getAbsolutePath() + pdf; OMRoom[] rooms = new OMRoom[7]; rooms[0] = (OMRoom) comboBoxRoom1.getSelectedItem(); rooms[1] = (OMRoom) comboBoxRoom2.getSelectedItem(); rooms[2] = (OMRoom) comboBoxRoom3.getSelectedItem(); rooms[3] = (OMRoom) comboBoxRoom4.getSelectedItem(); rooms[4] = (OMRoom) comboBoxRoom5.getSelectedItem(); rooms[5] = (OMRoom) comboBoxRoom6.getSelectedItem(); rooms[6] = (OMRoom) comboBoxRoom7.getSelectedItem(); int start = sliderStartTime.getValue(); OMCampaign campaign; try { if (isResult) { campaign = getResultCampaign(); } else { campaign = new OMCampaign(start, rooms, 0); } JFreeChart chart = OMCharts.createCampaignChart(campaign, false); String title = "Campaign: " + rooms[0].getId() + rooms[1].getId() + rooms[2].getId() + rooms[3].getId() + rooms[4].getId() + rooms[5].getId() + rooms[6].getId() + ", Start: " + start; int height = (int) PageSize.A4.getWidth(); int width = (int) PageSize.A4.getHeight(); try { OMExports.exportPdf(pdfPath, chart, width, height, new DefaultFontMapper(), title); JOptionPane.showMessageDialog(null, "PDF saved successfully!\n" + pdfPath, "Success", JOptionPane.INFORMATION_MESSAGE); } catch (IOException ioe) { JOptionPane.showMessageDialog(null, "Failed to write PDF. Please check permissions!\n" + ioe.getMessage(), "Failed", JOptionPane.ERROR_MESSAGE); ioe.printStackTrace(); } } catch (IOException ioe) { JOptionPane.showMessageDialog(null, "Failed to create chart!\n" + ioe.getMessage(), "Failed", JOptionPane.ERROR_MESSAGE); ioe.printStackTrace(); } } else { JOptionPane.showMessageDialog(null, "Failed to write PDF. Please check the file path!", "Failed", JOptionPane.ERROR_MESSAGE); } } }); btnPdf.setBounds(670, 475, 70, 23); btnPdf.setFont(new Font(Font.SANS_SERIF, Font.PLAIN, 11)); btnPdf.setVisible(false); add(btnPdf); lblSelectProject = new JLabel("Select Project"); lblSelectProject.setBounds(10, 65, 132, 14); lblSelectProject.setFont(new Font("SansSerif", Font.PLAIN, 11)); add(lblSelectProject); lblSelectRooms = new JLabel("Select Rooms"); lblSelectRooms.setBounds(10, 94, 132, 14); lblSelectRooms.setFont(new Font("SansSerif", Font.PLAIN, 11)); add(lblSelectRooms); lblStartTime = new JLabel("Start Time"); lblStartTime.setBounds(10, 123, 132, 14); lblStartTime.setFont(new Font("SansSerif", Font.PLAIN, 11)); add(lblStartTime); lblWarning = new JLabel("Select 6 rooms and 1 cellar!"); lblWarning.setForeground(Color.RED); lblWarning.setBounds(565, 123, 175, 14); lblWarning.setFont(new Font("SansSerif", Font.PLAIN, 11)); lblWarning.setVisible(false); add(lblWarning); sliderStartTime = new JSlider(); sliderStartTime.setMaximum(0); sliderStartTime.setBounds(152, 119, 285, 24); sliderStartTime.setFont(new Font("SansSerif", Font.PLAIN, 11)); add(sliderStartTime); spnrStartTime = new JSpinner(); spnrStartTime.setModel(new SpinnerNumberModel(0, 0, 0, 1)); spnrStartTime.setBounds(447, 120, 108, 22); spnrStartTime.setFont(new Font("SansSerif", Font.PLAIN, 11)); add(spnrStartTime); btnRefresh = new JButton("Load"); btnRefresh.setBounds(616, 61, 124, 23); btnRefresh.setFont(new Font("SansSerif", Font.PLAIN, 11)); add(btnRefresh); btnMaximize = new JButton("Fullscreen"); btnMaximize.setBounds(10, 475, 124, 23); btnMaximize.setFont(new Font("SansSerif", Font.PLAIN, 11)); add(btnMaximize); panelCampaign = new JPanel(); panelCampaign.setBounds(10, 150, 730, 315); panelCampaign.setFont(new Font("SansSerif", Font.PLAIN, 11)); add(panelCampaign); progressBar = new JProgressBar(); progressBar.setBounds(10, 475, 730, 23); progressBar.setFont(new Font("SansSerif", Font.PLAIN, 