JAL-2443 push getResidueBoxColour inside getResidueColour

[jalview.git] / src / jalview / ext / varna / VarnaCommands.java

diff --git a/src/jalview/ext/varna/VarnaCommands.java b/src/jalview/ext/varna/VarnaCommands.java
index 617dc8f..d65f1d5 100644 (file)
--- a/src/jalview/ext/varna/VarnaCommands.java
+++ b/src/jalview/ext/varna/VarnaCommands.java
@@ -48,7 +48,7 @@ public class VarnaCommands
   public static String[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
           SequenceI[][] sequence, SequenceRenderer sr,
-          FeatureColourFinder fr,
+          FeatureColourFinder finder,
           AlignmentI alignment)
   {
     ArrayList<String> str = new ArrayList<String>();
@@ -88,12 +88,9 @@ public class VarnaCommands
 
               lastPos = pos;
 
-              Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
+              Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
+                      finder);
 
-              if (fr != null)
-              {
-                col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
-              }
               String newSelcom = (mapping[m].getChain() != " " ? ":"
                       + mapping[m].getChain() : "")
                       + "/"