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

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.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

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.


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.


positionDelta

private PositionDelta positionDelta
How the zone deviates in position from the ArrayDesign.


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.


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.


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.


setZone

public void setZone(org.biomage.ArrayDesign.Zone zone)
Set method for zone

Specified by:
setZone in interface org.biomage.Interface.HasZone

getZone

public org.biomage.ArrayDesign.Zone getZone()
Get method for zone

Specified by:
getZone in interface org.biomage.Interface.HasZone

setPositionDelta

public void setPositionDelta(PositionDelta positionDelta)
Set method for positionDelta

Specified by:
setPositionDelta in interface org.biomage.Interface.HasPositionDelta

getPositionDelta

public PositionDelta getPositionDelta()
Get method for positionDelta

Specified by:
getPositionDelta in interface org.biomage.Interface.HasPositionDelta

setDefectType

public void setDefectType(org.biomage.Description.OntologyEntry defectType)
Set method for defectType

Specified by:
setDefectType in interface org.biomage.Interface.HasDefectType

getDefectType

public org.biomage.Description.OntologyEntry getDefectType()
Get method for defectType

Specified by:
getDefectType in interface org.biomage.Interface.HasDefectType