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JAL-1705 more lenient test for 'sequence retrieved'
[jalview.git]
/
src
/
jalview
/
ext
/
ensembl
/
EnsemblCdna.java
diff --git
a/src/jalview/ext/ensembl/EnsemblCdna.java
b/src/jalview/ext/ensembl/EnsemblCdna.java
index
139e44f
..
f60125b
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblCdna.java
+++ b/
src/jalview/ext/ensembl/EnsemblCdna.java
@@
-1,7
+1,8
@@
package jalview.ext.ensembl;
import jalview.datamodel.SequenceFeature;
package jalview.ext.ensembl;
import jalview.datamodel.SequenceFeature;
-import jalview.io.gff.SequenceOntology;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
import java.util.List;
import java.util.List;
@@
-9,8
+10,12
@@
import com.stevesoft.pat.Regex;
public class EnsemblCdna extends EnsemblSeqProxy
{
public class EnsemblCdna extends EnsemblSeqProxy
{
+ // TODO modify to accept other species e.g. ENSMUSPnnn
+ private static final Regex ACCESSION_REGEX = new Regex(
+ "(ENST|ENSG|CCDS)[0-9.]{3,}$");
+
/*
/*
- * fetch exon features on genomic sequence (to identify the cdnaregions)
+ * fetch exon features on genomic sequence (to identify the cdna regions)
* and cds and variation features (to retain)
*/
private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
* and cds and variation features (to retain)
*/
private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
@@
-37,7
+42,7
@@
public class EnsemblCdna extends EnsemblSeqProxy
@Override
public Regex getAccessionValidator()
{
@Override
public Regex getAccessionValidator()
{
- return new Regex("((ENST|ENSG|CCDS)[0-9.]{3,})");
+ return ACCESSION_REGEX;
}
@Override
}
@Override
@@
-68,8
+73,8
@@
public class EnsemblCdna extends EnsemblSeqProxy
@Override
protected boolean identifiesSequence(SequenceFeature sf, String accId)
{
@Override
protected boolean identifiesSequence(SequenceFeature sf, String accId)
{
- if (SequenceOntology.getInstance().isA(sf.getType(),
- SequenceOntology.EXON))
+ if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
+ SequenceOntologyI.EXON))
{
String parentFeature = (String) sf.getValue(PARENT);
if (("transcript:" + accId).equals(parentFeature))
{
String parentFeature = (String) sf.getValue(PARENT);
if (("transcript:" + accId).equals(parentFeature))