org.biomage.Array
Class Array

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

All Implemented Interfaces:

HasArrayDesign, HasArrayGroup, HasArrayManufactureDeviations, HasAuditTrail, HasDescriptions, HasInformation, HasPropertySets, HasSecurity, java.io.Serializable

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 inherited from class org.biomage.Interface.HasArrayManufactureDeviations

HasArrayManufactureDeviations.ArrayManufactureDeviations_list

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

HasAuditTrail.AuditTrail_list

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

HasDescriptions.Descriptions_list

Nested classes inherited from class 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 HasArrayManufactureDeviations.ArrayManufactureDeviations_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

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

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
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
float	getArrayXOrigin() Get method for arrayXOrigin
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	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(float arrayXOrigin) Set method for arrayXOrigin
void	setArrayYOrigin(float arrayYOrigin) Set method for arrayYOrigin
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

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, 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

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 HasArrayManufactureDeviations.ArrayManufactureDeviations_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

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 Identifiable

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 Identifiable

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

java.io.IOException

setArrayIdentifier

public void setArrayIdentifier(java.lang.String arrayIdentifier)

Set method for arrayIdentifier

getArrayIdentifier

public java.lang.String getArrayIdentifier()

Get method for arrayIdentifier

Returns:

value of the attribute

setArrayXOrigin

public void setArrayXOrigin(float arrayXOrigin)

Set method for arrayXOrigin

getArrayXOrigin

public float getArrayXOrigin()

Get method for arrayXOrigin

Returns:

value of the attribute

setArrayYOrigin

public void setArrayYOrigin(float arrayYOrigin)

Set method for arrayYOrigin

getArrayYOrigin

public float getArrayYOrigin()

Get method for arrayYOrigin

Returns:

value of the attribute

setOriginRelativeTo

public void setOriginRelativeTo(java.lang.String originRelativeTo)

Set method for originRelativeTo

getOriginRelativeTo

public java.lang.String getOriginRelativeTo()

Get method for originRelativeTo

Returns:

value of the attribute

setArrayDesign

public void setArrayDesign(ArrayDesign arrayDesign)

Set method for arrayDesign

Specified by:

setArrayDesign in interface HasArrayDesign

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

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

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

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