org.biomage.Array
Class ArrayManufacture

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Common.Identifiable
              extended by org.biomage.Array.ArrayManufacture
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasArrayManufacturers, HasArrays, HasAuditTrail, HasDescriptions, HasFeatureLIMSs, HasPropertySets, HasProtocolApplications, HasQualityControlStatistics, HasSecurity

public class ArrayManufacture
extends Identifiable
implements java.io.Serializable, HasArrays, HasProtocolApplications, HasFeatureLIMSs, HasArrayManufacturers, HasQualityControlStatistics

Describes the process by which arrays are produced.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasArrays
HasArrays.Arrays_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasProtocolApplications
HasProtocolApplications.ProtocolApplications_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasFeatureLIMSs
HasFeatureLIMSs.FeatureLIMSs_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasArrayManufacturers
HasArrayManufacturers.ArrayManufacturers_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasQualityControlStatistics
HasQualityControlStatistics.QualityControlStatistics_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  java.util.List arrayManufacturers
          The person or organization to contact for information concerning the ArrayManufacture.
protected  java.util.List arrays
          Association between the manufactured array and the information on that manufacture.
protected  java.util.List featureLIMSs
          Information on the manufacture of the features.
protected  java.util.List protocolApplications
          The protocols followed in the manufacturing of the arrays.
protected  java.util.List qualityControlStatistics
          Information on the quality of the ArrayManufacture.
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
ArrayManufacture()
          Default constructor.
ArrayManufacture(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToArrayManufacturers(Contact contact)
          Method to add Contact to ArrayManufacturers_list
 void addToArrayManufacturers(int position, Contact contact)
          Method to add Contact at position to ArrayManufacturers_list
 void addToArrays(Array array)
          Method to add Array to Arrays_list
 void addToArrays(int position, Array array)
          Method to add Array at position to Arrays_list
 void addToFeatureLIMSs(int position, ManufactureLIMS manufactureLIMS)
          Method to add ManufactureLIMS at position to FeatureLIMSs_list
 void addToFeatureLIMSs(ManufactureLIMS manufactureLIMS)
          Method to add ManufactureLIMS to FeatureLIMSs_list
 void addToProtocolApplications(int position, ProtocolApplication protocolApplication)
          Method to add ProtocolApplication at position to ProtocolApplications_list
 void addToProtocolApplications(ProtocolApplication protocolApplication)
          Method to add ProtocolApplication to ProtocolApplications_list
 void addToQualityControlStatistics(int position, NameValueType nameValueType)
          Method to add NameValueType at position to QualityControlStatistics_list
 void addToQualityControlStatistics(NameValueType nameValueType)
          Method to add NameValueType to QualityControlStatistics_list
 boolean emptyMAGEobject()
           
 HasArrayManufacturers.ArrayManufacturers_list getArrayManufacturers()
          Get method for arrayManufacturers
 HasArrays.Arrays_list getArrays()
          Get method for arrays
 HasFeatureLIMSs.FeatureLIMSs_list getFeatureLIMSs()
          Get method for featureLIMSs
 Contact getFromArrayManufacturers(int position)
          Method to get Contact from ArrayManufacturers_list
 Array getFromArrays(int position)
          Method to get Array from Arrays_list
 ManufactureLIMS getFromFeatureLIMSs(int position)
          Method to get ManufactureLIMS from FeatureLIMSs_list
 ProtocolApplication getFromProtocolApplications(int position)
          Method to get ProtocolApplication from ProtocolApplications_list
 NameValueType getFromQualityControlStatistics(int position)
          Method to get NameValueType from QualityControlStatistics_list
 java.util.Date getManufacturingDate()
          Get method for manufacturingDate
 java.lang.String getModelClassName()
           
