Merge hack/JAL-1617 fake DBRef to develop

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 54bdf20..0581845 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -193,4 +193,9 @@ public class DBRefEntry
     return ((source != null) ? source : "") + ":"
             + ((accessionId != null) ? accessionId : "");
   }
+
+  public String toString()
+  {
+    return getSrcAccString();
+  }
 }

diff --git a/src/jalview/datamodel/DBRefSource.java b/src/jalview/datamodel/DBRefSource.java
index b1824f7..6982594 100755 (executable)
--- a/src/jalview/datamodel/DBRefSource.java
+++ b/src/jalview/datamodel/DBRefSource.java
@@ -38,12 +38,15 @@ public class DBRefSource
   /**
    * UNIPROT Entry Name
    */
-  public static String UP_NAME = "UNIPROT_NAME";
+  public static String UP_NAME = "UNIPROT_NAME".toUpperCase();
 
   /**
    * Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
    */
-  public static final String UNIPROTKB = "UniProtKB/TrEMBL";
+  public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase();
+  
+  public static final String EMBLCDSProduct = "EMBLCDSProtein"
+          .toUpperCase();
 
   /**
    * PDB Entry Code
@@ -73,7 +76,7 @@ public class DBRefSource
   /**
    * GeneDB ID
    */
-  public static final String GENEDB = "GeneDB";
+  public static final String GENEDB = "GeneDB".toUpperCase();
 
   /**
    * List of databases whose sequences might have coding regions annotated
@@ -85,10 +88,10 @@ public class DBRefSource
   { EMBLCDS, GENEDB };
 
   public static final String[] PROTEINDBS =
-  { UNIPROT, PDB, UNIPROTKB };
+  { UNIPROT, PDB, UNIPROTKB, EMBLCDSProduct };
 
   public static final String[] PROTEINSEQ =
-  { UNIPROT, UNIPROTKB };
+  { UNIPROT, UNIPROTKB, EMBLCDSProduct };
 
   public static final String[] PROTEINSTR =
   { PDB };

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index d501ef1..fc57b27 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -590,8 +590,10 @@ public class EmblEntry
       }
     }
     Sequence product = null;
+    DBRefEntry protEMBLCDS = null;
     exon = adjustForPrStart(prstart, exon);
-
+    boolean noProteinDbref=true;
+    
     if (prseq != null && prname != null && prid != null)
     {
       // extract proteins.
@@ -669,8 +671,12 @@ public class EmblEntry
           if (product != null)
           {
             product.addDBRef(pcdnaref);
-          }
-
+            protEMBLCDS = new DBRefEntry(pcdnaref);
+            protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
+            product.addDBRef(protEMBLCDS);
+            
+          }     
+          
         }
       }
       // add cds feature to dna seq - this may include the stop codon
@@ -724,6 +730,7 @@ public class EmblEntry
                               + ref.getAccessionId());
             }
           }
+          noProteinDbref = false;
         }
         if (product != null)
         {
@@ -746,6 +753,33 @@ public class EmblEntry
         }
         dna.addDBRef(ref);
       }
+      if (noProteinDbref && product != null)
+      {
+        // add protein coding reference to dna sequence so xref matches
+        if (protEMBLCDS == null)
+        {
+          protEMBLCDS = new DBRefEntry();
+          protEMBLCDS.setAccessionId(prid);
+          protEMBLCDS.setSource(DBRefSource.EMBLCDSProduct);
+          protEMBLCDS.setVersion(getVersion());
+          protEMBLCDS
+                  .setMap(new Mapping(product, map.getMap().getInverse()));
+        }
+        product.addDBRef(protEMBLCDS);
+          
+        // Add converse mapping reference
+        if (map != null)
+        {
+          Mapping pmap = new Mapping(product, protEMBLCDS.getMap().getMap()
+                  .getInverse());
+          DBRefEntry ncMap = new DBRefEntry(protEMBLCDS);
+          ncMap.setMap(pmap);
+          if (map.getTo() != null)
+          {
+            dna.addDBRef(ncMap);
+          }
+        }
+      }
     }
   }
 

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 9a4ffc8..8163f05 100755 (executable)
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -20,9 +20,15 @@
  */
 package jalview.util;
 
