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A database of sequences. This may have several implementations with rich behaviour, but basically most of the time you will just use the interface methods to do stuff. A sequence database contains a finite number of sequences stored under unique keys.
Field Summary | |
static ChangeType |
SEQUENCES
Signals that sequences are being added to or remove from the database. |
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. |
void |
removeSequence(java.lang.String id)
Remove the sequence associated with an ID from the database. |
Methods inherited from interface org.biojava.utils.Changeable |
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener |
Field Detail |
public static final ChangeType SEQUENCES
Method Detail |
public java.lang.String getName()
public Sequence getSequence(java.lang.String id) throws IllegalIDException, BioException
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
seq
- the Sequence to add
IllegalIDException
- if a uniqe ID could not be generated for seq
BioException
- if something goes wrong with adding the sequence
ChangeVetoException
- if either the database does not allow
sequences to be added or the modification was vetoedpublic void removeSequence(java.lang.String id) throws IllegalIDException, BioException, ChangeVetoException
id
- the ID of the sequence to remove
IllegalIDException
- if there is no sequence for the ID
BioException
- if something failed while removing the sequence for
that ID
ChangeVetoException
- if either the database does not allow
sequences to be removed or the modification was vetoed
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