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
      • BioSQLSequenceDB

        public BioSQLSequenceDB​(javax.sql.DataSource ds,
                                java.lang.String biodatabase,
                                boolean create)
                         throws BioException
        Deprecated.
        Throws:
        BioException
    • Method Detail

      • createOntology

        public Ontology createOntology​(java.lang.String name,
                                       java.lang.String description)
                                throws java.lang.Exception
        Deprecated.
        Throws:
        java.lang.Exception
      • getOntology

        public Ontology getOntology​(java.lang.String name)
                             throws java.lang.Exception
        Deprecated.
        Throws:
        java.lang.Exception
      • addOntology

        public Ontology addOntology​(Ontology onto)
                             throws java.lang.Exception
        Deprecated.
        Throws:
        java.lang.Exception
      • getName

        public java.lang.String getName()
        Deprecated.
        Description copied from interface: SequenceDBLite
        Get the name of this sequence database.
        Specified by:
        getName in interface SequenceDBLite
        Returns:
        the name of the sequence database, which may be null.
      • getSequence

        public Sequence getSequence​(java.lang.String id)
                             throws BioException
        Deprecated.
        Description copied from interface: SequenceDBLite
        Retrieve a single sequence by its id.
        Specified by:
        getSequence in interface SequenceDBLite
        Parameters:
        id - the id to retrieve by
        Returns:
        the Sequence with that id
        Throws:
        IllegalIDException - if the database doesn't know about the id
        BioException - if there was a failure in retrieving the sequence
      • ids

        public java.util.Set ids()
        Deprecated.
        Description copied from interface: SequenceDB
        Get an immutable set of all of the IDs in the database. The ids are legal arguments to getSequence.
        Specified by:
        ids in interface SequenceDB
        Returns:
        a Set of ids - at the moment, strings
      • filter

        public FeatureHolder filter​(FeatureFilter ff)
        Deprecated.
        Description copied from interface: SequenceDB
        Query features attached to all sequences in this database. This is equivalent to applying filter to all sequences then merging the results.
        Specified by:
        filter in interface SequenceDB
        Parameters:
        ff - a FeatureFilter.
      • sequenceIterator

        public SequenceIterator sequenceIterator()
        Deprecated.
        Description copied from interface: SequenceDB
        Returns a SequenceIterator over all sequences in the database. The order of retrieval is undefined.
        Specified by:
        sequenceIterator in interface SequenceDB
        Returns:
        a SequenceIterator over all sequences