X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;h=37c787b37222a61a29e186554ec346ecbe22bc88;hb=defcce0ef74ffc0923b4387bcb5f0d867bf64831;hp=4dd1bba3161075043669341275565c1fea6a1a86;hpb=d547268f85f377f14dbeb169072caebad45f9e2b;p=jalview.git
diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index 4dd1bba..37c787b 100644
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.ext.ensembl;
import jalview.api.FeatureColourI;
@@ -8,7 +28,7 @@ import jalview.datamodel.SequenceFeature;
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;
@@ -118,7 +138,10 @@ public class EnsemblGene extends EnsemblSeqProxy
* 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);
@@ -167,14 +190,30 @@ public class EnsemblGene extends EnsemblSeqProxy
geneIds.add(geneId);
}
}
+ else if (isProteinIdentifier(acc))
+ {
+ String tscriptId = new EnsemblLookup(getDomain()).getParent(acc);
+ if (tscriptId != null)
+ {
+ String geneId = new EnsemblLookup(getDomain())
+ .getParent(tscriptId);
+ if (geneId != null && !geneIds.contains(geneId))
+ {
+ geneIds.add(geneId);
+ }
+ }
+ // NOTE - acc is lost if it resembles an ENS.+ ID but isn't actually
+ // resolving to one... e.g. ENSMICP00000009241
+ }
/*
* if given a gene or other external name, lookup and fetch
* the corresponding gene for all model organisms
*/
else
{
- List ids = new EnsemblSymbol(getDomain()).getIds(acc);
+ List ids = new EnsemblSymbol(getDomain(), getDbSource(),
+ getDbVersion()).getIds(acc);
for (String geneId : ids)
{
if (!geneIds.contains(geneId))
@@ -196,7 +235,8 @@ public class EnsemblGene extends EnsemblSeqProxy
*/
protected String getGeneIdentifiersForName(String query)
{
- List ids = new EnsemblSymbol(getDomain()).getIds(query);
+ List ids = new EnsemblSymbol(getDomain(), getDbSource(),
+ getDbVersion()).getIds(query);
if (ids != null)
{
for (String id : ids)
@@ -257,8 +297,7 @@ public class EnsemblGene extends EnsemblSeqProxy
}
}
gene.setSequenceFeatures(filtered
- .toArray(new SequenceFeature[filtered
- .size()]));
+ .toArray(new SequenceFeature[filtered.size()]));
}
}
@@ -524,6 +563,7 @@ public class EnsemblGene extends EnsemblSeqProxy
return new FeatureSettingsAdapter()
{
SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+
@Override
public boolean isFeatureDisplayed(String type)
{
@@ -536,7 +576,7 @@ public class EnsemblGene extends EnsemblSeqProxy
{
if (so.isA(type, SequenceOntologyI.EXON))
{
- return new FeatureColourAdapter()
+ return new FeatureColour()
{
@Override
public boolean isColourByLabel()
@@ -547,7 +587,7 @@ public class EnsemblGene extends EnsemblSeqProxy
}
if (so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT))
{
- return new FeatureColourAdapter()
+ return new FeatureColour()
{
@Override