From f4d531c14c933d33377556506adb70980fffda9e Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Sun, 27 Aug 2017 14:23:06 +0100
Subject: [PATCH] JAL-2691 discover any existing chain mappings for a
 structure view

---
 .../structures/models/AAStructureBindingModel.java |   50 +++++++++++++++++++-
 1 file changed, 49 insertions(+), 1 deletion(-)

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 9f4cea0..a3c4beb 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -142,7 +142,6 @@ public abstract class AAStructureBindingModel
    * @param ssm
    * @param pdbentry
    * @param sequenceIs
-   * @param chains
    * @param protocol
    */
   public AAStructureBindingModel(StructureSelectionManager ssm,
@@ -154,8 +153,57 @@ public abstract class AAStructureBindingModel
     this.nucleotide = Comparison.isNucleotide(sequenceIs);
     this.pdbEntry = pdbentry;
     this.protocol = protocol;
+    resolveChains();
   }
 
+  private boolean resolveChains()
+  {
+    /**
+     * final count of chain mappings discovered
+     */
+    int chainmaps = 0;
+    String[][] newchains = new String[pdbEntry.length][];
+    int pe = 0;
+    for (PDBEntry pdb : pdbEntry)
+    {
+      SequenceI[] seqsForPdb = sequence[pe];
+      if (seqsForPdb != null)
+      {
+        newchains[pe] = new String[seqsForPdb.length];
+        int se = 0;
+        for (SequenceI asq : seqsForPdb)
+        {
+          String chain = (chains != null && chains[pe] != null)
+                  ? chains[pe][se]
+                  : null;
+          SequenceI sq = asq.getDatasetSequence();
+          if (sq.getAllPDBEntries() != null)
+          {
+            for (PDBEntry pdbentry : sq.getAllPDBEntries())
+            {
+              if (pdb.getFile() != null && pdbentry.getFile() != null
+                      && pdb.getFile().equals(pdbentry.getFile()))
+              {
+                String chaincode = pdbentry.getChainCode();
+                if (chaincode != null && chaincode.length() > 0)
+                {
+                  chain = chaincode;
+                  chainmaps++;
+                  break;
+                }
+              }
+            }
+          }
+          newchains[pe][se] = chain;
+          se++;
+        }
+        pe++;
+      }
+    }
+
+    chains = newchains;
+    return chainmaps > 0;
+  }
   public StructureSelectionManager getSsm()
   {
     return ssm;
-- 
1.7.10.2