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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.BioAssay.BioAssay
public abstract class BioAssay
An abstract class which represents both physical and computational groupings of arrays and biomaterials.
Nested Class Summary |
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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 |
bioAssayFactorValues
The values that this BioAssay is associated with for the experiment. |
protected java.util.List |
channels
Channels can be non-null for all subclasses. |
protected boolean |
deleted
caARRAY-specific marker for a DELETED BioAssay. |
protected java.lang.String |
ojbConcreteClass
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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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BioAssay()
Default constructor. |
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BioAssay(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToBioAssayFactorValues(FactorValue factorValue)
Method to add FactorValue to BioAssayFactorValues_list |
void |
addToBioAssayFactorValues(int position,
FactorValue factorValue)
Method to add FactorValue at position to BioAssayFactorValues_list |
void |
addToChannels(Channel channel)
Method to add Channel to Channels_list |
void |
addToChannels(int position,
Channel channel)
Method to add Channel at position to Channels_list |
HasBioAssayFactorValues.BioAssayFactorValues_list |
getBioAssayFactorValues()
Get method for bioAssayFactorValues |
HasChannels.Channels_list |
getChannels()
Get method for channels |
FactorValue |
getFromBioAssayFactorValues(int position)
Method to get FactorValue from BioAssayFactorValues_list |
Channel |
getFromChannels(int position)
Method to get Channel from Channels_list |
java.lang.String |
getModelClassName()
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boolean |
isDeleted()
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void |
removeElementAtFromBioAssayFactorValues(int position)
Method to remove by position from BioAssayFactorValues_list |
void |
removeElementAtFromChannels(int position)
Method to remove by position from Channels_list |
void |
removeFromBioAssayFactorValues(FactorValue factorValue)
Method to remove first FactorValue from BioAssayFactorValues_list |
void |
removeFromChannels(Channel channel)
Method to remove first Channel from Channels_list |
void |
setAttributes(org.xml.sax.Attributes atts)
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void |
setBioAssayFactorValues(HasBioAssayFactorValues.BioAssayFactorValues_list bioAssayFactorValues)
Set method for bioAssayFactorValues |
void |
setChannels(HasChannels.Channels_list channels)
Set method for channels |
void |
setDeleted(boolean deleted)
Marks if this BioAssay is deleted. |
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.lang.String ojbConcreteClass
protected java.util.List channels
protected java.util.List bioAssayFactorValues
protected boolean deleted
Constructor Detail |
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public BioAssay()
public BioAssay(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 setChannels(HasChannels.Channels_list channels)
setChannels
in interface HasChannels
value
- to setpublic HasChannels.Channels_list getChannels()
getChannels
in interface HasChannels
public void addToChannels(Channel channel)
addToChannels
in interface HasChannels
public void addToChannels(int position, Channel channel)
addToChannels
in interface HasChannels
public Channel getFromChannels(int position)
getFromChannels
in interface HasChannels
public void removeElementAtFromChannels(int position)
removeElementAtFromChannels
in interface HasChannels
public void removeFromChannels(Channel channel)
removeFromChannels
in interface HasChannels
public void setBioAssayFactorValues(HasBioAssayFactorValues.BioAssayFactorValues_list bioAssayFactorValues)
setBioAssayFactorValues
in interface HasBioAssayFactorValues
value
- to setpublic HasBioAssayFactorValues.BioAssayFactorValues_list getBioAssayFactorValues()
getBioAssayFactorValues
in interface HasBioAssayFactorValues
public void addToBioAssayFactorValues(FactorValue factorValue)
addToBioAssayFactorValues
in interface HasBioAssayFactorValues
public void addToBioAssayFactorValues(int position, FactorValue factorValue)
addToBioAssayFactorValues
in interface HasBioAssayFactorValues
public FactorValue getFromBioAssayFactorValues(int position)
getFromBioAssayFactorValues
in interface HasBioAssayFactorValues
public void removeElementAtFromBioAssayFactorValues(int position)
removeElementAtFromBioAssayFactorValues
in interface HasBioAssayFactorValues
public void removeFromBioAssayFactorValues(FactorValue factorValue)
removeFromBioAssayFactorValues
in interface HasBioAssayFactorValues
public boolean isDeleted()
public void setDeleted(boolean deleted)
deleted
- - True if this BioAssay is deleted; false otherwise.
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