org.biomage.Array
Class ArrayGroup

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

All Implemented Interfaces:

HasArrays, HasAuditTrail, HasDescriptions, HasDistanceUnit, HasFiducials, HasPropertySets, HasSecurity, HasSubstrateType, java.io.Serializable

public class ArrayGroup

extends Identifiable

implements java.io.Serializable, HasArrays, HasFiducials, HasDistanceUnit, HasSubstrateType

An array package is a physical platform that contains one or more arrays that are separately addressable (e.g. several arrays that can be hybridized on a single microscope slide) or a virtual grouping together of arrays. The array package that has been manufactured has information about where certain artifacts about the array are located for scanning and feature extraction purposes.

See Also:

Serialized Form

Nested Class Summary

class

ArrayGroup.OrientationMarkPosition Inner class for the enumeration values that the attribute orientationMarkPosition can assume.

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

HasArrays.Arrays_list

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

HasFiducials.Fiducials_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 HasArrays.Arrays_list	arrays 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 DistanceUnit	distanceUnit The unit of the measurement attributes.
protected HasFiducials.Fiducials_list	fiducials Association to the marks on the Array for alignment for the scanner.
protected OntologyEntry	substrateType Commonly, arrays will be spotted on 1x3 glass microscope slides but there is nothing that says this must be the case.

Fields inherited from class org.biomage.Common.Describable

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

Constructor Summary

ArrayGroup()
Default constructor.

ArrayGroup(org.xml.sax.Attributes atts)
Attribute constructor.

Method Summary

void	addToArrays(Array array) Method to add Array to Arrays_list
void	addToArrays(int position, Array array) Method to add Array at position to Arrays_list
void	addToFiducials(Fiducial fiducial) Method to add Fiducial to Fiducials_list
void	addToFiducials(int position, Fiducial fiducial) Method to add Fiducial at position to Fiducials_list
HasArrays.Arrays_list	getArrays() Get method for arrays
float	getArraySpacingX() Get method for arraySpacingX
float	getArraySpacingY() Get method for arraySpacingY
java.lang.String	getBarcode() Get method for barcode
DistanceUnit	getDistanceUnit() Get method for distanceUnit
HasFiducials.Fiducials_list	getFiducials() Get method for fiducials
Array	getFromArrays(int position) Method to get Array from Arrays_list
Fiducial	getFromFiducials(int position) Method to get Fiducial from Fiducials_list
float	getLength() Get method for length
java.lang.String	getNameByValueOrientationMarkPosition(int val) For OrientationMarkPosition get the Name of the Enumeration type by passing a Value to it.
java.lang.String	getNameOrientationMarkPosition() Return the current name of the Enumeration type of OrientationMarkPosition.
int	getNumArrays() Get method for numArrays
java.lang.String	getOrientationMark() Get method for orientationMark
ArrayGroup.OrientationMarkPosition	getOrientationMarkPosition() Get method for orientationMarkPosition
OntologyEntry	getSubstrateType() Get method for substrateType
int	getValueByNameOrientationMarkPosition(java.lang.String name) For OrientationMarkPosition get the Value of the Enumeration type by passing a Name to it.
int	getValueOrientationMarkPosition() Return the currrent value of the Enumeration type of OrientationMarkPosition.
float	getWidth() Get method for width
void	removeElementAtFromArrays(int position) Method to remove by position from Arrays_list
void	removeElementAtFromFiducials(int position) Method to remove by position from Fiducials_list
void	removeFromArrays(Array array) Method to remove first Array from Arrays_list
void	removeFromFiducials(Fiducial fiducial) Method to remove first Fiducial from Fiducials_list
void	setArrays(HasArrays.Arrays_list arrays) Set method for arrays
void	setArraySpacingX(float arraySpacingX) Set method for arraySpacingX
void	setArraySpacingY(float arraySpacingY) Set method for arraySpacingY
void	setBarcode(java.lang.String barcode) Set method for barcode
void	setDistanceUnit(DistanceUnit distanceUnit) Set method for distanceUnit
void	setFiducials(HasFiducials.Fiducials_list fiducials) Set method for fiducials
void	setLength(float length) Set method for length
java.lang.String	setNameByValueOrientationMarkPosition(int val) For OrientationMarkPosition set the Name of the Enumeration type by passing a value (int)
void	setNumArrays(int numArrays) Set method for numArrays
void	setOrientationMark(java.lang.String orientationMark) Set method for orientationMark
void	setOrientationMarkPosition(ArrayGroup.OrientationMarkPosition orientationMarkPosition) Set method for orientationMarkPosition
void	setSubstrateType(OntologyEntry substrateType) Set method for substrateType
int	setValueByNameOrientationMarkPosition(java.lang.String name) For OrientationMarkPosition set the Value of the Enumeration type by passing a Name to it.
void	setWidth(float width) Set method for width
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

fiducials

protected HasFiducials.Fiducials_list fiducials

Association to the marks on the Array for alignment for the scanner.

arrays

protected HasArrays.Arrays_list arrays

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.

substrateType

protected OntologyEntry substrateType

Commonly, arrays will be spotted on 1x3 glass microscope slides but there is nothing that says this must be the case. This association is for scanners to inform them on the possible different formats of slides that can contain arrays.

distanceUnit

protected DistanceUnit distanceUnit

The unit of the measurement attributes.

Constructor Detail

ArrayGroup

public ArrayGroup()

Default constructor.

