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 ChangeTable.Changer.change(Object value)
           Produce a modified value from an old value.
 Object ChangeTable.ChainedChanger.change(Object value)
           
 Object RegexChanger.change(Object value)
           
 Object ChangeTable.change(Object tag, Object value)
           
 void SimpleTagValueWrapper.endRecord()
           
 void Indexer2.endRecord()
           
 void StateMachine.endRecord()
           
 void StateMachine.SimpleStateListener.endRecord()
           
 void AbstractWrapper.endRecord()
           
 void TagValueListener.endRecord()
          The current record has ended.
 void Indexer.endRecord()
           
 void TagDropper.endTag()
           
 void Aggregator.endTag()
           
 void SimpleTagValueWrapper.endTag()
           
 void MultiTagger.endTag()
           
 void StateMachine.endTag()
           
 void StateMachine.SimpleStateListener.endTag()
           
 void AbstractWrapper.endTag()
           
 void TagDelegator.endTag()
           
 void TagValueListener.endTag()
          End the current tag.
 void RegexFieldFinder.endTag()
           
 void StateMachine.ExitNotification.notifyExit()
           
 TagValue RegexParser.parse(Object o)
           
 TagValue TagValueParser.parse(Object record)
           
 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 SimpleTagValueWrapper.startRecord()
           
 void StateMachine.startRecord()
           
 void StateMachine.SimpleStateListener.startRecord()
           
 void AbstractWrapper.startRecord()
           
 void TagValueListener.startRecord()
          A new record is about to start.
 void ValueChanger.startTag(Object tag)
           
 void TagDropper.startTag(Object tag)
           
 void Aggregator.startTag(Object tag)
           
 void SimpleTagValueWrapper.startTag(Object tag)
           
 void TagRenamer.startTag(Object tag)
           
 void MultiTagger.startTag(Object tag)
           
 void StateMachine.startTag(Object tag)
          TagValueListener interface
 void StateMachine.SimpleStateListener.startTag(Object tag)
           
 void AbstractWrapper.startTag(Object tag)
           
 void TagDelegator.startTag(Object tag)
           
 void TagValueListener.startTag(Object tag)
          Start a new tag.
 void RegexFieldFinder.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 TagDropper.value(TagValueContext ctxt, Object value)
           
 void Aggregator.value(TagValueContext ctxt, Object value)
           
 void SimpleTagValueWrapper.value(TagValueContext ctxt, Object value)
           
 void MultiTagger.value(TagValueContext ctxt, Object value)
           
 void StateMachine.value(TagValueContext ctxt, Object value)
           
 void StateMachine.SimpleStateListener.value(TagValueContext ctxt, Object value)
           
 void AbstractWrapper.value(TagValueContext ctxt, Object value)
           
 void TagDelegator.value(TagValueContext tvc, Object value)
           
 void TagValueListener.value(TagValueContext ctxt, Object value)
          A value has been seen.
 void RegexFieldFinder.value(TagValueContext ctxt, Object val)
           
 

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.