X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=e2865a89e124b7caf20c6d0ba874bddf743ec05d;hb=075b2506c45bf8ae70e7a3ce3bb29029a21824b1;hp=546ce6514253706217dc0cf5e93d93ddf99231a1;hpb=c35461ed2a5a258cab842e8ccb89b7a973722799;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 546ce65..e2865a8 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
  * as published by the Free Software Foundation; either version 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  * GNU General Public License for more details.
- *
+ * 
  * You should have received a copy of the GNU General Public License
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -30,78 +30,125 @@ import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.io.*;
 import jalview.schemes.*;
+import jalview.util.UrlLink;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
-public class PopupMenu
-    extends JPopupMenu
+public class PopupMenu extends JPopupMenu
 {
   JMenu groupMenu = new JMenu();
+
   JMenuItem groupName = new JMenuItem();
+
   protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
-  protected JRadioButtonMenuItem hydrophobicityColour = new
-      JRadioButtonMenuItem();
+
+  protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
+
   protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
+
   protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
+
   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+
   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+
   AlignmentPanel ap;
+
   JMenu sequenceMenu = new JMenu();
+
   JMenuItem sequenceName = new JMenuItem();
+
   Sequence sequence;
+
   JMenuItem unGroupMenuItem = new JMenuItem();
+
   JMenuItem outline = new JMenuItem();
+
   JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
+
   JMenu colourMenu = new JMenu();
+
   JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
+
   JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
+
   JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
+
+  JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
+
   JMenu editMenu = new JMenu();
+
   JMenuItem cut = new JMenuItem();
+
   JMenuItem copy = new JMenuItem();
+
   JMenuItem upperCase = new JMenuItem();
+
   JMenuItem lowerCase = new JMenuItem();
+
   JMenuItem toggle = new JMenuItem();
+
   JMenu pdbMenu = new JMenu();
+
   JMenuItem pdbFromFile = new JMenuItem();
+
   JMenuItem enterPDB = new JMenuItem();
+
   JMenuItem discoverPDB = new JMenuItem();
+
   JMenu outputMenu = new JMenu();
+
   JMenuItem sequenceFeature = new JMenuItem();
+
   JMenuItem textColour = new JMenuItem();
+
   JMenu jMenu1 = new JMenu();
+
   JMenu structureMenu = new JMenu();
+
   JMenu viewStructureMenu = new JMenu();
- // JMenu colStructureMenu = new JMenu();
+
+  // JMenu colStructureMenu = new JMenu();
   JMenuItem editSequence = new JMenuItem();
- // JMenuItem annotationMenuItem = new JMenuItem();
+
+  // JMenuItem annotationMenuItem = new JMenuItem();
 
   /**
    * Creates a new PopupMenu object.
-   *
-   * @param ap DOCUMENT ME!
-   * @param seq DOCUMENT ME!
+   * 
+   * @param ap
+   *                DOCUMENT ME!
+   * @param seq
+   *                DOCUMENT ME!
    */
   public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
   {
-    ///////////////////////////////////////////////////////////
+    // /////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
     // edit or annotate a particular residue. Therefore display the residue menu
     //
     // If from the IDPanel, we must display the sequence menu
-    //////////////////////////////////////////////////////////
+    // ////////////////////////////////////////////////////////
     this.ap = ap;
     sequence = seq;
 
@@ -122,8 +169,8 @@ public class PopupMenu
 
     for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
     {
-      JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[
-                                     i]);
+      JMenuItem item = new JMenuItem(
+              jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
 
       item.addActionListener(new java.awt.event.ActionListener()
       {
@@ -139,8 +186,7 @@ public class PopupMenu
     try
     {
       jbInit();
-    }
-    catch (Exception e)
+    } catch (Exception e)
     {
       e.printStackTrace();
     }
@@ -151,10 +197,10 @@ public class PopupMenu
 
       JMenuItem menuItem;
       if (seq.getDatasetSequence().getPDBId() != null
-          && seq.getDatasetSequence().getPDBId().size()>0)
+              && seq.getDatasetSequence().getPDBId().size() > 0)
       {
-        java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
-            elements();
+        java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
+                .elements();
 
         while (e.hasMoreElements())
         {
@@ -169,48 +215,46 @@ public class PopupMenu
               Vector seqs = new Vector();
               for (int i = 0; i < ap.av.alignment.getHeight(); i++)
               {
-                Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();
-                if(pdbs==null)
+                Vector pdbs = ap.av.alignment.getSequenceAt(i)
+                        .getDatasetSequence().getPDBId();
+                if (pdbs == null)
                   continue;
 
-                for(int p=0; p<pdbs.size(); p++)
+                for (int p = 0; p < pdbs.size(); p++)
                 {
-                  PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);
-                  if(p1.getId().equals(pdb.getId()))
+                  PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
+                  if (p1.getId().equals(pdb.getId()))
                   {
                     if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
-                        seqs.addElement(ap.av.alignment.getSequenceAt(i));
+                      seqs.addElement(ap.av.alignment.getSequenceAt(i));
 
-                      continue;
+                    continue;
                   }
                 }
               }
 
-              SequenceI [] seqs2 = new SequenceI[seqs.size()];
+              SequenceI[] seqs2 = new SequenceI[seqs.size()];
               seqs.toArray(seqs2);
 
               new AppJmol(pdb, seqs2, null, ap);
-              //  new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
+              // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
             }
           });
           viewStructureMenu.add(menuItem);
 
-       /*   menuItem = new JMenuItem();
-          menuItem.setText(pdb.getId());
-          menuItem.addActionListener(new java.awt.event.ActionListener()
-          {
-            public void actionPerformed(ActionEvent e)
-            {
-              colourByStructure(pdb.getId());
-            }
-          });
-          colStructureMenu.add(menuItem);*/
+          /*
+           * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
+           * menuItem.addActionListener(new java.awt.event.ActionListener() {
+           * public void actionPerformed(ActionEvent e) {
+           * colourByStructure(pdb.getId()); } });
+           * colStructureMenu.add(menuItem);
+           */
         }
       }
       else
       {
         structureMenu.remove(viewStructureMenu);
-       // structureMenu.remove(colStructureMenu);
+        // structureMenu.remove(colStructureMenu);
       }
 
       menuItem = new JMenuItem("Hide Sequences");
@@ -224,7 +268,7 @@ public class PopupMenu
       add(menuItem);
 
       if (ap.av.getSelectionGroup() != null
-          && ap.av.getSelectionGroup().getSize() > 1)
+              && ap.av.getSelectionGroup().getSize() > 1)
       {
         menuItem = new JMenuItem("Represent Group with " + seq.getName());
         menuItem.addActionListener(new java.awt.event.ActionListener()
@@ -241,8 +285,8 @@ public class PopupMenu
       {
         final int index = ap.av.alignment.findIndex(seq);
 
-        if (ap.av.adjustForHiddenSeqs(index) -
-            ap.av.adjustForHiddenSeqs(index - 1) > 1)
+        if (ap.av.adjustForHiddenSeqs(index)
+                - ap.av.adjustForHiddenSeqs(index - 1) > 1)
         {
           menuItem = new JMenuItem("Reveal Sequences");
           menuItem.addActionListener(new ActionListener()
@@ -336,7 +380,7 @@ public class PopupMenu
       {
         conservationMenuItem.setSelected(true);
       }
-
+      displayNonconserved.setSelected(sg.getShowunconserved());
       showText.setSelected(sg.getDisplayText());
       showColourText.setSelected(sg.getColourText());
       showBoxes.setSelected(sg.getDisplayBoxes());
@@ -361,53 +405,110 @@ public class PopupMenu
     if (links != null && links.size() > 0)
     {
       JMenu linkMenu = new JMenu("Link");
-
+      Vector linkset = new Vector();
       for (int i = 0; i < links.size(); i++)
       {
         String link = links.elementAt(i).toString();
-        final String label = link.substring(0, link.indexOf("|"));
-        
-        
-        if (link.indexOf("$SEQUENCE_ID$") > -1)
+        UrlLink urlLink = null;
+        try
+        {
+          urlLink = new UrlLink(link);
+        } catch (Exception foo)
+        {
+          jalview.bin.Cache.log.error("Exception for URLLink '" + link
+                  + "'", foo);
+          continue;
+        }
+        ;
+        if (!urlLink.isValid())
+        {
+          jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+          continue;
+        }
+        final String label = urlLink.getLabel();
+        if (urlLink.isDynamic())
         {
-          // Substitute SEQUENCE_ID string and any matching database reference accessions
-          String url_pref = link.substring(link.indexOf("|") + 1,
-                  link.indexOf("$SEQUENCE_ID$"));
-          
-          String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13); 
 
