+ matches.add(dbref);
+ }
+ }
+ }
+ return matches;
+ }
+
+ /**
+ * promote direct database references to primary for nucleotide or protein
+ * sequences if they have an appropriate primary ref
+ * <table>
+ * <tr>
+ * <th>Seq Type</th>
+ * <th>Primary DB</th>
+ * <th>Direct which will be promoted</th>
+ * </tr>
+ * <tr align=center>
+ * <td>peptides</td>
+ * <td>Ensembl</td>
+ * <td>Uniprot</td>
+ * </tr>
+ * <tr align=center>
+ * <td>peptides</td>
+ * <td>Ensembl</td>
+ * <td>Uniprot</td>
+ * </tr>
+ * <tr align=center>
+ * <td>dna</td>
+ * <td>Ensembl</td>
+ * <td>ENA</td>
+ * </tr>
+ * </table>
+ *
+ * @param sequence
+ */
+ public static void ensurePrimaries(SequenceI sequence)
+ {
+ List<DBRefEntry> pr = sequence.getPrimaryDBRefs();
+ if (pr.size() == 0)
+ {
+ // nothing to do
+ return;
+ }
+ List<DBRefEntry> selfs = new ArrayList<DBRefEntry>();
+ {
+ DBRefEntry[] selfArray = selectDbRefs(!sequence.isProtein(),
+ sequence.getDBRefs());
+ if (selfArray == null || selfArray.length == 0)
+ {
+ // nothing to do
+ return;
+ }
+ selfs.addAll(Arrays.asList(selfArray));
+ }
+
+ // filter non-primary refs
+ for (DBRefEntry p : pr)
+ {
+ while (selfs.contains(p))
+ {
+ selfs.remove(p);
+ }
+ }
+ List<DBRefEntry> toPromote = new ArrayList<DBRefEntry>();
+
+ for (DBRefEntry p : pr)
+ {
+ List<String> promType = new ArrayList<String>();
+ if (sequence.isProtein())
+ {
+ switch (getCanonicalName(p.getSource()))
+ {
+ case DBRefSource.UNIPROT:
+ // case DBRefSource.UNIPROTKB:
+ // case DBRefSource.UP_NAME:
+ // search for and promote ensembl
+ promType.add(DBRefSource.ENSEMBL);
+ break;
+ case DBRefSource.ENSEMBL:
+ // search for and promote Uniprot
+ promType.add(DBRefSource.UNIPROT);
+ break;
+ }
+ }
+ else
+ {
+ // TODO: promote transcript refs
+ }
+
+ // collate candidates and promote them
+ DBRefEntry[] candidates = selectRefs(selfs.toArray(new DBRefEntry[0]),
+ promType.toArray(new String[0]));
+ if (candidates != null)
+ {
+ for (DBRefEntry cand : candidates)
+ {
+ if (cand.hasMap())