Improved encapsulation of thread synchronisation as follows

- replaced use of Object instance mutex with a private final Lock object
- replaced Object signaling with specific condition signalling

.gitignore

@@ -1,3 +1,4 @@
 build
 .gradle
 .metadata
+*.tmp

briar-android/src/org/briarproject/android/AndroidNotificationManagerImpl.java

@@ -11,6 +11,8 @@ import static java.util.logging.Level.WARNING;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.concurrent.Executor;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
 import java.util.logging.Logger;
 
 import javax.inject.Inject;
@@ -64,6 +66,8 @@ Service, EventListener {
 	private int nextRequestId = 0; // Locking: this
 
 	private volatile Settings settings = new Settings();
+	
+	private final Lock synchLock = new ReentrantLock();
 
 	@Inject
 	public AndroidNotificationManagerImpl(DatabaseComponent db,
@@ -103,19 +107,31 @@ Service, EventListener {
 		if(e instanceof SettingsUpdatedEvent) loadSettings();
 	}
 
-	public synchronized void showPrivateMessageNotification(ContactId c) {
-		Integer count = contactCounts.get(c);
-		if(count == null) contactCounts.put(c, 1);
-		else contactCounts.put(c, count + 1);
-		privateTotal++;
-		updatePrivateMessageNotification();
+	public void showPrivateMessageNotification(ContactId c) {
+		synchLock.lock();
+		try{
+			Integer count = contactCounts.get(c);
+			if(count == null) contactCounts.put(c, 1);
+			else contactCounts.put(c, count + 1);
+			privateTotal++;
+			updatePrivateMessageNotification();
+		}
+		finally{
+			synchLock.unlock();
+		}
 	}
 
-	public synchronized void clearPrivateMessageNotification(ContactId c) {
-		Integer count = contactCounts.remove(c);
-		if(count == null) return; // Already cleared
-		privateTotal -= count;
-		updatePrivateMessageNotification();
+	public void clearPrivateMessageNotification(ContactId c) {
+		synchLock.lock();
+		try{
+			Integer count = contactCounts.remove(c);
+			if(count == null) return; // Already cleared
+			privateTotal -= count;
+			updatePrivateMessageNotification();
+		}
+		finally{
+			synchLock.unlock();
+		}
 	}
 
 	// Locking: this
@@ -180,19 +196,31 @@ Service, EventListener {
 		return defaults;
 	}
 
-	public synchronized void showGroupPostNotification(GroupId g) {
-		Integer count = groupCounts.get(g);
-		if(count == null) groupCounts.put(g, 1);
-		else groupCounts.put(g, count + 1);
-		groupTotal++;
-		updateGroupPostNotification();
+	public void showGroupPostNotification(GroupId g) {
+		synchLock.lock();
+		try{
+			Integer count = groupCounts.get(g);
+			if(count == null) groupCounts.put(g, 1);
+			else groupCounts.put(g, count + 1);
+			groupTotal++;
+			updateGroupPostNotification();
+		}
+		finally{
+			synchLock.unlock();
+		}
 	}
 
-	public synchronized void clearGroupPostNotification(GroupId g) {
+	public void clearGroupPostNotification(GroupId g) {
+		synchLock.lock();
+		try{
 		Integer count = groupCounts.remove(g);
 		if(count == null) return; // Already cleared
 		groupTotal -= count;
 		updateGroupPostNotification();
+		}
+		finally{
+			synchLock.unlock();
+		}
 	}
 
 	// Locking: this
@@ -238,18 +266,23 @@ Service, EventListener {
 		}
 	}
 
-	// Locking: this
 	private void clearGroupPostNotification() {
 		Object o = appContext.getSystemService(NOTIFICATION_SERVICE);
 		NotificationManager nm = (NotificationManager) o;
 		nm.cancel(GROUP_POST_NOTIFICATION_ID);
 	}
 
-	public synchronized void clearNotifications() {
-		contactCounts.clear();
-		groupCounts.clear();
-		privateTotal = groupTotal = 0;
-		clearPrivateMessageNotification();
-		clearGroupPostNotification();
+	public void clearNotifications() {
+		synchLock.lock();
+		try{
+			contactCounts.clear();
+			groupCounts.clear();
+			privateTotal = groupTotal = 0;
+			clearPrivateMessageNotification();
+			clearGroupPostNotification();
+		}
+		finally{
+			synchLock.unlock();
+		}
 	}
 }

briar-android/src/org/briarproject/android/ReferenceManagerImpl.java

@@ -4,6 +4,8 @@ import static java.util.logging.Level.INFO;
 
 import java.util.HashMap;
 import java.util.Map;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
 import java.util.logging.Logger;
 
 import org.briarproject.api.android.ReferenceManager;
@@ -13,49 +15,70 @@ class ReferenceManagerImpl implements ReferenceManager {
 	private static final Logger LOG =
 			Logger.getLogger(ReferenceManagerImpl.class.getName());
 
-	// Locking: this
 	private final Map<Class<?>, Map<Long, Object>> outerMap =
 			new HashMap<Class<?>, Map<Long, Object>>();
 
 	private long nextHandle = 0; // Locking: this
 
-	public synchronized <T> T getReference(long handle, Class<T> c) {
-		Map<Long, Object> innerMap = outerMap.get(c);
-		if(innerMap == null) {
+	private final Lock synchLock = new ReentrantLock();
+
+	public <T> T getReference(long handle, Class<T> c) {
+		synchLock.lock();
+		try{
+			Map<Long, Object> innerMap = outerMap.get(c);
+			if(innerMap == null) {
+				if(LOG.isLoggable(INFO))
+					LOG.info("0 handles for " + c.getName());
+				return null;
+			}
 			if(LOG.isLoggable(INFO))
-				LOG.info("0 handles for " + c.getName());
-			return null;
+				LOG.info(innerMap.size() + " handles for " + c.getName());
+			Object o = innerMap.get(handle);
+			return c.cast(o);
 		}
-		if(LOG.isLoggable(INFO))
-			LOG.info(innerMap.size() + " handles for " + c.getName());
-		Object o = innerMap.get(handle);
-		return c.cast(o);
+		finally{
+			synchLock.unlock();
+		}
+		
 	}
 
-	public synchronized <T> long putReference(T reference, Class<T> c) {
-		Map<Long, Object> innerMap = outerMap.get(c);
-		if(innerMap == null) {
-			innerMap = new HashMap<Long, Object>();
-			outerMap.put(c, innerMap);
+	public <T> long putReference(T reference, Class<T> c) {
+		synchLock.lock();
+		try{
+			Map<Long, Object> innerMap = outerMap.get(c);
+			if(innerMap == null) {
+				innerMap = new HashMap<Long, Object>();
+				outerMap.put(c, innerMap);
+			}
+			long handle = nextHandle++;
+			innerMap.put(handle, reference);
+			if(LOG.isLoggable(INFO)) {
+				LOG.info(innerMap.size() + " handles for " + c.getName() +
+						" after put");
+			}
+			return handle;
 		}
-		long handle = nextHandle++;
-		innerMap.put(handle, reference);
-		if(LOG.isLoggable(INFO)) {
-			LOG.info(innerMap.size() + " handles for " + c.getName() +
-					" after put");
+		finally{
+			synchLock.unlock();
 		}
-		return handle;
 	}
 
-	public synchronized <T> T removeReference(long handle, Class<T> c) {
-		Map<Long, Object> innerMap = outerMap.get(c);
-		if(innerMap == null) return null;
-		Object o = innerMap.remove(handle);
-		if(innerMap.isEmpty()) outerMap.remove(c);
-		if(LOG.isLoggable(INFO)) {
-			LOG.info(innerMap.size() + " handles for " + c.getName() +
-					" after remove");
+	public <T> T removeReference(long handle, Class<T> c) {
+		synchLock.lock();
+		try{
+			Map<Long, Object> innerMap = outerMap.get(c);
+			if(innerMap == null) return null;
+			Object o = innerMap.remove(handle);
+			if(innerMap.isEmpty()) outerMap.remove(c);
+			if(LOG.isLoggable(INFO)) {
+				LOG.info(innerMap.size() + " handles for " + c.getName() +
+						" after remove");
+			}
+			return c.cast(o);
 		}
-		return c.cast(o);
+		finally{
+			synchLock.unlock();
+		}
+
 	}
 }

briar-core/src/org/briarproject/crypto/FortunaGenerator.java

@@ -1,5 +1,8 @@
 package org.briarproject.crypto;
 
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
+
 import org.briarproject.api.crypto.MessageDigest;
 import org.spongycastle.crypto.BlockCipher;
 import org.spongycastle.crypto.digests.SHA256Digest;
@@ -23,61 +26,89 @@ class FortunaGenerator {
 	private final byte[] counter = new byte[BLOCK_BYTES];
 	private final byte[] buffer = new byte[BLOCK_BYTES];
 	private final byte[] newKey = new byte[KEY_BYTES];
+	
+	private final Lock synchLock = new ReentrantLock(); 
 
 	FortunaGenerator(byte[] seed) {
 		reseed(seed);
 	}
 
-	synchronized void reseed(byte[] seed) {
-		digest.update(key);
-		digest.update(seed);
-		digest.digest(key, 0, KEY_BYTES);
-		incrementCounter();
+	void reseed(byte[] seed) {
+		synchLock.lock();
+		try{
+			digest.update(key);
+			digest.update(seed);
+			digest.digest(key, 0, KEY_BYTES);
+			incrementCounter();
+		}
+		finally{
+			synchLock.unlock();
+		}
+
 	}
 
 	// Package access for testing
-	synchronized void incrementCounter() {
-		counter[0]++;
-		for(int i = 0; counter[i] == 0; i++) {
-			if(i + 1 == BLOCK_BYTES)
-				throw new RuntimeException("Counter exhausted");
-			counter[i + 1]++;
+	void incrementCounter() {
+		synchLock.lock();
+		try{
+			counter[0]++;
+			for(int i = 0; counter[i] == 0; i++) {
+				if(i + 1 == BLOCK_BYTES)
+					throw new RuntimeException("Counter exhausted");
+				counter[i + 1]++;
+			}
 		}
-	}
+		finally{
+			synchLock.unlock();
+		}
+}
 
 	// Package access for testing
-	synchronized byte[] getCounter() {
-		return counter;
+	byte[] getCounter() {
+		synchLock.lock();
+		try{
+			return counter;
+		}
+		finally{
+			synchLock.unlock();
+		}
+
 	}
 
