Merge branch 'bug/JAL-3072scrollThread' into merge/JAL-3072_3073

[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 7e6f653..7648536 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -51,8 +51,6 @@ import com.stevesoft.pat.Regex;
  */
 public class EnsemblGene extends EnsemblSeqProxy
 {
-  private static final String GENE_PREFIX = "gene:";
-
   /*
    * accepts anything as we will attempt lookup of gene or 
    * transcript id or gene name
@@ -368,7 +366,7 @@ public class EnsemblGene extends EnsemblSeqProxy
      * look for exon features of the transcript, failing that for CDS
      * (for example ENSG00000124610 has 1 CDS but no exon features)
      */
-    String parentId = "transcript:" + accId;
+    String parentId = accId;
     List<SequenceFeature> splices = findFeatures(gene,
             SequenceOntologyI.EXON, parentId);
     if (splices.isEmpty())
@@ -399,7 +397,7 @@ public class EnsemblGene extends EnsemblSeqProxy
      * Ensembl has gene name as transcript Name
      * EnsemblGenomes doesn't, but has a url-encoded description field
      */
-    String description = (String) transcriptFeature.getValue(NAME);
+    String description = transcriptFeature.getDescription();
     if (description == null)
     {
       description = (String) transcriptFeature.getValue(DESCRIPTION);
@@ -488,7 +486,7 @@ public class EnsemblGene extends EnsemblSeqProxy
    */
   protected String getTranscriptId(SequenceFeature feature)
   {
-    return (String) feature.getValue("transcript_id");
+    return (String) feature.getValue(JSON_ID);
   }
 
   /**
@@ -510,7 +508,7 @@ public class EnsemblGene extends EnsemblSeqProxy
   {
     List<SequenceFeature> transcriptFeatures = new ArrayList<>();
 
-    String parentIdentifier = GENE_PREFIX + accId;
+    String parentIdentifier = accId;
 
     List<SequenceFeature> sfs = geneSequence.getFeatures()
             .getFeaturesByOntology(SequenceOntologyI.TRANSCRIPT);
@@ -548,23 +546,26 @@ public class EnsemblGene extends EnsemblSeqProxy
   }
 
   /**
-   * Answers true for a feature of type 'gene' (or a sub-type of gene in the
-   * Sequence Ontology), whose ID is the accession we are retrieving
+   * Answers a list of sequence features (if any) whose type is 'gene' (or a
+   * subtype of gene in the Sequence Ontology), and whose ID is the accession we
+   * are retrieving
    */
   @Override
-  protected boolean identifiesSequence(SequenceFeature sf, String accId)
+  protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
+          String accId)
   {
-    if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
-            SequenceOntologyI.GENE))
+    List<SequenceFeature> result = new ArrayList<>();
+    List<SequenceFeature> sfs = seq.getFeatures()
+            .getFeaturesByOntology(SequenceOntologyI.GENE);
+    for (SequenceFeature sf : sfs)
     {
-      // NB features as gff use 'ID'; rest services return as 'id'
-      String id = (String) sf.getValue("ID");
-      if ((GENE_PREFIX + accId).equalsIgnoreCase(id))
+      String id = (String) sf.getValue(JSON_ID);
+      if (accId.equalsIgnoreCase(id))
       {
-        return true;
+        result.add(sf);
       }
     }
-    return false;
+    return result;
   }
 
   /**
@@ -586,7 +587,7 @@ public class EnsemblGene extends EnsemblSeqProxy
     if (isTranscript(type))
     {
       String parent = (String) sf.getValue(PARENT);
-      if (!(GENE_PREFIX + accessionId).equalsIgnoreCase(parent))
+      if (!accessionId.equalsIgnoreCase(parent))
       {
         return false;
       }
@@ -595,17 +596,6 @@ public class EnsemblGene extends EnsemblSeqProxy
   }
 
   /**
-   * Answers false. This allows an optimisation - a single 'gene' feature is all
-   * that is needed to identify the positions of the gene on the genomic
-   * sequence.
-   */
-  @Override
-  protected boolean isSpliceable()
-  {
-    return false;
-  }
-
-  /**
    * Override to do nothing as Ensembl doesn't return a protein sequence for a
    * gene identifier
    */