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JAL-2999 release date for 2.10.4b1 set for 27th May 2018
[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)
{
}
if (geneAlignment.getHeight() == 1)
{
+ // ensure id has 'correct' case for the Ensembl identifier
+ geneId = geneAlignment.getSequenceAt(0).getName();
getTranscripts(geneAlignment, geneId);
}
if (al == null)
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);
for (SequenceFeature sf : sfs)
{
String parent = (String) sf.getValue(PARENT);
- if (parentIdentifier.equals(parent))
+ if (parentIdentifier.equalsIgnoreCase(parent))
{
transcriptFeatures.add(sf);
}
{
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");
{
// 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;
}
{
return true;
}
@@
-479,7
+481,7
@@
public class EnsemblGene extends EnsemblSeqProxy
if (isTranscript(type))
{
String parent = (String) sf.getValue(PARENT);
if (isTranscript(type))
{
String parent = (String) sf.getValue(PARENT);
- if (!(GENE_PREFIX + accessionId).equals(parent))
+ if (!(GENE_PREFIX + accessionId).equalsIgnoreCase(parent))
{
return false;
}
{
return false;
}