11)); progressBar.setVisible(false); add(progressBar); lblOpenOmbfile = new JLabel("Open OMB-File"); lblOpenOmbfile.setFont(new Font("SansSerif", Font.PLAIN, 11)); lblOpenOmbfile.setBounds(10, 36, 132, 14); add(lblOpenOmbfile); lblHelp = new JLabel("Select an OMB-Object file to manually simulate virtual campaigns."); lblHelp.setForeground(Color.GRAY); lblHelp.setFont(new Font("SansSerif", Font.PLAIN, 11)); lblHelp.setBounds(10, 10, 730, 14); add(lblHelp); txtOmbFile = new JTextField(); txtOmbFile.setFont(new Font("SansSerif", Font.PLAIN, 11)); txtOmbFile.setColumns(10); txtOmbFile.setBounds(152, 33, 454, 20); add(txtOmbFile); btnBrowse = new JButton("Browse"); btnBrowse.setFont(new Font("SansSerif", Font.PLAIN, 11)); btnBrowse.setBounds(616, 32, 124, 23); add(btnBrowse); comboBoxRoom1 = new JComboBox<OMRoom>(); comboBoxRoom1.setBounds(152, 90, 75, 22); comboBoxRoom1.setFont(new Font("SansSerif", Font.PLAIN, 11)); add(comboBoxRoom1); comboBoxRoom2 = new JComboBox<OMRoom>(); comboBoxRoom2.setBounds(237, 90, 75, 22); comboBoxRoom2.setFont(new Font("SansSerif", Font.PLAIN, 11)); add(comboBoxRoom2); comboBoxRoom3 = new JComboBox<OMRoom>(); comboBoxRoom3.setBounds(323, 90, 75, 22); comboBoxRoom3.setFont(new Font("SansSerif", Font.PLAIN, 11)); add(comboBoxRoom3); comboBoxRoom4 = new JComboBox<OMRoom>(); comboBoxRoom4.setBounds(408, 90, 75, 22); comboBoxRoom4.setFont(new Font("SansSerif", Font.PLAIN, 11)); add(comboBoxRoom4); comboBoxRoom5 = new JComboBox<OMRoom>(); comboBoxRoom5.setBounds(494, 90, 75, 22); comboBoxRoom5.setFont(new Font("SansSerif", Font.PLAIN, 11)); add(comboBoxRoom5); comboBoxRoom6 = new JComboBox<OMRoom>(); comboBoxRoom6.setBounds(579, 90, 75, 22); comboBoxRoom6.setFont(new Font("SansSerif", Font.PLAIN, 11)); add(comboBoxRoom6); comboBoxRoom7 = new JComboBox<OMRoom>(); comboBoxRoom7.setBounds(665, 90, 75, 22); comboBoxRoom7.setFont(new Font("SansSerif", Font.PLAIN, 11)); add(comboBoxRoom7); comboBoxProjects = new JComboBox<OMBuilding>(); comboBoxProjects.setBounds(152, 61, 454, 22); comboBoxProjects.setFont(new Font("SansSerif", Font.PLAIN, 11)); add(comboBoxProjects); comboBoxRoom1.addActionListener(this); comboBoxRoom1.addPropertyChangeListener(new PropertyChangeListener() { public void propertyChange(PropertyChangeEvent evt) { validateCampaign(); } }); comboBoxRoom2.addActionListener(this); comboBoxRoom2.addPropertyChangeListener(new PropertyChangeListener() { public void propertyChange(PropertyChangeEvent evt) { validateCampaign(); } }); comboBoxRoom3.addActionListener(this); comboBoxRoom3.addPropertyChangeListener(new PropertyChangeListener() { public void propertyChange(PropertyChangeEvent evt) { validateCampaign(); } }); comboBoxRoom4.addActionListener(this); comboBoxRoom4.addPropertyChangeListener(new PropertyChangeListener() { public void propertyChange(PropertyChangeEvent evt) { validateCampaign(); } }); comboBoxRoom5.addActionListener(this); comboBoxRoom5.addPropertyChangeListener(new PropertyChangeListener() { public void propertyChange(PropertyChangeEvent evt) { validateCampaign(); } }); comboBoxRoom6.addActionListener(this); comboBoxRoom6.addPropertyChangeListener(new PropertyChangeListener() { public void propertyChange(PropertyChangeEvent evt) { validateCampaign(); } }); comboBoxRoom7.addActionListener(this); comboBoxRoom7.addPropertyChangeListener(new PropertyChangeListener() { public void propertyChange(PropertyChangeEvent evt) { validateCampaign(); } }); sliderStartTime.