-	synchronized int nextBytes(byte[] dest, int off, int len) {
-		// Don't write more than the maximum number of bytes in one request
-		if(len > MAX_BYTES_PER_REQUEST) len = MAX_BYTES_PER_REQUEST;
-		cipher.init(true, new KeyParameter(key));
-		// Generate full blocks directly into the output buffer
-		int fullBlocks = len / BLOCK_BYTES;
-		for(int i = 0; i < fullBlocks; i++) {
-			cipher.processBlock(counter, 0, dest, off + i * BLOCK_BYTES);
-			incrementCounter();
+	int nextBytes(byte[] dest, int off, int len) {
+		synchLock.lock();
+		try{
+			// Don't write more than the maximum number of bytes in one request
+			if(len > MAX_BYTES_PER_REQUEST) len = MAX_BYTES_PER_REQUEST;
+			cipher.init(true, new KeyParameter(key));
+			// Generate full blocks directly into the output buffer
+			int fullBlocks = len / BLOCK_BYTES;
+			for(int i = 0; i < fullBlocks; i++) {
+				cipher.processBlock(counter, 0, dest, off + i * BLOCK_BYTES);
+				incrementCounter();
+			}
+			// Generate a partial block if needed
+			int done = fullBlocks * BLOCK_BYTES, remaining = len - done;
+			assert remaining < BLOCK_BYTES;
+			if(remaining > 0) {
+				cipher.processBlock(counter, 0, buffer, 0);
+				incrementCounter();
+				// Copy the partial block to the output buffer and erase our copy
+				System.arraycopy(buffer, 0, dest, off + done, remaining);
+				for(int i = 0; i < BLOCK_BYTES; i++) buffer[i] = 0;
+			}
+			// Generate a new key
+			for(int i = 0; i < KEY_BYTES / BLOCK_BYTES; i++) {
+				cipher.processBlock(counter, 0, newKey, i * BLOCK_BYTES);
+				incrementCounter();
+			}
+			System.arraycopy(newKey, 0, key, 0, KEY_BYTES);
+			for(int i = 0; i < KEY_BYTES; i++) newKey[i] = 0;
+			// Return the number of bytes written
+			return len;
 		}
-		// Generate a partial block if needed
-		int done = fullBlocks * BLOCK_BYTES, remaining = len - done;
-		assert remaining < BLOCK_BYTES;
-		if(remaining > 0) {
-			cipher.processBlock(counter, 0, buffer, 0);
-			incrementCounter();
-			// Copy the partial block to the output buffer and erase our copy
-			System.arraycopy(buffer, 0, dest, off + done, remaining);
-			for(int i = 0; i < BLOCK_BYTES; i++) buffer[i] = 0;
+		finally{
+			synchLock.unlock();
 		}
-		// Generate a new key
-		for(int i = 0; i < KEY_BYTES / BLOCK_BYTES; i++) {
-			cipher.processBlock(counter, 0, newKey, i * BLOCK_BYTES);
-			incrementCounter();
-		}
-		System.arraycopy(newKey, 0, key, 0, KEY_BYTES);
-		for(int i = 0; i < KEY_BYTES; i++) newKey[i] = 0;
-		// Return the number of bytes written
-		return len;
 	}
 }

briar-core/src/org/briarproject/crypto/PseudoRandomImpl.java

@@ -1,5 +1,8 @@
 package org.briarproject.crypto;
 
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
+
 import org.briarproject.api.crypto.MessageDigest;
 import org.briarproject.api.crypto.PseudoRandom;
 import org.briarproject.util.ByteUtils;
@@ -10,6 +13,8 @@ class PseudoRandomImpl implements PseudoRandom {
 
 	private byte[] state;
 	private int offset;
+	
+	private final Lock synchLock = new ReentrantLock();
 
 	PseudoRandomImpl(MessageDigest messageDigest, int seed1, int seed2) {
 		this.messageDigest = messageDigest;
@@ -21,21 +26,27 @@ class PseudoRandomImpl implements PseudoRandom {
 		offset = 0;
 	}
 
-	public synchronized byte[] nextBytes(int bytes) {
-		byte[] b = new byte[bytes];
-		int half = state.length / 2;
-		int off = 0, len = b.length, available = half - offset;
-		while(available < len) {
-			System.arraycopy(state, offset, b, off, available);
-			off += available;
-			len -= available;
-			messageDigest.update(state, half, half);
-			state = messageDigest.digest();
-			offset = 0;
-			available = half;
+	public byte[] nextBytes(int bytes) {
+		synchLock.lock();
+		try{
+			byte[] b = new byte[bytes];
+			int half = state.length / 2;
+			int off = 0, len = b.length, available = half - offset;
+			while(available < len) {
+				System.arraycopy(state, offset, b, off, available);
+				off += available;
+				len -= available;
+				messageDigest.update(state, half, half);
+				state = messageDigest.digest();
+				offset = 0;
+				available = half;
+			}
+			System.arraycopy(state, offset, b, off, len);
+			offset += len;
+			return b;
+		}
+		finally{
+			synchLock.unlock();
 		}
-		System.arraycopy(state, offset, b, off, len);
-		offset += len;
-		return b;
 	}
 }

briar-core/src/org/briarproject/crypto/SecretKeyImpl.java

@@ -1,5 +1,8 @@
 package org.briarproject.crypto;
 
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
+
 import org.briarproject.api.crypto.SecretKey;
 import org.briarproject.util.ByteUtils;
 
@@ -8,23 +11,38 @@ class SecretKeyImpl implements SecretKey {
 	private final byte[] key;
 
 	private boolean erased = false; // Locking: this
+	
+	private final Lock synchLock = new ReentrantLock();
 
 	SecretKeyImpl(byte[] key) {
 		this.key = key;
 	}
 
-	public synchronized byte[] getEncoded() {
-		if(erased) throw new IllegalStateException();
-		return key;
+	public byte[] getEncoded() {
+		synchLock.lock();
+		try{
+			if(erased) throw new IllegalStateException();
+			return key;
+		}
+		finally{
+			synchLock.unlock();
+		}
+
 	}
 
 	public SecretKey copy() {
 		return new SecretKeyImpl(key.clone());
 	}
 
-	public synchronized void erase() {
-		if(erased) throw new IllegalStateException();
-		ByteUtils.erase(key);
-		erased = true;
+	public void erase() {
+		synchLock.lock();
+		try{
+			if(erased) throw new IllegalStateException();
+			ByteUtils.erase(key);
+			erased = true;
+		}
+		finally{
+			synchLock.unlock();
+		}
 	}
 }

briar-core/src/org/briarproject/db/JdbcDatabase.java

@@ -27,6 +27,9 @@ import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Set;
 import java.util.concurrent.atomic.AtomicInteger;
+import java.util.concurrent.locks.Condition;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
 import java.util.logging.Logger;
 
 import org.briarproject.api.Author;
@@ -322,6 +325,9 @@ abstract class JdbcDatabase implements Database<Connection> {
 
 	protected abstract Connection createConnection() throws SQLException;
 	protected abstract void flushBuffersToDisk(Statement s) throws SQLException;
+	
+	private final Lock connectionsLock = new ReentrantLock();
+	private final Condition connectionsChanged = connectionsLock.newCondition();
 
 	JdbcDatabase(String hashType, String binaryType, String counterType,
 			String secretType, Clock clock) {
@@ -431,19 +437,28 @@ abstract class JdbcDatabase implements Database<Connection> {
 
 	public Connection startTransaction() throws DbException {
 		Connection txn = null;
-		synchronized(connections) {
+		connectionsLock.lock();
+		try {
 			if(closed) throw new DbClosedException();
 			txn = connections.poll();
 		}
+		finally{
+			connectionsLock.unlock();
+		}
+		
 		try {
 			if(txn == null) {
 				// Open a new connection
 				txn = createConnection();
 				if(txn == null) throw new DbException();
 				txn.setAutoCommit(false);
-				synchronized(connections) {
+				connectionsLock.lock();
+				try {
 					openConnections++;
 				}
+				finally{
+					connectionsLock.unlock();
+				}
 			}
 		} catch(SQLException e) {
 			throw new DbException(e);
@@ -455,9 +470,13 @@ abstract class JdbcDatabase implements Database<Connection> {
 	public void abortTransaction(Connection txn) {
 		try {
 			txn.rollback();
-			synchronized(connections) {
+			connectionsLock.lock();
+			try {
 				connections.add(txn);
-				connections.notifyAll();
+				connectionsChanged.signalAll();
+			}
+			finally{
+				connectionsLock.unlock();
 			}
 		} catch(SQLException e) {
 			// Try to close the connection
@@ -468,11 +487,14 @@ abstract class JdbcDatabase implements Database<Connection> {
 				if(LOG.isLoggable(WARNING)) LOG.log(WARNING, e1.toString(), e1);
 			}
 			// Whatever happens, allow the database to close
-			synchronized(connections) {
+			connectionsLock.lock();
+			try {
 				openConnections--;
-				connections.notifyAll();
+				connectionsChanged.signalAll();
 			}
-		}
+			finally{
+				connectionsLock.unlock();
+			}		}
 	}
 
 	public void commitTransaction(Connection txn) throws DbException {
@@ -486,9 +508,13 @@ abstract class JdbcDatabase implements Database<Connection> {
 			tryToClose(s);
 			throw new DbException(e);
 		}
-		synchronized(connections) {
+		connectionsLock.lock();
+		try{
 			connections.add(txn);
-			connections.notifyAll();
+			connectionsChanged.signalAll();
+		}
+		finally{
+			connectionsLock.unlock();
 		}
 	}
 
@@ -502,14 +528,15 @@ abstract class JdbcDatabase implements Database<Connection> {
 
 	protected void closeAllConnections() throws SQLException {
 		boolean interrupted = false;
-		synchronized(connections) {
+		connectionsLock.lock();
+		try{
 			closed = true;
 			for(Connection c : connections) c.close();
 			openConnections -= connections.size();
 			connections.clear();
 			while(openConnections > 0) {
 				try {
-					connections.wait();
+					connectionsChanged.await();
 				} catch(InterruptedException e) {
 					LOG.warning("Interrupted while closing connections");
 					interrupted = true;
@@ -519,6 +546,10 @@ abstract class JdbcDatabase implements Database<Connection> {
 				connections.clear();
 			}
 		}
+		finally{
+			connectionsLock.unlock();
+		}
+		
 		if(interrupted) Thread.currentThread().interrupt();
 	}
 

briar-core/src/org/briarproject/invitation/ConnectorGroup.java

@@ -10,6 +10,8 @@ import java.util.Map;
 import java.util.concurrent.CopyOnWriteArrayList;
 import java.util.concurrent.CountDownLatch;
 import java.util.concurrent.atomic.AtomicBoolean;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
 import java.util.logging.Logger;
 
 import org.briarproject.api.Author;
@@ -60,6 +62,8 @@ class ConnectorGroup extends Thread implements InvitationTask {
 	private final Collection<InvitationListener> listeners;
 	private final AtomicBoolean connected;
 	private final CountDownLatch localConfirmationLatch;
+	
+	private final Lock synchLock = new ReentrantLock();
 
