org.biomage.Array
Class ArrayManufactureDeviation

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Array.ArrayManufactureDeviation

All Implemented Interfaces:

HasAdjustments, HasFeatureDefects, HasPropertySets, java.io.Serializable

public class ArrayManufactureDeviation

extends Extendable

implements java.io.Serializable, HasFeatureDefects, 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).

See Also:

Serialized Form

Nested Class Summary

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

HasFeatureDefects.FeatureDefects_list

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

HasAdjustments.Adjustments_list

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

HasPropertySets.PropertySets_list

Field Summary

protected HasAdjustments.Adjustments_list	adjustments Descriptions of how a Zone has been printed differently than specified in the ArrayDesign.
protected 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

propertySets

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
HasAdjustments.Adjustments_list	getAdjustments() Get method for adjustments
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(HasAdjustments.Adjustments_list adjustments) Set method for adjustments
void	setFeatureDefects(HasFeatureDefects.FeatureDefects_list featureDefects) Set method for featureDefects
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.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

adjustments

protected HasAdjustments.Adjustments_list adjustments

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

featureDefects

protected HasFeatureDefects.FeatureDefects_list featureDefects

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

Constructor Detail

ArrayManufactureDeviation

public ArrayManufactureDeviation()

Default constructor.

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.

Overrides:

writeMAGEML in class Extendable

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 Extendable

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 Extendable

java.io.IOException

setAdjustments

public void setAdjustments(HasAdjustments.Adjustments_list adjustments)

Set method for adjustments

Specified by:

setAdjustments in interface HasAdjustments

getAdjustments

public HasAdjustments.Adjustments_list getAdjustments()

Get method for adjustments

Specified by:

getAdjustments in interface HasAdjustments

Returns:

value of the attribute

addToAdjustments

public void addToAdjustments(ZoneDefect zoneDefect)

Method to add ZoneDefect to Adjustments_list

Specified by:

addToAdjustments in interface HasAdjustments

addToAdjustments

public void addToAdjustments(int position,
                             ZoneDefect zoneDefect)

Method to add ZoneDefect at position to Adjustments_list

Specified by:

addToAdjustments in interface HasAdjustments

getFromAdjustments

public ZoneDefect getFromAdjustments(int position)

Method to get ZoneDefect from Adjustments_list

Specified by:

getFromAdjustments in interface HasAdjustments

removeElementAtFromAdjustments

public void removeElementAtFromAdjustments(int position)

Method to remove by position from Adjustments_list

Specified by:

removeElementAtFromAdjustments in interface HasAdjustments

removeFromAdjustments

public void removeFromAdjustments(ZoneDefect zoneDefect)

Method to remove first ZoneDefect from Adjustments_list

Specified by:

removeFromAdjustments in interface HasAdjustments

setFeatureDefects

public void setFeatureDefects(HasFeatureDefects.FeatureDefects_list featureDefects)

Set method for featureDefects

Specified by:

setFeatureDefects in interface HasFeatureDefects

getFeatureDefects

public HasFeatureDefects.FeatureDefects_list getFeatureDefects()

Get method for featureDefects

Specified by:

getFeatureDefects in interface HasFeatureDefects

Returns:

value of the attribute

addToFeatureDefects

public void addToFeatureDefects(FeatureDefect featureDefect)

Method to add FeatureDefect to FeatureDefects_list

Specified by:

addToFeatureDefects in interface HasFeatureDefects

addToFeatureDefects

public void addToFeatureDefects(int position,
                                FeatureDefect featureDefect)

Method to add FeatureDefect at position to FeatureDefects_list

Specified by:

addToFeatureDefects in interface HasFeatureDefects

getFromFeatureDefects

public FeatureDefect getFromFeatureDefects(int position)

Method to get FeatureDefect from FeatureDefects_list

Specified by:

getFromFeatureDefects in interface HasFeatureDefects

removeElementAtFromFeatureDefects

public void removeElementAtFromFeatureDefects(int position)

Method to remove by position from FeatureDefects_list

Specified by:

removeElementAtFromFeatureDefects in interface HasFeatureDefects

removeFromFeatureDefects

public void removeFromFeatureDefects(FeatureDefect featureDefect)

Method to remove first FeatureDefect from FeatureDefects_list

Specified by:

removeFromFeatureDefects in interface HasFeatureDefects