All Classes

Class	Description
AAindex	Symbol property table based on the Amino Acid Index Database.
AAindexStreamReader	Iterator over AAindex objects that are stored in a stream in the AAindex1 file format.
ABIFChromatogram	An implementation of Chromatogram to encapulsulate chromatogram data extracted from the files produced by ABI sequencers, such as the the 377 and the 3700.
ABIFParser	A general base parser for files produced by ABI software.
ABIFParser.DataAccess	Concatenation of the Seekable and DataInput interfaces.
ABIFParser.TaggedDataRecord	An aggregate immutable type for an ABIF tagged data record.
ABITools	Useful functionality for working with fasta files where the quality of the DNA is encoded as upper and lower case DNA characters.
ABITrace	Title: ABITrace ABITrace is a class for managing ABI file information, it is capable of opening an ABI file and storing the most important fields, which can be recalled as simple java types.
AbiTraceRenderer	Renders an ABI trace file as a chromatogram graph.
AbstractAlignmentStyler	Abstract implementation of AlignmentStyler, contains utility methods for generating a set of HTML styles from a list of RGB colours.
AbstractAlphabet	An abstract implementation of Alphabet.
AbstractAnnotation	A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.
AbstractBeadRenderer	AbstractBeadRenderer is a an abstract base class for the creation of FeatureRenderers which use a 'string of beads' metaphor for displaying features.
AbstractBean	a generic class that implements the toString method for a bean
AbstractBioEntryDB	An abstract implementation of BioEntryDB that provides the getBioEntryIterator method.
AbstractChangeable	Useful base-class for objects implementing Changeable
AbstractChromatogram	A basic, abstract implementation of Chromatogram.
AbstractCrossOverFunction	Abstract implementation of CrossOverFunction.
AbstractDistribution	An abstract implementation of Distribution.
AbstractFeatureHolder	An abstract implementation of FeatureHolder.
AbstractGeneticAlgorithm	Base class from which most implementations of GeneticAlgorithm will inherit.
AbstractLocation	An abstract implementation of Location.
AbstractLocationDecorator	Abstract Location decorator (wrapper).
AbstractManyToOneTranslationTable	an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.
AbstractMatrixPairDPCursor
AbstractMutationFunction	Abstract implementation of MutationFunction all custom implementations should inherit from here.
AbstractOrderNDistribution	Simple base class for OrderNDistributions.
AbstractOrganism	Abstract implementation of Organism.
AbstractOrthologueSet
AbstractOrthoPairCollection	An abstract implementation of the OrthoPairCollection interface.
AbstractOrthoPairSet	represents the Homologene Group.
AbstractPeptideDigestRenderer	A SequenceRenderer that renders a set of Features that match a FeatureFilter in such a way that they do not overlap in the display.
AbstractPopulation	Most Population implementations will want to inherit from here.
AbstractRangeLocation	Base class for simple contiguous Location implementations.
AbstractReversibleTranslationTable	an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.
AbstractRichSequenceDB	An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method.
AbstractSequenceDB	An abstract implementation of SequenceDB that provides the sequenceIterator method.
AbstractSVMClassifierModel	Abstract implementation of SVMClassifierModel.
AbstractSVMTarget	An abstract implementation of an SVMModel.
AbstractSymbol	The base-class for Symbol implementations.
AbstractSymbolList	Abstract helper implementation of the SymbolList core interface.
AbstractTaxon	Deprecated. replaced by classes in org.biojavax.bio.taxa
AbstractTerm	Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.
AbstractTrainer	An abstract implementation of TrainingAlgorithm that provides a framework for plugging in per-cycle code for parameter optimization.
AbstractULAlignment
AbstractWrapper	An abstract TagValueWrapper that does nothing!
AcnumHitReader	AcnumHitReader reads the "acnum.hit" file of an EMBL CD-ROM format binary index.
AcnumTrgReader	AcnumTrgReader reads the "acnum.trg" file of an EMBL CD-ROM format binary index.
ActivityListener	Interface for object which monitor long-running activities.
Agave2AgaveAnnotFilter	Dumping the data from biojava with source of agave into agave format
AGAVEAltIdsPropHandler	Deals with alternate sequence IDs
AGAVEAnnotationsHandler
AGAVEAnnotFilter	This interface defines mapping from BioJava into AGAVE format.
AGAVEAnnotFilterFactory
AGAVEAssemblyHandler
AGAVEBioSeqCallbackItf	An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEBioSeqHandler	Handles the AGAVE <bio_sequence> element
AGAVEBioSequenceHandler	Handles the AGAVE <bio_sequence> element
AGAVECallbackItf	An interface that can be tested for by nested handlers when trying to do a callback.
AGAVECdsHandler	Handles the AGAVE <cds> element
AGAVEChromosomeCallbackItf	An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEChromosomeHandler	Handles the AGAVE <chromosome> element
AGAVEClassificationHandler
AGAVECompResultHandler
AGAVEComputationHandler
AGAVEContigCallbackItf	An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEContigHandler	Handles the AGAVE <contig> element
AGAVEDbId
AGAVEDbIdCallbackItf	this is the interface implemented by several classes
AGAVEDbIdPropCallbackItf
AGAVEDbIdPropHandler	Deals with database crossreferences
AGAVEDescPropHandler	Deals with database crossreferences
AGAVEElementIdPropHandler
AGAVEEvidenceCallbackItf
AGAVEEvidenceHandler
AGAVEExonsPropHandler
AGAVEFeatureCallbackItf	An interface that can be tested for by nested handlers when trying to do a callback.
AGAVEFragmentOrderHandler
AGAVEFragmentOrientationHandler
AGAVEGeneHandler
AGAVEHandler	Handles the root AGAVE element modified for agave format
AGAVEIdAlias
AGAVEIdAliasCallbackItf
AGAVEIdAliasPropHandler
AGAVEKeywordPropHandler	Deals with AGAVE keywords
AGAVEMapLocation
AGAVEMapLocationPropHandler
AGAVEMapPosition
AGAVEMapPositionPropHandler
AGAVEMatchAlignPropHandler	Deals with match_align
AGAVEMatchDescPropHandler	Deals with match_desc
AGAVEMatchRegion	match_region
AGAVEMatchRegionPropHandler	Deals with match_region
AGAVEMrnaHandler	Handles the AGAVE <mrna> element
AGAVENotePropHandler	Deals with note
AGAVEPredictedProteinHandler	Handles the AGAVE <predicted_protein> element
AGAVEProperty
AGAVEQualifierPropHandler
AGAVEQueryRegion
AGAVEQueryRegionPropHandler
AGAVERelatedAnnot
AGAVERelatedAnnotPropHandler
AGAVEResultGroupHandler
AGAVEResultPropertyPropHandler
AGAVESciPropertyPropHandler	sci_property
AGAVESeqFeatureHandler	seq_feature
AGAVESeqLocationPropHandler	seq_location
AGAVESeqMapHandler	sequence_map
AGAVESeqPropHandler	Deals with sequence code
AGAVETranscriptHandler	transcript
AGAVEUnorderedFragmentsHandler	unordered_fragments
AGAVEViewPropHandler	Moves view attributes into annotation properties.
AgaveWriter	Writes Sequence into AGAVE XML document.
AGAVEXref	xref
AGAVEXrefCallbackItf
AGAVEXrefPropHandler	handle AGAVE xref
AGAVEXrefPropPropHandler	xref_property
AGAVEXrefs	xrefs
AGAVEXrefsPropHandler	Deals with database crossreferences (xrefs)
Aggregator	Joins multipel values into single values.
AligMatEl
Alignable
AlignedPosition
AlignIOConstants	AlignIOConstants contains constants used to identify sequence formats, alphabets etc, in the context of reading and writing alignments.
Alignment	Alignment object to contain/manage a DAS alignment.
Alignment	An alignment containing multiple SymbolLists.
Alignment.SymbolListIterator	Iterator implementation looping over symbol lists in an alignment using the labels.
AlignmentCalc	A class that obtains two structures via DAS and aligns them This is done in a separate thread.
AlignmentElement	AlignmentElement is a class which represents a SymbolList and its location within an Alignment This is for use in UnequalLengthAlignments and ARAlignments.
AlignmentFormat
AlignmentGui	A JFrame that allows to trigger a pairwise structure alignment, either from files in a directory, or after manual upload.
AlignmentMarker	Class to do simple HTML colouring of sequence alignments.
AlignmentPositionListener
AlignmentRenderer
AlignmentStAXHandler	AlignmentStAXHandler handles the BlastLikeAlignment element of BioJava BlastLike XML.
AligNPE
AlignTools
Alphabet	The set of AtomicSymbols which can be concatenated together to make a SymbolList.
AlphabetIndex	Map between Symbols and index numbers.
AlphabetManager	Utility methods for working with Alphabets.
AlphabetResolver	AlphabetResolvers are helpers which determine which type of sequence Alphabet to expect from a search result.
AlphaCTools	AlphaCTools is a collection of static convenience methods for dealing with Alpha Carbon Backbone Phi / Psi angles.
AlreadyExistsException	Thrown to indicate that a term or triple can't be added to an ontology because it is already present.
AltAligComparator	a comparator to sort AlternativeAlignments based on their number of equivalent residues and RMSD.
AlternateTokenization	Implementation of SymbolTokenization which binds symbols to strings of characters.
AlternativeAlignment	Implements a class which handles one possible (alternative) solution.
AlternativeAlignmentFrame	a frame showing the alternative alignments, which are the result of a structure superimposition
AminoAcid	A Group that represents an AminoAcid.
AminoAcidImpl	AminoAcid inherits most from Hetatom.
Annotatable	Indicates that an object has an associated annotation.
Annotatable.AnnotationForwarder	Deprecated. use new ChangeForwarder.Retyper(source, cs, Annotation.PROPERTY) instead
AnnotatedSequenceDB	SequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.
Annotation	Arbitrary annotation associated with one or more objects.
AnnotationBuilder	Builds an Annotation tree from TagValue events using an AnnotationType to work out which fields are of what type.
AnnotationChanger	AnnotationChanger remaps the values of an Annotation to new values specified by a ValueChanger.
AnnotationDB	A database of Annotation instances.
AnnotationFactory	AnnotationFactory is a utility class for making Annotations from Maps.
AnnotationRenamer	AnnotationRenamer remaps the keys of an Annotation to new keys specified by a TagMapper.
AnnotationTools	AnnotationTools is a set of static utility methods for manipulating Annotations and AnnotationTypes.
AnnotationType	A set of constraints on the data contained in an Annotation.
AnnotationType.Abstract	An abstract base class useful for implementing AnnotationType instances.
AnnotationType.Impl	An implementation of AnnotationType.
AppBeanRunner	Create a bean from an XML file, then attempt to enter it.
AppEntry
AppException
ARAlignment	ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.
ArrayStateMachineToolkit
ArrowedFeatureRenderer	A Feature Renderer that paints the Feature as a right facing arrow Based heavily on BasicFeatureRenderer
ArrowGlyph	A Glyph that paints an arrow shape within the bounds.
AssembledSymbolList	Support class for applications which need to patch together sections of sequence into a single SymbolList.
AssertionFailure	An unchecked exception representing an Assertion failure.
Atom	A simple interface for an Atom.
AtomicSymbol	A symbol that is not ambiguous.
AtomImpl	Implementation of an Atom of a PDB file.
AtomIterator	an iterator over all atoms of a structure / group.
AtomSite
Author	Describes author attributes for author information in a PDB file.
AutomatonException	An exception thrown by classes of this package.
BackMatrixPairDPCursor
BackPointer	A backpointer.
BarLogoPainter	A logo painter that paints in bars.
BaseXMLWriter	Base XMLWriter class for writing XML representations of Java Value Objects with bespoke architectures.
BasicFeatureRenderer
BasicImapRenderer	BasicImapRenderer is a decorator for BasicFeatureRenderer which adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by the BasicFeatureRenderer.
BasicXFFHelper
BasisSymbol	A symbol that can be represented as a string of Symbols.
BaumWelchSampler	Train a hidden markov model using a sampling algorithm.
BaumWelchTrainer	Train a hidden markov model using maximum likelihood.
BeadFeatureRenderer	BeadFeatureRenderers use a 'string of beads' metaphor for displaying features.
BeanAsAnnotation	Create an Annotation with properties matching those of a JavaBean instance.
BeanAsMap
BetweenLocation	Between view onto an underlying Location instance.
BiblioArticle	It represents an article.
BiblioBook	It represents a book.
BiblioBookArticle	It represents a book article.
BiblioCriterion	The criteria define how the matching or ordering should be done during queries.
BiblioDescription	It represents an account of the content of the cited resource.
BiblioEntryStatus	It defines information related to the citation itself rather than to the cited resource.
BiblioJournal	A class describing journals.
BiblioJournalArticle	It represents a journal article.
BiblioOrganisation	It represents an organisation dealing with the bibliographic resources.
BiblioPatent	It represents a patent.
BiblioPerson	It represents a person dealing with the bibliographic resources.
BiblioProceeding	It represents a conference proceeding.
BiblioProvider	This class and its sub-classes define active participants of the process of creation and dissemination of the bibliographic resources.
BiblioScope	It represent an extent or scope of the content of the cited resource.
BiblioService	It represents a service dealing with the bibliographic resources.
BiblioSubject	It represents the topic of the content of the cited resource.
BiblioTechReport	It represents a technical report.
BiblioThesis	It represents a thesis.
BiblioWebResource	It represents a WWW resource.
BibRef	This class is a core class of the bibliographic data model - it represents a bibliographic reference, a citation.
BibRefException	An exception raised when communciation with the BibRef APIs fails.
BibRefQuery	The interface BibRefQuery is a fundamental part of the Bibliographic Query Service.
BibRefSupport	This interface defines supporting utilities for working with bibliographic repositories.
BinarySearch	solves y = f(x) = 0 by binary search.
BioEntry	This class relates to the bioentry table in BioSQL.
BioEntryDB	.
BioEntryDBLite	A database of BioEntrys.
BioEntryIterator	Essentially the same as SequenceIterator.
BioEntryRelationship	Represents the relation between two bioentries.
BioError	A nestable biological error.
BioException	A nestable biological exception.
BioFetchSequenceDB	Simple SequenceDB implementation backed by a BioFetch (HTTP) server.
BioFetchSequenceDBProvider	Directory-services plugin for biofetch databases.
