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;
import jalview.schemes.FeatureColour;
import jalview.schemes.FeatureSettingsAdapter;
import jalview.util.MapList;
+import jalview.util.Platform;
import java.awt.Color;
import java.io.UnsupportedEncodingException;
*/
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
*/
- private static final Regex ACCESSION_REGEX = new Regex(".*");
+ private static final Regex ACCESSION_REGEX = Platform.newRegex(".*");
private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
EnsemblFeatureType.gene, EnsemblFeatureType.transcript,
EnsemblFeatureType.exon, EnsemblFeatureType.cds,
EnsemblFeatureType.variation };
+ private static final String CHROMOSOME = "chromosome";
+
/**
* Default constructor (to use rest.ensembl.org)
*/
* convert to a non-duplicated list of gene identifiers
*/
List<String> geneIds = getGeneIds(query);
-
AlignmentI al = null;
for (String geneId : geneIds)
{
{
// ensure id has 'correct' case for the Ensembl identifier
geneId = geneAlignment.getSequenceAt(0).getName();
-
findGeneLoci(geneAlignment.getSequenceAt(0), geneId);
-
getTranscripts(geneAlignment, geneId);
}
if (al == null)
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);
@Override
public String getTestQuery()
{
- return "ENSG00000157764"; // BRAF, 5 transcripts, reverse strand
+ return Platform.isJS() ? "ENSG00000123569" : "ENSG00000157764";
+ // ENSG00000123569 // H2BFWT histone, 2 transcripts, reverse strand
+ // ENSG00000157764 // BRAF, 5 transcripts, reverse strand
// ENSG00000090266 // NDUFB2, 15 transcripts, forward strand
// ENSG00000101812 // H2BFM histone, 3 transcripts, forward strand
- // ENSG00000123569 // H2BFWT histone, 2 transcripts, reverse strand
}
/**
- * Answers true for a feature of type 'gene' (or a sub-type of gene in the
- * Sequence Ontology), whose ID is the accession we are retrieving
+ * Answers a list of sequence features (if any) whose type is 'gene' (or a
+ * subtype of gene in the Sequence Ontology), and whose ID is the accession we
+ * are retrieving
*/
@Override
- protected boolean identifiesSequence(SequenceFeature sf, String accId)
+ protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
+ String accId)
{
- if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
- SequenceOntologyI.GENE))
+ List<SequenceFeature> result = new ArrayList<>();
+ List<SequenceFeature> sfs = seq.getFeatures()
+ .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))
{
- return true;
+ result.add(sf);
}
}
- return false;
+ return result;
}
/**
@Override
protected boolean retainFeature(SequenceFeature sf, String accessionId)
{
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
String type = sf.getType();
if (so.isA(type, SequenceOntologyI.GENE))
{
if (isTranscript(type))
{
String parent = (String) sf.getValue(PARENT);
- if (!(GENE_PREFIX + accessionId).equalsIgnoreCase(parent))
+ if (!accessionId.equalsIgnoreCase(parent))
{
return false;
}
}
/**
- * Answers false. This allows an optimisation - a single 'gene' feature is all
- * that is needed to identify the positions of the gene on the genomic
- * sequence.
- */
- @Override
- protected boolean isSpliceable()
- {
- return false;
- }
-
- /**
* Override to do nothing as Ensembl doesn't return a protein sequence for a
* gene identifier
*/
{
return new FeatureSettingsAdapter()
{
- SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
@Override
- public boolean isFeatureDisplayed(String type)
+ public boolean isFeatureHidden(String type)
{
- return (so.isA(type, SequenceOntologyI.EXON)
- || so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT));
+ return (!so.isA(type, SequenceOntologyI.EXON)
+ && !so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT));
}
@Override