Uses of Interface
org.biojava.bio.seq.io.SeqIOListener

Packages that use SeqIOListener

Package	Description
org.biojava.bio.program.phred	Parser for Phred output
org.biojava.bio.program.ssaha	SSAHA sequence searching API.
org.biojava.bio.program.xff	Event-driven parsing system for the Extensible Feature Format (XFF).
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.seq.io.agave	Classes for converting between AGAVE XML and BioJava objects.
org.biojava.bio.seq.io.game	Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
org.biojava.bio.seq.io.game12	Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.
org.biojavax.bio.seq.io	Classes to support the I/O of RichSequence and Bioentry objects.

Uses of SeqIOListener in org.biojava.bio.program.phred

Methods in org.biojava.bio.program.phred with parameters of type SeqIOListener

Modifier and Type	Method	Description
boolean	PhredFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol)

Uses of SeqIOListener in org.biojava.bio.program.ssaha

Methods in org.biojava.bio.program.ssaha with parameters of type SeqIOListener

Modifier and Type	Method	Description
void	SequenceStreamer.FileStreamer.streamNext(SeqIOListener listener)
void	SequenceStreamer.SequenceDBStreamer.streamNext(SeqIOListener listener)
void	SequenceStreamer.streamNext(SeqIOListener listener)

Uses of SeqIOListener in org.biojava.bio.program.xff

Methods in org.biojava.bio.program.xff that return SeqIOListener

Modifier and Type	Method	Description
SeqIOListener	XFFFeatureSetHandler.getFeatureListener()	Return the object which receives startFeature/endFeature notifications.

Methods in org.biojava.bio.program.xff with parameters of type SeqIOListener

Modifier and Type	Method	Description
void	XFFFeatureSetHandler.setFeatureListener(SeqIOListener siol)	Set the object which receives startFeature/endFeature notifications.

Uses of SeqIOListener in org.biojava.bio.seq.io

Subinterfaces of SeqIOListener in org.biojava.bio.seq.io

Modifier and Type	Interface	Description
interface	SeqFileFormer	Deprecated. Use org.biojavax.bio.seq.io framework instead
interface	SequenceBuilder	Interface for objects which accumulate state via SeqIOListener, then construct a Sequence object.

Classes in org.biojava.bio.seq.io that implement SeqIOListener

Modifier and Type	Class	Description
class	EmblFileFormer	Deprecated. Use org.biojavax.bio.seq.io framework instead
class	EmblProcessor	Deprecated. Use org.biojavax.bio.seq.io framework instead
class	FastaDescriptionLineParser	Deprecated. Use org.biojavax.bio.seq.io.FastaFormat
class	GenbankFileFormer	Deprecated. Use org.biojavax.bio.seq.io framework instead
class	GenbankProcessor	Deprecated. Use org.biojavax.bio.seq.io framework instead
class	OrganismParser	Deprecated. Use org.biojavax.bio.taxa framework instead
class	ProteinRefSeqFileFormer	Deprecated. Use org.biojavax.bio.seq.io framework instead
class	ProteinRefSeqProcessor	Deprecated. Use org.biojavax.bio.seq.io framework instead
class	SeqIOAdapter	Adapter class for SeqIOListener that has empty methods.
class	SeqIOFilter	Base-class for listeners that pass filtered events onto another listener.
class	SequenceBuilderBase	Basic SequenceBuilder implementation which accumulates all notified information.
class	SequenceBuilderFilter	Base-class for builders that pass filtered events onto another builder.
class	SimpleAssemblyBuilder	Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleAssembly.
class	SimpleSequenceBuilder	Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleSequence.
class	SmartSequenceBuilder	Basic SequenceBuilder implementation which accumulates all notified information and chooses a sequence implementation suited to the size of the sequence.
class	SwissprotFileFormer	Deprecated. Use org.biojavax.bio.seq.io framework instead
class	SwissprotProcessor	Deprecated. Use org.biojavax.bio.seq.io framework instead

Methods in org.biojava.bio.seq.io that return SeqIOListener

Modifier and Type	Method	Description
SeqIOListener	SeqIOFilter.getDelegate()	Retrieve the delegate that is wrapped.

