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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:

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

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public class Reporter

extends DesignElement

implements java.io.Serializable, org.biomage.Interface.HasFailTypes, org.biomage.Interface.HasWarningType, org.biomage.Interface.HasImmobilizedCharacteristics, org.biomage.Interface.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.

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Nested Class Summary

 

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

org.biomage.Interface.HasFailTypes.FailTypes_list

 

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

org.biomage.Interface.HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list

 

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

org.biomage.Interface.HasFeatureReporterMaps.FeatureReporterMaps_list

 

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

org.biomage.Interface.HasAuditTrail.AuditTrail_list

 

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

org.biomage.Interface.HasDescriptions.Descriptions_list

 

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

org.biomage.Interface.HasPropertySets.PropertySets_list

 

Field Summary
private  org.biomage.Interface.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.)
private  org.biomage.Interface.HasFeatureReporterMaps.FeatureReporterMaps_list	featureReporterMaps           Associates features with their reporter.
private  org.biomage.Interface.HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list	immobilizedCharacteristics           The sequence annotation on the BioMaterial this reporter represents.
private  org.biomage.Description.OntologyEntry	warningType           Similar to failType but indicates a warning rather than a failure.

 

Fields inherited from class org.biomage.DesignElement.DesignElement

 

Fields inherited from class org.biomage.Common.Identifiable

 

Fields inherited from class org.biomage.Common.Describable

 

Fields inherited from class org.biomage.Common.Extendable

 

Constructor Summary

Reporter()           Default constructor.

Reporter(org.xml.sax.Attributes atts)           Attribute constructor.

 

Method Summary
void	addToFailTypes(int position, org.biomage.Description.OntologyEntry ontologyEntry)           Method to add OntologyEntry at position to FailTypes_list
void	addToFailTypes(org.biomage.Description.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(org.biomage.BioSequence.BioSequence bioSequence)           Method to add BioSequence to ImmobilizedCharacteristics_list
void	addToImmobilizedCharacteristics(int position, org.biomage.BioSequence.BioSequence bioSequence)           Method to add BioSequence at position to ImmobilizedCharacteristics_list
org.biomage.Interface.HasFailTypes.FailTypes_list	getFailTypes()           Get method for failTypes
org.biomage.Interface.HasFeatureReporterMaps.FeatureReporterMaps_list	getFeatureReporterMaps()           Get method for featureReporterMaps
org.biomage.Description.OntologyEntry	getFromFailTypes(int position)           Method to get OntologyEntry from FailTypes_list
FeatureReporterMap	getFromFeatureReporterMaps(int position)           Method to get FeatureReporterMap from FeatureReporterMaps_list
org.biomage.BioSequence.BioSequence	getFromImmobilizedCharacteristics(int position)           Method to get BioSequence from ImmobilizedCharacteristics_list
org.biomage.Interface.HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list	getImmobilizedCharacteristics()           Get method for immobilizedCharacteristics
org.biomage.Description.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(org.biomage.Description.OntologyEntry ontologyEntry)           Method to remove first OntologyEntry from FailTypes_list
void	removeFromFeatureReporterMaps(FeatureReporterMap featureReporterMap)           Method to remove first FeatureReporterMap from FeatureReporterMaps_list
void	removeFromImmobilizedCharacteristics(org.biomage.BioSequence.BioSequence bioSequence)           Method to remove first BioSequence from ImmobilizedCharacteristics_list
void	setFailTypes(org.biomage.Interface.HasFailTypes.FailTypes_list failTypes)           Set method for failTypes
void	setFeatureReporterMaps(org.biomage.Interface.HasFeatureReporterMaps.FeatureReporterMaps_list featureReporterMaps)           Set method for featureReporterMaps
void	setImmobilizedCharacteristics(org.biomage.Interface.HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list immobilizedCharacteristics)           Set method for immobilizedCharacteristics
void	setWarningType(org.biomage.Description.OntologyEntry warningType)           Set method for warningType
void	writeAssociations(java.io.Writer out)           writeAssociations
void	writeAttributes(java.io.Writer out)           writeAttributes
void	writeMAGEML(java.io.Writer out)           writeMAGEML

 

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

failTypes

private org.biomage.Interface.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.)

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warningType

private org.biomage.Description.OntologyEntry warningType

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

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immobilizedCharacteristics

private org.biomage.Interface.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.

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featureReporterMaps

private org.biomage.Interface.HasFeatureReporterMaps.FeatureReporterMaps_list featureReporterMaps

Associates features with their reporter.

Constructor Detail

Reporter

public Reporter()

Default constructor.

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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

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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

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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

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setFailTypes

public void setFailTypes(org.biomage.Interface.HasFailTypes.FailTypes_list failTypes)

Set method for failTypes

Specified by:

setFailTypes in interface org.biomage.Interface.HasFailTypes

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getFailTypes

public org.biomage.Interface.HasFailTypes.FailTypes_list getFailTypes()

Get method for failTypes

Specified by:

getFailTypes in interface org.biomage.Interface.HasFailTypes

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addToFailTypes

public void addToFailTypes(org.biomage.Description.OntologyEntry ontologyEntry)

Method to add OntologyEntry to FailTypes_list

Specified by:

addToFailTypes in interface org.biomage.Interface.HasFailTypes

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addToFailTypes

public void addToFailTypes(int position,
                           org.biomage.Description.OntologyEntry ontologyEntry)

Method to add OntologyEntry at position to FailTypes_list

Specified by:

addToFailTypes in interface org.biomage.Interface.HasFailTypes

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getFromFailTypes

public org.biomage.Description.OntologyEntry getFromFailTypes(int position)

