JAL-1479 JAL- Fix to eradicate duplicate mapping output and further improvement for...

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 692cd18..b1a4fee 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -683,27 +683,42 @@ public class AlignViewport extends AlignmentViewport implements
     List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
     for (PDBEntry pdb : pdbEntries)
     {
-      List<SequenceI> seqs = new ArrayList<SequenceI>();
+      List<SequenceI> choosenSeqs = new ArrayList<SequenceI>();
       for (SequenceI sq : alignment.getSequences())
       {
-        Vector<PDBEntry> pdbs = sq.getDatasetSequence().getAllPDBEntries();
-        if (pdbs == null)
+        Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence().getAllPDBEntries();
+        if (pdbRefEntries == null)
         {
           continue;
         }
-        for (PDBEntry p1 : pdbs)
+        for (PDBEntry pdbRefEntry : pdbRefEntries)
         {
-          if (p1.getId().equals(pdb.getId()))
+          if (pdbRefEntry.getId().equals(pdb.getId()))
           {
-            if (!seqs.contains(sq))
+            if (pdbRefEntry.getChainCode() != null
+                    && pdb.getChainCode() != null)
             {
-              seqs.add(sq);
-              continue;
+              if (pdbRefEntry.getChainCode().equalsIgnoreCase(
+                      pdb.getChainCode())
+                      && !choosenSeqs.contains(sq))
+              {
+                choosenSeqs.add(sq);
+                continue;
+              }
             }
+            else
+            {
+              if (!choosenSeqs.contains(sq))
+              {
+                choosenSeqs.add(sq);
+                continue;
+              }
+            }
+
           }
         }
       }
-      seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
+      seqvectors.add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
     }
     return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
   }
@@ -1103,6 +1118,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @param featureSettings
    */
+  @Override
   public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
   {
     if (featureSettings == null)

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 6471795..2972c69 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -407,7 +407,6 @@ public class StructureChooser extends GStructureChooser implements
           FTSRestRequest pdbRequest = new FTSRestRequest();
           if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
           {
-            System.out.println(">>>>>> Filtering with uniprot coverate");
             pdbRequest.setAllowEmptySeq(false);
             pdbRequest.setResponseSize(1);
             pdbRequest.setFieldToSearchBy("(");
@@ -862,45 +861,19 @@ public class StructureChooser extends GStructureChooser implements
       ArrayList<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
       for (SequenceI seq : sequences)
       {
-        if (seq.getSourceDBRef() == null)
+        if (seq.getSourceDBRef() == null && seq.getDBRefs() == null)
         {
-          if (seq.getDBRefs() == null)
-          {
             seqsWithoutSourceDBRef.add(seq);
             continue;
           }
-          for (DBRefEntry dbRef : seq.getDBRefs())
-          {
-            if (dbRef.getSource().equalsIgnoreCase("uniprot"))
-            {
-              seq.setSourceDBRef(dbRef);
-              break;
-            }
-          }
-          for (DBRefEntry dbRef : seq.getDBRefs())
-          {
-            if (dbRef.getSource().equalsIgnoreCase("pdb"))
-            {
-              seq.setSourceDBRef(dbRef);
-              break;
-            }
-          }
-          if (seq.getSourceDBRef() == null)
-          {
-            seqsWithoutSourceDBRef.add(seq);
-          }
-        }
       }
       if (!seqsWithoutSourceDBRef.isEmpty())
       {
         int y = seqsWithoutSourceDBRef.size();
         ssm.setProgressBar(null);
-        ssm.setProgressBar(">>>>> Fetching Database refs for " + y
-                + " sequence" + (y > 1 ? "s" : "")
-                + " with no valid uniprot or pdb ref for SIFTS mapping");
-        System.out.println(">>>>> Fetching Database refs for " + y
+        ssm.setProgressBar("Fetching db refs for " + y
                 + " sequence" + (y > 1 ? "s" : "")
-                + " with no valid uniprot or pdb ref for SIFTS mapping");
+                + " without valid db ref required for SIFTS mapping");
         SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
         int x = 0;
         for (SequenceI fSeq : seqsWithoutSourceDBRef)

