private void loop() {
while (thread == Thread.currentThread()) {
try {
Request key = peekKey();
if (key == null) throw new IOException("end of stream");
synchronized (response_map) {
Response response = (Response) response_map.get(key);
if (response == null) {
if (log.level >= 4) log.println("Invalid key, skipping message");
doSkip();
} else {
doRecv(response);
response.isReceived = true;
response_map.notifyAll();
}
}
} catch (Exception ex) {
String msg = ex.getMessage();
boolean timeout = msg != null && msg.equals("Read timed out");
/* If just a timeout, try to disconnect gracefully
*/
boolean hard = timeout == false;
if (!timeout && log.level >= 3) ex.printStackTrace(log);
try {
disconnect(hard);
} catch (IOException ioe) {
ioe.printStackTrace(log);
}
}
}
}
public void run() {
String line;
String id = null;
seqs = new HashMap<String, StringBuffer>();
try {
// System.err.println("quality read start"); // debug
while (true) {
line = br.readLine();
// FIX ME: update to use reader...
if (line == null) break;
// EOF
if (line.indexOf(">") == 0) {
String[] stuff = line.substring(1).split("\\s+");
id = new String(stuff[0]);
// HACK, WRONG if line contains comments...
} else {
// sequence
StringBuffer sb = seqs.get(id);
if (sb == null) seqs.put(id, sb = new StringBuffer());
sb.append(line);
}
}
data_loaded = true;
// System.err.println("quality read end"); // debug
} catch (Exception e) {
System.err.println("FASTASequenceReader load error: " + e); // debug
System.exit(1);
}
}
/**
* Returns the index of the given relation in the relation sort order, or the index of "*" if the
* relation is not explicitly listed.
*/
public Integer getRelationSortIndex(String rel) {
Integer retval = _relationIndexMap.get(rel);
if (retval != null) return retval;
retval = _relationIndexMap.get("*");
if (retval != null) return retval;
return new Integer(-1);
}
/**
* Returns an icon for the specified file.
*
* @param file file reference
* @return icon
*/
public static Icon file(final IOFile file) {
if (file == null) return UNKNOWN;
// fallback code for displaying icons
final String path = file.path();
final MediaType type = MediaType.get(path);
if (type.isXML()) return XML;
if (type.isXQuery()) return XQUERY;
if (path.contains(IO.BASEXSUFFIX)) return BASEX;
// only works with standard dpi (https://bugs.openjdk.java.net/browse/JDK-6817929)
if (Prop.WIN && !GUIConstants.large()) {
// retrieve system icons (only supported on Windows)
final int p = path.lastIndexOf(path, '.');
final String suffix = p == -1 ? null : path.substring(p + 1);
Icon icon = null;
if (suffix != null) icon = FILES.get(suffix);
if (icon == null) {
icon = FS.getSystemIcon(file.file());
if (suffix != null) FILES.put(suffix, icon);
}
return icon;
}
// default icon chooser
return type.isText() ? TEXT : UNKNOWN;
}
public void save() {
for (String key : fields.keySet()) {
JComponent comp = fields.get(key);
if (comp instanceof JTextField) {
JTextField c = (JTextField) comp;
if (c.getText().trim().equals("")) {
sketch.configFile.unset(key);
} else {
sketch.configFile.set(key, c.getText());
}
} else if (comp instanceof JTextArea) {
JTextArea c = (JTextArea) comp;
if (c.getText().trim().equals("")) {
sketch.configFile.unset(key);
} else {
sketch.configFile.set(key, c.getText());
}
}
}
sketch.saveConfig();
}
public void setObjectValues() {
((JTextField) (fields.get("board"))).setText(sketch.getBoard().getName());
((JTextField) (fields.get("core"))).setText(sketch.getCore().getName());
((JTextField) (fields.get("compiler"))).setText(sketch.getCompiler().getName());
((JTextField) (fields.get("port"))).setText(sketch.getDevice().toString());
((JTextField) (fields.get("programmer"))).setText(sketch.getProgrammer());
}
/**
* Returns the specified image as icon.
