org.biomage.HigherLevelAnalysis
Class NodeValue

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.HigherLevelAnalysis.NodeValue

All Implemented Interfaces:

HasDataType, HasPropertySets, HasScale, HasType, java.io.Serializable

public class NodeValue

extends Extendable

implements java.io.Serializable, HasScale, HasDataType, HasType

A value associated with the Node that can rank it in relation to the other nodes produced by the clustering algorithm.

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class org.biomage.Interface.HasPropertySets

HasPropertySets.PropertySets_list

Field Summary

protected OntologyEntry	dataType The data type of the any element.
protected OntologyEntry	scale The scale (linear, log10, ln, etc.) of the value.
protected OntologyEntry	type The type of value, distance, etc.

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

NodeValue()
Default constructor.

NodeValue(org.xml.sax.Attributes atts)
Attribute constructor.

Method Summary

OntologyEntry	getDataType() Get method for dataType
java.lang.String	getName() Get method for name
OntologyEntry	getScale() Get method for scale
OntologyEntry	getType() Get method for type
java.lang.Object	getValue() Get method for value
void	setDataType(OntologyEntry dataType) Set method for dataType
void	setName(java.lang.String name) Set method for name
void	setScale(OntologyEntry scale) Set method for scale
void	setType(OntologyEntry type) Set method for type
void	setValue(java.lang.Object value) Set method for value
void	writeAssociations(java.io.Writer out) writeAssociations This method is responsible for assembling the association data into XML.
void	writeAttributes(java.io.Writer out) writeAttributes This method is responsible for assembling the attribute data into XML.
void	writeMAGEML(java.io.Writer out) writeMAGEML This method is responsible for assembling the attribute and association data into XML.

Methods inherited from class org.biomage.Common.Extendable

addToPropertySets, addToPropertySets, getFromPropertySets, getPropertySets, removeElementAtFromPropertySets, removeFromPropertySets, setPropertySets

Methods inherited from class java.lang.Object

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

Field Detail

type

protected OntologyEntry type

The type of value, distance, etc.

scale

protected OntologyEntry scale

The scale (linear, log10, ln, etc.) of the value.

dataType

protected OntologyEntry dataType

The data type of the any element.

Constructor Detail

NodeValue

public NodeValue()

Default constructor.

NodeValue

public NodeValue(org.xml.sax.Attributes atts)

Attribute constructor. Looks up the attributes in the parameter and casts them from strings appropriately

Method Detail

writeMAGEML

public void writeMAGEML(java.io.Writer out)
                 throws java.io.IOException

writeMAGEML This method is responsible for assembling the attribute and association data into XML. It creates the object tag and then calls the writeAttributes and writeAssociation methods.

Overrides:

writeMAGEML in class Extendable

java.io.IOException

writeAttributes

public void writeAttributes(java.io.Writer out)
                     throws java.io.IOException

writeAttributes This method is responsible for assembling the attribute data into XML. It calls the super method to write out all attributes of this class and it's ancestors.

Overrides:

writeAttributes in class Extendable

java.io.IOException

writeAssociations

public void writeAssociations(java.io.Writer out)
                       throws java.io.IOException

writeAssociations This method is responsible for assembling the association data into XML. It calls the super method to write out all associations of this class's ancestors.

Overrides:

writeAssociations in class Extendable

java.io.IOException

setName

public void setName(java.lang.String name)

Set method for name

getName

public java.lang.String getName()

Get method for name

Returns:

value of the attribute

setValue

public void setValue(java.lang.Object value)

Set method for value

Parameters:

value - to set

getValue

public java.lang.Object getValue()

Get method for value

Returns:

value of the attribute

setType

public void setType(OntologyEntry type)

Set method for type

Specified by:

setType in interface HasType

getType

public OntologyEntry getType()

Get method for type

Specified by:

getType in interface HasType

Returns:

value of the attribute

setScale

public void setScale(OntologyEntry scale)

Set method for scale

Specified by:

setScale in interface HasScale

getScale

public OntologyEntry getScale()

Get method for scale

Specified by:

getScale in interface HasScale

Returns:

value of the attribute

setDataType

public void setDataType(OntologyEntry dataType)

Set method for dataType

Specified by:

setDataType in interface HasDataType

getDataType

public OntologyEntry getDataType()

Get method for dataType

Specified by:

getDataType in interface HasDataType

Returns:

value of the attribute