All Classes and Interfaces
Class
Description
Symbol property table based on the Amino Acid Index Database.
Iterator over
AAindex objects that
are stored in a stream in the AAindex1 file format.An implementation of
Chromatogram to
encapulsulate chromatogram data extracted from the files produced by ABI
sequencers, such as the the 377 and the 3700.A general base parser for files produced by ABI software.
An aggregate immutable type for an ABIF tagged data record.
Useful functionality for working with fasta files where the quality of the
DNA is encoded as upper and lower case DNA characters.
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.
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.
Renders an ABI trace file as a chromatogram graph.
Abstract implementation of
AlignmentStyler, contains
utility methods for generating a set of HTML styles from a list of
RGB colours.
An abstract implementation of
Alphabet.A utility class to ease the problem of implementing an Annotation to that of
providing an apropreate implementation of Map.
AbstractBeadRenderer is a an abstract base class
for the creation of FeatureRenderers which use a
'string of beads' metaphor for displaying features.An abstract implementation of BioEntryDB that provides the getBioEntryIterator
method.
Useful base-class for objects implementing Changeable
A basic, abstract implementation of
Chromatogram.Abstract implementation of
CrossOverFunction.An abstract implementation of Distribution.
An abstract implementation of FeatureHolder.
Base class from which most implementations of GeneticAlgorithm will inherit.
An abstract implementation of
Location.Abstract
Location decorator (wrapper).an abstract class implementing basic functionality
of a translation table that translates Symbols from
one Alphabet to another.
Abstract implementation of
MutationFunction all custom
implementations should inherit from here.Simple base class for OrderNDistributions.
Abstract implementation of Organism.
An abstract implementation of the OrthoPairCollection
interface.
represents the Homologene Group.
A SequenceRenderer that renders a set of Features that match a FeatureFilter in such a way that
they do not overlap in the display.
Most Population implementations will want to inherit from here.
Base class for simple contiguous Location implementations.
an abstract class implementing basic functionality
of a translation table that translates Symbols from
one Alphabet to another.
An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator
method.
An abstract implementation of SequenceDB that provides the sequenceIterator
method.
Abstract implementation of SVMClassifierModel.
An abstract implementation of an SVMModel.
The base-class for Symbol implementations.
Abstract helper implementation of the SymbolList core interface.
Deprecated.
Abstract implementation of term
This provides basic change-forwarding functionality from
the annotation and ontology properties.
An abstract implementation of TrainingAlgorithm that provides a framework
for plugging in per-cycle code for parameter optimization.
An abstract TagValueWrapper that does nothing!
AcnumHitReader reads the "acnum.hit" file of an EMBL
CD-ROM format binary index.AcnumTrgReader reads the "acnum.trg" file of an EMBL
CD-ROM format binary index.Interface for object which monitor long-running activities.
Dumping the data from biojava with source of agave into agave format
Deals with alternate sequence IDs
This interface defines mapping from BioJava into AGAVE format.
An interface that can be tested for by nested handlers
when trying to do a callback.
Handles the AGAVE <bio_sequence> element
Handles the AGAVE <bio_sequence> element
An interface that can be tested for by nested handlers
when trying to do a callback.
Handles the AGAVE <cds> element
An interface that can be tested for by nested handlers
when trying to do a callback.
Handles the AGAVE <chromosome> element
An interface that can be tested for by nested handlers
when trying to do a callback.
Handles the AGAVE <contig> element
this is the interface implemented by several classes
Deals with database crossreferences
Deals with database crossreferences
An interface that can be tested for by nested handlers
when trying to do a callback.
Handles the root AGAVE element
modified for agave format
Deals with AGAVE keywords
Deals with match_align
Deals with match_desc
match_region
Deals with match_region
Handles the AGAVE <mrna> element
Deals with note
Handles the AGAVE <predicted_protein> element
sci_property
seq_feature
seq_location
sequence_map
Deals with sequence code
transcript
unordered_fragments
Moves view attributes into annotation properties.
Writes Sequence into AGAVE XML document.
xref
handle AGAVE xref
xref_property
xrefs
Deals with database crossreferences (xrefs)
Joins multipel values into single values.
AlignIOConstants contains constants used to identify
sequence formats, alphabets etc, in the context of reading and
writing alignments.An alignment containing multiple SymbolLists.
Iterator implementation looping over symbol lists in an alignment using
the labels.
