streamlined app and applet jmol console + event handling via component listener

[jalview.git] / src / jalview / appletgui / AppletJmol.java

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index afbc83c..bf38d32 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -98,13 +98,25 @@ public class AppletJmol extends EmbmenuFrame implements
    * datasource protocol for access to PDBEntry
    */
   String protocol = null;
-
+  /**
+   * Load a bunch of pdb entries associated with sequences in the alignment and display them - aligning them if necessary.
+   * @param pdbentries each pdb file (at least one needed)
+   * @param boundseqs each set of sequences for each pdb file (must match number of pdb files)
+   * @param boundchains the target pdb chain corresponding with each sequence associated with each pdb file (may be null at any level)
+   * @param align true/false
+   * @param ap associated alignment
+   * @param protocol how to get pdb data
+   */
+  public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs, String[][] boundchains, boolean align, AlignmentPanel ap, String protocol)
+  {
+    throw new Error("Not yet implemented.");
+  }
   public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
           AlignmentPanel ap, String protocol)
   {
     this.ap = ap;
     jmb = new AppletJmolBinding(this, new PDBEntry[]
-    { pdbentry }, seq, chains, protocol);
+    { pdbentry }, new SequenceI[][]{seq}, new String[][]{ chains }, protocol);
     jmb.setColourBySequence(true);
     if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
     {
@@ -172,17 +184,22 @@ public class AppletJmol extends EmbmenuFrame implements
     coloursMenu.add(user);
 
     helpMenu.add(jmolHelp);
+    this.setLayout(new BorderLayout());
 
     setMenuBar(menuBar);
 
     renderPanel = new RenderPanel();
     embedMenuIfNeeded(renderPanel);
     this.add(renderPanel, BorderLayout.CENTER);
+    scriptWindow = new Panel();
+    scriptWindow.setVisible(false);
+    // this.add(scriptWindow, BorderLayout.SOUTH);
+    
     try
     {
-      jmb.allocateViewer(renderPanel, "jalviewJmol",
+      jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()+"_jmol_",
               ap.av.applet.getDocumentBase(), ap.av.applet.getCodeBase(),
-              "");
+              "-applet", scriptWindow, null);
     } catch (Exception e)
     {
       System.err
@@ -203,12 +220,18 @@ public class AppletJmol extends EmbmenuFrame implements
         closeViewer();
       }
     });
-
+    if (pdbentry.getProperty()==null)
+    {
+      pdbentry.setProperty(new Hashtable());
+      pdbentry.getProperty().put("protocol", protocol);
+    }
     if (pdbentry.getFile() != null)
     {
       // import structure data from pdbentry.getFile based on given protocol
       if (protocol.equals(AppletFormatAdapter.PASTE))
       {
+        // TODO: JAL-623 : correctly record file contents for matching up later
+        // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode());
         loadInline(pdbentry.getFile());
       }
       else if (protocol.equals(AppletFormatAdapter.FILE)
@@ -276,7 +299,7 @@ public class AppletJmol extends EmbmenuFrame implements
   public void loadInline(String string)
   {
     loadedInline = true;
-    jmb.viewer.openStringInline(string);
+    jmb.loadInline(string);
   }
 
   void setChainMenuItems(Vector chains)
@@ -335,15 +358,24 @@ public class AppletJmol extends EmbmenuFrame implements
       Frame frame = new Frame();
       frame.add(cap);
 
-      jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
-              550, 600);
       StringBuffer sb = new StringBuffer();
+      try {
       for (int s = 0; s < jmb.pdbentry.length; s++)
       {
         sb.append(StructureSelectionManager.getStructureSelectionManager()
                 .printMapping(jmb.pdbentry[s].getFile()));
         sb.append("\n");
       }
+      cap.setText(sb.toString());
+      }
+      catch (OutOfMemoryError ex)
+      {
+        frame.dispose();
+        System.err.println("Out of memory when trying to create dialog box with sequence-structure mapping.");
+        return;
+      }
+      jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
+              550, 600);
     }
     else if (evt.getSource() == charge)
     {
@@ -493,23 +525,27 @@ public class AppletJmol extends EmbmenuFrame implements
     {
     }
   }
-
+  Panel splitPane=null;
   public void showConsole(boolean showConsole)
   {
-    if (scriptWindow == null)
+    if (showConsole)
     {
-      scriptWindow = new Panel(new BorderLayout());
-      inputLine = new TextField();
-      history = new TextArea(5, 40);
-      scriptWindow.add(history, BorderLayout.CENTER);
-      scriptWindow.add(inputLine, BorderLayout.SOUTH);
-      add(scriptWindow, BorderLayout.SOUTH);
+      remove(renderPanel);
+      splitPane = new Panel();
+      
+      splitPane.setLayout(new java.awt.GridLayout(2,1));
+      splitPane.add(renderPanel);
+      splitPane.add(scriptWindow);
+      scriptWindow.setVisible(true);
+      this.add(splitPane, BorderLayout.CENTER);
+      splitPane.setVisible(true);
+      splitPane.validate();
+    } else {
       scriptWindow.setVisible(false);
-      history.setEditable(false);
-      inputLine.addKeyListener(this);
+      remove(splitPane);
+      add(renderPanel, BorderLayout.CENTER);
+      splitPane=null;
     }
-
-    scriptWindow.setVisible(!scriptWindow.isVisible());
     validate();
   }