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org.biomage.ArrayDesign
Class ArrayDesign_package  

java.lang.Object
  org.biomage.ArrayDesign.ArrayDesign_package

All Implemented Interfaces:

java.io.Serializable

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public class ArrayDesign_package

extends java.lang.Object

implements java.io.Serializable

Describes a microarray design that can be printed and then, in the case of gene expression, hybridized. An array design consists of several features (also called spots) in which reporter sequences are placed. Many features may have the same reporter replicated and a reporter may be specified in one or more array designs. The nature of the reporter's biosequence placed on a spot will depend on the technology. Two well-known technologies differ significantly-spotter arrays draw material from a well and place a spot on the array whereas in situ oligo arrays are created through the synthesis of many, short (~20-100mer) nucleotide sequences onto the features. Reporters can be grouped together into CompositeSequences, typically representing a gene or one or more splice variants in gene expression experiments. There are then two distinct ways that DesignElements are grouped. The one described in the ArrayDesign package by FeatureGroup, ReporterGroup and CompositeGroup is by technology type, that is, one might want to segregate the controls to a Group and all the non-controls to another. Or if PCR Product and Oligos are both used on an array they would likely be in different groups. The grouping described in the DesignElement package by the mappings relates the Features to the Reporter, the Reporters to CompositeSequence, and at higher levels, CompositeSequences to CompositeSequence.

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Nested Class Summary
class	ArrayDesign_package.ArrayDesign_list           Inner list class for holding multiple entries for attribute arrayDesign_list.
class	ArrayDesign_package.CompositeGroup_list           Inner list class for holding multiple entries for attribute compositeGroup_list.
class	ArrayDesign_package.DesignElementGroup_list           Inner list class for holding multiple entries for attribute designElementGroup_list.
class	ArrayDesign_package.PhysicalArrayDesign_list           Inner list class for holding multiple entries for attribute physicalArrayDesign_list.
class	ArrayDesign_package.ReporterGroup_list           Inner list class for holding multiple entries for attribute reporterGroup_list.

 

Field Summary
ArrayDesign_package.ArrayDesign_list	arrayDesign_list           Describes the design of an gene expression layout.
ArrayDesign_package.CompositeGroup_list	compositeGroup_list           Allows specification of the type of Composite Design Element.
ArrayDesign_package.DesignElementGroup_list	designElementGroup_list           The DesignElementGroup holds information on either features, reporters, or compositeSequences, particularly that information that is common between all of the DesignElements contained.
ArrayDesign_package.PhysicalArrayDesign_list	physicalArrayDesign_list           A design that is expected to be used to manufacture physical arrays.
ArrayDesign_package.ReporterGroup_list	reporterGroup_list           Allows specification of the type of Reporter Design Element.

 

Constructor Summary

ArrayDesign_package()           Default constructor.

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

 

