X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=98787cbb749edd01f9eb5e9859940ba57fa9146a;hb=refs%2Fheads%2Ffeature%2FJAL-3551Pymol;hp=9f7090a784114426489197913625bdac40a06d6b;hpb=794501173d6cea5fc3a965cee3792ae78304abe9;p=jalview.git

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 9f7090a..98787cb 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -1,143 +1,192 @@
-/**
+/*
+ * 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.
+ *  
+ * 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.BitSet;
-import java.util.Vector;
+import java.awt.Container;
+import java.io.File;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.JComponent;
+
+import org.jmol.api.JmolAppConsoleInterface;
+import org.openscience.jmol.app.jmolpanel.console.AppConsole;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.io.DataSourceType;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.Platform;
+import javajs.util.BS;
 
-import org.jmol.popup.JmolPopup;
-
-class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
+public class AppJmolBinding extends JalviewJmolBinding
 {
-
-  /**
-   * 
-   */
-  private AppJmol appJmolWindow;
-
-  public AppJmolBinding(AppJmol appJmol, PDBEntry[] pdbentry,
-          SequenceI[] seq, String[] chains, String protocol)
+  public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+          DataSourceType protocol)
   {
-    super(pdbentry, seq, chains, protocol);
-    appJmolWindow = appJmol;
-  }
-  FeatureRenderer fr=null;
-  @Override
-  public jalview.api.FeatureRenderer getFeatureRenderer()
-  {
-    if (appJmolWindow.ap.av.showSequenceFeatures)
-    {
-      if (fr == null)
-      {
-        fr = new FeatureRenderer(appJmolWindow.ap);
-      }
-
-      fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas
-                      .getFeatureRenderer());
-    }
-
-    return fr;
+    super(sSm, pdbentry, sequenceIs, protocol);
+    setViewer(appJmol);
   }
 
   @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()
   {
+    if (getMappedStructureCount() == 0)
+    {
+      // too soon!
+      return;
+    }
     // appJmolWindow.repaint();
-    appJmolWindow.updateTitleAndMenus();
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        JalviewStructureDisplayI theViewer = getViewer();
+        // invokes colourbySequence() via seqColour_ActionPerformed()
+        theViewer.updateTitleAndMenus();
+        ((JComponent) theViewer).revalidate();
+      }
+    });
   }
 
-  public void updateColours(Object source)
+  @Override
+  public void notifyScriptTermination(String strStatus, int msWalltime)
   {
-    AlignmentPanel ap = (AlignmentPanel) source;
-    if (appJmolWindow.ap.alignFrame.getCurrentView()!=ap.av)
-      return;
-    
-    colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+    // todo - script termination doesn't happen ?
+    // if (console != null)
+    // console.notifyScriptTermination(strStatus,
+    // msWalltime);
   }
 
-  public void notifyScriptTermination(String strStatus, int msWalltime)
+  @Override
+  public void showUrl(String url)
   {
-    if (appJmolWindow.scriptWindow != null)
-      appJmolWindow.scriptWindow.notifyScriptTermination(strStatus, msWalltime);
+    showUrl(url, "jmol");
   }
 
-  public void showUrl(String url)
+  public void newJmolPopup(String menuName)
   {
-    showUrl(url,"jmol");
+    // jmolpopup = new JmolAwtPopup();
+    // jmolpopup.jpiInitialize((viewer), menuName);
   }
 
-  public void newJmolPopup(boolean translateLocale, String menuName,
-          boolean asPopup)
+  @Override
+  public void selectionChanged(BS arg0)
   {
+  }
 
-    jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
-            asPopup);
+  @Override
+  public void showConsole(boolean b)
+  {
+    getViewer().showConsole(b);
   }
-  public synchronized void addSequence(SequenceI[] seq)
+
+  @Override
+  protected JmolAppConsoleInterface createJmolConsole(
+          Container consolePanel, String buttonsToShow)
   {
-    Vector v = new Vector();
-    for (int i = 0; i < sequence.length; i++)
-      v.addElement(sequence[i]);
+    jmolViewer.setJmolCallbackListener(this);
+    // BH comment: can't do this yet [for JS only, or generally?]
+    return Platform.isJS() ? null
+            : new AppConsole(jmolViewer, consolePanel, buttonsToShow);
+  }
 
-    for (int i = 0; i < seq.length; i++)
-      if (!v.contains(seq[i]))
-        v.addElement(seq[i]);
+  @Override
+  protected void releaseUIResources()
+  {
+    setViewer(null);
+    closeConsole();
+  }
 
-    SequenceI[] tmp = new SequenceI[v.size()];
-    v.copyInto(tmp);
-    sequence = tmp;
+  @Override
+  public void releaseReferences(Object svl)
+  {
+    if (svl instanceof SeqPanel)
+    {
+      getViewer().removeAlignmentPanel(((SeqPanel) svl).ap);
+    }
   }
 
-  public void selectionChanged(BitSet arg0)
+  @Override
+  public Map<String, Object> getJSpecViewProperty(String arg0)
   {
     // TODO Auto-generated method stub
-    
+    return null;
   }
 
-  public void refreshPdbEntries()
+  @SuppressWarnings("unused")
+  public void cacheFiles(List<File> files)
   {
-    // TODO Auto-generated method stub
-    
+    if (files == null)
+    {
+      return;
+    }
+    for (File f : files)
+    {
+      Platform.cacheFileData(f);
+    }
   }
-}
\ No newline at end of file
+}