X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=1f2a3add6733a631069619b0044320275262e443;hb=b4ebd059827a953d3d54b14ff08eefc99825be5d;hp=2d24512bceb0d25cc74a9b884255c26e09cc082d;hpb=f8ead1fdb720982f5f02ee806ccb4cb5f260cba9;p=jalview.git

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 2d24512..1f2a3ad 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -48,8 +48,8 @@ import javax.swing.ToolTipManager;
  * @author $author$
  * @version $Revision$
  */
-public class IdPanel extends JPanel implements MouseListener,
-        MouseMotionListener, MouseWheelListener
+public class IdPanel extends JPanel
+        implements MouseListener, MouseMotionListener, MouseWheelListener
 {
   private IdCanvas idCanvas;
 
@@ -138,7 +138,7 @@ public class IdPanel extends JPanel implements MouseListener,
     }
 
     lastid = seq;
-    alignPanel.paintAlignment(false);
+    alignPanel.paintAlignment(false, false);
   }
 
   /**
@@ -154,7 +154,7 @@ public class IdPanel extends JPanel implements MouseListener,
       {
         av.getRanges().scrollRight(true);
       }
-      else if (!av.getWrapAlignment())
+      else
       {
         av.getRanges().scrollUp(false);
       }
@@ -165,7 +165,7 @@ public class IdPanel extends JPanel implements MouseListener,
       {
         av.getRanges().scrollRight(false);
       }
-      else if (!av.getWrapAlignment())
+      else
       {
         av.getRanges().scrollUp(true);
       }
@@ -293,8 +293,8 @@ public class IdPanel extends JPanel implements MouseListener,
     }
 
     if ((av.getSelectionGroup() == null)
-            || (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown() && av
-                    .getSelectionGroup() != null))
+            || (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown()
+                    && av.getSelectionGroup() != null))
     {
       av.setSelectionGroup(new SequenceGroup());
       av.getSelectionGroup().setStartRes(0);
@@ -313,7 +313,7 @@ public class IdPanel extends JPanel implements MouseListener,
 
     av.isSelectionGroupChanged(true);
 
-    alignPanel.paintAlignment(false);
+    alignPanel.paintAlignment(false, false);
   }
 
   /**
@@ -325,23 +325,19 @@ public class IdPanel extends JPanel implements MouseListener,
   {
     int seq2 = alignPanel.getSeqPanel().findSeq(e);
     Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2);
-    // build a new links menu based on the current links + any non-positional
-    // features
+
+    /*
+     *  build a new links menu based on the current links
+     *  and any non-positional features
+     */
     List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
-    SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures();
-    if (sfs != null)
+    for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
     {
-      for (SequenceFeature sf : sfs)
+      if (sf.links != null)
       {
-        if (sf.begin == sf.end && sf.begin == 0)
+        for (String link : sf.links)
         {
-          if (sf.links != null && sf.links.size() > 0)
-          {
-            for (int l = 0, lSize = sf.links.size(); l < lSize; l++)
-            {
-              nlinks.add(sf.links.elementAt(l));
-            }
-          }
+          nlinks.add(link);
         }
       }
     }
@@ -395,8 +391,8 @@ public class IdPanel extends JPanel implements MouseListener,
 
     for (int i = start; i <= end; i++)
     {
-      av.getSelectionGroup().addSequence(
-              av.getAlignment().getSequenceAt(i), i == end);
+      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+              i == end);
     }
   }
 
@@ -511,7 +507,7 @@ public class IdPanel extends JPanel implements MouseListener,
           running = false;
         }
 
-        alignPanel.paintAlignment(false);
+        alignPanel.paintAlignment(false, false);
 
         try
         {