JAL-1479 fixed off-by-one error in SIFTS mapping output and added the flag 'isGetEnti...

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index f866127..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;
@@ -284,6 +280,10 @@ public class SiftsClient implements SiftsClientI
    */
   public static File downloadSiftsFile(String pdbId) throws SiftsException
   {
+    if (pdbId.contains(".cif"))
+    {
+      pdbId = pdbId.replace(".cif", "");
+    }
     String siftFile = pdbId + ".xml.gz";
     String siftsFileFTPURL = SIFTS_FTP_BASE_URL + siftFile;
     String downloadedSiftsFile = SiftsSettings.getSiftDownloadDirectory()
@@ -530,7 +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
@@ -596,12 +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();
@@ -613,13 +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());
 
@@ -630,6 +635,58 @@ public class SiftsClient implements SiftsClientI
   }
 
   /**
+   * 
+   * @param chainId
+   *          Target chain to populate mapping of its atom positions.
+   * @param mapping
+   *          Two dimension array of residue index versus atom position
+   * @throws IllegalArgumentException
+   *           Thrown if chainId or mapping is null
+   */
+  void populateAtomPositions(String chainId,
+          HashMap<Integer, int[]> mapping) throws IllegalArgumentException
+  {
+    PDBChain chain = pdb.findChain(chainId);
+    if (chain == null || mapping == null)
+    {
+      throw new IllegalArgumentException(
+              "Chain id or mapping must not be null.");
+    }
+    for (int[] map : mapping.values())
+    {
+      if (map[PDB_RES_POS] != UNASSIGNED)
+      {
+        map[PDB_ATOM_POS] = getAtomIndex(map[PDB_RES_POS], chain.atoms);
+      }
+    }
+  }
+
+  /**
+   * 
+   * @param residueIndex
+   *          The residue index used for the search
+   * @param atoms
+   *          A collection of Atom to search
+   * @return atom position for the given residue index
+   */
+  int getAtomIndex(int residueIndex, Collection<Atom> atoms)
+  {
+    if (atoms == null)
+    {
+      throw new IllegalArgumentException(
+              "atoms collection must not be null!");
+    }
+    for (Atom atom : atoms)
+    {
+      if (atom.resNumber == residueIndex)
+      {
+        return atom.atomIndex;
+      }
+    }
+    return UNASSIGNED;
+  }
+
+  /**
    * Checks if the residue instance is marked 'Not_observed' or not
    * 
    * @param residue
@@ -716,69 +773,32 @@ public class SiftsClient implements SiftsClientI
     }
   }
 
-  /**
-   * 
-   * @param chainId
-   *          Target chain to populate mapping of its atom positions.
-   * @param mapping
-   *          Two dimension array of residue index versus atom position
-   * @throws IllegalArgumentException
-   *           Thrown if chainId or mapping is null
-   */
-  void populateAtomPositions(String chainId, HashMap<Integer, int[]> mapping)
-          throws IllegalArgumentException
-  {
-    PDBChain chain = pdb.findChain(chainId);
-    if (chain == null || mapping == null)
-    {
-      throw new IllegalArgumentException(
-              "Chain id or mapping must not be null.");
-    }
-    for (int[] map : mapping.values())
-    {
-      if (map[PDB_RES_POS] != UNASSIGNED)
-      {
-        map[PDB_ATOM_POS] = getAtomIndex(map[PDB_RES_POS], chain.atoms);
-      }
-    }
-  }
 
-  /**
-   * 
-   * @param residueIndex
-   *          The residue index used for the search
-   * @param atoms
-   *          A collection of Atom to search
-   * @return atom position for the given residue index
-   */
-  int getAtomIndex(int residueIndex, Collection<Atom> atoms)
-  {
-    if (atoms == null)
-    {
-      throw new IllegalArgumentException(
-              "atoms collection must not be null!");
-    }
-    for (Atom atom : atoms)
-    {
-      if (atom.resNumber == residueIndex)
-      {
-        return atom.atomIndex;
-      }
-    }
-    return UNASSIGNED;
-  }
 
   @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)
@@ -798,8 +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;
@@ -996,8 +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);