*
* @param name name of icon
* @return icon
*/
public static ImageIcon icon(final String name) {
ImageIcon ii = ICONS.get(name);
if (ii != null) return ii;
Image img;
if (GUIConstants.scale > 1) {
// choose large image or none
final URL url =
GUIConstants.large() ? BaseXImages.class.getResource("/img/" + name + "_32.png") : null;
if (url == null) {
// resize low-res image if no hi-res image exists
img = get(url(name));
final int w = (int) (img.getWidth(null) * GUIConstants.scale);
final int h = (int) (img.getHeight(null) * GUIConstants.scale);
final BufferedImage tmp = new BufferedImage(w, h, BufferedImage.TYPE_INT_ARGB);
final Graphics2D g2 = tmp.createGraphics();
g2.setRenderingHint(
RenderingHints.KEY_INTERPOLATION, RenderingHints.VALUE_INTERPOLATION_BICUBIC);
g2.drawImage(img, 0, 0, w, h, null);
g2.dispose();
img = tmp;
} else {
img = get(url);
}
} else {
img = get(name);
}
ii = new ImageIcon(img);
ICONS.put(name, ii);
return ii;
}
JarFile get(URL url, boolean useCaches) throws IOException {
JarFile result = null;
JarFile local_result = null;
if (useCaches) {
synchronized (this) {
result = getCachedJarFile(url);
}
if (result == null) {
local_result = URLJarFile.getJarFile(url);
synchronized (this) {
result = getCachedJarFile(url);
if (result == null) {
fileCache.put(url, local_result);
urlCache.put(local_result, url);
result = local_result;
} else {
if (local_result != null) {
local_result.close();
}
}
}
}
} else {
result = URLJarFile.getJarFile(url);
}
if (result == null) throw new FileNotFoundException(url.toString());
return result;
}
public void sendrecv(Request request, Response response, long timeout) throws IOException {
synchronized (response_map) {
makeKey(request);
response.isReceived = false;
try {
response_map.put(request, response);
doSend(request);
response.expiration = System.currentTimeMillis() + timeout;
while (!response.isReceived) {
response_map.wait(timeout);
timeout = response.expiration - System.currentTimeMillis();
if (timeout <= 0) {
throw new TransportException(name + " timedout waiting for response to " + request);
}
}
} catch (IOException ioe) {
if (log.level > 2) ioe.printStackTrace(log);
try {
disconnect(true);
} catch (IOException ioe2) {
ioe2.printStackTrace(log);
}
throw ioe;
} catch (InterruptedException ie) {
throw new TransportException(ie);
} finally {
response_map.remove(request);
}
}
}
public synchronized void messageReceived(int to, Message m) {
DrainMsg mhMsg = (DrainMsg) m;
log.debug(
"incoming: localDest: "
+ to
+ " type:"
+ mhMsg.get_type()
+ " hops:"
+ (16 - mhMsg.get_ttl())
+ " seqNo:"
+ mhMsg.get_seqNo()
+ " source:"
+ mhMsg.get_source()
+ " finalDest:"
+ mhMsg.get_dest());
// lets assume that the network cannot buffer more than 25 drain msgs from a single source at a
// time (should be more than reasonable)
if (seqNos.containsKey(new Integer(mhMsg.get_source()))) {
int oldSeqNo = ((Integer) seqNos.get(new Integer(mhMsg.get_source()))).intValue();
