git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-2743 fall back to parsing description if chromosome lookup fails;
[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
11322c8
..
cdcfa96
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblGene.java
+++ b/
src/jalview/ext/ensembl/EnsemblGene.java
@@
-166,25
+166,25
@@
public class EnsemblGene extends EnsemblSeqProxy
/**
* Calls the /lookup/id REST service, parses the response for gene
/**
* Calls the /lookup/id REST service, parses the response for gene
- * coordinates, and if successful, adds these to the sequence
+ * coordinates, and if successful, adds these to the sequence. If this fails,
+ * fall back on trying to parse the sequence description in case it is in
+ * Ensembl-gene format e.g. chromosome:GRCh38:17:45051610:45109016:1.
*
* @param seq
* @param geneId
*/
void findGeneLoci(SequenceI seq, String geneId)
{
*
* @param seq
* @param geneId
*/
void findGeneLoci(SequenceI seq, String geneId)
{
- /*
- * if sequence description is in gene loci format, parse this
- * - but try remote lookup anyway as 'better' if available
- */
- parseChromosomeLocations(seq);
-
GeneLociI geneLoci = new EnsemblLookup(getDomain()).getGeneLoci(geneId);
if (geneLoci != null)
{
seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
geneLoci.getChromosomeId(), geneLoci.getMap());
}
GeneLociI geneLoci = new EnsemblLookup(getDomain()).getGeneLoci(geneId);
if (geneLoci != null)
{
seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
geneLoci.getChromosomeId(), geneLoci.getMap());
}
+ else
+ {
+ parseChromosomeLocations(seq);
+ }
}
/**
}
/**