 HasProtocolApplications.ProtocolApplications_list getProtocolApplications()
          Get method for protocolApplications
 HasQualityControlStatistics.QualityControlStatistics_list getQualityControlStatistics()
          Get method for qualityControlStatistics
 java.lang.Float getTolerance()
          Get method for tolerance
 void removeElementAtFromArrayManufacturers(int position)
          Method to remove by position from ArrayManufacturers_list
 void removeElementAtFromArrays(int position)
          Method to remove by position from Arrays_list
 void removeElementAtFromFeatureLIMSs(int position)
          Method to remove by position from FeatureLIMSs_list
 void removeElementAtFromProtocolApplications(int position)
          Method to remove by position from ProtocolApplications_list
 void removeElementAtFromQualityControlStatistics(int position)
          Method to remove by position from QualityControlStatistics_list
 void removeFromArrayManufacturers(Contact contact)
          Method to remove first Contact from ArrayManufacturers_list
 void removeFromArrays(Array array)
          Method to remove first Array from Arrays_list
 void removeFromFeatureLIMSs(ManufactureLIMS manufactureLIMS)
          Method to remove first ManufactureLIMS from FeatureLIMSs_list
 void removeFromProtocolApplications(ProtocolApplication protocolApplication)
          Method to remove first ProtocolApplication from ProtocolApplications_list
 void removeFromQualityControlStatistics(NameValueType nameValueType)
          Method to remove first NameValueType from QualityControlStatistics_list
 void setArrayManufacturers(HasArrayManufacturers.ArrayManufacturers_list arrayManufacturers)
          Set method for arrayManufacturers
 void setArrays(HasArrays.Arrays_list arrays)
          Set method for arrays
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setFeatureLIMSs(HasFeatureLIMSs.FeatureLIMSs_list featureLIMSs)
          Set method for featureLIMSs
 void setManufacturingDate(java.util.Date manufacturingDate)
           
 void setProtocolApplications(HasProtocolApplications.ProtocolApplications_list protocolApplications)
          Set method for protocolApplications
 void setQualityControlStatistics(HasQualityControlStatistics.QualityControlStatistics_list qualityControlStatistics)
          Set method for qualityControlStatistics
 void setTolerance(java.lang.Float tolerance)
          Set method for tolerance
 void writeAssociations(java.io.Writer out)
          writeAssociations This method is responsible for assembling the association data into XML.
 void writeAttributes(java.io.Writer out)
          writeAttributes This method is responsible for assembling the attribute data into XML.
 void writeMAGEML(java.io.Writer out)
          writeMAGEML This method is responsible for assembling the attribute and association data into XML.
 
Methods inherited from class org.biomage.Common.Identifiable
getIdentifier, getName, setIdentifier, setName, toString
 
Methods inherited from class org.biomage.Common.Describable
addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity
 
Methods inherited from class org.biomage.Common.Extendable
addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

arrays

protected java.util.List arrays
Association between the manufactured array and the information on that manufacture.


arrayManufacturers

protected java.util.List arrayManufacturers
The person or organization to contact for information concerning the ArrayManufacture.


qualityControlStatistics

protected java.util.List qualityControlStatistics
Information on the quality of the ArrayManufacture.


featureLIMSs

protected java.util.List featureLIMSs
Information on the manufacture of the features.


protocolApplications

protected java.util.List protocolApplications
The protocols followed in the manufacturing of the arrays.

Constructor Detail

ArrayManufacture

public ArrayManufacture()
Default constructor.


ArrayManufacture

public ArrayManufacture(org.xml.sax.Attributes atts)
Attribute constructor. Looks up the attributes in the parameter and casts them from strings appropriately

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class Identifiable

writeMAGEML

public void writeMAGEML(java.io.Writer out)
                 throws java.io.IOException
writeMAGEML This method is responsible for assembling the attribute and association data into XML. It creates the object tag and then calls the writeAttributes and writeAssociation methods.

Overrides:
writeMAGEML in class Identifiable
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

writeAttributes

public void writeAttributes(java.io.Writer out)
                     throws java.io.IOException
writeAttributes This method is responsible for assembling the attribute data into XML. It calls the super method to write out all attributes of this class and it's ancestors.

Overrides:
writeAttributes in class Identifiable
Throws:
java.io.IOException

writeAssociations

public void writeAssociations(java.io.Writer out)
                       throws java.io.IOException
writeAssociations This method is responsible for assembling the association data into XML. It calls the super method to write out all associations of this class's ancestors.

