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

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

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.das	Development client for the Distributed Annotation System.
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
org.biojavax.bio.db.ncbi

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

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

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

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.das

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.program.gff

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

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

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

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

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

IllegalIDException

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

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

IllegalIDException

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

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

IllegalIDException

SequenceDBLite
A database of sequences.

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

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

IllegalIDException

SequenceDBLite
A database of sequences.

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

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

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

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

SequenceDBLite
A database of sequences.

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

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

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

IllegalIDException

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

SequenceDBLite
A database of sequences.