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org.biomage.Array
Class ZoneDefect  

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

All Implemented Interfaces:

org.biomage.Interface.HasDefectType, org.biomage.Interface.HasPositionDelta, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasZone, java.io.Serializable

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public class ZoneDefect

extends org.biomage.Common.Extendable

implements java.io.Serializable, org.biomage.Interface.HasZone, org.biomage.Interface.HasPositionDelta, org.biomage.Interface.HasDefectType

Stores the defect information for a zone.

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Nested Class Summary

 

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

org.biomage.Interface.HasPropertySets.PropertySets_list

 

Field Summary
private  org.biomage.Description.OntologyEntry	defectType           Indicates the type of defect (e.g.
private  PositionDelta	positionDelta           How the zone deviates in position from the ArrayDesign.
private  org.biomage.ArrayDesign.Zone	zone           Reference to the Zone that was misprinted.

 

Fields inherited from class org.biomage.Common.Extendable

 

Constructor Summary

ZoneDefect()           Default constructor.

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

 

Method Summary
org.biomage.Description.OntologyEntry	getDefectType()           Get method for defectType
PositionDelta	getPositionDelta()           Get method for positionDelta
org.biomage.ArrayDesign.Zone	getZone()           Get method for zone
void	setDefectType(org.biomage.Description.OntologyEntry defectType)           Set method for defectType
void	setPositionDelta(PositionDelta positionDelta)           Set method for positionDelta
void	setZone(org.biomage.ArrayDesign.Zone zone)           Set method for zone
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

zone

private org.biomage.ArrayDesign.Zone zone

Reference to the Zone that was misprinted.

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positionDelta

private PositionDelta positionDelta

How the zone deviates in position from the ArrayDesign.

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defectType

private org.biomage.Description.OntologyEntry defectType

Indicates the type of defect (e.g. a missing zone or a moved zone).

Constructor Detail

ZoneDefect

public ZoneDefect()

Default constructor.

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ZoneDefect

public ZoneDefect(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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setZone

public void setZone(org.biomage.ArrayDesign.Zone zone)

Set method for zone

Specified by:

setZone in interface org.biomage.Interface.HasZone

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getZone

public org.biomage.ArrayDesign.Zone getZone()

Get method for zone

Specified by:

getZone in interface org.biomage.Interface.HasZone

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setPositionDelta

public void setPositionDelta(PositionDelta positionDelta)

Set method for positionDelta

Specified by:

setPositionDelta in interface org.biomage.Interface.HasPositionDelta

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getPositionDelta

public PositionDelta getPositionDelta()

Get method for positionDelta

Specified by:

getPositionDelta in interface org.biomage.Interface.HasPositionDelta

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setDefectType

public void setDefectType(org.biomage.Description.OntologyEntry defectType)

Set method for defectType

Specified by:

setDefectType in interface org.biomage.Interface.HasDefectType

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getDefectType

public org.biomage.Description.OntologyEntry getDefectType()

Get method for defectType

Specified by:

getDefectType in interface org.biomage.Interface.HasDefectType

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