This Interface provides methods for the alignment of bio-sequences.
AlignmentElement is a class which represents a SymbolList and its
location within an Alignment This is for use in
UnequalLengthAlignments and ARAlignments.
Class to do simple HTML colouring of sequence alignments.
This class stores the result of an alignment procedure that creates a
pairwise alignment of two sequences.
AlignmentStAXHandler handles the BlastLikeAlignment
element of BioJava BlastLike XML.
The set of AtomicSymbols which can be concatenated together to make a
SymbolList.
Map between Symbols and index numbers.
Utility methods for working with Alphabets.
AlphabetResolvers are helpers which determine which
type of sequence Alphabet to expect from a search
result.Thrown to indicate that a term or triple can't be added to an ontology
because it is already present.
Implementation of SymbolTokenization which binds symbols to
strings of characters.
Indicates that an object has an associated annotation.
Deprecated.
use
new ChangeForwarder.Retyper(source, cs, Annotation.PROPERTY)
insteadSequenceDB implementation which lazily applies a SequenceAnnotator
to sequences retrieved from a SequenceDB.
Arbitrary annotation associated with one or more objects.
Builds an Annotation tree from TagValue events using an AnnotationType to
work out which fields are of what type.
AnnotationChanger remaps the values of an
Annotation to new values specified by a
ValueChanger.A database of Annotation instances.
AnnotationFactory is a utility class for making
Annotations from Maps.AnnotationRenamer remaps the keys of an
Annotation to new keys specified by a
TagMapper.AnnotationTools is a set of static utility methods for
manipulating Annotations and AnnotationTypes.A set of constraints on the data contained in an
Annotation.An abstract base class useful for implementing AnnotationType
instances.
An implementation of
AnnotationType.Hello world!
Create a bean from an XML file, then attempt to enter it.
ARAlignment is an interface that defines methods for adding and
removing seqeunces from an Alignment.
A Feature Renderer that paints the Feature as a right facing arrow Based heavily on
BasicFeatureRenderer
A Glyph that paints an arrow shape within the bounds.
Support class for applications which need to patch together sections
of sequence into a single SymbolList.
An unchecked exception representing an Assertion failure.
A symbol that is not ambiguous.
An exception thrown by classes of this package.
A backpointer.
A logo painter that paints in bars.
Base XMLWriter class for writing XML representations of Java Value
Objects with bespoke architectures.
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.
A symbol that can be represented as a string of Symbols.
Train a hidden markov model using a sampling algorithm.
Train a hidden markov model using maximum likelihood.
BeadFeatureRenderers use a 'string of beads'
metaphor for displaying features.Create an Annotation with properties matching those of a JavaBean instance.
Between view onto an underlying Location instance.
It represents an article.
It represents a book.
It represents a book article.
The criteria define how the matching or ordering should be done
during queries.
It represents an account of the content of the cited resource.
It defines information related to the citation itself rather than to the cited resource.
A class describing journals.
It represents a journal article.
It represents an organisation dealing with the bibliographic
resources.
It represents a patent.
It represents a person dealing with the bibliographic resources.
It represents a conference proceeding.
This class and its sub-classes define active participants of the process
of creation and dissemination of the bibliographic resources.
It represent an extent or scope of the content of the cited resource.
It represents a service dealing with the bibliographic
resources.
It represents the topic of the content of the cited resource.
It represents a technical report.
It represents a thesis.
It represents a WWW resource.
This class is a core class of the bibliographic data model - it
represents a bibliographic reference, a citation.
An exception raised when communciation with the BibRef APIs fails.
The interface BibRefQuery is a fundamental part of the Bibliographic Query
Service.
This interface defines supporting utilities for working with
bibliographic repositories.
solves y = f(x) = 0 by binary search.
This class relates to the bioentry table in BioSQL.
.
A database of BioEntrys.
Essentially the same as SequenceIterator.
Represents the relation between two bioentries.
A nestable biological error.
A nestable biological exception.
Simple SequenceDB implementation backed by a BioFetch (HTTP)
server.
Directory-services plugin for biofetch databases.
The original object for indexing sequence files.
Interface for things that perform matches.
A nestable biological exception.
The class that accepts all features.
The class that accepts no features.
A simple implementation of CrossReferenceResolver
A filter for accepting or rejecting a feature.
A filter that returns all features accepted by both child filter.
