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

Class ScanNode

java.lang.Object

uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode

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

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

All Implemented Interfaces:

Node, SDRFNode

public class ScanNode
extends AbstractSDRFNode

A scan node in the graph. Scan nodes are top level nodes and can have associated sets of comments.

Author:

Tony Burdett

Field Summary

Fields

Modifier and Type	Field and Description
Map<String,List<String>>	comments
List<FactorValueAttribute>	factorValues

Fields inherited from class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode

nodeName

Constructor Summary

Constructors

Constructor and Description
ScanNode()

Method Summary

Methods

Modifier and Type	Method and Description
String	getNodeType() Get the type of this node in the graph.
String[]	headers() Returns a string array representing the headers of this node and all it's attributes.
String[]	values() Delegates to values(int), using the channel labeled as channel one.
String[]	values(int channel) Request values by factor value attribute scanner channel.

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

toString

Methods inherited from class uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.AbstractNode

addChildNode, addChildNode, addParentNode, addParentNode, equals, getChildNodes, getLog, getNodeName, getParentNodes, hashCode, removeChildNode, removeParentNode, setNodeName, updateChildNode, updateParentNode

Methods inherited from class java.lang.Object

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

Methods inherited from interface uk.ac.ebi.arrayexpress2.magetab.datamodel.graph.Node

addChildNode, addChildNode, addParentNode, addParentNode, getChildNodes, getNodeName, getParentNodes, removeChildNode, removeParentNode, setNodeName, updateChildNode, updateParentNode

Field Detail

factorValues

public final List<FactorValueAttribute> factorValues

comments

public Map<String,List<String>> comments

Constructor Detail

ScanNode

public ScanNode()

Method Detail

headers

public String[] headers()

Description copied from interface: SDRFNode

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(int channel)

Request values by factor value attribute scanner channel. The returned String array will include only Cy3 or Cy5, and single channel, factor values depending on those requested.

Parameters:

channel - the channel to return values for

Returns:

the values, formatted by scanner channel

values

public String[] values()

Delegates to values(int), using the channel labeled as channel one. In single channel experiments, this will be all values, but in two or three channel experiments using this form of the method will only return channel one values, resulting in the loss of data. You should not use this form of the method in multichannel experiments.

Returns:

the default range of values, depending on experiment type

getNodeType

public String getNodeType()

Description copied from interface: Node

Get the type of this node in the graph.

Returns:

the standardised header string for this node