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

diff --git a/src/jalview/ext/ensembl/EnsemblFeatures.java b/src/jalview/ext/ensembl/EnsemblFeatures.java
index 7570822..cb6f548 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblFeatures.java
+++ b/src/jalview/ext/ensembl/EnsemblFeatures.java
@@ -82,7 +82,7 @@ class EnsemblFeatures extends EnsemblRestClient
   public AlignmentI getSequenceRecords(String query) throws IOException
   {
     // TODO: use a vararg String... for getSequenceRecords instead?
-    List<String> queries = new ArrayList<String>();
+    List<String> queries = new ArrayList<>();
     queries.add(query);
     FileParse fp = getSequenceReader(queries);
     if (fp == null || !fp.isValid())
@@ -109,9 +109,17 @@ class EnsemblFeatures extends EnsemblRestClient
     urlstring.append("?content-type=text/x-gff3");
 
     /*
+     * specify object_type=gene in case is shared by transcript and/or protein;
+     * currently only fetching features for gene sequences;
+     * refactor in future if needed to fetch for transcripts
+     */
+    urlstring.append("&").append(OBJECT_TYPE).append("=")
+            .append(OBJECT_TYPE_GENE);
+
+    /*
      * specify  features to retrieve
      * @see http://rest.ensembl.org/documentation/info/overlap_id
-     * could make the list a configurable entry in jalview.properties
+     * could make the list a configurable entry in .jalview_properties
      */
     for (EnsemblFeatureType feature : featuresWanted)
     {

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index 919134c..c8b59da 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -413,7 +413,7 @@ 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 +452,7 @@ 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 +479,7 @@ 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;
       }

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);
       }

diff --git a/test/jalview/ext/ensembl/EnsemblCdnaTest.java b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
index 6611e05..779962c 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblCdnaTest.java
+++ b/test/jalview/ext/ensembl/EnsemblCdnaTest.java
@@ -228,6 +228,9 @@ public class EnsemblCdnaTest
     sf.setValue("Parent", "transcript:" + accId);
     assertTrue(testee.retainFeature(sf, accId));
 
+    // test is not case-sensitive
+    assertTrue(testee.retainFeature(sf, accId.toLowerCase()));
+
     // feature with wrong parent is not retained
     sf.setValue("Parent", "transcript:XYZ");
     assertFalse(testee.retainFeature(sf, accId));

diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java
index 5920b89..1b1a2b4 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblGeneTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java
@@ -173,7 +173,8 @@ public class EnsemblGeneTest
     // NMD_transcript_variant treated like transcript in Ensembl
     SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
             22000, 22500, 0f, null);
-    sf3.setValue("Parent", "gene:" + geneId);
+    // id matching should not be case-sensitive
+    sf3.setValue("Parent", "gene:" + geneId.toLowerCase());
     sf3.setValue("transcript_id", "transcript3");
     genomic.addSequenceFeature(sf3);
 
@@ -259,6 +260,9 @@ public class EnsemblGeneTest
     sf.setValue("ID", "gene:" + accId);
     assertTrue(testee.identifiesSequence(sf, accId));
 
+    // test is not case-sensitive
+    assertTrue(testee.identifiesSequence(sf, accId.toLowerCase()));
+
     // transcript not valid:
     sf = new SequenceFeature("transcript", "", 1, 2, 0f, null);
     sf.setValue("ID", "gene:" + accId);