uk.ac.ebi.arrayexpress2.magetab.parser

Class ADFParser

java.lang.Object

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

uk.ac.ebi.arrayexpress2.magetab.parser.ADFParser

All Implemented Interfaces:

Parser<ADF>

public class ADFParser
extends AbstractParser<ADF>

Imports ADF documents into an ADF. The ADFParser implements a parser for ADF documents, creating an in-memory object model to cache this date. The data contained in the cache fairly closely models the structure of the spreadsheet as described by the MAGETAB specification.

As for the IDFParser, this importer processes the document in parallel and uses Handlers to distribute the work. As handlers may, at some point, require data that is being processed by another handler that is running in a parallel process, there is a degree of waiting and communication between threads.

Author:

Tony Burdett

See Also:

ADF

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

Constructor and Description
ADFParser()

Method Summary

Methods

Modifier and Type	Method and Description
ADF	parse(InputStream adfIn) Performs parsing from the specified input stream source, populating an ADF object which is returned.
ADF	parse(InputStream adfIn, ADF adf) Perform parsing from the supplied input stream to a new data model instance.
ADF	parse(InputStream adfIn, ADF adf, 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.
protected void	read(String[][] adfData, ADF adf, ExecutorService service)
void	validate(ADF adf)
void	validate(ADF adf, ExecutorService service)
void	write(ADF adf)
void	write(ADF adf, ExecutorService service)

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

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

Methods inherited from class java.lang.Object

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

Constructor Detail

ADFParser

public ADFParser()

Method Detail

parse

public ADF parse(InputStream adfIn)
          throws ParseException

Performs parsing from the specified input stream source, populating an ADF object which is returned. This class will generate ErrorItems in response to any errors in the ADF file it detects, and report them via any registered ErrorItemListeners.

A ParseException will be thrown if and only if there was a problem with the ADF input stream that meant the document was unparseable. You not use the absence of a parse exception to indicate that parsing was successful, rather you should register an ErrorItemListener and check any generated error items to determine whether the ADF is suitable for your own purposes.

Unlike the MAGETABArrayParser, this parse method does not roll in validation and writing of the ADF within the parse lifecycle. This is to allow for dependencies that may need to be checked (for example, between an SDRF and an ADF file) and also to remain consistent with the behaviour of MAGETABParser. As such, this class defines its own validate(uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF) and write(uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF) methods. You can perform either of these actions manually yourself if you wish to do so.

Calling this method is equivalent to calling parse(adfIn, new ADF());.

ADF files will be parsed in a single threaded manner when calling this form of the parse() method. This method blocks until parsing is complete.

Parameters:

adfIn - the input stream to use to read ADF data for parsing

Returns:

a reference the populated ADF object (which is a reference to the adf parameter passed)

Throws:

ParseException - if the input stream was unparseable

parse

public ADF parse(InputStream adfIn,
        ADF adf)
          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

adf - 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 ADF parse(InputStream adfIn,
        ADF adf,
        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

adf - 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.

read

protected void read(String[][] adfData,
        ADF adf,
        ExecutorService service)
             throws ExecutionException,
                    InterruptedException

Throws:

ExecutionException

InterruptedException

validate

public void validate(ADF adf)
              throws ValidateException

Throws:

ValidateException

validate

public void validate(ADF adf,
            ExecutorService service)

write

public void write(ADF adf)
           throws ConversionException

Throws:

ConversionException

write

public void write(ADF adf,
         ExecutorService service)