           // collect matching db-refs
-          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new String[]{label});
+          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
+                  .getDBRef(), new String[]
+          { urlLink.getTarget() });
           // collect id string too
           String id = seq.getName();
-          if (id.indexOf("|") > -1)
+          String descr = seq.getDescription();
+          if (descr!=null && descr.length()<1)
           {
-            id = id.substring(id.lastIndexOf("|") + 1);
+            descr = null;
           }
 
-          if (dbr!=null)
+          if (dbr != null)
           {
-            for (int r=0;r<dbr.length; r++)
+            for (int r = 0; r < dbr.length; r++)
             {
-              if (dbr[r].getAccessionId().equals(id))
+              if (id != null && dbr[r].getAccessionId().equals(id))
               {
-                // suppress duplicate link creation for the bare sequence ID string with this link
+                // suppress duplicate link creation for the bare sequence ID
+                // string with this link
                 id = null;
               }
-              addshowLink(linkMenu, dbr[r].getSource()+"|"+dbr[r].getAccessionId(), 
-                      url_pref+dbr[r].getAccessionId()+url_suff);
+              // create Bare ID link for this RUL
+              String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
+                      true);
+              if (urls != null)
+              {
+                for (int u = 0; u < urls.length; u += 2)
+                {
+                  if (!linkset.contains(urls[u]+"|"+urls[u+1]))
+                  {
+                    linkset.addElement(urls[u]+"|"+urls[u+1]);
+                    addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
+                  }
+                }
+              }
             }
           }
-          if (id!=null)
+          if (id != null)
           {
             // create Bare ID link for this RUL
-            addshowLink(linkMenu, label,  url_pref + id + url_suff);
+            String[] urls = urlLink.makeUrls(id, true);
+            if (urls != null)
+            {
+              for (int u = 0; u < urls.length; u += 2)
+              {
+                if (!linkset.contains(urls[u]+"|"+urls[u+1]))
+                {
+                  linkset.addElement(urls[u]+"|"+urls[u+1]);
+                  addshowLink(linkMenu, label, urls[u + 1]);
+                }
+              }
+            }
+          }
+          // Create urls from description but only for URL links which are regex links
+          if (descr != null && urlLink.getRegexReplace()!=null)
+          {
+            // create link for this URL from description where regex matches
+            String[] urls = urlLink.makeUrls(descr, true);
+            if (urls != null)
+            {
+              for (int u = 0; u < urls.length; u += 2)
+              {
+                if (!linkset.contains(urls[u]+"|"+urls[u+1]))
+                {
+                  linkset.addElement(urls[u]+"|"+urls[u+1]);
+                  addshowLink(linkMenu, label, urls[u + 1]);
+                }
+              }
+            }
           }
         }
         else
         {
-          // Add a non-dynamic link
-          addshowLink(linkMenu, label, link.substring(link.lastIndexOf("|") + 1));
+          if (!linkset.contains(label+"|"+urlLink.getUrl_prefix()))
+          {
+            linkset.addElement(label+"|"+urlLink.getUrl_prefix());
+            // Add a non-dynamic link
+            addshowLink(linkMenu, label, urlLink.getUrl_prefix());
+          }
         }
       }
       if (sequence != null)
@@ -423,38 +524,43 @@ public class PopupMenu
 
   /**
    * add a show URL menu item to the given linkMenu
+   * 
    * @param linkMenu
-   * @param label - menu label string
-   * @param url - url to open
+   * @param label -
+   *                menu label string
+   * @param url -
+   *                url to open
    */
   private void addshowLink(JMenu linkMenu, String label, final String url)
   {
     JMenuItem item = new JMenuItem(label);
+    item.setToolTipText("open URL: " + url);
     item.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
       {
-        new Thread(new Runnable() {
+        new Thread(new Runnable()
+        {
 
           public void run()
           {
             showLink(url);
           }
-          
+
         }).start();
       }
     });
 