 	/*
 	 * All of the following require locking: this. We don't want to call the
@@ -104,12 +108,18 @@ class ConnectorGroup extends Thread implements InvitationTask {
 		localConfirmationLatch = new CountDownLatch(1);
 	}
 
-	public synchronized InvitationState addListener(InvitationListener l) {
-		listeners.add(l);
-		return new InvitationState(localInvitationCode, remoteInvitationCode,
-				localConfirmationCode, remoteConfirmationCode, connected.get(),
-				connectionFailed, localCompared, remoteCompared, localMatched,
-				remoteMatched, remoteName);
+	public InvitationState addListener(InvitationListener l) {
+		synchLock.lock();
+		try{
+			listeners.add(l);
+			return new InvitationState(localInvitationCode, remoteInvitationCode,
+					localConfirmationCode, remoteConfirmationCode, connected.get(),
+					connectionFailed, localCompared, remoteCompared, localMatched,
+					remoteMatched, remoteName);
+		}
+		finally{
+			synchLock.unlock();
+		}
 	}
 
 	public void removeListener(InvitationListener l) {
@@ -130,9 +140,13 @@ class ConnectorGroup extends Thread implements InvitationTask {
 			localProps = db.getLocalProperties();
 		} catch(DbException e) {
 			if(LOG.isLoggable(WARNING)) LOG.log(WARNING, e.toString(), e);
-			synchronized(this) {
+			synchLock.lock();
+			try {
 				connectionFailed = true;
 			}
+			finally{
+				synchLock.unlock();
+			}
 			for(InvitationListener l : listeners) l.connectionFailed();
 			return;
 		}
@@ -163,9 +177,13 @@ class ConnectorGroup extends Thread implements InvitationTask {
 		}
 		// If none of the threads connected, inform the listeners
 		if(!connected.get()) {
-			synchronized(this) {
+			synchLock.lock();
+			try {
 				connectionFailed = true;
 			}
+			finally{
+				synchLock.unlock();
+			}
 			for(InvitationListener l : listeners) l.connectionFailed();
 		}
 	}
@@ -193,18 +211,26 @@ class ConnectorGroup extends Thread implements InvitationTask {
 	}
 
 	public void localConfirmationSucceeded() {
-		synchronized(this) {
+		synchLock.lock();
+		try {
 			localCompared = true;
 			localMatched = true;
 		}
+		finally{
+			synchLock.unlock();
+		}
 		localConfirmationLatch.countDown();
 	}
 
 	public void localConfirmationFailed() {
-		synchronized(this) {
+		synchLock.lock();
+		try {
 			localCompared = true;
 			localMatched = false;
 		}
+		finally{
+			synchLock.unlock();
+		}
 		localConfirmationLatch.countDown();
 	}
 
@@ -216,10 +242,14 @@ class ConnectorGroup extends Thread implements InvitationTask {
 	}
 
 	void keyAgreementSucceeded(int localCode, int remoteCode) {
-		synchronized(this) {
+		synchLock.lock();
+		try {
 			localConfirmationCode = localCode;
 			remoteConfirmationCode = remoteCode;
 		}
+		finally{
+			synchLock.unlock();
+		}
 		for(InvitationListener l : listeners)
 			l.keyAgreementSucceeded(localCode, remoteCode);
 	}
@@ -230,32 +260,48 @@ class ConnectorGroup extends Thread implements InvitationTask {
 
 	boolean waitForLocalConfirmationResult() throws InterruptedException {
 		localConfirmationLatch.await(CONFIRMATION_TIMEOUT, MILLISECONDS);
-		synchronized(this) {
+		synchLock.lock();
+		try {
 			return localMatched;
 		}
+		finally{
+			synchLock.unlock();
+		}
 	}
 
 	void remoteConfirmationSucceeded() {
-		synchronized(this) {
+		synchLock.lock();
+		try {
 			remoteCompared = true;
 			remoteMatched = true;
 		}
+		finally{
+			synchLock.unlock();
+		}
 		for(InvitationListener l : listeners) l.remoteConfirmationSucceeded();
 	}
 
 	void remoteConfirmationFailed() {
-		synchronized(this) {
+		synchLock.lock();
+		try {
 			remoteCompared = true;
 			remoteMatched = false;
 		}
+		finally{
+			synchLock.unlock();
+		}
 		for(InvitationListener l : listeners) l.remoteConfirmationFailed();
 	}
 
 	void pseudonymExchangeSucceeded(Author remoteAuthor) {
 		String name = remoteAuthor.getName();
-		synchronized(this) {
+		synchLock.lock();
+		try {
 			remoteName = name;
 		}
+		finally{
+			synchLock.unlock();
+		}
 		for(InvitationListener l : listeners)
 			l.pseudonymExchangeSucceeded(name);
 	}

briar-core/src/org/briarproject/lifecycle/ShutdownManagerImpl.java

@@ -2,6 +2,8 @@ package org.briarproject.lifecycle;
 
 import java.util.HashMap;
 import java.util.Map;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
 
 import org.briarproject.api.lifecycle.ShutdownManager;
 
@@ -10,26 +12,42 @@ class ShutdownManagerImpl implements ShutdownManager {
 	protected final Map<Integer, Thread> hooks; // Locking: this
 
 	private int nextHandle = 0; // Locking: this
+	
+	private final Lock synchLock = new ReentrantLock();
 
 	ShutdownManagerImpl() {
 		hooks = new HashMap<Integer, Thread>();
 	}
 
-	public synchronized int addShutdownHook(Runnable r) {
-		int handle = nextHandle++;
-		Thread hook = createThread(r);
-		hooks.put(handle, hook);
-		Runtime.getRuntime().addShutdownHook(hook);
-		return handle;
+	public int addShutdownHook(Runnable r) {
+		synchLock.lock();
+		try{
+			int handle = nextHandle++;
+			Thread hook = createThread(r);
+			hooks.put(handle, hook);
+			Runtime.getRuntime().addShutdownHook(hook);
+			return handle;
+		}
+		finally{
+			synchLock.unlock();
+		}
+
 	}
 
 	protected Thread createThread(Runnable r) {
 		return new Thread(r, "ShutdownManager");
 	}
 
-	public synchronized boolean removeShutdownHook(int handle) {
-		Thread hook = hooks.remove(handle);
-		if(hook == null) return false;
-		else return Runtime.getRuntime().removeShutdownHook(hook);
+	public boolean removeShutdownHook(int handle) {
+		synchLock.lock();
+		try{
+			Thread hook = hooks.remove(handle);
+			if(hook == null) return false;
+			else return Runtime.getRuntime().removeShutdownHook(hook);
+		}
+		finally{
+			synchLock.unlock();
+		}
+
 	}
 }

briar-core/src/org/briarproject/plugins/ConnectionRegistryImpl.java

@@ -8,6 +8,8 @@ import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
 import java.util.logging.Logger;
 
 import org.briarproject.api.ContactId;
@@ -29,6 +31,8 @@ class ConnectionRegistryImpl implements ConnectionRegistry {
 	private final Map<TransportId, Map<ContactId, Integer>> connections;
 	// Locking: this
 	private final Map<ContactId, Integer> contactCounts;
+	
+	private final Lock synchLock = new ReentrantLock();
 
 	@Inject
 	ConnectionRegistryImpl(EventBus eventBus) {
@@ -40,7 +44,8 @@ class ConnectionRegistryImpl implements ConnectionRegistry {
 	public void registerConnection(ContactId c, TransportId t) {
 		LOG.info("Connection registered");
 		boolean firstConnection = false;
-		synchronized(this) {
+		synchLock.lock();
+		try {
 			Map<ContactId, Integer> m = connections.get(t);
 			if(m == null) {
 				m = new HashMap<ContactId, Integer>();
@@ -57,6 +62,10 @@ class ConnectionRegistryImpl implements ConnectionRegistry {
 				contactCounts.put(c, count + 1);
 			}
 		}
+		finally{
+			synchLock.unlock();
+		}
+
 		if(firstConnection) {
 			LOG.info("Contact connected");
 			eventBus.broadcast(new ContactConnectedEvent(c));
@@ -66,7 +75,8 @@ class ConnectionRegistryImpl implements ConnectionRegistry {
 	public void unregisterConnection(ContactId c, TransportId t) {
 		LOG.info("Connection unregistered");
 		boolean lastConnection = false;
-		synchronized(this) {
+		synchLock.lock();
+		try {
 			Map<ContactId, Integer> m = connections.get(t);
 			if(m == null) throw new IllegalArgumentException();
 			Integer count = m.remove(c);
@@ -85,22 +95,40 @@ class ConnectionRegistryImpl implements ConnectionRegistry {
 				contactCounts.put(c, count - 1);
 			}
 		}
+		finally{
+			synchLock.unlock();
+		}
+
 		if(lastConnection) {
 			LOG.info("Contact disconnected");
 			eventBus.broadcast(new ContactDisconnectedEvent(c));
 		}
 	}
 
-	public synchronized Collection<ContactId> getConnectedContacts(
+	public Collection<ContactId> getConnectedContacts(
 			TransportId t) {
-		Map<ContactId, Integer> m = connections.get(t);
-		if(m == null) return Collections.emptyList();
-		List<ContactId> ids = new ArrayList<ContactId>(m.keySet());
-		if(LOG.isLoggable(INFO)) LOG.info(ids.size() + " contacts connected");
-		return Collections.unmodifiableList(ids);
+		synchLock.lock();
+		try{
+			Map<ContactId, Integer> m = connections.get(t);
+			if(m == null) return Collections.emptyList();
+			List<ContactId> ids = new ArrayList<ContactId>(m.keySet());
+			if(LOG.isLoggable(INFO)) LOG.info(ids.size() + " contacts connected");
+			return Collections.unmodifiableList(ids);
+		}
+		finally{
+			synchLock.unlock();
+		}
+
 	}
 
