X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;h=3d957f0e88ab36411e713a02cbe93173634f39b8;hb=401715f8745eeee967df8d60549b4c5d7f64530f;hp=0d73a474caff26542b7497998833acbad4b90dc2;hpb=86413dd6b73b097232ee5684c5c13604790317c3;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index 0d73a47..3d957f0 100644
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -23,7 +23,6 @@ package jalview.ext.ensembl;
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GeneLociI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
@@ -56,13 +55,15 @@ public class EnsemblGene extends EnsemblSeqProxy
    * accepts anything as we will attempt lookup of gene or 
    * transcript id or gene name
    */
-  private static final Regex ACCESSION_REGEX = new Regex(".*");
+  private static final Regex ACCESSION_REGEX = Platform.newRegex(".*");
 
   private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
       EnsemblFeatureType.gene, EnsemblFeatureType.transcript,
       EnsemblFeatureType.exon, EnsemblFeatureType.cds,
       EnsemblFeatureType.variation };
 
+  private static final String CHROMOSOME = "chromosome";
+
   /**
    * Default constructor (to use rest.ensembl.org)
    */
@@ -185,7 +186,7 @@ public class EnsemblGene extends EnsemblSeqProxy
     if (geneLoci != null)
     {
       seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
-              geneLoci.getChromosomeId(), geneLoci.getMap());
+              geneLoci.getChromosomeId(), geneLoci.getMapping());
     }
     else
     {
@@ -207,7 +208,7 @@ public class EnsemblGene extends EnsemblSeqProxy
       return false;
     }
     String[] tokens = description.split(":");
-    if (tokens.length == 6 && tokens[0].startsWith(DBRefEntry.CHROMOSOME))
+    if (tokens.length == 6 && tokens[0].startsWith(CHROMOSOME))
     {
       String ref = tokens[1];
       String chrom = tokens[2];
@@ -458,7 +459,7 @@ public class EnsemblGene extends EnsemblSeqProxy
       return;
     }
 
-    MapList geneMapping = loci.getMap();
+    MapList geneMapping = loci.getMapping();
 
     List<int[]> exons = mapping.getFromRanges();
     List<int[]> transcriptLoci = new ArrayList<>();
@@ -577,7 +578,7 @@ public class EnsemblGene extends EnsemblSeqProxy
   @Override
   protected boolean retainFeature(SequenceFeature sf, String accessionId)
   {
-    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+    SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
     String type = sf.getType();
     if (so.isA(type, SequenceOntologyI.GENE))
     {
@@ -624,7 +625,7 @@ public class EnsemblGene extends EnsemblSeqProxy
   {
     return new FeatureSettingsAdapter()
     {
-      SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+      SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
 
       @Override
       public boolean isFeatureDisplayed(String type)