X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=619d5226f20fa5d039f1f1f8e65be3d26ceeacc1;hb=9ff5fcbe6681e37c441656e2f704f8d9bab9179c;hp=afbc83c546fe528dbb420dbe3bc8380bf59ca8a9;hpb=9adeaab28df6873e67ebe42e1ccd3a87cf6507af;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index afbc83c..619d522 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -83,6 +83,7 @@ public class AppletJmol extends EmbmenuFrame implements
   RenderPanel renderPanel;
 
   AlignmentPanel ap;
+  ArrayList _aps = new ArrayList();
 
   String fileLoadingError;
 
@@ -99,12 +100,40 @@ public class AppletJmol extends EmbmenuFrame implements
    */
   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 +201,22 @@ 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",
-              ap.av.applet.getDocumentBase(), ap.av.applet.getCodeBase(),
-              "");
+      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 +237,18 @@ 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 +316,7 @@ 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 +375,26 @@ 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();
-      for (int s = 0; s < jmb.pdbentry.length; s++)
+      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)
       {
-        sb.append(StructureSelectionManager.getStructureSelectionManager()
-                .printMapping(jmb.pdbentry[s].getFile()));
-        sb.append("\n");
+        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)
     {
@@ -439,7 +490,7 @@ public class AppletJmol extends EmbmenuFrame implements
     if (evt.getSource() == seqColour)
     {
       setEnabled(seqColour);
-      jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+      jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
     }
     else if (!allChainsSelected)
       centerViewer();
@@ -467,7 +518,7 @@ public class AppletJmol extends EmbmenuFrame implements
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
-    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
   }
 
   public void updateTitleAndMenus()
@@ -478,7 +529,7 @@ public class AppletJmol extends EmbmenuFrame implements
       return;
     }
     setChainMenuItems(jmb.chainNames);
-    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
 
     setTitle(jmb.getViewerTitle());
   }
@@ -494,22 +545,30 @@ public class AppletJmol extends EmbmenuFrame implements
     }
   }
 
+  Panel splitPane = null;
+
   public void showConsole(boolean showConsole)
   {
-    if (scriptWindow == null)
-    {
-      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);
+    if (showConsole)
+    {
+      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();
   }
 
@@ -574,4 +633,16 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     jmb.setJalviewColourScheme(ucs);
   }
+
+  public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
+  {
+    for (int i=0;i<_aps.size();i++)
+    {
+      if (((AlignmentPanel)_aps.get(i)).av.getAlignment()==alignment)
+      {
+        return ((AlignmentPanel)_aps.get(i));
+      }
+    }
+    return ap;
+  }
 }