protected void load(ZipFile zipfile) throws IOException {
Enumeration entries = zipfile.entries();
while (entries.hasMoreElements()) {
ZipEntry entry = (ZipEntry) entries.nextElement();
fireBeginFile(entry.getName());
Logger.getLogger(getClass())
.debug("Starting file " + entry.getName() + " (" + entry.getSize() + " bytes)");
byte[] bytes = null;
InputStream in = null;
try {
in = zipfile.getInputStream(entry);
bytes = readBytes(in);
} finally {
if (in != null) {
try {
in.close();
} catch (IOException ex) {
// Ignore
}
}
}
Logger.getLogger(getClass())
.debug("Passing up file " + entry.getName() + " (" + bytes.length + " bytes)");
getLoader().load(entry.getName(), new ByteArrayInputStream(bytes));
fireEndFile(entry.getName());
}
}
protected void load(String filename, InputStream in) {
Logger.getLogger(getClass()).debug("Starting group in stream " + filename);
ZipInputStream zipfile = null;
try {
zipfile = new ZipInputStream(in);
fireBeginGroup(filename, -1);
Logger.getLogger(getClass()).debug("Loading ZipInputStream " + filename);
load(zipfile);
Logger.getLogger(getClass()).debug("Loaded ZipInputStream " + filename);
fireEndGroup(filename);
} catch (IOException ex) {
Logger.getLogger(getClass()).error("Cannot load Zip file \"" + filename + "\"", ex);
} finally {
if (zipfile != null) {
try {
zipfile.close();
} catch (IOException ex) {
// Ignore
}
}
}
}
/* Check: getLoggerNames() must return correct names
* for registered loggers and their parents.
* Returns boolean values: PASSED or FAILED
*/
public static boolean checkLoggers() {
String failMsg = "# checkLoggers: getLoggerNames() returned unexpected loggers";
Vector<String> expectedLoggerNames = new Vector<String>(getDefaultLoggerNames());
// Create the logger LOGGER_NAME_1
Logger.getLogger(LOGGER_NAME_1);
expectedLoggerNames.addElement(PARENT_NAME_1);
expectedLoggerNames.addElement(LOGGER_NAME_1);
// Create the logger LOGGER_NAME_2
Logger.getLogger(LOGGER_NAME_2);
expectedLoggerNames.addElement(PARENT_NAME_2);
expectedLoggerNames.addElement(LOGGER_NAME_2);
Enumeration<String> returnedLoggersEnum = logMgr.getLoggerNames();
Vector<String> returnedLoggerNames = new Vector<String>(0);
while (returnedLoggersEnum.hasMoreElements()) {
String logger = returnedLoggersEnum.nextElement();
if (!initialLoggerNames.contains(logger)) {
// filter out the loggers that have been added before this test runs
returnedLoggerNames.addElement(logger);
}
}
;
return checkNames(expectedLoggerNames, returnedLoggerNames, failMsg);
}
public static synchronized void createLoggers(boolean reinit) {
if (m_initialized == true && reinit == false) {
return;
}
if (!m_initialized) {
Logger.getLogger("").removeHandler(Logger.getLogger("").getHandlers()[0]);
}
if (m_initialized) {
m_severeLogger.removeHandler(m_severeLogger.getHandlers()[0]);
m_nonSevereLogger.removeHandler(m_nonSevereLogger.getHandlers()[0]);
}
Handler severeHandler = new AMyConsoleHandler(System.err);
severeHandler.setFormatter(new SingleLineFormatter());
m_severeLogger.addHandler(severeHandler);
m_severeLogger.setLevel(getLoggingLevel());
Handler nonSevereHandler = new AMyConsoleHandler(System.out);
nonSevereHandler.setFormatter(new SingleLineFormatter());
m_nonSevereLogger.addHandler(nonSevereHandler);
m_nonSevereLogger.setLevel(getLoggingLevel());
m_initialized = true;
}
public LocalVariableTable_attribute(ConstantPool constantPool, Visitable owner, DataInput in)
throws IOException {
super(constantPool, owner);
int byteCount = in.readInt();
Logger.getLogger(getClass()).debug("Attribute length: " + byteCount);
int localVariableTableLength = in.readUnsignedShort();
Logger.getLogger(getClass())
.debug("Reading " + localVariableTableLength + " local variable(s) ...");
for (int i = 0; i < localVariableTableLength; i++) {
Logger.getLogger(getClass()).debug("Local variable " + i + ":");
localVariables.add(new LocalVariable(this, in));
}
}
public void summaryAction(HttpServletRequest req, HttpServletResponse res) {
if (AccountController.redirectIfNoCookie(req, res)) return;
Map<String, Object> viewData = new HashMap<String, Object>();
DocumentManager docMan = new DocumentManager();
try {
if (req.getParameter("documentId") != null) {
// Get the document ID
int docId = Integer.parseInt(req.getParameter("documentId"));
// Get the document using document id
Document document = docMan.get(docId);
// Set title to name of the document
viewData.put("title", document.getDocumentName());
// Create List of access records
List<AccessRecord> accessRecords = new LinkedList<AccessRecord>();
// Add access records for document to the list
accessRecords = docMan.getAccessRecords(docId);
viewData.put("accessRecords", accessRecords);
} else {
// Go back to thread page.
