Merge branch 'features/JAL-2360colourSchemeApplicability' into

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index cda08c6..8393693 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -3373,6 +3373,7 @@ public class Jalview2XML
                 jGroup.getDisplayBoxes(), jGroup.getDisplayText(),
                 jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd());
         sg.getGroupColourScheme().setThreshold(pidThreshold, true);
+        sg.getGroupColourScheme().setConservationInc(jGroup.getConsThreshold());
         sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour()));
 
         sg.textColour = new java.awt.Color(jGroup.getTextCol1());
@@ -4418,10 +4419,12 @@ 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 +4471,6 @@ public class Jalview2XML
       {
         cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
       }
-
-      // if (cs != null)
-      // {
-      // cs.setThreshold(view.getPidThreshold(), true);
-      // cs.setConsensus(af.viewport.getSequenceConsensusHash());
-      // }
     }
 
     af.viewport.setGlobalColourScheme(cs);