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 TypeMethodDescriptionbooleanPhredFormat.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 voidFeatureHandler.fireEndFeature()Fire the endFeature event.protected voidFeatureHandler.fireStartFeature()Fire the startFeature event.protected voidFeatureHandler.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 TypeMethodDescriptionvoidGenbankFileFormer.addFeatureProperty(Object key, Object value) Deprecated.voidSeqIOAdapter.addFeatureProperty(Object key, Object value) voidSeqIOFilter.addFeatureProperty(Object key, Object value) voidSeqIOListener.addFeatureProperty(Object key, Object value) Notify the listener of a feature property.voidSequenceBuilderBase.addFeatureProperty(Object key, Object value) Add an annotation-bundle entry to the feature.voidSequenceBuilderFilter.addFeatureProperty(Object key, Object value) voidSwissprotFileFormer.addFeatureProperty(Object key, Object value) Deprecated.Null implementationvoidEmblFileFormer.addSequenceProperty(Object key, Object value) Deprecated.voidEmblProcessor.addSequenceProperty(Object key, Object value) Deprecated.voidFastaDescriptionLineParser.addSequenceProperty(Object key, Object value) Deprecated.voidGenbankFileFormer.addSequenceProperty(Object key, Object value) Deprecated.voidGenbankProcessor.addSequenceProperty(Object key, Object value) Deprecated.voidOrganismParser.addSequenceProperty(Object sciNameKey, Object value) Deprecated.voidSeqIOAdapter.addSequenceProperty(Object key, Object value) voidSeqIOFilter.addSequenceProperty(Object key, Object value) voidSeqIOListener.addSequenceProperty(Object key, Object value) Notify the listener of a sequence-wide property.voidSequenceBuilderFilter.addSequenceProperty(Object key, Object value) voidSwissprotFileFormer.addSequenceProperty(Object key, Object value) Deprecated.Notify the listener of a sequence-wide property.voidSwissprotProcessor.addSequenceProperty(Object key, Object value) Deprecated.voidEmblFileFormer.endFeature()Deprecated.voidGenbankFileFormer.endFeature()Deprecated.voidSeqIOAdapter.endFeature()voidSeqIOFilter.endFeature()voidSeqIOListener.endFeature()Mark the end of data associated with one specific feature.voidSequenceBuilderFilter.endFeature()voidSwissprotFileFormer.endFeature()Deprecated.Null implementation.voidEmblFileFormer.endSequence()Deprecated.voidEmblProcessor.endSequence()Deprecated.voidGenbankFileFormer.endSequence()Deprecated.voidGenbankProcessor.endSequence()Deprecated.voidOrganismParser.endSequence()Deprecated.voidSeqIOAdapter.endSequence()voidSeqIOFilter.endSequence()voidSeqIOListener.endSequence()Notify the listener that processing of the sequence is complete.voidSequenceBuilderFilter.endSequence()voidSwissprotFileFormer.endSequence()Deprecated.Notify the listener that processing of the sequence is complete.voidSwissprotProcessor.endSequence()Deprecated.protected voidEmblLikeFormat.processSequenceLine(String line, StreamParser parser) Deprecated.Dispatch symbol data from SQ-block line of an EMBL-like file.booleanEmblLikeFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Deprecated.booleanFastaFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener siol) Deprecated.Reads information from a flatfile to aSeqIOListenerusing aSymbolTokenizerto convert sequence strings toSymbolobjects.booleanGenbankFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Deprecated.Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided.booleanGenbankXmlFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Deprecated.voidDeprecated.voidDeprecated.voidvoidvoidNotify the listener that the current sequence is generally known by a particular name.voidvoidDeprecated.The name is printed out as part of the identifier line.voidDeprecated.voidDeprecated.voidvoidvoidNotify the listener of a URI identifying the current sequence.voidvoidDeprecated.Null implementation.voidEmblFileFormer.startFeature(Feature.Template templ) Deprecated.voidGenbankFileFormer.startFeature(Feature.Template templ) Deprecated.voidProteinRefSeqFileFormer.startFeature(Feature.Template templ) Deprecated.voidSeqIOAdapter.startFeature(Feature.Template templ) voidSeqIOFilter.startFeature(Feature.Template templ) voidSeqIOListener.startFeature(Feature.Template templ) Notify the listener that a new feature object is starting.voidSequenceBuilderFilter.startFeature(Feature.Template templ) voidSwissprotFileFormer.startFeature(Feature.Template templ) Deprecated.Null implementation.voidEmblFileFormer.startSequence()Deprecated.voidGenbankFileFormer.startSequence()Deprecated.voidSeqIOAdapter.startSequence()voidSeqIOFilter.startSequence()voidSeqIOListener.startSequence()Start the processing of a sequence.voidSequenceBuilderFilter.startSequence()voidSwissprotFileFormer.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 ListIteratorStAXPropertyHandler.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 ListIteratorStAXPropertyHandler.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 intOboFileParser.getNestedValue(org.biojava.ontology.obo.NestedValue nv, String str, int startIndex) voidOboFileParser.parseOBO(BufferedReader oboFile) parse an ontology fileprotected OboFileParser.SOPairOboFileParser.