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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:

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

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public class ArrayGroup

extends org.biomage.Common.Identifiable

implements java.io.Serializable, org.biomage.Interface.HasArrays, org.biomage.Interface.HasFiducials, org.biomage.Interface.HasDistanceUnit, org.biomage.Interface.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.

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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

org.biomage.Interface.HasArrays.Arrays_list

 

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

org.biomage.Interface.HasFiducials.Fiducials_list

 

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

org.biomage.Interface.HasAuditTrail.AuditTrail_list

 

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

org.biomage.Interface.HasDescriptions.Descriptions_list

 

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

org.biomage.Interface.HasPropertySets.PropertySets_list

 

Field Summary
private  org.biomage.Interface.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.
(package private)  float	arraySpacingX           If there exist more than one array on a slide or a chip, then the spacing between the arrays is useful so that scanning / feature extraction software can crop images representing 1 unique bioassay.
(package private)  float	arraySpacingY           If there exist more than one array on a slide or a chip, then the spacing between the arrays is useful so that scanning / feature extraction software can crop images representing 1 unique bioassay.
(package private)  java.lang.String	barcode           Identifier for the ArrayGroup.
private  org.biomage.Measurement.DistanceUnit	distanceUnit           The unit of the measurement attributes.
private  org.biomage.Interface.HasFiducials.Fiducials_list	fiducials           Association to the marks on the Array for alignment for the scanner.
(package private)  float	length           The length of the platform.
(package private)  int	numArrays           This attribute defines the number of arrays on a chip or a slide.
(package private)  java.lang.String	orientationMark           For a human to determine where the top left side of the array is, such as a barcode or frosted side of the glass, etc.
(package private)  ArrayGroup.OrientationMarkPosition	orientationMarkPosition           One of top, bottom, left or right.
private  org.biomage.Description.OntologyEntry	substrateType           Commonly, arrays will be spotted on 1x3 glass microscope slides but there is nothing that says this must be the case.
(package private)  float	width           The width of the platform

 

Fields inherited from class org.biomage.Common.Identifiable

 

Fields inherited from class org.biomage.Common.Describable

 

Fields inherited from class org.biomage.Common.Extendable

 

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
org.biomage.Interface.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
org.biomage.Measurement.DistanceUnit	getDistanceUnit()           Get method for distanceUnit
org.biomage.Interface.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
int	getNumArrays()           Get method for numArrays
java.lang.String	getOrientationMark()           Get method for orientationMark
ArrayGroup.OrientationMarkPosition	getOrientationMarkPosition()           Get method for orientationMarkPosition
org.biomage.Description.OntologyEntry	getSubstrateType()           Get method for substrateType
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(org.biomage.Interface.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(org.biomage.Measurement.DistanceUnit distanceUnit)           Set method for distanceUnit
void	setFiducials(org.biomage.Interface.HasFiducials.Fiducials_list fiducials)           Set method for fiducials
void	setLength(float length)           Set method for length
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(org.biomage.Description.OntologyEntry substrateType)           Set method for substrateType
void	setWidth(float width)           Set method for width
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.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

barcode

java.lang.String barcode

Identifier for the ArrayGroup.

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arraySpacingX

float arraySpacingX

If there exist more than one array on a slide or a chip, then the spacing between the arrays is useful so that scanning / feature extraction software can crop images representing 1 unique bioassay.

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arraySpacingY

float arraySpacingY

If there exist more than one array on a slide or a chip, then the spacing between the arrays is useful so that scanning / feature extraction software can crop images representing 1 unique bioassay.

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numArrays

int numArrays

This attribute defines the number of arrays on a chip or a slide.

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orientationMark

java.lang.String orientationMark

For a human to determine where the top left side of the array is, such as a barcode or frosted side of the glass, etc.

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orientationMarkPosition

ArrayGroup.OrientationMarkPosition orientationMarkPosition

One of top, bottom, left or right.

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width

float width

The width of the platform

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length

float length

The length of the platform.

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arrays

private org.biomage.Interface.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.

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fiducials

private org.biomage.Interface.HasFiducials.Fiducials_list fiducials

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

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distanceUnit

private org.biomage.Measurement.DistanceUnit distanceUnit

The unit of the measurement attributes.

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substrateType

private org.biomage.Description.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.

Constructor Detail

ArrayGroup

public ArrayGroup()

Default constructor.

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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.

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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.

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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.

