|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
Packages that use SequenceDBLite | |
---|---|
org.biojava.bio.program.das | Development client for the Distributed Annotation System. |
org.biojava.bio.seq.db | Collections of biological sequence data. |
org.biojava.bio.seq.db.biofetch | Client for the OBDA BioFetch protocol. |
org.biojava.bio.seq.db.biosql | General purpose Sequence storage in a relational database. |
org.biojava.bio.seq.db.flat | Support for OBDA flatfile databases. |
org.biojava.bio.seq.distributed | Sequences and SequenceDBs which are composed from data taken from a number of data sources. |
org.biojava.directory | Open Bio Sequence Database Access (OBDA) registry support. |
org.biojavax.bio.db | Interactions between biojavax objects and a DB. |
org.biojavax.bio.db.biosql | Interface between biojava and biosql databases |
org.biojavax.bio.db.ncbi | Interfaces to NCBI data. |
Uses of SequenceDBLite in org.biojava.bio.program.das |
---|
Classes in org.biojava.bio.program.das that implement SequenceDBLite | |
---|---|
class |
DASSequenceDB
Collection of sequences retrieved from the DAS network. |
Methods in org.biojava.bio.program.das that return SequenceDBLite | |
---|---|
SequenceDBLite |
DASSequenceDB.allEntryPointsDB()
|
SequenceDBLite |
DASSequenceDBProvider.getSequenceDB(Map config)
|
Uses of SequenceDBLite in org.biojava.bio.seq.db |
---|
Subinterfaces of SequenceDBLite in org.biojava.bio.seq.db | |
---|---|
interface |
SequenceDB
A database of sequences with accessible keys and iterators over all sequences. |
Classes in org.biojava.bio.seq.db that implement SequenceDBLite | |
---|---|
class |
AbstractSequenceDB
An abstract implementation of SequenceDB that provides the sequenceIterator method. |
class |
AnnotatedSequenceDB
SequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB. |
class |
CachingSequenceDB
SequenceDB implementation that caches the results of another SequenceDB. |
class |
DummySequenceDB
DummySequenceDB is an implementation which contains
only a DummySequence . |
class |
HashSequenceDB
An implementation of SequenceDB that uses an underlying HashMap to store the sequence objects. |
class |
IndexedSequenceDB
This class implements SequenceDB on top of a set of sequence files and sequence offsets within these files. |
class |
NCBISequenceDB
|
class |
SequenceDBWrapper
An abstract implementation of SequenceDB that wraps up another database. |
class |
SubSequenceDB
|
class |
ViewingSequenceDB
SequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database. |
class |
WebSequenceDB
Functions for access to a web based database that returns sequences in a variety of formats. |
Methods in org.biojava.bio.seq.db that return SequenceDBLite | |
---|---|
SequenceDBLite |
DummySequenceDBInstallation.getSequenceDB(String identifier)
|
SequenceDBLite |
SequenceDBInstallation.getSequenceDB(String identifier)
Return the SequenceDB for the given identifier. |
SequenceDBLite |
SimpleSequenceDBInstallation.getSequenceDB(String identifier)
If the given identifier is known to this sequence db installation because it has been used in a call to addSequenceDB(), then this method returns the SequenceDB associated with this identifier. |
Methods in org.biojava.bio.seq.db with parameters of type SequenceDBLite | |
---|---|
void |
DummySequenceDBInstallation.addSequenceDB(SequenceDBLite sequenceDB,
Set otherIdentifiers)
As this is a dummy implementation adding a sequenceDB doesn't do anything |
void |
SequenceDBInstallation.addSequenceDB(SequenceDBLite sequenceDB,
Set otherIdentifiers)
addSequenceDB adds a new SequenceDB
under its own identifier which will additionally be recognised
by the set of other identifiers. |
void |
SimpleSequenceDBInstallation.addSequenceDB(SequenceDBLite sequenceDB,
Set otherIdentifiers)
addSequenceDB adds a new SequenceDB which will be
accessible via the name returned by its getName() method and
via all other given identifiers. |
Uses of SequenceDBLite in org.biojava.bio.seq.db.biofetch |
---|
Classes in org.biojava.bio.seq.db.biofetch that implement SequenceDBLite | |
---|---|
class |
BioFetchSequenceDB
Simple SequenceDB implementation backed by a BioFetch (HTTP) server. |
Methods in org.biojava.bio.seq.db.biofetch that return SequenceDBLite | |
---|---|
SequenceDBLite |
BioFetchSequenceDBProvider.getSequenceDB(Map config)
|
Uses of SequenceDBLite in org.biojava.bio.seq.db.biosql |
---|
Classes in org.biojava.bio.seq.db.biosql that implement SequenceDBLite | |
---|---|
class |
BioSQLSequenceDB
Deprecated. Use hibernate and org.biojavax.bio.db.* |
Methods in org.biojava.bio.seq.db.biosql that return SequenceDBLite | |
---|---|
SequenceDBLite |
BioSQLSequenceDBProvider.getSequenceDB(Map config)
Deprecated. |
Uses of SequenceDBLite in org.biojava.bio.seq.db.flat |
---|
Classes in org.biojava.bio.seq.db.flat that implement SequenceDBLite | |
---|---|
class |
FlatSequenceDB
FlatSequenceDB is an OBDA flatfile sequence databank
implementation. |
Methods in org.biojava.bio.seq.db.flat that return SequenceDBLite | |
---|---|
SequenceDBLite |
FlatSequenceDBProvider.getSequenceDB(Map config)
|
Uses of SequenceDBLite in org.biojava.bio.seq.distributed |
---|
Classes in org.biojava.bio.seq.distributed that implement SequenceDBLite | |
---|---|
class |
DistributedSequenceDB
Sequence database from the meta-DAS system. |
Uses of SequenceDBLite in org.biojava.directory |
---|
Methods in org.biojava.directory that return SequenceDBLite | |
---|---|
SequenceDBLite |
Registry.getDatabase(String dbName)
getDatabase retrieves a database instance known by
a name String . |
SequenceDBLite |
SequenceDBProvider.getSequenceDB(Map config)
Get a sequence database. |
Uses of SequenceDBLite in org.biojavax.bio.db |
---|
Subinterfaces of SequenceDBLite in org.biojavax.bio.db | |
---|---|
interface |
RichSequenceDB
A database of RichSequences with accessible keys and iterators over all sequences. |
interface |
RichSequenceDBLite
A database of RichSequences. |
Classes in org.biojavax.bio.db that implement SequenceDBLite | |
---|---|
class |
AbstractRichSequenceDB
An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method. |
class |
HashRichSequenceDB
An implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects. |
Uses of SequenceDBLite in org.biojavax.bio.db.biosql |
---|
Classes in org.biojavax.bio.db.biosql that implement SequenceDBLite | |
---|---|
class |
BioSQLRichSequenceDB
|
Uses of SequenceDBLite in org.biojavax.bio.db.ncbi |
---|
Classes in org.biojavax.bio.db.ncbi that implement SequenceDBLite | |
---|---|
class |
GenbankRichSequenceDB
This class contains functions accessing DNA sequences in Genbank format. |
class |
GenpeptRichSequenceDB
This class contains functions accessing Peptide sequences in Genpept format. |
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |