Merge branch 'features/JAL-2360colourSchemeApplicability' into

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 4fdb25a..47b0694 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -35,6 +35,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.SequenceAnnotationReport;
+import jalview.schemes.CollectionColourSchemeI;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.SelectionListener;
 import jalview.structure.SelectionSource;
@@ -1654,13 +1655,13 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       if (av.getConservationSelected())
       {
-        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
+        SliderPanel.setConservationSlider(ap, av.getViewportColourScheme(),
                 "Background");
       }
 
       if (av.getAbovePIDThreshold())
       {
-        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
+        SliderPanel.setPIDSliderSource(ap, av.getViewportColourScheme(),
                 "Background");
       }
       if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
@@ -1732,15 +1733,15 @@ public class SeqPanel extends JPanel implements MouseListener,
       stretchGroup.cs.alignmentChanged(stretchGroup,
               av.getHiddenRepSequences());
 
+      CollectionColourSchemeI groupColourScheme = stretchGroup.getGroupColourScheme();
+      String name = stretchGroup.getName();
       if (stretchGroup.cs.conservationApplied())
       {
-        SliderPanel.setConservationSlider(ap, stretchGroup.cs,
-                stretchGroup.getName());
+        SliderPanel.setConservationSlider(ap, groupColourScheme, name);
       }
       if (stretchGroup.cs.getThreshold() > 0)
       {
-        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
-                stretchGroup.getName());
+        SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
       }
     }
     PaintRefresher.Refresh(this, av.getSequenceSetId());