Method to get OntologyEntry from FailTypes_list

Specified by:

getFromFailTypes in interface org.biomage.Interface.HasFailTypes

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removeElementAtFromFailTypes

public void removeElementAtFromFailTypes(int position)

Method to remove by position from FailTypes_list

Specified by:

removeElementAtFromFailTypes in interface org.biomage.Interface.HasFailTypes

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removeFromFailTypes

public void removeFromFailTypes(org.biomage.Description.OntologyEntry ontologyEntry)

Method to remove first OntologyEntry from FailTypes_list

Specified by:

removeFromFailTypes in interface org.biomage.Interface.HasFailTypes

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setWarningType

public void setWarningType(org.biomage.Description.OntologyEntry warningType)

Set method for warningType

Specified by:

setWarningType in interface org.biomage.Interface.HasWarningType

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getWarningType

public org.biomage.Description.OntologyEntry getWarningType()

Get method for warningType

Specified by:

getWarningType in interface org.biomage.Interface.HasWarningType

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setImmobilizedCharacteristics

public void setImmobilizedCharacteristics(org.biomage.Interface.HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list immobilizedCharacteristics)

Set method for immobilizedCharacteristics

Specified by:

setImmobilizedCharacteristics in interface org.biomage.Interface.HasImmobilizedCharacteristics

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getImmobilizedCharacteristics

public org.biomage.Interface.HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list getImmobilizedCharacteristics()

Get method for immobilizedCharacteristics

Specified by:

getImmobilizedCharacteristics in interface org.biomage.Interface.HasImmobilizedCharacteristics

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addToImmobilizedCharacteristics

public void addToImmobilizedCharacteristics(org.biomage.BioSequence.BioSequence bioSequence)

Method to add BioSequence to ImmobilizedCharacteristics_list

Specified by:

addToImmobilizedCharacteristics in interface org.biomage.Interface.HasImmobilizedCharacteristics

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addToImmobilizedCharacteristics

public void addToImmobilizedCharacteristics(int position,
                                            org.biomage.BioSequence.BioSequence bioSequence)

Method to add BioSequence at position to ImmobilizedCharacteristics_list

Specified by:

addToImmobilizedCharacteristics in interface org.biomage.Interface.HasImmobilizedCharacteristics

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getFromImmobilizedCharacteristics

public org.biomage.BioSequence.BioSequence getFromImmobilizedCharacteristics(int position)

Method to get BioSequence from ImmobilizedCharacteristics_list

Specified by:

getFromImmobilizedCharacteristics in interface org.biomage.Interface.HasImmobilizedCharacteristics

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removeElementAtFromImmobilizedCharacteristics

public void removeElementAtFromImmobilizedCharacteristics(int position)

Method to remove by position from ImmobilizedCharacteristics_list

Specified by:

removeElementAtFromImmobilizedCharacteristics in interface org.biomage.Interface.HasImmobilizedCharacteristics

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removeFromImmobilizedCharacteristics

public void removeFromImmobilizedCharacteristics(org.biomage.BioSequence.BioSequence bioSequence)

Method to remove first BioSequence from ImmobilizedCharacteristics_list

Specified by:

removeFromImmobilizedCharacteristics in interface org.biomage.Interface.HasImmobilizedCharacteristics

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setFeatureReporterMaps

public void setFeatureReporterMaps(org.biomage.Interface.HasFeatureReporterMaps.FeatureReporterMaps_list featureReporterMaps)

Set method for featureReporterMaps

Specified by:

setFeatureReporterMaps in interface org.biomage.Interface.HasFeatureReporterMaps

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getFeatureReporterMaps

public org.biomage.Interface.HasFeatureReporterMaps.FeatureReporterMaps_list getFeatureReporterMaps()

Get method for featureReporterMaps

Specified by:

getFeatureReporterMaps in interface org.biomage.Interface.HasFeatureReporterMaps

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addToFeatureReporterMaps

public void addToFeatureReporterMaps(FeatureReporterMap featureReporterMap)

Method to add FeatureReporterMap to FeatureReporterMaps_list

Specified by:

addToFeatureReporterMaps in interface org.biomage.Interface.HasFeatureReporterMaps

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addToFeatureReporterMaps

public void addToFeatureReporterMaps(int position,
                                     FeatureReporterMap featureReporterMap)

Method to add FeatureReporterMap at position to FeatureReporterMaps_list

Specified by:

addToFeatureReporterMaps in interface org.biomage.Interface.HasFeatureReporterMaps

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getFromFeatureReporterMaps

public FeatureReporterMap getFromFeatureReporterMaps(int position)

Method to get FeatureReporterMap from FeatureReporterMaps_list

Specified by:

getFromFeatureReporterMaps in interface org.biomage.Interface.HasFeatureReporterMaps

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removeElementAtFromFeatureReporterMaps

public void removeElementAtFromFeatureReporterMaps(int position)

Method to remove by position from FeatureReporterMaps_list

Specified by:

removeElementAtFromFeatureReporterMaps in interface org.biomage.Interface.HasFeatureReporterMaps

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removeFromFeatureReporterMaps

public void removeFromFeatureReporterMaps(FeatureReporterMap featureReporterMap)

Method to remove first FeatureReporterMap from FeatureReporterMaps_list

Specified by:

removeFromFeatureReporterMaps in interface org.biomage.Interface.HasFeatureReporterMaps

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> biomage >> [ DesignElement overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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