Docjar: A Java Source and Docuemnt Enginecom.*    java.*    javax.*    org.*    all    new    plug-in

Quick Search    Search Deep

org.biomage.DesignElement
Class Reporter  view Reporter download Reporter.java

java.lang.Object
  extended byorg.biomage.Common.Extendable
      extended byorg.biomage.Common.Describable
          extended byorg.biomage.Common.Identifiable
              extended byorg.biomage.DesignElement.DesignElement
                  extended byorg.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

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.


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.)


warningType

private org.biomage.Description.OntologyEntry warningType
Similar to failType but indicates a warning rather than a failure.


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.


featureReporterMaps

private org.biomage.Interface.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

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

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

setFailTypes

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

Specified by:
setFailTypes in interface org.biomage.Interface.HasFailTypes

getFailTypes

public org.biomage.Interface.HasFailTypes.FailTypes_list getFailTypes()
Get method for failTypes

Specified by:
getFailTypes in interface org.biomage.Interface.HasFailTypes

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

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

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

removeElementAtFromFailTypes

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

Specified by:
removeElementAtFromFailTypes in interface org.biomage.Interface.HasFailTypes

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

setWarningType

public void setWarningType(org.biomage.Description.OntologyEntry warningType)
Set method for warningType

Specified by:
setWarningType in interface org.biomage.Interface.HasWarningType

getWarningType

public org.biomage.Description.OntologyEntry getWarningType()
Get method for warningType

Specified by:
getWarningType in interface org.biomage.Interface.HasWarningType

setImmobilizedCharacteristics

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

Specified by:
setImmobilizedCharacteristics in interface org.biomage.Interface.HasImmobilizedCharacteristics

getImmobilizedCharacteristics

public org.biomage.Interface.HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list getImmobilizedCharacteristics()
Get method for immobilizedCharacteristics

Specified by:
getImmobilizedCharacteristics in interface org.biomage.Interface.HasImmobilizedCharacteristics

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

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

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

removeElementAtFromImmobilizedCharacteristics

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

Specified by:
removeElementAtFromImmobilizedCharacteristics in interface org.biomage.Interface.HasImmobilizedCharacteristics

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

setFeatureReporterMaps

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

Specified by:
setFeatureReporterMaps in interface org.biomage.Interface.HasFeatureReporterMaps

getFeatureReporterMaps

public org.biomage.Interface.HasFeatureReporterMaps.FeatureReporterMaps_list getFeatureReporterMaps()
Get method for featureReporterMaps

Specified by:
getFeatureReporterMaps in interface org.biomage.Interface.HasFeatureReporterMaps

addToFeatureReporterMaps

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

Specified by:
addToFeatureReporterMaps in interface org.biomage.Interface.HasFeatureReporterMaps

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

getFromFeatureReporterMaps

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

Specified by:
getFromFeatureReporterMaps in interface org.biomage.Interface.HasFeatureReporterMaps

removeElementAtFromFeatureReporterMaps

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

Specified by:
removeElementAtFromFeatureReporterMaps in interface org.biomage.Interface.HasFeatureReporterMaps

removeFromFeatureReporterMaps

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

Specified by:
removeFromFeatureReporterMaps in interface org.biomage.Interface.HasFeatureReporterMaps