Package org.biojava.bio.seq.impl

Class SimpleSequenceFactory

java.lang.Object

org.biojava.bio.seq.impl.SimpleSequenceFactory

All Implemented Interfaces:

Serializable, SequenceFactory

public class SimpleSequenceFactory
extends Object
implements SequenceFactory, Serializable

A no-frills implementation of SequenceFactory that produces SimpleSequence objects.

Author:

Matthew Pocock, Thomas Down

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
SimpleSequenceFactory()

Method Summary

Modifier and Type	Method	Description
Sequence	createSequence(SymbolList symList, String uri, String name, Annotation annotation)	Creates a sequence using these parameters.
FeatureRealizer	getFeatureRealizer()	Returns the FeatureRealizer set by "setFeatureRealizer".
void	setFeatureRealizer(FeatureRealizer fr)	Set the FeatureRealizer used by new sequences created by this factory.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SimpleSequenceFactory

public SimpleSequenceFactory()

Method Detail

getFeatureRealizer

public FeatureRealizer getFeatureRealizer()

Returns the FeatureRealizer set by "setFeatureRealizer".

setFeatureRealizer

public void setFeatureRealizer(FeatureRealizer fr)

Set the FeatureRealizer used by new sequences created by this factory.

createSequence

public Sequence createSequence(SymbolList symList,
                               String uri,
                               String name,
                               Annotation annotation)

Description copied from interface: SequenceFactory

Creates a sequence using these parameters.

Specified by:

createSequence in interface SequenceFactory

Parameters:

symList - the SymbolList defining the 'sequence'

uri - the uri of the sequence. This will be returned by the getURN() method on Sequence.

name - the name

annotation - a hint for the annotation of the resulting sequence

Returns:

a new Sequence object