import jalview.api.FeatureColourI;
import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
import jalview.datamodel.GeneLociI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
*/
public class EnsemblGene extends EnsemblSeqProxy
{
- private static final String GENE_PREFIX = "gene:";
-
/*
* accepts anything as we will attempt lookup of gene or
* transcript id or gene name
EnsemblFeatureType.exon, EnsemblFeatureType.cds,
EnsemblFeatureType.variation };
+ private static final String CHROMOSOME = "chromosome";
+
/**
* Default constructor (to use rest.ensembl.org)
*/
if (geneLoci != null)
{
seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(),
- geneLoci.getChromosomeId(), geneLoci.getMap());
+ geneLoci.getChromosomeId(), geneLoci.getMapping());
}
else
{
return false;
}
String[] tokens = description.split(":");
- if (tokens.length == 6 && tokens[0].startsWith(DBRefEntry.CHROMOSOME))
+ if (tokens.length == 6 && tokens[0].startsWith(CHROMOSOME))
{
String ref = tokens[1];
String chrom = tokens[2];
* look for exon features of the transcript, failing that for CDS
* (for example ENSG00000124610 has 1 CDS but no exon features)
*/
- String parentId = "transcript:" + accId;
+ String parentId = accId;
List<SequenceFeature> splices = findFeatures(gene,
SequenceOntologyI.EXON, parentId);
if (splices.isEmpty())
* Ensembl has gene name as transcript Name
* EnsemblGenomes doesn't, but has a url-encoded description field
*/
- String description = (String) transcriptFeature.getValue(NAME);
+ String description = transcriptFeature.getDescription();
if (description == null)
{
description = (String) transcriptFeature.getValue(DESCRIPTION);
return;
}
- MapList geneMapping = loci.getMap();
+ MapList geneMapping = loci.getMapping();
List<int[]> exons = mapping.getFromRanges();
List<int[]> transcriptLoci = new ArrayList<>();
*/
protected String getTranscriptId(SequenceFeature feature)
{
- return (String) feature.getValue("transcript_id");
+ return (String) feature.getValue(JSON_ID);
}
/**
{
List<SequenceFeature> transcriptFeatures = new ArrayList<>();
- String parentIdentifier = GENE_PREFIX + accId;
+ String parentIdentifier = accId;
List<SequenceFeature> sfs = geneSequence.getFeatures()
.getFeaturesByOntology(SequenceOntologyI.TRANSCRIPT);
.getFeaturesByOntology(SequenceOntologyI.GENE);
for (SequenceFeature sf : sfs)
{
- // NB features as gff use 'ID'; rest services return as 'id'
- String id = (String) sf.getValue("ID");
- if ((GENE_PREFIX + accId).equalsIgnoreCase(id))
+ String id = (String) sf.getValue(JSON_ID);
+ if (accId.equalsIgnoreCase(id))
{
result.add(sf);
}
if (isTranscript(type))
{
String parent = (String) sf.getValue(PARENT);
- if (!(GENE_PREFIX + accessionId).equalsIgnoreCase(parent))
+ if (!accessionId.equalsIgnoreCase(parent))
{
return false;
}