Java Code Examples for java.io.File#toString()

@Test
public void testLoadDynamicalProperties() throws IOException, FlinkParseException {
	final File tmpDir = temporaryFolder.newFolder();
	final File confFile = new File(tmpDir, GlobalConfiguration.FLINK_CONF_FILENAME);
	final PrintWriter pw1 = new PrintWriter(confFile);
	final long managedMemory = 1024 * 1024 * 256;
	pw1.println(JobManagerOptions.ADDRESS.key() + ": localhost");
	pw1.println(TaskManagerOptions.MANAGED_MEMORY_SIZE.key() + ": " + managedMemory + "b");
	pw1.close();

	final String jmHost = "host1";
	final int jmPort = 12345;
	String[] args = new String[] {
		"--configDir", tmpDir.toString(),
		"-D" + JobManagerOptions.ADDRESS.key() + "=" + jmHost,
		"-D" + JobManagerOptions.PORT.key() + "=" + jmPort
	};
	Configuration configuration = TaskManagerRunner.loadConfiguration(args);
	assertEquals(MemorySize.parse(managedMemory + "b"), configuration.get(TaskManagerOptions.MANAGED_MEMORY_SIZE));
	assertEquals(jmHost, configuration.get(JobManagerOptions.ADDRESS));
	assertEquals(jmPort, configuration.getInteger(JobManagerOptions.PORT));
}
 

@Test
public void testSimple() throws Exception {
    final File dreamDir =  new File(publicTestDir, "org/broadinstitute/hellbender/tools/mutect/dream");
    final File output = createTempFile("output", ".txt");
    final String[] args = {
            "-V", dreamDir + "/vcfs/dream3-chr20.vcf",
            "-R", b37_reference_20_21,
            "-L", dreamDir + "/dream-chr20.interval_list",
            "-O", output.toString()
    };
    runCommandLine(args);

    FalsePositiveRecordReader reader = new FalsePositiveRecordReader(output);
    FalsePositiveRecord record = reader.readRecord();

    // check that the tool agrees with the false positive counts using AWK
    // SNP: grep PASS dream3-chr20.vcf | awk 'length($4) == length($5) { print $0 }' | wc -l
    // INDEL: grep PASS dream3-chr20.vcf | awk 'length($4) != length($5) { print $0 }' | wc -l
    Assert.assertEquals(record.getSnpFalsePositives(), 173);
    Assert.assertEquals(record.getIndelFalsePositives(), 276);
}
 

/**
 * Fills a report and saves it directly into a PDF file. 
 * The intermediate JasperPrint object is not saved on disk.
 */
public String runToPdfFile(
	String sourceFileName, 
	Map<String,Object> params, 
	JRDataSource jrDataSource
	) throws JRException
{
	File sourceFile = new File(sourceFileName);

	/*   */
	JasperPrint jasperPrint = JRFiller.fill(jasperReportsContext, 
			JasperFillManager.getReportSource(jasperReportsContext, sourceFile), 
			params, jrDataSource);

	/*   */
	File destFile = new File(sourceFile.getParent(), jasperPrint.getName() + ".pdf");
	String destFileName = destFile.toString();

	JasperExportManager.getInstance(jasperReportsContext).exportToPdfFile(jasperPrint, destFileName);
	
	return destFileName;
}
 

private Save(File worldFolder) {
	data = new ArrayList<>();
	
	
	if(worldFolder.getParent().equals("saves")) {
		String worldName = worldFolder.getName();
		if (!worldName.toLowerCase().equals(worldName)) {
			if (Game.debug) System.out.println("Renaming world in " + worldFolder + " to lowercase");
			String path = worldFolder.toString();
			path = path.substring(0, path.lastIndexOf(worldName));
			File newFolder = new File(path + worldName.toLowerCase());
			if (worldFolder.renameTo(newFolder))
				worldFolder = newFolder;
			else
				System.err.println("Failed to rename world folder " + worldFolder + " to " + newFolder);
		}
	}
	
	folder = worldFolder;
	location = worldFolder.getPath() + "/";
	
	folder.mkdirs();
}
 

/**
 * Returns an alternate path name for the given file
 * such that if the original pathname did not exist, then the
 * file may be located at the alternate location.
 * For mac, this replaces the final .dylib suffix with .jnilib
 */
static File mapAlternativeName(File lib) {
    String name = lib.toString();
    int index = name.lastIndexOf('.');
    if (index < 0) {
        return null;
    }
    return new File(name.substring(0, index) + ".jnilib");
}
 

