Uses of Package
org.biojava.bio
Packages that use org.biojava.bio
Package
Description
The core classes that will be used throughout the bio packages.
Classes to generate and describe sequence alignments.
Databases of generic structured data (annotation) objects.
Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
Graphical interfaces for biojava objects.
The classes and interfaces in this package cover common molecular
biological techniques such as restriction digests and PCR.
ABI Trace Handling.
Experimental parsers using the tagvalue framework.
GFF manipulation.
Support for reading and writing GFF3.
Tools for working with profile Hidden Markov Models from the HMMer package.
Support classes for Homologene data.
A flat-file ascii index of ascii flat files as per the OBDA specification.
Parser for Phred output
Parsers for the XML output from NCBI blast.
SSAHA sequence searching API.
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
Process files as streams of records, each with tags with values.
Objects for representing Unigene clusters.
Event-driven parsing system for the Extensible Feature Format (XFF).
Utilities to aid in performing various physical analysis of proteins.
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.
The classes and interfaces for defining sequence similarity and
honology.
Standard in-memory implementations of
Sequence
and
Feature
.Classes and interfaces for processing and producing flat-file representations
of sequences.
Classes for converting between AGAVE XML and BioJava objects.
Tools for reading and writing an XML representation of BioJava's FeatureFilter language.
Code for projecting Feature objects and systematically altering their
properties.
Representation of the Symbols that make up a sequence, and locations within
them.
Taxonomy object for representing species information.
Open Bio Sequence Database Access (OBDA) registry support.
A general-purpose API for ontologies.
Mathematical utility classes.
This package is used to perform regular expression searches of
SymbolLists defined in arbitrary Alphabets.
The Biojava extensions packages, classes that extend the core biojava
functionality
Classes to represent biological entities and their relationships.
This package contains the interfaces that need to be implemented by discrete alignment services.
This package holds implementations of the org.biojava3.ws.alignment interfaces for the NCBI remote QBlast services
through the WWW.
Interactions between biojavax objects and a DB.
Interface between biojava and biosql databases
Interfaces to NCBI data.
Rich implementations of Sequences, Locations and Features.
Classes to support the I/O of RichSequence and
Bioentry objects.
Extensions to the biojava ontology model that represent BioSQL ontology.
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Classes in org.biojava.bio used by org.biojava.bioClassDescriptionA utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.Arbitrary annotation associated with one or more objects.A set of constraints on the data contained in an
Annotation
.An abstract base class useful for implementing AnnotationType instances.Used byAnnotationType
to represent the constraint on the collection of values in a property-slot.An ec (enzyme classification) number.A simple implementation of EcNumber.PropertyConstraint
s describes a constraint applied to the members of an annotation bundle. -
Classes in org.biojava.bio used by org.biojava.bio.alignmentClassDescriptionA nestable biological error.A nestable biological exception.A nestable biological exception.
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Classes in org.biojava.bio used by org.biojava.bio.annodbClassDescriptionA set of constraints on the data contained in an
Annotation
.A nestable biological exception. -
Classes in org.biojava.bio used by org.biojava.bio.chromatogram
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Classes in org.biojava.bio used by org.biojava.bio.dist
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Classes in org.biojava.bio used by org.biojava.bio.dpClassDescriptionIndicates that an object has an associated annotation.Arbitrary annotation associated with one or more objects.A nestable biological exception.
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Classes in org.biojava.bio used by org.biojava.bio.dp.onehead
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Classes in org.biojava.bio used by org.biojava.bio.dp.twohead
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Classes in org.biojava.bio used by org.biojava.bio.gui
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Classes in org.biojava.bio used by org.biojava.bio.molbioClassDescriptionIndicates that an object has an associated annotation.Arbitrary annotation associated with one or more objects.A nestable biological exception.
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Classes in org.biojava.bio used by org.biojava.bio.program.abi
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Classes in org.biojava.bio used by org.biojava.bio.program.formatsClassDescriptionA set of constraints on the data contained in an
Annotation
.A nestable biological exception. -
Classes in org.biojava.bio used by org.biojava.bio.program.gff
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Classes in org.biojava.bio used by org.biojava.bio.program.gff3ClassDescriptionIndicates that an object has an associated annotation.Arbitrary annotation associated with one or more objects.A nestable biological exception.
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Classes in org.biojava.bio used by org.biojava.bio.program.hmmerClassDescriptionIndicates that an object has an associated annotation.Arbitrary annotation associated with one or more objects.
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Classes in org.biojava.bio used by org.biojava.bio.program.homologene
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Classes in org.biojava.bio used by org.biojava.bio.program.indexdbClassDescriptionArbitrary annotation associated with one or more objects.A set of constraints on the data contained in an
Annotation
.A nestable biological exception. -
Classes in org.biojava.bio used by org.biojava.bio.program.phredClassDescriptionIndicates that an object has an associated annotation.Arbitrary annotation associated with one or more objects.A nestable biological exception.
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Classes in org.biojava.bio used by org.biojava.bio.program.sax.blastxml
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Classes in org.biojava.bio used by org.biojava.bio.program.ssaha
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Classes in org.biojava.bio used by org.biojava.bio.program.ssbindClassDescriptionArbitrary annotation associated with one or more objects.A nestable biological exception.
