Uses of Class
org.biojava.bio.seq.io.ParseException
Packages that use ParseException
Package
Description
Parser for Phred output
Event-driven parsing system for the Extensible Feature Format (XFF).
Classes and interfaces for processing and producing flat-file representations
of sequences.
Classes for converting between AGAVE XML and BioJava objects.
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
Tools for loading and saving ontologies.
Classes to support the I/O of Nexus files.
Classes to support the reading and writing of PHYLIP format.
Classes to support the I/O of RichSequence and
Bioentry objects.
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Uses of ParseException in org.biojava.bio.program.phred
Methods in org.biojava.bio.program.phred that throw ParseExceptionModifier and TypeMethodDescriptionboolean
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 ParseExceptionModifier and TypeMethodDescriptionprotected 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 ParseExceptionModifier and TypeMethodDescriptionvoid
GenbankFileFormer.addFeatureProperty
(Object key, Object value) Deprecated.void
SeqIOAdapter.addFeatureProperty
(Object key, Object value) void
SeqIOFilter.addFeatureProperty
(Object key, Object value) void
SeqIOListener.addFeatureProperty
(Object key, Object value) Notify the listener of a feature property.void
SequenceBuilderBase.addFeatureProperty
(Object key, Object value) Add an annotation-bundle entry to the feature.void
SequenceBuilderFilter.addFeatureProperty
(Object key, Object value) void
SwissprotFileFormer.addFeatureProperty
(Object key, Object value) Deprecated.Null implementationvoid
EmblFileFormer.addSequenceProperty
(Object key, Object value) Deprecated.void
EmblProcessor.addSequenceProperty
(Object key, Object value) Deprecated.void
FastaDescriptionLineParser.addSequenceProperty
(Object key, Object value) Deprecated.void
GenbankFileFormer.addSequenceProperty
(Object key, Object value) Deprecated.void
GenbankProcessor.addSequenceProperty
(Object key, Object value) Deprecated.void
OrganismParser.addSequenceProperty
(Object sciNameKey, Object value) Deprecated.void
SeqIOAdapter.addSequenceProperty
(Object key, Object value) void
SeqIOFilter.addSequenceProperty
(Object key, Object value) void
SeqIOListener.addSequenceProperty
(Object key, Object value) Notify the listener of a sequence-wide property.void
SequenceBuilderFilter.addSequenceProperty
(Object key, Object value) void
SwissprotFileFormer.addSequenceProperty
(Object key, Object value) Deprecated.Notify the listener of a sequence-wide property.void
SwissprotProcessor.addSequenceProperty
(Object key, Object value) Deprecated.void
EmblFileFormer.endFeature()
Deprecated.void
GenbankFileFormer.endFeature()
Deprecated.void
SeqIOAdapter.endFeature()
void
SeqIOFilter.endFeature()
void
SeqIOListener.endFeature()
Mark the end of data associated with one specific feature.void
SequenceBuilderFilter.endFeature()
void
SwissprotFileFormer.endFeature()
Deprecated.Null implementation.void
EmblFileFormer.endSequence()
Deprecated.void
EmblProcessor.endSequence()
Deprecated.void
GenbankFileFormer.endSequence()
Deprecated.void
GenbankProcessor.endSequence()
Deprecated.void
OrganismParser.endSequence()
Deprecated.void
SeqIOAdapter.endSequence()
void
SeqIOFilter.endSequence()
void
SeqIOListener.endSequence()
Notify the listener that processing of the sequence is complete.void
SequenceBuilderFilter.endSequence()
void
SwissprotFileFormer.endSequence()
Deprecated.Notify the listener that processing of the sequence is complete.void
SwissprotProcessor.endSequence()
Deprecated.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 aSeqIOListener
using aSymbolTokenizer
to convert sequence strings toSymbol
objects.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.void
Deprecated.void
Deprecated.void
void
void
Notify the listener that the current sequence is generally known by a particular name.void
void
Deprecated.The name is printed out as part of the identifier line.void
Deprecated.void
Deprecated.void
void
void
Notify the listener of a URI identifying the current sequence.void
void
Deprecated.Null implementation.void
EmblFileFormer.startFeature
(Feature.Template templ) Deprecated.void
GenbankFileFormer.startFeature
(Feature.Template templ) Deprecated.void
ProteinRefSeqFileFormer.startFeature
(Feature.Template templ) Deprecated.void
SeqIOAdapter.startFeature
(Feature.Template templ) void
SeqIOFilter.startFeature
(Feature.Template templ) void
SeqIOListener.startFeature
(Feature.Template templ) Notify the listener that a new feature object is starting.void
SequenceBuilderFilter.startFeature
(Feature.Template templ) void
SwissprotFileFormer.startFeature
(Feature.Template templ) Deprecated.Null implementation.void
EmblFileFormer.startSequence()
Deprecated.void
GenbankFileFormer.startSequence()
Deprecated.void
SeqIOAdapter.startSequence()
void
SeqIOFilter.startSequence()
void
SeqIOListener.startSequence()
Start the processing of a sequence.void
SequenceBuilderFilter.startSequence()
void
SwissprotFileFormer.startSequence()
Deprecated.Start the processing of a sequence. -
Uses of ParseException in org.biojava.bio.seq.io.agave