Construct one of these to filter features by display name.
A filter that returns all features that have the given note, and
the value and rank is checked as well.
A filter that returns all features that have a note with the given term.
Construct one of these to filter features by rank.
Accept features that reside on a sequence with a particular name.
Construct one of these to filter features by source.
Construct one of these to filter features by source (name only - parent ontology
is ignored).
A filter that returns all features having locations on a given strand.
Construct one of these to filter features by type.
Construct one of these to filter features by type (name only - parent ontology
is ignored).
A filter that returns all features contained within a location.
A filter for Hibernate-BioSQL filters to extend.
A filter that returns all features not accepted by a child filter.
A filter that returns all features accepted by at least one child filter.
A filter that returns all features overlapping a location.
A class representing some useful stuff you can do with BioSQLFeatureFilters,
for instance converting plain FeatureFilters into a their BioSQLFeatureFilter
equivalents (where possible).
Takes requests for RichObjects and sees if it can load them from a Hibernate
database.
A handler which loads sequence data from a BioSQL database, caching it where possible.
Deprecated.
Use hibernate and org.biojavax.bio.db
Deprecated.
Use hibernate and org.biojavax.bio.db
BioStores represent directory and file structures
which index flat files according to the OBDA specification.BioStoreFactory creates BioStore
instances.Takes a SAX event stream and a HTMLRenderer to produce
a HTML Blast like program report.
BlastLikeHomologyBuilder populates a
List with Homology instances created from
SAX events supplied via a SeqSimilarityAdapter.A facade class allowing for direct SAX2-like parsing of the native
output from Blast-like bioinformatics software.
BlastLikeSearchBuilder will create
SeqSimilaritySearchResults from SAX events via a
SeqSimilarityAdapter.A SearchContentHandler class that implements filtering
in chains of SearchContentHandler instances.
Applies test to the value specified by the key in hit properties.
Applies test to the value specified by the key in search properties.
Applies test to the value specified by the key in subhit properties.
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.
This class parses NCBI Blast XML output.
A facade class that wraps the NCBI Blast XML
parsing framework in a more user-friendly form.
StAX handler for any element which just contains a string representation of
an boolean.
A Comparator similar to Feature.ByLocationComparator except that the min and max positions of
the location are both compared
Comparator that compares the min and max positions of Features
Required by org.biojava.bio.gui.sequence.AbstractPeptideDigestRenderer instances.
Factory for objects which encapsulate individual Java bytecode instructions.
StAX handler for any element which just contains a string representation of
a byte.
Interface for managing caches of objects.
Interface for managing caches of objects fetchable by key.
Interface for a reference to an object, analogous to
java.lang.ref.Referencce, but more flexible.A wrapper around
InputStream that provides in-memory
caching of the input data.
Caches the results of a nested kernel so that k(a, b) need only be calculated
once.
SequenceDB implementation that caches the results of another SequenceDB.
This is a basic container for a vocabulary entry.
This interface is a main entry point to a set of controlled
vocabularies.
This interface defines functionality of a controlled vocabulary.
A constraint on the number of values a property can have.
A single cell in the DP matrix.
The interface for all functions that can calculate the 'scores' array for
a given cell.
The interface for all functions that can calculate the 'scores' array for
a given cell.
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.
A cache that clears values as the keys fire ChangeEvents of a given type.
This is a ChangeListener that ignores everything.
Event which encapsulates a change in any mutable BioJava object.
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.
A ChangeForwarder that systematically uses a given type and wraps the old
event.
Interface implemented by ChangeHubs, i.e.
Interface for objects which listen to ChangeEvents.
An implementation that always vetoes everything.
A listener that remembers the ChangeEvent of the last change.
A listener that writes information about the event stream to a PrintStream.
A utility class to provide management for informing ChangeListeners of
ChangeEvents.
A mapping between keys and actions to turn old values into new values.
An implementation of Changer that applies a list of Changer instances to
the value in turn.
Callback used to produce a new value from an old one.
Callback used to produce a list of values from a single old one.
Class for all constants which are used to indicate change
types.
Exception which is thrown when a ChangeListener does not
wish a change to take place.
Represents Nexus characters blocks.
Builds Nexus characters blocks.
Listens to events that represent Nexus characters blocks.
Parses Nexus characters blocks.
Implementation of SymbolTokenization which binds symbols to
single unicode characters.
StAX handler for any element which just contains a string representation of
a char.
