JAL-3148 SequenceRenderer, ResidueColourFinder overloads and

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

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 6c934c8..12bb21d 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -26,6 +26,7 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.structures.models.AAStructureBindingModel;
+import jalview.structures.models.AAStructureBindingModel.ColourBy;
 import jalview.util.BrowserLauncher;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -113,14 +114,14 @@ public class AppJmol extends StructureViewerBase
     initMenus();
     if (leaveColouringToJmol || !usetoColour)
     {
-      jmb.setColourBySequence(false);
+      jmb.setColourBy(ColourBy.Viewer);
       seqColour.setSelected(false);
       viewerColour.setSelected(true);
     }
     else if (usetoColour)
     {
       useAlignmentPanelForColourbyseq(ap);
-      jmb.setColourBySequence(true);
+      jmb.setColourBy(ColourBy.Sequence);
       seqColour.setSelected(true);
       viewerColour.setSelected(false);
     }
@@ -193,7 +194,7 @@ public class AppJmol extends StructureViewerBase
     alignAddedStructures = alignAdded;
     useAlignmentPanelForSuperposition(ap);
 
-    jmb.setColourBySequence(true);
+    jmb.setColourBy(ColourBy.Sequence);
     setSize(400, 400); // probably should be a configurable/dynamic default here
     initMenus();
     addingStructures = false;