org.biomage.HigherLevelAnalysis
Class NodeValue

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.HigherLevelAnalysis.NodeValue
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasDataType, HasPropertySets, HasScale, HasType

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/interfaces inherited from interface 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
editable, id, securedElementId
 
Constructor Summary
NodeValue()
          Default constructor.
NodeValue(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 boolean emptyMAGEobject()
           
 OntologyEntry getDataType()
          Get method for dataType
 java.lang.String getModelClassName()
           
 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, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setAttributes, setId, setIsEditable, setPropertySets, setSecuredElementId, toString
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, 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

Parameters:
atts: - the attribute list.
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
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

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
Throws:
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
Throws:
java.io.IOException

setName

public void setName(java.lang.String name)
Set method for name

Parameters:
value - to set

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

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class Extendable

setType

public void setType(OntologyEntry type)
Set method for type

Specified by:
setType in interface HasType
Parameters:
value - to set

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
Parameters:
value - to set

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
Parameters:
value - to set

getDataType

public OntologyEntry getDataType()
Get method for dataType

Specified by:
getDataType in interface HasDataType
Returns:
value of the attribute