Encapsulates the basic information you would want from a chromatogram.
A factory that creates
Chromatogram objects from files or streams.Encapsulates a configurable method for drawing a
Chromatogram
into a graphics context.A typesafe enumeration of the options available for configuring
the behavior of a
ChromatogramGraphic instance.Provides the mechanism whereby a ChromatogramGraphic can display
a Chromatogram with a non-linear horizontal scale.
The default scaler that displays the chromatogram 1:1.
Utility class for dealing with
Chromatograms.SymbolList implementation using constant-size chunks.
class that makes ChunkedSymbolLists with the chunks
implemented as SymbolLists themselves.
Circular view onto an underlying Location instance.
Renders multiple renderers, each in their own concentric rings.
Deprecated.
replaced by classes in
org.biojavax.bio.taxaRender information from a CircularRendererContext onto a graphics context.
A context providing information for rendering sequences into circular coordinate systems.
Renders a sequence as a circle using a CircularRenderer.
A circular view onto another Sequence object.
A simple toy example that allows you to put points on a canvas, and find a
polynomial hyperplane to seperate them.
An extention of JComponent that contains the points invalid input: '&' encapsulates the
classifier.
Utility methods for manipulating class objects and resources.
A SAX2 parser for dealing with a multiple sequence
alignment as produced by ClustalW outputing .aln format.
Interface for Java classes within the bytecode generation framework.
Interface which encapsulates the stream to which Java bytecode can
be written.
An exception indicating that something went wrong generating byte code.
Wrap up details about a field in a Java class file.
Interface for an object which can produce Java bytecode.
Wrap up details about a method in a Java class file
Utility code for things you will frequently need.
An utility class for codon preferences
Used by
AnnotationType to represent the constraint on
the collection of values in a property-slot.CollectionConstraint which validates all members of a Collection.
A collection constraint that accpepts collections iff they are accepted by both
child constraints.
CollectionConstraint which validates a portion of a Collection.
A collection constraint that accepts items iff they are accepted by either
child constraints.
Interface for specifying whether a particular pair
of residues/bases should be coloured.
A simple ranked comment designed to be used for BioEntry comments
in BioSQL.
Implementations of
Commitable support atomic changes
from one known state to another via commit/rollback semantics.An implementation of DataStore that will map onto a file using the NIO
constructs.
Builder for a data store that is backed by a java.nio.MappedByteBuffer.
An Ontology that can be compared to another.
Makes Term objects comparable properly and adds some extra features to them.
Comparable triples, obviously.
Feature which represents a component in an assembly (contig).
Template for constructing a new ComponentFeature.
Computes composition statistics about a
SymbolList.An implementation of RichLocation which covers multiple locations,
but on the same strand of the same (optionally circular) sequence.
interface for classes that return a single
double precision value for a single double
precision argument.
Build a Java class file constant pool.
Some usefull constants for working with binary files.
An encapsulation of a count over the Symbols within an alphabet.
Utility class that calculates a CRC64 checksum on a stream of bytes.
CrosshairRenderer draws a crosshair, optionally
with coordinates.Crosses two chromosomes.
A place holder CrossOverFunction that doesn't perform cross overs
Tokenization for cross-product alphabets.
Represents a cross reference to another database.
An exception that indicates that an attempt to resolve a
CrossRef
has failed.This interface returns symbols or sequence for a given cross-reference.
Takes a database ID and some configuration properties
( such as base URL ) and returns either a URL or
a full anchor tag.
Represents Nexus data blocks.
Builds Nexus characters blocks.
Listens to events that represent Nexus data blocks.
Parses Nexus data blocks.
A repository that can be searched with a sequence.
Builder for a data store.
Deprecated.
Use hibernate and org.biojavax.bio.db
This is purely for debugging purposes.
Default implementation of OntologyOps.
A simple default
URLGeneratorFactory which returns
a single NcbiDatabaseURLGenerator instance.Interface which exposes delegation services offered by a StAX
event source.
Interface which exposes delegation services offered by a StAX
event source.
Adds a class specific constant to k(x, x).
Caches the leading diagonal of a kernel matrix.
This class contains methods for calculating the results of proteolytic digestion
of a protein sequence
this class is not designed to be thread safe
Represents Nexus distances blocks.
Builds Nexus distances blocks.
Listens to events that represent Nexus distances blocks.
