X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=329850993db02ecf857847a2696002926e436b50;hb=2107a91322a1988a8a6b724c74f9d244795341e3;hp=2104399e22bc8f20ab05af78c46123f94d9c1729;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 2104399..3298509 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -21,65 +21,43 @@
 package jalview.gui;
 
 import java.awt.Container;
-import java.util.BitSet;
+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.api.JmolAppConsoleInterface;
-import org.jmol.api.JmolViewer;
-import org.jmol.popup.JmolPopup;
-import org.openscience.jmol.app.jmolpanel.AppConsole;
-
-public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
+public class AppJmolBinding extends JalviewJmolBinding
 {
-
-  /**
-   * 
-   */
-  private AppJmol appJmolWindow;
-
   public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
-          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
-          String protocol)
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+          DataSourceType protocol)
   {
-    super(sSm, pdbentry, sequenceIs, chains, protocol);
-    appJmolWindow = appJmol;
+    super(sSm, pdbentry, sequenceIs, protocol);
+    setViewer(appJmol);
   }
 
-  FeatureRenderer fr = null;
-
   @Override
-  public jalview.api.FeatureRenderer getFeatureRenderer(
-          AlignmentViewPanel alignment)
-  {
-    AlignmentPanel ap = (alignment == null) ? appJmolWindow.ap
-            : (AlignmentPanel) alignment;
-    if (ap.av.showSequenceFeatures)
-    {
-      if (fr == null)
-      {
-        fr = ap.cloneFeatureRenderer();
-      }
-      else
-      {
-        ap.updateFeatureRenderer(fr);
-      }
-    }
-
-    return fr;
-  }
-
-  @Override
-  public jalview.api.SequenceRenderer getSequenceRenderer(
-          AlignmentViewPanel alignment)
+  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
     return new SequenceRenderer(((AlignmentPanel) alignment).av);
   }
 
+  @Override
   public void sendConsoleEcho(String strEcho)
   {
     if (console != null)
@@ -88,6 +66,7 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     }
   }
 
+  @Override
   public void sendConsoleMessage(String strStatus)
   {
     if (console != null && strStatus != null)
@@ -117,26 +96,18 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     // appJmolWindow.repaint();
     javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
+      @Override
       public void run()
       {
-        appJmolWindow.updateTitleAndMenus();
-        appJmolWindow.revalidate();
+        JalviewStructureDisplayI theViewer = getViewer();
+        // invokes colourbySequence() via seqColour_ActionPerformed()
+        theViewer.updateTitleAndMenus();
+        ((JComponent) theViewer).revalidate();
       }
     });
   }
 
-  public void updateColours(Object source)
-  {
-    AlignmentPanel ap = (AlignmentPanel) source, topap;
-    // ignore events from panels not used to colour this view
-    if (!appJmolWindow.isUsedforcolourby(ap))
-      return;
-    if (!isLoadingFromArchive())
-    {
-      colourBySequence(ap.av.getShowSequenceFeatures(), ap);
-    }
-  }
-
+  @Override
   public void notifyScriptTermination(String strStatus, int msWalltime)
   {
     // todo - script termination doesn't happen ?
@@ -145,80 +116,44 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     // msWalltime);
   }
 
+  @Override
   public void showUrl(String url)
   {
     showUrl(url, "jmol");
   }
 
-  public void newJmolPopup(boolean translateLocale, String menuName,
-          boolean asPopup)
-  {
-
-    jmolpopup = new JmolPopup();
-    jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
-  }
-
-  public void selectionChanged(BitSet arg0)
+  public void newJmolPopup(String menuName)
   {
-    // TODO Auto-generated method stub
-
+    // jmolpopup = new JmolAwtPopup();
+    // jmolpopup.jpiInitialize((viewer), menuName);
   }
 
-  public void refreshPdbEntries()
+  @Override
+  public void selectionChanged(BS arg0)
   {
-    // TODO Auto-generated method stub
-
   }
 
+  @Override
   public void showConsole(boolean b)
   {
-    appJmolWindow.showConsole(b);
-  }
-
-  /**
-   * add the given sequences to the mapping scope for the given pdb file handle
-   * 
-   * @param pdbFile
-   *          - pdbFile identifier
-   * @param seq
-   *          - set of sequences it can be mapped to
-   */
-  public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
-  {
-    for (int pe = 0; pe < pdbentry.length; pe++)
-    {
-      if (pdbentry[pe].getFile().equals(pdbFile))
-      {
-        addSequence(pe, seq);
-      }
-    }
+    getViewer().showConsole(b);
   }
 
   @Override
-  protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+  protected JmolAppConsoleInterface createJmolConsole(
           Container consolePanel, String buttonsToShow)
   {
-    return new AppConsole(viewer, consolePanel, buttonsToShow);
+    jmolViewer.setJmolCallbackListener(this);
+    // BH comment: can't do this yet [for JS only, or generally?]
+    return Platform.isJS() ? null
+            : new AppConsole(jmolViewer, consolePanel, buttonsToShow);
   }
 
   @Override
   protected void releaseUIResources()
   {
-    appJmolWindow = null;
-    if (console != null)
-    {
-      try
-      {
-        console.setVisible(false);
-      } catch (Error e)
-      {
-      } catch (Exception x)
-      {
-      }
-      ;
-      console = null;
-    }
-
+    setViewer(null);
+    closeConsole();
   }
 
   @Override
@@ -226,9 +161,27 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   {
     if (svl instanceof SeqPanel)
     {
-      appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
+      getViewer().removeAlignmentPanel(((SeqPanel) svl).ap);
+    }
+  }
+
+  @Override
+  public Map<String, Object> getJSpecViewProperty(String arg0)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
 
+  @SuppressWarnings("unused")
+  public void cacheFiles(List<File> files)
+  {
+    if (files == null)
+    {
+      return;
+    }
+    for (File f : files)
+    {
+      Platform.cacheFileData(f);
     }
-    ;
   }
 }