JAL-1761 need to pass molecule type when generating superposition commands

[jalview.git] / src / jalview / ext / rbvi / chimera / ChimeraCommands.java

diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index 43cdeb1..bfad8fb 100644 (file)
--- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@ -20,6 +20,8 @@
  */
 package jalview.ext.rbvi.chimera;
 
+import java.util.Locale;
+
 import java.awt.Color;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -181,7 +183,7 @@ public class ChimeraCommands extends StructureCommandsBase
      * Chimera treats an attribute name ending in 'color' as colour-valued;
      * Jalview doesn't, so prevent this by appending an underscore
      */
-    if (attName.toUpperCase().endsWith("COLOR"))
+    if (attName.toUpperCase(Locale.ROOT).endsWith("COLOR"))
     {
       attName += "_";
     }
@@ -257,7 +259,7 @@ public class ChimeraCommands extends StructureCommandsBase
 
   @Override
   public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
-          AtomSpecModel spec)
+          AtomSpecModel spec, boolean isNucleotide)
   {
     /*
      * Form Chimera match command to match spec to ref
@@ -388,33 +390,6 @@ public class ChimeraCommands extends StructureCommandsBase
     return new StructureCommand("open " + file);
   }
 
-  /**
-   * Overrides the default method to concatenate colour commands into one
-   */
-  @Override
-  public List<StructureCommandI> colourBySequence(
-          Map<Object, AtomSpecModel> colourMap)
-  {
-    List<StructureCommandI> commands = new ArrayList<>();
-    StringBuilder sb = new StringBuilder(colourMap.size() * 20);
-    boolean first = true;
-    for (Object key : colourMap.keySet())
-    {
-      Color colour = (Color) key;
-      final AtomSpecModel colourData = colourMap.get(colour);
-      StructureCommandI command = getColourCommand(colourData, colour);
-      if (!first)
-      {
-        sb.append(getCommandSeparator());
-      }
-      first = false;
-      sb.append(command.getCommand());
-    }
-
-    commands.add(new StructureCommand(sb.toString()));
-    return commands;
-  }
-
   @Override
   public StructureCommandI openSession(String filepath)
   {