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java.lang.Objectorg.biomage.BioAssayData.BioAssayData_package
public class BioAssayData_package
The classes defined here provide data and the information and annotation on the derivation of that data. Some of the scenarios that might occur are the following. FeatureExtraction of a single PhysicalBioAssay produces MeasuredBioAssayData that has a single BioAssay on the BioAssayDimension, typically the Features described in the ArrayDesign on the DesignElementDimension, and the Quantitations associated with the application of a FeatureExtraction protocol on the QuantitationDimension. An error model transformation might be applied that doesn't change the BioAssayDimension or the DesignElementDimension but likely changes the QuantitationDimension. A transformation on replicate Reporters or CompositeSequences might be applied on the single BioAssay that would change the DesignElementDimension and the QuantitationDimension both. Replicate and Control BioAssays might be added to the BioAssayDimension and a transformation could change the BioAssayDimension and the QuantitationDimension but not change the DesignElementDimension to produce a new DerivedBioAssayData. Or some combination of the above transformations could be performed at once to change all three dimensions. Because the classes derive from Describable, the Experimenter can provide as much detail at each level of the class hierarchy as desired.
Nested Class Summary | |
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class |
BioAssayData_package.BioAssayData_list
Inner list class for holding multiple entries for attribute bioAssayData. |
class |
BioAssayData_package.BioAssayDimension_list
Inner list class for holding multiple entries for attribute bioAssayDimension. |
class |
BioAssayData_package.BioAssayMap_list
Inner list class for holding multiple entries for attribute bioAssayMap. |
class |
BioAssayData_package.DesignElementDimension_list
Inner list class for holding multiple entries for attribute designElementDimension. |
class |
BioAssayData_package.QuantitationTypeDimension_list
Inner list class for holding multiple entries for attribute quantitationTypeDimension. |
class |
BioAssayData_package.QuantitationTypeMap_list
Inner list class for holding multiple entries for attribute quantitationTypeMap. |
Field Summary | |
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BioAssayData_package.BioAssayData_list |
bioAssayData_list
Represents the dataset created when the BioAssays are created. |
BioAssayData_package.BioAssayDimension_list |
bioAssayDimension_list
An ordered list of bioAssays. |
BioAssayData_package.BioAssayMap_list |
bioAssayMap_list
The BioAssayMap is the description of how source MeasuredBioAssays and/or DerivedBioAssays are manipulated (mathematically) to produce DerivedBioAssays. |
BioAssayData_package.DesignElementDimension_list |
designElementDimension_list
An ordered list of designElements. |
BioAssayData_package.QuantitationTypeDimension_list |
quantitationTypeDimension_list
An ordered list of quantitationTypes. |
BioAssayData_package.QuantitationTypeMap_list |
quantitationTypeMap_list
A QuantitationTypeMap is the description of how source QuantitationTypes are mathematically transformed into a target QuantitationType. |
Constructor Summary | |
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BioAssayData_package()
Default constructor. |
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BioAssayData_package(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToBioAssayData_list(BioAssayData bioAssayData)
Method to add BioAssayData to BioAssayData_list |
void |
addToBioAssayData_list(int position,
BioAssayData bioAssayData)
Method to add BioAssayData at position to BioAssayData_list |
void |
addToBioAssayDimension_list(BioAssayDimension bioAssayDimension)
Method to add BioAssayDimension to BioAssayDimension_list |
void |
addToBioAssayDimension_list(int position,
BioAssayDimension bioAssayDimension)
Method to add BioAssayDimension at position to BioAssayDimension_list |
void |
addToBioAssayMap_list(BioAssayMap bioAssayMap)
Method to add BioAssayMap to BioAssayMap_list |
void |
addToBioAssayMap_list(int position,
BioAssayMap bioAssayMap)
Method to add BioAssayMap at position to BioAssayMap_list |
void |
addToDesignElementDimension_list(DesignElementDimension designElementDimension)
Method to add DesignElementDimension to DesignElementDimension_list |
void |
addToDesignElementDimension_list(int position,
DesignElementDimension designElementDimension)
Method to add DesignElementDimension at position to DesignElementDimension_list |
void |
