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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.PhysicalBioAssay
public class PhysicalBioAssay
A bioAssay created by the bioAssayCreation event (e.g. in gene expression analysis this event is represented by the hybridization event).
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasPhysicalBioAssayData |
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HasPhysicalBioAssayData.PhysicalBioAssayData_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasBioAssayTreatments |
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HasBioAssayTreatments.BioAssayTreatments_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 BioAssayCreation |
bioAssayCreation
The association between the BioAssayCreation event (typically Hybridization) and the PhysicalBioAssay and its annotation of this event. |
protected java.util.List |
bioAssayTreatments
The set of treatments undergone by this PhysicalBioAssay. |
protected java.util.List |
physicalBioAssayData
The Images associated with this PhysicalBioAssay by ImageAcquisition. |
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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PhysicalBioAssay()
Default constructor. |
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PhysicalBioAssay(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToBioAssayTreatments(BioAssayTreatment bioAssayTreatment)
Method to add BioAssayTreatment to BioAssayTreatments_list |
void |
addToBioAssayTreatments(int position,
BioAssayTreatment bioAssayTreatment)
Method to add BioAssayTreatment at position to BioAssayTreatments_list |
void |
addToPhysicalBioAssayData(Image image)
Method to add Image to PhysicalBioAssayData_list |
void |
addToPhysicalBioAssayData(int position,
Image image)
Method to add Image at position to PhysicalBioAssayData_list |
boolean |
emptyMAGEobject()
|
BioAssayCreation |
getBioAssayCreation()
Get method for bioAssayCreation |
HasBioAssayTreatments.BioAssayTreatments_list |
getBioAssayTreatments()
Get method for bioAssayTreatments |
BioAssayTreatment |
getFromBioAssayTreatments(int position)
Method to get BioAssayTreatment from BioAssayTreatments_list |
Image |
getFromPhysicalBioAssayData(int position)
Method to get Image from PhysicalBioAssayData_list |
java.lang.String |
getModelClassName()
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HasPhysicalBioAssayData.PhysicalBioAssayData_list |
getPhysicalBioAssayData()
Get method for physicalBioAssayData |
void |
removeElementAtFromBioAssayTreatments(int position)
Method to remove by position from BioAssayTreatments_list |
void |
removeElementAtFromPhysicalBioAssayData(int position)
Method to remove by position from PhysicalBioAssayData_list |
void |
removeFromBioAssayTreatments(BioAssayTreatment bioAssayTreatment)
Method to remove first BioAssayTreatment from BioAssayTreatments_list |
void |
removeFromPhysicalBioAssayData(Image image)
Method to remove first Image from PhysicalBioAssayData_list |
void |
setAttributes(org.xml.sax.Attributes atts)
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void |
setBioAssayCreation(BioAssayCreation bioAssayCreation)
Set method for bioAssayCreation |
void |
setBioAssayTreatments(HasBioAssayTreatments.BioAssayTreatments_list bioAssayTreatments)
Set method for bioAssayTreatments |
void |
setPhysicalBioAssayData(HasPhysicalBioAssayData.PhysicalBioAssayData_list physicalBioAssayData)
Set method for physicalBioAssayData |
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 java.util.List physicalBioAssayData
protected BioAssayCreation bioAssayCreation
protected java.util.List bioAssayTreatments
Constructor Detail |
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public PhysicalBioAssay()
public PhysicalBioAssay(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 setPhysicalBioAssayData(HasPhysicalBioAssayData.PhysicalBioAssayData_list physicalBioAssayData)
setPhysicalBioAssayData
in interface HasPhysicalBioAssayData
value
- to setpublic HasPhysicalBioAssayData.PhysicalBioAssayData_list getPhysicalBioAssayData()
getPhysicalBioAssayData
in interface HasPhysicalBioAssayData
public void addToPhysicalBioAssayData(Image image)
addToPhysicalBioAssayData
in interface HasPhysicalBioAssayData
public void addToPhysicalBioAssayData(int position, Image image)
addToPhysicalBioAssayData
in interface HasPhysicalBioAssayData
public Image getFromPhysicalBioAssayData(int position)
getFromPhysicalBioAssayData
in interface HasPhysicalBioAssayData
public void removeElementAtFromPhysicalBioAssayData(int position)
removeElementAtFromPhysicalBioAssayData
in interface HasPhysicalBioAssayData
public void removeFromPhysicalBioAssayData(Image image)
removeFromPhysicalBioAssayData
in interface HasPhysicalBioAssayData
public void setBioAssayCreation(BioAssayCreation bioAssayCreation)
setBioAssayCreation
in interface HasBioAssayCreation
value
- to setpublic BioAssayCreation getBioAssayCreation()
getBioAssayCreation
in interface HasBioAssayCreation
public void setBioAssayTreatments(HasBioAssayTreatments.BioAssayTreatments_list bioAssayTreatments)
setBioAssayTreatments
in interface HasBioAssayTreatments
value
- to setpublic HasBioAssayTreatments.BioAssayTreatments_list getBioAssayTreatments()
getBioAssayTreatments
in interface HasBioAssayTreatments
public void addToBioAssayTreatments(BioAssayTreatment bioAssayTreatment)
addToBioAssayTreatments
in interface HasBioAssayTreatments
public void addToBioAssayTreatments(int position, BioAssayTreatment bioAssayTreatment)
addToBioAssayTreatments
in interface HasBioAssayTreatments
public BioAssayTreatment getFromBioAssayTreatments(int position)
getFromBioAssayTreatments
in interface HasBioAssayTreatments
public void removeElementAtFromBioAssayTreatments(int position)
removeElementAtFromBioAssayTreatments
in interface HasBioAssayTreatments
public void removeFromBioAssayTreatments(BioAssayTreatment bioAssayTreatment)
removeFromBioAssayTreatments
in interface HasBioAssayTreatments
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