JAL-2320 thread to close Chimera viewer panel if Chimera shut down

[jalview.git] / src / jalview / ext / rbvi / chimera / JalviewChimeraBinding.java

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index af87e44..501e345 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;
@@ -101,17 +102,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
 
   private String lastCommand;
 
-  private boolean loadedInline;
-
-  /**
-   * current set of model filenames loaded
-   */
-  String[] modelFileNames = null;
-
   String lastHighlightCommand;
 
-  private List<String> lastReply;
-
   /*
    * incremented every time a load notification is successfully handled -
    * lightweight mechanism for other threads to detect when they can start
@@ -119,6 +111,8 @@ 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.
    * 
@@ -204,8 +198,38 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
           String protocol)
   {
     super(ssm, pdbentry, sequenceIs, chains, 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();
   }
 
   /**
@@ -290,6 +314,10 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     lastCommand = null;
     viewer = null;
 
+    if (chimeraMonitor != null)
+    {
+      chimeraMonitor.interrupt();
+    }
     releaseUIResources();
   }
 
@@ -570,23 +598,29 @@ 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;
   }
 
   /**
@@ -617,7 +651,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     if (lastCommand == null || !lastCommand.equals(command))
     {
       // trim command or it may never find a match in the replyLog!!
-      lastReply = viewer.sendChimeraCommand(command.trim(), logResponse);
+      List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
+              logResponse);
       if (logResponse && debug)
       {
         log("Response from command ('" + command + "') was:\n" + lastReply);
@@ -715,17 +750,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   // End StructureListener
   // //////////////////////////
 
-  public Color getColour(int atomIndex, int pdbResNum, String chain,
-          String pdbfile)
-  {
-    if (getModelNum(pdbfile) < 0)
-    {
-      return null;
-    }
-    log("get model / residue colour attribute unimplemented");
-    return null;
-  }
-
   /**
    * returns the current featureRenderer that should be used to colour the
    * structures
@@ -795,15 +819,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   }
 
   /**
-   * map from string to applet
-   */
-  public Map getRegistryInfo()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  /**
    * returns the current sequenceRenderer that should be used to colour the
    * structures
    * 
@@ -815,20 +830,18 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
           AlignmentViewPanel alignment);
 
   /**
-   * Construct and send a command to highlight zero, one or more atoms.
-   * 
-   * <pre>
-   * Done by generating a command like (to 'highlight' positions 44 and 46)
-   *   show #0:44,46.C
-   * </pre>
+   * Construct and send a command to highlight zero, one or more atoms. We do
+   * this by sending an "rlabel" command to show the residue label at that
+   * position.
    */
   @Override
   public void highlightAtoms(List<AtomSpec> atoms)
   {
-    if (atoms == null)
+    if (atoms == null || atoms.size() == 0)
     {
       return;
     }
+
     StringBuilder cmd = new StringBuilder(128);
     boolean first = true;
     boolean found = false;
@@ -843,7 +856,7 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
       {
         if (first)
         {
-          cmd.append("show #").append(cms.get(0).getModelNumber())
+          cmd.append("rlabel #").append(cms.get(0).getModelNumber())
                   .append(":");
         }
         else
@@ -851,7 +864,6 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
           cmd.append(",");
         }
         first = false;
-        cmd.append(cms.get(0).getModelNumber()).append(":");
         cmd.append(pdbResNum);
         if (!chain.equals(" "))
         {
@@ -863,19 +875,24 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
     String command = cmd.toString();
 
     /*
-     * Avoid repeated commands for the same residue
+     * avoid repeated commands for the same residue
      */
     if (command.equals(lastHighlightCommand))
     {
       return;
     }
 
-    viewerCommandHistory(false);
+    /*
+     * unshow the label for the previous residue
+     */
+    if (lastHighlightCommand != null)
+    {
+      viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
+    }
     if (found)
     {
-      viewer.sendChimeraCommand(command.toString(), false);
+      viewer.sendChimeraCommand(command, false);
     }
-    viewerCommandHistory(true);
     this.lastHighlightCommand = command;
   }
 
@@ -1127,6 +1144,8 @@ public abstract class JalviewChimeraBinding extends AAStructureBindingModel
   /**
    * Send a 'show' command for all atoms in the currently selected columns
    * 
+   * TODO: pull up to abstract structure viewer interface
+   * 
    * @param vp
    */
   public void highlightSelection(AlignmentViewPanel vp)