Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV CLASS NEXT CLASS | FRAMES NO FRAMES
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD

## org.biojava.bio.seq.distributed
Class DistributedSequenceDB

    java.lang.Object
      org.biojava.utils.AbstractChangeable
          org.biojava.bio.seq.db.AbstractSequenceDB
              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
`static ChangeType` | `DATASOURCE`
`static ChangeType` | `DATASOURCE_SELECTION`

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

Constructor Summary
`DistributedSequenceDB()`

Method Summary
`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.bio.seq.db.SequenceDB
`filter, sequenceIterator`

Methods inherited from interface org.biojava.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

Field Detail

### DATASOURCE

    public static final ChangeType DATASOURCE

### DATASOURCE_SELECTION

    public static final ChangeType DATASOURCE_SELECTION

Constructor Detail

### DistributedSequenceDB

    public DistributedSequenceDB()

Method Detail

### 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

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV CLASS NEXT CLASS | FRAMES NO FRAMES
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD