uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node

Class SampleHandler

java.lang.Object

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

uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadHandler

uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.node.SampleHandler

All Implemented Interfaces:

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

@ServiceProvider
public class SampleHandler
extends SDRFReadHandler

A handler that handles Sample nodes in the SDRF graph

Tag: Sample Name
Allowed attributes: Characteristics, Material Type, Description, Comment, Array Design File/Ref

Author:

Tony Burdett

Field Summary

Fields inherited from class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadHandler

PROTOCOL_DELIMITER

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

listeners

Constructor Summary

Constructors

Constructor and Description
SampleHandler()

Method Summary

Methods

Modifier and Type	Method and Description
int	assess(String[] header) Return the index of the last header this handler can read from in the supplied header.
boolean	canReadHeader(String[] header) Determine whether this handler can read the data referenced by this header.
void	readData(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber) Performs the unit of work to read the data into the internal datamodel.

Methods inherited from class uk.ac.ebi.arrayexpress2.magetab.handler.sdrf.SDRFReadHandler

assessAttribute, canRead, read, readAttribute, updateChildNode

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

SampleHandler

public SampleHandler()

Method Detail

canReadHeader

public boolean canReadHeader(String[] header)

Description copied from class: SDRFReadHandler

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.

Specified by:

canReadHeader in class SDRFReadHandler

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

assess

public int assess(String[] header)

Description copied from class: SDRFReadHandler

Return the index of the last header this handler can read from in the supplied header. This can be used to determine the start and finish indices that a handler can read from/to.

Specified by:

assess in class SDRFReadHandler

Parameters:

header - the header to assess

Returns:

the last column index that can be read

readData

public void readData(String[] header,
            String[] data,
            SDRF sdrf,
            int lineNumber,
            int columnNumber)
              throws ParseException

Description copied from class: SDRFReadHandler

Performs the unit of work to read the data into the internal datamodel. Override this method in implementations, so that you don't need to implement status updating and checking code. Implementations should determine how much data should be read from the data queue - access the data that still needs to be read by calling

Specified by:

readData in class SDRFReadHandler

Parameters:

header - the header identifying the data to read

data - the data to read

sdrf - the SDRF to add data to

lineNumber - the lin number this data was read from

columnNumber - the first column of the data being read

Throws:

ParseException - if the header cannot be parsed or there was an error reading the value