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Merge branch 'feature/JAL-3187linkedFeatures' into feature/JAL-3251biotypedMappings
[jalview.git]
/
src
/
jalview
/
ext
/
ensembl
/
EnsemblSequenceFetcher.java
diff --git
a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
index
4da0e3c
..
7454eb6
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
+++ b/
src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
@@
-42,7
+42,8
@@
abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
// domain properties default values:
protected static final String DEFAULT_ENSEMBL_BASEURL = "https://rest.ensembl.org";
// domain properties default values:
protected static final String DEFAULT_ENSEMBL_BASEURL = "https://rest.ensembl.org";
- protected static final String DEFAULT_ENSEMBL_GENOMES_BASEURL = "https://rest.ensemblgenomes.org";
+ // ensemblgenomes REST service merged to ensembl 9th April 2019
+ protected static final String DEFAULT_ENSEMBL_GENOMES_BASEURL = DEFAULT_ENSEMBL_BASEURL;
/*
* accepts ENSG/T/E/P with 11 digits
/*
* accepts ENSG/T/E/P with 11 digits
@@
-92,9
+93,9
@@
abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
* this allows an easy change from http to https in future if needed
*/
ensemblDomain = Cache.getDefault(ENSEMBL_BASEURL,
* this allows an easy change from http to https in future if needed
*/
ensemblDomain = Cache.getDefault(ENSEMBL_BASEURL,
- DEFAULT_ENSEMBL_BASEURL);
+ DEFAULT_ENSEMBL_BASEURL).trim();
ensemblGenomesDomain = Cache.getDefault(ENSEMBL_GENOMES_BASEURL,
ensemblGenomesDomain = Cache.getDefault(ENSEMBL_GENOMES_BASEURL,
- DEFAULT_ENSEMBL_GENOMES_BASEURL);
+ DEFAULT_ENSEMBL_GENOMES_BASEURL).trim();
domain = ensemblDomain;
}
domain = ensemblDomain;
}
@@
-102,10
+103,6
@@
abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
public String getDbSource()
{
// NB ensure Uniprot xrefs are canonicalised from "Ensembl" to "ENSEMBL"
public String getDbSource()
{
// NB ensure Uniprot xrefs are canonicalised from "Ensembl" to "ENSEMBL"
- if (ensemblGenomesDomain.equals(getDomain()))
- {
- return DBRefSource.ENSEMBLGENOMES;
- }
return DBRefSource.ENSEMBL;
}
return DBRefSource.ENSEMBL;
}
@@
-169,6
+166,6
@@
abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
protected void setDomain(String d)
{
protected void setDomain(String d)
{
- domain = d;
+ domain = d == null ? null : d.trim();
}
}
}
}