-    linkMenu.add(item);    
+    linkMenu.add(item);
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @throws Exception DOCUMENT ME!
+   * 
+   * @throws Exception
+   *                 DOCUMENT ME!
    */
-  private void jbInit()
-      throws Exception
+  private void jbInit() throws Exception
   {
     groupMenu.setText("Group");
     groupMenu.setText("Selection");
@@ -528,6 +634,15 @@ public class PopupMenu
         showColourText_actionPerformed();
       }
     });
+    displayNonconserved.setText("Show Nonconserved");
+    displayNonconserved.setState(true);
+    displayNonconserved.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showNonconserved_actionPerformed();
+      }
+    });
     editMenu.setText("Edit");
     cut.setText("Cut");
     cut.addActionListener(new ActionListener()
@@ -614,7 +729,7 @@ public class PopupMenu
     jMenu1.setText("Group");
     structureMenu.setText("Structure");
     viewStructureMenu.setText("View Structure");
-  //  colStructureMenu.setText("Colour By Structure");
+    // colStructureMenu.setText("Colour By Structure");
     editSequence.setText("Edit Sequence...");
     editSequence.addActionListener(new ActionListener()
     {
@@ -623,14 +738,12 @@ public class PopupMenu
         editSequence_actionPerformed(actionEvent);
       }
     });
-   /* annotationMenuItem.setText("By Annotation");
-    annotationMenuItem.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        annotationMenuItem_actionPerformed(actionEvent);
-      }
-    });*/
+    /*
+     * annotationMenuItem.setText("By Annotation");
+     * annotationMenuItem.addActionListener(new ActionListener() { public void
+     * actionPerformed(ActionEvent actionEvent) {
+     * annotationMenuItem_actionPerformed(actionEvent); } });
+     */
 
     add(groupMenu);
 
@@ -658,13 +771,12 @@ public class PopupMenu
 
     if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
     {
-      java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
-          getUserColourSchemes().keys();
+      java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+              .getUserColourSchemes().keys();
 
       while (userColours.hasMoreElements())
       {
-        JMenuItem item = new JMenuItem(userColours.
-                                       nextElement().toString());
+        JMenuItem item = new JMenuItem(userColours.nextElement().toString());
         item.addActionListener(new ActionListener()
         {
           public void actionPerformed(ActionEvent evt)
@@ -679,7 +791,7 @@ public class PopupMenu
     colourMenu.addSeparator();
     colourMenu.add(abovePIDColour);
     colourMenu.add(conservationMenuItem);
-    //colourMenu.add(annotationMenuItem);
+    // colourMenu.add(annotationMenuItem);
     editMenu.add(copy);
     editMenu.add(cut);
     editMenu.add(editSequence);
@@ -696,9 +808,10 @@ public class PopupMenu
     jMenu1.add(showText);
     jMenu1.add(showColourText);
     jMenu1.add(outline);
+    jMenu1.add(displayNonconserved);
     structureMenu.add(pdbMenu);
     structureMenu.add(viewStructureMenu);
-   // structureMenu.add(colStructureMenu);
+    // structureMenu.add(colStructureMenu);
     noColourmenuItem.setText("None");
     noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -733,13 +846,14 @@ public class PopupMenu
       }
     });
     hydrophobicityColour.setText("Hydrophobicity");
-    hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        hydrophobicityColour_actionPerformed();
-      }
-    });
+    hydrophobicityColour
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                hydrophobicityColour_actionPerformed();
+              }
+            });
     helixColour.setText("Helix propensity");
     helixColour.addActionListener(new java.awt.event.ActionListener()
     {
@@ -805,17 +919,24 @@ public class PopupMenu
       }
     });
     conservationMenuItem.setText("Conservation");
-    conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        conservationMenuItem_actionPerformed();
-      }
-    });
+    conservationMenuItem
+            .addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                conservationMenuItem_actionPerformed();
+              }
+            });
+  }
+
+  protected void showNonconserved_actionPerformed()
+  {
+    getGroup().setShowunconserved(displayNonconserved.isSelected());
+    refresh();
   }
 
