JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

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

diff --git a/src/jalview/ext/ensembl/EnsemblProtein.java b/src/jalview/ext/ensembl/EnsemblProtein.java
index 1554a0b..f586ed6 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblProtein.java
+++ b/src/jalview/ext/ensembl/EnsemblProtein.java
@@ -22,7 +22,10 @@ package jalview.ext.ensembl;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.Platform;
 
+import java.util.ArrayList;
 import java.util.List;
 
 import com.stevesoft.pat.Regex;
@@ -40,8 +43,7 @@ public class EnsemblProtein extends EnsemblSeqProxy
    * or ENSMUSP or similar for other species
    * or CCDSnnnnn.nn with at least 3 digits
    */
-  private static final Regex ACCESSION_REGEX = new Regex(
-          "(ENS([A-Z]{3}|)P[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
+  private static Regex ACCESSION_REGEX;
 
   /**
    * Default constructor (to use rest.ensembl.org)
@@ -108,15 +110,20 @@ public class EnsemblProtein extends EnsemblSeqProxy
   }
 
   @Override
-  protected boolean identifiesSequence(SequenceFeature sf, String accId)
+  protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
+          String accId)
   {
-    // not applicable - protein sequence is not a 'subset' of genomic sequence
-    return false;
+    return new ArrayList<>();
   }
 
   @Override
   public Regex getAccessionValidator()
   {
+    if (ACCESSION_REGEX == null)
+    {
+      ACCESSION_REGEX = Platform.newRegex(
+              "(ENS([A-Z]{3}|)P[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)", null);
+    }
     return ACCESSION_REGEX;
   }