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setBarcode

public void setBarcode(java.lang.String barcode)

Set method for barcode

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getBarcode

public java.lang.String getBarcode()

Get method for barcode

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setArraySpacingX

public void setArraySpacingX(float arraySpacingX)

Set method for arraySpacingX

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getArraySpacingX

public float getArraySpacingX()

Get method for arraySpacingX

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setArraySpacingY

public void setArraySpacingY(float arraySpacingY)

Set method for arraySpacingY

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getArraySpacingY

public float getArraySpacingY()

Get method for arraySpacingY

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setNumArrays

public void setNumArrays(int numArrays)

Set method for numArrays

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getNumArrays

public int getNumArrays()

Get method for numArrays

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setOrientationMark

public void setOrientationMark(java.lang.String orientationMark)

Set method for orientationMark

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getOrientationMark

public java.lang.String getOrientationMark()

Get method for orientationMark

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setOrientationMarkPosition

public void setOrientationMarkPosition(ArrayGroup.OrientationMarkPosition orientationMarkPosition)

Set method for orientationMarkPosition

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getOrientationMarkPosition

public ArrayGroup.OrientationMarkPosition getOrientationMarkPosition()

Get method for orientationMarkPosition

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setWidth

public void setWidth(float width)

Set method for width

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getWidth

public float getWidth()

Get method for width

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setLength

public void setLength(float length)

Set method for length

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getLength

public float getLength()

Get method for length

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setArrays

public void setArrays(org.biomage.Interface.HasArrays.Arrays_list arrays)

Set method for arrays

Specified by:

setArrays in interface org.biomage.Interface.HasArrays

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getArrays

public org.biomage.Interface.HasArrays.Arrays_list getArrays()

Get method for arrays

Specified by:

getArrays in interface org.biomage.Interface.HasArrays

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addToArrays

public void addToArrays(Array array)

Method to add Array to Arrays_list

Specified by:

addToArrays in interface org.biomage.Interface.HasArrays

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addToArrays

public void addToArrays(int position,
                        Array array)

Method to add Array at position to Arrays_list

Specified by:

addToArrays in interface org.biomage.Interface.HasArrays

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getFromArrays

public Array getFromArrays(int position)

Method to get Array from Arrays_list

Specified by:

getFromArrays in interface org.biomage.Interface.HasArrays

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removeElementAtFromArrays

public void removeElementAtFromArrays(int position)

Method to remove by position from Arrays_list

Specified by:

removeElementAtFromArrays in interface org.biomage.Interface.HasArrays

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removeFromArrays

public void removeFromArrays(Array array)

Method to remove first Array from Arrays_list

Specified by:

removeFromArrays in interface org.biomage.Interface.HasArrays

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setFiducials

public void setFiducials(org.biomage.Interface.HasFiducials.Fiducials_list fiducials)

Set method for fiducials

Specified by:

setFiducials in interface org.biomage.Interface.HasFiducials

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getFiducials

public org.biomage.Interface.HasFiducials.Fiducials_list getFiducials()

Get method for fiducials

Specified by:

getFiducials in interface org.biomage.Interface.HasFiducials

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addToFiducials

public void addToFiducials(Fiducial fiducial)

Method to add Fiducial to Fiducials_list

Specified by:

addToFiducials in interface org.biomage.Interface.HasFiducials

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addToFiducials

public void addToFiducials(int position,
                           Fiducial fiducial)

Method to add Fiducial at position to Fiducials_list

Specified by:

addToFiducials in interface org.biomage.Interface.HasFiducials

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getFromFiducials

public Fiducial getFromFiducials(int position)

Method to get Fiducial from Fiducials_list

Specified by:

getFromFiducials in interface org.biomage.Interface.HasFiducials

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removeElementAtFromFiducials

public void removeElementAtFromFiducials(int position)

Method to remove by position from Fiducials_list

Specified by:

removeElementAtFromFiducials in interface org.biomage.Interface.HasFiducials

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removeFromFiducials

public void removeFromFiducials(Fiducial fiducial)

Method to remove first Fiducial from Fiducials_list

Specified by:

removeFromFiducials in interface org.biomage.Interface.HasFiducials

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setDistanceUnit

public void setDistanceUnit(org.biomage.Measurement.DistanceUnit distanceUnit)

Set method for distanceUnit

Specified by:

setDistanceUnit in interface org.biomage.Interface.HasDistanceUnit

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getDistanceUnit

public org.biomage.Measurement.DistanceUnit getDistanceUnit()

Get method for distanceUnit

Specified by:

getDistanceUnit in interface org.biomage.Interface.HasDistanceUnit

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setSubstrateType

public void setSubstrateType(org.biomage.Description.OntologyEntry substrateType)

Set method for substrateType

Specified by:

setSubstrateType in interface org.biomage.Interface.HasSubstrateType

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getSubstrateType

public org.biomage.Description.OntologyEntry getSubstrateType()

Get method for substrateType

Specified by:

getSubstrateType in interface org.biomage.Interface.HasSubstrateType

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ Array overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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