Merge branch 'bug/JAL-3288splitFrameMenusJava11' into develop

[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 36b19e2..9c7ce63 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -23,7 +23,6 @@ package jalview.ext.ensembl;
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GeneLociI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
@@ -51,8 +50,6 @@ 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
@@ -64,6 +61,8 @@ public class EnsemblGene extends EnsemblSeqProxy
       EnsemblFeatureType.exon, EnsemblFeatureType.cds,
       EnsemblFeatureType.variation };
 
+  private static final String CHROMOSOME = "chromosome";
+
   /**
    * Default constructor (to use rest.ensembl.org)
    */
@@ -189,7 +188,7 @@ public class EnsemblGene extends EnsemblSeqProxy
     if (geneLoci != null)
     {
       seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
-              geneLoci.getChromosomeId(), geneLoci.getMap());
+              geneLoci.getChromosomeId(), geneLoci.getMapping());
     }
     else
     {
@@ -211,7 +210,7 @@ public class EnsemblGene extends EnsemblSeqProxy
       return false;
     }
     String[] tokens = description.split(":");
-    if (tokens.length == 6 && tokens[0].startsWith(DBRefEntry.CHROMOSOME))
+    if (tokens.length == 6 && tokens[0].startsWith(CHROMOSOME))
     {
       String ref = tokens[1];
       String chrom = tokens[2];
@@ -368,7 +367,7 @@ 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 +398,7 @@ 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);
@@ -462,7 +461,7 @@ public class EnsemblGene extends EnsemblSeqProxy
       return;
     }
 
-    MapList geneMapping = loci.getMap();
+    MapList geneMapping = loci.getMapping();
 
     List<int[]> exons = mapping.getFromRanges();
     List<int[]> transcriptLoci = new ArrayList<>();
@@ -488,7 +487,7 @@ public class EnsemblGene extends EnsemblSeqProxy
    */
   protected String getTranscriptId(SequenceFeature feature)
   {
-    return (String) feature.getValue("transcript_id");
+    return (String) feature.getValue(JSON_ID);
   }
 
   /**
@@ -510,7 +509,7 @@ 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);
@@ -561,9 +560,8 @@ public class EnsemblGene extends EnsemblSeqProxy
             .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))
       {
         result.add(sf);
       }
@@ -590,7 +588,7 @@ 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;
       }