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java.lang.Objectorg.biomage.Common.Extendable
org.biomage.Common.Describable
org.biomage.Common.Identifiable
org.biomage.DesignElement.DesignElement
org.biomage.DesignElement.Reporter
public class Reporter
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 |
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Nested classes/interfaces inherited from interface org.biomage.Interface.HasFailTypes |
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HasFailTypes.FailTypes_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasImmobilizedCharacteristics |
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HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasFeatureReporterMaps |
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HasFeatureReporterMaps.FeatureReporterMaps_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasAuditTrail |
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HasAuditTrail.AuditTrail_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasDescriptions |
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HasDescriptions.Descriptions_list |
Nested classes/interfaces inherited from interface org.biomage.Interface.HasPropertySets |
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HasPropertySets.PropertySets_list |
Field Summary | |
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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 |
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controlType |
Fields inherited from class org.biomage.Common.Describable |
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security |
Fields inherited from class org.biomage.Common.Extendable |
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editable, id, securedElementId |
Constructor Summary | |
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Reporter()
Default constructor. |
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Reporter(org.xml.sax.Attributes atts)
Attribute constructor. |
Method Summary | |
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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()
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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()
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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)
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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 |
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getControlType, setControlType |
Methods inherited from class org.biomage.Common.Identifiable |
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getIdentifier, getName, setIdentifier, setName, toString |
Methods inherited from class org.biomage.Common.Describable |
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addToAuditTrail, addToAuditTrail, addToDescriptions, addToDescriptions, getAuditTrail, getDescriptions, getFromAuditTrail, getFromDescriptions, getSecurity, removeElementAtFromAuditTrail, removeElementAtFromDescriptions, removeFromAuditTrail, removeFromDescriptions, setAuditTrail, setDescriptions, setSecurity |
Methods inherited from class org.biomage.Common.Extendable |
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addToPropertySets, addToPropertySets, equals, getFromPropertySets, getId, getIsEditable, getPropertySets, getSecuredElementId, isEditable, removeElementAtFromPropertySets, removeFromPropertySets, setId, setIsEditable, setPropertySets, setSecuredElementId |
Methods inherited from class java.lang.Object |
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clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected OntologyEntry warningType
protected java.util.List featureReporterMaps
Constructor Detail |
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public Reporter()
public Reporter(org.xml.sax.Attributes atts)
atts:
- the attribute list.Method Detail |
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public void setAttributes(org.xml.sax.Attributes atts)
setAttributes
in class DesignElement
public void writeMAGEML(java.io.Writer out) throws java.io.IOException
writeMAGEML
in class DesignElement
java.io.IOException
public boolean emptyMAGEobject()
public void writeAttributes(java.io.Writer out) throws java.io.IOException
writeAttributes
in class DesignElement
java.io.IOException
public void writeAssociations(java.io.Writer out) throws java.io.IOException
writeAssociations
in class DesignElement
java.io.IOException
public java.lang.String getModelClassName()
getModelClassName
in class DesignElement
public void setImmobilizedCharacteristics(HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list immobilizedCharacteristics)
setImmobilizedCharacteristics
in interface HasImmobilizedCharacteristics
value
- to setpublic HasImmobilizedCharacteristics.ImmobilizedCharacteristics_list getImmobilizedCharacteristics()
getImmobilizedCharacteristics
in interface HasImmobilizedCharacteristics
public void addToImmobilizedCharacteristics(BioSequence bioSequence)
addToImmobilizedCharacteristics
in interface HasImmobilizedCharacteristics
public void addToImmobilizedCharacteristics(int position, BioSequence bioSequence)
addToImmobilizedCharacteristics
in interface HasImmobilizedCharacteristics
public BioSequence getFromImmobilizedCharacteristics(int position)
getFromImmobilizedCharacteristics
in interface HasImmobilizedCharacteristics
public void removeElementAtFromImmobilizedCharacteristics(int position)
removeElementAtFromImmobilizedCharacteristics
in interface HasImmobilizedCharacteristics
public void removeFromImmobilizedCharacteristics(BioSequence bioSequence)
removeFromImmobilizedCharacteristics
in interface HasImmobilizedCharacteristics
public void setWarningType(OntologyEntry warningType)
setWarningType
in interface HasWarningType
value
- to setpublic OntologyEntry getWarningType()
getWarningType
in interface HasWarningType
public void setFailTypes(HasFailTypes.FailTypes_list failTypes)
setFailTypes
in interface HasFailTypes
value
- to setpublic HasFailTypes.FailTypes_list getFailTypes()
getFailTypes
in interface HasFailTypes
public void addToFailTypes(OntologyEntry ontologyEntry)
addToFailTypes
in interface HasFailTypes
public void addToFailTypes(int position, OntologyEntry ontologyEntry)
addToFailTypes
in interface HasFailTypes
public OntologyEntry getFromFailTypes(int position)
getFromFailTypes
in interface HasFailTypes
public void removeElementAtFromFailTypes(int position)
removeElementAtFromFailTypes
in interface HasFailTypes
public void removeFromFailTypes(OntologyEntry ontologyEntry)
removeFromFailTypes
in interface HasFailTypes
public void setFeatureReporterMaps(HasFeatureReporterMaps.FeatureReporterMaps_list featureReporterMaps)
setFeatureReporterMaps
in interface HasFeatureReporterMaps
value
- to setpublic HasFeatureReporterMaps.FeatureReporterMaps_list getFeatureReporterMaps()
getFeatureReporterMaps
in interface HasFeatureReporterMaps
public void addToFeatureReporterMaps(FeatureReporterMap featureReporterMap)
addToFeatureReporterMaps
in interface HasFeatureReporterMaps
public void addToFeatureReporterMaps(int position, FeatureReporterMap featureReporterMap)
addToFeatureReporterMaps
in interface HasFeatureReporterMaps
public FeatureReporterMap getFromFeatureReporterMaps(int position)
getFromFeatureReporterMaps
in interface HasFeatureReporterMaps
public void removeElementAtFromFeatureReporterMaps(int position)
removeElementAtFromFeatureReporterMaps
in interface HasFeatureReporterMaps
public void removeFromFeatureReporterMaps(FeatureReporterMap featureReporterMap)
removeFromFeatureReporterMaps
in interface HasFeatureReporterMaps
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