-	public synchronized boolean isConnected(ContactId c) {
-		return contactCounts.containsKey(c);
+	public boolean isConnected(ContactId c) {
+		synchLock.lock();
+		try{
+			return contactCounts.containsKey(c);
+		}
+		finally{
+			synchLock.unlock();
+		}
+
 	}
 }

briar-core/src/org/briarproject/reliability/Receiver.java

@@ -5,6 +5,10 @@ import java.util.Comparator;
 import java.util.Iterator;
 import java.util.SortedSet;
 import java.util.TreeSet;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.locks.Condition;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
 
 import org.briarproject.api.reliability.ReadHandler;
 import org.briarproject.api.system.Clock;
@@ -23,6 +27,8 @@ class Receiver implements ReadHandler {
 	private long nextSequenceNumber = 1;
 
 	private volatile boolean valid = true;
+	private Lock synchLock = new ReentrantLock();
+	private Condition dataFrameAvailable = synchLock.newCondition();
 
 	Receiver(Clock clock, Sender sender) {
 		this.sender = sender;
@@ -30,36 +36,46 @@ class Receiver implements ReadHandler {
 		dataFrames = new TreeSet<Data>(new SequenceNumberComparator());
 	}
 
-	synchronized Data read() throws IOException, InterruptedException {
-		long now = clock.currentTimeMillis(), end = now + READ_TIMEOUT;
-		while(now < end && valid) {
-			if(dataFrames.isEmpty()) {
-				// Wait for a data frame
-				wait(end - now);
-			} else {
-				Data d = dataFrames.first();
-				if(d.getSequenceNumber() == nextSequenceNumber) {
-					dataFrames.remove(d);
-					// Update the window
-					windowSize += d.getPayloadLength();
-					sender.sendAck(0, windowSize);
-					nextSequenceNumber++;
-					return d;
+	Data read() throws IOException, InterruptedException {
+		synchLock.lock();
+		try{
+			long now = clock.currentTimeMillis(), end = now + READ_TIMEOUT;
+			while(now < end && valid) {
+				if(dataFrames.isEmpty()) {
+					// Wait for a data frame
+					dataFrameAvailable.await(end - now, TimeUnit.MILLISECONDS);
 				} else {
-					// Wait for the next in-order data frame
-					wait(end - now);
+					Data d = dataFrames.first();
+					if(d.getSequenceNumber() == nextSequenceNumber) {
+						dataFrames.remove(d);
+						// Update the window
+						windowSize += d.getPayloadLength();
+						sender.sendAck(0, windowSize);
+						nextSequenceNumber++;
+						return d;
+					} else {
+						// Wait for the next in-order data frame
+						dataFrameAvailable.await(end - now, TimeUnit.MILLISECONDS);
+					}
 				}
+				now = clock.currentTimeMillis();
 			}
-			now = clock.currentTimeMillis();
+			if(valid) throw new IOException("Read timed out");
+			throw new IOException("Connection closed");
+		}
+		finally{
+			synchLock.unlock();
 		}
-		if(valid) throw new IOException("Read timed out");
-		throw new IOException("Connection closed");
 	}
 
 	void invalidate() {
 		valid = false;
-		synchronized(this) {
-			notifyAll();
+		synchLock.lock();
+		try {
+			dataFrameAvailable.signalAll();
+		}
+		finally{
+			synchLock.unlock();
 		}
 	}
 
@@ -79,43 +95,49 @@ class Receiver implements ReadHandler {
 		}
 	}
 
-	private synchronized void handleData(byte[] b) throws IOException {
-		if(b.length < Data.MIN_LENGTH || b.length > Data.MAX_LENGTH) {
-			// Ignore data frame with invalid length
-			return;
-		}
-		Data d = new Data(b);
-		int payloadLength = d.getPayloadLength();
-		if(payloadLength > windowSize) return; // No space in the window
-		if(d.getChecksum() != d.calculateChecksum()) {
-			// Ignore data frame with invalid checksum
-			return;
-		}
-		long sequenceNumber = d.getSequenceNumber();
-		if(sequenceNumber == 0) {
-			// Window probe
-		} else if(sequenceNumber < nextSequenceNumber) {
-			// Duplicate data frame
-		} else if(d.isLastFrame()) {
-			finalSequenceNumber = sequenceNumber;
-			// Remove any data frames with higher sequence numbers
-			Iterator<Data> it = dataFrames.iterator();
-			while(it.hasNext()) {
-				Data d1 = it.next();
-				if(d1.getSequenceNumber() >= finalSequenceNumber) it.remove();
+	private void handleData(byte[] b) throws IOException {
+		synchLock.lock();
+		try{
+			if(b.length < Data.MIN_LENGTH || b.length > Data.MAX_LENGTH) {
+				// Ignore data frame with invalid length
+				return;
 			}
-			if(dataFrames.add(d)) {
-				windowSize -= payloadLength;
-				notifyAll();
+			Data d = new Data(b);
+			int payloadLength = d.getPayloadLength();
+			if(payloadLength > windowSize) return; // No space in the window
+			if(d.getChecksum() != d.calculateChecksum()) {
+				// Ignore data frame with invalid checksum
+				return;
 			}
-		} else if(sequenceNumber < finalSequenceNumber) {
-			if(dataFrames.add(d)) {
-				windowSize -= payloadLength;
-				notifyAll();
+			long sequenceNumber = d.getSequenceNumber();
+			if(sequenceNumber == 0) {
+				// Window probe
+			} else if(sequenceNumber < nextSequenceNumber) {
+				// Duplicate data frame
+			} else if(d.isLastFrame()) {
+				finalSequenceNumber = sequenceNumber;
+				// Remove any data frames with higher sequence numbers
+				Iterator<Data> it = dataFrames.iterator();
+				while(it.hasNext()) {
+					Data d1 = it.next();
+					if(d1.getSequenceNumber() >= finalSequenceNumber) it.remove();
+				}
+				if(dataFrames.add(d)) {
+					windowSize -= payloadLength;
+					dataFrameAvailable.signalAll();
+				}
+			} else if(sequenceNumber < finalSequenceNumber) {
+				if(dataFrames.add(d)) {
+					windowSize -= payloadLength;
+					dataFrameAvailable.signalAll();
+				}
 			}
+			// Acknowledge the data frame even if it's a duplicate
+			sender.sendAck(sequenceNumber, windowSize);
+		}
+		finally{
+			synchLock.unlock();
 		}
-		// Acknowledge the data frame even if it's a duplicate
-		sender.sendAck(sequenceNumber, windowSize);
 	}
 
 	private static class SequenceNumberComparator implements Comparator<Data> {

briar-core/src/org/briarproject/reliability/Sender.java

@@ -5,6 +5,10 @@ import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.LinkedList;
 import java.util.List;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.locks.Condition;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
 
 import org.briarproject.api.reliability.WriteHandler;
 import org.briarproject.api.system.Clock;
@@ -31,6 +35,9 @@ class Sender {
 	private long lastWindowUpdateOrProbe = Long.MAX_VALUE;
 	private boolean dataWaiting = false;
 
+	private Lock synchLock = new ReentrantLock();
+	private Condition sendWindowAvailable = synchLock.newCondition();
+
 	Sender(Clock clock, WriteHandler writeHandler) {
 		this.clock = clock;
 		this.writeHandler = writeHandler;
@@ -58,7 +65,8 @@ class Sender {
 		long sequenceNumber = a.getSequenceNumber();
 		long now = clock.currentTimeMillis();
 		Outstanding fastRetransmit = null;
-		synchronized(this) {
+		synchLock.lock();
+		try {
 			// Remove the acked data frame if it's outstanding
 			int foundIndex = -1;
 			Iterator<Outstanding> it = outstanding.iterator();
@@ -96,6 +104,9 @@ class Sender {
 			// If space has become available, notify any waiting writers
 			if(windowSize > oldWindowSize || foundIndex != -1) notifyAll();
 		}
+		finally{
+			synchLock.unlock();
+		}
 		// Fast retransmission
 		if(fastRetransmit != null)
 			writeHandler.handleWrite(fastRetransmit.data.getBuffer());
@@ -105,7 +116,8 @@ class Sender {
 		long now = clock.currentTimeMillis();
 		List<Outstanding> retransmit = null;
 		boolean sendProbe = false;
-		synchronized(this) {
+		synchLock.lock();
+		try {
 			if(outstanding.isEmpty()) {
 				if(dataWaiting && now - lastWindowUpdateOrProbe > rto) {
 					sendProbe = true;
@@ -135,6 +147,9 @@ class Sender {
 				}
 			}
 		}
+		finally{
+			synchLock.unlock();
+		}
 		// Send a window probe if necessary
 		if(sendProbe) {
 			byte[] buf = new byte[Data.MIN_LENGTH];
@@ -151,12 +166,13 @@ class Sender {
 
 	void write(Data d) throws IOException, InterruptedException {
 		int payloadLength = d.getPayloadLength();
-		synchronized(this) {
+		synchLock.lock();
+		try {
 			// Wait for space in the window
 			long now = clock.currentTimeMillis(), end = now + WRITE_TIMEOUT;
 			while(now < end && outstandingBytes + payloadLength >= windowSize) {
 				dataWaiting = true;
-				wait(end - now);
+				sendWindowAvailable.await(end - now, TimeUnit.MILLISECONDS);
 				now = clock.currentTimeMillis();
 			}
 			if(outstandingBytes + payloadLength >= windowSize)
@@ -165,11 +181,20 @@ class Sender {
 			outstandingBytes += payloadLength;
 			dataWaiting = false;
 		}
+		finally{
+			synchLock.unlock();
+		}
 		writeHandler.handleWrite(d.getBuffer());
 	}
 
-	synchronized void flush() throws IOException, InterruptedException {
-		while(dataWaiting || !outstanding.isEmpty()) wait();
+	void flush() throws IOException, InterruptedException {
+		synchLock.lock();
+		try{
+			while(dataWaiting || !outstanding.isEmpty()) sendWindowAvailable.await();
+		}
+		finally{
+			synchLock.unlock();
+		}
 	}
 
 	private static class Outstanding {

briar-core/src/org/briarproject/transport/KeyManagerImpl.java

@@ -11,6 +11,8 @@ import java.util.Iterator;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.TimerTask;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
 import java.util.logging.Logger;
 
 import javax.inject.Inject;
@@ -56,6 +58,8 @@ class KeyManagerImpl extends TimerTask implements KeyManager, EventListener {
 	private final Map<EndpointKey, TemporarySecret> currentSecrets;
 	private final Map<EndpointKey, TemporarySecret> newSecrets;
 
