* add/define mechanism for retrieval of Trees and distance matrices from a\r
* database (unify with io)\r
* \r
- * @author JimP\r
- * \r
+ * @author JimP TODO: promote to API\r
*/\r
public interface DbSourceProxy\r
{\r
\r
/**\r
* Regular expression for checking form of query string understood by this\r
- * source.\r
+ * source. If the Regex includes parenthesis, then the first parenthesis\r
+ * should yield the same accession string as the one used to annotate the\r
+ * sequence. This is used to match query strings to returned sequences.\r
* \r
* @return null or a validation regex\r
*/\r
* into an alignment\r
* \r
* @param queries\r
+ * - one or more queries for database in expected form\r
* @return null if queries were successful but result was not parsable\r
* @throws Exception\r
- * TODO\r
+ * - propagated from underlying transport to database (note -\r
+ * exceptions are not raised if query not found in database)\r
+ * \r
*/\r
public AlignmentI getSequenceRecords(String queries) throws Exception;\r
\r
*/\r
public StringBuffer getRawRecords();\r
\r
- \r
/**\r
* Find out more info about the source.\r
- * @param dbsourceproperty - one of the database reference source properties in jalview.datamodel.DBRefSource\r
+ * \r
+ * @param dbsourceproperty\r
+ * - one of the database reference source properties in\r
+ * jalview.datamodel.DBRefSource\r
* @return true if the source has this property\r
*/\r
public boolean isA(Object dbsourceproperty);\r