Methods in org.biojava.bio.seq.io with parameters of type SeqIOListener

Modifier and Type	Method	Description
void	SeqIOEventEmitter.getSeqIOEvents(Sequence seq, SeqIOListener listener)	Deprecated. getSeqIOEvents scans a Sequence object and sends events describing its data to the SeqIOListener.
StreamParser	AlternateTokenization.parseStream(SeqIOListener listener)	Will throw an exception.
StreamParser	CharacterTokenization.parseStream(SeqIOListener listener)
StreamParser	SymbolTokenization.parseStream(SeqIOListener listener)	Return an object which can parse an arbitrary character stream into symbols.
StreamParser	WordTokenization.parseStream(SeqIOListener siol)
boolean	EmblLikeFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)	Deprecated.
boolean	FastaFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol)	Deprecated. Reads information from a flatfile to a SeqIOListener using a SymbolTokenizer to convert sequence strings to Symbol objects.
boolean	GAMEFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)	this version only reads annotations (no symbols)
boolean	GenbankFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)	Deprecated. Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided.
boolean	GenbankXmlFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)	Deprecated.
boolean	SequenceFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)	Read a sequence and pass data on to a SeqIOListener.

Constructors in org.biojava.bio.seq.io with parameters of type SeqIOListener

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

Uses of SeqIOListener in org.biojava.bio.seq.io.agave

Fields in org.biojava.bio.seq.io.agave declared as SeqIOListener

Modifier and Type	Field	Description
protected SeqIOListener	StAXFeatureHandler.featureListener
protected SeqIOListener	StAXPropertyHandler.featureListener

Methods in org.biojava.bio.seq.io.agave that return SeqIOListener

Modifier and Type	Method	Description
SeqIOListener	StAXFeatureHandler.getFeatureListener()	Return current feature listener

Methods in org.biojava.bio.seq.io.agave with parameters of type SeqIOListener

Modifier and Type	Method	Description
void	StAXFeatureHandler.setFeatureListener(SeqIOListener siol)

Uses of SeqIOListener in org.biojava.bio.seq.io.game

Fields in org.biojava.bio.seq.io.game declared as SeqIOListener

Modifier and Type	Field	Description
protected SeqIOListener	StAXFeatureHandler.featureListener
protected SeqIOListener	StAXPropertyHandler.featureListener

Methods in org.biojava.bio.seq.io.game that return SeqIOListener

Modifier and Type	Method	Description
SeqIOListener	StAXFeatureHandler.getFeatureListener()	Return current feature listener

Methods in org.biojava.bio.seq.io.game with parameters of type SeqIOListener

Modifier and Type	Method	Description
void	StAXFeatureHandler.setFeatureListener(SeqIOListener siol)

Uses of SeqIOListener in org.biojava.bio.seq.io.game12

Constructors in org.biojava.bio.seq.io.game12 with parameters of type SeqIOListener

Constructor	Description
GAMEHandler(SeqIOListener listener)	Constructor for the GAMEHandler object

Uses of SeqIOListener in org.biojava.bio.symbol

Methods in org.biojava.bio.symbol with parameters of type SeqIOListener

Modifier and Type	Method	Description
StreamParser	SoftMaskedAlphabet.CaseSensitiveTokenization.parseStream(SeqIOListener l)	The current implementation only supports character parsing.

Uses of SeqIOListener in org.biojavax.bio.seq.io

Subinterfaces of SeqIOListener in org.biojavax.bio.seq.io

Modifier and Type	Interface	Description
interface	RichSeqIOListener	An interface for classes that listen to BioEntry or RichSequence I/O streams.
interface	RichSequenceBuilder	An interface for objects that can build RichSequences.

Classes in org.biojavax.bio.seq.io that implement SeqIOListener

Modifier and Type	Class	Description
class	DebuggingRichSeqIOListener	This is purely for debugging purposes.
class	RichSeqIOAdapter	This class implements all methods of RichSeqIOListener and takes no action.
class	SimpleRichSequenceBuilder	Constructs BioEntry objects by listening to events.

Methods in org.biojavax.bio.seq.io with parameters of type SeqIOListener

Modifier and Type	Method	Description
boolean	EMBLFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)	Read a sequence and pass data on to a SeqIOListener.
boolean	EMBLxmlFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)	Read a sequence and pass data on to a SeqIOListener.
boolean	FastaFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)	Read a sequence and pass data on to a SeqIOListener.
boolean	GenbankFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)	Read a sequence and pass data on to a SeqIOListener.
boolean	INSDseqFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)	Read a sequence and pass data on to a SeqIOListener.
boolean	UniProtFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)	Read a sequence and pass data on to a SeqIOListener.
boolean	UniProtXMLFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)	Read a sequence and pass data on to a SeqIOListener.