List of usage examples for javafx.stage FileChooser getExtensionFilters
public ObservableList<ExtensionFilter> getExtensionFilters()
From source file:de.bayern.gdi.gui.Controller.java
/** * Handle config saving./* w w w . java 2s. com*/ * * @param event The event. */ @FXML protected void handleSaveConfig(ActionEvent event) { extractStoredQuery(); extractBoundingBox(); extractCql(); if (validateInput() && validateCqlInput()) { FileChooser fileChooser = new FileChooser(); DirectoryChooser dirChooser = new DirectoryChooser(); File downloadDir; File initDir; dirChooser.setTitle(I18n.getMsg("gui.save-dir")); if (downloadConfig == null) { downloadDir = dirChooser.showDialog(getPrimaryStage()); String basedir = Config.getInstance().getServices().getBaseDirectory(); initDir = new File(basedir.isEmpty() ? System.getProperty(USER_DIR) : basedir); File uniqueName = Misc.uniqueFile(downloadDir, "config", "xml", null); fileChooser.setInitialFileName(uniqueName.getName()); } else { File downloadInitDir = new File(downloadConfig.getDownloadPath()); if (!downloadInitDir.exists()) { downloadInitDir = new File(System.getProperty(USER_DIR)); } dirChooser.setInitialDirectory(downloadInitDir); downloadDir = dirChooser.showDialog(getPrimaryStage()); String path = downloadConfig.getFile().getAbsolutePath(); path = path.substring(0, path.lastIndexOf(File.separator)); initDir = new File(path); fileChooser.setInitialFileName(downloadConfig.getFile().getName()); } fileChooser.setInitialDirectory(initDir); FileChooser.ExtensionFilter xmlFilter = new FileChooser.ExtensionFilter("xml files (*.xml)", "*.xml"); fileChooser.getExtensionFilters().add(xmlFilter); fileChooser.setSelectedExtensionFilter(xmlFilter); fileChooser.setTitle(I18n.getMsg("gui.save-conf")); File configFile = fileChooser.showSaveDialog(getPrimaryStage()); if (configFile == null) { return; } if (!configFile.toString().endsWith(".xml")) { configFile = new File(configFile.toString() + ".xml"); } this.dataBean.setProcessingSteps(extractProcessingSteps()); String savePath = downloadDir.getPath(); DownloadStep ds = dataBean.convertToDownloadStep(savePath); try { ds.write(configFile); } catch (IOException ex) { log.warn(ex.getMessage(), ex); } } }
From source file:snpviewer.SnpViewer.java
public void loadColourScheme(ActionEvent e) { FileChooser fileChooser = new FileChooser(); fileChooser.getExtensionFilters() .add(new FileChooser.ExtensionFilter("SNP Viewer Colour Scheme", "*.svcols")); fileChooser.setTitle("Open SNP Viewer Colour Scheme (.svcols) file"); File loadFile = fileChooser.showOpenDialog(mainWindow); if (loadFile != null) { try {// www.j a v a 2s. co m ObjectInputStream is = new ObjectInputStream( new BufferedInputStream(new FileInputStream(loadFile))); ArrayList<Color> loadedColors = new ArrayList<>(); for (Color c : colorComp) { String colorString = (String) is.readObject(); loadedColors.add(Color.valueOf(colorString)); } for (int ci = 0; ci < loadedColors.size(); ci++) { colorComponantSelector.getSelectionModel().clearAndSelect(ci); colorPicker.setValue(loadedColors.get(ci)); colorPicker.fireEvent(new ActionEvent()); } colorComponantSelector.getSelectionModel().selectFirst(); colorComp.clear(); colorComp.addAll(loadedColors); is.close(); saveProject(); removeSavedChromosomeImages(); refreshView((String) chromosomeSelector.getSelectionModel().getSelectedItem(), true); } catch (IOException | ClassNotFoundException ex) { } } }
From source file:snpviewer.SnpViewer.java