BioIndex	The original object for indexing sequence files.
BiojavaJmol	A class that provides a simple GUI for Jmol
BioMatcher	Interface for things that perform matches.
BioPattern
BioRuntimeException	A nestable biological exception.
BioSQLAcceptAllFilter	The class that accepts all features.
BioSQLAcceptNoneFilter	The class that accepts no features.
BioSQLBioEntryDB
BioSQLCrossReferenceResolver	A simple implementation of CrossReferenceResolver
BioSQLFeatureFilter	A filter for accepting or rejecting a feature.
BioSQLFeatureFilter.And	A filter that returns all features accepted by both child filter.
BioSQLFeatureFilter.ByName	Construct one of these to filter features by display name.
BioSQLFeatureFilter.ByNote	A filter that returns all features that have the given note, and the value and rank is checked as well.
BioSQLFeatureFilter.ByNoteTermOnly	A filter that returns all features that have a note with the given term.
BioSQLFeatureFilter.ByRank	Construct one of these to filter features by rank.
BioSQLFeatureFilter.BySequenceName	Accept features that reside on a sequence with a particular name.
BioSQLFeatureFilter.BySourceTerm	Construct one of these to filter features by source.
BioSQLFeatureFilter.BySourceTermName	Construct one of these to filter features by source (name only - parent ontology is ignored).
BioSQLFeatureFilter.ByStrand	A filter that returns all features having locations on a given strand.
BioSQLFeatureFilter.ByTypeTerm	Construct one of these to filter features by type.
BioSQLFeatureFilter.ByTypeTermName	Construct one of these to filter features by type (name only - parent ontology is ignored).
BioSQLFeatureFilter.ContainedByRichLocation	A filter that returns all features contained within a location.
BioSQLFeatureFilter.HibernateFeatureFilter	A filter for Hibernate-BioSQL filters to extend.
BioSQLFeatureFilter.Not	A filter that returns all features not accepted by a child filter.
BioSQLFeatureFilter.Or	A filter that returns all features accepted by at least one child filter.
BioSQLFeatureFilter.OverlapsRichLocation	A filter that returns all features overlapping a location.
BioSQLFeatureFilter.Tools	A class representing some useful stuff you can do with BioSQLFeatureFilters, for instance converting plain FeatureFilters into a their BioSQLFeatureFilter equivalents (where possible).
BioSQLRichObjectBuilder	Takes requests for RichObjects and sees if it can load them from a Hibernate database.
BioSQLRichSequenceDB
BioSQLRichSequenceHandler	A handler which loads sequence data from a BioSQL database, caching it where possible.
BioSQLSequenceDB	Deprecated. Use hibernate and org.biojavax.bio.db.*
BioSQLSequenceDBProvider	Deprecated. Use hibernate and org.biojavax.bio.db.*
BioStore	BioStores represent directory and file structures which index flat files according to the OBDA specification.
BioStoreFactory	BioStoreFactory creates BioStore instances.
Blast2HTMLHandler	Takes a SAX event stream and a HTMLRenderer to produce a HTML Blast like program report.
BlastLikeHomologyBuilder	BlastLikeHomologyBuilder populates a List with Homology instances created from SAX events supplied via a SeqSimilarityAdapter.
BlastLikeSAXParser	A facade class allowing for direct SAX2-like parsing of the native output from Blast-like bioinformatics software.
BlastLikeSearchBuilder	BlastLikeSearchBuilder will create SeqSimilaritySearchResults from SAX events via a SeqSimilarityAdapter.
BlastLikeSearchFilter	A SearchContentHandler class that implements filtering in chains of SearchContentHandler instances.
BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
BlastLikeSearchFilter.And
BlastLikeSearchFilter.ByHitProperty	Applies test to the value specified by the key in hit properties.
BlastLikeSearchFilter.BySearchProperty	Applies test to the value specified by the key in search properties.
BlastLikeSearchFilter.BySubHitProperty	Applies test to the value specified by the key in subhit properties.
BlastLikeSearchFilter.Node
BlastLikeSearchFilter.Not
BlastLikeSearchFilter.Or
BlastLikeToXMLConverter	A class that converts the raw output from a variety of bioinformatics software and converts it to XML that will validate against the biojava:BlastLikeDataSetCollection DTD.
BlastXMLParser	This class parses NCBI Blast XML output.
BlastXMLParserFacade	A facade class that wraps the NCBI Blast XML parsing framework in a more user-friendly form.
BlockPainter
BooleanElementHandlerBase	StAX handler for any element which just contains a string representation of an boolean.
BoundaryFinder
BumpedRenderer
ByLocationMinMaxComparator	A Comparator similar to Feature.ByLocationComparator except that the min and max positions of the location are both compared
ByLocationMinMaxFeatureComparator	Comparator that compares the min and max positions of Features Required by org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer instances.
ByteElementHandlerBase	StAX handler for any element which just contains a string representation of a byte.
Cache	Interface for managing caches of objects.
CacheMap	Interface for managing caches of objects fetchable by key.
CacheReference	Interface for a reference to an object, analogous to java.lang.ref.Referencce, but more flexible.
CachingInputStream	A wrapper around InputStream that provides in-memory caching of the input data.
CachingKernel	Caches the results of a nested kernel so that k(a, b) need only be calculated once.
CachingSequenceDB	SequenceDB implementation that caches the results of another SequenceDB.
CAConverter	Converts full atom representations to Calpha only ones.
Calc	utility operations on Atoms, AminoAcids, etc.
CandyEntry	This is a basic container for a vocabulary entry.
CandyException
CandyFinder	This interface is a main entry point to a set of controlled vocabularies.
CandyVocabulary	This interface defines functionality of a controlled vocabulary.
CardinalityConstraint	A constraint on the number of values a property can have.
Cell	A single cell in the DP matrix.
CellCalculator	The interface for all functions that can calculate the 'scores' array for a given cell.
CellCalculatorFactory
CellCalculatorFactoryMaker	The interface for all functions that can calculate the 'scores' array for a given cell.
Chain	Defines the interface for a Chain.
ChainImpl	A Chain in a PDB file.
Changeable	This is a flag interface that defines the common add/remove listener methods for classes and interfaces that wish to indicate that they are sources of ChangeEvents.
ChangeableCache	A cache that clears values as the keys fire ChangeEvents of a given type.
ChangeAdapter	This is a ChangeListener that ignores everything.
ChangeEvent	Event which encapsulates a change in any mutable BioJava object.
ChangeForwarder	This is a ChangeListener that is designed to adapt events of one type from one source to events of another type emitted by another source.
ChangeForwarder.Retyper	A ChangeForwarder that systematically uses a given type and wraps the old event.
ChangeHub	Interface implemented by ChangeHubs, i.e.
ChangeListener	Interface for objects which listen to ChangeEvents.
ChangeListener.AlwaysVetoListener	An implementation that always vetoes everything.
ChangeListener.ChangeEventRecorder	A listener that remembers the ChangeEvent of the last change.
ChangeListener.LoggingListener	A listener that writes information about the event stream to a PrintStream.
ChangeSupport	A utility class to provide management for informing ChangeListeners of ChangeEvents.
ChangeTable	A mapping between keys and actions to turn old values into new values.
ChangeTable.ChainedChanger	An implementation of Changer that applies a list of Changer instances to the value in turn.
ChangeTable.Changer	Callback used to produce a new value from an old one.
ChangeTable.Splitter	Callback used to produce a list of values from a single old one.
ChangeType	Class for all constants which are used to indicate change types.
ChangeVetoException	Exception which is thrown when a ChangeListener does not wish a change to take place.
CharacterTokenization	Implementation of SymbolTokenization which binds symbols to single unicode characters.
CharElementHandlerBase	StAX handler for any element which just contains a string representation of a char.
ChemComp
ChemCompConsumer
ChemCompTools	Some tools for working with chemical compounds.
ChemicalComponentDictionary	A representation of the Chemical Component Dictionary.
CholeskyDecomposition	Cholesky Decomposition.
Chromatogram	Encapsulates the basic information you would want from a chromatogram.
ChromatogramFactory	A factory that creates Chromatogram objects from files or streams.
ChromatogramGraphic	Encapsulates a configurable method for drawing a Chromatogram into a graphics context.
ChromatogramGraphic.Option	A typesafe enumeration of the options available for configuring the behavior of a ChromatogramGraphic instance.
ChromatogramNonlinearScaler	Provides the mechanism whereby a ChromatogramGraphic can display a Chromatogram with a non-linear horizontal scale.
ChromatogramNonlinearScaler.Identity	The default scaler that displays the chromatogram 1:1.
ChromatogramTools	Utility class for dealing with Chromatograms.
ChunkedSymbolList	SymbolList implementation using constant-size chunks.
ChunkedSymbolListFactory	class that makes ChunkedSymbolLists with the chunks implemented as SymbolLists themselves.
CircularFeatureFilteringRenderer
CircularFeatureRenderer
CircularFeaturesRenderer
CircularLocation	Circular view onto an underlying Location instance.
CircularMLR	Renders multiple renderers, each in their own concentric rings.
CircularPaddedRenderer
CircularReferenceException	Deprecated. replaced by classes in org.biojavax.bio.taxa
CircularRenderer	Render information from a CircularRendererContext onto a graphics context.
CircularRendererContext	A context providing information for rendering sequences into circular coordinate systems.
CircularRendererPanel	Renders a sequence as a circle using a CircularRenderer.
CircularView	A circular view onto another Sequence object.
ClassifierExample	A simple toy example that allows you to put points on a canvas, and find a polynomial hyperplane to seperate them.
ClassifierExample.PointClassifier	An extention of JComponent that contains the points & encapsulates the classifier.
Classify
ClassTools	Utility methods for manipulating class objects and resources.
ClustalWAlignmentSAXParser	A SAX2 parser for dealing with a multiple sequence alignment as produced by ClustalW outputing .aln format.
ClusterAltAligs	A class that clusters alternative alignments according to their similarity.
CodonPref
CodonPrefFilter
CodonPrefFilter.AcceptAll
CodonPrefFilter.ByName
CodonPrefFilter.EverythingToXML
CodonPrefTools	An utility class for codon preferences
CollectionConstraint	Used by AnnotationType to represent the constraint on the collection of values in a property-slot.
CollectionConstraint.AllValuesIn	CollectionConstraint which validates all members of a Collection.
CollectionConstraint.And	A collection constraint that accpepts collections iff they are accepted by both child constraints.
CollectionConstraint.Contains	CollectionConstraint which validates a portion of a Collection.
CollectionConstraint.Or	A collection constraint that accepts items iff they are accepted by either child constraints.
ColourCommand	Interface for specifying whether a particular pair of residues/bases should be coloured.
Comment	A simple ranked comment designed to be used for BioEntry comments in BioSQL.
Commitable	Implementations of Commitable support atomic changes from one known state to another via commit/rollback semantics.
CommitFailure
CompactedDataStore	An implementation of DataStore that will map onto a file using the NIO constructs.
CompactedDataStoreFactory	Builder for a data store that is backed by a java.nio.MappedByteBuffer.
ComparableOntology	An Ontology that can be compared to another.
ComparableTerm	Makes Term objects comparable properly and adds some extra features to them.
ComparableTriple	Comparable triples, obviously.
ComponentFeature	Feature which represents a component in an assembly (contig).
ComponentFeature.Template	Template for constructing a new ComponentFeature.
Composition	Computes composition statistics about a SymbolList.
Compound	Created by IntelliJ IDEA.
CompoundRichLocation	An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.
ComputeObject	interface for classes that return a single double precision value for a single double precision argument.
Constants	Some usefull constants for working with binary files.
CoordManager	a class that manages the conversion of sequence coordinate system to JPanel drawing coordinates
Count	An encapsulation of a count over the Symbols within an alphabet.
CountedBufferedReader
CRC64Checksum	Utility class that calculates a CRC64 checksum on a stream of bytes.
CrosshairRenderer	CrosshairRenderer draws a crosshair, optionally with coordinates.
CrossOverFunction	Crosses two chromosomes.
CrossOverFunction.NoCross	A place holder CrossOverFunction that doesn't perform cross overs
CrossProductTokenization	Tokenization for cross-product alphabets.
CrossRef	Represents a cross reference to another database.
CrossReferenceResolutionException	An exception that indicates that an attempt to resolve a CrossRef has failed.
CrossReferenceResolver	This interface returns symbols or sequence for a given cross-reference.
DAS	A collection of DAS datasources.
DASAlignmentCall	takes care of the communication with a DAS Alignment service.
DASAlignmentClient	A DAS client that connects to a DAS aligmnent service and returns a Biojava Alignment object.
DASAlignmentXMLResponseParser	A class to Parse the XML response of a DAS Alignment service.
DASException	An exception of one of the DAS classes.
DASLink	A memento class for storing a link.
DASSequence	Sequence reflecting a DAS reference sequence, possibly decorated with one of more annotation sets.
DASSequenceDB	Collection of sequences retrieved from the DAS network.
DASSequenceDBProvider	Hook DAS into the OBDA directory system.
DASStructureCall	Calls a DAS - Structure server.
DASStructureClient	A DAS client that connects to a DAS structure service and returns a Biojava structure class.
DASStructureXMLResponseParser	a class to Parse the XML response of a DAS structure service.
DatabasePDBremark
DatabasePDBrev
DatabaseURLGenerator	Takes a database ID and some configuration properties ( such as base URL ) and returns either a URL or a full anchor tag.
DataSource	Reflect a datasource (reference or annotation) in the DAS1 network.
DataStore	A repository that can be searched with a sequence.
DataStoreFactory	Builder for a data store.
DBHelper	Deprecated. Use hibernate and org.biojavax.bio.db.*
DBHelper.BioSequenceStyle
DBHelper.DeleteStyle
DBHelper.JoinStyle
DBRef	A class to represent database cross references.
DebuggingRichSeqIOListener	This is purely for debugging purposes.
DefaultOps	Default implementation of OntologyOps.
DefaultURLGeneratorFactory	A simple default URLGeneratorFactory which returns a single NcbiDatabaseURLGenerator instance.
DelegationManager	Interface which exposes delegation services offered by a StAX event source.
DelegationManager	Interface which exposes delegation services offered by a StAX event source.
DemoStructureServer
DfaBuilder
DiagonalAddKernel	Adds a class specific constant to k(x, x).
DiagonalCachingKernel	Caches the leading diagonal of a kernel matrix.
