X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=2a0e2a7dfa4721b76bb4585c21fef1712e509e51;hb=6486a5333807ca300db4a28a6bf9899f5dddf5a6;hp=d6535e3d961a2f571f35ed48182a0703f45e1202;hpb=4fe775d619d3587a4037a79a67b7391a82b8a130;p=jalview.git

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index d6535e3..2a0e2a7 100644
--- 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
 {
 
   /**
@@ -54,19 +56,19 @@ 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)
+    if (console != null && strStatus != null)
     // && !strStatus.equals("Script completed"))
     // should we squash the script completed string ?
     {
-      appJmolWindow.scriptWindow.sendConsoleMessage(strStatus);
+      console.sendConsoleMessage(strStatus);
     }
   }
 
@@ -87,7 +89,11 @@ class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   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)
@@ -101,9 +107,10 @@ class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 
   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)
@@ -119,144 +126,6 @@ class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
             asPopup);
   }
 
-  /**
-   * add structures and any known sequence associations
-   * 
-   * @returns the pdb entries added to the current set.
-   */
-  private PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
-          SequenceI[][] seq, String[][] chns)
-  {
-    int pe = -1;
-    Vector v = new Vector();
-    Vector rtn = new Vector();
-    for (int i = 0; i < pdbentry.length; i++)
-    {
-      v.addElement(pdbentry[i]);
-    }
-    for (int i = 0; i < pdbe.length; i++)
-    {
-      int r = v.indexOf(pdbe[i]);
-      if (r == -1 || r >= pdbentry.length)
-      {
-        rtn.addElement(new int[]
-        { v.size(), i });
-        v.addElement(pdbe[i]);
-      }
-      else
-      {
-        // just make sure the sequence/chain entries are all up to date
-        addSequenceAndChain(r, seq[i], chns[i]);
-      }
-    }
-    pdbe = new PDBEntry[v.size()];
-    v.copyInto(pdbe);
-    pdbentry = pdbe;
-    if (rtn.size() > 0)
-    {
-      // expand the tied seuqence[] and string[] arrays
-      SequenceI[][] sqs = new SequenceI[pdbentry.length][];
-      String[][] sch = new String[pdbentry.length][];
-      System.arraycopy(sequence, 0, sqs, 0, sequence.length);
-      System.arraycopy(chains, 0, sch, 0, this.chains.length);
-      sequence = sqs;
-      chains = sch;
-      pdbe = new PDBEntry[rtn.size()];
-      for (int r = 0; r < pdbe.length; r++)
-      {
-        int[] stri = ((int[]) rtn.elementAt(r));
-        // record the pdb file as a new addition
-        pdbe[r] = pdbentry[stri[0]];
-        // and add the new sequence/chain entries
-        addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]);
-      }
-    }
-    else
-    {
-      pdbe = null;
-    }
-    return pdbe;
-  }
-
-  void addSequence(int pe, SequenceI[] seq)
-  {
-    // add sequences to the pe'th pdbentry's seuqence set.
-    addSequenceAndChain(pe, seq, null);
-  }
-
-  private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain)
-  {
-    if (pe < 0 || pe >= pdbentry.length)
-    {
-      throw new Error(
-              "Implementation error - no corresponding pdbentry (for index "
-                      + pe + ") to add sequences mappings to");
-    }
-    final String nullChain = "TheNullChain";
-    Vector s = new Vector();
-    Vector c = new Vector();
-    if (chains == null)
-    {
-      chains = new String[pdbentry.length][];
-    }
-    if (sequence[pe] != null)
-    {
-      for (int i = 0; i < sequence[pe].length; i++)
-      {
-        s.addElement(sequence[pe][i]);
-        if (chains[pe] != null)
-        {
-          if (i < chains[pe].length)
-          {
-            c.addElement(chains[pe][i]);
-          }
-          else
-          {
-            c.addElement(nullChain);
-          }
-        }
-        else
-        {
-          if (tchain != null && tchain.length > 0)
-          {
-            c.addElement(nullChain);
-          }
-        }
-      }
-    }
-    for (int i = 0; i < seq.length; i++)
-    {
-      if (!s.contains(seq[i]))
-      {
-        s.addElement(seq[i]);
-        if (tchain != null && i < tchain.length)
-        {
-          c.addElement(tchain[i] == null ? nullChain : tchain[i]);
-        }
-      }
-    }
-    SequenceI[] tmp = new SequenceI[s.size()];
-    s.copyInto(tmp);
-    sequence[pe] = tmp;
-    if (c.size() > 0)
-    {
-      String[] tch = new String[c.size()];
-      c.copyInto(tch);
-      for (int i = 0; i < tch.length; i++)
-      {
-        if (tch[i] == nullChain)
-        {
-          tch[i] = null;
-        }
-      }
-      chains[pe] = tch;
-    }
-    else
-    {
-      chains[pe] = null;
-    }
-  }
-
   public void selectionChanged(BitSet arg0)
   {
     // TODO Auto-generated method stub
@@ -269,58 +138,8 @@ class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 
   }
 
-  /**
-   * add another pdb entry into the view, with associated sequences and chains
-   * 
-   * @param pdbentry
-   * @param seq
-   * @param chains
-   * @param align
-   *          if true, new structure(s) will be align using associated alignment
-   */
-  public synchronized void addStructure(PDBEntry pdbentry, SequenceI[] seq,
-          String[] chains, final boolean align)
-  {
-    PDBEntry[] pe = addSequenceAndChain(new PDBEntry[]
-    { pdbentry }, new SequenceI[][]
-    { seq }, new String[][]
-    { chains });
-    if (pe != null)
-    {
-      StringBuffer cmd = new StringBuffer();
-      cmd.append("load APPEND");
-      for (int p = 0; p < pe.length; p++)
-      {
-        cmd.append(" \"");
-        cmd.append(pe[p].getFile());
-        cmd.append("\"");
-      }
-      cmd.append("\n");
-      final String command = cmd.toString();
-      cmd = null;
-      new Thread(new Runnable()
-      {
-        public void run()
-        {
-          evalStateCommand(command);
-          if (align)
-          {
-            // may need to wait around until script has finished
-            while (viewer.isScriptExecuting())
-            {
-              try
-              {
-                Thread.sleep(20);
-              } catch (Exception e)
-              {
-              }
-              ;
-            }
-            superposeStructures(appJmolWindow.ap.av.getAlignment(), -1, null);
-          }
-        }
-      }).start();
-    }
+  public void showConsole(boolean b) {
+    appJmolWindow.showConsole(b);
   }
 
   /**
@@ -341,5 +160,4 @@ class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
       }
     }
   }
-
 }
\ No newline at end of file