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

Class FactorValueNodeHandler

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.SDRFReadInContextHandler

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

All Implemented Interfaces:

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

@ServiceProvider
public class FactorValueNodeHandler
extends SDRFReadInContextHandler

A special type of 'dummy' handler for handling factor values. As factor value attributes can "float" around in the SDRF spreadsheet, they are not always explicitly attached to their parent node. As such, they are handled by this handler as if they were nodes. However, once their location has been determined, this handler tracks back to the parent "data" type node and invokes an attribute handler, passing the parent node in. Essentially, this acts as a wrapper to accommodate for the floating nature of factor value attributes.

Tag: Factor Value
Allowed Attributes (none here - see FactorValueAttributeReader

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
FactorValueNodeHandler()

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.
int	assessFrom(String[] header, int columnNumber) A specialised alternate form of the assess(String[]) method, specialised for handling Factor Value "floating" nodes.
boolean	canReadFrom(String[] header, int startIndex) A specialised alternate form of the SDRFReadInContextHandler.canReadHeader(String[]) method, specialised for handling Factor Value "floating" nodes.
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.
void	readDataFrom(String[] header, String[] data, SDRF sdrf, int lineNumber, int columnNumber) A specialised alternate form of the SDRFReadHandler.readData(String[], String[], uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF, int, int) method, specialised for handling Factor Value "floating" nodes.

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

canReadHeader, fetchUpstreamNode, handleUpstreamNode, read, readFrom

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

assessAttribute, canRead, 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

FactorValueNodeHandler

public FactorValueNodeHandler()

Method Detail

canReadFrom

public boolean canReadFrom(String[] header,
                  int startIndex)

A specialised alternate form of the SDRFReadInContextHandler.canReadHeader(String[]) method, specialised for handling Factor Value "floating" nodes. Because Factor Values can move left and right in the SDRF spreadsheet, the handler requires extra information to work out hybridization to attach the factor value to. This means more data must be passed than normal, including the column at which the factor value is located. This column index is passed via this method.

Specified by:

canReadFrom in class SDRFReadInContextHandler

Parameters:

header - the header - includes more data than normal (to enable read-back to the last hyb)

startIndex - the index at which the factor value column is located

Returns:

true if this handler can read the header tag at 'startIndex', 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

assessFrom

public int assessFrom(String[] header,
             int columnNumber)

A specialised alternate form of the assess(String[]) method, specialised for handling Factor Value "floating" nodes. Because Factor Values can move left and right in the SDRF spreadsheet, the handler requires extra information to work out hybridization to attach the factor value to. This means more data must be passed than normal, including the column at which the factor value is located. This column index is passed via this method.

Specified by:

assessFrom in class SDRFReadInContextHandler

Parameters:

header - the header - includes more data than normal (to enable read-back to the last hyb)

columnNumber - the index at which the factor value column is located

Returns:

the integer representing the point that can be read to

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

readDataFrom

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

A specialised alternate form of the SDRFReadHandler.readData(String[], String[], uk.ac.ebi.arrayexpress2.magetab.datamodel.SDRF, int, int) method, specialised for handling Factor Value "floating" nodes. Because Factor Values can move left and right in the SDRF spreadsheet, the handler requires extra information to work out hybridization to attach the factor value to. This means more data must be passed than normal, including the column at which the factor value is located. This column index is passed via this method.

Specified by:

readDataFrom in class SDRFReadInContextHandler

Parameters:

header - the header identifying the data to read

data - the data to read

sdrf - the sdrf to read the data into

lineNumber -

columnNumber - the index of the column to start reading from @throws ParseException if the data cannot be read

Throws:

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