JAL-634 and JAL-635

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index c361ab9..74a9c22 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -59,24 +59,60 @@ public class AppJmol extends GStructureViewer implements Runnable,
 
   private boolean addingStructures = false;
 
+  /**
+   * 
+   * @param file
+   * @param id
+   * @param seq
+   * @param ap
+   * @param loadStatus
+   * @param bounds
+   * @deprecated defaults to AppJmol(String[] files, ... , viewid);
+   */
   public AppJmol(String file, String id, SequenceI[] seq,
           AlignmentPanel ap, String loadStatus, Rectangle bounds)
   {
     this(file, id, seq, ap, loadStatus, bounds, null);
   }
 
+  /**
+   * @deprecated
+   */
   public AppJmol(String file, String id, SequenceI[] seq,
           AlignmentPanel ap, String loadStatus, Rectangle bounds,
           String viewid)
   {
-    PDBEntry pdbentry = new PDBEntry();
-    pdbentry.setFile(file);
-    pdbentry.setId(id);
+    this(new String[]
+    { file }, new String[]
+    { id }, new SequenceI[][]
+    { seq }, ap, loadStatus, bounds, viewid);
+  }
+
+  /**
+   * 
+   * @param files
+   * @param ids
+   * @param seqs
+   * @param ap
+   * @param loadStatus
+   * @param bounds
+   * @param viewid
+   */
+  public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,
+          AlignmentPanel ap, String loadStatus, Rectangle bounds,
+          String viewid)
+  {
+    PDBEntry[] pdbentrys = new PDBEntry[files.length];
+    for (int i = 0; i < pdbentrys.length; i++)
+    {
+      PDBEntry pdbentry = new PDBEntry();
+      pdbentry.setFile(files[i]);
+      pdbentry.setId(ids[i]);
+      pdbentrys[i] = pdbentry;
+    }
     // / TODO: check if protocol is needed to be set, and if chains are
     // autodiscovered.
-    jmb = new AppJmolBinding(this, new PDBEntry[]
-    { pdbentry }, new SequenceI[][]
-    { seq }, null, null);
+    jmb = new AppJmolBinding(this, pdbentrys, seqs, null, null);
 
     jmb.setLoadingFromArchive(true);
     this.ap = ap;
@@ -98,9 +134,12 @@ public class AppJmol extends GStructureViewer implements Runnable,
 
   }
 
+  IProgressIndicator progressBar = null;
+
   public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
           AlignmentPanel ap)
   {
+    progressBar = ap.alignFrame;
     // ////////////////////////////////
     // Is the pdb file already loaded?
     String alreadyMapped = StructureSelectionManager
@@ -169,7 +208,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
                 JOptionPane.YES_NO_OPTION);
         if (option == JOptionPane.YES_OPTION)
         {
-          topJmol.addStructure(pdbentry, seq, chains, true);
+          topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
           return;
         }
       }
@@ -215,11 +254,12 @@ public class AppJmol extends GStructureViewer implements Runnable,
    * @param pdbentry
    * @param seq
    * @param chains
+   * @param alignFrame 
    * @param align
    *          if true, new structure(s) will be align using associated alignment
    */
   private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq,
-          final String[] chains, final boolean b)
+          final String[] chains, final boolean b, final IProgressIndicator alignFrame)
   {
     if (pdbentry.getFile() == null)
     {
@@ -243,7 +283,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
 
             }
             // and call ourselves again.
-            addStructure(pdbentry, seq, chains, b);
+            addStructure(pdbentry, seq, chains, b, alignFrame);
           }
         }).start();
         return;
@@ -256,6 +296,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
     { chains });
     addingStructures = true;
     _started = false;
+    alignAddedStructures = b;
+    progressBar = alignFrame; // visual indication happens on caller frame. 
     (worker = new Thread(this)).start();
     return;
   }
@@ -392,6 +434,13 @@ public class AppJmol extends GStructureViewer implements Runnable,
         {
           // retrieve the pdb and store it locally
           AlignmentI pdbseq = null;
+          pdbid = jmb.pdbentry[pi].getId();
+          long hdl=pdbid.hashCode()-System.currentTimeMillis();
+          if (progressBar != null)
+          {
+            progressBar.setProgressBar("Fetching PDB " + pdbid,
+                    hdl);
+          }
           try
           {
             pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
@@ -404,6 +453,10 @@ public class AppJmol extends GStructureViewer implements Runnable,
             ex.printStackTrace();
             errormsgs.append("'" + pdbid + "'");
           }
+          if (progressBar != null)
+          {
+            progressBar.setProgressBar("Finished.", hdl);
+          }
           if (pdbseq != null)
           {
             // just transfer the file name from the first sequence's first
@@ -472,51 +525,55 @@ public class AppJmol extends GStructureViewer implements Runnable,
         {
           Cache.log.error("Couldn't open Jmol viewer!", ex);
         }
-    }
-    else
-    {
-      StringBuffer cmd = new StringBuffer();
-      cmd.append("load APPEND ");
-      cmd.append(files.toString());
-      cmd.append("\n");
-      final String command = cmd.toString();
-      cmd = null;
-      try
-      {
-        jmb.evalStateCommand(command);
-      } catch (OutOfMemoryError oomerror)
-      {
-        new OOMWarning("When trying to add structures to the Jmol viewer!",
-                oomerror);
-        Cache.log.debug("File locations are " + files);
-      } catch (Exception ex)
-      {
-        Cache.log.error("Couldn't add files to Jmol viewer!", ex);
       }
-      if (alignAddedStructures)
+      else
       {
-        // may need to wait around until script has finished
-        while (jmb.viewer.isScriptExecuting())
+        StringBuffer cmd = new StringBuffer();
+        cmd.append("loadingJalviewdata=true\nload APPEND ");
+        cmd.append(files.toString());
+        cmd.append("\nloadingJalviewdata=null");
+        final String command = cmd.toString();
+        cmd = null;
+        try
         {
-          try
-          {
-            Thread.sleep(20);
-          } catch (Exception e)
-          {
-          }
-          ;
-        }
-        javax.swing.SwingUtilities.invokeLater(new Runnable()
+          jmb.evalStateCommand(command);
+        } catch (OutOfMemoryError oomerror)
         {
-          public void run()
+          new OOMWarning(
+                  "When trying to add structures to the Jmol viewer!",
+                  oomerror);
+          Cache.log.debug("File locations are " + files);
+        } catch (Exception ex)
+        {
+          Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+        }
+          long lastnotify=jmb.getLoadNotifiesHandled();
+          // need to wait around until script has finished
+          while (lastnotify>=jmb.getLoadNotifiesHandled()); 
           {
-            jmb.superposeStructures(ap.av.getAlignment(), -1, null);
+            try
+            {
+              Thread.sleep(35);
+            } catch (Exception e)
+            {
+            }
           }
-        });
-        alignAddedStructures = false;
+          // refresh the sequence colours for the new structure(s)
+          jmb.updateColours(ap);
+          // do superposition if asked to
+          if (alignAddedStructures)
+          {
+            javax.swing.SwingUtilities.invokeLater(new Runnable()
+          {
+            public void run()
+            {
+              jmb.superposeStructures(ap.av.getAlignment(), -1, null);
+            }
+          });
+          alignAddedStructures = false;
+        }
+        addingStructures = false;
       }
-      addingStructures = false;
-    }
     }
     _started = false;
     worker = null;