+	private final Lock synchLock = new ReentrantLock();
+
 	@Inject
 	KeyManagerImpl(CryptoComponent crypto, DatabaseComponent db,
 			EventBus eventBus, TagRecogniser tagRecogniser, Clock clock,
@@ -72,41 +76,47 @@ class KeyManagerImpl extends TimerTask implements KeyManager, EventListener {
 		newSecrets = new HashMap<EndpointKey, TemporarySecret>();
 	}
 
-	public synchronized boolean start() {
-		eventBus.addListener(this);
-		// Load the temporary secrets and transport latencies from the database
-		Collection<TemporarySecret> secrets;
+	public boolean start() {
+		synchLock.lock();
 		try {
-			secrets = db.getSecrets();
-			maxLatencies.putAll(db.getTransportLatencies());
-		} catch(DbException e) {
-			if(LOG.isLoggable(WARNING)) LOG.log(WARNING, e.toString(), e);
-			return false;
-		}
-		// Work out what phase of its lifecycle each secret is in
-		long now = clock.currentTimeMillis();
-		Collection<TemporarySecret> dead = assignSecretsToMaps(now, secrets);
-		// Replace any dead secrets
-		Collection<TemporarySecret> created = replaceDeadSecrets(now, dead);
-		if(!created.isEmpty()) {
-			// Store any secrets that have been created, removing any dead ones
+			eventBus.addListener(this);
+			// Load the temporary secrets and transport latencies from the database
+			Collection<TemporarySecret> secrets;
 			try {
-				db.addSecrets(created);
+				secrets = db.getSecrets();
+				maxLatencies.putAll(db.getTransportLatencies());
 			} catch(DbException e) {
 				if(LOG.isLoggable(WARNING)) LOG.log(WARNING, e.toString(), e);
 				return false;
 			}
+			// Work out what phase of its lifecycle each secret is in
+			long now = clock.currentTimeMillis();
+			Collection<TemporarySecret> dead = assignSecretsToMaps(now, secrets);
+			// Replace any dead secrets
+			Collection<TemporarySecret> created = replaceDeadSecrets(now, dead);
+			if(!created.isEmpty()) {
+				// Store any secrets that have been created, removing any dead ones
+				try {
+					db.addSecrets(created);
+				} catch(DbException e) {
+					if(LOG.isLoggable(WARNING)) LOG.log(WARNING, e.toString(), e);
+					return false;
+				}
+			}
+			// Pass the old, current and new secrets to the recogniser
+			for(TemporarySecret s : oldSecrets.values())
+				tagRecogniser.addSecret(s);
+			for(TemporarySecret s : currentSecrets.values())
+				tagRecogniser.addSecret(s);
+			for(TemporarySecret s : newSecrets.values())
+				tagRecogniser.addSecret(s);
+			// Schedule periodic key rotation
+			timer.scheduleAtFixedRate(this, MS_BETWEEN_CHECKS, MS_BETWEEN_CHECKS);
+			return true;
+		}
+		finally{
+			synchLock.unlock();
 		}
-		// Pass the old, current and new secrets to the recogniser
-		for(TemporarySecret s : oldSecrets.values())
-			tagRecogniser.addSecret(s);
-		for(TemporarySecret s : currentSecrets.values())
-			tagRecogniser.addSecret(s);
-		for(TemporarySecret s : newSecrets.values())
-			tagRecogniser.addSecret(s);
-		// Schedule periodic key rotation
-		timer.scheduleAtFixedRate(this, MS_BETWEEN_CHECKS, MS_BETWEEN_CHECKS);
-		return true;
 	}
 
 	// Assigns secrets to the appropriate maps and returns any dead secrets
@@ -215,15 +225,21 @@ class KeyManagerImpl extends TimerTask implements KeyManager, EventListener {
 		return created;
 	}
 
-	public synchronized boolean stop() {
-		eventBus.removeListener(this);
-		timer.cancel();
-		tagRecogniser.removeSecrets();
-		maxLatencies.clear();
-		removeAndEraseSecrets(oldSecrets);
-		removeAndEraseSecrets(currentSecrets);
-		removeAndEraseSecrets(newSecrets);
-		return true;
+	public boolean stop() {
+		synchLock.lock();
+		try{
+			eventBus.removeListener(this);
+			timer.cancel();
+			tagRecogniser.removeSecrets();
+			maxLatencies.clear();
+			removeAndEraseSecrets(oldSecrets);
+			removeAndEraseSecrets(currentSecrets);
+			removeAndEraseSecrets(newSecrets);
+			return true;
+		}
+		finally{
+			synchLock.unlock();
+		}
 	}
 
 	// Locking: this
@@ -232,98 +248,116 @@ class KeyManagerImpl extends TimerTask implements KeyManager, EventListener {
 		m.clear();
 	}
 
-	public synchronized StreamContext getStreamContext(ContactId c,
+	public StreamContext getStreamContext(ContactId c,
 			TransportId t) {
-		TemporarySecret s = currentSecrets.get(new EndpointKey(c, t));
-		if(s == null) {
-			LOG.info("No secret for endpoint");
-			return null;
-		}
-		long streamNumber;
-		try {
-			streamNumber = db.incrementStreamCounter(c, t, s.getPeriod());
-			if(streamNumber == -1) {
-				LOG.info("No counter for period");
+		synchLock.lock();
+		try{
+			TemporarySecret s = currentSecrets.get(new EndpointKey(c, t));
+			if(s == null) {
+				LOG.info("No secret for endpoint");
 				return null;
 			}
-		} catch(DbException e) {
-			if(LOG.isLoggable(WARNING)) LOG.log(WARNING, e.toString(), e);
-			return null;
+			long streamNumber;
+			try {
+				streamNumber = db.incrementStreamCounter(c, t, s.getPeriod());
+				if(streamNumber == -1) {
+					LOG.info("No counter for period");
+					return null;
+				}
+			} catch(DbException e) {
+				if(LOG.isLoggable(WARNING)) LOG.log(WARNING, e.toString(), e);
+				return null;
+			}
+			// Clone the secret - the original will be erased
+			byte[] secret = s.getSecret().clone();
+			return new StreamContext(c, t, secret, streamNumber, s.getAlice());
+		}
+		finally{
+			synchLock.unlock();
 		}
-		// Clone the secret - the original will be erased
-		byte[] secret = s.getSecret().clone();
-		return new StreamContext(c, t, secret, streamNumber, s.getAlice());
 	}
 
-	public synchronized void endpointAdded(Endpoint ep, long maxLatency,
+	public void endpointAdded(Endpoint ep, long maxLatency,
 			byte[] initialSecret) {
-		maxLatencies.put(ep.getTransportId(), maxLatency);
-		// Work out which rotation period we're in
-		long elapsed = clock.currentTimeMillis() - ep.getEpoch();
-		long rotation = maxLatency + MAX_CLOCK_DIFFERENCE;
-		long period = (elapsed / rotation) + 1;
-		if(period < 1) throw new IllegalStateException();
-		// Derive the old, current and new secrets
-		byte[] b1 = initialSecret;
-		for(long p = 0; p < period; p++) {
-			byte[] temp = crypto.deriveNextSecret(b1, p);
-			ByteUtils.erase(b1);
-			b1 = temp;
+		synchLock.lock();
+		try{
+			maxLatencies.put(ep.getTransportId(), maxLatency);
+			// Work out which rotation period we're in
+			long elapsed = clock.currentTimeMillis() - ep.getEpoch();
+			long rotation = maxLatency + MAX_CLOCK_DIFFERENCE;
+			long period = (elapsed / rotation) + 1;
+			if(period < 1) throw new IllegalStateException();
+			// Derive the old, current and new secrets
+			byte[] b1 = initialSecret;
+			for(long p = 0; p < period; p++) {
+				byte[] temp = crypto.deriveNextSecret(b1, p);
+				ByteUtils.erase(b1);
+				b1 = temp;
+			}
+			byte[] b2 = crypto.deriveNextSecret(b1, period);
+			byte[] b3 = crypto.deriveNextSecret(b2, period + 1);
+			TemporarySecret s1 = new TemporarySecret(ep, period - 1, b1);
+			TemporarySecret s2 = new TemporarySecret(ep, period, b2);
+			TemporarySecret s3 = new TemporarySecret(ep, period + 1, b3);
+			// Add the incoming secrets to their respective maps
+			EndpointKey k = new EndpointKey(ep);
+			oldSecrets.put(k, s1);
+			currentSecrets.put(k, s2);
+			newSecrets.put(k, s3);
+			// Store the new secrets
+			try {
+				db.addSecrets(Arrays.asList(s1, s2, s3));
+			} catch(DbException e) {
+				if(LOG.isLoggable(WARNING)) LOG.log(WARNING, e.toString(), e);
+				return;
+			}
+			// Pass the new secrets to the recogniser
+			tagRecogniser.addSecret(s1);
+			tagRecogniser.addSecret(s2);
+			tagRecogniser.addSecret(s3);
 		}
-		byte[] b2 = crypto.deriveNextSecret(b1, period);
-		byte[] b3 = crypto.deriveNextSecret(b2, period + 1);
-		TemporarySecret s1 = new TemporarySecret(ep, period - 1, b1);
-		TemporarySecret s2 = new TemporarySecret(ep, period, b2);
-		TemporarySecret s3 = new TemporarySecret(ep, period + 1, b3);
-		// Add the incoming secrets to their respective maps
-		EndpointKey k = new EndpointKey(ep);
-		oldSecrets.put(k, s1);
-		currentSecrets.put(k, s2);
-		newSecrets.put(k, s3);
-		// Store the new secrets
-		try {
-			db.addSecrets(Arrays.asList(s1, s2, s3));
-		} catch(DbException e) {
-			if(LOG.isLoggable(WARNING)) LOG.log(WARNING, e.toString(), e);
-			return;
+		finally{
+			synchLock.unlock();
 		}
-		// Pass the new secrets to the recogniser
-		tagRecogniser.addSecret(s1);
-		tagRecogniser.addSecret(s2);
-		tagRecogniser.addSecret(s3);
 	}
 
