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

also tidied up javadoc

diff --cc src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java
Simple merge

diff --cc src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 4a9bf5f,501e345..327d787
--- 1/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
--- 2/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@@ -64,9 -64,6 +65,10 @@@ public abstract class JalviewChimeraBin
  
    private static final String ALPHACARBON = "CA";
  
 +  private List<String> chainNames = new ArrayList<String>();
 +
 +  private Hashtable<String, String> chainFile = new Hashtable<String, String>();
++
    /*
     * Object through which we talk to Chimera
     */
@@@ -195,11 -194,42 +199,41 @@@
     * @param protocol
     */
    public JalviewChimeraBinding(StructureSelectionManager ssm,
 -          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
 -          String protocol)
 +          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String protocol)
    {
 -    super(ssm, pdbentry, sequenceIs, chains, 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();
    }
  
    /**
@@@ -1056,13 -1105,35 +1100,6 @@@
    }
  
    /**
--   * Returns a list of chains mapped in this viewer. Note this list is not
--   * currently scoped per structure.
--   * 
--   * @return
--   */
- 
-   /**
 -  public List<String> getChainNames()
 -  {
 -    List<String> names = new ArrayList<String>();
 -    String[][] allNames = getChains();
 -    if (allNames != null)
 -    {
 -      for (String[] chainsForPdb : allNames)
 -      {
 -        if (chainsForPdb != null)
 -        {
 -          for (String chain : chainsForPdb)
 -          {
 -            if (chain != null && !names.contains(chain))
 -            {
 -              names.add(chain);
 -            }
 -          }
 -        }
 -      }
 -    }
 -    return names;
 -  }
 -
 -  /**
     * Send a 'focus' command to Chimera to recentre the visible display
     */
    public void focusView()
@@@ -1097,31 -1168,4 +1134,30 @@@
        sm.highlightStructure(this, seq, positions);
      }
    }
 +
- 
 +  @Override
 +  public List<String> getChainNames()
 +  {
 +    return chainNames;
 +  }
 +
 +  public Hashtable<String, String> getChainFile()
 +  {
 +    return chainFile;
 +  }
 +
 +  public List<ChimeraModel> getChimeraModelByChain(String chain)
 +  {
 +    return chimeraMaps.get(chainFile.get(chain));
 +  }
 +
 +  public int getModelNoForChain(String chain)
 +  {
 +    List<ChimeraModel> foundModels = getChimeraModelByChain(chain);
 +    if (foundModels != null && !foundModels.isEmpty())
 +    {
 +      return foundModels.get(0).getModelNumber();
 +    }
 +    return -1;
 +  }
  }

diff --cc src/jalview/gui/AppJmolBinding.java
Simple merge

diff --cc src/jalview/gui/JalviewChimeraBindingModel.java
Simple merge

diff --cc src/jalview/structures/models/AAStructureBindingModel.java
index 5dc3465,b618bc0..2b3e23a
--- 1/src/jalview/structures/models/AAStructureBindingModel.java
--- 2/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@@ -135,8 -136,8 +136,7 @@@ public abstract class AAStructureBindin
     * @param protocol
     */
    public AAStructureBindingModel(StructureSelectionManager ssm,
-           PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
-           String protocol)
 -          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
 -          String protocol)
++          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String protocol)
    {
      this.ssm = ssm;
      this.sequence = sequenceIs;
@@@ -671,10 -677,12 +671,19 @@@
    }
  
    /**
 +   * Returns a list of chains mapped in this viewer.
 +   * 
 +   * @return
 +   */
 +  public abstract List<String> getChainNames();
 +
++  /**
+    * Returns the Jalview panel hosting the structure viewer (if any)
+    * 
+    * @return
+    */
+   public JalviewStructureDisplayI getViewer()
+   {
+     return null;
+   }
  }