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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.QuantitationType.QuantitationType
public abstract class QuantitationType
A method for calculating a single datum of the matrix (e.g. raw intensity, background, error).
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasQuantitationTypeMaps |
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HasQuantitationTypeMaps.QuantitationTypeMaps_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasConfidenceIndicators |
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HasConfidenceIndicators.ConfidenceIndicators_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 Channel |
channel
The optional channel associated with the QuantitationType. |
protected java.util.List |
confidenceIndicators
The association between a ConfidenceIndicator and the QuantitationType its is an indicator for. |
protected OntologyEntry |
dataType
The specific type for the quantitations. |
protected java.lang.String |
ojbConcreteClass
|
protected java.util.List |
quantitationTypeMaps
The QuantitationType whose value will be produced from the values of the source QuantitationType according to the Protocol. |
protected OntologyEntry |
scale
Indication of how to interpret the value. |
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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QuantitationType()
Default constructor. |
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QuantitationType(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToConfidenceIndicators(ConfidenceIndicator confidenceIndicator)
Method to add ConfidenceIndicator to ConfidenceIndicators_list |
void |
addToConfidenceIndicators(int position,
ConfidenceIndicator confidenceIndicator)
Method to add ConfidenceIndicator at position to ConfidenceIndicators_list |
void |
addToQuantitationTypeMaps(int position,
QuantitationTypeMap quantitationTypeMap)
Method to add QuantitationTypeMap at position to QuantitationTypeMaps_list |
void |
addToQuantitationTypeMaps(QuantitationTypeMap quantitationTypeMap)
Method to add QuantitationTypeMap to QuantitationTypeMaps_list |
Channel |
getChannel()
Get method for channel |
HasConfidenceIndicators.ConfidenceIndicators_list |
getConfidenceIndicators()
Get method for confidenceIndicators |
OntologyEntry |
getDataType()
Get method for dataType |
ConfidenceIndicator |
getFromConfidenceIndicators(int position)
Method to get ConfidenceIndicator from ConfidenceIndicators_list |
QuantitationTypeMap |
getFromQuantitationTypeMaps(int position)
Method to get QuantitationTypeMap from QuantitationTypeMaps_list |
java.lang.Boolean |
getIsBackground()
Get method for isBackground |
java.lang.String |
getModelClassName()
|
HasQuantitationTypeMaps.QuantitationTypeMaps_list |
getQuantitationTypeMaps()
Get method for quantitationTypeMaps |
OntologyEntry |
getScale()
Get method for scale |
void |
removeElementAtFromConfidenceIndicators(int position)
Method to remove by position from ConfidenceIndicators_list |
void |
removeElementAtFromQuantitationTypeMaps(int position)
Method to remove by position from QuantitationTypeMaps_list |
void |
removeFromConfidenceIndicators(ConfidenceIndicator confidenceIndicator)
Method to remove first ConfidenceIndicator from ConfidenceIndicators_list |
void |
removeFromQuantitationTypeMaps(QuantitationTypeMap quantitationTypeMap)
Method to remove first QuantitationTypeMap from QuantitationTypeMaps_list |
void |
setAttributes(org.xml.sax.Attributes atts)
|
void |
setChannel(Channel channel)
Set method for channel |
void |
setConfidenceIndicators(HasConfidenceIndicators.ConfidenceIndicators_list confidenceIndicators)
Set method for confidenceIndicators |
void |
setDataType(OntologyEntry dataType)
Set method for dataType |
void |
setIsBackground(java.lang.Boolean isBackground)
Set method for isBackground |
void |
setQuantitationTypeMaps(HasQuantitationTypeMaps.QuantitationTypeMaps_list quantitationTypeMaps)
Set method for quantitationTypeMaps |
void |
setScale(OntologyEntry scale)
Set method for scale |
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.lang.String ojbConcreteClass
protected Channel channel
protected OntologyEntry scale
protected OntologyEntry dataType
protected java.util.List confidenceIndicators
protected java.util.List quantitationTypeMaps
Constructor Detail |
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public QuantitationType()
public QuantitationType(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 void setIsBackground(java.lang.Boolean isBackground)
value
- to setpublic java.lang.Boolean getIsBackground()
public java.lang.String getModelClassName()
getModelClassName
in class Identifiable
public void setChannel(Channel channel)
setChannel
in interface HasChannel
value
- to setpublic Channel getChannel()
getChannel
in interface HasChannel
public void setScale(OntologyEntry scale)
setScale
in interface HasScale
value
- to setpublic OntologyEntry getScale()
getScale
in interface HasScale
public void setDataType(OntologyEntry dataType)
setDataType
in interface HasDataType
value
- to setpublic OntologyEntry getDataType()
getDataType
in interface HasDataType
public void setConfidenceIndicators(HasConfidenceIndicators.ConfidenceIndicators_list confidenceIndicators)
setConfidenceIndicators
in interface HasConfidenceIndicators
value
- to setpublic HasConfidenceIndicators.ConfidenceIndicators_list getConfidenceIndicators()
getConfidenceIndicators
in interface HasConfidenceIndicators
public void addToConfidenceIndicators(ConfidenceIndicator confidenceIndicator)
addToConfidenceIndicators
in interface HasConfidenceIndicators
public void addToConfidenceIndicators(int position, ConfidenceIndicator confidenceIndicator)
addToConfidenceIndicators
in interface HasConfidenceIndicators
public ConfidenceIndicator getFromConfidenceIndicators(int position)
getFromConfidenceIndicators
in interface HasConfidenceIndicators
public void removeElementAtFromConfidenceIndicators(int position)
removeElementAtFromConfidenceIndicators
in interface HasConfidenceIndicators
public void removeFromConfidenceIndicators(ConfidenceIndicator confidenceIndicator)
removeFromConfidenceIndicators
in interface HasConfidenceIndicators
public void setQuantitationTypeMaps(HasQuantitationTypeMaps.QuantitationTypeMaps_list quantitationTypeMaps)
setQuantitationTypeMaps
in interface HasQuantitationTypeMaps
value
- to setpublic HasQuantitationTypeMaps.QuantitationTypeMaps_list getQuantitationTypeMaps()
getQuantitationTypeMaps
in interface HasQuantitationTypeMaps
public void addToQuantitationTypeMaps(QuantitationTypeMap quantitationTypeMap)
addToQuantitationTypeMaps
in interface HasQuantitationTypeMaps
public void addToQuantitationTypeMaps(int position, QuantitationTypeMap quantitationTypeMap)
addToQuantitationTypeMaps
in interface HasQuantitationTypeMaps
public QuantitationTypeMap getFromQuantitationTypeMaps(int position)
getFromQuantitationTypeMaps
in interface HasQuantitationTypeMaps
public void removeElementAtFromQuantitationTypeMaps(int position)
removeElementAtFromQuantitationTypeMaps
in interface HasQuantitationTypeMaps
public void removeFromQuantitationTypeMaps(QuantitationTypeMap quantitationTypeMap)
removeFromQuantitationTypeMaps
in interface HasQuantitationTypeMaps
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