added d martin to authors and fixed faq/discuss message

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 39a7fac..1320aa0 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1,19 +1,19 @@
 /*
- * 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 Softwarechang
+ * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
 package jalview.gui;
@@ -45,7 +45,7 @@ import jalview.ws.*;
  * @version $Revision$
  */
 public class AlignFrame
-    extends GAlignFrame implements DropTargetListener
+    extends GAlignFrame implements DropTargetListener, IProgressIndicator
 {
   /** DOCUMENT ME!! */
   public static final int DEFAULT_WIDTH = 700;
@@ -515,11 +515,17 @@ public class AlignFrame
     {
       calculateMenu.remove(calculateMenu.getItemCount()-2);
     }
-    setShowProductsEnabled();
   }
 
 
-
+  /**
+   * set up menus for the currently viewport.
+   * This may be called after any operation that affects the data in the current view (selection changed, etc) to update the menus to reflect the new state.
+   */
+  public void setMenusForViewport()
+  {
+    setMenusFromViewport(viewport);
+  }
   /**
    * Need to call this method when tabs are selected for multiple views,
    * or when loading from Jalview2XML.java
@@ -550,11 +556,16 @@ public class AlignFrame
     hiddenMarkers.setState(av.showHiddenMarkers);
     applyToAllGroups.setState(av.colourAppliesToAllGroups);
 
+    setShowProductsEnabled();
+
     updateEditMenuBar();
   }
 
 
   Hashtable progressBars;
+  /* (non-Javadoc)
+   * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
+   */
   public void setProgressBar(String message, long id)
   {
     if(progressBars == null)
@@ -592,7 +603,8 @@ public class AlignFrame
 
       progressBars.put(new Long(id), progressPanel);
     }
-
+    // update GUI
+    setMenusForViewport();
     validate();
   }
   /**
@@ -3468,7 +3480,7 @@ public class AlignFrame
       Vector seqsrch = (Vector) Discoverer.services.get("SeqSearch");
       // TODO: move GUI generation code onto service implementation - so a client instance attaches itself to the GUI with method call like jalview.ws.MsaWSClient.bind(servicehandle, Desktop.instance, alignframe)
       Vector wsmenu = new Vector();
-      final AlignFrame af = this;
+      final IProgressIndicator af = this;
       if (msaws != null)
       {
         // Add any Multiple Sequence Alignment Services
@@ -3534,15 +3546,22 @@ public class AlignFrame
     webService.removeAll();
     // Temporary hack - DBRef Fetcher always top level ws entry.
     JMenuItem rfetch = new JMenuItem("Fetch DB References");
-    rfetch.setToolTipText("Retrieve and parse uniprot records for the alignment or the currently selected sequences");
+    rfetch.setToolTipText("Retrieve and parse sequence database records for the alignment or the currently selected sequences");
     webService.add(rfetch);
     rfetch.addActionListener(new ActionListener() {
 
       public void actionPerformed(ActionEvent e)
       {
-        new jalview.ws.DBRefFetcher(
-                alignPanel.av.getSequenceSelection(),
-                alignPanel.alignFrame).fetchDBRefs(false);
+        new Thread(new Runnable() {
+
+          public void run()
+          {
+            new jalview.ws.DBRefFetcher(
+                    alignPanel.av.getSequenceSelection(),
+                    alignPanel.alignFrame).fetchDBRefs(false);
+          }
+        }).start();
+        
       }
 
     });
@@ -3610,7 +3629,7 @@ public class AlignFrame
           public void actionPerformed(ActionEvent e)
           {
             // TODO: new thread for this call with vis-delay
-            af.showProductsFor(sel, ds, isRegSel, dna, source);
+            af.showProductsFor(af.viewport.getSequenceSelection(), ds, isRegSel, dna, source);
           }
           
         });
@@ -3911,6 +3930,7 @@ public void drop(DropTargetDropEvent evt)
       {
         
         alignPanel.adjustAnnotationHeight();
+        viewport.updateSequenceIdColours();
         buildSortByAnnotationScoresMenu();
         alignPanel.paintAlignment(true);
       }
@@ -3961,8 +3981,9 @@ public void drop(DropTargetDropEvent evt)
   protected void extractScores_actionPerformed(ActionEvent e)
   {
     ParseProperties pp = new jalview.analysis.ParseProperties(viewport.alignment);
-    if (pp.getScoresFromDescription("col", "score column ", "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)", true)>0)
-    {
+    // TODO: verify regex and introduce GUI dialog for version 2.5
+    //if (pp.getScoresFromDescription("col", "score column ", "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)", true)>0)
+    if (pp.getScoresFromDescription("description column", "score in description column ", "\\W*([-+eE0-9.]+)", true)>0)    {
       buildSortByAnnotationScoresMenu();
     }
   }