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Classes in org.biojava.bio used by org.biojava.bio.program.tagvalueClassDescriptionArbitrary annotation associated with one or more objects.A set of constraints on the data contained in an
Annotation
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Classes in org.biojava.bio used by org.biojava.bio.program.unigeneClassDescriptionIndicates that an object has an associated annotation.A set of constraints on the data contained in an
Annotation
.A nestable biological exception. -
Classes in org.biojava.bio used by org.biojava.bio.program.xffClassDescriptionArbitrary annotation associated with one or more objects.A nestable biological exception.
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Classes in org.biojava.bio used by org.biojava.bio.proteomics
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Classes in org.biojava.bio used by org.biojava.bio.proteomics.aaindex
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Classes in org.biojava.bio used by org.biojava.bio.searchClassDescriptionIndicates that an object has an associated annotation.Arbitrary annotation associated with one or more objects.A nestable biological exception.
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Classes in org.biojava.bio used by org.biojava.bio.seqClassDescriptionIndicates that an object has an associated annotation.Arbitrary annotation associated with one or more objects.A set of constraints on the data contained in an
Annotation
.A nestable biological exception. -
Classes in org.biojava.bio used by org.biojava.bio.seq.dbClassDescriptionA nestable biological exception.A nestable biological exception.
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Classes in org.biojava.bio used by org.biojava.bio.seq.db.biofetch
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Classes in org.biojava.bio used by org.biojava.bio.seq.db.biosqlClassDescriptionA nestable biological exception.A nestable biological exception.
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Classes in org.biojava.bio used by org.biojava.bio.seq.db.flat
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Classes in org.biojava.bio used by org.biojava.bio.seq.distributed
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Classes in org.biojava.bio used by org.biojava.bio.seq.homolClassDescriptionIndicates that an object has an associated annotation.A nestable biological exception.
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Classes in org.biojava.bio used by org.biojava.bio.seq.implClassDescriptionIndicates that an object has an associated annotation.Arbitrary annotation associated with one or more objects.A nestable biological exception.
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Classes in org.biojava.bio used by org.biojava.bio.seq.ioClassDescriptionA utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.Indicates that an object has an associated annotation.Arbitrary annotation associated with one or more objects.A nestable biological exception.
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Classes in org.biojava.bio used by org.biojava.bio.seq.io.agaveClassDescriptionIndicates that an object has an associated annotation.Arbitrary annotation associated with one or more objects.A no-frills implementation of Annotation that is just a wrapper around a
LinkedHashMap
. -
Classes in org.biojava.bio used by org.biojava.bio.seq.io.filterxmlClassDescriptionA set of constraints on the data contained in an
Annotation
.Used byAnnotationType
to represent the constraint on the collection of values in a property-slot.PropertyConstraint
s describes a constraint applied to the members of an annotation bundle. -
Classes in org.biojava.bio used by org.biojava.bio.seq.projectionClassDescriptionIndicates that an object has an associated annotation.A nestable biological exception.
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Classes in org.biojava.bio used by org.biojava.bio.symbolClassDescriptionIndicates that an object has an associated annotation.Arbitrary annotation associated with one or more objects.A nestable biological exception.
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Classes in org.biojava.bio used by org.biojava.bio.taxaClassDescriptionIndicates that an object has an associated annotation.Arbitrary annotation associated with one or more objects.A nestable biological exception.
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Classes in org.biojava.bio used by org.biojava.directory
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Classes in org.biojava.bio used by org.biojava.ontologyClassDescriptionIndicates that an object has an associated annotation.Arbitrary annotation associated with one or more objects.
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Classes in org.biojava.bio used by org.biojava.utils.automata
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Classes in org.biojava.bio used by org.biojava.utils.math
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Classes in org.biojava.bio used by org.biojava.utils.regex
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Classes in org.biojava.bio used by org.biojava.utils.walker
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Classes in org.biojava.bio used by org.biojavaxClassDescriptionIndicates that an object has an associated annotation.Arbitrary annotation associated with one or more objects.
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Classes in org.biojava.bio used by org.biojavax.bioClassDescriptionIndicates that an object has an associated annotation.Arbitrary annotation associated with one or more objects.A nestable biological exception.
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Classes in org.biojava.bio used by org.biojavax.bio.alignment
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Classes in org.biojava.bio used by org.biojavax.bio.alignment.blast
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Classes in org.biojava.bio used by org.biojavax.bio.db
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Classes in org.biojava.bio used by org.biojavax.bio.db.biosql
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Classes in org.biojava.bio used by org.biojavax.bio.db.ncbi
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Classes in org.biojava.bio used by org.biojavax.bio.seqClassDescriptionIndicates that an object has an associated annotation.Arbitrary annotation associated with one or more objects.A nestable biological exception.
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Classes in org.biojava.bio used by org.biojavax.bio.seq.io
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Classes in org.biojava.bio used by org.biojavax.ontologyClassDescriptionIndicates that an object has an associated annotation.Arbitrary annotation associated with one or more objects.