Uses of Class org.biojava.bio.seq.io.ParseException (BioJava-1.5-beta API)

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES

## 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.
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
`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.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
`void` | `SequenceBuilderFilter.addFeatureProperty(Object key, Object value)`
`void` | `SeqIOFilter.addFeatureProperty(Object key, Object value)`
`void` | `SequenceBuilderBase.addFeatureProperty(Object key, Object value)` Add an annotation-bundle entry to the feature.
`void` | `SwissprotFileFormer.addFeatureProperty(Object key, Object value)` Deprecated. Null implementation
`void` | `GenbankFileFormer.addFeatureProperty(Object key, Object value)` Deprecated.
`void` | `SeqIOListener.addFeatureProperty(Object key, Object value)` Notify the listener of a feature property.
`void` | `SeqIOAdapter.addFeatureProperty(Object key, Object value)`
`void` | `SequenceBuilderFilter.addSequenceProperty(Object key, Object value)`
`void` | `SeqIOFilter.addSequenceProperty(Object key, Object value)`
`void` | `SwissprotFileFormer.addSequenceProperty(Object key, Object value)` Deprecated. Notify the listener of a sequence-wide property.
`void` | `OrganismParser.addSequenceProperty(Object sciNameKey, Object value)` Deprecated.
`void` | `EmblProcessor.addSequenceProperty(Object key, Object value)` Deprecated.
`void` | `GenbankProcessor.addSequenceProperty(Object key, Object value)` Deprecated.
`void` | `GenbankFileFormer.addSequenceProperty(Object key, Object value)` Deprecated.
`void` | `FastaDescriptionLineParser.addSequenceProperty(Object key, Object value)` Deprecated.
`void` | `SeqIOListener.addSequenceProperty(Object key, Object value)` Notify the listener of a sequence-wide property.
`void` | `EmblFileFormer.addSequenceProperty(Object key, Object value)` Deprecated.
`void` | `SwissprotProcessor.addSequenceProperty(Object key, Object value)` Deprecated.
`void` | `SeqIOAdapter.addSequenceProperty(Object key, Object value)`
`void` | `SequenceBuilderFilter.endFeature()`
`void` | `SeqIOFilter.endFeature()`
`void` | `SwissprotFileFormer.endFeature()` Deprecated. Null implementation.
`void` | `GenbankFileFormer.endFeature()` Deprecated.
`void` | `SeqIOListener.endFeature()` Mark the end of data associated with one specific feature.
`void` | `EmblFileFormer.endFeature()` Deprecated.
`void` | `SeqIOAdapter.endFeature()`
`void` | `SequenceBuilderFilter.endSequence()`
`void` | `SeqIOFilter.endSequence()`
`void` | `SwissprotFileFormer.endSequence()` Deprecated. Notify the listener that processing of the sequence is complete.
`void` | `OrganismParser.endSequence()` Deprecated.
`void` | `EmblProcessor.endSequence()` Deprecated.
`void` | `GenbankProcessor.endSequence()` Deprecated.
`void` | `GenbankFileFormer.endSequence()` Deprecated.
`void` | `SeqIOListener.endSequence()` Notify the listener that processing of the sequence is complete.
`void` | `EmblFileFormer.endSequence()` Deprecated.
`void` | `SwissprotProcessor.endSequence()` Deprecated.
`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` | `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` | `EmblLikeFormat.readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)` Deprecated.
`boolean` | `GenbankXmlFormat.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.
`void` | `SequenceBuilderFilter.setName(String name)`
`void` | `SeqIOFilter.setName(String name)`
`void` | `SwissprotFileFormer.setName(String theName)` Deprecated. The name is printed out as part of the identifier line.
`void` | `GenbankFileFormer.setName(String id)` Deprecated.
`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` | `SeqIOAdapter.setName(String name)`
`void` | `SequenceBuilderFilter.setURI(String uri)`
`void` | `SeqIOFilter.setURI(String uri)`
`void` | `SwissprotFileFormer.setURI(String theURI)` Deprecated. Null implementation.
`void` | `GenbankFileFormer.setURI(String uri)` Deprecated.
`void` | `SeqIOListener.setURI(String uri)` Notify the listener of a URI identifying the current sequence.
`void` | `EmblFileFormer.setURI(String uri)` Deprecated.
`void` | `SeqIOAdapter.setURI(String uri)`
`void` | `SequenceBuilderFilter.startFeature(Feature.Template templ)`
`void` | `SeqIOFilter.startFeature(Feature.Template templ)`
`void` | `SwissprotFileFormer.startFeature(Feature.Template templ)` Deprecated. Null implementation.
`void` | `GenbankFileFormer.startFeature(Feature.Template templ)` Deprecated.
`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` | `SeqIOAdapter.startFeature(Feature.Template templ)`
`void` | `SequenceBuilderFilter.startSequence()`
`void` | `SeqIOFilter.startSequence()`
`void` | `SwissprotFileFormer.startSequence()` Deprecated. Start the processing of a sequence.
`void` | `GenbankFileFormer.startSequence()` Deprecated.
`void` | `SeqIOListener.startSequence()` Start the processing of a sequence.
`void` | `EmblFileFormer.startSequence()` Deprecated.
`void` | `SeqIOAdapter.startSequence()`

