uk.ac.ebi.arrayexpress2.magetab.converter

Class MAGETABConverter<O>

java.lang.Object

uk.ac.ebi.arrayexpress2.magetab.converter.AbstractConverter<MAGETABInvestigation,O>

uk.ac.ebi.arrayexpress2.magetab.converter.MAGETABConverter<O>

All Implemented Interfaces:

Converter<MAGETABInvestigation,O>

public class MAGETABConverter<O>
extends AbstractConverter<MAGETABInvestigation,O>

Performs conversion of a MAGE-TAB object model using any ConversionHandlers available. Only handlers that can convert an entire MAGETABInvestigation object will be used. For more fine-grained conversion, see IDFConverter or SDRFConverter implementations.

Author:

Tony Burdett

Constructor Summary

Constructors

Constructor and Description
MAGETABConverter()

Method Summary

Methods

Modifier and Type	Method and Description
void	addErrorItemListener(ErrorItemListener listener) Register an ErrorItemListener with this parser.
void	convert(MAGETABInvestigation investigation, O outputResource) Converts source objects into target objects.
void	convert(MAGETABInvestigation investigation, O outputResource, ExecutorService service) Perform validation of the supplied validator source, delegating all work to the supplied Executor Service to enable validation in parallel.

Methods inherited from class uk.ac.ebi.arrayexpress2.magetab.converter.AbstractConverter

addProgressListener, fireConversionCompletedEvent, fireConversionEvent, fireConversionFailedEvent, fireConversionStartedEvent, fireErrorItemEvent, getErrorItemListeners, getProgressListeners, removeErrorItemListener, removeProgressListener

Methods inherited from class java.lang.Object

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

Constructor Detail

MAGETABConverter

public MAGETABConverter()

Method Detail

convert

public void convert(MAGETABInvestigation investigation,
           O outputResource)
             throws ConversionException

Description copied from interface: Converter

Converts source objects into target objects.

A ConversionException 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:

investigation - the source objects to convert

outputResource - the resulting target objects

Throws:

ConversionException - if the source

convert

public void convert(MAGETABInvestigation investigation,
           O outputResource,
           ExecutorService service)
             throws ConversionException,
                    InterruptedException

Description copied from interface: Converter

Perform validation of the supplied validator source, delegating all work to the supplied Executor Service to enable validation in parallel.

A ValidateException will be thrown if the supplied data could not be validated at all. You should not rely on an exception being thrown to determine whether the supplied MAGE-TAB is valid, as validator 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 validate operation.

Parameters:

investigation - the datamodel objects to convert from

outputResource - the type of object data is being converted into

service - the service to use to execute conversion tasks

Throws:

ConversionException - if the supplied source could not be converted

InterruptedException - if execution of a task sent to the Executor Service was interrrupted

addErrorItemListener

public void addErrorItemListener(ErrorItemListener listener)

Description copied from interface: Converter

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 Converter<MAGETABInvestigation,O>

Overrides:

addErrorItemListener in class AbstractConverter<MAGETABInvestigation,O>

Parameters:

listener - the listener to register