}
} catch (Exception e) {
Logger.getLogger("").log(Level.SEVERE, "An error occurred when getting profile user", e);
}
view(req, res, "/views/group/Document.jsp", viewData);
}
/** Creates a new AjaxMetricsFilterConfiguration populated with the default values. */
protected AjaxMetricsFilterConfiguration() {
log = Logger.getLogger(getClass());
// ==========================================================================
// Set default property values
// ==========================================================================
parameterNames.put(pUri, "AG_U");
parameterNames.put(pElapsed, "AG_E");
parameterNames.put(pConcurrent, "AG_C");
parameterNames.put(pException, "AG_X");
parameterNames.put(pHcode, "AG_H");
parameterNames.put(pDelta, "AG_D");
parameterNames.put(pFailure, "AG_F");
parameterNames.put(pInteractive, "AG_I");
parameterNames.put(pInteractiveTime, "AG_T");
parameterNames.put(pInteractiveCallbacks, "AG_B");
parameterNames.put(pSerialNumber, "AG_S");
parameterNames.put(pParameter, "AG_P");
parameterNames.put(pRunOption, "AG_O");
runOptions.put(reportInteractive, false);
runOptions.put(reportDelta, true);
runOptions.put(logging, false);
runOptions.put(uploadBatch, false);
runOptions.put(uploadInParams, false);
batchOptions.put(batchTime, 40);
batchOptions.put(batchSize, 5);
}
protected void load(ZipInputStream in) throws IOException {
ZipEntry entry;
while ((entry = in.getNextEntry()) != null) {
fireBeginFile(entry.getName());
Logger.getLogger(getClass())
.debug("Starting file " + entry.getName() + " (" + entry.getSize() + " bytes)");
byte[] bytes = readBytes(in);
Logger.getLogger(getClass())
.debug("Passing up file " + entry.getName() + " (" + bytes.length + " bytes)");
getLoader().load(entry.getName(), new ByteArrayInputStream(bytes));
fireEndFile(entry.getName());
}
}
/**
* Main method. Begins the GUI, and the rest of the program.