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent e) { if (comboBoxProjects.isEnabled() || isResult) { if (comboBoxProjects.getSelectedItem() != null) { spnrStartTime.setValue((int) sliderStartTime.getValue()); updateChart(); } } } }); spnrStartTime.addChangeListener(new ChangeListener() { public void stateChanged(ChangeEvent arg0) { if (comboBoxProjects.isEnabled() || isResult) { if (comboBoxProjects.getSelectedItem() != null) { sliderStartTime.setValue((Integer) spnrStartTime.getValue()); updateChart(); } } } }); btnRefresh.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent arg0) { if (txtOmbFile.getText() != null && !txtOmbFile.getText().equals("") && !txtOmbFile.getText().equals(" ")) { txtOmbFile.setBackground(Color.WHITE); String ombPath = txtOmbFile.getText(); String omb; String[] tmpFileName = ombPath.split("\\."); if (tmpFileName[tmpFileName.length - 1].equals("omb")) { omb = ""; } else { omb = ".omb"; } txtOmbFile.setText(ombPath + omb); setOmbFile(ombPath + omb); File ombFile = new File(ombPath + omb); if (ombFile.exists()) { txtOmbFile.setBackground(Color.WHITE); btnRefresh.setEnabled(false); comboBoxProjects.setEnabled(false); setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); progressBar.setVisible(true); btnPdf.setVisible(false); btnCsv.setVisible(false); btnMaximize.setVisible(false); lblExportChartTo.setVisible(false); progressBar.setIndeterminate(true); progressBar.setStringPainted(true); refreshTask = new Refresh(); refreshTask.execute(); } else { txtOmbFile.setBackground(new Color(255, 222, 222, 128)); JOptionPane.showMessageDialog(null, "OMB-file not found, please check the file path!", "Error", JOptionPane.ERROR_MESSAGE); } } else { txtOmbFile.setBackground(new Color(255, 222, 222, 128)); JOptionPane.showMessageDialog(null, "Please select an OMB-file!", "Warning", JOptionPane.WARNING_MESSAGE); } } }); btnMaximize.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent arg0) { try { OMRoom[] rooms = new OMRoom[7]; rooms[0] = (OMRoom) comboBoxRoom1.getSelectedItem(); rooms[1] = (OMRoom) comboBoxRoom2.getSelectedItem(); rooms[2] = (OMRoom) comboBoxRoom3.getSelectedItem(); rooms[3] = (OMRoom) comboBoxRoom4.getSelectedItem(); rooms[4] = (OMRoom) comboBoxRoom5.getSelectedItem(); rooms[5] = (OMRoom) comboBoxRoom6.getSelectedItem(); rooms[6] = (OMRoom) comboBoxRoom7.getSelectedItem(); int start = sliderStartTime.getValue(); String title = "Campaign: " + rooms[0].getId() + rooms[1].getId() + rooms[2].getId() + rooms[3].getId() + rooms[4].getId() + rooms[5].getId() + rooms[6].getId() + ", Start: " + start; OMCampaign campaign; if (isResult) { campaign = getResultCampaign(); } else { campaign = new OMCampaign(start, rooms, 0); } JPanel campaignChart = createCampaignPanel(campaign, false, true); JFrame chartFrame = new JFrame(); chartFrame.getContentPane().add(campaignChart); chartFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE); Dimension dim = Toolkit.getDefaultToolkit().getScreenSize(); chartFrame.setBounds(0, 0, (int) dim.getWidth(), (int) dim.getHeight()); chartFrame.setTitle(title); chartFrame.setResizable(true); chartFrame.setExtendedState(JFrame.MAXIMIZED_BOTH); chartFrame.setVisible(true); } catch (IOException ioe) { ioe.printStackTrace(); } } }); txtOmbFile.addFocusListener(new FocusAdapter() { @Override public void focusLost(FocusEvent arg0) { setOmbFile(txtOmbFile.getText()); } }); btnBrowse.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent arg0) { JFileChooser fileDialog = new JFileChooser(); fileDialog.setFileFilter(new FileNameExtensionFilter("*.omb", "omb")); fileDialog.showOpenDialog(getParent()); final File file = fileDialog.getSelectedFile(); if (file != null) { String omb; String[] tmpFileName = file.getAbsolutePath().split("\\."); if (tmpFileName[tmpFileName.length - 1].equals("omb")) { omb = ""; } else { omb = ".omb"; } txtOmbFile.setText(file.getAbsolutePath() + omb); setOmbFile(file.getAbsolutePath() + omb); } } }); }