 	@Override
-	public synchronized void run() {
+	public void run() {
+		synchLock.lock();
+		try{
 		// Rebuild the maps because we may be running a whole period late
-		Collection<TemporarySecret> secrets = new ArrayList<TemporarySecret>();
-		secrets.addAll(oldSecrets.values());
-		secrets.addAll(currentSecrets.values());
-		secrets.addAll(newSecrets.values());
-		oldSecrets.clear();
-		currentSecrets.clear();
-		newSecrets.clear();
-		// Work out what phase of its lifecycle each secret is in
-		long now = clock.currentTimeMillis();
-		Collection<TemporarySecret> dead = assignSecretsToMaps(now, secrets);
-		// Remove any dead secrets from the recogniser
-		for(TemporarySecret s : dead) {
-			ContactId c = s.getContactId();
-			TransportId t = s.getTransportId();
-			long period = s.getPeriod();
-			tagRecogniser.removeSecret(c, t, period);
-		}
-		// Replace any dead secrets
-		Collection<TemporarySecret> created = replaceDeadSecrets(now, dead);
-		if(!created.isEmpty()) {
-			// Store any secrets that have been created
-			try {
-				db.addSecrets(created);
-			} catch(DbException e) {
-				if(LOG.isLoggable(WARNING)) LOG.log(WARNING, e.toString(), e);
+			Collection<TemporarySecret> secrets = new ArrayList<TemporarySecret>();
+			secrets.addAll(oldSecrets.values());
+			secrets.addAll(currentSecrets.values());
+			secrets.addAll(newSecrets.values());
+			oldSecrets.clear();
+			currentSecrets.clear();
+			newSecrets.clear();
+			// Work out what phase of its lifecycle each secret is in
+			long now = clock.currentTimeMillis();
+			Collection<TemporarySecret> dead = assignSecretsToMaps(now, secrets);
+			// Remove any dead secrets from the recogniser
+			for(TemporarySecret s : dead) {
+				ContactId c = s.getContactId();
+				TransportId t = s.getTransportId();
+				long period = s.getPeriod();
+				tagRecogniser.removeSecret(c, t, period);
 			}
-			// Pass any secrets that have been created to the recogniser
-			for(TemporarySecret s : created) tagRecogniser.addSecret(s);
+			// Replace any dead secrets
+			Collection<TemporarySecret> created = replaceDeadSecrets(now, dead);
+			if(!created.isEmpty()) {
+				// Store any secrets that have been created
+				try {
+					db.addSecrets(created);
+				} catch(DbException e) {
+					if(LOG.isLoggable(WARNING)) LOG.log(WARNING, e.toString(), e);
+				}
+				// Pass any secrets that have been created to the recogniser
+				for(TemporarySecret s : created) tagRecogniser.addSecret(s);
+			}
+		}
+		finally{
+			synchLock.unlock();
 		}
 	}
 
@@ -407,11 +441,15 @@ class KeyManagerImpl extends TimerTask implements KeyManager, EventListener {
 		public void run() {
 			ContactId c = event.getContactId();
 			tagRecogniser.removeSecrets(c);
-			synchronized(KeyManagerImpl.this) {
+			synchLock.lock();
+			try {
 				removeAndEraseSecrets(c, oldSecrets);
 				removeAndEraseSecrets(c, currentSecrets);
 				removeAndEraseSecrets(c, newSecrets);
 			}
+			finally{
+				synchLock.unlock();
+			}
 		}
 	}
 
@@ -425,9 +463,13 @@ class KeyManagerImpl extends TimerTask implements KeyManager, EventListener {
 
 		@Override
 		public void run() {
-			synchronized(KeyManagerImpl.this) {
+			synchLock.lock();
+			try {
 				maxLatencies.put(event.getTransportId(), event.getMaxLatency());
 			}
+			finally{
+				synchLock.unlock();
+			}
 		}
 	}
 
@@ -443,12 +485,16 @@ class KeyManagerImpl extends TimerTask implements KeyManager, EventListener {
 		public void run() {
 			TransportId t = event.getTransportId();
 			tagRecogniser.removeSecrets(t);
-			synchronized(KeyManagerImpl.this) {
+			synchLock.lock();
+			try {
 				maxLatencies.remove(t);
 				removeAndEraseSecrets(t, oldSecrets);
 				removeAndEraseSecrets(t, currentSecrets);
 				removeAndEraseSecrets(t, newSecrets);
 			}
+			finally{
+				synchLock.unlock();
+			}
 		}
 	}
 }

briar-core/src/org/briarproject/transport/TagRecogniserImpl.java

@@ -2,6 +2,8 @@ package org.briarproject.transport;
 
 import java.util.HashMap;
 import java.util.Map;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
 
 import javax.inject.Inject;
 
@@ -20,6 +22,9 @@ class TagRecogniserImpl implements TagRecogniser {
 	private final DatabaseComponent db;
 	// Locking: this
 	private final Map<TransportId, TransportTagRecogniser> recognisers;
+	
+	private final Lock synchLock = new ReentrantLock();
+
 
 	@Inject
 	TagRecogniserImpl(CryptoComponent crypto, DatabaseComponent db) {
@@ -31,9 +36,13 @@ class TagRecogniserImpl implements TagRecogniser {
 	public StreamContext recogniseTag(TransportId t, byte[] tag)
 			throws DbException {
 		TransportTagRecogniser r;
-		synchronized(this) {
+		synchLock.lock();
+		try {
 			r = recognisers.get(t);
 		}
+		finally{
+			synchLock.unlock();
+		}
 		if(r == null) return null;
 		return r.recogniseTag(tag);
 	}
@@ -41,35 +50,63 @@ class TagRecogniserImpl implements TagRecogniser {
 	public void addSecret(TemporarySecret s) {
 		TransportId t = s.getTransportId();
 		TransportTagRecogniser r;
-		synchronized(this) {
+		synchLock.lock();
+		try {
 			r = recognisers.get(t);
 			if(r == null) {
 				r = new TransportTagRecogniser(crypto, db, t);
 				recognisers.put(t, r);
 			}
 		}
+		finally{
+			synchLock.unlock();
+		}
 		r.addSecret(s);
 	}
 
 	public void removeSecret(ContactId c, TransportId t, long period) {
 		TransportTagRecogniser r;
-		synchronized(this) {
+		synchLock.lock();
+		try {
 			r = recognisers.get(t);
 		}
+		finally{
+			synchLock.unlock();
+		}
 		if(r != null) r.removeSecret(c, period);
 	}
 
-	public synchronized void removeSecrets(ContactId c) {
-		for(TransportTagRecogniser r : recognisers.values())
-			r.removeSecrets(c);
+	public void removeSecrets(ContactId c) {
+		synchLock.lock();
+		try{
+			for(TransportTagRecogniser r : recognisers.values())
+				r.removeSecrets(c);
+		}
+		finally{
+			synchLock.unlock();
+		}
 	}
 
-	public synchronized void removeSecrets(TransportId t) {
-		recognisers.remove(t);
+	public void removeSecrets(TransportId t) {
+		synchLock.lock();
+		try{
+			recognisers.remove(t);
+		}
+		finally{
+			synchLock.unlock();
+		}
+
 	}
 
-	public synchronized void removeSecrets() {
-		for(TransportTagRecogniser r : recognisers.values())
-			r.removeSecrets();
+	public void removeSecrets() {
+		synchLock.lock();
+		try{
+			for(TransportTagRecogniser r : recognisers.values())
+				r.removeSecrets();
+		}
+		finally{
+			synchLock.unlock();
+		}
+
 	}
 }

briar-core/src/org/briarproject/transport/TransportTagRecogniser.java

@@ -6,6 +6,8 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.Map;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
 
 import org.briarproject.api.Bytes;
 import org.briarproject.api.ContactId;
@@ -30,6 +32,8 @@ class TransportTagRecogniser {
 	private final Map<Bytes, TagContext> tagMap; // Locking: this
 	private final Map<RemovalKey, RemovalContext> removalMap; // Locking: this
 
+	private final Lock synchLock = new ReentrantLock();
+
 	TransportTagRecogniser(CryptoComponent crypto, DatabaseComponent db,
 			TransportId transportId) {
 		this.crypto = crypto;
@@ -39,62 +43,80 @@ class TransportTagRecogniser {
 		removalMap = new HashMap<RemovalKey, RemovalContext>();
 	}
 
-	synchronized StreamContext recogniseTag(byte[] tag) throws DbException {
-		TagContext t = tagMap.remove(new Bytes(tag));
-		if(t == null) return null; // The tag was not expected
-		// Update the reordering window and the expected tags
-		SecretKey key = crypto.deriveTagKey(t.secret, !t.alice);
-		for(long streamNumber : t.window.setSeen(t.streamNumber)) {
-			byte[] tag1 = new byte[TAG_LENGTH];
-			crypto.encodeTag(tag1, key, streamNumber);
-			if(streamNumber < t.streamNumber) {
-				TagContext removed = tagMap.remove(new Bytes(tag1));
-				assert removed != null;
-			} else {
-				TagContext added = new TagContext(t, streamNumber);
-				TagContext duplicate = tagMap.put(new Bytes(tag1), added);
+	StreamContext recogniseTag(byte[] tag) throws DbException {
+		synchLock.lock();
+		try{
+			TagContext t = tagMap.remove(new Bytes(tag));
+			if(t == null) return null; // The tag was not expected
+			// Update the reordering window and the expected tags
+			SecretKey key = crypto.deriveTagKey(t.secret, !t.alice);
+			for(long streamNumber : t.window.setSeen(t.streamNumber)) {
+				byte[] tag1 = new byte[TAG_LENGTH];
+				crypto.encodeTag(tag1, key, streamNumber);
+				if(streamNumber < t.streamNumber) {
+					TagContext removed = tagMap.remove(new Bytes(tag1));
+					assert removed != null;
+				} else {
+					TagContext added = new TagContext(t, streamNumber);
+					TagContext duplicate = tagMap.put(new Bytes(tag1), added);
+					assert duplicate == null;
+				}
+			}
+			key.erase();
+			// Store the updated reordering window in the DB
+			db.setReorderingWindow(t.contactId, transportId, t.period,
+					t.window.getCentre(), t.window.getBitmap());
+			// Clone the secret - the key manager will erase the original
+			byte[] secret = t.secret.clone();
+			return new StreamContext(t.contactId, transportId, secret,
+					t.streamNumber, t.alice);
+		}
+		finally{
+			synchLock.unlock();
+		}
+	}
+
+	void addSecret(TemporarySecret s) {
+		synchLock.lock();
+		try{
+			ContactId contactId = s.getContactId();
+			boolean alice = s.getAlice();
+			long period = s.getPeriod();
+			byte[] secret = s.getSecret();
+			long centre = s.getWindowCentre();
+			byte[] bitmap = s.getWindowBitmap();
+			// Create the reordering window and the expected tags
+			SecretKey key = crypto.deriveTagKey(secret, !alice);
+			ReorderingWindow window = new ReorderingWindow(centre, bitmap);
+			for(long streamNumber : window.getUnseen()) {
+				byte[] tag = new byte[TAG_LENGTH];
+				crypto.encodeTag(tag, key, streamNumber);
+				TagContext added = new TagContext(contactId, alice, period,
+						secret, window, streamNumber);
+				TagContext duplicate = tagMap.put(new Bytes(tag), added);
 				assert duplicate == null;
 			}
+			key.erase();
+			// Create a removal context to remove the window and the tags later
+			RemovalContext r = new RemovalContext(window, secret, alice);
+			removalMap.put(new RemovalKey(contactId, period), r);
+		}
+		finally{
+			synchLock.unlock();
 		}
-		key.erase();
-		// Store the updated reordering window in the DB
-		db.setReorderingWindow(t.contactId, transportId, t.period,
-				t.window.getCentre(), t.window.getBitmap());
-		// Clone the secret - the key manager will erase the original
-		byte[] secret = t.secret.clone();
-		return new StreamContext(t.contactId, transportId, secret,
-				t.streamNumber, t.alice);
 	}
 
