org.jbei.ice.storage.model

Class Sequence

java.lang.Object

org.jbei.ice.storage.model.Sequence

All Implemented Interfaces:

DataModel

@Entity
public class Sequence
extends Object
implements DataModel

Stores the unique sequence for an Entry object.

• sequence: Normalized (lower cased, trimmed) sequence for Entry.
• sequenceUser: Original sequence uploaded by the user. For example, the unparsed genbank file, if that was the original upload. If the original upload does not exist, then this field is the same as sequence.
• fwdHash, revHash: sha1 hash of the normalized sequence for fast searches.
• sequenceFeatures: SequenceFeature objects.

Author:

Timothy Ham, Zinovii Dmytriv

Constructor Summary

Constructors

Constructor and Description
Sequence()
Sequence(String sequence, String sequenceUser, String fwdHash, String revHash, Entry entry)

Method Summary

Modifier and Type	Method and Description
String	getComponentUri()
Entry	getEntry()
String	getFileName()
SequenceFormat	getFormat()
String	getFwdHash()
long	getId()
String	getIdentifier()
String	getRevHash()
String	getSequence()
Set<SequenceFeature>	getSequenceFeatures()
String	getSequenceUser()
String	getUri()
void	setComponentUri(String componentUri)
void	setEntry(Entry entry)
void	setFileName(String fileName)
void	setFormat(SequenceFormat format)
void	setFwdHash(String fwdHash)
void	setId(long id)
void	setIdentifier(String identifier)
void	setRevHash(String revHash)
void	setSequence(String sequence)
void	setSequenceFeatures(Set<SequenceFeature> features)
void	setSequenceUser(String sequenceUser)
void	setUri(String uri)
SequenceInfo	toDataTransferObject()

Methods inherited from class java.lang.Object

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

Constructor Detail

Sequence

public Sequence()

Sequence

public Sequence(String sequence,
                String sequenceUser,
                String fwdHash,
                String revHash,
                Entry entry)

Method Detail

getId

public long getId()

Specified by:

getId in interface DataModel

setId

public void setId(long id)

getSequence

public String getSequence()

setSequence

public void setSequence(String sequence)

getSequenceUser

public String getSequenceUser()

setSequenceUser

public void setSequenceUser(String sequenceUser)

getFwdHash

public String getFwdHash()

setFwdHash

public void setFwdHash(String fwdHash)

getRevHash

public String getRevHash()

setRevHash

public void setRevHash(String revHash)

getEntry

public Entry getEntry()

setEntry

public void setEntry(Entry entry)

getSequenceFeatures

public Set<SequenceFeature> getSequenceFeatures()

setSequenceFeatures

public void setSequenceFeatures(Set<SequenceFeature> features)

getUri

public String getUri()

setUri

public void setUri(String uri)

getComponentUri

public String getComponentUri()

Returns:

uri for component that this sequence is a part of

setComponentUri

public void setComponentUri(String componentUri)

getIdentifier

public String getIdentifier()

setIdentifier

public void setIdentifier(String identifier)

getFileName

public String getFileName()

setFileName

public void setFileName(String fileName)

setFormat

public void setFormat(SequenceFormat format)

getFormat

public SequenceFormat getFormat()

toDataTransferObject

public SequenceInfo toDataTransferObject()

Specified by:

toDataTransferObject in interface DataModel