X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolCommands.java;h=a1ff3c57079e3a127f850a2ea125266ee68ce167;hb=2888e7307e1f7c8239234941498cb86e8c65ab36;hp=a809caecc1b7126cae8d62fb243590c64ccdaa01;hpb=799c26111d6936a2e70cb5f1fd7d7312311e6db9;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index a809cae..a1ff3c5 100644
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -21,11 +21,13 @@
 package jalview.ext.jmol;
 
 import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
@@ -53,9 +55,12 @@ public class JmolCommands
    */
   public static StructureMappingcommandSet[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
-          SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
-          AlignViewportI viewport)
+          SequenceI[][] sequence, SequenceRenderer sr,
+          AlignmentViewPanel viewPanel)
   {
+    FeatureRenderer fr = viewPanel.getFeatureRenderer();
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
+    AlignViewportI viewport = viewPanel.getAlignViewport();
     ColumnSelection cs = viewport.getColumnSelection();
     AlignmentI al = viewport.getAlignment();
     List<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
@@ -101,7 +106,8 @@ public class JmolCommands
 
               if (fr != null)
               {
-                col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
+                col = finder
+                        .findFeatureColour(col, sequence[pdbfnum][s], r);
               }
 
               /*