Overrides:
writeAssociations in class Identifiable
Throws:
java.io.IOException

getManufacturingDate

public java.util.Date getManufacturingDate()
Get method for manufacturingDate

Returns:
value of the attribute

setTolerance

public void setTolerance(java.lang.Float tolerance)
Set method for tolerance

Parameters:
value - to set

getTolerance

public java.lang.Float getTolerance()
Get method for tolerance

Returns:
value of the attribute

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class Identifiable

setArrays

public void setArrays(HasArrays.Arrays_list arrays)
Set method for arrays

Specified by:
setArrays in interface HasArrays
Parameters:
value - to set

getArrays

public HasArrays.Arrays_list getArrays()
Get method for arrays

Specified by:
getArrays in interface HasArrays
Returns:
value of the attribute

addToArrays

public void addToArrays(Array array)
Method to add Array to Arrays_list

Specified by:
addToArrays in interface HasArrays

addToArrays

public void addToArrays(int position,
                        Array array)
Method to add Array at position to Arrays_list

Specified by:
addToArrays in interface HasArrays

getFromArrays

public Array getFromArrays(int position)
Method to get Array from Arrays_list

Specified by:
getFromArrays in interface HasArrays

removeElementAtFromArrays

public void removeElementAtFromArrays(int position)
Method to remove by position from Arrays_list

Specified by:
removeElementAtFromArrays in interface HasArrays

removeFromArrays

public void removeFromArrays(Array array)
Method to remove first Array from Arrays_list

Specified by:
removeFromArrays in interface HasArrays

setArrayManufacturers

public void setArrayManufacturers(HasArrayManufacturers.ArrayManufacturers_list arrayManufacturers)
Set method for arrayManufacturers

Specified by:
setArrayManufacturers in interface HasArrayManufacturers
Parameters:
value - to set

getArrayManufacturers

public HasArrayManufacturers.ArrayManufacturers_list getArrayManufacturers()
Get method for arrayManufacturers

Specified by:
getArrayManufacturers in interface HasArrayManufacturers
Returns:
value of the attribute

addToArrayManufacturers

public void addToArrayManufacturers(Contact contact)
Method to add Contact to ArrayManufacturers_list

Specified by:
addToArrayManufacturers in interface HasArrayManufacturers

addToArrayManufacturers

public void addToArrayManufacturers(int position,
                                    Contact contact)
Method to add Contact at position to ArrayManufacturers_list

Specified by:
addToArrayManufacturers in interface HasArrayManufacturers

getFromArrayManufacturers

public Contact getFromArrayManufacturers(int position)
Method to get Contact from ArrayManufacturers_list

Specified by:
getFromArrayManufacturers in interface HasArrayManufacturers

removeElementAtFromArrayManufacturers

public void removeElementAtFromArrayManufacturers(int position)
Method to remove by position from ArrayManufacturers_list

Specified by:
removeElementAtFromArrayManufacturers in interface HasArrayManufacturers

removeFromArrayManufacturers

public void removeFromArrayManufacturers(Contact contact)
Method to remove first Contact from ArrayManufacturers_list

Specified by:
removeFromArrayManufacturers in interface HasArrayManufacturers

setQualityControlStatistics

public void setQualityControlStatistics(HasQualityControlStatistics.QualityControlStatistics_list qualityControlStatistics)
Set method for qualityControlStatistics

Specified by:
setQualityControlStatistics in interface HasQualityControlStatistics
Parameters:
value - to set

getQualityControlStatistics

public HasQualityControlStatistics.QualityControlStatistics_list getQualityControlStatistics()
Get method for qualityControlStatistics

Specified by:
getQualityControlStatistics in interface HasQualityControlStatistics
Returns:
value of the attribute

addToQualityControlStatistics

public void addToQualityControlStatistics(NameValueType nameValueType)
Method to add NameValueType to QualityControlStatistics_list

Specified by:
addToQualityControlStatistics in interface HasQualityControlStatistics

addToQualityControlStatistics

public void addToQualityControlStatistics(int position,
                                          NameValueType nameValueType)
Method to add NameValueType at position to QualityControlStatistics_list

Specified by:
addToQualityControlStatistics in interface HasQualityControlStatistics

getFromQualityControlStatistics

public NameValueType getFromQualityControlStatistics(int position)
Method to get NameValueType from QualityControlStatistics_list

