X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FDBRefUtils.java;h=a1f06e5faf993764db1ae985606cfecf99cb1f8e;hb=3ed5c0f91614bb7a3620ec3a968a54bafdbd74ad;hp=424d40bd45f4f83b975e0d0e2eead6682ee19109;hpb=964f27f06912574ac9d0c65c3f741852f48e558a;p=jalview.git

diff --git a/src/jalview/util/DBRefUtils.java b/src/jalview/util/DBRefUtils.java
index 424d40b..a1f06e5 100755
--- a/src/jalview/util/DBRefUtils.java
+++ b/src/jalview/util/DBRefUtils.java
@@ -31,6 +31,7 @@ import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import com.stevesoft.pat.Regex;
 
@@ -59,6 +60,18 @@ public class DBRefUtils
 
     canonicalSourceNameLookup.put("pdb", DBRefSource.PDB);
     canonicalSourceNameLookup.put("ensembl", DBRefSource.ENSEMBL);
+    // Ensembl Gn and Tr are for Ensembl genomic and transcript IDs as served
+    // from ENA.
+    canonicalSourceNameLookup.put("ensembl-tr", DBRefSource.ENSEMBL);
+    canonicalSourceNameLookup.put("ensembl-gn", DBRefSource.ENSEMBL);
+
+    // Make sure we have lowercase entries for all canonical string lookups
+    Set<String> keys = canonicalSourceNameLookup.keySet();
+    for (String k : keys)
+    {
+      canonicalSourceNameLookup.put(k.toLowerCase(),
+              canonicalSourceNameLookup.get(k));
+    }
 
     dasCoordinateSystemsLookup.put("pdbresnum", DBRefSource.PDB);
     dasCoordinateSystemsLookup.put("uniprot", DBRefSource.UNIPROT);
@@ -67,11 +80,14 @@ public class DBRefUtils
   }
 
   /**
+   * Returns those DBRefEntry objects whose source identifier (once converted to
+   * Jalview's canonical form) is in the list of sources to search for. Returns
+   * null if no matches found.
    * 
    * @param dbrefs
-   *          array of DBRef objects to search
+   *          DBRefEntry objects to search
    * @param sources
-   *          String[] array of source DBRef IDs to retrieve
+   *          array of sources to select
    * @return
    */
   public static DBRefEntry[] selectRefs(DBRefEntry[] dbrefs,
@@ -148,8 +164,8 @@ public class DBRefUtils
   }
 
   /**
-   * Returns an array of those references that match the given entry, or null if
-   * no matches. Currently uses a comparator which matches if
+   * Returns a (possibly empty) list of those references that match the given
+   * entry. Currently uses a comparator which matches if
    * <ul>
    * <li>database sources are the same</li>
    * <li>accession ids are the same</li>
@@ -162,34 +178,35 @@ public class DBRefUtils
    *          pattern to match
    * @return
    */
-  public static DBRefEntry[] searchRefs(DBRefEntry[] ref, DBRefEntry entry)
+  public static List<DBRefEntry> searchRefs(DBRefEntry[] ref,
+          DBRefEntry entry)
   {
     return searchRefs(ref, entry,
             matchDbAndIdAndEitherMapOrEquivalentMapList);
   }
 
   /**
-   * Returns an array of those references that match the given accession id
+   * Returns a list of those references that match the given accession id
    * <ul>
    * <li>database sources are the same</li>
    * <li>accession ids are the same</li>
    * <li>both have no mapping, or the mappings are the same</li>
    * </ul>
    * 
-   * @param ref
+   * @param refs
    *          Set of references to search
-   * @param entry
-   *          pattern to match
+   * @param accId
+   *          accession id to match
    * @return
    */
-  public static DBRefEntry[] searchRefs(DBRefEntry[] ref, String accId)
+  public static List<DBRefEntry> searchRefs(DBRefEntry[] refs, String accId)
   {
-    return searchRefs(ref, new DBRefEntry("", "", accId), matchId);
+    return searchRefs(refs, new DBRefEntry("", "", accId), matchId);
   }
 
