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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.BioEvent.BioEvent
public abstract class BioEvent
An abstract class to capture the concept of an event (either in the laboratory or a computational analysis).
Nested Class Summary |
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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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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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BioEvent()
Default constructor. |
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BioEvent(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToProtocolApplications(int position,
ProtocolApplication protocolApplication)
Method to add ProtocolApplication at position to ProtocolApplications_list |
void |
addToProtocolApplications(ProtocolApplication protocolApplication)
Method to add ProtocolApplication to ProtocolApplications_list |
ProtocolApplication |
getFromProtocolApplications(int position)
Method to get ProtocolApplication from ProtocolApplications_list |
java.lang.String |
getModelClassName()
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HasProtocolApplications.ProtocolApplications_list |
getProtocolApplications()
Get method for protocolApplications |
void |
removeElementAtFromProtocolApplications(int position)
Method to remove by position from ProtocolApplications_list |
void |
removeFromProtocolApplications(ProtocolApplication protocolApplication)
Method to remove first ProtocolApplication from ProtocolApplications_list |
void |
setAttributes(org.xml.sax.Attributes atts)
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void |
setProtocolApplications(HasProtocolApplications.ProtocolApplications_list protocolApplications)
Set method for protocolApplications |
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 |
Constructor Detail |
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public BioEvent()
public BioEvent(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 Identifiable
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class Identifiable
java.io.IOException
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Identifiable
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Identifiable
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class Identifiable
public void setProtocolApplications(HasProtocolApplications.ProtocolApplications_list protocolApplications)
setProtocolApplications
in interface HasProtocolApplications
value
- to setpublic HasProtocolApplications.ProtocolApplications_list getProtocolApplications()
getProtocolApplications
in interface HasProtocolApplications
public void addToProtocolApplications(ProtocolApplication protocolApplication)
addToProtocolApplications
in interface HasProtocolApplications
public void addToProtocolApplications(int position, ProtocolApplication protocolApplication)
addToProtocolApplications
in interface HasProtocolApplications
public ProtocolApplication getFromProtocolApplications(int position)
getFromProtocolApplications
in interface HasProtocolApplications
public void removeElementAtFromProtocolApplications(int position)
removeElementAtFromProtocolApplications
in interface HasProtocolApplications
public void removeFromProtocolApplications(ProtocolApplication protocolApplication)
removeFromProtocolApplications
in interface HasProtocolApplications
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