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.