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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.BioEvent.BioEvent
org.biomage.BioAssay.BioAssayCreation
public class BioAssayCreation
The process by which an array and one or more biomaterials are combined to create a bioAssayCreation.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasSourceBioMaterialMeasurements |
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HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_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 Array |
array
The array used in the BioAssayCreation event. |
protected java.lang.String |
ojbConcreteClass
|
protected PhysicalBioAssay |
physicalBioAssayTarget
The association between the BioAssayCreation event (typically Hybridization) and the PhysicalBioAssay and its annotation of this event. |
protected java.util.List |
sourceBioMaterialMeasurements
The BioSample and its amount used in the BioAssayCreation event. |
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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BioAssayCreation()
Default constructor. |
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BioAssayCreation(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToSourceBioMaterialMeasurements(BioMaterialMeasurement bioMaterialMeasurement)
Method to add BioMaterialMeasurement to SourceBioMaterialMeasurements_list |
void |
addToSourceBioMaterialMeasurements(int position,
BioMaterialMeasurement bioMaterialMeasurement)
Method to add BioMaterialMeasurement at position to SourceBioMaterialMeasurements_list |
boolean |
emptyMAGEobject()
|
Array |
getArray()
Get method for array |
BioMaterialMeasurement |
getFromSourceBioMaterialMeasurements(int position)
Method to get BioMaterialMeasurement from SourceBioMaterialMeasurements_list |
java.lang.String |
getModelClassName()
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PhysicalBioAssay |
getPhysicalBioAssayTarget()
Get method for physicalBioAssayTarget |
HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list |
getSourceBioMaterialMeasurements()
Get method for sourceBioMaterialMeasurements |
void |
removeElementAtFromSourceBioMaterialMeasurements(int position)
Method to remove by position from SourceBioMaterialMeasurements_list |
void |
removeFromSourceBioMaterialMeasurements(BioMaterialMeasurement bioMaterialMeasurement)
Method to remove first BioMaterialMeasurement from SourceBioMaterialMeasurements_list |
void |
setArray(Array array)
Set method for array |
void |
setAttributes(org.xml.sax.Attributes atts)
|
void |
setPhysicalBioAssayTarget(PhysicalBioAssay physicalBioAssayTarget)
Set method for physicalBioAssayTarget |
void |
setSourceBioMaterialMeasurements(HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list sourceBioMaterialMeasurements)
Set method for sourceBioMaterialMeasurements |
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.lang.String ojbConcreteClass
protected java.util.List sourceBioMaterialMeasurements
protected Array array
protected PhysicalBioAssay physicalBioAssayTarget
Constructor Detail |
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public BioAssayCreation()
public BioAssayCreation(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 setSourceBioMaterialMeasurements(HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list sourceBioMaterialMeasurements)
setSourceBioMaterialMeasurements
in interface HasSourceBioMaterialMeasurements
value
- to setpublic HasSourceBioMaterialMeasurements.SourceBioMaterialMeasurements_list getSourceBioMaterialMeasurements()
getSourceBioMaterialMeasurements
in interface HasSourceBioMaterialMeasurements
public void addToSourceBioMaterialMeasurements(BioMaterialMeasurement bioMaterialMeasurement)
addToSourceBioMaterialMeasurements
in interface HasSourceBioMaterialMeasurements
public void addToSourceBioMaterialMeasurements(int position, BioMaterialMeasurement bioMaterialMeasurement)
addToSourceBioMaterialMeasurements
in interface HasSourceBioMaterialMeasurements
public BioMaterialMeasurement getFromSourceBioMaterialMeasurements(int position)
getFromSourceBioMaterialMeasurements
in interface HasSourceBioMaterialMeasurements
public void removeElementAtFromSourceBioMaterialMeasurements(int position)
removeElementAtFromSourceBioMaterialMeasurements
in interface HasSourceBioMaterialMeasurements
public void removeFromSourceBioMaterialMeasurements(BioMaterialMeasurement bioMaterialMeasurement)
removeFromSourceBioMaterialMeasurements
in interface HasSourceBioMaterialMeasurements
public void setArray(Array array)
setArray
in interface HasArray
value
- to setpublic Array getArray()
getArray
in interface HasArray
public void setPhysicalBioAssayTarget(PhysicalBioAssay physicalBioAssayTarget)
setPhysicalBioAssayTarget
in interface HasPhysicalBioAssayTarget
value
- to setpublic PhysicalBioAssay getPhysicalBioAssayTarget()
getPhysicalBioAssayTarget
in interface HasPhysicalBioAssayTarget
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