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

Packages that use ParseException

Package	Description
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.
org.biojava.ontology.obo
org.biojavax.bio.phylo.io.nexus	Classes to support the I/O of Nexus files.
org.biojavax.bio.phylo.io.phylip	Classes to support the reading and writing of PHYLIP format.
org.biojavax.bio.seq.io	Classes to support the I/O of RichSequence and Bioentry objects.
org.biojavax.bio.taxa.io

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

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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
protected void	FeatureHandler.fireEndFeature() Fire the endFeature event.
protected void	FeatureHandler.fireStartFeature() Fire the startFeature 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

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

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

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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
Ontology	GOParser.parseGO(BufferedReader goFile, String ontoName, String ontoDescription, OntologyFactory factory)
Ontology	OboParser.parseOBO(BufferedReader oboFile, String ontoName, String ontoDescription) Parse a OBO file and return its content as a BioJava Ontology object

Uses of ParseException in org.biojava.ontology.obo

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

Modifier and Type	Method and Description
protected Map<String,Object>[]	OboFileParser.getDbxrefList(String line, int startoffset, int endoffset)
protected int	OboFileParser.getNestedValue(org.biojava.ontology.obo.NestedValue nv, String str, int startIndex)
void	OboFileParser.parseOBO(BufferedReader oboFile) parse an ontology file
protected Map<String,Object>	OboFileParser.parseXref(String line, int startoffset, int endoffset)
protected OboFileParser.SOPair	OboFileParser.readQuotedString(String value, int startIndex, int stopIndex, char terminatingChar, boolean requireQuotes, boolean legalEndOfLine)
String	OboFileParser.unescape(String str)
OboFileParser.SOPair	OboFileParser.unescape(String str, char toChar, int startindex, boolean mustFindChar)
OboFileParser.SOPair	OboFileParser.unescape(String str, char toChar, int startindex, int endindex, boolean mustFindChar)

Uses of ParseException in org.biojavax.bio.phylo.io.nexus

Methods in org.biojavax.bio.phylo.io.nexus that throw ParseException

Modifier and Type	Method and Description
void	CharactersBlockListener.addTaxLabel(String taxLabel) Add a TAXLABEL.
void	DistancesBlockListener.addTaxLabel(String taxLabel) Add a TAXLABEL.
void	DistancesBlock.addTaxLabel(String taxLabel) Add a TAXLABEL.
void	TaxaBlock.addTaxLabel(String taxLabel) Add a TAXLABEL.
void	TaxaBlockBuilder.addTaxLabel(String taxLabel)
void	DistancesBlockBuilder.addTaxLabel(String taxLabel)
void	TaxaBlockListener.addTaxLabel(String taxLabel) Add another value after the TAXLABEL tag.
void	CharactersBlockBuilder.addTaxLabel(String taxLabel)
void	CharactersBlock.addTaxLabel(String taxLabel) Add a TAXLABEL.
void	TreesBlockParser.commentText(String comment)
void	NexusBlockParser.commentText(String comment) Receiving free text inside a comment tag.
void	NexusBlockParser.Abstract.commentText(String comment)
void	NexusBlockListener.commentText(String comment) Receiving free text inside a comment tag.
void	NexusFileListener.commentText(String comment) Receiving free text inside a comment tag.
void	NexusFileListener.Abstract.commentText(String comment)
org.jgrapht.WeightedGraph<String,org.jgrapht.graph.DefaultWeightedEdge>	TreesBlock.getTreeAsWeightedJGraphT(String label) Get given (NewickString) tree by label, converts it to weighted graph (JGraphT).
static void	NexusFileFormat.parseFile(NexusFileListener listener, File inputFile) Parse a file and send events to the given listener.
static void	NexusFileFormat.parseInputStream(NexusFileListener listener, InputStream inputStream) Parse a stream and send events to the given listener.
static void	NexusFileFormat.parseReader(NexusFileListener listener, Reader inputReader) Parse a reader and send events to the given listener.
void	DistancesBlockParser.parseToken(String token)
void	TaxaBlockParser.parseToken(String token)
void	TreesBlockParser.parseToken(String token)
void	NexusBlockParser.parseToken(String token) Notifies the parser of the next token.
abstract void	NexusBlockParser.Abstract.parseToken(String token)
void	CharactersBlockParser.parseToken(String token)
void	NexusFileListener.parseToken(String token) Encountered a token.
void	NexusFileListener.Abstract.parseToken(String token)

Uses of ParseException in org.biojavax.bio.phylo.io.phylip

Methods in org.biojavax.bio.phylo.io.phylip that throw ParseException

Modifier and Type	Method and Description
void	PHYLIPFileListener.endFile() Finished reading a file.
void	PHYLIPFileBuilder.endFile()
static void	PHYLIPFileFormat.parse(PHYLIPFileListener listener, BufferedReader reader)
static void	PHYLIPFileFormat.parseFile(PHYLIPFileListener listener, File inputFile)
static void	PHYLIPFileFormat.parseInputStream(PHYLIPFileListener listener, InputStream inputStream)
static void	PHYLIPFileFormat.parseReader(PHYLIPFileListener listener, Reader inputReader)

