gov.nih.nci.mageom.domain.Description.impl
Class OntologyEntryImpl

java.lang.Object
  extended by gov.nih.nci.mageom.domain.impl.MAGEOMObject
      extended by gov.nih.nci.mageom.domain.impl.ExtendableImpl
          extended by gov.nih.nci.mageom.domain.Description.impl.OntologyEntryImpl
All Implemented Interfaces:
OntologyEntry, Extendable, java.io.Serializable

public class OntologyEntryImpl
extends ExtendableImpl
implements OntologyEntry

A single entry from an ontology or a controlled vocabulary. For instance, category could be 'species name', value could be 'homo sapiens' and ontology would be taxonomy database, NCBI.

Version:
%I%, %G%
See Also:
Serialized Form

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected static java.util.Hashtable associationMethods
           
protected  OntologyEntry[] associations
          DOCUMENT ME
protected  int associationsCount
          The count of OntologyEntry objects.
protected  java.lang.String category
          The category to which this entry belongs.
protected  java.lang.String description
          The description of the meaning for this entry.
protected  DatabaseEntry ontologyReference
          DOCUMENT ME
protected  java.lang.Long ontologyReferenceId
          The internal ID of the associated ontologyReference object.
protected  java.lang.String value
          The value for this entry in this category.
 
Fields inherited from class gov.nih.nci.mageom.domain.impl.ExtendableImpl
propertySets, propertySetsCount, securedElementId
 
Constructor Summary
OntologyEntryImpl()
          Default constructor
 
Method Summary
 OntologyEntry[] getAssociations()
          Returns the value of this OntologyEntry object's associations attribute.
 int getAssociationsCount()
          Returns the count of all OntologyEntry associated with this OntologyEntry object.
 java.lang.String getCategory()
          Returns the value of this OntologyEntry object's category attribute.
 java.lang.String getDescription()
          Returns the value of this OntologyEntry object's description attribute.
 DatabaseEntry getOntologyReference()
          Returns the value of this OntologyEntry object's ontologyReference attribute.
 java.lang.String getValue()
          Returns the value of this OntologyEntry object's value attribute.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 OntologyEntry[] searchOntologyEntries(OntologyEntrySearchCriteria criteria)
          Returns an array of OntologyEntry objects that satisfy the given OntologyEntrySearchCriteria.
 void setAssociations(OntologyEntry[] p_associations)
          Sets the associations attribute.
 void setCategory(java.lang.String p_category)
          Sets the category attribute.
 void setDescription(java.lang.String p_description)
          Sets the description attribute.
 void setOntologyReference(DatabaseEntry p_ontologyReference)
          Sets the ontologyReference attribute.
 void setValue(java.lang.String p_value)
          Sets the value attribute.
 java.lang.String toString()
          Returns a String representation of this object suitable for console display.
 org.w3c.dom.Element toXML(org.w3c.dom.Document doc)
           
 org.w3c.dom.Element toXMLDoc(org.w3c.dom.Document doc)
           
 org.w3c.dom.Element toXMLProcessor(org.w3c.dom.Document doc, java.util.ArrayList fillOutValues)
          Returns an XML representation of the object.
 
Methods inherited from class gov.nih.nci.mageom.domain.impl.ExtendableImpl
getPropertySets, getPropertySetsCount, getSecuredElementId, searchExtendables, setPropertySets, setSecuredElementId
 
Methods inherited from class gov.nih.nci.mageom.domain.impl.MAGEOMObject
getId, getIsEditable, setId
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface gov.nih.nci.mageom.domain.Extendable
getPropertySets, setPropertySets
 

Field Detail

allAssociationMethods

protected static java.util.ArrayList allAssociationMethods

associationMethods

protected static java.util.Hashtable associationMethods

category

protected java.lang.String category
The category to which this entry belongs.


value

protected java.lang.String value
The value for this entry in this category.


description

protected java.lang.String description
The description of the meaning for this entry.


ontologyReference

protected DatabaseEntry ontologyReference
DOCUMENT ME


ontologyReferenceId

protected java.lang.Long ontologyReferenceId
The internal ID of the associated ontologyReference object.


associationsCount

protected int associationsCount
The count of OntologyEntry objects.


associations

protected OntologyEntry[] associations
DOCUMENT ME

Constructor Detail

OntologyEntryImpl

public OntologyEntryImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class ExtendableImpl

searchOntologyEntries

public OntologyEntry[] searchOntologyEntries(OntologyEntrySearchCriteria criteria)
                                      throws gov.nih.nci.common.search.SearchException
Returns an array of OntologyEntry objects that satisfy the given OntologyEntrySearchCriteria.

