org.biomage.Array
Class Array

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Common.Identifiable
              extended by org.biomage.Array.Array
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasArrayDesign, HasArrayGroup, HasArrayManufactureDeviations, HasAuditTrail, HasDescriptions, HasInformation, HasPropertySets, HasSecurity

public class Array
extends Identifiable
implements java.io.Serializable, HasArrayDesign, HasArrayGroup, HasInformation, HasArrayManufactureDeviations

The physical substrate along with its features and their annotation

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasArrayManufactureDeviations
HasArrayManufactureDeviations.ArrayManufactureDeviations_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
protected  ArrayDesign arrayDesign
          The association of a physical array with its array design.
protected  ArrayGroup arrayGroup
          Association between an ArrayGroup and its Arrays, typically the ArrayGroup will represent a slide and the Arrays will be the manufactured so that they may be hybridized separately on that slide.
protected  java.util.List arrayManufactureDeviations
          Association to classes to describe deviations from the ArrayDesign.
protected  ArrayManufacture information
          Association between the manufactured array and the information on that manufacture.
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
Array()
          Default constructor.
Array(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToArrayManufactureDeviations(ArrayManufactureDeviation arrayManufactureDeviation)
          Method to add ArrayManufactureDeviation to ArrayManufactureDeviations_list
 void addToArrayManufactureDeviations(int position, ArrayManufactureDeviation arrayManufactureDeviation)
          Method to add ArrayManufactureDeviation at position to ArrayManufactureDeviations_list
 boolean emptyMAGEobject()
           
 ArrayDesign getArrayDesign()
          Get method for arrayDesign
 ArrayGroup getArrayGroup()
          Get method for arrayGroup
 java.lang.String getArrayIdentifier()
          Get method for arrayIdentifier
 HasArrayManufactureDeviations.ArrayManufactureDeviations_list getArrayManufactureDeviations()
          Get method for arrayManufactureDeviations
 java.lang.Float getArrayXOrigin()
          Get method for arrayXOrigin
 java.lang.Float getArrayYOrigin()
          Get method for arrayYOrigin
 ArrayManufactureDeviation getFromArrayManufactureDeviations(int position)
          Method to get ArrayManufactureDeviation from ArrayManufactureDeviations_list
 ArrayManufacture getInformation()
          Get method for information
 java.lang.String getModelClassName()
           
 java.lang.String getOriginRelativeTo()
          Get method for originRelativeTo
 void removeElementAtFromArrayManufactureDeviations(int position)
          Method to remove by position from ArrayManufactureDeviations_list
 void removeFromArrayManufactureDeviations(ArrayManufactureDeviation arrayManufactureDeviation)
          Method to remove first ArrayManufactureDeviation from ArrayManufactureDeviations_list
 void setArrayDesign(ArrayDesign arrayDesign)
          Set method for arrayDesign
 void setArrayGroup(ArrayGroup arrayGroup)
          Set method for arrayGroup
 void setArrayIdentifier(java.lang.String arrayIdentifier)
          Set method for arrayIdentifier
 void setArrayManufactureDeviations(HasArrayManufactureDeviations.ArrayManufactureDeviations_list arrayManufactureDeviations)
          Set method for arrayManufactureDeviations
 void setArrayXOrigin(java.lang.Float arrayXOrigin)
          Set method for arrayXOrigin
 void setArrayYOrigin(java.lang.Float arrayYOrigin)
          Set method for arrayYOrigin
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setInformation(ArrayManufacture information)
          Set method for information
 void setOriginRelativeTo(java.lang.String originRelativeTo)
          Set method for originRelativeTo
 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.Identifiable
getIdentifier, getName, setIdentifier, setName, toString
 
Methods inherited from class org.biomage.Common.Describable
addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity
 
Methods inherited from class org.biomage.Common.Extendable
addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

arrayDesign

protected ArrayDesign arrayDesign
The association of a physical array with its array design.


information

protected ArrayManufacture information
Association between the manufactured array and the information on that manufacture.


arrayGroup

protected ArrayGroup arrayGroup
Association between an ArrayGroup and its Arrays, typically the ArrayGroup will represent a slide and the Arrays will be the manufactured so that they may be hybridized separately on that slide.


arrayManufactureDeviations

protected java.util.List arrayManufactureDeviations
Association to classes to describe deviations from the ArrayDesign.

Constructor Detail

Array

public Array()
Default constructor.