*
* @param args the command line arguments
*/
public static void main(String args[]) {
// playSound();
try {
for (UIManager.LookAndFeelInfo info : UIManager.getInstalledLookAndFeels()) {
if ("Nimbus".equals(info.getName())) {
UIManager.setLookAndFeel(info.getClassName());
break;
}
}
} catch (ClassNotFoundException
| InstantiationException
| IllegalAccessException
| UnsupportedLookAndFeelException ex) {
Logger.getLogger(mainForm.class.getName()).log(Level.SEVERE, null, ex);
}
// </editor-fold>
/* Create and display the form */
EventQueue.invokeLater(
new Runnable() {
@Override
public void run() {
new mainForm().setVisible(true);
}
});
}
/** @author Symphorien Wanko */
public class PopupMessageHandlerSLick extends TestSuite implements BundleActivator {
/** Logger for this class */
private static Logger logger = Logger.getLogger(PopupMessageHandlerSLick.class);
/** our bundle context */
protected static BundleContext bundleContext = null;
/** implements BundleActivator.start() */
public void start(BundleContext bc) throws Exception {
logger.info("starting popup message test ");
bundleContext = bc;
setName("PopupMessageHandlerSLick");
Hashtable<String, String> properties = new Hashtable<String, String>();
properties.put("service.pid", getName());
// we maybe are running on machine without WM and systray
// (test server machine), skip tests
if (ServiceUtils.getService(bc, SystrayService.class) != null) {
addTest(TestPopupMessageHandler.suite());
}
bundleContext.registerService(getClass().getName(), this, properties);
}
/** implements BundleActivator.stop() */
public void stop(BundleContext bc) throws Exception {}
}
public void preprocess(Run run) {
File logFile = new File(getRunDir(run), "genetik.log");
try {
SimpleFileHandler fh = new SimpleFileHandler(logFile);
fh.setFormatter(new CompactFormatter());
Logger logger = Logger.getLogger(GenetikConstants.LOGGER);
logger.setLevel(Level.INFO);
logger.setUseParentHandlers(false);
Handler handlers[] = logger.getHandlers();
logger.addHandler(fh);
for (Handler h : handlers) {
logger.removeHandler(h);
if (h instanceof SimpleFileHandler) h.close(); // close our old one
}
} catch (Exception exp) {
throw new IllegalArgumentException(
"Unable to create log file at " + logFile.getAbsolutePath());
}
super.preprocess(run);
}
/**
* Add a named logger. This does nothing and returns false if a logger
* with the same name is already registered.
* <p>
* The Logger factory methods call this method to register each
* newly created Logger.
* <p>
* The application should retain its own reference to the Logger
* object to avoid it being garbage collected. The LogManager
* may only retain a weak reference.
*
* @param logger the new logger.
* @return true if the argument logger was registered successfully,
* false if a logger of that name already exists.
* @exception NullPointerException if the logger name is null.
*/
public synchronized boolean addLogger(Logger logger) {
String name = logger.getName();
if (name == null) {
throw new NullPointerException();
}
Logger old = (Logger) loggers.get(name);
if (old != null) {
// We already have a registered logger with the given name.
return false;
}
// We're adding a new logger.
// Note that we are creating a strong reference here that will
// keep the Logger in existence indefinitely.
loggers.put(name, logger);
// Apply any initial level defined for the new logger.
Level level = getLevelProperty(name+".level", null);
if (level != null) {
doSetLevel(logger, level);
}
// If any of the logger's parents have levels defined,
// make sure they are instantiated.
int ix = 1;
for (;;) {
int ix2 = name.indexOf(".", ix);
if (ix2 < 0) {
break;
}
String pname = name.substring(0,ix2);
if (getProperty(pname+".level") != null) {
// This pname has a level definition. Make sure it exists.
Logger plogger = Logger.getLogger(pname);
}
ix = ix2+1;
}
// Find the new node and its parent.
LogNode node = findNode(name);
node.logger = logger;
Logger parent = null;
LogNode nodep = node.parent;
while (nodep != null) {
if (nodep.logger != null) {
parent = nodep.logger;
break;
}
nodep = nodep.parent;
}
if (parent != null) {
doSetParent(logger, parent);
}
// Walk over the children and tell them we are their new parent.
