org.biomage.DesignElement
Class Reporter

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.DesignElement.DesignElement
                  extended by org.biomage.DesignElement.Reporter
All Implemented Interfaces:
SecuredElementItf, java.io.Serializable, HasAuditTrail, HasControlType, HasDescriptions, HasFailTypes, HasFeatureReporterMaps, HasImmobilizedCharacteristics, HasPropertySets, HasSecurity, HasWarningType

public class Reporter
extends DesignElement
implements java.io.Serializable, HasFailTypes, HasWarningType, HasImmobilizedCharacteristics, HasFeatureReporterMaps

A Design Element that represents some biological material (clone, oligo, etc.) on an array which will report on some biosequence or biosequences. The derived data from the measured data of its Features represents the presence or absence of the biosequence or biosequences it is reporting on in the BioAssay. Reporters are Identifiable and several Features on the same array can be mapped to the same reporter as can Features from a different ArrayDesign. The granularity of the Reporters independence is dependent on the technology and the intent of the ArrayDesign. Oligos using mature technologies can in general be assumed to be safely replicated on many features where as with PCR Products there might be the desire for quality assurence to make reporters one to one with features and use the mappings to CompositeSequences for replication purposes.

See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasFailTypes
HasFailTypes.FailTypes_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasImmobilizedCharacteristics
HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list
 
Nested classes/interfaces inherited from interface org.biomage.Interface.HasFeatureReporterMaps
HasFeatureReporterMaps.FeatureReporterMaps_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 featureReporterMaps
          Associates features with their reporter.
protected  OntologyEntry warningType
          Similar to failType but indicates a warning rather than a failure.
 
Fields inherited from class org.biomage.DesignElement.DesignElement
controlType
 
Fields inherited from class org.biomage.Common.Describable
security
 
Fields inherited from class org.biomage.Common.Extendable
editable, id, securedElementId
 
Constructor Summary
Reporter()
          Default constructor.
Reporter(org.xml.sax.Attributes atts)
          Attribute constructor.
 
Method Summary
 void addToFailTypes(int position, OntologyEntry ontologyEntry)
          Method to add OntologyEntry at position to FailTypes_list
 void addToFailTypes(OntologyEntry ontologyEntry)
          Method to add OntologyEntry to FailTypes_list
 void addToFeatureReporterMaps(FeatureReporterMap featureReporterMap)
          Method to add FeatureReporterMap to FeatureReporterMaps_list
 void addToFeatureReporterMaps(int position, FeatureReporterMap featureReporterMap)
          Method to add FeatureReporterMap at position to FeatureReporterMaps_list
 void addToImmobilizedCharacteristics(BioSequence bioSequence)
          Method to add BioSequence to ImmobilizedCharacteristics_list
 void addToImmobilizedCharacteristics(int position, BioSequence bioSequence)
          Method to add BioSequence at position to ImmobilizedCharacteristics_list
 boolean emptyMAGEobject()
           
 HasFailTypes.FailTypes_list getFailTypes()
          Get method for failTypes
 HasFeatureReporterMaps.FeatureReporterMaps_list getFeatureReporterMaps()
          Get method for featureReporterMaps
 OntologyEntry getFromFailTypes(int position)
          Method to get OntologyEntry from FailTypes_list
 FeatureReporterMap getFromFeatureReporterMaps(int position)
          Method to get FeatureReporterMap from FeatureReporterMaps_list
 BioSequence getFromImmobilizedCharacteristics(int position)
          Method to get BioSequence from ImmobilizedCharacteristics_list
 HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list getImmobilizedCharacteristics()
          Get method for immobilizedCharacteristics
 java.lang.String getModelClassName()
           
 OntologyEntry getWarningType()
          Get method for warningType
 void removeElementAtFromFailTypes(int position)
          Method to remove by position from FailTypes_list
 void removeElementAtFromFeatureReporterMaps(int position)
          Method to remove by position from FeatureReporterMaps_list
 void removeElementAtFromImmobilizedCharacteristics(int position)
          Method to remove by position from ImmobilizedCharacteristics_list
 void removeFromFailTypes(OntologyEntry ontologyEntry)
          Method to remove first OntologyEntry from FailTypes_list
 void removeFromFeatureReporterMaps(FeatureReporterMap featureReporterMap)
          Method to remove first FeatureReporterMap from FeatureReporterMaps_list
 void removeFromImmobilizedCharacteristics(BioSequence bioSequence)
          Method to remove first BioSequence from ImmobilizedCharacteristics_list
 void setAttributes(org.xml.sax.Attributes atts)
           
 void setFailTypes(HasFailTypes.FailTypes_list failTypes)
          Set method for failTypes
 void setFeatureReporterMaps(HasFeatureReporterMaps.FeatureReporterMaps_list featureReporterMaps)
          Set method for featureReporterMaps
 void setImmobilizedCharacteristics(HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list immobilizedCharacteristics)
          Set method for immobilizedCharacteristics
 void setWarningType(OntologyEntry warningType)
          Set method for warningType
 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.DesignElement.DesignElement
getControlType, setControlType
 
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

warningType

protected OntologyEntry warningType
Similar to failType but indicates a warning rather than a failure.


featureReporterMaps

protected java.util.List featureReporterMaps
Associates features with their reporter.

Constructor Detail

Reporter

public Reporter()
Default constructor.