int upperBound = mhMsg.get_seqNo() + 25;
int wrappedUpperBound = 25 - (255 - mhMsg.get_seqNo());
if ((oldSeqNo >= mhMsg.get_seqNo() && oldSeqNo < upperBound)
|| (oldSeqNo >= 0 && oldSeqNo < wrappedUpperBound)) {
log.debug(
"Dropping message from "
+ mhMsg.get_source()
+ " with duplicate seqNo: "
+ mhMsg.get_seqNo());
return;
}
}
seqNos.put(new Integer(mhMsg.get_source()), new Integer(mhMsg.get_seqNo()));
if (to != spAddr && to != MoteIF.TOS_BCAST_ADDR && to != TOS_UART_ADDR) {
log.debug("Dropping message not for me.");
return;
}
HashSet promiscuousSet = (HashSet) idTable.get(new Integer(BCAST_ID));
HashSet listenerSet = (HashSet) idTable.get(new Integer(mhMsg.get_type()));
if (listenerSet != null && promiscuousSet != null) {
listenerSet.addAll(promiscuousSet);
} else if (listenerSet == null && promiscuousSet != null) {
listenerSet = promiscuousSet;
}
if (listenerSet == null) {
log.debug("No Listener for type: " + mhMsg.get_type());
return;
}
for (Iterator it = listenerSet.iterator(); it.hasNext(); ) {
MessageListener ml = (MessageListener) it.next();
ml.messageReceived(to, mhMsg);
}
}
/** Looks up the local database, creating if necessary. */
private DataSource findDatabaseImpl(String url, String driverName) throws SQLException {
try {
synchronized (_databaseMap) {
DBPool db = _databaseMap.get(url);
if (db == null) {
db = new DBPool();
db.setVar(url + "-" + _gId++);
DriverConfig driver = db.createDriver();
ClassLoader loader = Thread.currentThread().getContextClassLoader();
Class driverClass = Class.forName(driverName, false, loader);
driver.setType(driverClass);
driver.setURL(url);
db.init();
_databaseMap.put(url, db);
}
return db;
}
} catch (RuntimeException e) {
throw e;
} catch (SQLException e) {
throw e;
} catch (Exception e) {
throw ConfigException.create(e);
}
}
public ArrayList getPointList(long handId) {
ArrayList curList;
if (_pointLists.containsKey(handId)) curList = (ArrayList) _pointLists.get(handId);
else {
curList = new ArrayList(_maxPoints);
_pointLists.put(handId, curList);
}
return curList;
}
/**
* Add a ServiceMonitorFilter to this MonitorFilter
*
* @param serviceMonitorFilter Service Specific Filter
* @exception MonitorFilterException
* @return ServiceMonitorFilter Modified Filter to the capabilities of the service
*/
public ServiceMonitorFilter addServiceMonitorFilter(ServiceMonitorFilter serviceMonitorFilter)
throws MonitorFilterException {
ModuleClassID moduleClassID = serviceMonitorFilter.getModuleClassID();
if (serviceMonitorFilters.get(moduleClassID) != null)
throw new MonitorFilterException(
"Attempt to add a second Monitor Filter for: " + moduleClassID);
serviceMonitorFilters.put(moduleClassID, serviceMonitorFilter);
return serviceMonitorFilter;
}
/**
* Obtient le socket enregistré correspondant à l'addresse IP donnée.
*
* @return le socket correspondant à l'IP source donnée s'il a été enregistré null sinon.