Method Summary
void	addToArrayDesign_list(ArrayDesign arrayDesign)           Method to add ArrayDesign to ArrayDesign_list
void	addToArrayDesign_list(int position, ArrayDesign arrayDesign)           Method to add ArrayDesign at position to ArrayDesign_list
void	addToCompositeGroup_list(CompositeGroup compositeGroup)           Method to add CompositeGroup to CompositeGroup_list
void	addToCompositeGroup_list(int position, CompositeGroup compositeGroup)           Method to add CompositeGroup at position to CompositeGroup_list
void	addToDesignElementGroup_list(DesignElementGroup designElementGroup)           Method to add DesignElementGroup to DesignElementGroup_list
void	addToDesignElementGroup_list(int position, DesignElementGroup designElementGroup)           Method to add DesignElementGroup at position to DesignElementGroup_list
void	addToPhysicalArrayDesign_list(int position, PhysicalArrayDesign physicalArrayDesign)           Method to add PhysicalArrayDesign at position to PhysicalArrayDesign_list
void	addToPhysicalArrayDesign_list(PhysicalArrayDesign physicalArrayDesign)           Method to add PhysicalArrayDesign to PhysicalArrayDesign_list
void	addToReporterGroup_list(int position, ReporterGroup reporterGroup)           Method to add ReporterGroup at position to ReporterGroup_list
void	addToReporterGroup_list(ReporterGroup reporterGroup)           Method to add ReporterGroup to ReporterGroup_list
ArrayDesign_package.ArrayDesign_list	getArrayDesign_list()           Get method for arrayDesign_list
ArrayDesign_package.CompositeGroup_list	getCompositeGroup_list()           Get method for compositeGroup_list
ArrayDesign_package.DesignElementGroup_list	getDesignElementGroup_list()           Get method for designElementGroup_list
ArrayDesign	getFromArrayDesign_list(int position)           Method to get ArrayDesign from ArrayDesign_list
CompositeGroup	getFromCompositeGroup_list(int position)           Method to get CompositeGroup from CompositeGroup_list
DesignElementGroup	getFromDesignElementGroup_list(int position)           Method to get DesignElementGroup from DesignElementGroup_list
PhysicalArrayDesign	getFromPhysicalArrayDesign_list(int position)           Method to get PhysicalArrayDesign from PhysicalArrayDesign_list
ReporterGroup	getFromReporterGroup_list(int position)           Method to get ReporterGroup from ReporterGroup_list
ArrayDesign_package.PhysicalArrayDesign_list	getPhysicalArrayDesign_list()           Get method for physicalArrayDesign_list
ArrayDesign_package.ReporterGroup_list	getReporterGroup_list()           Get method for reporterGroup_list
void	removeElementAtFromArrayDesign_list(int position)           Method to remove by position from ArrayDesign_list
void	removeElementAtFromCompositeGroup_list(int position)           Method to remove by position from CompositeGroup_list
void	removeElementAtFromDesignElementGroup_list(int position)           Method to remove by position from DesignElementGroup_list
void	removeElementAtFromPhysicalArrayDesign_list(int position)           Method to remove by position from PhysicalArrayDesign_list
void	removeElementAtFromReporterGroup_list(int position)           Method to remove by position from ReporterGroup_list
void	removeFromArrayDesign_list(ArrayDesign arrayDesign)           Method to remove first ArrayDesign from ArrayDesign_list
void	removeFromCompositeGroup_list(CompositeGroup compositeGroup)           Method to remove first CompositeGroup from CompositeGroup_list
void	removeFromDesignElementGroup_list(DesignElementGroup designElementGroup)           Method to remove first DesignElementGroup from DesignElementGroup_list
void	removeFromPhysicalArrayDesign_list(PhysicalArrayDesign physicalArrayDesign)           Method to remove first PhysicalArrayDesign from PhysicalArrayDesign_list
void	removeFromReporterGroup_list(ReporterGroup reporterGroup)           Method to remove first ReporterGroup from ReporterGroup_list
void	setArrayDesign_list(ArrayDesign_package.ArrayDesign_list arrayDesign_list)           Set method for arrayDesign_list
void	setCompositeGroup_list(ArrayDesign_package.CompositeGroup_list compositeGroup_list)           Set method for compositeGroup_list
void	setDesignElementGroup_list(ArrayDesign_package.DesignElementGroup_list designElementGroup_list)           Set method for designElementGroup_list
void	setPhysicalArrayDesign_list(ArrayDesign_package.PhysicalArrayDesign_list physicalArrayDesign_list)           Set method for physicalArrayDesign_list
void	setReporterGroup_list(ArrayDesign_package.ReporterGroup_list reporterGroup_list)           Set method for reporterGroup_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

arrayDesign_list

public ArrayDesign_package.ArrayDesign_list arrayDesign_list

Describes the design of an gene expression layout. In some cases this might be virtual and, for instance, represent the output from analysis software at the composite level without reporters or features.

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physicalArrayDesign_list

public ArrayDesign_package.PhysicalArrayDesign_list physicalArrayDesign_list

A design that is expected to be used to manufacture physical arrays.

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reporterGroup_list

public ArrayDesign_package.ReporterGroup_list reporterGroup_list

Allows specification of the type of Reporter Design Element.

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designElementGroup_list

public ArrayDesign_package.DesignElementGroup_list designElementGroup_list

The DesignElementGroup holds information on either features, reporters, or compositeSequences, particularly that information that is common between all of the DesignElements contained.

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compositeGroup_list

public ArrayDesign_package.CompositeGroup_list compositeGroup_list

Allows specification of the type of Composite Design Element.

Constructor Detail

ArrayDesign_package

public ArrayDesign_package()

Default constructor.

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ArrayDesign_package

public ArrayDesign_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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setArrayDesign_list

public void setArrayDesign_list(ArrayDesign_package.ArrayDesign_list arrayDesign_list)

Set method for arrayDesign_list

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getArrayDesign_list

public ArrayDesign_package.ArrayDesign_list getArrayDesign_list()

Get method for arrayDesign_list

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addToArrayDesign_list

public void addToArrayDesign_list(ArrayDesign arrayDesign)

Method to add ArrayDesign to ArrayDesign_list

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addToArrayDesign_list

public void addToArrayDesign_list(int position,
                                  ArrayDesign arrayDesign)

Method to add ArrayDesign at position to ArrayDesign_list

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getFromArrayDesign_list

public ArrayDesign getFromArrayDesign_list(int position)

Method to get ArrayDesign from ArrayDesign_list

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removeElementAtFromArrayDesign_list

public void removeElementAtFromArrayDesign_list(int position)

Method to remove by position from ArrayDesign_list

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removeFromArrayDesign_list

public void removeFromArrayDesign_list(ArrayDesign arrayDesign)

Method to remove first ArrayDesign from ArrayDesign_list

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setPhysicalArrayDesign_list

public void setPhysicalArrayDesign_list(ArrayDesign_package.PhysicalArrayDesign_list physicalArrayDesign_list)

