+
+ /**
+ * access a mapping, if present that can be used to map positions from the
+ * associated dataset sequence to the DBRef's sequence frame.
+ *
+ * @return null or a valid mapping.
+ */
+ public Mapping getMap();
+
+ /**
+ * Answers true if this object is either equivalent to, or can be 'improved'
+ * by, the given entry. Specifically, answers true if
+ * <ul>
+ * <li>source and accession are identical</li>
+ * <li>version is identical, or this version is of the format "someSource:0",
+ * in which case the version for the other entry replaces it</li>
+ * <li>mappings are not compared but if this entry has no mapping, replace
+ * with that for the other entry</li>
+ * </ul>
+ *
+ * @param otherEntry
+ * @return
+ */
+ public boolean updateFrom(DBRefEntryI otherEntry);
+
+ /**
+ * Answers true if the ref looks like a primary (direct) database reference.
+ * <br>
+ * The only way a dbref's mappings can be fully verified is via the local
+ * sequence frame, so rather than use isPrimaryCandidate directly, please use
+ * SequenceI.getPrimaryDbRefs(). <br>
+ * Primary references indicate the local sequence data directly corresponds
+ * with the database record. All other references are secondary. Direct
+ * references indicate that part or all of the local sequence data can be
+ * mapped with another sequence, enabling annotation transfer.
+ * Cross-references indicate the local sequence data can be corresponded to
+ * some other linear coordinate system via a transformation. <br>
+ * This method is also sufficient to distinguish direct DBRefEntry mappings
+ * from other relationships - e.g. coding relationships (imply a 1:3/3:1
+ * mapping), but not transcript relationships, which imply a (possibly
+ * non-contiguous) 1:1 mapping.
+ *
+ * @return true if this reference provides a primary accession for the
+ * associated sequence object
+ */
+ public boolean isPrimaryCandidate();