gov.nih.nci.mageom.domain.BioMaterial.impl
Class BioMaterialImpl

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.impl.DescribableImpl
              extended by gov.nih.nci.mageom.domain.impl.IdentifiableImpl
                  extended by gov.nih.nci.mageom.domain.BioMaterial.impl.BioMaterialImpl
All Implemented Interfaces:
BioMaterial, Describable, Extendable, Identifiable, java.io.Serializable
Direct Known Subclasses:
BioSampleImpl, BioSourceImpl, LabeledExtractImpl

public class BioMaterialImpl
extends IdentifiableImpl
implements BioMaterial

BioMaterial is an abstract class that represents the important substances such as cells, tissues, DNA, proteins, etc... Biomaterials can be related to other biomaterial through a directed acyclic graph (represented by treatment(s)).

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

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected static java.util.Hashtable associationMethods
           
protected  OntologyEntry[] characteristics
          DOCUMENT ME
protected  int characteristicsCount
          The count of OntologyEntry objects.
protected  OntologyEntry materialType
          DOCUMENT ME
protected  java.lang.Long materialTypeId
          The internal ID of the associated materialType object.
protected  NameValueType[] qualityControlStatistics
          DOCUMENT ME
protected  int qualityControlStatisticsCount
          The count of NameValueType objects.
protected  Treatment[] treatments
          DOCUMENT ME
protected  int treatmentsCount
          The count of Treatment objects.
 
Fields inherited from class gov.nih.nci.mageom.domain.impl.IdentifiableImpl
identifier, name
 
Fields inherited from class gov.nih.nci.mageom.domain.impl.DescribableImpl
auditTrail, auditTrailCount, descriptions, descriptionsCount, security, securityId
 
Fields inherited from class gov.nih.nci.mageom.domain.impl.ExtendableImpl
propertySets, propertySetsCount, securedElementId
 
Constructor Summary
BioMaterialImpl()
          Default constructor
 
Method Summary
 OntologyEntry[] getCharacteristics()
          Returns the value of this BioMaterial object's characteristics attribute.
 int getCharacteristicsCount()
          Returns the count of all OntologyEntry associated with this BioMaterial object.
 OntologyEntry getMaterialType()
          Returns the value of this BioMaterial object's materialType attribute.
 NameValueType[] getQualityControlStatistics()
          Returns the value of this BioMaterial object's qualityControlStatistics attribute.
 int getQualityControlStatisticsCount()
          Returns the count of all NameValueType associated with this BioMaterial object.
 Treatment[] getTreatments()
          Returns the value of this BioMaterial object's treatments attribute.
 int getTreatmentsCount()
          Returns the count of all Treatment associated with this BioMaterial object.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 BioMaterial[] searchBioMaterials(BioMaterialSearchCriteria criteria)
          Returns an array of BioMaterial objects that satisfy the given BioMaterialSearchCriteria.
 void setCharacteristics(OntologyEntry[] p_characteristics)
          Sets the characteristics attribute.
 void setMaterialType(OntologyEntry p_materialType)
          Sets the materialType attribute.
 void setQualityControlStatistics(NameValueType[] p_qualityControlStatistics)
          Sets the qualityControlStatistics attribute.
 void setTreatments(Treatment[] p_treatments)
          Sets the treatments 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.IdentifiableImpl
getIdentifier, getName, searchIdentifiables, setIdentifier, setName
 
Methods inherited from class gov.nih.nci.mageom.domain.impl.DescribableImpl
getAuditTrail, getAuditTrailCount, getDescriptions, getDescriptionsCount, getSecurity, searchDescribables, setAuditTrail, setDescriptions, setSecurity
 
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.Identifiable
getIdentifier, getName, setIdentifier, setName
 
Methods inherited from interface gov.nih.nci.mageom.domain.Describable
getAuditTrail, getDescriptions, getSecurity, setAuditTrail, setDescriptions, setSecurity
 
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

treatmentsCount

protected int treatmentsCount
The count of Treatment objects.


