From 602686d713d7b4554b96d09847a77a675dae3aab Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Sun, 11 Feb 2018 11:04:57 +0000
Subject: [PATCH] JAL-2781 use SIFTs mapping rather than maxChain AlignSeq to
 propagate annotation and sequence features to sequence
 being associated

---
 .../structure/StructureSelectionManager.java       |   23 ++++++++++----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 35e2536..2b429d7 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -526,10 +526,10 @@ public class StructureSelectionManager
             siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
                     pdb, maxChain, sqmpping, maxAlignseq);
             seqToStrucMapping.add(siftsMapping);
-            maxChain.makeExactMapping(maxAlignseq, seq);
-            maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
+            maxChain.makeExactMapping(siftsMapping, seq);
+            maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
                                                        // "IEA:SIFTS" ?
-            maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
+            maxChain.transferResidueAnnotation(siftsMapping, null);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
 
           } catch (SiftsException e)
@@ -540,7 +540,8 @@ public class StructureSelectionManager
                     targetChainId, maxChain, pdb, maxAlignseq);
             seqToStrucMapping.add(nwMapping);
             maxChain.makeExactMapping(maxAlignseq, seq);
-            maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+            maxChain.transferRESNUMFeatures(seq, "IEA:Jalview"); // FIXME: is
+                                                                 // this
                                                         // "IEA:Jalview" ?
             maxChain.transferResidueAnnotation(nwMapping, sqmpping);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
@@ -551,11 +552,16 @@ public class StructureSelectionManager
           List<StructureMapping> foundSiftsMappings = new ArrayList<>();
           for (PDBChain chain : pdb.getChains())
           {
+            StructureMapping siftsMapping = null;
             try
             {
-              StructureMapping siftsMapping = getStructureMapping(seq,
+              siftsMapping = getStructureMapping(seq,
                       pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
               foundSiftsMappings.add(siftsMapping);
+              chain.makeExactMapping(siftsMapping, seq);
+              chain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
+              // "IEA:SIFTS" ?
+              chain.transferResidueAnnotation(siftsMapping, null);
             } catch (SiftsException e)
             {
               System.err.println(e.getMessage());
@@ -564,11 +570,6 @@ public class StructureSelectionManager
           if (!foundSiftsMappings.isEmpty())
           {
             seqToStrucMapping.addAll(foundSiftsMappings);
-            maxChain.makeExactMapping(maxAlignseq, seq);
-            maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
-                                                       // "IEA:SIFTS" ?
-            maxChain.transferResidueAnnotation(foundSiftsMappings.get(0),
-                    sqmpping);
             ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0));
           }
           else
@@ -639,7 +640,7 @@ public class StructureSelectionManager
       PDBChain chain = pdb.findChain(targetChainId);
       if (chain != null)
       {
-        chain.transferResidueAnnotation(curChainMapping, sqmpping);
+        chain.transferResidueAnnotation(curChainMapping, null);
       }
     } catch (Exception e)
     {
-- 
1.7.10.2