Parses Nexus distances blocks.
Object which contributes data to a DistributedSequenceDB.
Sequence database from the meta-DAS system.
An encapsulation of a probability distribution over the Symbols within an
alphabet.
Deprecated.
use
new ChangeForwarder.Retyper(this, cs, Annotation.PROPERTY)
instead
A thing that can make Distributions.
The default DistributionFactory implementation.
The GUI component for rendering a DistributionLogo.
A class to hold static methods for calculations and manipulations using
Distributions.
An object that can be used to train a distribution up.
A context within a group of DistributionTrainers can be trained together.
DivisionLkpReader reads the "division.lkp" file of an
EMBL CD-ROM format binary index.Packing utility class for DNA.
Computes composition statistics about a DNA
SymbolList.A
Packing implementation which handles the DNA alphabet, without any
support for ambiguity symbols.A simple implementation of SymbolStyle optimized for DNA.
Useful functionality for processing DNA sequences.
Represents a documentary reference.
Represents an author of a documentary reference.
Useful tools for working with authors.
A Dot state.
An efficient implementation of an Alphabet over the infinite set of double
values.
A range of double values.
A single double value.
A class to represent a contiguous range of double symbols.
StAX handler for any element which just contains a string representation of
a double.
Objects that can perform dymamic programming operations upon sequences with
HMMs.
This is an implementation of CellCalculatorFactoryMaker that compiles the
HMM object down to Java byte-code that is equivalent in behaviour to the
interpreter.
Encapsulates the dynamic programmming matrix, and the context within algorithms work.
The interface for objects that can generate a DP object for a MarkovModel.
A simple implementation of CrossReferenceResolver.
A Sequence implementation that has a name and URI but no features,
and a zero length symbol list.
DummySequenceDB is an implementation which contains
only a DummySequence.DummySequenceDBInstallation is an implementation which
returns the same DummySequenceDB instance regardless
of the identifier used to retrieve a database.Symbol list which just consists of non-informative symbols.
Simple URL generator for EMBL at the EBI.
Deprecated.
replaced by classes in
org.biojavax.bio.taxa
A simple listener that just echoes events back to the console.
An ec (enzyme classification) number.
A simple implementation of EcNumber.
Encapsulates an edit operation on a SymbolList.
EditableAlignment is an interface that defines methods for
shifting bases within an Alignment.
Simple interface for filtering SAX/StAX startElement events.
This class is copied to agave package
Simple interface for filtering SAX/StAX startElement events
Simple interface for filtering SAX/StAX startElement events
Filter elements by local name (not recommended).
Filter elements by local name (not recommended).
Filter elements by local name (not recommended).
Filter elements by name and namespace.
Filter elements by name and namespace.
Filter elements by name and namespace.
Filter elements on the existence of a specified attribute.
Filter elements on the existence of a specified attribute.
Filter elements on the existence of a specified attribute.
EllipticalBeadRenderer renders features as simple
ellipses.Map EMBL data into AGAVE format
EmblCDROMIndexReader is an abstract class whose
concrete subclasses read EMBL CD-ROM format indices from an
underlying InputStream.EmblCDROMIndexStores implement a read-only
IndexStore backed by EMBL CD-ROM format binary
indices.EmblCDROMRandomAccess is an abstract class whose
concrete subclasses can perform fast lookups in EMBL CD-ROM format
index files.Deprecated.
Use org.biojavax.bio.seq.io framework instead
Format reader for EMBL files.
Implements some EMBL-specific terms.
Deprecated.
Use org.biojavax.bio.seq.io.EMBLFormat instead
Deprecated.
Use org.biojavax.bio.seq.io framework instead
Deprecated.
Use org.biojavax.bio.seq.io framework instead
Factory which wraps SequenceBuilders in an EmblProcessor
Format reader for EMBLxml files.
Implements some EMBLxml-specific terms.
Cache for columns of emission probabilities in pair-wise alignment
algorithms.
A state in a markov process that has an emission spectrum.
A place holder for a RichAnnotation that prevents null having to be used
An Empty implementation of RichLocation.
EntryNamIdxReader reads the "entrynam.idx" file of an
EMBL CD-ROM format binary index.EntryNamRandomAccess objects provide random access to
records within the "entrynam.idx" file of an EMBL CD-ROM format
binary index.Makes running external executables easier, optionally under a watched thread.