*/
public Socket popSocket(InetAddress addr) {
String addrname = toId(addr);
if (acceptedSockets.containsKey(addrname)) {
Socket sock = acceptedSockets.get(addrname);
acceptedSockets.remove(addrname);
return sock;
}
return null;
}
public void registerListener(int id, MessageListener m) {
HashSet listenerSet = (HashSet) idTable.get(new Integer(id));
if (listenerSet == null) {
listenerSet = new HashSet();
idTable.put(new Integer(id), listenerSet);
}
listenerSet.add(m);
log.info("New Listener for id=" + id);
}
void send(String msg) {
Iterator it = clients.keySet().iterator();
while (it.hasNext()) {
try {
DataOutputStream out = (DataOutputStream) clients.get(it.next());
out.writeUTF(msg);
} catch (IOException e) {
}
}
}
private static void writeDuplicates() {
Main.status("Writing duplicates.");
if (!dup_post_list.isEmpty()) {
Main.status(String.format("%s\t%s", "older_post", "newer_post"));
for (Post post : dup_post_list.keySet()) {
Main.status(String.format("%s\t%s", post.post_id, dup_post_list.get(post).post_id));
}
} else {
Main.status("There are no duplicates.");
}
Main.status("Writing duplicates done.");
}
public boolean startProxy(long from, long to) {
// lazy init for proxy support check quickly in isReadable
if (ProxyConnections == null) {
ProxyConnections = new HashMap<Long, EventableChannel>();
}
EventableChannel target = Connections.get(to);
if (target != null) {
ProxyConnections.put(from, target);
return true;
} else {
return false;
}
}
private void addMenuToTray() {
HashMap categories = new HashMap();
// create menu list
Iterator plugins = PluginManager.getInstance().getAvailablePlugins();
plugins = PluginComparator.sortPlugins(plugins);
while (plugins.hasNext()) {
Plugin p = (Plugin) plugins.next();
JMenu category = (JMenu) categories.get(p.getCategory());
if (category == null) {
category = new JMenu(p.getCategory());
categories.put(p.getCategory(), category);
// copy menu to real one
if (!p.getCategory().equals("Invisible")) this.trayIcon.add(category);
}
ImageIcon icon = new ImageIcon();
try {
icon = new ImageIcon(new URL(p.getDirectory() + p.getIcon()));
icon = new ImageIcon(icon.getImage().getScaledInstance(16, 16, Image.SCALE_SMOOTH));
} catch (Exception e) {
// error at icon loading
}
JMenuItem menu = new JMenuItem(p.getTitle(), icon);
menu.setName(p.getName());
menu.setToolTipText(p.getToolTip());
menu.addActionListener(this);
category.add(menu);
}
this.trayIcon.addSeparator();
// windows
this.trayIcon.add(new WindowMenu(this));
// open main interface
JMenuItem menu = new JMenuItem(tr("open"));
menu.setName("org.lucane.applications.maininterface");
menu.addActionListener(this);
this.trayIcon.add(menu);
// exit
menu = new JMenuItem(tr("exit"));
menu.setName("exit");
menu.addActionListener(this);
this.trayIcon.add(menu);
}
// get relation sort order, or use defaults
private void loadRelationSortOrder(Element relationSortingElt) {
// use defaults if no order specified
if (relationSortingElt == null) {
for (int i = 0; i < defaultRelationSortOrder.length; i++) {
_relationIndexMap.put(defaultRelationSortOrder[i], new Integer(i));
}
return;
}
// otherwise load from 'order' attribute
String orderAttr = relationSortingElt.getAttributeValue("order");
String[] relSortOrder = orderAttr.split("\\s+");
for (int i = 0; i < relSortOrder.length; i++) {
_relationIndexMap.put(relSortOrder[i], new Integer(i));
}
}
void close() {
try {
if (mySelector != null) mySelector.close();
} catch (IOException e) {
}
mySelector = null;
// run down open connections and sockets.
Iterator<ServerSocketChannel> i = Acceptors.values().iterator();
while (i.hasNext()) {
try {
i.next().close();
} catch (IOException e) {
}
}
// 29Sep09: We create an ArrayList of the existing connections, then iterate over
// that to call unbind on them. This is because an unbind can trigger a reconnect,
// which will add to the Connections HashMap, causing a ConcurrentModificationException.
// XXX: The correct behavior here would be to latch the various reactor methods to return
// immediately if the reactor is shutting down.
