uk.ac.ebi.arrayexpress2.magetab.parser

Class MAGETABArrayParser<O>

java.lang.Object

uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser<MAGETABArrayDesign>

uk.ac.ebi.arrayexpress2.magetab.parser.MAGETABArrayParser<O>

All Implemented Interfaces:

Parser<MAGETABArrayDesign>

public class MAGETABArrayParser<O>
extends AbstractParser<MAGETABArrayDesign>

Imports MAGETAB Array Design documents into a MAGETABArrayDesign. Unlike MAGETABInvestigations, MAGETABArrayDesigns normally only have one component (the ADF). Therefore this parser functions mostly as a wrapper around an ADFParser, but takes care of appropriate instantiation of services and MAGETABArrayDesign objects for you. appropriate.

Author:

Tony Burdett

See Also:

ADFParser, MAGETABArrayDesign

Nested Class Summary

Nested classes/interfaces inherited from class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser

AbstractParser.DefaultHandlerListener

Field Summary

Fields inherited from interface uk.ac.ebi.arrayexpress2.magetab.parser.Parser

DEFAULT_ENCODING

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	MAGETABArrayParser()

Method Summary

Methods

Modifier and Type	Method and Description
void	addErrorItemListener(ErrorItemListener listener) Register an ErrorItemListener with this parser.
O	getOutputResource() Get the currently configured output resource for this parser
Validator<MAGETABArrayDesign>	getValidator() Get the currently configured validator for this parser.
MAGETABArrayDesign	parse(File adfFile)
MAGETABArrayDesign	parse(InputStream adfIn) Perform parsing from the supplied input stream to a new data model instance.
MAGETABArrayDesign	parse(InputStream adfIn, MAGETABArrayDesign arrayDesign) Perform parsing from the supplied input stream to a new data model instance.
MAGETABArrayDesign	parse(InputStream adfIn, MAGETABArrayDesign arrayDesign, ExecutorService service) Perform parsing from the supplied input stream to a new data model instance, delegating all work to the supplied Executor Service to enable parsing in parallel.
MAGETABArrayDesign	parse(URL adfURL)
void	removeErrorItemListener(ErrorItemListener listener) Deregister an ErrorItemListener with this parser.
void	setOutputResource(O outputResource) Configure this parser with an output resource to convert data to.
void	setStripEscaping(boolean stripEscaping)
void	setValidator(Validator<MAGETABArrayDesign> validator) Configure this parser with a Validator.

Methods inherited from class uk.ac.ebi.arrayexpress2.magetab.parser.AbstractParser

addProgressListener, fireErrorItemEvent, fireParseEvent, fireParsingCompletedEvent, fireParsingFailedEvent, fireParsingStartedEvent, getEncoding, getErrorItemListeners, getLog, getProgressListeners, isStrippingEscaping, removeProgressListener, setEncoding

Methods inherited from class java.lang.Object

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

Constructor Detail

MAGETABArrayParser

protected MAGETABArrayParser()

Method Detail

setStripEscaping

public void setStripEscaping(boolean stripEscaping)

Overrides:

setStripEscaping in class AbstractParser<MAGETABArrayDesign>

setValidator

public void setValidator(Validator<MAGETABArrayDesign> validator)

Configure this parser with a Validator. Normally, the validate() method on the Validator will be called once reading has completed.

It is possible to share an ErrorItemListener between a Parser and a Validator

Parameters:

validator - the validator this parser should use to validate once parsing has completed.

getValidator

public Validator<MAGETABArrayDesign> getValidator()

Get the currently configured validator for this parser.

Returns:

the validator for this parser, or null if there has not been one set.

setOutputResource

public void setOutputResource(O outputResource)

Configure this parser with an output resource to convert data to.

Parameters:

outputResource - the output resource to convert to

getOutputResource

public O getOutputResource()

Get the currently configured output resource for this parser

Returns:

the output resource for this parser, or null if there has not been one set.

addErrorItemListener

public void addErrorItemListener(ErrorItemListener listener)

Description copied from interface: Parser

Register an ErrorItemListener with this parser. Whenever an error is encountered when parsing from the a parserSource, this listener should be notified.

Specified by:

addErrorItemListener in interface Parser<MAGETABArrayDesign>

Overrides:

addErrorItemListener in class AbstractParser<MAGETABArrayDesign>

Parameters:

listener - the listener to register

removeErrorItemListener

public void removeErrorItemListener(ErrorItemListener listener)

Description copied from interface: Parser

Deregister an ErrorItemListener with this parser. This listener will no longer be notified when error items are generated.

Specified by:

removeErrorItemListener in interface Parser<MAGETABArrayDesign>

Overrides:

removeErrorItemListener in class AbstractParser<MAGETABArrayDesign>

Parameters:

listener - the listener to register

parse

public MAGETABArrayDesign parse(File adfFile)
                         throws ParseException

Throws:

ParseException

parse

public MAGETABArrayDesign parse(URL adfURL)
                         throws ParseException

Throws:

ParseException

parse

public MAGETABArrayDesign parse(InputStream adfIn)
                         throws ParseException

Description copied from interface: Parser

Perform parsing from the supplied input stream to a new data model instance.

A ParseException will be thrown if data could not be read from the supplied stream. You should not rely on an exception being thrown to determine whether the supplied MAGE-TAB is valid or complete, as parser implementations may ignore invalid or unreadable sections. Instead you should register an ErrorItem listener and check that there are no critical error events fired during the parse operation.

Parameters:

adfIn - the input stream to parse from

Returns:

the data model that has been populated by this parse operation

Throws:

ParseException - if the source format was invalid, or the URL could not be read.

parse

public MAGETABArrayDesign parse(InputStream adfIn,
                       MAGETABArrayDesign arrayDesign)
                         throws ParseException

Description copied from interface: Parser

Perform parsing from the supplied input stream to a new data model instance. The supplied target will be populated with data - the result of this method will be simply a reference to the passed parameter.

A ParseException will be thrown if data could not be read from the supplied stream. You should not rely on an exception being thrown to determine whether the supplied MAGE-TAB is valid or complete, as parser implementations may ignore invalid or unreadable sections. Instead you should register an ErrorItem listener and check that there are no critical error events fired during the parse operation.

Parameters:

adfIn - the input stream to parse from

arrayDesign - the data model to populate with data during this parse operation

Returns:

the data model that has been populated by this import operation

Throws:

ParseException - if the source format was invalid, or the URL could not be read.

parse

public MAGETABArrayDesign parse(InputStream adfIn,
                       MAGETABArrayDesign arrayDesign,
                       ExecutorService service)
                         throws ParseException

Description copied from interface: Parser

Perform parsing from the supplied input stream to a new data model instance, delegating all work to the supplied Executor Service to enable parsing in parallel.

A ParseException will be thrown if data could not be read from the supplied stream. You should not rely on an exception being thrown to determine whether the supplied MAGE-TAB is valid or complete, as parser implementations may ignore invalid or unreadable sections. Instead you should register an ErrorItem listener and check that there are no critical error events fired during the parse operation.

Parameters:

adfIn - the input stream to parse from

arrayDesign - the data model to populate with data during this parse operation

service - the service to use to execute parsing tasks

Returns:

the data model that has been populated by this import operation

Throws:

ParseException - if the source format was invalid, or the URL could not be read.