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

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
                      extended by gov.nih.nci.mageom.domain.BioMaterial.impl.BioSampleImpl
All Implemented Interfaces:
BioMaterial, BioSample, Describable, Extendable, Identifiable, java.io.Serializable

public class BioSampleImpl
extends BioMaterialImpl
implements BioSample

BioSamples are products of treatments that are of interest. BioSamples are often used as the sources for other biosamples. The Type attribute describes the role the BioSample holds in the treatment hierarchy. This type can be an extract.

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

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected static java.util.Hashtable associationMethods
           
protected  OntologyEntry type
          DOCUMENT ME
protected  java.lang.Long typeId
          The internal ID of the associated type object.
 
Fields inherited from class gov.nih.nci.mageom.domain.BioMaterial.impl.BioMaterialImpl
characteristics, characteristicsCount, materialType, materialTypeId, qualityControlStatistics, qualityControlStatisticsCount, treatments, treatmentsCount
 
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
BioSampleImpl()
          Default constructor
 
Method Summary
 OntologyEntry getType()
          Returns the value of this BioSample object's type attribute.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 BioSample[] searchBioSamples(BioSampleSearchCriteria criteria)
          Returns an array of BioSample objects that satisfy the given BioSampleSearchCriteria.
 void setType(OntologyEntry p_type)
          Sets the type 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.BioMaterial.impl.BioMaterialImpl
getCharacteristics, getCharacteristicsCount, getMaterialType, getQualityControlStatistics, getQualityControlStatisticsCount, getTreatments, getTreatmentsCount, searchBioMaterials, setCharacteristics, setMaterialType, setQualityControlStatistics, setTreatments
 
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.BioMaterial.BioMaterial
getCharacteristics, getMaterialType, getQualityControlStatistics, getTreatments, setCharacteristics, setMaterialType, setQualityControlStatistics, setTreatments
 
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

type

protected OntologyEntry type
DOCUMENT ME


typeId

protected java.lang.Long typeId
The internal ID of the associated type object.

Constructor Detail

BioSampleImpl

public BioSampleImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class BioMaterialImpl

searchBioSamples

public BioSample[] searchBioSamples(BioSampleSearchCriteria criteria)
                             throws gov.nih.nci.common.search.SearchException
Returns an array of BioSample objects that satisfy the given BioSampleSearchCriteria.

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

setType

public void setType(OntologyEntry p_type)
Sets the type attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioSample object.

Specified by:
setType in interface BioSample
Parameters:
p_type - The new value for type.
See Also:
BioSample.getType()

getType

public OntologyEntry getType()
Description copied from interface: BioSample
Returns the value of this BioSample object's type attribute.

Specified by:
getType in interface BioSample
Returns:
gov.nih.nci.mageom.bean.Description.OntologyEntry The value of type.
See Also:
BioSample.getType()

toXML

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

toXMLDoc

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

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 BioMaterialImpl
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 BioMaterialImpl
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 BioMaterialImpl
Returns:
the String representation.