@Entity @Configurable public class Sequence extends AnnotatableEntity implements java.lang.Cloneable
single sequences
to a consensus sequence.
This sequence is a part of (or the complete) DNA sequences of the related DNA Sample
,
while
single sequences
to one consensus sequence
(singleReads
, contigFile
)
as well as sequence related information.
The later includes the sequence string
itself,
important genetic information about the DNA that has been sequenced
(marker
, getHaplotype()
haplotype) as well as
registration information (genetic accession number
),
citations, and barcoding information (BOLD-id
,
barcode sequence
, ...).annotations, markers
CLOB_LENGTH, uuid
Modifier | Constructor and Description |
---|---|
protected |
Sequence() |
Modifier and Type | Method and Description |
---|---|
void |
addCitation(Reference citation) |
SingleReadAlignment |
addSingleRead(SingleRead singleRead)
Convenience method to add a single read to a consensus sequence
by creating a
SingleReadAlignment . |
void |
addSingleReadAlignment(SingleReadAlignment singleReadAlignment) |
java.lang.Object |
clone()
Clones this sequence.
|
SequenceString |
getBarcodeSequencePart()
If the barcode sequence string does not include 100% of the (consensus) sequence
the part used as barcode is provided here.
|
java.lang.String |
getBoldProcessId()
The identifier used by the Barcode of Life Data Systems (BOLD, http://www.boldsystems.org/).
|
java.net.URI |
getBoldUri()
Returns the URI for the BOLD entry.
|
java.util.Set<Reference> |
getCitations()
Citations are the set of references in which this sequence was published.
|
SequenceString |
getConsensusSequence()
The resulting consensus sequence represened by this
sequence . |
Media |
getContigFile()
The contigFile containing all data and data processing for this sequencing.
|
java.net.URI |
getDdbjUri()
Returns the computed DDBJ uri.
|
DefinedTerm |
getDnaMarker()
Sets the
DNA marker examined and described by this sequencing. |
DnaSample |
getDnaSample()
The
dna sample this sequencing belongs too. |
java.net.URI |
getEmblUri()
Returns the computed EMBL uri.
|
java.net.URI |
getGenBankUri()
Returns the computed genBank uri.
|
java.lang.String |
getGeneticAccessionNumber()
The accession number used in GenBank, EMBL and DDBJ.
|
java.lang.String |
getHaplotype()
Returns the name of the haplotype.
|
java.lang.Boolean |
getIsBarcode()
The isBarcode flag should be set to true if this (consensus) sequence is or includes
a barcoding sequence.
|
java.util.Set<Media> |
getPherograms()
Convenience method which computes the set of all related pherograms
|
java.lang.String |
getSequenceString()
Delegate method to get the text representation of the consensus sequence
|
java.util.Set<SingleReadAlignment> |
getSingleReadAlignments()
The
single reads that were used to build this consensus sequence. |
java.util.Set<SingleRead> |
getSingleReads()
Convenience method that returns all single reads this consensus sequence
is based on via
SingleReadAlignment s. |
static Sequence |
NewInstance(DnaSample dnaSample,
java.lang.String consensusSequence,
java.lang.Integer length) |
static Sequence |
NewInstance(java.lang.String consensusSequence) |
static Sequence |
NewInstance(java.lang.String consensusSequence,
java.lang.Integer length) |
void |
removeCitation(Reference citation) |
void |
removeSingleRead(SingleRead singleRead) |
void |
removeSingleReadAlignment(SingleReadAlignment singleReadAlignment) |
void |
setBarcodeSequencePart(SequenceString barcodeSequencePart) |
void |
setBoldProcessId(java.lang.String boldProcessId) |
protected void |
setCitations(java.util.Set<Reference> citations) |
void |
setConsensusSequence(SequenceString sequenceString) |
void |
setContigFile(Media contigFile) |
void |
setDnaMarker(DefinedTerm dnaMarker) |
protected void |
setDnaSample(DnaSample dnaSample)
To be called only from
DnaSample.addSequence(Sequence) |
void |
setGeneticAccessionNumber(java.lang.String geneticAccessionNumber)
Sets the genetic accession number.
|
void |
setHaplotype(java.lang.String haplotype) |
void |
setIsBarcode(java.lang.Boolean isBarcode) |
void |
setSequenceString(java.lang.String sequence)
Delegate method to set the text representation of the
consensus sequence . |
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 Sequence NewInstance(java.lang.String consensusSequence)
public static Sequence NewInstance(java.lang.String consensusSequence, java.lang.Integer length)
public static Sequence NewInstance(DnaSample dnaSample, java.lang.String consensusSequence, java.lang.Integer length)
public DnaSample getDnaSample()
dna sample
this sequencing belongs too.protected void setDnaSample(DnaSample dnaSample)
DnaSample.addSequence(Sequence)
getDnaSample()
public SequenceString getConsensusSequence()
sequence
.
