JAL-1528 Chimera tidy errors, focus after align, close option

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 72801dd..9eee9cc 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -383,7 +383,7 @@ label.pdb_entry_is_already_displayed = {0} is already displayed.\nDo you want to
 label.map_sequences_to_visible_window = Map Sequences to Visible Window: {0}
 label.add_pdbentry_to_view = Do you want to add {0} to the view called\n{1}\n
 label.align_to_existing_structure_view = Align to existing structure view
-label.pdb_entries_couldnt_be_retrieved = The following pdb entries could not be retrieved from the PDB\:\n{0}\nPlease try downloading them manually.
+label.pdb_entries_couldnt_be_retrieved = The following pdb entries could not be retrieved from the PDB\:\n{0}\nPlease retry, or try downloading them manually.
 label.couldnt_load_file = Couldn't load file
 label.couldnt_find_pdb_id_in_file = Couldn't find a PDB id in the file supplied. Please enter an Id to identify this structure.
 label.no_pdb_id_in_file = No PDB Id in File
@@ -487,7 +487,7 @@ label.sequence_details = Sequence Details
 label.jmol_help = Jmol Help
 label.chimera_help = Chimera Help
 label.close_viewer = Close Viewer
-label.confirm_close_chimera = Do you want to close the Chimera window?
+label.confirm_close_chimera = This will close Jalview''s connection to {0}.<br>Do you want to close the Chimera window as well?
 label.chimera_help = Chimera Help
 label.all = All
 label.sort_by = Sort alignment by

diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 3f2d5e4..7033ba7 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@ -254,12 +254,13 @@ public abstract class JalviewChimeraBinding extends
   }
 
   /**
-   * construct a title string for the viewer window based on the data jalview
+   * Construct a title string for the viewer window based on the data Jalview
    * knows about
    * 
+   * @param verbose
    * @return
    */
-  public String getViewerTitle()
+  public String getViewerTitle(boolean verbose)
   {
     if (sequence == null || pdbentry == null || sequence.length < 1
             || pdbentry.length < 1 || sequence[0].length < 1)
@@ -268,20 +269,24 @@ public abstract class JalviewChimeraBinding extends
     }
     // TODO: give a more informative title when multiple structures are
     // displayed.
-    StringBuffer title = new StringBuffer("Chimera view for "
-            + sequence[0][0].getName() + ":" + pdbentry[0].getId());
+    StringBuilder title = new StringBuilder(64);
+    title.append("Chimera view for " + sequence[0][0].getName() + ":"
+            + pdbentry[0].getId());
 
-    if (pdbentry[0].getProperty() != null)
+    if (verbose)
     {
-      if (pdbentry[0].getProperty().get("method") != null)
+      if (pdbentry[0].getProperty() != null)
       {
-        title.append(" Method: ");
-        title.append(pdbentry[0].getProperty().get("method"));
-      }
-      if (pdbentry[0].getProperty().get("chains") != null)
-      {
-        title.append(" Chain:");
-        title.append(pdbentry[0].getProperty().get("chains"));
+        if (pdbentry[0].getProperty().get("method") != null)
+        {
+          title.append(" Method: ");
+          title.append(pdbentry[0].getProperty().get("method"));
+        }
+        if (pdbentry[0].getProperty().get("chains") != null)
+        {
+          title.append(" Chain:");
+          title.append(pdbentry[0].getProperty().get("chains"));
+        }
       }
     }
     return title.toString();
@@ -319,11 +324,17 @@ public abstract class JalviewChimeraBinding extends
             + ";focus " + cmdstring, false);
   }
 
-  public void closeViewer()
+  /**
+   * Close down the Jalview viewer, and (optionally) the associate Chimera
+   * window.
+   */
+  public void closeViewer(boolean closeChimera)
   {
     ssm.removeStructureViewerListener(this, this.getPdbFile());
-    // and shut down Chimera
-    viewer.exitChimera();
+    if (closeChimera)
+    {
+      viewer.exitChimera();
+    }
     // viewer.evalStringQuiet("zap");
     // viewer.setJmolStatusListener(null);
     lastCommand = null;
@@ -670,7 +681,7 @@ public abstract class JalviewChimeraBinding extends
       }
       System.out.println("Select regions:\n" + selectioncom.toString());
       allComs.append("; ~display all; chain @CA|P; ribbon "
-              + selectioncom.toString() + "");
+              + selectioncom.toString() + "; focus");
       // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString());
       evalStateCommand(allComs.toString(), true /* false */);
     }
@@ -689,7 +700,24 @@ public abstract class JalviewChimeraBinding extends
     }
   }
 
