JAL-3201 restore group colours correctly from project

[jalview.git] / src / jalview / project / Jalview2XML.java

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index f772cf5..1797fb7 100644 (file)
--- 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
@@ -5067,7 +5068,8 @@ public class Jalview2XML
           float min = safeFloat(safeFloat(setting.getMin()));
           float max = setting.getMax() == null ? 1f
                   : setting.getMax().floatValue();
-          FeatureColourI gc = new FeatureColour(minColour, maxColour,
+          FeatureColourI gc = new FeatureColour(maxColour, minColour,
+                  maxColour,
                   noValueColour, min, max);
           if (setting.getAttributeName().size() > 0)
           {
@@ -6562,7 +6564,7 @@ public class Jalview2XML
         noValueColour = maxcol;
       }
   
-      colour = new FeatureColour(mincol, maxcol, noValueColour,
+      colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
               safeFloat(colourModel.getMin()),
               safeFloat(colourModel.getMax()));
       final List<String> attributeName = colourModel.getAttributeName();