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index a5d9736..4dff04d 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -506,17 +506,41 @@ public class StructureSelectionManager
                 .getMappingFromS1(false);
         if (targetChainId != null && !targetChainId.trim().isEmpty())
         {
-          StructureMapping mapping = getStructureMapping(seq, pdbFile,
-                  targetChainId, pdb, maxChain, sqmpping, maxAlignseq);
-          seqToStrucMapping.add(mapping);
+          StructureMapping mapping;
+          try
+          {
+            mapping = getStructureMapping(seq, pdbFile, targetChainId, pdb,
+                    maxChain, sqmpping, maxAlignseq);
+            seqToStrucMapping.add(mapping);
+          } catch (SiftsException e)
+          {
+            // e.printStackTrace();
+            // fall back to NW alignment
+            System.err.println(e.getMessage());
+            seqToStrucMapping.add(getNWMappings(seq, pdbFile,
+                    targetChainId,
+                    maxChain, pdb, maxAlignseq));
+          }
         }
         else
         {
-          for (PDBChain chain : pdb.getChains())
+          try
           {
-            StructureMapping mapping = getStructureMapping(seq, pdbFile,
-                    chain.id, pdb, chain, sqmpping, maxAlignseq);
-            seqToStrucMapping.add(mapping);
+            ArrayList<StructureMapping> tempMapping = new ArrayList<StructureMapping>();
+            for (PDBChain chain : pdb.getChains())
+            {
+              StructureMapping mapping = getStructureMapping(seq, pdbFile,
+                      chain.id, pdb, chain, sqmpping, maxAlignseq);
+              tempMapping.add(mapping);
+            }
+            seqToStrucMapping.addAll(tempMapping);
+          } catch (SiftsException e)
+          {
+            // e.printStackTrace();
+            // fall back to NW alignment
+            System.err.println(e.getMessage());
+            seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
+                    maxChain, pdb, maxAlignseq));
           }
         }
       }
@@ -546,11 +570,8 @@ public class StructureSelectionManager
   private StructureMapping getStructureMapping(SequenceI seq,
           String pdbFile, String targetChainId, StructureFile pdb,
           PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
-          AlignSeq maxAlignseq)
+          AlignSeq maxAlignseq) throws SiftsException
   {
-    String maxChainId = targetChainId;
-    try
-    {
       StructureMapping curChainMapping = siftsClient
               .getSiftsStructureMapping(seq, pdbFile, targetChainId);
       try
@@ -565,15 +586,6 @@ public class StructureSelectionManager
         e.printStackTrace();
       }
       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,

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index e04bbb7..3c2e703 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -360,7 +360,8 @@ public class SiftsClient implements SiftsClientI
       DBRefEntry[] dbRefs = seq.getDBRefs();
       if (dbRefs == null || dbRefs.length < 1)
       {
-        throw new SiftsException("Could not get source DB Ref");
+        throw new SiftsException(
+                "Source DBRef could not be determined. DBRefs might not have been retrieved.");
       }
 
       for (DBRefEntryI dbRef : dbRefs)
@@ -374,6 +375,7 @@ public class SiftsClient implements SiftsClientI
                 && (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT) || dbRef
                         .getSource().equalsIgnoreCase(DBRefSource.PDB)))
         {
+          seq.setSourceDBRef(dbRef);
           return dbRef;
         }
       }
@@ -413,7 +415,8 @@ public class SiftsClient implements SiftsClientI
                 .getMapRegion();
         for (MapRegion mapRegion : mapRegions)
         {
-          accessions.add(mapRegion.getDb().getDbAccessionId());
+          accessions
+                  .add(mapRegion.getDb().getDbAccessionId().toLowerCase());
         }
       }
     }
@@ -464,12 +467,9 @@ public class SiftsClient implements SiftsClientI
             jalview.util.Comparison.GapChars, seq.getSequenceAsString());
     HashMap<Integer, int[]> mapping = new HashMap<Integer, int[]>();
     DBRefEntryI sourceDBRef = seq.getSourceDBRef();
-    if (sourceDBRef == null)
-    {
-      sourceDBRef = getValidSourceDBRef(seq);
-      // TODO ensure sequence start/end is in the same coordinate system and
-      // consistent with the choosen sourceDBRef
-    }
+    sourceDBRef = getValidSourceDBRef(seq);
+    // TODO ensure sequence start/end is in the same coordinate system and
+    // consistent with the choosen sourceDBRef
 
     // set sequence coordinate system - default value is UniProt
     if (sourceDBRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
@@ -752,8 +752,9 @@ public class SiftsClient implements SiftsClientI
 
   private boolean isFoundInSiftsEntry(String accessionId)
   {
+    HashSet<String> siftsDBRefs = getAllMappingAccession();
     return accessionId != null
-            && getAllMappingAccession().contains(accessionId);
+            && siftsDBRefs.contains(accessionId.toLowerCase());
   }
 
   /**