Digest	This class contains methods for calculating the results of proteolytic digestion of a protein sequence this class is not designed to be thread safe
DistDataSource	Object which contributes data to a DistributedSequenceDB.
DistributedSequenceDB	Sequence database from the meta-DAS system.
Distribution	An encapsulation of a probability distribution over the Symbols within an alphabet.
Distribution.NullModelForwarder	Deprecated. use new ChangeForwarder.Retyper(this, cs, Annotation.PROPERTY) instead
DistributionFactory	A thing that can make Distributions.
DistributionFactory.DefaultDistributionFactory	The default DistributionFactory implementation.
DistributionLogo	The GUI component for rendering a DistributionLogo.
DistributionTools	A class to hold static methods for calculations and manipulations using Distributions.
DistributionTrainer	An object that can be used to train a distribution up.
DistributionTrainerContext	A context within a group of DistributionTrainers can be trained together.
DivisionLkpReader	DivisionLkpReader reads the "division.lkp" file of an EMBL CD-ROM format binary index.
DNAAmbPack	Packing utility class for DNA.
DNAComposition	Computes composition statistics about a DNA SymbolList.
DNANoAmbPack	A Packing implementation which handles the DNA alphabet, without any support for ambiguity symbols.
DNAStyle	A simple implementation of SymbolStyle optimized for DNA.
DNATools	Useful functionality for processing DNA sequences.
DocRef	Represents a documentary reference.
DocRefAuthor	Represents an author of a documentary reference.
DocRefAuthor.Tools	Useful tools for working with authors.
DotState	A Dot state.
DoubleAlphabet	An efficient implementation of an Alphabet over the infinite set of double values.
DoubleAlphabet.DoubleRange	A range of double values.
DoubleAlphabet.DoubleSymbol	A single double value.
DoubleAlphabet.SubDoubleAlphabet	A class to represent a contiguous range of double symbols.
DoubleElementHandlerBase	StAX handler for any element which just contains a string representation of a double.
DoubleTokenization
DP	Objects that can perform dymamic programming operations upon sequences with HMMs.
DP.ReverseIterator
DPCompiler	This is an implementation of CellCalculatorFactoryMaker that compiles the HMM object down to Java byte-code that is equivalent in behaviour to the interpreter.
DPCursor	Encapsulates the dynamic programmming matrix, and the context within algorithms work.
DPFactory	The interface for objects that can generate a DP object for a MarkovModel.
DPFactory.DefaultFactory
DPInterpreter
DPInterpreter.Maker
DPMatrix
DummyCrossReferenceResolver	A simple implementation of CrossReferenceResolver.
DummyRichSequenceHandler
DummySequence	A Sequence implementation that has a name and URI but no features, and a zero length symbol list.
DummySequenceDB	DummySequenceDB is an implementation which contains only a DummySequence.
DummySequenceDBInstallation	DummySequenceDBInstallation is an implementation which returns the same DummySequenceDB instance regardless of the identifier used to retrieve a database.
DummySymbolList	Symbol list which just consists of non-informative symbols.
DuplicateTaxonException
EbiDatabaseURLGenerator	Simple URL generator for EMBL at the EBI.
EbiFormat	Deprecated. replaced by classes in org.biojavax.bio.taxa
Echo	A simple listener that just echoes events back to the console.
EcNumber	An ec (enzyme classification) number.
EcNumber.Impl	A simple implementation of EcNumber.
Edit	Encapsulates an edit operation on a SymbolList.
EditableAlignment	EditableAlignment is an interface that defines methods for shifting bases within an Alignment.
EigenvalueDecomposition	Eigenvalues and eigenvectors of a real matrix.
ElementRecognizer	Simple interface for filtering SAX/StAX startElement events.
ElementRecognizer	This class is copied to agave package Simple interface for filtering SAX/StAX startElement events
ElementRecognizer	Simple interface for filtering SAX/StAX startElement events
ElementRecognizer.AllElementRecognizer
ElementRecognizer.AllElementRecognizer
ElementRecognizer.AllElementRecognizer
ElementRecognizer.ByLocalName	Filter elements by local name (not recommended).
ElementRecognizer.ByLocalName	Filter elements by local name (not recommended).
ElementRecognizer.ByLocalName	Filter elements by local name (not recommended).
ElementRecognizer.ByNSName	Filter elements by name and namespace.
ElementRecognizer.ByNSName	Filter elements by name and namespace.
ElementRecognizer.ByNSName	Filter elements by name and namespace.
ElementRecognizer.HasAttribute	Filter elements on the existence of a specified attribute.
ElementRecognizer.HasAttribute	Filter elements on the existence of a specified attribute.
ElementRecognizer.HasAttribute	Filter elements on the existence of a specified attribute.
EllipticalBeadRenderer	EllipticalBeadRenderer renders features as simple ellipses.
Embl
Embl2AgaveAnnotFilter	Map EMBL data into AGAVE format
EmblCDROMIndexReader	EmblCDROMIndexReader is an abstract class whose concrete subclasses read EMBL CD-ROM format indices from an underlying InputStream.
EmblCDROMIndexStore	EmblCDROMIndexStores implement a read-only IndexStore backed by EMBL CD-ROM format binary indices.
EmblCDROMRandomAccess	EmblCDROMRandomAccess is an abstract class whose concrete subclasses can perform fast lookups in EMBL CD-ROM format index files.
EmblFileFormer	Deprecated. Use org.biojavax.bio.seq.io framework instead
EMBLFormat	Format reader for EMBL files.
EMBLFormat.Terms	Implements some EMBL-specific terms.
EmblLikeFormat	Deprecated. Use org.biojavax.bio.seq.io.EMBLFormat instead
EmblLikeLocationParser	Deprecated. Use org.biojavax.bio.seq.io framework instead
EmblProcessor	Deprecated. Use org.biojavax.bio.seq.io framework instead
EmblProcessor.Factory	Factory which wraps SequenceBuilders in an EmblProcessor
EmblReferenceComparator
EMBLxmlFormat	Format reader for EMBLxml files.
EMBLxmlFormat.Terms	Implements some EMBLxml-specific terms.
EmissionCache	Cache for columns of emission probabilities in pair-wise alignment algorithms.
EmissionState	A state in a markov process that has an emission spectrum.
EmptyRichAnnotation	A place holder for a RichAnnotation that prevents null having to be used
EmptyRichLocation	An Empty implementation of RichLocation.
Entity	A simple class to represent Entity records in mmCif files
EntityPolySeq	Container for _entity_poly_seq records
EntryNamIdxReader	EntryNamIdxReader reads the "entrynam.idx" file of an EMBL CD-ROM format binary index.
EntryNamRandomAccess	EntryNamRandomAccess objects provide random access to records within the "entrynam.idx" file of an EMBL CD-ROM format binary index.
Enzyme
ExecRunner	Makes running external executables easier, optionally under a watched thread.
Exptl
ExternalProcess	Utility class to execute an external process and to handle the STDOUT, STDERR and STDIN streams in multiple threads managed by a thread pool.
FastaAlignmentFormat	This class implements the AlignmentFormat interface to read FASTA alignments.
FastaDescriptionLineParser	Deprecated. Use org.biojavax.bio.seq.io.FastaFormat
FastaDescriptionLineParser.Factory	Factory which wraps SequenceBuilders in a FastaDescriptionLineParser
FastaFormat	Deprecated. Use org.biojavax.bio.seq.io.FastaFormat
FastaFormat	Format object representing FASTA files.
FastaHeader	This class is used by FastaFormat to determine which fields are in the fasta header.
FastaSearchSAXParser	FastaSearchSAXParser is a SAX2 compliant parser for '-m 10' format output from the the Fasta search program (see the Fasta documentation for details of this format).
FastaSequenceSAXParser	A SAX2 parser for dealing with multiple sequences in FASTA format.
Fastq	FASTQ formatted sequence.
FastqBuilder	Fluent builder API for creating FASTQ formatted sequences.
FastqReader	Reader for FASTQ formatted sequences.
FastqVariant	FASTQ sequence format variant.
FastqWriter	Writer for FASTQ formatted sequences.
FastXMLWriter	Simple implementation of XMLWriter, optimized for speed.
Feature	A feature within a sequence, or nested within another feature.
Feature.ByLocationComparator	ByLocationComparator compares Features by the minimum base position of their Location.
Feature.Template	Template class for a plain feature.
FeatureBlockSequenceRenderer	FeatureBlockSequenceRenderer forms a bridge between Sequence rendering and Feature rendering.
FeatureFilter	A filter for accepting or rejecting a feature.
FeatureFilter.And	A filter that returns all features accepted by both child filter.
FeatureFilter.AnnotationContains	Retrieve features that contain a given annotation, and that the set of values contains the value given.
FeatureFilter.ByAncestor	Filter by applying a nested FeatureFilter to all ancestor features.
FeatureFilter.ByAnnotation	Retrieve features that contain a given annotation with a given value.
FeatureFilter.ByAnnotationType	A filter that returns all features that have an annotation bundle that is of a given annotation type.
FeatureFilter.ByChild	Filter by applying a nested FeatureFilter to the child features.
FeatureFilter.ByClass	Filter which accepts only those filters which are an instance of a specific Java class
FeatureFilter.ByComponentName	Accepts features which are ComponentFeatures and have a componentSequenceName property of the specified value.
FeatureFilter.ByDescendant	Filter by applying a nested FeatureFilter to all descendant features.
FeatureFilter.ByFeature	Accept only features which are equal to the specified feature
FeatureFilter.ByPairwiseScore	ByPairwiseScore is used to filter SimilarityPairFeatures by their score.
FeatureFilter.ByParent	Filter by applying a nested FeatureFilter to the parent feature.
FeatureFilter.BySequenceName	Accept features that reside on a sequence with a particular name.
FeatureFilter.BySource	Construct one of these to filter features by source.
FeatureFilter.ByType	Construct one of these to filter features by type.
FeatureFilter.ContainedByLocation	A filter that returns all features contained within a location.
FeatureFilter.FrameFilter	Accept features with a given reading frame.
FeatureFilter.HasAnnotation	Retrieve features that contain a given annotation with any value.
FeatureFilter.Not	A filter that returns all features not accepted by a child filter.
FeatureFilter.OnlyChildren	Accepts features where all immediate children meet the supplied filter.
FeatureFilter.OnlyDescendants	Accepts features where all descendants meet the supplied filter.
FeatureFilter.Or	A filter that returns all features accepted by at least one child filter.
FeatureFilter.OverlapsLocation	A filter that returns all features overlapping a location.
FeatureFilter.ShadowContainedByLocation	A filter that accepts all features whose shadow is contained by a specified Location.
FeatureFilter.ShadowOverlapsLocation	A filter that accepts all features whose shadow overlaps a specified Location.
FeatureFilter.StrandFilter	Accept features with a given strandedness.
FeatureHandler	StAX handler for the basic feature type of XFF.
FeatureHolder	The interface for objects that contain features.
FeatureHolder.EmptyFeatureHolder
FeatureHolderUtils	This class intendes to provide some FeatureHolder utilities.
FeatureImpl	Wrap up default sets of Feature implementations.
FeatureLabelRenderer
FeatureLabelRenderer.AnnotationLabelMaker
FeatureLabelRenderer.LabelMaker
FeatureLabelRenderer.SourceLabelMaker
FeatureLabelRenderer.TypeLabelMaker
FeatureRealizer	Interface for translators which map from Feature.Template instances to real Feature objects.
FeatureRenderer
FeatureSource	A closure that allows AbstractPeptideDigestRenderer implementations to obtain the features of the rendered sequence.
FeatureTableParser	Deprecated. Use org.biojavax.bio.seq.io framework instead
FeatureTree	FeatureTree is GUI tree to display the features and annotations of the sequences in a SequenceDB Nested Features are displayed as expandable leaves.
FeatureTypes	Registry of known types of features.
FeatureTypes.Repository	A named collection of Types.
FeatureTypes.RepositoryImpl	A simple implementation of a Repository.
FeatureTypes.Type	A type of feature.
FetchURL
FileAsList	FileAsList creates a writable List implementation backed by a random access file.
FileConvert	Methods to convert a structure object into different file formats.
FilteringContentHandler
FilteringRenderer
FilterTest	Class for implementing tests with BlastLikeSearchFilter objects.
FilterTest.Equals	Tests that the value associated with the specified key is equal to the value supplied here by whatever criterion of equality appropriate to those objects.
FilterTest.FindRegex	Tests that the value associated with the specified key contains a part matched by the supplied regex.
FilterTest.GreaterThan	Tests that the value associated with the specified key is greater than the specified threshold.
FilterTest.LessThan	Tests that the value associated with the specified key is less than the specified threshold.
FilterTest.MatchRegex	Tests that the value associated with the specified key is matched in its entirety by the supplied regex.
FilterTransformer	Base-class for visitors that re-write a filter tree.
FilterUtils	A set of FeatureFilter algebraic operations.
FilterUtils.FilterTransformer	An object able to transform some FeatureFilter instances sytematically into others.
FiniteAlphabet	An alphabet over a finite set of Symbols.
FiniteAutomaton	Class for modelling finite automata.
FitnessFunction	Calculates the fitness of an Organism in a Population of Organisms
FixedBaseWidthScaler	A ChromatogramNonlinearScaler that scales all the base calls in a chromatogram to the same width in pixels, optionally biasing the peak of the call to the center.
FixedSizeCache	Cache which stores up to limit Objects.
FixedSizeMap	A cache that only remembers a given number of keys.
FlatFileInstallation	a PDB installation that reads all files from one directory in the file system.
FlatFileUnigeneFactory	A UnigeneFactory that will use flat-file indexing of the unigene ascii-art files.
FlatSequenceDB	FlatSequenceDB is an OBDA flatfile sequence databank implementation.
FlatSequenceDBProvider	FlatSequenceDBProvider directory-services plugin for flatfile databases.
FlexibleAlignment	FlexibleAlignment is a class which implements UnequalLengthAlignment, ARAlignment and EditableAlignment It places no restriction on where any sequence can be in the alignment so there could be gaps in the alignment.
FloatElementHandlerBase	StAX handler for any element which just contains a string representation of a float.
Format	A file format supported by the tag-value event-based parsing system.
Formats	This is intended as a repository for tag-value and AnnotationType information about common file formats.
FormatTools
FragmentJoiner	Joins the initial Fragments together to larger Fragments
FragmentPair	a pair of fragments of two protein structures
Frame	Title: Frame.
