org.jbei.ice.storage.hibernate.dao

Class SequenceDAO

java.lang.Object

org.jbei.ice.storage.hibernate.HibernateRepository<Sequence>

org.jbei.ice.storage.hibernate.dao.SequenceDAO

All Implemented Interfaces:

IRepository<Sequence>

public class SequenceDAO
extends HibernateRepository<Sequence>

Manipulate Sequence and associated objects in the database.

Author:

Hector Plahar

Constructor Summary

Constructors

Constructor and Description
SequenceDAO()

Method Summary

Modifier and Type	Method and Description
void	deleteSequence(Sequence sequence, String pigeonImageFolder) Delete the given Sequence object in the database.
Sequence	get(long id)
Sequence	getByEntry(Entry entry) Retrieve the Sequence object associated with the given Entry object.
Sequence	getSequence(int offset) Enables retrieving sequences in the database without loading everything in memory Expected usage is long count = getSequenceCount(); int offset = 0; while( offset < count ) { Sequence sequence = dao.getSequence(offset); // do something with sequence }
int	getSequenceCount()
String	getSequenceFilename(Entry entry)
Optional<String>	getSequenceString(Entry entry)
boolean	hasOriginalSequence(long entryId) Determines if the user uploaded a sequence file and associated it with an entry
boolean	hasSequence(long entryId)
Sequence	saveSequence(Sequence sequence) Save the given Sequence object in the database.
Sequence	updateSequence(Sequence sequence, Set<SequenceFeature> newFeatures) Updates an existing feature with a new set of features

Methods inherited from class org.jbei.ice.storage.hibernate.HibernateRepository

create, currentSession, delete, get, getBuilder, update

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceDAO

public SequenceDAO()

Method Detail

saveSequence

public Sequence saveSequence(Sequence sequence)

Save the given Sequence object in the database.

Parameters:

sequence - sequence to save

Returns:

Saved Sequence object

Throws:

IllegalArgumentException - if the sequence object is null or does not have a valid entry associated with it

DAOException

updateSequence

public Sequence updateSequence(Sequence sequence,
                               Set<SequenceFeature> newFeatures)

Updates an existing feature with a new set of features

Parameters:

sequence - existing feature to update

newFeatures - optional new set of features that need updating. If this is null, the features associated with the specified sequence is cleared

Returns:

updated sequence

Throws:

IllegalArgumentException - if sequence is null or does not have an associated entry

deleteSequence

public void deleteSequence(Sequence sequence,
                           String pigeonImageFolder)

Delete the given Sequence object in the database.

Parameters:

sequence - sequence to delete

pigeonImageFolder - path of the image folder where the pigeon images are cached

getByEntry

public Sequence getByEntry(Entry entry)

Retrieve the Sequence object associated with the given Entry object.

Parameters:

entry - entry associated with sequence

Returns:

Sequence object.

getSequenceString

public Optional<String> getSequenceString(Entry entry)

hasSequence

public boolean hasSequence(long entryId)

getSequenceFilename

public String getSequenceFilename(Entry entry)

hasOriginalSequence

public boolean hasOriginalSequence(long entryId)

Determines if the user uploaded a sequence file and associated it with an entry

Parameters:

entryId - unique identifier for entry

Returns:

true if there is a sequence file that was originally uploaded by user, false otherwise

Throws:

DAOException

getSequence

public Sequence getSequence(int offset)

Enables retrieving sequences in the database without loading everything in memory

Expected usage is long count = getSequenceCount(); int offset = 0; while( offset < count ) { Sequence sequence = dao.getSequence(offset); // do something with sequence }

Returns:

Sequence at the specified offset

Throws:

DAOException

getSequenceCount

public int getSequenceCount()

Returns:

number of sequences available for all valid (visibility=9) entry object

get

public Sequence get(long id)