X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;h=e832eff3693d24879a6e7a3c9848ae4625dfd722;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=37c787b37222a61a29e186554ec346ecbe22bc88;hpb=7d9e8749e06f98fd14f72086faef8b6dd5c5adf4;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java index 37c787b..e832eff 100644 --- a/src/jalview/ext/ensembl/EnsemblGene.java +++ b/src/jalview/ext/ensembl/EnsemblGene.java @@ -23,14 +23,17 @@ package jalview.ext.ensembl; import jalview.api.FeatureColourI; import jalview.api.FeatureSettingsModelI; import jalview.datamodel.AlignmentI; +import jalview.datamodel.GeneLociI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.datamodel.features.SequenceFeatures; import jalview.io.gff.SequenceOntologyFactory; import jalview.io.gff.SequenceOntologyI; import jalview.schemes.FeatureColour; import jalview.schemes.FeatureSettingsAdapter; import jalview.util.MapList; +import jalview.util.Platform; import java.awt.Color; import java.io.UnsupportedEncodingException; @@ -48,19 +51,19 @@ import com.stevesoft.pat.Regex; */ 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) */ @@ -97,6 +100,12 @@ public class EnsemblGene extends EnsemblSeqProxy return EnsemblSeqType.GENOMIC; } + @Override + protected String getObjectType() + { + return OBJECT_TYPE_GENE; + } + /** * Returns an alignment containing the gene(s) for the given gene or * transcript identifier, or external identifier (e.g. Uniprot id). If given a @@ -109,7 +118,8 @@ public class EnsemblGene extends EnsemblSeqProxy *
+ * Transcript features are those of type "transcript", or any of its sub-types
+ * in the Sequence Ontology e.g. "mRNA", "processed_transcript". We also
+ * include "NMD_transcript_variant", because this type behaves like a
+ * transcript identifier in Ensembl, although strictly speaking it is not in
+ * the SO.
*
* @param accId
* @param geneSequence
@@ -434,23 +505,21 @@ public class EnsemblGene extends EnsemblSeqProxy
protected List