JAL-1479 added transfer of residue annotation for SIFTS mapping, then did some minor...

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 3d5a975..1541a6a 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -328,7 +328,7 @@ public class StructureSelectionManager
    * 
    * @param sequenceArray
    *          - one or more sequences to be mapped to pdbFile
-   * @param targetChains
+   * @param targetChainIds
    *          - optional chain specification for mapping each sequence to pdb
    *          (may be nill, individual elements may be nill)
    * @param pdbFile
@@ -338,7 +338,8 @@ public class StructureSelectionManager
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public PDBfile setMapping(boolean forStructureView,
-          SequenceI[] sequenceArray, String[] targetChains, String pdbFile,
+          SequenceI[] sequenceArray, String[] targetChainIds,
+          String pdbFile,
           String protocol)
   {
     /*
@@ -379,54 +380,60 @@ public class StructureSelectionManager
     {
       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();
       return null;
     }
 
-    String targetChain;
+    try
+    {
+      if (isMapUsingSIFTs)
+      {
+        siftsClient = new SiftsClient(pdb);
+      }
+    } catch (SiftsException e)
+    {
+      isMapUsingSIFTs = false;
+      e.printStackTrace();
+    }
+
+    String targetChainId;
     for (int s = 0; s < sequenceArray.length; s++)
     {
       boolean infChain = true;
       final SequenceI seq = sequenceArray[s];
-      if (targetChains != null && targetChains[s] != null)
+      if (targetChainIds != null && targetChainIds[s] != null)
       {
         infChain = false;
-        targetChain = targetChains[s];
+        targetChainId = targetChainIds[s];
       }
       else if (seq.getName().indexOf("|") > -1)
       {
-        targetChain = seq.getName().substring(
+        targetChainId = seq.getName().substring(
                 seq.getName().lastIndexOf("|") + 1);
-        if (targetChain.length() > 1)
+        if (targetChainId.length() > 1)
         {
-          if (targetChain.trim().length() == 0)
+          if (targetChainId.trim().length() == 0)
           {
-            targetChain = " ";
+            targetChainId = " ";
           }
           else
           {
             // not a valid chain identifier
-            targetChain = "";
+            targetChainId = "";
           }
         }
       }
       else
       {
-        targetChain = "";
+        targetChainId = "";
       }
 
       /*
@@ -440,7 +447,7 @@ public class StructureSelectionManager
       boolean first = true;
       for (PDBChain chain : pdb.chains)
       {
-        if (targetChain.length() > 0 && !targetChain.equals(chain.id)
+        if (targetChainId.length() > 0 && !targetChainId.equals(chain.id)
                 && !infChain)
         {
           continue; // don't try to map chains don't match.
@@ -456,7 +463,7 @@ public class StructureSelectionManager
         // as.traceAlignment();
 
         if (first || as.maxscore > max
-                || (as.maxscore == max && chain.id.equals(targetChain)))
+                || (as.maxscore == max && chain.id.equals(targetChainId)))
         {
           first = false;
           maxChain = chain;
@@ -480,26 +487,35 @@ public class StructureSelectionManager
       {
         try
         {
+          jalview.datamodel.Mapping sqmpping = maxAlignseq
+                  .getMappingFromS1(false);
           seqToStrucMapping = new ArrayList<StructureMapping>();
-          if (targetChain != null && !targetChain.trim().isEmpty())
+          if (targetChainId != null && !targetChainId.trim().isEmpty())
           {
-            maxChainId = targetChain;
             StructureMapping curChainMapping = siftsClient
-                    .getSiftsStructureMapping(seq, pdbFile, targetChain);
+                    .getSiftsStructureMapping(seq, pdbFile, targetChainId);
             seqToStrucMapping.add(curChainMapping);
+            maxChainId = targetChainId;
+            PDBChain chain = pdb.findChain(targetChainId);
+            if (chain != null)
+            {
+              chain.transferResidueAnnotation(curChainMapping, sqmpping);
+            }
           }
           else
           {
             for (PDBChain chain : pdb.chains)
             {
-              maxChainId = chain.id;
               StructureMapping curChainMapping = siftsClient
                       .getSiftsStructureMapping(seq, pdbFile, chain.id);
               seqToStrucMapping.add(curChainMapping);
+              maxChainId = chain.id;
+              chain.transferResidueAnnotation(curChainMapping, sqmpping);
             }
           }
         } catch (SiftsException e)
         {
+          e.printStackTrace();
           System.err
                   .println(">>>>>>> SIFTs mapping could not be obtained... Now mapping with NW alignment");
           seqToStrucMapping = getNWMappings(seq, pdbFile, maxChainId,