-import java.util.*;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Map;
+import java.util.Vector;
 
 public class DBRefUtils
 {
@@ -48,8 +54,8 @@ public class DBRefUtils
     {
       return dbrefs;
     }
-    Hashtable srcs = new Hashtable();
-    Vector res = new Vector();
+    Map<String, Integer> srcs = new HashMap<String, Integer>();
+    ArrayList<DBRefEntry> res = new ArrayList<DBRefEntry>();
 
     for (int i = 0; i < sources.length; i++)
     {
@@ -59,18 +65,14 @@ public class DBRefUtils
     {
       if (srcs.containsKey(dbrefs[i].getSource()))
       {
-        res.addElement(dbrefs[i]);
+        res.add(dbrefs[i]);
       }
     }
 
     if (res.size() > 0)
     {
       DBRefEntry[] reply = new DBRefEntry[res.size()];
-      for (int i = 0; i < res.size(); i++)
-      {
-        reply[i] = (DBRefEntry) res.elementAt(i);
-      }
-      return reply;
+      return res.toArray(reply);
     }
     res = null;
     // there are probable memory leaks in the hashtable!
@@ -169,7 +171,9 @@ public class DBRefUtils
           DbRefComp comparator)
   {
     if (ref == null || entry == null)
+    {
       return null;
+    }
     Vector rfs = new Vector();
     for (int i = 0; i < ref.length; i++)
     {
@@ -303,6 +307,7 @@ public class DBRefUtils
         {
           if ((refa.getMap() == null && refb.getMap() == null)
                   || (refa.getMap() != null && refb.getMap() != null))
+          {
             if ((refb.getMap().getMap() == null && refa.getMap().getMap() == null)
                     || (refb.getMap().getMap() != null
                             && refa.getMap().getMap() != null && refb
@@ -311,6 +316,7 @@ public class DBRefUtils
             {
               return true;
             }
+          }
         }
       }
       return false;

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index afaadbb..f58ead5 100644 (file)
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -50,6 +50,7 @@ public class DbRefFetcherTest
   @BeforeClass
   public static void setUpBeforeClass() throws Exception
   {
+    jalview.bin.Cache.initLogger();
   }
 
   /**
@@ -102,13 +103,33 @@ public class DbRefFetcherTest
   {
     String retrievalId = "CAA23748"; // "V00488";
     DbSourceProxy embl = new SequenceFetcher().getSourceProxy(DBRefSource.EMBL).get(0);
-    assertNotNull("Couldn't find the EMBL retrieval client",embl);
+    assertNotNull("Couldn't find the EMBL retrieval client", embl);
+    verifyProteinNucleotideXref(retrievalId, embl);
+  }
+
+  @Test
+  public void testEmblCDSUniprotProductRecovery() throws Exception
+  {
+    String retrievalId = "AAH29712";
+    DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
+            DBRefSource.EMBLCDS).get(0);
+    assertNotNull("Couldn't find the EMBL retrieval client", embl);
+    verifyProteinNucleotideXref(retrievalId, embl);
+  }
+
+  private void verifyProteinNucleotideXref(String retrievalId,
+          DbSourceProxy embl) throws Exception
+  {
     AlignmentI alsq = embl.getSequenceRecords(retrievalId);
     assertNotNull("Couldn't find the EMBL record " + retrievalId, alsq);
     assertEquals("Didn't retrieve right number of records", 1, alsq.getHeight());
     DBRefEntry[] dr = DBRefUtils.selectRefs(alsq.getSequenceAt(0).getDBRef(), DBRefSource.PROTEINSEQ);
     assertNotNull(dr);
     assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
+    assertEquals("Expected cross refernce map to be one amino acid", dr[0]
+            .getMap().getMappedWidth(), 1);
+    assertEquals("Expected local refernce map to be 3 nucleotides", dr[0]
+            .getMap().getWidth(), 3);
     AlignmentI sprods = CrossRef.findXrefSequences(alsq.getSequencesArray(), true, dr[0].getSource(), alsq.getDataset());
     assertNotNull(
             "Couldn't recover cross reference sequence from dataset. Was it ever added ?",