java: add test with deeper paths

also format test files

java/ql/test/query-tests/ThreadSafe/ThreadSafe.expected

@@ -9,6 +9,7 @@
 | examples/C.java:26:9:26:14 | this.y | This field access (publicly accessible via $@) is not protected by any monitor, but the class is annotated as @ThreadSafe. | examples/C.java:26:9:26:14 | this.y | this expression |
 | examples/C.java:30:13:30:13 | y | This field access (publicly accessible via $@) is not protected by any monitor, but the class is annotated as @ThreadSafe. | examples/C.java:30:13:30:13 | y | this expression |
 | examples/C.java:33:9:33:9 | y | This field access (publicly accessible via $@) is not protected by any monitor, but the class is annotated as @ThreadSafe. | examples/C.java:33:9:33:9 | y | this expression |
+| examples/DeepPaths.java:8:17:8:17 | y | This field is not properly synchronized in that no single monitor covers all accesses, but the class $@ is annotated as @ThreadSafe. | examples/DeepPaths.java:7:14:7:22 | DeepPaths | DeepPaths |
 | examples/FaultyTurnstileExample.java:18:5:18:9 | count | This field access (publicly accessible via $@) is not protected by any monitor, but the class is annotated as @ThreadSafe. | examples/FaultyTurnstileExample.java:18:5:18:9 | count | this expression |
 | examples/FaultyTurnstileExample.java:26:15:26:19 | count | This field is not properly synchronized in that no single monitor covers all accesses, but the class $@ is annotated as @ThreadSafe. | examples/FaultyTurnstileExample.java:23:7:23:29 | FaultyTurnstileExample2 | FaultyTurnstileExample2 |
 | examples/FlawedSemaphore.java:15:14:15:18 | state | This field access (publicly accessible via $@) is not protected by any monitor, but the class is annotated as @ThreadSafe. | examples/FlawedSemaphore.java:15:14:15:18 | state | this expression |
@@ -34,7 +35,7 @@
 | examples/LockExample.java:124:5:124:21 | notRelatedToOther | This field access (publicly accessible via $@) is not protected by any monitor, but the class is annotated as @ThreadSafe. | examples/LockExample.java:124:5:124:21 | notRelatedToOther | this expression |
 | examples/LockExample.java:145:5:145:21 | notRelatedToOther | This field access (publicly accessible via $@) is not protected by any monitor, but the class is annotated as @ThreadSafe. | examples/LockExample.java:145:5:145:21 | notRelatedToOther | this expression |
 | examples/LockExample.java:153:5:153:21 | notRelatedToOther | This field access (publicly accessible via $@) is not protected by any monitor, but the class is annotated as @ThreadSafe. | examples/LockExample.java:153:5:153:21 | notRelatedToOther | this expression |
-| examples/ManyLocks.java:8:15:8:15 | y | This field is not properly synchronized in that no single monitor covers all accesses, but the class $@ is annotated as @ThreadSafe. | examples/ManyLocks.java:7:14:7:22 | ManyLocks | ManyLocks |
+| examples/ManyLocks.java:8:17:8:17 | y | This field is not properly synchronized in that no single monitor covers all accesses, but the class $@ is annotated as @ThreadSafe. | examples/ManyLocks.java:7:14:7:22 | ManyLocks | ManyLocks |
 | examples/SyncLstExample.java:45:5:45:7 | lst | This field access (publicly accessible via $@) is not protected by any monitor, but the class is annotated as @ThreadSafe. | examples/SyncLstExample.java:45:5:45:7 | lst | this expression |
 | examples/SyncStackExample.java:37:5:37:7 | stc | This field access (publicly accessible via $@) is not protected by any monitor, but the class is annotated as @ThreadSafe. | examples/SyncStackExample.java:37:5:37:7 | stc | this expression |
 | examples/SynchronizedAndLock.java:10:17:10:22 | length | This field is not properly synchronized in that no single monitor covers all accesses, but the class $@ is annotated as @ThreadSafe. | examples/SynchronizedAndLock.java:7:14:7:32 | SynchronizedAndLock | SynchronizedAndLock |

java/ql/test/query-tests/ThreadSafe/examples/DeepPaths.java

@@ -0,0 +1,61 @@
+package examples;
+
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
+
+@ThreadSafe
+public class DeepPaths {
+    private int y; // $ Alert
+
+    private final Lock lock1 = new ReentrantLock();
+    private final Lock lock2 = new ReentrantLock();
+    private final Lock lock3 = new ReentrantLock();
+
+    public void layer1Locked() {
+        lock1.lock();
+        this.layer2Locked();
+        lock1.unlock();
+    }
+
+    private void layer2Locked() {
+        lock2.lock();
+        this.layer3Unlocked();
+        lock2.unlock();
+    }
+
+    private void layer3Locked() {
+        lock3.lock();
+        y++;
+        lock3.unlock();
+    }
+
+    public void layer1Skip() {
+        lock2.lock();
+        this.layer3Locked();
+        lock2.unlock();
+    }
+
+    public void layer1Indirect() {
+        this.layer2();
+    }
+
+    private void layer2() {
+        this.layer2Locked();
+    }
+
+    public void layer1Unlocked() {
+        this.layer2Unlocked();
+    }
+
+    private void layer2Unlocked() {
+        this.layer3();
+    }
+
+    private void layer3() {
+        this.layer3Locked();
+    }
+
+    private void layer3Unlocked() {
+        y++;
+    }
+}

java/ql/test/query-tests/ThreadSafe/examples/ManyLocks.java

@@ -5,33 +5,33 @@ import java.util.concurrent.locks.ReentrantLock;
 
 @ThreadSafe
 public class ManyLocks {
-  private int y; // $ Alert
+    private int y; // $ Alert
 
-  private final Lock lock1 = new ReentrantLock();
-  private final Lock lock2 = new ReentrantLock();
-  private final Lock lock3 = new ReentrantLock();
+    private final Lock lock1 = new ReentrantLock();
+    private final Lock lock2 = new ReentrantLock();
+    private final Lock lock3 = new ReentrantLock();
 
-  public void inc() {
-    lock1.lock();
-    lock2.lock();
-    y++;
-    lock2.unlock();
-    lock1.unlock();
-  }
+    public void inc() {
+        lock1.lock();
+        lock2.lock();
+        y++;
+        lock2.unlock();
+        lock1.unlock();
+    }
 
-  public void dec() {
-    lock2.lock();
-    lock3.lock();
-    y--;
-    lock3.unlock();
-    lock2.unlock();
-  }
+    public void dec() {
+        lock2.lock();
+        lock3.lock();
+        y--;
+        lock3.unlock();
+        lock2.unlock();
+    }
 
-  public void reset() {
-    lock1.lock();
-    lock3.lock();
-    y = 0;
-    lock3.unlock();
-    lock1.unlock();
-  }
+    public void reset() {
+        lock1.lock();
+        lock3.lock();
+        y = 0;
+        lock3.unlock();
+        lock1.unlock();
+    }
 }