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org.biomage.HigherLevelAnalysis
Class NodeContents  

java.lang.Object
  org.biomage.Common.Extendable
      org.biomage.Common.Describable
          org.biomage.HigherLevelAnalysis.NodeContents

All Implemented Interfaces:

org.biomage.Interface.HasAuditTrail, org.biomage.Interface.HasBioAssayDimension, org.biomage.Interface.HasDescriptions, org.biomage.Interface.HasDesignElementDimension, org.biomage.Interface.HasPropertySets, org.biomage.Interface.HasQuantitationDimension, org.biomage.Interface.HasSecurity, java.io.Serializable

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public class NodeContents

extends org.biomage.Common.Describable

implements java.io.Serializable, org.biomage.Interface.HasDesignElementDimension, org.biomage.Interface.HasQuantitationDimension, org.biomage.Interface.HasBioAssayDimension

The contents of a node for any or all of the three Dimensions. If a node only contained genes just the DesignElementDimension would be defined.

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Nested Class Summary

 

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.BioAssayData.BioAssayDimension	bioAssayDimension           The relevant BioAssays for this NodeContents from the BioAssayData.
private  org.biomage.BioAssayData.DesignElementDimension	designElementDimension           The relevant DesignElements for this NodeContents from the BioAssayData.
private  org.biomage.BioAssayData.QuantitationTypeDimension	quantitationDimension           The relevant QuantitationTypes for this NodeContents from the BioAssayData.

 

Fields inherited from class org.biomage.Common.Describable

 

Fields inherited from class org.biomage.Common.Extendable

 

Constructor Summary

NodeContents()           Default constructor.

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

 

Method Summary
org.biomage.BioAssayData.BioAssayDimension	getBioAssayDimension()           Get method for bioAssayDimension
org.biomage.BioAssayData.DesignElementDimension	getDesignElementDimension()           Get method for designElementDimension
org.biomage.BioAssayData.QuantitationTypeDimension	getQuantitationDimension()           Get method for quantitationDimension
void	setBioAssayDimension(org.biomage.BioAssayData.BioAssayDimension bioAssayDimension)           Set method for bioAssayDimension
void	setDesignElementDimension(org.biomage.BioAssayData.DesignElementDimension designElementDimension)           Set method for designElementDimension
void	setQuantitationDimension(org.biomage.BioAssayData.QuantitationTypeDimension quantitationDimension)           Set method for quantitationDimension
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.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

designElementDimension

private org.biomage.BioAssayData.DesignElementDimension designElementDimension

The relevant DesignElements for this NodeContents from the BioAssayData.

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quantitationDimension

private org.biomage.BioAssayData.QuantitationTypeDimension quantitationDimension

The relevant QuantitationTypes for this NodeContents from the BioAssayData.

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bioAssayDimension

private org.biomage.BioAssayData.BioAssayDimension bioAssayDimension

The relevant BioAssays for this NodeContents from the BioAssayData.

Constructor Detail

NodeContents

public NodeContents()

Default constructor.

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NodeContents

public NodeContents(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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setDesignElementDimension

public void setDesignElementDimension(org.biomage.BioAssayData.DesignElementDimension designElementDimension)

Set method for designElementDimension

Specified by:

setDesignElementDimension in interface org.biomage.Interface.HasDesignElementDimension

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getDesignElementDimension

public org.biomage.BioAssayData.DesignElementDimension getDesignElementDimension()

Get method for designElementDimension

Specified by:

getDesignElementDimension in interface org.biomage.Interface.HasDesignElementDimension

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setQuantitationDimension

public void setQuantitationDimension(org.biomage.BioAssayData.QuantitationTypeDimension quantitationDimension)

Set method for quantitationDimension

Specified by:

setQuantitationDimension in interface org.biomage.Interface.HasQuantitationDimension

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getQuantitationDimension

public org.biomage.BioAssayData.QuantitationTypeDimension getQuantitationDimension()

Get method for quantitationDimension

Specified by:

getQuantitationDimension in interface org.biomage.Interface.HasQuantitationDimension

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setBioAssayDimension

public void setBioAssayDimension(org.biomage.BioAssayData.BioAssayDimension bioAssayDimension)

Set method for bioAssayDimension

Specified by:

setBioAssayDimension in interface org.biomage.Interface.HasBioAssayDimension

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getBioAssayDimension

public org.biomage.BioAssayData.BioAssayDimension getBioAssayDimension()

Get method for bioAssayDimension

Specified by:

getBioAssayDimension in interface org.biomage.Interface.HasBioAssayDimension

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

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