JAL-3210 Barebones gradle/buildship/eclipse. See README

[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 63a6a6c..0d73a47 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -56,7 +56,7 @@ public class EnsemblGene extends EnsemblSeqProxy
    * accepts anything as we will attempt lookup of gene or 
    * transcript id or gene name
    */
-  private static Regex ACCESSION_REGEX;
+  private static final Regex ACCESSION_REGEX = new Regex(".*");
 
   private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
       EnsemblFeatureType.gene, EnsemblFeatureType.transcript,
@@ -577,7 +577,7 @@ public class EnsemblGene extends EnsemblSeqProxy
   @Override
   protected boolean retainFeature(SequenceFeature sf, String accessionId)
   {
-    SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
+    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
     String type = sf.getType();
     if (so.isA(type, SequenceOntologyI.GENE))
     {
@@ -606,10 +606,6 @@ public class EnsemblGene extends EnsemblSeqProxy
   @Override
   public Regex getAccessionValidator()
   {
-    if (ACCESSION_REGEX == null)
-    {
-      ACCESSION_REGEX = Platform.newRegex(".*", null);
-    }
     return ACCESSION_REGEX;
   }
 
@@ -628,7 +624,7 @@ public class EnsemblGene extends EnsemblSeqProxy
   {
     return new FeatureSettingsAdapter()
     {
-      SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
+      SequenceOntologyI so = SequenceOntologyFactory.getInstance();
 
       @Override
       public boolean isFeatureDisplayed(String type)