JAL-1957 JAL-1479 Further optimisation of SIFTs Client and addition of support for...

diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java
index 19f535c..d5676c5 100644 (file)
--- a/src/jalview/ext/jmol/JmolCommands.java
+++ b/src/jalview/ext/jmol/JmolCommands.java
@@ -64,7 +64,9 @@ public class JmolCommands
       ArrayList<String> str = new ArrayList<String>();
 
       if (mapping == null || mapping.length < 1)
+      {
         continue;
+      }
 
       int lastPos = -1;
       for (int s = 0; s < sequence[pdbfnum].length; s++)
@@ -85,14 +87,18 @@ public class JmolCommands
               int pos = mapping[m].getPDBResNum(asp.findPosition(r));
 
               if (pos < 1 || pos == lastPos)
+              {
                 continue;
+              }
 
               lastPos = pos;
 
               Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
 
               if (fr != null)
+              {
                 col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
+              }
               String newSelcom = (mapping[m].getChain() != " " ? ":"
                       + mapping[m].getChain() : "")
                       + "/"
@@ -125,7 +131,7 @@ public class JmolCommands
               command.append("select " + pos);
               command.append(newSelcom);
             }
-            break;
+            // break;
           }
         }
       }

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 13aae26..3d5a975 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -326,7 +326,7 @@ public class StructureSelectionManager
    * @param forStructureView
    *          when true, record the mapping for use in mouseOvers
    * 
-   * @param sequence
+   * @param sequenceArray
    *          - one or more sequences to be mapped to pdbFile
    * @param targetChains
    *          - optional chain specification for mapping each sequence to pdb
@@ -338,7 +338,7 @@ public class StructureSelectionManager
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public PDBfile setMapping(boolean forStructureView,
-          SequenceI[] sequence, String[] targetChains, String pdbFile,
+          SequenceI[] sequenceArray, String[] targetChains, String pdbFile,
           String protocol)
   {
     /*
@@ -348,7 +348,7 @@ public class StructureSelectionManager
     boolean parseSecStr = processSecondaryStructure;
     if (isPDBFileRegistered(pdbFile))
     {
-      for (SequenceI sq : sequence)
+      for (SequenceI sq : sequenceArray)
       {
         SequenceI ds = sq;
         while (ds.getDatasetSequence() != null)
@@ -372,15 +372,25 @@ public class StructureSelectionManager
       }
     }
     PDBfile pdb = null;
+    boolean isMapUsingSIFTs = Boolean.valueOf(jalview.bin.Cache.getDefault(
+            "MAP_WITH_SIFTS", "false"));
+    SiftsClient siftsClient = null;
     try
     {
       pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
               pdbFile, protocol);
+      if (isMapUsingSIFTs)
+      {
+        siftsClient = new SiftsClient(pdb);
+      }
       if (pdb.id != null && pdb.id.trim().length() > 0
               && AppletFormatAdapter.FILE.equals(protocol))
       {
         registerPDBFile(pdb.id.trim(), pdbFile);
       }
+    } catch (SiftsException e)
+    {
+      e.printStackTrace();
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -388,10 +398,10 @@ public class StructureSelectionManager
     }
 
     String targetChain;
-    for (int s = 0; s < sequence.length; s++)
+    for (int s = 0; s < sequenceArray.length; s++)
     {
       boolean infChain = true;
-      final SequenceI seq = sequence[s];
+      final SequenceI seq = sequenceArray[s];
       if (targetChains != null && targetChains[s] != null)
       {
         infChain = false;
@@ -465,16 +475,29 @@ public class StructureSelectionManager
         pdbFile = "INLINE" + pdb.id;
       }
 
-      StructureMapping seqToStrucMapping = null;
-      boolean isMapViaSIFTs = Boolean.valueOf(jalview.bin.Cache.getDefault(
-              "MAP_WITH_SIFTS", "false"));
-      if (isMapViaSIFTs)
+      ArrayList<StructureMapping> seqToStrucMapping = null;
+      if (isMapUsingSIFTs)
       {
-        SiftsClient siftsClient = new SiftsClient(pdb);
         try
         {
-          seqToStrucMapping = siftsClient.getSiftsStructureMapping(seq,
-                  pdbFile, maxChainId);
+          seqToStrucMapping = new ArrayList<StructureMapping>();
+          if (targetChain != null && !targetChain.trim().isEmpty())
+          {
+            maxChainId = targetChain;
+            StructureMapping curChainMapping = siftsClient
+                    .getSiftsStructureMapping(seq, pdbFile, targetChain);
+            seqToStrucMapping.add(curChainMapping);
+          }
+          else
+          {
+            for (PDBChain chain : pdb.chains)
+            {
+              maxChainId = chain.id;
+              StructureMapping curChainMapping = siftsClient
+                      .getSiftsStructureMapping(seq, pdbFile, chain.id);
+              seqToStrucMapping.add(curChainMapping);
+            }
+          }
         } catch (SiftsException e)
         {
           System.err
@@ -492,13 +515,15 @@ public class StructureSelectionManager
 