-  public void evalStateCommand(final String command, boolean resp)
+  /**
+   * Answers true if the Chimera process is still running, false if ended or not
+   * started.
+   * 
+   * @return
+   */
+  public boolean isChimeraRunning()
+  {
+    return viewer.isChimeraLaunched();
+  }
+
+  /**
+   * Send a command to Chimera, and optionally log any responses.
+   * 
+   * @param command
+   * @param logResponse
+   */
+  public void evalStateCommand(final String command, boolean logResponse)
   {
     viewerCommandHistory(false);
     checkLaunched();
@@ -701,8 +729,8 @@ public abstract class JalviewChimeraBinding extends
 //        public void run()
 //        {
       // trim command or it may never find a match in the replyLog!!
-      lastReply = viewer.sendChimeraCommand(command.trim(), resp);
-      if (debug && resp)
+      lastReply = viewer.sendChimeraCommand(command.trim(), logResponse);
+      if (debug && logResponse)
           {
             log("Response from command ('" + command + "') was:\n"
                     + lastReply);

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 6278536..3c53762 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -546,7 +546,7 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable,
     jmb.setFinishedInit(false);
     // TODO: consider waiting until the structure/view is fully loaded before
     // displaying
-    jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
+    jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(true),
             getBounds().width, getBounds().height);
     if (command == null)
     {
@@ -619,9 +619,24 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable,
     jmb.centerViewer(toshow);
   }
 
+  /**
+   * Close down this instance of Jalview's Chimera viewer, giving the user the
+   * option to close the associated Chimera window (process). They may wish to
+   * keep it open until they have had an opportunity to save any work.
+   */
   public void closeViewer()
   {
-    jmb.closeViewer();
+    if (jmb.isChimeraRunning())
+    {
+      String prompt = MessageManager
+              .formatMessage("label.confirm_close_chimera", new Object[]
+              { jmb.getViewerTitle(false) });
+      prompt = JvSwingUtils.wrapTooltip(true, prompt);
+      int confirm = JOptionPane.showConfirmDialog(this, prompt,
+              MessageManager.getString("label.close_viewer"),
+              JOptionPane.YES_NO_OPTION);
+      jmb.closeViewer(confirm == JOptionPane.YES_OPTION);
+    }
     ap = null;
     _aps.clear();
     _alignwith.clear();
@@ -698,7 +713,7 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable,
     } catch (Exception ex)
     {
       ex.printStackTrace();
-      errormsgs.append("When retrieving pdbfiles : current was: '"
+      errormsgs.append("When retrieving pdbfiles for '"
               + thePdbEntry.getId() + "'");
     }
     if (errormsgs.length() > 0)
@@ -818,11 +833,13 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable,
     } catch (OutOfMemoryError oomerror)
     {
       new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
-    }
-    if (progressBar != null)
+    } finally
     {
-      progressBar.setProgressBar(
-              MessageManager.getString("label.state_completed"), hdl);
+      if (progressBar != null)
+      {
+        progressBar.setProgressBar(
+                MessageManager.getString("label.state_completed"), hdl);
+      }
     }
     /*
      * If PDB data were saved and are not invalid (empty alignment), return the
@@ -1082,7 +1099,7 @@ public class ChimeraViewFrame extends GStructureViewer implements Runnable,
     }
     setChainMenuItems(jmb.chainNames);
 
-    this.setTitle(jmb.getViewerTitle());
+    this.setTitle(jmb.getViewerTitle(true));
     if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1)
     {
       viewerActionMenu.setVisible(true);

diff --git a/src/jalview/gui/JalviewChimeraBindingModel.java b/src/jalview/gui/JalviewChimeraBindingModel.java
index f7c4878..c582c5d 100644 (file)
--- a/src/jalview/gui/JalviewChimeraBindingModel.java
+++ b/src/jalview/gui/JalviewChimeraBindingModel.java
@@ -66,7 +66,9 @@ public class JalviewChimeraBindingModel extends JalviewChimeraBinding
     AlignmentPanel ap = (AlignmentPanel) source, topap;
     // ignore events from panels not used to colour this view
     if (!cvf.isUsedforcolourby(ap))
+    {
       return;
+    }
     if (!isLoadingFromArchive())
     {
       colourBySequence(ap.av.getShowSequenceFeatures(), ap);