/**
 * 获取工程路径
 *
 * @return
 */
public static String getProjectPath(String fileName, String relativeUiPath) {
	String projectPath = "";
	try {
		File file = new DefaultResourceLoader().getResource("").getFile();
		if (file != null) {
			while (true) {
				File f = new File(file.getPath() + File.separator + "src" + File.separator + "main");
				if (f == null || f.exists()) {
					break;
				}
				if (file.getParentFile() != null) {
					file = file.getParentFile();
				} else {
					break;
				}
			}
			if (!fileName.endsWith(DOT_JAVA) && isNotEmpty(relativeUiPath)) {
				File fileTemp = new File(file.getPath() + File.separator + relativeUiPath);
				if (fileTemp == null || fileTemp.exists()) {
					file = fileTemp;
				}
			}

			projectPath = file.toString();
		}
	} catch (IOException e) {
		e.printStackTrace();
	}
	return projectPath;
}
 

private void choosePhotoFromCamera() {
    String dir = getTakePhotoDir();
    File photoDir = new File(dir);
    if (!photoDir.exists()) {
        //noinspection ResultOfMethodCallIgnored
        photoDir.mkdirs();
    }
    File mCurrentFile = new File(dir, getPhotoName());
    mImagePath = mCurrentFile.toString();
    Intent intent = getCameraIntent(mCurrentFile);
    startActivityForResult(intent, ConstantData.REQUEST_CODE_TAKE_PHOTO);
    getActivity().overridePendingTransition(0, 0);
}
 

public final static  void destroyLocalFileSystem (String testName) throws IOException {            
    File mountPoint = TestUtilHid.locationOfTempFolder("lfstest");
    
    if (mountPoint.exists()) {
            if (TestUtilHid.deleteFolder(mountPoint) == false)
                throw new IOException("Cannot delete test folder: " + mountPoint.toString());
    }
    
}
 

/**
 * Add the .jar elements of a directory to the DCache classpath, optionally
 * recursively.
 */
private static void addDirToCache(File dir, FileSystem fs,
  Set<String> localUrls, boolean recursive) {
  if (dir != null) {
    File[] fileList = dir.listFiles();

    if (fileList != null) {
      for (File libFile : dir.listFiles()) {
        if (libFile.exists() && !libFile.isDirectory()
          && libFile.getName().endsWith("jar")) {
          Path p = new Path(libFile.toString());
          if (libFile.canRead()) {
            String qualified = p.makeQualified(fs).toString();
            LOG.info("Adding to job classpath: " + qualified);
            localUrls.add(qualified);
          } else {
            LOG.warn("Ignoring unreadable file " + libFile);
          }
        }
        if (recursive && libFile.isDirectory()) {
          addDirToCache(libFile, fs, localUrls, recursive);
        }
      }
    } else {
      LOG.warn("No files under " + dir
        + " to add to distributed cache for Accumulo job");
    }
  }
}
 

/**
 * Add the given fileName to the zip stream with the given entry name.
 * @param entryName the entry name
 * @param fileName the file name and path
 * @param zout the output stream
 * @throws IOException on error
 */
static void addFile(String entryName, String fileName, ZipOutputStream zout)
throws IOException {
	ZipEntry mf = new ZipEntry(entryName);
	File mfm = new File(fileName);
	if (mfm.canRead()) {
		mf.setSize(mfm.length());
		mf.setTime(mfm.lastModified());
		zout.putNextEntry(mf);
		zout.write(IOUtils.load(mfm));
	} else {
		throw new RuntimeException("File not found: " + mfm.toString());
	}
}
 

private DotNetCoreNugetInspector findDotnetCoreInspector(File nupkgFolder, String dotnetExecutable) throws DetectorException {
    //new inspector
    final String dotnetInspectorName = "BlackduckNugetInspector.dll";
    logger.info("Searching for: " + dotnetInspectorName);
    File toolsFolder = new File(nupkgFolder, "tools");
    Optional<File> foundExe = detectFileFinder.findFilesToDepth(toolsFolder, dotnetInspectorName, 3).stream().findFirst();
    if (foundExe.isPresent() && foundExe.get().exists()) {
        String inspectorExe = foundExe.get().toString();
        logger.info("Found nuget inspector: " + inspectorExe);
        return new DotNetCoreNugetInspector(dotnetExecutable, inspectorExe, executableRunner);
    } else {
        throw new DetectorException("Unable to find nuget inspector, looking for " + dotnetInspectorName + " in " + toolsFolder.toString());
    }
}
 

private File extractAssetToCacheDirectory(String assetPath, String filename, boolean force)
        throws ProoferException {
    File outFile = new File(Util.getCacheDirectory(), filename);
    if (force || !outFile.exists()) {
        if (!Util.extractResource("assets/" + assetPath, outFile)) {
            throw new ProoferException("Error extracting to " + outFile.toString());
        }
    }
    return outFile;
}
 

