gov.nih.nci.mageom.domain.Experiment.impl
Class ExperimentDesignImpl

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.Experiment.impl.ExperimentDesignImpl
All Implemented Interfaces:
Describable, ExperimentDesign, Extendable, java.io.Serializable

public class ExperimentDesignImpl
extends DescribableImpl
implements ExperimentDesign

The ExperimentDesign is the description and collection of ExperimentalFactors and the hierarchy of BioAssays to which they pertain.

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

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected static java.util.Hashtable associationMethods
           
protected  ExperimentalFactor[] experimentalFactors
          DOCUMENT ME
protected  int experimentalFactorsCount
          The count of ExperimentalFactor objects.
protected  Description normalizationDescription
          DOCUMENT ME
protected  java.lang.Long normalizationDescriptionId
          The internal ID of the associated normalizationDescription object.
protected  Description qualityControlDescription
          DOCUMENT ME
protected  java.lang.Long qualityControlDescriptionId
          The internal ID of the associated qualityControlDescription object.
protected  Description replicateDescription
          DOCUMENT ME
protected  java.lang.Long replicateDescriptionId
          The internal ID of the associated replicateDescription object.
protected  BioAssay[] topLevelBioAssays
          DOCUMENT ME
protected  int topLevelBioAssaysCount
          The count of BioAssay objects.
protected  OntologyEntry[] types
          DOCUMENT ME
protected  int typesCount
          The count of OntologyEntry objects.
 
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
ExperimentDesignImpl()
          Default constructor
 
Method Summary
 ExperimentalFactor[] getExperimentalFactors()
          Returns the value of this ExperimentDesign object's experimentalFactors attribute.
 int getExperimentalFactorsCount()
          Returns the count of all ExperimentalFactor associated with this ExperimentDesign object.
 Description getNormalizationDescription()
          Returns the value of this ExperimentDesign object's normalizationDescription attribute.
 Description getQualityControlDescription()
          Returns the value of this ExperimentDesign object's qualityControlDescription attribute.
 Description getReplicateDescription()
          Returns the value of this ExperimentDesign object's replicateDescription attribute.
 BioAssay[] getTopLevelBioAssays()
          Returns the value of this ExperimentDesign object's topLevelBioAssays attribute.
 int getTopLevelBioAssaysCount()
          Returns the count of all BioAssay associated with this ExperimentDesign object.
 OntologyEntry[] getTypes()
          Returns the value of this ExperimentDesign object's types attribute.
 int getTypesCount()
          Returns the count of all OntologyEntry associated with this ExperimentDesign object.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 ExperimentDesign[] searchExperimentDesigns(ExperimentDesignSearchCriteria criteria)
          Returns an array of ExperimentDesign objects that satisfy the given ExperimentDesignSearchCriteria.
 void setExperimentalFactors(ExperimentalFactor[] p_experimentalFactors)
          Sets the experimentalFactors attribute.
 void setNormalizationDescription(Description p_normalizationDescription)
          Sets the normalizationDescription attribute.
 void setQualityControlDescription(Description p_qualityControlDescription)
          Sets the qualityControlDescription attribute.
 void setReplicateDescription(Description p_replicateDescription)
          Sets the replicateDescription attribute.
 void setTopLevelBioAssays(BioAssay[] p_topLevelBioAssays)
          Sets the topLevelBioAssays attribute.
 void setTypes(OntologyEntry[] p_types)
          Sets the types 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.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.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

experimentalFactorsCount

protected int experimentalFactorsCount
The count of ExperimentalFactor objects.


experimentalFactors

protected ExperimentalFactor[] experimentalFactors
DOCUMENT ME


topLevelBioAssaysCount

protected int topLevelBioAssaysCount
The count of BioAssay objects.


topLevelBioAssays

protected BioAssay[] topLevelBioAssays
DOCUMENT ME


replicateDescription

protected Description replicateDescription
DOCUMENT ME


replicateDescriptionId

protected java.lang.Long replicateDescriptionId
The internal ID of the associated replicateDescription object.


qualityControlDescription

protected Description qualityControlDescription
DOCUMENT ME


qualityControlDescriptionId

protected java.lang.Long qualityControlDescriptionId
The internal ID of the associated qualityControlDescription object.


normalizationDescription

protected Description normalizationDescription
DOCUMENT ME


normalizationDescriptionId

protected java.lang.Long normalizationDescriptionId
The internal ID of the associated normalizationDescription object.


typesCount

protected int typesCount
The count of OntologyEntry objects.


types

protected OntologyEntry[] types
DOCUMENT ME

Constructor Detail

ExperimentDesignImpl

public ExperimentDesignImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class DescribableImpl

searchExperimentDesigns

public ExperimentDesign[] searchExperimentDesigns(ExperimentDesignSearchCriteria criteria)
                                           throws gov.nih.nci.common.search.SearchException
Returns an array of ExperimentDesign objects that satisfy the given ExperimentDesignSearchCriteria.

