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org.biomage.Array
Class ArrayManufacture  view ArrayManufacture download ArrayManufacture.java

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

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

Describes the process by which arrays are produced.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasArrays
org.biomage.Interface.HasArrays.Arrays_list
 
Nested classes inherited from class org.biomage.Interface.HasProtocolApplications
org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list
 
Nested classes inherited from class org.biomage.Interface.HasFeatureLIMSs
org.biomage.Interface.HasFeatureLIMSs.FeatureLIMSs_list
 
Nested classes inherited from class org.biomage.Interface.HasArrayManufacturers
org.biomage.Interface.HasArrayManufacturers.ArrayManufacturers_list
 
Nested classes inherited from class org.biomage.Interface.HasQualityControlStatistics
org.biomage.Interface.HasQualityControlStatistics.QualityControlStatistics_list
 
Nested classes inherited from class org.biomage.Interface.HasAuditTrail
org.biomage.Interface.HasAuditTrail.AuditTrail_list
 
Nested classes inherited from class org.biomage.Interface.HasDescriptions
org.biomage.Interface.HasDescriptions.Descriptions_list
 
Nested classes inherited from class org.biomage.Interface.HasPropertySets
org.biomage.Interface.HasPropertySets.PropertySets_list
 
Field Summary
private  org.biomage.Interface.HasArrayManufacturers.ArrayManufacturers_list arrayManufacturers
          The person or organization to contact for information concerning the ArrayManufacture.
private  org.biomage.Interface.HasArrays.Arrays_list arrays
          Association between the manufactured array and the information on that manufacture.
private  org.biomage.Interface.HasFeatureLIMSs.FeatureLIMSs_list featureLIMSs
          Information on the manufacture of the features.
(package private)  java.lang.String manufacturingDate
          The date the arrays were manufactured
private  org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list protocolApplications
          The protocols followed in the manufacturing of the arrays.
private  org.biomage.Interface.HasQualityControlStatistics.QualityControlStatistics_list qualityControlStatistics
          Information on the quality of the ArrayManufacture.
(package private)  float tolerance
          The allowable error of a feature printed to its intended position.
 
Fields inherited from class org.biomage.Common.Identifiable
 
Fields inherited from class org.biomage.Common.Describable
 
Fields inherited from class org.biomage.Common.Extendable
 
Constructor Summary
ArrayManufacture()
          Default constructor.
ArrayManufacture(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToArrayManufacturers(org.biomage.AuditAndSecurity.Contact contact)
          Method to add Contact to ArrayManufacturers_list
 void addToArrayManufacturers(int position, org.biomage.AuditAndSecurity.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, org.biomage.Protocol.ProtocolApplication protocolApplication)
          Method to add ProtocolApplication at position to ProtocolApplications_list
 void addToProtocolApplications(org.biomage.Protocol.ProtocolApplication protocolApplication)
          Method to add ProtocolApplication to ProtocolApplications_list
 void addToQualityControlStatistics(int position, org.biomage.Common.NameValueType nameValueType)
          Method to add NameValueType at position to QualityControlStatistics_list
 void addToQualityControlStatistics(org.biomage.Common.NameValueType nameValueType)
          Method to add NameValueType to QualityControlStatistics_list
 org.biomage.Interface.HasArrayManufacturers.ArrayManufacturers_list getArrayManufacturers()
          Get method for arrayManufacturers
 org.biomage.Interface.HasArrays.Arrays_list getArrays()
          Get method for arrays
 org.biomage.Interface.HasFeatureLIMSs.FeatureLIMSs_list getFeatureLIMSs()
          Get method for featureLIMSs
 org.biomage.AuditAndSecurity.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
 org.biomage.Protocol.ProtocolApplication getFromProtocolApplications(int position)
          Method to get ProtocolApplication from ProtocolApplications_list
 org.biomage.Common.NameValueType getFromQualityControlStatistics(int position)
          Method to get NameValueType from QualityControlStatistics_list
 java.lang.String getManufacturingDate()
          Get method for manufacturingDate
 org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list getProtocolApplications()
          Get method for protocolApplications
 org.biomage.Interface.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(org.biomage.AuditAndSecurity.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(org.biomage.Protocol.ProtocolApplication protocolApplication)
          Method to remove first ProtocolApplication from ProtocolApplications_list
 void removeFromQualityControlStatistics(org.biomage.Common.NameValueType nameValueType)
          Method to remove first NameValueType from QualityControlStatistics_list
 void setArrayManufacturers(org.biomage.Interface.HasArrayManufacturers.ArrayManufacturers_list arrayManufacturers)
          Set method for arrayManufacturers
 void setArrays(org.biomage.Interface.HasArrays.Arrays_list arrays)
          Set method for arrays
 void setFeatureLIMSs(org.biomage.Interface.HasFeatureLIMSs.FeatureLIMSs_list featureLIMSs)
          Set method for featureLIMSs
 void setManufacturingDate(java.lang.String manufacturingDate)
          Set method for manufacturingDate
 void setProtocolApplications(org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list protocolApplications)
          Set method for protocolApplications
 void setQualityControlStatistics(org.biomage.Interface.HasQualityControlStatistics.QualityControlStatistics_list qualityControlStatistics)
          Set method for qualityControlStatistics
 void setTolerance(float tolerance)
          Set method for tolerance
 void writeAssociations(java.io.Writer out)
          writeAssociations
 void writeAttributes(java.io.Writer out)
          writeAttributes
 void writeMAGEML(java.io.Writer out)
          writeMAGEML
 
