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Packages that use org.biojava.bio.seq.db | |
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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 | 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 | |
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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 | |
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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 | |
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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 | |
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IllegalIDException
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SequenceDB
A database of sequences with accessible keys and iterators over all sequences. |
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SequenceDBLite
A database of sequences. |
Classes in org.biojava.bio.seq.db used by org.biojava.bio.program.gff | |
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IllegalIDException
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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 | |
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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 | |
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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 | |
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IllegalIDException
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SequenceDB
A database of sequences with accessible keys and iterators over all sequences. |
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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 | |
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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 | |
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IllegalIDException
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.search | |
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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 | |
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IllegalIDException
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Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq.db | |
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AbstractSequenceDB
An abstract implementation of SequenceDB that provides the sequenceIterator method. |
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IDMaker
Interface for objects that define how to make an ID for a sequence. |
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IllegalIDException
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Index
This defines an index entry for an individual sequence within a set of indexed files. |
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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. |
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SequenceDB
A database of sequences with accessible keys and iterators over all sequences. |
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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. |
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SequenceDBLite
A database of sequences. |
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SequenceDBWrapper
An abstract implementation of SequenceDB that wraps up another database. |
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TabIndexStore
Implements IndexStore as a serialized file for the java data and a tab-delimited file of offsets. |
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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 | |
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IllegalIDException
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SequenceDBLite
A database of sequences. |
Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq.db.biosql | |
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SequenceDB
A database of sequences with accessible keys and iterators over all sequences. |
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SequenceDBLite
A database of sequences. |
Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq.db.flat | |
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IllegalIDException
|
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SequenceDBLite
A database of sequences. |
Classes in org.biojava.bio.seq.db used by org.biojava.bio.seq.distributed | |
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AbstractSequenceDB
An abstract implementation of SequenceDB that provides the sequenceIterator method. |
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IllegalIDException
|
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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 | |
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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 | |
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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 | |
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SequenceDBLite
A database of sequences. |
Classes in org.biojava.bio.seq.db used by org.biojavax.bio.db | |
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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 | |
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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 | |
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IllegalIDException
|
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SequenceDB
A database of sequences with accessible keys and iterators over all sequences. |
|
SequenceDBLite
A database of sequences. |
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