X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fvarna%2FVarnaCommands.java;h=4dd0648618d005f24297479b49500c0685cb27e2;hb=7b733539862769ff2438a3149d120aedd044b1be;hp=617dc8fd422800fb799b88915eec62422d5d606c;hpb=2888e7307e1f7c8239234941498cb86e8c65ab36;p=jalview.git

diff --git a/src/jalview/ext/varna/VarnaCommands.java b/src/jalview/ext/varna/VarnaCommands.java
index 617dc8f..4dd0648 100644
--- a/src/jalview/ext/varna/VarnaCommands.java
+++ b/src/jalview/ext/varna/VarnaCommands.java
@@ -48,8 +48,7 @@ public class VarnaCommands
   public static String[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
           SequenceI[][] sequence, SequenceRenderer sr,
-          FeatureColourFinder fr,
-          AlignmentI alignment)
+          FeatureColourFinder finder, AlignmentI alignment)
   {
     ArrayList<String> str = new ArrayList<String>();
     StringBuffer command = new StringBuffer();
@@ -88,27 +87,17 @@ 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() : "")
-                      + "/"
-                      + (pdbfnum + 1)
-                      + ".1"
-                      + ";color["
-                      + col.getRed()
-                      + ","
-                      + col.getGreen()
-                      + ","
+              String newSelcom = (mapping[m].getChain() != " "
+                      ? ":" + mapping[m].getChain()
+                      : "") + "/" + (pdbfnum + 1) + ".1" + ";color["
+                      + col.getRed() + "," + col.getGreen() + ","
                       + col.getBlue() + "]";
-              if (command.length() > newSelcom.length()
-                      && command.substring(
-                              command.length() - newSelcom.length())
-                              .equals(newSelcom))
+              if (command.length() > newSelcom.length() && command
+                      .substring(command.length() - newSelcom.length())
+                      .equals(newSelcom))
               {
                 command = VarnaCommands.condenseCommand(command, pos);
                 continue;