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)`

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

Methods in org.biojavax.bio.seq.io that throw ParseException
`void` | `SimpleRichSequenceBuilder.addFeatureProperty(Object key, Object value)` Notify the listener of a feature property.
`void` | `DebuggingRichSeqIOListener.addFeatureProperty(Object key, Object value)`
`void` | `RichSeqIOAdapter.addFeatureProperty(Object key, Object value)`
`void` | `SimpleRichSequenceBuilder.addSequenceProperty(Object key, Object value)` Notify the listener of a sequence-wide property.
`void` | `DebuggingRichSeqIOListener.addSequenceProperty(Object key, Object value)`
`void` | `RichSeqIOAdapter.addSequenceProperty(Object key, Object value)`
`void` | `SimpleRichSequenceBuilder.endFeature()` Mark the end of data associated with one specific feature.
`void` | `DebuggingRichSeqIOListener.endFeature()`
`void` | `RichSeqIOAdapter.endFeature()`
`void` | `SimpleRichSequenceBuilder.endSequence()` Notify the listener that processing of the sequence is complete.
`void` | `DebuggingRichSeqIOListener.endSequence()`
`void` | `RichSeqIOAdapter.endSequence()`
`String` | `UniProtCommentParser.generate()` Generates a comment string based on the current values of the internal fields.
`RichFeature` | `SimpleRichSequenceBuilder.getCurrentFeature()` Gets the feature currently being created.
`RichFeature` | `DebuggingRichSeqIOListener.getCurrentFeature()`
`RichFeature` | `RichSeqIOAdapter.getCurrentFeature()`
`RichFeature` | `RichSeqIOListener.getCurrentFeature()` Gets the feature currently being created.
`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.
`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` | `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` | `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` | `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. If namespace is null, then the namespace of the sequence in the fasta is used.
`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. If namespace is null, then the namespace of the sequence in the fasta is used.
`boolean` | `EMBLFormat.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` | `EMBLxmlFormat.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.
`void` | `SimpleRichSequenceBuilder.setAccession(String accession)` Call back method so the event emitter can tell the listener the accession of the record being read. The last accession passed to this routine will always be the one used.
`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.setCircular(boolean circular)` Defined this sequence being parser as circular.
`void` | `DebuggingRichSeqIOListener.setCircular(boolean circular)`
`void` | `RichSeqIOAdapter.setCircular(boolean circular)`
`void` | `RichSeqIOListener.setCircular(boolean circular)` Defined this sequence being parser as circular.
`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.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.setDescription(String description)` Call back method so the event emitter can tell the listener the description of 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.setDivision(String division)` Call back method so the event emitter can tell the listener the division 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.setIdentifier(String identifier)` Call back method so the event emitter can tell the listener the identifier 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.setName(String name)` Notify the listener that the current sequence is generally known by a particular name.
`void` | `DebuggingRichSeqIOListener.setName(String name)`
`void` | `RichSeqIOAdapter.setName(String name)`
`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.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.setRankedCrossRef(RankedCrossRef ref)` Call back method so the event emitter can tell the listener about a cross reference.
`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.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.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.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.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.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` | `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.setTaxon(NCBITaxon taxon)` Call back method so the event emitter can tell the listener the Taxon of the record being read.
`void` | `DebuggingRichSeqIOListener.setTaxon(NCBITaxon taxon)`
`void` | `RichSeqIOAdapter.setTaxon(NCBITaxon taxon)`
`void` | `RichSeqIOListener.setTaxon(NCBITaxon taxon)` Call back method so the event emitter can tell the listener the Taxon of the record being read.
`void` | `SimpleRichSequenceBuilder.setURI(String uri)` Notify the listener of a URI identifying the current sequence. NOT IMPLEMENTED
`void` | `DebuggingRichSeqIOListener.setURI(String uri)`
`void` | `RichSeqIOAdapter.setURI(String uri)`
`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` | `SimpleRichSequenceBuilder.setVersion(int version)` Call back method so the event emitter can tell the listener the version of the record being read.
`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.startFeature(Feature.Template templ)` Notify the listener that a new feature object is starting.
`void` | `DebuggingRichSeqIOListener.startFeature(Feature.Template templ)`
`void` | `RichSeqIOAdapter.startFeature(Feature.Template templ)`
`void` | `SimpleRichSequenceBuilder.startSequence()` Start the processing of a sequence.
`void` | `DebuggingRichSeqIOListener.startSequence()`
`void` | `RichSeqIOAdapter.startSequence()`

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

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

Overview | Package | Class | Use | Tree | Deprecated | Index | Help
PREV NEXT | FRAMES NO FRAMES