FramedFeature	Title: FramedFeature.
FramedFeature.ReadingFrame	A singleton to hold the frame information
FramedFeature.Template
FullHmmerProfileHMM	This is a class for representing the full HMMER generated Profile HMM (including loop states N and C terminal looping states).
FundamentalAtomicSymbol	An atomic symbol consisting only of itself.
FuzzyLocation	A 'fuzzy' location a-la Embl fuzzy locations.
FuzzyLocation.RangeResolver	Determines how a FuzzyLocation should be treated when used as a normal Location.
FuzzyPointLocation	FuzzyPointLocation represents two types of EMBL-style partially-defined locations.
FuzzyPointLocation.PointResolver	Determines how a FuzzyPointLocation should be treated when used as a normal Location.
GACross	Holds the results of a CrossOver event, objects of this type are made by CrossOverFunctions
GACrossResult	Holds the results of a CrossOver event, objects of this type are made by CrossOverFunctions
GAMEAnnotationHandler	Handles the GAME <annotation> element
GAMEAnnotationHandler	Handles the GAME <annotation> element
GAMEAspectHandler	Handles the GAME <aspect> element
GAMEAspectPropHandler	Handles the GAME <aspect> element
GAMEDbxrefHandler	Handles the GAME <dbxref> element
GAMEDbxrefPropHandler	Deals with database crossreferences
GAMEDescriptionPropHandler	StAX handler for GAME <description> elements.
GAMEFeatureCallbackItf	An interface that can be tested for by nested handlers when trying to do a callback.
GAMEFeatureSetHandler	Handles the <feature_set> element
GAMEFeatureSetHandler	Handles the GAME <feature_set> element this element is used to represent transcripts.
GAMEFeatureSetPropHandler	Handles the GAME element
GAMEFeatureSpanHandler	Handles the <feature_span> element
GAMEFeatureSpanHandler	Handles the GAME <feature_span> element
GAMEFormat	A rudimentary read-only GAME 1.2 Format object.
GAMEGeneHandler	Handles the GAME <annotation> element
GAMEGenePropHandler	Handles the GAME <gene> element
GAMEHandler	Handles the root GAME element
GAMEHandler	Handles the root GAME element
GAMEMapPosPropHandler	Handles the GAME <map_position> element Currently, it just ignores it!
GAMENameCallbackItf	An interface that can be tested for by nested handlers when trying to do a callback.
GAMENamePropHandler	StAX handler for the GAME <name> element.
GAMEPropertyHandler	Handles the GAME <dbxref> element
GAMEResiduesPropHandler	StAX handler for GAME <residues> elements.
GAMESeqHandler	Handles the GAME <seq> element
GAMESeqPropHandler	Handles the GAME <seq> element
GAMESeqRelHandler	Handles the GAME <> element
GAMESeqRelPropHandler	Handles the GAME <aspect> element
GAMESpanHandler	Handles the GAME <> element.
GAMESpanPropHandler	Handles the GAME <span> element Currently, it just ignores it!
GAMETranscriptCallbackItf	An interface that can be tested for by nested handlers when trying to do a callback.
GAMETypePropHandler	StAX handler for GAME <type> elements.
GapArray
GapDistribution	This distribution emits gap symbols.
GappedRenderer	A renderer that will display a gapped sequence as a discontinuous series of regions.
GappedSequence	Extension of GappedSymbolList which also projects features into the gapped coordinate system.
GappedSymbolList	This extends SymbolList with API for manipulating, inserting and deleting gaps.
GAStoppingCriteria	Used by a GeneticAlgorithm.run() method to determine when the algorithm should stop
GAStoppingCriteria.MaximumGeneration	Simple Implementation of GAStoppingCriteria, signals a GeneticAlgorithm to stop after n generations
GATools	Utility methods for the GA library
GenbankFileFormer	Deprecated. Use org.biojavax.bio.seq.io framework instead
GenbankFormat	Deprecated. Use org.biojavax.bio.seq.io.GenbankFormat
GenbankFormat	Format reader for GenBank files.
GenbankFormat.Terms	Implements some GenBank-specific terms.
GenbankLocationParser	Parses Genbank location strings into RichLocation objects.
GenbankProcessor	Deprecated. Use org.biojavax.bio.seq.io framework instead
GenbankProcessor.Factory	Factory which wraps sequence builders in a GenbankProcessor
GenbankRichSequenceDB	This class contains functions accessing DNA sequences in Genbank format.
GenbankSequenceDB	This class contains functions accessing DNA sequences in Genbank format.
GenbankXmlFormat	Deprecated. Use org.biojavax.bio.seq.io.INSDseqFormat
GenEmblFeatureComparator	Deprecated. Use org.biojavax.bio.seq.io framework instead
GenEmblPropertyComparator	Deprecated. Use org.biojavax.bio.seq.io framework instead
GeneticAlgorithm	The class that runs the cycles of reproduction, evolution and selection, potentially on multiple Populations
GeneticCodes	Collects the references to translation methods in one place.
GenpeptFormat	Deprecated. Use org.biojavax.bio.seq.io framework instead
GenpeptRichSequenceDB	This class contains functions accessing Peptide sequences in Genpept format.
GenpeptSequenceDB
GFF3DocumentHandler	The interface for things that listen to GFF event streams.
GFF3Parser	Parse a stream of GFF text into a stream of records and comments.
GFF3Record	A record in a GFF3 formatted file.
GFF3Record.Impl
GFFDataSource	Use a GFFEntrySet as a DataSource for adding annotation to sequences.
GFFDocumentHandler	The interface for things that listen to GFF event streams.
GFFEntrySet	A set of entries and comments as a representation of a GFF file.
GFFErrorHandler	Interface which captures any errors which occur when parsing a GFF stream.
GFFErrorHandler.AbortErrorHandler
GFFErrorHandler.SkipRecordErrorHandler
GFFFilterer	An object that filters a stream of GFF, forwarding some GFFRecords to a listening GFFDocumentHandler, and dropping others.
GFFParser	Parse a stream of GFF text into a stream of records and comments.
GFFRecord	A single GFF record.
GFFRecordFilter	A filter that will accept or reject a GFFEntry.
GFFRecordFilter.AcceptAll	Implementation of GFFRecordFilter that accepts everything.
GFFRecordFilter.FeatureFilter	Implementation of GFFRecordFilter that accepts records based upon the feature field.
GFFRecordFilter.FrameFilter
GFFRecordFilter.NotFilter
GFFRecordFilter.SequenceFilter	Implementation of GFFRecordFilter that accepts records based upon the sequence name.
GFFRecordFilter.SourceFilter	Implementation of GFFRecordFilter that accepts records based upon the source field.
GFFRecordFilter.StrandFilter
GFFTools
GFFWriter	Listens to a stream of GFF events and writes the lines to a PrintWriter.
Glyph	The Glyph interface for painting a shape within bounds
GlyphFeatureRenderer	A FeatureRenderer that renders a particular Glyph for Features accepted by a particular FeatureFilter
GlyphUtils	Utils class used by Glyph implementors.
GOParser	Simple parser for the Gene Ontology (GO) flatfile format.
Gotoh	a class to perform Gotoh algorithm
Group	This is the data structure for a single Group of atoms.
GroupIterator	An iterator over all groups of a structure.
GroupType	contains only the static declaration of which types of Groups are available
GUITools
HashBioEntryDB	An implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects.
HashedFastaIterator	Iterates over a Fasta file that is kept in memory for optimized access.
HashRichSequenceDB	An implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects.
HashSequenceDB	An implementation of SequenceDB that uses an underlying HashMap to store the sequence objects.
HeaderStAXHandler	HeaderStAXHandler handles the Header element of BioJava BlastLike XML.
HeadlessRenderContext	A stand-alone SequenceRenderContext to make it easy to render to an image.
HelixGlyph	A Glyph that paints a Helix within the bounds
HetatomImpl	Generic Implementation of a Group interface.
HitMerger	A listener that merges overlapping hits and culls all hits under a given length.
HitStAXHandler	AlignmentStAXHandler handles the Hit element of BioJava BlastLike XML.
HmmerProfileHMM	This is a class for representing HMMER generated Profile HMM.
HmmerProfileParser	A class for parsing in Hmmer markov models from HMM_ls files generated by HMMER training note that this class is still currently experimental.
HMMTrainer	interface implemented by objects that train HMMs.
HomologeneBuilder	an interface for Homologene dataset Builders
HomologeneDB	Homologene is a NCBI dataset that curates sets of orthologues from the reference model organisms.
HomologeneTools	Homologene is a NCBI dataset that curates sets of orthologues from the reference model ogranisms.
Homology	Signifies that two or more features are homologous.
HomologyDB
HomologyFeature
HomologyFeature.Template
HSPStAXHandler	HSPStAXHandler handles the HSP element of BioJava BlastLike XML.
HSPSummaryStAXHandler	HSPSummaryStAXHandler handles the HSPSummary element of BioJava BlastLike XML.
HTMLRenderer	Renders HTML version of blast-like output.
HypersonicDBHelper	Deprecated. Use hibernate and org.biojavax.bio.db.*
Identifiable	Marks an implementor as having a LifeScienceIdentifier.
IDMaker	Interface for objects that define how to make an ID for a sequence.
IDMaker.ByName
IDMaker.ByURN
IgnoreCountsTrainer	A distribution trainer that just ignores all counts.
IgnoreRecordException	Ignore this record in the stream.
IllegalAlignmentEditException	The usual reason for throwing an IllegalAlignmentEditException is that you are trying to shift a group of bases in such a way that it would require deleting bases.
IllegalAlphabetException	The exception to indicate that an invalid alphabet has been used.
IllegalIDException
IllegalOrganismException	Indicates an invalid organism
IllegalSymbolException	The exception to indicate that a symbol is not valid within a context.
IllegalTransitionException	This exception indicates that there is no transition between two states.
IlluminaFastqReader	Reader for FastqVariant.FASTQ_ILLUMINA formatted sequences.
IlluminaFastqWriter	Writer for FastqVariant.FASTQ_ILLUMINA formatted sequences.
ImageMap	ImageMap represents a collection of image map hotspots.
ImageMap.ClientSide	ClientSide represents a client-side style image map.
ImageMap.HotSpot	HotSpots represent an image map hotspot.
ImageMap.ServerSide	ServerSide represents a server-side style image map.
ImageMapRenderer	ImageMapRenderers create strings representing Features suitable for use in HTML image maps.
Index	This defines an index entry for an individual sequence within a set of indexed files.
Index2Model
IndexedAnnotationDB	A database of Annotation instances backed by an indexed file set.
IndexedAnnotationDB.ParserListenerFactory	A factory for retrieving parsers and listeners.
IndexedAnnotationDB.StaticMethodRPFactory	An implementation of ParserListenerFactory that uses a static method.
IndexedChangeHub	implements Changeable support with a ChangeHub that stores ChangeListener by key.
IndexedCount	An encapsulation of a count over the Symbols within a FiniteAlphabet using an AlphabetIndex object.
IndexedSequenceDB	This class implements SequenceDB on top of a set of sequence files and sequence offsets within these files.
Indexer	Listens to tag-value events and passes on indexing events to an IndexStore.
Indexer2	Listens to tag-value events and passes on indexing events to an IndexStore.
IndexPair
IndexStore	IndexStore is an interface for indexing flatfiles according to the OBDA specification.
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.
IndexTools	IndexTools contains static utility methods for creating flatfile indices according to the OBDA standard.
InfinitelyAmbiguousSymbolList	A symbol list that is Integer.MAX_VALUElong, never gives index out of bounds and always returns ambiguity symbols for everything.
Initializable
InputHandler	Interface to a threadable input handler for an external process.
InputStreamProvider	A class that provides an InputStream from a File.
INSDseqFormat	Format reader for INSDseq files.
INSDseqFormat.Terms	Implements some INSDseq-specific terms.
IntegerAlphabet	An efficient implementation of an Alphabet over the infinite set of integer values.
IntegerAlphabet.IntegerSymbol	A single int value.
IntegerAlphabet.SubIntegerAlphabet	A class to represent a finite contiguous subset of the infinite IntegerAlphabet
IntegerOntology
IntegerTokenization
IntElementHandlerBase	StAX handler for any element which just contains a string representation of an integer.
InvalidTermException	Thrown to indicate that an ontology term is not acceptable or appropriate in a given context
IsoelectricPointCalc	Class that computes isoelectric point for denaturated proteins.
ItemValue	A simple Object-double tuple.
JDBCConnectionPool	Really simple connection pool for JDBC databases.
JDBCPooledDataSource	Returns a DataSource that implements connection pooling Uses Jakarta Commons DBCP and Pool packages.
JMatrixPanel	a JPanel that can display a difference of distance matrix and paths that have been taken for the alignment
JmolAlignedPositionListener
JointFragments	A utility class that defines which set of atoms are considered to be on equivalent positions.
JournalArticle	PDB-specific
KeyedWeakReference	Subclass of WeakReference which includes and extra field (the key) which can be used to help cleanup once this reference has been enqueued.
KnuthMorrisPrattSearch	An object to find exact subsequences within a sequence.
LabelledSequenceRenderer	Renderer which draws a track of sequence with a textual label.
LabelRenderer	The interface for things that can render labels for a line of information about a sequence.
LabelRenderer.RenderNothing
LargeBuffer	Wrapper arround MappedByteBuffers to allow long-indexed access to files larger than 2 gigs.
LayeredRenderer	LayeredRenderer handles the lane offsets for MultiLineRenders.
LazyFeatureHolder	Wrapper implementation of FeatureHolder which calls a method to create a contained FeatureHolder on demand.
LazyFilteredAnnotationDB	An implementation of AnnotationDB that lazily applies a filter.
LazyFilterFeatureHolder	FeatureHolder which lazily applies a specified filter to another FeatureHolder.
LazySearchedAnnotationDB	An implementation of AnnotationDB that does a JIT search on another set.
LifeScienceIdentifier	Life Science Identifier (LSID).
LifeScienceIdentifierParseException	Exception thrown in the event of an error in parsing a LSID-formatted string.
Ligand
Ligand.Compound
Ligand.Enzyme
Ligand.Reaction
LightPairDPCursor	A LIGHT implementation of PairDPCursor.
LinearKernel	Deprecated. Just use SparseVector.kernel instead...