treatments

protected Treatment[] treatments
DOCUMENT ME


materialType

protected OntologyEntry materialType
DOCUMENT ME


materialTypeId

protected java.lang.Long materialTypeId
The internal ID of the associated materialType object.


characteristicsCount

protected int characteristicsCount
The count of OntologyEntry objects.


characteristics

protected OntologyEntry[] characteristics
DOCUMENT ME


qualityControlStatisticsCount

protected int qualityControlStatisticsCount
The count of NameValueType objects.


qualityControlStatistics

protected NameValueType[] qualityControlStatistics
DOCUMENT ME

Constructor Detail

BioMaterialImpl

public BioMaterialImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class IdentifiableImpl

searchBioMaterials

public BioMaterial[] searchBioMaterials(BioMaterialSearchCriteria criteria)
                                 throws gov.nih.nci.common.search.SearchException
Returns an array of BioMaterial objects that satisfy the given BioMaterialSearchCriteria.

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

setTreatments

public void setTreatments(Treatment[] p_treatments)
Sets the treatments attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioMaterial object.

Specified by:
setTreatments in interface BioMaterial
Parameters:
p_treatments - The new value for treatments.
See Also:
BioMaterial.getTreatments()

getTreatments

public Treatment[] getTreatments()
Description copied from interface: BioMaterial
Returns the value of this BioMaterial object's treatments attribute.

Specified by:
getTreatments in interface BioMaterial
Returns:
gov.nih.nci.mageom.bean.BioMaterial.Treatment[] The value of treatments.
See Also:
BioMaterial.getTreatments()

setMaterialType

public void setMaterialType(OntologyEntry p_materialType)
Sets the materialType attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioMaterial object.

Specified by:
setMaterialType in interface BioMaterial
Parameters:
p_materialType - The new value for materialType.
See Also:
BioMaterial.getMaterialType()

getMaterialType

public OntologyEntry getMaterialType()
Description copied from interface: BioMaterial
Returns the value of this BioMaterial object's materialType attribute.

Specified by:
getMaterialType in interface BioMaterial
Returns:
gov.nih.nci.mageom.bean.Description.OntologyEntry The value of materialType.
See Also:
BioMaterial.getMaterialType()

setCharacteristics

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

Specified by:
setCharacteristics in interface BioMaterial
Parameters:
p_characteristics - The new value for characteristics.
See Also:
BioMaterial.getCharacteristics()

getCharacteristics

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

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

setQualityControlStatistics

public void setQualityControlStatistics(NameValueType[] p_qualityControlStatistics)
Sets the qualityControlStatistics attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioMaterial object.

Specified by:
setQualityControlStatistics in interface BioMaterial
Parameters:
p_qualityControlStatistics - The new value for qualityControlStatistics.
See Also:
BioMaterial.getQualityControlStatistics()

getQualityControlStatistics

public NameValueType[] getQualityControlStatistics()
Description copied from interface: BioMaterial
Returns the value of this BioMaterial object's qualityControlStatistics attribute.

Specified by:
getQualityControlStatistics in interface BioMaterial
Returns:
gov.nih.nci.mageom.bean.NameValueType[] The value of qualityControlStatistics.
See Also:
BioMaterial.getQualityControlStatistics()

getTreatmentsCount

public int getTreatmentsCount()
Returns the count of all Treatment associated with this BioMaterial object.

Returns:
the count
See Also:
BioMaterial.getTreatments()

getCharacteristicsCount

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

Returns:
the count
See Also:
BioMaterial.getCharacteristics()

getQualityControlStatisticsCount

public int getQualityControlStatisticsCount()
Returns the count of all NameValueType associated with this BioMaterial object.

Returns:
the count
See Also:
BioMaterial.getQualityControlStatistics()

toXML

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

toXMLDoc

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

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 IdentifiableImpl
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 IdentifiableImpl
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 IdentifiableImpl
Returns:
the String representation.