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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.BioAssayData.BioAssayData
public abstract class BioAssayData
Represents the dataset created when the BioAssays are created. BioAssayData is the entry point to the values. Because the actual values are represented by a different object, BioDataValues, which can be memory intensive, the annotation of the transformation can be gotten separate from the data.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasSummaryStatistics |
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HasSummaryStatistics.SummaryStatistics_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 BioAssayDimension |
bioAssayDimension
The BioAssays of the BioAssayData. |
protected BioDataValues |
bioDataValues
The data values of the BioAssayData. |
protected DesignElementDimension |
designElementDimension
The DesignElements of the BioAssayData. |
protected QuantitationTypeDimension |
quantitationTypeDimension
The QuantitationTypes of the BioAssayData. |
protected java.util.List |
summaryStatistics
Statistics on the Quality of the BioAssayData. |
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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BioAssayData()
Default constructor. |
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BioAssayData(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToSummaryStatistics(int position,
NameValueType nameValueType)
Method to add NameValueType at position to SummaryStatistics_list |
void |
addToSummaryStatistics(NameValueType nameValueType)
Method to add NameValueType to SummaryStatistics_list |
BioAssayDimension |
getBioAssayDimension()
Get method for bioAssayDimension |
BioDataValues |
getBioDataValues()
Get method for bioDataValues |
DesignElementDimension |
getDesignElementDimension()
Get method for designElementDimension |
NameValueType |
getFromSummaryStatistics(int position)
Method to get NameValueType from SummaryStatistics_list |
java.lang.String |
getModelClassName()
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QuantitationTypeDimension |
getQuantitationTypeDimension()
Get method for quantitationTypeDimension |
HasSummaryStatistics.SummaryStatistics_list |
getSummaryStatistics()
Get method for summaryStatistics |
void |
removeElementAtFromSummaryStatistics(int position)
Method to remove by position from SummaryStatistics_list |
void |
removeFromSummaryStatistics(NameValueType nameValueType)
Method to remove first NameValueType from SummaryStatistics_list |
void |
setAttributes(org.xml.sax.Attributes atts)
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void |
setBioAssayDimension(BioAssayDimension bioAssayDimension)
Set method for bioAssayDimension |
void |
setBioDataValues(BioDataValues bioDataValues)
Set method for bioDataValues |
void |
setDesignElementDimension(DesignElementDimension designElementDimension)
Set method for designElementDimension |
void |
setQuantitationTypeDimension(QuantitationTypeDimension quantitationTypeDimension)
Set method for quantitationTypeDimension |
void |
setSummaryStatistics(HasSummaryStatistics.SummaryStatistics_list summaryStatistics)
Set method for summaryStatistics |
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.util.List summaryStatistics
protected BioAssayDimension bioAssayDimension
protected DesignElementDimension designElementDimension
protected QuantitationTypeDimension quantitationTypeDimension
protected BioDataValues bioDataValues
Constructor Detail |
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public BioAssayData()
public BioAssayData(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 setSummaryStatistics(HasSummaryStatistics.SummaryStatistics_list summaryStatistics)
setSummaryStatistics
in interface HasSummaryStatistics
value
- to setpublic HasSummaryStatistics.SummaryStatistics_list getSummaryStatistics()
getSummaryStatistics
in interface HasSummaryStatistics
public void addToSummaryStatistics(NameValueType nameValueType)
addToSummaryStatistics
in interface HasSummaryStatistics
public void addToSummaryStatistics(int position, NameValueType nameValueType)
addToSummaryStatistics
in interface HasSummaryStatistics
public NameValueType getFromSummaryStatistics(int position)
getFromSummaryStatistics
in interface HasSummaryStatistics
public void removeElementAtFromSummaryStatistics(int position)
removeElementAtFromSummaryStatistics
in interface HasSummaryStatistics
public void removeFromSummaryStatistics(NameValueType nameValueType)
removeFromSummaryStatistics
in interface HasSummaryStatistics
public void setBioAssayDimension(BioAssayDimension bioAssayDimension)
setBioAssayDimension
in interface HasBioAssayDimension
value
- to setpublic BioAssayDimension getBioAssayDimension()
getBioAssayDimension
in interface HasBioAssayDimension
public void setDesignElementDimension(DesignElementDimension designElementDimension)
setDesignElementDimension
in interface HasDesignElementDimension
value
- to setpublic DesignElementDimension getDesignElementDimension()
getDesignElementDimension
in interface HasDesignElementDimension
public void setQuantitationTypeDimension(QuantitationTypeDimension quantitationTypeDimension)
setQuantitationTypeDimension
in interface HasQuantitationTypeDimension
value
- to setpublic QuantitationTypeDimension getQuantitationTypeDimension()
getQuantitationTypeDimension
in interface HasQuantitationTypeDimension
public void setBioDataValues(BioDataValues bioDataValues)
setBioDataValues
in interface HasBioDataValues
value
- to setpublic BioDataValues getBioDataValues()
getBioDataValues
in interface HasBioDataValues
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