+ @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
+ */
+ @Override
+ protected void addProteinProduct(SequenceI querySeq)
+ {
+ }
+
+ @Override
+ public Regex getAccessionValidator()
+ {
+ return ACCESSION_REGEX;
+ }
+
+ @Override
+ public FeatureSettingsI 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;
+ }
+ };
+ }
+