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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.Experiment.ExperimentalFactor
public class ExperimentalFactor
ExperimentFactors are the dependent variables of an experiment (e.g. time, glucose concentration, ...).
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasFactorValues |
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HasFactorValues.FactorValues_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAnnotations |
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HasAnnotations.Annotations_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 |
annotations
Allows describing additional information such as concentration of Tamoxafin with a CASRegistry #. |
protected OntologyEntry |
category
The category of an ExperimentalFactor could be biological (time, [glucose]) or a methodological factor (differing cDNA preparation protocols). |
protected java.util.List |
factorValues
The pairing of BioAssay FactorValues with the ExperimentDesign ExperimentFactor. |
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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ExperimentalFactor()
Default constructor. |
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ExperimentalFactor(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToAnnotations(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Annotations_list |
void |
addToAnnotations(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Annotations_list |
void |
addToFactorValues(FactorValue factorValue)
Method to add FactorValue to FactorValues_list |
void |
addToFactorValues(int position,
FactorValue factorValue)
Method to add FactorValue at position to FactorValues_list |
boolean |
emptyMAGEobject()
|
HasAnnotations.Annotations_list |
getAnnotations()
Get method for annotations |
OntologyEntry |
getCategory()
Get method for category |
HasFactorValues.FactorValues_list |
getFactorValues()
Get method for factorValues |
OntologyEntry |
getFromAnnotations(int position)
Method to get OntologyEntry from Annotations_list |
FactorValue |
getFromFactorValues(int position)
Method to get FactorValue from FactorValues_list |
java.lang.String |
getModelClassName()
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void |
removeElementAtFromAnnotations(int position)
Method to remove by position from Annotations_list |
void |
removeElementAtFromFactorValues(int position)
Method to remove by position from FactorValues_list |
void |
removeFromAnnotations(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Annotations_list |
void |
removeFromFactorValues(FactorValue factorValue)
Method to remove first FactorValue from FactorValues_list |
void |
setAnnotations(HasAnnotations.Annotations_list annotations)
Set method for annotations |
void |
setAttributes(org.xml.sax.Attributes atts)
|
void |
setCategory(OntologyEntry category)
Set method for category |
void |
setFactorValues(HasFactorValues.FactorValues_list factorValues)
Set method for factorValues |
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 category
protected java.util.List factorValues
protected java.util.List annotations
Constructor Detail |
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public ExperimentalFactor()
public ExperimentalFactor(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 boolean emptyMAGEobject()
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 setCategory(OntologyEntry category)
setCategory
in interface HasCategory
value
- to setpublic OntologyEntry getCategory()
getCategory
in interface HasCategory
public void setFactorValues(HasFactorValues.FactorValues_list factorValues)
setFactorValues
in interface HasFactorValues
value
- to setpublic HasFactorValues.FactorValues_list getFactorValues()
getFactorValues
in interface HasFactorValues
public void addToFactorValues(FactorValue factorValue)
addToFactorValues
in interface HasFactorValues
public void addToFactorValues(int position, FactorValue factorValue)
addToFactorValues
in interface HasFactorValues
public FactorValue getFromFactorValues(int position)
getFromFactorValues
in interface HasFactorValues
public void removeElementAtFromFactorValues(int position)
removeElementAtFromFactorValues
in interface HasFactorValues
public void removeFromFactorValues(FactorValue factorValue)
removeFromFactorValues
in interface HasFactorValues
public void setAnnotations(HasAnnotations.Annotations_list annotations)
setAnnotations
in interface HasAnnotations
value
- to setpublic HasAnnotations.Annotations_list getAnnotations()
getAnnotations
in interface HasAnnotations
public void addToAnnotations(OntologyEntry ontologyEntry)
addToAnnotations
in interface HasAnnotations
public void addToAnnotations(int position, OntologyEntry ontologyEntry)
addToAnnotations
in interface HasAnnotations
public OntologyEntry getFromAnnotations(int position)
getFromAnnotations
in interface HasAnnotations
public void removeElementAtFromAnnotations(int position)
removeElementAtFromAnnotations
in interface HasAnnotations
public void removeFromAnnotations(OntologyEntry ontologyEntry)
removeFromAnnotations
in interface HasAnnotations
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