- public DBRefEntry(DBRefEntry entry)
- {
- this((entry.source==null ? "" : new String(entry.source)),
- (entry.version==null ? "" : new String(entry.version)),
- (entry.accessionId==null ? "" : new String(entry.accessionId)),
- (entry.map==null ? null : new Mapping(entry.map)));
- }
- public boolean equals(DBRefEntry entry) {
- if (entry==this)
- return true;
- if (entry==null)
- return false;
- if (equalRef(entry)
- &&
- ((map==null && entry.map==null) || (map!=null && entry.map!=null && map.equals(entry.map)))) {
- return true;
- }
+
+ public DBRefEntry(DBRefEntryI entry)
+ {
+ this((entry.getSource() == null ? "" : new String(entry.getSource())),
+ (entry.getVersion() == null ? "" : new String(
+ entry.getVersion())),
+ (entry.getAccessionId() == null ? "" : new String(
+ entry.getAccessionId())),
+ (entry.getMap() == null ? null : new Mapping(entry.getMap())));
+ }
+
+ @Override
+ public boolean equals(Object o)
+ {
+ // TODO should also override hashCode to ensure equal objects have equal
+ // hashcodes
+ if (o == null || !(o instanceof DBRefEntry))
+ {
+ return false;
+ }
+ DBRefEntry entry = (DBRefEntry) o;
+ if (entry == this)
+ {
+ return true;
+ }
+ if (equalRef(entry)
+ && ((map == null && entry.map == null) || (map != null
+ && entry.map != null && map.equals(entry.map))))
+ {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * 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 (ignoring case)</li>
+ * <li>version is identical (ignoring case), 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 other
+ * @return
+ */
+ @Override
+ public boolean updateFrom(DBRefEntry other)
+ {
+ if (other == null)
+ {
+ return false;
+ }
+ if (other == this)
+ {
+ return true;
+ }
+
+ /*
+ * source must either match or be both null
+ */
+ String otherSource = other.getSource();
+ if ((source == null && otherSource != null)
+ || (source != null && otherSource == null)
+ || (source != null && !source.equalsIgnoreCase(otherSource)))
+ {
+ return false;
+ }
+
+ /*
+ * accession id must either match or be both null
+ */
+ String otherAccession = other.getAccessionId();
+ if ((accessionId == null && otherAccession != null)
+ || (accessionId != null && otherAccession == null)
+ || (accessionId != null && !accessionId.equalsIgnoreCase(otherAccession)))
+ {