Utility class to execute an external process and to handle
the
STDOUT, STDERR and STDIN streams
in multiple threads managed by a thread pool.This class implements the AlignmentFormat interface to read FASTA alignments.
Deprecated.
Use org.biojavax.bio.seq.io.FastaFormat
Factory which wraps SequenceBuilders in a FastaDescriptionLineParser
Deprecated.
Use org.biojavax.bio.seq.io.FastaFormat
Format object representing FASTA files.
This class is used by
FastaFormat to determine which fields are in the
fasta header.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).A SAX2 parser for dealing with multiple sequences in
FASTA format.
FASTQ formatted sequence.
Fluent builder API for creating FASTQ formatted sequences.
Reader for FASTQ formatted sequences.
Utility methods for FASTQ formatted sequences.
FASTQ sequence format variant.
Writer for FASTQ formatted sequences.
Simple implementation of XMLWriter, optimized for speed.
A feature within a sequence, or nested within another feature.
ByLocationComparator compares
Features by the minimum base position of their
Location.Template class for a plain feature.
FeatureBlockSequenceRenderer forms a bridge between
Sequence rendering and Feature
rendering.A filter for accepting or rejecting a feature.
A filter that returns all features accepted by both child filter.
Retrieve features that contain a given annotation, and that the set of values
contains the value given.
Filter by applying a nested
FeatureFilter to all
ancestor features.Retrieve features that contain a given annotation with a given value.
A filter that returns all features that have an annotation bundle that is of a given
annotation type.
Filter by applying a nested
FeatureFilter to the
child features.Filter which accepts only those filters which are an instance
of a specific Java class
Accepts features which are ComponentFeatures and have a
componentSequenceName
property of the specified value.Filter by applying a nested
FeatureFilter to all
descendant features.Accept only features which are equal to the specified feature
ByPairwiseScore is used to filter
SimilarityPairFeatures by their score.Filter by applying a nested
FeatureFilter to the
parent feature.Accept features that reside on a sequence with a particular name.
Construct one of these to filter features by source.
Construct one of these to filter features by type.
A filter that returns all features contained within a location.
Accept features with a given reading frame.
Retrieve features that contain a given annotation with any value.
A filter that returns all features not accepted by a child filter.
Accepts features where all immediate children meet the supplied filter.
Accepts features where all descendants meet the supplied filter.
A filter that returns all features accepted by at least one child filter.
A filter that returns all features overlapping a location.
A filter that accepts all features whose shadow is contained by a specified
Location.A filter that accepts all features whose shadow overlaps a specified
Location.Accept features with a given strandedness.
StAX handler for the basic
feature type of XFF.The interface for objects that contain features.
This class intendes to provide some FeatureHolder utilities.
Wrap up default sets of Feature implementations.
Interface for translators which map from Feature.Template
instances to real Feature objects.
A closure that allows AbstractPeptideDigestRenderer implementations to obtain the features of the rendered sequence.
Deprecated.
Use org.biojavax.bio.seq.io framework instead
FeatureTree is GUI tree to display the features and annotations
of the sequences in a
SequenceDB Nested Features are
displayed as expandable leaves.Registry of known types of features.
A named collection of Types.
A simple implementation of a Repository.
A type of feature.
FileAsList creates a writable List
implementation backed by a random access file.Class for implementing tests with BlastLikeSearchFilter
objects.
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.
Tests that the value associated with the specified
key contains a part matched by the supplied regex.
Tests that the value associated with the specified
key is greater than the specified threshold.
Tests that the value associated with the specified
key is less than the specified threshold.
Tests that the value associated with the specified
key is matched in its entirety by the supplied regex.
Base-class for visitors that re-write a filter tree.
A set of FeatureFilter algebraic operations.
An object able to transform some FeatureFilter instances sytematically into others.
An alphabet over a finite set of Symbols.
Class for modelling finite automata.
Calculates the fitness of an
Organism in a
Population of OrganismsA
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.Cache which stores up to
limit Objects.A cache that only remembers a given number of keys.
Provides a cache for storing multiple small files in memory.
A UnigeneFactory that will use flat-file indexing of the unigene ascii-art
files.
FlatSequenceDB is an OBDA flatfile sequence databank
implementation.FlatSequenceDBProvider directory-services plugin for
flatfile databases.
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.
StAX handler for any element which just contains a string representation of
a float.
A file format supported by the tag-value event-based parsing system.
