Uses of Class
org.biojava.utils.ParserException
Packages that use ParserException
Package
Description
Databases of generic structured data (annotation) objects.
GFF manipulation.
Support for reading and writing GFF3.
A flat-file ascii index of ascii flat files as per the OBDA specification.
Process files as streams of records, each with tags with values.
Objects for representing Unigene clusters.
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Uses of ParserException in org.biojava.bio.annodb
Constructors in org.biojava.bio.annodb that throw ParserExceptionModifierConstructorDescriptionIndexedAnnotationDB(String dbName, File storeLoc, Index2Model model, List toIndex, int maxKeyLen, AnnotationType schema, IndexedAnnotationDB.ParserListenerFactory plFactory) Create a new IndexedAnnotationDB. -
Uses of ParserException in org.biojava.bio.program.gff
Methods in org.biojava.bio.program.gff that throw ParserExceptionModifier and TypeMethodDescriptionprotected GFFRecordGFFParser.createRecord(GFFDocumentHandler handler, List aList, String rest, String comment) Actually turns a list of tokens, some value string and a comment into a GFFRecord and informs handler.intGFFErrorHandler.AbortErrorHandler.invalidEnd(String token) intGFFErrorHandler.invalidEnd(String token) The `end' field of the GFF entry was not a valid value.intGFFErrorHandler.AbortErrorHandler.invalidFrame(String token) intGFFErrorHandler.invalidFrame(String token) The `frame' field of the GFF entry was not a valid value.doubleGFFErrorHandler.AbortErrorHandler.invalidScore(String token) doubleGFFErrorHandler.invalidScore(String token) The `score' field of the GFF entry was not a valid value.intGFFErrorHandler.AbortErrorHandler.invalidStart(String token) intGFFErrorHandler.invalidStart(String token) The `start' field of the GFF entry was not a valid value.GFFErrorHandler.AbortErrorHandler.invalidStrand(String token) GFFErrorHandler.invalidStrand(String token) The `strand' field of the GFF entry was not a valid value.voidGFFParser.parse(BufferedReader bReader, GFFDocumentHandler handler) Informs handler of each line of gff read from bReader.voidGFFParser.parse(BufferedReader bReader, GFFDocumentHandler handler, String locator) Informs handler of each line of GFF read from bReaderstatic GFFEntrySetGFFTools.readGFF(BufferedReader gffIn) Read all GFF entries from a buffered reader.static GFFEntrySetGFFTools.readGFF(BufferedReader gffIn, GFFRecordFilter recFilt) Read all GFF entries matching a filter from a buffered reader.static GFFEntrySetReads aGFFEntrySetfrom a file with no filtering.static GFFEntrySetGFFTools.readGFF(File inFile, GFFRecordFilter recFilt) Reads a GFFEntrySet from a file with the specified filter.static GFFEntrySetDeprecated.use: readGff(File)static GFFEntrySetGFFTools.readGFF(String fileName, GFFRecordFilter recFilt) Deprecated.use: readGff(File,GFFRecordFilter) -
Uses of ParserException in org.biojava.bio.program.gff3
Methods in org.biojava.bio.program.gff3 that throw ParserExceptionModifier and TypeMethodDescriptionprotected GFF3RecordGFF3Parser.createRecord(GFF3DocumentHandler handler, List aList, String rest, String comment, Ontology ontology, Ontology fallBack) Actually turns a list of tokens, some value string and a comment into a GFF3Record and informs handler.voidGFF3Parser.parse(BufferedReader bReader, GFF3DocumentHandler handler, Ontology ontology) Informs handler of each line of gff read from bReader.voidGFF3Parser.parse(BufferedReader bReader, GFF3DocumentHandler handler, Ontology ontology, String locator) Informs handler of each line of GFF read from bReader -
Uses of ParserException in org.biojava.bio.program.indexdb
