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

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Array.ArrayManufactureDeviation
All Implemented Interfaces:
org.biomage.Interface.HasAdjustments, org.biomage.Interface.HasFeatureDefects, org.biomage.Interface.HasPropertySets, java.io.Serializable

public class ArrayManufactureDeviation
extends org.biomage.Common.Extendable
implements java.io.Serializable, org.biomage.Interface.HasFeatureDefects, org.biomage.Interface.HasAdjustments

Stores information of the potential difference between an array design and arrays that have been manufactured using that design (e.g. a tip failed to print several spots).


Nested Class Summary
 
Nested classes inherited from class org.biomage.Interface.HasFeatureDefects
org.biomage.Interface.HasFeatureDefects.FeatureDefects_list
 
Nested classes inherited from class org.biomage.Interface.HasAdjustments
org.biomage.Interface.HasAdjustments.Adjustments_list
 
Nested classes inherited from class org.biomage.Interface.HasPropertySets
org.biomage.Interface.HasPropertySets.PropertySets_list
 
Field Summary
private  org.biomage.Interface.HasAdjustments.Adjustments_list adjustments
          Descriptions of how a Zone has been printed differently than specified in the ArrayDesign.
private  org.biomage.Interface.HasFeatureDefects.FeatureDefects_list featureDefects
          Description on features who are manufactured in a different location than specified in the ArrayDesign.
 
Fields inherited from class org.biomage.Common.Extendable
 
Constructor Summary
ArrayManufactureDeviation()
          Default constructor.
ArrayManufactureDeviation(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToAdjustments(int position, ZoneDefect zoneDefect)
          Method to add ZoneDefect at position to Adjustments_list
 void addToAdjustments(ZoneDefect zoneDefect)
          Method to add ZoneDefect to Adjustments_list
 void addToFeatureDefects(FeatureDefect featureDefect)
          Method to add FeatureDefect to FeatureDefects_list
 void addToFeatureDefects(int position, FeatureDefect featureDefect)
          Method to add FeatureDefect at position to FeatureDefects_list
 org.biomage.Interface.HasAdjustments.Adjustments_list getAdjustments()
          Get method for adjustments
 org.biomage.Interface.HasFeatureDefects.FeatureDefects_list getFeatureDefects()
          Get method for featureDefects
 ZoneDefect getFromAdjustments(int position)
          Method to get ZoneDefect from Adjustments_list
 FeatureDefect getFromFeatureDefects(int position)
          Method to get FeatureDefect from FeatureDefects_list
 void removeElementAtFromAdjustments(int position)
          Method to remove by position from Adjustments_list
 void removeElementAtFromFeatureDefects(int position)
          Method to remove by position from FeatureDefects_list
 void removeFromAdjustments(ZoneDefect zoneDefect)
          Method to remove first ZoneDefect from Adjustments_list
 void removeFromFeatureDefects(FeatureDefect featureDefect)
          Method to remove first FeatureDefect from FeatureDefects_list
 void setAdjustments(org.biomage.Interface.HasAdjustments.Adjustments_list adjustments)
          Set method for adjustments
 void setFeatureDefects(org.biomage.Interface.HasFeatureDefects.FeatureDefects_list featureDefects)
          Set method for featureDefects
 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

featureDefects

private org.biomage.Interface.HasFeatureDefects.FeatureDefects_list featureDefects
Description on features who are manufactured in a different location than specified in the ArrayDesign.


adjustments

private org.biomage.Interface.HasAdjustments.Adjustments_list adjustments
Descriptions of how a Zone has been printed differently than specified in the ArrayDesign.

Constructor Detail

ArrayManufactureDeviation

public ArrayManufactureDeviation()
Default constructor.


ArrayManufactureDeviation

public ArrayManufactureDeviation(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.


setFeatureDefects

public void setFeatureDefects(org.biomage.Interface.HasFeatureDefects.FeatureDefects_list featureDefects)
Set method for featureDefects

Specified by:
setFeatureDefects in interface org.biomage.Interface.HasFeatureDefects

getFeatureDefects

public org.biomage.Interface.HasFeatureDefects.FeatureDefects_list getFeatureDefects()
Get method for featureDefects

Specified by:
getFeatureDefects in interface org.biomage.Interface.HasFeatureDefects

addToFeatureDefects

public void addToFeatureDefects(FeatureDefect featureDefect)
Method to add FeatureDefect to FeatureDefects_list

Specified by:
addToFeatureDefects in interface org.biomage.Interface.HasFeatureDefects

addToFeatureDefects

public void addToFeatureDefects(int position,
                                FeatureDefect featureDefect)
Method to add FeatureDefect at position to FeatureDefects_list

Specified by:
addToFeatureDefects in interface org.biomage.Interface.HasFeatureDefects

getFromFeatureDefects

public FeatureDefect getFromFeatureDefects(int position)
Method to get FeatureDefect from FeatureDefects_list

Specified by:
getFromFeatureDefects in interface org.biomage.Interface.HasFeatureDefects

removeElementAtFromFeatureDefects

public void removeElementAtFromFeatureDefects(int position)
Method to remove by position from FeatureDefects_list

Specified by:
removeElementAtFromFeatureDefects in interface org.biomage.Interface.HasFeatureDefects

removeFromFeatureDefects

public void removeFromFeatureDefects(FeatureDefect featureDefect)
Method to remove first FeatureDefect from FeatureDefects_list

Specified by:
removeFromFeatureDefects in interface org.biomage.Interface.HasFeatureDefects

setAdjustments

public void setAdjustments(org.biomage.Interface.HasAdjustments.Adjustments_list adjustments)
Set method for adjustments

Specified by:
setAdjustments in interface org.biomage.Interface.HasAdjustments

getAdjustments

public org.biomage.Interface.HasAdjustments.Adjustments_list getAdjustments()
Get method for adjustments

Specified by:
getAdjustments in interface org.biomage.Interface.HasAdjustments

addToAdjustments

public void addToAdjustments(ZoneDefect zoneDefect)
Method to add ZoneDefect to Adjustments_list

Specified by:
addToAdjustments in interface org.biomage.Interface.HasAdjustments

addToAdjustments

public void addToAdjustments(int position,
                             ZoneDefect zoneDefect)
Method to add ZoneDefect at position to Adjustments_list

Specified by:
addToAdjustments in interface org.biomage.Interface.HasAdjustments

getFromAdjustments

public ZoneDefect getFromAdjustments(int position)
Method to get ZoneDefect from Adjustments_list

Specified by:
getFromAdjustments in interface org.biomage.Interface.HasAdjustments

removeElementAtFromAdjustments

public void removeElementAtFromAdjustments(int position)
Method to remove by position from Adjustments_list

Specified by:
removeElementAtFromAdjustments in interface org.biomage.Interface.HasAdjustments

removeFromAdjustments

public void removeFromAdjustments(ZoneDefect zoneDefect)
Method to remove first ZoneDefect from Adjustments_list

Specified by:
removeFromAdjustments in interface org.biomage.Interface.HasAdjustments