   /**
-   * Returns an array of those references that match the given entry, according
-   * to the given comparator. Returns null if no matches.
+   * Returns a (possibly empty) list of those references that match the given
+   * entry, according to the given comparator.
    * 
    * @param refs
    *          an array of database references to search
@@ -198,14 +215,14 @@ public class DBRefUtils
    * @param comparator
    * @return
    */
-  static DBRefEntry[] searchRefs(DBRefEntry[] refs, DBRefEntry entry,
+  static List<DBRefEntry> searchRefs(DBRefEntry[] refs, DBRefEntry entry,
           DbRefComp comparator)
   {
+    List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
     if (refs == null || entry == null)
     {
-      return null;
+      return rfs;
     }
-    List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
     for (int i = 0; i < refs.length; i++)
     {
       if (comparator.matches(entry, refs[i]))
@@ -213,7 +230,7 @@ public class DBRefUtils
         rfs.add(refs[i]);
       }
     }
-    return rfs.size() == 0 ? null : rfs.toArray(new DBRefEntry[rfs.size()]);
+    return rfs;
   }
 
   interface DbRefComp
@@ -380,9 +397,9 @@ public class DBRefUtils
   };
 
   /**
-   * accession ID and DB must be identical. Version is ignored. No map on either
-   * or map but no maplist on either or maplist of map on a is equivalent to the
-   * maplist of map on b.
+   * accession ID and DB must be identical, or null on a. Version is ignored. No
+   * map on either or map but no maplist on either or maplist of map on a is
+   * equivalent to the maplist of map on b.
    */
   public static DbRefComp matchDbAndIdAndEitherMapOrEquivalentMapList = new DbRefComp()
   {
@@ -393,8 +410,9 @@ public class DBRefUtils
               && refb.getSource().equals(refa.getSource()))
       {
         // We dont care about version
-        if (refa.getAccessionId() != null && refb.getAccessionId() != null
-                && refb.getAccessionId().equals(refa.getAccessionId()))
+
+        if (refa.getAccessionId() == null
+                || refa.getAccessionId().equals(refb.getAccessionId()))
         {
           if (refa.getMap() == null || refb.getMap() == null)
           {
@@ -406,7 +424,7 @@ public class DBRefUtils
                   || (refb.getMap().getMap() != null
                           && refa.getMap().getMap() != null && (refb
                           .getMap().getMap().equals(refa.getMap().getMap()))))
-          { // getMap().getMap().containsEither(false,refa.getMap().getMap())
+          {
             return true;
           }
         }
@@ -516,7 +534,52 @@ public class DBRefUtils
     {
       return true;
     }
-    return (o1 == null ? o2.equals(o1) : o1.equals(o2));
+    return o1.equals(o2);
+  }
+
+  /**
+   * Selects just the DNA or protein references from a set of references
+   * 
+   * @param selectDna
+   *          if true, select references to 'standard' DNA databases, else to
+   *          'standard' peptide databases
+   * @param refs
+   *          a set of references to select from
+   * @return
+   */
+  public static DBRefEntry[] selectDbRefs(boolean selectDna,
+          DBRefEntry[] refs)
+  {
+    return selectRefs(refs, selectDna ? DBRefSource.DNACODINGDBS
+            : DBRefSource.PROTEINDBS);
+    // could attempt to find other cross
+    // refs here - ie PDB xrefs
+    // (not dna, not protein seq)
+  }
+
+  /**
+   * Returns the (possibly empty) list of those supplied dbrefs which have the
+   * specified source database, with a case-insensitive match of source name
+   * 
+   * @param dbRefs
+   * @param source
+   * @return
+   */
+  public static List<DBRefEntry> searchRefsForSource(DBRefEntry[] dbRefs,
+          String source)
+  {
+    List<DBRefEntry> matches = new ArrayList<DBRefEntry>();
+    if (dbRefs != null && source != null)
+    {
+      for (DBRefEntry dbref : dbRefs)
+      {
+        if (source.equalsIgnoreCase(dbref.getSource()))
+        {
+          matches.add(dbref);
+        }
+      }
+    }
+    return matches;
   }
 
 }