org.biomage.Array
Class Fiducial

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

All Implemented Interfaces:

HasAuditTrail, HasDescriptions, HasDistanceUnit, HasFiducialType, HasPosition, HasPropertySets, HasSecurity, java.io.Serializable

public class Fiducial

extends Describable

implements java.io.Serializable, HasDistanceUnit, HasFiducialType, HasPosition

A marking on the surface of the array that can be used to identify the array's origin, the coordinates of which are the fiducial's centroid.

See Also:

Serialized Form

Nested Class Summary

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

HasAuditTrail.AuditTrail_list

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

HasDescriptions.Descriptions_list

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

HasPropertySets.PropertySets_list

Field Summary

protected DistanceUnit	distanceUnit The units the fiducial is measured in.
protected OntologyEntry	fiducialType A descriptive string that indicates the type of a fiducial (e.g.
protected Position	position The position, relative to the upper left corner, of the fiducial

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

Fiducial()
Default constructor.

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

Method Summary

DistanceUnit	getDistanceUnit() Get method for distanceUnit
OntologyEntry	getFiducialType() Get method for fiducialType
Position	getPosition() Get method for position
void	setDistanceUnit(DistanceUnit distanceUnit) Set method for distanceUnit
void	setFiducialType(OntologyEntry fiducialType) Set method for fiducialType
void	setPosition(Position position) Set method for position
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.Describable

addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity

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

fiducialType

protected OntologyEntry fiducialType

A descriptive string that indicates the type of a fiducial (e.g. the chrome border on an Affymetrix array, a laser ablation mark).

distanceUnit

protected DistanceUnit distanceUnit

The units the fiducial is measured in.

position

protected Position position

The position, relative to the upper left corner, of the fiducial

Constructor Detail

Fiducial

public Fiducial()

Default constructor.

Fiducial

public Fiducial(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 Describable

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 Describable

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 Describable

java.io.IOException

setFiducialType

public void setFiducialType(OntologyEntry fiducialType)

Set method for fiducialType

Specified by:

setFiducialType in interface HasFiducialType

getFiducialType

public OntologyEntry getFiducialType()

Get method for fiducialType

Specified by:

getFiducialType in interface HasFiducialType

Returns:

value of the attribute

setDistanceUnit

public void setDistanceUnit(DistanceUnit distanceUnit)

Set method for distanceUnit

Specified by:

setDistanceUnit in interface HasDistanceUnit

getDistanceUnit

public DistanceUnit getDistanceUnit()

Get method for distanceUnit

Specified by:

getDistanceUnit in interface HasDistanceUnit

Returns:

value of the attribute

setPosition

public void setPosition(Position position)

Set method for position

Specified by:

setPosition in interface HasPosition

getPosition

public Position getPosition()

Get method for position

Specified by:

getPosition in interface HasPosition

Returns:

value of the attribute