   /**
-   * DOCUMENT ME!
+   * call to refresh view after settings change
    */
   void refresh()
   {
@@ -826,21 +947,24 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void clustalColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
-    sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
-                                     ap.av.alignment.getWidth());
+    sg.cs = new ClustalxColourScheme(sg
+            .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
+            .getWidth());
     refresh();
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void zappoColour_actionPerformed()
   {
@@ -850,8 +974,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void taylorColour_actionPerformed()
   {
@@ -861,8 +986,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void hydrophobicityColour_actionPerformed()
   {
@@ -872,8 +998,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void helixColour_actionPerformed()
   {
@@ -883,8 +1010,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void strandColour_actionPerformed()
   {
@@ -894,8 +1022,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void turnColour_actionPerformed()
   {
@@ -905,8 +1034,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void buriedColour_actionPerformed()
   {
@@ -916,8 +1046,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void nucleotideMenuItem_actionPerformed()
   {
@@ -927,8 +1058,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void abovePIDColour_actionPerformed()
   {
@@ -940,18 +1072,19 @@ public class PopupMenu
 
     if (abovePIDColour.isSelected())
     {
-      sg.cs.setConsensus(AAFrequency.calculate(
-          sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
-          sg.getEndRes() + 1));
+      sg.cs.setConsensus(AAFrequency.calculate(sg
+              .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
+              .getEndRes() + 1));
 
-      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
-          getGroup().getName());
+      int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+              .getName());
 
       sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
 
       SliderPanel.showPIDSlider();
     }
-    else // remove PIDColouring
+    else
+    // remove PIDColouring
     {
       sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
     }
@@ -961,8 +1094,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void userDefinedColour_actionPerformed(ActionEvent e)
   {
@@ -974,8 +1108,8 @@ public class PopupMenu
     }
     else
     {
-      UserColourScheme udc = (UserColourScheme) UserDefinedColours.
-          getUserColourSchemes().get(e.getActionCommand());
+      UserColourScheme udc = (UserColourScheme) UserDefinedColours
+              .getUserColourSchemes().get(e.getActionCommand());
 
       sg.cs = udc;
     }
@@ -984,24 +1118,25 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void PIDColour_actionPerformed()
   {
     SequenceGroup sg = getGroup();
     sg.cs = new PIDColourScheme();
-    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
-        hiddenRepSequences),
-                                             sg.getStartRes(),
-                                             sg.getEndRes() + 1));
+    sg.cs.setConsensus(AAFrequency.calculate(sg
+            .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
+            .getEndRes() + 1));
     refresh();
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void BLOSUM62Colour_actionPerformed()
   {
@@ -1009,18 +1144,18 @@ public class PopupMenu
 
     sg.cs = new Blosum62ColourScheme();
 
-    sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
-        hiddenRepSequences),
-                                             sg.getStartRes(),
-                                             sg.getEndRes() + 1));
+    sg.cs.setConsensus(AAFrequency.calculate(sg
+            .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg
+            .getEndRes() + 1));
 
     refresh();
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void noColourmenuItem_actionPerformed()
   {
@@ -1030,8 +1165,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void conservationMenuItem_actionPerformed()
   {
@@ -1044,11 +1180,9 @@ public class PopupMenu
     if (conservationMenuItem.isSelected())
     {
       Conservation c = new Conservation("Group",
-                                        ResidueProperties.propHash, 3,
-                                        sg.getSequences(ap.av.
-          hiddenRepSequences),
-                                        sg.getStartRes(),
-                                        sg.getEndRes() + 1);
+              ResidueProperties.propHash, 3, sg
+                      .getSequences(ap.av.hiddenRepSequences), sg
+                      .getStartRes(), sg.getEndRes() + 1);
 
       c.calculate();
       c.verdict(false, ap.av.ConsPercGaps);
@@ -1058,7 +1192,8 @@ public class PopupMenu
       SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
       SliderPanel.showConservationSlider();
     }
-    else // remove ConservationColouring
+    else
+    // remove ConservationColouring
     {
       sg.cs.setConservation(null);
     }
@@ -1074,8 +1209,9 @@ public class PopupMenu
       return;
     }
 
