JAL-1705 include stop codons in derived CDS; support ensemblgenomes

[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 6507ff5..cec7a8d 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -40,10 +40,28 @@ public class EnsemblGene extends EnsemblSeqProxy
       EnsemblFeatureType.exon, EnsemblFeatureType.cds,
       EnsemblFeatureType.variation };
 
+  /**
+   * Default constructor (to use rest.ensembl.org)
+   */
+  public EnsemblGene()
+  {
+    super();
+  }
+
+  /**
+   * Constructor given the target domain to fetch data from
+   * 
+   * @param d
+   */
+  public EnsemblGene(String d)
+  {
+    super(d);
+  }
+
   @Override
   public String getDbName()
   {
-    return "ENSEMBL (GENE)";
+    return "ENSEMBL";
   }
 
   @Override
@@ -97,7 +115,7 @@ public class EnsemblGene extends EnsemblSeqProxy
     if (isTranscriptIdentifier(query))
     {
       // we are assuming all transcripts have the same gene parent here
-      query = new EnsemblLookup().getParent(queries[0]);
+      query = new EnsemblLookup(getDomain()).getParent(queries[0]);
       if (query == null)
       {
         return null;
@@ -110,7 +128,7 @@ public class EnsemblGene extends EnsemblSeqProxy
      */
     if (!isGeneIdentifier(query))
     {
-      List<String> geneIds = new EnsemblSymbol().getIds(query);
+      List<String> geneIds = new EnsemblSymbol(getDomain()).getIds(query);
       if (geneIds.isEmpty())
       {
         return null;
@@ -145,7 +163,7 @@ public class EnsemblGene extends EnsemblSeqProxy
    */
   protected String getGeneIdentifiersForName(String query)
   {
-    List<String> ids = new EnsemblSymbol().getIds(query);
+    List<String> ids = new EnsemblSymbol(getDomain()).getIds(query);
     if (ids != null)
     {
       for (String id : ids)
@@ -290,8 +308,9 @@ public class EnsemblGene extends EnsemblSeqProxy
     List<int[]> mapTo = new ArrayList<int[]>();
     mapTo.add(new int[] { 1, transcriptLength });
     MapList mapping = new MapList(mappedFrom, mapTo, 1, 1);
-    new EnsemblCdna().transferFeatures(gene.getSequenceFeatures(),
-            transcript.getDatasetSequence(), mapping, parentId);
+    new EnsemblCdna(getDomain()).transferFeatures(
+            gene.getSequenceFeatures(), transcript.getDatasetSequence(),
+            mapping, parentId);
 
     /*
      * fetch and save cross-references
@@ -301,7 +320,7 @@ public class EnsemblGene extends EnsemblSeqProxy
     /*
      * and finally fetch the protein product and save as a cross-reference
      */
-    new EnsemblCdna().addProteinProduct(transcript);
+    new EnsemblCdna(getDomain()).addProteinProduct(transcript);
 
     return transcript;
   }