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org.biomage.Array
Class Fiducial  

java.lang.Object
  org.biomage.Common.Extendable
      org.biomage.Common.Describable
          org.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

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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.

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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.

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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).

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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.

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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.

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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.

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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.

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setDistanceUnit

public void setDistanceUnit(org.biomage.Measurement.DistanceUnit distanceUnit)

Set method for distanceUnit

Specified by:

setDistanceUnit in interface org.biomage.Interface.HasDistanceUnit

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getDistanceUnit

public org.biomage.Measurement.DistanceUnit getDistanceUnit()

Get method for distanceUnit

Specified by:

getDistanceUnit in interface org.biomage.Interface.HasDistanceUnit

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setFiducialType

public void setFiducialType(org.biomage.Description.OntologyEntry fiducialType)

Set method for fiducialType

Specified by:

setFiducialType in interface org.biomage.Interface.HasFiducialType

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getFiducialType

public org.biomage.Description.OntologyEntry getFiducialType()

Get method for fiducialType

Specified by:

getFiducialType in interface org.biomage.Interface.HasFiducialType

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setPosition

public void setPosition(org.biomage.DesignElement.Position position)

Set method for position

Specified by:

setPosition in interface org.biomage.Interface.HasPosition

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getPosition

public org.biomage.DesignElement.Position getPosition()

Get method for position

Specified by:

getPosition in interface org.biomage.Interface.HasPosition

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ Array overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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