JAL-2679 use object_type=Transcript for lookup of Parent for Protein

[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 50dfa90..919134c 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -98,6 +98,12 @@ public class EnsemblGene extends EnsemblSeqProxy
     return EnsemblSeqType.GENOMIC;
   }
 
+  @Override
+  protected String getObjectType()
+  {
+    return OBJECT_TYPE_GENE;
+  }
+
   /**
    * Returns an alignment containing the gene(s) for the given gene or
    * transcript identifier, or external identifier (e.g. Uniprot id). If given a
@@ -170,7 +176,7 @@ public class EnsemblGene extends EnsemblSeqProxy
    */
   List<String> getGeneIds(String accessions)
   {
-    List<String> geneIds = new ArrayList<String>();
+    List<String> geneIds = new ArrayList<>();
 
     for (String acc : accessions.split(getAccessionSeparator()))
     {
@@ -305,7 +311,7 @@ public class EnsemblGene extends EnsemblSeqProxy
     int transcriptLength = 0;
     final char[] geneChars = gene.getSequence();
     int offset = gene.getStart(); // to convert to 0-based positions
-    List<int[]> mappedFrom = new ArrayList<int[]>();
+    List<int[]> mappedFrom = new ArrayList<>();
 
     for (SequenceFeature sf : splices)
     {
@@ -347,7 +353,7 @@ public class EnsemblGene extends EnsemblSeqProxy
      * transfer features to the new sequence; we use EnsemblCdna to do this,
      * to filter out unwanted features types (see method retainFeature)
      */
-    List<int[]> mapTo = new ArrayList<int[]>();
+    List<int[]> mapTo = new ArrayList<>();
     mapTo.add(new int[] { 1, transcriptLength });
     MapList mapping = new MapList(mappedFrom, mapTo, 1, 1);
     EnsemblCdna cdna = new EnsemblCdna(getDomain());
@@ -395,7 +401,7 @@ public class EnsemblGene extends EnsemblSeqProxy
   protected List<SequenceFeature> getTranscriptFeatures(String accId,
           SequenceI geneSequence)
   {
-    List<SequenceFeature> transcriptFeatures = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> transcriptFeatures = new ArrayList<>();
 
     String parentIdentifier = GENE_PREFIX + accId;
 
@@ -444,7 +450,8 @@ public class EnsemblGene extends EnsemblSeqProxy
     if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
             SequenceOntologyI.GENE))
     {
-      String id = (String) sf.getValue(ID);
+      // NB features as gff use 'ID'; rest services return as 'id'
+      String id = (String) sf.getValue("ID");
       if ((GENE_PREFIX + accId).equals(id))
       {
         return true;