From 2dc7f485be2afd841461e5eafc71dee47b44f14a Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 11 Jan 2024 15:15:28 +0000
Subject: [PATCH] JAL-4366 remove some tortuous repetition in computeMapping,
 so SIFTs failures result in NW mappings being created in
 the same way as if sifts mappings was disabled in
 preferences.

---
 .../structure/StructureSelectionManager.java       |   41 ++++++--------------
 1 file changed, 12 insertions(+), 29 deletions(-)

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 735d814..6761cc3 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -598,6 +598,7 @@ public class StructureSelectionManager
       }
       List<StructureMapping> seqToStrucMapping = new ArrayList<>();
 
+      List<StructureMapping> foundSiftsMappings = new ArrayList<>();
       if (isMapUsingSIFTs && seq.isProtein())
       {
         if (progress != null)
@@ -622,26 +623,15 @@ public class StructureSelectionManager
                     pdb.getId().toLowerCase(Locale.ROOT));
             maxChain.transferResidueAnnotation(siftsMapping, null);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+            foundSiftsMappings.add(siftsMapping);
 
           } catch (SiftsException e)
           {
-            // fall back to NW alignment
             Console.error(e.getMessage());
-            StructureMapping nwMapping = getNWMappings(seq, pdbFile,
-                    targetChainId, maxChain, pdb, maxAlignseq);
-            seqToStrucMapping.add(nwMapping);
-            maxChain.makeExactMapping(maxAlignseq, seq);
-            maxChain.transferRESNUMFeatures(seq, "IEA:Jalview",
-                    pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is
-            // this
-            // "IEA:Jalview" ?
-            maxChain.transferResidueAnnotation(nwMapping, sqmpping);
-            ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
           }
         }
         else
         {
-          List<StructureMapping> foundSiftsMappings = new ArrayList<>();
           for (PDBChain chain : pdb.getChains())
           {
             StructureMapping siftsMapping = null;
@@ -665,30 +655,23 @@ public class StructureSelectionManager
               jalview.bin.Console.errPrintln(e.getMessage());
             }
           }
+          // If sifts was successful, add mappings and return
           if (!foundSiftsMappings.isEmpty())
           {
-            seqToStrucMapping.addAll(foundSiftsMappings);
             ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0));
           }
-          else
-          {
-            /*
-             * fallback to NeedlemanWunch.
-             */
-            StructureMapping nwMapping = getNWMappings(seq, pdbFile,
-                    maxChainId, maxChain, pdb, maxAlignseq);
-            seqToStrucMapping.add(nwMapping);
-            maxChain.transferRESNUMFeatures(seq, null,
-                    pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is this
-            // "IEA:Jalview" ?
-            maxChain.transferResidueAnnotation(nwMapping, sqmpping);
-            ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
-          }
+        }
+        
+        // If sifts was successful, add mappings and return
+        if (!foundSiftsMappings.isEmpty())
+        {
+          seqToStrucMapping.addAll(foundSiftsMappings);
         }
       }
-      else
+      if (foundSiftsMappings.isEmpty())
       {
-        // Not doing SIFTS
+        // Not doing SIFTS, or SIFTS failed for some reason.
+        
         // first check if we should use an identity mapping
         if (idLengthChain != null && maxAlignseq.getS2Coverage() < 0.5)
         {
-- 
1.7.10.2