Array

public Array(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

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class Identifiable

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 Identifiable
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 Identifiable
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 Identifiable
Throws:
java.io.IOException

setArrayIdentifier

public void setArrayIdentifier(java.lang.String arrayIdentifier)
Set method for arrayIdentifier

Parameters:
value - to set

getArrayIdentifier

public java.lang.String getArrayIdentifier()
Get method for arrayIdentifier

Returns:
value of the attribute

setArrayXOrigin

public void setArrayXOrigin(java.lang.Float arrayXOrigin)
Set method for arrayXOrigin

Parameters:
value - to set

getArrayXOrigin

public java.lang.Float getArrayXOrigin()
Get method for arrayXOrigin

Returns:
value of the attribute

setArrayYOrigin

public void setArrayYOrigin(java.lang.Float arrayYOrigin)
Set method for arrayYOrigin

Parameters:
value - to set

getArrayYOrigin

public java.lang.Float getArrayYOrigin()
Get method for arrayYOrigin

Returns:
value of the attribute

setOriginRelativeTo

public void setOriginRelativeTo(java.lang.String originRelativeTo)
Set method for originRelativeTo

Parameters:
value - to set

getOriginRelativeTo

public java.lang.String getOriginRelativeTo()
Get method for originRelativeTo

Returns:
value of the attribute

getModelClassName

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

setArrayDesign

public void setArrayDesign(ArrayDesign arrayDesign)
Set method for arrayDesign

Specified by:
setArrayDesign in interface HasArrayDesign
Parameters:
value - to set

getArrayDesign

public ArrayDesign getArrayDesign()
Get method for arrayDesign

Specified by:
getArrayDesign in interface HasArrayDesign
Returns:
value of the attribute

setInformation

public void setInformation(ArrayManufacture information)
Set method for information

Specified by:
setInformation in interface HasInformation
Parameters:
value - to set

getInformation

public ArrayManufacture getInformation()
Get method for information

Specified by:
getInformation in interface HasInformation
Returns:
value of the attribute

setArrayGroup

public void setArrayGroup(ArrayGroup arrayGroup)
Set method for arrayGroup

Specified by:
setArrayGroup in interface HasArrayGroup
Parameters:
value - to set

getArrayGroup

public ArrayGroup getArrayGroup()
Get method for arrayGroup

Specified by:
getArrayGroup in interface HasArrayGroup
Returns:
value of the attribute

setArrayManufactureDeviations

public void setArrayManufactureDeviations(HasArrayManufactureDeviations.ArrayManufactureDeviations_list arrayManufactureDeviations)
Set method for arrayManufactureDeviations

Specified by:
setArrayManufactureDeviations in interface HasArrayManufactureDeviations
Parameters:
value - to set

getArrayManufactureDeviations

public HasArrayManufactureDeviations.ArrayManufactureDeviations_list getArrayManufactureDeviations()
Get method for arrayManufactureDeviations

Specified by:
getArrayManufactureDeviations in interface HasArrayManufactureDeviations
Returns:
value of the attribute

addToArrayManufactureDeviations

public void addToArrayManufactureDeviations(ArrayManufactureDeviation arrayManufactureDeviation)
Method to add ArrayManufactureDeviation to ArrayManufactureDeviations_list

Specified by:
addToArrayManufactureDeviations in interface HasArrayManufactureDeviations

addToArrayManufactureDeviations

public void addToArrayManufactureDeviations(int position,
                                            ArrayManufactureDeviation arrayManufactureDeviation)
Method to add ArrayManufactureDeviation at position to ArrayManufactureDeviations_list

Specified by:
addToArrayManufactureDeviations in interface HasArrayManufactureDeviations

getFromArrayManufactureDeviations

public ArrayManufactureDeviation getFromArrayManufactureDeviations(int position)
Method to get ArrayManufactureDeviation from ArrayManufactureDeviations_list

Specified by:
getFromArrayManufactureDeviations in interface HasArrayManufactureDeviations

removeElementAtFromArrayManufactureDeviations

public void removeElementAtFromArrayManufactureDeviations(int position)
Method to remove by position from ArrayManufactureDeviations_list

Specified by:
removeElementAtFromArrayManufactureDeviations in interface HasArrayManufactureDeviations

removeFromArrayManufactureDeviations

public void removeFromArrayManufactureDeviations(ArrayManufactureDeviation arrayManufactureDeviation)
Method to remove first ArrayManufactureDeviation from ArrayManufactureDeviations_list

Specified by:
removeFromArrayManufactureDeviations in interface HasArrayManufactureDeviations