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

Interface SDRFAttributeReader

All Known Implementing Classes:

ArrayDesignAttributeReader, ArrayDesignFileAttributeReader, ArrayDesignRefAttributeReader, CharacteristicsAttributeReader, FactorValueAttributeReader, LabelAttributeReader, MaterialTypeAttributeReader, ParameterValueAttributeReader, PerformerAttributeReader, ProviderAttributeReader, TechnologyTypeAttributeReader

public interface SDRFAttributeReader

An interface that allows SDRFReadHandlers to delegate functionality of attribute reading to this interface rather than check all possible attribute combinations themselves.

Attribute readers are analogous in general to ReadHandlers, but are implemented slightly differently, firstly because they do not read data into a MAGETAB investigation (instead working only on specific SDRF node types) and secondly because they should not be eligibly for service discovery: each SDRF node has a constrained number of attributes it can contain.

The constructor for each SDRF handler should set up the instances of attribute readers it can defer to.

Author:

Tony Burdett

Method Summary

Methods

Modifier and Type	Method and Description
int	assess(String[] header) Returns an integer representing the number of columns this handler can read forward of the given header.
boolean	canRead(String firstHeader) Determine whether this reader can read the attributes referenced by this header.
void	readAttributes(String[] header, String[] data, SDRF sdrf, SDRFNode sdrfNode, int lineNumber, int columnNumber) Reads the attributes from the data and sets them on the supplied SDRFNode

Method Detail

canRead

boolean canRead(String firstHeader)

Determine whether this reader can read the attributes referenced by this header.

Parameters:

firstHeader - the first column heading to read from

Returns:

true if this attribute reader can read attributes following this column heading, false otherwise

assess

int assess(String[] header)

Returns an integer representing the number of columns this handler can read forward of the given header.

Parameters:

header - the header to be passed to this attribute reader. This should start at a column this reader can actually read

Returns:

the number of columns this handler can read

readAttributes

void readAttributes(String[] header,
                  String[] data,
                  SDRF sdrf,
                  SDRFNode sdrfNode,
                  int lineNumber,
                  int columnNumber)
                    throws ParseException

Reads the attributes from the data and sets them on the supplied SDRFNode

Parameters:

header - the header to read from, starting from attributes this reader can actually read

data - the data to read

sdrf - the sdrf being read to

sdrfNode - the SDRF node that these attributes should be set on

lineNumber - the line this data is read from

columnNumber - the column this data is read from @throws ParseException if the data could not be read for any reason

Throws:

ParseException