JAL-2693 TODO comments

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index fbfa486..b973f45 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -340,7 +340,9 @@ public class StructureSelectionManager
    *          - one or more sequences to be mapped to pdbFile
    * @param targetChainIds
    *          - optional chain specification for mapping each sequence to pdb
-   *          (may be nill, individual elements may be nill)
+   *          (may be nill, individual elements may be nill) - JBPNote: JAL-2693
+   *          - this should be List<List<String>>, empty lists indicate no
+   *          predefined mappings
    * @param pdbFile
    *          - structure data resource
    * @param sourceType

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index a3c4beb..ffd865f 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -162,6 +162,8 @@ public abstract class AAStructureBindingModel
      * final count of chain mappings discovered
      */
     int chainmaps = 0;
+    // JBPNote: JAL-2693 - this should be a list of chain mappings per
+    // [pdbentry][sequence]
     String[][] newchains = new String[pdbEntry.length][];
     int pe = 0;
     for (PDBEntry pdb : pdbEntry)