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

Class ProtocolHandler

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.ProtocolHandler

All Implemented Interfaces:

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

@ServiceProvider
public class ProtocolHandler
extends SDRFReadInContextHandler

A handler that handles Protocol edges in the SDRF graph. Protocols are not actually true nodes in the SDRF spreadsheet - they are actually edges, labelled with the name of the protocol used to generate the child node from the parent. This is represented in the data model as a Protocol Application node, which is the "implicit" node that exists in the spreadsheet. To accomplish this, this handler needs to do extra work - it has to read backwards to the parent node and forwards to the child (and any parameter values that modify this protocol). The unique name for the protocol application node can then be generated from a combination of these identifiers.

Tag: Protocol Ref
Allowed attributes: Parameter Value, Performer, Date, Term Source Ref, Term Accession NUmber, Comment

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
ProtocolHandler()

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 SDRFReadInContextHandler.canReadHeader(String[]) method for handling Protocol Application Nodes.
boolean	canReadFrom(String[] header, int startIndex) A specialised alternate form of the SDRFReadInContextHandler.canReadHeader(String[]) method for handling Protocol Application 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 SDRFReadInContextHandler.canReadHeader(String[]) method for handling Protocol Application 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

ProtocolHandler

public ProtocolHandler()

Method Detail

canReadFrom

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

A specialised alternate form of the SDRFReadInContextHandler.canReadHeader(String[]) method for handling Protocol Application Nodes. Because Protocols resemble nodes, but are really edges, they cannot be handled in the same way as other nodes. Extra data must be passed to enable the Protocol Application Nodes that are created to be linked to both upstream and downstream nodes. This requires the start index (the location of the protocol being handled) to be passed.

Specified by:

canReadFrom in class SDRFReadInContextHandler

Parameters:

header - the header to handle

startIndex - the starting index to read from

Returns:

true if this handler can read the header from the given 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 SDRFReadInContextHandler.canReadHeader(String[]) method for handling Protocol Application Nodes. Because Protocols resemble nodes, but are really edges, they cannot be handled in the same way as other nodes. Extra data must be passed to enable the Protocol Application Nodes that are created to be linked to both upstream and downstream nodes. This requires the start index (the location of the protocol being handled) to be passed.

Specified by:

assessFrom in class SDRFReadInContextHandler

Parameters:

header - the header to assess

columnNumber - the index of the header to start assessing from

Returns:

the index of the header 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 SDRFReadInContextHandler.canReadHeader(String[]) method for handling Protocol Application Nodes. Because Protocols resemble nodes, but are really edges, they cannot be handled in the same way as other nodes. Extra data must be passed to enable the Protocol Application Nodes that are created to be linked to both upstream and downstream nodes. This requires the start index (the location of the protocol being handled) to be passed.

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 - the line number data is being read from

columnNumber - the index to start read 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