uk.ac.ebi.arrayexpress2.magetab.handler.adf

Class ADFHeaderReadHandler

java.lang.Object

uk.ac.ebi.arrayexpress2.magetab.handler.AbstractHandler

uk.ac.ebi.arrayexpress2.magetab.handler.adf.ADFHeaderReadHandler

All Implemented Interfaces:

Handler, ReadHandler<String,String[],ADF>

Direct Known Subclasses:

AccessionHandler, ArrayDesignNameHandler, CommentHandler, PrintingProtocolHandler, ProviderHandler, SequencePolymerTypeHandler, SequencePolymerTypeTermAccessionHandler, SequencePolymerTypeTermSourceRefHandler, SubstrateTypeHandler, SubstrateTypeTermAccessionHandler, SubstrateTypeTermSourceRefHandler, SurfaceTypeHandler, SurfaceTypeTermAccessionHandler, SurfaceTypeTermSourceRefHandler, TechnologyTypeHandler, TechnologyTypeTermAccessionHandler, TechnologyTypeTermSourceRefHandler, TermSourceFileHandler, TermSourceNameHandler, TermSourceVersionHandler, VersionHandler

public abstract class ADFHeaderReadHandler
extends AbstractHandler
implements ReadHandler<String,String[],ADF>

An abstract implementation of ReadHandler for reading from the header part of an ADF file into a MAGETABArrayDesign. This implementation governs all common functionality including general handling order and progress tracking. Specific concrete handlers only need define the header they can read, the maximum number of values allowed on the line marked by this tag, and how to set the field on the MAGETABArrayDesign object.

Author:

Tony Burdett

Field Summary

Fields inherited from class uk.ac.ebi.arrayexpress2.magetab.handler.AbstractHandler

listeners

Constructor Summary

Constructors

Constructor and Description
ADFHeaderReadHandler()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	canRead(Object header) Determine whether this handler can read the supplied header.
protected abstract boolean	canReadHeader(String header) Determine whether this handler can read the data referenced by this header.
int	getAllowedLength() Get the legal number of data entries for this type of handler, as specified by the MAGE-TAB specification.
void	read(String header, String[] data, ADF adf, int lineNumber, int columnNumber) Invoke this read handler.
protected abstract void	readValue(ADF adf, String value, int lineNumber, String... types) Performs the unit of work to read the data into the internal MAGE-TAB investigation.

Methods inherited from class uk.ac.ebi.arrayexpress2.magetab.handler.AbstractHandler

accept, addListener, fireHandlingFailedEvent, fireHandlingStartedEvent, fireHandlingSucceededEvent, getListeners, getLog, removeListener

Methods inherited from class java.lang.Object

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

Methods inherited from interface uk.ac.ebi.arrayexpress2.magetab.handler.Handler

accept, addListener, getListeners, removeListener

Constructor Detail

ADFHeaderReadHandler

public ADFHeaderReadHandler()

Method Detail

canRead

public boolean canRead(Object header)

Description copied from interface: ReadHandler

Determine whether this handler can read the supplied header. Typically, the data will be a String or String array depending on whether IDF, SDRF or ADF is being read, although the general framework can be extended to parse any data type.

This header should be passed to the handler prior to reading to determine whether this handler can handle it

Specified by:

canRead in interface ReadHandler<String,String[],ADF>

Parameters:

header - the data that will be validated

Returns:

true if this handler can handle this tag, false otherwise

getAllowedLength

public int getAllowedLength()

Get the legal number of data entries for this type of handler, as specified by the MAGE-TAB specification. Usually, this will not be set unless there is a specific cardinality=1 requirement (only found in some places in the ADF spec).

If the allowed length is -1 (the default) this means the cardinality is unrestricted

Returns:

the allowed length

read

public void read(String header,
        String[] data,
        ADF adf,
        int lineNumber,
        int columnNumber)
          throws ParseException

Invoke this read handler. This will read the supplied data assigned to this handler into the MAGETABArrayDesign object.

This abstract implementation delegates the responsibility for setting the correct fields to concrete implementations via readValue(uk.ac.ebi.arrayexpress2.magetab.datamodel.ADF, String, int, String...). This method itself governs the update of progress tracking and status information. Before this handler has completed reading, the status of the current task index is updated to Status.COMPLETE if everything succeeded, or Status.FAILED otherwise

Specified by:

read in interface ReadHandler<String,String[],ADF>

Parameters:

header - the header describing the data to parse

data - the data to read into the object model

adf - the ADF object to populate

lineNumber -

columnNumber -

Throws:

ParseException - if the handler failed to read data from it's source

canReadHeader

protected abstract boolean canReadHeader(String header)

Determine whether this handler can read the data referenced by this header. Typically, the header in an IDF file (or ADF header) is the first token on any given line, and the header in an SDRF file (or ADF graph part) is the column heading for each tab-separated column. Other types of data referencing can be supplied - for example, an XML type reader might pass the tag qname as the header.

The header should be passed to the handler prior to reading to determine whether this handler can handle this line.

Parameters:

header - the first token on a line, or the column heading, which is the string describing this line contents

Returns:

true if this handler can handle this tag, false otherwise

readValue

protected abstract void readValue(ADF adf,
             String value,
             int lineNumber,
             String... types)
                           throws ParseException

Performs the unit of work to read the data into the internal MAGE-TAB investigation. Override this method in implementations, so that you don't need to implement status updating and checking code.

This method is passed the array design to read into, the next value that should be read and (optionally) the type. The type parameter will normally be zero or one value indicating the absence or presence of a type variable on the header.

Parameters:

adf - the ADF to populate with parsed data

value - the value to read into the cache

lineNumber - the line number this value is being read from

types - a single string representing the type, if present. Should not normally be greater than 1 element long @throws ParseException if the header cannot be parsed or there was an error reading the value

Throws:

ParseException - if the given data failed to parse