       if (forStructureView)
       {
-        mappings.add(seqToStrucMapping);
+        // mappings.add(seqToStrucMapping);
+        mappings.addAll(seqToStrucMapping);
       }
     }
     return pdb;
   }
 
-  private StructureMapping getNWMappings(SequenceI seq, String pdbFile,
+  private ArrayList<StructureMapping> getNWMappings(SequenceI seq,
+          String pdbFile,
           String maxChainId, PDBChain maxChain, PDBfile pdb,
           AlignSeq maxAlignseq)
   {
@@ -574,7 +599,9 @@ public class StructureSelectionManager
     StructureMapping nwMapping = new StructureMapping(seq, pdbFile,
             pdb.id, maxChainId, mapping, mappingDetails.toString());
     maxChain.transferResidueAnnotation(nwMapping, sqmpping);
-    return nwMapping;
+    ArrayList<StructureMapping> mappings = new ArrayList<StructureMapping>();
+    mappings.add(nwMapping);
+    return mappings;
   }
 
   public void removeStructureViewerListener(Object svl, String[] pdbfiles)

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index e054b29..10e14f4 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -78,11 +78,7 @@ public class SiftsClient implements SiftsClientI
 
   private String segStartEnd;
 
-  private static final String UNIPROT_COORDINATE_SYS = "UniProt";
-
-  private static final String PDB_COORDINATE_SYS = "PDBresnum";
-
-  private String seqCoordSys = UNIPROT_COORDINATE_SYS;
+  private CoordinateSys seqCoordSys = CoordinateSys.UNIPROT;
 
   private static final int BUFFER_SIZE = 4096;
 
@@ -104,45 +100,55 @@ public class SiftsClient implements SiftsClientI
 
   private final static String NEWLINE = System.lineSeparator();
 
+  private String curSourceDBRef;
+
+  private HashSet<String> curDBRefAccessionIdsString;
+
+  public enum CoordinateSys
+  {
+    UNIPROT("UniProt"), PDB("PDBresnum"), PDBe("PDBe");
+    private String name;
+
+    private CoordinateSys(String name)
+    {
+      this.name = name;
+    }
+
+    public String getName()
+    {
+      return name;
+    }
+  };
+  
   /**
    * Fetch SIFTs file for the given PDB Id and construct an instance of
    * SiftsClient
    * 
    * @param pdbId
+   * @throws SiftsException
    */
-  public SiftsClient(PDBfile pdb)
+  public SiftsClient(PDBfile pdb) throws SiftsException
   {
     this.pdb = pdb;
     this.pdbId = pdb.id;
-    try
-    {
-      File siftsFile = getSiftsFile(pdbId);
-      siftsEntry = parseSIFTs(siftsFile);
-    } catch (Exception e)
-    {
-      e.printStackTrace();
-    }
+    File siftsFile = getSiftsFile(pdbId);
+    siftsEntry = parseSIFTs(siftsFile);
   }
 
   /**
-   * Construct an instance of SiftsClient using the supplied SIFTs file - 
-   * the SIFTs file should correspond to the given PDB Id
+   * Construct an instance of SiftsClient using the supplied SIFTs file - the
+   * SIFTs file should correspond to the given PDB Id
    * 
    * @param pdbId
    * @param siftsFile
+   * @throws SiftsException
+   * @throws Exception
    */
-  public SiftsClient(PDBfile pdb, File siftsFile)
+  public SiftsClient(PDBfile pdb, File siftsFile) throws SiftsException
   {
     this.pdb = pdb;
     this.pdbId = pdb.id;
-    try
-    {
-      siftsEntry = parseSIFTs(siftsFile);
-    } catch (Exception e)
-    {
-      e.printStackTrace();
-    }
-
+    siftsEntry = parseSIFTs(siftsFile);
   }
 
