## Uses of Class
org.biojava.utils.ParserException

Packages that use ParserException
org.biojava.bio.annodb: Databases of generic structured data (annotation) objects.
org.biojava.bio.program.gff: GFF manipulation.
org.biojava.bio.program.gff3: Support for reading and writing GFF3.
org.biojava.bio.program.indexdb: A flat-file ascii index of ascii flat files as per the OBDA specification.
org.biojava.bio.program.tagvalue: Process files as streams of records, each with tags with values.
org.biojava.bio.program.unigene: Objects for representing Unigene clusters.

Uses of ParserException in org.biojava.bio.annodb

Constructors in org.biojava.bio.annodb that throw ParserException
`IndexedAnnotationDB(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 ParserException
`protected GFFRecord` `GFFParser.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.
`int` `GFFErrorHandler.invalidEnd(String token)` The `end' field of the GFF entry was not a valid value.
`int` `GFFErrorHandler.AbortErrorHandler.invalidEnd(String token)`
`int` `GFFErrorHandler.invalidFrame(String token)` The `frame' field of the GFF entry was not a valid value.
`int` `GFFErrorHandler.AbortErrorHandler.invalidFrame(String token)`
`double` `GFFErrorHandler.invalidScore(String token)` The `score' field of the GFF entry was not a valid value.
`double` `GFFErrorHandler.AbortErrorHandler.invalidScore(String token)`
`int` `GFFErrorHandler.invalidStart(String token)` The `start' field of the GFF entry was not a valid value.
`int` `GFFErrorHandler.AbortErrorHandler.invalidStart(String token)`
`StrandedFeature.Strand` `GFFErrorHandler.invalidStrand(String token)` The `strand' field of the GFF entry was not a valid value.
`StrandedFeature.Strand` `GFFErrorHandler.AbortErrorHandler.invalidStrand(String token)`
`void` `GFFParser.parse(BufferedReader bReader, GFFDocumentHandler handler)` Informs handler of each line of gff read from bReader.
`void` `GFFParser.parse(BufferedReader bReader, GFFDocumentHandler handler, String locator)` Informs handler of each line of GFF read from bReader
`static GFFEntrySet` `GFFTools.readGFF(BufferedReader gffIn)` Read all GFF entries from a buffered reader.
`static GFFEntrySet` `GFFTools.readGFF(BufferedReader gffIn, GFFRecordFilter recFilt)` Read all GFF entries matching a filter from a buffered reader.
`static GFFEntrySet` `GFFTools.readGFF(File inFile)` Reads a `GFFEntrySet` from a file with no filtering.
`static GFFEntrySet` `GFFTools.readGFF(File inFile, GFFRecordFilter recFilt)` Reads a GFFEntrySet from a file with the specified filter.
`static GFFEntrySet` `GFFTools.readGFF(String fileName)` Deprecated. use: readGff(File)
`static GFFEntrySet` `GFFTools.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 ParserException
`protected GFF3Record` `GFF3Parser.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.
`void` `GFF3Parser.parse(BufferedReader bReader, GFF3DocumentHandler handler, Ontology ontology)` Informs handler of each line of gff read from bReader.
`void` `GFF3Parser.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 ParserException
`static void` `IndexTools.indexEmbl(String name, File location, File[] seqFiles, int alphabetIdentifier)` `indexEmbl` indexes DNA, RNA or protein EMBL format sequence files on ID as primary identifier and AC as secondary.
`static void` `IndexTools.indexFasta(String name, File location, File[] seqFiles, int alphabetIdentifier)` `indexFasta` indexes DNA, RNA or protein Fasta format sequence files on primary identifier.
`static void` `IndexTools.indexGenbank(String name, File location, File[] seqFiles, int alphabetIdentifier)` `indexGenbank` indexes DNA, RNA or protein Genbank format sequence files on LOCUS as primary identifier and ACCESSION as secondary.
`static void` `IndexTools.indexSwissprot(String name, File location, File[] seqFiles)` `indexSwissprot` indexes 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 ParserException
`Object` `RegexChanger.change(Object value)`
