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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Experiment.ExperimentDesign
public class ExperimentDesign
The ExperimentDesign is the description and collection of ExperimentalFactors and the hierarchy of BioAssays to which they pertain.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasTopLevelBioAssays |
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HasTopLevelBioAssays.TopLevelBioAssays_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasExperimentalFactors |
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HasExperimentalFactors.ExperimentalFactors_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasTypes |
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HasTypes.Types_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 |
experimentalFactors
The description of the factors (TimeCourse, Dosage, etc.) that group the BioAssays. |
protected Description |
normalizationDescription
Description of the normalization strategy of the Experiment. |
protected Description |
qualityControlDescription
Description of the quality control aspects of the Experiment. |
protected Description |
replicateDescription
Description of the replicate strategy of the Experiment. |
protected java.util.List |
topLevelBioAssays
The organization of the BioAssays as specified by the ExperimentDesign (TimeCourse, Dosage, etc.) |
protected java.util.List |
types
Classification of an experiment. |
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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ExperimentDesign()
Default constructor. |
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ExperimentDesign(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToExperimentalFactors(ExperimentalFactor experimentalFactor)
Method to add ExperimentalFactor to ExperimentalFactors_list |
void |
addToExperimentalFactors(int position,
ExperimentalFactor experimentalFactor)
Method to add ExperimentalFactor at position to ExperimentalFactors_list |
void |
addToTopLevelBioAssays(BioAssay bioAssay)
Method to add BioAssay to TopLevelBioAssays_list |
void |
addToTopLevelBioAssays(int position,
BioAssay bioAssay)
Method to add BioAssay at position to TopLevelBioAssays_list |
void |
addToTypes(int position,
OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to Types_list |
void |
addToTypes(OntologyEntry ontologyEntry)
Method to add OntologyEntry to Types_list |
boolean |
emptyMAGEobject()
|
HasExperimentalFactors.ExperimentalFactors_list |
getExperimentalFactors()
Get method for experimentalFactors |
ExperimentalFactor |
getFromExperimentalFactors(int position)
Method to get ExperimentalFactor from ExperimentalFactors_list |
BioAssay |
getFromTopLevelBioAssays(int position)
Method to get BioAssay from TopLevelBioAssays_list |
OntologyEntry |
getFromTypes(int position)
Method to get OntologyEntry from Types_list |
java.lang.String |
getModelClassName()
|
Description |
getNormalizationDescription()
Get method for normalizationDescription |
Description |
getQualityControlDescription()
Get method for qualityControlDescription |
Description |
getReplicateDescription()
Get method for replicateDescription |
HasTopLevelBioAssays.TopLevelBioAssays_list |
getTopLevelBioAssays()
Get method for topLevelBioAssays |
HasTypes.Types_list |
getTypes()
Get method for types |
void |
removeElementAtFromExperimentalFactors(int position)
Method to remove by position from ExperimentalFactors_list |
void |
removeElementAtFromTopLevelBioAssays(int position)
Method to remove by position from TopLevelBioAssays_list |
void |
removeElementAtFromTypes(int position)
Method to remove by position from Types_list |
void |
removeFromExperimentalFactors(ExperimentalFactor experimentalFactor)
Method to remove first ExperimentalFactor from ExperimentalFactors_list |
void |
removeFromTopLevelBioAssays(BioAssay bioAssay)
Method to remove first BioAssay from TopLevelBioAssays_list |
void |
removeFromTypes(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from Types_list |
void |
setExperimentalFactors(HasExperimentalFactors.ExperimentalFactors_list experimentalFactors)
Set method for experimentalFactors |
void |
setNormalizationDescription(Description normalizationDescription)
Set method for normalizationDescription |
void |
setQualityControlDescription(Description qualityControlDescription)
Set method for qualityControlDescription |
void |
setReplicateDescription(Description replicateDescription)
Set method for replicateDescription |
void |
setTopLevelBioAssays(HasTopLevelBioAssays.TopLevelBioAssays_list topLevelBioAssays)
