Uses of Package
org.biojava.bio.seq.db
Packages that use org.biojava.bio.seq.db
Package
Description
Classes to generate and describe sequence alignments.
HMM and Dynamic Programming Algorithms.
Graphical interfaces for biojava objects.
GFF manipulation.
Parser for Phred output
SSAHA sequence searching API.
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
Objects for representing Unigene clusters.
Classes and interfaces to load Amino Acid Index database files.
Interfaces and classes for representing sequence similarity search results.
Classes and interfaces for defining biological sequences and informatics
objects.
Collections of biological sequence data.
Client for the OBDA BioFetch protocol.
General purpose Sequence storage in a relational database.
Support for OBDA flatfile databases.
Sequences and SequenceDBs which are composed from data taken
from a number of data sources.
Standard in-memory implementations of
Sequence
and
Feature
.Classes and interfaces for processing and producing flat-file representations
of sequences.
Open Bio Sequence Database Access (OBDA) registry support.
Interactions between biojavax objects and a DB.
Interface between biojava and biosql databases
Interfaces to NCBI data.
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.alignmentClassDescriptionA database of sequences with accessible keys and iterators over all sequences.
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.dpClassDescriptionA database of sequences with accessible keys and iterators over all sequences.
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.guiClassDescriptionA database of sequences with accessible keys and iterators over all sequences.
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.program.gffClassDescriptionA database of sequences with accessible keys and iterators over all sequences.
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.program.phredClassDescriptionA database of sequences with accessible keys and iterators over all sequences.
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.program.ssahaClassDescriptionA database of sequences with accessible keys and iterators over all sequences.
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.program.ssbindClassDescriptionA database of sequences with accessible keys and iterators over all sequences.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.
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.program.unigeneClassDescriptionA database of sequences with accessible keys and iterators over all sequences.
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.proteomics.aaindex
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.searchClassDescriptionA database of sequences with accessible keys and iterators over all sequences.
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq.dbClassDescriptionAn abstract implementation of SequenceDB that provides the sequenceIterator method.Interface for objects that define how to make an ID for a sequence.This defines an index entry for an individual sequence within a set of indexed files.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.A database of sequences with accessible keys and iterators over all sequences.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.A database of sequences.An abstract implementation of SequenceDB that wraps up another database.Implements IndexStore as a serialized file for the java data and a tab-delimited file of offsets.Functions for access to a web based database that returns sequences in a variety of formats.
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq.db.biofetch
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq.db.biosqlClassDescriptionA database of sequences with accessible keys and iterators over all sequences.A database of sequences.
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq.db.flat
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq.distributedClassDescriptionAn abstract implementation of SequenceDB that provides the sequenceIterator method.A database of sequences with accessible keys and iterators over all sequences.A database of sequences.
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq.implClassDescriptionA database of sequences with accessible keys and iterators over all sequences.
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq.ioClassDescriptionA database of sequences with accessible keys and iterators over all sequences.
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Classes in org.biojava.bio.seq.db used by org.biojava.directory
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Classes in org.biojava.bio.seq.db used by org.biojavax.bio.dbClassDescriptionInterface for objects that define how to make an ID for a sequence.A database of sequences with accessible keys and iterators over all sequences.A database of sequences.
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Classes in org.biojava.bio.seq.db used by org.biojavax.bio.db.biosqlClassDescriptionA database of sequences with accessible keys and iterators over all sequences.A database of sequences.
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Classes in org.biojava.bio.seq.db used by org.biojavax.bio.db.ncbiClassDescriptionA database of sequences with accessible keys and iterators over all sequences.A database of sequences.