Examples with UncheckedIOException java.io.UncheckedIOException used on opensource projects

Example 26 with UncheckedIOException

use of java.io.UncheckedIOException in project gatk-protected by broadinstitute.

the class XHMMSegmentCallerBaseIntegrationTest method writeChainInTempFile.

public static File writeChainInTempFile(final XHMMData chain) {
    final File result = createTempFile("chain-", ".tab");
    //final File result = new File("/tmp/input");
    final List<String> sampleNames = IntStream.range(0, chain.data.size()).mapToObj(a -> "SAMPLE_" + a).collect(Collectors.toList());
    final List<String> columnNames = new ArrayList<>(sampleNames.size() + 4);
    columnNames.addAll(Arrays.asList(TargetTableColumn.CONTIG.toString(), TargetTableColumn.START.toString(), TargetTableColumn.END.toString(), TargetTableColumn.NAME.toString()));
    columnNames.addAll(sampleNames);
    try (final TableWriter<Integer> writer = new TableWriter<Integer>(result, new TableColumnCollection(columnNames)) {

        @Override
        protected void composeLine(final Integer record, final DataLine dataLine) {
            dataLine.append(chain.targets.get(record).getContig()).append(chain.targets.get(record).getStart()).append(chain.targets.get(record).getEnd()).append(chain.targets.get(record).getName());
            for (final List<Double> sampleData : chain.data) {
                dataLine.append(sampleData.get(record));
            }
        }
    }) {
        writer.writeAllRecords(IntStream.range(0, chain.targets.size()).boxed().collect(Collectors.toList()));
    } catch (final IOException ex) {
        throw new UncheckedIOException(ex);
    }
    return result;
}

Example 27 with UncheckedIOException

use of java.io.UncheckedIOException in project gatk by broadinstitute.

the class XHMMSegmentCallerBaseIntegrationTest method writeChainInTempFile.

public static File writeChainInTempFile(final XHMMData chain) {
    final File result = createTempFile("chain-", ".tab");
    //final File result = new File("/tmp/input");
    final List<String> sampleNames = IntStream.range(0, chain.data.size()).mapToObj(a -> "SAMPLE_" + a).collect(Collectors.toList());
    final List<String> columnNames = new ArrayList<>(sampleNames.size() + 4);
    columnNames.addAll(Arrays.asList(TargetTableColumn.CONTIG.toString(), TargetTableColumn.START.toString(), TargetTableColumn.END.toString(), TargetTableColumn.NAME.toString()));
    columnNames.addAll(sampleNames);
    try (final TableWriter<Integer> writer = new TableWriter<Integer>(result, new TableColumnCollection(columnNames)) {

        @Override
        protected void composeLine(final Integer record, final DataLine dataLine) {
            dataLine.append(chain.targets.get(record).getContig()).append(chain.targets.get(record).getStart()).append(chain.targets.get(record).getEnd()).append(chain.targets.get(record).getName());
            for (final List<Double> sampleData : chain.data) {
                dataLine.append(sampleData.get(record));
            }
        }
    }) {
        writer.writeAllRecords(IntStream.range(0, chain.targets.size()).boxed().collect(Collectors.toList()));
    } catch (final IOException ex) {
        throw new UncheckedIOException(ex);
    }
    return result;
}

Example 28 with UncheckedIOException

use of java.io.UncheckedIOException in project jgnash by ccavanaugh.

the class FXMLUtils method load.

/**
     * Creates a new Stage with application defaults {@code StageStyle.DECORATED}, {@code Modality.APPLICATION_MODAL}
     * with the specified fxml {@code URL} as the {@code Scene}.  The default resource bundle is used.
     *
     * @param fxmlUrl the fxml {@code URL}
     * @param title the Stage title
     * @param <C> the fxml controller type
     * @return Pair containing the Stage and controller
     */
public static <C> Pair<C> load(@NotNull final URL fxmlUrl, final String title) {
    final FXMLLoader fxmlLoader = new FXMLLoader(fxmlUrl, ResourceUtils.getBundle());
    final Stage stage = new Stage(StageStyle.DECORATED);
    stage.initModality(Modality.APPLICATION_MODAL);
    stage.initOwner(MainView.getPrimaryStage());
    try {
        final Scene scene = new Scene(fxmlLoader.load());
        scene.getStylesheets().addAll(MainView.DEFAULT_CSS);
        scene.getRoot().styleProperty().bind(ThemeManager.styleProperty());
        final C controller = fxmlLoader.getController();
        stage.setScene(scene);
        stage.getIcons().add(StaticUIMethods.getApplicationIcon());
        stage.setTitle(title);
        // force a resize, some stages need a push
        stage.sizeToScene();
        // Inject the scene into the controller
        injectParent(controller, scene);
        stage.setOnShown(event -> Platform.runLater(() -> {
            stage.sizeToScene();
            stage.setMinHeight(stage.getHeight());
            stage.setMinWidth(stage.getWidth());
        }));
        return new Pair<>(controller, stage);
    } catch (final IOException ioe) {
        // log and throw an unchecked exception
        Logger.getLogger(FXMLUtils.class.getName()).log(Level.SEVERE, ioe.getMessage(), ioe);
        throw new UncheckedIOException(ioe);
    }
}

Example 29 with UncheckedIOException

use of java.io.UncheckedIOException in project chuidiang-ejemplos by chuidiang.

the class WriteFile method writeWithFilesAndStream.

private static void writeWithFilesAndStream() {
    String[] lines = new String[] { "line 1", "line 2", "line 2" };
    Path path = Paths.get("outputfile.txt");
    try (BufferedWriter br = Files.newBufferedWriter(path, Charset.defaultCharset(), StandardOpenOption.CREATE)) {
        Arrays.stream(lines).forEach((s) -> {
            try {
                br.write(s);
                br.newLine();
            } catch (IOException e) {
                throw new UncheckedIOException(e);
            }
        });
    } catch (Exception e) {
        e.printStackTrace();
    }
}

Example 30 with UncheckedIOException

use of java.io.UncheckedIOException in project ddf by codice.

the class IngestCommand method buildQueue.

private void buildQueue(File inputFile, ArrayBlockingQueue<Metacard> metacardQueue, long start) {
    try {
        if (includeContent) {
            processIncludeContent(metacardQueue);
        } else {
            try {
                Stream<Path> ingestStream = Files.walk(inputFile.toPath(), FileVisitOption.FOLLOW_LINKS);
                ingestStream.map(Path::toFile).filter(file -> !file.isDirectory()).forEach(file -> addFileToQueue(metacardQueue, start, file));
            } catch (IOException e) {
                throw new UncheckedIOException(e);
            }
        }
    } finally {
        phaser.arriveAndDeregister();
    }
}