X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;h=ae85b453a1180397cd245bb46b85c29d8ed9c911;hb=5d60cda87940311cfff2679e6f0e96890d3e1fd6;hp=ac756fc553e282f2bd262299720b5a3b145f694f;hpb=c904a8042a8fb0894738c98fc67459766532571d;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index ac756fc..ae85b45 100644
--- 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,
@@ -151,7 +151,7 @@ public class EnsemblGene extends EnsemblSeqProxy
       {
         continue;
       }
-      
+
       if (geneAlignment.getHeight() == 1)
       {
         // ensure id has 'correct' case for the Ensembl identifier
@@ -318,8 +318,8 @@ public class EnsemblGene extends EnsemblSeqProxy
         SequenceOntologyI.NMD_TRANSCRIPT_VARIANT,
         SequenceOntologyI.TRANSCRIPT, SequenceOntologyI.EXON,
         SequenceOntologyI.CDS };
-    List<SequenceFeature> sfs = gene.getFeatures().getFeaturesByOntology(
-            soTerms);
+    List<SequenceFeature> sfs = gene.getFeatures()
+            .getFeaturesByOntology(soTerms);
     for (SequenceFeature sf : sfs)
     {
       gene.deleteFeature(sf);
@@ -469,8 +469,9 @@ public class EnsemblGene extends EnsemblSeqProxy
       transcriptLoci.add(geneMapping.locateInTo(exon[0], exon[1]));
     }
 
-    List<int[]> transcriptRange = Arrays.asList(new int[] {
-        transcript.getStart(), transcript.getEnd() });
+    List<int[]> transcriptRange = Arrays
+            .asList(new int[]
+            { transcript.getStart(), transcript.getEnd() });
     MapList mapList = new MapList(transcriptRange, transcriptLoci, 1, 1);
 
     transcript.setGeneLoci(loci.getSpeciesId(), loci.getAssemblyId(),
@@ -578,7 +579,7 @@ 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 +626,7 @@ public class EnsemblGene extends EnsemblSeqProxy
   {
     return new FeatureSettingsAdapter()
     {
-      SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+      SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
 
       @Override
       public boolean isFeatureHidden(String type)