List of usage examples for javafx.concurrent Task messageProperty
@Override
public final ReadOnlyStringProperty messageProperty()
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//from w w w.j a v 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:com.bekwam.resignator.ResignatorAppMainViewController.java
@FXML public void sign() { if (logger.isDebugEnabled()) { logger.debug("[SIGN] activeProfile sourceFile={}, targetFile={}", activeProfile.getSourceFileFileName(), activeProfile.getTargetFileFileName()); }/*from w w w . j a v a2 s.co 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:com.bekwam.resignator.ResignatorAppMainViewController.java
@FXML public void initialize() { try {//from w w w. jav a 2 s . c om miHelp.setAccelerator(KeyCombination.keyCombination("F1")); cbType.getItems().add(SigningArgumentsType.JAR); cbType.getItems().add(SigningArgumentsType.FOLDER); cbType.getSelectionModel().select(SigningArgumentsType.JAR); cbType.setConverter(new StringConverter<SigningArgumentsType>() { @Override public String toString(SigningArgumentsType type) { return StringUtils.capitalize(StringUtils.lowerCase(String.valueOf(type))); } @Override public SigningArgumentsType fromString(String type) { return Enum.valueOf(SigningArgumentsType.class, StringUtils.upperCase(type)); } }); activeConfiguration.activeProfileProperty().bindBidirectional(activeProfile.profileNameProperty()); tfSourceFile.textProperty().bindBidirectional(activeProfile.sourceFileFileNameProperty()); tfTargetFile.textProperty().bindBidirectional(activeProfile.targetFileFileNameProperty()); ckReplace.selectedProperty().bindBidirectional(activeProfile.replaceSignaturesProperty()); cbType.valueProperty().bindBidirectional(activeProfile.argsTypeProperty()); miSave.disableProperty().bind(needsSave.not()); tfSourceFile.textProperty().addListener(new WeakInvalidationListener(needsSaveListener)); tfTargetFile.textProperty().addListener(new WeakInvalidationListener(needsSaveListener)); ckReplace.selectedProperty().addListener(new WeakInvalidationListener(needsSaveListener)); cbType.valueProperty().addListener(new WeakInvalidationListener(needsSaveListener)); lblSource.setText(SOURCE_LABEL_JAR); lblTarget.setText(TARGET_LABEL_JAR); cbType.getSelectionModel().selectedItemProperty().addListener((ov, old_v, new_v) -> { if (new_v == SigningArgumentsType.FOLDER) { if (!lblSource.getText().equalsIgnoreCase(SOURCE_LABEL_FOLDER)) { lblSource.setText(SOURCE_LABEL_FOLDER); } if (!lblSource.getText().equalsIgnoreCase(TARGET_LABEL_FOLDER)) { lblTarget.setText(TARGET_LABEL_FOLDER); } } else { if (!lblSource.getText().equalsIgnoreCase(SOURCE_LABEL_JAR)) { lblSource.setText(SOURCE_LABEL_JAR); } if (!lblSource.getText().equalsIgnoreCase(TARGET_LABEL_JAR)) { lblTarget.setText(TARGET_LABEL_JAR); } } }); lvProfiles.getSelectionModel().selectedItemProperty().addListener((ov, old_v, new_v) -> { if (new_v == null) { // coming from clearSelection or sort return; } if (needsSave.getValue()) { Alert alert = new Alert(Alert.AlertType.CONFIRMATION, "Discard unsaved profile?"); alert.setHeaderText("Unsaved profile"); Optional<ButtonType> response = alert.showAndWait(); if (!response.isPresent() || response.get() != ButtonType.OK) { if (logger.isDebugEnabled()) { logger.debug("[SELECT] discard canceled"); } return; } } if (logger.isDebugEnabled()) { logger.debug("[SELECT] nv={}", new_v); } doLoadProfile(new_v); }); lvProfiles.setCellFactory(TextFieldListCell.forListView()); Task<Void> t = new Task<Void>() { @Override protected Void call() throws Exception { updateMessage("Loading configuration"); configurationDS.loadConfiguration(); if (!configurationDS.isSecured()) { if (logger.isDebugEnabled()) { logger.debug("[CALL] config not secured; getting password"); } NewPasswordController npc = newPasswordControllerProvider.get(); if (logger.isDebugEnabled()) { logger.debug("[INIT TASK] npc id={}", npc.hashCode()); } Platform.runLater(() -> { try { npc.showAndWait(); } catch (Exception exc) { logger.error("error showing npc", exc); } }); synchronized (npc) { try { npc.wait(MAX_WAIT_TIME); // 10 minutes to enter the password } catch (InterruptedException exc) { logger.error("new password operation interrupted", exc); } } if (logger.isDebugEnabled()) { logger.debug("[INIT TASK] npc={}", npc.getHashedPassword()); } if (StringUtils.isNotEmpty(npc.getHashedPassword())) { activeConfiguration.setHashedPassword(npc.getHashedPassword()); activeConfiguration.setUnhashedPassword(npc.getUnhashedPassword()); activeConfiguration.setLastUpdatedDateTime(LocalDateTime.now()); configurationDS.saveConfiguration(); configurationDS.loadConfiguration(); configurationDS.decrypt(activeConfiguration.getUnhashedPassword()); } else { Platform.runLater(() -> { Alert noPassword = new Alert(Alert.AlertType.INFORMATION, "You'll need to provide a password to save your keystore credentials."); noPassword.showAndWait(); }); return null; } } else { PasswordController pc = passwordControllerProvider.get(); Platform.runLater(() -> { try { pc.showAndWait(); } catch (Exception exc) { logger.error("error showing pc", exc); } }); synchronized (pc) { try { pc.wait(MAX_WAIT_TIME); // 10 minutes to enter the password } catch (InterruptedException exc) { logger.error("password operation interrupted", exc); } } Platform.runLater(() -> { if (pc.getStage().isShowing()) { // ended in timeout timeout pc.getStage().hide(); } if (pc.wasCancelled() || pc.wasReset() || !pc.doesPasswordMatch()) { if (logger.isDebugEnabled()) { logger.debug("[INIT TASK] was cancelled or the number of retries was exceeded"); } String msg = ""; if (pc.wasCancelled()) { msg = "You must provide a password to the datastore. Exitting..."; } else if (pc.wasReset()) { msg = "Data file removed. Exitting..."; } else { msg = "Exceeded maximum number of retries. Exitting..."; } Alert alert = new Alert(Alert.AlertType.WARNING, msg); alert.setOnCloseRequest((evt) -> { Platform.exit(); System.exit(1); }); alert.showAndWait(); } else { // // save password for later decryption ops // activeConfiguration.setUnhashedPassword(pc.getPassword()); configurationDS.decrypt(activeConfiguration.getUnhashedPassword()); // // init profileBrowser // if (logger.isDebugEnabled()) { logger.debug("[INIT TASK] loading profiles from source"); } long startTimeMillis = System.currentTimeMillis(); final List<String> profileNames = configurationDS.getProfiles().stream() .map(Profile::getProfileName).sorted((o1, o2) -> o1.compareToIgnoreCase(o2)) .collect(Collectors.toList()); final List<String> recentProfiles = configurationDS.getRecentProfileNames(); if (logger.isDebugEnabled()) { logger.debug("[INIT TASK] loading profiles into UI"); } lvProfiles.setItems(FXCollections.observableArrayList(profileNames)); if (CollectionUtils.isNotEmpty(recentProfiles)) { mRecentProfiles.getItems().clear(); mRecentProfiles.getItems().addAll( FXCollections.observableArrayList(recentProfiles.stream().map((s) -> { MenuItem mi = new MenuItem(s); mi.setOnAction(recentProfileLoadHandler); return mi; }).collect(Collectors.toList()))); } // // #31 preload the last active profile // if (StringUtils.isNotEmpty(activeConfiguration.getActiveProfile())) { if (logger.isDebugEnabled()) { logger.debug("[INIT TASK] preloading last active profile={}", activeConfiguration.getActiveProfile()); } doLoadProfile(activeConfiguration.getActiveProfile()); } long endTimeMillis = System.currentTimeMillis(); if (logger.isDebugEnabled()) { logger.debug("[INIT TASK] loading profiles took {} ms", (endTimeMillis - startTimeMillis)); } } }); } return null; } @Override protected void succeeded() { super.succeeded(); updateMessage(""); lblStatus.textProperty().unbind(); } @Override protected void cancelled() { super.cancelled(); logger.error("task cancelled", getException()); updateMessage(""); lblStatus.textProperty().unbind(); } @Override protected void failed() { super.failed(); logger.error("task failed", getException()); updateMessage(""); lblStatus.textProperty().unbind(); } }; lblStatus.textProperty().bind(t.messageProperty()); new Thread(t).start(); } catch (Exception exc) { logger.error("can't load configuration", exc); String msg = "Verify that the user has access to the directory '" + configFile + "' under " + System.getProperty("user.home") + "."; Alert alert = new Alert(Alert.AlertType.ERROR, msg); alert.setHeaderText("Can't load config file"); alert.showAndWait(); Platform.exit(); } }
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 a v a 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: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 www . j a 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(); }