merge from develop

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index b3b5708..6bc8f84 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -73,6 +73,8 @@ public class StructureSelectionManager
 
   private IProgressIndicator progressIndicator;
 
+  private SiftsClient siftsClient = null;
+
   private long progressSessionId;
 
   /*
@@ -380,7 +382,6 @@ public class StructureSelectionManager
     }
     PDBfile pdb = null;
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
-    SiftsClient siftsClient = null;
     try
     {
       pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
@@ -487,69 +488,73 @@ public class StructureSelectionManager
         pdbFile = "INLINE" + pdb.id;
       }
 
-      ArrayList<StructureMapping> seqToStrucMapping = null;
+      ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
       if (isMapUsingSIFTs)
       {
         setProgressBar(null);
         setProgressBar("Obtaining mapping with SIFTS");
-        try
+        jalview.datamodel.Mapping sqmpping = maxAlignseq
+                .getMappingFromS1(false);
+        if (targetChainId != null && !targetChainId.trim().isEmpty())
         {
-          jalview.datamodel.Mapping sqmpping = maxAlignseq
-                  .getMappingFromS1(false);
-          seqToStrucMapping = new ArrayList<StructureMapping>();
-          if (targetChainId != null && !targetChainId.trim().isEmpty())
-          {
-            StructureMapping curChainMapping = siftsClient
-                    .getSiftsStructureMapping(seq, pdbFile, targetChainId);
-            seqToStrucMapping.add(curChainMapping);
-            maxChainId = targetChainId;
-            PDBChain chain = pdb.findChain(targetChainId);
-            if (chain != null)
-            {
-              chain.transferResidueAnnotation(curChainMapping, sqmpping);
-            }
-          }
-          else
+          StructureMapping mapping = getStructureMapping(seq, pdbFile,
+                  targetChainId, pdb, maxChain, sqmpping, maxAlignseq);
+          seqToStrucMapping.add(mapping);
+        }
+        else
+        {
+          for (PDBChain chain : pdb.chains)
           {
-            for (PDBChain chain : pdb.chains)
-            {
-              StructureMapping curChainMapping = siftsClient
-                      .getSiftsStructureMapping(seq, pdbFile, chain.id);
-              seqToStrucMapping.add(curChainMapping);
-              maxChainId = chain.id;
-              chain.transferResidueAnnotation(curChainMapping, sqmpping);
-            }
+            StructureMapping mapping = getStructureMapping(seq, pdbFile,
+                    chain.id, pdb, chain, sqmpping, maxAlignseq);
+            seqToStrucMapping.add(mapping);
           }
-        } catch (SiftsException e)
-        {
-          System.err.println(e.getMessage());
-          System.err
-                  .println(">>> Now switching mapping with NW alignment...");
-          setProgressBar(null);
-          setProgressBar(">>> Now switching mapping with NW alignment...");
-          seqToStrucMapping = getNWMappings(seq, pdbFile, maxChainId,
-                  maxChain, pdb, maxAlignseq);
         }
       }
       else
       {
         setProgressBar(null);
         setProgressBar("Obtaining mapping with NW alignment");
-        seqToStrucMapping = getNWMappings(seq, pdbFile,
-                maxChainId, maxChain, pdb,
-                maxAlignseq);
+        seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
+                maxChain, pdb, maxAlignseq));
       }
 
       if (forStructureView)
       {
-        // mappings.add(seqToStrucMapping);
         mappings.addAll(seqToStrucMapping);
       }
     }
     return pdb;
   }
 
-  private ArrayList<StructureMapping> getNWMappings(SequenceI seq,
+  private StructureMapping getStructureMapping(SequenceI seq,
+          String pdbFile, String targetChainId, PDBfile pdb,
+          PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
+          AlignSeq maxAlignseq)
+  {
+    String maxChainId = targetChainId;
+    try
+    {
+      StructureMapping curChainMapping = siftsClient
+              .getSiftsStructureMapping(seq, pdbFile, targetChainId);
+      PDBChain chain = pdb.findChain(targetChainId);
+      if (chain != null)
+      {
+        chain.transferResidueAnnotation(curChainMapping, sqmpping);
+      }
+      return curChainMapping;
+    } catch (SiftsException e)
+    {
+      System.err.println(e.getMessage());
+      System.err.println(">>> Now switching mapping with NW alignment...");
+      setProgressBar(null);
+      setProgressBar(">>> Now switching mapping with NW alignment...");
+      return getNWMappings(seq, pdbFile, maxChainId, maxChain, pdb,
+              maxAlignseq);
+    }
+  }
+
+  private StructureMapping getNWMappings(SequenceI seq,
           String pdbFile,
           String maxChainId, PDBChain maxChain, PDBfile pdb,
           AlignSeq maxAlignseq)
@@ -624,9 +629,7 @@ public class StructureSelectionManager
     StructureMapping nwMapping = new StructureMapping(seq, pdbFile,
             pdb.id, maxChainId, mapping, mappingDetails.toString());
     maxChain.transferResidueAnnotation(nwMapping, sqmpping);
-    ArrayList<StructureMapping> mappings = new ArrayList<StructureMapping>();
-    mappings.add(nwMapping);
-    return mappings;
+    return nwMapping;
   }
 
   public void removeStructureViewerListener(Object svl, String[] pdbfiles)

