org.biomage.Array
Class ArrayManufacture

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.Array.ArrayManufacture

All Implemented Interfaces:

HasArrayManufacturers, HasArrays, HasAuditTrail, HasDescriptions, HasFeatureLIMSs, HasPropertySets, HasProtocolApplications, HasQualityControlStatistics, HasSecurity, java.io.Serializable

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 inherited from class org.biomage.Interface.HasArrays

HasArrays.Arrays_list

Nested classes inherited from class org.biomage.Interface.HasProtocolApplications

HasProtocolApplications.ProtocolApplications_list

Nested classes inherited from class org.biomage.Interface.HasFeatureLIMSs

HasFeatureLIMSs.FeatureLIMSs_list

Nested classes inherited from class org.biomage.Interface.HasArrayManufacturers

HasArrayManufacturers.ArrayManufacturers_list

Nested classes inherited from class org.biomage.Interface.HasQualityControlStatistics

HasQualityControlStatistics.QualityControlStatistics_list

Nested classes inherited from class org.biomage.Interface.HasAuditTrail

HasAuditTrail.AuditTrail_list

Nested classes inherited from class org.biomage.Interface.HasDescriptions

HasDescriptions.Descriptions_list

Nested classes inherited from class org.biomage.Interface.HasPropertySets

HasPropertySets.PropertySets_list

Field Summary

protected HasArrayManufacturers.ArrayManufacturers_list	arrayManufacturers The person or organization to contact for information concerning the ArrayManufacture.
protected HasArrays.Arrays_list	arrays Association between the manufactured array and the information on that manufacture.
protected HasFeatureLIMSs.FeatureLIMSs_list	featureLIMSs Information on the manufacture of the features.
protected HasProtocolApplications.ProtocolApplications_list	protocolApplications The protocols followed in the manufacturing of the arrays.
protected HasQualityControlStatistics.QualityControlStatistics_list	qualityControlStatistics Information on the quality of the ArrayManufacture.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

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
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.lang.String	getManufacturingDate() Get method for manufacturingDate
HasProtocolApplications.ProtocolApplications_list	getProtocolApplications() Get method for protocolApplications
HasQualityControlStatistics.QualityControlStatistics_list	getQualityControlStatistics() Get method for qualityControlStatistics
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	setFeatureLIMSs(HasFeatureLIMSs.FeatureLIMSs_list featureLIMSs) Set method for featureLIMSs
void	setManufacturingDate(java.lang.String manufacturingDate) Set method for manufacturingDate
void	setProtocolApplications(HasProtocolApplications.ProtocolApplications_list protocolApplications) Set method for protocolApplications
void	setQualityControlStatistics(HasQualityControlStatistics.QualityControlStatistics_list qualityControlStatistics) Set method for qualityControlStatistics
void	setTolerance(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

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, getFromPropertySets, getPropertySets, removeElementAtFromPropertySets, removeFromPropertySets, setPropertySets

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

arrays

protected HasArrays.Arrays_list arrays

Association between the manufactured array and the information on that manufacture.

arrayManufacturers

protected HasArrayManufacturers.ArrayManufacturers_list arrayManufacturers

The person or organization to contact for information concerning the ArrayManufacture.

qualityControlStatistics

protected HasQualityControlStatistics.QualityControlStatistics_list qualityControlStatistics

Information on the quality of the ArrayManufacture.

featureLIMSs

protected HasFeatureLIMSs.FeatureLIMSs_list featureLIMSs

Information on the manufacture of the features.

protocolApplications

protected HasProtocolApplications.ProtocolApplications_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

Method Detail

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

java.io.IOException

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

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

java.io.IOException

setManufacturingDate

public void setManufacturingDate(java.lang.String manufacturingDate)

Set method for manufacturingDate

getManufacturingDate

public java.lang.String getManufacturingDate()

Get method for manufacturingDate

Returns:

value of the attribute

setTolerance

public void setTolerance(float tolerance)

Set method for tolerance

getTolerance

public float getTolerance()

Get method for tolerance

Returns:

value of the attribute

setArrays

public void setArrays(HasArrays.Arrays_list arrays)

Set method for arrays

Specified by:

setArrays in interface HasArrays

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

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

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

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

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