## 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.seq.ragbag: The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code.

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

Methods in org.biojava.bio.program.phred with parameters of type SeqIOListener
`boolean` `PhredFormat.readSequence(java.io.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` Objects implementing the `SeqFileFormer` interface are responsible for the detailed formatting of sequence data prior to writing to a `PrintStream`.
`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` `EmblFileFormer` performs the detailed formatting of EMBL entries for writing to a `PrintStream`.
`class` `EmblProcessor` Simple filter which handles attribute lines from an EMBL file.
`class` `FastaDescriptionLineParser` Simple filter which performs a default extraction of data from the description lines of FASTA files.
`class` `GenbankFileFormer` `GenbankFileFormer` performs the detailed formatting of Genbank entries for writing to a `PrintStream`.
`class` `GenbankProcessor` Simple filter which handles attribute lines from a Genbank file
`class` `OrganismParser` A parser that is able to generate Taxon entries for sequence builder event streams.
`class` `ProteinRefSeqFileFormer` This class performs the detailed formatting of refseq protein entries.
`class` `ProteinRefSeqProcessor` Class description
`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` Formats a sequence into Swissprot/TrEMBL format.
`class` `SwissprotProcessor` Simple filter which handles attribute lines from an Swissprot entry.

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
`boolean` `GenbankFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)` Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided.
`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` `SequenceFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)` Read a sequence and pass data on to a SeqIOListener.
`boolean` `GAMEFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)` this version only reads annotations (no symbols)
`boolean` `FastaFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol)`
`boolean` `EmblLikeFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)`

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` `StAXPropertyHandler.featureListener`
`protected SeqIOListener` `StAXFeatureHandler.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` `StAXPropertyHandler.featureListener`
`protected SeqIOListener` `StAXFeatureHandler.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.seq.ragbag

Classes in org.biojava.bio.seq.ragbag that implement SeqIOListener
`class` `RagbagIdleSequenceBuilder` A breakfast cereal of a SequenceBuilder, jes' sits there soakin' up all those events and doin' absolutely nuffin'.