public void addInputFiles(final boolean isAffected) { setProgressMode(true);//from ww w. j a v a 2 s.c om FileChooser fileChooser = new FileChooser(); fileChooser.getExtensionFilters() .add(new FileChooser.ExtensionFilter("Text Files", "*.txt", "AutoSNPa Files", "*.xls")); fileChooser.setTitle("Select one or more input (birdseed) files"); List<File> chosen = fileChooser.showOpenMultipleDialog(null); if (chosen == null) { setProgressMode(false); return; } cancelButton.setOnAction(new EventHandler<ActionEvent>() { @Override public void handle(ActionEvent actionEvent) { setProgressMode(false); }; }); ArrayList<File> inputFiles = new ArrayList<>(); inputFiles.addAll(chosen); ArrayList<File> duplicates = new ArrayList<>(); ArrayList<Integer> indicesToRemove = new ArrayList<>(); for (int i = 0; i < inputFiles.size(); i++) { for (SnpFile s : affFiles) { if (inputFiles.get(i).getName().equals(s.getInputFileName())) { duplicates.add(inputFiles.get(i)); indicesToRemove.add(i); } } for (SnpFile s : unFiles) { if (inputFiles.get(i).getName().equals(s.getInputFileName())) { duplicates.add(inputFiles.get(i)); indicesToRemove.add(i); } } } if (!duplicates.isEmpty()) { StringBuilder duplicateString = new StringBuilder(); for (File d : duplicates) { duplicateString.append(d.getName()).append("\n"); } Collections.sort(indicesToRemove, Collections.reverseOrder()); for (int i : indicesToRemove) { inputFiles.remove(i); } DialogResponse response = Dialogs.showWarningDialog(null, "This project already includes the following file(s) with " + "matching names to the file(s) you have just tried to add:" + "\n\n" + duplicateString + "\nIf you want to change the affected " + "status of a file please remove it first. Any remaining " + "(non-duplicate) files will be processed if you click 'OK'.", "Duplicate Input File", "SnpViewer", Dialogs.DialogOptions.OK_CANCEL); if (!response.equals(DialogResponse.OK)) { setProgressMode(false); return; } } if (inputFiles.isEmpty()) { setProgressMode(false); return; } final Iterator iter = inputFiles.iterator(); File input = (File) iter.next(); int fileCounter = 1; if (snpViewSaveDirectory == null) { Dialogs.showWarningDialog(null, "Before processing input files " + "please create a project", "Create Project", "SNP Viewer"); boolean success = startNewProject(); if (!success) { setProgressMode(false); return; } } addInputFilesWithIterator(isAffected, input, iter, fileCounter, inputFiles.size()); }
From source file:snpviewer.SnpViewer.java
public void drawPaneToPng() { if (chromosomeSelector.getSelectionModel().isEmpty()) { return;//from ww w. j a va 2 s.c om } FileChooser fileChooser = new FileChooser(); FileChooser.ExtensionFilter extFilter = new FileChooser.ExtensionFilter("PNG Image Files (*.png)", "*.png"); fileChooser.getExtensionFilters().add(extFilter); fileChooser.setTitle("Save View as Image (.png) File..."); File pngFile = fileChooser.showSaveDialog(mainWindow); if (pngFile == null) { return; } else if (!pngFile.getName().endsWith(".png")) { pngFile = new File(pngFile.getAbsolutePath() + ".png"); } WritableImage image = chromSplitPane.snapshot(null, null); if (image == null) { Dialogs.showErrorDialog(null, "Error attempting to convert" + " dynamic view to image file", "PNG conversion failed", "SNP Viewer"); return; } try { ImageIO.write(SwingFXUtils.fromFXImage(image, null), "png", pngFile); Dialogs.showInformationDialog(null, "Sucessfully saved current view " + "to " + pngFile.getName(), "Image Saved", "SNP Viewer"); } catch (IOException ex) { Dialogs.showErrorDialog(null, "Error attempting to convert" + " dynamic view to image file", "PNG conversion failed", "SNP Viewer", ex); } }
From source file:snpviewer.SnpViewer.java
public void loadProject() { if (projectRunning) { /*setProgressMode(true); DialogResponse response = Dialogs.showConfirmDialog(null, "Do you want to save your current project before starting a new one?", "Save Current Project?", "SNP View"); if (DialogResponse.YES.equals(response)){ boolean saved = saveProject();/* www. j ava 2 s .c o m*/ if (! saved){ setProgressMode(false); return; }else{ Dialogs.showInformationDialog(null, projectFile.getName() + " saved sucessfully", "Save Successful", "SNP View"); } }else if (DialogResponse.CANCEL.equals(response)){ setProgressMode(false); return; }*/ } loadProjectButton.setDisable(true); newProjectButton.setDisable(true); FileChooser fileChooser = new FileChooser(); fileChooser.getExtensionFilters().add(new FileChooser.ExtensionFilter("SNP Viewer Projects", "*.svproj")); fileChooser.setTitle("Open SNP Viewer