org.biomage.Array
Class Fiducial

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

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/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface 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
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
Fiducial()
          Default constructor.
Fiducial(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 boolean emptyMAGEobject()
           
 DistanceUnit getDistanceUnit()
          Get method for distanceUnit
 OntologyEntry getFiducialType()
          Get method for fiducialType
 java.lang.String getModelClassName()
           
 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, setAttributes, setAuditTrail, setDescriptions, setSecurity
 
Methods inherited from class org.biomage.Common.Extendable
addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId, toString
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, 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

Parameters:
atts: - the attribute list.
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
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

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
Throws:
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
Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class Describable

setFiducialType

public void setFiducialType(OntologyEntry fiducialType)
Set method for fiducialType

Specified by:
setFiducialType in interface HasFiducialType
Parameters:
value - to set

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
Parameters:
value - to set

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
Parameters:
value - to set

getPosition

public Position getPosition()
Get method for position

Specified by:
getPosition in interface HasPosition
Returns:
value of the attribute