org.biomage.DesignElement
Class Reporter

java.lang.Object
  |
  +--org.biomage.Common.Extendable
        |
        +--org.biomage.Common.Describable
              |
              +--org.biomage.Common.Identifiable
                    |
                    +--org.biomage.DesignElement.DesignElement
                          |
                          +--org.biomage.DesignElement.Reporter

All Implemented Interfaces:

HasAuditTrail, HasControlType, HasDescriptions, HasFailTypes, HasFeatureReporterMaps, HasImmobilizedCharacteristics, HasPropertySets, HasSecurity, HasWarningType, java.io.Serializable

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 inherited from class org.biomage.Interface.HasFailTypes

HasFailTypes.FailTypes_list

Nested classes inherited from class org.biomage.Interface.HasImmobilizedCharacteristics

HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list

Nested classes inherited from class org.biomage.Interface.HasFeatureReporterMaps

HasFeatureReporterMaps.FeatureReporterMaps_list

Nested classes inherited from class org.biomage.Interface.HasAuditTrail

HasAuditTrail.AuditTrail_list

Nested classes inherited from class org.biomage.Interface.HasDescriptions

HasDescriptions.Descriptions_list

Nested classes inherited from class org.biomage.Interface.HasPropertySets

HasPropertySets.PropertySets_list

Field Summary

protected HasFailTypes.FailTypes_list	failTypes If at some time the reporter is determined to be failed this indicts the failure (doesn't report on what it was intended to report on, etc.)
protected HasFeatureReporterMaps.FeatureReporterMaps_list	featureReporterMaps Associates features with their reporter.
protected HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list	immobilizedCharacteristics The sequence annotation on the BioMaterial this reporter represents.
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

auditTrail, descriptions, security

Fields inherited from class org.biomage.Common.Extendable

propertySets

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
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
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	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

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, getFromPropertySets, getPropertySets, removeElementAtFromPropertySets, removeFromPropertySets, setPropertySets

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

immobilizedCharacteristics

protected HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list immobilizedCharacteristics

The sequence annotation on the BioMaterial this reporter represents. Typically the sequences will be an Oligo Sequence, Clone or PCR Primer.

warningType

protected OntologyEntry warningType

Similar to failType but indicates a warning rather than a failure.

failTypes

protected HasFailTypes.FailTypes_list failTypes

If at some time the reporter is determined to be failed this indicts the failure (doesn't report on what it was intended to report on, etc.)

featureReporterMaps

protected HasFeatureReporterMaps.FeatureReporterMaps_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

Method Detail

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

java.io.IOException

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

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

java.io.IOException

setImmobilizedCharacteristics

public void setImmobilizedCharacteristics(HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list immobilizedCharacteristics)

Set method for immobilizedCharacteristics

Specified by:

setImmobilizedCharacteristics in interface HasImmobilizedCharacteristics

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

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

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

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