JAL-2945 resolve model as PDB file. Need to verify behaviour with multiple model...

[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 919134c..0d5fc26 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -152,6 +152,8 @@ public class EnsemblGene extends EnsemblSeqProxy
       }
       if (geneAlignment.getHeight() == 1)
       {
+        // ensure id has 'correct' case for the Ensembl identifier
+        geneId = geneAlignment.getSequenceAt(0).getName();
         getTranscripts(geneAlignment, geneId);
       }
       if (al == null)
@@ -413,7 +415,7 @@ public class EnsemblGene extends EnsemblSeqProxy
     for (SequenceFeature sf : sfs)
     {
       String parent = (String) sf.getValue(PARENT);
-      if (parentIdentifier.equals(parent))
+      if (parentIdentifier.equalsIgnoreCase(parent))
       {
         transcriptFeatures.add(sf);
       }
@@ -452,7 +454,7 @@ public class EnsemblGene extends EnsemblSeqProxy
     {
       // NB features as gff use 'ID'; rest services return as 'id'
       String id = (String) sf.getValue("ID");
-      if ((GENE_PREFIX + accId).equals(id))
+      if ((GENE_PREFIX + accId).equalsIgnoreCase(id))
       {
         return true;
       }
@@ -479,7 +481,7 @@ public class EnsemblGene extends EnsemblSeqProxy
     if (isTranscript(type))
     {
       String parent = (String) sf.getValue(PARENT);
-      if (!(GENE_PREFIX + accessionId).equals(parent))
+      if (!(GENE_PREFIX + accessionId).equalsIgnoreCase(parent))
       {
         return false;
       }