uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl

Class ExperimentalDesignHandler

java.lang.Object

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

uk.ac.ebi.arrayexpress2.magetab.handler.idf.IDFReadHandler

uk.ac.ebi.arrayexpress2.magetab.handler.idf.impl.ExperimentalDesignHandler

All Implemented Interfaces:

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

@ServiceProvider
public class ExperimentalDesignHandler
extends IDFReadHandler

A handler implementation that will handle Experimental Design fields in the IDF.

Tag: Experimental Design

Author:

Tony Burdett

Field Summary

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

listeners

Constructor Summary

Constructors

Constructor and Description
ExperimentalDesignHandler()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	canReadHeader(String header) Determine whether this handler can read the data referenced by this header.
protected void	readValue(IDF idf, 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.idf.IDFReadHandler

canRead, getAllowedLength, read

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

ExperimentalDesignHandler

public ExperimentalDesignHandler()

Method Detail

readValue

protected void readValue(IDF idf,
             String value,
             int lineNumber,
             String... types)
                  throws ParseException

Description copied from class: IDFReadHandler

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 investigation 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.

Specified by:

readValue in class IDFReadHandler

Parameters:

idf - the IDF to read data into

value - the value to read into the cache

lineNumber - the line number this data is 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 supplied data could not be parsed

canReadHeader

public boolean canReadHeader(String header)

Description copied from class: IDFReadHandler

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 IDFReadHandler

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