- /*
- * accepts ENSG/T/E/P with 11 digits
- * or ENSMUSP or similar for other species
- * or CCDSnnnnn.nn with at least 3 digits
- */
- private static final Regex ACCESSION_REGEX = new Regex(
- "(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
+ // domain properties lookup keys:
+ protected static final String ENSEMBL_BASEURL = "ENSEMBL_BASEURL";
+
+ protected static final String ENSEMBL_GENOMES_BASEURL = "ENSEMBL_GENOMES_BASEURL";
+
+ // domain properties default values:
+ protected static final String DEFAULT_ENSEMBL_BASEURL = "https://rest.ensembl.org";
+
+ // ensemblgenomes REST service merged to ensembl 9th April 2019
+ protected static final String DEFAULT_ENSEMBL_GENOMES_BASEURL = DEFAULT_ENSEMBL_BASEURL;
+
+ private static Regex ACCESSION_REGEX;
+
+ protected final String ensemblGenomesDomain;
+
+ protected final String ensemblDomain;
+
+ protected static final String OBJECT_TYPE_TRANSLATION = "Translation";
+
+ protected static final String OBJECT_TYPE_TRANSCRIPT = "Transcript";
+
+ protected static final String OBJECT_TYPE_GENE = "Gene";
+
+ protected static final String PARENT = "Parent";
+
+ protected static final String JSON_ID = AlignmentUtils.VARIANT_ID; // "id";
+
+ protected static final String OBJECT_TYPE = "object_type";