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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.BioEvent.BioEvent
org.biomage.BioAssayData.Transformation
public class Transformation
The process by which derivedBioAssays are created from measuredBioAssays and/or derivedBioAssays. It uses mappings to indicate the input and output dimensions.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasBioAssayDataSources |
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HasBioAssayDataSources.BioAssayDataSources_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasProtocolApplications |
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HasProtocolApplications.ProtocolApplications_list |
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 java.util.List |
bioAssayDataSources
The BioAssayData sources that the Transformation event uses to produce the target DerivedBioAssayData. |
protected BioAssayMapping |
bioAssayMapping
The collection of mappings for the BioAssays. |
protected DerivedBioAssayData |
derivedBioAssayDataTarget
The association between the DerivedBioAssayData and the Transformation event that produced it. |
protected DesignElementMapping |
designElementMapping
The collection of mappings for the DesignElements. |
protected QuantitationTypeMapping |
quantitationTypeMapping
The collection of mappings for the QuantitationTypes. |
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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Transformation()
Default constructor. |
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Transformation(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToBioAssayDataSources(BioAssayData bioAssayData)
Method to add BioAssayData to BioAssayDataSources_list |
void |
addToBioAssayDataSources(int position,
BioAssayData bioAssayData)
Method to add BioAssayData at position to BioAssayDataSources_list |
boolean |
emptyMAGEobject()
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HasBioAssayDataSources.BioAssayDataSources_list |
getBioAssayDataSources()
Get method for bioAssayDataSources |
BioAssayMapping |
getBioAssayMapping()
Get method for bioAssayMapping |
DerivedBioAssayData |
getDerivedBioAssayDataTarget()
Get method for derivedBioAssayDataTarget |
DesignElementMapping |
getDesignElementMapping()
Get method for designElementMapping |
BioAssayData |
getFromBioAssayDataSources(int position)
Method to get BioAssayData from BioAssayDataSources_list |
java.lang.String |
getModelClassName()
|
QuantitationTypeMapping |
getQuantitationTypeMapping()
Get method for quantitationTypeMapping |
void |
removeElementAtFromBioAssayDataSources(int position)
Method to remove by position from BioAssayDataSources_list |
void |
removeFromBioAssayDataSources(BioAssayData bioAssayData)
Method to remove first BioAssayData from BioAssayDataSources_list |
void |
setAttributes(org.xml.sax.Attributes atts)
|
void |
setBioAssayDataSources(HasBioAssayDataSources.BioAssayDataSources_list bioAssayDataSources)
Set method for bioAssayDataSources |
void |
setBioAssayMapping(BioAssayMapping bioAssayMapping)
Set method for bioAssayMapping |
void |
setDerivedBioAssayDataTarget(DerivedBioAssayData derivedBioAssayDataTarget)
Set method for derivedBioAssayDataTarget |
void |
setDesignElementMapping(DesignElementMapping designElementMapping)
Set method for designElementMapping |
void |
setQuantitationTypeMapping(QuantitationTypeMapping quantitationTypeMapping)
Set method for quantitationTypeMapping |
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.BioEvent.BioEvent |
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addToProtocolApplications, addToProtocolApplications, getFromProtocolApplications, getProtocolApplications, removeElementAtFromProtocolApplications, removeFromProtocolApplications, setProtocolApplications |
Methods inherited from class org.biomage.Common.Identifiable |
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getIdentifier, getName, setIdentifier, setName, toString |
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, 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 |
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 java.util.List bioAssayDataSources
protected DerivedBioAssayData derivedBioAssayDataTarget
protected QuantitationTypeMapping quantitationTypeMapping
protected DesignElementMapping designElementMapping
protected BioAssayMapping bioAssayMapping
Constructor Detail |
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public Transformation()
public Transformation(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
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public void setAttributes(org.xml.sax.Attributes atts)
setAttributes
in class BioEvent
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class BioEvent
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class BioEvent
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class BioEvent
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class BioEvent
public void setBioAssayDataSources(HasBioAssayDataSources.BioAssayDataSources_list bioAssayDataSources)
setBioAssayDataSources
in interface HasBioAssayDataSources
value
- to setpublic HasBioAssayDataSources.BioAssayDataSources_list getBioAssayDataSources()
getBioAssayDataSources
in interface HasBioAssayDataSources
public void addToBioAssayDataSources(BioAssayData bioAssayData)
addToBioAssayDataSources
in interface HasBioAssayDataSources
public void addToBioAssayDataSources(int position, BioAssayData bioAssayData)
addToBioAssayDataSources
in interface HasBioAssayDataSources
public BioAssayData getFromBioAssayDataSources(int position)
getFromBioAssayDataSources
in interface HasBioAssayDataSources
public void removeElementAtFromBioAssayDataSources(int position)
removeElementAtFromBioAssayDataSources
in interface HasBioAssayDataSources
public void removeFromBioAssayDataSources(BioAssayData bioAssayData)
removeFromBioAssayDataSources
in interface HasBioAssayDataSources
public void setDerivedBioAssayDataTarget(DerivedBioAssayData derivedBioAssayDataTarget)
setDerivedBioAssayDataTarget
in interface HasDerivedBioAssayDataTarget
value
- to setpublic DerivedBioAssayData getDerivedBioAssayDataTarget()
getDerivedBioAssayDataTarget
in interface HasDerivedBioAssayDataTarget
public void setQuantitationTypeMapping(QuantitationTypeMapping quantitationTypeMapping)
setQuantitationTypeMapping
in interface HasQuantitationTypeMapping
value
- to setpublic QuantitationTypeMapping getQuantitationTypeMapping()
getQuantitationTypeMapping
in interface HasQuantitationTypeMapping
public void setDesignElementMapping(DesignElementMapping designElementMapping)
setDesignElementMapping
in interface HasDesignElementMapping
value
- to setpublic DesignElementMapping getDesignElementMapping()
getDesignElementMapping
in interface HasDesignElementMapping
public void setBioAssayMapping(BioAssayMapping bioAssayMapping)
setBioAssayMapping
in interface HasBioAssayMapping
value
- to setpublic BioAssayMapping getBioAssayMapping()
getBioAssayMapping
in interface HasBioAssayMapping
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