LineInfo	Encapsulates the rendering info for a single line of the display.
LineSplitParser	A parser that splits a line into tag/value at a given column number.
ListSumKernel	This kernel computes the sum of the dot products between items of two lists at corresponding indexes.
ListTools
ListTools.Doublet
ListTools.Mapper	Maps one object to another.
ListTools.SeriesList	A list that represents a series of values.
ListTools.Triplet
Location	A set of integers, often used to represent positions on biological sequences.
LocationHandlerBase	Handler to the XFF location type.
LocationTools	Tools class containing a number of operators for working with Location objects.
LogoContext
LogoPainter	The interface for something that will draw the sequence logo for a state.
LongElementHandlerBase	StAX handler for any element which just contains a string representation of a long.
LUDecomposition	LU Decomposition.
MagicalState	Start/end state for HMMs.
ManyToOneTranslationTable	A translation table that will handle the many-to-one mappings that you see, for example, with genetic codes.
MappedDataStoreFactory	Builder for a data store that is backed by a java.nio.MappedByteBuffer.
MarkovModel	A markov model.
MassCalc	MassCalc calculates the mass of peptides which for our purposes are SymbolLists which contain Symbolsfrom the protein Alphabet.
Matcher	This class is analogous to java.util.Matcher except that it works on SymbolLists instead of Strings.
Maths
Matrix	Jama = Java Matrix class.
MatrixPairDPCursor
MaxMismatchMatcher	A BioMatcher class returned by MaxMismatchPattern.matcher() that implements searching of a SymbolList.
MaxMismatchPattern	This class permits searching a SymbolList with another SymbolList while permitting a specified number of mismatches.
Meme	The results of a meme run.
MenuCreator	Create the menu for BiojavaJmol
MergeAnnotation	Merged view onto a list of underlying Annotation objects.
MergeFeatureHolder	FeatureHolder which exposes all the features in a set of sub-FeatureHolders.
MergeLocation	Produced by LocationTools as a result of union operations.
MergingAnnotationDB	An AnnotationDB that provides a merged view of a list of underlying DBs.
MergingIterator
MergingSet
MMcifConsumer	An interface for the events triggered by a MMcifParser.
MMCIFFileInstallation
MMCIFFileReader	How to parse an mmCif file:
MMcifParser	Interface that needs to be implemented by an MMcifParser
ModelInState	A state that contains an entire sub-model.
ModelTrainer	Encapsulates the training of an entire model.
MotifTools	MotifTools contains utility methods for sequence motifs.
MSFAlignmentFormat
MultiLineRenderer	MultiLineRenderer is a SequenceRenderer which collects a number of other SequenceRenderers each of which render their own view of a Sequence.
MultipleHitCorrection
MultiSourceCompoundRichLocation	An implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences.
MultiTagger	Partician multiple values for a tag into their own tag groups.
MutationFunction	A class that mutates a SymbolList
MutationFunction.NoMutation	Place Holder class that doesn't mutate its SymbolLists
Mutator	A class that can change one amino acid to another.
MySQLDBHelper	Deprecated. Use hibernate and org.biojavax.bio.db.*
Namespace	The namespace of an entry in a database schema.
NameTokenization	Simple implementation of SymbolTokenization which uses the `name' field of the symbols.
NcbiDatabaseURLGenerator	Simple URL generator for Entrez at the NCBI.
NCBISequenceDB
NCBITaxon	Represents an NCBI Taxon entry, a combination of the taxon and taxon_name tables in BioSQL.
NCBITaxonomyLoader	Implementors are able to load taxonomy files and generate sets of NCBITaxon objects that represent them.
NeedlemanWunsch	Needleman and Wunsch defined the problem of global sequence alignments, from the first till the last symbol of a sequence.
NestedKernel	Encapsulates a kernel that wraps another kernel up.
NewAssembledSymbolList	Support class for applications which need to patch together sections of sequence into a single SymbolList.
NewSimpleAssembly	A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
Nfa	Class for modelling non-deterministic finite automata.
NfaBuilder
NfaSubModel	This class caches a reference to all objects that it directs its delegate to make.
NIODataStoreFactory	Builder for a datastore that has no practical file size limit.
NormalizingKernel	Performs a normalization on the results of a nested kernel.
Note	Note is a generic class intended to hold a term describing the note, a value to associate with that term, and a rank.
NucleotideImpl	A nucleotide group is almost the same as a Hetatm group.
NucleotideTools	Useful functionality for processing nucleotide sequences.
ObdaContext
ObdaInitialContextFactory
OBDARegistryParser	This class encapsulates all the parsing of the OBDA registry configuration file.
ObdaUriParser	Singleton class for parsers that understand OBDA URIs.
ObjectUtil	utility methods for implementing the equals() and hashCode() methods of Objects.
OboFileEventListener	an interface for events that occur during parsing of .obo files
OboFileHandler	A file handler for .obo files
OboFileParser	A class to parse the content of an OBO file.
OboFileParser.SOPair
OboParser	Parses an OBO file.
OffsetRulerRenderer	OffsetRulerRenderer can render the ruler starting from an arbitrary offset from the sequence.
Ontology	An ontology.
Ontology.Impl	A basic in-memory implementation of an ontology
OntologyException	Thrown to indicate an error in an Ontology object
OntologyFactory	A factory for Ontology instances.
OntologyOps	This is an interface for optimizing ontology operators.
OntologyTerm	A term in an ontology which identifies another ontology.
OntologyTerm.Impl	Simple in-memory implementation of a remote ontology term.
OntoTools	Tools for manipulating ontologies.
OptimizableFilter	The interface for filters that can potentialy optimize themselves, and compare themselves with other filters.
OracleDBHelper	Deprecated. Use hibernate and org.biojavax.bio.db.*
OrderCrossover	This does a 2-point-crossover on two chromosomes keeping the Symbols in each chromosome constant.
OrderNDistribution	Provides an N'th order distribution.
OrderNDistributionFactory	Default factory for Order-N distributions.
Organism	A GA 'organism' contains one or more Chromosomes
OrganismParser	Deprecated. Use org.biojavax.bio.taxa framework instead
OrganismParser.Factory	Factory which wraps SequenceBuilders in an OrganismParser.
Orthologue	this entry contains data about the orthologue.
OrthologueFilter
OrthologueFilter.AcceptAll
OrthologueFilter.And
OrthologueFilter.ByAccession
OrthologueFilter.ByHomologeneID
OrthologueFilter.ByLocusID
OrthologueFilter.ByTaxon
OrthologueFilter.ByTaxonID
OrthologueFilter.ByTitle
OrthologueFilter.Not
OrthologueFilter.Or
OrthologueFilter.Xor
OrthologueSet	Interface for classes that store and manipulate orthologues.
OrthologueSet.Iterator	An iterator for the contents of an OrthologueSet.
OrthoPair	Each HomologeneEntry represents a single Homologene record that relates two presumptive orthologues.
OrthoPairCollection	Interface for a Set of OrthoPairSets
OrthoPairCollection.Iterator	Iterator for a OrthoPairCollection
OrthoPairFilter
OrthoPairFilter.AcceptAll
OrthoPairFilter.And
OrthoPairFilter.ByMaxIdentity
OrthoPairFilter.ByMinIdentity
OrthoPairFilter.ByRef
OrthoPairFilter.BySimilarityType
OrthoPairFilter.Not
OrthoPairFilter.Or
OrthoPairFilter.Xor
OrthoPairSet	represents the Homologene Group.
OrthoPairSet.Iterator
OrthoPairSetFilter
OrthoPairSetFilter.AcceptAll
OrthoPairSetFilter.AllPairsInCollection	all OrthoPairs must meet the requirement defined by filter.
OrthoPairSetFilter.And
OrthoPairSetFilter.ByMinIdentity
OrthoPairSetFilter.ByTaxon
OrthoPairSetFilter.Not
OrthoPairSetFilter.Or
OrthoPairSetFilter.SomePairsInCollection	at least one OrthoPair must meet the requirement defined by filter.
OrthoPairSetFilter.Xor
OutputHandler	Interface to a threadable output handler for an external process.
OverlayAnnotation	Annotation implementation which allows new key-value pairs to be layered on top of an underlying Annotation.
OverlayMap	Overlap one map onto another.
OverlayMarker	This is a dummy interface to permit identification of renderers whose output is to be overlaid along the lines of the Marker Interface pattern.
OverlayRendererWrapper	This class wraps SequenceRenderer classes to present an Overlay Marker interface that will indicate to LayeredRenderer that subsequent renderers should overdraw the same space as the wrapped renderer.
PackedSymbolList	A SymbolList that stores symbols as bit-patterns in an array of longs.
PackedSymbolListFactory	This class makes PackedSymbolLists.
Packing	An encapsulation of the way symbols map to bit-patterns.
PackingFactory	A factory that is used to maintain associations between alphabets and preferred bit-packings for them.
PaddingRenderer	A renderer that adds padding before and after a delegate renderer.
PairDistribution	Class for pairing up two independant distributions.
PairDPCursor	A cursor over a DP matrix.
PairDPMatrix	Storage structure for intermediate values from a pairwise dynamic programming run.
PairwiseDiagonalRenderer	PairwiseDiagonalRenderer renders a region of similarity between two sequences as a straight line.
PairwiseDP	Algorithms for dynamic programming (alignments) between pairs of SymbolLists.
PairwiseFilteringRenderer	PairwiseFilteringRenderer wraps a PairwiseSequenceRenderer and filters the PairwiseRenderContexts passed to it.
PairwiseOverlayRenderer	PairwiseOverlayRenderer allows a list of other PairwiseSequenceRenderers to superimpose their output.
PairwiseRenderContext	PairwiseRenderContext encapsulates information required for the rendering of a pair of sequences.
PairwiseSequencePanel	A PairwiseSequencePanel is a panel that displays a pair of sequences; one sequence (the primary) may be either left-to-right (HORIZONTAL) or from top-to-bottom (VERTICAL).
PairwiseSequenceRenderer	PairwiseSequenceRenderers render information about the relationship between two sequences.
PairwiseSequenceRenderer.PairwiseRendererForwarder	PairwiseRendererForwarder forward events to other renderers.
ParseErrorEvent	Event which signals a bad line when parsing a record.
ParseErrorListener	Listener for a ParseErrorEvent.
ParseErrorSource	Source for a ParseErrorEvent.
ParseException	ParseException should be thrown to indicate that there was a problem with parsing sequence information.
Parser	Encapsulate the parsing of lines from a buffered reader into tag-value events.
ParserException	Exception thrown when an error occurs in document parsing.
ParserListener	ParserListener is an immutable pairing of a parser and listener.
Pattern	A class analogous to java.util.regex.Pattern but for SymbolLists.
PatternBlitz
PatternFactory	A class that creates Patterns for regex matching on SymbolLists of a specific Alphabet.
PatternListener
PatternMaker
PDBDirPanel	A class to define where a structure for the alignment is coming from
PDBFileParser	This class implements the actual PDB file parsing.
PDBFileReader	The wrapper class for parsing a PDB file.
PDBFilter	defines how a filter of PDB files has to behave
PDBHeader	A class that contains PDB Header information.
PDBInstallation	an interface that defines different access methods to PDB installations.
PDBMSDReader	retreive a structure from an installation of the MSD - search database ( http://www.ebi.ac.uk/msd/index.html , http://www.ebi.ac.uk/msd-srv/docs/dbdoc/ )
PDBParseException	An exception during the parsing of a PDB file.
PDBRecord	An interface implemented by all classes that represent PDB records
PdbSAXParser	A SAX2 parser for dealing with native PDB files.
PDBServerPanel	A class to define where a structure for the alignment is coming from
PDBSRSReader	reads a PDB file from a local SRS installation using getz Actually is the same as PDBFileReader, but instead of reading from a file stream, reads from a buffered stream.
PdbToXMLConverter	A class that converts Protein Data Bank (PDB) to XML that will validate against the biojava:MacromolecularStructure DTD.
PDBUploadPanel	A JPanel to upload 2 PDB files.
PdbxEntityNonPoly	A bean for the Pdbx_entity_nonpoly category.
PdbxNonPolyScheme	A bean for the PDBX_NONPOLY_SCHEME category, which provides residue level nomenclature mapping for non-polymer entities.
PdbxPolySeqScheme	A bean for the PDBX_POLY_SEQ_SCHEME category, which provides residue level nomenclature mapping for polymer entities.
PeptideDigestRenderer	A concrete AbstractPeptideDigestRenderer.
PhredFormat	Format object representing Phred Quality files.
PhredSequence	PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores.
PhredTools	PhredTools contains static methods for working with phred quality data.
PHYLIPFileBuilder	Builds a PHYLIP file by listening to events.
PHYLIPFileFormat	Reads PHYLIP interleaved alignment files and fires events at a PHYLIPFileListener object.
PHYLIPFileListener	Listens to events fired by the PHYLIP parser.
PlainBlock	A painter that just draws a block (or bar).
PlainStyle	A simple implementation of SymbolStyle that just uses a single paint for outlines and a single paint for filling.
PointLocation	A location representing a single point.
PolymerType	Enumerates the classification of polymers.
PolynomialKernel	This kernel computes all possible products of order features in feature space.
Population	A collection of GA organisms
Position	Holds info about base positions.
PositionResolver	Resolves a position that is fuzzy or covers a range of bases by converting it to a single base.
PositionResolver.AverageResolver	The minimal resolver returns the base which provides the average range, halfway between maximal and minimal.
PositionResolver.MaximalResolver	The maximal resolver returns the base which provides the largest possible range.
PositionResolver.MinimalResolver	The minimal resolver returns the base which provides the smallest possible range.
PostgreSQLDBHelper
PrepareIndexFile
PrepareMMcifIndexFile	A class to index all files in a PDB installation
PrettyXMLWriter	Implementation of XMLWriter which emits nicely formatted documents to a PrintWriter.
ProcessTimeoutException	Exception which is thrown if a child process managed by ProcessTools exceeds a specified time limit.
ProcessTools	Deprecated. preferable to use org.biojava.utils.ExecRunner or the org.biojava.utils.process package.
ProfileEmissionState	A state in a HMMer model.
ProfileHMM
ProjectedFeature	Internal class used by ProjectionEngine to wrap Feature objects.
ProjectedFeatureHolder	Helper class for projecting Feature objects into an alternative coordinate system.
Projection	Interface implemented by all projected feature objects.
