CachingSequenceDB (biojava-legacy 1.9.5 API)

CachingSequenceDB (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.CachingSequenceDB

All Implemented Interfaces:

Serializable, SequenceDB, SequenceDBLite, Changeable
```
public class CachingSequenceDB
extends SequenceDBWrapper
```
SequenceDB implementation that caches the results of another SequenceDB.

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

CachingSequenceDB(SequenceDB parent)
Create a new CachingSequenceDB that caches 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
  - CachingSequenceDB
```
public CachingSequenceDB(SequenceDB parent)
```
    Create a new CachingSequenceDB that caches the sequences in parent.
    
    Parameters:
    
    parent - the SequenceDB to cache
- Method Detail
  - getName
```
public String getName()
```
    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
```
    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