Specified by:
getFromQualityControlStatistics in interface HasQualityControlStatistics

removeElementAtFromQualityControlStatistics

public void removeElementAtFromQualityControlStatistics(int position)
Method to remove by position from QualityControlStatistics_list

Specified by:
removeElementAtFromQualityControlStatistics in interface HasQualityControlStatistics

removeFromQualityControlStatistics

public void removeFromQualityControlStatistics(NameValueType nameValueType)
Method to remove first NameValueType from QualityControlStatistics_list

Specified by:
removeFromQualityControlStatistics in interface HasQualityControlStatistics

setFeatureLIMSs

public void setFeatureLIMSs(HasFeatureLIMSs.FeatureLIMSs_list featureLIMSs)
Set method for featureLIMSs

Specified by:
setFeatureLIMSs in interface HasFeatureLIMSs
Parameters:
value - to set

getFeatureLIMSs

public HasFeatureLIMSs.FeatureLIMSs_list getFeatureLIMSs()
Get method for featureLIMSs

Specified by:
getFeatureLIMSs in interface HasFeatureLIMSs
Returns:
value of the attribute

addToFeatureLIMSs

public void addToFeatureLIMSs(ManufactureLIMS manufactureLIMS)
Method to add ManufactureLIMS to FeatureLIMSs_list

Specified by:
addToFeatureLIMSs in interface HasFeatureLIMSs

addToFeatureLIMSs

public void addToFeatureLIMSs(int position,
                              ManufactureLIMS manufactureLIMS)
Method to add ManufactureLIMS at position to FeatureLIMSs_list

Specified by:
addToFeatureLIMSs in interface HasFeatureLIMSs

getFromFeatureLIMSs

public ManufactureLIMS getFromFeatureLIMSs(int position)
Method to get ManufactureLIMS from FeatureLIMSs_list

Specified by:
getFromFeatureLIMSs in interface HasFeatureLIMSs

removeElementAtFromFeatureLIMSs

public void removeElementAtFromFeatureLIMSs(int position)
Method to remove by position from FeatureLIMSs_list

Specified by:
removeElementAtFromFeatureLIMSs in interface HasFeatureLIMSs

removeFromFeatureLIMSs

public void removeFromFeatureLIMSs(ManufactureLIMS manufactureLIMS)
Method to remove first ManufactureLIMS from FeatureLIMSs_list

Specified by:
removeFromFeatureLIMSs in interface HasFeatureLIMSs

setProtocolApplications

public void setProtocolApplications(HasProtocolApplications.ProtocolApplications_list protocolApplications)
Set method for protocolApplications

Specified by:
setProtocolApplications in interface HasProtocolApplications
Parameters:
value - to set

getProtocolApplications

public HasProtocolApplications.ProtocolApplications_list getProtocolApplications()
Get method for protocolApplications

Specified by:
getProtocolApplications in interface HasProtocolApplications
Returns:
value of the attribute

addToProtocolApplications

public void addToProtocolApplications(ProtocolApplication protocolApplication)
Method to add ProtocolApplication to ProtocolApplications_list

Specified by:
addToProtocolApplications in interface HasProtocolApplications

addToProtocolApplications

public void addToProtocolApplications(int position,
                                      ProtocolApplication protocolApplication)
Method to add ProtocolApplication at position to ProtocolApplications_list

Specified by:
addToProtocolApplications in interface HasProtocolApplications

getFromProtocolApplications

public ProtocolApplication getFromProtocolApplications(int position)
Method to get ProtocolApplication from ProtocolApplications_list

Specified by:
getFromProtocolApplications in interface HasProtocolApplications

removeElementAtFromProtocolApplications

public void removeElementAtFromProtocolApplications(int position)
Method to remove by position from ProtocolApplications_list

Specified by:
removeElementAtFromProtocolApplications in interface HasProtocolApplications

removeFromProtocolApplications

public void removeFromProtocolApplications(ProtocolApplication protocolApplication)
Method to remove first ProtocolApplication from ProtocolApplications_list

Specified by:
removeFromProtocolApplications in interface HasProtocolApplications

setManufacturingDate

public void setManufacturingDate(java.util.Date manufacturingDate)
Parameters:
manufacturingDate - The manufacturingDate to set.