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'.