org.biojavax.bio.db.AbstractRichSequenceDB

All Implemented Interfaces:: SequenceDB, SequenceDBLite, Changeable, BioEntryDB, BioEntryDBLite, RichSequenceDB, RichSequenceDBLite

Direct Known Subclasses:: BioSQLRichSequenceDB, GenbankRichSequenceDB, GenpeptRichSequenceDB, HashRichSequenceDB

public abstract class AbstractRichSequenceDB extends AbstractBioEntryDB implements RichSequenceDB

An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method.

Since:: 1.5
Author:: Matthew Pocock, Thomas Down, Richard Holland

Field Summary

Fields inherited from interface org.biojavax.bio.db.BioEntryDBLite
BIOENTRYS

Fields inherited from interface org.biojava.bio.seq.db.SequenceDBLite
SEQUENCES
Constructor Summary

Constructors

Constructor

Description

AbstractRichSequenceDB()
Method Summary

Modifier and Type

Method

Description

void

addBioEntry(BioEntry seq)

Adds a sequence to the database.

void

addRichSequence(RichSequence seq)

Adds a sequence to the database.

void

addSequence(Sequence seq)

Adds a sequence to the database.

FeatureHolder

filter(FeatureFilter ff)

Query features attached to all sequences in this database.

BioEntry

getBioEntry(String id)

Retrieve a single BioEntry by its id.

BioEntryIterator

getBioEntryIterator()

Returns a BioEntryIterator over all BioEntrys in the database.

BioEntryDB

getBioEntrys(Set ids)

Retrieve multiple BioEntry by their ids.

BioEntryDB

getBioEntrys(Set ids, BioEntryDB db)

Retrieve multiple BioEntry into a specific sequence database.

RichSequenceIterator

getRichSequenceIterator()

Returns a RichSequenceIterator over all sequences in the database.

Sequence

getSequence(String id)

Retrieve a single sequence by its id.

void

removeBioEntry(String id)

Remove the BioEntry associated with an ID from the database.

void

removeRichSequence(String id)

Remove the RichSequence associated with an ID from the database.

void

removeSequence(String id)

Remove the sequence associated with an ID from the database.

SequenceIterator

sequenceIterator()

Returns a SequenceIterator over all sequences in the database.

Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojavax.bio.db.BioEntryDB
ids

Methods inherited from interface org.biojavax.bio.db.BioEntryDBLite
getName

Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojavax.bio.db.RichSequenceDBLite
getRichSequence, getRichSequences, getRichSequences

Methods inherited from interface org.biojava.bio.seq.db.SequenceDB
ids

Methods inherited from interface org.biojava.bio.seq.db.SequenceDBLite
getName

Constructor Details
- AbstractRichSequenceDB
  
  public AbstractRichSequenceDB()
Method Details
- getSequence
  
  public Sequence getSequence(String id) throws BioException, IllegalIDException
  
  Description copied from interface: SequenceDBLite
  
  Retrieve a single sequence by its id.
  
  Specified by:
  
  getSequence in interface SequenceDBLite
  
  Parameters:
  
  id - the id to retrieve by
  
  Returns:
  
  the Sequence with that id
  
  Throws:
  
  IllegalIDException - if the database doesn't know about the id
  
  BioException - if there was a failure in retrieving the sequence
- getBioEntry
  
  public BioEntry getBioEntry(String id) throws BioException, IllegalIDException
  
  Description copied from interface: BioEntryDBLite
  
  Retrieve a single BioEntry by its id.
  
  Specified by:
  
  getBioEntry in interface BioEntryDBLite
  
  Parameters:
  
  id - the id to retrieve by
  
  Returns:
  
  the BioEntry with that id
  
  Throws:
  
  IllegalIDException - if the database doesn't know about the id
  
  BioException - if there was a failure in retrieving the BioEntry
- getBioEntrys
  
  public BioEntryDB getBioEntrys(Set ids) throws BioException, IllegalIDException
  
  Description copied from interface: BioEntryDBLite
  
  Retrieve multiple BioEntry by their ids.
  
  Specified by:
  
  getBioEntrys in interface BioEntryDBLite
  
  Parameters:
  
  ids - a set of ids to retrieve by
  
  Returns:
  
  the BioEntrys with those ids
  
  Throws:
  
  IllegalIDException - if the database doesn't know about the id
  
  BioException
- getBioEntrys
  
  public BioEntryDB getBioEntrys(Set ids, BioEntryDB db) throws BioException, IllegalIDException
  
  Description copied from interface: BioEntryDBLite
  
  Retrieve multiple BioEntry into a specific sequence database. If that database is null, a new HashBioEntryDB is used.
  
  Specified by:
  
  getBioEntrys in interface BioEntryDBLite
  
  Parameters:
  
  ids - a set of ids to retrieve by
  
  db - a database to load the seqs into
  
  Returns:
  
  the BioEntrys with that id
  
  Throws:
  
  IllegalIDException - if the database doesn't know about the id
  
  BioException
- addSequence
  
  public void addSequence(Sequence seq) throws IllegalIDException, BioException, ChangeVetoException
  
  Description copied from interface: SequenceDBLite
  
  Adds a sequence to the database.
  
  Specified by:
  
  addSequence in interface SequenceDBLite
  
  Parameters:
  
  seq - the Sequence to add
  
  Throws:
  
  IllegalIDException - if a uniqe ID could not be generated for seq
  
  BioException - if something goes wrong with adding the sequence
  
  ChangeVetoException - if either the database does not allow sequences to be added or the modification was vetoed
- removeSequence
  
  public void removeSequence(String id) throws IllegalIDException, BioException, ChangeVetoException
  
  Description copied from interface: SequenceDBLite
  
  Remove the sequence associated with an ID from the database.
  