ProjectionContext	Interface that defines the projection between original features and projected features.
ProjectionEngine	Factory for proxy objects which project BioJava features into alternate coordinate systems.
ProjectionEngine.Instantiator	Internal helper class.
ProjectionEngine.TemplateProjector	This is an interface for things that project feature templates.
ProjectionUtils	Some common things you want to do while projecting features.
PropDetailHandler	StAX handler for xff:prop detail elements.
PropertyChanger	Interface for objects that change tag names or properties systematically.
PropertyConstraint	PropertyConstraints describes a constraint applied to the members of an annotation bundle.
PropertyConstraint.And	A property constraint that accpepts items iff they are accepted by both child constraints.
PropertyConstraint.ByAnnotationType	ByAnnotationType accepts a property value if it belongs to type defined by AnnotationType.
PropertyConstraint.ByClass	ByClass accepts a property value if it is an instance of a specific Java class.
PropertyConstraint.Enumeration	Enumeration accepts a property if it is present in the specified set of values.
PropertyConstraint.ExactValue	Matches properties if they have exactly this one value.
PropertyConstraint.Or	A property constraint that accepts items iff they are accepted by either child constraints.
PropertyWriter
ProportionalSelection	A Selection function that determines the proportion of individuals in a new population proportionally to their fitness.
Protease	The protease class stores parameters needed by Digest to digest a protein sequence.
ProteaseManager	Registry and utility methods for Proteases.
ProteinRefSeqFileFormer	Deprecated. Use org.biojavax.bio.seq.io framework instead
ProteinRefSeqProcessor	Deprecated. Use org.biojavax.bio.seq.io framework instead
ProteinRefSeqProcessor.Factory	Factory which wraps sequence builders in a ProteinRefSeqProcessor
ProteinTools	The central port-of-call for all information and functionality specific to SymbolLists over the protein alphabet.
ProviderNotFoundException	ProviderNotFoundException is thrown when a sequence database provider can not be located.
QRDecomposition	QR Decomposition.
Qualitative	Qualitative is an interface for classes wanting to hold quality data in symbolic form such as Phred scores.
QualitativeAlignment
RadialBaseKernel	This kernel computes the radial base kernel that corresponds to a gausian distribution.
RAF
RandomAccessReader	RandomAccessReader extends Reader to provide a means to create buffered Readers from RandomAccessFiles.
RangeLocation	A simple implementation of Location that contains all points between getMin and getMax inclusive.
RankedCrossRef	Allows cross-references to other databases to be ranked.
RankedCrossRefable	Defines an object as being able to have ranked cross references associated with it.
RankedDocRef	Represents a documentary reference.
RasmolCommandListener	a utility class that listens to Ramsol script commands in the @link BiojavaJmol class
ReaderInputHandler	Reader input handler that reads the input for an external process from a reader.
ReaderWriterPipe	A multi threaded class which pipes the contents of an input reader to an output writer.
RealizingFeatureHolder	Interface for FeatureHolder objects which know how to instantiate new child Features.
Record	Record represents a record within an indexed flat file databank as defined by the OBDA standard.
Record.Impl	Impl is the default implementation of Record.
RectangleGlyph	A Glyph that paints a rectangle shape within the bounds.
RectangularBeadRenderer	RectangularBeadRenderer renders features as simple rectangles.
RectangularImapRenderer	RectangularImapRenderer is a decorator for RectangularBeadRenderer which adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by the RectangularBeadRenderer.
ReferenceAnnotation	Deprecated. Use org.biojavax.bio.seq.io framework instead
ReferenceServer	Reflects a reference server on the DAS network.
Refine
RegexChanger	A ValueChanger.Changer that returns a specific match value using a regex Pattern.
RegexException	An exception thrown by classes of this package.
RegexFieldFinder
RegexParser	A TagValueParser that splits a line based upon a regular expression.
RegexSplitter	A ValueChanger.Splitter that splits a line of text using a regular expression, returning one value per match.
Registry	Registry is a factory which gets implementations of the BioJava SequenceDBLite interface.
RegistryConfiguration	The BioDirectory Registry is a simple system for specifying where to find services which provide sequence databases.
RegistryConfiguration.Composite	A RegistryConfiguration that allows you to treat other configurations as providing important or default configuration information.
RegistryConfiguration.Impl	A simple implementation of RegistryConfiguration backed by a Map.
RegistryException	A RegistryException thrown when the registry cannot find an implementation of a requested SequenceDB.
RelabeledAlignment	An alignment that relabels another alignment.
RemoteFeature	A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.
RemoteFeature.Region	A tuple of Location and sequence ID.
RemoteFeature.Resolver	The interface for objects that actually can take a RemoteFeature and return a Sequence object with the feature resolved into a real feature.
RemoteFeature.Template
RemoteTerm	A term in another ontology.
RemoteTerm.Impl	Simple in-memory implementation of a remote ontology term.
ReparentContext	A good base class to implement ProjectionContext from.
RepeatedCharSequence
ResidueType	Enumerates the possible classifications of residues.
ResourceEntityResolver	SAX EntityResolve which looks up system IDs as resources from a Java ClassLoader.
RestrictionEnzyme	RestrictionEnzyme represents a restriction enzyme according to the REBASE standard.
RestrictionEnzymeManager	RestrictionEnzymeManager manages collections of static RestrictionEnzyme instances.
RestrictionMapper	RestrictionMapper is a class for annotating Sequences with Features which represent restriction sites.
RestrictionSite	RestrictionSite represents the recognition site of a restriction enzyme.
RestrictionSite.Template	Template for construction of RestrictionSites.
RevCompSequence	A reverse complement view onto Sequence interface.
ReversibleTranslationTable	A translation table that can also translate from the target to source alphabet.
RichAnnotatable	Annotatable objects that can have rich annotations.
RichAnnotation	An annotation collection which stores annotations as Note objects.
RichFeature	Represents a feature that can be given name and rank and be moved from one sequence to another.
RichFeature.Template	Added-value extension of Feature.Template including bits we're interested in, eg.
RichFeature.Tools	Some useful tools for working with features.
RichFeatureRelationship	Represents the relation between two features.
RichFeatureRelationshipHolder	Holds feature relationships.
RichLocation	Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.
RichLocation.Strand	This class represents a strand on which a location may lie.
RichLocation.Tools	Some useful tools for working with Locations.
RichObjectBuilder	This interface allows a class to generate Rich objects based on a class name and some parameters.
RichObjectFactory	Runs a service that builds rich objects, and provides some default values for things like default ontology, default namespace, etc.
RichSeqIOAdapter	This class implements all methods of RichSeqIOListener and takes no action.
RichSeqIOListener	An interface for classes that listen to BioEntry or RichSequence I/O streams.
RichSequence	A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.
RichSequence.IOTools	A set of convenience methods for handling common file formats.
RichSequence.IOTools.SingleRichSeqIterator	Used to iterate over a single rich sequence
RichSequence.Terms	Stores a number of useful terms used across many sequence formats for consistency's sake.
RichSequence.Tools	Some useful tools for working with RichSequence objects.
RichSequenceBuilder	An interface for objects that can build RichSequences.
RichSequenceBuilderFactory	Simple factory for constructing new RichSequenceBuilder objects.
RichSequenceDB	A database of RichSequences with accessible keys and iterators over all sequences.
RichSequenceDBLite	A database of RichSequences.
RichSequenceFormat	Allows a file format to be read/written as RichSequences.
RichSequenceFormat.BasicFormat	Provides a basic format with simple things like line-widths precoded.
RichSequenceFormat.HeaderlessFormat	Provides the basic implementation required for simple header/footer-less files such as Genbank.
RichSequenceHandler	An interface for classes that know how to handle subsequence operations.
RichSequenceIterator	Essentially the same as SequenceIterator.
RichStreamReader	Parses a stream into sequences.
RichStreamWriter	Writes all of the sequences from a SequenceIterator to a stream with a particular format.
RNATools	Useful functionality for processing DNA and RNA sequences.
RoundRectangularBeadRenderer	RoundRectangularBeadRenderer renders features as rectangles with rounded corners.
RulerRenderer	RulerRenderer renders numerical scales in sequence coordinates.
SangerFastqReader	Reader for FastqVariant.FASTQ_SANGER formatted sequences.
SangerFastqWriter	Writer for FastqVariant.FASTQ_SANGER formatted sequences.
SAX2StAXAdaptor	Lightweight adaptor which translates SAX content events into StAX form, and provides delegation services.
SAX2StAXAdaptor	Lightweight adaptor which translates SAX content events into StAX form, and provides delegation services.
ScaleableMatrixPanel	A JPanel that can display the underlying distance matrix data of the protein structure alignment algorithm.
SCF	A Chromatogram as loaded from an SCF v2 or v3 file.
ScoreType	This class computes the score that is used to be used in a DP optimisation.
ScoreType.NullModel	In this class, calculateScore returns the probability of a Symbol being emitted by the null model.
ScoreType.Odds	In this class, calculateScore returns the odds ratio of a symbol being emitted.
ScoreType.Probability	In this class, calculateScore returns the probability of a Symbol being emitted.
Search	A utility class to make searching a Sequence with many regex patterns easier.
Search.Listener	Interface for a class that will recieve match information from this class.
SearchBuilder	The SearchBuilder interface is to be used by objects which accumulate state via a SearchContentHandler and then construct a SeqSimilaritySearchResult object.
SearchContentAdapter	An adapter for SearchContentHandler.
SearchContentFilter	Filtering implementation of SearchContentHandler that by default passes all messages on to the next delegate in the chain.
SearchContentHandler	SearchContentHandler is a notification interface for objects which listen to search stream parsers.
SearchContentHandlerDebugger	This class prints to a PrintStream calls to the SearchContentHandler interface in human readable form.
SearchException	There has been some failure that prevents a search from completing.
SearchListener	The interface used to inform interested parties that some sequence has been searched and something found.
SearchListener.Echo	A SearchListener that prints events out to a PrintStream.
SearchListener.FilterByLength	A simple listener that filters out all hits that are too short.
SearchListener.Tee	A SearchListener that passes events on to two delegate listeners.
SearchListener.Wrapper	A simple wrapper implementation.
SecondaryStructureFeatureRenderer	A GlyphRenderer subclass that specificatlly handles Features pertaining to Secondary Structure (Helices, Turns and Strands).
Seekable	This interface provides a collective name for IO classes that implement a seek function (e.g., RandomAccessFile).
SelectionFunction	Selects Organisms for Replication and returns the offspring.
SelectionFunction.SelectAll
SelectionFunction.Threshold	Selects individuals who's fitness exceeds a threshold value.
SeqContentPattern	A pattern that can be used to find regions with given sequence content.
SeqFileFormer	Deprecated. Use org.biojavax.bio.seq.io framework instead
SeqIOAdapter	Adapter class for SeqIOListener that has empty methods.
SeqIOConstants	SeqIOConstants contains constants used to identify sequence formats, alphabets etc, in the context of reading and writing sequences.
SeqIOEventEmitter	Deprecated. Use org.biojavax.bio.seq.io framework instead
SeqIOFilter	Base-class for listeners that pass filtered events onto another listener.
SeqIOListener	Notification interface for objects which listen to a sequence stream parser.
SeqIOTools	Deprecated. use org.biojavax.bio.seq.RichSequence.IOTools
SeqRes2AtomAligner	Aligns the SEQRES residues to the ATOM residues.
SeqSimilarityAdapter	A SeqSimilarityAdapter converts SAX events into method calls on a SearchContentHandler implementation.
SeqSimilaritySearcher	Objects of this type represent one particular installation (not just implementation) of a sequence similarity searcher such as BLASTP.
SeqSimilaritySearchHit	Objects of this type represent one particular hit (sequence and associated information) from a sequence similarity search.
SeqSimilaritySearchHit.ByScoreComparator	ByScoreComparator compares SeqSimilaritySearchHits by their score.
SeqSimilaritySearchHit.BySubHitCountComparator	BySubHitCountComparator compares SeqSimilaritySearchHits by their number of sub-hits.
SeqSimilaritySearchResult	Objects of this type represent one particular result of a sequence similarity search.
SeqSimilaritySearchSubHit	Objects of this type represent one particular sub-hit (one concrete sequence stretch within a sequence and associated information) from a sequence similarity search hit.
SeqSimilaritySearchSubHit.ByScoreComparator	ByScoreComparator compares SeqSimilaritySearchSubHits by their score.
SeqSimilaritySearchSubHit.BySubjectStartComparator	BySubjectStartComparator compares SeqSimilaritySearchSubHits by their start position on the subject sequence.
SeqSimilarityStAXAdapter	SeqSimilarityStAXAdapter is a handler for XML conforming to the BioJava BlastLike DTD.
SeqSimilarityStAXHandler	SeqSimilarityStAXHandler is a base class for creating modular StAX handlers which send callbacks to a SeqSimilarityStAXAdapter.
Sequence	A biological sequence.
SequenceAlignment	This Interface provides methods for the alignment of bio-sequences.
SequenceAlignmentSAXParser	A SAX2 parser for dealing with a sequence alignments.
SequenceAnnotator	An object which adds some additional information to a Sequence.
SequenceBuilder	Interface for objects which accumulate state via SeqIOListener, then construct a Sequence object.
SequenceBuilderBase	Basic SequenceBuilder implementation which accumulates all notified information.
SequenceBuilderFactory	Simple factory for constructing new SequenceBuilder objects.
SequenceBuilderFilter	Base-class for builders that pass filtered events onto another builder.
SequenceContentHandlerBase	StAX handler for elements containing sequence
SequenceDB	A database of sequences with accessible keys and iterators over all sequences.
SequenceDBDataSource	Turn an entire SequenceDB instance into a DistDataSource.
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.
SequenceDBProvider	Interfaces for named resources that can provide sequences via a database given some configuration information as defined by the OBDA standard.
SequenceDBSearchHit	Deprecated. SimpleSeqSimilaritySearchHit has been made Annotatable and is now functionally identical.
SequenceDBSearchResult	Deprecated. SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical.
SequenceDBSearchSubHit	Deprecated. SimpleSeqSimilaritySearchSubHit has been made Annotatable and is now functionally identical.
SequenceDBSequenceBuilder	This SequenceBuilder has a variety of modes of operation.
SequenceDBWrapper	An abstract implementation of SequenceDB that wraps up another database.
SequenceDisplay	A sequence display that can show the results of a protein structure alignment.
