Package org.biojava.bio.seq.distributed

Class GFFDataSource

java.lang.Object

org.biojava.bio.seq.distributed.GFFDataSource

All Implemented Interfaces:

DistDataSource

public class GFFDataSource
extends Object
implements DistDataSource

Use a GFFEntrySet as a DataSource for adding annotation to sequences. Instantiate this and add it to an instance of DistributeSequenceDB. All of the GFF features that have sequence fields matching sequence IDs in the db will be merged in.

Author:

Thomas Down, Matthew Pocock

Constructor Summary

Constructors

Constructor	Description
GFFDataSource(GFFEntrySet gffe)

Method Summary

Modifier and Type	Method	Description
FeatureHolder	getFeatures(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(String id)	Get a Sequence object for an ID.
boolean	hasFeatures(String id)	Find out if this DistDataSource can provide features on a sequence with a particular ID.
boolean	hasSequence(String id)	Find out if this DistDataSource provides the sequence information for a sequence ID.
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

Constructor Detail

GFFDataSource

public GFFDataSource(GFFEntrySet gffe)

Method Detail

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