Package org.biojava.bio.seq.io

Class SequenceBuilderFilter

java.lang.Object

org.biojava.bio.seq.io.SequenceBuilderFilter

All Implemented Interfaces:

SeqIOListener, SequenceBuilder

Direct Known Subclasses:

EmblProcessor, FastaDescriptionLineParser, GenbankProcessor, OrganismParser, SwissprotProcessor

public class SequenceBuilderFilter
extends Object
implements SequenceBuilder

Base-class for builders that pass filtered events onto another builder.

Since:

1.1

Author:

Matthew Pocock

See Also:

RichSeqIOAdapter

Constructor Summary

Constructors

Constructor	Description
SequenceBuilderFilter(SequenceBuilder delegate)	Create a new SeqIOFilter that will forward events on to another listener.

Method Summary

Modifier and Type	Method	Description
void	addFeatureProperty(Object key, Object value)	Notify the listener of a feature property.
void	addSequenceProperty(Object key, Object value)	Notify the listener of a sequence-wide property.
void	addSymbols(Alphabet alpha, Symbol[] syms, int start, int length)	Notify the listener of symbol data.
void	endFeature()	Mark the end of data associated with one specific feature.
void	endSequence()	Notify the listener that processing of the sequence is complete.
SequenceBuilder	getDelegate()	Retrieve the delegate that is wrapped.
Sequence	makeSequence()	Return the Sequence object which has been constructed by this builder.
void	setName(String name)	Notify the listener that the current sequence is generally known by a particular name.
void	setURI(String uri)	Notify the listener of a URI identifying the current sequence.
void	startFeature(Feature.Template templ)	Notify the listener that a new feature object is starting.
void	startSequence()	Start the processing of a sequence.

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceBuilderFilter

public SequenceBuilderFilter(SequenceBuilder delegate)

Create a new SeqIOFilter that will forward events on to another listener.

Parameters:

delegate - the SequenceBuilder to wrap

Method Detail

getDelegate

public SequenceBuilder getDelegate()

Retrieve the delegate that is wrapped.

Returns:

the SequenceBuilder delegate

startSequence

public void startSequence()
                   throws ParseException

Description copied from interface: SeqIOListener

Start the processing of a sequence. This method exists primarily to enforce the life-cycles of SeqIOListener objects.

Specified by:

startSequence in interface SeqIOListener

Throws:

ParseException

endSequence

public void endSequence()
                 throws ParseException

Description copied from interface: SeqIOListener

Notify the listener that processing of the sequence is complete.

Specified by:

endSequence in interface SeqIOListener

Throws:

ParseException

setName

public void setName(String name)
             throws ParseException

Description copied from interface: SeqIOListener

Notify the listener that the current sequence is generally known by a particular name.

Specified by:

setName in interface SeqIOListener

Parameters:

name - the String that should be returned by getName for the sequence being parsed

Throws:

ParseException

setURI

public void setURI(String uri)
            throws ParseException

Description copied from interface: SeqIOListener

Notify the listener of a URI identifying the current sequence.

Specified by:

setURI in interface SeqIOListener

Throws:

ParseException

addSymbols

public void addSymbols(Alphabet alpha,
                       Symbol[] syms,
                       int start,
                       int length)
                throws IllegalAlphabetException

Description copied from interface: SeqIOListener

Notify the listener of symbol data. All symbols passed to this method are guarenteed to be contained within the specified alphabet. Generally all calls to a given Listener should have the same alphabet -- if not, the listener implementation is likely to throw an exception

Specified by:

addSymbols in interface SeqIOListener

Parameters:

alpha - The alphabet of the symbol data

syms - An array containing symbols

start - The start offset of valid data within the array

length - The number of valid symbols in the array

Throws:

IllegalAlphabetException - if we can't cope with this alphabet.

addSequenceProperty

public void addSequenceProperty(Object key,
                                Object value)
                         throws ParseException

Description copied from interface: SeqIOListener

Notify the listener of a sequence-wide property. This might be stored as an entry in the sequence's annotation bundle.

Specified by:

addSequenceProperty in interface SeqIOListener

Throws:

ParseException

startFeature

public void startFeature(Feature.Template templ)
                  throws ParseException

Description copied from interface: SeqIOListener

Notify the listener that a new feature object is starting. Every call to startFeature should have a corresponding call to endFeature. If the listener is concerned with a hierarchy of features, it should maintain a stack of `open' features.

Specified by:

startFeature in interface SeqIOListener

Throws:

ParseException

endFeature

public void endFeature()
                throws ParseException

Description copied from interface: SeqIOListener

Mark the end of data associated with one specific feature.

Specified by:

endFeature in interface SeqIOListener

Throws:

ParseException

addFeatureProperty

public void addFeatureProperty(Object key,
                               Object value)
                        throws ParseException

Description copied from interface: SeqIOListener

Notify the listener of a feature property.

Specified by:

addFeatureProperty in interface SeqIOListener

Throws:

ParseException

makeSequence

public Sequence makeSequence()
                      throws BioException

Description copied from interface: SequenceBuilder

Return the Sequence object which has been constructed by this builder. This method is only expected to succeed after the endSequence() notifier has been called.

Specified by:

makeSequence in interface SequenceBuilder

Throws:

BioException