Uses of Interface org.biojava.bio.seq.io.SeqIOListener (BioJava-1.5-beta API)

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

Packages that use SeqIOListener
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
`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
`void` | `SequenceStreamer.streamNext(SeqIOListener listener)`
`void` | `SequenceStreamer.SequenceDBStreamer.streamNext(SeqIOListener listener)`
`void` | `SequenceStreamer.FileStreamer.streamNext(SeqIOListener listener)`

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

Methods in org.biojava.bio.program.xff that return SeqIOListener
`SeqIOListener` | `XFFFeatureSetHandler.getFeatureListener()` Return the object which receives startFeature/endFeature notifications.

Methods in org.biojava.bio.program.xff with parameters of type SeqIOListener
`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
`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
`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` | `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 instead
`class` | `SwissprotProcessor` Deprecated. Use org.biojavax.bio.seq.io framework instead

Methods in org.biojava.bio.seq.io that return SeqIOListener
`SeqIOListener` | `SeqIOFilter.getDelegate()` Retrieve the delegate that is wrapped.

Methods in org.biojava.bio.seq.io with parameters of type SeqIOListener
`void` | `SeqIOEventEmitter.getSeqIOEvents(Sequence seq, SeqIOListener listener)` Deprecated. `getSeqIOEvents` scans a `Sequence` object and sends events describing its data to the `SeqIOListener`.
`StreamParser` | `SymbolTokenization.parseStream(SeqIOListener listener)` Return an object which can parse an arbitrary character stream into symbols.
`StreamParser` | `WordTokenization.parseStream(SeqIOListener siol)`
`StreamParser` | `CharacterTokenization.parseStream(SeqIOListener listener)`
`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` | `SequenceFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)` Read a sequence and pass data on to a SeqIOListener.
`boolean` | `EmblLikeFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)` Deprecated.
`boolean` | `GenbankXmlFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)` Deprecated.
`boolean` | `GAMEFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)` this version only reads annotations (no symbols)
`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.

Constructors in org.biojava.bio.seq.io with parameters of type SeqIOListener
`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
`protected SeqIOListener` | `StAXFeatureHandler.featureListener`
`protected SeqIOListener` | `StAXPropertyHandler.featureListener`

Methods in org.biojava.bio.seq.io.agave that return SeqIOListener
`SeqIOListener` | `StAXFeatureHandler.getFeatureListener()` Return current feature listener

Methods in org.biojava.bio.seq.io.agave with parameters of type SeqIOListener
`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
`protected SeqIOListener` | `StAXFeatureHandler.featureListener`
`protected SeqIOListener` | `StAXPropertyHandler.featureListener`

Methods in org.biojava.bio.seq.io.game that return SeqIOListener
`SeqIOListener` | `StAXFeatureHandler.getFeatureListener()` Return current feature listener

Methods in org.biojava.bio.seq.io.game with parameters of type SeqIOListener
`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
`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
`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
`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
`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
`boolean` | `EMBLFormat.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` | `EMBLxmlFormat.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.
`boolean` | `FastaFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)` Read a sequence and pass data on to a SeqIOListener.

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