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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Array.Fiducial
public class Fiducial
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 |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail |
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HasAuditTrail.AuditTrail_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions |
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HasDescriptions.Descriptions_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets |
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HasPropertySets.PropertySets_list |
Field Summary | |
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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 |
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security |
Fields inherited from class org.biomage.Common.Extendable |
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editable, id, securedElementId |
Constructor Summary | |
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Fiducial()
Default constructor. |
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Fiducial(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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boolean |
emptyMAGEobject()
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DistanceUnit |
getDistanceUnit()
Get method for distanceUnit |
OntologyEntry |
getFiducialType()
Get method for fiducialType |
java.lang.String |
getModelClassName()
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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 |
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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 |
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addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId, toString |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected OntologyEntry fiducialType
protected DistanceUnit distanceUnit
protected Position position
Constructor Detail |
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public Fiducial()
public Fiducial(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
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public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class Describable
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Describable
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Describable
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class Describable
public void setFiducialType(OntologyEntry fiducialType)
setFiducialType
in interface HasFiducialType
value
- to setpublic OntologyEntry getFiducialType()
getFiducialType
in interface HasFiducialType
public void setDistanceUnit(DistanceUnit distanceUnit)
setDistanceUnit
in interface HasDistanceUnit
value
- to setpublic DistanceUnit getDistanceUnit()
getDistanceUnit
in interface HasDistanceUnit
public void setPosition(Position position)
setPosition
in interface HasPosition
value
- to setpublic Position getPosition()
getPosition
in interface HasPosition
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