From source file:ffx.algorithms.TransitionTemperedOSRW.java
@Override public double energyAndGradient(double[] x, double[] gradient) { double e = potential.energyAndGradient(x, gradient); /**//from w w w . j a v a2 s .c om * OSRW is propagated with the slowly varying terms. */ if (state == STATE.FAST) { return e; } if (osrwOptimization && lambda > osrwOptimizationLambdaCutoff) { if (energyCount % osrwOptimizationFrequency == 0) { logger.info(String.format(" OSRW Minimization (Step %d)", energyCount)); // Set Lambda value to 1.0. lambdaInterface.setLambda(1.0); potential.setEnergyTermState(Potential.STATE.BOTH); // Optimize the system. Minimize minimize = new Minimize(null, potential, null); minimize.minimize(osrwOptimizationEps); // Collect the minimum energy. double minEnergy = potential.getTotalEnergy(); // If a new minimum has been found, save its coordinates. if (minEnergy < osrwOptimum) { osrwOptimum = minEnergy; logger.info(String.format(" New minimum energy found: %16.8f (Step %d).", osrwOptimum, energyCount)); int n = potential.getNumberOfVariables(); osrwOptimumCoords = new double[n]; osrwOptimumCoords = potential.getCoordinates(osrwOptimumCoords); if (pdbFilter.writeFile(pdbFile, false)) { logger.info(String.format(" Wrote PDB file to " + pdbFile.getName())); } } // Reset lambda value. lambdaInterface.setLambda(lambda); // Remove the scaling of coordinates & gradient set by the minimizer. potential.setScaling(null); // Reset the Potential State potential.setEnergyTermState(state); // Revert to the coordinates and gradient prior to optimization. double eCheck = potential.energyAndGradient(x, gradient); if (abs(eCheck - e) > osrwOptimizationTolerance) { logger.warning(String.format( " OSRW optimization could not revert coordinates %16.8f vs. %16.8f.", e, eCheck)); } } } double biasEnergy = 0.0; dEdLambda = lambdaInterface.getdEdL(); d2EdLambda2 = lambdaInterface.getd2EdL2(); int lambdaBin = binForLambda(lambda); int FLambdaBin = binForFLambda(dEdLambda); double dEdU = dEdLambda; if (propagateLambda) { energyCount++; detectTransition(); } /** * Calculate recursion kernel G(L, F_L) and its derivatives with respect * to L and F_L. */ double dGdLambda = 0.0; double dGdFLambda = 0.0; double ls2 = (2.0 * dL) * (2.0 * dL); double FLs2 = (2.0 * dFL) * (2.0 * dFL); for (int iL = -biasCutoff; iL <= biasCutoff; iL++) { int lcenter = lambdaBin + iL; double deltaL = lambda - (lcenter * dL); double deltaL2 = deltaL * deltaL; // Mirror conditions for recursion kernel counts. int lcount = lcenter; double mirrorFactor = 1.0; if (lcount == 0 || lcount == lambdaBins - 1) { mirrorFactor = 2.0; } else if (lcount < 0) { lcount = -lcount; } else if (lcount > lambdaBins - 1) { // Number of bins past the last bin lcount -= (lambdaBins - 1); // Mirror bin lcount = lambdaBins - 1 - lcount; } for (int iFL = -biasCutoff; iFL <= biasCutoff; iFL++) { int FLcenter = FLambdaBin + iFL; /** * If either of the following FL edge conditions are true, then * there are no counts and we continue. */ if (FLcenter < 0 || FLcenter >= FLambdaBins) { continue; } double deltaFL = dEdLambda - (minFLambda + FLcenter * dFL + dFL_2); double deltaFL2 = deltaFL * deltaFL; double weight = mirrorFactor * recursionKernel[lcount][FLcenter]; double bias = weight * biasMag * exp(-deltaL2 / (2.0 * ls2)) * exp(-deltaFL2 / (2.0 * FLs2)); biasEnergy += bias; dGdLambda -= deltaL / ls2 * bias; dGdFLambda -= deltaFL / FLs2 * bias; } } /** * Lambda gradient due to recursion kernel G(L, F_L). */ dEdLambda += dGdLambda + dGdFLambda * d2EdLambda2; /** * Cartesian coordinate gradient due to recursion kernel G(L, F_L). */ fill(dUdXdL, 0.0); lambdaInterface.getdEdXdL(dUdXdL); for (int i = 0; i < nVariables; i++) { gradient[i] += dGdFLambda * dUdXdL[i]; } if (propagateLambda && energyCount > 0) { /** * Update free energy F(L) every ~10 steps. */ if (energyCount % 10 == 0) { fLambdaUpdates++; boolean printFLambda = fLambdaUpdates % fLambdaPrintInterval == 0; totalFreeEnergy = updateFLambda(printFLambda); /** * Calculating Moving Average & Standard Deviation */ totalAverage += totalFreeEnergy; totalSquare += Math.pow(totalFreeEnergy, 2); periodCount++; if (periodCount == window - 1) { lastAverage = totalAverage / window; //lastStdDev = Math.sqrt((totalSquare - Math.pow(totalAverage, 2) / window) / window); lastStdDev = Math.sqrt((totalSquare - (totalAverage * totalAverage)) / (window * window)); logger.info(String.format( " The running average is %12.4f kcal/mol and the stdev is %8.4f kcal/mol.", lastAverage, lastStdDev)); totalAverage = 0; totalSquare = 0; periodCount = 0; } } if (energyCount % saveFrequency == 0) { if (algorithmListener != null) { algorithmListener.algorithmUpdate(lambdaOneAssembly); } /** * Only the rank 0 process writes the histogram restart file. */ if (rank == 0) { try { TTOSRWHistogramWriter ttOSRWHistogramRestart = new TTOSRWHistogramWriter( new BufferedWriter(new FileWriter(histogramFile))); ttOSRWHistogramRestart.writeHistogramFile(); ttOSRWHistogramRestart.flush(); ttOSRWHistogramRestart.close(); logger.info(String.format(" Wrote TTOSRW histogram restart file to %s.", histogramFile.getName())); } catch (IOException ex) { String message = " Exception writing TTOSRW histogram restart file."; logger.log(Level.INFO, message, ex); } } /** * All ranks write a lambda restart file. */ try { TTOSRWLambdaWriter ttOSRWLambdaRestart = new TTOSRWLambdaWriter( new BufferedWriter(new FileWriter(lambdaFile))); ttOSRWLambdaRestart.writeLambdaFile(); ttOSRWLambdaRestart.flush(); ttOSRWLambdaRestart.close(); logger.info(String.format(" Wrote TTOSRW lambda restart file to %s.", lambdaFile.getName())); } catch (IOException ex) { String message = " Exception writing TTOSRW lambda restart file."; logger.log(Level.INFO, message, ex); } } /** * Write out snapshot upon each full lambda traversal. */ if (writeTraversalSnapshots) { double heldTraversalLambda = 0.5; if (!traversalInHand.isEmpty()) { heldTraversalLambda = Double.parseDouble(traversalInHand.get(0).split(",")[0]); if ((lambda > 0.2 && traversalSnapshotTarget == 0) || (lambda < 0.8 && traversalSnapshotTarget == 1)) { int snapshotCounts = Integer.parseInt(traversalInHand.get(0).split(",")[1]); traversalInHand.remove(0); File fileToWrite; int numStructures; if (traversalSnapshotTarget == 0) { fileToWrite = lambdaZeroFile; numStructures = ++lambdaZeroStructures; } else { fileToWrite = lambdaOneFile; numStructures = ++lambdaOneStructures; } try { FileWriter fw = new FileWriter(fileToWrite, true); BufferedWriter bw = new BufferedWriter(fw); bw.write(String.format("MODEL %d L=%.4f counts=%d", numStructures, heldTraversalLambda, snapshotCounts)); for (int i = 0; i < 50; i++) { bw.write(" "); } bw.newLine(); for (int i = 0; i < traversalInHand.size(); i++) { bw.write(traversalInHand.get(i)); bw.newLine(); } bw.write(String.format("ENDMDL")); for (int i = 0; i < 75; i++) { bw.write(" "); } bw.newLine(); bw.close(); logger.info(String.format(" Wrote traversal structure L=%.4f", heldTraversalLambda)); } catch (Exception exception) { logger.warning(String.format("Exception writing to file: %s", fileToWrite.getName())); } heldTraversalLambda = 0.5; traversalInHand.clear(); traversalSnapshotTarget = 1 - traversalSnapshotTarget; } } if (((lambda < 0.1 && traversalInHand.isEmpty()) || (lambda < heldTraversalLambda - 0.025 && !traversalInHand.isEmpty())) && (traversalSnapshotTarget == 0 || traversalSnapshotTarget == -1)) { if (lambdaZeroFilter == null) { lambdaZeroFilter = new PDBFilter(lambdaZeroFile, lambdaZeroAssembly, null, null); lambdaZeroFilter.setListMode(true); } lambdaZeroFilter.clearListOutput(); lambdaZeroFilter.writeFileWithHeader(lambdaFile, new StringBuilder(String.format("%.4f,%d", lambda, totalWeight))); traversalInHand = lambdaZeroFilter.getListOutput(); traversalSnapshotTarget = 0; } else if (((lambda > 0.9 && traversalInHand.isEmpty()) || (lambda > heldTraversalLambda + 0.025 && !traversalInHand.isEmpty())) && (traversalSnapshotTarget == 1 || traversalSnapshotTarget == -1)) { if (lambdaOneFilter == null) { lambdaOneFilter = new PDBFilter(lambdaOneFile, lambdaOneAssembly, null, null); lambdaOneFilter.setListMode(true); } lambdaOneFilter.clearListOutput(); lambdaOneFilter.writeFileWithHeader(lambdaFile, new StringBuilder(String.format("%.4f,%d", lambda, totalWeight))); traversalInHand = lambdaOneFilter.getListOutput(); traversalSnapshotTarget = 1; } } } /** * Compute the energy and gradient for the recursion slave at F(L) using * interpolation. */ double freeEnergy = currentFreeEnergy(); biasEnergy += freeEnergy; if (print) { logger.info(String.format(" %s %16.8f", "Bias Energy ", biasEnergy)); logger.info(String.format(" %s %16.8f %s", "OSRW Potential ", e + biasEnergy, "(Kcal/mole)")); } if (propagateLambda && energyCount > 0) { /** * Log the current Lambda state. */ if (energyCount % printFrequency == 0) { if (lambdaBins < 1000) { logger.info(String.format(" L=%6.4f (%3d) F_LU=%10.4f F_LB=%10.4f F_L=%10.4f", lambda, lambdaBin, dEdU, dEdLambda - dEdU, dEdLambda)); } else { logger.info(String.format(" L=%6.4f (%4d) F_LU=%10.4f F_LB=%10.4f F_L=%10.4f", lambda, lambdaBin, dEdU, dEdLambda - dEdU, dEdLambda)); } } /** * Metadynamics grid counts (every 'countInterval' steps). */ if (energyCount % countInterval == 0) { if (jobBackend != null) { if (world.size() > 1) { jobBackend.setComment(String.format( "Overall dG=%10.4f at %7.3e psec, Current: [L=%6.4f, F_L=%10.4f, dG=%10.4f] at %7.3e psec", totalFreeEnergy, totalWeight * dt * countInterval, lambda, dEdU, -freeEnergy, energyCount * dt)); } else { jobBackend.setComment(String.format( "Overall dG=%10.4f at %7.3e psec, Current: [L=%6.4f, F_L=%10.4f, dG=%10.4f]", totalFreeEnergy, totalWeight * dt * countInterval, lambda, dEdU, -freeEnergy)); } } if (asynchronous) { asynchronousSend(lambda, dEdU); } else { synchronousSend(lambda, dEdU); } } } /** * Propagate the Lambda particle. */ if (propagateLambda) { langevin(); } else { equilibrationCounts++; if (jobBackend != null) { jobBackend.setComment(String.format("Equilibration [L=%6.4f, F_L=%10.4f]", lambda, dEdU)); } if (equilibrationCounts % 10 == 0) { logger.info(String.format(" L=%6.4f, F_L=%10.4f", lambda, dEdU)); } } totalEnergy = e + biasEnergy; return totalEnergy; }
From source file:com.cisco.dvbu.ps.common.util.CommonUtils.java
