Package org.biojava.bio.seq.distributed

Interface DistDataSource

  • All Known Implementing Classes:
    GFFDataSource, SequenceDBDataSource
    public interface DistDataSource

    Object which contributes data to a DistributedSequenceDB.

    DistDataSource is responsible for providing some information about what sequences exist, what the SymbolList associated with it and what features are here. Typically, the objects returned from DistributedSequenceDB will be composed from information from multiple DistDataSource instances.

    Since:
    1.2 Take an instance of this interface and add it to a DistributedSequenceDB. Implement this if you have information about some seqeunces but do not wish to or can not integrate this with the main sequence at source. For example, if you have some locally annotated features for SwissProt entries, you could create a DistDataSource providing just your features and let the DistDataSource API integrate these in software with a SwissProt sequence db provider. DistDataSource instances can provided sequence information and feature information. These are integrated seperately. To provide sequences, implement hasSequence(), getSequence() and ids(). ids(false).contains(id) should equal hasSequence(id). Features are provided by implementing hasFeatures(), and the two getFeatures() methods. In the case where hasFeatures() returns true, getFeatures() should return a FeatureHolder. If it is false, getFeatures() may raise a BioException. If these rules are not followed, the results are undefined and may not be consistent.
    Author:
    Thomas Down

    • Method Detail

      • hasSequence

        boolean hasSequence​(String id)
             throws BioException
        Find out if this DistDataSource provides the sequence information for a sequence ID.
        Parameters:
        id - the String id of a sequence
        Returns:
        true if this DistDataSource provides the primary sequence, false otherwise
        Throws:
        BioException

      • hasFeatures

        boolean hasFeatures​(String id)
             throws BioException
        Find out if this DistDataSource can provide features on a sequence with a particular ID.
        Parameters:
        id - the String id of a sequence
        Returns:
        true if this DistDataSource provides features for the sequence, false otherwise
        Throws:
        BioException

      • getFeatures

        FeatureHolder getFeatures​(FeatureFilter ff)
                   throws BioException
        Get all features matching a FeatureFilter provided by this DistDataSource. You can simulate getFeatures(id, ff, recurse) by using the advanced FeatureFilter implementations.
        Parameters:
        ff - the FeatureFilter to search with
        Returns:
        a FeatureHolder with all matching filters
        Throws:
        BioException

      • getFeatures

        FeatureHolder getFeatures​(String id,
                          FeatureFilter ff,
                          boolean recurse)
                   throws BioException
        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.
        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

        Sequence getSequence​(String id)
              throws BioException
        Get a Sequence object for an ID.
        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

        Set ids​(boolean topLevel)
 throws BioException

        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.

        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