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JAL-1705 include stop codons in derived CDS; support ensemblgenomes
[jalview.git]
/
src
/
jalview
/
ext
/
ensembl
/
EnsemblGenome.java
diff --git
a/src/jalview/ext/ensembl/EnsemblGenome.java
b/src/jalview/ext/ensembl/EnsemblGenome.java
index
e977e62
..
20987e1
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblGenome.java
+++ b/
src/jalview/ext/ensembl/EnsemblGenome.java
@@
-2,6
+2,14
@@
package jalview.ext.ensembl;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceFeature;
+/**
+ * A client to fetch genomic sequence from Ensembl
+ *
+ * TODO: not currently used - delete?
+ *
+ * @author gmcarstairs
+ *
+ */
public class EnsemblGenome extends EnsemblSeqProxy
{
/*
public class EnsemblGenome extends EnsemblSeqProxy
{
/*
@@
-12,11
+20,24
@@
public class EnsemblGenome extends EnsemblSeqProxy
EnsemblFeatureType.transcript, EnsemblFeatureType.exon,
EnsemblFeatureType.cds, EnsemblFeatureType.variation };
EnsemblFeatureType.transcript, EnsemblFeatureType.exon,
EnsemblFeatureType.cds, EnsemblFeatureType.variation };
+ /**
+ * Default constructor (to use rest.ensembl.org)
+ */
public EnsemblGenome()
{
super();
}
public EnsemblGenome()
{
super();
}
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblGenome(String d)
+ {
+ super(d);
+ }
+
@Override
public String getDbName()
{
@Override
public String getDbName()
{