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index cd132df..6e7b988 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -103,10 +103,6 @@ public class SiftsClient implements SiftsClientI
 
   private final static String NEWLINE = System.lineSeparator();
 
-  // private final static int CACHE_THRESHOLD_IN_DAYS = 2;
-  //
-  // private final static int FAIL_SAFE_PID_THRESHOLD = 30;
-
   private String curSourceDBRef;
 
   private HashSet<String> curDBRefAccessionIdsString;
@@ -534,7 +530,7 @@ public class SiftsClient implements SiftsClientI
         {
           continue;
         }
-        if (currSeqIndex > seq.getStart() && currSeqIndex <= seq.getEnd())
+        if (currSeqIndex >= seq.getStart() && currSeqIndex <= seq.getEnd())
         {
           int resNum;
           try
@@ -600,12 +596,17 @@ public class SiftsClient implements SiftsClientI
       int orignalSeqStart = seq.getStart();
       if (orignalSeqStart >= 1)
       {
-        int subSeqStart = seqStart - orignalSeqStart;
+        int subSeqStart = (seqStart >= orignalSeqStart) ? seqStart
+                - orignalSeqStart : 0;
         int subSeqEnd = seqEnd - (orignalSeqStart - 1);
         subSeqEnd = originalSeq.length() < subSeqEnd ? originalSeq.length()
                 : subSeqEnd;
         matchedSeq = originalSeq.substring(subSeqStart, subSeqEnd);
       }
+      else
+      {
+        matchedSeq = originalSeq.substring(1, originalSeq.length());
+      }
     }
 
     StringBuilder targetStrucSeqs = new StringBuilder();
@@ -617,13 +618,13 @@ public class SiftsClient implements SiftsClientI
     if (os != null)
     {
       MappingOutputPojo mop = new MappingOutputPojo();
-      mop.setSeqStart(seqStart);
-      mop.setSeqEnd(seqEnd);
+      mop.setSeqStart(pdbStart);
+      mop.setSeqEnd(pdbEnd);
       mop.setSeqName(seq.getName());
       mop.setSeqResidue(matchedSeq);
 
-      mop.setStrStart(pdbStart);
-      mop.setStrEnd(pdbEnd);
+      mop.setStrStart(seqStart);
+      mop.setStrEnd(seqEnd);
       mop.setStrName(structId);
       mop.setStrResidue(targetStrucSeqs.toString());
 
@@ -777,14 +778,27 @@ public class SiftsClient implements SiftsClientI
   @Override
   public Entity getEntityById(String id) throws SiftsException
   {
-    List<Entity> entities = siftsEntry.getEntity();
-    for (Entity entity : entities)
+    // Sometimes SIFTS mappings are wrongly swapped between different chains of
+    // a PDB entry. This results to wrong mappings being generated. The boolean
+    // flag 'isGetEntityIdDirectly, determines whether an entity to process is
+    // determined by a greedy heuristic search or by just matching the Chain Id
+    // directly against the entity Id tag. Setting the default value to 'false'
+    // utilise the heuristic search which always produces correct mappings but
+    // less optimised processing, where as changing the value to 'true'
+    // optimises performance but might result to incorrect mapping in some cases
+    // where SIFTS mappings are wrongly swapped between different chains.
+    boolean isGetEntityIdDirectly = false;
+    if (isGetEntityIdDirectly)
     {
-      if (!entity.getEntityId().equalsIgnoreCase(id))
+      List<Entity> entities = siftsEntry.getEntity();
+      for (Entity entity : entities)
       {
-        continue;
+        if (!entity.getEntityId().equalsIgnoreCase(id))
+        {
+          continue;
+        }
+        return entity;
       }
-      return entity;
     }
     Entity entity = getEntityByMostOptimalMatchedId(id);
     if (entity != null)
@@ -804,8 +818,7 @@ public class SiftsClient implements SiftsClientI
    */
   public Entity getEntityByMostOptimalMatchedId(String chainId)
   {
-    System.out
-            .println("--------------> advanced greedy entityId matching block entered..");
+    // System.out.println("---> advanced greedy entityId matching block entered..");
     List<Entity> entities = siftsEntry.getEntity();
     SiftsEntitySortPojo[] sPojo = new SiftsEntitySortPojo[entities.size()];
     int count = 0;
@@ -1002,8 +1015,7 @@ public class SiftsClient implements SiftsClientI
     float pid = (float) matchedSeqCount / seqRes.length() * 100;
     if (pid < SiftsSettings.getFailSafePIDThreshold())
     {
-      throw new SiftsException(
-">>> Low PID detected for SIFTs mapping...");
+      throw new SiftsException(">>> Low PID detected for SIFTs mapping...");
     }
     output.append("Length of alignment = " + seqRes.length()).append(
             NEWLINE);