Uses of Interface
org.biojava.bio.seq.io.SeqIOListener
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Packages that use SeqIOListener Package Description org.biojava.bio.program.phred Parser for Phred outputorg.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. -
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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)
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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)
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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 insteadinterface
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 insteadclass
EmblProcessor
Deprecated.Use org.biojavax.bio.seq.io framework insteadclass
FastaDescriptionLineParser
Deprecated.Use org.biojavax.bio.seq.io.FastaFormatclass
GenbankFileFormer
Deprecated.Use org.biojavax.bio.seq.io framework insteadclass
GenbankProcessor
Deprecated.Use org.biojavax.bio.seq.io framework insteadclass
OrganismParser
Deprecated.Use org.biojavax.bio.taxa framework insteadclass
ProteinRefSeqFileFormer
Deprecated.Use org.biojavax.bio.seq.io framework insteadclass
ProteinRefSeqProcessor
Deprecated.Use org.biojavax.bio.seq.io framework insteadclass
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
SequenceDBSequenceBuilder
This SequenceBuilder has a variety of modes of operation.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 insteadclass
SwissprotProcessor
Deprecated.Use org.biojavax.bio.seq.io framework insteadMethods 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 aSequence
object and sends events describing its data to theSeqIOListener
.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 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 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 listenerMethods in org.biojava.bio.seq.io.agave with parameters of type SeqIOListener Modifier and Type Method Description void
StAXFeatureHandler. setFeatureListener(SeqIOListener siol)
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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 listenerMethods in org.biojava.bio.seq.io.game with parameters of type SeqIOListener Modifier and Type Method Description void
StAXFeatureHandler. setFeatureListener(SeqIOListener siol)
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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.
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