org.jbei.ice.storage.model

Class SequenceFeature

java.lang.Object

org.jbei.ice.storage.model.SequenceFeature

All Implemented Interfaces:

DataModel

@Entity
public class SequenceFeature
extends Object
implements DataModel

Stores the sequence annotation information, and associates Feature objects to a Sequence object.

SequenceFeature represents is a many-to-many mapping. In addition, this class has fields to store sequence specific annotation information.

Author:

Timothy Ham, Zinovii Dmytriv

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SequenceFeature.AnnotationType Annotation type for "parts".

Constructor Summary

Constructors

Constructor and Description
SequenceFeature()
SequenceFeature(Sequence sequence, Feature feature, int strand, String name, String genbankType, SequenceFeature.AnnotationType annotationType)

Method Summary

Modifier and Type	Method and Description
Set<AnnotationLocation>	getAnnotationLocations()
SequenceFeature.AnnotationType	getAnnotationType()
Feature	getFeature()
String	getGenbankType()
long	getId()
String	getName()
Sequence	getSequence()
Set<SequenceFeatureAttribute>	getSequenceFeatureAttributes()
int	getStrand()
Integer	getUniqueEnd()
Integer	getUniqueGenbankStart()
String	getUri()
void	setFeature(Feature feature)
void	setId(long id)
void	setName(String name)
void	setSequence(Sequence sequence)
void	setStrand(int strand) +1 for forward, -1 for reverse.
void	setUri(String uri)
DNAFeature	toDataTransferObject()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SequenceFeature

public SequenceFeature()

SequenceFeature

public SequenceFeature(Sequence sequence,
                       Feature feature,
                       int strand,
                       String name,
                       String genbankType,
                       SequenceFeature.AnnotationType annotationType)

Method Detail

getUri

public String getUri()

setUri

public void setUri(String uri)

toDataTransferObject

public DNAFeature toDataTransferObject()

Specified by:

toDataTransferObject in interface DataModel

setId

public void setId(long id)

getId

public long getId()

Specified by:

getId in interface DataModel

getSequence

public Sequence getSequence()

setSequence

public void setSequence(Sequence sequence)

getFeature

public Feature getFeature()

setFeature

public void setFeature(Feature feature)

getAnnotationLocations

public Set<AnnotationLocation> getAnnotationLocations()

getStrand

public int getStrand()

setStrand

public void setStrand(int strand)

+1 for forward, -1 for reverse.

getName

public String getName()

setName

public void setName(String name)

getGenbankType

public String getGenbankType()

getAnnotationType

public SequenceFeature.AnnotationType getAnnotationType()

getSequenceFeatureAttributes

public Set<SequenceFeatureAttribute> getSequenceFeatureAttributes()

getUniqueGenbankStart

public Integer getUniqueGenbankStart()

getUniqueEnd

public Integer getUniqueEnd()