JAL-2679 case-insensitive comparison of query and retrieved accession

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

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index 24d1b95..b2ebb1a 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -203,7 +203,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     try
     {
       /*
-       * get 'dummy' genomic sequence with exon, cds and variation features
+       * get 'dummy' genomic sequence with gene, transcript, 
+       * exon, cds and variation features
        */
       SequenceI genomicSequence = null;
       EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain());
@@ -219,7 +220,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
         /*
          * transfer features to the query sequence
          */
-        SequenceI querySeq = alignment.findName(accId);
+        SequenceI querySeq = alignment.findName(accId, true);
         if (transferFeatures(accId, genomicSequence, querySeq))
         {
 
@@ -861,7 +862,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   {
     String parent = (String) sf.getValue(PARENT);
     // using contains to allow for prefix "gene:", "transcript:" etc
-    if (parent != null && !parent.contains(identifier))
+    if (parent != null
+            && !parent.toUpperCase().contains(identifier.toUpperCase()))
     {
       // this genomic feature belongs to a different transcript
       return false;
@@ -896,7 +898,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     for (SequenceFeature sf : sfs)
     {
       String parent = (String) sf.getValue(PARENT);
-      if (parent != null && parent.equals(parentId))
+      if (parent != null && parent.equalsIgnoreCase(parentId))
       {
         result.add(sf);
       }