ArrayList<EventableChannel> conns = new ArrayList<EventableChannel>();
Iterator<EventableChannel> i2 = Connections.values().iterator();
while (i2.hasNext()) {
EventableChannel ec = i2.next();
if (ec != null) {
conns.add(ec);
}
}
Connections.clear();
ListIterator<EventableChannel> i3 = conns.listIterator(0);
while (i3.hasNext()) {
EventableChannel ec = i3.next();
eventCallback(ec.getBinding(), EM_CONNECTION_UNBOUND, null);
ec.close();
EventableSocketChannel sc = (EventableSocketChannel) ec;
if (sc != null && sc.isAttached()) DetachedConnections.add(sc);
}
ListIterator<EventableSocketChannel> i4 = DetachedConnections.listIterator(0);
while (i4.hasNext()) {
EventableSocketChannel ec = i4.next();
ec.cleanup();
}
DetachedConnections.clear();
}
private JarFile getCachedJarFile(URL url) {
JarFile result = (JarFile) fileCache.get(url);
/* if the JAR file is cached, the permission will always be there */
if (result != null) {
Permission perm = getPermission(result);
if (perm != null) {
SecurityManager sm = System.getSecurityManager();
if (sm != null) {
try {
sm.checkPermission(perm);
} catch (SecurityException se) {
// fallback to checkRead/checkConnect for pre 1.2
// security managers
if ((perm instanceof java.io.FilePermission)
&& perm.getActions().indexOf("read") != -1) {
sm.checkRead(perm.getName());
} else if ((perm instanceof java.net.SocketPermission)
&& perm.getActions().indexOf("connect") != -1) {
sm.checkConnect(url.getHost(), url.getPort());
} else {
throw se;
}
}
}
}
}
return result;
}
/** {@inheritDoc} */
public void initializeFrom(Element element) throws DocumentSerializationException {
for (Enumeration e = element.getChildren(); e.hasMoreElements(); ) {
Element serviceElement = (TextElement) e.nextElement();
String tagName = (String) serviceElement.getKey();
if (tagName.equals("service")) {
try {
ModuleClassID moduleClassID =
(ModuleClassID)
IDFactory.fromURI(
new URI(
DocumentSerializableUtilities.getString(
serviceElement, "moduleClassID", "ERROR")));
try {
ServiceMonitorFilter serviceMonitorFilter =
MonitorResources.createServiceMonitorFilter(moduleClassID);
serviceMonitorFilter.init(moduleClassID);
Element serviceMonitorFilterElement =
DocumentSerializableUtilities.getChildElement(serviceElement, "serviceFilter");
serviceMonitorFilter.initializeFrom(serviceMonitorFilterElement);
serviceMonitorFilters.put(moduleClassID, serviceMonitorFilter);
} catch (Exception ex) {
if (unknownModuleClassIDs == null) unknownModuleClassIDs = new LinkedList();
unknownModuleClassIDs.add(moduleClassID);
}
} catch (URISyntaxException jex) {
throw new DocumentSerializationException("Can't get ModuleClassID", jex);
}
}
}
}
public void disconnect(boolean hard) throws IOException {
synchronized (setupDiscoLock) {
synchronized (this) {
switch (state) {
case 0: /* not connected - just return */
return;
case 2:
hard = true;
case 3: /* connected - go ahead and disconnect */
if (response_map.size() != 0 && !hard) {
break; /* outstanding requests */
}
doDisconnect(hard);
case 4: /* in error - reset the transport */
thread = null;
state = 0;
break;
default:
if (log.level >= 1) log.println("Invalid state: " + state);
thread = null;
state = 0;
break;
}
}
}
}
// returns a macro adder for the given morph item
private MacroAdder getMacAdder(MorphItem mi) {
// check map
MacroAdder retval = macAdderMap.get(mi);
if (retval != null) return retval;
// set up macro adder
IntHashSetMap macrosFromLex = new IntHashSetMap();
String[] newMacroNames = mi.getMacros();
