Merge branch 'feature/JAL-3127_seqidChainshading' into merge/JAL-3127

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

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index f772cf5..11404dc 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -3859,7 +3859,7 @@ public class Jalview2XML
           }
           else
           {
-            cs = ColourSchemeProperty.getColourScheme(al,
+            cs = ColourSchemeProperty.getColourScheme(null, al,
                     jGroup.getColour());
           }
         }
@@ -4973,7 +4973,8 @@ public class Jalview2XML
       }
       else
       {
-        cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
+        cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
+                view.getBgColour());
       }
     }
 
@@ -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)
           {
@@ -5269,7 +5271,7 @@ public class Jalview2XML
     else
     {
       cs = new AnnotationColourGradient(matchedAnnotation,
-              ColourSchemeProperty.getColourScheme(al,
+              ColourSchemeProperty.getColourScheme(af.getViewport(), al,
                       viewAnnColour.getColourScheme()),
               safeInt(viewAnnColour.getAboveThreshold()));
     }
@@ -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();