Uses of Package
org.biojava.bio.seq.db

Packages that use org.biojava.bio.seq.db

Package	Description
org.biojava.bio.alignment	Classes to generate and describe sequence alignments.
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.gui	Graphical interfaces for biojava objects.
org.biojava.bio.program.gff	GFF manipulation.
org.biojava.bio.program.phred	Parser for Phred output
org.biojava.bio.program.ssaha	SSAHA sequence searching API.
org.biojava.bio.program.ssbind	Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
org.biojava.bio.program.unigene	Objects for representing Unigene clusters.
org.biojava.bio.proteomics.aaindex	Classes and interfaces to load Amino Acid Index database files.
org.biojava.bio.search	Interfaces and classes for representing sequence similarity search results.
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
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.bio.seq.impl	Standard in-memory implementations of Sequence and Feature.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
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.

Classes in org.biojava.bio.seq.db used by org.biojava.bio.alignment

Class and Description
SequenceDB A database of sequences with accessible keys and iterators over all sequences.

Classes in org.biojava.bio.seq.db used by org.biojava.bio.dp

Class and Description
SequenceDB A database of sequences with accessible keys and iterators over all sequences.

Classes in org.biojava.bio.seq.db used by org.biojava.bio.gui

Class and Description
SequenceDB A database of sequences with accessible keys and iterators over all sequences.

Classes in org.biojava.bio.seq.db used by org.biojava.bio.program.gff

Class and Description
IllegalIDException
SequenceDB A database of sequences with accessible keys and iterators over all sequences.

Classes in org.biojava.bio.seq.db used by org.biojava.bio.program.phred

Class and Description
SequenceDB A database of sequences with accessible keys and iterators over all sequences.

Classes in org.biojava.bio.seq.db used by org.biojava.bio.program.ssaha

Class and Description
SequenceDB A database of sequences with accessible keys and iterators over all sequences.

Classes in org.biojava.bio.seq.db used by org.biojava.bio.program.ssbind

Class and Description
IllegalIDException
SequenceDB A database of sequences with accessible keys and iterators over all sequences.
SequenceDBInstallation A SequenceDBInstallation has the functionality of a factory for SequenceDB objects and additionally manages the SequenceDB objects created by itself such that the minimum number of SequenceDB objects is created by a particular SequenceDBInstallation object.

Classes in org.biojava.bio.seq.db used by org.biojava.bio.program.unigene

Class and Description
SequenceDB A database of sequences with accessible keys and iterators over all sequences.

Classes in org.biojava.bio.seq.db used by org.biojava.bio.proteomics.aaindex

Class and Description
IllegalIDException

Classes in org.biojava.bio.seq.db used by org.biojava.bio.search

Class and Description
SequenceDB A database of sequences with accessible keys and iterators over all sequences.

Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq

Class and Description
IllegalIDException

Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq.db

Class and Description
AbstractSequenceDB An abstract implementation of SequenceDB that provides the sequenceIterator method.
IDMaker Interface for objects that define how to make an ID for a sequence.
IllegalIDException
Index This defines an index entry for an individual sequence within a set of indexed files.
IndexStore This defines the objects that IndexedSequenceDB uses to store all of the database state, such as name, format, sequence builder and the actual file offsets.
SequenceDB A database of sequences with accessible keys and iterators over all sequences.
SequenceDBInstallation A SequenceDBInstallation has the functionality of a factory for SequenceDB objects and additionally manages the SequenceDB objects created by itself such that the minimum number of SequenceDB objects is created by a particular SequenceDBInstallation object.
SequenceDBLite A database of sequences.
SequenceDBWrapper An abstract implementation of SequenceDB that wraps up another database.
TabIndexStore Implements IndexStore as a serialized file for the java data and a tab-delimited file of offsets.
WebSequenceDB Functions for access to a web based database that returns sequences in a variety of formats.

Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq.db.biofetch

Class and Description
IllegalIDException
SequenceDBLite A database of sequences.

Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq.db.biosql

Class and Description
SequenceDB A database of sequences with accessible keys and iterators over all sequences.
SequenceDBLite A database of sequences.

Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq.db.flat

Class and Description
IllegalIDException
SequenceDBLite A database of sequences.

Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq.distributed

Class and Description
AbstractSequenceDB An abstract implementation of SequenceDB that provides the sequenceIterator method.
IllegalIDException
SequenceDB A database of sequences with accessible keys and iterators over all sequences.
SequenceDBLite A database of sequences.

Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq.impl

Class and Description
SequenceDB A database of sequences with accessible keys and iterators over all sequences.

Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq.io

Class and Description
SequenceDB A database of sequences with accessible keys and iterators over all sequences.

Classes in org.biojava.bio.seq.db used by org.biojava.directory

Class and Description
SequenceDBLite A database of sequences.

Classes in org.biojava.bio.seq.db used by org.biojavax.bio.db

Class and Description
IDMaker Interface for objects that define how to make an ID for a sequence.
IllegalIDException
SequenceDB A database of sequences with accessible keys and iterators over all sequences.
SequenceDBLite A database of sequences.

Classes in org.biojava.bio.seq.db used by org.biojavax.bio.db.biosql

Class and Description
IllegalIDException
SequenceDB A database of sequences with accessible keys and iterators over all sequences.
SequenceDBLite A database of sequences.

Classes in org.biojava.bio.seq.db used by org.biojavax.bio.db.ncbi

Class and Description
IllegalIDException
SequenceDB A database of sequences with accessible keys and iterators over all sequences.
SequenceDBLite A database of sequences.