-	synchronized void addSecret(TemporarySecret s) {
-		ContactId contactId = s.getContactId();
-		boolean alice = s.getAlice();
-		long period = s.getPeriod();
-		byte[] secret = s.getSecret();
-		long centre = s.getWindowCentre();
-		byte[] bitmap = s.getWindowBitmap();
-		// Create the reordering window and the expected tags
-		SecretKey key = crypto.deriveTagKey(secret, !alice);
-		ReorderingWindow window = new ReorderingWindow(centre, bitmap);
-		for(long streamNumber : window.getUnseen()) {
-			byte[] tag = new byte[TAG_LENGTH];
-			crypto.encodeTag(tag, key, streamNumber);
-			TagContext added = new TagContext(contactId, alice, period,
-					secret, window, streamNumber);
-			TagContext duplicate = tagMap.put(new Bytes(tag), added);
-			assert duplicate == null;
+	void removeSecret(ContactId contactId, long period) {
+		synchLock.lock();
+		try{
+			RemovalKey k = new RemovalKey(contactId, period);
+			RemovalContext removed = removalMap.remove(k);
+			if(removed == null) throw new IllegalArgumentException();
+			removeSecret(removed);
+		}
+		finally{
+			synchLock.unlock();
 		}
-		key.erase();
-		// Create a removal context to remove the window and the tags later
-		RemovalContext r = new RemovalContext(window, secret, alice);
-		removalMap.put(new RemovalKey(contactId, period), r);
-	}
-
-	synchronized void removeSecret(ContactId contactId, long period) {
-		RemovalKey k = new RemovalKey(contactId, period);
-		RemovalContext removed = removalMap.remove(k);
-		if(removed == null) throw new IllegalArgumentException();
-		removeSecret(removed);
 	}
 
 	// Locking: this
@@ -110,17 +132,29 @@ class TransportTagRecogniser {
 		key.erase();
 	}
 
-	synchronized void removeSecrets(ContactId c) {
-		Collection<RemovalKey> keysToRemove = new ArrayList<RemovalKey>();
-		for(RemovalKey k : removalMap.keySet())
-			if(k.contactId.equals(c)) keysToRemove.add(k);
-		for(RemovalKey k : keysToRemove) removeSecret(k.contactId, k.period);
+	void removeSecrets(ContactId c) {
+		synchLock.lock();
+		try{
+			Collection<RemovalKey> keysToRemove = new ArrayList<RemovalKey>();
+			for(RemovalKey k : removalMap.keySet())
+				if(k.contactId.equals(c)) keysToRemove.add(k);
+			for(RemovalKey k : keysToRemove) removeSecret(k.contactId, k.period);
+		}
+		finally{
+			synchLock.unlock();
+		}
 	}
 
-	synchronized void removeSecrets() {
-		for(RemovalContext r : removalMap.values()) removeSecret(r);
-		assert tagMap.isEmpty();
-		removalMap.clear();
+	void removeSecrets() {
+		synchLock.lock();
+		try{
+			for(RemovalContext r : removalMap.values()) removeSecret(r);
+			assert tagMap.isEmpty();
+			removalMap.clear();
+		}
+		finally{
+			synchLock.unlock();
+		}
 	}
 
 	private static class TagContext {

briar-desktop/src/org/briarproject/lifecycle/WindowsShutdownManagerImpl.java

@@ -8,6 +8,8 @@ import java.util.Collections;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.concurrent.atomic.AtomicBoolean;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
 import java.util.logging.Logger;
 
 import org.briarproject.util.OsUtils;
@@ -38,6 +40,9 @@ class WindowsShutdownManagerImpl extends ShutdownManagerImpl {
 	private final Map<String, Object> options;
 
 	private boolean initialised = false; // Locking: this
+	
+	private final Lock synchLock = new ReentrantLock();
+
 
 	WindowsShutdownManagerImpl() {
 		// Use the Unicode versions of Win32 API calls
@@ -48,9 +53,15 @@ class WindowsShutdownManagerImpl extends ShutdownManagerImpl {
 	}
 
 	@Override
-	public synchronized int addShutdownHook(Runnable r) {
-		if(!initialised) initialise();
-		return super.addShutdownHook(r);
+	public int addShutdownHook(Runnable r) {
+		synchLock.lock();
+		try {
+			if(!initialised) initialise();
+			return super.addShutdownHook(r);
+		} 
+		finally{
+			synchLock.unlock();
+		}
 	}
 
 	@Override
@@ -69,20 +80,26 @@ class WindowsShutdownManagerImpl extends ShutdownManagerImpl {
 	}
 
 	// Package access for testing
-	synchronized void runShutdownHooks() {
-		boolean interrupted = false;
-		// Start each hook in its own thread
-		for(Thread hook : hooks.values()) hook.start();
-		// Wait for all the hooks to finish
-		for(Thread hook : hooks.values()) {
-			try {
-				hook.join();
-			} catch(InterruptedException e) {
-				LOG.warning("Interrupted while running shutdown hooks");
-				interrupted = true;
+	void runShutdownHooks() {
+		synchLock.lock();
+		try {
+			boolean interrupted = false;
+			// Start each hook in its own thread
+			for(Thread hook : hooks.values()) hook.start();
+			// Wait for all the hooks to finish
+			for(Thread hook : hooks.values()) {
+				try {
+					hook.join();
+				} catch(InterruptedException e) {
+					LOG.warning("Interrupted while running shutdown hooks");
+					interrupted = true;
+				}
 			}
+			if(interrupted) Thread.currentThread().interrupt();
+		} 
+		finally{
+			synchLock.unlock();
 		}
-		if(interrupted) Thread.currentThread().interrupt();
 	}
 
 	private class EventLoop extends Thread {

briar-desktop/src/org/briarproject/plugins/file/PollingRemovableDriveMonitor.java

@@ -4,6 +4,10 @@ import java.io.File;
 import java.io.IOException;
 import java.util.Collection;
 import java.util.concurrent.Executor;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.locks.Condition;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
 import java.util.logging.Logger;
 
 class PollingRemovableDriveMonitor implements RemovableDriveMonitor, Runnable {
@@ -14,11 +18,14 @@ class PollingRemovableDriveMonitor implements RemovableDriveMonitor, Runnable {
 	private final Executor ioExecutor;
 	private final RemovableDriveFinder finder;
 	private final long pollingInterval;
-	private final Object pollingLock = new Object();
 
 	private volatile boolean running = false;
 	private volatile Callback callback = null;
 
+	private final Lock synchLock = new ReentrantLock();
+	private final Condition stopPolling = synchLock.newCondition();
+
+
 	public PollingRemovableDriveMonitor(Executor ioExecutor,
 			RemovableDriveFinder finder, long pollingInterval) {
 		this.ioExecutor = ioExecutor;
@@ -34,8 +41,12 @@ class PollingRemovableDriveMonitor implements RemovableDriveMonitor, Runnable {
 
 	public void stop() throws IOException {
 		running = false;
-		synchronized(pollingLock) {
-			pollingLock.notifyAll();
+		synchLock.lock();
+		try {
+			stopPolling.signalAll();
+		} 
+		finally {
+			synchLock.unlock();
 		}
 	}
 
@@ -43,8 +54,12 @@ class PollingRemovableDriveMonitor implements RemovableDriveMonitor, Runnable {
 		try {
 			Collection<File> drives = finder.findRemovableDrives();
 			while(running) {
-				synchronized(pollingLock) {
-					pollingLock.wait(pollingInterval);
+				synchLock.lock();
+				try {
+					stopPolling.await(pollingInterval, TimeUnit.MILLISECONDS);
+				} 
+				finally{
+					synchLock.unlock();
 				}
 				if(!running) return;
 				Collection<File> newDrives = finder.findRemovableDrives();

briar-desktop/src/org/briarproject/plugins/file/UnixRemovableDriveMonitor.java

@@ -4,6 +4,9 @@ import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.concurrent.locks.Condition;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
 
 import net.contentobjects.jnotify.JNotify;
 import net.contentobjects.jnotify.JNotifyListener;
@@ -21,7 +24,11 @@ JNotifyListener {
 	private Callback callback = null; // Locking: this
 
 	protected abstract String[] getPathsToWatch();
-
+	
+	//TODO: rationalise this in a further refactor
+	private final Lock synchLock = new ReentrantLock();
+	private static final Lock staticSynchLock = new ReentrantLock();
+	
 	private static Throwable tryLoad() {
 		try {
 			Class.forName("net.contentobjects.jnotify.JNotify");
@@ -33,12 +40,18 @@ JNotifyListener {
 		}
 	}
 
