Package org.biojava.bio.seq.db.biosql
Class BioSQLSequenceDB
java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB
- All Implemented Interfaces:
SequenceDB
,SequenceDBLite
,Changeable
Deprecated.
Use hibernate and org.biojavax.bio.db.*
SequenceDB keyed off a BioSQL database. This is an almost-complete
implementation of the BioJava Sequence, SequenceDB, and Feature interfaces,
and can be used in a wide range of applications.
Note: It now uses BioSQL schema version 1.0 (Post Singapore)
All previous versions are no longer supported.
- Since:
- 1.3
- Author:
- Thomas Down, Matthew Pocock, Simon Foote, Len Trigg, Mark Schreiber, Richard Holland
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Field Summary
Fields inherited from interface org.biojava.bio.seq.db.SequenceDBLite
SEQUENCES
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Constructor Summary
ConstructorsConstructorDescriptionBioSQLSequenceDB
(String dbURL, String dbUser, String dbPass, String biodatabase, boolean create) Deprecated.Connect to a BioSQL database.BioSQLSequenceDB
(String dbDriver, String dbURL, String dbUser, String dbPass, String biodatabase, boolean create) Deprecated.Connect to a BioSQL database.BioSQLSequenceDB
(DataSource ds, String biodatabase, boolean create) Deprecated. -
Method Summary
Modifier and TypeMethodDescriptionaddOntology
(Ontology onto) Deprecated.void
addSequence
(Sequence seq) Deprecated.Adds a sequence to the database.void
createDummySequence
(String id, Alphabet alphabet, int length) Deprecated.createOntology
(String name, String description) Deprecated.filter
(FeatureFilter ff) Deprecated.Query features attached to all sequences in this database.getName()
Deprecated.Get the name of this sequence database.getOntology
(String name) Deprecated.getSequence
(int bioentry_id) Deprecated.getSequence
(String id) Deprecated.Retrieve a single sequence by its id.ids()
Deprecated.Get an immutable set of all of the IDs in the database.void
removeSequence
(String id) Deprecated.Remove the sequence associated with an ID from the database.Deprecated.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.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
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Constructor Details
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BioSQLSequenceDB
public BioSQLSequenceDB(String dbDriver, String dbURL, String dbUser, String dbPass, String biodatabase, boolean create) throws BioException Deprecated.Connect to a BioSQL database.- Parameters:
dbDriver
- A JDBC database driver. For example,com.jdbc.mysql.Driver
dbURL
- A JDBC database URL. For example,jdbc:postgresql://localhost/thomasd_biosql
dbUser
- The username to use when connecting to the database (or an empty string).dbPass
- The password to use when connecting to the database (or an empty string).biodatabase
- The identifier of a namespace within the physical BioSQL database.create
- If the requested namespace doesn't exist, and this flag istrue
, a new namespace will be created.- Throws:
BioException
- if an error occurs communicating with the database
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BioSQLSequenceDB
public BioSQLSequenceDB(String dbURL, String dbUser, String dbPass, String biodatabase, boolean create) throws BioException Deprecated.Connect to a BioSQL database.- Parameters:
dbURL
- A JDBC database URL. For example,jdbc:postgresql://localhost/thomasd_biosql
dbUser
- The username to use when connecting to the database (or an empty string).dbPass
- The password to use when connecting to the database (or an empty string).biodatabase
- The identifier of a namespace within the physical BioSQL database.create
- If the requested namespace doesn't exist, and this flag istrue
, a new namespace will be created.- Throws:
BioException
- if an error occurs communicating with the database
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BioSQLSequenceDB
Deprecated.- Throws:
BioException
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Method Details
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createOntology
Deprecated.- Throws:
Exception
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getOntology
Deprecated.- Throws:
Exception
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addOntology
Deprecated.- Throws:
Exception
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getName
Deprecated.Description copied from interface:SequenceDBLite
Get the name of this sequence database.- Specified by:
getName
in interfaceSequenceDBLite
- Returns:
- the name of the sequence database, which may be null.
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createDummySequence
public void createDummySequence(String id, Alphabet alphabet, int length) throws ChangeVetoException, BioException Deprecated.- Throws:
ChangeVetoException
BioException
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addSequence
Deprecated.Description copied from interface:SequenceDBLite
Adds a sequence to the database.- Specified by:
addSequence
in interfaceSequenceDBLite
- Parameters:
seq
- the Sequence to add- Throws:
ChangeVetoException
- if either the database does not allow sequences to be added or the modification was vetoedBioException
- if something goes wrong with adding the sequence
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getSequence
Deprecated.Description copied from interface:SequenceDBLite
Retrieve a single sequence by its id.- Specified by:
getSequence
in interfaceSequenceDBLite
- Parameters:
id
- the id to retrieve by- Returns:
- the Sequence with that id
- Throws:
BioException
- if there was a failure in retrieving the sequence
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getSequence
Deprecated.- Throws:
BioException
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removeSequence
Deprecated.Description copied from interface:SequenceDBLite
Remove the sequence associated with an ID from the database.- Specified by:
removeSequence
in interfaceSequenceDBLite
- Parameters:
id
- the ID of the sequence to remove- Throws:
ChangeVetoException
- if either the database does not allow sequences to be removed or the modification was vetoedBioException
- if something failed while removing the sequence for that ID
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ids
Deprecated.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 interfaceSequenceDB
- Returns:
- a Set of ids - at the moment, strings
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filter
Deprecated.Description copied from interface:SequenceDB
Query features attached to all sequences in this database. This is equivalent to applyingfilter
to all sequences then merging the results.- Specified by:
filter
in interfaceSequenceDB
- Parameters:
ff
- aFeatureFilter
.
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sequenceIterator
Deprecated.Description copied from interface:SequenceDB
Returns a SequenceIterator over all sequences in the database. The order of retrieval is undefined.- Specified by:
sequenceIterator
in interfaceSequenceDB
- Returns:
- a SequenceIterator over all sequences
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