@Entity public class AmplificationResult extends AnnotatableEntity 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
.
Amplification
,
Serialized Formannotations, markers
CLOB_LENGTH, uuid
Modifier | Constructor and Description |
---|---|
protected |
AmplificationResult() |
Modifier and Type | Method and Description |
---|---|
void |
addSingleRead(SingleRead singleRead) |
java.lang.Object |
clone()
Clones this amplification.
|
Amplification |
getAmplification()
The
amplification event this amplification result resulted from. |
Cloning |
getCloning()
The
cloning process involved in this amplification. |
DnaSample |
getDnaSample()
The
dna sample which is the input for this amplification . |
Media |
getGelPhoto()
The photo taken from the electrophoresis result showing the quality of the amplification.
|
java.util.Set<SingleRead> |
getSingleReads()
The
single sequences created by using this amplification's result (PCR). |
java.lang.Boolean |
getSuccessful()
Information if this amplification was successful or not.
|
java.lang.String |
getSuccessText()
Freetext about the success of this amplification explaining
in detail why it is concidered to be successful/unsucessful
|
static AmplificationResult |
NewInstance() |
static AmplificationResult |
NewInstance(DnaSample dnaSample) |
static AmplificationResult |
NewInstance(DnaSample dnaSample,
Amplification amplification) |
static AmplificationResult |
NewInstance(SingleRead singleRead) |
void |
removeSingleRead(SingleRead singleRead) |
void |
setAmplification(Amplification amplification)
|
void |
setCloning(Cloning cloning) |
protected void |
setDnaSample(DnaSample dnaSample)
For use by DnaSample.addAmplification(ampl.) only.
|
void |
setGelPhoto(Media gelPhoto) |
void |
setSuccessful(java.lang.Boolean successful) |
void |
setSuccessText(java.lang.String successText) |
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 AmplificationResult NewInstance(DnaSample dnaSample)
public static AmplificationResult NewInstance(SingleRead singleRead)
public static AmplificationResult NewInstance(DnaSample dnaSample, Amplification amplification)
public static AmplificationResult NewInstance()
public DnaSample getDnaSample()
dna sample
which is the input for this amplification
.protected void setDnaSample(DnaSample dnaSample)
getDnaSample()
public Amplification getAmplification()
amplification event
this amplification result resulted from.setAmplification(Amplification)
,
Amplification
public void setAmplification(Amplification amplification)
amplification
- public java.util.Set<SingleRead> getSingleReads()
single sequences
created by using this amplification's result (PCR).public void addSingleRead(SingleRead singleRead)
public void removeSingleRead(SingleRead singleRead)
public java.lang.Boolean getSuccessful()
getSuccessText()
public void setSuccessful(java.lang.Boolean successful)
getSuccessful()
,
getSuccessText()
public java.lang.String getSuccessText()
getSuccessful()
public void setSuccessText(java.lang.String successText)
getSuccessText()
,
getSuccessful()
public Cloning getCloning()
cloning process
involved in this amplification.public void setCloning(Cloning cloning)
getCloning()
public Media getGelPhoto()
this
amplification. However, this may make
the concrete media file unusable for other amplifications also represented by the same image.#getElectrophoresisVoltage()
,
#getLadderUsed()
,
#getGelConcentration()
,
#getGelRunningTime()
public void setGelPhoto(Media gelPhoto)
gelPhoto
- the gelPhoto to setpublic java.lang.Object clone()
clone
in class AnnotatableEntity
EventBase.clone()
,
Object.clone()
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