X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=3432911ea37c37905d1cd71eebd656a081abe9f4;hb=c6018dc0dc12720e13b75850a5303279ac7094b7;hp=f051838f30ab6875c281d086ac8ae9dbbdc8f6ca;hpb=1b5f1de68f3f4dadcd4eecc80a5db17441eb7ab6;p=jalview.git

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index f051838..3432911 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -1,66 +1,66 @@
-/**
+/*
+ * 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.awt.Container;
-import java.awt.event.ComponentEvent;
-import java.awt.event.ComponentListener;
-import java.awt.event.ContainerEvent;
-import java.awt.event.ContainerListener;
-import java.util.BitSet;
-
-import javax.swing.JPanel;
-
+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 java.awt.Container;
+import java.util.Map;
 
 import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.api.JmolViewer;
-import org.jmol.popup.JmolPopup;
-import org.openscience.jmol.app.jmolpanel.AppConsole;
+import org.jmol.java.BS;
+import org.openscience.jmol.app.jmolpanel.console.AppConsole;
 
-public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding 
+public class AppJmolBinding extends 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,
+          DataSourceType protocol)
   {
-    super(pdbentry, sequenceIs, chains, protocol);
+    super(sSm, pdbentry, sequenceIs, protocol);
     appJmolWindow = appJmol;
   }
 
-  FeatureRenderer fr = null;
-
   @Override
-  public jalview.api.FeatureRenderer getFeatureRenderer()
+  protected IProgressIndicator getIProgressIndicator()
   {
-    if (appJmolWindow.ap.av.showSequenceFeatures)
-    {
-      if (fr == null)
-      {
-        fr = new FeatureRenderer(appJmolWindow.ap);
-      }
-
-      fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas
-              .getFeatureRenderer());
-    }
-
-    return fr;
+    return appJmolWindow.progressBar;
   }
 
   @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 (console != null)
@@ -69,6 +69,7 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     }
   }
 
+  @Override
   public void sendConsoleMessage(String strStatus)
   {
     if (console != null && strStatus != null)
@@ -96,82 +97,78 @@ 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()
+    {
+      @Override
+      public void run()
+      {
         appJmolWindow.updateTitleAndMenus();
         appJmolWindow.revalidate();
-      }});
+      }
+    });
   }
 
+  @Override
   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)
   {
     // todo - script termination doesn't happen ?
-    //if (console != null)
-      //console.notifyScriptTermination(strStatus,
-      //        msWalltime);
+    // if (console != null)
+    // console.notifyScriptTermination(strStatus,
+    // msWalltime);
   }
 
+  @Override
   public void showUrl(String url)
   {
     showUrl(url, "jmol");
   }
 
-  public void newJmolPopup(boolean translateLocale, String menuName,
-          boolean asPopup)
+  public void newJmolPopup(String menuName)
   {
-
-    jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
-            asPopup);
+    // jmolpopup = new JmolAwtPopup();
+    // jmolpopup.jpiInitialize((viewer), menuName);
   }
 
-  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
 
   }
 
-  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)
+  @Override
+  public void showConsole(boolean b)
   {
-    for (int pe = 0; pe < pdbentry.length; pe++)
-    {
-      if (pdbentry[pe].getFile().equals(pdbFile))
-      {
-        addSequence(pe, seq);
-      }
-    }
+    appJmolWindow.showConsole(b);
   }
 
   @Override
-  protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+  protected JmolAppConsoleInterface createJmolConsole(
           Container consolePanel, String buttonsToShow)
   {
+    viewer.setJmolCallbackListener(this);
     return new AppConsole(viewer, consolePanel, buttonsToShow);
   }
 
@@ -179,12 +176,38 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   protected void releaseUIResources()
   {
     appJmolWindow = null;
-    if (console!=null) {
-      try {
-        console.setVisible(false);
-      } catch (Error e) {} catch (Exception x) {};
-      console=null;
+    closeConsole();
+  }
+
+  @Override
+  public void releaseReferences(Object svl)
+  {
+    if (svl instanceof SeqPanel)
+    {
+      appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
     }
-    
   }
-}
\ No newline at end of file
+
+  @Override
+  public Map<String, Object> getJSpecViewProperty(String arg0)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+  @Override
+  public JalviewStructureDisplayI getViewer()
+  {
+    return appJmolWindow;
+  }
+
+  @Override
+  public jalview.api.FeatureRenderer getFeatureRenderer(
+          AlignmentViewPanel alignment)
+  {
+    AlignmentPanel ap = (alignment == null)
+            ? appJmolWindow.getAlignmentPanel()
+            : (AlignmentPanel) alignment;
+    return ap.av.getAlignPanel().getFeatureRenderer();
+  }
+}