-	public static synchronized void checkEnabled() throws IOException {
-		if(!triedLoad) {
-			loadError = tryLoad();
-			triedLoad = true;
+	public static void checkEnabled() throws IOException {
+		staticSynchLock.lock();
+		try {
+			if(!triedLoad) {
+				loadError = tryLoad();
+				triedLoad = true;
+			}
+			if(loadError != null) throw new IOException(loadError.toString());
+		} 
+		finally{
+			staticSynchLock.unlock();
 		}
-		if(loadError != null) throw new IOException(loadError.toString());
 	}
 
 	public void start(Callback callback) throws IOException {
@@ -49,34 +62,46 @@ JNotifyListener {
 			if(new File(path).exists())
 				watches.add(JNotify.addWatch(path, mask, false, this));
 		}
-		synchronized(this) {
-			assert !started;
-			assert this.callback == null;
-			started = true;
-			this.callback = callback;
-			this.watches.addAll(watches);
-		}
+			synchLock.lock();
+			try {
+				assert !started;
+				assert this.callback == null;
+				started = true;
+				this.callback = callback;
+				this.watches.addAll(watches);
+			} 
+			finally{
+				synchLock.unlock();
+			}
 	}
 
 	public void stop() throws IOException {
 		checkEnabled();
 		List<Integer> watches;
-		synchronized(this) {
-			assert started;
-			assert callback != null;
-			started = false;
-			callback = null;
-			watches = new ArrayList<Integer>(this.watches);
-			this.watches.clear();
-		}
+			synchLock.lock();
+			try {
+				assert started;
+				assert callback != null;
+				started = false;
+				callback = null;
+				watches = new ArrayList<Integer>(this.watches);
+				this.watches.clear();
+			} 
+			finally{
+				synchLock.unlock();
+			}
 		for(Integer w : watches) JNotify.removeWatch(w);
 	}
 
 	public void fileCreated(int wd, String rootPath, String name) {
 		Callback callback;
-		synchronized(this) {
-			callback = this.callback;
-		}
+			synchLock.lock();
+			try {
+				callback = this.callback;
+			} 
+			finally{
+				synchLock.unlock();
+			}
 		if(callback != null)
 			callback.driveInserted(new File(rootPath + "/" + name));
 	}

briar-desktop/src/org/briarproject/plugins/modem/ModemImpl.java

@@ -10,6 +10,10 @@ import java.io.InputStream;
 import java.io.OutputStream;
 import java.util.concurrent.Executor;
 import java.util.concurrent.Semaphore;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.locks.Condition;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
 import java.util.logging.Logger;
 
 import jssc.SerialPortEvent;
@@ -44,6 +48,11 @@ class ModemImpl implements Modem, WriteHandler, SerialPortEventListener {
 
 	private ReliabilityLayer reliability = null; // Locking: this
 	private boolean initialised = false, connected = false; // Locking: this
+	
+	private final Lock synchLock = new ReentrantLock();
+	private final Condition connectedStateChanged = synchLock.newCondition();
+	private final Condition initialisedStateChanged = synchLock.newCondition();
+
 
 	ModemImpl(Executor executor, ReliabilityLayerFactory reliabilityFactory,
 			Clock clock, Callback callback, SerialPort port) {
@@ -91,14 +100,18 @@ class ModemImpl implements Modem, WriteHandler, SerialPortEventListener {
 			// Wait for the event thread to receive "OK"
 			boolean success = false;
 			try {
-				synchronized(this) {
+				synchLock.lock();
+				try {
 					long now = clock.currentTimeMillis();
 					long end = now + OK_TIMEOUT;
 					while(now < end && !initialised) {
-						wait(end - now);
+						initialisedStateChanged.await(end - now, TimeUnit.MILLISECONDS);
 						now = clock.currentTimeMillis();
 					}
 					success = initialised;
+				} 
+				finally{
+					synchLock.unlock();
 				}
 			} catch(InterruptedException e) {
 				tryToClose(port);
@@ -123,11 +136,16 @@ class ModemImpl implements Modem, WriteHandler, SerialPortEventListener {
 
 	public void stop() throws IOException {
 		LOG.info("Stopping");
-		// Wake any threads that are waiting to connect
-		synchronized(this) {
+		synchLock.lock();
+		try {
+			// Wake any threads that are waiting to connect
 			initialised = false;
 			connected = false;
-			notifyAll();
+			initialisedStateChanged.signalAll();
+			connectedStateChanged.signalAll();
+		} 
+		finally{
+			synchLock.unlock();
 		}
 		// Hang up if necessary and close the port
 		try {
@@ -148,7 +166,8 @@ class ModemImpl implements Modem, WriteHandler, SerialPortEventListener {
 	// Locking: stateChange
 	private void hangUpInner() throws IOException {
 		ReliabilityLayer reliability;
-		synchronized(this) {
+		synchLock.lock();
+		try {
 			if(this.reliability == null) {
 				LOG.info("Not hanging up - already on the hook");
 				return;
@@ -156,6 +175,9 @@ class ModemImpl implements Modem, WriteHandler, SerialPortEventListener {
 			reliability = this.reliability;
 			this.reliability = null;
 			connected = false;
+		} 
+		finally{
+			synchLock.unlock();
 		}
 		reliability.stop();
 		LOG.info("Hanging up");
@@ -182,7 +204,8 @@ class ModemImpl implements Modem, WriteHandler, SerialPortEventListener {
 		try {
 			ReliabilityLayer reliability =
 					reliabilityFactory.createReliabilityLayer(this);
-			synchronized(this) {
+			synchLock.lock();
+			try {
 				if(!initialised) {
 					LOG.info("Not dialling - modem not initialised");
 					return false;
@@ -192,6 +215,9 @@ class ModemImpl implements Modem, WriteHandler, SerialPortEventListener {
 					return false;
 				}
 				this.reliability = reliability;
+			} 
+			finally{
+				synchLock.unlock();
 			}
 			reliability.start();
 			LOG.info("Dialling");
@@ -204,14 +230,18 @@ class ModemImpl implements Modem, WriteHandler, SerialPortEventListener {
 			}
 			// Wait for the event thread to receive "CONNECT"
 			try {
-				synchronized(this) {
+				synchLock.lock();
+				try {
 					long now = clock.currentTimeMillis();
 					long end = now + CONNECT_TIMEOUT;
 					while(now < end && initialised && !connected) {
-						wait(end - now);
+						connectedStateChanged.await(end - now, TimeUnit.MILLISECONDS);
 						now = clock.currentTimeMillis();
 					}
 					if(connected) return true;
+				} 
+				finally{
+					synchLock.unlock();
 				}
 			} catch(InterruptedException e) {
 				tryToClose(port);
@@ -227,8 +257,12 @@ class ModemImpl implements Modem, WriteHandler, SerialPortEventListener {
 
 	public InputStream getInputStream() throws IOException {
 		ReliabilityLayer reliability;
-		synchronized(this) {
+		synchLock.lock();
+		try {
 			reliability = this.reliability;
+		} 
+		finally{
+			synchLock.unlock();
 		}
 		if(reliability == null) throw new IOException("Not connected");
 		return reliability.getInputStream();
@@ -236,8 +270,12 @@ class ModemImpl implements Modem, WriteHandler, SerialPortEventListener {
 
 	public OutputStream getOutputStream() throws IOException {
 		ReliabilityLayer reliability;
-		synchronized(this) {
+		synchLock.lock();
+		try {
 			reliability = this.reliability;
+		} 
+		finally{
+			synchLock.unlock();
 		}
 		if(reliability == null) throw new IOException("Not connected");
 		return reliability.getOutputStream();
@@ -288,8 +326,12 @@ class ModemImpl implements Modem, WriteHandler, SerialPortEventListener {
 
 	private boolean handleData(byte[] b) throws IOException {
 		ReliabilityLayer reliability;
-		synchronized(this) {
+		synchLock.lock();
+		try {
 			reliability = this.reliability;
+		} 
+		finally{
+			synchLock.unlock();
 		}
 		if(reliability == null) return false;
 		reliability.handleRead(b);
@@ -309,9 +351,13 @@ class ModemImpl implements Modem, WriteHandler, SerialPortEventListener {
 				lineLen = 0;
 				if(LOG.isLoggable(INFO)) LOG.info("Modem status: " + s);
 				if(s.startsWith("CONNECT")) {
-					synchronized(this) {
+					synchLock.lock();
+					try {
 						connected = true;
-						notifyAll();
+						connectedStateChanged.signalAll();
+					} 
+					finally{
+						synchLock.unlock();
 					}
 					// There might be data in the buffer as well as text
 					int off = i + 1;
@@ -323,14 +369,22 @@ class ModemImpl implements Modem, WriteHandler, SerialPortEventListener {
 					return;
 				} else if(s.equals("BUSY") || s.equals("NO DIALTONE")
 						|| s.equals("NO CARRIER")) {
-					synchronized(this) {
+					synchLock.lock();
+					try {
 						connected = false;
-						notifyAll();
+						connectedStateChanged.signalAll();
+					} 
+					finally{
+						synchLock.unlock();
 					}
 				} else if(s.equals("OK")) {
-					synchronized(this) {
+					synchLock.lock();
+					try {
 						initialised = true;
-						notifyAll();
+						initialisedStateChanged.signalAll();
+					} 
+					finally{
+						synchLock.unlock();
 					}
 				} else if(s.equals("RING")) {
 					executor.execute(new Runnable() {
@@ -358,7 +412,8 @@ class ModemImpl implements Modem, WriteHandler, SerialPortEventListener {
 		try {
 			ReliabilityLayer reliability =
 					reliabilityFactory.createReliabilityLayer(this);
-			synchronized(this) {
+			synchLock.lock();
+			try {
 				if(!initialised) {
 					LOG.info("Not answering - modem not initialised");
 					return;
@@ -368,6 +423,9 @@ class ModemImpl implements Modem, WriteHandler, SerialPortEventListener {
 					return;
 				}
 				this.reliability = reliability;
+			} 
+			finally{
+				synchLock.unlock();
 			}
 			reliability.start();
 			LOG.info("Answering");
@@ -380,14 +438,18 @@ class ModemImpl implements Modem, WriteHandler, SerialPortEventListener {
 			// Wait for the event thread to receive "CONNECT"
 			boolean success = false;
 			try {
-				synchronized(this) {
+				synchLock.lock();
+				try {
 					long now = clock.currentTimeMillis();
 					long end = now + CONNECT_TIMEOUT;
 					while(now < end && initialised && !connected) {
-						wait(end - now);
+						connectedStateChanged.await(end - now, TimeUnit.MILLISECONDS);
 						now = clock.currentTimeMillis();
 					}
 					success = connected;
+				} 
+				finally{
+					synchLock.unlock();
 				}
 			} catch(InterruptedException e) {
 				tryToClose(port);