node.walkAndSetParent(logger);
return true;
}
public class IdlePointCron extends HttpServlet {
/** */
private static final long serialVersionUID = 1L;
private static final Logger log = Logger.getLogger(IdlePointCron.class.getName());
@Override
@SuppressWarnings(Const.WARNING_UNCHECKED)
public void doGet(final HttpServletRequest req, final HttpServletResponse resp)
throws IOException {
// PrintWriter out;
// out = resp.getWriter();
try {
processGet();
} catch (NimbitsException e) {
LogHelper.logException(IdlePointCron.class, e);
}
}
protected static int processGet() throws NimbitsException {
final List<Entity> points = EntityServiceFactory.getInstance().getIdleEntities();
log.info("Processing " + points.size() + " potentially idle points");
for (final Entity p : points) {
try {
checkIdle((Point) p);
} catch (NimbitsException e) {
LogHelper.logException(IdlePointCron.class, e);
}
}
return points.size();
}
protected static boolean checkIdle(final Point p) throws NimbitsException {
final Calendar c = Calendar.getInstance();
c.add(Calendar.SECOND, p.getIdleSeconds() * -1);
boolean retVal = false;
final List<Entity> result =
EntityServiceFactory.getInstance()
.getEntityByKey(
UserServiceFactory.getServerInstance().getAdmin(), p.getOwner(), EntityType.user);
if (!result.isEmpty()) {
final User u = (User) result.get(0);
final List<Value> v = ValueServiceFactory.getInstance().getCurrentValue(p);
if (p.getIdleSeconds() > 0
&& !v.isEmpty()
&& v.get(0).getTimestamp().getTime() <= c.getTimeInMillis()
&& !p.getIdleAlarmSent()) {
p.setIdleAlarmSent(true);
EntityServiceFactory.getInstance().addUpdateEntity(u, p);
// PointServiceFactory.getInstance().updatePoint(u, p);
final Value va = ValueFactory.createValueModel(v.get(0), AlertType.IdleAlert);
SubscriptionServiceFactory.getInstance().processSubscriptions(u, p, va);
retVal = true;
}
}
return retVal;
}
}
/** Export to an ARC file */
public class ArcExporter extends Exporter {
private static Logger log = Logger.getLogger("ArcExporter");
protected CIProperties arcProps = null;
String arcFilePrefix = "SimulatedCrawl";
AtomicInteger serialNo = new AtomicInteger(0);
ARCWriter aw;
boolean isResponse;
public ArcExporter(LockssDaemon daemon, ArchivalUnit au, boolean isResponse) {
super(daemon, au);
this.isResponse = isResponse;
}
protected void start() {
aw = makeARCWriter();
}
protected void finish() throws IOException {
aw.close();
}
private ARCWriter makeARCWriter() {
return new ARCWriter(
serialNo, ListUtil.list(dir), prefix, compress, maxSize >= 0 ? maxSize : Long.MAX_VALUE);
}
protected void writeCu(CachedUrl cu) throws IOException {
String url = cu.getUrl();
long contentSize = cu.getContentSize();
CIProperties props = cu.getProperties();
long fetchTime = Long.parseLong(props.getProperty(CachedUrl.PROPERTY_FETCH_TIME));
InputStream contentIn = cu.getUnfilteredInputStream();
try {
if (isResponse) {
String hdrString = getHttpResponseString(cu);
long size = contentSize + hdrString.length();
InputStream headerIn = new ReaderInputStream(new StringReader(hdrString));
InputStream concat = new SequenceInputStream(headerIn, contentIn);
try {
aw.write(xlateFilename(url), cu.getContentType(), getHostIp(), fetchTime, size, concat);
} finally {
IOUtil.safeClose(concat);
}
} else {
aw.write(
xlateFilename(url),
cu.getContentType(),
getHostIp(),
fetchTime,
cu.getContentSize(),
contentIn);
}
} finally {
AuUtil.safeRelease(cu);
}
}
}
// @Override
public synchronized String getIP() {
try {
return NetUtils.getIPAddress();
} catch (ConnectException ex) {
Logger.getLogger(Mapa.class.getName()).log(Level.SEVERE, null, ex);
}
return "";
}
public void actionPerformed(ActionEvent e) {
try {
undo.redo();
} catch (CannotRedoException ex) {
Logger.getLogger(RedoAction.class.getName()).log(Level.SEVERE, "Unable to redo", ex);
}
update();
undoAction.update();
}
DBPort(InetSocketAddress addr, DBPortPool pool, MongoOptions options) throws IOException {
_options = options;
_addr = addr;
_pool = pool;
_hashCode = _addr.hashCode();
_logger = Logger.getLogger(_rootLogger.getName() + "." + addr.toString());
}
/**
* Construye el objeto que gestionara la comunicacion de datos.
*
* @param s Socket de conexion.