ArrayGroup

public ArrayGroup(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

setBarcode

public void setBarcode(java.lang.String barcode)

Set method for barcode

getBarcode

public java.lang.String getBarcode()

Get method for barcode

Returns:

value of the attribute

setArraySpacingX

public void setArraySpacingX(float arraySpacingX)

Set method for arraySpacingX

getArraySpacingX

public float getArraySpacingX()

Get method for arraySpacingX

Returns:

value of the attribute

setArraySpacingY

public void setArraySpacingY(float arraySpacingY)

Set method for arraySpacingY

getArraySpacingY

public float getArraySpacingY()

Get method for arraySpacingY

Returns:

value of the attribute

setNumArrays

public void setNumArrays(int numArrays)

Set method for numArrays

getNumArrays

public int getNumArrays()

Get method for numArrays

Returns:

value of the attribute

setOrientationMark

public void setOrientationMark(java.lang.String orientationMark)

Set method for orientationMark

getOrientationMark

public java.lang.String getOrientationMark()

Get method for orientationMark

Returns:

value of the attribute

setOrientationMarkPosition

public void setOrientationMarkPosition(ArrayGroup.OrientationMarkPosition orientationMarkPosition)

Set method for orientationMarkPosition

getOrientationMarkPosition

public ArrayGroup.OrientationMarkPosition getOrientationMarkPosition()

Get method for orientationMarkPosition

Returns:

value of the attribute

setNameByValueOrientationMarkPosition

public java.lang.String setNameByValueOrientationMarkPosition(int val)

For OrientationMarkPosition set the Name of the Enumeration type by passing a value (int)

setValueByNameOrientationMarkPosition

public int setValueByNameOrientationMarkPosition(java.lang.String name)

For OrientationMarkPosition set the Value of the Enumeration type by passing a Name to it.

getNameByValueOrientationMarkPosition

public java.lang.String getNameByValueOrientationMarkPosition(int val)

For OrientationMarkPosition get the Name of the Enumeration type by passing a Value to it.

getValueByNameOrientationMarkPosition

public int getValueByNameOrientationMarkPosition(java.lang.String name)

For OrientationMarkPosition get the Value of the Enumeration type by passing a Name to it.

getNameOrientationMarkPosition

public java.lang.String getNameOrientationMarkPosition()

Return the current name of the Enumeration type of OrientationMarkPosition.

getValueOrientationMarkPosition

public int getValueOrientationMarkPosition()

Return the currrent value of the Enumeration type of OrientationMarkPosition.

setWidth

public void setWidth(float width)

Set method for width

getWidth

public float getWidth()

Get method for width

Returns:

value of the attribute

setLength

public void setLength(float length)

Set method for length

getLength

public float getLength()

Get method for length

Returns:

value of the attribute

setFiducials

public void setFiducials(HasFiducials.Fiducials_list fiducials)

Set method for fiducials

Specified by:

setFiducials in interface HasFiducials

getFiducials

public HasFiducials.Fiducials_list getFiducials()

Get method for fiducials

Specified by:

getFiducials in interface HasFiducials

Returns:

value of the attribute

addToFiducials

public void addToFiducials(Fiducial fiducial)

Method to add Fiducial to Fiducials_list

Specified by:

addToFiducials in interface HasFiducials

addToFiducials

public void addToFiducials(int position,
                           Fiducial fiducial)

Method to add Fiducial at position to Fiducials_list

Specified by:

addToFiducials in interface HasFiducials

getFromFiducials

public Fiducial getFromFiducials(int position)

Method to get Fiducial from Fiducials_list

Specified by:

getFromFiducials in interface HasFiducials

removeElementAtFromFiducials

public void removeElementAtFromFiducials(int position)

Method to remove by position from Fiducials_list

Specified by:

removeElementAtFromFiducials in interface HasFiducials

removeFromFiducials

public void removeFromFiducials(Fiducial fiducial)

Method to remove first Fiducial from Fiducials_list

Specified by:

removeFromFiducials in interface HasFiducials

setArrays

public void setArrays(HasArrays.Arrays_list arrays)

Set method for arrays

Specified by:

setArrays in interface HasArrays

getArrays

public HasArrays.Arrays_list getArrays()

Get method for arrays

Specified by:

getArrays in interface HasArrays

Returns:

value of the attribute

addToArrays

public void addToArrays(Array array)

Method to add Array to Arrays_list

Specified by:

addToArrays in interface HasArrays

addToArrays

public void addToArrays(int position,
                        Array array)

Method to add Array at position to Arrays_list

Specified by:

addToArrays in interface HasArrays

getFromArrays

public Array getFromArrays(int position)

Method to get Array from Arrays_list

Specified by:

getFromArrays in interface HasArrays

removeElementAtFromArrays

public void removeElementAtFromArrays(int position)

Method to remove by position from Arrays_list

Specified by:

removeElementAtFromArrays in interface HasArrays

removeFromArrays

public void removeFromArrays(Array array)

Method to remove first Array from Arrays_list

Specified by:

removeFromArrays in interface HasArrays

setSubstrateType

public void setSubstrateType(OntologyEntry substrateType)

Set method for substrateType

Specified by:

setSubstrateType in interface HasSubstrateType

getSubstrateType

public OntologyEntry getSubstrateType()

Get method for substrateType

Specified by:

getSubstrateType in interface HasSubstrateType

Returns:

value of the attribute

setDistanceUnit

public void setDistanceUnit(DistanceUnit distanceUnit)

Set method for distanceUnit

Specified by:

setDistanceUnit in interface HasDistanceUnit

getDistanceUnit

public DistanceUnit getDistanceUnit()

Get method for distanceUnit

Specified by:

getDistanceUnit in interface HasDistanceUnit

Returns:

value of the attribute