/**
 * Exports the generated report file specified by the parameter into PDF format.
 * The resulting PDF file has the same name as the report object inside the source file,
 * plus the <code>*.pdf</code> extension and it is located in the same directory as the source file.
 *  
 * @param sourceFileName source file containing the generated report
 * @return resulting PDF file name
 * @see net.sf.jasperreports.engine.export.JRPdfExporter
 */
public String exportToPdfFile(String sourceFileName) throws JRException
{
	File sourceFile = new File(sourceFileName);

	/* We need the report name. */
	JasperPrint jasperPrint = (JasperPrint)JRLoader.loadObject(sourceFile);

	File destFile = new File(sourceFile.getParent(), jasperPrint.getName() + ".pdf");
	String destFileName = destFile.toString();
	
	exportToPdfFile(jasperPrint, destFileName);
	
	return destFileName;
}
 

public static boolean deleteDirectory(String path,String fileName) {
	boolean status;
	SecurityManager checker = new SecurityManager();

	if (!fileName.equals("")) {

		File newPath = new File(path.toString() + fileName);
		checker.checkDelete(newPath.toString());
		if (newPath.isDirectory()) {
			String[] listfile = newPath.list();
			try {
				for (int i = 0; i < listfile.length; i++) {
					File deletedFile = new File(newPath.toString() + "/"
							+ listfile[i].toString());
					deletedFile.delete();
				}
				newPath.delete();
				System.out.println("DirectoryManager deleteDirectory"+ fileName);
				status = true;
			} catch (Exception e) {
				e.printStackTrace();
				status = false;
			}

		} else
			status = false;
	} else
		status = false;
	return status;
}
 

public static void main(String[] args) throws Exception {
	final OptionParser parser = new OptionParser();

	final OptionSpec<Void> help = parser.acceptsAll(Arrays.asList("help")).forHelp();
	final OptionSpec<String> schema = parser.accepts("schema").withOptionalArg()
			.describedAs("The schema is written to standard output.");
	final OptionSpec<String> withHeader = parser.accepts("with-header").withOptionalArg()
			.describedAs("When with-header is included, a header line of column names is written to each data file.");
	final OptionSpec<File> input = parser.accepts("input").withRequiredArg().ofType(File.class).required()
			.describedAs("The input accdb file.");
	final OptionSpec<String> table = parser.accepts("table").withRequiredArg().ofType(String.class).describedAs("The table name to export, or all if it is not specified.");
	final OptionSpec<File> output = parser.accepts("output").requiredUnless("schema").withRequiredArg().ofType(File.class)
			.describedAs("The output directory for data files. This is required for writing data output. This not required for schema output.");
	final OptionSpec<String> csvPrefix = parser.accepts("csv-prefix").withRequiredArg().ofType(String.class).defaultsTo("").describedAs("A prefix to add to all of the generated CSV file names");    
	final OptionSpec<Boolean> quoteAll = parser.accepts("quote-all").withOptionalArg().ofType(Boolean.class).defaultsTo(true)
			.describedAs("Set quote-all to true if all values are to be quoted. " +
			"Set to false if quotes are only to be applied to values which contain " + 
			"the separator, secape, quote, or new line characters. The default is true.");
	final OptionSpec<String> writeNull = parser.accepts("write-null").withOptionalArg().ofType(String.class).defaultsTo("")
			.describedAs("The text to write when entry is NULL. Defaults to empty output if not specified or if no argument supplied. " +
			"If quote-all is set to true then the value for write-null is also quoted.");
  
   
	OptionSet options = null;

	try {
		options = parser.parse(args);
	} catch (final OptionException e) {
		System.out.println(e.getMessage());
		parser.printHelpOn(System.out);
		throw e;
	}

	if (options.has(help)) {
		parser.printHelpOn(System.out);
		return;
	}
     
	File inputFile = input.value(options);
	if(!inputFile.exists()) {
		throw new FileNotFoundException("Could not find input file: " + inputFile.toString());
	}
	