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

manufacturingDate

java.lang.String manufacturingDate
The date the arrays were manufactured


tolerance

float tolerance
The allowable error of a feature printed to its intended position.


arrays

private org.biomage.Interface.HasArrays.Arrays_list arrays
Association between the manufactured array and the information on that manufacture.


protocolApplications

private org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list protocolApplications
The protocols followed in the manufacturing of the arrays.


featureLIMSs

private org.biomage.Interface.HasFeatureLIMSs.FeatureLIMSs_list featureLIMSs
Information on the manufacture of the features.


arrayManufacturers

private org.biomage.Interface.HasArrayManufacturers.ArrayManufacturers_list arrayManufacturers
The person or organization to contact for information concerning the ArrayManufacture.


qualityControlStatistics

private org.biomage.Interface.HasQualityControlStatistics.QualityControlStatistics_list qualityControlStatistics
Information on the quality of the ArrayManufacture.

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.


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.


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.


setManufacturingDate

public void setManufacturingDate(java.lang.String manufacturingDate)
Set method for manufacturingDate


getManufacturingDate

public java.lang.String getManufacturingDate()
Get method for manufacturingDate


setTolerance

public void setTolerance(float tolerance)
Set method for tolerance


getTolerance

public float getTolerance()
Get method for tolerance


setArrays

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

Specified by:
setArrays in interface org.biomage.Interface.HasArrays

getArrays

public org.biomage.Interface.HasArrays.Arrays_list getArrays()
Get method for arrays

Specified by:
getArrays in interface org.biomage.Interface.HasArrays

addToArrays

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

Specified by:
addToArrays in interface org.biomage.Interface.HasArrays

addToArrays

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

Specified by:
addToArrays in interface org.biomage.Interface.HasArrays

getFromArrays

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

Specified by:
getFromArrays in interface org.biomage.Interface.HasArrays

removeElementAtFromArrays

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

Specified by:
removeElementAtFromArrays in interface org.biomage.Interface.HasArrays

removeFromArrays

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

Specified by:
removeFromArrays in interface org.biomage.Interface.HasArrays

setProtocolApplications

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

Specified by:
setProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

getProtocolApplications

public org.biomage.Interface.HasProtocolApplications.ProtocolApplications_list getProtocolApplications()
Get method for protocolApplications

Specified by:
getProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

addToProtocolApplications

public void addToProtocolApplications(org.biomage.Protocol.ProtocolApplication protocolApplication)
Method to add ProtocolApplication to ProtocolApplications_list

Specified by:
addToProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

addToProtocolApplications

public void addToProtocolApplications(int position,
                                      org.biomage.Protocol.ProtocolApplication protocolApplication)
Method to add ProtocolApplication at position to ProtocolApplications_list

Specified by:
addToProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

getFromProtocolApplications

public org.biomage.Protocol.ProtocolApplication getFromProtocolApplications(int position)
Method to get ProtocolApplication from ProtocolApplications_list

Specified by:
getFromProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

removeElementAtFromProtocolApplications

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

Specified by:
removeElementAtFromProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

removeFromProtocolApplications

public void removeFromProtocolApplications(org.biomage.Protocol.ProtocolApplication protocolApplication)
Method to remove first ProtocolApplication from ProtocolApplications_list

