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 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
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 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.