Uses of Package org.biojava.bio.seq.db (BioJava-1.5-beta API)

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## 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.

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