package jalview.api;
+import jalview.datamodel.Mapping;
+
+//JBPComment: this is a datamodel API - so it should be in datamodel (it's a peer of SequenceI)
public interface DBRefEntryI
{
public boolean equalRef(DBRefEntryI entry);
+ /**
+ *
+ * @return Source DB name for this entry
+ */
public String getSource();
- public String getVersion();
-
+ /**
+ *
+ * @return Accession Id for this entry
+ */
public String getAccessionId();
+ /**
+ *
+ * @param accessionId
+ * Accession Id for this entry
+ */
public void setAccessionId(String accessionId);
+ /**
+ *
+ * @param source
+ * Source DB name for this entry
+ */
public void setSource(String source);
- public void setVersion(String version);
-
- public void setStartRes(int startRes);
+ /**
+ *
+ * @return Source DB version for this entry
+ */
+ public String getVersion();
- public int getStartRes();
+ /**
+ *
+ * @param version
+ * Source DB version for this entry
+ */
+ public void setVersion(String version);
- public void setEndRes(int endRes);
+ /**
+ * 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();
- public int getEndRes();
+ /**
+ * 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);
}