Changeset 106 for trunk/corelib/src/org/bridgedb/rdb/SimpleGdbImpl2.java

Timestamp:

07/19/09 19:24:43 (3 years ago)

Author:

martijn

Message:

Fixed style and javadoc issues

Files:

• trunk/corelib/src/org/bridgedb/rdb/SimpleGdbImpl2.java (modified) (4 diffs)

trunk/corelib/src/org/bridgedb/rdb/SimpleGdbImpl2.java

@@ -103 +103 @@
                         "id = ? AND code = ?"
                 );
-        private final LazyPst pstGeneSymbol = new LazyPst(
-                        "SELECT attrvalue FROM attribute WHERE " +
-                        "attrname = 'Symbol' AND id = ? " +
-                        "AND code = ?"
-                );
         private final LazyPst pstBackpage = new LazyPst(
                         "SELECT backpageText FROM datanode " +
@@ -165 +160 @@
          * get Backpage info. In Schema v2, this was not stored in 
          * the attribute table but as a separate column, so this is treated
-         * as a special case.
+         * as a special case. This method is called by <pre>getAttribute (ref, "Backpage")</pre>
+         * @param ref the entity to get backpage info for.
+         * @return Backpage info as string
+         * @throws IDMapperException when database is unavailable
          */
         private String getBpInfo(Xref ref) throws IDMapperException 
@@ -245 +243 @@
         /**
          * Opens a connection to the Gene Database located in the given file.
+         * A new instance of this class is created automatically.
          * @param dbName The file containing the Gene Database. 
-         * @param connector An instance of DBConnector, to determine the type of database (e.g. DataDerby).
-         * A new instance of this class is created automatically.
+         * @param newDbConnector An instance of DBConnector, to determine the type of database (e.g. DataDerby).
+         * @param props PROP_RECREATE if you want to create a new database (possibly overwriting an existing one) 
+         *      or PROP_NONE if you want to connect read-only
+         * @throws IDMapperException when the database could not be created or connected to
          */
         public SimpleGdbImpl2(String dbName, DBConnector newDbConnector, int props) throws IDMapperException
@@ -539 +540 @@
         /**
          * @return a list of data sources present in this database. 
+           @throws IDMapperException when the database is unavailable
          */
         private Set<DataSource> getDataSources() throws IDMapperException