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org.biomage.Array
Class ArrayManufactureDeviation  

java.lang.Object
  org.biomage.Common.Extendable
      org.biomage.Array.ArrayManufactureDeviation

All Implemented Interfaces:

org.biomage.Interface.HasAdjustments, org.biomage.Interface.HasFeatureDefects, org.biomage.Interface.HasPropertySets, java.io.Serializable

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public class ArrayManufactureDeviation

extends org.biomage.Common.Extendable

implements java.io.Serializable, org.biomage.Interface.HasFeatureDefects, org.biomage.Interface.HasAdjustments

Stores information of the potential difference between an array design and arrays that have been manufactured using that design (e.g. a tip failed to print several spots).

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Nested Class Summary

 

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

org.biomage.Interface.HasFeatureDefects.FeatureDefects_list

 

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

org.biomage.Interface.HasAdjustments.Adjustments_list

 

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

org.biomage.Interface.HasPropertySets.PropertySets_list

 

Field Summary
private  org.biomage.Interface.HasAdjustments.Adjustments_list	adjustments           Descriptions of how a Zone has been printed differently than specified in the ArrayDesign.
private  org.biomage.Interface.HasFeatureDefects.FeatureDefects_list	featureDefects           Description on features who are manufactured in a different location than specified in the ArrayDesign.

 

Fields inherited from class org.biomage.Common.Extendable

 

Constructor Summary

ArrayManufactureDeviation()           Default constructor.

ArrayManufactureDeviation(org.xml.sax.Attributes atts)           Attribute constructor.

 

Method Summary
void	addToAdjustments(int position, ZoneDefect zoneDefect)           Method to add ZoneDefect at position to Adjustments_list
void	addToAdjustments(ZoneDefect zoneDefect)           Method to add ZoneDefect to Adjustments_list
void	addToFeatureDefects(FeatureDefect featureDefect)           Method to add FeatureDefect to FeatureDefects_list
void	addToFeatureDefects(int position, FeatureDefect featureDefect)           Method to add FeatureDefect at position to FeatureDefects_list
org.biomage.Interface.HasAdjustments.Adjustments_list	getAdjustments()           Get method for adjustments
org.biomage.Interface.HasFeatureDefects.FeatureDefects_list	getFeatureDefects()           Get method for featureDefects
ZoneDefect	getFromAdjustments(int position)           Method to get ZoneDefect from Adjustments_list
FeatureDefect	getFromFeatureDefects(int position)           Method to get FeatureDefect from FeatureDefects_list
void	removeElementAtFromAdjustments(int position)           Method to remove by position from Adjustments_list
void	removeElementAtFromFeatureDefects(int position)           Method to remove by position from FeatureDefects_list
void	removeFromAdjustments(ZoneDefect zoneDefect)           Method to remove first ZoneDefect from Adjustments_list
void	removeFromFeatureDefects(FeatureDefect featureDefect)           Method to remove first FeatureDefect from FeatureDefects_list
void	setAdjustments(org.biomage.Interface.HasAdjustments.Adjustments_list adjustments)           Set method for adjustments
void	setFeatureDefects(org.biomage.Interface.HasFeatureDefects.FeatureDefects_list featureDefects)           Set method for featureDefects
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.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

featureDefects

private org.biomage.Interface.HasFeatureDefects.FeatureDefects_list featureDefects

Description on features who are manufactured in a different location than specified in the ArrayDesign.

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adjustments

private org.biomage.Interface.HasAdjustments.Adjustments_list adjustments

Descriptions of how a Zone has been printed differently than specified in the ArrayDesign.

Constructor Detail

ArrayManufactureDeviation

public ArrayManufactureDeviation()

Default constructor.

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ArrayManufactureDeviation

public ArrayManufactureDeviation(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.

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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.

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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.

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setFeatureDefects

public void setFeatureDefects(org.biomage.Interface.HasFeatureDefects.FeatureDefects_list featureDefects)

Set method for featureDefects

Specified by:

setFeatureDefects in interface org.biomage.Interface.HasFeatureDefects

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getFeatureDefects

public org.biomage.Interface.HasFeatureDefects.FeatureDefects_list getFeatureDefects()

Get method for featureDefects

Specified by:

getFeatureDefects in interface org.biomage.Interface.HasFeatureDefects

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addToFeatureDefects

public void addToFeatureDefects(FeatureDefect featureDefect)

Method to add FeatureDefect to FeatureDefects_list

Specified by:

addToFeatureDefects in interface org.biomage.Interface.HasFeatureDefects

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addToFeatureDefects

public void addToFeatureDefects(int position,
                                FeatureDefect featureDefect)

Method to add FeatureDefect at position to FeatureDefects_list

Specified by:

addToFeatureDefects in interface org.biomage.Interface.HasFeatureDefects

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getFromFeatureDefects

public FeatureDefect getFromFeatureDefects(int position)

Method to get FeatureDefect from FeatureDefects_list

Specified by:

getFromFeatureDefects in interface org.biomage.Interface.HasFeatureDefects

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removeElementAtFromFeatureDefects

public void removeElementAtFromFeatureDefects(int position)

Method to remove by position from FeatureDefects_list

Specified by:

removeElementAtFromFeatureDefects in interface org.biomage.Interface.HasFeatureDefects

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removeFromFeatureDefects

public void removeFromFeatureDefects(FeatureDefect featureDefect)

Method to remove first FeatureDefect from FeatureDefects_list

Specified by:

removeFromFeatureDefects in interface org.biomage.Interface.HasFeatureDefects

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setAdjustments

public void setAdjustments(org.biomage.Interface.HasAdjustments.Adjustments_list adjustments)

Set method for adjustments

Specified by:

setAdjustments in interface org.biomage.Interface.HasAdjustments

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getAdjustments

public org.biomage.Interface.HasAdjustments.Adjustments_list getAdjustments()

Get method for adjustments

Specified by:

getAdjustments in interface org.biomage.Interface.HasAdjustments

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addToAdjustments

public void addToAdjustments(ZoneDefect zoneDefect)

Method to add ZoneDefect to Adjustments_list

Specified by:

addToAdjustments in interface org.biomage.Interface.HasAdjustments

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addToAdjustments

public void addToAdjustments(int position,
                             ZoneDefect zoneDefect)

Method to add ZoneDefect at position to Adjustments_list

Specified by:

addToAdjustments in interface org.biomage.Interface.HasAdjustments

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getFromAdjustments

public ZoneDefect getFromAdjustments(int position)

Method to get ZoneDefect from Adjustments_list

Specified by:

getFromAdjustments in interface org.biomage.Interface.HasAdjustments

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removeElementAtFromAdjustments

public void removeElementAtFromAdjustments(int position)

Method to remove by position from Adjustments_list

Specified by:

removeElementAtFromAdjustments in interface org.biomage.Interface.HasAdjustments

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removeFromAdjustments

public void removeFromAdjustments(ZoneDefect zoneDefect)

Method to remove first ZoneDefect from Adjustments_list

Specified by:

removeFromAdjustments in interface org.biomage.Interface.HasAdjustments

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ Array overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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