`Object` `ChangeTable.Changer.change(Object value)` Produce a modified value from an old value.
`Object` `ChangeTable.ChainedChanger.change(Object value)`
`Object` `ChangeTable.change(Object tag, Object value)`
`void` `TagValueListener.endRecord()` The current record has ended.
`void` `StateMachine.endRecord()`
`void` `StateMachine.SimpleStateListener.endRecord()`
`void` `SimpleTagValueWrapper.endRecord()`
`void` `Indexer2.endRecord()`
`void` `Indexer.endRecord()`
`void` `AbstractWrapper.endRecord()`
`void` `TagValueListener.endTag()` End the current tag.
`void` `TagDropper.endTag()`
`void` `TagDelegator.endTag()`
`void` `StateMachine.endTag()`
`void` `StateMachine.SimpleStateListener.endTag()`
`void` `SimpleTagValueWrapper.endTag()`
`void` `RegexFieldFinder.endTag()`
`void` `MultiTagger.endTag()`
`void` `Aggregator.endTag()`
`void` `AbstractWrapper.endTag()`
`void` `StateMachine.ExitNotification.notifyExit()`
`TagValue` `TagValueParser.parse(Object record)`
`TagValue` `RegexParser.parse(Object o)`
`void` `StateMachine.TransitionTable.put(Object tag, StateMachine.Transition transition)` set a Transition within this TransitionTable (2-argument form)
`boolean` `Parser.read(BufferedReader reader, TagValueParser parser, TagValueListener listener)`
`void` `StateMachine.BasicState.setTransition(Object tag, StateMachine.State destination)` set a Transition for this State setting notifyOnExit to false.
`void` `StateMachine.TransitionTable.setTransition(Object tag, StateMachine.State destination, boolean notifyOnExit)` set a Transition within this TransitionTable (3-argument form)
`void` `StateMachine.BasicState.setTransition(Object tag, StateMachine.State destination, boolean notifyOnExit)` set a Transition for this State
`List` `ChangeTable.Splitter.split(Object value)` Produce a list of values from an old value.
`void` `TagValueListener.startRecord()` A new record is about to start.
`void` `StateMachine.startRecord()`
`void` `StateMachine.SimpleStateListener.startRecord()`
`void` `SimpleTagValueWrapper.startRecord()`
`void` `AbstractWrapper.startRecord()`
`void` `ValueChanger.startTag(Object tag)`
`void` `TagValueListener.startTag(Object tag)` Start a new tag.
`void` `TagRenamer.startTag(Object tag)`
`void` `TagDropper.startTag(Object tag)`
`void` `TagDelegator.startTag(Object tag)`
`void` `StateMachine.startTag(Object tag)` TagValueListener interface
`void` `StateMachine.SimpleStateListener.startTag(Object tag)`
`void` `SimpleTagValueWrapper.startTag(Object tag)`
`void` `RegexFieldFinder.startTag(Object tag)`
`void` `MultiTagger.startTag(Object tag)`
`void` `Aggregator.startTag(Object tag)`
`void` `AbstractWrapper.startTag(Object tag)`
`void` `StateMachine.State.transit(Object tag)`
`void` `StateMachine.BasicState.transit(Object tag)` Find the destination State when the specified tag is encountered.
`void` `ValueChanger.value(TagValueContext ctxt, Object value)`
`void` `TagValueListener.value(TagValueContext ctxt, Object value)` A value has been seen.
`void` `TagDropper.value(TagValueContext ctxt, Object value)`
`void` `TagDelegator.value(TagValueContext tvc, Object value)`
`void` `StateMachine.value(TagValueContext ctxt, Object value)`
`void` `StateMachine.SimpleStateListener.value(TagValueContext ctxt, Object value)`
`void` `SimpleTagValueWrapper.value(TagValueContext ctxt, Object value)`
`void` `RegexFieldFinder.value(TagValueContext ctxt, Object val)`
`void` `MultiTagger.value(TagValueContext ctxt, Object value)`
`void` `Aggregator.value(TagValueContext ctxt, Object value)`
`void` `AbstractWrapper.value(TagValueContext ctxt, Object value)`

Uses of ParserException in org.biojava.bio.program.unigene

Methods in org.biojava.bio.program.unigene that throw ParserException
`static ParserListener` `UnigeneTools.buildDataParser(TagValueListener listener)` Generate a tag-value parser for unigene data files that will pass all parsing events on to your listener.
`static ParserListener` `UnigeneTools.buildLibInfoParser(TagValueListener listener)` Generate a tag-value parser for the library info unigene files.