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

setExperimentalFactors

public void setExperimentalFactors(ExperimentalFactor[] p_experimentalFactors)
Sets the experimentalFactors attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ExperimentDesign object.

Specified by:
setExperimentalFactors in interface ExperimentDesign
Parameters:
p_experimentalFactors - The new value for experimentalFactors.
See Also:
ExperimentDesign.getExperimentalFactors()

getExperimentalFactors

public ExperimentalFactor[] getExperimentalFactors()
Description copied from interface: ExperimentDesign
Returns the value of this ExperimentDesign object's experimentalFactors attribute.

Specified by:
getExperimentalFactors in interface ExperimentDesign
Returns:
gov.nih.nci.mageom.bean.Experiment.ExperimentalFactor[] The value of experimentalFactors.
See Also:
ExperimentDesign.getExperimentalFactors()

setTopLevelBioAssays

public void setTopLevelBioAssays(BioAssay[] p_topLevelBioAssays)
Sets the topLevelBioAssays attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ExperimentDesign object.

Specified by:
setTopLevelBioAssays in interface ExperimentDesign
Parameters:
p_topLevelBioAssays - The new value for topLevelBioAssays.
See Also:
ExperimentDesign.getTopLevelBioAssays()

getTopLevelBioAssays

public BioAssay[] getTopLevelBioAssays()
Description copied from interface: ExperimentDesign
Returns the value of this ExperimentDesign object's topLevelBioAssays attribute.

Specified by:
getTopLevelBioAssays in interface ExperimentDesign
Returns:
gov.nih.nci.mageom.bean.BioAssay.BioAssay[] The value of topLevelBioAssays.
See Also:
ExperimentDesign.getTopLevelBioAssays()

setReplicateDescription

public void setReplicateDescription(Description p_replicateDescription)
Sets the replicateDescription attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ExperimentDesign object.

Specified by:
setReplicateDescription in interface ExperimentDesign
Parameters:
p_replicateDescription - The new value for replicateDescription.
See Also:
ExperimentDesign.getReplicateDescription()

getReplicateDescription

public Description getReplicateDescription()
Description copied from interface: ExperimentDesign
Returns the value of this ExperimentDesign object's replicateDescription attribute.

Specified by:
getReplicateDescription in interface ExperimentDesign
Returns:
gov.nih.nci.mageom.bean.Description.Description The value of replicateDescription.
See Also:
ExperimentDesign.getReplicateDescription()

setQualityControlDescription

public void setQualityControlDescription(Description p_qualityControlDescription)
Sets the qualityControlDescription attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ExperimentDesign object.

Specified by:
setQualityControlDescription in interface ExperimentDesign
Parameters:
p_qualityControlDescription - The new value for qualityControlDescription.
See Also:
ExperimentDesign.getQualityControlDescription()

getQualityControlDescription

public Description getQualityControlDescription()
Description copied from interface: ExperimentDesign
Returns the value of this ExperimentDesign object's qualityControlDescription attribute.

Specified by:
getQualityControlDescription in interface ExperimentDesign
Returns:
gov.nih.nci.mageom.bean.Description.Description The value of qualityControlDescription.
See Also:
ExperimentDesign.getQualityControlDescription()

setNormalizationDescription

public void setNormalizationDescription(Description p_normalizationDescription)
Sets the normalizationDescription attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ExperimentDesign object.

Specified by:
setNormalizationDescription in interface ExperimentDesign
Parameters:
p_normalizationDescription - The new value for normalizationDescription.
See Also:
ExperimentDesign.getNormalizationDescription()

getNormalizationDescription

public Description getNormalizationDescription()
Description copied from interface: ExperimentDesign
Returns the value of this ExperimentDesign object's normalizationDescription attribute.

Specified by:
getNormalizationDescription in interface ExperimentDesign
Returns:
gov.nih.nci.mageom.bean.Description.Description The value of normalizationDescription.
See Also:
ExperimentDesign.getNormalizationDescription()

setTypes

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

Specified by:
setTypes in interface ExperimentDesign
Parameters:
p_types - The new value for types.
See Also:
ExperimentDesign.getTypes()

getTypes

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

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

getExperimentalFactorsCount

public int getExperimentalFactorsCount()
Returns the count of all ExperimentalFactor associated with this ExperimentDesign object.

Returns:
the count
See Also:
ExperimentDesign.getExperimentalFactors()

getTopLevelBioAssaysCount

public int getTopLevelBioAssaysCount()
Returns the count of all BioAssay associated with this ExperimentDesign object.

Returns:
the count
See Also:
ExperimentDesign.getTopLevelBioAssays()

getTypesCount

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

Returns:
the count
See Also:
ExperimentDesign.getTypes()

toXML

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

toXMLDoc

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

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 DescribableImpl
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 DescribableImpl
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 DescribableImpl
Returns:
the String representation.