org.biojava.bio.program.gff3

Class GFF3Parser

java.lang.Object

org.biojava.bio.program.gff3.GFF3Parser

public class GFF3Parser
extends Object

Parse a stream of GFF text into a stream of records and comments.

Developed from GFFParser.

Author:

Matthew Pocock

Constructor Summary

Constructors

Constructor and Description
GFF3Parser()

Method Summary

Modifier and Type	Method and Description
protected GFF3Record	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.
GFFErrorHandler	getErrorHandler() Find the error handler used by this parser.
void	parse(BufferedReader bReader, GFF3DocumentHandler handler, Ontology ontology) Informs handler of each line of gff read from bReader.
void	parse(BufferedReader bReader, GFF3DocumentHandler handler, Ontology ontology, String locator) Informs handler of each line of GFF read from bReader
protected void	parseAttribute(String attValList, Annotation anno, Ontology onto, Ontology fallBack) Parse attValList into a Map of attributes and value lists.
void	setErrorHandler(GFFErrorHandler errors) Set the error handler used by this parser.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GFF3Parser

public GFF3Parser()

Method Detail

setErrorHandler

public void setErrorHandler(GFFErrorHandler errors)

Set the error handler used by this parser.

getErrorHandler

public GFFErrorHandler getErrorHandler()

Find the error handler used by this parser.

parse

public void parse(BufferedReader bReader,
                  GFF3DocumentHandler handler,
                  Ontology ontology)
           throws IOException,
                  BioException,
                  ParserException

Informs handler of each line of gff read from bReader. This form of the method should only be used if no locator string is available for the resource being parsed.

Parameters:

bReader - the BufferedReader to parse

handler - the GFF3DocumentHandler that will listen for 'stuff'

ontology - an Ontology that all terms should come from

Throws:

- class="type">IOException if for any reason bReader throws one

- class="type">BioException if handler can not correct a parse error

IOException

BioException

ParserException

parse

public void parse(BufferedReader bReader,
                  GFF3DocumentHandler handler,
                  Ontology ontology,
                  String locator)
           throws IOException,
                  BioException,
                  ParserException

Informs handler of each line of GFF read from bReader

Parameters:

bReader - the BufferedReader to parse

handler - the GFF3DocumentHandler that will listen for 'stuff'

ontology - an Ontology that all terms should come from

Throws:

- class="type">IOException if for any reason bReader throws one

- class="type">BioException if handler can not correct a parse error

IOException

BioException

ParserException

createRecord

protected GFF3Record createRecord(GFF3DocumentHandler handler,
                                  List aList,
                                  String rest,
                                  String comment,
                                  Ontology ontology,
                                  Ontology fallBack)
                           throws BioException,
                                  ParserException,
                                  IgnoreRecordException

Actually turns a list of tokens, some value string and a comment into a GFF3Record and informs handler.

Parameters:

handler - a GFF3DocumentHandler to inform of any parse errors, and the completed GFF3Record

aList - a List containing the 8 mandatory GFF columns

rest - a String representing the unparsed attribute-value text, or null if there is none

comment - a String containing the comment (without the leading '#' character.

ontology - the Ontology to resolve Terms in

Throws:

- class="type">BioException if handler could not correct a parse error

BioException

ParserException

IgnoreRecordException

parseAttribute

protected void parseAttribute(String attValList,
                              Annotation anno,
                              Ontology onto,
                              Ontology fallBack)
                       throws ChangeVetoException

Parse attValList into a Map of attributes and value lists.

Populates an Annotation instance with Ontology Term keys and string/list values.

Parameters:

attValList - the String to parse

Throws:

ChangeVetoException