   /**
@@ -154,7 +160,7 @@ public class SiftsClient implements SiftsClientI
    * @throws Exception
    *           if a problem occurs while parsing the SIFTs XML
    */
-  private Entry parseSIFTs(File siftFile) throws Exception
+  private Entry parseSIFTs(File siftFile) throws SiftsException
   {
     try
     {
@@ -182,7 +188,7 @@ public class SiftsClient implements SiftsClientI
     {
       e.printStackTrace();
     }
-    throw new Exception("Error parsing siftFile");
+    throw new SiftsException("Error parsing siftFile");
   }
 
   /**
@@ -308,8 +314,8 @@ public class SiftsClient implements SiftsClientI
           continue;
         }
         if (isFoundInSiftsEntry(dbRef.getAccessionId())
-                && (dbRef.getSource().equalsIgnoreCase("uniprot") || dbRef
-                        .getSource().equalsIgnoreCase("pdb")))
+                && (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT) || dbRef
+                        .getSource().equalsIgnoreCase(DBRefSource.PDB)))
         {
           return dbRef;
         }
@@ -414,14 +420,18 @@ public class SiftsClient implements SiftsClientI
     // set sequence coordinate system - default value is UniProt
     if (sourceDBRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
     {
-      seqCoordSys = PDB_COORDINATE_SYS;
+      seqCoordSys = CoordinateSys.PDB;
     }
 
-    ArrayList<String> dbRefAccessionIdsString = new ArrayList<String>();
+    HashSet<String> dbRefAccessionIdsString = new HashSet<String>();
     for (DBRefEntry dbref : seq.getDBRefs())
     {
-      dbRefAccessionIdsString.add(dbref.getAccessionId());
+      dbRefAccessionIdsString.add(dbref.getAccessionId().toLowerCase());
     }
+    dbRefAccessionIdsString.add(sourceDBRef.getAccessionId().toLowerCase());
+
+    curDBRefAccessionIdsString = dbRefAccessionIdsString;
+    curSourceDBRef = sourceDBRef.getAccessionId();
 
     // initialise all mapping positions to unassigned
     for (int residuePos[] : mapping)
@@ -442,17 +452,25 @@ public class SiftsClient implements SiftsClientI
       {
         int currSeqIndex = UNASSIGNED;
         List<CrossRefDb> cRefDbs = residue.getCrossRefDb();
+        CrossRefDb pdbRefDb = null;
         for (CrossRefDb cRefDb : cRefDbs)
         {
-          if (cRefDb.getDbCoordSys().equalsIgnoreCase(seqCoordSys)
-                  && dbRefAccessionIdsString.contains(cRefDb
-                          .getDbAccessionId()))
+          if (cRefDb.getDbSource().equalsIgnoreCase(DBRefSource.PDB))
+          {
+            pdbRefDb = cRefDb;
+          }
+          if (cRefDb.getDbCoordSys()
+                  .equalsIgnoreCase(seqCoordSys.getName())
+                  && hasAccessionId(cRefDb.getDbAccessionId()))
           {
             String resNumIndexString = cRefDb.getDbResNum()
                     .equalsIgnoreCase("None") ? String.valueOf(UNASSIGNED)
                     : cRefDb.getDbResNum();
             currSeqIndex = Integer.valueOf(resNumIndexString);
-            break;
+            if (pdbRefDb != null)
+            {
+              break;// exit loop if pdb and uniprot are already found
+            }
           }
         }
         if (currSeqIndex == UNASSIGNED)
@@ -461,8 +479,24 @@ public class SiftsClient implements SiftsClientI
         }
         if (currSeqIndex > seq.getStart() && currSeqIndex <= seq.getEnd())
         {
-          int resNum = Integer.valueOf(residue.getDbResNum());
-          mapping[currSeqIndex][PDB_RES_POS] = Integer.valueOf(resNum);
+          int resNum;
+          try
+          {
+            resNum = (pdbRefDb == null) ? Integer.valueOf(residue
+                  .getDbResNum()) : Integer.valueOf(pdbRefDb.getDbResNum());
+          } catch (NumberFormatException nfe)
+          {
+            resNum = (pdbRefDb == null) ? Integer.valueOf(residue
+                    .getDbResNum()) : Integer.valueOf(pdbRefDb
+                    .getDbResNum().split("[a-zA-Z]")[0]);
+          }
+          try
+          {
+            mapping[currSeqIndex][PDB_RES_POS] = Integer.valueOf(resNum);
+          } catch (ArrayIndexOutOfBoundsException e)
+          {
+            // do nothing..
+          }
           char resCharCode = ResidueProperties
                   .getSingleCharacterCode(residue.getDbResName());
           resNumMap.put(currSeqIndex, String.valueOf(resCharCode));
@@ -478,10 +512,10 @@ public class SiftsClient implements SiftsClientI
     }
     padWithGaps(resNumMap);
     int counter = 0;
-    int seqStart = 0;
-    int seqEnd = 0;
-    int pdbStart = 0;
-    int pdbEnd = 0;
+    int seqStart = UNASSIGNED;
+    int seqEnd = UNASSIGNED;
+    int pdbStart = UNASSIGNED;
+    int pdbEnd = UNASSIGNED;
     boolean startDetected = false;
     for (int[] x : mapping)
     {
@@ -520,31 +554,32 @@ public class SiftsClient implements SiftsClientI
       targetStrucSeqs.append(res);
     }
 
