Package org.biojava.bio.seq.distributed

Class SequenceDBDataSource

java.lang.Object
org.biojava.bio.seq.distributed.SequenceDBDataSource
All Implemented Interfaces:
DistDataSource
public class SequenceDBDataSource extends 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

  • Constructor Details

  • Method Details

    • hasSequence

      public boolean hasSequence(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(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(FeatureFilter ff) throws BioException
      Description copied from interface: DistDataSource
      Get all features matching a FeatureFilter provided by this DistDataSource. You can simulate getFeatures(id, ff, recurse) by using the advanced FeatureFilter implementations.
      Specified by:
      getFeatures in interface DistDataSource
      Parameters:
      ff - the FeatureFilter to search with
      Returns:
      a FeatureHolder with all matching filters
      Throws:
      BioException

    • getFeatures

      public FeatureHolder getFeatures(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(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 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