@Entity public class Amplification extends EventBase implements java.lang.Cloneable
DNA Sample
. The part of the DNA being replicated is defined by the
marker
(also called locus) - implemented in CDM as a DefinedTerm
of term type TermType.DnaMarker
.
primers
(short DNA fractions) are
used. They may work in both directions of the DNA part therefore we do have a
forward primer
and a reverse primer
.
Most (or all?) amplifications require a purification process
. Additionally
some use #getCloning()
for replication.
photo
are also relevant for an amplification.
We have 2 classes to store the core data for an amplification: Amplification
and AmplificationResult
.
Amplification
we store all data that is equal for an amplification event which includes amplification
of many dna samples
. Those data which are relevant only for a specific dna sample are
stored in AmplificationResult
. Theoretically this includes data on the resulting PCR. However, as the
PCR itself is not persistent we do not store further information on it in the CDM and do not handle
AmplificationResult
as a DerivedUnit
.
AmplificationResult
,
Serialized Formannotations, markers
CLOB_LENGTH, uuid
Modifier | Constructor and Description |
---|---|
protected |
Amplification() |
Modifier and Type | Method and Description |
---|---|
java.lang.Object |
clone()
Clones this amplification.
|
DefinedTerm |
getDnaMarker()
The
DNA marker used for this amplification. |
java.lang.Double |
getElectrophoresisVoltage()
The voltage used for running the electrophoresis quality check.
|
Primer |
getForwardPrimer()
The primer used for forward amplification.
|
java.lang.Double |
getGelConcentration()
The gel concentration used for the electrophoresis.
|
java.lang.Double |
getGelRunningTime()
The time for running the electrophoresis quality check.
|
Institution |
getInstitution()
The institution in which the amplification event took place.
|
java.lang.String |
getLabelCache()
Returns the labelCache
|
java.lang.String |
getLadderUsed()
Material and method used for testing quality of this amplification.
|
MaterialOrMethodEvent |
getPurification()
The material and/or method used for purification.
|
Primer |
getReversePrimer()
The primer used for reverse amplification.
|
static Amplification |
NewInstance() |
void |
setDnaMarker(DefinedTerm marker) |
void |
setElectrophoresisVoltage(java.lang.Double electrophoresisVoltage) |
void |
setForwardPrimer(Primer forwardPrimer) |
void |
setGelConcentration(java.lang.Double gelConcentration) |
void |
setGelRunningTime(java.lang.Double gelRunningTime) |
void |
setInstitution(Institution institution) |
void |
setLadderUsed(java.lang.String ladderUsed) |
void |
setPurification(MaterialOrMethodEvent purification) |
void |
setReversePrimer(Primer reversePrimer) |
void |
updateCache()
This method pushes the
label cache update. |
getActor, getDescription, getTimeperiod, setActor, setDescription, setTimeperiod
addAnnotation, addMarker, addMarker, getAnnotations, getAnnotations, getMarkers, getMarkers, hasMarker, hasMarker, markerValue, removeAnnotation, removeMarker, removeMarker, setAnnotations
cloneLanguageString, equals, getUpdated, getUpdatedBy, setUpdated, setUpdatedBy
addPropertyChangeListener, addPropertyChangeListener, addToSetWithChangeEvent, deproxy, deproxy, fireOnCreateEvent, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getCreated, getCreatedBy, getId, getUserFriendlyDescription, getUserFriendlyFieldName, getUserFriendlyTypeName, getUuid, hashCode, hasListeners, initListener, instanceToString, invokeSetMethod, invokeSetMethodWithNull, isBlank, isInstanceOf, isNotBlank, isPersited, removeFromSetWithChangeEvent, removePropertyChangeListener, removePropertyChangeListener, replaceInList, setCreated, setCreatedBy, setId, setNewEntityListener, setUuid, toString
finalize, getClass, notify, notifyAll, wait, wait, wait
getUpdated, getUpdatedBy, setUpdated, setUpdatedBy
getCreated, getCreatedBy, getId, getUuid, isInstanceOf, isPersited, setCreated, setCreatedBy, setId, setUuid
public static Amplification NewInstance()
public DefinedTerm getDnaMarker()
DNA marker
used for this amplification.
The DNA marker also defines the part (locality) of the DNA/RNA examined.
It may also be called locuspublic void setDnaMarker(DefinedTerm marker)
getDnaMarker()
public Primer getForwardPrimer()
getReversePrimer()
public void setForwardPrimer(Primer forwardPrimer)
getForwardPrimer()
,
getReversePrimer()
public Primer getReversePrimer()
getForwardPrimer()
public void setReversePrimer(Primer reversePrimer)
getReversePrimer()
,
getForwardPrimer()
public MaterialOrMethodEvent getPurification()
public void setPurification(MaterialOrMethodEvent purification)
getPurification()
public Institution getInstitution()
EventBase.getActor()
should be a person
or team that works for this institution at the given timepublic void setInstitution(Institution institution)
getInstitution()
public java.lang.Double getElectrophoresisVoltage()
getGelRunningTime()
,
#getGelPhoto()
,
getLadderUsed()
,
getGelConcentration()
public void setElectrophoresisVoltage(java.lang.Double electrophoresisVoltage)
getElectrophoresisVoltage()
public java.lang.Double getGelRunningTime()
public void setGelRunningTime(java.lang.Double gelRunningTime)
getGelRunningTime()
public java.lang.Double getGelConcentration()
getElectrophoresisVoltage()
,
getGelRunningTime()
,
#getGelPhoto()
,
getLadderUsed()
public void setGelConcentration(java.lang.Double gelConcentration)
getGelConcentration()
public java.lang.String getLadderUsed()
getElectrophoresisVoltage()
,
#getGelPhoto()
,
getGelConcentration()
,
getGelRunningTime()
public void setLadderUsed(java.lang.String ladderUsed)
getLadderUsed()
public java.lang.String getLabelCache()
public void updateCache()
label cache
update.
The cache is otherwise updated during persist in CacheStrategyUpdater.public java.lang.Object clone()
clone
in class EventBase
EventBase.clone()
,
Object.clone()
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