Package org.biojava.bio.seq.db
Class AnnotatedSequenceDB
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.db.AbstractSequenceDB
org.biojava.bio.seq.db.AnnotatedSequenceDB
- All Implemented Interfaces:
Serializable
,SequenceDB
,SequenceDBLite
,Changeable
SequenceDB implementation which lazily applies a SequenceAnnotator
to sequences retrieved from a SequenceDB.
- Author:
- Thomas Down, Matthew Pocock
- See Also:
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Field Summary
Fields inherited from interface org.biojava.bio.seq.db.SequenceDBLite
SEQUENCES
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected Sequence
doAnnotation
(Sequence seq) Apply the annotation to a sequence.getName()
Get the name of this sequence database.Get the original sequenceDB from this annotated sequenceDB.getSequence
(String id) Retrieve a single sequence by its id.ids()
Get an immutable set of all of the IDs in the database.Returns a SequenceIterator over all sequences in the database.Methods inherited from class org.biojava.bio.seq.db.AbstractSequenceDB
addSequence, filter, removeSequence
Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from interface org.biojava.bio.seq.db.SequenceDB
filter
Methods inherited from interface org.biojava.bio.seq.db.SequenceDBLite
addSequence, removeSequence
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Constructor Details
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AnnotatedSequenceDB
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Method Details
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getParent
Get the original sequenceDB from this annotated sequenceDB. -
getName
Description copied from interface:SequenceDBLite
Get the name of this sequence database.- Specified by:
getName
in interfaceSequenceDBLite
- Returns:
- the name of the sequence database, which may be null.
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getSequence
Description copied from interface:SequenceDBLite
Retrieve a single sequence by its id.- Specified by:
getSequence
in interfaceSequenceDBLite
- Parameters:
id
- the id to retrieve by- Returns:
- the Sequence with that id
- Throws:
BioException
- if there was a failure in retrieving the sequence
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ids
Description copied from interface:SequenceDB
Get an immutable set of all of the IDs in the database. The ids are legal arguments to getSequence.- Specified by:
ids
in interfaceSequenceDB
- Returns:
- a Set of ids - at the moment, strings
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sequenceIterator
Description copied from interface:SequenceDB
Returns a SequenceIterator over all sequences in the database. The order of retrieval is undefined.- Specified by:
sequenceIterator
in interfaceSequenceDB
- Overrides:
sequenceIterator
in classAbstractSequenceDB
- Returns:
- a SequenceIterator over all sequences
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doAnnotation
Apply the annotation to a sequence.- Parameters:
seq
- the sequence to annotate.- Throws:
BioException
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