org.biomage.DesignElement
Class FeatureReporterMap

java.lang.Object
  extended by org.biomage.Common.Extendable
      extended by org.biomage.Common.Describable
          extended by org.biomage.Common.Identifiable
              extended by org.biomage.BioEvent.BioEvent
                  extended by org.biomage.BioEvent.Map
                      extended by org.biomage.BioAssayData.DesignElementMap
                          extended by org.biomage.DesignElement.FeatureReporterMap
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasDescriptions, HasFeatureInformationSources, HasPropertySets, HasProtocolApplications, HasReporter, HasSecurity

public class FeatureReporterMap
extends DesignElementMap
implements java.io.Serializable, HasReporter, HasFeatureInformationSources

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.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasFeatureInformationSources
HasFeatureInformationSources.FeatureInformationSources_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasProtocolApplications
HasProtocolApplications.ProtocolApplications_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail
HasAuditTrail.AuditTrail_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions
HasDescriptions.Descriptions_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets
HasPropertySets.PropertySets_list
 
Field Summary
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
ojbConcreteClass
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
FeatureReporterMap()
          Default constructor.
FeatureReporterMap(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 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()
           
 HasFeatureInformationSources.FeatureInformationSources_list getFeatureInformationSources()
          Get method for featureInformationSources
 FeatureInformation getFromFeatureInformationSources(int position)
          Method to get FeatureInformation from FeatureInformationSources_list
 java.lang.String getModelClassName()
           
 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
addToProtocolApplications, addToProtocolApplications, getFromProtocolApplications, getProtocolApplications, removeElementAtFromProtocolApplications, removeFromProtocolApplications, setProtocolApplications
 
Methods inherited from class org.biomage.Common.Identifiable
getIdentifier, getName, setIdentifier, setName, toString
 
Methods inherited from class org.biomage.Common.Describable
addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity
 
Methods inherited from class org.biomage.Common.Extendable
addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId
 
Methods inherited from class java.lang.Object
clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

reporter

protected Reporter reporter
Associates features with their reporter.


featureInformationSources

protected java.util.List featureInformationSources
Typically, the features on an array that are manufactured with this reporter's BioSequence.

Constructor Detail

FeatureReporterMap

public FeatureReporterMap()
Default constructor.


FeatureReporterMap

public FeatureReporterMap(org.xml.sax.Attributes atts)
Attribute constructor. Looks up the attributes in the parameter and casts them from strings appropriately

Parameters:
atts: - the attribute list.
Method Detail

setAttributes

public void setAttributes(org.xml.sax.Attributes atts)
Overrides:
setAttributes in class DesignElementMap

writeMAGEML

public void writeMAGEML(java.io.Writer out)
                 throws java.io.IOException
writeMAGEML This method is responsible for assembling the attribute and association data into XML. It creates the object tag and then calls the writeAttributes and writeAssociation methods.

Overrides:
writeMAGEML in class DesignElementMap
Throws:
java.io.IOException

emptyMAGEobject

public boolean emptyMAGEobject()

writeAttributes

public void writeAttributes(java.io.Writer out)
                     throws java.io.IOException
writeAttributes This method is responsible for assembling the attribute data into XML. It calls the super method to write out all attributes of this class and it's ancestors.

Overrides:
writeAttributes in class DesignElementMap
Throws:
java.io.IOException

writeAssociations

public void writeAssociations(java.io.Writer out)
                       throws java.io.IOException
writeAssociations This method is responsible for assembling the association data into XML. It calls the super method to write out all associations of this class's ancestors.

Overrides:
writeAssociations in class DesignElementMap
Throws:
java.io.IOException

getModelClassName

public java.lang.String getModelClassName()
Overrides:
getModelClassName in class DesignElementMap

setReporter

public void setReporter(Reporter reporter)
Set method for reporter

Specified by:
setReporter in interface HasReporter
Parameters:
value - to set

getReporter

public Reporter getReporter()
Get method for reporter

Specified by:
getReporter in interface HasReporter
Returns:
value of the attribute

setFeatureInformationSources

public void setFeatureInformationSources(HasFeatureInformationSources.FeatureInformationSources_list featureInformationSources)
Set method for featureInformationSources

Specified by:
setFeatureInformationSources in interface HasFeatureInformationSources
Parameters:
value - to set

getFeatureInformationSources

public HasFeatureInformationSources.FeatureInformationSources_list getFeatureInformationSources()
Get method for featureInformationSources

Specified by:
getFeatureInformationSources in interface HasFeatureInformationSources
Returns:
value of the attribute

addToFeatureInformationSources

public void addToFeatureInformationSources(FeatureInformation featureInformation)
Method to add FeatureInformation to FeatureInformationSources_list

Specified by:
addToFeatureInformationSources in interface HasFeatureInformationSources

addToFeatureInformationSources

public void addToFeatureInformationSources(int position,
                                           FeatureInformation featureInformation)
Method to add FeatureInformation at position to FeatureInformationSources_list

Specified by:
addToFeatureInformationSources in interface HasFeatureInformationSources

getFromFeatureInformationSources

public FeatureInformation getFromFeatureInformationSources(int position)
Method to get FeatureInformation from FeatureInformationSources_list

Specified by:
getFromFeatureInformationSources in interface HasFeatureInformationSources

removeElementAtFromFeatureInformationSources

public void removeElementAtFromFeatureInformationSources(int position)
Method to remove by position from FeatureInformationSources_list

Specified by:
removeElementAtFromFeatureInformationSources in interface HasFeatureInformationSources

removeFromFeatureInformationSources

public void removeFromFeatureInformationSources(FeatureInformation featureInformation)
Method to remove first FeatureInformation from FeatureInformationSources_list

Specified by:
removeFromFeatureInformationSources in interface HasFeatureInformationSources