JAL-3210 Barebones gradle/buildship/eclipse. See README

[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 a3c4beb..2528286 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)
@@ -176,7 +178,8 @@ public abstract class AAStructureBindingModel
           String chain = (chains != null && chains[pe] != null)
                   ? chains[pe][se]
                   : null;
-          SequenceI sq = asq.getDatasetSequence();
+          SequenceI sq = (asq.getDatasetSequence() == null) ? asq
+                  : asq.getDatasetSequence();
           if (sq.getAllPDBEntries() != null)
           {
             for (PDBEntry pdbentry : sq.getAllPDBEntries())