JAL-1517 update copyright to version 2.8.2

[jalview.git] / src / jalview / gui / AppJmolBinding.java

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 2a0e2a7..af40504 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -1,16 +1,34 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
+import java.awt.Container;
 import java.util.BitSet;
 
-import javax.swing.JPanel;
-
+import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.structure.StructureSelectionManager;
 
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.api.JmolViewer;
 import org.jmol.popup.JmolPopup;
 import org.openscience.jmol.app.jmolpanel.AppConsole;
 
@@ -22,36 +40,42 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
    */
   private AppJmol appJmolWindow;
 
-  public AppJmolBinding(AppJmol appJmol, PDBEntry[] pdbentry,
-          SequenceI[][] sequenceIs, String[][] chains, String protocol)
+  public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+          String protocol)
   {
-    super(pdbentry, sequenceIs, chains, protocol);
+    super(sSm, pdbentry, sequenceIs, chains, protocol);
     appJmolWindow = appJmol;
   }
 
   FeatureRenderer fr = null;
 
   @Override
-  public jalview.api.FeatureRenderer getFeatureRenderer()
+  public jalview.api.FeatureRenderer getFeatureRenderer(
+          AlignmentViewPanel alignment)
   {
-    if (appJmolWindow.ap.av.showSequenceFeatures)
+    AlignmentPanel ap = (alignment == null) ? appJmolWindow.ap
+            : (AlignmentPanel) alignment;
+    if (ap.av.showSequenceFeatures)
     {
       if (fr == null)
       {
-        fr = new FeatureRenderer(appJmolWindow.ap);
+        fr = ap.cloneFeatureRenderer();
+      }
+      else
+      {
+        ap.updateFeatureRenderer(fr);
       }
-
-      fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas
-              .getFeatureRenderer());
     }
 
     return fr;
   }
 
   @Override
-  public jalview.api.SequenceRenderer getSequenceRenderer()
+  public jalview.api.SequenceRenderer getSequenceRenderer(
+          AlignmentViewPanel alignment)
   {
-    return new SequenceRenderer(appJmolWindow.ap.av);
+    return new SequenceRenderer(((AlignmentPanel) alignment).av);
   }
 
   public void sendConsoleEcho(String strEcho)
@@ -89,28 +113,34 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   public void refreshGUI()
   {
     // appJmolWindow.repaint();
-    javax.swing.SwingUtilities.invokeLater(new Runnable() {
-      public void run() {
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
         appJmolWindow.updateTitleAndMenus();
         appJmolWindow.revalidate();
-      }});
+      }
+    });
   }
 
   public void updateColours(Object source)
   {
-    AlignmentPanel ap = (AlignmentPanel) source;
-    if (appJmolWindow.ap.alignFrame.getCurrentView() != ap.av)
+    AlignmentPanel ap = (AlignmentPanel) source, topap;
+    // ignore events from panels not used to colour this view
+    if (!appJmolWindow.isUsedforcolourby(ap))
       return;
-
-    colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+    if (!isLoadingFromArchive())
+    {
+      colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+    }
   }
 
   public void notifyScriptTermination(String strStatus, int msWalltime)
   {
     // todo - script termination doesn't happen ?
-    //if (console != null)
-      //console.notifyScriptTermination(strStatus,
-      //        msWalltime);
+    // if (console != null)
+    // console.notifyScriptTermination(strStatus,
+    // msWalltime);
   }
 
   public void showUrl(String url)
@@ -122,8 +152,8 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
           boolean asPopup)
   {
 
-    jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
-            asPopup);
+    jmolpopup = new JmolPopup();
+    jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
   }
 
   public void selectionChanged(BitSet arg0)
@@ -138,7 +168,8 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 
   }
 
-  public void showConsole(boolean b) {
+  public void showConsole(boolean b)
+  {
     appJmolWindow.showConsole(b);
   }
 
@@ -160,4 +191,42 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
       }
     }
   }
-}
\ No newline at end of file
+
+  @Override
+  protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+          Container consolePanel, String buttonsToShow)
+  {
+    return new AppConsole(viewer, consolePanel, buttonsToShow);
+  }
+
+  @Override
+  protected void releaseUIResources()
+  {
+    appJmolWindow = null;
+    if (console != null)
+    {
+      try
+      {
+        console.setVisible(false);
+      } catch (Error e)
+      {
+      } catch (Exception x)
+      {
+      }
+      ;
+      console = null;
+    }
+
+  }
+
+  @Override
+  public void releaseReferences(Object svl)
+  {
+    if (svl instanceof SeqPanel)
+    {
+      appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
+
+    }
+    ;
+  }
+}