gov.nih.nci.mageom.domain.ArrayDesign.impl
Class ArrayDesignImpl

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.ArrayDesign.impl.ArrayDesignImpl
All Implemented Interfaces:
ArrayDesign, Describable, Extendable, Identifiable, java.io.Serializable
Direct Known Subclasses:
PhysicalArrayDesignImpl

public class ArrayDesignImpl
extends IdentifiableImpl
implements ArrayDesign

Describes the design of an gene expression layout. In some cases this might be virtual and, for instance, represent the output from analysis software at the composite level without reporters or features.

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

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected static java.util.Hashtable associationMethods
           
protected  CompositeGroup[] compositeGroups
          DOCUMENT ME
protected  int compositeGroupsCount
          The count of CompositeGroup objects.
protected  Contact[] designProviders
          DOCUMENT ME
protected  int designProvidersCount
          The count of Contact objects.
protected  FeatureGroup[] featureGroups
          DOCUMENT ME
protected  int featureGroupsCount
          The count of FeatureGroup objects.
protected  java.lang.Integer numberOfFeatures
          The number of features for this array
protected  ProtocolApplication[] protocolApplications
          DOCUMENT ME
protected  int protocolApplicationsCount
          The count of ProtocolApplication objects.
protected  ReporterGroup[] reporterGroups
          DOCUMENT ME
protected  int reporterGroupsCount
          The count of ReporterGroup objects.
protected  java.lang.String version
          The version of this design.
 
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
ArrayDesignImpl()
          Default constructor
 
Method Summary
 CompositeGroup[] getCompositeGroups()
          Returns the value of this ArrayDesign object's compositeGroups attribute.
 int getCompositeGroupsCount()
          Returns the count of all CompositeGroup associated with this ArrayDesign object.
 Contact[] getDesignProviders()
          Returns the value of this ArrayDesign object's designProviders attribute.
 int getDesignProvidersCount()
          Returns the count of all Contact associated with this ArrayDesign object.
 FeatureGroup[] getFeatureGroups()
          Returns the value of this ArrayDesign object's featureGroups attribute.
 int getFeatureGroupsCount()
          Returns the count of all FeatureGroup associated with this ArrayDesign object.
 java.lang.Integer getNumberOfFeatures()
          Returns the value of this ArrayDesign object's numberOfFeatures attribute.
 ProtocolApplication[] getProtocolApplications()
          Returns the value of this ArrayDesign object's protocolApplications attribute.
 int getProtocolApplicationsCount()
          Returns the count of all ProtocolApplication associated with this ArrayDesign object.
 ReporterGroup[] getReporterGroups()
          Returns the value of this ArrayDesign object's reporterGroups attribute.
 int getReporterGroupsCount()
          Returns the count of all ReporterGroup associated with this ArrayDesign object.
 java.lang.String getVersion()
          Returns the value of this ArrayDesign object's version attribute.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 ArrayDesign[] searchArrayDesigns(ArrayDesignSearchCriteria criteria)
          Returns an array of ArrayDesign objects that satisfy the given ArrayDesignSearchCriteria.
 void setCompositeGroups(CompositeGroup[] p_compositeGroups)
          Sets the compositeGroups attribute.
 void setDesignProviders(Contact[] p_designProviders)
          Sets the designProviders attribute.
 void setFeatureGroups(FeatureGroup[] p_featureGroups)
          Sets the featureGroups attribute.
 void setNumberOfFeatures(java.lang.Integer p_numberOfFeatures)
          Sets the numberOfFeatures attribute.
 void setProtocolApplications(ProtocolApplication[] p_protocolApplications)
          Sets the protocolApplications attribute.
 void setReporterGroups(ReporterGroup[] p_reporterGroups)
          Sets the reporterGroups attribute.
 void setVersion(java.lang.String p_version)
          Sets the version 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

version

protected java.lang.String version
The version of this design.


numberOfFeatures

protected java.lang.Integer numberOfFeatures
The number of features for this array


protocolApplicationsCount

protected int protocolApplicationsCount
The count of ProtocolApplication objects.


protocolApplications

protected ProtocolApplication[] protocolApplications
DOCUMENT ME


compositeGroupsCount

protected int compositeGroupsCount
The count of CompositeGroup objects.


compositeGroups

protected CompositeGroup[] compositeGroups
DOCUMENT ME


designProvidersCount

protected int designProvidersCount
The count of Contact objects.


designProviders

protected Contact[] designProviders
DOCUMENT ME


reporterGroupsCount

protected int reporterGroupsCount
The count of ReporterGroup objects.


reporterGroups

protected ReporterGroup[] reporterGroups
DOCUMENT ME


featureGroupsCount

protected int featureGroupsCount
The count of FeatureGroup objects.


featureGroups

protected FeatureGroup[] featureGroups
DOCUMENT ME

Constructor Detail

ArrayDesignImpl

public ArrayDesignImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class IdentifiableImpl

searchArrayDesigns

public ArrayDesign[] searchArrayDesigns(ArrayDesignSearchCriteria criteria)
                                 throws gov.nih.nci.common.search.SearchException
Returns an array of ArrayDesign objects that satisfy the given ArrayDesignSearchCriteria.

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

setVersion

public void setVersion(java.lang.String p_version)
Sets the version attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ArrayDesign object.

Specified by:
setVersion in interface ArrayDesign
Parameters:
p_version - The new value for version.
See Also:
ArrayDesign.getVersion()

getVersion

public java.lang.String getVersion()
Description copied from interface: ArrayDesign
Returns the value of this ArrayDesign object's version attribute. Description of version: The version of this design.

