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

[jalview.git] / src / jalview / structure / StructureCommandsI.java

diff --git a/src/jalview/structure/StructureCommandsI.java b/src/jalview/structure/StructureCommandsI.java
index 91e0494..734f275 100644 (file)
--- a/src/jalview/structure/StructureCommandsI.java
+++ b/src/jalview/structure/StructureCommandsI.java
@@ -86,10 +86,12 @@ public interface StructureCommandsI
    * 
    * @param refAtoms
    * @param atomSpec
+   * @param isNucleotide TODO
+   * @param nucleotide - when true, superposition is based on phoshpate backbone, not peptide
    * @return
    */
   List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
-          AtomSpecModel atomSpec);
+          AtomSpecModel atomSpec, boolean isNucleotide);
 
   /**
    * Returns a command to open a file of commands at the given path