/** * Append passed in content to the file. * Create file if it does not exist. /*from www . java 2 s . c o m*/ * Create the sub-directories if they do not exist. * * @param file - file name with path * @param content - the content to append to the file */ public static void appendContentToFile(String file, String content) { if (file == null || file.length() <= 0) { throw new CompositeException("File path is not defined."); } // Create the sub-directories if they do not already exist String fileDir = getDirectory(file); if (fileDir != null && !fileExists(fileDir)) { mkdirs(fileDir); } // Write to the file BufferedWriter bw = null; try { if (file != null && file.trim().length() > 0) { bw = new BufferedWriter(new FileWriter(file, true)); if (content != null && content.trim().length() > 0) { bw.write(content); bw.newLine(); bw.flush(); } } } catch (IOException e) { CompositeLogger.logException(e, "Could not append to file " + file); throw new ValidationException(e.getMessage(), e); } finally { // always close the file if (bw != null) try { bw.close(); } catch (IOException ioe2) { // just ignore it } } // end try/catch/finally }
From source file:de.tudarmstadt.ukp.dkpro.core.io.ditop.DiTopWriter.java
/** * This method has been copied and slightly adapted from MalletLDA#printTopics in the original * DiTop code./*from w w w . j a va 2 s . c o m*/ * * @throws IOException * if a low-level I/O error occurs */ private void writetermMatrixFiles() throws IOException { File topicTermFile = new File(collectionDir, TOPIC_TERM_FILE); File topicTermMatrixFile = new File(collectionDir, TOPIC_TERM_MATRIX_FILE); File topicSummaryFile = new File(collectionDir, TOPIC_SUMMARY_FILE); BufferedWriter writerTopicTerm = new BufferedWriter(new FileWriter(topicTermFile)); BufferedWriter writerTopicTermMatrix = new BufferedWriter(new FileWriter(topicTermMatrixFile)); BufferedWriter writerTopicTermShort = new BufferedWriter(new FileWriter(topicSummaryFile)); getLogger().info(String.format("Writing file '%s'.", topicTermFile)); getLogger().info(String.format("Writing file '%s'.", topicTermMatrixFile)); getLogger().info(String.format("Writing file '%s'.", topicSummaryFile)); /* Write topic term associations */ Alphabet alphabet = model.getAlphabet(); for (int i = 0; i < model.getSortedWords().size(); i++) { writerTopicTerm.write("TOPIC " + i + ": "); writerTopicTermShort.write("TOPIC " + i + ": "); writerTopicTermMatrix.write("TOPIC " + i + ": "); /** topic for the label */ int count = 0; TreeSet<IDSorter> set = model.getSortedWords().get(i); for (IDSorter s : set) { if (count <= maxTopicWords) { writerTopicTermShort.write(alphabet.lookupObject(s.getID()) + ", "); } count++; writerTopicTerm.write(alphabet.lookupObject(s.getID()) + ", "); writerTopicTermMatrix.write(alphabet.lookupObject(s.getID()) + " (" + s.getWeight() + "), "); /** add to topic label */ } writerTopicTerm.newLine(); writerTopicTermShort.newLine(); writerTopicTermMatrix.newLine(); } writerTopicTermMatrix.close(); writerTopicTerm.close(); writerTopicTermShort.close(); }
From source file:it.unibas.spicy.persistence.csv.ExportCSVInstances.java
private void appendToCSVDocument(ResultSet allRows, int columnCount, String filePath) throws SQLException, IOException { //the flag 'true' means that the writer will go to the end of the file and append the new data BufferedWriter bfout = new BufferedWriter(new FileWriter(filePath, true)); try {/*from w w w . j a v a 2 s.co m*/ while (allRows.next()) { String row = ""; for (int j = 1; j <= columnCount; j++) { String dataType = allRows.getMetaData().getColumnTypeName(j); String value = allRows.getString(j); //if the value is null write null to