@Entity public class SingleRead extends EventBase implements java.lang.Cloneable
SingleRead
class describe the process and the result of a single
sequence generation (read). It has as an input the PCR result (AmplificationResult
). A primer
is used for expressing the DNA in either forward
or
reverse
direction.
The result of the process is a pherogram
which by interpretation results
in the most probable sequence
.
The event dates like the sequencing date and the sequencing agent(person) are inherited by EventBase
.AmplificationResult
,
SequenceString
,
Sequence
,
Serialized Formannotations, markers
CLOB_LENGTH, uuid
Modifier | Constructor and Description |
---|---|
protected |
SingleRead() |
Modifier and Type | Method and Description |
---|---|
java.lang.Object |
clone()
Clones this sequence.
|
AmplificationResult |
getAmplificationResult()
Returns the
amplification product that was the input for this
single sequence . |
TimePeriod |
getDateSequenced()
Transient convenience method which wrapps
EventBase.getActor() . |
SequenceDirection |
getDirection()
The
direction in which this single sequence has been created. |
MaterialOrMethodEvent |
getMaterialOrMethod()
The material and/or method used for this sequencing.
|
Media |
getPherogram()
The pherogram (chromatogram) which visualizes the result of this single sequence.
|
Primer |
getPrimer()
The
primer used for processing this single sequence. |
SequenceString |
getSequence()
The
sequence string of this single sequence process (e.g. |
AgentBase |
getSequencedBy()
Transient convenience method which wrapps
EventBase.getActor() . |
java.lang.String |
getSequenceString()
Delegate method to get the text representation of the
sequence . |
static SingleRead |
NewInstance() |
protected void |
setAmplificationResult(AmplificationResult amplificationResult)
TODO this method is protected as long as bidirectionality is not clear.
|
void |
setDateSequenced(TimePeriod dateSequenced) |
void |
setDirection(SequenceDirection direction) |
void |
setMaterialOrMethod(MaterialOrMethodEvent materialOrMethod) |
void |
setPherogram(Media pherogram) |
void |
setPrimer(Primer primer) |
void |
setSequence(SequenceString sequence) |
void |
setSequencedBy(AgentBase sequencedBy) |
void |
setSequenceString(java.lang.String sequence)
Delegate method to set the text representation of the
sequence . |
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 SingleRead NewInstance()
public AmplificationResult getAmplificationResult()
amplification product
that was the input for this
single sequence
.protected void setAmplificationResult(AmplificationResult amplificationResult)
getAmplificationResult()
public Primer getPrimer()
primer
used for processing this single sequence.
Often this primer already has been used in the according amplification
.
However, there are exceptions from this rule.public void setPrimer(Primer primer)
getPrimer()
public SequenceString getSequence()
sequence string
of this single sequence process (e.g. AGTGGTAGGATG)public void setSequence(SequenceString sequence)
getSequence()
public SequenceDirection getDirection()
direction
in which this single sequence has been created.
Usually an amplification
leads to 2 single sequences per DnaSample
,
a forward
and a reverse
one.
These 2 result then in a consensus sequence
.
But there are exceptions from this rule.public void setDirection(SequenceDirection direction)
getDirection()
public Media getPherogram()
public void setPherogram(Media pherogram)
getPherogram()
public MaterialOrMethodEvent getMaterialOrMethod()
public void setMaterialOrMethod(MaterialOrMethodEvent materialOrMethod)
getMaterialOrMethod()
public java.lang.String getSequenceString()
sequence
.setSequenceString(String)
public void setSequenceString(java.lang.String sequence)
sequence
.public TimePeriod getDateSequenced()
EventBase.getActor()
.date/period
when this sequence was created.public void setDateSequenced(TimePeriod dateSequenced)
getDateSequenced()
public AgentBase getSequencedBy()
EventBase.getActor()
.agent
who sequenced this single sequence.public void setSequencedBy(AgentBase sequencedBy)
getSequencedBy()
public java.lang.Object clone()
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