Specified by:
getVersion in interface ArrayDesign
Returns:
String The value of version.
See Also:
ArrayDesign.getVersion()

setNumberOfFeatures

public void setNumberOfFeatures(java.lang.Integer p_numberOfFeatures)
Sets the numberOfFeatures attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ArrayDesign object.

Specified by:
setNumberOfFeatures in interface ArrayDesign
Parameters:
p_numberOfFeatures - The new value for numberOfFeatures.
See Also:
ArrayDesign.getNumberOfFeatures()

getNumberOfFeatures

public java.lang.Integer getNumberOfFeatures()
Description copied from interface: ArrayDesign
Returns the value of this ArrayDesign object's numberOfFeatures attribute. Description of numberOfFeatures: The number of features for this array

Specified by:
getNumberOfFeatures in interface ArrayDesign
Returns:
int The value of numberOfFeatures.
See Also:
ArrayDesign.getNumberOfFeatures()

setProtocolApplications

public void setProtocolApplications(ProtocolApplication[] p_protocolApplications)
Sets the protocolApplications attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ArrayDesign object.

Specified by:
setProtocolApplications in interface ArrayDesign
Parameters:
p_protocolApplications - The new value for protocolApplications.
See Also:
ArrayDesign.getProtocolApplications()

getProtocolApplications

public ProtocolApplication[] getProtocolApplications()
Description copied from interface: ArrayDesign
Returns the value of this ArrayDesign object's protocolApplications attribute.

Specified by:
getProtocolApplications in interface ArrayDesign
Returns:
gov.nih.nci.mageom.bean.Protocol.ProtocolApplication[] The value of protocolApplications.
See Also:
ArrayDesign.getProtocolApplications()

setCompositeGroups

public void setCompositeGroups(CompositeGroup[] p_compositeGroups)
Sets the compositeGroups attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ArrayDesign object.

Specified by:
setCompositeGroups in interface ArrayDesign
Parameters:
p_compositeGroups - The new value for compositeGroups.
See Also:
ArrayDesign.getCompositeGroups()

getCompositeGroups

public CompositeGroup[] getCompositeGroups()
Description copied from interface: ArrayDesign
Returns the value of this ArrayDesign object's compositeGroups attribute.

Specified by:
getCompositeGroups in interface ArrayDesign
Returns:
gov.nih.nci.mageom.bean.ArrayDesign.CompositeGroup[] The value of compositeGroups.
See Also:
ArrayDesign.getCompositeGroups()

setDesignProviders

public void setDesignProviders(Contact[] p_designProviders)
Sets the designProviders attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ArrayDesign object.

Specified by:
setDesignProviders in interface ArrayDesign
Parameters:
p_designProviders - The new value for designProviders.
See Also:
ArrayDesign.getDesignProviders()

getDesignProviders

public Contact[] getDesignProviders()
Description copied from interface: ArrayDesign
Returns the value of this ArrayDesign object's designProviders attribute.

Specified by:
getDesignProviders in interface ArrayDesign
Returns:
gov.nih.nci.mageom.bean.AuditAndSecurity.Contact[] The value of designProviders.
See Also:
ArrayDesign.getDesignProviders()

setReporterGroups

public void setReporterGroups(ReporterGroup[] p_reporterGroups)
Sets the reporterGroups attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ArrayDesign object.

Specified by:
setReporterGroups in interface ArrayDesign
Parameters:
p_reporterGroups - The new value for reporterGroups.
See Also:
ArrayDesign.getReporterGroups()

getReporterGroups

public ReporterGroup[] getReporterGroups()
Description copied from interface: ArrayDesign
Returns the value of this ArrayDesign object's reporterGroups attribute.

Specified by:
getReporterGroups in interface ArrayDesign
Returns:
gov.nih.nci.mageom.bean.ArrayDesign.ReporterGroup[] The value of reporterGroups.
See Also:
ArrayDesign.getReporterGroups()

setFeatureGroups

public void setFeatureGroups(FeatureGroup[] p_featureGroups)
Sets the featureGroups attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a ArrayDesign object.

Specified by:
setFeatureGroups in interface ArrayDesign
Parameters:
p_featureGroups - The new value for featureGroups.
See Also:
ArrayDesign.getFeatureGroups()

getFeatureGroups

public FeatureGroup[] getFeatureGroups()
Description copied from interface: ArrayDesign
Returns the value of this ArrayDesign object's featureGroups attribute.

Specified by:
getFeatureGroups in interface ArrayDesign
Returns:
gov.nih.nci.mageom.bean.ArrayDesign.FeatureGroup[] The value of featureGroups.
See Also:
ArrayDesign.getFeatureGroups()

getProtocolApplicationsCount

public int getProtocolApplicationsCount()
Returns the count of all ProtocolApplication associated with this ArrayDesign object.

Returns:
the count
See Also:
ArrayDesign.getProtocolApplications()

getCompositeGroupsCount

public int getCompositeGroupsCount()
Returns the count of all CompositeGroup associated with this ArrayDesign object.

Returns:
the count
See Also:
ArrayDesign.getCompositeGroups()

getDesignProvidersCount

public int getDesignProvidersCount()
Returns the count of all Contact associated with this ArrayDesign object.

Returns:
the count
See Also:
ArrayDesign.getDesignProviders()

getReporterGroupsCount

public int getReporterGroupsCount()
Returns the count of all ReporterGroup associated with this ArrayDesign object.

Returns:
the count
See Also:
ArrayDesign.getReporterGroups()

getFeatureGroupsCount

public int getFeatureGroupsCount()
Returns the count of all FeatureGroup associated with this ArrayDesign object.

Returns:
the count
See Also:
ArrayDesign.getFeatureGroups()

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.