Package org.biojavax.bio.db
Class HashBioEntryDB
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojavax.bio.db.AbstractBioEntryDB
org.biojavax.bio.db.HashBioEntryDB
- All Implemented Interfaces:
Changeable
,BioEntryDB
,BioEntryDBLite
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
-
Constructor Summary
ConstructorsConstructorDescriptionGenerate a HashRichSequenceDB object that will use byName to generate ids for sequences and have a null name.HashBioEntryDB
(String name) Generate a HashRichSequenceDB object that will use byName to generate ids and will have the requested name. -
Method Summary
Modifier and TypeMethodDescriptionprotected void
addBioEntry
(String id, BioEntry seq) void
addBioEntry
(BioEntry seq) Add a BioEntry, the name of the BioEntry will be used as the IDgetBioEntry
(String id) Retrieve a single BioEntry by its id.getBioEntrys
(Set ids) Retrieve multiple BioEntry by their ids.getBioEntrys
(Set ids, BioEntryDB db) Retrieve multiple BioEntry into a specific sequence database.getName()
Get the name of this sequence database.ids()
Get an immutable set of all of the IDs in the database.void
removeBioEntry
(String id) Remove the BioEntry associated with an ID from the database.Methods inherited from class org.biojavax.bio.db.AbstractBioEntryDB
getBioEntryIterator
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
-
Constructor Details
-
HashBioEntryDB
public HashBioEntryDB()Generate a HashRichSequenceDB object that will use byName to generate ids for sequences and have a null name. -
HashBioEntryDB
Generate a HashRichSequenceDB object that will use byName to generate ids and will have the requested name.- Parameters:
name
- the name for this database
-
-
Method Details
-
getName
Description copied from interface:BioEntryDBLite
Get the name of this sequence database.- Specified by:
getName
in interfaceBioEntryDBLite
- Returns:
- the name of the sequence database, which may be null.
-
getBioEntry
Description copied from interface:BioEntryDBLite
Retrieve a single BioEntry by its id.- Specified by:
getBioEntry
in interfaceBioEntryDBLite
- Parameters:
id
- the id to retrieve by- Returns:
- the BioEntry with that id
- Throws:
BioException
- if there was a failure in retrieving the BioEntryIllegalIDException
- if the database doesn't know about the id
-
getBioEntrys
Description copied from interface:BioEntryDBLite
Retrieve multiple BioEntry by their ids.- Specified by:
getBioEntrys
in interfaceBioEntryDBLite
- 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 idBioException
-
getBioEntrys
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 interfaceBioEntryDBLite
- Parameters:
ids
- a set of ids to retrieve bydb
- a database to load the seqs into- Returns:
- the BioEntrys with that id
- Throws:
IllegalIDException
- if the database doesn't know about the idBioException
-
ids
Description copied from interface:BioEntryDB
Get an immutable set of all of the IDs in the database. The ids are legal arguments to getBioEntry.- Specified by:
ids
in interfaceBioEntryDB
- Returns:
- a Set of ids - at the moment, strings
-
addBioEntry
Add a BioEntry, the name of the BioEntry will be used as the ID- Specified by:
addBioEntry
in interfaceBioEntryDBLite
- Overrides:
addBioEntry
in classAbstractBioEntryDB
- Parameters:
seq
- the BioEntry to add- Throws:
ChangeVetoException
- if this addition was vetoedIllegalIDException
- if a uniqe ID could not be generated for BioEntryBioException
- if something goes wrong with adding the BioEntry
-
addBioEntry
protected void addBioEntry(String id, BioEntry seq) throws IllegalIDException, BioException, ChangeVetoException -
removeBioEntry
Description copied from interface:BioEntryDBLite
Remove the BioEntry associated with an ID from the database.- Specified by:
removeBioEntry
in interfaceBioEntryDBLite
- Overrides:
removeBioEntry
in classAbstractBioEntryDB
- Parameters:
id
- the ID of the BioEntry to remove- Throws:
IllegalIDException
- if there is no BioEntry for the IDBioException
- if something failed while removing the BioEntry for that IDChangeVetoException
- if either the database does not allow BioEntrys to be removed or the modification was vetoed
-