-    try
+    if (os != null)
     {
-      if (os != null)
-      {
-        MappingOutputPojo mop = new MappingOutputPojo();
-        mop.setSeqStart(seqStart);
-        mop.setSeqEnd(seqEnd);
-        mop.setSeqName(seq.getName());
-        mop.setSeqResidue(matchedSeq);
-
-        mop.setStrStart(pdbStart);
-        mop.setStrEnd(pdbEnd);
-        mop.setStrName(structId);
-        mop.setStrResidue(targetStrucSeqs.toString());
-
-        mop.setType("pep");
-        os.print(getMappingOutput(mop).toString());
-      }
-    } catch (Exception ex)
-    {
-      ex.printStackTrace();
+      MappingOutputPojo mop = new MappingOutputPojo();
+      mop.setSeqStart(seqStart);
+      mop.setSeqEnd(seqEnd);
+      mop.setSeqName(seq.getName());
+      mop.setSeqResidue(matchedSeq);
+
+      mop.setStrStart(pdbStart);
+      mop.setStrEnd(pdbEnd);
+      mop.setStrName(structId);
+      mop.setStrResidue(targetStrucSeqs.toString());
+
+      mop.setType("pep");
+      os.print(getMappingOutput(mop).toString());
     }
     return mapping;
   }
 
+  private boolean hasAccessionId(String accession)
+  {
+    boolean isStrictMatch = true;
+    return isStrictMatch ? curSourceDBRef.equalsIgnoreCase(accession)
+            : curDBRefAccessionIdsString.contains(accession.toLowerCase());
+  }
+
   @Override
   public boolean isFoundInSiftsEntry(String accessionId)
   {
@@ -559,6 +594,10 @@ public class SiftsClient implements SiftsClientI
    */
   void padWithGaps(TreeMap<Integer, String> resNumMap)
   {
+    if (resNumMap == null || resNumMap.isEmpty())
+    {
+      return;
+    }
     Integer[] keys = resNumMap.keySet().toArray(new Integer[0]);
     Arrays.sort(keys);
     int firstIndex = keys[0];
@@ -766,6 +805,10 @@ public class SiftsClient implements SiftsClientI
       output.append(NEWLINE).append(NEWLINE);
     }
     float pid = (float) matchedSeqCount / seqRes.length() * 100;
+    if (pid < 2)
+    {
+      throw new SiftsException("Low PID detected for SIFTs mapping...");
+    }
     output.append("Length of alignment = " + seqRes.length())
             .append(NEWLINE);
     output.append(new Format("Percentage ID = %2.2f").form(pid));

diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java
index 7443f4a..4c94f66 100644 (file)
--- a/test/jalview/ws/sifts/SiftsClientTest.java
+++ b/test/jalview/ws/sifts/SiftsClientTest.java
@@ -78,7 +78,7 @@ public class SiftsClientTest
       { 94, u }, { 95, u }, { 96, u }, { 97, u } };
 
   @BeforeTest(alwaysRun = true)
-  public void setUpSiftsClient()
+  public void setUpSiftsClient() throws SiftsException
   {
     // SIFTs entries are updated weekly - so use saved SIFTs file to enforce
     // test reproducibility