X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewerBase.java;h=ed42ffa7c98761275a3e42a9015e8dc12e183c9e;hb=7f09e6ac5717bc78373c5d77f309831403e6ebf8;hp=9a575ffc06cb1b7b8f072db319dcc6bd71ded4aa;hpb=b865b46f6f34e82f5d10fccfe646f00b8ae2e7a1;p=jalview.git

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 9a575ff..ed42ffa 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -37,9 +37,6 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Random;
 import java.util.Vector;
-import java.util.concurrent.Callable;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.TimeUnit;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
@@ -50,6 +47,7 @@ import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
 import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.datamodel.AlignmentI;
@@ -91,6 +89,29 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   /**
+   * Singleton list of all (open) instances of structureViewerBase
+   * TODO: JAL-3362 - review and adopt the swingJS-safe singleton pattern so each structure viewer base instance is kept to its own JalviewJS parent
+   */
+  private static List<JalviewStructureDisplayI> svbs = new ArrayList<>();
+
+  /**
+   * 
+   * @return list with all existing StructureViewers instance
+   */
+  public static List<JalviewStructureDisplayI> getAllStructureViewerBases()
+  {
+    List<JalviewStructureDisplayI> goodSvbs = new ArrayList<>();
+    for (JalviewStructureDisplayI s : svbs)
+    {
+      if (s != null && !goodSvbs.contains(s))
+      {
+        goodSvbs.add(s);
+      }
+    }
+    return goodSvbs;
+  }
+
+  /**
    * list of sequenceSet ids associated with the view
    */
   protected List<String> _aps = new ArrayList<>();
@@ -140,6 +161,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   {
     super();
     setFrameIcon(null);
+    svbs.add(this);
   }
 
   /**
@@ -183,6 +205,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     return _aps.contains(ap2.av.getSequenceSetId());
   }
 
+  @Override
   public boolean isUsedforaligment(AlignmentViewPanel ap2)
   {
 
@@ -1200,7 +1223,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       }
     } catch (Exception e)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Error retrieving PDB id " + pdbid + ": " + e.getMessage());
     } finally
     {
@@ -1255,6 +1278,20 @@ public abstract class StructureViewerBase extends GStructureViewer
     return session;
   }
 
+  private static boolean quitClose = false;
+
+  public static void setQuitClose(boolean b)
+  {
+    quitClose = b;
+  }
+
+  @Override
+  public boolean stillRunning()
+  {
+    AAStructureBindingModel binding = getBinding();
+    return binding != null && binding.isViewerRunning();
+  }
+
   /**
    * 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
@@ -1267,19 +1304,29 @@ public abstract class StructureViewerBase extends GStructureViewer
   public void closeViewer(boolean forceClose)
   {
     AAStructureBindingModel binding = getBinding();
-    if (binding != null && binding.isViewerRunning())
+    if (stillRunning())
     {
       if (!forceClose)
       {
         String viewerName = getViewerName();
 
         int confirm = JvOptionPane.CANCEL_OPTION;
-        String prompt = MessageManager
-                .formatMessage("label.confirm_close_viewer", new Object[]
-                { binding.getViewerTitle(viewerName, false), viewerName });
-        prompt = JvSwingUtils.wrapTooltip(true, prompt);
-        String title = MessageManager.getString("label.close_viewer");
-        confirm = showCloseDialog(title, prompt);
+        if (QuitHandler.quitting())
+        {
+          // already asked about closing external windows
+          confirm = quitClose ? JvOptionPane.YES_OPTION
+                  : JvOptionPane.NO_OPTION;
+        }
+        else
+        {
+          String prompt = MessageManager
+                  .formatMessage("label.confirm_close_viewer", new Object[]
+                  { binding.getViewerTitle(viewerName, false),
+                      viewerName });
+          prompt = JvSwingUtils.wrapTooltip(true, prompt);
+          String title = MessageManager.getString("label.close_viewer");
+          confirm = showCloseDialog(title, prompt);
+        }
 
         /*
          * abort closure if user hits escape or Cancel
@@ -1315,59 +1362,23 @@ public abstract class StructureViewerBase extends GStructureViewer
     // TODO: check for memory leaks where instance isn't finalised because jmb
     // holds a reference to the window
     // jmb = null;
+    
+    try {
+      svbs.remove(this);
+    } catch (Throwable t)
+    {
+      Console.info("Unexpected exception when deregistering structure viewer",t);
+    }
     dispose();
   }
 
   private int showCloseDialog(final String title, final String prompt)
   {
-    confirmResponse = JvOptionPane.CANCEL_OPTION;
-
-    if (QuitHandler.quitting())
-    {
-
-      Callable<Void> yesCall = () -> {
-        Console.debug("YES");
-        confirmResponse = JvOptionPane.YES_OPTION;
-        return null;
-      };
-      Callable<Void> noCall = () -> {
-        Console.debug("NO");
-        confirmResponse = JvOptionPane.NO_OPTION;
-        return null;
-      };
-      Callable<Void> cancelCall = () -> {
-        Console.debug("CANCEL");
-        confirmResponse = JvOptionPane.CANCEL_OPTION;
-        return null;
-      };
-      Callable<Void>[] calls = new Callable[] { yesCall, noCall,
-          cancelCall };
-      String cancelQuit = MessageManager.getString("action.cancel_quit");
-      String[] buttonsText = { MessageManager.getString("action.yes"),
-          MessageManager.getString("action.no"), cancelQuit };
-      JvOptionPane dialog = JvOptionPane.frameDialog(prompt,
-              MessageManager.getString("label.close_viewer"),
-              JvOptionPane.WARNING_MESSAGE, buttonsText, cancelQuit, calls,
-              false);
-      // wait for response
-      ExecutorService executor = dialog.getExecutor();
-      executor.shutdown();
-      try
-      {
-        Console.debug("### executor.awaitTermination() starting");
-        executor.awaitTermination(60, TimeUnit.SECONDS);
-        Console.debug("### executor.awaitTermination() finished");
-      } catch (InterruptedException e)
-      {
-      }
-    }
-    else
-    {
-      confirmResponse = JvOptionPane.showConfirmDialog(this, prompt,
-              MessageManager.getString("label.close_viewer"),
-              JvOptionPane.YES_NO_CANCEL_OPTION,
-              JvOptionPane.WARNING_MESSAGE);
-    }
+    int confirmResponse = JvOptionPane.CANCEL_OPTION;
+    confirmResponse = JvOptionPane.showConfirmDialog(this, prompt,
+            MessageManager.getString("label.close_viewer"),
+            JvOptionPane.YES_NO_CANCEL_OPTION,
+            JvOptionPane.WARNING_MESSAGE);
     return confirmResponse;
   }
 
@@ -1402,5 +1413,4 @@ public abstract class StructureViewerBase extends GStructureViewer
             && viewerActionMenu.isVisible();
   }
 
-  private static int confirmResponse = 0;
 }