* @throws Exception
*/
public DataAttendant(Socket s) throws Exception {
mylogger = Logger.getLogger("isabel.nereda.DataAttendant");
mylogger.fine("Creating DataAttendant object.");
sock = s;
myPP = new PacketProcessor(sock);
NeReDa.peers.Add(this);
}
/** Test class for <code>org.lockss.scheduler.StepperTask</code> */
public class TestStepperTask extends LockssTestCase {
public static Class testedClasses[] = {
org.lockss.scheduler.StepTask.class, org.lockss.scheduler.StepperTask.class,
};
static Logger log = Logger.getLogger("TestStepperTask");
public void setUp() throws Exception {
super.setUp();
TimeBase.setSimulated();
}
public void tearDown() throws Exception {
TimeBase.setReal();
super.tearDown();
}
static StepperTask taskBetween(long minStart, long deadline, int duration, Stepper stepper) {
return new StepperTask(
Deadline.at(minStart), Deadline.at(deadline), duration, null, null, stepper);
}
Stepper newSt(final boolean isFinished) {
return new Stepper() {
public int computeStep(int metric) {
return 0;
}
public boolean isFinished() {
return isFinished;
}
};
}
public void testStepper() {
Stepper st = newSt(false);
StepperTask t = taskBetween(100, 200, 50, st);
assertEquals(st, t.getStepper());
assertFalse(t.isBackgroundTask());
assertFalse(t.isFinished());
t.e = new Exception();
assertTrue(t.isFinished());
Stepper st2 = newSt(true);
StepperTask t2 = taskBetween(100, 200, 50, st2);
assertTrue(t2.isFinished());
}
public void testToString() {
Stepper st = newSt(false);
StepperTask t = taskBetween(100, 200, 50, st);
t.toString();
t.cookie = "foo";
t.toString();
}
}
@Override
public void delete(IMatchresultDto value) {
try {
server.domain.classes.Matchresult matchresult = createDomain(value);
DomainFacade.getInstance().delete(matchresult);
} catch (IdNotFoundException | CouldNotDeleteException ex) {
Logger.getLogger(MatchresultMapper.class.getName()).log(Level.SEVERE, null, ex);
}
}
/**
* The <tt>Resources</tt> class manages the access to the internationalization properties files and
* the image resources used in this plugin.
*
* @author Yana Stamcheva
*/
public class Resources {
private static Logger log = Logger.getLogger(Resources.class);
/** The name of the resource, where internationalization strings for this plugin are stored. */
private static final String STRING_RESOURCE_NAME =
"resources.languages.plugin.contactinfo.resources";
/** The name of the resource, where paths to images used in this bundle are stored. */
private static final String IMAGE_RESOURCE_NAME =
"net.java.sip.communicator.plugin.contactinfo.resources";
/** The string resource bundle. */
private static final ResourceBundle STRING_RESOURCE_BUNDLE =
ResourceBundle.getBundle(STRING_RESOURCE_NAME);
/** The image resource bundle. */
private static final ResourceBundle IMAGE_RESOURCE_BUNDLE =
ResourceBundle.getBundle(IMAGE_RESOURCE_NAME);
/**
* Returns an internationalized string corresponding to the given key.
*
* @param key The key of the string.
* @return An internationalized string corresponding to the given key.
*/
public static String getString(String key) {
try {
return STRING_RESOURCE_BUNDLE.getString(key);
} catch (MissingResourceException e) {
return '!' + key + '!';
}
}
/**
* Loads an image from a given image identifier.
*
* @param imageID The identifier of the image.
* @return The image for the given identifier.
