eu.etaxonomy.cdm.model.molecular
Class Sequence

java.lang.Object
  eu.etaxonomy.cdm.model.common.CdmBase
      eu.etaxonomy.cdm.model.common.VersionableEntity
          eu.etaxonomy.cdm.model.common.AnnotatableEntity
              eu.etaxonomy.cdm.model.common.IdentifiableEntity<IIdentifiableEntityCacheStrategy<Sequence>>
                  eu.etaxonomy.cdm.model.molecular.Sequence

All Implemented Interfaces:

IAnnotatableEntity, ICdmBase, IIdentifiableEntity, IReferencedEntity, ISourceable<IdentifiableSource>, IVersionableEntity, IMediaDocumented, Serializable, Cloneable

@Configurable
public class Sequence
extends IdentifiableEntity<IIdentifiableEntityCacheStrategy<Sequence>>
implements IReferencedEntity, IMediaDocumented

Version:

1.0

Author:

m.doering

See Also:

Serialized Form

Field Summary

Fields inherited from class eu.etaxonomy.cdm.model.common.IdentifiableEntity

cacheStrategy, NOT_PROTECTED, PROTECTED, protectedTitleCache, titleCache

Fields inherited from class eu.etaxonomy.cdm.model.common.AnnotatableEntity

annotations, markers

Fields inherited from class eu.etaxonomy.cdm.model.common.CdmBase

uuid

Constructor Summary

protected

Sequence()

Method Summary

void	addChromatogram(Media chromatogram)
void	addCitation(Reference citation)
void	addGenBankAccession(GenBankAccession genBankAccession)
Object	clone() Clones this sequence.
Set<Media>	getChromatograms()
Reference	getCitation()
String	getCitationMicroReference()
Set<Reference>	getCitations()
org.joda.time.DateTime	getDateSequenced()
Set<GenBankAccession>	getGenBankAccession()
Integer	getLength()
Locus	getLocus()
Set<Media>	getMedia()
Reference	getPublishedIn()
String	getSequence()
boolean	isBarcode()
void	removeChromatogram(Media chromatogram)
void	removeCitation(Reference citation)
void	removeGenBankAccession(GenBankAccession genBankAccession)
void	setBarcode(boolean barcode)
void	setCitationMicroReference(String citationMicroReference)
protected void	setCitations(Set<Reference> citations)
void	setDateSequenced(org.joda.time.DateTime dateSequenced)
void	setLength(Integer length)
void	setLocus(Locus locus)
void	setPublishedIn(Reference publishedIn)
void	setSequence(String sequence)

Methods inherited from class eu.etaxonomy.cdm.model.common.IdentifiableEntity

addCredit, addCredit, addExtension, addExtension, addRights, addSource, addSource, compareTo, generateTitle, getCacheStrategy, getCredits, getCredits, getData, getExtensions, getExtensions, getExtensions, getLsid, getRights, getSources, getTitleCache, getTruncatedCache, initListener, isProtectedTitleCache, removeCredit, removeCredit, removeExtension, removeRights, removeSource, setCacheStrategy, setLsid, setProtectedTitleCache, setTitleCache, setTitleCache, toString

Methods inherited from class eu.etaxonomy.cdm.model.common.AnnotatableEntity

addAnnotation, addMarker, getAnnotations, getMarkers, hasMarker, hasMarker, removeAnnotation, removeMarker

Methods inherited from class eu.etaxonomy.cdm.model.common.VersionableEntity

equals, getUpdated, getUpdatedBy, setUpdated, setUpdatedBy

Methods inherited from class eu.etaxonomy.cdm.model.common.CdmBase

addPropertyChangeListener, addPropertyChangeListener, clone, deproxy, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getCreated, getCreatedBy, getId, getUuid, hashCode, hasListeners, invokeSetMethod, invokeSetMethodWithNull, isInstanceOf, removePropertyChangeListener, removePropertyChangeListener, setCreated, setCreatedBy, setId, setUuid

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface eu.etaxonomy.cdm.model.common.IAnnotatableEntity

addAnnotation, addMarker, getAnnotations, getMarkers, hasMarker, hasMarker, removeAnnotation, removeMarker

Methods inherited from interface eu.etaxonomy.cdm.model.common.IVersionableEntity

getUpdated, getUpdatedBy, setUpdated, setUpdatedBy

Methods inherited from interface eu.etaxonomy.cdm.model.common.ICdmBase

getCreated, getCreatedBy, getId, getUuid, setCreated, setCreatedBy, setId, setUuid

Constructor Detail

Sequence

protected Sequence()

Method Detail

getLocus

public Locus getLocus()

setLocus

public void setLocus(Locus locus)

getPublishedIn

public Reference getPublishedIn()

setPublishedIn

public void setPublishedIn(Reference publishedIn)

getCitations

public Set<Reference> getCitations()

setCitations

protected void setCitations(Set<Reference> citations)

addCitation

public void addCitation(Reference citation)

removeCitation

public void removeCitation(Reference citation)

getGenBankAccession

public Set<GenBankAccession> getGenBankAccession()

addGenBankAccession

public void addGenBankAccession(GenBankAccession genBankAccession)

removeGenBankAccession

public void removeGenBankAccession(GenBankAccession genBankAccession)

getChromatograms

public Set<Media> getChromatograms()

addChromatogram

public void addChromatogram(Media chromatogram)

removeChromatogram

public void removeChromatogram(Media chromatogram)

getMedia

public Set<Media> getMedia()

Specified by:

getMedia in interface IMediaDocumented

getSequence

public String getSequence()

setSequence

public void setSequence(String sequence)

Parameters:

sequence - sequence

getLength

public Integer getLength()

setLength

public void setLength(Integer length)

Parameters:

length - length

getDateSequenced

public org.joda.time.DateTime getDateSequenced()

setDateSequenced

public void setDateSequenced(org.joda.time.DateTime dateSequenced)

Parameters:

dateSequenced - dateSequenced

isBarcode

public boolean isBarcode()

setBarcode

public void setBarcode(boolean barcode)

Parameters:

isBarcode - isBarcode

getCitationMicroReference

public String getCitationMicroReference()

setCitationMicroReference

public void setCitationMicroReference(String citationMicroReference)

Parameters:

citationMicroReference - citationMicroReference

getCitation

public Reference getCitation()

Specified by:

getCitation in interface IReferencedEntity

clone

public Object clone()

Clones this sequence. This is a shortcut that enables to create a new instance that differs only slightly from this sequence by modifying only some of the attributes.

Overrides:

clone in class IdentifiableEntity<IIdentifiableEntityCacheStrategy<Sequence>>

See Also:

eu.etaxonomy.cdm.model.media.IdentifiableEntity#clone(), Object.clone()