-    AnnotationColourGradient acg = new AnnotationColourGradient(
-        sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);
+    AnnotationColourGradient acg = new AnnotationColourGradient(sequence
+            .getAnnotation()[0], null,
+            AnnotationColourGradient.NO_THRESHOLD);
 
     acg.predefinedColours = true;
     sg.cs = acg;
@@ -1085,18 +1221,17 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void groupName_actionPerformed()
   {
 
     SequenceGroup sg = getGroup();
-    EditNameDialog dialog = new EditNameDialog(sg.getName(),
-                                               sg.getDescription(),
-                                               "       Group Name ",
-                                               "Group Description ",
-                                               "Edit Group Name/Description");
+    EditNameDialog dialog = new EditNameDialog(sg.getName(), sg
+            .getDescription(), "       Group Name ", "Group Description ",
+            "Edit Group Name/Description");
 
     if (!dialog.accept)
     {
@@ -1109,7 +1244,7 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   SequenceGroup getGroup()
@@ -1126,16 +1261,15 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   void sequenceName_actionPerformed()
   {
-    EditNameDialog dialog = new EditNameDialog(sequence.getName(),
-                                               sequence.getDescription(),
-                                               "       Sequence Name ",
-                                               "Sequence Description ",
-                                               "Edit Sequence Name/Description");
+    EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence
+            .getDescription(), "       Sequence Name ",
+            "Sequence Description ", "Edit Sequence Name/Description");
 
     if (!dialog.accept)
     {
@@ -1147,9 +1281,9 @@ public class PopupMenu
       if (dialog.getName().indexOf(" ") > -1)
       {
         JOptionPane.showMessageDialog(ap,
-                                      "Spaces have been converted to \"_\"",
-                                      "No spaces allowed in Sequence Name",
-                                      JOptionPane.WARNING_MESSAGE);
+                "Spaces have been converted to \"_\"",
+                "No spaces allowed in Sequence Name",
+                JOptionPane.WARNING_MESSAGE);
       }
 
       sequence.setName(dialog.getName().replace(' ', '_'));
@@ -1158,15 +1292,16 @@ public class PopupMenu
 
     sequence.setDescription(dialog.getDescription());
 
-    ap.av.firePropertyChange("alignment", null,
-                             ap.av.getAlignment().getSequences());
+    ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+            .getSequences());
 
   }
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   void unGroupMenuItem_actionPerformed()
   {
@@ -1178,14 +1313,15 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   protected void outline_actionPerformed()
   {
     SequenceGroup sg = getGroup();
     Color col = JColorChooser.showDialog(this, "Select Outline Colour",
-                                         Color.BLUE);
+            Color.BLUE);
 
     if (col != null)
     {
@@ -1197,8 +1333,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void showBoxes_actionPerformed()
   {
@@ -1208,8 +1345,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void showText_actionPerformed()
   {
@@ -1219,8 +1357,9 @@ public class PopupMenu
 
   /**
    * DOCUMENT ME!
-   *
-   * @param e DOCUMENT ME!
+   * 
+   * @param e
+   *                DOCUMENT ME!
    */
   public void showColourText_actionPerformed()
   {
@@ -1233,15 +1372,14 @@ public class PopupMenu
     try
     {
       jalview.util.BrowserLauncher.openURL(url);
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                            "Unixers: Couldn't find default web browser."
-                                            +
-          "\nAdd the full path to your browser in Preferences.",
-                                            "Web browser not found",
-                                            JOptionPane.WARNING_MESSAGE);
+      JOptionPane
+              .showInternalMessageDialog(
+                      Desktop.desktop,
+                      "Unixers: Couldn't find default web browser."
+                              + "\nAdd the full path to your browser in Preferences.",
+                      "Web browser not found", JOptionPane.WARNING_MESSAGE);
 
       ex.printStackTrace();
     }
@@ -1253,7 +1391,7 @@ public class PopupMenu
     if (sg == null || sg.getSize() < 1)
     {
       ap.av.hideSequence(new SequenceI[]
-                         {sequence});
+      { sequence });
       return;
     }
 
