List of usage examples for javafx.concurrent Task progressProperty
@Override
public final ReadOnlyDoubleProperty progressProperty()
From source file:editeurpanovisu.EquiCubeDialogController.java
/** * *///from w ww . ja v a 2s . c o m private void validerE2C() { if (fileLstFichier == null) { Alert alert = new Alert(AlertType.ERROR); alert.setTitle(rbLocalisation.getString("transformation.traiteImages")); alert.setHeaderText(null); alert.setContentText(rbLocalisation.getString("transformation.traiteImagesPasFichiers")); alert.showAndWait(); } else { Alert alert = new Alert(AlertType.WARNING); alert.setTitle(rbLocalisation.getString("transformation.traiteImages")); alert.setHeaderText(null); alert.setContentText(rbLocalisation.getString("transformation.traiteImagesMessage")); alert.showAndWait(); lblTermine = new Label(); lblTermine.setText("Traitement en cours"); lblTermine.setLayoutX(24); lblTermine.setLayoutY(250); paneChoixTypeFichier.getChildren().add(lblTermine); pbBarreAvancement.setId("bar"); lblTermine.setId("lblTermine"); pbBarreAvancement.setVisible(true); pbBarreImage.setVisible(true); Task taskTraitement; taskTraitement = tskTraitement(); pbBarreAvancement.progressProperty().unbind(); pbBarreImage.setProgress(0.001); pbBarreAvancement.setProgress(0.001); pbBarreAvancement.progressProperty().bind(taskTraitement.progressProperty()); lblTermine.textProperty().unbind(); lblTermine.textProperty().bind(taskTraitement.messageProperty()); Thread thrTraitement = new Thread(taskTraitement); thrTraitement.setDaemon(true); thrTraitement.start(); } }
From source file:com.bekwam.resignator.JarsignerConfigController.java
private void loadAliases() { if (StringUtils.isNotEmpty(tfKeystore.getText()) && StringUtils.isNotEmpty(pfStorepass.getText())) { if (logger.isDebugEnabled()) { logger.debug("[LOAD ALIASES] there are values for the keytool command"); }// ww w .j a v a 2 s.co m hboxAliasProgress.setVisible(true); cbAlias.valueProperty().unbindBidirectional(activeProfile.jarsignerConfigAliasProperty()); cbAlias.getItems().clear(); final String ks = tfKeystore.getText(); final String sp = pfStorepass.getText(); Task<Void> t = new Task<Void>() { public Void call() { try { updateMessage("Loading..."); updateProgress(0.1d, 1.0d); final List<String> aliases = keytoolCommand .findAliases(activeConfiguration.getKeytoolCommand().toString(), ks, sp); updateMessage("Updating..."); updateProgress(0.8d, 1.0d); Platform.runLater(() -> { if (CollectionUtils.isNotEmpty(aliases)) { cbAlias.getItems().addAll(aliases); cbAlias.valueProperty() .bindBidirectional(activeProfile.jarsignerConfigAliasProperty()); } cbAlias.setDisable(false); // might be an empty list for empty keystore cbAlias.requestFocus(); // leave the PasswordField hboxAliasProgress.setVisible(false); }); } catch (CommandExecutionException exc) { if (logger.isWarnEnabled()) { logger.warn("error getting aliases", exc); } Platform.runLater(() -> { cbAlias.setDisable(true); hboxAliasProgress.setVisible(false); }); } finally { updateMessage(""); updateProgress(0.0d, 1.0d); } return null; } }; lblAliasProgress.textProperty().bind(t.messageProperty()); pbAlias.progressProperty().bind(t.progressProperty()); new Thread(t).start(); } else { cbAlias.getItems().clear(); cbAlias.setDisable(true); } }
From source file:frontend.GUIController.java
public Thread processInput(Runnable rSuccess, Runnable rFail) throws Exception { System.out.println("Steping to next step..."); progressBar.progressProperty().unbind(); progressMessage.textProperty().unbind(); next1.setDisable(true);//from www. j a v a 2 s. co m final ArrayList<String> comboBoxValues = new ArrayList<String>(); for (ComboBox<String> c : comboBoxes) { comboBoxValues.add(c.getValue()); } Task<Boolean> t = new Task<Boolean>() { @Override protected Boolean call() throws Exception { updateMessage("Doing Prediction"); updateProgress(3, 10); int status = at.processAfterLoadFile(comboBoxValues, predModel.getValue(), visualize.isSelected(), predicted.isSelected()); if (status > 0) { System.err.println("ProcessAfterLoadFile Error occured."); return false; } updateMessage("Finished Prediction"); if (visualize.isSelected()) { updateProgress(5, 10); at.showVisualization(); updateMessage("Finished Visualization"); updateProgress(8, 10); } updateProgress(10, 10); updateMessage("Done"); //webpage.getChildren().add(new Browser(url)); //at.addTweets(at.outputDir+"/visualization/Sentiment.tsv", personData); return true; }; @Override protected void succeeded() { super.succeeded(); updateMessage("Done!"); } @Override protected void cancelled() { super.cancelled(); updateMessage("Cancelled!"); } @Override protected void failed() { super.failed(); updateMessage("Failed!"); } @Override protected void done() { super.done(); updateMessage("Done!"); } }; progressBar.progressProperty().bind(t.progressProperty()); progressMessage.textProperty().bind(t.messageProperty()); t.setOnSucceeded(new EventHandler<WorkerStateEvent>() { @Override public void handle(WorkerStateEvent event) { if (t.getValue()) { Platform.runLater(rSuccess); } else { Platform.runLater(rFail); } } }); Thread mythread = new Thread(t); mythread.start(); return mythread; }
