Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' 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 ac756fc..e832eff 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -55,7 +55,7 @@ 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,
@@ -578,7 +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))
     {
@@ -625,7 +625,7 @@ public class EnsemblGene extends EnsemblSeqProxy
   {
     return new FeatureSettingsAdapter()
     {
-      SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+      SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
 
       @Override
       public boolean isFeatureHidden(String type)