	File outputDir = null;
	if (options.has(output)) {
		outputDir = output.value(options);
		if(!outputDir.exists()) {
			outputDir.mkdirs();
		}	
	}
   		
	boolean applyQuotesToAll = quoteAll.value(options);    
   String nullText = writeNull.value(options);
   
	if (options.has(schema)) {
		schema(inputFile);
	}
	
	if (null != outputDir) {
		if (options.has(table)){
			export(inputFile, table.value(options), options.has(withHeader), outputDir, csvPrefix.value(options), applyQuotesToAll, nullText);
		}
		else {
			exportAll(inputFile, options.has(withHeader), outputDir, csvPrefix.value(options), applyQuotesToAll, nullText);
		}	
	}
}
 

public String getFileName() {
	File f = getFile();
	return f == null ? null : f.toString();
}
 

/**
 * Saves the EGL surface to a file.
 * <p>
 * Expects that this object's EGL surface is current.
 */
public void saveFrame(File file) throws IOException {
    if (!mEglCore.isCurrent(mEGLSurface)) {
        throw new RuntimeException("Expected EGL context/surface is not current");
    }

    // glReadPixels fills in a "direct" ByteBuffer with what is essentially big-endian RGBA
    // data (i.e. a byte of red, followed by a byte of green...).  While the Bitmap
    // constructor that takes an int[] wants little-endian ARGB (blue/red swapped), the
    // Bitmap "copy pixels" method wants the same format GL provides.
    //
    // Ideally we'd have some way to re-use the ByteBuffer, especially if we're calling
    // here often.
    //
    // Making this even more interesting is the upside-down nature of GL, which means
    // our output will look upside down relative to what appears on screen if the
    // typical GL conventions are used.

    String filename = file.toString();

    int width = getWidth();
    int height = getHeight();
    ByteBuffer buf = ByteBuffer.allocateDirect(width * height * 4);
    buf.order(ByteOrder.LITTLE_ENDIAN);
    GLES20.glReadPixels(0, 0, width, height,
            GLES20.GL_RGBA, GLES20.GL_UNSIGNED_BYTE, buf);
    GlUtil.checkGlError("glReadPixels");
    buf.rewind();

    BufferedOutputStream bos = null;
    try {
        bos = new BufferedOutputStream(new FileOutputStream(filename));
        Bitmap bmp = Bitmap.createBitmap(width, height, Bitmap.Config.ARGB_8888);
        bmp.copyPixelsFromBuffer(buf);
        bmp.compress(Bitmap.CompressFormat.PNG, 90, bos);
        bmp.recycle();
    } finally {
        if (bos != null)
            bos.close();
    }
    Log.d(TAG, "Saved " + width + "x" + height + " frame as '" + filename + "'");
}
 

@Deprecated
public Config(File file, int type, LinkedHashMap<String, Object> defaultMap) {
    this(file.toString(), type, new ConfigSection(defaultMap));
}
 

private void addComponents() {
    Property property = getProperty();
    try {
        Template template = this.modifiedParameter.getTemplate();
        property.setValue(template.getPath());
    } catch (ValidationException e) {
        logger.warning(e.getMessage());
    }

    FileEditor fileEditor = new FileEditor();
    JComponent filePathComponent = fileEditor.createEditorComponent(property.getDescriptor(), this.paramContext);
    filePathComponent.setPreferredSize(new Dimension(770, 25));

    JPanel topPanel = new JPanel(new BorderLayout());
    JPanel filePanel = new JPanel();
    final JLabel label = new JLabel("File:");
    filePanel.add(label);
    filePanel.add(filePathComponent);
    topPanel.add(filePanel, BorderLayout.NORTH);

    JPanel outFilePanel = new JPanel();
    final JLabel jLabel = new JLabel("Output File:");
    outFilePanel.add(jLabel);
    File outputFile = this.modifiedParameter.getOutputFile();
    outFileName = new JTextField(outputFile != null ? outputFile.toString() : "");
    outFileName.setPreferredSize(
            new Dimension(filePathComponent.getPreferredSize().width + label.getPreferredSize().width - jLabel.getPreferredSize().width, 25));
    org.esa.snap.utils.UIUtils.addPromptSupport(outFileName, "Enter the name of transformed file here");
    outFilePanel.add(outFileName);
    topPanel.add(outFilePanel, BorderLayout.WEST);

    JPanel mainPanel = new JPanel(new BorderLayout());
    mainPanel.setPreferredSize(new Dimension(800, 550));
    mainPanel.add(topPanel, BorderLayout.PAGE_START);

