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Merge branch 'develop' into features/JAL-2094_colourInterface
[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
9a4952e
..
dd1739b
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
+++ b/
src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
@@
-20,6
+20,10
@@
abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
private static final Regex ACCESSION_REGEX = new Regex(
"(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
private static final Regex ACCESSION_REGEX = new Regex(
"(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
+ protected static final String ENSEMBL_GENOMES_REST = "http://rest.ensemblgenomes.org";
+
+ protected static final String ENSEMBL_REST = "http://rest.ensembl.org";
+
/*
* possible values for the 'feature' parameter of the /overlap REST service
* @see http://rest.ensembl.org/documentation/info/overlap_id
/*
* possible values for the 'feature' parameter of the /overlap REST service
* @see http://rest.ensembl.org/documentation/info/overlap_id
@@
-31,17
+35,17
@@
abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
constrained, regulatory
}
constrained, regulatory
}
+ private String domain = ENSEMBL_REST;
+
@Override
public String getDbSource()
{
// NB ensure Uniprot xrefs are canonicalised from "Ensembl" to "ENSEMBL"
@Override
public String getDbSource()
{
// NB ensure Uniprot xrefs are canonicalised from "Ensembl" to "ENSEMBL"
- return DBRefSource.ENSEMBL; // "ENSEMBL"
- }
-
- @Override
- public String getDbVersion()
- {
- return "0";
+ if (ENSEMBL_GENOMES_REST.equals(getDomain()))
+ {
+ return DBRefSource.ENSEMBLGENOMES;
+ }
+ return DBRefSource.ENSEMBL;
}
@Override
}
@Override
@@
-90,4
+94,20
@@
abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
{
return true;
}
{
return true;
}
+
+ /**
+ * Returns the domain name to query e.g. http://rest.ensembl.org or
+ * http://rest.ensemblgenomes.org
+ *
+ * @return
+ */
+ protected String getDomain()
+ {
+ return domain;
+ }
+
+ protected void setDomain(String d)
+ {
+ domain = d;
+ }
}
}