org.biomage.Array
Class ArrayManufactureDeviation

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

public class ArrayManufactureDeviation
extends Extendable
implements java.io.Serializable, HasFeatureDefects, 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).

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasFeatureDefects
HasFeatureDefects.FeatureDefects_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAdjustments
HasAdjustments.Adjustments_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  java.util.List adjustments
          Descriptions of how a Zone has been printed differently than specified in the ArrayDesign.
protected  java.util.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
editable, id, securedElementId
 
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
 boolean emptyMAGEobject()
           
 HasAdjustments.Adjustments_list getAdjustments()
          Get method for adjustments
 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
 java.lang.String getModelClassName()
           
 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(HasAdjustments.Adjustments_list adjustments)
          Set method for adjustments
 void setFeatureDefects(HasFeatureDefects.FeatureDefects_list featureDefects)
          Set method for featureDefects
 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, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setAttributes, setId, setIsEditable, setPropertySets, setSecuredElementId, toString
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

adjustments

protected java.util.List adjustments
Descriptions of how a Zone has been printed differently than specified in the ArrayDesign.


featureDefects

protected java.util.List featureDefects
Description on features who are manufactured in a different location 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

Parameters:
atts: - the attribute list.
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
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

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
Throws:
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
Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class Extendable

setAdjustments

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

Specified by:
setAdjustments in interface HasAdjustments
Parameters:
value - to set

getAdjustments

public HasAdjustments.Adjustments_list getAdjustments()
Get method for adjustments

Specified by:
getAdjustments in interface HasAdjustments
Returns:
value of the attribute

addToAdjustments

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

Specified by:
addToAdjustments in interface HasAdjustments

addToAdjustments

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

Specified by:
addToAdjustments in interface HasAdjustments

getFromAdjustments

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

Specified by:
getFromAdjustments in interface HasAdjustments

removeElementAtFromAdjustments

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

Specified by:
removeElementAtFromAdjustments in interface HasAdjustments

removeFromAdjustments

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

Specified by:
removeFromAdjustments in interface HasAdjustments

setFeatureDefects

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

Specified by:
setFeatureDefects in interface HasFeatureDefects
Parameters:
value - to set

getFeatureDefects

public HasFeatureDefects.FeatureDefects_list getFeatureDefects()
Get method for featureDefects

Specified by:
getFeatureDefects in interface HasFeatureDefects
Returns:
value of the attribute

addToFeatureDefects

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

Specified by:
addToFeatureDefects in interface HasFeatureDefects

addToFeatureDefects

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

Specified by:
addToFeatureDefects in interface HasFeatureDefects

getFromFeatureDefects

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

Specified by:
getFromFeatureDefects in interface HasFeatureDefects

removeElementAtFromFeatureDefects

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

Specified by:
removeElementAtFromFeatureDefects in interface HasFeatureDefects

removeFromFeatureDefects

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

Specified by:
removeFromFeatureDefects in interface HasFeatureDefects