    //to create UI component for outputFile
    fileContentArea.setAutoCompleteEntries(getAutocompleteEntries());
    fileContentArea.setTriggerChar('$');
    mainPanel.add(new JScrollPane(fileContentArea), BorderLayout.CENTER);

    updateFileAreaContent();

    mainPanel.add(createParametersPanel(), BorderLayout.PAGE_END);

    setContent(mainPanel);
}
 

/**
 * For a given normal or tumor BAM file, walks through the list of common SNPs,
 * {@link BayesianHetPulldownCalculator#snpIntervals}), detects heterozygous sites, and returns
 * a {@link Pulldown} containing detailed information on the called heterozygous SNP sites.
 *
 * The {@code hetCallingStrigency} parameters sets the threshold posterior for calling a Het SNP site:
 *
 *      hetPosteriorThreshold = 1 - 10^{-hetCallingStringency}
 *      hetThresholdLogOdds = log(hetPosteriorThreshold/(1-hetPosteriorThreshold))
 *                          = log(10^{hetCallingStringency} - 1)
 *
 * (see CNV-methods.pdf for details)
 *
 * @param bamFile sorted BAM file for sample
 * @param hetCallingStringency strigency for calling a Het site
 * @return Pulldown of heterozygous SNP sites in 1-based format
 */
public Pulldown getHetPulldown(final File bamFile, final double hetCallingStringency) {
    /* log odds from stringency */
    final double hetThresholdLogOdds = FastMath.log(FastMath.pow(10, hetCallingStringency) - 1);

    try (final SamReader bamReader = SamReaderFactory.makeDefault().validationStringency(validationStringency)
            .referenceSequence(refFile).open(bamFile);
         final ReferenceSequenceFileWalker refWalker = new ReferenceSequenceFileWalker(refFile)) {
        if (bamReader.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
            throw new UserException.BadInput("BAM file " + bamFile.toString() + " must be coordinate sorted.");
        }

        final Pulldown hetPulldown = new Pulldown(bamReader.getFileHeader());
        final SamLocusIterator locusIterator = getSamLocusIteratorWithDefaultFilters(bamReader);

        final int totalNumberOfSNPs = snpIntervals.size();
        logger.info("Examining " + totalNumberOfSNPs + " sites in total...");
        int locusCount = 0;
        for (final SamLocusIterator.LocusInfo locus : locusIterator) {
            if (locusCount % NUMBER_OF_SITES_PER_LOGGED_STATUS_UPDATE == 0) {
                logger.info("Examined " + locusCount + " covered sites.");
            }
            locusCount++;

            final int totalReadCount = locus.getRecordAndOffsets().size();
            if (totalReadCount <= readDepthThreshold) {
                continue;
            }
            final Nucleotide refBase = Nucleotide.valueOf(refWalker.get(locus.getSequenceIndex())
                    .getBases()[locus.getPosition() - 1]);
            if (!isProperBase(refBase)) {
                logger.warn(String.format("The reference position at %d has an unknown base call (value: %s). Even though" +
                        " this position is indicated to be a possible heterozygous SNP in the provided SNP interval list," +
                        " no inference can be made. Continuing ...", locus.getPosition(), refBase.toString()));
                continue;
            }

            final Map<Nucleotide, List<BaseQuality>> baseQualities = getPileupBaseQualities(locus);
            final Nucleotide altBase = inferAltFromPileup(baseQualities, refBase);

            /* calculate Het log odds */
            final double hetLogLikelihood = getHetLogLikelihood(baseQualities, refBase, altBase);
            final double homLogLikelihood = getHomLogLikelihood(baseQualities, refBase, altBase,
                    DEFAULT_PRIOR_REF_HOM);
            final double hetLogOdds = (hetLogLikelihood + FastMath.log(DEFAULT_PRIOR_HET)) -
                    (homLogLikelihood + FastMath.log(1 - DEFAULT_PRIOR_HET));

            if (hetLogOdds > hetThresholdLogOdds) {
                hetPulldown.add(new AllelicCount(
                        new SimpleInterval(locus.getSequenceName(), locus.getPosition(), locus.getPosition()),
                        baseQualities.get(refBase).size(), baseQualities.get(altBase).size(),
                        refBase, altBase, totalReadCount, hetLogOdds));
            }
        }

        logger.info(locusCount + " covered sites out of " + totalNumberOfSNPs + " total sites were examined.");

        return hetPulldown;

    } catch (final IOException | SAMFormatException e) {
        throw new UserException(e.getMessage());
    }
}