Merge branch 'features/JAL-2320_closeChimeraAction' into releases/Release_2_10_Branch

also tidied up javadoc

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
index 736e459..439d479 100644 (file)
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
@@ -380,6 +380,8 @@ public class ChimeraManager
       sendChimeraCommand("stop really", false);
       try
       {
+        // TODO is this too violent? could it force close the process
+        // before it has done an orderly shutdown?
         chimera.destroy();
       } catch (Exception ex)
       {
@@ -886,4 +888,9 @@ public class ChimeraManager
   {
     return busy;
   }
+
+  public Process getChimeraProcess()
+  {
+    return chimera;
+  }
 }

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 4a9bf5f..327d787 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -23,6 +23,7 @@ package jalview.ext.rbvi.chimera;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
@@ -67,6 +68,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   private List<String> chainNames = new ArrayList<String>();
 
   private Hashtable<String, String> chainFile = new Hashtable<String, String>();
+
   /*
    * Object through which we talk to Chimera
    */
@@ -114,6 +116,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
    */
   private long loadNotifiesHandled = 0;
 
+  private Thread chimeraMonitor;
+
   /**
    * Open a PDB structure file in Chimera and set up mappings from Jalview.
    * 
@@ -198,8 +202,38 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
           PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String protocol)
   {
     super(ssm, pdbentry, sequenceIs, protocol);
-    viewer = new ChimeraManager(
-            new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
+    viewer = new ChimeraManager(new StructureManager(true));
+  }
+
+  /**
+   * Starts a thread that waits for the Chimera process to finish, so that we
+   * can then close the associated resources. This avoids leaving orphaned
+   * Chimera viewer panels in Jalview if the user closes Chimera.
+   */
+  protected void startChimeraProcessMonitor()
+  {
+    final Process p = viewer.getChimeraProcess();
+    chimeraMonitor = new Thread(new Runnable()
+    {
+
+      @Override
+      public void run()
+      {
+        try
+        {
+          p.waitFor();
+          JalviewStructureDisplayI display = getViewer();
+          if (display != null)
+          {
+            display.closeViewer(false);
+          }
+        } catch (InterruptedException e)
+        {
+          // exit thread if Chimera Viewer is closed in Jalview
+        }
+      }
+    });
+    chimeraMonitor.start();
   }
 
   /**
@@ -287,6 +321,10 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     lastCommand = null;
     viewer = null;
 
+    if (chimeraMonitor != null)
+    {
+      chimeraMonitor.interrupt();
+    }
     releaseUIResources();
   }
 
@@ -567,23 +605,29 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
   /**
    * Launch Chimera, unless an instance linked to this object is already
-   * running. Returns true if chimera is successfully launched, or already
+   * running. Returns true if Chimera is successfully launched, or already
    * running, else false.
    * 
    * @return
    */
   public boolean launchChimera()
   {
-    if (!viewer.isChimeraLaunched())
-    {
-      return viewer.launchChimera(StructureManager.getChimeraPaths());
-    }
     if (viewer.isChimeraLaunched())
     {
       return true;
     }
-    log("Failed to launch Chimera!");
-    return false;
+
+    boolean launched = viewer.launchChimera(StructureManager
+            .getChimeraPaths());
+    if (launched)
+    {
+      startChimeraProcessMonitor();
+    }
+    else
+    {
+      log("Failed to launch Chimera!");
+    }
+    return launched;
   }
 
   /**
@@ -1056,13 +1100,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   }
 
   /**
-   * Returns a list of chains mapped in this viewer. Note this list is not
-   * currently scoped per structure.
-   * 
-   * @return
-   */
-
-  /**
    * Send a 'focus' command to Chimera to recentre the visible display
    */
   public void focusView()
@@ -1098,7 +1135,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     }
   }
 
-
   @Override
   public List<String> getChainNames()
   {

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 546890e..a6d699f 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
@@ -207,4 +208,10 @@ public class AppJmolBinding extends JalviewJmolBinding
     // TODO Auto-generated method stub
     return null;
   }
+
+  @Override
+  public JalviewStructureDisplayI getViewer()
+  {
+    return appJmolWindow;
+  }
 }

diff --git a/src/jalview/gui/JalviewChimeraBindingModel.java b/src/jalview/gui/JalviewChimeraBindingModel.java
index 78ab68d..94724d1 100644 (file)
--- a/src/jalview/gui/JalviewChimeraBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraBindingModel.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
@@ -140,5 +141,10 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
 
   }
 
+  @Override
+  public JalviewStructureDisplayI getViewer()
+  {
+    return cvf;
+  }
 
 }

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 5dc3465..2b3e23a 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -21,6 +21,7 @@
 package jalview.structures.models;
 
 import jalview.api.StructureSelectionManagerProvider;
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
@@ -135,8 +136,7 @@ public abstract class AAStructureBindingModel extends
    * @param protocol
    */
   public AAStructureBindingModel(StructureSelectionManager ssm,
-          PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
-          String protocol)
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String protocol)
   {
     this.ssm = ssm;
     this.sequence = sequenceIs;
@@ -677,4 +677,13 @@ public abstract class AAStructureBindingModel extends
    */
   public abstract List<String> getChainNames();
 
+  /**
+   * Returns the Jalview panel hosting the structure viewer (if any)
+   * 
+   * @return
+   */
+  public JalviewStructureDisplayI getViewer()
+  {
+    return null;
+  }
 }