JAL-1632 similarity options on TreeChooser panel affect tree by PID

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index d5ec6ac..68184e9 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1294,7 +1294,7 @@ public class Jalview2XML
                 .getGlobalColourScheme()));
       }
 
-      ResidueShaderI vcs = av.getViewportColourScheme();
+      ResidueShaderI vcs = av.getResidueShading();
       ColourSchemeI cs = av.getGlobalColourScheme();
 
       if (cs != null)
@@ -3666,7 +3666,7 @@ public class Jalview2XML
         TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
         if (tp == null)
         {
-          tp = af.ShowNewickTree(
+          tp = af.showNewickTree(
                   new jalview.io.NewickFile(tree.getNewick()),
                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
                   tree.getXpos(), tree.getYpos());
@@ -4474,15 +4474,15 @@ public class Jalview2XML
     }
 
     af.viewport.setGlobalColourScheme(cs);
-    af.viewport.getViewportColourScheme().setThreshold(
+    af.viewport.getResidueShading().setThreshold(
             view.getPidThreshold(), true);
-    af.viewport.getViewportColourScheme().setConsensus(
+    af.viewport.getResidueShading().setConsensus(
             af.viewport.getSequenceConsensusHash());
     af.viewport.setColourAppliesToAllGroups(false);
 
     if (view.getConservationSelected() && cs != null)
     {
-      af.viewport.getViewportColourScheme().setConservationInc(
+      af.viewport.getResidueShading().setConservationInc(
               view.getConsThreshold());
     }