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(java.io.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(java.lang.Object key, java.lang.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 SequenceBuilderBase.addFeatureProperty(java.lang.Object key, java.lang.Object value)
          Add an annotation-bundle entry to the feature.
 void SwissprotFileFormer.addFeatureProperty(java.lang.Object key, java.lang.Object value)
          Deprecated. Null implementation
 void SeqIOFilter.addFeatureProperty(java.lang.Object key, java.lang.Object value)
           
 void SequenceBuilderFilter.addFeatureProperty(java.lang.Object key, java.lang.Object value)
           
 void SeqIOAdapter.addFeatureProperty(java.lang.Object key, java.lang.Object value)
           
 void GenbankFileFormer.addFeatureProperty(java.lang.Object key, java.lang.Object value)
          Deprecated.  
 void SeqIOListener.addFeatureProperty(java.lang.Object key, java.lang.Object value)
          Notify the listener of a feature property.
 void FastaDescriptionLineParser.addSequenceProperty(java.lang.Object key, java.lang.Object value)
          Deprecated.  
 void SwissprotFileFormer.addSequenceProperty(java.lang.Object key, java.lang.Object value)
          Deprecated. Notify the listener of a sequence-wide property.
 void EmblFileFormer.addSequenceProperty(java.lang.Object key, java.lang.Object value)
          Deprecated.  
 void OrganismParser.addSequenceProperty(java.lang.Object sciNameKey, java.lang.Object value)
          Deprecated.  
 void GenbankProcessor.addSequenceProperty(java.lang.Object key, java.lang.Object value)
          Deprecated.  
 void EmblProcessor.addSequenceProperty(java.lang.Object key, java.lang.Object value)
          Deprecated.  
 void SeqIOFilter.addSequenceProperty(java.lang.Object key, java.lang.Object value)
           
 void SequenceBuilderFilter.addSequenceProperty(java.lang.Object key, java.lang.Object value)
           
 void SeqIOAdapter.addSequenceProperty(java.lang.Object key, java.lang.Object value)
           
 void SwissprotProcessor.addSequenceProperty(java.lang.Object key, java.lang.Object value)
          Deprecated.  
 void GenbankFileFormer.addSequenceProperty(java.lang.Object key, java.lang.Object value)
          Deprecated.  
 void SeqIOListener.addSequenceProperty(java.lang.Object key, java.lang.Object value)
          Notify the listener of a sequence-wide property.
 void SwissprotFileFormer.endFeature()
          Deprecated. Null implementation.
 void EmblFileFormer.endFeature()
          Deprecated.  
 void SeqIOFilter.endFeature()
           
 void SequenceBuilderFilter.endFeature()
           
 void SeqIOAdapter.endFeature()
           
 void GenbankFileFormer.endFeature()
          Deprecated.  
 void SeqIOListener.endFeature()
          Mark the end of data associated with one specific feature.
 void SwissprotFileFormer.endSequence()
          Deprecated. Notify the listener that processing of the sequence is complete.
 void EmblFileFormer.endSequence()
          Deprecated.  
 void OrganismParser.endSequence()
          Deprecated.  
 void GenbankProcessor.endSequence()
          Deprecated.  
 void EmblProcessor.endSequence()
          Deprecated.  
 void SeqIOFilter.endSequence()
           
 void SequenceBuilderFilter.endSequence()
           
 void SeqIOAdapter.endSequence()
           
 void SwissprotProcessor.endSequence()
          Deprecated.  
 void GenbankFileFormer.endSequence()
          Deprecated.  
 void SeqIOListener.endSequence()
          Notify the listener that processing of the sequence is complete.
protected  void EmblLikeFormat.processSequenceLine(java.lang.String line, StreamParser parser)
          Deprecated. Dispatch symbol data from SQ-block line of an EMBL-like file.
 boolean FastaFormat.readSequence(java.io.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(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)
          Deprecated.  
 boolean GenbankFormat.readSequence(java.io.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(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)
          Deprecated.  
 void SwissprotFileFormer.setName(java.lang.String theName)
          Deprecated. The name is printed out as part of the identifier line.
 void EmblFileFormer.setName(java.lang.String id)
          Deprecated.  
 void SeqIOFilter.setName(java.lang.String name)
           
 void SequenceBuilderFilter.setName(java.lang.String name)
           
 void SeqIOAdapter.setName(java.lang.String name)
           
 void GenbankFileFormer.setName(java.lang.String id)
          Deprecated.  
 void SeqIOListener.setName(java.lang.String name)
          Notify the listener that the current sequence is generally known by a particular name.
 void SwissprotFileFormer.setURI(java.lang.String theURI)
          Deprecated. Null implementation.
 void EmblFileFormer.setURI(java.lang.String uri)
          Deprecated.  
 void SeqIOFilter.setURI(java.lang.String uri)
           