  Specified by:
  
  removeSequence in interface SequenceDBLite
  
  Parameters:
  
  id - the ID of the sequence to remove
  
  Throws:
  
  IllegalIDException - if there is no sequence for the ID
  
  BioException - if something failed while removing the sequence for that ID
  
  ChangeVetoException - if either the database does not allow sequences to be removed or the modification was vetoed
- addBioEntry
  
  public void addBioEntry(BioEntry seq) throws IllegalIDException, BioException, ChangeVetoException
  
  Description copied from interface: BioEntryDBLite
  
  Adds a sequence to the database.
  
  Specified by:
  
  addBioEntry in interface BioEntryDBLite
  
  Overrides:
  
  addBioEntry in class AbstractBioEntryDB
  
  Parameters:
  
  seq - the BioEntry to add
  
  Throws:
  
  IllegalIDException - if a uniqe ID could not be generated for BioEntry
  
  BioException - if something goes wrong with adding the BioEntry
  
  ChangeVetoException - if either the database does not allow BioEntrys to be added or the modification was vetoed
- removeBioEntry
  
  public void removeBioEntry(String id) throws IllegalIDException, BioException, ChangeVetoException
  
  Description copied from interface: BioEntryDBLite
  
  Remove the BioEntry associated with an ID from the database.
  
  Specified by:
  
  removeBioEntry in interface BioEntryDBLite
  
  Overrides:
  
  removeBioEntry in class AbstractBioEntryDB
  
  Parameters:
  
  id - the ID of the BioEntry to remove
  
  Throws:
  
  IllegalIDException - if there is no BioEntry for the ID
  
  BioException - if something failed while removing the BioEntry for that ID
  
  ChangeVetoException - if either the database does not allow BioEntrys to be removed or the modification was vetoed
- addRichSequence
  
  public void addRichSequence(RichSequence seq) throws IllegalIDException, BioException, ChangeVetoException
  
  Description copied from interface: RichSequenceDBLite
  
  Adds a sequence to the database.
  
  Specified by:
  
  addRichSequence in interface RichSequenceDBLite
  
  Parameters:
  
  seq - the RichSequence to add
  
  Throws:
  
  IllegalIDException - if a uniqe ID could not be generated for RichSequence
  
  BioException - if something goes wrong with adding the RichSequence
  
  ChangeVetoException - if either the database does not allow RichSequences to be added or the modification was vetoed
- removeRichSequence
  
  public void removeRichSequence(String id) throws IllegalIDException, BioException, ChangeVetoException
  
  Description copied from interface: RichSequenceDBLite
  
  Remove the RichSequence associated with an ID from the database.
  
  Specified by:
  
  removeRichSequence in interface RichSequenceDBLite
  
  Parameters:
  
  id - the ID of the RichSequence to remove
  
  Throws:
  
  IllegalIDException - if there is no RichSequence for the ID
  
  BioException - if something failed while removing the RichSequence for that ID
  
  ChangeVetoException - if either the database does not allow RichSequences to be removed or the modification was vetoed
- sequenceIterator
  
  public SequenceIterator sequenceIterator()
  
  Description copied from interface: RichSequenceDB
  
  Returns a SequenceIterator over all sequences in the database. The order of retrieval is undefined. Will always return an instance of RichSequenceIterator.
  
  Specified by:
  
  sequenceIterator in interface RichSequenceDB
  
  Specified by:
  
  sequenceIterator in interface SequenceDB
  
  Returns:
  
  a SequenceIterator over all sequences
- getBioEntryIterator
  
  public BioEntryIterator getBioEntryIterator()
  
  Description copied from interface: BioEntryDB
  
  Returns a BioEntryIterator over all BioEntrys in the database. The order of retrieval is undefined.
  
  Specified by:
  
  getBioEntryIterator in interface BioEntryDB
  
  Overrides:
  
  getBioEntryIterator in class AbstractBioEntryDB
  
  Returns:
  
  a BioEntryIterator over all BioEntrys
- getRichSequenceIterator
  
  public RichSequenceIterator getRichSequenceIterator()
  
  Description copied from interface: RichSequenceDB
  
  Returns a RichSequenceIterator over all sequences in the database. The order of retrieval is undefined.
  
  Specified by:
  
  getRichSequenceIterator in interface RichSequenceDB
  
  Returns:
  
  a RichSequenceIterator over all sequences
- filter
  
  public FeatureHolder filter(FeatureFilter ff)
  
  Description copied from interface: SequenceDB
  
  Query features attached to all sequences in this database. This is equivalent to applying filter to all sequences then merging the results.
  
  Specified by:
  
  filter in interface SequenceDB
  
  Parameters:
  
  ff - a FeatureFilter.

Class AbstractRichSequenceDB

Field Summary

Fields inherited from interface org.biojavax.bio.db.BioEntryDBLite

Fields inherited from interface org.biojava.bio.seq.db.SequenceDBLite

Constructor Summary

Method Summary

Methods inherited from class org.biojava.utils.AbstractChangeable

Methods inherited from class java.lang.Object

Methods inherited from interface org.biojavax.bio.db.BioEntryDB

Methods inherited from interface org.biojavax.bio.db.BioEntryDBLite

Methods inherited from interface org.biojava.utils.Changeable

Methods inherited from interface org.biojavax.bio.db.RichSequenceDBLite

Methods inherited from interface org.biojava.bio.seq.db.SequenceDB

Methods inherited from interface org.biojava.bio.seq.db.SequenceDBLite

Constructor Details

AbstractRichSequenceDB

Method Details

getSequence

getBioEntry

getBioEntrys

getBioEntrys

addSequence

removeSequence

addBioEntry

removeBioEntry

addRichSequence

removeRichSequence

sequenceIterator

getBioEntryIterator

getRichSequenceIterator

filter