JAL-4371 minimal test and move PDBEntryUtils to correct package

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 735d814..0f82650 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -26,10 +26,12 @@ import java.util.Arrays;
 import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.IdentityHashMap;
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
+import java.util.Set;
 import java.util.Vector;
 
 import jalview.analysis.AlignSeq;
@@ -522,32 +524,15 @@ public class StructureSelectionManager
       {
         ds = ds.getDatasetSequence();
       }
-
+      List <PDBEntry> putativePDBe = PDBEntryUtils.selectPutativePDBe(seq,ds, pdb); 
+      
       if (targetChainIds != null && targetChainIds[s] != null)
       {
         infChain = false;
         targetChainId = targetChainIds[s];
       }
-      else if (seq.getName().indexOf("|") > -1)
-      {
-        targetChainId = seq.getName()
-                .substring(seq.getName().lastIndexOf("|") + 1);
-        if (targetChainId.length() > 1)
-        {
-          if (targetChainId.trim().length() == 0)
-          {
-            targetChainId = " ";
-          }
-          else
-          {
-            // not a valid chain identifier
-            targetChainId = "";
-          }
-        }
-      }
-      else
-      {
-        targetChainId = "";
+      else {
+        targetChainId = PDBEntryUtils.inferChainId(seq);
       }
 
       /*
@@ -567,6 +552,12 @@ public class StructureSelectionManager
         {
           continue; // don't try to map chains don't match.
         }
+        PDBEntry putativeChain = null;
+        if (!putativePDBe.isEmpty() && (putativeChain = PDBEntryUtils
+                .selectPutativePDBEntry(putativePDBe, chain)) == null)
+        {
+          continue;
+        }
         // TODO: correctly determine sequence type for mixed na/peptide
         // structures
         final String type = chain.isNa ? AlignSeq.DNA : AlignSeq.PEP;
@@ -598,6 +589,7 @@ public class StructureSelectionManager
       }
       List<StructureMapping> seqToStrucMapping = new ArrayList<>();
 
+      List<StructureMapping> foundSiftsMappings = new ArrayList<>();
       if (isMapUsingSIFTs && seq.isProtein())
       {
         if (progress != null)
@@ -622,26 +614,15 @@ 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 +646,25 @@ 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");
@@ -702,6 +676,11 @@ public class StructureSelectionManager
         }
         else
         {
+          if (maxAlignseq.getS1Coverage()<0.15 && maxAlignseq.getS2Coverage()<0.15)
+          {
+            // skip this - the NW alignment is spurious
+            continue;
+          }
           // Construct a needleman wunsch mapping instead.
           if (progress != null)
           {