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 TypeMethodDescriptionvoidCharactersBlock.addTaxLabel(String taxLabel) Add a TAXLABEL.voidCharactersBlockBuilder.addTaxLabel(String taxLabel) voidCharactersBlockListener.addTaxLabel(String taxLabel) Add a TAXLABEL.voidDistancesBlock.addTaxLabel(String taxLabel) Add a TAXLABEL.voidDistancesBlockBuilder.addTaxLabel(String taxLabel) voidDistancesBlockListener.addTaxLabel(String taxLabel) Add a TAXLABEL.voidTaxaBlock.addTaxLabel(String taxLabel) Add a TAXLABEL.voidTaxaBlockBuilder.addTaxLabel(String taxLabel) voidTaxaBlockListener.addTaxLabel(String taxLabel) Add another value after the TAXLABEL tag.voidNexusBlockListener.commentText(String comment) Receiving free text inside a comment tag.voidNexusBlockParser.Abstract.commentText(String comment) voidNexusBlockParser.commentText(String comment) Receiving free text inside a comment tag.voidNexusFileListener.Abstract.commentText(String comment) voidNexusFileListener.commentText(String comment) Receiving free text inside a comment tag.voidTreesBlockParser.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 voidNexusFileFormat.parseFile(NexusFileListener listener, File inputFile) Parse a file and send events to the given listener.static voidNexusFileFormat.parseInputStream(NexusFileListener listener, InputStream inputStream) Parse a stream and send events to the given listener.static voidNexusFileFormat.parseReader(NexusFileListener listener, Reader inputReader) Parse a reader and send events to the given listener.voidCharactersBlockParser.parseToken(String token) voidDistancesBlockParser.parseToken(String token) abstract voidNexusBlockParser.Abstract.parseToken(String token) voidNexusBlockParser.parseToken(String token) Notifies the parser of the next token.voidNexusFileListener.Abstract.parseToken(String token) voidNexusFileListener.parseToken(String token) Encountered a token.voidTaxaBlockParser.parseToken(String token) voidTreesBlockParser.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 TypeMethodDescriptionvoidPHYLIPFileBuilder.endFile()voidPHYLIPFileListener.endFile()Finished reading a file.static voidPHYLIPFileFormat.parse(PHYLIPFileListener listener, BufferedReader reader) static voidPHYLIPFileFormat.parseFile(PHYLIPFileListener listener, File inputFile) static voidPHYLIPFileFormat.parseInputStream(PHYLIPFileListener listener, InputStream inputStream) static voidPHYLIPFileFormat.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 TypeMethodDescriptionvoidDebuggingRichSeqIOListener.addFeatureProperty(Object key, Object value) voidRichSeqIOAdapter.addFeatureProperty(Object key, Object value) voidSimpleRichSequenceBuilder.addFeatureProperty(Object key, Object value) Notify the listener of a feature property.voidDebuggingRichSeqIOListener.addSequenceProperty(Object key, Object value) voidRichSeqIOAdapter.addSequenceProperty(Object key, Object value) voidSimpleRichSequenceBuilder.addSequenceProperty(Object key, Object value) Notify the listener of a sequence-wide property.voidDebuggingRichSeqIOListener.endFeature()voidRichSeqIOAdapter.endFeature()voidSimpleRichSequenceBuilder.endFeature()Mark the end of data associated with one specific feature.voidDebuggingRichSeqIOListener.endSequence()voidRichSeqIOAdapter.endSequence()voidSimpleRichSequenceBuilder.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.voidUniProtCommentParser.parseComment(String c) Parses the comment string from the given comment and populates the internal fields appropriately.voidUniProtCommentParser.parseComment(Comment c) Parses the comment string from the given comment and populates the internal fields appropriately.static RichLocationGenbankLocationParser.parseLocation(Namespace featureNS, String featureAccession, String locationString) Parses a location.static RichLocationUniProtLocationParser.parseLocation(String loc) Parses a location.voidFastaFormat.processHeader(String line, RichSeqIOListener rsiol, Namespace ns) Parse the Header information from the Fasta Description linebooleanEMBLFormat.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.booleanEMBLxmlFormat.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.booleanFastaFormat.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.booleanGenbankFormat.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.booleanINSDseqFormat.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.booleanUniProtFormat.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.booleanUniProtXMLFormat.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.booleanEMBLFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.booleanEMBLxmlFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.booleanFastaFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.booleanGenbankFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.booleanINSDseqFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.booleanUniProtFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.booleanUniProtXMLFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) Read a sequence and pass data on to a SeqIOListener.voidDebuggingRichSeqIOListener.setAccession(String accession) voidRichSeqIOAdapter.setAccession(String accession) voidRichSeqIOListener.setAccession(String accession) Call back method so the event emitter can tell the listener the accession of the record being read.voidSimpleRichSequenceBuilder.setAccession(String accession) Call back method so the event emitter can tell the listener the accession of the record being