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

Class TermSourceVersionHandler

java.lang.Object

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

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

uk.ac.ebi.arrayexpress2.magetab.handler.adf.impl.TermSourceVersionHandler

All Implemented Interfaces:

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

@ServiceProvider
public class TermSourceVersionHandler
extends ADFHeaderReadHandler

A handler that handles the term source version declaration rows in ADF. These elements are tied to a term source name.

Tag: Term Source Version

Author:

Tony Burdett

Field Summary

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

listeners

Constructor Summary

Constructors

Constructor and Description
TermSourceVersionHandler()

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(ADF adf, 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.adf.ADFHeaderReadHandler

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

TermSourceVersionHandler

public TermSourceVersionHandler()

Method Detail

readValue

protected void readValue(ADF adf,
             String value,
             int lineNumber,
             String... types)
                  throws ParseException

Description copied from class: ADFHeaderReadHandler

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 array design 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 ADFHeaderReadHandler

Parameters:

adf - the ADF to populate with parsed data

value - the value to read into the cache

lineNumber - the line number this value is being 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 given data failed to parse

canReadHeader

public boolean canReadHeader(String header)

Description copied from class: ADFHeaderReadHandler

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 ADFHeaderReadHandler

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