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org.biomage.Array
Class Array_package  

java.lang.Object
  org.biomage.Array.Array_package

All Implemented Interfaces:

java.io.Serializable

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public class Array_package

extends java.lang.Object

implements java.io.Serializable

Describes the process of creating arrays from array designs. Includes information on how arrays are grouped together, if relevant, how an array deviates from its array design both in layout and per feature and potentially contains references to LIMS data that might contain more detail on the BioMaterial used to create the reporters.

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Nested Class Summary
class	Array_package.Array_list           Inner list class for holding multiple entries for attribute array_list.
class	Array_package.ArrayGroup_list           Inner list class for holding multiple entries for attribute arrayGroup_list.
class	Array_package.ArrayManufacture_list           Inner list class for holding multiple entries for attribute arrayManufacture_list.

 

Field Summary
Array_package.Array_list	array_list           The physical substrate along with its features and their annotation
Array_package.ArrayGroup_list	arrayGroup_list           An array package is a physical platform that contains one or more arrays that are separately addressable (e.g.
Array_package.ArrayManufacture_list	arrayManufacture_list           Describes the process by which arrays are produced.

 

Constructor Summary

Array_package()           Default constructor.

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

 

Method Summary
void	addToArray_list(Array array)           Method to add Array to Array_list
void	addToArray_list(int position, Array array)           Method to add Array at position to Array_list
void	addToArrayGroup_list(ArrayGroup arrayGroup)           Method to add ArrayGroup to ArrayGroup_list
void	addToArrayGroup_list(int position, ArrayGroup arrayGroup)           Method to add ArrayGroup at position to ArrayGroup_list
void	addToArrayManufacture_list(ArrayManufacture arrayManufacture)           Method to add ArrayManufacture to ArrayManufacture_list
void	addToArrayManufacture_list(int position, ArrayManufacture arrayManufacture)           Method to add ArrayManufacture at position to ArrayManufacture_list
Array_package.Array_list	getArray_list()           Get method for array_list
Array_package.ArrayGroup_list	getArrayGroup_list()           Get method for arrayGroup_list
Array_package.ArrayManufacture_list	getArrayManufacture_list()           Get method for arrayManufacture_list
Array	getFromArray_list(int position)           Method to get Array from Array_list
ArrayGroup	getFromArrayGroup_list(int position)           Method to get ArrayGroup from ArrayGroup_list
ArrayManufacture	getFromArrayManufacture_list(int position)           Method to get ArrayManufacture from ArrayManufacture_list
void	removeElementAtFromArray_list(int position)           Method to remove by position from Array_list
void	removeElementAtFromArrayGroup_list(int position)           Method to remove by position from ArrayGroup_list
void	removeElementAtFromArrayManufacture_list(int position)           Method to remove by position from ArrayManufacture_list
void	removeFromArray_list(Array array)           Method to remove first Array from Array_list
void	removeFromArrayGroup_list(ArrayGroup arrayGroup)           Method to remove first ArrayGroup from ArrayGroup_list
void	removeFromArrayManufacture_list(ArrayManufacture arrayManufacture)           Method to remove first ArrayManufacture from ArrayManufacture_list
void	setArray_list(Array_package.Array_list array_list)           Set method for array_list
void	setArrayGroup_list(Array_package.ArrayGroup_list arrayGroup_list)           Set method for arrayGroup_list
void	setArrayManufacture_list(Array_package.ArrayManufacture_list arrayManufacture_list)           Set method for arrayManufacture_list
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 java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

 

Field Detail

array_list

public Array_package.Array_list array_list

The physical substrate along with its features and their annotation

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arrayGroup_list

public Array_package.ArrayGroup_list arrayGroup_list

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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arrayManufacture_list

public Array_package.ArrayManufacture_list arrayManufacture_list

Describes the process by which arrays are produced.

Constructor Detail

Array_package

public Array_package()

Default constructor.

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Array_package

public Array_package(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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setArray_list

public void setArray_list(Array_package.Array_list array_list)

Set method for array_list

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getArray_list

public Array_package.Array_list getArray_list()

Get method for array_list

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addToArray_list

public void addToArray_list(Array array)

Method to add Array to Array_list

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addToArray_list

public void addToArray_list(int position,
                            Array array)

Method to add Array at position to Array_list

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getFromArray_list

public Array getFromArray_list(int position)

Method to get Array from Array_list

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removeElementAtFromArray_list

public void removeElementAtFromArray_list(int position)

Method to remove by position from Array_list

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removeFromArray_list

public void removeFromArray_list(Array array)

Method to remove first Array from Array_list

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setArrayGroup_list

public void setArrayGroup_list(Array_package.ArrayGroup_list arrayGroup_list)

Set method for arrayGroup_list

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getArrayGroup_list

public Array_package.ArrayGroup_list getArrayGroup_list()

Get method for arrayGroup_list

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addToArrayGroup_list

public void addToArrayGroup_list(ArrayGroup arrayGroup)

Method to add ArrayGroup to ArrayGroup_list

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addToArrayGroup_list

public void addToArrayGroup_list(int position,
                                 ArrayGroup arrayGroup)

Method to add ArrayGroup at position to ArrayGroup_list

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getFromArrayGroup_list

public ArrayGroup getFromArrayGroup_list(int position)

Method to get ArrayGroup from ArrayGroup_list

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removeElementAtFromArrayGroup_list

public void removeElementAtFromArrayGroup_list(int position)

Method to remove by position from ArrayGroup_list

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removeFromArrayGroup_list

public void removeFromArrayGroup_list(ArrayGroup arrayGroup)

Method to remove first ArrayGroup from ArrayGroup_list

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setArrayManufacture_list

public void setArrayManufacture_list(Array_package.ArrayManufacture_list arrayManufacture_list)

Set method for arrayManufacture_list

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getArrayManufacture_list

public Array_package.ArrayManufacture_list getArrayManufacture_list()

Get method for arrayManufacture_list

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addToArrayManufacture_list

public void addToArrayManufacture_list(ArrayManufacture arrayManufacture)

Method to add ArrayManufacture to ArrayManufacture_list

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addToArrayManufacture_list

public void addToArrayManufacture_list(int position,
                                       ArrayManufacture arrayManufacture)

Method to add ArrayManufacture at position to ArrayManufacture_list

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getFromArrayManufacture_list

public ArrayManufacture getFromArrayManufacture_list(int position)

Method to get ArrayManufacture from ArrayManufacture_list

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removeElementAtFromArrayManufacture_list

public void removeElementAtFromArrayManufacture_list(int position)

Method to remove by position from ArrayManufacture_list

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removeFromArrayManufacture_list

public void removeFromArrayManufacture_list(ArrayManufacture arrayManufacture)

Method to remove first ArrayManufacture from ArrayManufacture_list

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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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