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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.BioAssay.BioAssay
org.biomage.BioAssay.MeasuredBioAssay
public class MeasuredBioAssay
A measured bioAssay is the direct processing of information in a physical bioAssay by the featureExtraction event. Often uses images which are referenced through the physical bioAssay.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasMeasuredBioAssayData |
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HasMeasuredBioAssayData.MeasuredBioAssayData_list |
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 FeatureExtraction |
featureExtraction
The association between the MeasuredBioAssay and the FeatureExtraction Event. |
protected java.util.List |
measuredBioAssayData
The data associated with the MeasuredBioAssay. |
Fields inherited from class org.biomage.BioAssay.BioAssay |
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bioAssayFactorValues, channels, deleted, ojbConcreteClass |
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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MeasuredBioAssay()
Default constructor. |
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MeasuredBioAssay(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToMeasuredBioAssayData(int position,
MeasuredBioAssayData measuredBioAssayData)
Method to add MeasuredBioAssayData at position to MeasuredBioAssayData_list |
void |
addToMeasuredBioAssayData(MeasuredBioAssayData measuredBioAssayData)
Method to add MeasuredBioAssayData to MeasuredBioAssayData_list |
boolean |
emptyMAGEobject()
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FeatureExtraction |
getFeatureExtraction()
Get method for featureExtraction |
MeasuredBioAssayData |
getFromMeasuredBioAssayData(int position)
Method to get MeasuredBioAssayData from MeasuredBioAssayData_list |
HasMeasuredBioAssayData.MeasuredBioAssayData_list |
getMeasuredBioAssayData()
Get method for measuredBioAssayData |
java.lang.String |
getModelClassName()
|
void |
removeElementAtFromMeasuredBioAssayData(int position)
Method to remove by position from MeasuredBioAssayData_list |
void |
removeFromMeasuredBioAssayData(MeasuredBioAssayData measuredBioAssayData)
Method to remove first MeasuredBioAssayData from MeasuredBioAssayData_list |
void |
setAttributes(org.xml.sax.Attributes atts)
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void |
setFeatureExtraction(FeatureExtraction featureExtraction)
Set method for featureExtraction |
void |
setMeasuredBioAssayData(HasMeasuredBioAssayData.MeasuredBioAssayData_list measuredBioAssayData)
Set method for measuredBioAssayData |
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 FeatureExtraction featureExtraction
protected java.util.List measuredBioAssayData
Constructor Detail |
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public MeasuredBioAssay()
public MeasuredBioAssay(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 BioAssay
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class BioAssay
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class BioAssay
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class BioAssay
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class BioAssay
public void setFeatureExtraction(FeatureExtraction featureExtraction)
setFeatureExtraction
in interface HasFeatureExtraction
value
- to setpublic FeatureExtraction getFeatureExtraction()
getFeatureExtraction
in interface HasFeatureExtraction
public void setMeasuredBioAssayData(HasMeasuredBioAssayData.MeasuredBioAssayData_list measuredBioAssayData)
setMeasuredBioAssayData
in interface HasMeasuredBioAssayData
value
- to setpublic HasMeasuredBioAssayData.MeasuredBioAssayData_list getMeasuredBioAssayData()
getMeasuredBioAssayData
in interface HasMeasuredBioAssayData
public void addToMeasuredBioAssayData(MeasuredBioAssayData measuredBioAssayData)
addToMeasuredBioAssayData
in interface HasMeasuredBioAssayData
public void addToMeasuredBioAssayData(int position, MeasuredBioAssayData measuredBioAssayData)
addToMeasuredBioAssayData
in interface HasMeasuredBioAssayData
public MeasuredBioAssayData getFromMeasuredBioAssayData(int position)
getFromMeasuredBioAssayData
in interface HasMeasuredBioAssayData
public void removeElementAtFromMeasuredBioAssayData(int position)
removeElementAtFromMeasuredBioAssayData
in interface HasMeasuredBioAssayData
public void removeFromMeasuredBioAssayData(MeasuredBioAssayData measuredBioAssayData)
removeFromMeasuredBioAssayData
in interface HasMeasuredBioAssayData
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