SequenceFactory	Deprecated. use org.biojavax.bio.seq.io.RichSequenceBuilder or use org.biojavax.bio.seq.io.SequenceBuilder
SequenceFormat	Defines what a sequence format does.
SequenceHandler	mark interface
SequenceIterator	An iterator over a bag of sequences.
SequenceMouseListener	a mouse listener for the AbstractChainRenderer class it listens to all mouse events and triggeres appropriate SequenceListener and FeatureListener events
SequencePanel	A panel that displays a Sequence.
SequencePanelWrapper	Handles multiple SequencePanels and Ranges so that a Sequence can be wrapped over more than one line on screen.
SequencePoster	Deprecated. This doesn't handle loads of stuff.
SequenceRenderContext	A context within which sequence information may be rendered.
SequenceRenderContext.Border	The metric object for the 'border' area - the area between the extent of the rendered area and the beginning or end of the sequence.
SequenceRenderer	The interface for things that can render a line of information about a sequence.
SequenceRenderer.RendererForwarder
SequenceRendererWrapper	An implementation of SequenceRenderer that delegates rendering to another renderer.
SequencesAsGFF	Turns a sequence database into a GFF event stream.
SequenceScalePanel	A class that draws a Sequence as a rectangle, a scale display over it.
SequenceStreamer
SequenceStreamer.FileStreamer
SequenceStreamer.SequenceDBStreamer
SequenceTools	Methods for manipulating sequences.
SequenceViewerEvent	An event indicating that a mouse gesture was recognised within a widget that renders sequences.
SequenceViewerListener
SequenceViewerMotionListener
SequenceViewerMotionSupport
SequenceViewerSupport
Services	Utility methods for handling META-INF/services files
SigmoidKernel	This kernel implements a three layer neural net.
SimilarityPairBuilder	SimilarityPairBuilder annotates query and subject Sequence with SimilarityPairFeatures created from SAX events supplied via a SeqSimilarityAdapter.
SimilarityPairFeature	SimilarityPairFeature describes a pairwise similarity between two nucleotide sequences (as it extends StrandedFeature).
SimilarityPairFeature.EmptyPairwiseAlignment	EmptyPairwiseAlignment empty pairwise alignment which has labels to empty symbol lists.
SimilarityPairFeature.Template	Template for construction of SimilarityPairFeatures.
SimilarityType	Each HomologeneEntry represents a single Homologene record that relates two presumptive orthologues.
SimilarityType.PlaceHolder
SimpleAlignment	A simple implementation of an Alignment.
SimpleAlignmentElement	SimpleSimpleAlignment is a simple implementation of AlignmentElement.
SimpleAlignmentStyler	Simple implementation for specifying markup styles.
SimpleAlphabet	A simple no-frills implementation of the FiniteAlphabet interface.
SimpleAnnotation	A no-frills implementation of Annotation that is just a wrapper around a LinkedHashMap.
SimpleAnnotationDB	A no-frills implementation of AnnotationDB.
SimpleAnnotFilter	Basic implementation of AGAVEAnnotFilter
SimpleAssembly	A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
SimpleAssemblyBuilder	Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleAssembly.
SimpleAtomicSymbol	A basic implementation of AtomicSymbol.
SimpleBioEntry	Reference implementation of a BioEntry object which has no features or sequence.
SimpleBioEntryRelationship	Represents a relationship between two bioentries that is described by a term and given a rank.
SimpleChromatogram	A basic chromatogram implementation which provides public mutators for setting the various attributes of the chromatogram.
SimpleCodonPref	a simple no-frills implementation of the CodonPref object that encapsulates codon preference data.
SimpleComment	An implementaion of Comment.
SimpleComparableOntology	Represents an ontology that can be compared to other ontologies.
SimpleComparableTerm	A Term object that can be compared and thus sorted.
SimpleComparableTriple	Basic comparable triple, BioSQL style.
SimpleCrossOverFunction	Simple Implementation of the CrossOverFunction interface
SimpleCrossRef	A basic CrossRef implementation.
SimpleDistribution	A simple implementation of a distribution, which works with any finite alphabet.
SimpleDistributionTrainer	Deprecated. Distribution impls should be providing custom trainers.
SimpleDistributionTrainerContext	A no-frills implementation of DistributionTrainerContext.
SimpleDocRef	A basic DocRef implementation.
SimpleDocRefAuthor	Represents an author of a documentary reference.
SimpleDotState	A Dot state that you can make and use.
SimpleEmissionState
SimpleFeature	A no-frills implementation of a feature.
SimpleFeatureHolder	A no-frills implementation of FeatureHolder.
SimpleFeatureRealizer	FeatureRealizer which uses a lookup table to map template classes to implementations.
SimpleFramedFeature	Title: SimpleFramedFeature.
SimpleGACrossResult	Simple implementation of the GACross interface.
SimpleGappedSequence	Simple implementation of GappedSequence.
SimpleGappedSymbolList	This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.
SimpleGappedSymbolList.Block	An aligned block.
SimpleGeneticAlgorithm	A simple implementation of the GeneticAlgorithm interface it is not intended that this class be overidden, hence it is final.
SimpleGeneticCodeTable	A genetic code translation table representing a translation table in the DDBJ/EMBL/GenBank Feature Table (appendix V).
SimpleGFFRecord	A no-frills implementation of a GFFRecord.
SimpleHMMTrainer
SimpleHomologeneBuilder	A simple no-frills implementation of the HomologeneBuilder interface.
SimpleHomologeneDB
SimpleHomology	A no-frills implementation of Homology.
SimpleHomologyFeature
SimpleIndex	This is a no-frills implementation of the Index interface.
SimpleInputHandler	Simple input handler that reads the input for an external process from an input stream.
SimpleItemValue	A no-frills implementation of ItemValue.
SimpleLabelRenderer
SimpleManyToOneTranslationTable	A no-frills implementation of a translation table that maps between two alphabets.
SimpleMarkovModel
SimpleMMcifConsumer	A MMcifConsumer implementation that build a in-memory representation of the content of a mmcif file as a BioJava Structure object.
SimpleMMcifParser	A simple mmCif file parser
SimpleModelInState
SimpleModelTrainer
SimpleMutationFunction	Simple no frills Implementation of the MutationFunction interface
SimpleNamespace	A basic Namespace implemenation.
SimpleNCBITaxon	Reference implementation of NCBITaxon.
SimpleNCBITaxonName	Represents a name class plus name combination for an NCBITaxon object.
SimpleNCBITaxonomyLoader	Loads NCBI taxon information from names.dmp and nodes.dmp, which are two of the files in the archive downloadable at ftp://ftp.ncbi.nih.gov/pub/taxonomy/ .
SimpleNote	Simple implementation of Note.
SimpleOrganism	A Simple Haploid Organism implementation
SimpleOrthologue	this entry contains data about the orthologue.
SimpleOrthologueSet
SimpleOrthoPair	A no-frills implementation of the OrthoPair interface
SimpleOrthoPairCollection
SimpleOrthoPairSet	a no-frills implementation of a Homologene Group
SimpleOutputHandler	Simple output handler that pipes the output of an external process to an output stream.
SimplePopulation	Simple concrete implementation of the Population interface
SimplePosition	A simple implementation of the Position interface.
SimpleRankedCrossRef	Simple implementation of RankedCrossRef.
SimpleRankedDocRef	Represents a documentary reference.
SimpleRemoteFeature	A no-frills implementation of a remote feature.
SimpleRemoteFeature.DBResolver
SimpleRestrictionSite	SimpleRestrictionSite represents the recognition site of a restriction enzyme.
SimpleReversibleTranslationTable	A no-frills implementation of TranslationTable that uses a Map to map from symbols in a finite source alphabet into a target alphabet.
SimpleRichAnnotation	Simple annotation wrapper.
SimpleRichFeature	A simple implementation of RichFeature.
SimpleRichFeatureRelationship	Represents a relationship between two features that is described by a term.
SimpleRichLocation	A simple implementation of RichLocation.
SimpleRichObjectBuilder	Creates objects and returns them, and stores them in an internal map of singletons for reference.
SimpleRichSequence	A simple implementation of RichSequence.
SimpleRichSequenceBuilder	Constructs BioEntry objects by listening to events.
SimpleRichSequenceBuilderFactory	Generates RichSequenceBuilder objects.
SimpleSeqSimilaritySearchHit	SimpleSeqSimilaritySearchHit objects represent a similarity search hit of a query sequence to a sequence referenced in a SequenceDB object.
SimpleSeqSimilaritySearchResult	SimpleSeqSimilaritySearchResult objects represent a result of a search of a SymbolList against the sequences within a SequenceDB object.
SimpleSeqSimilaritySearchSubHit	SimpleSeqSimilaritySearchSubHit objects represent sub-hits which make up a hit.
SimpleSequence	A basic implementation of the Sequence interface.
SimpleSequenceBuilder	Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleSequence.
SimpleSequenceDBInstallation	This class is an implementation of interface SequenceDBInstallation that manages a set of SequenceDB objects.
SimpleSequenceFactory	A no-frills implementation of SequenceFactory that produces SimpleSequence objects.
SimpleSimilarityPairFeature	SimpleSimilarityPairFeature represents a similarity between a query sequence and a subject sequence as produced by a search program.
SimpleStatePath	A no-frills implementation of StatePath.
SimpleStrandedFeature	A no-frills implementation of StrandedFeature.
SimpleStructureServer
SimpleSVMClassifierModel	A no-frills implementation of an SVM classifier model.
SimpleSVMTarget	No-frills implementation of SVMTarget.
SimpleSymbolList	Basic implementation of SymbolList.
SimpleSymbolListFactory	This class makes SimpleSymbolLists.
SimpleSymbolPropertyTable	Class that implements the SymbolPropertyTable interface
SimpleSymbolPropertyTableDB	A simple implementation of a symbol property table database.
SimpleSymbolStyle	A no-frills implementation of SymbolStyle.
SimpleTagValueWrapper	Helper class to wrap one TagValueListener inside another one.
SimpleTaxon	Deprecated. replaced by classes in org.biojavax.bio.taxa
SimpleTaxonFactory	Deprecated. replaced by classes in org.biojavax.bio.taxa
SimpleThreadPool	SimpleThreadPool is a basic implementation of ThreadPool for use where we don't wish to introduce a dependency on a 3rd-party pool.
SimpleTrackLayout	A TrackLayout implenentation that wraps the sequence smoothly after a set number of residues
SimpleTranslationTable	A no-frills implementation of TranslationTable that uses a Map to map from symbols in a finite source alphabet into a target alphabet.
SimpleWeightMatrix
SimpleXMLEmitter	A simple XML DocumentHandler that processes SAX2 events to create a sensibly formatted XML as it parsed without populating objects with data.
SingleDP	An implementation of DP that aligns a single sequence against a single model.
SingleDPMatrix	The dynamic programming matrix for a single sequence.
SingletonAlphabet	An alphabet that contains a single atomic symbol.
SingletonList
SingularValueDecomposition	Singular Value Decomposition.
SixFrameRenderer	Class that handles drawing in six frames for other classes.
SixFrameZiggyRenderer	A feature renderer that computes the data necessary to render multi-exon transcripts without CDS data.
SmallAnnotation	Annotation that is optimized for memory usage.
SmallCursor	Constant-memory implementation of single-head DP cursor.
SmallMap	Lightweight implementation of Map which uses little memory to store a small number of mappings, at the expense of scalability.
SmallSet	Lightweight implementation of Set which uses little memory to store a small number of items, at the expense of scalability.
SmartSequenceBuilder	Basic SequenceBuilder implementation which accumulates all notified information and chooses a sequence implementation suited to the size of the sequence.
SmithWaterman	Smith and Waterman developed an efficient dynamic programming algorithm to perform local sequence alignments, which returns the most conserved region of two sequences (longest common substring with modifications).
SMORegressionTrainer	Train a regression support vector machine using the Sequential Minimal Optimization algorithm.
SMOTrainer	Train a support vector machine using the Sequential Minimal Optimization algorithm.
SoftMaskedAlphabet	Soft masking is usually displayed by making the masked regions somehow different from the non masked regions.
SoftMaskedAlphabet.MaskingDetector	Implementations will define how soft masking looks.
SoftMaskedAlphabet.MaskingDetector.DefaultMaskingDetector
SoftReferenceCache	Cache which is cleared according to memory pressure.
SolexaFastqReader	Reader for FastqVariant.FASTQ_SOLEXA formatted sequences.
SolexaFastqWriter	Writer for FastqVariant.FASTQ_SOLEXA formatted sequences.
SparseVector	An implementation of a sparse vector.
SparseVector.NormalizingKernel	A version of the standard dot-product kernel that scales each column independently.
SQLUnigeneFactory	An implementatoin of UnigeneFactory that manages it's data in an SQL database.
SSBond	A simple bean to store disulfid bridge information, the SSBOND records in the PDB files.
StackedFeatureRenderer	Allows you to stack multiple feature renderers up (for example a label renderer and a beaded renderer) and have them treated as a single renderer for layout.
StackedLogoPainter	A logo painter that paints in stacked areas.
StandardAminoAcid	A class that provides a set of standard amino acids.
State	A state in a markov process.
StateMachine	This class implements a state machine for parsing events from the Parser class.
StateMachine.ExitNotification	Interface implemented by State listeners that want notification when a transition leaves the State.
StateMachine.State	Interface for a State within this StateMachine
StateMachineFactory	Class that produces StateMachineInstance objects.
StateMachineInstance
StatePath	Extends the Alignment interface so that it is explicitly used to represent a state path through an HMM, and the associated emitted sequence and likelihoods.
StaticMemberPlaceHolder
StAXContentHandler	Interface for StAX content handlers.
StAXContentHandler	Interface for StAX content handlers.
StAXContentHandlerBase	Simple implementation of the StAXContentHandler interface, with empty implementations for all the methods.
StAXContentHandlerBase	Simple implementation of the StAXContentHandler interface, with empty implementations for all the methods.
StAXFeatureHandler	StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXFeatureHandler	StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXFeatureHandler	StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXHandlerBinding	StAXHandlerBindings associates an ElementRecognizer with a factory which creates StAXContentHandlers for elements which it the ElementRecognizer accepts.
StAXHandlerFactory	StAXHandlerFactory is an interface for factories producing StAXContentHandlers which are used by the SeqSimilarityStAXAdapter.
StAXHandlerFactory	Factory for StAX content handlers.