Methods in org.biojava.bio.seq.io.agave that throw ParseExceptionModifier and TypeMethodDescriptionprotected 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 ParseExceptionModifier and TypeMethodDescriptionprotected 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 ParseExceptionModifier and TypeMethodDescriptionGOParser.parseGO
(BufferedReader goFile, String ontoName, String ontoDescription, OntologyFactory factory) 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 ParseExceptionModifier and TypeMethodDescriptionOboFileParser.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 fileprotected OboFileParser.SOPair
OboFileParser.readQuotedString
(String value, int startIndex, int stopIndex, char terminatingChar, boolean requireQuotes, boolean legalEndOfLine) -
Uses of ParseException in org.biojavax.bio.phylo.io.nexus
Methods in org.biojavax.bio.phylo.io.nexus that throw ParseExceptionModifier and TypeMethodDescriptionvoid
CharactersBlock.addTaxLabel
(String taxLabel) Add a TAXLABEL.void
CharactersBlockBuilder.addTaxLabel
(String taxLabel) void
CharactersBlockListener.addTaxLabel
(String taxLabel) Add a TAXLABEL.void
DistancesBlock.addTaxLabel
(String taxLabel) Add a TAXLABEL.void
DistancesBlockBuilder.addTaxLabel
(String taxLabel) void
DistancesBlockListener.addTaxLabel
(String taxLabel) Add a TAXLABEL.void
TaxaBlock.addTaxLabel
(String taxLabel) Add a TAXLABEL.void
TaxaBlockBuilder.addTaxLabel
(String taxLabel) void
TaxaBlockListener.addTaxLabel
(String taxLabel) Add another value after the TAXLABEL tag.void
NexusBlockListener.commentText
(String comment) Receiving free text inside a comment tag.void
NexusBlockParser.Abstract.commentText
(String comment) void
NexusBlockParser.commentText
(String comment) Receiving free text inside a comment tag.void
NexusFileListener.Abstract.commentText
(String comment) void
NexusFileListener.commentText
(String comment) Receiving free text inside a comment tag.void
TreesBlockParser.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
CharactersBlockParser.parseToken
(String token) void
DistancesBlockParser.parseToken
(String token) abstract void
NexusBlockParser.Abstract.parseToken
(String token) void
NexusBlockParser.parseToken
(String token) Notifies the parser of the next token.void
NexusFileListener.Abstract.parseToken
(String token) void
NexusFileListener.parseToken
(String token) Encountered a token.void
TaxaBlockParser.parseToken
(String token) void
TreesBlockParser.parseToken
(String token) -
Uses of ParseException in org.biojavax.bio.phylo.io.phylip
Methods in org.biojavax.bio.phylo.io.phylip that throw ParseExceptionModifier and TypeMethodDescriptionvoid
PHYLIPFileBuilder.endFile()
void
PHYLIPFileListener.endFile()
Finished reading a file.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 ParseExceptionModifier and TypeMethodDescriptionvoid
DebuggingRichSeqIOListener.addFeatureProperty
(Object key, Object value) void
RichSeqIOAdapter.addFeatureProperty
(Object key, Object value) void
SimpleRichSequenceBuilder.addFeatureProperty
(Object key, Object value) Notify the listener of a feature property.void
DebuggingRichSeqIOListener.addSequenceProperty
(Object key, Object value) void
RichSeqIOAdapter.addSequenceProperty
(Object key, Object value) void
SimpleRichSequenceBuilder.addSequenceProperty
(Object key, Object value) Notify the listener of a sequence-wide property.void
DebuggingRichSeqIOListener.endFeature()
void
RichSeqIOAdapter.endFeature()
void
SimpleRichSequenceBuilder.endFeature()
Mark the end of data associated with one specific feature.void
DebuggingRichSeqIOListener.endSequence()
void
RichSeqIOAdapter.endSequence()
void
SimpleRichSequenceBuilder.endSequence()
Notify the listener that processing of the sequence is complete.UniProtCommentParser.generate()
Generates a comment string based on the current values of the internal fields.DebuggingRichSeqIOListener.getCurrentFeature()
RichSeqIOAdapter.getCurrentFeature()
RichSeqIOListener.getCurrentFeature()
Gets the feature currently being created.SimpleRichSequenceBuilder.getCurrentFeature()
Gets the feature currently being created.void
UniProtCommentParser.parseComment
(String c) Parses the comment string from the given comment and populates the internal fields appropriately.void
UniProtCommentParser.parseComment
(Comment 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 lineboolean
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
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
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
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
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
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
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
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.void
DebuggingRichSeqIOListener.setAccession
(String accession) void
RichSeqIOAdapter.setAccession
(String accession) void
RichSeqIOListener.setAccession
(String accession) Call back method so the event emitter can tell the listener the accession of the record being read.void
SimpleRichSequenceBuilder.setAccession
(String accession) Call back method so the event emitter can tell the listener the accession of the record being read.void
DebuggingRichSeqIOListener.setCircular
(boolean circular) void
RichSeqIOAdapter.setCircular
(boolean circular) void
RichSeqIOListener.setCircular
(boolean circular) Defined this sequence being parser as circular.void
