uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor

Class SDRFNodeWrapper<T extends SDRFNode>

java.lang.Object

org.isatools.tablib.export.graph2tab.DefaultAbstractNode

uk.ac.ebi.arrayexpress2.magetab.renderer.adaptor.SDRFNodeWrapper<T>

All Implemented Interfaces:

Comparable<org.isatools.tablib.export.graph2tab.Node>, org.isatools.tablib.export.graph2tab.Node

Direct Known Subclasses:

ArrayDataMatrixNodeWrapper, ArrayDataNodeWrapper, ArrayDesignNodeWrapper, AssayNodeWrapper, DerivedArrayDataMatrixNodeWrapper, DerivedArrayDataNodeWrapper, ExtractNodeWrapper, HybridizationNodeWrapper, ImageNodeWrapper, LabeledExtractNodeWrapper, NormalizationNodeWrapper, ProtocolApplicationNodeWrapper, SampleNodeWrapper, ScanNodeWrapper, SourceNodeWrapper

public class SDRFNodeWrapper<T extends SDRFNode>
extends org.isatools.tablib.export.graph2tab.DefaultAbstractNode

Class needed for graph2tab algorithm

Creates wrappers for the SDRF graph's nodes

Author:

Natalja Kurbatova

Field Summary

Fields inherited from class org.isatools.tablib.export.graph2tab.DefaultAbstractNode

inputs, outputs

Constructor Summary

Constructors

Constructor and Description
SDRFNodeWrapper(T base, int order, WrapperNodeFactory factory)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	appendAttributeCommentsToGroup(org.isatools.tablib.export.graph2tab.DefaultTabValueGroup group, Map<String,String> comments)
protected void	appendAttributeToGroup(org.isatools.tablib.export.graph2tab.DefaultTabValueGroup group, AbstractSDRFAttribute attribute)
protected void	appendFactorValuesToGroup(org.isatools.tablib.export.graph2tab.DefaultTabValueGroup group)
protected void	appendFactorValuesToGroup(org.isatools.tablib.export.graph2tab.DefaultTabValueGroup group, SDRFNodeWrapper<T> node)
protected void	appendNodeCommentsToGroup(org.isatools.tablib.export.graph2tab.DefaultTabValueGroup group, Map<String,List<String>> comments)
protected void	appendValueToGroup(org.isatools.tablib.export.graph2tab.DefaultTabValueGroup group, String header, String value)
int	compareTo(org.isatools.tablib.export.graph2tab.Node other)
T	getBase()
protected int	getCurrentChannel()
protected org.isatools.tablib.export.graph2tab.DefaultTabValueGroup	getDefaultTabValueGroup()
SortedSet<org.isatools.tablib.export.graph2tab.Node>	getInputs()
int	getOrder()
SortedSet<org.isatools.tablib.export.graph2tab.Node>	getOutputs()
List<org.isatools.tablib.export.graph2tab.TabValueGroup>	getTabValues()
String	getType()
protected boolean	isEndNode()
protected boolean	isMultiChannel()
protected void	setCurrentChannel(String label)

Methods inherited from class org.isatools.tablib.export.graph2tab.DefaultAbstractNode

equals, hashCode, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

SDRFNodeWrapper

public SDRFNodeWrapper(T base,
               int order,
               WrapperNodeFactory factory)

Method Detail

getBase

public T getBase()

getInputs

public SortedSet<org.isatools.tablib.export.graph2tab.Node> getInputs()

Specified by:

getInputs in interface org.isatools.tablib.export.graph2tab.Node

Overrides:

getInputs in class org.isatools.tablib.export.graph2tab.DefaultAbstractNode

getOutputs

public SortedSet<org.isatools.tablib.export.graph2tab.Node> getOutputs()

Specified by:

getOutputs in interface org.isatools.tablib.export.graph2tab.Node

Overrides:

getOutputs in class org.isatools.tablib.export.graph2tab.DefaultAbstractNode

getTabValues

public final List<org.isatools.tablib.export.graph2tab.TabValueGroup> getTabValues()

getType

public String getType()

Specified by:

getType in interface org.isatools.tablib.export.graph2tab.Node

Overrides:

getType in class org.isatools.tablib.export.graph2tab.DefaultAbstractNode

getOrder

public int getOrder()

Specified by:

getOrder in interface org.isatools.tablib.export.graph2tab.Node

Overrides:

getOrder in class org.isatools.tablib.export.graph2tab.DefaultAbstractNode

isEndNode

protected boolean isEndNode()

isMultiChannel

protected boolean isMultiChannel()

setCurrentChannel

protected void setCurrentChannel(String label)

getCurrentChannel

protected int getCurrentChannel()

getDefaultTabValueGroup

protected org.isatools.tablib.export.graph2tab.DefaultTabValueGroup getDefaultTabValueGroup()

appendFactorValuesToGroup

protected void appendFactorValuesToGroup(org.isatools.tablib.export.graph2tab.DefaultTabValueGroup group,
                             SDRFNodeWrapper<T> node)

appendFactorValuesToGroup

protected void appendFactorValuesToGroup(org.isatools.tablib.export.graph2tab.DefaultTabValueGroup group)

appendValueToGroup

protected void appendValueToGroup(org.isatools.tablib.export.graph2tab.DefaultTabValueGroup group,
                      String header,
                      String value)

compareTo

public int compareTo(org.isatools.tablib.export.graph2tab.Node other)

Specified by:

compareTo in interface Comparable<org.isatools.tablib.export.graph2tab.Node>

Overrides:

compareTo in class org.isatools.tablib.export.graph2tab.DefaultAbstractNode

appendAttributeToGroup

protected void appendAttributeToGroup(org.isatools.tablib.export.graph2tab.DefaultTabValueGroup group,
                          AbstractSDRFAttribute attribute)

appendAttributeCommentsToGroup

protected void appendAttributeCommentsToGroup(org.isatools.tablib.export.graph2tab.DefaultTabValueGroup group,
                                  Map<String,String> comments)

appendNodeCommentsToGroup

protected void appendNodeCommentsToGroup(org.isatools.tablib.export.graph2tab.DefaultTabValueGroup group,
                             Map<String,List<String>> comments)