 void SequenceBuilderFilter.setURI(java.lang.String uri)
           
 void SeqIOAdapter.setURI(java.lang.String uri)
           
 void GenbankFileFormer.setURI(java.lang.String uri)
          Deprecated.  
 void SeqIOListener.setURI(java.lang.String uri)
          Notify the listener of a URI identifying the current sequence.
 void ProteinRefSeqFileFormer.startFeature(Feature.Template templ)
          Deprecated.  
 void SwissprotFileFormer.startFeature(Feature.Template templ)
          Deprecated. Null implementation.
 void EmblFileFormer.startFeature(Feature.Template templ)
          Deprecated.  
 void SeqIOFilter.startFeature(Feature.Template templ)
           
 void SequenceBuilderFilter.startFeature(Feature.Template templ)
           
 void SeqIOAdapter.startFeature(Feature.Template templ)
           
 void GenbankFileFormer.startFeature(Feature.Template templ)
          Deprecated.  
 void SeqIOListener.startFeature(Feature.Template templ)
          Notify the listener that a new feature object is starting.
 void SwissprotFileFormer.startSequence()
          Deprecated. Start the processing of a sequence.
 void EmblFileFormer.startSequence()
          Deprecated.  
 void SeqIOFilter.startSequence()
           
 void SequenceBuilderFilter.startSequence()
           
 void SeqIOAdapter.startSequence()
           
 void GenbankFileFormer.startSequence()
          Deprecated.  
 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  java.util.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  java.util.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(java.io.BufferedReader goFile, java.lang.String ontoName, java.lang.String ontoDescription, OntologyFactory factory)
           
 Ontology OboParser.parseOBO(java.io.BufferedReader oboFile, java.lang.String ontoName, java.lang.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  java.util.Map<java.lang.String,java.lang.Object>[] OboFileParser.getDbxrefList(java.lang.String line, int startoffset, int endoffset)
           
protected  int OboFileParser.getNestedValue(org.biojava.ontology.obo.NestedValue nv, java.lang.String str, int startIndex)
           
 void OboFileParser.parseOBO(java.io.BufferedReader oboFile)
          parse an ontology file
protected  java.util.Map<java.lang.String,java.lang.Object> OboFileParser.parseXref(java.lang.String line, int startoffset, int endoffset)
           
protected  OboFileParser.SOPair OboFileParser.readQuotedString(java.lang.String value, int startIndex, int stopIndex, char terminatingChar, boolean requireQuotes, boolean legalEndOfLine)
           
 java.lang.String OboFileParser.unescape(java.lang.String str)
           
 OboFileParser.SOPair OboFileParser.unescape(java.lang.String str, char toChar, int startindex, boolean mustFindChar)
           
 OboFileParser.SOPair OboFileParser.unescape(java.lang.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, java.io.BufferedReader reader)
           
static void PHYLIPFileFormat.parseFile(PHYLIPFileListener listener, java.io.File inputFile)
           
static void PHYLIPFileFormat.parseInputStream(PHYLIPFileListener listener, java.io.InputStream inputStream)
           
static void PHYLIPFileFormat.parseReader(PHYLIPFileListener listener, java.io.Reader inputReader)
           
 

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

Methods in org.biojavax.bio.seq.io that throw ParseException
 void DebuggingRichSeqIOListener.addFeatureProperty(java.lang.Object key, java.lang.Object value)
           
 void SimpleRichSequenceBuilder.addFeatureProperty(java.lang.Object key, java.lang.Object value)
          Notify the listener of a feature property.
 void RichSeqIOAdapter.addFeatureProperty(java.lang.Object key, java.lang.Object value)
           
 void DebuggingRichSeqIOListener.addSequenceProperty(java.lang.Object key, java.lang.Object value)
           
 void SimpleRichSequenceBuilder.addSequenceProperty(java.lang.Object key, java.lang.Object value)
          Notify the listener of a sequence-wide property.
 void RichSeqIOAdapter.addSequenceProperty(java.lang.Object key, java.lang.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()
           