Set method for topLevelBioAssays |
void |
setTypes(HasTypes.Types_list types)
Set method for types |
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.Describable |
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addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAttributes, 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, toString |
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 types
protected java.util.List topLevelBioAssays
protected java.util.List experimentalFactors
protected Description qualityControlDescription
protected Description normalizationDescription
protected Description replicateDescription
Constructor Detail |
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public ExperimentDesign()
public ExperimentDesign(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
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public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class Describable
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class Describable
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class Describable
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class Describable
public void setTypes(HasTypes.Types_list types)
setTypes
in interface HasTypes
value
- to setpublic HasTypes.Types_list getTypes()
getTypes
in interface HasTypes
public void addToTypes(OntologyEntry ontologyEntry)
addToTypes
in interface HasTypes
public void addToTypes(int position, OntologyEntry ontologyEntry)
addToTypes
in interface HasTypes
public OntologyEntry getFromTypes(int position)
getFromTypes
in interface HasTypes
public void removeElementAtFromTypes(int position)
removeElementAtFromTypes
in interface HasTypes
public void removeFromTypes(OntologyEntry ontologyEntry)
removeFromTypes
in interface HasTypes
public void setTopLevelBioAssays(HasTopLevelBioAssays.TopLevelBioAssays_list topLevelBioAssays)
setTopLevelBioAssays
in interface HasTopLevelBioAssays
value
- to setpublic HasTopLevelBioAssays.TopLevelBioAssays_list getTopLevelBioAssays()
getTopLevelBioAssays
in interface HasTopLevelBioAssays
public void addToTopLevelBioAssays(BioAssay bioAssay)
addToTopLevelBioAssays
in interface HasTopLevelBioAssays
public void addToTopLevelBioAssays(int position, BioAssay bioAssay)
addToTopLevelBioAssays
in interface HasTopLevelBioAssays
public BioAssay getFromTopLevelBioAssays(int position)
getFromTopLevelBioAssays
in interface HasTopLevelBioAssays
public void removeElementAtFromTopLevelBioAssays(int position)
removeElementAtFromTopLevelBioAssays
in interface HasTopLevelBioAssays
public void removeFromTopLevelBioAssays(BioAssay bioAssay)
removeFromTopLevelBioAssays
in interface HasTopLevelBioAssays
public void setExperimentalFactors(HasExperimentalFactors.ExperimentalFactors_list experimentalFactors)
setExperimentalFactors
in interface HasExperimentalFactors
value
- to setpublic HasExperimentalFactors.ExperimentalFactors_list getExperimentalFactors()
getExperimentalFactors
in interface HasExperimentalFactors
public void addToExperimentalFactors(ExperimentalFactor experimentalFactor)
addToExperimentalFactors
in interface HasExperimentalFactors
public void addToExperimentalFactors(int position, ExperimentalFactor experimentalFactor)
addToExperimentalFactors
in interface HasExperimentalFactors
public ExperimentalFactor getFromExperimentalFactors(int position)
getFromExperimentalFactors
in interface HasExperimentalFactors
public void removeElementAtFromExperimentalFactors(int position)
removeElementAtFromExperimentalFactors
in interface HasExperimentalFactors
public void removeFromExperimentalFactors(ExperimentalFactor experimentalFactor)
removeFromExperimentalFactors
in interface HasExperimentalFactors
public void setQualityControlDescription(Description qualityControlDescription)
setQualityControlDescription
in interface HasQualityControlDescription
value
- to setpublic Description getQualityControlDescription()
getQualityControlDescription
in interface HasQualityControlDescription
public void setNormalizationDescription(Description normalizationDescription)
setNormalizationDescription
in interface HasNormalizationDescription
value
- to setpublic Description getNormalizationDescription()
getNormalizationDescription
in interface HasNormalizationDescription
public void setReplicateDescription(Description replicateDescription)
setReplicateDescription
in interface HasReplicateDescription
value
- to setpublic Description getReplicateDescription()
getReplicateDescription
in interface HasReplicateDescription
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