SimpleRichSequenceBuilder.setCircular
(boolean circular) Defined this sequence being parser as circular.void
DebuggingRichSeqIOListener.setComment
(String comment) void
RichSeqIOAdapter.setComment
(String comment) 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
SimpleRichSequenceBuilder.setComment
(String comment) Call back method so the event emitter can tell the listener about a comment in the record being read.void
DebuggingRichSeqIOListener.setDescription
(String description) void
RichSeqIOAdapter.setDescription
(String description) void
RichSeqIOListener.setDescription
(String description) Call back method so the event emitter can tell the listener the description of the record being read.void
SimpleRichSequenceBuilder.setDescription
(String description) Call back method so the event emitter can tell the listener the description of the record being read.void
DebuggingRichSeqIOListener.setDivision
(String division) void
RichSeqIOAdapter.setDivision
(String division) void
RichSeqIOListener.setDivision
(String division) Call back method so the event emitter can tell the listener the division of the record being read.void
SimpleRichSequenceBuilder.setDivision
(String division) Call back method so the event emitter can tell the listener the division of the record being read.void
DebuggingRichSeqIOListener.setIdentifier
(String identifier) void
RichSeqIOAdapter.setIdentifier
(String identifier) void
RichSeqIOListener.setIdentifier
(String identifier) Call back method so the event emitter can tell the listener the identifier of the record being read.void
SimpleRichSequenceBuilder.setIdentifier
(String identifier) Call back method so the event emitter can tell the listener the identifier of the record being read.void
void
void
Notify the listener that the current sequence is generally known by a particular name.void
DebuggingRichSeqIOListener.setNamespace
(Namespace namespace) void
RichSeqIOAdapter.setNamespace
(Namespace namespace) void
RichSeqIOListener.setNamespace
(Namespace namespace) Call back method so the event emitter can tell the listener the namespace of the record being read.void
SimpleRichSequenceBuilder.setNamespace
(Namespace namespace) Call back method so the event emitter can tell the listener the namespace of the record being read.void
DebuggingRichSeqIOListener.setRankedCrossRef
(RankedCrossRef crossRef) void
RichSeqIOAdapter.setRankedCrossRef
(RankedCrossRef crossRef) void
RichSeqIOListener.setRankedCrossRef
(RankedCrossRef crossRef) Call back method so the event emitter can tell the listener about a cross reference.void
SimpleRichSequenceBuilder.setRankedCrossRef
(RankedCrossRef ref) Call back method so the event emitter can tell the listener about a cross reference.void
DebuggingRichSeqIOListener.setRankedDocRef
(RankedDocRef ref) void
RichSeqIOAdapter.setRankedDocRef
(RankedDocRef ref) 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
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
DebuggingRichSeqIOListener.setRelationship
(BioEntryRelationship relationship) void
RichSeqIOAdapter.setRelationship
(BioEntryRelationship relationship) 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
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
DebuggingRichSeqIOListener.setSeqVersion
(String version) void
RichSeqIOAdapter.setSeqVersion
(String version) 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
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
void
void
Call back method so the event emitter can tell the listener the Taxon of the record being read.void
Call back method so the event emitter can tell the listener the Taxon of the record being read.void
void
void
Deprecated.There is no clear mapping between URI and BioSQL.void
Notify the listener of a URI identifying the current sequence.void
DebuggingRichSeqIOListener.setVersion
(int version) void
RichSeqIOAdapter.setVersion
(int version) void
RichSeqIOListener.setVersion
(int version) Call back method so the event emitter can tell the listener the version of the record being read.void
SimpleRichSequenceBuilder.setVersion
(int version) Call back method so the event emitter can tell the listener the version of the record being read.void
DebuggingRichSeqIOListener.startFeature
(Feature.Template templ) void
RichSeqIOAdapter.startFeature
(Feature.Template templ) void
SimpleRichSequenceBuilder.startFeature
(Feature.Template templ) Notify the listener that a new feature object is starting.void
DebuggingRichSeqIOListener.startSequence()
void
RichSeqIOAdapter.startSequence()
void
SimpleRichSequenceBuilder.startSequence()
Start the processing of a sequence. -
Uses of ParseException in org.biojavax.bio.taxa.io
Methods in org.biojavax.bio.taxa.io that throw ParseExceptionModifier and TypeMethodDescriptionNCBITaxonomyLoader.readName
(BufferedReader names) Reads the next entry from the names.dmp file and returns the corresponding NCBITaxon object with the name added in already.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.NCBITaxonomyLoader.readNode
(BufferedReader nodes) Reads the next entry from the nodes.dmp file and returns the corresponding NCBITaxon object.SimpleNCBITaxonomyLoader.readNode
(BufferedReader nodes) Reads the next entry from the nodes.dmp file and returns the corresponding NCBITaxon object.