Parameters:
criteria - The OntologyEntrySearchCriteria which represents a query for OntologyEntry objects.
Returns:
An array of OntologyEntry objects.
Throws:
A - gov.nih.nci.common.search.SearchException if there is a problem searching.
gov.nih.nci.common.search.SearchException

setCategory

public void setCategory(java.lang.String p_category)
Sets the category attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a OntologyEntry object.

Specified by:
setCategory in interface OntologyEntry
Parameters:
p_category - The new value for category.
See Also:
OntologyEntry.getCategory()

getCategory

public java.lang.String getCategory()
Description copied from interface: OntologyEntry
Returns the value of this OntologyEntry object's category attribute. Description of category: The category to which this entry belongs.

Specified by:
getCategory in interface OntologyEntry
Returns:
String The value of category.
See Also:
OntologyEntry.getCategory()

setValue

public void setValue(java.lang.String p_value)
Sets the value attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a OntologyEntry object.

Specified by:
setValue in interface OntologyEntry
Parameters:
p_value - The new value for value.
See Also:
OntologyEntry.getValue()

getValue

public java.lang.String getValue()
Description copied from interface: OntologyEntry
Returns the value of this OntologyEntry object's value attribute. Description of value: The value for this entry in this category.

Specified by:
getValue in interface OntologyEntry
Returns:
String The value of value.
See Also:
OntologyEntry.getValue()

setDescription

public void setDescription(java.lang.String p_description)
Sets the description attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a OntologyEntry object.

Specified by:
setDescription in interface OntologyEntry
Parameters:
p_description - The new value for description.
See Also:
OntologyEntry.getDescription()

getDescription

public java.lang.String getDescription()
Description copied from interface: OntologyEntry
Returns the value of this OntologyEntry object's description attribute. Description of description: The description of the meaning for this entry.

Specified by:
getDescription in interface OntologyEntry
Returns:
String The value of description.
See Also:
OntologyEntry.getDescription()

setOntologyReference

public void setOntologyReference(DatabaseEntry p_ontologyReference)
Sets the ontologyReference attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a OntologyEntry object.

Specified by:
setOntologyReference in interface OntologyEntry
Parameters:
p_ontologyReference - The new value for ontologyReference.
See Also:
OntologyEntry.getOntologyReference()

getOntologyReference

public DatabaseEntry getOntologyReference()
Description copied from interface: OntologyEntry
Returns the value of this OntologyEntry object's ontologyReference attribute.

Specified by:
getOntologyReference in interface OntologyEntry
Returns:
gov.nih.nci.mageom.bean.Description.DatabaseEntry The value of ontologyReference.
See Also:
OntologyEntry.getOntologyReference()

setAssociations

public void setAssociations(OntologyEntry[] p_associations)
Sets the associations attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a OntologyEntry object.

Specified by:
setAssociations in interface OntologyEntry
Parameters:
p_associations - The new value for associations.
See Also:
OntologyEntry.getAssociations()

getAssociations

public OntologyEntry[] getAssociations()
Description copied from interface: OntologyEntry
Returns the value of this OntologyEntry object's associations attribute.

Specified by:
getAssociations in interface OntologyEntry
Returns:
gov.nih.nci.mageom.bean.Description.OntologyEntry[] The value of associations.
See Also:
OntologyEntry.getAssociations()

getAssociationsCount

public int getAssociationsCount()
Returns the count of all OntologyEntry associated with this OntologyEntry object.

Returns:
the count
See Also:
OntologyEntry.getAssociations()

toXML

public org.w3c.dom.Element toXML(org.w3c.dom.Document doc)
Overrides:
toXML in class ExtendableImpl

toXMLDoc

public org.w3c.dom.Element toXMLDoc(org.w3c.dom.Document doc)
Overrides:
toXMLDoc in class ExtendableImpl

toXMLProcessor

public org.w3c.dom.Element toXMLProcessor(org.w3c.dom.Document doc,
                                          java.util.ArrayList fillOutValues)
Returns an XML representation of the object. The document is not modified.

Overrides:
toXMLProcessor in class ExtendableImpl
Parameters:
doc - the working document
fillOutValues - a list of attribute names that should have full XML for their values.
Returns:
org.w3c.dom.Element an XML representation

getXMLMethodDescriptors

public java.util.Hashtable getXMLMethodDescriptors()
Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.

Overrides:
getXMLMethodDescriptors in class ExtendableImpl
Returns:
Hashtable The Hashtable of descriptors.

toString

public java.lang.String toString()
Returns a String representation of this object suitable for console display.

Overrides:
toString in class ExtendableImpl
Returns:
the String representation.