Class DASSequenceDB

  • All Implemented Interfaces:
    SequenceDB, SequenceDBLite, Changeable

    public class DASSequenceDB
    extends Unchangeable
    implements SequenceDB

    Collection of sequences retrieved from the DAS network.

    The DAS-specific parts of this API are still subject to change.

    Since:
    1.1
    Author:
    Thomas Down
    • Method Detail

      • filter

        public FeatureHolder filter​(FeatureFilter ff)
        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.
      • getURL

        public java.net.URL getURL()
        Return the URL of the reference server for this database.
      • getName

        public java.lang.String getName()
        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.
      • ids

        public java.util.Set ids()
        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
      • removeSequence

        public void removeSequence​(java.lang.String id)
                            throws ChangeVetoException
        Description copied from interface: SequenceDBLite
        Remove the sequence associated with an ID from the database.
        Specified by:
        removeSequence in interface SequenceDBLite
        Parameters:
        id - the ID of the sequence to remove
        Throws:
        ChangeVetoException - if either the database does not allow sequences to be removed or the modification was vetoed
      • sequenceIterator

        public SequenceIterator sequenceIterator()
        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