org.biojavax.bio.db.HashRichSequenceDB

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

public class HashRichSequenceDB extends AbstractRichSequenceDB implements RichSequenceDB

An implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects.

Since:: 1.5
Author:: Matthew Pocock, Gerald Loeffler, 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

HashRichSequenceDB()

Generate a HashRichSequenceDB object that will use byName to generate ids for sequences and have a null name.

HashRichSequenceDB(String name)

Generate a HashRichSequenceDB object that will use byName to generate ids and will have the requested name.

HashRichSequenceDB(IDMaker idMaker)

Generate a HashRichSequenceDB object that will use idMaker to generate ids for sequences and have a null name.

HashRichSequenceDB(IDMaker idMaker, String name)

Generate a HashRichSequenceDB object that will use idMaker to generate ids for sequences and have the requested name.
Method Summary

Modifier and Type

Method

Description

protected void

addRichSequence(String id, RichSequence seq)

void

addRichSequence(RichSequence seq)

Add a sequence.

IDMaker

getIDMaker()

Retrieve the IDMaker associated with this database.

String

getName()

Get the name of this sequence database.

RichSequence

getRichSequence(String id)

Retrieve a single RichSequence by its id.

RichSequenceDB

getRichSequences(Set ids)

Retrieve multiple RichSequence by its id.

RichSequenceDB

getRichSequences(Set ids, RichSequenceDB db)

Retrieve multiple RichSequence into a specific sequence database.

Set

ids()

Get an immutable set of all of the IDs in the database.

void

removeSequence(String id)

Remove the sequence associated with an ID from the database.

Methods inherited from class org.biojavax.bio.db.AbstractRichSequenceDB
addBioEntry, addSequence, filter, getBioEntry, getBioEntryIterator, getBioEntrys, getBioEntrys, getRichSequenceIterator, getSequence, removeBioEntry, removeRichSequence, sequenceIterator

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
getBioEntryIterator

Methods inherited from interface org.biojavax.bio.db.BioEntryDBLite
addBioEntry, getBioEntry, getBioEntrys, getBioEntrys, removeBioEntry

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

Methods inherited from interface org.biojavax.bio.db.RichSequenceDB
getRichSequenceIterator, sequenceIterator

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

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

Methods inherited from interface org.biojava.bio.seq.db.SequenceDBLite
addSequence, getSequence

Constructor Details
- HashRichSequenceDB
  
  public HashRichSequenceDB()
  
  Generate a HashRichSequenceDB object that will use byName to generate ids for sequences and have a null name.
- HashRichSequenceDB
  
  public HashRichSequenceDB(IDMaker idMaker)
  
  Generate a HashRichSequenceDB object that will use idMaker to generate ids for sequences and have a null name.
  
  Parameters:
  
  idMaker - the object that will work out the default id for a sequence
- HashRichSequenceDB
  
  public HashRichSequenceDB(String name)
  
  Generate a HashRichSequenceDB object that will use byName to generate ids and will have the requested name.
  
  Parameters:
  
  name - the name for this database
- HashRichSequenceDB
  
  public HashRichSequenceDB(IDMaker idMaker, String name)
  
  Generate a HashRichSequenceDB object that will use idMaker to generate ids for sequences and have the requested name.
  
  Parameters:
  
  idMaker - the object that will work out the default id for a sequence
  
  name - the name for this database
Method Details
- getName
  
  public String getName()
  
  Description copied from interface: SequenceDBLite
  
  Get the name of this sequence database.
  
  Specified by:
  
  getName in interface BioEntryDBLite
  
  Specified by:
  
  getName in interface SequenceDBLite
  
  Returns:
  
  the name of the sequence database, which may be null.
- getIDMaker
  
  public IDMaker getIDMaker()
  
  Retrieve the IDMaker associated with this database.
  
  Returns:
  
  the current IDMaker object
- getRichSequence
  
  public RichSequence getRichSequence(String id) throws BioException, IllegalIDException
  
  Description copied from interface: RichSequenceDBLite
  
  Retrieve a single RichSequence by its id.
  
  Specified by:
  
  getRichSequence in interface RichSequenceDBLite
  
  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
- getRichSequences
  
  public RichSequenceDB getRichSequences(Set ids) throws BioException, IllegalIDException
  
  Description copied from interface: RichSequenceDBLite
  
  Retrieve multiple RichSequence by its id.
  
  Specified by:
  
  getRichSequences in interface RichSequenceDBLite
  
  Parameters:
  
  ids - a set of ids to retrieve by
  
  Returns:
  
  the RichSequences with that id
  
  Throws:
  
  IllegalIDException - if the database doesn't know about the id
  
  BioException
- getRichSequences
  
  public RichSequenceDB getRichSequences(Set ids, RichSequenceDB db) throws BioException, IllegalIDException
  
  Description copied from interface: RichSequenceDBLite
  
  Retrieve multiple RichSequence into a specific sequence database. If that database is null, a new HashRichSequenceDB is used.
  
  Specified by:
  
  getRichSequences in interface RichSequenceDBLite
  
  Parameters:
  
  ids - a set of ids to retrieve by
  
  db - a database to load the seqs into
  
  Returns:
  
  the RichSequences with that id
  
  Throws:
  
  IllegalIDException - if the database doesn't know about the id
  
  BioException
- ids
  
  public Set ids()
  
  Description copied from interface: SequenceDB
  
  Get an immutable set of all of the IDs in the database. The ids are legal arguments to getSequence.
  
  Specified by:
  
  ids in interface BioEntryDB
  
  Specified by:
  
  ids in interface SequenceDB
  
  Returns:
  
  a Set of ids - at the moment, strings
- addRichSequence
  
  public void addRichSequence(RichSequence seq) throws IllegalIDException, BioException, ChangeVetoException
  
  Add a sequence.
  
  Specified by:
  
  addRichSequence in interface RichSequenceDBLite
  
  Overrides:
  
  addRichSequence in class AbstractRichSequenceDB
  
  Parameters:
  
  seq - the RichSequence to add
  
  Throws:
  
  ChangeVetoException - if this addition was vetoed
  
  IllegalIDException - if a uniqe ID could not be generated for RichSequence
  
  BioException - if something goes wrong with adding the RichSequence
- addRichSequence
  
  protected void addRichSequence(String id, RichSequence seq) throws IllegalIDException, BioException, ChangeVetoException
  
  Throws:
  
  IllegalIDException
  
  BioException
  
  ChangeVetoException
- 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
  
  Overrides:
  
  removeSequence in class AbstractRichSequenceDB
  
  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

Class HashRichSequenceDB

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.biojavax.bio.db.AbstractRichSequenceDB

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.RichSequenceDB

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

HashRichSequenceDB

HashRichSequenceDB

HashRichSequenceDB

HashRichSequenceDB

Method Details

getName

getIDMaker

getRichSequence

getRichSequences

getRichSequences

ids

addRichSequence

addRichSequence

removeSequence