org.jbei.ice.lib.entry.sequence

Class SequenceController

java.lang.Object

org.jbei.ice.lib.entry.HasEntry

org.jbei.ice.lib.entry.sequence.SequenceController

public class SequenceController
extends HasEntry

ABI to manipulate Sequences.

Author:

Hector Plahar, Timothy Ham, Zinovii Dmytriv

Field Summary

Fields inherited from class org.jbei.ice.lib.entry.HasEntry

accountDAO

Constructor Summary

Constructors

Constructor and Description
SequenceController()

Method Summary

Modifier and Type	Method and Description
protected String	compose(Sequence sequence, IFormatter formatter) Generate a formatted text of a given IFormatter from the given Sequence.
boolean	deleteSequence(String requester, long partId)
static Sequence	dnaSequenceToSequence(DNASequence dnaSequence) Create a Sequence object from an DNASequence object.
protected FeaturedDNASequence	getFeaturedSequence(Entry entry, boolean canEdit)
FeaturedDNASequence	getRequestedSequence(RegistryPartner requestingPartner, String remoteUserId, String token, String entryId, long folderId)
ByteArrayWrapper	getSequenceFile(String userId, long partId, SequenceFormat format)
FeaturedDNASequence	retrievePartSequence(String userId, String recordId)
Sequence	save(String userId, Sequence sequence) Save the given Sequence into the database, with the option to rebuild the search index.
FeaturedDNASequence	sequenceToDNASequence(Sequence sequence) Generate a FeaturedDNASequence from a given Sequence object.
protected Sequence	update(String userId, Sequence sequence) Update the Sequence in the database, with the option to rebuild the search index.
FeaturedDNASequence	updateSequence(String userId, long entryId, FeaturedDNASequence featuredDNASequence, boolean addFeatures)

Methods inherited from class org.jbei.ice.lib.entry.HasEntry

getEntry

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceController

public SequenceController()

Method Detail

save

public Sequence save(String userId,
                     Sequence sequence)

Save the given Sequence into the database, with the option to rebuild the search index.

Parameters:

userId - unique identifier of user saving sequence

sequence - sequence to save

Returns:

Saved Sequence

updateSequence

public FeaturedDNASequence updateSequence(String userId,
                                          long entryId,
                                          FeaturedDNASequence featuredDNASequence,
                                          boolean addFeatures)

update

protected Sequence update(String userId,
                          Sequence sequence)

Update the Sequence in the database, with the option to rebuild the search index.

Parameters:

userId - unique identifier for user performing action

sequence - sequence to be updated

Returns:

Saved Sequence.

deleteSequence

public boolean deleteSequence(String requester,
                              long partId)

compose

protected String compose(Sequence sequence,
                         IFormatter formatter)

Generate a formatted text of a given IFormatter from the given Sequence.

Parameters:

sequence -

formatter -

Returns:

Text of a formatted sequence.

getRequestedSequence

public FeaturedDNASequence getRequestedSequence(RegistryPartner requestingPartner,
                                                String remoteUserId,
                                                String token,
                                                String entryId,
                                                long folderId)

retrievePartSequence

public FeaturedDNASequence retrievePartSequence(String userId,
                                                String recordId)

getFeaturedSequence

protected FeaturedDNASequence getFeaturedSequence(Entry entry,
                                                  boolean canEdit)

sequenceToDNASequence

public FeaturedDNASequence sequenceToDNASequence(Sequence sequence)

Generate a FeaturedDNASequence from a given Sequence object.

Parameters:

sequence -

Returns:

FeaturedDNASequence

dnaSequenceToSequence

public static Sequence dnaSequenceToSequence(DNASequence dnaSequence)

Create a Sequence object from an DNASequence object.

Parameters:

dnaSequence -

Returns:

Translated Sequence object.

getSequenceFile

public ByteArrayWrapper getSequenceFile(String userId,
                                        long partId,
                                        SequenceFormat format)