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

Class ADFGraphReadHandler

java.lang.Object

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

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

All Implemented Interfaces:

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

Direct Known Subclasses:

CompositeElementHandler, FeatureHandler, ReporterHandler

public abstract class ADFGraphReadHandler
extends AbstractHandler
implements ReadHandler<String[],String[],ADF>

An abstract implementation of a ReadHandler for reading from the graph part of an ADF file into a ADF object. This implementation governs all common functionality including general handling order and progress tracking. Specific concrete handlers only need define the header they can read, the maximum number of values allowed on the line marked by this tag, and how to set the field on the ADF object.

Author:

Tony Burdett

Field Summary

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

listeners

Constructor Summary

Constructors

Constructor and Description
ADFGraphReadHandler()

Method Summary

Methods

Modifier and Type	Method and Description
abstract int	assess(String[] header) Return the index of the last header this handler can read from in the supplied header.
protected int	assessAttribute(ADFAttributeReader reader, String[] header, int startIndex)
boolean	canRead(Object header) Determine whether this handler can read the supplied header.
protected abstract boolean	canReadHeader(String[] header) Determine whether this handler can read the data referenced by this header.
void	read(String[] header, String[] data, ADF adf, int lineNumber, int columnNumber) Cause the handler to read the supplied data into the supplied target object.
protected int	readAttribute(ADFAttributeReader reader, String[] header, String[] data, ADFNode parentNode, int startIndex)
protected abstract void	readData(String[] header, String[] data, ADF adf, int lineNumber, int columnNumber) Performs the unit of work to read the data into the internal datamodel.
protected void	updateChildNode(String[] header, String[] data, ADFNode node, int valueIndex)

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

ADFGraphReadHandler

public ADFGraphReadHandler()

Method Detail

canRead

public boolean canRead(Object header)

Description copied from interface: ReadHandler

Determine whether this handler can read the supplied header. Typically, the data will be a String or String array depending on whether IDF, SDRF or ADF is being read, although the general framework can be extended to parse any data type.

This header should be passed to the handler prior to reading to determine whether this handler can handle it

Specified by:

canRead in interface ReadHandler<String[],String[],ADF>

Parameters:

header - the data that will be validated

Returns:

true if this handler can handle this tag, false otherwise

read

public void read(String[] header,
        String[] data,
        ADF adf,
        int lineNumber,
        int columnNumber)
          throws ParseException

Description copied from interface: ReadHandler

Cause the handler to read the supplied data into the supplied target object.

Specified by:

read in interface ReadHandler<String[],String[],ADF>

Parameters:

header - the header identifying the type of the data

data - the data to be read

adf - the object that the data will be read into

lineNumber - the line number of the field this data was read from

columnNumber - the column number of the field this data was read from

Throws:

ParseException - if parsing failed

assessAttribute

protected int assessAttribute(ADFAttributeReader reader,
                  String[] header,
                  int startIndex)

readAttribute

protected int readAttribute(ADFAttributeReader reader,
                String[] header,
                String[] data,
                ADFNode parentNode,
                int startIndex)
                     throws ParseException

Throws:

ParseException

updateChildNode

protected void updateChildNode(String[] header,
                   String[] data,
                   ADFNode node,
                   int valueIndex)

canReadHeader

protected abstract boolean canReadHeader(String[] header)

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.

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 abstract int assess(String[] header)

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.

Parameters:

header - the header to assess

Returns:

the last column index that can be read

readData

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

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

Parameters:

header - the header identifying the data to read

data - 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