ViewingSequenceDB (biojava-legacy 1.9.5 API)

java.lang.Object
- org.biojava.utils.AbstractChangeable
- - org.biojava.bio.seq.db.AbstractSequenceDB
  - - org.biojava.bio.seq.db.SequenceDBWrapper
    - - org.biojava.bio.seq.db.ViewingSequenceDB

All Implemented Interfaces:

Serializable, SequenceDB, SequenceDBLite, Changeable
```
public class ViewingSequenceDB
extends SequenceDBWrapper
```
SequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database. One appropriate use of this would be to wrap a DB in one of these and then wrap this in an annotating db so that the annotation is added to views, not the underlying sequences.

Since:

1.2

Author:

Matthew Pocock

See Also:

Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from class org.biojava.bio.seq.db.SequenceDBWrapper
  SequenceDBWrapper.SequencesForwarder

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

Constructor Summary

Constructors
Constructor Description

ViewingSequenceDB(SequenceDB parent)
Create a new ViewingSequenceDB that views the sequences in parent.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`String`	`getName()`	Get the name of this sequence database.
`Sequence`	`getSequence(String id)`	Retrieve a single sequence by its id.
`Set`	`ids()`	Get an immutable set of all of the IDs in the database.

Methods inherited from class org.biojava.bio.seq.db.SequenceDBWrapper
getChangeSupport, getParent

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

Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, 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

- Constructor Detail
  - ViewingSequenceDB
```
public ViewingSequenceDB(SequenceDB parent)
```
    Create a new ViewingSequenceDB that views the sequences in parent.
    
    Parameters:
    
    parent - the SequenceDB to view
- Method Detail
  - getName
```
public String getName()
```
    Description copied from interface: SequenceDBLite
    
    Get the name of this sequence database.
    
    Returns:
    
    the name of the sequence database, which may be null.
  - getSequence
```
public Sequence getSequence(String id)
                     throws BioException
```
    Description copied from interface: SequenceDBLite
    
    Retrieve a single sequence by its id.
    
    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.
    
    Returns:
    
    a Set of ids - at the moment, strings