StAXHandlerFactory	Factory for StAX content handlers.
StAXHandlerFactory	Factory for StAX content handlers.
StAXPropertyHandler	StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXPropertyHandler	StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StoppingCriteria	A callback that is invoked during the training of an HMM.
StopRenderer	Compute sites of stop codons.
StrandedFeature	Adds the concept of 'strand' to features.
StrandedFeature.Strand	Class to represent the 'strandedness' of a feature.
StrandedFeature.Template	Template class for parameterizing the creation of a new StrandedFeature.
StrandedFeatureHandler	StAX handler for XFF strandedFeature type.
StrandParser	Process strings and return strand objects.
StrCompAlignment
StreamParser	Parse a stream of characters into BioJava symbols.
StreamPipe	A multi threaded class which pipes the contents of an input stream to an output stream.
StreamReader	Parses a stream into sequences.
StreamWriter	Writes all of the sequences from a SequenceIterator to a stream with a particular format.
StringElementHandlerBase	StAX handler for any element which just contains a string.
StringTools	Utility class for formatting strings into regular-sized blocks.
StrucAligParameters	A class that contains all the parameters of the structure alignment algorithm.
Struct	a bean to contain the data of the _struct lines
StructAsym	Contains the data for _struct_asym
StructKeywords
StructRef	A class to containt the _struct_ref field data
StructRefSeq
Structure	Interface for a structure object.
StructureEvent
StructureEventImpl
StructureException	An exception during the parsing of a PDB file.
StructureFetcherRunnable	a Runnable class that talks to a PDBInstallation and requests a new protein structure.
StructureImpl	Implementation of a PDB Structure.
StructureIO	Defines the interface how to access Structure (- PDB file) input,output readers, writers.
StructureIOFile	interface StructureIOFile extends the StructureIO interface and adds a few File specific methods.
StructureListener
StructurePairAligner	Perform a pairwise protein structure superimposition.
StructurePairSelector	To be implemented by JPanels that are part of the GUI to trigger structure aligmnents.
StructureServer	a server that pre-loads PDB files in memory, for quicker processing by StructureListeners
StructureTools	Simple access to protein seccondary structure assignments.
StructureTools	A class that provides some tool methods.
SubCircularRendererContext	A renderer context that allows some or all properties of another context to be over-ridden.
SubIntegerTokenization
SubPairwiseRenderContext	SubPairwiseRenderContext is a rendering context which wraps a delegate context and effectively hides some of the delegate's properties with its own.
SubSequence	View a sub-section of a given sequence object, including all the features intersecting that region.
SubSequence.SubProjectedFeatureContext	TargetContext that implements the mapping between the parent sequence and this sub-sequence.
SubSequenceDB
SubSequenceRenderContext	Allows a new renderer to "wrap" another one, replacing one or more values.
SubstitutionMatrix	This object is able to read a substitution matrix file and constructs a short matrix in memory.
SuffixTree	Suffix tree implementation.
SuffixTree.SuffixNode	A node in the suffix tree.
SuffixTreeKernel	Computes the dot-product of two suffix-trees as the sum of the products of the counts of all nodes they have in common.
SuffixTreeKernel.DepthScaler	Encapsulates the scale factor to apply at a given depth.
SuffixTreeKernel.MultipleScalar	Scale using a multiple of two DepthScalers.
SuffixTreeKernel.NullModelScaler	Scales by 4^depth - equivalent to dividing by a probablistic flatt prior null model
SuffixTreeKernel.SelectionScalar	Scale using a BitSet to allow/disallow depths.
SuffixTreeKernel.UniformScaler	Scale all depths by 1.0
SVDSuperimposer	A class that calculates the superimposition between two sets of atoms inspired by the biopython SVDSuperimposer class...
SVM_Light
SVM_Light.LabelledVector
SVMClassifierModel	An SVM classifier model.
SVMKernel	Kernel for support vector machines and related methods.
SVMRegressionModel
SVMTarget	An SVM classifier model.
SwapMutationFunction	This class does a sort of mutation by exchanging two positions on the chromosome.
Swissprot
SwissprotFileFormer	Deprecated. Use org.biojavax.bio.seq.io framework instead
SwissprotProcessor	Deprecated. Use org.biojavax.bio.seq.io framework instead
SwissprotProcessor.Factory	Factory which wraps SequenceBuilders in a SwissprotProcessor
SwissprotSequenceDB	This class contains functions accessing sequences in swiss-prot.
Symbol	A single symbol.
SymbolList	A sequence of symbols that belong to an alphabet.
SymbolListCharSequence	SymbolListCharSequence is a CharSequence implementation which wraps a SymbolList.
SymbolListFactory	This interface exists to hide implementational details of SymbolLists when making chunked symbol lists.
SymbolListViews	Tools class for constructing views of SymbolList objects.
SymbolPropertyTable	class for maintaining properties associated with a symbol
SymbolPropertyTableDB	Database of SymbolPropertyTable objects.
SymbolPropertyTableIterator	Iterator over SymbolPropertyTable objects.
SymbolReader	Encapsulate a stream of Symbols being parsed from some input stream.
SymbolSequenceRenderer	SymbolSequenceRenderer renders symbols of a SymbolList.
SymbolStyle	The interface for things that say how to paint a symbol.
SymbolTokenization	Encapsulate a mapping between BioJava Symbol objects and some string representation.
SymbolTokenization.TokenType
Synonym
SystemRegistry	A registry that loads up the standard biodirectory files.
TabDelimParser	Parse tab-delimited ontology files into Ontology objects.
TabIndexStore	Implements IndexStore as a serialized file for the java data and a tab-delimited file of offsets.
TagDelegator	Pushes a new parser and listener, or delegate to a listener depending on the tag.
TagDropper	Silently drop all tags except those specified, and pass the rest onto a delegate.
TagMapper	TagMapper maps arbitrary object keys to new keys.
TagRenamer	Rename tags using a TagMapper.
TagValue	Utility class for representing tag-value pairs for TagValueParser implementors.
TagValueContext	Communication interface between Parser and a TagValueListener that allows listeners to request that a parser/listener pair be pushed onto the stack to handle the current tag.
TagValueListener	An object that wishes to be informed of events during the parsing of a file.
TagValueParser	Tokenize single records (lines of text, objects) into a tag and a value.
TagValueWrapper	Interface for TagValueListeners that wrap other TagValueListeners
Taxon
Taxon	Deprecated. replaced by classes in org.biojavax.bio.taxa
Taxon.TaxonStub
TaxonFactory	Deprecated. replaced by classes in org.biojavax.bio.taxa
TaxonParser	Deprecated. replaced by classes in org.biojavax.bio.taxa
TaxonSQL	Deprecated. Use hibernate and org.biojavax.bio.db.*
TemplateUtils	Common things you may want to do with feature templates.
Term	A term in an ontology.
Term.Impl	Simple in-memory implementation of an ontology term.
TextBlock	A BlockPainter that renders letters in proportion to the size of the signal.
TextLogoPainter	A logo painter that paints in stacked letters.
ThinRichSequence	A simple implementation of RichSequence.
ThreadPool	ThreadPool specifies basic thread-pooling operations such that third-party implementations may be used without requiring changes to BioJava.
TickFeatureRenderer
TournamentSelection	Tournament Selection chooses the best organisms from n random subsets of a given population.
TrackLayout	An interface for the handling of the layout of a WrappedSequencePanel.
Train
Trainable	Flags an object as being able to register itself with a model trainer.
TrainerTransition	This is a small and ugly class for storing a trainer and a transition.
TrainingAlgorithm
TrainingContext
TrainingEvent
TrainingListener
TrainRegression
Transition	This is a small and ugly class for storing a transition.
TransitionTrainer	An object that can be used to train the transitions within a MarkovModel.
TranslatedDistribution	A translated view of some underlying distribution.
TranslatedSequencePanel	TranslatedSequencePanel is a panel that displays a Sequence.
TranslateFlipContext	A ProjectionContext that translates and optionaly flips features.
TranslationTable	Encapsulates the mapping from a source to a destination alphabet.
Triple	A triple in an ontology.
Triple.Impl	Basic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriple
TriState	Class that represents the tristate values possible in a logical operation: true, false and indeterminate.
TurnGlyph	A Glyph that paints a wide 'H' line within the bounds
TwoHeadedArrowGlyph	A Glyph that paints a two headed arrow within the bounds
TypedProperties	a sub-class of java.util.Properties that provides the same constructors, adds two convenient load methods to load the properties from files and, most importantly, adds getPropertyAsXXX() methods to get a property as an object of type XXX.
UkkonenSuffixTree	A suffix tree is an efficient method for encoding the frequencies of motifs in a sequence.
UkkonenSuffixTree.SuffixNode	end Tree modification methods
Unchangeable	This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.
UncompressInputStream	This class decompresses an input stream containing data compressed with the unix "compress" utility (LZC, a LZW variant).
UnequalLengthAlignment	UnequalLengthAlignment has the following behavior.
UniformDistribution	An implementation of an uniform distribution
UnigeneCluster	A single unigene cluster.
UnigeneDB	A database of Unigene clusters.
UnigeneFactory	Objects that can be used to produce a UnigeneDB instance given a URL.
UnigeneTools	Usefull tools for working with Unigene.
UniProtCommentParser
UniProtCommentParser.Event	A class to describe events for alternative product comments.
UniProtCommentParser.Interaction	A class to describe protein-protein interactions.
UniProtCommentParser.Isoform	A class to describe isoforms for alternative product comments.
UniProtCommentParser.SeqCaution	A class to describe seq caution entries.
UniProtFormat	Format reader for UniProt files.
UniProtFormat.Terms	Implements some UniProt-specific terms.
UniProtLocationParser	Parses UniProt location strings into RichLocation objects.
UniProtXMLFormat	Format reader for UniProtXML files.
UniProtXMLFormat.Terms	Implements some UniProtXML-specific terms.
UnknownDBHelper	Deprecated. Use hibernate and org.biojavax.bio.db.*
UnsupportedChromatogramFormatException	Exception indicating that some provided data does not represent a supported chromatogram format.
UntrainableDistribution	A distribution which does not interact with the training framework.
URLFactory	URLFactory defines a means of obtaining a URL associated with an object.
URLGeneratorFactory	Interface for a factory method to return a list of 0, 1 or more DatabaseURLGenerator instances.
UserDefinedTrackLayout	An implementation of TrackLayout that that wraps a sequence over an arbitrary set of ranges
UtilHelper	Just make the property follow the common case
ValueChanger	Intercept the values associated with some tags and change them systematically.
Variable
Variable.Impl
ViewingSequenceDB	SequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database.
ViewSequence	A view onto another Sequence object.
ViewSequenceFactory	ViewSequenceFactory is a base class for creating search handlers which create and cache views on the query and subject sequences.
Visitor	Things that will be shown filters.
Walker	Objects that can walk over a filter expression, showing each element to a visitor.
WalkerFactory
WeakCacheMap	A cache which retains weak references to objects
WeakTaxon	Deprecated. replaced by classes in org.biojavax.bio.taxa
WeakTaxonFactory	Deprecated. replaced by classes in org.biojavax.bio.taxa
WeakValueHashMap	Map implementation which keeps weak references to values.
WebSequenceDB	Functions for access to a web based database that returns sequences in a variety of formats.
WeightedSet	Inspred by the BioJava Distribution objects the WeightedSet is a map from a Key to a Weight.
WeightMatrix	A log odds weight matrix.
WeightMatrixAnnotator	Annotates a sequence with hits to a weight-matrix.
WMAsMM	Wraps a weight matrix up so that it appears to be a very simple HMM.
WobbleDistribution	an object to return statistics about the frequency of the wobble base in a set of synonymous codons.
WordTokenization	Base class for tokenizations which accept whitespace-separated `words'.
WriterOutputHandler	Simple output handler that writes the output of an external process to an writer.
XFFFeatureSetHandler	StAX handler which converts and stream of parse events for an XFF featureSet element into BioJava SeqIO events.
XFFHelper
XFFPartHandlerFactory	Factory for StAX content handlers.
XFFTools	Common functionality for manipulating XFF.
XFFWriter	Simple XFF writing code, ripped off from Dazzle 0.08.
XMLAnnotationTypeHandler	StAX handler for parsing AnnotationTypes in FilterXML documents.
XMLAnnotationTypeHandler.CollectionConstraintHandler	Handler for an individual CollectionConstraint in an AnnotationType.
XMLAnnotationTypeHandler.CollectionConstraintHandlerFactory	Handler Factory for a CollectionConstraint in an AnnotationType.
XMLAnnotationTypeHandler.PropertyConstraintHandler	Handler for an individual PropertyConstraint in an AnnotationType.
XMLAnnotationTypeHandler.PropertyConstraintHandlerFactory	Handler Factory for a PropertyConstraint in an AnnotationType.
XMLAnnotationTypeWriter	Main class for writing AnnotationTypes as XML.
XMLAnnotationTypeWriter.XMLCollectionConstraintWriter	Writer for types of CollectionConstraint.
XMLAnnotationTypeWriter.XMLPropertyConstraintWriter	Writer for types of PropertyConstraint.
XMLBeans	Construct java beans from XML elements
XMLDistributionReader	A SAX parser that reads an XML representation of a Distribution from a file and recreates it as a Distribution Object.
XMLDistributionWriter	Writes an OrderNDistribution or simple Distribution to an XML file.
XMLFilterHandler	Factory producing content handlers for parsing FilterXML elements.
XMLFilterHandler.FilterHandler	StAXContentHandler for a particular type of FeatureFilter.
XMLFilterHandler.FilterHandlerFactory	Factory of StAXContentHandlers for a particular type of FeatureFilter.
XMLFilterWriter	Write FeatureFilters in XML format.
XMLFilterWriter.FilterWriter	Interface for an object which can write a FeatureFilter as XML.
XmlMarkovModel
XMLTools	Utility class for reading chunks of XML files and feeding them to SAX.
XMLWritable	Object which knows how to represent itself as an XML element.
XMLWriter	Simple interface for building XML documents.
ZiggyFeatureRenderer	A feature renderer that draws non-contiguous features as a set of boxes joined by zig-zags.
ZiggyImapRenderer	ZiggyImapRenderer is a decorator for ZiggyFeatureRenderer which adds the ability to create HTML image map coordinates which correspond to the feature rendering produced by the ZiggyFeatureRenderer.