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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.BioEvent.BioEvent
org.biomage.BioEvent.Map
org.biomage.BioAssayData.DesignElementMap
org.biomage.DesignElement.FeatureReporterMap
public class FeatureReporterMap
A FeatureReporterMap is the description of how source features are transformed into a target reporter. These would map replicate features for a reporter to the reporter.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasFeatureInformationSources |
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HasFeatureInformationSources.FeatureInformationSources_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasProtocolApplications |
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HasProtocolApplications.ProtocolApplications_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 |
featureInformationSources
Typically, the features on an array that are manufactured with this reporter's BioSequence. |
protected Reporter |
reporter
Associates features with their reporter. |
Fields inherited from class org.biomage.BioAssayData.DesignElementMap |
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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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FeatureReporterMap()
Default constructor. |
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FeatureReporterMap(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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void |
addToFeatureInformationSources(FeatureInformation featureInformation)
Method to add FeatureInformation to FeatureInformationSources_list |
void |
addToFeatureInformationSources(int position,
FeatureInformation featureInformation)
Method to add FeatureInformation at position to FeatureInformationSources_list |
boolean |
emptyMAGEobject()
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HasFeatureInformationSources.FeatureInformationSources_list |
getFeatureInformationSources()
Get method for featureInformationSources |
FeatureInformation |
getFromFeatureInformationSources(int position)
Method to get FeatureInformation from FeatureInformationSources_list |
java.lang.String |
getModelClassName()
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Reporter |
getReporter()
Get method for reporter |
void |
removeElementAtFromFeatureInformationSources(int position)
Method to remove by position from FeatureInformationSources_list |
void |
removeFromFeatureInformationSources(FeatureInformation featureInformation)
Method to remove first FeatureInformation from FeatureInformationSources_list |
void |
setAttributes(org.xml.sax.Attributes atts)
|
void |
setFeatureInformationSources(HasFeatureInformationSources.FeatureInformationSources_list featureInformationSources)
Set method for featureInformationSources |
void |
setReporter(Reporter reporter)
Set method for reporter |
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.BioEvent.BioEvent |
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addToProtocolApplications, addToProtocolApplications, getFromProtocolApplications, getProtocolApplications, removeElementAtFromProtocolApplications, removeFromProtocolApplications, setProtocolApplications |
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 Reporter reporter
protected java.util.List featureInformationSources
Constructor Detail |
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public FeatureReporterMap()
public FeatureReporterMap(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 DesignElementMap
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class DesignElementMap
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class DesignElementMap
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class DesignElementMap
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class DesignElementMap
public void setReporter(Reporter reporter)
setReporter
in interface HasReporter
value
- to setpublic Reporter getReporter()
getReporter
in interface HasReporter
public void setFeatureInformationSources(HasFeatureInformationSources.FeatureInformationSources_list featureInformationSources)
setFeatureInformationSources
in interface HasFeatureInformationSources
value
- to setpublic HasFeatureInformationSources.FeatureInformationSources_list getFeatureInformationSources()
getFeatureInformationSources
in interface HasFeatureInformationSources
public void addToFeatureInformationSources(FeatureInformation featureInformation)
addToFeatureInformationSources
in interface HasFeatureInformationSources
public void addToFeatureInformationSources(int position, FeatureInformation featureInformation)
addToFeatureInformationSources
in interface HasFeatureInformationSources
public FeatureInformation getFromFeatureInformationSources(int position)
getFromFeatureInformationSources
in interface HasFeatureInformationSources
public void removeElementAtFromFeatureInformationSources(int position)
removeElementAtFromFeatureInformationSources
in interface HasFeatureInformationSources
public void removeFromFeatureInformationSources(FeatureInformation featureInformation)
removeFromFeatureInformationSources
in interface HasFeatureInformationSources
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