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JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...
[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
0d73a47
..
63a6a6c
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblGene.java
+++ b/
src/jalview/ext/ensembl/EnsemblGene.java
@@
-56,7
+56,7
@@
public class EnsemblGene extends EnsemblSeqProxy
* accepts anything as we will attempt lookup of gene or
* transcript id or gene name
*/
* accepts anything as we will attempt lookup of gene or
* transcript id or gene name
*/
- private static final Regex ACCESSION_REGEX = new Regex(".*");
+ private static Regex ACCESSION_REGEX;
private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
EnsemblFeatureType.gene, EnsemblFeatureType.transcript,
private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
EnsemblFeatureType.gene, EnsemblFeatureType.transcript,
@@
-577,7
+577,7
@@
public class EnsemblGene extends EnsemblSeqProxy
@Override
protected boolean retainFeature(SequenceFeature sf, String accessionId)
{
@Override
protected boolean retainFeature(SequenceFeature sf, String accessionId)
{
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
String type = sf.getType();
if (so.isA(type, SequenceOntologyI.GENE))
{
String type = sf.getType();
if (so.isA(type, SequenceOntologyI.GENE))
{
@@
-606,6
+606,10
@@
public class EnsemblGene extends EnsemblSeqProxy
@Override
public Regex getAccessionValidator()
{
@Override
public Regex getAccessionValidator()
{
+ if (ACCESSION_REGEX == null)
+ {
+ ACCESSION_REGEX = Platform.newRegex(".*", null);
+ }
return ACCESSION_REGEX;
}
return ACCESSION_REGEX;
}
@@
-624,7
+628,7
@@
public class EnsemblGene extends EnsemblSeqProxy
{
return new FeatureSettingsAdapter()
{
{
return new FeatureSettingsAdapter()
{
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
@Override
public boolean isFeatureDisplayed(String type)
@Override
public boolean isFeatureDisplayed(String type)