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 10e14f4..245d38f 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -35,6 +35,7 @@ import jalview.xml.binding.sifts.Entry.Entity.Segment;
 import jalview.xml.binding.sifts.Entry.Entity.Segment.ListMapRegion.MapRegion;
 import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue;
 import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.CrossRefDb;
+import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.ResidueDetail;
 import jalview.xml.binding.sifts.Entry.ListDB.Db;
 
 import java.io.File;
@@ -119,7 +120,24 @@ public class SiftsClient implements SiftsClientI
       return name;
     }
   };
-  
+
+  public enum ResidueDetailType
+  {
+    NAME_SEC_STRUCTURE("nameSecondaryStructure"), CODE_SEC_STRUCTURE(
+            "codeSecondaryStructure"), ANNOTATION("Annotation");
+    private String code;
+
+    private ResidueDetailType(String code)
+    {
+      this.code = code;
+    }
+
+    public String getCode()
+    {
+      return code;
+    }
+  };
+
   /**
    * Fetch SIFTs file for the given PDB Id and construct an instance of
    * SiftsClient
@@ -175,20 +193,24 @@ public class SiftsClient implements SiftsClientI
     } catch (JAXBException e)
     {
       e.printStackTrace();
+      throw new SiftsException(e.getMessage());
     } catch (FileNotFoundException e)
     {
       e.printStackTrace();
+      throw new SiftsException(e.getMessage());
     } catch (XMLStreamException e)
     {
       e.printStackTrace();
+      throw new SiftsException(e.getMessage());
     } catch (FactoryConfigurationError e)
     {
       e.printStackTrace();
+      throw new SiftsException(e.getMessage());
     } catch (IOException e)
     {
       e.printStackTrace();
+      throw new SiftsException(e.getMessage());
     }
-    throw new SiftsException("Error parsing siftFile");
   }
 
   /**
@@ -196,8 +218,9 @@ public class SiftsClient implements SiftsClientI
    * 
    * @param pdbId
    * @return SIFTs XML file
+   * @throws SiftsException
    */
-  public static File getSiftsFile(String pdbId)
+  public static File getSiftsFile(String pdbId) throws SiftsException
   {
     File siftsFile = new File(SIFTS_DOWNLOAD_DIR + pdbId.toLowerCase()
             + ".xml.gz");
@@ -218,8 +241,9 @@ public class SiftsClient implements SiftsClientI
    * 
    * @param pdbId
    * @return downloaded SIFTs XML file
+   * @throws SiftsException
    */
-  public static File downloadSiftsFile(String pdbId)
+  public static File downloadSiftsFile(String pdbId) throws SiftsException
   {
     String siftFile = pdbId + ".xml.gz";
     String siftsFileFTPURL = SIFTS_FTP_BASE_URL + siftFile;
@@ -248,7 +272,7 @@ public class SiftsClient implements SiftsClientI
       System.out.println(">>> File downloaded : " + downloadedSiftsFile);
     } catch (IOException ex)
     {
-      ex.printStackTrace();
+      throw new SiftsException(ex.getMessage());
     }
     return new File(downloadedSiftsFile);
   }
@@ -401,7 +425,6 @@ public class SiftsClient implements SiftsClientI
           java.io.PrintStream os)
  throws SiftsException
   {
-
     System.out.println("Generating mappings for : " + entityId);
     Entity entity = null;
     entity = getEntityById(entityId);
@@ -439,7 +462,6 @@ public class SiftsClient implements SiftsClientI
       residuePos[PDB_RES_POS] = UNASSIGNED;
       residuePos[PDB_ATOM_POS] = UNASSIGNED;
     }
-    
     TreeMap<Integer, String> resNumMap = new TreeMap<Integer, String>();
     List<Segment> segments = entity.getSegment();
     for (Segment segment : segments)
@@ -492,7 +514,8 @@ public class SiftsClient implements SiftsClientI
           }
           try
           {
-            mapping[currSeqIndex][PDB_RES_POS] = Integer.valueOf(resNum);
+            mapping[currSeqIndex][PDB_RES_POS] = Integer
+                    .valueOf(resNum);
           } catch (ArrayIndexOutOfBoundsException e)
           {
             // do nothing..
@@ -573,6 +596,36 @@ public class SiftsClient implements SiftsClientI
     return mapping;
   }
 
+  private boolean isResidueObserved(Residue residue)
+  {
+    String annotation = getResidueAnnotaiton(residue,
+            ResidueDetailType.ANNOTATION);
+    if (annotation == null)
+    {
+      return true;
+    }
+    if (!annotation.equalsIgnoreCase("Not_Found")
+            && annotation.equalsIgnoreCase("Not_Observed"))
+    {
+      return false;
+    }
+    return true;
+  }
+
+  private String getResidueAnnotaiton(Residue residue,
+          ResidueDetailType type)
+  {
+    List<ResidueDetail> resDetails = residue.getResidueDetail();
+    for (ResidueDetail resDetail : resDetails)
+    {
+      if (resDetail.getProperty().equalsIgnoreCase(type.getCode()))
+      {
+        return resDetail.getContent();
+      }
+    }
+    return "Not_Found";
+  }
+
   private boolean hasAccessionId(String accession)
   {
     boolean isStrictMatch = true;

diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java
index 4c94f66..4a57a88 100644 (file)
--- a/test/jalview/ws/sifts/SiftsClientTest.java
+++ b/test/jalview/ws/sifts/SiftsClientTest.java
@@ -107,7 +107,7 @@ public class SiftsClientTest
   }
 
   @Test(groups = { "Functional" })
-  public void getSIFTsFileTest()
+  public void getSIFTsFileTest() throws SiftsException
   {
     Assert.assertTrue(SiftsClient.deleteSiftsFileByPDBId(testPDBId));
     SiftsClient.getSiftsFile(testPDBId);
@@ -121,7 +121,7 @@ public class SiftsClientTest
   }
 
   @Test(groups = { "Functional" })
-  public void downloadSiftsFileTest()
+  public void downloadSiftsFileTest() throws SiftsException
   {
     // Assert that file isn't yet downloaded - if already downloaded, assert it
     // is deleted