Uses of Class
org.biojava.bio.seq.io.ParseException

Packages that use ParseException

org.biojava.bio.program.phred	Parser for Phred output
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.ontology.io	Tools for loading and saving ontologies.

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

Methods in org.biojava.bio.program.phred that throw ParseException

boolean

PhredFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol)

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

Methods in org.biojava.bio.program.xff that throw ParseException

protected void	FeatureHandler.fireStartFeature() Fire the startFeature event.
protected void	FeatureHandler.fireEndFeature() Fire the endFeature event.
protected void	FeatureHandler.setFeatureProperty(Object key, Object value) Set a property.

Uses of ParseException in org.biojava.bio.seq.io

Methods in org.biojava.bio.seq.io that throw ParseException

void	SwissprotProcessor.endSequence()
void	SwissprotProcessor.addSequenceProperty(Object key, Object value)
void	SwissprotFileFormer.startSequence() Start the processing of a sequence.
void	SwissprotFileFormer.endSequence() Notify the listener that processing of the sequence is complete.
void	SwissprotFileFormer.setName(String theName) The name is printed out as part of the identifier line.
void	SwissprotFileFormer.setURI(String theURI) Null implementation.
void	SwissprotFileFormer.addSequenceProperty(Object key, Object value) Notify the listener of a sequence-wide property.
void	SwissprotFileFormer.startFeature(Feature.Template templ) Null implementation.
void	SwissprotFileFormer.endFeature() Null implementation.
void	SwissprotFileFormer.addFeatureProperty(Object key, Object value) Null implementation
void	SequenceBuilderFilter.startSequence()
void	SequenceBuilderFilter.endSequence()
void	SequenceBuilderFilter.setName(String name)
void	SequenceBuilderFilter.setURI(String uri)
void	SequenceBuilderFilter.addSequenceProperty(Object key, Object value)
void	SequenceBuilderFilter.startFeature(Feature.Template templ)
void	SequenceBuilderFilter.endFeature()
void	SequenceBuilderFilter.addFeatureProperty(Object key, Object value)
void	SequenceBuilderBase.addFeatureProperty(Object key, Object value) Add an annotation-bundle entry to the feature.
void	SeqIOListener.startSequence() Start the processing of a sequence.
void	SeqIOListener.endSequence() Notify the listener that processing of the sequence is complete.
void	SeqIOListener.setName(String name) Notify the listener that the current sequence is generally known by a particular name.
void	SeqIOListener.setURI(String uri) Notify the listener of a URI identifying the current sequence.
void	SeqIOListener.addSequenceProperty(Object key, Object value) Notify the listener of a sequence-wide property.
void	SeqIOListener.startFeature(Feature.Template templ) Notify the listener that a new feature object is starting.
void	SeqIOListener.endFeature() Mark the end of data associated with one specific feature.
void	SeqIOListener.addFeatureProperty(Object key, Object value) Notify the listener of a feature property.
void	SeqIOFilter.startSequence()
void	SeqIOFilter.endSequence()
void	SeqIOFilter.setName(String name)
void	SeqIOFilter.setURI(String uri)
void	SeqIOFilter.addSequenceProperty(Object key, Object value)
void	SeqIOFilter.startFeature(Feature.Template templ)
void	SeqIOFilter.endFeature()
void	SeqIOFilter.addFeatureProperty(Object key, Object value)
void	SeqIOAdapter.startSequence()
void	SeqIOAdapter.endSequence()
void	SeqIOAdapter.setName(String name)
void	SeqIOAdapter.setURI(String uri)
void	SeqIOAdapter.addSequenceProperty(Object key, Object value)
void	SeqIOAdapter.startFeature(Feature.Template templ)
void	SeqIOAdapter.endFeature()
void	SeqIOAdapter.addFeatureProperty(Object key, Object value)
void	ProteinRefSeqFileFormer.startFeature(Feature.Template templ)
void	OrganismParser.addSequenceProperty(Object sciNameKey, Object value)
void	OrganismParser.endSequence()
void	GenbankProcessor.endSequence()
void	GenbankProcessor.addSequenceProperty(Object key, Object value)
boolean	GenbankFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided.
void	GenbankFileFormer.setName(String id)
void	GenbankFileFormer.startSequence()
void	GenbankFileFormer.endSequence()
void	GenbankFileFormer.setURI(String uri)
void	GenbankFileFormer.addSequenceProperty(Object key, Object value)
void	GenbankFileFormer.startFeature(Feature.Template templ)
void	GenbankFileFormer.endFeature()
void	GenbankFileFormer.addFeatureProperty(Object key, Object value)
boolean	FastaFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol)
void	FastaDescriptionLineParser.addSequenceProperty(Object key, Object value)
void	EmblProcessor.endSequence()
void	EmblProcessor.addSequenceProperty(Object key, Object value)
boolean	EmblLikeFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)
protected void	EmblLikeFormat.processSequenceLine(String line, StreamParser parser) Dispatch symbol data from SQ-block line of an EMBL-like file.
void	EmblFileFormer.setName(String id)
void	EmblFileFormer.startSequence()
void	EmblFileFormer.endSequence()
void	EmblFileFormer.setURI(String uri)
void	EmblFileFormer.addSequenceProperty(Object key, Object value)
void	EmblFileFormer.startFeature(Feature.Template templ)
void	EmblFileFormer.endFeature()

Uses of ParseException in org.biojava.bio.seq.io.agave

Methods in org.biojava.bio.seq.io.agave that throw ParseException

protected ListIterator

StAXPropertyHandler.getHandlerStackIterator() get iterator for current stack starting at the position below mine.

Uses of ParseException in org.biojava.bio.seq.io.game

Methods in org.biojava.bio.seq.io.game that throw ParseException

protected ListIterator

StAXPropertyHandler.getHandlerStackIterator() get iterator for current stack starting at the position below mine.

Uses of ParseException in org.biojava.ontology.io

Methods in org.biojava.ontology.io that throw ParseException

Ontology

GOParser.parseGO(BufferedReader goFile, String ontoName, String ontoDescription, OntologyFactory factory)