下面列出了java.io.File#toString ( ) 实例代码，或者点击链接到github查看源代码，也可以在右侧发表评论。
@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));
}
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();
}
/**
* 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;
}
@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);
}
/**
* 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());
}
}
/**
* 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");
}
}
}
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;
}
/**
* 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());
}
}
@Deprecated
public Config(File file, int type, LinkedHashMap<String, Object> defaultMap) {
this(file.toString(), type, new ConfigSection(defaultMap));
}
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 + "'");
}
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);
}