 java.lang.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 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(java.lang.String c)
          Parses the comment string from the given comment and populates the internal fields appropriately.
static RichLocation GenbankLocationParser.parseLocation(Namespace featureNS, java.lang.String featureAccession, java.lang.String locationString)
          Parses a location.
static RichLocation UniProtLocationParser.parseLocation(java.lang.String loc)
          Parses a location.
 void FastaFormat.processHeader(java.lang.String line, RichSeqIOListener rsiol, Namespace ns)
          Parse the Header information from the Fasta Description line
 boolean EMBLxmlFormat.readRichSequence(java.io.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(java.io.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 UniProtXMLFormat.readRichSequence(java.io.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(java.io.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(java.io.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(java.io.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(java.io.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(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)
          Read a sequence and pass data on to a SeqIOListener.
 boolean FastaFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)
          Read a sequence and pass data on to a SeqIOListener.
 boolean UniProtXMLFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)
          Read a sequence and pass data on to a SeqIOListener.
 boolean EMBLFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)
          Read a sequence and pass data on to a SeqIOListener.
 boolean UniProtFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)
          Read a sequence and pass data on to a SeqIOListener.
 boolean GenbankFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)
          Read a sequence and pass data on to a SeqIOListener.
 boolean INSDseqFormat.readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener)
          Read a sequence and pass data on to a SeqIOListener.
 void DebuggingRichSeqIOListener.setAccession(java.lang.String accession)
           
 void SimpleRichSequenceBuilder.setAccession(java.lang.String accession)
          Call back method so the event emitter can tell the listener the accession of the record being read.
 void RichSeqIOAdapter.setAccession(java.lang.String accession)
           
 void RichSeqIOListener.setAccession(java.lang.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 SimpleRichSequenceBuilder.setCircular(boolean circular)
          Defined this sequence being parser as circular.
 void RichSeqIOAdapter.setCircular(boolean circular)
           
 void RichSeqIOListener.setCircular(boolean circular)
          Defined this sequence being parser as circular.
 void DebuggingRichSeqIOListener.setComment(java.lang.String comment)
           
 void SimpleRichSequenceBuilder.setComment(java.lang.String comment)
          Call back method so the event emitter can tell the listener about a comment in the record being read.
 void RichSeqIOAdapter.setComment(java.lang.String comment)
           
 void RichSeqIOListener.setComment(java.lang.String comment)
          Call back method so the event emitter can tell the listener about a comment in the record being read.
 void DebuggingRichSeqIOListener.setDescription(java.lang.String description)
           
 void SimpleRichSequenceBuilder.setDescription(java.lang.String description)
          Call back method so the event emitter can tell the listener the description of the record being read.
 void RichSeqIOAdapter.setDescription(java.lang.String description)
           
 void RichSeqIOListener.setDescription(java.lang.String description)
          Call back method so the event emitter can tell the listener the description of the record being read.
 void DebuggingRichSeqIOListener.setDivision(java.lang.String division)
           
 void SimpleRichSequenceBuilder.setDivision(java.lang.String division)
          Call back method so the event emitter can tell the listener the division of the record being read.
 void RichSeqIOAdapter.setDivision(java.lang.String division)
           
 void RichSeqIOListener.setDivision(java.lang.String division)
          Call back method so the event emitter can tell the listener the division of the record being read.
 void DebuggingRichSeqIOListener.setIdentifier(java.lang.String identifier)
           
 void SimpleRichSequenceBuilder.setIdentifier(java.lang.String identifier)
          Call back method so the event emitter can tell the listener the identifier of the record being read.
 void RichSeqIOAdapter.setIdentifier(java.lang.String identifier)
           
 void RichSeqIOListener.setIdentifier(java.lang.String identifier)
          Call back method so the event emitter can tell the listener the identifier of the record being read.
 void DebuggingRichSeqIOListener.setName(java.lang.String name)
           
 void SimpleRichSequenceBuilder.setName(java.lang.String name)
          Notify the listener that the current sequence is generally known by a particular name.
 void RichSeqIOAdapter.setName(java.lang.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 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 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 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 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 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 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 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 DebuggingRichSeqIOListener.setSeqVersion(java.lang.String version)
           
 void SimpleRichSequenceBuilder.setSeqVersion(java.lang.String seqVersion)
          Call back method so the event emitter can tell the listener the version of the sequence of the record being read.
 void RichSeqIOAdapter.setSeqVersion(java.lang.String version)
           
 void RichSeqIOListener.setSeqVersion(java.lang.String version)
          Call back method so the event emitter can tell the listener the version of the sequence of the record being read.
 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 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 DebuggingRichSeqIOListener.setURI(java.lang.String uri)
           
 void SimpleRichSequenceBuilder.setURI(java.lang.String uri)
          Notify the listener of a URI identifying the current sequence.
 void RichSeqIOAdapter.setURI(java.lang.String uri)
           
 void RichSeqIOListener.setURI(java.lang.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 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 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 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
 NCBITaxon SimpleNCBITaxonomyLoader.readName(java.io.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(java.io.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(java.io.BufferedReader nodes)
          Reads the next entry from the nodes.dmp file and returns the corresponding NCBITaxon object.
 NCBITaxon NCBITaxonomyLoader.readNode(java.io.BufferedReader nodes)
          Reads the next entry from the nodes.dmp file and returns the corresponding NCBITaxon object.