Package org.biojava.bio.seq.distributed
Class GFFDataSource
java.lang.Object
org.biojava.bio.seq.distributed.GFFDataSource
- All Implemented Interfaces:
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 -
Method Summary
Modifier and TypeMethodDescriptiongetFeatures
(String id, FeatureFilter ff, boolean recurse) Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats.Get all features matching a FeatureFilter provided by this DistDataSource.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.ids
(boolean topLevel) Get the complete set of sequence IDs provided by this DistDataSource.
-
Constructor Details
-
GFFDataSource
-
-
Method Details
-
hasSequence
Description copied from interface:DistDataSource
Find out if this DistDataSource provides the sequence information for a sequence ID.- Specified by:
hasSequence
in interfaceDistDataSource
- Parameters:
id
- the String id of a sequence- Returns:
- true if this DistDataSource provides the primary sequence, false otherwise
- Throws:
BioException
-
hasFeatures
Description copied from interface:DistDataSource
Find out if this DistDataSource can provide features on a sequence with a particular ID.- Specified by:
hasFeatures
in interfaceDistDataSource
- Parameters:
id
- the String id of a sequence- Returns:
- true if this DistDataSource provides features for the sequence, false otherwise
- Throws:
BioException
-
getFeatures
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 interfaceDistDataSource
- Parameters:
ff
- the FeatureFilter to search with- Returns:
- a FeatureHolder with all matching filters
- Throws:
BioException
-
getFeatures
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 interfaceDistDataSource
- Parameters:
id
- the ID of the Sequenceff
- the FeatureFilter to search withrecurse
- 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
Description copied from interface:DistDataSource
Get a Sequence object for an ID.- Specified by:
getSequence
in interfaceDistDataSource
- 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
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 interfaceDistDataSource
- 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
-