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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.HigherLevelAnalysis.NodeContents
public class NodeContents
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.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail |
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HasAuditTrail.AuditTrail_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions |
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HasDescriptions.Descriptions_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets |
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HasPropertySets.PropertySets_list |
Field Summary | |
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protected BioAssayDimension |
bioAssayDimension
The relevant BioAssays for this NodeContents from the BioAssayData. |
protected DesignElementDimension |
designElementDimension
The relevant DesignElements for this NodeContents from the BioAssayData. |
protected QuantitationTypeDimension |
quantitationDimension
The relevant QuantitationTypes for this NodeContents from the BioAssayData. |
Fields inherited from class org.biomage.Common.Describable |
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security |
Fields inherited from class org.biomage.Common.Extendable |
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editable, id, securedElementId |
Constructor Summary | |
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NodeContents()
Default constructor. |
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NodeContents(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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boolean |
emptyMAGEobject()
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BioAssayDimension |
getBioAssayDimension()
Get method for bioAssayDimension |
DesignElementDimension |
getDesignElementDimension()
Get method for designElementDimension |
java.lang.String |
getModelClassName()
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QuantitationTypeDimension |
getQuantitationDimension()
Get method for quantitationDimension |
void |
setBioAssayDimension(BioAssayDimension bioAssayDimension)
Set method for bioAssayDimension |
void |
setDesignElementDimension(DesignElementDimension designElementDimension)
Set method for designElementDimension |
void |
setQuantitationDimension(QuantitationTypeDimension quantitationDimension)
Set method for quantitationDimension |
void |
writeAssociations(java.io.Writer out)
writeAssociations This method is responsible for assembling the association data into XML. |
void |
writeAttributes(java.io.Writer out)
writeAttributes This method is responsible for assembling the attribute data into XML. |
void |
writeMAGEML(java.io.Writer out)
writeMAGEML This method is responsible for assembling the attribute and association data into XML. |
Methods inherited from class org.biomage.Common.Describable |
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addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAttributes, setAuditTrail, setDescriptions, setSecurity |
Methods inherited from class org.biomage.Common.Extendable |
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addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId, toString |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected BioAssayDimension bioAssayDimension
protected DesignElementDimension designElementDimension
protected QuantitationTypeDimension quantitationDimension
Constructor Detail |
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public NodeContents()
public NodeContents(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
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public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class Describable
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Describable
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Describable
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class Describable
public void setBioAssayDimension(BioAssayDimension bioAssayDimension)
setBioAssayDimension
in interface HasBioAssayDimension
value
- to setpublic BioAssayDimension getBioAssayDimension()
getBioAssayDimension
in interface HasBioAssayDimension
public void setDesignElementDimension(DesignElementDimension designElementDimension)
setDesignElementDimension
in interface HasDesignElementDimension
value
- to setpublic DesignElementDimension getDesignElementDimension()
getDesignElementDimension
in interface HasDesignElementDimension
public void setQuantitationDimension(QuantitationTypeDimension quantitationDimension)
setQuantitationDimension
in interface HasQuantitationDimension
value
- to setpublic QuantitationTypeDimension getQuantitationDimension()
getQuantitationDimension
in interface HasQuantitationDimension
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