This is intended as a repository for tag-value and AnnotationType information
about common file formats.
Title: Frame.
Title: FramedFeature.
A singleton to hold the frame information
This is a class for representing the full HMMER generated Profile HMM (including loop
states N and C terminal looping states).
An atomic symbol consisting only of itself.
A 'fuzzy' location a-la Embl fuzzy locations.
Determines how a
FuzzyLocation should be treated when used
as a normal Location.FuzzyPointLocation represents two types of EMBL-style
partially-defined locations.Determines how a
FuzzyPointLocation should be treated when used
as a normal Location.Holds the results of a CrossOver event, objects of this type are made by
CrossOverFunctionsHolds the results of a CrossOver event, objects of this type are made by
CrossOverFunctionsHandles the GAME <annotation> element
Handles the GAME <annotation> element
Handles the GAME <aspect> element
Handles the GAME <aspect> element
Handles the GAME <dbxref> element
Deals with database crossreferences
StAX handler for GAME <description> elements.
An interface that can be tested for by nested handlers
when trying to do a callback.
Handles the <feature_set> element
Handles the GAME <feature_set> element
this element is used to represent transcripts.
Handles the GAME element
Handles the <feature_span> element
Handles the GAME <feature_span> element
A rudimentary read-only GAME 1.2 Format object.
Handles the GAME <annotation> element
Handles the GAME <gene> element
Handles the root GAME element
Handles the root GAME element
Handles the GAME <map_position> element
Currently, it just ignores it!
An interface that can be tested for by nested handlers
when trying to do a callback.
StAX handler for the GAME <name> element.
Handles the GAME <dbxref> element
StAX handler for GAME <residues> elements.
Handles the GAME <seq> element
Handles the GAME <seq> element
Handles the GAME <> element
Handles the GAME <aspect> element
Handles the GAME <> element.
Handles the GAME <span> element
Currently, it just ignores it!
An interface that can be tested for by nested handlers
when trying to do a callback.
StAX handler for GAME <type> elements.
This distribution emits gap symbols.
A renderer that will display a gapped sequence as a discontinuous series of
regions.
Extension of GappedSymbolList which also projects features
into the gapped coordinate system.
This extends SymbolList with API for manipulating, inserting and deleting
gaps.
Used by a
GeneticAlgorithm.run() method
to determine when the algorithm should stopSimple Implementation of GAStoppingCriteria, signals
a
GeneticAlgorithm to stop after n generations Utility methods for the GA library
Deprecated.
Use org.biojavax.bio.seq.io framework instead
Deprecated.
Use org.biojavax.bio.seq.io.GenbankFormat
Format reader for GenBank files.
Implements some GenBank-specific terms.
Parses Genbank location strings into RichLocation objects.
Deprecated.
Use org.biojavax.bio.seq.io framework instead
Factory which wraps sequence builders in a GenbankProcessor
This class contains functions accessing DNA sequences in Genbank format.
This class contains functions accessing DNA sequences in Genbank format.
Deprecated.
Use org.biojavax.bio.seq.io.INSDseqFormat
Deprecated.
Use org.biojavax.bio.seq.io framework instead
Deprecated.
Use org.biojavax.bio.seq.io framework instead
A class loader that actually produces real Java classes from
GeneratedCodeClass instances.
A CodeClass implementation that is used to generate new classes.
A method that will be generated.
The class that runs the cycles of reproduction, evolution and selection,
potentially on multiple
PopulationsCollects the references to translation methods in one place.
Deprecated.
Use org.biojavax.bio.seq.io framework instead
This class contains functions accessing Peptide sequences in Genpept format.
The interface for things that listen to GFF event streams.
Parse a stream of GFF text into a stream of records and comments.
A record in a GFF3 formatted file.
Use a GFFEntrySet as a DataSource for adding annotation to sequences.
The interface for things that listen to GFF event streams.
A set of entries and comments as a representation of a GFF file.
Interface which captures any errors which occur when parsing
a GFF stream.
An object that filters a stream of GFF, forwarding some
GFFRecords to a
listening GFFDocumentHandler, and dropping others.
Parse a stream of GFF text into a stream of records and comments.
A single GFF record.
A filter that will accept or reject a GFFEntry.
Implementation of GFFRecordFilter that accepts everything.
Implementation of GFFRecordFilter that accepts
records based upon the feature field.
