org.jbei.ice.storage.hibernate.dao

Class TraceSequenceDAO

java.lang.Object

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

org.jbei.ice.storage.hibernate.dao.TraceSequenceDAO

All Implemented Interfaces:

IRepository<TraceSequence>

public class TraceSequenceDAO
extends HibernateRepository<TraceSequence>

Data accessor for TraceSequences

Author:

Hector Plahar

Constructor Summary

Constructors

Constructor and Description
TraceSequenceDAO()

Method Summary

Modifier and Type	Method and Description
TraceSequence	create(Path traceDir, TraceSequence traceSequence, InputStream inputStream) Create a new TraceSequence object in the database, and write the file data to disk.
void	delete(Path tracesDir, TraceSequence traceSequence) Delete the trace file from the referenced directory and if that succeeds, deletes the given TraceSequence object in the database
TraceSequence	get(long id)
List<TraceSequence>	getByEntry(Entry entry, int start, int limit) Retrieve all TraceSequence objects associated with the given Entry object using the paging parameters, ordered by creation time in ascending order
Optional<TraceSequence>	getByFileId(String fileId) Retrieve the TraceSequence object by its fileId.
int	getCountByEntry(Entry entry) Get number of trace sequences available for specified entry
TraceSequence	save(TraceSequence traceSequence) Save the given TraceSequence object in the database.

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

TraceSequenceDAO

public TraceSequenceDAO()

Method Detail

create

public TraceSequence create(Path traceDir,
                            TraceSequence traceSequence,
                            InputStream inputStream)

Create a new TraceSequence object in the database, and write the file data to disk.

Parameters:

traceDir - storage directory for the new trace sequence file

traceSequence - information about the new file to store, including a unique identifier

inputStream - byte stream for file

Returns:

Saved TraceSequence object.

Throws:

DAOException - if the filename for the new trace sequence already exists or if there is an error saving

save

public TraceSequence save(TraceSequence traceSequence)

Save the given TraceSequence object in the database.

Parameters:

traceSequence - object to save

Returns:

Saved TraceSequence object.

Throws:

DAOException - on hibernate exception saving

getByFileId

public Optional<TraceSequence> getByFileId(String fileId)

Retrieve the TraceSequence object by its fileId.

Parameters:

fileId - unique file identifier

Returns:

Optional container that contains the trace sequence if found.

Throws:

DAOException

delete

public void delete(Path tracesDir,
                   TraceSequence traceSequence)

Delete the trace file from the referenced directory and if that succeeds, deletes the given TraceSequence object in the database

Parameters:

tracesDir - directory for trace files

traceSequence - trace object to delete from database

Throws:

DAOException - on hibernate or IO Exception when attempting to save the trace sequence object or

getByEntry

public List<TraceSequence> getByEntry(Entry entry,
                                      int start,
                                      int limit)

Retrieve all TraceSequence objects associated with the given Entry object using the paging parameters, ordered by creation time in ascending order

Parameters:

entry - entry whose trace sequences are being retrieved

start - start for traces retrieval

limit - maximum number of trace records to retrieve

Returns:

List of TraceSequence objects.

Throws:

DAOException

getCountByEntry

public int getCountByEntry(Entry entry)

Get number of trace sequences available for specified entry

Parameters:

entry - entry whose entry count is being retrieved

Returns:

number of traces available for the specified entry

get

public TraceSequence get(long id)