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

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.CompoundImpl
All Implemented Interfaces:
Compound, Describable, Extendable, Identifiable, java.io.Serializable

public class CompoundImpl
extends IdentifiableImpl
implements Compound

A Compound can be a simple compound such as SDS (sodium dodecyl sulfate). It may also be made of other Compounds in proportions using CompoundMeasurements to enumerate the Compounds and their amounts such as LB (Luria Broth) Media.

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

Field Summary
protected static java.util.ArrayList allAssociationMethods
           
protected static java.util.Hashtable associationMethods
           
protected  CompoundMeasurement[] componentCompounds
          DOCUMENT ME
protected  int componentCompoundsCount
          The count of CompoundMeasurement objects.
protected  OntologyEntry[] compoundIndices
          DOCUMENT ME
protected  int compoundIndicesCount
          The count of OntologyEntry objects.
protected  DatabaseEntry externalLIMS
          DOCUMENT ME
protected  java.lang.Long externalLIMSId
          The internal ID of the associated externalLIMS object.
protected  java.lang.Boolean isSolvent
          A Compound may be a special case Solvent.
 
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
CompoundImpl()
          Default constructor
 
Method Summary
 CompoundMeasurement[] getComponentCompounds()
          Returns the value of this Compound object's componentCompounds attribute.
 int getComponentCompoundsCount()
          Returns the count of all CompoundMeasurement associated with this Compound object.
 OntologyEntry[] getCompoundIndices()
          Returns the value of this Compound object's compoundIndices attribute.
 int getCompoundIndicesCount()
          Returns the count of all OntologyEntry associated with this Compound object.
 DatabaseEntry getExternalLIMS()
          Returns the value of this Compound object's externalLIMS attribute.
 java.lang.Boolean getIsSolvent()
          Returns the value of this Compound object's isSolvent attribute.
 java.util.Hashtable getXMLMethodDescriptors()
          Returns a Hashtable containing XMLMethodDescriptors descriptors of the association methods of this object.
protected  void init()
           
 Compound[] searchCompounds(CompoundSearchCriteria criteria)
          Returns an array of Compound objects that satisfy the given CompoundSearchCriteria.
 void setComponentCompounds(CompoundMeasurement[] p_componentCompounds)
          Sets the componentCompounds attribute.
 void setCompoundIndices(OntologyEntry[] p_compoundIndices)
          Sets the compoundIndices attribute.
 void setExternalLIMS(DatabaseEntry p_externalLIMS)
          Sets the externalLIMS attribute.
 void setIsSolvent(java.lang.Boolean p_isSolvent)
          Sets the isSolvent 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

isSolvent

protected java.lang.Boolean isSolvent
A Compound may be a special case Solvent.


componentCompoundsCount

protected int componentCompoundsCount
The count of CompoundMeasurement objects.


componentCompounds

protected CompoundMeasurement[] componentCompounds
DOCUMENT ME


compoundIndicesCount

protected int compoundIndicesCount
The count of OntologyEntry objects.


compoundIndices

protected OntologyEntry[] compoundIndices
DOCUMENT ME


externalLIMS

protected DatabaseEntry externalLIMS
DOCUMENT ME


externalLIMSId

protected java.lang.Long externalLIMSId
The internal ID of the associated externalLIMS object.

Constructor Detail

CompoundImpl

public CompoundImpl()
Default constructor

Method Detail

init

protected void init()
Overrides:
init in class IdentifiableImpl

searchCompounds

public Compound[] searchCompounds(CompoundSearchCriteria criteria)
                           throws gov.nih.nci.common.search.SearchException
Returns an array of Compound objects that satisfy the given CompoundSearchCriteria.

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

setIsSolvent

public void setIsSolvent(java.lang.Boolean p_isSolvent)
Sets the isSolvent attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Compound object.

Specified by:
setIsSolvent in interface Compound
Parameters:
p_isSolvent - The new value for isSolvent.
See Also:
Compound.getIsSolvent()

getIsSolvent

public java.lang.Boolean getIsSolvent()
Description copied from interface: Compound
Returns the value of this Compound object's isSolvent attribute. Description of isSolvent: A Compound may be a special case Solvent.

Specified by:
getIsSolvent in interface Compound
Returns:
boolean The value of isSolvent.
See Also:
Compound.getIsSolvent()

setComponentCompounds

public void setComponentCompounds(CompoundMeasurement[] p_componentCompounds)
Sets the componentCompounds attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Compound object.

Specified by:
setComponentCompounds in interface Compound
Parameters:
p_componentCompounds - The new value for componentCompounds.
See Also:
Compound.getComponentCompounds()

getComponentCompounds

public CompoundMeasurement[] getComponentCompounds()
Description copied from interface: Compound
Returns the value of this Compound object's componentCompounds attribute.

Specified by:
getComponentCompounds in interface Compound
Returns:
gov.nih.nci.mageom.bean.BioMaterial.CompoundMeasurement[] The value of componentCompounds.
See Also:
Compound.getComponentCompounds()

setCompoundIndices

public void setCompoundIndices(OntologyEntry[] p_compoundIndices)
Sets the compoundIndices attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Compound object.

Specified by:
setCompoundIndices in interface Compound
Parameters:
p_compoundIndices - The new value for compoundIndices.
See Also:
Compound.getCompoundIndices()

getCompoundIndices

public OntologyEntry[] getCompoundIndices()
Description copied from interface: Compound
Returns the value of this Compound object's compoundIndices attribute.

Specified by:
getCompoundIndices in interface Compound
Returns:
gov.nih.nci.mageom.bean.Description.OntologyEntry[] The value of compoundIndices.
See Also:
Compound.getCompoundIndices()

setExternalLIMS

public void setExternalLIMS(DatabaseEntry p_externalLIMS)
Sets the externalLIMS attribute. This API is currently read-only. So, calling this method does not affect the persistent state of a Compound object.

Specified by:
setExternalLIMS in interface Compound
Parameters:
p_externalLIMS - The new value for externalLIMS.
See Also:
Compound.getExternalLIMS()

getExternalLIMS

public DatabaseEntry getExternalLIMS()
Description copied from interface: Compound
Returns the value of this Compound object's externalLIMS attribute.

Specified by:
getExternalLIMS in interface Compound
Returns:
gov.nih.nci.mageom.bean.Description.DatabaseEntry The value of externalLIMS.
See Also:
Compound.getExternalLIMS()

getComponentCompoundsCount

public int getComponentCompoundsCount()
Returns the count of all CompoundMeasurement associated with this Compound object.

Returns:
the count
See Also:
Compound.getComponentCompounds()

getCompoundIndicesCount

public int getCompoundIndicesCount()
Returns the count of all OntologyEntry associated with this Compound object.

Returns:
the count
See Also:
Compound.getCompoundIndices()

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.