addToQuantitationTypeDimension_list(int position,
QuantitationTypeDimension quantitationTypeDimension)
Method to add QuantitationTypeDimension at position to QuantitationTypeDimension_list |
void |
addToQuantitationTypeDimension_list(QuantitationTypeDimension quantitationTypeDimension)
Method to add QuantitationTypeDimension to QuantitationTypeDimension_list |
void |
addToQuantitationTypeMap_list(int position,
QuantitationTypeMap quantitationTypeMap)
Method to add QuantitationTypeMap at position to QuantitationTypeMap_list |
void |
addToQuantitationTypeMap_list(QuantitationTypeMap quantitationTypeMap)
Method to add QuantitationTypeMap to QuantitationTypeMap_list |
boolean |
emptyMAGEobject()
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BioAssayData_package.BioAssayData_list |
getBioAssayData_list()
Get method for bioAssayData_list |
BioAssayData_package.BioAssayDimension_list |
getBioAssayDimension_list()
Get method for bioAssayDimension_list |
BioAssayData_package.BioAssayMap_list |
getBioAssayMap_list()
Get method for bioAssayMap_list |
BioAssayData_package.DesignElementDimension_list |
getDesignElementDimension_list()
Get method for designElementDimension_list |
BioAssayData |
getFromBioAssayData_list(int position)
Method to get BioAssayData from BioAssayData_list |
BioAssayDimension |
getFromBioAssayDimension_list(int position)
Method to get BioAssayDimension from BioAssayDimension_list |
BioAssayMap |
getFromBioAssayMap_list(int position)
Method to get BioAssayMap from BioAssayMap_list |
DesignElementDimension |
getFromDesignElementDimension_list(int position)
Method to get DesignElementDimension from DesignElementDimension_list |
QuantitationTypeDimension |
getFromQuantitationTypeDimension_list(int position)
Method to get QuantitationTypeDimension from QuantitationTypeDimension_list |
QuantitationTypeMap |
getFromQuantitationTypeMap_list(int position)
Method to get QuantitationTypeMap from QuantitationTypeMap_list |
java.lang.String |
getModelClassName()
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BioAssayData_package.QuantitationTypeDimension_list |
getQuantitationTypeDimension_list()
Get method for quantitationTypeDimension_list |
BioAssayData_package.QuantitationTypeMap_list |
getQuantitationTypeMap_list()
Get method for quantitationTypeMap_list |
void |
removeElementAtFromBioAssayData_list(int position)
Method to remove by position from BioAssayData_list |
void |
removeElementAtFromBioAssayDimension_list(int position)
Method to remove by position from BioAssayDimension_list |
void |
removeElementAtFromBioAssayMap_list(int position)
Method to remove by position from BioAssayMap_list |
void |
removeElementAtFromDesignElementDimension_list(int position)
Method to remove by position from DesignElementDimension_list |
void |
removeElementAtFromQuantitationTypeDimension_list(int position)
Method to remove by position from QuantitationTypeDimension_list |
void |
removeElementAtFromQuantitationTypeMap_list(int position)
Method to remove by position from QuantitationTypeMap_list |
void |
removeFromBioAssayData_list(BioAssayData bioAssayData)
Method to remove first BioAssayData from BioAssayData_list |
void |
removeFromBioAssayDimension_list(BioAssayDimension bioAssayDimension)
Method to remove first BioAssayDimension from BioAssayDimension_list |
void |
removeFromBioAssayMap_list(BioAssayMap bioAssayMap)
Method to remove first BioAssayMap from BioAssayMap_list |
void |
removeFromDesignElementDimension_list(DesignElementDimension designElementDimension)
Method to remove first DesignElementDimension from DesignElementDimension_list |
void |
removeFromQuantitationTypeDimension_list(QuantitationTypeDimension quantitationTypeDimension)
Method to remove first QuantitationTypeDimension from QuantitationTypeDimension_list |
void |
removeFromQuantitationTypeMap_list(QuantitationTypeMap quantitationTypeMap)
Method to remove first QuantitationTypeMap from QuantitationTypeMap_list |
void |
setBioAssayData_list(BioAssayData_package.BioAssayData_list bioAssayData_list)
Set method for bioAssayData_list |
void |
setBioAssayDimension_list(BioAssayData_package.BioAssayDimension_list bioAssayDimension_list)
Set method for bioAssayDimension_list |
void |
setBioAssayMap_list(BioAssayData_package.BioAssayMap_list bioAssayMap_list)
Set method for bioAssayMap_list |
void |
setDesignElementDimension_list(BioAssayData_package.DesignElementDimension_list designElementDimension_list)
Set method for designElementDimension_list |
void |
setQuantitationTypeDimension_list(BioAssayData_package.QuantitationTypeDimension_list quantitationTypeDimension_list)
Set method for quantitationTypeDimension_list |
