Uses of Interface
org.biojava.bio.seq.io.SeqIOListener
Packages that use SeqIOListener
Package
Description
Parser for Phred output
SSAHA sequence searching API.
Event-driven parsing system for the Extensible Feature Format (XFF).
Classes and interfaces for processing and producing flat-file representations
of sequences.
Classes for converting between AGAVE XML and BioJava objects.
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
Representation of the Symbols that make up a sequence, and locations within
them.
Classes to support the I/O of RichSequence and
Bioentry objects.
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Uses of SeqIOListener in org.biojava.bio.program.phred
Methods in org.biojava.bio.program.phred with parameters of type SeqIOListenerModifier and TypeMethodDescriptionboolean
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 SeqIOListenerModifier and TypeMethodDescriptionvoid
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 SeqIOListenerModifier and TypeMethodDescriptionXFFFeatureSetHandler.getFeatureListener()
Return the object which receives startFeature/endFeature notifications.Methods in org.biojava.bio.program.xff with parameters of type SeqIOListenerModifier and TypeMethodDescriptionvoid
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.ioModifier and TypeInterfaceDescriptioninterface
Deprecated.Use org.biojavax.bio.seq.io framework insteadinterface
Interface for objects which accumulate state via SeqIOListener, then construct a Sequence object.Classes in org.biojava.bio.seq.io that implement SeqIOListenerModifier and TypeClassDescriptionclass
Deprecated.Use org.biojavax.bio.seq.io framework insteadclass
Deprecated.Use org.biojavax.bio.seq.io framework insteadclass
Deprecated.Use org.biojavax.bio.seq.io.FastaFormatclass
Deprecated.Use org.biojavax.bio.seq.io framework insteadclass
Deprecated.Use org.biojavax.bio.seq.io framework insteadclass
Deprecated.Use org.biojavax.bio.taxa framework insteadclass
Deprecated.Use org.biojavax.bio.seq.io framework insteadclass
Deprecated.Use org.biojavax.bio.seq.io framework insteadclass
Adapter class for SeqIOListener that has empty methods.class
Base-class for listeners that pass filtered events onto another listener.class
Basic SequenceBuilder implementation which accumulates all notified information.class
Base-class for builders that pass filtered events onto another builder.class
This SequenceBuilder has a variety of modes of operation.class
Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleAssembly.class
Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleSequence.class
Basic SequenceBuilder implementation which accumulates all notified information and chooses a sequence implementation suited to the size of the sequence.class
Deprecated.Use org.biojavax.bio.seq.io framework insteadclass
Deprecated.Use org.biojavax.bio.seq.io framework insteadMethods in org.biojava.bio.seq.io that return SeqIOListenerModifier and TypeMethodDescriptionSeqIOFilter.getDelegate()
Retrieve the delegate that is wrapped.Methods in org.biojava.bio.seq.io with parameters of type SeqIOListenerModifier and TypeMethodDescriptionvoid
SeqIOEventEmitter.getSeqIOEvents
(Sequence seq, SeqIOListener listener) Deprecated.getSeqIOEvents
scans aSequence
object and sends events describing its data to theSeqIOListener
.AlternateTokenization.parseStream
(SeqIOListener listener) Will throw an exception.CharacterTokenization.parseStream
(SeqIOListener listener) SymbolTokenization.parseStream
(SeqIOListener listener) Return an object which can parse an arbitrary character stream into symbols.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 aSeqIOListener
using aSymbolTokenizer
to convert sequence strings toSymbol
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 SeqIOListenerModifierConstructorDescriptionSeqIOFilter
(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 SeqIOListenerModifier and TypeFieldDescriptionprotected SeqIOListener
StAXFeatureHandler.featureListener
protected SeqIOListener
StAXPropertyHandler.featureListener
Methods in org.biojava.bio.seq.io.agave that return SeqIOListenerModifier and TypeMethodDescriptionStAXFeatureHandler.getFeatureListener()
Return current feature listenerMethods in org.biojava.bio.seq.io.agave with parameters of type SeqIOListener -
Uses of SeqIOListener in org.biojava.bio.seq.io.game
Fields in org.biojava.bio.seq.io.game declared as SeqIOListenerModifier and TypeFieldDescriptionprotected SeqIOListener
StAXFeatureHandler.featureListener
protected SeqIOListener
StAXPropertyHandler.featureListener
Methods in org.biojava.bio.seq.io.game that return SeqIOListenerModifier and TypeMethodDescriptionStAXFeatureHandler.getFeatureListener()
Return current feature listenerMethods in org.biojava.bio.seq.io.game with parameters of type SeqIOListener -
Uses of SeqIOListener in org.biojava.bio.seq.io.game12
Constructors in org.biojava.bio.seq.io.game12 with parameters of type SeqIOListenerModifierConstructorDescriptionGAMEHandler
(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 SeqIOListenerModifier and TypeMethodDescriptionSoftMaskedAlphabet.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.ioModifier and TypeInterfaceDescriptioninterface
An interface for classes that listen to BioEntry or RichSequence I/O streams.interface
An interface for objects that can build RichSequences.Classes in org.biojavax.bio.seq.io that implement SeqIOListenerModifier and TypeClassDescriptionclass
This is purely for debugging purposes.class
This class implements all methods of RichSeqIOListener and takes no action.class
Constructs BioEntry objects by listening to events.Methods in org.biojavax.bio.seq.io with parameters of type SeqIOListenerModifier and TypeMethodDescriptionboolean
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.