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JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob
[jalview.git] / src / jalview / gui / IdPanel.java
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index a22e918..b5569c3 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -27,6 +27,7 @@ import jalview.datamodel.SequenceI;
 import jalview.io.SequenceAnnotationReport;
 import jalview.util.MessageManager;
 import jalview.util.UrlLink;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.BorderLayout;
 import java.awt.event.MouseEvent;
@@ -54,7 +55,7 @@ public class IdPanel extends JPanel implements MouseListener,
 {
   private IdCanvas idCanvas;
 
-  protected AlignViewport av;
+  protected AlignmentViewport av;
 
   protected AlignmentPanel alignPanel;
 
@@ -108,10 +109,9 @@ public class IdPanel extends JPanel implements MouseListener,
     {
       SequenceI sequence = av.getAlignment().getSequenceAt(seq);
       StringBuffer tip = new StringBuffer(64);
-      seqAnnotReport
-              .createSequenceAnnotationReport(tip, sequence,
-                      av.isShowDbRefs(), av.isShowNpFeats(),
-                      sp.seqCanvas.fr.getMinMax());
+      seqAnnotReport.createSequenceAnnotationReport(tip, sequence,
+              av.isShowDBRefs(), av.isShowNPFeats(),
+              sp.seqCanvas.fr.getMinMax());
       setToolTipText("<html>" + sequence.getDisplayId(true) + " "
               + tip.toString() + "</html>");
     }
@@ -244,11 +244,10 @@ public class IdPanel extends JPanel implements MouseListener,
       jalview.util.BrowserLauncher.openURL(url);
     } catch (Exception ex)
     {
-      JOptionPane
-              .showInternalMessageDialog(
-                      Desktop.desktop,
-                      MessageManager.getString("label.web_browser_not_found_unix"),
-                      MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+              MessageManager.getString("label.web_browser_not_found_unix"),
+              MessageManager.getString("label.web_browser_not_found"),
+              JOptionPane.WARNING_MESSAGE);
       ex.printStackTrace();
     }
   }
@@ -323,8 +322,7 @@ public class IdPanel extends JPanel implements MouseListener,
       // build a new links menu based on the current links + any non-positional
       // features
       Vector nlinks = new Vector(Preferences.sequenceURLLinks);
-      SequenceFeature sf[] = sq == null ? null : sq.getDatasetSequence()
-              .getSequenceFeatures();
+      SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
       for (int sl = 0; sf != null && sl < sf.length; sl++)
       {
         if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
@@ -363,6 +361,9 @@ public class IdPanel extends JPanel implements MouseListener,
     {
       selectSeq(seq);
     }
+    // TODO is this addition ok here?
+    av.isSelectionGroupChanged(true);
+
     alignPanel.paintAlignment(true);
   }