Methods in org.biojava.bio.program.indexdb that throw ParserExceptionModifier and TypeMethodDescriptionstatic voidindexEmblindexes DNA, RNA or protein EMBL format sequence files on ID as primary identifier and AC as secondary.static voidIndexTools.indexFasta(String name, File location, File[] seqFiles, int alphabetIdentifier) indexFastaindexes DNA, RNA or protein Fasta format sequence files on primary identifier.static voidIndexTools.indexGenbank(String name, File location, File[] seqFiles, int alphabetIdentifier) indexGenbankindexes DNA, RNA or protein Genbank format sequence files on LOCUS as primary identifier and ACCESSION as secondary.static voidIndexTools.indexSwissprot(String name, File location, File[] seqFiles) indexSwissprotindexes Swissprot format protein sequence files on ID as primary identifier. -
Uses of ParserException in org.biojava.bio.program.tagvalue
Methods in org.biojava.bio.program.tagvalue that throw ParserExceptionModifier and TypeMethodDescriptionProduce a modified value from an old value.voidAbstractWrapper.endRecord()voidIndexer.endRecord()voidIndexer2.endRecord()voidSimpleTagValueWrapper.endRecord()voidStateMachine.endRecord()voidStateMachine.SimpleStateListener.endRecord()voidTagValueListener.endRecord()The current record has ended.voidAbstractWrapper.endTag()voidAggregator.endTag()voidMultiTagger.endTag()voidRegexFieldFinder.endTag()voidSimpleTagValueWrapper.endTag()voidStateMachine.endTag()voidStateMachine.SimpleStateListener.endTag()voidTagDelegator.endTag()voidTagDropper.endTag()voidTagValueListener.endTag()End the current tag.voidStateMachine.ExitNotification.notifyExit()voidStateMachine.TransitionTable.put(Object tag, StateMachine.Transition transition) set a Transition within this TransitionTable (2-argument form)booleanParser.read(BufferedReader reader, TagValueParser parser, TagValueListener listener) voidStateMachine.BasicState.setTransition(Object tag, StateMachine.State destination) set a Transition for this State setting notifyOnExit to false.voidStateMachine.BasicState.setTransition(Object tag, StateMachine.State destination, boolean notifyOnExit) set a Transition for this StatevoidStateMachine.TransitionTable.setTransition(Object tag, StateMachine.State destination, boolean notifyOnExit) set a Transition within this TransitionTable (3-argument form)Produce a list of values from an old value.voidAbstractWrapper.startRecord()voidSimpleTagValueWrapper.startRecord()voidStateMachine.SimpleStateListener.startRecord()voidStateMachine.startRecord()voidTagValueListener.startRecord()A new record is about to start.voidvoidvoidvoidvoidvoidvoidTagValueListener interfacevoidvoidvoidvoidStart a new tag.voidvoidFind the destination State when the specified tag is encountered.voidvoidAbstractWrapper.value(TagValueContext ctxt, Object value) voidAggregator.value(TagValueContext ctxt, Object value) voidMultiTagger.value(TagValueContext ctxt, Object value) voidRegexFieldFinder.value(TagValueContext ctxt, Object val) voidSimpleTagValueWrapper.value(TagValueContext ctxt, Object value) voidStateMachine.SimpleStateListener.value(TagValueContext ctxt, Object value) voidStateMachine.value(TagValueContext ctxt, Object value) voidTagDelegator.value(TagValueContext tvc, Object value) voidTagDropper.value(TagValueContext ctxt, Object value) voidTagValueListener.value(TagValueContext ctxt, Object value) A value has been seen.voidValueChanger.value(TagValueContext ctxt, Object value) -
Uses of ParserException in org.biojava.bio.program.unigene
Methods in org.biojava.bio.program.unigene that throw ParserExceptionModifier and TypeMethodDescriptionstatic ParserListenerUnigeneTools.buildDataParser(TagValueListener listener) Generate a tag-value parser for unigene data files that will pass all parsing events on to your listener.static ParserListenerUnigeneTools.buildLibInfoParser(TagValueListener listener) Generate a tag-value parser for the library info unigene files.