From source file:com.bekwam.resignator.ResignatorAppMainViewController.java
@FXML public void sign() { if (logger.isDebugEnabled()) { logger.debug("[SIGN] activeProfile sourceFile={}, targetFile={}", activeProfile.getSourceFileFileName(), activeProfile.getTargetFileFileName()); }//from www. ja v a 2 s . c o m boolean isValid = validateSign(); if (!isValid) { if (logger.isDebugEnabled()) { logger.debug("[SIGN] form not valid; returning"); } return; } final Boolean doUnsign = ckReplace.isSelected(); UnsignCommand unsignCommand = unsignCommandProvider.get(); SignCommand signCommand = signCommandProvider.get(); if (activeProfile.getArgsType() == SigningArgumentsType.FOLDER) { if (logger.isDebugEnabled()) { logger.debug("[SIGN] signing folder full of jars"); } // // Get list of source JARs // File[] sourceJars = new File(activeProfile.getSourceFileFileName()) .listFiles((d, n) -> StringUtils.endsWithIgnoreCase(n, ".jar")); // // Report if no jars to sign and exit // if (sourceJars == null || sourceJars.length == 0) { Alert alert = new Alert(Alert.AlertType.INFORMATION, "There aren't any JARs to sign in '" + activeProfile.getTargetFileFileName() + "'"); alert.setHeaderText("No JARs to Sign"); alert.showAndWait(); return; } if (logger.isDebugEnabled()) { for (File f : sourceJars) { logger.debug("[SIGN] source jar={}, filename={}", f.getAbsolutePath(), f.getName()); } } // // Confirm replace operation // if (doUnsign && !confirmReplaceExisting()) { return; } // // Confirm overwriting of files // if (!confirmOverwrite(sourceJars)) { return; } // // This number is applied to the progress bar to report a particular // iterations unit-of-work (2 operations per jar) // double unitFactor = 1.0d / (sourceJars.length * 2.0d); Task<Void> task = new Task<Void>() { @Override protected Void call() throws Exception { double accruedProgress = 0.0d; for (File sf : sourceJars) { File tf = new File(activeProfile.getTargetFileFileName(), sf.getName()); if (logger.isDebugEnabled()) { logger.debug("[SIGN] progress={}", accruedProgress); } updateMessage(""); Platform.runLater(() -> piSignProgress.setVisible(true)); updateProgress(accruedProgress, 1.0d); accruedProgress += unitFactor; if (doUnsign) { if (logger.isDebugEnabled()) { logger.debug("[SIGN] doing bulk unsign operation"); } updateTitle("Unsigning JAR"); unsignCommand.unsignJAR(Paths.get(sf.getAbsolutePath()), Paths.get(tf.getAbsolutePath()), s -> Platform.runLater( () -> txtConsole.appendText(s + System.getProperty("line.separator")))); if (isCancelled()) { return null; } } else { if (logger.isDebugEnabled()) { logger.debug("[SIGN] copying bulk for sign operation"); } updateTitle("Copying JAR"); Platform.runLater(() -> txtConsole .appendText("Copying JAR" + System.getProperty("line.separator"))); unsignCommand.copyJAR(sf.getAbsolutePath(), tf.getAbsolutePath()); } updateProgress(accruedProgress, 1.0d); accruedProgress += unitFactor; updateTitle("Signing JAR"); signCommand.signJAR(Paths.get(tf.getAbsolutePath()), Paths.get(activeProfile.getJarsignerConfigKeystore()), activeProfile.getJarsignerConfigStorepass(), activeProfile.getJarsignerConfigAlias(), activeProfile.getJarsignerConfigKeypass(), s -> Platform.runLater( () -> txtConsole.appendText(s + System.getProperty("line.separator")))); } return null; } @Override protected void succeeded() { super.succeeded(); updateProgress(1.0d, 1.0d); updateMessage("JARs signed successfully"); piSignProgress.progressProperty().unbind(); lblStatus.textProperty().unbind(); } @Override protected void failed() { super.failed(); logger.error("error unsigning and signing jar", exceptionProperty().getValue()); updateProgress(1.0d, 1.0d); updateMessage("Error signing JARs"); piSignProgress.progressProperty().unbind(); lblStatus.textProperty().unbind(); piSignProgress.setVisible(false); Alert alert = new Alert(Alert.AlertType.ERROR, exceptionProperty().getValue().getMessage()); alert.showAndWait(); } @Override protected void cancelled() { super.cancelled(); if (logger.isWarnEnabled()) { logger.warn("signing jar operation cancelled"); } updateProgress(1.0d, 1.0d); updateMessage("JARs signing cancelled"); Platform.runLater(() -> { piSignProgress.progressProperty().unbind(); lblStatus.textProperty().unbind(); piSignProgress.setVisible(false); Alert alert = new Alert(Alert.AlertType.INFORMATION, "JARs signing cancelled"); alert.showAndWait(); }); } }; piSignProgress.progressProperty().bind(task.progressProperty()); lblStatus.textProperty().bind(task.messageProperty()); new Thread(task).start(); } else { if (logger.isDebugEnabled()) { logger.debug("[SIGN] signing single JAR"); } // // #2 confirm an overwrite (if needed); factored // if (doUnsign && !confirmReplaceExisting()) { return; } else { // // #6 sign-only to a different target filename needs a copy and // possible overwrite // File tf = new File(activeProfile.getTargetFileFileName()); if (tf.exists()) { Alert alert = new Alert(Alert.AlertType.CONFIRMATION, "Overwrite existing file '" + tf.getName() + "'?"); alert.setHeaderText("Overwrite existing file"); Optional<ButtonType> response = alert.showAndWait(); if (!response.isPresent() || response.get() != ButtonType.OK) { if (logger.isDebugEnabled()) { logger.debug("[SIGN] overwrite file cancelled"); } return; } } } Task<Void> task = new Task<Void>() { @Override protected Void call() throws Exception { updateMessage(""); Platform.runLater(() -> piSignProgress.setVisible(true)); updateProgress(0.1d, 1.0d); if (doUnsign) { if (logger.isDebugEnabled()) { logger.debug("[SIGN] doing unsign operation"); } updateTitle("Unsigning JAR"); unsignCommand.unsignJAR(Paths.get(activeProfile.getSourceFileFileName()), Paths.get(activeProfile.getTargetFileFileName()), s -> Platform.runLater( () -> txtConsole.appendText(s + System.getProperty("line.separator")))); if (isCancelled()) { return null; } } else { // // #6 needs a copy to the target if target file doesn't // exist // if (logger.isDebugEnabled()) { logger.debug("[SIGN] copying for sign operation"); } updateTitle("Copying JAR"); Platform.runLater( () -> txtConsole.appendText("Copying JAR" + System.getProperty("line.separator"))); unsignCommand.copyJAR(activeProfile.getSourceFileFileName(), activeProfile.getTargetFileFileName()); } updateProgress(0.5d, 1.0d); updateTitle("Signing JAR"); signCommand.signJAR(Paths.get(activeProfile.getTargetFileFileName()), Paths.get(activeProfile.getJarsignerConfigKeystore()), activeProfile.getJarsignerConfigStorepass(), activeProfile.getJarsignerConfigAlias(), activeProfile.getJarsignerConfigKeypass(), s -> Platform.runLater( () -> txtConsole.appendText(s + System.getProperty("line.separator")))); return null; } @Override protected void succeeded() { super.succeeded(); updateProgress(1.0d, 1.0d); updateMessage("JAR signed successfully"); piSignProgress.progressProperty().unbind(); lblStatus.textProperty().unbind(); } @Override protected void failed() { super.failed(); logger.error("error unsigning and signing jar", exceptionProperty().getValue()); updateProgress(1.0d, 1.0d); updateMessage("Error signing JAR"); piSignProgress.progressProperty().unbind(); lblStatus.textProperty().unbind(); piSignProgress.setVisible(false); Alert alert = new Alert(Alert.AlertType.ERROR, exceptionProperty().getValue().getMessage()); alert.showAndWait(); } @Override protected void cancelled() { super.cancelled(); if (logger.isWarnEnabled()) { logger.warn("signing jar operation cancelled"); } updateProgress(1.0d, 1.0d); updateMessage("JAR signing cancelled"); piSignProgress.progressProperty().unbind(); lblStatus.textProperty().unbind(); piSignProgress.setVisible(false); Alert alert = new Alert(Alert.AlertType.INFORMATION, "JAR signing cancelled"); alert.showAndWait(); } }; piSignProgress.progressProperty().bind(task.progressProperty()); lblStatus.textProperty().bind(task.messageProperty()); new Thread(task).start(); } }
From source file:sh.isaac.api.util.DownloadUnzipTask.java
/** * Call.//from w w w . j a va 2 s . c om * * @return the file * @throws Exception the exception * @see javafx.concurrent.Task#call() */ @Override protected File call() throws Exception { final File dataFile = download(this.url); String calculatedSha1Value = null; String expectedSha1Value = null; ; try { LOG.debug("Attempting to get .sha1 file"); final File sha1File = download(new URL(this.url.toString() + ".sha1")); expectedSha1Value = Files.readAllLines(sha1File.toPath()).get(0); final Task<String> calculateTask = ChecksumGenerator.calculateChecksum("SHA1", dataFile); calculateTask.messageProperty().addListener( (ChangeListener<String>) (observable, oldValue, newValue) -> updateMessage(newValue)); calculateTask.progressProperty().addListener((ChangeListener<Number>) (observable, oldValue, newValue) -> updateProgress(calculateTask.getProgress(), calculateTask.getTotalWork())); WorkExecutors.get().getExecutor().execute(calculateTask); calculatedSha1Value = calculateTask.get(); sha1File.delete(); } catch (final Exception e1) { LOG.debug("Failed to get .sha1 file", e1); } if ((calculatedSha1Value != null) && !calculatedSha1Value.equals(expectedSha1Value)) { if (this.failOnBadCheksum) { throw new RuntimeException("Checksum of downloaded file '" + this.url.toString() + "' does not match the expected value!"); } else { LOG.warn("Checksum of downloaded file '" + this.url.toString() + "' does not match the expected value!"); } } if (this.cancel) { LOG.debug("Download cancelled"); throw new Exception("Cancelled!"); } if (this.unzip) { updateTitle("Unzipping"); try { final ZipFile zipFile = new ZipFile(dataFile); zipFile.setRunInThread(true); zipFile.extractAll(this.targetFolder.getAbsolutePath()); while (zipFile.getProgressMonitor().getState() == ProgressMonitor.STATE_BUSY) { if (this.cancel) { zipFile.getProgressMonitor().cancelAllTasks(); LOG.debug("Download cancelled"); throw new Exception("Cancelled!"); } updateProgress(zipFile.getProgressMonitor().getPercentDone(), 100); updateMessage("Unzipping " + dataFile.getName() + " at " + zipFile.getProgressMonitor().getPercentDone() + "%"); try { // TODO see if there is an API where I don't have to poll for completion Thread.sleep(25); } catch (final InterruptedException e) { // noop } } LOG.debug("Unzip complete"); } catch (final Exception e) { LOG.error("error unzipping", e); throw new Exception("The downloaded file doesn't appear to be a zip file"); } finally { dataFile.delete(); } return this.targetFolder; } else { return dataFile; } }
From source file:snpviewer.SnpViewer.java
public void saveRegion(final String chromosome, final double startCoordinate, final double endCoordinate) { final Task<RegionSummary> saveSelectionTask = new Task<RegionSummary>() { @Override/* ww w. j av a 2 s . c o m*/ protected RegionSummary call() throws Exception { try { updateProgress(-1, -1); updateTitle("Finding flanking SNPs"); updateMessage("Searching for nearest SNP in all files..."); /* read SnpFiles to find closest SNPs - use binary search * to find nearby SNP and refine to closest */ List<SnpFile.SnpLine> startAndEndSnps = searchCoordinate(chromosome, (int) startCoordinate, (int) endCoordinate); if (startAndEndSnps == null) { System.out.println("Start and End SNPS ARE NULL!"); //DISPLAY ERROR HERE? return null; } RegionSummary region = new RegionSummary(chromosome, startAndEndSnps.get(0).getPosition(), startAndEndSnps.get(1).getPosition(), 0, 0, startAndEndSnps.get(0).getId(), startAndEndSnps.get(1).getId()); return region; } catch (NumberFormatException ex) { Dialogs.showErrorDialog(null, "Can't display flanking SNP IDs" + " - missing required componant!\n\nPlease report this error.", "Error!", "SNP Viewer", ex); } return null; } }; setProgressMode(true); progressBar.progressProperty().bind(saveSelectionTask.progressProperty()); progressMessage.textProperty().unbind(); progressMessage.textProperty().bind(saveSelectionTask.messageProperty()); progressTitle.textProperty().unbind(); progressTitle.textProperty().bind(saveSelectionTask.titleProperty()); saveSelectionTask.setOnSucceeded(new EventHandler<WorkerStateEvent>() { @Override public void handle(WorkerStateEvent e) { setProgressMode(false); RegionSummary result = (RegionSummary) e.getSource().getValue(); savedRegions.add(result); RegionSummary sorter = new RegionSummary(); sorter.mergeRegionsByPosition(savedRegions); saveProject(); clearDragSelectRectangle(); savedRegionsDisplay.clear(); savedRegionsReference.clear(); drawSavedRegions( (String) chromosomeBoxList[chromosomeSelector.getSelectionModel().getSelectedIndex()]); progressBar.progressProperty().unbind(); progressBar.progressProperty().set(0); progressTitle.textProperty().unbind(); progressMessage.textProperty().unbind(); progressTitle.setText(""); progressMessage.setText(""); } }); saveSelectionTask.setOnFailed(new EventHandler<WorkerStateEvent>() { @Override public void handle(WorkerStateEvent e) { setProgressMode(false); progressBar.progressProperty().unbind(); progressBar.progressProperty().set(0); progressTitle.textProperty().unbind(); progressMessage.textProperty().unbind(); progressTitle.setText(""); progressMessage.setText(""); Dialogs.showErrorDialog(null, "Error finding flanking SNPs\n", "Save Region error", "SNP Viewer", saveSelectionTask.getException()); } }); saveSelectionTask.setOnCancelled(new EventHandler<WorkerStateEvent>() { @Override public void handle(WorkerStateEvent e) { progressMessage.setText("Region write cancelled"); setProgressMode(false); progressBar.progressProperty().unbind(); progressBar.progressProperty().set(0); progressTitle.textProperty().unbind(); progressMessage.textProperty().unbind(); progressTitle.setText(""); progressMessage.setText(""); Dialogs.showErrorDialog(null, "User cancelled region save.", "Save Region", "SNP Viewer", saveSelectionTask.getException()); } }); cancelButton.setOnAction(new EventHandler<ActionEvent>() { @Override public void handle(ActionEvent actionEvent) { saveSelectionTask.cancel(); } }); new Thread(saveSelectionTask).start(); }
From source file:snpviewer.SnpViewer.java
