JAL-3466 higher ‘crummy alignment’ threshold when deciding to create an identity...

[jalview.git] / src / jalview / structure / StructureSelectionManager.java

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 735d814..9906582 100644 (file)
--- 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;
@@ -665,32 +655,25 @@ 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)
+        if (idLengthChain != null && maxAlignseq.getS2Coverage() < 0.75)
         {
           Console.info(
                   "Assuming 3Dsi identity mapping between structure and sequence");