From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 11 Mar 2019 15:04:23 +0000 (+0000)
Subject: Merge branch 'feature/JAL-2250colourAllGroups' into develop
X-Git-Tag: Release_2_11_0~17^2~47^2~1
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=a510e9b4726214441e4fdac8a1d6752263c4c73d;hp=7091ed4ecff294623230f96ed93f9a5689ea5938

Merge branch 'feature/JAL-2250colourAllGroups' into develop
---

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 53e9a83..1797fb7 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -4977,21 +4977,22 @@ public class Jalview2XML
       }
     }
 
+    /*
+     * turn off 'alignment colour applies to all groups'
+     * while restoring global colour scheme
+     */
+    viewport.setColourAppliesToAllGroups(false);
     viewport.setGlobalColourScheme(cs);
     viewport.getResidueShading().setThreshold(pidThreshold,
             view.isIgnoreGapsinConsensus());
     viewport.getResidueShading()
             .setConsensus(viewport.getSequenceConsensusHash());
-    viewport.setColourAppliesToAllGroups(false);
-
     if (safeBoolean(view.isConservationSelected()) && cs != null)
     {
       viewport.getResidueShading()
               .setConservationInc(safeInt(view.getConsThreshold()));
     }
-
     af.changeColour(cs);
-
     viewport.setColourAppliesToAllGroups(true);
 
     viewport
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 0f56561..0ea31d7 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -662,7 +662,8 @@ public abstract class AlignmentViewport
          * retain any colour thresholds per group while
          * changing choice of colour scheme (JAL-2386)
          */
-        sg.setColourScheme(cs.getInstance(sg, hiddenRepSequences));
+        sg.setColourScheme(
+                cs == null ? null : cs.getInstance(sg, hiddenRepSequences));
         if (cs != null)
         {
           sg.getGroupColourScheme().alignmentChanged(sg,
diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index afc445e..ea3f00b 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -818,6 +818,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     /*
      * Colour alignment by Buried Index, Above 10% PID, By Conservation 20%
      */
+    av.setColourAppliesToAllGroups(false);
     af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString());
     assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme);
     af.abovePIDThreshold_actionPerformed(true);