org.biojava.bio.seq.distributed.DistributedSequenceDB

All Implemented Interfaces:: SequenceDB, SequenceDBLite, Changeable

public class DistributedSequenceDB extends AbstractSequenceDB implements SequenceDB

Sequence database from the meta-DAS system.

Since:: 1.2 Once you've made one of these and populated it with a few DistDataSource instances, you should be able to prety much forget about it and use it directly as a normal SequenceDB implementation. DataSources can be added and removed while the object is live.
Author:: Thomas Down, Matthew Pocock

Field Summary

Fields

Modifier and Type

Field

Description

static final ChangeType

DATASOURCE

static final ChangeType

DATASOURCE_SELECTION

Fields inherited from interface org.biojava.bio.seq.db.SequenceDBLite
SEQUENCES
Constructor Summary

Constructors

Constructor

Description

DistributedSequenceDB()
Method Summary

Modifier and Type

Method

Description

void

addDataSource(DistDataSource dds)

Add a distributed data source.

void

addSequence(Sequence seq)

Adds a sequence to the database.

protected ChangeSupport

getChangeSupport()

Set

getDataSources()

Get the current set of all currently registered data sources.

String

getName()

Get the name of this sequence database.

Sequence

getSequence(String id)

Retrieve a single sequence by its id.

protected boolean

hasChangeSupport()

Set

ids()

Get an immutable set of all of the IDs in the database.

void

removeDataSource(DistDataSource dds)

Remove a distributed data source.

void

removeSequence(String id)

Remove the sequence associated with an ID from the database.

Methods inherited from class org.biojava.bio.seq.db.AbstractSequenceDB
filter, sequenceIterator

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, sequenceIterator

Field Details
- DATASOURCE
  
  public static final ChangeType DATASOURCE
- DATASOURCE_SELECTION
  
  public static final ChangeType DATASOURCE_SELECTION
Constructor Details
- DistributedSequenceDB
  
  public DistributedSequenceDB()
Method Details
- hasChangeSupport
  
  protected boolean hasChangeSupport()
- getChangeSupport
  
  protected ChangeSupport getChangeSupport()
- getDataSources
  
  public Set getDataSources()
  
  Get the current set of all currently registered data sources.
  The returned Set is totaly independant of any future changes made to the distributed sequence DB.
  
  Returns:
  
  a new Set containing all DistDataSource instances registered at the time
- addDataSource
  
  public void addDataSource(DistDataSource dds) throws ChangeVetoException
  
  Add a distributed data source.
  
  Parameters:
  
  dds - the DistDataSource to add
  
  Throws:
  
  ChangeVetoException - if the data source could not be added
- removeDataSource
  
  public void removeDataSource(DistDataSource dds) throws ChangeVetoException
  
  Remove a distributed data source.
  
  Parameters:
  
  dds - the DistributedDataSource to remove
  
  Throws:
  
  ChangeVetoException - if the data source could not be removed
- getName
  
  public String getName()
  
  Description copied from interface: SequenceDBLite
  
  Get the name of this sequence database.
  
  Specified by:
  
  getName in interface SequenceDBLite
  
  Returns:
  
  the name of the sequence database, which may be null.
- addSequence
  
  public void addSequence(Sequence seq) throws ChangeVetoException
  
  Description copied from interface: SequenceDBLite
  
  Adds a sequence to the database.
  
  Specified by:
  
  addSequence in interface SequenceDBLite
  
  Overrides:
  
  addSequence in class AbstractSequenceDB
  
  Parameters:
  
  seq - the Sequence to add
  
  Throws:
  
  ChangeVetoException - if either the database does not allow sequences to be added or the modification was vetoed
- removeSequence
  
  public void removeSequence(String id) throws ChangeVetoException
  
  Description copied from interface: SequenceDBLite
  
  Remove the sequence associated with an ID from the database.
  
  Specified by:
  
  removeSequence in interface SequenceDBLite
  
  Overrides:
  
  removeSequence in class AbstractSequenceDB
  
  Parameters:
  
  id - the ID of the sequence to remove
  
  Throws:
  
  ChangeVetoException - if either the database does not allow sequences to be removed or the modification was vetoed
- getSequence
  
  public Sequence getSequence(String id) throws IllegalIDException, BioException
  
  Description copied from interface: SequenceDBLite
  
  Retrieve a single sequence by its id.
  
  Specified by:
  
  getSequence in interface SequenceDBLite
  
  Parameters:
  
  id - the id to retrieve by
  
  Returns:
  
  the Sequence with that id
  
  Throws:
  
  IllegalIDException - if the database doesn't know about the id
  
  BioException - if there was a failure in retrieving the sequence
- ids
  
  public Set 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 interface SequenceDB
  
  Returns:
  
  a Set of ids - at the moment, strings

Class DistributedSequenceDB

Field Summary

Fields inherited from interface org.biojava.bio.seq.db.SequenceDBLite

Constructor Summary

Method Summary

Methods inherited from class org.biojava.bio.seq.db.AbstractSequenceDB

Methods inherited from class org.biojava.utils.AbstractChangeable

Methods inherited from class java.lang.Object

Methods inherited from interface org.biojava.utils.Changeable

Methods inherited from interface org.biojava.bio.seq.db.SequenceDB

Field Details

DATASOURCE

DATASOURCE_SELECTION

Constructor Details

DistributedSequenceDB

Method Details

hasChangeSupport

getChangeSupport

getDataSources

addDataSource

removeDataSource

getName

addSequence

removeSequence

getSequence

ids