Set method for physicalArrayDesign_list

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getPhysicalArrayDesign_list

public ArrayDesign_package.PhysicalArrayDesign_list getPhysicalArrayDesign_list()

Get method for physicalArrayDesign_list

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addToPhysicalArrayDesign_list

public void addToPhysicalArrayDesign_list(PhysicalArrayDesign physicalArrayDesign)

Method to add PhysicalArrayDesign to PhysicalArrayDesign_list

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addToPhysicalArrayDesign_list

public void addToPhysicalArrayDesign_list(int position,
                                          PhysicalArrayDesign physicalArrayDesign)

Method to add PhysicalArrayDesign at position to PhysicalArrayDesign_list

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getFromPhysicalArrayDesign_list

public PhysicalArrayDesign getFromPhysicalArrayDesign_list(int position)

Method to get PhysicalArrayDesign from PhysicalArrayDesign_list

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removeElementAtFromPhysicalArrayDesign_list

public void removeElementAtFromPhysicalArrayDesign_list(int position)

Method to remove by position from PhysicalArrayDesign_list

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removeFromPhysicalArrayDesign_list

public void removeFromPhysicalArrayDesign_list(PhysicalArrayDesign physicalArrayDesign)

Method to remove first PhysicalArrayDesign from PhysicalArrayDesign_list

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setReporterGroup_list

public void setReporterGroup_list(ArrayDesign_package.ReporterGroup_list reporterGroup_list)

Set method for reporterGroup_list

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getReporterGroup_list

public ArrayDesign_package.ReporterGroup_list getReporterGroup_list()

Get method for reporterGroup_list

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addToReporterGroup_list

public void addToReporterGroup_list(ReporterGroup reporterGroup)

Method to add ReporterGroup to ReporterGroup_list

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addToReporterGroup_list

public void addToReporterGroup_list(int position,
                                    ReporterGroup reporterGroup)

Method to add ReporterGroup at position to ReporterGroup_list

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getFromReporterGroup_list

public ReporterGroup getFromReporterGroup_list(int position)

Method to get ReporterGroup from ReporterGroup_list

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removeElementAtFromReporterGroup_list

public void removeElementAtFromReporterGroup_list(int position)

Method to remove by position from ReporterGroup_list

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removeFromReporterGroup_list

public void removeFromReporterGroup_list(ReporterGroup reporterGroup)

Method to remove first ReporterGroup from ReporterGroup_list

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setDesignElementGroup_list

public void setDesignElementGroup_list(ArrayDesign_package.DesignElementGroup_list designElementGroup_list)

Set method for designElementGroup_list

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getDesignElementGroup_list

public ArrayDesign_package.DesignElementGroup_list getDesignElementGroup_list()

Get method for designElementGroup_list

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addToDesignElementGroup_list

public void addToDesignElementGroup_list(DesignElementGroup designElementGroup)

Method to add DesignElementGroup to DesignElementGroup_list

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addToDesignElementGroup_list

public void addToDesignElementGroup_list(int position,
                                         DesignElementGroup designElementGroup)

Method to add DesignElementGroup at position to DesignElementGroup_list

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getFromDesignElementGroup_list

public DesignElementGroup getFromDesignElementGroup_list(int position)

Method to get DesignElementGroup from DesignElementGroup_list

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removeElementAtFromDesignElementGroup_list

public void removeElementAtFromDesignElementGroup_list(int position)

Method to remove by position from DesignElementGroup_list

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removeFromDesignElementGroup_list

public void removeFromDesignElementGroup_list(DesignElementGroup designElementGroup)

Method to remove first DesignElementGroup from DesignElementGroup_list

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setCompositeGroup_list

public void setCompositeGroup_list(ArrayDesign_package.CompositeGroup_list compositeGroup_list)

Set method for compositeGroup_list

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getCompositeGroup_list

public ArrayDesign_package.CompositeGroup_list getCompositeGroup_list()

Get method for compositeGroup_list

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addToCompositeGroup_list

public void addToCompositeGroup_list(CompositeGroup compositeGroup)

Method to add CompositeGroup to CompositeGroup_list

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addToCompositeGroup_list

public void addToCompositeGroup_list(int position,
                                     CompositeGroup compositeGroup)

Method to add CompositeGroup at position to CompositeGroup_list

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getFromCompositeGroup_list

public CompositeGroup getFromCompositeGroup_list(int position)

Method to get CompositeGroup from CompositeGroup_list

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removeElementAtFromCompositeGroup_list

public void removeElementAtFromCompositeGroup_list(int position)

Method to remove by position from CompositeGroup_list

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removeFromCompositeGroup_list

public void removeFromCompositeGroup_list(CompositeGroup compositeGroup)

Method to remove first CompositeGroup from CompositeGroup_list

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

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