csv file if (value == null) { // avenet 20170215 - using "" is the copy csv format for Postgres value = ""; } //if the type is String/text etc and is not null put the value between double quotes else if (dataType.toLowerCase().startsWith("varchar") || dataType.toLowerCase().startsWith("char") || dataType.toLowerCase().startsWith("text") || dataType.equalsIgnoreCase("bpchar") || dataType.equalsIgnoreCase("bit") || dataType.equalsIgnoreCase("mediumtext") || dataType.equalsIgnoreCase("longtext") || dataType.equalsIgnoreCase("serial") || dataType.equalsIgnoreCase("enum")) { value = "\"" + value + "\""; } row = row + value + ","; } //take out the last ',' character row = row.substring(0, row.length() - 1); bfout.write(row); bfout.newLine(); } } finally { bfout.close(); } }
From source file:com.holycityaudio.SpinCAD.SpinCADFile.java
public void fileSaveHex(int patchIndex, int[] codeListing, String fileName) throws IOException { BufferedWriter writer = new BufferedWriter(new FileWriter(fileName, true)); int i = -1;// w w w . j av a2s . c o m String outputString = new String(); for (int ii = 0, index = 0; ii < 128; ii++) { if (ii < codeListing.length) { i = codeListing[ii]; } else { i = 0; } if (i != -1) { if (i == 0) { // do NOP conversion i = 0x11; } outputString = String.format("04%04X00%08X", (patchIndex * 0x200) + index, i); // outputString = String.format("04%04X00%08X", index, i); long message = Long.parseLong(outputString, 16); int checksum = 0; for (int iii = 0; iii < 8; iii++) { checksum = checksum + (int) (message & 0xff); message = message >> 8; } checksum = (((~checksum) & 0xff) + 1) & 0xff; writer.write(":" + outputString + String.format("%02X", checksum)); writer.newLine(); index += 4; } } if (patchIndex == 7) { writer.write(":00000001FF\n"); } writer.close(); }
From source file:io.snappydata.hydra.cluster.SnappyTest.java
/** * Task(ENDTASK) for cleaning up snappy processes, because they are not stopped by Hydra in case of Test failure. *///from w w w .j av a 2s.c om public static void HydraTask_cleanUpSnappyProcessesOnFailure() { Process pr = null; ProcessBuilder pb = null; File logFile = null, log = null, nukeRunOutput = null; try { List<String> pidList = new ArrayList(); HostDescription hd = TestConfig.getInstance().getMasterDescription().getVmDescription() .getHostDescription(); pidList = snappyTest.getPidList(); log = new File("."); String nukerun = log.getCanonicalPath() + File.separator + "snappyNukeRun.sh"; logFile = new File(nukerun); String nukeRunOutputString = log.getCanonicalPath() + File.separator + "nukeRunOutput.log"; nukeRunOutput = new File(nukeRunOutputString); FileWriter fw = new FileWriter(logFile.getAbsoluteFile(), true); BufferedWriter bw = new BufferedWriter(fw); for (String pidString : pidList) { int pid = Integer.parseInt(pidString); bw.write("/bin/kill -KILL " + pid); bw.newLine(); try { RemoteTestModule.Master.removePID(hd, pid); } catch (RemoteException e) { String s = "Failed to remove PID from nukerun script: " + pid; throw new HydraRuntimeException(s, e); } } bw.close(); fw.close(); logFile.setExecutable(true); pb = new ProcessBuilder(nukerun); pb.redirectErrorStream(true); pb.redirectOutput(ProcessBuilder.Redirect.appendTo(nukeRunOutput)); pr = pb.start(); pr.waitFor(); } catch (IOException e) { throw new TestException("IOException occurred while retriving logFile path " + log + "\nError Message:" + e.getMessage()); } catch (InterruptedException e) { String s = "Exception occurred while waiting for the process execution : " + pr; throw new TestException(s, e); } }