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

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

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.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
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.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.