The consensus is usually computed from the single reads
.
The result of which is stored in a file called contig file
#see getContigFile()
#see getSingleReads()
public void setConsensusSequence(SequenceString sequenceString)
getConsensusSequence()
public java.lang.Boolean getIsBarcode()
barcoding sequence part
.
A isBarcode value of null
indicates that we do have no knowledge
whether the sequence is a barcoding sequence or not.getBarcodeSequencePart()
,
getSequenceString()
public void setIsBarcode(java.lang.Boolean isBarcode)
getIsBarcode()
,
getBarcodeSequencePart()
public SequenceString getBarcodeSequencePart()
getIsBarcode()
public void setBarcodeSequencePart(SequenceString barcodeSequencePart)
getBarcodeSequencePart()
public DefinedTerm getDnaMarker()
DNA marker
examined and described by this sequencing.
The marker should usually be similar to the one used in the according amplification process
. However, it may slightly differ, or, if multiple amplifications where
used to build this consensus sequence it may be the super set of the markers used in amplification.public void setDnaMarker(DefinedTerm dnaMarker)
marker
- getDnaMarker()
public java.lang.String getGeneticAccessionNumber()
public void setGeneticAccessionNumber(java.lang.String geneticAccessionNumber)
getGeneticAccessionNumber()
public java.lang.String getBoldProcessId()
public void setBoldProcessId(java.lang.String boldProcessId)
public java.lang.String getHaplotype()
public void setHaplotype(java.lang.String haplotype)
getHaplotype()
public Media getContigFile()
getConsensusSequence()
,
getSingleReads()
public void setContigFile(Media contigFile)
getContigFile()
public java.util.Set<Reference> getCitations()
protected void setCitations(java.util.Set<Reference> citations)
getCitations()
public void addCitation(Reference citation)
getCitations()
public void removeCitation(Reference citation)
getCitations()
public java.util.Set<SingleReadAlignment> getSingleReadAlignments()
single reads
that were used to build this consensus sequence.getConsensusSequence()
,
getContigFile()
public void addSingleReadAlignment(SingleReadAlignment singleReadAlignment)
getSingleReads()
public void removeSingleReadAlignment(SingleReadAlignment singleReadAlignment)
getSingleReads()
public SingleReadAlignment addSingleRead(SingleRead singleRead)
SingleReadAlignment
.singleRead
- the SingleRead
to addpublic void removeSingleRead(SingleRead singleRead)
public java.util.Set<SingleRead> getSingleReads()
SingleReadAlignment
s.public java.lang.String getSequenceString()
setSequenceString(String)
public void setSequenceString(java.lang.String sequence)
consensus sequence
.public java.util.Set<Media> getPherograms()
public java.net.URI getGenBankUri() throws java.net.URISyntaxException
GENBANK_BASE_URI
and geneticAccessionNumber
java.net.URISyntaxException
- when URI could not be created with geneticAccessionNumber
public java.net.URI getEmblUri() throws java.net.URISyntaxException
EMBL_BASE_URI
and geneticAccessionNumber
java.net.URISyntaxException
- when URI could not be created with geneticAccessionNumber
public java.net.URI getDdbjUri() throws java.net.URISyntaxException
DDBJ_BASE_URI
and geneticAccessionNumber
java.net.URISyntaxException
- when URI could not be created with geneticAccessionNumber
public java.net.URI getBoldUri() throws java.net.URISyntaxException
BOLD_BASE_URI
and boldProcessId
java.net.URISyntaxException
- when URI could not be created with boldProcessId
getBoldProcessId()
public java.lang.Object clone()
clone
in class AnnotatableEntity
eu.etaxonomy.cdm.model.media.IdentifiableEntity#clone()
,
Object.clone()
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