From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 9 Aug 2017 19:00:09 +0000 (+0100)
Subject: Merge commit '326d48e' into HEAD
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2Ffeatures%2FJAL-2253ensemblGenomes;p=jalview.git

Merge commit '326d48e' into HEAD
---

b342c421914723ac1b3403280cb8bc346011326e
diff --cc src/jalview/ext/ensembl/EnsemblGene.java
index 37c787b,902f745..84a0824
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@@ -190,35 -183,19 +183,39 @@@ public class EnsemblGene extends Ensemb
            geneIds.add(geneId);
          }
        }
 +      else if (isProteinIdentifier(acc))
 +      {
 +        String tscriptId = new EnsemblLookup(getDomain()).getParent(acc);
 +        if (tscriptId != null)
 +        {
 +          String geneId = new EnsemblLookup(getDomain())
 +                  .getParent(tscriptId);
 +
 +          if (geneId != null && !geneIds.contains(geneId))
 +          {
 +            geneIds.add(geneId);
 +          }
 +        }
 +        // NOTE - acc is lost if it resembles an ENS.+ ID but isn't actually
 +        // resolving to one... e.g. ENSMICP00000009241
 +      }
 +      /*
 +       * if given a gene or other external name, lookup and fetch 
 +       * the corresponding gene for all model organisms 
 +       */
        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);
            }
          }
        }
diff --cc src/jalview/ext/ensembl/EnsemblRestClient.java
index 2437588,e315dc1..4c4ba76
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@@ -114,42 -102,6 +112,43 @@@ abstract class EnsemblRestClient extend
      setDomain(d);
    }
  
++<<<<<<< HEAD
 +  /**
 +   * Answers true if the query matches the regular expression pattern for an
 +   * Ensembl transcript stable identifier
 +   * 
 +   * @param query
 +   * @return
 +   */
 +  public boolean isTranscriptIdentifier(String query)
 +  {
 +    return query == null ? false : TRANSCRIPT_REGEX.search(query);
 +  }
 +
 +  /**
 +   * Answers true if the query matches the regular expression pattern for an
 +   * Ensembl protein stable identifier
 +   * 
 +   * @param query
 +   * @return
 +   */
 +  public boolean isProteinIdentifier(String query)
 +  {
 +    return query == null ? false : PROTEIN_REGEX.search(query);
 +  }
 +
 +  /**
 +   * Answers true if the query matches the regular expression pattern for an
 +   * Ensembl gene stable identifier
 +   * 
 +   * @param query
 +   * @return
 +   */
 +  public boolean isGeneIdentifier(String query)
 +  {
 +    return query == null ? false : GENE_REGEX.search(query);
 +  }
 +
    @Override
    public boolean queryInProgress()
    {