List<MacroItem> macroItems = new ArrayList<MacroItem>();
for (int i = 0; i < newMacroNames.length; i++) {
Set<FeatureStructure> featStrucs = (Set<FeatureStructure>) _macros.get(newMacroNames[i]);
if (featStrucs != null) {
for (Iterator<FeatureStructure> fsIt = featStrucs.iterator(); fsIt.hasNext(); ) {
FeatureStructure fs = fsIt.next();
macrosFromLex.put(fs.getIndex(), fs);
}
}
MacroItem macroItem = _macroItems.get(newMacroNames[i]);
if (macroItem != null) {
macroItems.add(macroItem);
} else {
// should be checked earlier too
System.err.println(
"Warning: macro " + newMacroNames[i] + " not found for word '" + mi.getWord() + "'");
}
}
retval = new MacroAdder(macrosFromLex, macroItems);
// update map and return
macAdderMap.put(mi, retval);
return retval;
}
void isReadable(SelectionKey k) {
EventableChannel ec = (EventableChannel) k.attachment();
long b = ec.getBinding();
if (ec.isWatchOnly()) {
if (ec.isNotifyReadable()) eventCallback(b, EM_CONNECTION_NOTIFY_READABLE, null);
} else {
myReadBuffer.clear();
try {
ec.readInboundData(myReadBuffer);
myReadBuffer.flip();
if (myReadBuffer.limit() > 0) {
if (ProxyConnections != null) {
EventableChannel target = ProxyConnections.get(b);
if (target != null) {
ByteBuffer myWriteBuffer = ByteBuffer.allocate(myReadBuffer.limit());
myWriteBuffer.put(myReadBuffer);
myWriteBuffer.flip();
target.scheduleOutboundData(myWriteBuffer);
} else {
eventCallback(b, EM_CONNECTION_READ, myReadBuffer);
}
} else {
eventCallback(b, EM_CONNECTION_READ, myReadBuffer);
}
}
} catch (IOException e) {
UnboundConnections.add(b);
}
}
}
/**
* @param key
* @param options
*/
private void addSuffixPluralPattern(String key, HashMap<String, String> options) {
String option = options.get(key);
if (option != null) {
patternMap.put(
key, Pattern.compile("\\b(\\w{" + minPrefixLength + ",})(" + option + ")s?\\b"));
}
}
void bundleAndSend() {
Map.Entry entry;
IpAddress dest;
ObjectOutputStream out;
InetAddress addr;
int port;
byte[] data;
List l;
if (Trace.trace) {
Trace.info(
"UDP.BundlingOutgoingPacketHandler.bundleAndSend()",
"\nsending msgs:\n" + dumpMessages(msgs));
}
synchronized (msgs) {
stopTimer();
if (msgs.size() == 0) {
return;
}
for (Iterator it = msgs.entrySet().iterator(); it.hasNext(); ) {
entry = (Map.Entry) it.next();
dest = (IpAddress) entry.getKey();
addr = dest.getIpAddress();
port = dest.getPort();
l = (List) entry.getValue();
try {
out_stream.reset();
// BufferedOutputStream bos=new BufferedOutputStream(out_stream);
out_stream.write(Version.version_id, 0, Version.version_id.length); // write the version
// bos.write(Version.version_id, 0, Version.version_id.length); // write the version
out = new ObjectOutputStream(out_stream);
// out=new ObjectOutputStream(bos);
l.writeExternal(out);
out.close(); // needed if out buffers its output to out_stream
data = out_stream.toByteArray();
doSend(data, addr, port);
} catch (IOException e) {
Trace.error(
"UDP.BundlingOutgoingPacketHandle.bundleAndSend()",
"exception sending msg (to dest=" + dest + "): " + e);
}
}
msgs.clear();
}
}
public void deregisterListener(int id, MessageListener m) {
HashSet listenerSet = (HashSet) idTable.get(new Integer(id));
if (listenerSet == null) {
throw new IllegalArgumentException("No listeners registered for message type " + id);
}
listenerSet.remove(m);
}
public SocketChannel detachChannel(long sig) {
EventableSocketChannel ec = (EventableSocketChannel) Connections.get(sig);
if (ec != null) {
UnboundConnections.add(sig);
return ec.getChannel();
} else {
return null;
}
}