Package org.biojava.bio.seq.db
Class DummySequenceDB
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.db.AbstractSequenceDB
org.biojava.bio.seq.db.DummySequenceDB
- All Implemented Interfaces:
SequenceDB
,SequenceDBLite
,Changeable
DummySequenceDB
is an implementation which contains
only a DummySequence
. It will return the same
DummySequence
instance regardless of the sequence id
used to retrieve a sequence.- Since:
- 1.2
- Author:
- Keith James
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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.getName()
Get the name of this sequence database.getSequence
(String id) Retrieve a single sequence by its id.ids()
Get an immutable set of all of the IDs in the 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.bio.seq.db.AbstractSequenceDB
filter
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
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Constructor Details
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DummySequenceDB
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Method Details
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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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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:
IllegalIDException
- if the database doesn't know about the idBioException
- if there was a failure in retrieving the sequence
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addSequence
Description copied from interface:SequenceDBLite
Adds a sequence to the database.- Specified by:
addSequence
in interfaceSequenceDBLite
- Overrides:
addSequence
in classAbstractSequenceDB
- Parameters:
seq
- the Sequence to add- Throws:
IllegalIDException
- if a uniqe ID could not be generated for seqBioException
- 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
- Overrides:
removeSequence
in classAbstractSequenceDB
- Parameters:
id
- the ID of the sequence to remove- Throws:
IllegalIDException
- if there is no sequence for the IDBioException
- 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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