JAL-1761 backbone type parameter for configuring which atoms are used for superpositi...

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

diff --git a/src/jalview/structure/StructureCommandsI.java b/src/jalview/structure/StructureCommandsI.java
index 734f275..0489bda 100644 (file)
--- a/src/jalview/structure/StructureCommandsI.java
+++ b/src/jalview/structure/StructureCommandsI.java
@@ -86,12 +86,11 @@ public interface StructureCommandsI
    * 
    * @param refAtoms
    * @param atomSpec
-   * @param isNucleotide TODO
-   * @param nucleotide - when true, superposition is based on phoshpate backbone, not peptide
+   * @param backbone - superpose based on which kind of atomType
    * @return
    */
   List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
-          AtomSpecModel atomSpec, boolean isNucleotide);
+          AtomSpecModel atomSpec, AtomSpecType backbone);
 
   /**
    * Returns a command to open a file of commands at the given path
@@ -110,16 +109,17 @@ public interface StructureCommandsI
    */
   StructureCommandI saveSession(String filepath);
 
+  enum AtomSpecType { RESIDUE_ONLY, ALPHA, PHOSPHATE }; 
   /**
    * Returns a representation of the atom set represented by the model, in
    * viewer syntax format. If {@code alphaOnly} is true, this is restricted to
    * Alpha Carbon (peptide) or Phosphorous (rna) only
    * 
    * @param model
-   * @param alphaOnly
+   * @param specType
    * @return
    */
-  String getAtomSpec(AtomSpecModel model, boolean alphaOnly);
+  String getAtomSpec(AtomSpecModel model, AtomSpecType specType);
 
   /**
    * Returns the lowest model number used by the structure viewer (likely 0 or