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Merge branch 'features/mchmmer' into features/mchmmer_merge_JAL-1950
[jalview.git]
/
src
/
jalview
/
ext
/
ensembl
/
EnsemblSeqProxy.java
diff --git
a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index
b2ebb1a
..
9229379
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/
src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@
-34,6
+34,7
@@
import jalview.datamodel.features.SequenceFeatures;
import jalview.exceptions.JalviewException;
import jalview.io.FastaFile;
import jalview.io.FileParse;
import jalview.exceptions.JalviewException;
import jalview.io.FastaFile;
import jalview.io.FileParse;
+import jalview.io.gff.Gff3Helper;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
import jalview.util.Comparison;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
import jalview.util.Comparison;
@@
-57,8
+58,6
@@
import java.util.List;
*/
public abstract class EnsemblSeqProxy extends EnsemblRestClient
{
*/
public abstract class EnsemblSeqProxy extends EnsemblRestClient
{
- private static final String ALLELES = "alleles";
-
protected static final String NAME = "Name";
protected static final String DESCRIPTION = "description";
protected static final String NAME = "Name";
protected static final String DESCRIPTION = "description";
@@
-708,7
+707,7
@@
public abstract class EnsemblSeqProxy extends EnsemblRestClient
*/
static void reverseComplementAlleles(SequenceFeature sf)
{
*/
static void reverseComplementAlleles(SequenceFeature sf)
{
- final String alleles = (String) sf.getValue(ALLELES);
+ final String alleles = (String) sf.getValue(Gff3Helper.ALLELES);
if (alleles == null)
{
return;
if (alleles == null)
{
return;
@@
-719,7
+718,7
@@
public abstract class EnsemblSeqProxy extends EnsemblRestClient
reverseComplementAllele(complement, allele);
}
String comp = complement.toString();
reverseComplementAllele(complement, allele);
}
String comp = complement.toString();
- sf.setValue(ALLELES, comp);
+ sf.setValue(Gff3Helper.ALLELES, comp);
sf.setDescription(comp);
/*
sf.setDescription(comp);
/*
@@
-729,7
+728,8
@@
public abstract class EnsemblSeqProxy extends EnsemblRestClient
String atts = sf.getAttributes();
if (atts != null)
{
String atts = sf.getAttributes();
if (atts != null)
{
- atts = atts.replace(ALLELES + "=" + alleles, ALLELES + "=" + comp);
+ atts = atts.replace(Gff3Helper.ALLELES + "=" + alleles,
+ Gff3Helper.ALLELES + "=" + comp);
sf.setAttributes(atts);
}
}
sf.setAttributes(atts);
}
}