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

Packages that use ParserException
org.biojava.bio.program.gff: GFF manipulation.
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.program.gff

Methods in org.biojava.bio.program.gff that throw ParserException
`int` `GFFErrorHandler.invalidStart(java.lang.String token)` The `start' field of the GFF entry was not a valid value.
`int` `GFFErrorHandler.invalidEnd(java.lang.String token)` The `end' field of the GFF entry was not a valid value.
`double` `GFFErrorHandler.invalidScore(java.lang.String token)` The `score' field of the GFF entry was not a valid value.
`int` `GFFErrorHandler.invalidFrame(java.lang.String token)` The `frame' field of the GFF entry was not a valid value.
`StrandedFeature.Strand` `GFFErrorHandler.invalidStrand(java.lang.String token)` The `strand' field of the GFF entry was not a valid value.
`int` `GFFErrorHandler.AbortErrorHandler.invalidStart(java.lang.String token)`
`int` `GFFErrorHandler.AbortErrorHandler.invalidEnd(java.lang.String token)`
`double` `GFFErrorHandler.AbortErrorHandler.invalidScore(java.lang.String token)`
`int` `GFFErrorHandler.AbortErrorHandler.invalidFrame(java.lang.String token)`
`StrandedFeature.Strand` `GFFErrorHandler.AbortErrorHandler.invalidStrand(java.lang.String token)`
`void` `GFFParser.parse(java.io.BufferedReader bReader, GFFDocumentHandler handler)` Informs handler of each line of gff read from bReader.
`void` `GFFParser.parse(java.io.BufferedReader bReader, GFFDocumentHandler handler, java.lang.String locator)` Informs handler of each line of GFF read from bReader
`protected GFFRecord` `GFFParser.createRecord(GFFDocumentHandler handler, java.util.List aList, java.lang.String rest, java.lang.String comment)` Actually turns a list of tokens, some value string and a comment into a GFFRecord and informs handler.
`static GFFEntrySet` `GFFTools.readGFF(java.lang.String fileName)` Reads a `GFFEntrySet` from a file with no filtering
`static GFFEntrySet` `GFFTools.readGFF(java.lang.String fileName, GFFRecordFilter recFilt)` Reads a GFFEntrySet from a file with the specified filter
`static GFFEntrySet` `GFFTools.readGFF(java.io.BufferedReader gffIn)`
`static GFFEntrySet` `GFFTools.readGFF(java.io.BufferedReader gffIn, GFFRecordFilter recFilt)`

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

Methods in org.biojava.bio.program.indexdb that throw ParserException
`static void` `IndexTools.indexFasta(java.lang.String name, java.io.File location, java.io.File[] seqFiles, int alphabetIdentifier)` `indexFasta` indexes DNA, RNA or protein Fasta format sequence files on primary identifier.
`static void` `IndexTools.indexEmbl(java.lang.String name, java.io.File location, java.io.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.indexGenbank(java.lang.String name, java.io.File location, java.io.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(java.lang.String name, java.io.File location, java.io.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
`void` `RegexFieldFinder.startTag(java.lang.Object tag)`
`void` `RegexFieldFinder.endTag()`
`void` `RegexFieldFinder.value(TagValueContext ctxt, java.lang.Object val)`
`TagValue` `RegexParser.parse(java.lang.Object o)`
`java.lang.Object` `RegexChanger.change(java.lang.Object value)`
`void` `TagRenamer.startTag(java.lang.Object tag)`
`void` `TagValueListener.startRecord()` A new record is about to start.
`void` `TagValueListener.endRecord()` The current record has ended.
`void` `TagValueListener.startTag(java.lang.Object tag)` Start a new tag.
`void` `TagValueListener.endTag()` End the current tag.
`void` `TagValueListener.value(TagValueContext ctxt, java.lang.Object value)` A value has been seen.
`boolean` `Parser.read(java.io.BufferedReader reader, TagValueParser parser, TagValueListener listener)`
`void` `Indexer2.endRecord()`
`void` `Indexer.endRecord()`
`void` `ValueChanger.startTag(java.lang.Object tag)`
`void` `ValueChanger.value(TagValueContext ctxt, java.lang.Object value)`
`TagValue` `TagValueParser.parse(java.lang.Object record)`
`void` `TagDelegator.startTag(java.lang.Object tag)`
`void` `TagDelegator.endTag()`
`void` `TagDelegator.value(TagValueContext tvc, java.lang.Object value)`
`java.lang.Object` `ChangeTable.change(java.lang.Object tag, java.lang.Object value)`
`java.lang.Object` `ChangeTable.Changer.change(java.lang.Object value)` Produce a modified value from an old value.
`java.util.List` `ChangeTable.Splitter.split(java.lang.Object value)` Produce a list of values from an old value.
`java.lang.Object` `ChangeTable.ChainedChanger.change(java.lang.Object value)`
`void` `TagDropper.startTag(java.lang.Object tag)`
`void` `TagDropper.endTag()`
`void` `TagDropper.value(TagValueContext ctxt, java.lang.Object value)`
`void` `TagValueWrapper.startRecord()`
`void` `TagValueWrapper.endRecord()`
`void` `TagValueWrapper.startTag(java.lang.Object tag)`
`void` `TagValueWrapper.endTag()`
`void` `TagValueWrapper.value(TagValueContext ctxt, java.lang.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.