*/
public static ImageIcon getImage(String imageID) {
BufferedImage image = null;
String path = IMAGE_RESOURCE_BUNDLE.getString(imageID);
try {
image = ImageIO.read(Resources.class.getClassLoader().getResourceAsStream(path));
} catch (IOException e) {
log.error("Failed to load image:" + path, e);
}
return new ImageIcon(image);
}
}
public class TestElsevierXmlLinkExtractorFactory extends LinkExtractorTestCase {
private static Logger logger = Logger.getLogger("TestElsevierXmlLinkExtractorFactory");
String srcUrl = "http://www.example.com/";
private static final String withLinks =
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
+ "<!DOCTYPE dataset SYSTEM \"http://support.sciencedirect.com/xml/sdosftp10.dtd\">\n"
+ "<dataset identifier=\"OXM10160\" customer=\"OHL\""
+ " status=\"Announcement\""
+ " version=\"Network Dataset Announcement/Confirmation v1.0\">"
+ " <date year=\"2007\" month=\"May\" day=\"1\"/>\n"
+ "<file name=\"01407007.tar\" size=\"21780480\""
+ " md5=\"6c7266e0e246bf3e8cf1cd8b659a7a73\"/>\n"
+ "<file name=\"03064530.tar\" size=\"12748800\""
+ " md5=\"df9519d3075e164d22f5dd4988a693c3\"/>\n"
+ "<file name=\"dataset.toc\" size=\"2216587\""
+ " md5=\"cd21741eb91fa0fdfef2fa36485e21a0\"/>\n"
+ "</dataset>\n";
private static final String withoutLinks =
"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
+ "<!DOCTYPE dataset SYSTEM \"http://support.sciencedirect.com/xml/sdosftp10.dtd\">\n"
+ "<dataset identifier=\"OXM10160\" customer=\"OHL\""
+ " status=\"Announcement\""
+ " version=\"Network Dataset Announcement/Confirmation v1.0\">"
+ " <date year=\"2007\" month=\"May\" day=\"1\"/>\n"
+ "</dataset>\n";
private static final String[] links = {
"01407007.tar", "03064530.tar", "dataset.toc",
};
public String getMimeType() {
return "text/xml";
}
public LinkExtractorFactory getFactory() {
return new ElsevierXmlLinkExtractorFactory();
}
public void testFindCorrectEntries() throws Exception {
Set expected = new HashSet();
for (String link : links) {
expected.add(srcUrl + link);
}
assertEquals(expected, extractUrls(withLinks));
}
public void testFindNoEntries() throws Exception {
assertEmpty(extractUrls(withoutLinks));
}
}
@Override
public Integer set(IMatchresultDto value) {
try {
server.domain.classes.Matchresult matchresult = createDomain(value);
return DomainFacade.getInstance().set(matchresult);
} catch (IdNotFoundException | CouldNotSaveException ex) {
Logger.getLogger(MatchresultMapper.class.getName()).log(Level.SEVERE, null, ex);
}
return 0;
}
/** * 这是LWTownIndicatorAppend-直供乡追加电费指针记录表的数据访问对象类<br> * 创建于 2008-12-17 11:27:43.218<br> * JToolpad(1.6.0) Vendor:[email protected] */ public class DBLwTownIndicatorAppend extends DBLwTownIndicatorAppendBase { private static Logger logger = Logger.getLogger(DBLwTownIndicatorAppend.class); /** * 构造函数 * * @param dbManager 资源管理类 */ public DBLwTownIndicatorAppend(DBManager dbManager) { super(dbManager); } }
@Override
@SuppressWarnings("SleepWhileHoldingLock")
public void run() {
try {
// initialize the statusbar
status.removeAll();
JProgressBar progress = new JProgressBar();
progress.setMinimum(0);
progress.setMaximum(doc.getLength());
status.add(progress);
status.revalidate();
// start writing
Writer out = new FileWriter(f);
Segment text = new Segment();
text.setPartialReturn(true);
int charsLeft = doc.getLength();
int offset = 0;
while (charsLeft > 0) {
doc.getText(offset, Math.min(4096, charsLeft), text);
out.write(text.array, text.offset, text.count);
charsLeft -= text.count;
offset += text.count;
progress.setValue(offset);
try {
Thread.sleep(10);
} catch (InterruptedException e) {
Logger.getLogger(FileSaver.class.getName()).log(Level.SEVERE, null, e);
}
}
out.flush();
out.close();
} catch (IOException e) {
final String msg = e.getMessage();
SwingUtilities.invokeLater(
new Runnable() {
public void run() {
JOptionPane.showMessageDialog(
getFrame(),
"Could not save file: " + msg,
"Error saving file",
JOptionPane.ERROR_MESSAGE);
}
});
} catch (BadLocationException e) {
System.err.println(e.getMessage());
}
// we are done... get rid of progressbar
status.removeAll();