Reporter

public Reporter(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 DesignElement

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 DesignElement
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 DesignElement
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 DesignElement
Throws:
java.io.IOException

getModelClassName

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

setImmobilizedCharacteristics

public void setImmobilizedCharacteristics(HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list immobilizedCharacteristics)
Set method for immobilizedCharacteristics

Specified by:
setImmobilizedCharacteristics in interface HasImmobilizedCharacteristics
Parameters:
value - to set

getImmobilizedCharacteristics

public HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list getImmobilizedCharacteristics()
Get method for immobilizedCharacteristics

Specified by:
getImmobilizedCharacteristics in interface HasImmobilizedCharacteristics
Returns:
value of the attribute

addToImmobilizedCharacteristics

public void addToImmobilizedCharacteristics(BioSequence bioSequence)
Method to add BioSequence to ImmobilizedCharacteristics_list

Specified by:
addToImmobilizedCharacteristics in interface HasImmobilizedCharacteristics

addToImmobilizedCharacteristics

public void addToImmobilizedCharacteristics(int position,
                                            BioSequence bioSequence)
Method to add BioSequence at position to ImmobilizedCharacteristics_list

Specified by:
addToImmobilizedCharacteristics in interface HasImmobilizedCharacteristics

getFromImmobilizedCharacteristics

public BioSequence getFromImmobilizedCharacteristics(int position)
Method to get BioSequence from ImmobilizedCharacteristics_list

Specified by:
getFromImmobilizedCharacteristics in interface HasImmobilizedCharacteristics

removeElementAtFromImmobilizedCharacteristics

public void removeElementAtFromImmobilizedCharacteristics(int position)
Method to remove by position from ImmobilizedCharacteristics_list

Specified by:
removeElementAtFromImmobilizedCharacteristics in interface HasImmobilizedCharacteristics

removeFromImmobilizedCharacteristics

public void removeFromImmobilizedCharacteristics(BioSequence bioSequence)
Method to remove first BioSequence from ImmobilizedCharacteristics_list

Specified by:
removeFromImmobilizedCharacteristics in interface HasImmobilizedCharacteristics

setWarningType

public void setWarningType(OntologyEntry warningType)
Set method for warningType

Specified by:
setWarningType in interface HasWarningType
Parameters:
value - to set

getWarningType

public OntologyEntry getWarningType()
Get method for warningType

Specified by:
getWarningType in interface HasWarningType
Returns:
value of the attribute

setFailTypes

public void setFailTypes(HasFailTypes.FailTypes_list failTypes)
Set method for failTypes

Specified by:
setFailTypes in interface HasFailTypes
Parameters:
value - to set

getFailTypes

public HasFailTypes.FailTypes_list getFailTypes()
Get method for failTypes

Specified by:
getFailTypes in interface HasFailTypes
Returns:
value of the attribute

addToFailTypes

public void addToFailTypes(OntologyEntry ontologyEntry)
Method to add OntologyEntry to FailTypes_list

Specified by:
addToFailTypes in interface HasFailTypes

addToFailTypes

public void addToFailTypes(int position,
                           OntologyEntry ontologyEntry)
Method to add OntologyEntry at position to FailTypes_list

Specified by:
addToFailTypes in interface HasFailTypes

getFromFailTypes

public OntologyEntry getFromFailTypes(int position)
Method to get OntologyEntry from FailTypes_list

Specified by:
getFromFailTypes in interface HasFailTypes

removeElementAtFromFailTypes

public void removeElementAtFromFailTypes(int position)
Method to remove by position from FailTypes_list

Specified by:
removeElementAtFromFailTypes in interface HasFailTypes

removeFromFailTypes

public void removeFromFailTypes(OntologyEntry ontologyEntry)
Method to remove first OntologyEntry from FailTypes_list

Specified by:
removeFromFailTypes in interface HasFailTypes

setFeatureReporterMaps

public void setFeatureReporterMaps(HasFeatureReporterMaps.FeatureReporterMaps_list featureReporterMaps)
Set method for featureReporterMaps

Specified by:
setFeatureReporterMaps in interface HasFeatureReporterMaps
Parameters:
value - to set

getFeatureReporterMaps

public HasFeatureReporterMaps.FeatureReporterMaps_list getFeatureReporterMaps()
Get method for featureReporterMaps

Specified by:
getFeatureReporterMaps in interface HasFeatureReporterMaps
Returns:
value of the attribute

addToFeatureReporterMaps

public void addToFeatureReporterMaps(FeatureReporterMap featureReporterMap)
Method to add FeatureReporterMap to FeatureReporterMaps_list

Specified by:
addToFeatureReporterMaps in interface HasFeatureReporterMaps

addToFeatureReporterMaps

public void addToFeatureReporterMaps(int position,
                                     FeatureReporterMap featureReporterMap)
Method to add FeatureReporterMap at position to FeatureReporterMaps_list

Specified by:
addToFeatureReporterMaps in interface HasFeatureReporterMaps

getFromFeatureReporterMaps

public FeatureReporterMap getFromFeatureReporterMaps(int position)
Method to get FeatureReporterMap from FeatureReporterMaps_list

Specified by:
getFromFeatureReporterMaps in interface HasFeatureReporterMaps

removeElementAtFromFeatureReporterMaps

public void removeElementAtFromFeatureReporterMaps(int position)
Method to remove by position from FeatureReporterMaps_list

Specified by:
removeElementAtFromFeatureReporterMaps in interface HasFeatureReporterMaps

removeFromFeatureReporterMaps

public void removeFromFeatureReporterMaps(FeatureReporterMap featureReporterMap)
Method to remove first FeatureReporterMap from FeatureReporterMaps_list

Specified by:
removeFromFeatureReporterMaps in interface HasFeatureReporterMaps