@@ -1278,6 +1416,7 @@ public class PopupMenu
     }
 
     ap.av.hideSequence(hseqs);
+    ap.av.sendSelection();
   }
 
   public void copy_actionPerformed()
@@ -1297,8 +1436,8 @@ public class PopupMenu
 
     if (sg != null)
     {
-      int[][] startEnd = ap.av.getVisibleRegionBoundaries(
-          sg.getStartRes(), sg.getEndRes() + 1);
+      int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
+              sg.getEndRes() + 1);
 
       String description;
       int caseChange;
@@ -1319,15 +1458,14 @@ public class PopupMenu
         caseChange = ChangeCaseCommand.TO_LOWER;
       }
 
-      ChangeCaseCommand caseCommand = new ChangeCaseCommand(
-          description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
-          startEnd, caseChange
-          );
+      ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg
+              .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
+              caseChange);
 
       ap.alignFrame.addHistoryItem(caseCommand);
 
-      ap.av.firePropertyChange("alignment", null,
-                               ap.av.getAlignment().getSequences());
+      ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+              .getSequences());
 
     }
   }
@@ -1336,36 +1474,33 @@ public class PopupMenu
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     cap.setForInput(null);
-    Desktop.addInternalFrame(cap,
-                             "Alignment output - " + e.getActionCommand(), 600,
-                             500);
+    Desktop.addInternalFrame(cap, "Alignment output - "
+            + e.getActionCommand(), 600, 500);
 
     String[] omitHidden = null;
 
-    System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens or we simply trust the user wants wysiwig behaviour
+    System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
+                                            // or we simply trust the user wants
+                                            // wysiwig behaviour
     SequenceGroup sg = ap.av.getSelectionGroup();
     ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
     omitHidden = ap.av.getViewAsString(true);
     Alignment oal = new Alignment(ap.av.getSequenceSelection());
     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
-    for (int i=0; i<nala.length; i++)
+    for (int i = 0; i < nala.length; i++)
     {
-      AlignmentAnnotation na =nala[i];
+      AlignmentAnnotation na = nala[i];
       oal.addAnnotation(na);
     }
-    cap.setText(new FormatAdapter().formatSequences(
-            e.getActionCommand(),
-            oal,
-            omitHidden, csel, sg));
-    oal=null;
+    cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
+            oal, omitHidden, csel, sg));
+    oal = null;
   }
 
   public void pdbFromFile_actionPerformed()
   {
-    jalview.io.JalviewFileChooser chooser
-        = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
-                                            getProperty(
-                                                "LAST_DIRECTORY"));
+    jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle("Select a PDB file");
     chooser.setToolTipText("Load a PDB file");
@@ -1380,15 +1515,16 @@ public class PopupMenu
       try
       {
         MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
-            jalview.io.AppletFormatAdapter.FILE);
+                jalview.io.AppletFormatAdapter.FILE);
 
         if (pdbfile.id == null)
         {
-          String reply = JOptionPane.showInternalInputDialog(
-              Desktop.desktop,
-              "Couldn't find a PDB id in the file supplied."
-              + "Please enter an Id to identify this structure.",
-              "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
+          String reply = JOptionPane
+                  .showInternalInputDialog(
+                          Desktop.desktop,
+                          "Couldn't find a PDB id in the file supplied."
+                                  + "Please enter an Id to identify this structure.",
+                          "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
           if (reply == null)
           {
             return;
@@ -1400,8 +1536,7 @@ public class PopupMenu
         {
           entry.setId(pdbfile.id);
         }
-      }
-      catch (java.io.IOException ex)
+      } catch (java.io.IOException ex)
       {
         ex.printStackTrace();
       }
@@ -1415,26 +1550,33 @@ public class PopupMenu
   public void enterPDB_actionPerformed()
   {
     String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
-        "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
+            "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
 
     if (id != null && id.length() > 0)
     {
       PDBEntry entry = new PDBEntry();
       entry.setId(id.toUpperCase());
-      sequence.getDatasetSequence()
-          .addPDBId(entry);
+      sequence.getDatasetSequence().addPDBId(entry);
     }
   }
 
   public void discoverPDB_actionPerformed()
   {
-    SequenceI[] sequences =
-         ap.av.selectionGroup == null ?
-           new Sequence[]{sequence}
-         : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment);
 
