org.biomage.Array
Class ZoneDefect

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

All Implemented Interfaces:

HasDefectType, HasPositionDelta, HasPropertySets, HasZone, java.io.Serializable

public class ZoneDefect

extends Extendable

implements java.io.Serializable, HasZone, HasPositionDelta, HasDefectType

Stores the defect information for a zone.

See Also:

Serialized Form

Nested Class Summary

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

HasPropertySets.PropertySets_list

Field Summary

protected OntologyEntry	defectType Indicates the type of defect (e.g.
protected PositionDelta	positionDelta How the zone deviates in position from the ArrayDesign.
protected Zone	zone Reference to the Zone that was misprinted.

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

ZoneDefect()
Default constructor.

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

Method Summary

OntologyEntry	getDefectType() Get method for defectType
PositionDelta	getPositionDelta() Get method for positionDelta
Zone	getZone() Get method for zone
void	setDefectType(OntologyEntry defectType) Set method for defectType
void	setPositionDelta(PositionDelta positionDelta) Set method for positionDelta
void	setZone(Zone zone) Set method for zone
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

defectType

protected OntologyEntry defectType

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

positionDelta

protected PositionDelta positionDelta

How the zone deviates in position from the ArrayDesign.

zone

protected Zone zone

Reference to the Zone that was misprinted.

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.

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

setDefectType

public void setDefectType(OntologyEntry defectType)

Set method for defectType

Specified by:

setDefectType in interface HasDefectType

getDefectType

public OntologyEntry getDefectType()

Get method for defectType

Specified by:

getDefectType in interface HasDefectType

Returns:

value of the attribute

setPositionDelta

public void setPositionDelta(PositionDelta positionDelta)

Set method for positionDelta

Specified by:

setPositionDelta in interface HasPositionDelta

getPositionDelta

public PositionDelta getPositionDelta()

Get method for positionDelta

Specified by:

getPositionDelta in interface HasPositionDelta

Returns:

value of the attribute

setZone

public void setZone(Zone zone)

Set method for zone

Specified by:

setZone in interface HasZone

getZone

public Zone getZone()

Get method for zone

Specified by:

getZone in interface HasZone

Returns:

value of the attribute