JAL-2374 JAL-2419 - TODO suspiciously redundant nested if clauses probably need a...

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 6214a7c..37b4852 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1587,34 +1587,15 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     stretchGroup = av.getSelectionGroup();
 
-    if (stretchGroup == null)
+    if (stretchGroup == null || !stretchGroup.contains(sequence, res))
     {
       stretchGroup = av.getAlignment().findGroup(sequence, res);
-      av.setSelectionGroup(stretchGroup);
-    }
-    if (stretchGroup == null
-            || !stretchGroup.getSequences(null).contains(sequence)
-            || (stretchGroup.getStartRes() > res)
-            || (stretchGroup.getEndRes() < res))
-    {
-      stretchGroup = null;
-
-      SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
-
-      if (allGroups != null)
+      if (stretchGroup != null)
       {
-        for (int i = 0; i < allGroups.length; i++)
-        {
-          if ((allGroups[i].getStartRes() <= res)
-                  && (allGroups[i].getEndRes() >= res))
-          {
-            stretchGroup = allGroups[i];
-            break;
-          }
-        }
+        // only update the current selection if the popup menu has a group to
+        // focus on
+        av.setSelectionGroup(stretchGroup);
       }
-
-      av.setSelectionGroup(stretchGroup);
     }
 
     if (evt.isPopupTrigger()) // Mac: mousePressed
@@ -1655,15 +1636,16 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       if (av.getConservationSelected())
       {
-        SliderPanel.setConservationSlider(ap, av.getViewportColourScheme(),
+        SliderPanel.setConservationSlider(ap, av.getResidueShading(),
                 ap.getViewName());
       }
 
       if (av.getAbovePIDThreshold())
       {
-        SliderPanel.setPIDSliderSource(ap, av.getViewportColourScheme(),
+        SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
                 ap.getViewName());
       }
+      // TODO: stretchGroup will always be not null. Is this a merge error ?
       if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
       {
         // Edit end res position of selected group