void |
setQuantitationTypeMap_list(BioAssayData_package.QuantitationTypeMap_list quantitationTypeMap_list)
Set method for quantitationTypeMap_list |
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 java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public BioAssayData_package.BioAssayDimension_list bioAssayDimension_list
public BioAssayData_package.DesignElementDimension_list designElementDimension_list
public BioAssayData_package.QuantitationTypeDimension_list quantitationTypeDimension_list
public BioAssayData_package.BioAssayMap_list bioAssayMap_list
public BioAssayData_package.QuantitationTypeMap_list quantitationTypeMap_list
public BioAssayData_package.BioAssayData_list bioAssayData_list
Constructor Detail |
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public BioAssayData_package()
public BioAssayData_package(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
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
java.io.IOException
public java.lang.String getModelClassName()
public void setBioAssayDimension_list(BioAssayData_package.BioAssayDimension_list bioAssayDimension_list)
value
- to setpublic BioAssayData_package.BioAssayDimension_list getBioAssayDimension_list()
public void addToBioAssayDimension_list(BioAssayDimension bioAssayDimension)
public void addToBioAssayDimension_list(int position, BioAssayDimension bioAssayDimension)
public BioAssayDimension getFromBioAssayDimension_list(int position)
public void removeElementAtFromBioAssayDimension_list(int position)
public void removeFromBioAssayDimension_list(BioAssayDimension bioAssayDimension)
public void setDesignElementDimension_list(BioAssayData_package.DesignElementDimension_list designElementDimension_list)
value
- to setpublic BioAssayData_package.DesignElementDimension_list getDesignElementDimension_list()
public void addToDesignElementDimension_list(DesignElementDimension designElementDimension)
public void addToDesignElementDimension_list(int position, DesignElementDimension designElementDimension)
public DesignElementDimension getFromDesignElementDimension_list(int position)
public void removeElementAtFromDesignElementDimension_list(int position)
public void removeFromDesignElementDimension_list(DesignElementDimension designElementDimension)
public void setQuantitationTypeDimension_list(BioAssayData_package.QuantitationTypeDimension_list quantitationTypeDimension_list)
value
- to setpublic BioAssayData_package.QuantitationTypeDimension_list getQuantitationTypeDimension_list()
public void addToQuantitationTypeDimension_list(QuantitationTypeDimension quantitationTypeDimension)
public void addToQuantitationTypeDimension_list(int position, QuantitationTypeDimension quantitationTypeDimension)
public QuantitationTypeDimension getFromQuantitationTypeDimension_list(int position)
public void removeElementAtFromQuantitationTypeDimension_list(int position)
public void removeFromQuantitationTypeDimension_list(QuantitationTypeDimension quantitationTypeDimension)
public void setBioAssayMap_list(BioAssayData_package.BioAssayMap_list bioAssayMap_list)
value
- to setpublic BioAssayData_package.BioAssayMap_list getBioAssayMap_list()
public void addToBioAssayMap_list(BioAssayMap bioAssayMap)
public void addToBioAssayMap_list(int position, BioAssayMap bioAssayMap)
public BioAssayMap getFromBioAssayMap_list(int position)
public void removeElementAtFromBioAssayMap_list(int position)
public void removeFromBioAssayMap_list(BioAssayMap bioAssayMap)
public void setQuantitationTypeMap_list(BioAssayData_package.QuantitationTypeMap_list quantitationTypeMap_list)
value
- to setpublic BioAssayData_package.QuantitationTypeMap_list getQuantitationTypeMap_list()
public void addToQuantitationTypeMap_list(QuantitationTypeMap quantitationTypeMap)
public void addToQuantitationTypeMap_list(int position, QuantitationTypeMap quantitationTypeMap)
public QuantitationTypeMap getFromQuantitationTypeMap_list(int position)
public void removeElementAtFromQuantitationTypeMap_list(int position)
public void removeFromQuantitationTypeMap_list(QuantitationTypeMap quantitationTypeMap)
public void setBioAssayData_list(BioAssayData_package.BioAssayData_list bioAssayData_list)
value
- to setpublic BioAssayData_package.BioAssayData_list getBioAssayData_list()
public void addToBioAssayData_list(BioAssayData bioAssayData)
public void addToBioAssayData_list(int position, BioAssayData bioAssayData)
public BioAssayData getFromBioAssayData_list(int position)
public void removeElementAtFromBioAssayData_list(int position)
public void removeFromBioAssayData_list(BioAssayData bioAssayData)
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