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java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.seq.db.AbstractSequenceDB
org.biojava.bio.seq.db.DummySequenceDB
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.
Field Summary |
Fields inherited from interface org.biojava.bio.seq.db.SequenceDBLite |
SEQUENCES |
Constructor Summary | |
DummySequenceDB(java.lang.String name)
|
Method Summary | |
void |
addSequence(Sequence seq)
Adds a sequence to the database. |
java.lang.String |
getName()
Get the name of this sequence database. |
Sequence |
getSequence(java.lang.String id)
Retrieve a single sequence by its id. |
java.util.Set |
ids()
Get an immutable set of all of the IDs in the database. |
void |
removeSequence(java.lang.String id)
Remove the sequence associated with an ID from the database. |
SequenceIterator |
sequenceIterator()
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, 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.bio.seq.db.SequenceDB |
filter |
Methods inherited from interface org.biojava.utils.Changeable |
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Constructor Detail |
public DummySequenceDB(java.lang.String name)
Method Detail |
public java.util.Set ids()
SequenceDB
ids
in interface SequenceDB
public SequenceIterator sequenceIterator()
SequenceDB
sequenceIterator
in interface SequenceDB
sequenceIterator
in class AbstractSequenceDB
public java.lang.String getName()
SequenceDBLite
getName
in interface SequenceDBLite
public Sequence getSequence(java.lang.String id) throws IllegalIDException, BioException
SequenceDBLite
getSequence
in interface SequenceDBLite
IllegalIDException
- if the database doesn't know about the id
BioException
- if there was a failure in retrieving the sequencepublic void addSequence(Sequence seq) throws IllegalIDException, BioException, ChangeVetoException
SequenceDBLite
addSequence
in interface SequenceDBLite
addSequence
in class AbstractSequenceDB
IllegalIDException
BioException
ChangeVetoException
public void removeSequence(java.lang.String id) throws IllegalIDException, BioException, ChangeVetoException
SequenceDBLite
removeSequence
in interface SequenceDBLite
removeSequence
in class AbstractSequenceDB
IllegalIDException
BioException
ChangeVetoException
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