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org.biomage.Array
Class FeatureDefect  

java.lang.Object
  org.biomage.Common.Extendable
      org.biomage.Array.FeatureDefect

All Implemented Interfaces:

org.biomage.Interface.HasDefectType, org.biomage.Interface.HasFeature, org.biomage.Interface.HasPositionDelta, org.biomage.Interface.HasPropertySets, java.io.Serializable

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public class FeatureDefect

extends org.biomage.Common.Extendable

implements java.io.Serializable, org.biomage.Interface.HasPositionDelta, org.biomage.Interface.HasFeature, org.biomage.Interface.HasDefectType

Stores the defect information for a feature.

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Nested Class Summary

 

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

org.biomage.Interface.HasPropertySets.PropertySets_list

 

Field Summary
private  org.biomage.Description.OntologyEntry	defectType           Indicates the type of defect (e.g.
private  org.biomage.DesignElement.Feature	feature           The feature that was manufactured defectively.
private  PositionDelta	positionDelta           How the feature deviates in position from the ArrayDesign.

 

Fields inherited from class org.biomage.Common.Extendable

 

Constructor Summary

FeatureDefect()           Default constructor.

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

 

Method Summary
org.biomage.Description.OntologyEntry	getDefectType()           Get method for defectType
org.biomage.DesignElement.Feature	getFeature()           Get method for feature
PositionDelta	getPositionDelta()           Get method for positionDelta
void	setDefectType(org.biomage.Description.OntologyEntry defectType)           Set method for defectType
void	setFeature(org.biomage.DesignElement.Feature feature)           Set method for feature
void	setPositionDelta(PositionDelta positionDelta)           Set method for positionDelta
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.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

positionDelta

private PositionDelta positionDelta

How the feature deviates in position from the ArrayDesign.

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feature

private org.biomage.DesignElement.Feature feature

The feature that was manufactured defectively.

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defectType

private org.biomage.Description.OntologyEntry defectType

Indicates the type of defect (e.g. a missing feature or a moved feature).

Constructor Detail

FeatureDefect

public FeatureDefect()

Default constructor.

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FeatureDefect

public FeatureDefect(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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setPositionDelta

public void setPositionDelta(PositionDelta positionDelta)

Set method for positionDelta

Specified by:

setPositionDelta in interface org.biomage.Interface.HasPositionDelta

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getPositionDelta

public PositionDelta getPositionDelta()

Get method for positionDelta

Specified by:

getPositionDelta in interface org.biomage.Interface.HasPositionDelta

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setFeature

public void setFeature(org.biomage.DesignElement.Feature feature)

Set method for feature

Specified by:

setFeature in interface org.biomage.Interface.HasFeature

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getFeature

public org.biomage.DesignElement.Feature getFeature()

Get method for feature

Specified by:

getFeature in interface org.biomage.Interface.HasFeature

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setDefectType

public void setDefectType(org.biomage.Description.OntologyEntry defectType)

Set method for defectType

Specified by:

setDefectType in interface org.biomage.Interface.HasDefectType

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getDefectType

public org.biomage.Description.OntologyEntry getDefectType()

Get method for defectType

Specified by:

getDefectType in interface org.biomage.Interface.HasDefectType

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