X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmolBinding.java;h=e5767b68c8b06b8e1b10d9bc87248d6f553caaa3;hb=4a0a4a012676c3ebee341d667eab07ea60c5770e;hp=eca64064174600a52bc764a554f8be6bdefc2fa0;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index eca6406..e5767b6 100644
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -1,37 +1,40 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
- * 
+ * 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/>.
+ * 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.appletgui;
 
-import java.awt.Container;
-import java.util.BitSet;
-
 import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.io.DataSourceType;
 import jalview.structure.StructureSelectionManager;
 
+import java.awt.Container;
+import java.util.Map;
+
 import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.api.JmolViewer;
-import org.jmol.applet.AppletConsole;
-import org.jmol.popup.JmolPopup;
+import org.jmol.console.AppletConsole;
+import org.jmol.java.BS;
 
-class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
+class AppletJmolBinding extends JalviewJmolBinding
 {
 
   /**
@@ -39,77 +42,76 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
    */
   private AppletJmol appletJmolBinding;
 
-  public AppletJmolBinding(AppletJmol appletJmol, StructureSelectionManager sSm, PDBEntry[] pdbentry,
-          SequenceI[][] seq, String[][] chains, String protocol)
+  public AppletJmolBinding(AppletJmol appletJmol,
+          StructureSelectionManager sSm, PDBEntry[] pdbentry,
+          SequenceI[][] seq, DataSourceType protocol)
   {
-    super(sSm, pdbentry, seq, chains, protocol);
+    super(sSm, pdbentry, seq, protocol);
     appletJmolBinding = appletJmol;
   }
 
-  public jalview.api.FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+  @Override
+  public jalview.api.FeatureRenderer getFeatureRenderer(
+          AlignmentViewPanel alignment)
   {
-    AlignmentPanel ap = (AlignmentPanel)alignment;
-    if (appletJmolBinding.ap.av.showSequenceFeatures)
-    {
-      if (appletJmolBinding.fr == null)
-      {
-        appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(
-                appletJmolBinding.ap.av);
-      }
-
-      appletJmolBinding.fr
-              .transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas
-                      .getFeatureRenderer());
-    }
-
-    return appletJmolBinding.fr;
+    return appletJmolBinding.ap.getFeatureRenderer();
   }
 
-  public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
+  @Override
+  public jalview.api.SequenceRenderer getSequenceRenderer(
+          AlignmentViewPanel alignment)
   {
-    return new SequenceRenderer(((AlignmentPanel)alignment).av);
+    return new SequenceRenderer(((AlignmentPanel) alignment).av);
   }
 
+  @Override
   public void sendConsoleEcho(String strEcho)
   {
     if (appletJmolBinding.scriptWindow == null)
+    {
       appletJmolBinding.showConsole(true);
+    }
 
-    appletJmolBinding.history.append("\n" + strEcho);
+    appletJmolBinding.addToHistory(strEcho);
   }
 
+  @Override
   public void sendConsoleMessage(String strStatus)
   {
     if (appletJmolBinding.history != null && strStatus != null
             && !strStatus.equals("Script completed"))
     {
-      appletJmolBinding.history.append("\n" + strStatus);
+      appletJmolBinding.addToHistory(strStatus);
     }
   }
 
+  @Override
   public void showUrl(String url, String target)
   {
     appletJmolBinding.ap.alignFrame.showURL(url, target);
 
   }
 
+  @Override
   public void refreshGUI()
   {
     appletJmolBinding.updateTitleAndMenus();
   }
 
+  @Override
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
-    colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+    colourBySequence(ap);
   }
 
+  @Override
   public void showUrl(String url)
   {
     try
     {
-      appletJmolBinding.ap.av.applet.getAppletContext().showDocument(
-              new java.net.URL(url), "jmol");
+      appletJmolBinding.ap.av.applet.getAppletContext()
+              .showDocument(new java.net.URL(url), "jmol");
     } catch (java.net.MalformedURLException ex)
     {
     }
@@ -118,26 +120,27 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   public void newJmolPopup(boolean translateLocale, String menuName,
           boolean asPopup)
   {
-
-    jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
-            asPopup);
+    // jmolpopup = new JmolAwtPopup(); // is this used?
+    // jmolpopup.jpiInitialize((viewer), menuName);
   }
 
+  @Override
   public void notifyScriptTermination(String strStatus, int msWalltime)
   {
     // do nothing.
   }
 
-  public void selectionChanged(BitSet arg0)
+  @Override
+  public void selectionChanged(BS arg0)
   {
     // TODO Auto-generated method stub
 
   }
 
+  @Override
   public void refreshPdbEntries()
   {
-    // TODO Auto-generated method stub
-
+    // noop
   }
 
   @Override
@@ -147,30 +150,19 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   }
 
   @Override
-  protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+  protected JmolAppConsoleInterface createJmolConsole(
           Container consolePanel, String buttonsToShow)
   {
-    return new AppletConsole(viewer2, consolePanel);
+    JmolAppConsoleInterface appc = new AppletConsole();
+    appc.start(viewer);
+    return appc;
   }
 
   @Override
   protected void releaseUIResources()
   {
     appletJmolBinding = null;
-    if (console != null)
-    {
-      try
-      {
-        console.setVisible(false);
-      } catch (Error e)
-      {
-      } catch (Exception x)
-      {
-      }
-      ;
-      console = null;
-    }
-
+    closeConsole();
   }
 
   @Override
@@ -178,4 +170,15 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   {
   }
 
+  @Override
+  public int[] resizeInnerPanel(String data)
+  {
+    return null;
+  }
+
+  @Override
+  public Map<String, Object> getJSpecViewProperty(String arg0)
+  {
+    return null;
+  }
 }