Class SequenceDBDataSource

  • All Implemented Interfaces:
    DistDataSource

    public class SequenceDBDataSource
    extends java.lang.Object
    implements DistDataSource
    Turn an entire SequenceDB instance into a DistDataSource. This is very usefull for providing the 'reference' sequence and feature set upon which you can layer any other features you have.
    Author:
    Thomas Down
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      FeatureHolder getFeatures​(java.lang.String id, FeatureFilter ff, boolean recurse)
      Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.
      FeatureHolder getFeatures​(FeatureFilter ff)
      Get all features matching a FeatureFilter provided by this DistDataSource.
      Sequence getSequence​(java.lang.String id)
      Get a Sequence object for an ID.
      boolean hasFeatures​(java.lang.String id)
      Find out if this DistDataSource can provide features on a sequence with a particular ID.
      boolean hasSequence​(java.lang.String id)
      Find out if this DistDataSource provides the sequence information for a sequence ID.
      java.util.Set ids​(boolean topLevel)
      Get the complete set of sequence IDs provided by this DistDataSource.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Method Detail

      • hasSequence

        public boolean hasSequence​(java.lang.String id)
                            throws BioException
        Description copied from interface: DistDataSource
        Find out if this DistDataSource provides the sequence information for a sequence ID.
        Specified by:
        hasSequence in interface DistDataSource
        Parameters:
        id - the String id of a sequence
        Returns:
        true if this DistDataSource provides the primary sequence, false otherwise
        Throws:
        BioException
      • hasFeatures

        public boolean hasFeatures​(java.lang.String id)
                            throws BioException
        Description copied from interface: DistDataSource
        Find out if this DistDataSource can provide features on a sequence with a particular ID.
        Specified by:
        hasFeatures in interface DistDataSource
        Parameters:
        id - the String id of a sequence
        Returns:
        true if this DistDataSource provides features for the sequence, false otherwise
        Throws:
        BioException
      • getFeatures

        public FeatureHolder getFeatures​(java.lang.String id,
                                         FeatureFilter ff,
                                         boolean recurse)
                                  throws BioException
        Description copied from interface: DistDataSource
        Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats. You can simulate getFeatures(ff) by adding the apropreate FeatureFilter implementations.
        Specified by:
        getFeatures in interface DistDataSource
        Parameters:
        id - the ID of the Sequence
        ff - the FeatureFilter to search with
        recurse - true if we are to recurse the feature hierachy, false otherwise
        Returns:
        a FeatureHolder containing all feature matching
        Throws:
        BioException - if the features could not be fetched
      • getSequence

        public Sequence getSequence​(java.lang.String id)
                             throws BioException
        Description copied from interface: DistDataSource
        Get a Sequence object for an ID.
        Specified by:
        getSequence in interface DistDataSource
        Parameters:
        id - the ID of the Sequence to fetch
        Returns:
        a Seqeunce if hasSequence(id) would return true
        Throws:
        BioException - if either the ID could not be resolved or if the sequence could not be fetched
      • ids

        public java.util.Set ids​(boolean topLevel)
                          throws BioException
        Description copied from interface: DistDataSource

        Get the complete set of sequence IDs provided by this DistDataSource.

        If the recurse flat is true, the IDs associated with the top level will be returned. However, if it is false, then IDs should be returned for all levels of an assembly hierachy including the top level IDs.

        Specified by:
        ids in interface DistDataSource
        Parameters:
        topLevel - if true, return top level IDs, otherwise all IDs
        Returns:
        a Set of String IDs
        Throws:
        BioException - if the IDs could not be fetched