package jalview.ext.ensembl;
+import jalview.api.FeatureColourI;
+import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
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.FeatureSettingsAdapter;
import jalview.util.MapList;
import jalview.util.StringUtils;
+import java.awt.Color;
+import java.io.UnsupportedEncodingException;
+import java.net.URLDecoder;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
EnsemblFeatureType.exon, EnsemblFeatureType.cds,
EnsemblFeatureType.variation };
+ /**
+ * Default constructor (to use rest.ensembl.org)
+ */
+ public EnsemblGene()
+ {
+ super();
+ }
+
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblGene(String d)
+ {
+ super(d);
+ }
+
@Override
public String getDbName()
{
- return "ENSEMBL (GENE)";
+ return "ENSEMBL";
}
@Override
if (isTranscriptIdentifier(query))
{
// we are assuming all transcripts have the same gene parent here
- query = new EnsemblLookup().getParent(queries[0]);
+ query = new EnsemblLookup(getDomain()).getParent(queries[0]);
if (query == null)
{
return null;
*/
if (!isGeneIdentifier(query))
{
- List<String> geneIds = new EnsemblSymbol().getIds(query);
+ List<String> geneIds = new EnsemblSymbol(getDomain()).getIds(query);
if (geneIds.isEmpty())
{
return null;
return getSequenceRecords(theIds);
}
+ /*
+ * fetch the gene sequence(s) with features and xrefs
+ */
AlignmentI al = super.getSequenceRecords(query);
/*
*/
protected String getGeneIdentifiersForName(String query)
{
- List<String> ids = new EnsemblSymbol().getIds(query);
+ List<String> ids = new EnsemblSymbol(getDomain()).getIds(query);
if (ids != null)
{
for (String id : ids)
{
makeTranscript(transcriptFeature, al, gene);
}
+
+ clearGeneFeatures(gene);
+ }
+
+ /**
+ * Remove unwanted features (transcript, exon, CDS) from the gene sequence
+ * after we have used them to derive transcripts and transfer features
+ *
+ * @param gene
+ */
+ protected void clearGeneFeatures(SequenceI gene)
+ {
+ SequenceFeature[] sfs = gene.getSequenceFeatures();
+ if (sfs != null)
+ {
+ SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ List<SequenceFeature> filtered = new ArrayList<SequenceFeature>();
+ for (SequenceFeature sf : sfs)
+ {
+ String type = sf.getType();
+ if (!isTranscript(type) && !so.isA(type, SequenceOntologyI.EXON)
+ && !so.isA(type, SequenceOntologyI.CDS))
+ {
+ filtered.add(sf);
+ }
+ }
+ gene.setSequenceFeatures(filtered
+ .toArray(new SequenceFeature[filtered
+ .size()]));
+ }
}
/**
}
Sequence transcript = new Sequence(accId, seqChars, 1, transcriptLength);
- String geneName = (String) transcriptFeature.getValue(NAME);
- if (geneName != null)
+
+ /*
+ * Ensembl has gene name as transcript Name
+ * EnsemblGenomes doesn't, but has a url-encoded description field
+ */
+ String description = (String) transcriptFeature.getValue(NAME);
+ if (description == null)
{
- transcript.setDescription(geneName);
+ description = (String) transcriptFeature.getValue(DESCRIPTION);
+ }
+ if (description != null)
+ {
+ try
+ {
+ transcript.setDescription(URLDecoder.decode(description, "UTF-8"));
+ } catch (UnsupportedEncodingException e)
+ {
+ e.printStackTrace(); // as if
+ }
}
transcript.createDatasetSequence();
List<int[]> mapTo = new ArrayList<int[]>();
mapTo.add(new int[] { 1, transcriptLength });
MapList mapping = new MapList(mappedFrom, mapTo, 1, 1);
- new EnsemblCdna().transferFeatures(gene.getSequenceFeatures(),
+ EnsemblCdna cdna = new EnsemblCdna(getDomain());
+ cdna.transferFeatures(gene.getSequenceFeatures(),
transcript.getDatasetSequence(), mapping, parentId);
/*
* fetch and save cross-references
*/
- super.getCrossReferences(transcript);
+ cdna.getCrossReferences(transcript);
/*
* and finally fetch the protein product and save as a cross-reference
*/
- new EnsemblCdna().addProteinProduct(transcript);
+ cdna.addProteinProduct(transcript);
return transcript;
}
@Override
protected boolean retainFeature(SequenceFeature sf, String accessionId)
{
- if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
- SequenceOntologyI.GENE))
+ SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ String type = sf.getType();
+ if (so.isA(type, SequenceOntologyI.GENE))
{
return false;
}
-
- if (isTranscript(sf.getType()))
+ if (isTranscript(type))
{
String parent = (String) sf.getValue(PARENT);
if (!(GENE_PREFIX + accessionId).equals(parent))
return false;
}
- @Override
- protected List<String> getCrossReferenceDatabases()
- {
- // found these for ENSG00000157764 on 30/01/2016:
- // return new String[] {"Vega_gene", "OTTG", "ENS_LRG_gene", "ArrayExpress",
- // "EntrezGene", "HGNC", "MIM_GENE", "MIM_MORBID", "WikiGene"};
- return super.getCrossReferenceDatabases();
- }
-
/**
* Override to do nothing as Ensembl doesn't return a protein sequence for a
* gene identifier
return ACCESSION_REGEX;
}
+ /**
+ * Returns a descriptor for suitable feature display settings with
+ * <ul>
+ * <li>only exon or sequence_variant features (or their subtypes in the
+ * Sequence Ontology) visible</li>
+ * <li>variant features coloured red</li>
+ * <li>exon features coloured by label (exon name)</li>
+ * <li>variants displayed above (on top of) exons</li>
+ * </ul>
+ */
+ @Override
+ public FeatureSettingsModelI getFeatureColourScheme()
+ {
+ return new FeatureSettingsAdapter()
+ {
+ SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ @Override
+ public boolean isFeatureDisplayed(String type)
+ {
+ return (so.isA(type, SequenceOntologyI.EXON) || so.isA(type,
+ SequenceOntologyI.SEQUENCE_VARIANT));
+ }
+
+ @Override
+ public FeatureColourI getFeatureColour(String type)
+ {
+ if (so.isA(type, SequenceOntologyI.EXON))
+ {
+ return new FeatureColourAdapter()
+ {
+ @Override
+ public boolean isColourByLabel()
+ {
+ return true;
+ }
+ };
+ }
+ if (so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT))
+ {
+ return new FeatureColourAdapter()
+ {
+
+ @Override
+ public Color getColour()
+ {
+ return Color.RED;
+ }
+ };
+ }
+ return null;
+ }
+
+ /**
+ * order to render sequence_variant after exon after the rest
+ */
+ @Override
+ public int compare(String feature1, String feature2)
+ {
+ if (so.isA(feature1, SequenceOntologyI.SEQUENCE_VARIANT))
+ {
+ return +1;
+ }
+ if (so.isA(feature2, SequenceOntologyI.SEQUENCE_VARIANT))
+ {
+ return -1;
+ }
+ if (so.isA(feature1, SequenceOntologyI.EXON))
+ {
+ return +1;
+ }
+ if (so.isA(feature2, SequenceOntologyI.EXON))
+ {
+ return -1;
+ }
+ return 0;
+ }
+ };
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff