Package org.biojava.bio.seq.db
Class AbstractSequenceDB
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.db.AbstractSequenceDB
- All Implemented Interfaces:
SequenceDB
,SequenceDBLite
,Changeable
- Direct Known Subclasses:
AnnotatedSequenceDB
,DistributedSequenceDB
,DummySequenceDB
,HashSequenceDB
,IndexedSequenceDB
,SequenceDBWrapper
An abstract implementation of SequenceDB that provides the sequenceIterator
method.
- Author:
- Matthew Pocock, Thomas Down
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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 TypeMethodDescriptionvoid
addSequence
(Sequence seq) Adds a sequence to the database.filter
(FeatureFilter ff) Query features attached to all sequences in this database.void
removeSequence
(String id) Remove the sequence associated with an ID from the database.Returns a SequenceIterator over all sequences in the database.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
ids
Methods inherited from interface org.biojava.bio.seq.db.SequenceDBLite
getName, getSequence
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Constructor Details
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AbstractSequenceDB
public AbstractSequenceDB()
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Method Details
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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
- Returns:
- a SequenceIterator over all sequences
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filter
Description copied from interface:SequenceDB
Query features attached to all sequences in this database. This is equivalent to applyingfilter
to all sequences then merging the results.- Specified by:
filter
in interfaceSequenceDB
- Parameters:
ff
- aFeatureFilter
.
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addSequence
Description copied from interface:SequenceDBLite
Adds a sequence to the database.- Specified by:
addSequence
in interfaceSequenceDBLite
- Parameters:
seq
- the Sequence to add- Throws:
BioException
- if something goes wrong with adding the sequenceChangeVetoException
- if either the database does not allow sequences to be added or the modification was vetoed
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removeSequence
Description copied from interface:SequenceDBLite
Remove the sequence associated with an ID from the database.- Specified by:
removeSequence
in interfaceSequenceDBLite
- Parameters:
id
- the ID of the sequence to remove- Throws:
BioException
- if something failed while removing the sequence for that IDChangeVetoException
- if either the database does not allow sequences to be removed or the modification was vetoed
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