org.biomage.Array
Class FeatureDefect

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Array.FeatureDefect

All Implemented Interfaces:

HasDefectType, HasFeature, HasPositionDelta, HasPropertySets, java.io.Serializable

public class FeatureDefect

extends Extendable

implements java.io.Serializable, HasPositionDelta, HasFeature, HasDefectType

Stores the defect information for a feature.

See Also:

Serialized Form

Nested Class Summary

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

HasPropertySets.PropertySets_list

Field Summary

protected OntologyEntry	defectType Indicates the type of defect (e.g.
protected Feature	feature The feature that was manufactured defectively.
protected PositionDelta	positionDelta How the feature deviates in position from the ArrayDesign.

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

FeatureDefect()
Default constructor.

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

Method Summary

OntologyEntry	getDefectType() Get method for defectType
Feature	getFeature() Get method for feature
PositionDelta	getPositionDelta() Get method for positionDelta
void	setDefectType(OntologyEntry defectType) Set method for defectType
void	setFeature(Feature feature) Set method for feature
void	setPositionDelta(PositionDelta positionDelta) Set method for positionDelta
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.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

defectType

protected OntologyEntry defectType

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

positionDelta

protected PositionDelta positionDelta

How the feature deviates in position from the ArrayDesign.

feature

protected Feature feature

The feature that was manufactured defectively.

Constructor Detail

FeatureDefect

public FeatureDefect()

Default constructor.

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.

Overrides:

writeMAGEML in class Extendable

java.io.IOException

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 Extendable

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 Extendable

java.io.IOException

setDefectType

public void setDefectType(OntologyEntry defectType)

Set method for defectType

Specified by:

setDefectType in interface HasDefectType

getDefectType

public OntologyEntry getDefectType()

Get method for defectType

Specified by:

getDefectType in interface HasDefectType

Returns:

value of the attribute

setPositionDelta

public void setPositionDelta(PositionDelta positionDelta)

Set method for positionDelta

Specified by:

setPositionDelta in interface HasPositionDelta

getPositionDelta

public PositionDelta getPositionDelta()

Get method for positionDelta

Specified by:

getPositionDelta in interface HasPositionDelta

Returns:

value of the attribute

setFeature

public void setFeature(Feature feature)

Set method for feature

Specified by:

setFeature in interface HasFeature

getFeature

public Feature getFeature()

Get method for feature

Specified by:

getFeature in interface HasFeature

Returns:

value of the attribute