Specified by:
removeFromProtocolApplications in interface org.biomage.Interface.HasProtocolApplications

setFeatureLIMSs

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

Specified by:
setFeatureLIMSs in interface org.biomage.Interface.HasFeatureLIMSs

getFeatureLIMSs

public org.biomage.Interface.HasFeatureLIMSs.FeatureLIMSs_list getFeatureLIMSs()
Get method for featureLIMSs

Specified by:
getFeatureLIMSs in interface org.biomage.Interface.HasFeatureLIMSs

addToFeatureLIMSs

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

Specified by:
addToFeatureLIMSs in interface org.biomage.Interface.HasFeatureLIMSs

addToFeatureLIMSs

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

Specified by:
addToFeatureLIMSs in interface org.biomage.Interface.HasFeatureLIMSs

getFromFeatureLIMSs

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

Specified by:
getFromFeatureLIMSs in interface org.biomage.Interface.HasFeatureLIMSs

removeElementAtFromFeatureLIMSs

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

Specified by:
removeElementAtFromFeatureLIMSs in interface org.biomage.Interface.HasFeatureLIMSs

removeFromFeatureLIMSs

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

Specified by:
removeFromFeatureLIMSs in interface org.biomage.Interface.HasFeatureLIMSs

setArrayManufacturers

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

Specified by:
setArrayManufacturers in interface org.biomage.Interface.HasArrayManufacturers

getArrayManufacturers

public org.biomage.Interface.HasArrayManufacturers.ArrayManufacturers_list getArrayManufacturers()
Get method for arrayManufacturers

Specified by:
getArrayManufacturers in interface org.biomage.Interface.HasArrayManufacturers

addToArrayManufacturers

public void addToArrayManufacturers(org.biomage.AuditAndSecurity.Contact contact)
Method to add Contact to ArrayManufacturers_list

Specified by:
addToArrayManufacturers in interface org.biomage.Interface.HasArrayManufacturers

addToArrayManufacturers

public void addToArrayManufacturers(int position,
                                    org.biomage.AuditAndSecurity.Contact contact)
Method to add Contact at position to ArrayManufacturers_list

Specified by:
addToArrayManufacturers in interface org.biomage.Interface.HasArrayManufacturers

getFromArrayManufacturers

public org.biomage.AuditAndSecurity.Contact getFromArrayManufacturers(int position)
Method to get Contact from ArrayManufacturers_list

Specified by:
getFromArrayManufacturers in interface org.biomage.Interface.HasArrayManufacturers

removeElementAtFromArrayManufacturers

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

Specified by:
removeElementAtFromArrayManufacturers in interface org.biomage.Interface.HasArrayManufacturers

removeFromArrayManufacturers

public void removeFromArrayManufacturers(org.biomage.AuditAndSecurity.Contact contact)
Method to remove first Contact from ArrayManufacturers_list

Specified by:
removeFromArrayManufacturers in interface org.biomage.Interface.HasArrayManufacturers

setQualityControlStatistics

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

Specified by:
setQualityControlStatistics in interface org.biomage.Interface.HasQualityControlStatistics

getQualityControlStatistics

public org.biomage.Interface.HasQualityControlStatistics.QualityControlStatistics_list getQualityControlStatistics()
Get method for qualityControlStatistics

Specified by:
getQualityControlStatistics in interface org.biomage.Interface.HasQualityControlStatistics

addToQualityControlStatistics

public void addToQualityControlStatistics(org.biomage.Common.NameValueType nameValueType)
Method to add NameValueType to QualityControlStatistics_list

Specified by:
addToQualityControlStatistics in interface org.biomage.Interface.HasQualityControlStatistics

addToQualityControlStatistics

public void addToQualityControlStatistics(int position,
                                          org.biomage.Common.NameValueType nameValueType)
Method to add NameValueType at position to QualityControlStatistics_list

Specified by:
addToQualityControlStatistics in interface org.biomage.Interface.HasQualityControlStatistics

getFromQualityControlStatistics

public org.biomage.Common.NameValueType getFromQualityControlStatistics(int position)
Method to get NameValueType from QualityControlStatistics_list

Specified by:
getFromQualityControlStatistics in interface org.biomage.Interface.HasQualityControlStatistics

removeElementAtFromQualityControlStatistics

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

Specified by:
removeElementAtFromQualityControlStatistics in interface org.biomage.Interface.HasQualityControlStatistics

removeFromQualityControlStatistics

public void removeFromQualityControlStatistics(org.biomage.Common.NameValueType nameValueType)
Method to remove first NameValueType from QualityControlStatistics_list

Specified by:
removeFromQualityControlStatistics in interface org.biomage.Interface.HasQualityControlStatistics