Project (.svproj) file"); //setProgressMode(false); File loadFile = fileChooser.showOpenDialog(mainWindow); loadProjectButton.setDisable(false); newProjectButton.setDisable(false); if (loadFile != null) { try { ObjectInputStream is = new ObjectInputStream( new BufferedInputStream(new FileInputStream(loadFile))); try { projectFile = null; projectLabel.setText("Project: none"); chromSplitPane.getItems().clear(); labelSplitPane.getItems().clear(); clearDragSelectRectangle(); savedRegions.clear(); savedRegionsDisplay.clear(); savedRegionsReference.clear(); selectionOverlayPane.getChildren().clear(); selectionOverlayPane.getChildren().add(dragSelectRectangle); resetObservables(); genomeVersion = ""; qualityFilter = null; noFilteringRadio.setSelected(true); chromosomeSelector.getItems().clear(); projectFile = (File) is.readObject();//get rid of this? projectFile = loadFile;//allow relative referencing ArrayList<Color> loadedColors = new ArrayList<>(); ArrayList<SnpFile> tempAff = new ArrayList<>(); ArrayList<SnpFile> tempUn = new ArrayList<>(); tempAff.addAll((ArrayList<SnpFile>) is.readObject()); tempUn.addAll((ArrayList<SnpFile>) is.readObject()); ArrayList<SnpFile> tempBoth = new ArrayList<>(); tempBoth.addAll(tempAff); tempBoth.addAll(tempUn); genomeVersion = (String) is.readObject(); qualityFilter = (Double) is.readObject(); buildLabel.setText(genomeVersion); snpViewSaveDirectory = (File) is.readObject(); savedRegions = (ArrayList<RegionSummary>) is.readObject(); String projectName = projectFile.getName().replaceAll(".svproj", ""); if (!snpViewSaveDirectory.exists()) { snpViewSaveDirectory = new File( projectFile.getParentFile() + "/" + projectName + " SNP Viewer files"); if (!snpViewSaveDirectory.exists()) { DialogResponse response = Dialogs.showErrorDialog(null, "Can't find project directory (" + snpViewSaveDirectory.getName() + ") - do you " + "want to try to find it?", "Project directory " + "not found", "SnpViewer", Dialogs.DialogOptions.YES_NO); if (DialogResponse.YES.equals(response)) { DirectoryChooser dirChooser = new DirectoryChooser(); dirChooser.setTitle("Locate Project Folder"); snpViewSaveDirectory = dirChooser.showDialog(mainWindow); if (snpViewSaveDirectory == null) { returnToInitialState(); return; } } else { returnToInitialState(); return; } } } boolean check = checkProjectFolder(snpViewSaveDirectory, tempBoth); if (!check) { Dialogs.showErrorDialog(null, "Corrupt project" + " folder - missing files.", "Invalid " + "project folder.", "SnpViewer"); returnToInitialState(); return; } for (Color c : colorComp) { String colorString = (String) is.readObject(); loadedColors.add(Color.valueOf(colorString)); } for (int ci = 0; ci < loadedColors.size(); ci++) { colorComponantSelector.getSelectionModel().clearAndSelect(ci); colorPicker.setValue(loadedColors.get(ci)); colorPicker.fireEvent(new ActionEvent()); } affObserve.addAll(tempAff); unObserve.addAll(tempUn); colorComponantSelector.getSelectionModel().selectFirst(); colorComp.clear(); colorComp.addAll(loadedColors); is.close(); setQualityLabel(); checkQualitySelection(); saveProject(); projectLabel.setText("Project: " + projectFile.getName()); //addToChromosomeSelector(affFiles); //addToChromosomeSelector(unFiles); if (!chromosomeSelector.getItems().isEmpty()) { chromosomeSelector.getSelectionModel().selectFirst(); } if (chromosomeSelector.isDisabled()) { chromosomeSelector.setDisable(false); } //setProgressMode(false); if (affObserve.isEmpty() && unObserve.isEmpty()) { resetView(); } projectRunning = true; } catch (IOException | ClassNotFoundException ex) { resetView(); projectLabel.setText("Project: none"); savedRegions.clear(); savedRegionsDisplay.clear(); savedRegionsReference.clear(); resetObservables(); genomeVersion = ""; qualityFilter = null; noFilteringRadio.setSelected(true); chromosomeSelector.getItems().clear(); ex.printStackTrace(); Dialogs.showErrorDialog(null, "Could not load project file", "Load Failed", "SNP Viewer", ex); } } catch (IOException ex) { resetView(); projectLabel.setText("Project: none"); savedRegions.clear(); savedRegionsDisplay.clear(); savedRegionsReference.clear(); resetObservables(); genomeVersion = ""; qualityFilter = null; noFilteringRadio.setSelected(true); chromosomeSelector.getItems().clear(); ex.printStackTrace(); Dialogs.showErrorDialog(null, "Could not load project file - IO error", "Load Failed", "SNP Viewer", ex); } } }
