gov.nih.nci.mageom.domain.BioAssayData.impl
Class TransformationImpl

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.BioEvent.impl.BioEventImpl
                      extended by gov.nih.nci.mageom.domain.BioAssayData.impl.TransformationImpl
All Implemented Interfaces:
Transformation, BioEvent, Describable, Extendable, Identifiable, java.io.Serializable

public class TransformationImpl
extends BioEventImpl
implements Transformation

The process by which derivedBioAssays are created from measuredBioAssays and/or derivedBioAssays. It uses mappings to indicate the input and output dimensions.

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

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected static java.util.Hashtable associationMethods
           
protected  BioAssayData[] bioAssayDataSources
          DOCUMENT ME
protected  int bioAssayDataSourcesCount
          The count of BioAssayData objects.
protected  BioAssayMapping bioAssayMapping
          DOCUMENT ME
protected  java.lang.Long bioAssayMappingId
          The internal ID of the associated bioAssayMapping object.
protected  DerivedBioAssayData[] derivedBioAssayDataTarget
          DOCUMENT ME
protected  DesignElementMapping designElementMapping
          DOCUMENT ME
protected  java.lang.Long designElementMappingId
          The internal ID of the associated designElementMapping object.
protected  QuantitationTypeMapping quantitationTypeMapping
          rank: 3
protected  java.lang.Long quantitationTypeMappingId
          The internal ID of the associated quantitationTypeMapping object.
 
Fields inherited from class gov.nih.nci.mageom.domain.BioEvent.impl.BioEventImpl
protocolApplications, protocolApplicationsCount
 
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
TransformationImpl()
          Default constructor
 
Method Summary
 BioAssayData[] getBioAssayDataSources()
          Returns the value of this Transformation object's bioAssayDataSources attribute.
 int getBioAssayDataSourcesCount()
          Returns the count of all BioAssayData associated with this Transformation object.
 BioAssayMapping getBioAssayMapping()
          Returns the value of this Transformation object's bioAssayMapping attribute.
 DerivedBioAssayData getDerivedBioAssayDataTarget()
          Returns the value of this Transformation object's derivedBioAssayDataTarget attribute.
 DesignElementMapping getDesignElementMapping()
          Returns the value of this Transformation object's designElementMapping attribute.
 QuantitationTypeMapping getQuantitationTypeMapping()
          Returns the value of this Transformation object's quantitationTypeMapping attribute.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 Transformation[] searchTransformations(TransformationSearchCriteria criteria)
          Returns an array of Transformation objects that satisfy the given TransformationSearchCriteria.
 void setBioAssayDataSources(BioAssayData[] p_bioAssayDataSources)
          Sets the bioAssayDataSources attribute.
 void setBioAssayMapping(BioAssayMapping p_bioAssayMapping)
          Sets the bioAssayMapping attribute.
 void setDerivedBioAssayDataTarget(DerivedBioAssayData p_derivedBioAssayDataTarget)
          Sets the derivedBioAssayDataTarget attribute.
 void setDesignElementMapping(DesignElementMapping p_designElementMapping)
          Sets the designElementMapping attribute.
 void setQuantitationTypeMapping(QuantitationTypeMapping p_quantitationTypeMapping)
          Sets the quantitationTypeMapping 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.BioEvent.impl.BioEventImpl
getProtocolApplications, getProtocolApplicationsCount, searchBioEvents, setProtocolApplications
 
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.BioEvent.BioEvent
getProtocolApplications, setProtocolApplications
 
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

derivedBioAssayDataTarget

protected DerivedBioAssayData[] derivedBioAssayDataTarget
DOCUMENT ME


bioAssayDataSourcesCount

protected int bioAssayDataSourcesCount
The count of BioAssayData objects.


bioAssayDataSources

protected BioAssayData[] bioAssayDataSources
DOCUMENT ME


bioAssayMapping

protected BioAssayMapping bioAssayMapping
DOCUMENT ME


bioAssayMappingId

protected java.lang.Long bioAssayMappingId
The internal ID of the associated bioAssayMapping object.


designElementMapping

protected DesignElementMapping designElementMapping
DOCUMENT ME


designElementMappingId

protected java.lang.Long designElementMappingId
The internal ID of the associated designElementMapping object.


quantitationTypeMapping

protected QuantitationTypeMapping quantitationTypeMapping
rank: 3


quantitationTypeMappingId

protected java.lang.Long quantitationTypeMappingId
The internal ID of the associated quantitationTypeMapping object.

Constructor Detail

TransformationImpl

public TransformationImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class BioEventImpl

searchTransformations

public Transformation[] searchTransformations(TransformationSearchCriteria criteria)
                                       throws gov.nih.nci.common.search.SearchException
Returns an array of Transformation objects that satisfy the given TransformationSearchCriteria.

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

setDerivedBioAssayDataTarget

public void setDerivedBioAssayDataTarget(DerivedBioAssayData p_derivedBioAssayDataTarget)
Sets the derivedBioAssayDataTarget attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Transformation object.

Specified by:
setDerivedBioAssayDataTarget in interface Transformation
Parameters:
p_derivedBioAssayDataTarget - The new value for derivedBioAssayDataTarget.
See Also:
Transformation.getDerivedBioAssayDataTarget()

getDerivedBioAssayDataTarget

public DerivedBioAssayData getDerivedBioAssayDataTarget()
Description copied from interface: Transformation
Returns the value of this Transformation object's derivedBioAssayDataTarget attribute.

Specified by:
getDerivedBioAssayDataTarget in interface Transformation
Returns:
gov.nih.nci.mageom.bean.BioAssayData.DerivedBioAssayData The value of derivedBioAssayDataTarget.
See Also:
Transformation.getDerivedBioAssayDataTarget()

setBioAssayDataSources

public void setBioAssayDataSources(BioAssayData[] p_bioAssayDataSources)
Sets the bioAssayDataSources attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Transformation object.

Specified by:
setBioAssayDataSources in interface Transformation
Parameters:
p_bioAssayDataSources - The new value for bioAssayDataSources.
See Also:
Transformation.getBioAssayDataSources()

getBioAssayDataSources

public BioAssayData[] getBioAssayDataSources()
Description copied from interface: Transformation
Returns the value of this Transformation object's bioAssayDataSources attribute.

Specified by:
getBioAssayDataSources in interface Transformation
Returns:
gov.nih.nci.mageom.bean.BioAssayData.BioAssayData[] The value of bioAssayDataSources.
See Also:
Transformation.getBioAssayDataSources()

setBioAssayMapping

public void setBioAssayMapping(BioAssayMapping p_bioAssayMapping)
Sets the bioAssayMapping attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Transformation object.

Specified by:
setBioAssayMapping in interface Transformation
Parameters:
p_bioAssayMapping - The new value for bioAssayMapping.
See Also:
Transformation.getBioAssayMapping()

getBioAssayMapping

public BioAssayMapping getBioAssayMapping()
Description copied from interface: Transformation
Returns the value of this Transformation object's bioAssayMapping attribute.

Specified by:
getBioAssayMapping in interface Transformation
Returns:
gov.nih.nci.mageom.bean.BioAssayData.BioAssayMapping The value of bioAssayMapping.
See Also:
Transformation.getBioAssayMapping()

setDesignElementMapping

public void setDesignElementMapping(DesignElementMapping p_designElementMapping)
Sets the designElementMapping attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Transformation object.

Specified by:
setDesignElementMapping in interface Transformation
Parameters:
p_designElementMapping - The new value for designElementMapping.
See Also:
Transformation.getDesignElementMapping()

getDesignElementMapping

public DesignElementMapping getDesignElementMapping()
Description copied from interface: Transformation
Returns the value of this Transformation object's designElementMapping attribute.

Specified by:
getDesignElementMapping in interface Transformation
Returns:
gov.nih.nci.mageom.bean.BioAssayData.DesignElementMapping The value of designElementMapping.
See Also:
Transformation.getDesignElementMapping()

setQuantitationTypeMapping

public void setQuantitationTypeMapping(QuantitationTypeMapping p_quantitationTypeMapping)
Sets the quantitationTypeMapping attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Transformation object.

Specified by:
setQuantitationTypeMapping in interface Transformation
Parameters:
p_quantitationTypeMapping - The new value for quantitationTypeMapping.
See Also:
Transformation.getQuantitationTypeMapping()

getQuantitationTypeMapping

public QuantitationTypeMapping getQuantitationTypeMapping()
Description copied from interface: Transformation
Returns the value of this Transformation object's quantitationTypeMapping attribute.

Specified by:
getQuantitationTypeMapping in interface Transformation
Returns:
gov.nih.nci.mageom.bean.BioAssayData.QuantitationTypeMapping The value of quantitationTypeMapping.
See Also:
Transformation.getQuantitationTypeMapping()

getBioAssayDataSourcesCount

public int getBioAssayDataSourcesCount()
Returns the count of all BioAssayData associated with this Transformation object.

Returns:
the count
See Also:
Transformation.getBioAssayDataSources()

toXML

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

toXMLDoc

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

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 BioEventImpl
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 BioEventImpl
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 BioEventImpl
Returns:
the String representation.