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

Class FactorValueAttribute

java.lang.Object

uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.AbstractSDRFAttribute

uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.FactorValueAttribute

All Implemented Interfaces:

SDRFAttribute

public class FactorValueAttribute
extends AbstractSDRFAttribute

A factor value attribute node in the graph. Factor Values are annotations on specific named nodes, and can be applied to hybridization nodes. Factor Values can have sub-attributes type, optionalType, unit and termSourceREF.

Factor Values are unique amongst SDRF attributes, in that they have an implicit channel they are keyed on. In the SDRF document, this channel can be inferred by the row in which the attribute occurs. The same hybridization can therefore have different factor values in different rows of the spreadsheet, depending on the label specified in that row. At first glance, this would seem to break the graph representation, but actually this is just a convenient way of indexing the factor value by channel.

Author:

Tony Burdett

Field Summary

Fields

Modifier and Type	Field and Description
String	optionalType
int	scannerChannel Scanner channel attribute allows factors to be detected on a specific channel.
String	termAccessionNumber
String	termSourceREF
String	type
UnitAttribute	unit

Fields inherited from class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.AbstractSDRFAttribute

attributeValue

Constructor Summary

Constructors

Constructor and Description
FactorValueAttribute()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object o)
String	getAttributeType() Get the type of this attribute.
int	hashCode()
String[]	headers() Returns a string array representing the headers of this node and all it's attributes.
String[]	values() Returns the strings representing the values of this node and all it's attributes, indexed by the matching headers.

Methods inherited from class uk.ac.ebi.arrayexpress2.magetab.datamodel.sdrf.node.attribute.AbstractSDRFAttribute

getAttributeValue, getLog, getNodeName, getNodeType, setAttributeValue

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Field Detail

scannerChannel

public int scannerChannel

Scanner channel attribute allows factors to be detected on a specific channel. This means that the same hybridization could show different factor values, depending on the channel it was associated with. Channel number is 1 by default, but in multichannel experiments should be overridden.

type

public String type

optionalType

public String optionalType

unit

public UnitAttribute unit

termSourceREF

public String termSourceREF

termAccessionNumber

public String termAccessionNumber

Constructor Detail

FactorValueAttribute

public FactorValueAttribute()

Method Detail

getAttributeType

public String getAttributeType()

Description copied from interface: SDRFAttribute

Get the type of this attribute. The attribute is typed (like Nodes) by the standardised "Name" tag for the node, including any option qualifiers (such as contents of square brackets, parentheses, or prefixes in some cases).

Returns:

the attribute type, including qualifiers

headers

public String[] headers()

Description copied from interface: SDRFAttribute

Returns a string array representing the headers of this node and all it's attributes.

Returns:

the headers unique to this node

values

public String[] values()

Description copied from interface: SDRFAttribute

Returns the strings representing the values of this node and all it's attributes, indexed by the matching headers. So, SDRFAttribute.headers() and values have exactly the same length and the same order.

Returns:

the values for this node

equals

public boolean equals(Object o)

Overrides:

equals in class AbstractSDRFAttribute

hashCode

public int hashCode()

Overrides:

hashCode in class AbstractSDRFAttribute