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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
{
/*
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());
*/
SequenceI genomicSequence = null;
EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain());
@@
-219,7
+220,7
@@
public abstract class EnsemblSeqProxy extends EnsemblRestClient
/*
* transfer features to the query sequence
*/
/*
* transfer features to the query sequence
*/
- SequenceI querySeq = alignment.findName(accId);
+ SequenceI querySeq = alignment.findName(accId, true);
if (transferFeatures(accId, genomicSequence, querySeq))
{
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
{
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;
{
// 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);
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);
}
{
result.add(sf);
}