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

Methods in org.biojavax.bio.phylo.io.phylip that throw ParseException
 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
 void RichSeqIOAdapter.addFeatureProperty(Object key, Object value)
           
 void DebuggingRichSeqIOListener.addFeatureProperty(Object key, Object value)
           
 void SimpleRichSequenceBuilder.addFeatureProperty(Object key, Object value)
          Notify the listener of a feature property.
 void RichSeqIOAdapter.addSequenceProperty(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.endFeature()
           
 void DebuggingRichSeqIOListener.endFeature()
           
 void SimpleRichSequenceBuilder.endFeature()
          Mark the end of data associated with one specific feature.
 void RichSeqIOAdapter.endSequence()
           
 void DebuggingRichSeqIOListener.endSequence()
           
 void SimpleRichSequenceBuilder.endSequence()
          Notify the listener that processing of the sequence is complete.
 String UniProtCommentParser.generate()
          Generates a comment string based on the current values of the internal fields.
 RichFeature RichSeqIOAdapter.getCurrentFeature()
           
 RichFeature DebuggingRichSeqIOListener.getCurrentFeature()
           
 RichFeature SimpleRichSequenceBuilder.getCurrentFeature()
          Gets the feature currently being created.
 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.
 void FastaFormat.processHeader(String line, RichSeqIOListener rsiol, Namespace ns)
          Parse the Header information from the Fasta Description line
 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 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 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 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 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 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.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 EMBLFormat.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 GenbankFormat.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.
 void RichSeqIOAdapter.setAccession(String accession)
           
 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.setCircular(boolean circular)
           
 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.setComment(String comment)
           
 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.setDescription(String description)
           
 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.setDivision(String division)
           
 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.setIdentifier(String identifier)
           
 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.setName(String name)
           
 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.setNamespace(Namespace namespace)
           
 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.setRankedCrossRef(RankedCrossRef crossRef)
           
 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.setRankedDocRef(RankedDocRef ref)
           
 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.setRelationship(BioEntryRelationship relationship)
           
 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.setSeqVersion(String version)
           
 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.setTaxon(NCBITaxon taxon)
           
 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.setURI(String uri)
           
 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.setVersion(int version)
           
 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.startFeature(Feature.Template templ)
           
 void DebuggingRichSeqIOListener.startFeature(Feature.Template templ)
           
 void SimpleRichSequenceBuilder.startFeature(Feature.Template templ)
          Notify the listener that a new feature object is starting.
 void RichSeqIOAdapter.startSequence()
           
 void DebuggingRichSeqIOListener.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 ParseException
 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.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.readNode(BufferedReader nodes)
          Reads the next entry from the nodes.dmp file and returns the corresponding NCBITaxon object.
 NCBITaxon SimpleNCBITaxonomyLoader.readNode(BufferedReader nodes)
          Reads the next entry from the nodes.dmp file and returns the corresponding NCBITaxon object.