Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 2629f0a..7057c2a 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -3344,7 +3344,7 @@ public class Jalview2XML
           }
           else
           {
-            cs = ColourSchemeProperty.getColour(al, jGroup.getColour());
+            cs = ColourSchemeProperty.getColourScheme(al, jGroup.getColour());
           }
 
           if (cs != null)
@@ -4420,10 +4420,12 @@ public class Jalview2XML
 
     af.viewport.setShowAnnotation(view.getShowAnnotation());
     af.viewport.setAbovePIDThreshold(view.getPidSelected());
+    af.viewport.setThreshold(view.getPidThreshold());
 
     af.viewport.setColourText(view.getShowColourText());
 
     af.viewport.setConservationSelected(view.getConservationSelected());
+    af.viewport.setIncrement(view.getConsThreshold());
     af.viewport.setShowJVSuffix(view.getShowFullId());
     af.viewport.setRightAlignIds(view.getRightAlignIds());
     af.viewport.setFont(
@@ -4468,12 +4470,11 @@ public class Jalview2XML
       }
       else
       {
-        cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+        cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
       }
 
       if (cs != null)
       {
-        cs.setThreshold(view.getPidThreshold(), true);
         cs.setConsensus(af.viewport.getSequenceConsensusHash());
       }
     }
@@ -4749,7 +4750,7 @@ public class Jalview2XML
           {
             cs = new AnnotationColourGradient(
                     annAlignment.getAlignmentAnnotation()[i],
-                    ColourSchemeProperty.getColour(al,
+                    ColourSchemeProperty.getColourScheme(al,
                             viewAnnColour.getColourScheme()),
                     viewAnnColour.getAboveThreshold());
           }