patched Jmol and code for embedding JmolAppConsole in a JPanel (JAL-638)

[jalview.git] / src / jalview / gui / AppJmolBinding.java

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 9f7090a..2a0e2a7 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -4,15 +4,17 @@
 package jalview.gui;
 
 import java.util.BitSet;
-import java.util.Vector;
+
+import javax.swing.JPanel;
 
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 
 import org.jmol.popup.JmolPopup;
+import org.openscience.jmol.app.jmolpanel.AppConsole;
 
-class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
+public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 {
 
   /**
@@ -21,12 +23,14 @@ class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   private AppJmol appJmolWindow;
 
   public AppJmolBinding(AppJmol appJmol, PDBEntry[] pdbentry,
-          SequenceI[] seq, String[] chains, String protocol)
+          SequenceI[][] sequenceIs, String[][] chains, String protocol)
   {
-    super(pdbentry, seq, chains, protocol);
+    super(pdbentry, sequenceIs, chains, protocol);
     appJmolWindow = appJmol;
   }
-  FeatureRenderer fr=null;
+
+  FeatureRenderer fr = null;
+
   @Override
   public jalview.api.FeatureRenderer getFeatureRenderer()
   {
@@ -38,7 +42,7 @@ class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
       }
 
       fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas
-                      .getFeatureRenderer());
+              .getFeatureRenderer());
     }
 
     return fr;
@@ -52,59 +56,66 @@ class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 
   public void sendConsoleEcho(String strEcho)
   {
-    if (appJmolWindow.scriptWindow != null)
+    if (console != null)
     {
-      appJmolWindow.scriptWindow.sendConsoleEcho(strEcho);
+      console.sendConsoleEcho(strEcho);
     }
   }
 
   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)
+    if (appJmolWindow.ap.alignFrame.getCurrentView() != ap.av)
       return;
-    
+
     colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
   }
 
   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,
@@ -114,30 +125,39 @@ class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
             asPopup);
   }
-  public synchronized void addSequence(SequenceI[] seq)
-  {
-    Vector v = new Vector();
-    for (int i = 0; i < sequence.length; i++)
-      v.addElement(sequence[i]);
-
-    for (int i = 0; i < seq.length; i++)
-      if (!v.contains(seq[i]))
-        v.addElement(seq[i]);
-
-    SequenceI[] tmp = new SequenceI[v.size()];
-    v.copyInto(tmp);
-    sequence = tmp;
-  }
 
   public void selectionChanged(BitSet arg0)
   {
     // TODO Auto-generated method stub
-    
+
   }
 
   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)
+  {
+    for (int pe = 0; pe < pdbentry.length; pe++)
+    {
+      if (pdbentry[pe].getFile().equals(pdbFile))
+      {
+        addSequence(pe, seq);
+      }
+    }
   }
 }
\ No newline at end of file