X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=eb15a651246d1705184426f7d4c8e8a8f18594a3;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=831fd5a184461ba5dcab7a7602f01779cafde4f9;hpb=b32b824388dea3107cd1598d63f8759f00b75e1f;p=jalview.git

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 831fd5a..eb15a65 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -1,130 +1,208 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.util.Vector;
-
+import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.structure.StructureSelectionManager;
 
-import org.jmol.popup.JmolPopup;
+import java.awt.Container;
+import java.util.Map;
 
-class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
-{
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.java.BS;
+import org.openscience.jmol.app.jmolpanel.console.AppConsole;
 
-  /**
-   * 
-   */
+public class AppJmolBinding extends JalviewJmolBinding
+{
   private AppJmol appJmolWindow;
 
-  public AppJmolBinding(AppJmol appJmol, PDBEntry[] pdbentry,
-          SequenceI[] seq, String[] chains, String protocol)
+  private FeatureRenderer fr = null;
+
+  public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+          String protocol)
   {
-    super(pdbentry, seq, chains, protocol);
+    super(sSm, pdbentry, sequenceIs, chains, protocol);
     appJmolWindow = appJmol;
   }
-  FeatureRenderer fr=null;
+
   @Override
-  public jalview.api.FeatureRenderer getFeatureRenderer()
+  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
-    if (appJmolWindow.ap.av.showSequenceFeatures)
+    AlignmentPanel ap = (alignment == null) ? appJmolWindow
+            .getAlignmentPanel() : (AlignmentPanel) alignment;
+    if (ap.av.isShowSequenceFeatures())
     {
       if (fr == null)
       {
-        fr = new FeatureRenderer(appJmolWindow.ap);
+        fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
+      }
+      else
+      {
+        ap.updateFeatureRenderer(fr);
       }
-
-      fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas
-                      .getFeatureRenderer());
     }
 
     return fr;
   }
 
   @Override
-  public jalview.api.SequenceRenderer getSequenceRenderer()
+  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
-    return new SequenceRenderer(appJmolWindow.ap.av);
+    return new SequenceRenderer(((AlignmentPanel) alignment).av);
   }
 
+  @Override
   public void sendConsoleEcho(String strEcho)
   {
-    if (appJmolWindow.scriptWindow != null)
+    if (console != null)
     {
-      appJmolWindow.scriptWindow.sendConsoleEcho(strEcho);
+      console.sendConsoleEcho(strEcho);
     }
   }
 
+  @Override
   public void sendConsoleMessage(String strStatus)
   {
-    if (appJmolWindow.scriptWindow!=null && strStatus != null
-            )
-      //      && !strStatus.equals("Script completed"))
-      // should we squash the script completed string ?
+    if (console != null && strStatus != null)
+    // && !strStatus.equals("Script completed"))
+    // should we squash the script completed string ?
     {
-      appJmolWindow.scriptWindow.sendConsoleMessage(strStatus);
+      console.sendConsoleMessage(strStatus);
     }
   }
 
   @Override
   public void showUrl(String url, String target)
   {
-    try {
+    try
+    {
       jalview.util.BrowserLauncher.openURL(url);
-    } catch (Exception e) {
+    } catch (Exception e)
+    {
       Cache.log.error("Failed to launch Jmol-associated url " + url, e);
       // TODO: 2.6 : warn user if browser was not configured.
     }
   }
 
   @Override
-  public void updateUI()
+  public void refreshGUI()
   {
     // appJmolWindow.repaint();
-    appJmolWindow.updateTitleAndMenus();
+    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)
+    // 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);
+    }
   }
 
+  @Override
   public void notifyScriptTermination(String strStatus, int msWalltime)
   {
-    if (appJmolWindow.scriptWindow != null)
-      appJmolWindow.scriptWindow.notifyScriptTermination(strStatus, msWalltime);
+    // todo - script termination doesn't happen ?
+    // if (console != null)
+    // console.notifyScriptTermination(strStatus,
+    // msWalltime);
   }
 
   public void showUrl(String url)
   {
-    showUrl(url,"jmol");
+    showUrl(url, "jmol");
   }
 
-  public void newJmolPopup(boolean translateLocale, String menuName,
-          boolean asPopup)
+  public void newJmolPopup(String menuName)
   {
+    // jmolpopup = new JmolAwtPopup();
+    // jmolpopup.jpiInitialize((viewer), menuName);
+  }
 
-    jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
-            asPopup);
+  @Override
+  public void selectionChanged(BS arg0)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void refreshPdbEntries()
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  @Override
+  public void showConsole(boolean b)
+  {
+    appJmolWindow.showConsole(b);
+  }
+
+  @Override
+  protected JmolAppConsoleInterface createJmolConsole(
+          Container consolePanel, String buttonsToShow)
+  {
+    viewer.setJmolCallbackListener(this);
+    return new AppConsole(viewer, consolePanel, buttonsToShow);
   }
-  public synchronized void addSequence(SequenceI[] seq)
+
+  @Override
+  protected void releaseUIResources()
   {
-    Vector v = new Vector();
-    for (int i = 0; i < sequence.length; i++)
-      v.addElement(sequence[i]);
+    appJmolWindow = null;
+    closeConsole();
+  }
 
-    for (int i = 0; i < seq.length; i++)
-      if (!v.contains(seq[i]))
-        v.addElement(seq[i]);
+  @Override
+  public void releaseReferences(Object svl)
+  {
+    if (svl instanceof SeqPanel)
+    {
+      appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
+    }
+  }
 
-    SequenceI[] tmp = new SequenceI[v.size()];
-    v.copyInto(tmp);
-    sequence = tmp;
+  @Override
+  public Map<String, Object> getJSpecViewProperty(String arg0)
+  {
+    // TODO Auto-generated method stub
+    return null;
   }
-}
\ No newline at end of file
+}