read.voidDebuggingRichSeqIOListener.setCircular(boolean circular) voidRichSeqIOAdapter.setCircular(boolean circular) voidRichSeqIOListener.setCircular(boolean circular) Defined this sequence being parser as circular.voidSimpleRichSequenceBuilder.setCircular(boolean circular) Defined this sequence being parser as circular.voidDebuggingRichSeqIOListener.setComment(String comment) voidRichSeqIOAdapter.setComment(String comment) voidRichSeqIOListener.setComment(String comment) Call back method so the event emitter can tell the listener about a comment in the record being read.voidSimpleRichSequenceBuilder.setComment(String comment) Call back method so the event emitter can tell the listener about a comment in the record being read.voidDebuggingRichSeqIOListener.setDescription(String description) voidRichSeqIOAdapter.setDescription(String description) voidRichSeqIOListener.setDescription(String description) Call back method so the event emitter can tell the listener the description of the record being read.voidSimpleRichSequenceBuilder.setDescription(String description) Call back method so the event emitter can tell the listener the description of the record being read.voidDebuggingRichSeqIOListener.setDivision(String division) voidRichSeqIOAdapter.setDivision(String division) voidRichSeqIOListener.setDivision(String division) Call back method so the event emitter can tell the listener the division of the record being read.voidSimpleRichSequenceBuilder.setDivision(String division) Call back method so the event emitter can tell the listener the division of the record being read.voidDebuggingRichSeqIOListener.setIdentifier(String identifier) voidRichSeqIOAdapter.setIdentifier(String identifier) voidRichSeqIOListener.setIdentifier(String identifier) Call back method so the event emitter can tell the listener the identifier of the record being read.voidSimpleRichSequenceBuilder.setIdentifier(String identifier) Call back method so the event emitter can tell the listener the identifier of the record being read.voidvoidvoidNotify the listener that the current sequence is generally known by a particular name.voidDebuggingRichSeqIOListener.setNamespace(Namespace namespace) voidRichSeqIOAdapter.setNamespace(Namespace namespace) voidRichSeqIOListener.setNamespace(Namespace namespace) Call back method so the event emitter can tell the listener the namespace of the record being read.voidSimpleRichSequenceBuilder.setNamespace(Namespace namespace) Call back method so the event emitter can tell the listener the namespace of the record being read.voidDebuggingRichSeqIOListener.setRankedCrossRef(RankedCrossRef crossRef) voidRichSeqIOAdapter.setRankedCrossRef(RankedCrossRef crossRef) voidRichSeqIOListener.setRankedCrossRef(RankedCrossRef crossRef) Call back method so the event emitter can tell the listener about a cross reference.voidSimpleRichSequenceBuilder.setRankedCrossRef(RankedCrossRef ref) Call back method so the event emitter can tell the listener about a cross reference.voidDebuggingRichSeqIOListener.setRankedDocRef(RankedDocRef ref) voidRichSeqIOAdapter.setRankedDocRef(RankedDocRef ref) voidRichSeqIOListener.setRankedDocRef(RankedDocRef ref) Call back method so the event emitter can tell the listener about a literature reference in the record being read.voidSimpleRichSequenceBuilder.setRankedDocRef(RankedDocRef ref) Call back method so the event emitter can tell the listener about a literature reference in the record being read.voidDebuggingRichSeqIOListener.setRelationship(BioEntryRelationship relationship) voidRichSeqIOAdapter.setRelationship(BioEntryRelationship relationship) voidRichSeqIOListener.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.voidSimpleRichSequenceBuilder.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.voidDebuggingRichSeqIOListener.setSeqVersion(String version) voidRichSeqIOAdapter.setSeqVersion(String version) voidRichSeqIOListener.setSeqVersion(String version) Call back method so the event emitter can tell the listener the version of the sequence of the record being read.voidSimpleRichSequenceBuilder.setSeqVersion(String seqVersion) Call back method so the event emitter can tell the listener the version of the sequence of the record being read.voidvoidvoidCall back method so the event emitter can tell the listener the Taxon of the record being read.voidCall back method so the event emitter can tell the listener the Taxon of the record being read.voidvoidvoidDeprecated.There is no clear mapping between URI and BioSQL.voidNotify the listener of a URI identifying the current sequence.voidDebuggingRichSeqIOListener.setVersion(int version) voidRichSeqIOAdapter.setVersion(int version) voidRichSeqIOListener.setVersion(int version) Call back method so the event emitter can tell the listener the version of the record being read.voidSimpleRichSequenceBuilder.setVersion(int version) Call back method so the event emitter can tell the listener the version of the record being read.voidDebuggingRichSeqIOListener.startFeature(Feature.Template templ) voidRichSeqIOAdapter.startFeature(Feature.Template templ) voidSimpleRichSequenceBuilder.startFeature(Feature.Template templ) Notify the listener that a new feature object is starting.voidDebuggingRichSeqIOListener.startSequence()voidRichSeqIOAdapter.startSequence()voidSimpleRichSequenceBuilder.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.