Merge commit '326d48e' into HEAD

[jalview.git] / src / jalview / ext / ensembl / EnsemblGene.java

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index 37c787b..84a0824 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -159,8 +159,9 @@ public class EnsemblGene extends EnsemblSeqProxy
   }
 
   /**
-   * Converts a query, which may contain one or more gene or transcript
-   * identifiers, into a non-redundant list of gene identifiers.
+   * Converts a query, which may contain one or more gene, transcript, or
+   * external (to Ensembl) identifiers, into a non-redundant list of gene
+   * identifiers.
    * 
    * @param accessions
    * @return
@@ -171,21 +172,13 @@ public class EnsemblGene extends EnsemblSeqProxy
 
     for (String acc : accessions.split(getAccessionSeparator()))
     {
-      if (isGeneIdentifier(acc))
-      {
-        if (!geneIds.contains(acc))
-        {
-          geneIds.add(acc);
-        }
-      }
-
       /*
-       * if given a transcript id, look up its gene parent
+       * First try lookup as an Ensembl (gene or transcript) identifier
        */
-      else if (isTranscriptIdentifier(acc))
+      String geneId = new EnsemblLookup(getDomain()).getGeneId(acc);
+      if (geneId != null)
       {
-        String geneId = new EnsemblLookup(getDomain()).getParent(acc);
-        if (geneId != null && !geneIds.contains(geneId))
+        if (!geneIds.contains(geneId))
         {
           geneIds.add(geneId);
         }
@@ -212,13 +205,17 @@ public class EnsemblGene extends EnsemblSeqProxy
        */
       else
       {
+        /*
+         * if given a gene or other external name, lookup and fetch 
+         * the corresponding gene for all model organisms 
+         */
         List<String> ids = new EnsemblSymbol(getDomain(), getDbSource(),
-                getDbVersion()).getIds(acc);
-        for (String geneId : ids)
+                getDbVersion()).getGeneIds(acc);
+        for (String id : ids)
         {
-          if (!geneIds.contains(geneId))
+          if (!geneIds.contains(id))
           {
-            geneIds.add(geneId);
+            geneIds.add(id);
           }
         }
       }
@@ -227,30 +224,6 @@ public class EnsemblGene extends EnsemblSeqProxy
   }
 
   /**
-   * Attempts to get Ensembl stable identifiers for model organisms for a gene
-   * name by calling the xrefs symbol REST service to resolve the gene name.
-   * 
-   * @param query
-   * @return
-   */
-  protected String getGeneIdentifiersForName(String query)
-  {
-    List<String> ids = new EnsemblSymbol(getDomain(), getDbSource(),
-            getDbVersion()).getIds(query);
-    if (ids != null)
-    {
-      for (String id : ids)
-      {
-        if (isGeneIdentifier(id))
-        {
-          return id;
-        }
-      }
-    }
-    return null;
-  }
-
-  /**
    * Constructs all transcripts for the gene, as identified by "transcript"
    * features whose Parent is the requested gene. The coding transcript
    * sequences (i.e. with introns omitted) are added to the alignment.