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

Class FeatureHandler

java.lang.Object

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

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

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

All Implemented Interfaces:

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

@ServiceProvider
public class FeatureHandler
extends ADFGraphReadHandler

A handler that handles feature nodes in the ADF graph. Features are special types of nodes in as much as they are not explicity named (with a *** Name) column header, like all other nodes. Instead, they are the aggregation of the four integer-type column headers.

Tags: Block Column, Block Row, Column, Row Allowed Attributes: Comment

Author:

Tony Burdett

Field Summary

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

listeners

Constructor Summary

Constructors

Constructor and Description
FeatureHandler()

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.
protected void	readData(String[] header, String[] value, ADF adf, 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.adf.ADFGraphReadHandler

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

FeatureHandler

public FeatureHandler()

Method Detail

canReadHeader

public boolean canReadHeader(String[] header)

Description copied from class: ADFGraphReadHandler

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 ADFGraphReadHandler

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: ADFGraphReadHandler

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 ADFGraphReadHandler

Parameters:

header - the header to assess

Returns:

the last column index that can be read

readData

protected void readData(String[] header,
            String[] value,
            ADF adf,
            int lineNumber,
            int columnNumber)
                 throws ParseException

Description copied from class: ADFGraphReadHandler

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 ADFGraphReadHandler

Parameters:

header - the header identifying the data to read

value - the data to read

adf - the ADF to populate with parsed data

lineNumber - the line this data is read from

columnNumber - the column this data is read from

Throws:

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