JAL-1705 various refactoring towards Uniprot-to-Ensembl fetching

[jalview.git] / src / jalview / ext / ensembl / EnsemblCdna.java

diff --git a/src/jalview/ext/ensembl/EnsemblCdna.java b/src/jalview/ext/ensembl/EnsemblCdna.java
index 139e44f..f60125b 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/src/jalview/ext/ensembl/EnsemblCdna.java
@@ -1,7 +1,8 @@
 package jalview.ext.ensembl;
 
 import jalview.datamodel.SequenceFeature;
-import jalview.io.gff.SequenceOntology;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
 
 import java.util.List;
 
@@ -9,8 +10,12 @@ import com.stevesoft.pat.Regex;
 
 public class EnsemblCdna extends EnsemblSeqProxy
 {
+  // TODO modify to accept other species e.g. ENSMUSPnnn
+  private static final Regex ACCESSION_REGEX = new Regex(
+          "(ENST|ENSG|CCDS)[0-9.]{3,}$");
+  
   /*
-   * fetch exon features on genomic sequence (to identify the cdnaregions)
+   * fetch exon features on genomic sequence (to identify the cdna regions)
    * and cds and variation features (to retain)
    */
   private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
@@ -37,7 +42,7 @@ public class EnsemblCdna extends EnsemblSeqProxy
   @Override
   public Regex getAccessionValidator()
   {
-    return new Regex("((ENST|ENSG|CCDS)[0-9.]{3,})");
+    return ACCESSION_REGEX;
   }
 
   @Override
@@ -68,8 +73,8 @@ public class EnsemblCdna extends EnsemblSeqProxy
   @Override
   protected boolean identifiesSequence(SequenceFeature sf, String accId)
   {
-    if (SequenceOntology.getInstance().isA(sf.getType(),
-            SequenceOntology.EXON))
+    if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
+            SequenceOntologyI.EXON))
     {
       String parentFeature = (String) sf.getValue(PARENT);
       if (("transcript:" + accId).equals(parentFeature))