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

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

Modifier and Type	Method and Description
void	DebuggingRichSeqIOListener.addFeatureProperty(Object key, Object value)
void	SimpleRichSequenceBuilder.addFeatureProperty(Object key, Object value) Notify the listener of a feature property.
void	RichSeqIOAdapter.addFeatureProperty(Object key, Object value)
void	DebuggingRichSeqIOListener.addSequenceProperty(Object key, Object value)
void	SimpleRichSequenceBuilder.addSequenceProperty(Object key, Object value) Notify the listener of a sequence-wide property.
void	RichSeqIOAdapter.addSequenceProperty(Object key, Object value)
void	DebuggingRichSeqIOListener.endFeature()
void	SimpleRichSequenceBuilder.endFeature() Mark the end of data associated with one specific feature.
void	RichSeqIOAdapter.endFeature()
void	DebuggingRichSeqIOListener.endSequence()
void	SimpleRichSequenceBuilder.endSequence() Notify the listener that processing of the sequence is complete.
void	RichSeqIOAdapter.endSequence()
String	UniProtCommentParser.generate() Generates a comment string based on the current values of the internal fields.
RichFeature	DebuggingRichSeqIOListener.getCurrentFeature()
RichFeature	SimpleRichSequenceBuilder.getCurrentFeature() Gets the feature currently being created.
RichFeature	RichSeqIOListener.getCurrentFeature() Gets the feature currently being created.
RichFeature	RichSeqIOAdapter.getCurrentFeature()
void	UniProtCommentParser.parseComment(Comment c) Parses the comment string from the given comment and populates the internal fields appropriately.
void	UniProtCommentParser.parseComment(String c) Parses the comment string from the given comment and populates the internal fields appropriately.
static RichLocation	GenbankLocationParser.parseLocation(Namespace featureNS, String featureAccession, String locationString) Parses a location.
static RichLocation	UniProtLocationParser.parseLocation(String loc) Parses a location.
void	FastaFormat.processHeader(String line, RichSeqIOListener rsiol, Namespace ns) Parse the Header information from the Fasta Description line
boolean	UniProtFormat.readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
boolean	INSDseqFormat.readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
boolean	UniProtXMLFormat.readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
boolean	FastaFormat.readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rsiol, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
boolean	EMBLxmlFormat.readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
boolean	GenbankFormat.readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
boolean	EMBLFormat.readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rlistener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.
boolean	UniProtFormat.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	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.
boolean	EMBLxmlFormat.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	EMBLFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.
void	DebuggingRichSeqIOListener.setAccession(String accession)
void	SimpleRichSequenceBuilder.setAccession(String accession) Call back method so the event emitter can tell the listener the accession of the record being read.
void	RichSeqIOListener.setAccession(String accession) Call back method so the event emitter can tell the listener the accession of the record being read.
void	RichSeqIOAdapter.setAccession(String accession)
void	DebuggingRichSeqIOListener.setCircular(boolean circular)
void	SimpleRichSequenceBuilder.setCircular(boolean circular) Defined this sequence being parser as circular.
void	RichSeqIOListener.setCircular(boolean circular) Defined this sequence being parser as circular.
void	RichSeqIOAdapter.setCircular(boolean circular)
void	DebuggingRichSeqIOListener.setComment(String comment)
void	SimpleRichSequenceBuilder.setComment(String comment) Call back method so the event emitter can tell the listener about a comment in the record being read.
void	RichSeqIOListener.setComment(String comment) Call back method so the event emitter can tell the listener about a comment in the record being read.
void	RichSeqIOAdapter.setComment(String comment)
void	DebuggingRichSeqIOListener.setDescription(String description)
void	SimpleRichSequenceBuilder.setDescription(String description) Call back method so the event emitter can tell the listener the description of the record being read.
void	RichSeqIOListener.setDescription(String description) Call back method so the event emitter can tell the listener the description of the record being read.
void	RichSeqIOAdapter.setDescription(String description)
void	DebuggingRichSeqIOListener.setDivision(String division)
void	SimpleRichSequenceBuilder.setDivision(String division) Call back method so the event emitter can tell the listener the division of the record being read.
void	RichSeqIOListener.setDivision(String division) Call back method so the event emitter can tell the listener the division of the record being read.
void	RichSeqIOAdapter.setDivision(String division)
void	DebuggingRichSeqIOListener.setIdentifier(String identifier)
void	SimpleRichSequenceBuilder.setIdentifier(String identifier) Call back method so the event emitter can tell the listener the identifier of the record being read.
