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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:

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

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public class Array

extends org.biomage.Common.Identifiable

implements java.io.Serializable, org.biomage.Interface.HasArrayDesign, org.biomage.Interface.HasArrayGroup, org.biomage.Interface.HasInformation, org.biomage.Interface.HasArrayManufactureDeviations

The physical substrate along with its features and their annotation

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Nested Class Summary

 

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

org.biomage.Interface.HasArrayManufactureDeviations.ArrayManufactureDeviations_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.ArrayDesign.ArrayDesign	arrayDesign           The association of a physical array with its array design.
private  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.
(package private)  java.lang.String	arrayIdentifier           An identifying string, e.g.
private  org.biomage.Interface.HasArrayManufactureDeviations.ArrayManufactureDeviations_list	arrayManufactureDeviations           Association to classes to describe deviations from the ArrayDesign.
(package private)  float	arrayXOrigin           This can indicate the x position on a slide, chip, etc.
(package private)  float	arrayYOrigin           This can indicate the y position on a slide, chip, etc.
private  ArrayManufacture	information           Association between the manufactured array and the information on that manufacture.
(package private)  java.lang.String	originRelativeTo           What the array origin is relative to, e.g.

 

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

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
org.biomage.ArrayDesign.ArrayDesign	getArrayDesign()           Get method for arrayDesign
ArrayGroup	getArrayGroup()           Get method for arrayGroup
java.lang.String	getArrayIdentifier()           Get method for arrayIdentifier
org.biomage.Interface.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(org.biomage.ArrayDesign.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(org.biomage.Interface.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
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

arrayIdentifier

java.lang.String arrayIdentifier

An identifying string, e.g. a barcode.

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arrayXOrigin

float arrayXOrigin

This can indicate the x position on a slide, chip, etc. of the first Feature and is usually specified relative to the fiducial.

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arrayYOrigin

float arrayYOrigin

This can indicate the y position on a slide, chip, etc. of the first Feature and is usually specified relative to the fiducial.

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originRelativeTo

java.lang.String originRelativeTo

What the array origin is relative to, e.g. upper left corner, fiducial, etc.

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arrayDesign

private org.biomage.ArrayDesign.ArrayDesign arrayDesign

The association of a physical array with its array design.

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arrayGroup

private 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.

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information

private ArrayManufacture information

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

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arrayManufactureDeviations

private org.biomage.Interface.HasArrayManufactureDeviations.ArrayManufactureDeviations_list arrayManufactureDeviations

Association to classes to describe deviations from the ArrayDesign.

Constructor Detail

Array

public Array()

Default constructor.

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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.

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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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setArrayIdentifier

public void setArrayIdentifier(java.lang.String arrayIdentifier)

Set method for arrayIdentifier

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getArrayIdentifier

public java.lang.String getArrayIdentifier()

Get method for arrayIdentifier

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setArrayXOrigin

public void setArrayXOrigin(float arrayXOrigin)

Set method for arrayXOrigin

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getArrayXOrigin

public float getArrayXOrigin()

Get method for arrayXOrigin

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setArrayYOrigin

public void setArrayYOrigin(float arrayYOrigin)

Set method for arrayYOrigin

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getArrayYOrigin

public float getArrayYOrigin()

Get method for arrayYOrigin

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setOriginRelativeTo

public void setOriginRelativeTo(java.lang.String originRelativeTo)

Set method for originRelativeTo

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getOriginRelativeTo

public java.lang.String getOriginRelativeTo()

Get method for originRelativeTo

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setArrayDesign

public void setArrayDesign(org.biomage.ArrayDesign.ArrayDesign arrayDesign)

Set method for arrayDesign

Specified by:

setArrayDesign in interface org.biomage.Interface.HasArrayDesign

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getArrayDesign

public org.biomage.ArrayDesign.ArrayDesign getArrayDesign()

Get method for arrayDesign

Specified by:

getArrayDesign in interface org.biomage.Interface.HasArrayDesign

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setArrayGroup

public void setArrayGroup(ArrayGroup arrayGroup)

Set method for arrayGroup

Specified by:

setArrayGroup in interface org.biomage.Interface.HasArrayGroup

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getArrayGroup

public ArrayGroup getArrayGroup()

Get method for arrayGroup

Specified by:

getArrayGroup in interface org.biomage.Interface.HasArrayGroup

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setInformation

public void setInformation(ArrayManufacture information)

Set method for information

Specified by:

setInformation in interface org.biomage.Interface.HasInformation

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getInformation

public ArrayManufacture getInformation()

Get method for information

Specified by:

getInformation in interface org.biomage.Interface.HasInformation

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setArrayManufactureDeviations

public void setArrayManufactureDeviations(org.biomage.Interface.HasArrayManufactureDeviations.ArrayManufactureDeviations_list arrayManufactureDeviations)

Set method for arrayManufactureDeviations

Specified by:

setArrayManufactureDeviations in interface org.biomage.Interface.HasArrayManufactureDeviations

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getArrayManufactureDeviations

public org.biomage.Interface.HasArrayManufactureDeviations.ArrayManufactureDeviations_list getArrayManufactureDeviations()

Get method for arrayManufactureDeviations

Specified by:

getArrayManufactureDeviations in interface org.biomage.Interface.HasArrayManufactureDeviations

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addToArrayManufactureDeviations

public void addToArrayManufactureDeviations(ArrayManufactureDeviation arrayManufactureDeviation)

Method to add ArrayManufactureDeviation to ArrayManufactureDeviations_list

Specified by:

addToArrayManufactureDeviations in interface org.biomage.Interface.HasArrayManufactureDeviations

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addToArrayManufactureDeviations

public void addToArrayManufactureDeviations(int position,
                                            ArrayManufactureDeviation arrayManufactureDeviation)

Method to add ArrayManufactureDeviation at position to ArrayManufactureDeviations_list

Specified by:

addToArrayManufactureDeviations in interface org.biomage.Interface.HasArrayManufactureDeviations

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getFromArrayManufactureDeviations

public ArrayManufactureDeviation getFromArrayManufactureDeviations(int position)

Method to get ArrayManufactureDeviation from ArrayManufactureDeviations_list

Specified by:

getFromArrayManufactureDeviations in interface org.biomage.Interface.HasArrayManufactureDeviations

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removeElementAtFromArrayManufactureDeviations

public void removeElementAtFromArrayManufactureDeviations(int position)

Method to remove by position from ArrayManufactureDeviations_list

Specified by:

removeElementAtFromArrayManufactureDeviations in interface org.biomage.Interface.HasArrayManufactureDeviations

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removeFromArrayManufactureDeviations

public void removeFromArrayManufactureDeviations(ArrayManufactureDeviation arrayManufactureDeviation)

Method to remove first ArrayManufactureDeviation from ArrayManufactureDeviations_list

Specified by:

removeFromArrayManufactureDeviations in interface org.biomage.Interface.HasArrayManufactureDeviations

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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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