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 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.AbortErrorHandler.invalidEnd
(String token) int
GFFErrorHandler.invalidEnd
(String token) The `end' field of the GFF entry was not a valid value.int
GFFErrorHandler.AbortErrorHandler.invalidFrame
(String token) int
GFFErrorHandler.invalidFrame
(String token) The `frame' field of the GFF entry was not a valid value.double
GFFErrorHandler.AbortErrorHandler.invalidScore
(String token) double
GFFErrorHandler.invalidScore
(String token) The `score' field of the GFF entry was not a valid value.int
GFFErrorHandler.AbortErrorHandler.invalidStart
(String token) int
GFFErrorHandler.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.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 bReaderstatic 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
Reads aGFFEntrySet
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
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 ParserExceptionModifier and TypeMethodDescriptionprotected 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 ParserExceptionModifier and TypeMethodDescriptionstatic void
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 ParserExceptionModifier and TypeMethodDescriptionProduce a modified value from an old value.void
AbstractWrapper.endRecord()
void
Indexer.endRecord()
void
Indexer2.endRecord()
void
SimpleTagValueWrapper.endRecord()
void
StateMachine.endRecord()
void
StateMachine.SimpleStateListener.endRecord()
void
TagValueListener.endRecord()
The current record has ended.void
AbstractWrapper.endTag()
void
Aggregator.endTag()
void
MultiTagger.endTag()
void
RegexFieldFinder.endTag()
void
SimpleTagValueWrapper.endTag()
void
StateMachine.endTag()
void
StateMachine.SimpleStateListener.endTag()
void
TagDelegator.endTag()
void
TagDropper.endTag()
void
TagValueListener.endTag()
End the current tag.void
StateMachine.ExitNotification.notifyExit()
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.BasicState.setTransition
(Object tag, StateMachine.State destination, boolean notifyOnExit) set a Transition for this Statevoid
StateMachine.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.void
AbstractWrapper.startRecord()
void
SimpleTagValueWrapper.startRecord()
void
StateMachine.SimpleStateListener.startRecord()
void
StateMachine.startRecord()
void
TagValueListener.startRecord()
A new record is about to start.void
void
void
void
void
void
void
TagValueListener interfacevoid
void
void
void
Start a new tag.void
void
Find the destination State when the specified tag is encountered.void
void
AbstractWrapper.value
(TagValueContext ctxt, Object value) void
Aggregator.value
(TagValueContext ctxt, Object value) void
MultiTagger.value
(TagValueContext ctxt, Object value) void
RegexFieldFinder.value
(TagValueContext ctxt, Object val) void
SimpleTagValueWrapper.value
(TagValueContext ctxt, Object value) void
StateMachine.SimpleStateListener.value
(TagValueContext ctxt, Object value) void
StateMachine.value
(TagValueContext ctxt, Object value) void
TagDelegator.value
(TagValueContext tvc, Object value) void
TagDropper.value
(TagValueContext ctxt, Object value) void
TagValueListener.value
(TagValueContext ctxt, Object value) A value has been seen.void
ValueChanger.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 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.