void	RichSeqIOListener.setIdentifier(String identifier) Call back method so the event emitter can tell the listener the identifier of the record being read.
void	RichSeqIOAdapter.setIdentifier(String identifier)
void	DebuggingRichSeqIOListener.setName(String name)
void	SimpleRichSequenceBuilder.setName(String name) Notify the listener that the current sequence is generally known by a particular name.
void	RichSeqIOAdapter.setName(String name)
void	DebuggingRichSeqIOListener.setNamespace(Namespace namespace)
void	SimpleRichSequenceBuilder.setNamespace(Namespace namespace) Call back method so the event emitter can tell the listener the namespace of the record being read.
void	RichSeqIOListener.setNamespace(Namespace namespace) Call back method so the event emitter can tell the listener the namespace of the record being read.
void	RichSeqIOAdapter.setNamespace(Namespace namespace)
void	DebuggingRichSeqIOListener.setRankedCrossRef(RankedCrossRef crossRef)
void	SimpleRichSequenceBuilder.setRankedCrossRef(RankedCrossRef ref) Call back method so the event emitter can tell the listener about a cross reference.
void	RichSeqIOListener.setRankedCrossRef(RankedCrossRef crossRef) Call back method so the event emitter can tell the listener about a cross reference.
void	RichSeqIOAdapter.setRankedCrossRef(RankedCrossRef crossRef)
void	DebuggingRichSeqIOListener.setRankedDocRef(RankedDocRef ref)
void	SimpleRichSequenceBuilder.setRankedDocRef(RankedDocRef ref) Call back method so the event emitter can tell the listener about a literature reference in the record being read.
void	RichSeqIOListener.setRankedDocRef(RankedDocRef ref) Call back method so the event emitter can tell the listener about a literature reference in the record being read.
void	RichSeqIOAdapter.setRankedDocRef(RankedDocRef ref)
void	DebuggingRichSeqIOListener.setRelationship(BioEntryRelationship relationship)
void	SimpleRichSequenceBuilder.setRelationship(BioEntryRelationship relationship) Call back method so the event emitter can tell the listener about a relationship between the bioentry or sequence in the record being read and another bioentry.
void	RichSeqIOListener.setRelationship(BioEntryRelationship relationship) Call back method so the event emitter can tell the listener about a relationship between the bioentry or sequence in the record being read and another bioentry.
void	RichSeqIOAdapter.setRelationship(BioEntryRelationship relationship)
void	DebuggingRichSeqIOListener.setSeqVersion(String version)
void	SimpleRichSequenceBuilder.setSeqVersion(String seqVersion) Call back method so the event emitter can tell the listener the version of the sequence of the record being read.
void	RichSeqIOListener.setSeqVersion(String version) Call back method so the event emitter can tell the listener the version of the sequence of the record being read.
void	RichSeqIOAdapter.setSeqVersion(String version)
void	DebuggingRichSeqIOListener.setTaxon(NCBITaxon taxon)
void	SimpleRichSequenceBuilder.setTaxon(NCBITaxon taxon) Call back method so the event emitter can tell the listener the Taxon of the record being read.
void	RichSeqIOListener.setTaxon(NCBITaxon taxon) Call back method so the event emitter can tell the listener the Taxon of the record being read.
void	RichSeqIOAdapter.setTaxon(NCBITaxon taxon)
void	DebuggingRichSeqIOListener.setURI(String uri)
void	SimpleRichSequenceBuilder.setURI(String uri) Notify the listener of a URI identifying the current sequence.
void	RichSeqIOListener.setURI(String uri) Deprecated. There is no clear mapping between URI and BioSQL. This method is no longer used or supported in biojavax. Don't use it. Calling it may result in exceptions. Use instead setName(String name), setAccession(String accession), setVersion(int version) etc as appropriate.
void	RichSeqIOAdapter.setURI(String uri)
void	DebuggingRichSeqIOListener.setVersion(int version)
void	SimpleRichSequenceBuilder.setVersion(int version) Call back method so the event emitter can tell the listener the version of the record being read.
void	RichSeqIOListener.setVersion(int version) Call back method so the event emitter can tell the listener the version of the record being read.
void	RichSeqIOAdapter.setVersion(int version)
void	DebuggingRichSeqIOListener.startFeature(Feature.Template templ)
void	SimpleRichSequenceBuilder.startFeature(Feature.Template templ) Notify the listener that a new feature object is starting.
void	RichSeqIOAdapter.startFeature(Feature.Template templ)
void	DebuggingRichSeqIOListener.startSequence()
void	SimpleRichSequenceBuilder.startSequence() Start the processing of a sequence.
void	RichSeqIOAdapter.startSequence()

Uses of ParseException in org.biojavax.bio.taxa.io

Methods in org.biojavax.bio.taxa.io that throw ParseException

Modifier and Type	Method and Description
NCBITaxon	SimpleNCBITaxonomyLoader.readName(BufferedReader names) Reads the next entry from the names.dmp file and returns the corresponding NCBITaxon object with the name added in already.
NCBITaxon	NCBITaxonomyLoader.readName(BufferedReader names) Reads the next entry from the names.dmp file and returns the corresponding NCBITaxon object with the name added in already.
NCBITaxon	SimpleNCBITaxonomyLoader.readNode(BufferedReader nodes) Reads the next entry from the nodes.dmp file and returns the corresponding NCBITaxon object.
NCBITaxon	NCBITaxonomyLoader.readNode(BufferedReader nodes) Reads the next entry from the nodes.dmp file and returns the corresponding NCBITaxon object.