public void displayFlankingSnpIDs(final String chrom, final double start, final double end) { final Task<List<String>> displayTask = new Task<List<String>>() { @Override//from w w w .j a v a2s .c o m protected List<String> call() { updateProgress(-1, -1); updateTitle("Finding flanking SNPs"); updateMessage("Searching for nearest SNP in all files..."); //work out coordinates based on chromosome and pane sizes /* read SnpFiles to find closest SNPs - use binary search * to find nearby SNP and refine to closest */ List<SnpFile.SnpLine> startAndEndSnps = searchCoordinate(chrom, (int) start, (int) end); if (startAndEndSnps == null) { //DISPLAY ERROR HERE? return null; } String coordResult = "chr" + chrom + ":" + nf.format(startAndEndSnps.get(0).getPosition()) + "-" + nf.format(startAndEndSnps.get(1).getPosition()); String idResult = startAndEndSnps.get(0).getId() + ";" + startAndEndSnps.get(1).getId(); List<String> result = new ArrayList(); result.add(coordResult); result.add(idResult); return result; } }; setProgressMode(true); progressBar.progressProperty().bind(displayTask.progressProperty()); progressMessage.textProperty().unbind(); progressMessage.textProperty().bind(displayTask.messageProperty()); progressTitle.textProperty().unbind(); progressTitle.textProperty().bind(displayTask.titleProperty()); displayTask.setOnSucceeded(new EventHandler<WorkerStateEvent>() { @Override public void handle(WorkerStateEvent e) { setProgressMode(false); progressBar.progressProperty().unbind(); progressBar.progressProperty().set(0); progressTitle.textProperty().unbind(); progressMessage.textProperty().unbind(); progressTitle.setText(""); progressMessage.setText(""); } }); displayTask.setOnFailed(new EventHandler<WorkerStateEvent>() { @Override public void handle(WorkerStateEvent e) { setProgressMode(false); progressBar.progressProperty().unbind(); progressBar.progressProperty().set(0); progressTitle.textProperty().unbind(); progressMessage.textProperty().unbind(); progressTitle.setText(""); progressMessage.setText(""); Dialogs.showErrorDialog(null, "Error displaying flanking SNPs\n", "Display error", "SNP Viewer", displayTask.getException()); } }); displayTask.setOnCancelled(new EventHandler<WorkerStateEvent>() { @Override public void handle(WorkerStateEvent e) { progressMessage.setText("Display flanking SNPs cancelled"); setProgressMode(false); progressBar.progressProperty().unbind(); progressBar.progressProperty().set(0); progressTitle.textProperty().unbind(); progressMessage.textProperty().unbind(); progressTitle.setText(""); progressMessage.setText(""); Dialogs.showErrorDialog(null, "User cancelled display.", "Display error", "SNP Viewer", displayTask.getException()); } }); cancelButton.setOnAction(new EventHandler<ActionEvent>() { @Override public void handle(ActionEvent actionEvent) { displayTask.cancel(); } }); new Thread(displayTask).start(); try { List<String> result = displayTask.get(); FXMLLoader loader = new FXMLLoader(getClass().getResource("RegionReporter.fxml")); Stage stage = new Stage(); Pane page = (Pane) loader.load(); Scene scene = new Scene(page); stage.setScene(scene); stage.setTitle("SNP Viewer Region Summary"); stage.getIcons().add(new Image(this.getClass().getResourceAsStream("icon.png"))); RegionReporterController regionReporter = loader.<RegionReporterController>getController(); if (result == null) { regionReporter.setCoordinates("Error!"); regionReporter.setIds("Error!"); } else { regionReporter.setCoordinates(result.get(0)); regionReporter.setIds(result.get(1)); } scene.getStylesheets().add(SnpViewer.class.getResource("SnpViewerStyleSheet.css").toExternalForm()); stage.setResizable(false); stage.initModality(Modality.NONE); stage.show(); } catch (InterruptedException | ExecutionException | IOException ex) { Dialogs.showErrorDialog(null, "Can't display flanking SNP IDs" + " - exception caught!\n\nPlease report this error.", "Error!", "SNP Viewer", ex); } }
From source file:snpviewer.SnpViewer.java
public void writeSavedRegionsToFile() { if (savedRegions.size() < 1) { Dialogs.showErrorDialog(null, "No Saved Regions exist to write!", "No Saved Regions", "SnpViewer"); return;/*from w w w . ja va 2 s. co m*/ } final int flanks = 10; FileChooser fileChooser = new FileChooser(); FileChooser.ExtensionFilter extFilter = new FileChooser.ExtensionFilter("Excel (*.xlsx)", "*.xlsx"); fileChooser.getExtensionFilters().add(extFilter); fileChooser.setTitle("Write regions to Excel file (.xlsx)..."); File rFile = fileChooser.showSaveDialog(mainWindow); if (rFile == null) { return; } else if (!rFile.getName().endsWith(".xlsx")) { rFile = new File(rFile.getAbsolutePath() + ".xlsx"); } final File regionFile = rFile; final Task<Boolean> writeTask = new Task() { @Override protected Boolean call() throws Exception { try { updateProgress(-1, -1); BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(regionFile)); Workbook wb = new XSSFWorkbook(); //first create a summary sheet of all regions Sheet sheet = wb.createSheet(); Row row = null; int rowNo = 0; int sheetNo = 0; wb.setSheetName(sheetNo++, "Summary"); row = sheet.createRow(rowNo++); String header[] = { "Coordinates", "rsIDs", "Size (Mb)" }; for (int col = 0; col < header.length; col++) { Cell cell = row.createCell(col); cell.setCellValue(header[col]); } for (int i = 0; i < savedRegions.size(); i++) { row = sheet.createRow(rowNo++); int col = 0; Cell cell = row.createCell(col++); cell.setCellValue("chr" + savedRegions.get(i).getCoordinateString()); cell = row.createCell(col++); cell.setCellValue(savedRegions.get(i).getIdLine()); cell = row.createCell(col++); double mB = (double) savedRegions.get(i).getLength() / 1000000; cell.setCellValue(mB); } ArrayList<SnpFile> bothFiles = new ArrayList<>(); bothFiles.addAll(affFiles); bothFiles.addAll(unFiles); String prevChrom = new String(); double prog = 0; double total = savedRegions.size() * bothFiles.size() * 2; updateProgress(prog, total); int regCounter = 0; for (RegionSummary reg : savedRegions) { updateMessage("Writing region " + ++regCounter + " of " + savedRegions.size()); //create a sheet for each chromosome if (!reg.getChromosome().equalsIgnoreCase(prevChrom)) { if (!prevChrom.isEmpty()) { CellRangeAddress[] regions = { new CellRangeAddress(0, rowNo, 2, 2 + bothFiles.size()) }; SheetConditionalFormatting sheetCF = sheet.getSheetConditionalFormatting(); ConditionalFormattingRule rule1 = sheetCF .createConditionalFormattingRule(ComparisonOperator.EQUAL, "\"AA\""); PatternFormatting fill1 = rule1.createPatternFormatting(); fill1.setFillBackgroundColor(IndexedColors.LIGHT_GREEN.index); fill1.setFillPattern(PatternFormatting.SOLID_FOREGROUND); ConditionalFormattingRule rule2 = sheetCF .createConditionalFormattingRule(ComparisonOperator.EQUAL, "\"BB\""); PatternFormatting fill2 = rule2.createPatternFormatting(); fill2.setFillBackgroundColor(IndexedColors.PALE_BLUE.index); fill2.setFillPattern(PatternFormatting.SOLID_FOREGROUND); ConditionalFormattingRule rule3 = sheetCF .createConditionalFormattingRule(ComparisonOperator.EQUAL, "\"AB\""); PatternFormatting fill3 = rule3.createPatternFormatting(); fill3.setFillBackgroundColor(IndexedColors.ROSE.index); fill3.setFillPattern(PatternFormatting.SOLID_FOREGROUND); sheetCF.addConditionalFormatting(regions, rule3, rule2); sheetCF.addConditionalFormatting(regions, rule1); } rowNo = 0; sheet = wb.createSheet(); wb.setSheetName(sheetNo++, reg.getChromosome()); prevChrom = reg.getChromosome(); } else {//pad regions with an empty line rowNo++; } TreeMap<Integer, HashMap<String, String>> coordMap = new TreeMap(); /*coordmap - key is position, key of hashmap * is input filename and value call */ HashMap<Integer, String> coordToId = new HashMap<>(); //coordinate to rs ID try { for (SnpFile f : bothFiles) { updateProgress(prog++, total); if (isCancelled()) { return false; } List<SnpFile.SnpLine> lines = f.getSnpsInRegion(reg.getChromosome(), reg.getStartPos(), reg.getEndPos(), flanks); for (SnpFile.SnpLine snpLine : lines) { if (isCancelled()) { return false; } Integer coord = snpLine.getPosition(); if (!coordMap.containsKey(coord)) { coordMap.put(coord, new HashMap<String, String>()); } String filename = f.inputFile.getName(); String rsId = snpLine.getId(); String call = snpLine.getCall(); coordMap.get(coord).put(filename, call); coordToId.put(coord, rsId); } } row = sheet.createRow(rowNo++); Cell cell = row.createCell(0); cell.setCellValue(reg.getCoordinateString()); row = sheet.createRow(rowNo++); cell = row.createCell(0); cell.setCellValue(reg.getIdLine()); int col = 0; row = sheet.createRow(rowNo++); cell = row.createCell(col++); cell.setCellValue("Position"); cell = row.createCell(col++); cell.setCellValue("rsID"); for (SnpFile f : bothFiles) { updateProgress(prog++, total); cell = row.createCell(col++); if (f.getSampleName() != null && !f.getSampleName().isEmpty()) { cell.setCellValue(f.getSampleName()); } else { cell.setCellValue(f.inputFile.getName()); } } for (Entry current : coordMap.entrySet()) { if (isCancelled()) { return false; } col = 0; Integer coord = (Integer) current.getKey(); row = sheet.createRow(rowNo++); cell = row.createCell(col++); cell.setCellValue(coord); cell = row.createCell(col++); cell.setCellValue(coordToId.get(coord)); HashMap<String, String> fileToCall = (HashMap<String, String>) current.getValue(); for (SnpFile f : bothFiles) { cell = row.createCell(col++); if (fileToCall.containsKey(f.inputFile.getName())) { cell.setCellValue(fileToCall.get(f.inputFile.getName())); } else { cell.setCellValue("-"); } } } } catch (Exception ex) { return false; } } CellRangeAddress[] regions = { new CellRangeAddress(0, rowNo, 2, 2 + bothFiles.size()) }; SheetConditionalFormatting sheetCF = sheet.getSheetConditionalFormatting(); ConditionalFormattingRule rule1 = sheetCF .createConditionalFormattingRule(ComparisonOperator.EQUAL, "\"AA\""); PatternFormatting fill1 = rule1.createPatternFormatting(); fill1.setFillBackgroundColor(IndexedColors.LIGHT_GREEN.index); fill1.setFillPattern(PatternFormatting.SOLID_FOREGROUND); ConditionalFormattingRule rule2 = sheetCF .createConditionalFormattingRule(ComparisonOperator.EQUAL, "\"BB\""); PatternFormatting fill2 = rule2.createPatternFormatting(); fill2.setFillBackgroundColor(IndexedColors.PALE_BLUE.index); fill2.setFillPattern(PatternFormatting.SOLID_FOREGROUND); ConditionalFormattingRule rule3 = sheetCF .createConditionalFormattingRule(ComparisonOperator.EQUAL, "\"AB\""); PatternFormatting fill3 = rule3.createPatternFormatting(); fill3.setFillBackgroundColor(IndexedColors.ROSE.index); fill3.setFillPattern(PatternFormatting.SOLID_FOREGROUND); sheetCF.addConditionalFormatting(regions, rule3, rule2); sheetCF.addConditionalFormatting(regions, rule1); wb.write(out); updateProgress(total, total); out.close(); } catch (IOException | NumberFormatException ex) { ex.printStackTrace(); return false; } return true; } };//end of task setProgressMode(true); progressBar.progressProperty().bind(writeTask.progressProperty()); progressMessage.textProperty().bind(writeTask.messageProperty()); writeTask.setOnSucceeded(new EventHandler<WorkerStateEvent>() { @Override public void handle(WorkerStateEvent e) { if (e.getSource().getValue() == true) { Dialogs.showInformationDialog(null, "Saved regions written " + "to file " + "(" + regionFile.getName() + ")successfully", "Regions Written", "SNP Viewer"); } else { Dialogs.showErrorDialog(null, "Region write failed.", "Write Failed", "SNP Viewer"); } setProgressMode(false); progressBar.progressProperty().unbind(); progressBar.progressProperty().set(0); progressMessage.textProperty().unbind(); progressMessage.setText(""); progressTitle.setText(""); } }); writeTask.setOnFailed(new EventHandler<WorkerStateEvent>() { @Override public void handle(WorkerStateEvent e) { setProgressMode(false); progressBar.progressProperty().unbind(); progressBar.progressProperty().set(0); progressMessage.textProperty().unbind(); progressMessage.setText(""); progressTitle.setText("Region write failed!"); Dialogs.showErrorDialog(null, "Error writing region to file\n", "Region write error", "SNP Viewer", e.getSource().getException()); } }); writeTask.setOnCancelled(new EventHandler<WorkerStateEvent>() { @Override public void handle(WorkerStateEvent e) { progressMessage.setText("Region write cancelled"); progressTitle.setText("Cancelled"); setProgressMode(false); progressBar.progressProperty().unbind(); progressBar.progressProperty().set(0); Dialogs.showErrorDialog(null, "Error writing region to file\n", "Region write error", "SNP Viewer"); } }); cancelButton.setOnAction(new EventHandler<ActionEvent>() { @Override public void handle(ActionEvent actionEvent) { writeTask.cancel(); } }); progressTitle.setText("Writing regions to .xlsx file"); new Thread(writeTask).start(); }
From source file:snpviewer.SnpViewer.java
public void writeRegionToFile(final String chromosome, final double start, final double end) { /* get coordinates of selection and report back * write SNPs in region to file//w w w. j ava 2 s . co m */ FileChooser fileChooser = new FileChooser(); FileChooser.ExtensionFilter extFilter = new FileChooser.ExtensionFilter("Excel (*.xlsx)", "*.xlsx"); fileChooser.getExtensionFilters().add(extFilter); fileChooser.setTitle("Write region to Excel file (.xlsx)..."); File rFile = fileChooser.showSaveDialog(mainWindow); if (rFile == null) { return; } else if (!rFile.getName().endsWith(".xlsx")) { rFile = new File(rFile.getAbsolutePath() + ".xlsx"); } final File regionFile = rFile; final Task<Boolean> writeTask = new Task() { @Override protected Boolean call() throws Exception { try { updateProgress(-1, -1); ArrayList<SnpFile> bothFiles = new ArrayList<>(); bothFiles.addAll(affFiles); bothFiles.addAll(unFiles); TreeMap<Integer, HashMap<String, String>> coordMap = new TreeMap(); /*coordmap - key is position, key of hashmap * is input filename and value call */ HashMap<Integer, String> coordToId = new HashMap<>(); double progress = 0; double total = bothFiles.size() * 5; try { BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(regionFile)); Workbook wb = new XSSFWorkbook(); Sheet sheet = wb.createSheet(); int rowNo = 0; Row row = sheet.createRow(rowNo++); for (SnpFile f : bothFiles) { if (isCancelled()) { return false; } updateProgress(++progress, total); updateMessage("Reading region in " + f.inputFile.getName()); List<SnpFile.SnpLine> lines = f.getSnpsInRegion(chromosome, (int) start, (int) end); for (SnpFile.SnpLine snpLine : lines) { if (isCancelled()) { return false; } Integer coord = snpLine.getPosition(); if (!coordMap.containsKey(coord)) { coordMap.put(coord, new HashMap<String, String>()); } String filename = f.inputFile.getName(); String rsId = snpLine.getId(); String call = snpLine.getCall(); coordMap.get(coord).put(filename, call); coordToId.put(coord, rsId); } } Cell cell = row.createCell(0); cell.setCellValue( "chr" + chromosome + ":" + coordMap.firstKey() + "-" + coordMap.lastKey()); row = sheet.createRow(rowNo++); cell = row.createCell(0); cell.setCellValue( coordToId.get(coordMap.firstKey()) + ";" + coordToId.get(coordMap.lastKey())); row = sheet.createRow(rowNo++); int colNo = 0; cell = row.createCell(colNo++); cell.setCellValue("Position"); cell = row.createCell(colNo++); cell.setCellValue("rsID"); for (SnpFile f : bothFiles) { cell = row.createCell(colNo++); if (f.getSampleName() != null && f.getSampleName().length() > 0) { cell.setCellValue(f.getSampleName()); } else { cell.setCellValue(f.getInputFileName()); } } progress = coordMap.size(); total = 5 * coordMap.size(); updateMessage("Writing region to file..."); for (Entry current : coordMap.entrySet()) { if (isCancelled()) { return false; } progress += 4; updateProgress(progress, total); row = sheet.createRow(rowNo++); colNo = 0; Integer coord = (Integer) current.getKey(); cell = row.createCell(colNo++); cell.setCellValue(coord); String rsId = coordToId.get(coord); cell = row.createCell(colNo++); cell.setCellValue(rsId); HashMap<String, String> fileToCall = (HashMap<String, String>) current.getValue(); for (SnpFile f : bothFiles) { cell = row.createCell(colNo++); if (fileToCall.containsKey(f.inputFile.getName())) { cell.setCellValue(fileToCall.get(f.inputFile.getName())); } else { cell.setCellValue("-"); } } } CellRangeAddress[] regions = { new CellRangeAddress(0, rowNo, 2, 2 + bothFiles.size()) }; SheetConditionalFormatting sheetCF = sheet.getSheetConditionalFormatting(); ConditionalFormattingRule rule1 = sheetCF .createConditionalFormattingRule(ComparisonOperator.EQUAL, "\"AA\""); PatternFormatting fill1 = rule1.createPatternFormatting(); fill1.setFillBackgroundColor(IndexedColors.LIGHT_GREEN.index); fill1.setFillPattern(PatternFormatting.SOLID_FOREGROUND); ConditionalFormattingRule rule2 = sheetCF .createConditionalFormattingRule(ComparisonOperator.EQUAL, "\"BB\""); PatternFormatting fill2 = rule2.createPatternFormatting(); fill2.setFillBackgroundColor(IndexedColors.PALE_BLUE.index); fill2.setFillPattern(PatternFormatting.SOLID_FOREGROUND); ConditionalFormattingRule rule3 = sheetCF .createConditionalFormattingRule(ComparisonOperator.EQUAL, "\"AB\""); PatternFormatting fill3 = rule3.createPatternFormatting(); fill3.setFillBackgroundColor(IndexedColors.ROSE.index); fill3.setFillPattern(PatternFormatting.SOLID_FOREGROUND); sheetCF.addConditionalFormatting(regions, rule3, rule2); sheetCF.addConditionalFormatting(regions, rule1); wb.write(out); out.close(); return true; } catch (IOException ex) { return false; } } catch (Exception ex) { return false; } } };//end of task setProgressMode(true); progressBar.progressProperty().bind(writeTask.progressProperty()); progressMessage.textProperty().bind(writeTask.messageProperty()); writeTask.setOnSucceeded(new EventHandler<WorkerStateEvent>() { @Override public void handle(WorkerStateEvent e) { if (e.getSource().getValue() == true) { Dialogs.showInformationDialog(null, "Region written to file " + "(" + regionFile.getName() + ") successfully", "Region Written", "SNP Viewer"); } else { Dialogs.showErrorDialog(null, "Region write failed.", "Write Failed", "SNP Viewer"); } setProgressMode(false); progressBar.progressProperty().unbind(); progressBar.progressProperty().set(0); progressMessage.textProperty().unbind(); progressMessage.setText(""); progressTitle.setText(""); } }); writeTask.setOnFailed(new EventHandler<WorkerStateEvent>() { @Override public void handle(WorkerStateEvent e) { setProgressMode(false); progressBar.progressProperty().unbind(); progressBar.progressProperty().set(0); progressMessage.textProperty().unbind(); progressMessage.setText(""); progressTitle.setText("Region write failed!"); Dialogs.showErrorDialog(null, "Error writing region to file\n", "Region write error", "SNP Viewer", e.getSource().getException()); } }); writeTask.setOnCancelled(new EventHandler<WorkerStateEvent>() { @Override public void handle(WorkerStateEvent e) { progressMessage.setText("Region write cancelled"); progressTitle.setText("Cancelled"); setProgressMode(false); progressBar.progressProperty().unbind(); progressBar.progressProperty().set(0); Dialogs.showErrorDialog(null, "Error writing region to file\n", "Region write error", "SNP Viewer"); } }); cancelButton.setOnAction(new EventHandler<ActionEvent>() { @Override public void handle(ActionEvent actionEvent) { writeTask.cancel(); } }); progressTitle.setText("Writing region to .xlsx file"); new Thread(writeTask).start(); }
From source file:uk.bl.dpt.qa.gui.DissimilarGUIThread.java
/** * Calculate and display a record/*w w w.jav a 2s . com*/ * @param pRecord record to calculate and display */ private void internalCalcAndDisplayRecord(final int pRecord) { List<CheckResult> single = new LinkedList<CheckResult>(); single.add(gResults.get(pRecord)); //this is a hack - create a list with only one entry for processing //third param is true to ignore isProcessing checks as the record //should be claimed for us by this point Task<Integer> task = new ProcessingLoadTask(single, true, true, false); progressIndicator.progressProperty().bind(task.progressProperty()); imageLeftLabel.setText(gResults.get(pRecord).getFileOne().getName()); imageRightLabel.setText(gResults.get(pRecord).getFileTwo().getName()); Thread loader = new Thread(task); loader.setDaemon(true); loader.start(); }