JAL-2438 FeatureColourFinder refactored from FeatureRenderer, fr not

[jalview.git] / src / jalview / ext / jmol / JmolCommands.java

diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index a809cae..a1ff3c5 100644 (file)
--- 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);
               }
 
               /*