JAL-3193 removal of rest.ensemblgenomes.org

[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 7648536..0da3a29 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -70,16 +70,6 @@ public class EnsemblGene extends EnsemblSeqProxy
     super();
   }
 
-  /**
-   * Constructor given the target domain to fetch data from
-   * 
-   * @param d
-   */
-  public EnsemblGene(String d)
-  {
-    super(d);
-  }
-
   @Override
   public String getDbName()
   {
@@ -183,7 +173,7 @@ public class EnsemblGene extends EnsemblSeqProxy
    */
   void findGeneLoci(SequenceI seq, String geneId)
   {
-    GeneLociI geneLoci = new EnsemblLookup(getDomain()).getGeneLoci(geneId);
+    GeneLociI geneLoci = new EnsemblLookup().getGeneLoci(geneId);
     if (geneLoci != null)
     {
       seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
@@ -250,7 +240,7 @@ public class EnsemblGene extends EnsemblSeqProxy
       /*
        * First try lookup as an Ensembl (gene or transcript) identifier
        */
-      String geneId = new EnsemblLookup(getDomain()).getGeneId(acc);
+      String geneId = new EnsemblLookup().getGeneId(acc);
       if (geneId != null)
       {
         if (!geneIds.contains(geneId))
@@ -264,8 +254,8 @@ public class EnsemblGene extends EnsemblSeqProxy
          * 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()).getGeneIds(acc);
+        List<String> ids = new EnsemblSymbol(getDbSource(), getDbVersion())
+                .getGeneIds(acc);
         for (String id : ids)
         {
           if (!geneIds.contains(id))
@@ -423,7 +413,7 @@ public class EnsemblGene extends EnsemblSeqProxy
     List<int[]> mapTo = new ArrayList<>();
     mapTo.add(new int[] { 1, transcriptLength });
     MapList mapping = new MapList(mappedFrom, mapTo, 1, 1);
-    EnsemblCdna cdna = new EnsemblCdna(getDomain());
+    EnsemblCdna cdna = new EnsemblCdna();
     cdna.transferFeatures(gene.getFeatures().getPositionalFeatures(),
             transcript.getDatasetSequence(), mapping, parentId);