X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGenome.java;h=4f59bc59c0aa042d8ecf99e924c98923d24651b7;hb=fdde9a078d7bdb46ed9fb7fe115ea83c84a19c81;hp=60f8c464a1d7d44b1306934137125e3201fe4ddc;hpb=ecc50d775a514f9840cdcc10a9d5b1e49c60582c;p=jalview.git
diff --git a/src/jalview/ext/ensembl/EnsemblGenome.java b/src/jalview/ext/ensembl/EnsemblGenome.java
index 60f8c46..4f59bc5 100644
--- a/src/jalview/ext/ensembl/EnsemblGenome.java
+++ b/src/jalview/ext/ensembl/EnsemblGenome.java
@@ -1,8 +1,40 @@
+/*
+ * 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.datamodel.SequenceFeature;
-import jalview.io.gff.SequenceOntology;
+import jalview.datamodel.SequenceI;
+import jalview.io.gff.SequenceOntologyI;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * A client to fetch genomic sequence from Ensembl
+ *
+ * TODO: not currently used - delete?
+ *
+ * @author gmcarstairs
+ *
+ */
public class EnsemblGenome extends EnsemblSeqProxy
{
/*
@@ -13,15 +45,28 @@ public class EnsemblGenome extends EnsemblSeqProxy
EnsemblFeatureType.transcript, EnsemblFeatureType.exon,
EnsemblFeatureType.cds, EnsemblFeatureType.variation };
+ /**
+ * Default constructor (to use rest.ensembl.org)
+ */
public EnsemblGenome()
{
super();
}
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblGenome(String d)
+ {
+ super(d);
+ }
+
@Override
public String getDbName()
{
- return "ENSEMBL (Genome)";
+ return "ENSEMBL (Genomic)";
}
@Override
@@ -38,35 +83,47 @@ public class EnsemblGenome extends EnsemblSeqProxy
/**
* Answers true unless the feature type is 'transcript' (or a sub-type of
- * transcript in the Sequence Ontology). Transcript features are only
- * retrieved in order to identify the transcript sequence range, and are
- * redundant information on the transcript sequence itself.
+ * transcript in the Sequence Ontology), or has a parent other than the given
+ * accession id. Transcript features are only retrieved in order to identify
+ * the transcript sequence range, and are redundant information on the
+ * transcript sequence itself.
*/
@Override
- protected boolean retainFeature(String type)
+ protected boolean retainFeature(SequenceFeature sf, String accessionId)
{
- return !SequenceOntology.getInstance().isA(type,
- SequenceOntology.TRANSCRIPT);
+ if (isTranscript(sf.getType()))
+ {
+ return false;
+ }
+ return featureMayBelong(sf, accessionId);
}
/**
- * Answers true if the sequence feature type is 'transcript' (or a subtype of
- * transcript in the Sequence Ontology), and the ID of the feature is the
- * transcript we are retrieving
+ * Answers a list of sequence features (if any) whose type is 'transcript' (or
+ * a subtype of transcript in the Sequence Ontology), and whose ID is the
+ * accession we are retrieving.
+ *
+ * Note we also include features of type "NMD_transcript_variant", although
+ * not strictly 'transcript' in the SO, as they used in Ensembl as if they
+ * were.
*/
@Override
- protected boolean identifiesSequence(SequenceFeature sf, String accId)
+ protected List getIdentifyingFeatures(SequenceI seq,
+ String accId)
{
- if (SequenceOntology.getInstance().isA(sf.getType(),
- SequenceOntology.TRANSCRIPT))
+ List result = new ArrayList<>();
+ List sfs = seq.getFeatures().getFeaturesByOntology(
+ SequenceOntologyI.TRANSCRIPT,
+ SequenceOntologyI.NMD_TRANSCRIPT_VARIANT);
+ for (SequenceFeature sf : sfs)
{
- String id = (String) sf.getValue(ID);
- if (("transcript:" + accId).equals(id))
+ String id = (String) sf.getValue(JSON_ID);
+ if (accId.equals(id))
{
- return true;
+ result.add(sf);
}
}
- return false;
+ return result;
}
}