status.revalidate();
}
public static TypeList load(String gamePath, String dataName) {
System.out.println("load:" + dataName);
InputStream is = null;
Savable sav = null;
try {
File file =
new File(
System.getProperty("user.dir")
+ File.separator
+ gamePath
+ File.separator
+ dataName);
if (!file.exists()) {
return null;
}
is = new BufferedInputStream(new FileInputStream(file));
// is = new GZIPInputStream(new BufferedInputStream(new FileInputStream(file)));
XMLImporter imp = XMLImporter.getInstance();
// if (manager != null) {
// imp.setAssetManager(manager);
// }
sav = imp.load(is);
} catch (IOException ex) {
Logger.getLogger(Type.class.getName()).log(Level.SEVERE, "Error loading data: {0}", ex);
ex.printStackTrace();
} finally {
if (is != null) {
try {
is.close();
} catch (IOException ex) {
Logger.getLogger(Type.class.getName()).log(Level.SEVERE, "Error loading data: {0}", ex);
ex.printStackTrace();
}
}
}
return (TypeList) sav;
}
public void save(String gamePath, String dataName) {
XMLExporter ex = XMLExporter.getInstance();
OutputStream os = null;
try {
File daveFolder = new File(System.getProperty("user.dir") + File.separator + gamePath);
if (!daveFolder.exists() && !daveFolder.mkdirs()) {
Logger.getLogger(Type.class.getName()).log(Level.SEVERE, "Error creating save file!");
throw new IllegalStateException("SaveGame dataset cannot be created");
}
File saveFile = new File(daveFolder.getAbsolutePath() + File.separator + dataName);
if (!saveFile.exists()) {
if (!saveFile.createNewFile()) {
Logger.getLogger(Type.class.getName()).log(Level.SEVERE, "Error creating save file!");
throw new IllegalStateException("SaveGame dataset cannot be created");
}
}
os = new BufferedOutputStream(new FileOutputStream(saveFile));
// os = new GZIPOutputStream(new BufferedOutputStream(new FileOutputStream(saveFile)));
ex.save(this, os);
} catch (IOException ex1) {
Logger.getLogger(Type.class.getName()).log(Level.SEVERE, "Error saving data: {0}", ex1);
ex1.printStackTrace();
throw new IllegalStateException("SaveGame dataset cannot be saved");
} finally {
try {
if (os != null) {
os.close();
}
} catch (IOException ex1) {
Logger.getLogger(Type.class.getName()).log(Level.SEVERE, "Error saving data: {0}", ex1);
ex1.printStackTrace();
throw new IllegalStateException("SaveGame dataset cannot be saved");
}
}
}
/**
* Load the application information from the properties file specified by the application adaptor.
* The resource bundle information is stored in a Map for convenient access.
*
* @param path Path to the source information.
* @return The map containing the application information
*/
private Map loadApplicationInfo(final String path) {
Map infoMap;
try {
infoMap = Util.loadResourceBundle(path);
} catch (MissingResourceException exception) {
final String message = "No application \"About Box\" information resource found at: " + path;
Logger.getLogger("global").log(Level.WARNING, message, exception);
System.err.println(message);
// substitute with default information
infoMap = new HashMap();
infoMap.put("name", Application.getAdaptor().getClass().getName());
}
return infoMap;
}
public UkkonenSuffixTree() {
logger =
Logger.getLogger(
"edu.psu.compbio.seqcode.gse.projects.chipseq.assembler.UkkonenSuffixTree");
isLogging = true;
minLogLevel = Level.SEVERE;
logger.setFilter(new LoggingFilter());
logger.addHandler(new LoggingHandler(System.err, false));
logger.setUseParentHandlers(false);
logger.setLevel(Level.SEVERE);
logger.log(Level.FINE, "Logger setup complete.");
strings = new Vector<TreeString>();
terminal = '$';
root = new TreeNode(null);
totalStringEdges = new Vector<TreeEdge>();
extState = null;
}
private byte[] readBytes(InputStream in) {
byte[] result = null;
try {
ByteArrayOutputStream out = new ByteArrayOutputStream();
byte[] buffer = new byte[BUFFER_SIZE];
int bytesRead = 0;
while ((bytesRead = in.read(buffer, 0, BUFFER_SIZE)) != -1) {
out.write(buffer, 0, bytesRead);
}
out.close();
result = out.toByteArray();
} catch (IOException ex) {
Logger.getLogger(getClass()).debug("Error loading Zip entry", ex);
}
return (result);
}