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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.BioAssay.BioAssay
org.biomage.BioAssay.DerivedBioAssay
public class DerivedBioAssay
A BioAssay that is created by the Transformation BioEvent from one or more MeasuredBioAssays or DerivedBioAssays.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasDerivedBioAssayData |
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HasDerivedBioAssayData.DerivedBioAssayData_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDerivedBioAssayMap |
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HasDerivedBioAssayMap.DerivedBioAssayMap_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasChannels |
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HasChannels.Channels_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasBioAssayFactorValues |
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HasBioAssayFactorValues.BioAssayFactorValues_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 |
derivedBioAssayData
The data associated with the DerivedBioAssay. |
protected java.util.List |
derivedBioAssayMap
The DerivedBioAssay that is produced by the sources of the BioAssayMap. |
protected OntologyEntry |
type
The derivation type, for instance collapsed spot replicate, ratio, averaged intensity, bioassay replicates, etc. |
Fields inherited from class org.biomage.BioAssay.BioAssay |
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bioAssayFactorValues, channels, deleted, ojbConcreteClass |
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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DerivedBioAssay()
Default constructor. |
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DerivedBioAssay(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToDerivedBioAssayData(DerivedBioAssayData derivedBioAssayData)
Method to add DerivedBioAssayData to DerivedBioAssayData_list |
void |
addToDerivedBioAssayData(int position,
DerivedBioAssayData derivedBioAssayData)
Method to add DerivedBioAssayData at position to DerivedBioAssayData_list |
void |
addToDerivedBioAssayMap(BioAssayMap bioAssayMap)
Method to add BioAssayMap to DerivedBioAssayMap_list |
void |
addToDerivedBioAssayMap(int position,
BioAssayMap bioAssayMap)
Method to add BioAssayMap at position to DerivedBioAssayMap_list |
boolean |
emptyMAGEobject()
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HasDerivedBioAssayData.DerivedBioAssayData_list |
getDerivedBioAssayData()
Get method for derivedBioAssayData |
HasDerivedBioAssayMap.DerivedBioAssayMap_list |
getDerivedBioAssayMap()
Get method for derivedBioAssayMap |
DerivedBioAssayData |
getFromDerivedBioAssayData(int position)
Method to get DerivedBioAssayData from DerivedBioAssayData_list |
BioAssayMap |
getFromDerivedBioAssayMap(int position)
Method to get BioAssayMap from DerivedBioAssayMap_list |
java.lang.String |
getModelClassName()
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OntologyEntry |
getType()
Get method for type |
void |
removeElementAtFromDerivedBioAssayData(int position)
Method to remove by position from DerivedBioAssayData_list |
void |
removeElementAtFromDerivedBioAssayMap(int position)
Method to remove by position from DerivedBioAssayMap_list |
void |
removeFromDerivedBioAssayData(DerivedBioAssayData derivedBioAssayData)
Method to remove first DerivedBioAssayData from DerivedBioAssayData_list |
void |
removeFromDerivedBioAssayMap(BioAssayMap bioAssayMap)
Method to remove first BioAssayMap from DerivedBioAssayMap_list |
void |
setAttributes(org.xml.sax.Attributes atts)
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void |
setDerivedBioAssayData(HasDerivedBioAssayData.DerivedBioAssayData_list derivedBioAssayData)
Set method for derivedBioAssayData |
void |
setDerivedBioAssayMap(HasDerivedBioAssayMap.DerivedBioAssayMap_list derivedBioAssayMap)
Set method for derivedBioAssayMap |
void |
setType(OntologyEntry type)
Set method for type |
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.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 OntologyEntry type
protected java.util.List derivedBioAssayData
protected java.util.List derivedBioAssayMap
Constructor Detail |
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public DerivedBioAssay()
public DerivedBioAssay(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 BioAssay
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class BioAssay
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class BioAssay
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class BioAssay
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class BioAssay
public void setType(OntologyEntry type)
setType
in interface HasType
value
- to setpublic OntologyEntry getType()
getType
in interface HasType
public void setDerivedBioAssayData(HasDerivedBioAssayData.DerivedBioAssayData_list derivedBioAssayData)
setDerivedBioAssayData
in interface HasDerivedBioAssayData
value
- to setpublic HasDerivedBioAssayData.DerivedBioAssayData_list getDerivedBioAssayData()
getDerivedBioAssayData
in interface HasDerivedBioAssayData
public void addToDerivedBioAssayData(DerivedBioAssayData derivedBioAssayData)
addToDerivedBioAssayData
in interface HasDerivedBioAssayData
public void addToDerivedBioAssayData(int position, DerivedBioAssayData derivedBioAssayData)
addToDerivedBioAssayData
in interface HasDerivedBioAssayData
public DerivedBioAssayData getFromDerivedBioAssayData(int position)
getFromDerivedBioAssayData
in interface HasDerivedBioAssayData
public void removeElementAtFromDerivedBioAssayData(int position)
removeElementAtFromDerivedBioAssayData
in interface HasDerivedBioAssayData
public void removeFromDerivedBioAssayData(DerivedBioAssayData derivedBioAssayData)
removeFromDerivedBioAssayData
in interface HasDerivedBioAssayData
public void setDerivedBioAssayMap(HasDerivedBioAssayMap.DerivedBioAssayMap_list derivedBioAssayMap)
setDerivedBioAssayMap
in interface HasDerivedBioAssayMap
value
- to setpublic HasDerivedBioAssayMap.DerivedBioAssayMap_list getDerivedBioAssayMap()
getDerivedBioAssayMap
in interface HasDerivedBioAssayMap
public void addToDerivedBioAssayMap(BioAssayMap bioAssayMap)
addToDerivedBioAssayMap
in interface HasDerivedBioAssayMap
public void addToDerivedBioAssayMap(int position, BioAssayMap bioAssayMap)
addToDerivedBioAssayMap
in interface HasDerivedBioAssayMap
public BioAssayMap getFromDerivedBioAssayMap(int position)
getFromDerivedBioAssayMap
in interface HasDerivedBioAssayMap
public void removeElementAtFromDerivedBioAssayMap(int position)
removeElementAtFromDerivedBioAssayMap
in interface HasDerivedBioAssayMap
public void removeFromDerivedBioAssayMap(BioAssayMap bioAssayMap)
removeFromDerivedBioAssayMap
in interface HasDerivedBioAssayMap
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