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Merge branch 'develop' of https://source.jalview.org/git/jalview into develop
[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
4dd1bba
..
0c20e12
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblGene.java
+++ b/
src/jalview/ext/ensembl/EnsemblGene.java
@@
-8,7
+8,7
@@
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
import jalview.datamodel.SequenceI;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
-import jalview.schemes.FeatureColourAdapter;
+import jalview.schemes.FeatureColour;
import jalview.schemes.FeatureSettingsAdapter;
import jalview.util.MapList;
import jalview.schemes.FeatureSettingsAdapter;
import jalview.util.MapList;
@@
-118,7
+118,10
@@
public class EnsemblGene extends EnsemblSeqProxy
* fetch the gene sequence(s) with features and xrefs
*/
AlignmentI geneAlignment = super.getSequenceRecords(geneId);
* fetch the gene sequence(s) with features and xrefs
*/
AlignmentI geneAlignment = super.getSequenceRecords(geneId);
-
+ if (geneAlignment == null)
+ {
+ continue;
+ }
if (geneAlignment.getHeight() == 1)
{
getTranscripts(geneAlignment, geneId);
if (geneAlignment.getHeight() == 1)
{
getTranscripts(geneAlignment, geneId);
@@
-174,7
+177,8
@@
public class EnsemblGene extends EnsemblSeqProxy
*/
else
{
*/
else
{
- List<String> ids = new EnsemblSymbol(getDomain()).getIds(acc);
+ List<String> ids = new EnsemblSymbol(getDomain(), getDbSource(),
+ getDbVersion()).getIds(acc);
for (String geneId : ids)
{
if (!geneIds.contains(geneId))
for (String geneId : ids)
{
if (!geneIds.contains(geneId))
@@
-196,7
+200,8
@@
public class EnsemblGene extends EnsemblSeqProxy
*/
protected String getGeneIdentifiersForName(String query)
{
*/
protected String getGeneIdentifiersForName(String query)
{
- List<String> ids = new EnsemblSymbol(getDomain()).getIds(query);
+ List<String> ids = new EnsemblSymbol(getDomain(), getDbSource(),
+ getDbVersion()).getIds(query);
if (ids != null)
{
for (String id : ids)
if (ids != null)
{
for (String id : ids)
@@
-536,7
+541,7
@@
public class EnsemblGene extends EnsemblSeqProxy
{
if (so.isA(type, SequenceOntologyI.EXON))
{
{
if (so.isA(type, SequenceOntologyI.EXON))
{
- return new FeatureColourAdapter()
+ return new FeatureColour()
{
@Override
public boolean isColourByLabel()
{
@Override
public boolean isColourByLabel()
@@
-547,7
+552,7
@@
public class EnsemblGene extends EnsemblSeqProxy
}
if (so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT))
{
}
if (so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT))
{
- return new FeatureColourAdapter()
+ return new FeatureColour()
{
@Override
{
@Override