From source file:snpviewer.SnpViewer.java
public boolean startNewProject() { affFiles.clear();/* ww w . j a v a 2 s . c om*/ unFiles.clear(); resetObservables(); genomeVersion = ""; qualityFilter = null; noFilteringRadio.setSelected(true); chromSplitPane.getItems().clear(); labelSplitPane.getItems().clear(); chromosomeSelector.getItems().clear(); snpViewSaveDirectory = null; clearDragSelectRectangle(); savedRegions.clear(); savedRegionsDisplay.clear(); savedRegionsReference.clear(); selectionOverlayPane.getChildren().clear(); selectionOverlayPane.getChildren().add(dragSelectRectangle); if (projectRunning) { setProgressMode(true); } FileChooser fileChooser = new FileChooser(); FileChooser.ExtensionFilter extFilter = new FileChooser.ExtensionFilter("SNP Viewer Projects (*.svproj)", "*.svproj"); fileChooser.getExtensionFilters().add(extFilter); fileChooser.setTitle("Save New SNP Viewer (.svproj) Project As..."); projectFile = fileChooser.showSaveDialog(mainWindow); if (projectFile != null) { if (!projectFile.getName().endsWith(".svproj")) { projectFile = new File(projectFile.getAbsolutePath() + ".svproj"); } try { String projectName = projectFile.getName().replaceAll(".svproj", ""); File snpViewDir = new File(projectFile.getParentFile() + "/" + projectName + " SNP Viewer files"); if (snpViewDir.exists()) { FileUtils.deleteDirectory(snpViewDir); } boolean madeDir = snpViewDir.mkdir(); if (madeDir) { snpViewSaveDirectory = snpViewDir; } else { //display error? return false; } } catch (Exception ex) { Dialogs.showErrorDialog(null, "Project Directory Creation Failed", "Error Creating New Project", "Snp Viewer", ex); } return saveProject(projectFile); } else { resetView(); return false; } }
From source file:snpviewer.SnpViewer.java
public void saveColours(ActionEvent e) { FileChooser fileChooser = new FileChooser(); fileChooser.setTitle("Save Colour Scheme (.svcols) As..."); FileChooser.ExtensionFilter extFilter = new FileChooser.ExtensionFilter("SNP Viewer Colour Scheme", "*.svcols"); fileChooser.getExtensionFilters().add(extFilter); File colorFile = fileChooser.showSaveDialog(mainWindow); if (colorFile != null) { if (!colorFile.getName().endsWith(".svcols")) { colorFile = new File(colorFile.getAbsolutePath() + ".svcols"); }//from ww w.j a v a2s. c om try { FileOutputStream fos = new FileOutputStream(colorFile); try (ObjectOutputStream out = new ObjectOutputStream(new BufferedOutputStream(fos))) { for (Color c : colorComp) { out.writeObject(c.toString()); } out.close(); projectLabel.setText("Project: " + projectFile.getName()); } } catch (IOException ex) { Dialogs.showErrorDialog(null, "Could not save colour scheme - IO error", "Save Failed", "SNP Viewer", ex); } } }
From source file:snpviewer.SnpViewer.java
public boolean saveProject() { if (projectFile != null) { return saveProject(projectFile); } else {/* w w w .j a va2s . c o m*/ FileChooser fileChooser = new FileChooser(); fileChooser.setTitle("Save Snp Viewer Project (.svproj) As..."); FileChooser.ExtensionFilter extFilter = new FileChooser.ExtensionFilter("SNP Viewer Projects", "*.svproj"); fileChooser.getExtensionFilters().add(extFilter); projectFile = fileChooser.showSaveDialog(mainWindow); if (projectFile != null) { if (!projectFile.getName().endsWith(".svproj")) { projectFile = new File(projectFile.getAbsolutePath() + ".svproj"); } return saveProject(projectFile); } else { return false; } } }
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/*from w ww. j a v a 2s. c om*/ */ 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 w w w . ja va2s . c o 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(); }