Docjar: A Java Source and Docuemnt Enginecom.*    java.*    javax.*    org.*    all    new    plug-in

Quick Search    Search Deep

org.biomage.Array
Class FeatureDefect  view FeatureDefect download FeatureDefect.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.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

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.


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.


feature

private org.biomage.DesignElement.Feature feature
The feature that was manufactured defectively.


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.


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.


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.


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.


setPositionDelta

public void setPositionDelta(PositionDelta positionDelta)
Set method for positionDelta

Specified by:
setPositionDelta in interface org.biomage.Interface.HasPositionDelta

getPositionDelta

public PositionDelta getPositionDelta()
Get method for positionDelta

Specified by:
getPositionDelta in interface org.biomage.Interface.HasPositionDelta

setFeature

public void setFeature(org.biomage.DesignElement.Feature feature)
Set method for feature

Specified by:
setFeature in interface org.biomage.Interface.HasFeature

getFeature

public org.biomage.DesignElement.Feature getFeature()
Get method for feature

Specified by:
getFeature in interface org.biomage.Interface.HasFeature

setDefectType

public void setDefectType(org.biomage.Description.OntologyEntry defectType)
Set method for defectType

Specified by:
setDefectType in interface org.biomage.Interface.HasDefectType

getDefectType

public org.biomage.Description.OntologyEntry getDefectType()
Get method for defectType

Specified by:
getDefectType in interface org.biomage.Interface.HasDefectType