JAL-3518 more pull up / test coverage of structure command generation

[jalview.git] / src / jalview / structures / models / AAStructureBindingModel.java

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 4dfdc2a..0c1cd50 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -867,7 +867,7 @@ public abstract class AAStructureBindingModel
       executeCommand(commandGenerator.showBackbone(), false);
 
       /*
-       * superpose each (other) sequence to it in turn
+       * superpose each (other) structure to the reference in turn
        */
       for (int i = 0; i < structures.length; i++)
       {
@@ -1273,16 +1273,20 @@ public abstract class AAStructureBindingModel
   }
 
   /**
+   * Builds a data structure which records mapped structure residues for each
+   * colour. From this we can easily generate the viewer commands for colour by
+   * sequence. Constructs and returns a map of {@code Color} to
+   * {@code AtomSpecModel}, where the atomspec model holds
+   * 
    * <pre>
-   * Build a data structure which records residues for each colour. 
-   * From this we can easily generate the viewer command for colour by sequence.
-   * Color
-   *     Model number
-   *         Chain
-   *             Residue positions
-   * Ordering is by order of addition (for colours and positions), natural ordering (for models and chains)
+   *   Model numbers
+   *     Chains
+   *       Residue positions
    * </pre>
    * 
+   * Ordering is by order of addition (for colours), natural ordering (for
+   * models and chains)
+   * 
    * @param ssm
    * @param files
    * @param sequence