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java.lang.Objectorg.biojava.bio.seq.distributed.SequenceDBDataSource
public class SequenceDBDataSource
Turn an entire SequenceDB instance into a DistDataSource.
Constructor Summary | |
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SequenceDBDataSource(SequenceDB seqDB)
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Method Summary | |
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FeatureHolder |
getFeatures(FeatureFilter ff)
Get all features matching a FeatureFilter provided by this DistDataSource. |
FeatureHolder |
getFeatures(String id,
FeatureFilter ff,
boolean recurse)
Get all features matching a FeatureFilter on a Sequence with an ID and recurse flats. |
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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public SequenceDBDataSource(SequenceDB seqDB)
Method Detail |
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public boolean hasSequence(String id) throws BioException
DistDataSource
hasSequence
in interface DistDataSource
id
- the String id of a sequence
BioException
public boolean hasFeatures(String id) throws BioException
DistDataSource
hasFeatures
in interface DistDataSource
id
- the String id of a sequence
BioException
public FeatureHolder getFeatures(FeatureFilter ff) throws BioException
DistDataSource
getFeatures
in interface DistDataSource
ff
- the FeatureFilter to search with
BioException
public FeatureHolder getFeatures(String id, FeatureFilter ff, boolean recurse) throws BioException
DistDataSource
getFeatures
in interface DistDataSource
id
- the ID of the Sequenceff
- the FeatureFilter to search withrecurse
- true if we are to recurse the feature hierachy, false otherwise
BioException
- if the features could not be fetchedpublic Sequence getSequence(String id) throws BioException
DistDataSource
getSequence
in interface DistDataSource
id
- the ID of the Sequence to fetch
BioException
- if either the ID could not be resolved or if the
sequence could not be fetchedpublic Set ids(boolean topLevel) throws BioException
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.
ids
in interface DistDataSource
topLevel
- if true, return top level IDs, otherwise all IDs
BioException
- if the IDs could not be fetched
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