-    new jalview.ws.DBRefFetcher(sequences,
-        ap.alignFrame).fetchDBRefs(false);
+    final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
+    { sequence }
+            : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
+    Thread discpdb = new Thread(new Runnable()
+    {
+      public void run()
+      {
+
+        new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
+                .fetchDBRefs(false);
+      }
+
+    });
+    discpdb.start();
   }
 
   public void sequenceFeature_actionPerformed()
@@ -1454,14 +1596,14 @@ public class PopupMenu
       seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
       int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
       int end = sg.findEndRes(sg.getSequenceAt(i));
-      features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");
+      features[i] = new SequenceFeature(null, null, null, start, end,
+              "Jalview");
     }
 
-    if (ap.seqPanel.seqCanvas.getFeatureRenderer()
-        .amendFeatures(seqs, features, true, ap))
+    if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+            features, true, ap))
     {
-      ap.alignFrame.showSeqFeatures.setSelected(true);
-      ap.av.setShowSequenceFeatures(true);
+      ap.alignFrame.setShowSeqFeatures(true);
       ap.highlightSearchResults(null);
     }
   }
@@ -1477,57 +1619,51 @@ public class PopupMenu
 
   public void colourByStructure(String pdbid)
   {
-    Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()
-        .colourSequenceFromStructure(sequence, pdbid);
+    Annotation[] anots = jalview.structure.StructureSelectionManager
+            .getStructureSelectionManager().colourSequenceFromStructure(
+                    sequence, pdbid);
 
-    AlignmentAnnotation an = new AlignmentAnnotation(
-      "Structure", "Coloured by "+pdbid, anots);
+    AlignmentAnnotation an = new AlignmentAnnotation("Structure",
+            "Coloured by " + pdbid, anots);
 
     ap.av.alignment.addAnnotation(an);
     an.createSequenceMapping(sequence, 0, true);
-    //an.adjustForAlignment();
-    ap.av.alignment.setAnnotationIndex(an,0);
+    // an.adjustForAlignment();
+    ap.av.alignment.setAnnotationIndex(an, 0);
 
     ap.adjustAnnotationHeight();
 
     sequence.addAlignmentAnnotation(an);
 
-    }
+  }
 
   public void editSequence_actionPerformed(ActionEvent actionEvent)
   {
-      SequenceGroup sg = ap.av.getSelectionGroup();
+    SequenceGroup sg = ap.av.getSelectionGroup();
 
-      if(sg!=null)
-      {
-        if (sequence == null)
-          sequence = (Sequence) sg.getSequenceAt(0);
+    if (sg != null)
+    {
+      if (sequence == null)
+        sequence = (Sequence) sg.getSequenceAt(0);
 
-        EditNameDialog dialog = new EditNameDialog(
-            sequence.getSequenceAsString(
-                sg.getStartRes(),
-                sg.getEndRes() + 1),
-            null,
-            "Edit Sequence ",
-            null,
-            "Edit Sequence");
+      EditNameDialog dialog = new EditNameDialog(sequence
+              .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
+              null, "Edit Sequence ", null, "Edit Sequence");
 
-        if (dialog.accept)
-        {
-          EditCommand editCommand = new EditCommand(
-              "Edit Sequences", EditCommand.REPLACE,
-              dialog.getName().replace(' ', ap.av.getGapCharacter()),
-              sg.getSequencesAsArray(ap.av.hiddenRepSequences),
-              sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment
-              );
+      if (dialog.accept)
+      {
+        EditCommand editCommand = new EditCommand("Edit Sequences",
+                EditCommand.REPLACE, dialog.getName().replace(' ',
+                        ap.av.getGapCharacter()), sg
+                        .getSequencesAsArray(ap.av.hiddenRepSequences), sg
+                        .getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
 
-          ap.alignFrame.addHistoryItem(editCommand);
+        ap.alignFrame.addHistoryItem(editCommand);
 
-          ap.av.firePropertyChange("alignment", null,
-                                   ap.av.getAlignment().getSequences());
-        }
+        ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+                .getSequences());
       }
+    }
   }
 
-
 }