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

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Array.Fiducial
All Implemented Interfaces:
org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasDistanceUnit, org.biomage.Interface.HasFiducialType, org.biomage.Interface.HasPosition, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasSecurity, java.io.Serializable

public class Fiducial
extends org.biomage.Common.Describable
implements java.io.Serializable, org.biomage.Interface.HasDistanceUnit, org.biomage.Interface.HasFiducialType, org.biomage.Interface.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.


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasAuditTrail
org.biomage.Interface.HasAuditTrail.AuditTrail_list
 
Nested classes inherited from class org.biomage.Interface.HasDescriptions
org.biomage.Interface.HasDescriptions.Descriptions_list
 
Nested classes inherited from class org.biomage.Interface.HasPropertySets
org.biomage.Interface.HasPropertySets.PropertySets_list
 
Field Summary
private  org.biomage.Measurement.DistanceUnit distanceUnit
          The units the fiducial is measured in.
private  org.biomage.Description.OntologyEntry fiducialType
          A descriptive string that indicates the type of a fiducial (e.g.
private  org.biomage.DesignElement.Position position
          The position, relative to the upper left corner, of the fiducial
 
Fields inherited from class org.biomage.Common.Describable
 
Fields inherited from class org.biomage.Common.Extendable
 
Constructor Summary
Fiducial()
          Default constructor.
Fiducial(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 org.biomage.Measurement.DistanceUnit getDistanceUnit()
          Get method for distanceUnit
 org.biomage.Description.OntologyEntry getFiducialType()
          Get method for fiducialType
 org.biomage.DesignElement.Position getPosition()
          Get method for position
 void setDistanceUnit(org.biomage.Measurement.DistanceUnit distanceUnit)
          Set method for distanceUnit
 void setFiducialType(org.biomage.Description.OntologyEntry fiducialType)
          Set method for fiducialType
 void setPosition(org.biomage.DesignElement.Position position)
          Set method for position
 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.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

distanceUnit

private org.biomage.Measurement.DistanceUnit distanceUnit
The units the fiducial is measured in.


fiducialType

private org.biomage.Description.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).


position

private org.biomage.DesignElement.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.


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.


setDistanceUnit

public void setDistanceUnit(org.biomage.Measurement.DistanceUnit distanceUnit)
Set method for distanceUnit

Specified by:
setDistanceUnit in interface org.biomage.Interface.HasDistanceUnit

getDistanceUnit

public org.biomage.Measurement.DistanceUnit getDistanceUnit()
Get method for distanceUnit

Specified by:
getDistanceUnit in interface org.biomage.Interface.HasDistanceUnit

setFiducialType

public void setFiducialType(org.biomage.Description.OntologyEntry fiducialType)
Set method for fiducialType

Specified by:
setFiducialType in interface org.biomage.Interface.HasFiducialType

getFiducialType

public org.biomage.Description.OntologyEntry getFiducialType()
Get method for fiducialType

Specified by:
getFiducialType in interface org.biomage.Interface.HasFiducialType

setPosition

public void setPosition(org.biomage.DesignElement.Position position)
Set method for position

Specified by:
setPosition in interface org.biomage.Interface.HasPosition

getPosition

public org.biomage.DesignElement.Position getPosition()
Get method for position

Specified by:
getPosition in interface org.biomage.Interface.HasPosition