gov.nih.nci.mageom.domain.BioAssay.impl
Class BioAssayImpl

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.BioAssay.impl.BioAssayImpl
All Implemented Interfaces:
BioAssay, Describable, Extendable, Identifiable, java.io.Serializable
Direct Known Subclasses:
DerivedBioAssayImpl, MeasuredBioAssayImpl, PhysicalBioAssayImpl

public class BioAssayImpl
extends IdentifiableImpl
implements BioAssay

An abstract class which represents both physical and computational groupings of arrays and biomaterials.

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

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected static java.util.Hashtable associationMethods
           
protected  FactorValue[] bioAssayFactorValues
          DOCUMENT ME
protected  int bioAssayFactorValuesCount
          The count of FactorValue objects.
protected  Channel[] channels
          DOCUMENT ME
protected  int channelsCount
          The count of Channel 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
BioAssayImpl()
          Default constructor
 
Method Summary
 FactorValue[] getBioAssayFactorValues()
          Returns the value of this BioAssay object's bioAssayFactorValues attribute.
 int getBioAssayFactorValuesCount()
          Returns the count of all FactorValue associated with this BioAssay object.
 Channel[] getChannels()
          Returns the value of this BioAssay object's channels attribute.
 int getChannelsCount()
          Returns the count of all Channel associated with this BioAssay object.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 BioAssay[] searchBioAssays(BioAssaySearchCriteria criteria)
          Returns an array of BioAssay objects that satisfy the given BioAssaySearchCriteria.
 void setBioAssayFactorValues(FactorValue[] p_bioAssayFactorValues)
          Sets the bioAssayFactorValues attribute.
 void setChannels(Channel[] p_channels)
          Sets the channels 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

bioAssayFactorValuesCount

protected int bioAssayFactorValuesCount
The count of FactorValue objects.


bioAssayFactorValues

protected FactorValue[] bioAssayFactorValues
DOCUMENT ME


channelsCount

protected int channelsCount
The count of Channel objects.


channels

protected Channel[] channels
DOCUMENT ME

Constructor Detail

BioAssayImpl

public BioAssayImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class IdentifiableImpl

searchBioAssays

public BioAssay[] searchBioAssays(BioAssaySearchCriteria criteria)
                           throws gov.nih.nci.common.search.SearchException
Returns an array of BioAssay objects that satisfy the given BioAssaySearchCriteria.

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

setBioAssayFactorValues

public void setBioAssayFactorValues(FactorValue[] p_bioAssayFactorValues)
Sets the bioAssayFactorValues attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioAssay object.

Specified by:
setBioAssayFactorValues in interface BioAssay
Parameters:
p_bioAssayFactorValues - The new value for bioAssayFactorValues.
See Also:
BioAssay.getBioAssayFactorValues()

getBioAssayFactorValues

public FactorValue[] getBioAssayFactorValues()
Description copied from interface: BioAssay
Returns the value of this BioAssay object's bioAssayFactorValues attribute.

Specified by:
getBioAssayFactorValues in interface BioAssay
Returns:
gov.nih.nci.mageom.bean.Experiment.FactorValue[] The value of bioAssayFactorValues.
See Also:
BioAssay.getBioAssayFactorValues()

setChannels

public void setChannels(Channel[] p_channels)
Sets the channels attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a BioAssay object.

Specified by:
setChannels in interface BioAssay
Parameters:
p_channels - The new value for channels.
See Also:
BioAssay.getChannels()

getChannels

public Channel[] getChannels()
Description copied from interface: BioAssay
Returns the value of this BioAssay object's channels attribute.

Specified by:
getChannels in interface BioAssay
Returns:
gov.nih.nci.mageom.bean.BioAssay.Channel[] The value of channels.
See Also:
BioAssay.getChannels()

getBioAssayFactorValuesCount

public int getBioAssayFactorValuesCount()
Returns the count of all FactorValue associated with this BioAssay object.

Returns:
the count
See Also:
BioAssay.getBioAssayFactorValues()

getChannelsCount

public int getChannelsCount()
Returns the count of all Channel associated with this BioAssay object.

Returns:
the count
See Also:
BioAssay.getChannels()

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.