org.biojava.bio.program.gff

Class GFFParser

java.lang.Object

org.biojava.bio.program.gff.GFFParser

public class GFFParser
extends java.lang.Object

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

Author:

Matthew Pocock, Thomas Down, Keith James (docs)

Constructor Summary

Constructors

Constructor and Description
GFFParser()

Method Summary

Modifier and Type	Method and Description
protected GFFRecord	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.
GFFErrorHandler	getErrorHandler() Find the error handler used by this parser.
void	parse(java.io.BufferedReader bReader, GFFDocumentHandler handler) Informs handler of each line of gff read from bReader.
void	parse(java.io.BufferedReader bReader, GFFDocumentHandler handler, java.lang.String locator) Informs handler of each line of GFF read from bReader
protected java.util.Map	parseAttribute(java.lang.String attValList) 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

GFFParser

public GFFParser()

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(java.io.BufferedReader bReader,
                  GFFDocumentHandler handler)
           throws java.io.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 GFFDocumentHandler that will listen for 'stuff'

Throws:

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

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

java.io.IOException

BioException

ParserException

parse

public void parse(java.io.BufferedReader bReader,
                  GFFDocumentHandler handler,
                  java.lang.String locator)
           throws java.io.IOException,
                  BioException,
                  ParserException

Informs handler of each line of GFF read from bReader

Parameters:

bReader - the BufferedReader to parse

handler - the GFFDocumentHandler that will listen for 'stuff'

Throws:

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

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

java.io.IOException

BioException

ParserException

createRecord

protected GFFRecord createRecord(GFFDocumentHandler handler,
                                 java.util.List aList,
                                 java.lang.String rest,
                                 java.lang.String comment)
                          throws BioException,
                                 ParserException,
                                 IgnoreRecordException

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

Parameters:

handler - a GFFDocumentHandler to inform of any parse errors, and the completed GFFRecord

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.

Throws:

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

BioException

ParserException

IgnoreRecordException

parseAttribute

protected java.util.Map parseAttribute(java.lang.String attValList)

Parse attValList into a Map of attributes and value lists.

The resulting Map will have String keys, with List values. If there are no values associated with a key, then it will have an empty List, not null as its value.

Parameters:

attValList - the String to parse

Returns:

a Map of parsed attributes and value lists