Class BioSQLSequenceDB

  • All Implemented Interfaces:
    SequenceDB, SequenceDBLite, Changeable

    public class BioSQLSequenceDB
    extends AbstractChangeable
    implements SequenceDB
    Deprecated.
    Use hibernate and org.biojavax.bio.db.*
    SequenceDB keyed off a BioSQL database. This is an almost-complete implementation of the BioJava Sequence, SequenceDB, and Feature interfaces, and can be used in a wide range of applications. Note: It now uses BioSQL schema version 1.0 (Post Singapore) All previous versions are no longer supported.
    Since:
    1.3
    Author:
    Thomas Down, Matthew Pocock, Simon Foote, Len Trigg, Mark Schreiber, Richard Holland
    • Constructor Detail

      • BioSQLSequenceDB

        public BioSQLSequenceDB​(java.lang.String dbDriver,
                                java.lang.String dbURL,
                                java.lang.String dbUser,
                                java.lang.String dbPass,
                                java.lang.String biodatabase,
                                boolean create)
                         throws BioException
        Deprecated.
        Connect to a BioSQL database.
        Parameters:
        dbDriver - A JDBC database driver. For example, com.jdbc.mysql.Driver
        dbURL - A JDBC database URL. For example, jdbc:postgresql://localhost/thomasd_biosql
        dbUser - The username to use when connecting to the database (or an empty string).
        dbPass - The password to use when connecting to the database (or an empty string).
        biodatabase - The identifier of a namespace within the physical BioSQL database.
        create - If the requested namespace doesn't exist, and this flag is true, a new namespace will be created.
        Throws:
        BioException - if an error occurs communicating with the database
      • BioSQLSequenceDB

        public BioSQLSequenceDB​(java.lang.String dbURL,
                                java.lang.String dbUser,
                                java.lang.String dbPass,
                                java.lang.String biodatabase,
                                boolean create)
                         throws BioException
        Deprecated.
        Connect to a BioSQL database.
        Parameters:
        dbURL - A JDBC database URL. For example, jdbc:postgresql://localhost/thomasd_biosql
        dbUser - The username to use when connecting to the database (or an empty string).
        dbPass - The password to use when connecting to the database (or an empty string).
        biodatabase - The identifier of a namespace within the physical BioSQL database.
        create - If the requested namespace doesn't exist, and this flag is true, a new namespace will be created.
        Throws:
        BioException - if an error occurs communicating with the database