List of usage examples for org.apache.poi.ss.usermodel PatternFormatting SOLID_FOREGROUND
short SOLID_FOREGROUND
To view the source code for org.apache.poi.ss.usermodel PatternFormatting SOLID_FOREGROUND.
Click Source Link
From source file:snpviewer.SnpViewer.java
License:Open Source License
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 w w .j a va 2 s . c o 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(); }