X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblGene.java;h=9c7ce638fdf95fca1caca1a5347c0d27115dbb55;hb=456e5c765ac1e85336fd9f9b1a35453069bb2298;hp=915fa0aa04e5067731f1ebd8dceae9dc7a79f9d0;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java index 915fa0a..9c7ce63 100644 --- a/src/jalview/ext/ensembl/EnsemblGene.java +++ b/src/jalview/ext/ensembl/EnsemblGene.java @@ -23,6 +23,7 @@ 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; @@ -49,8 +50,6 @@ 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 @@ -62,6 +61,8 @@ public class EnsemblGene extends EnsemblSeqProxy EnsemblFeatureType.exon, EnsemblFeatureType.cds, EnsemblFeatureType.variation }; + private static final String CHROMOSOME = "chromosome"; + /** * Default constructor (to use rest.ensembl.org) */ @@ -98,6 +99,12 @@ 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 @@ -110,7 +117,8 @@ 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
@@ -434,22 +507,21 @@ public class EnsemblGene extends EnsemblSeqProxy
protected List