JAL-3253 miscellaneous tidying up before merge to JS-develop

[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..56d2e9b 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())
@@ -352,8 +355,8 @@ public abstract class AAStructureBindingModel
               { Integer.valueOf(pe).toString() }));
     }
     final String nullChain = "TheNullChain";
-    List<SequenceI> s = new ArrayList<SequenceI>();
-    List<String> c = new ArrayList<String>();
+    List<SequenceI> s = new ArrayList<>();
+    List<String> c = new ArrayList<>();
     if (getChains() == null)
     {
       setChains(new String[getPdbCount()][]);
@@ -422,8 +425,8 @@ public abstract class AAStructureBindingModel
   public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
           SequenceI[][] seq, String[][] chns)
   {
-    List<PDBEntry> v = new ArrayList<PDBEntry>();
-    List<int[]> rtn = new ArrayList<int[]>();
+    List<PDBEntry> v = new ArrayList<>();
+    List<int[]> rtn = new ArrayList<>();
     for (int i = 0; i < getPdbCount(); i++)
     {
       v.add(getPdbEntry(i));
@@ -512,9 +515,7 @@ public abstract class AAStructureBindingModel
    * Returns a readable description of all mappings for the wrapped pdbfile to
    * any mapped sequences
    * 
-   * @param pdbfile
-   * @param seqs
-   * @return
+   * @return 
    */
   public String printMappings()
   {