Implementation of GFFRecordFilter that accepts
records based upon the sequence name.
Implementation of GFFRecordFilter that accepts
records based upon the source field.
Listens to a stream of GFF events and writes the lines to a
PrintWriter.
The Glyph interface for painting a shape within bounds
A FeatureRenderer that renders a particular Glyph for Features accepted by a
particular FeatureFilter
Utils class used by Glyph implementors.
Simple parser for the Gene Ontology (GO) flatfile format.
An implementation of RichSequenceDB that uses an underlying HashMap to store the
RichSequence objects.
Iterates over a Fasta file that is kept in memory for optimized access.
An implementation of RichSequenceDB that uses an underlying HashMap to store the
RichSequence objects.
An implementation of SequenceDB that uses an underlying HashMap to store the
sequence objects.
HeaderStAXHandler handles the Header element of
BioJava BlastLike XML.
A stand-alone SequenceRenderContext to make it easy to render to an image.
A Glyph that paints a Helix within the bounds
A listener that merges overlapping hits and culls all hits under a given
length.
AlignmentStAXHandler handles the Hit element of
BioJava BlastLike XML.This is a class for representing HMMER generated Profile HMM.
A class for parsing in Hmmer markov models from HMM_ls files generated by HMMER training
note that this class is still currently experimental.
interface implemented by objects that train HMMs.
an interface for Homologene dataset Builders
Homologene is a NCBI dataset that curates sets
of orthologues from the reference model organisms.
Homologene is a NCBI dataset that curates sets
of orthologues from the reference model ogranisms.
Signifies that two or more features are homologous.
HSPStAXHandler handles the HSP element of BioJava
BlastLike XML.HSPSummaryStAXHandler handles the HSPSummary element
of BioJava BlastLike XML.Renders HTML version of blast-like output.
Deprecated.
Use hibernate and org.biojavax.bio.db
Marks an implementor as having a LifeScienceIdentifier.
Interface for objects that define how to make an ID for a sequence.
A CodeGenerator that provides something semanticaly identical to if.
A distribution trainer that just ignores all counts.
Ignore this record in the stream.
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.
The exception to indicate that an invalid alphabet has been used.
Indicates an invalid organism
The exception to indicate that a symbol is not valid within a context.
This exception indicates that there is no transition between two states.
Reader for
FastqVariant.FASTQ_ILLUMINA formatted sequences.Writer for
FastqVariant.FASTQ_ILLUMINA formatted sequences.ImageMap represents a collection of image map
hotspots.ClientSide represents a client-side style image
map.HotSpots represent an image map hotspot.ServerSide represents a server-side style image
map.ImageMapRenderers create strings representing
Features suitable for use in HTML image
maps.This defines an index entry for an individual sequence within a set of
indexed files.
A database of Annotation instances backed by an indexed file set.
A factory for retrieving parsers and listeners.
An implementation of ParserListenerFactory that uses a static method.
implements Changeable support with a ChangeHub that
stores ChangeListener by key.
An encapsulation of a count over the Symbols within a FiniteAlphabet using
an AlphabetIndex object.
This class implements SequenceDB on top of a set of sequence files
and sequence offsets within these files.
Listens to tag-value events and passes on indexing events to an IndexStore.
Listens to tag-value events and passes on indexing events to an IndexStore.
IndexStore is an interface for indexing flatfiles
according to the OBDA specification.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 contains static utility methods for
creating flatfile indices according to the OBDA standard.A symbol list that is
Integer.MAX_VALUElong, never gives index out of
bounds and always returns ambiguity symbols for everything.Interface to a threadable input handler for
an external process.
A class that provides an InputStream from a File.
Format reader for INSDseq files.
Implements some INSDseq-specific terms.
Base class for java bytecode instructions.
A list of Instructions and/or other CodeGenerator objects.
An efficient implementation of an Alphabet over the infinite set of integer
values.
A single int value.
A class to represent a finite contiguous subset of the infinite IntegerAlphabet
StAX handler for any element which just contains a string representation of
an integer.
CodeClass instances that represent normal Java Class objects.
Thrown to indicate that an ontology term is not acceptable or
appropriate in a given context
Class that computes isoelectric point for denaturated proteins.
A simple Object-double tuple.
Really simple connection pool for JDBC databases.
Returns a DataSource that implements connection pooling
Uses Jakarta Commons DBCP and Pool packages.
Subclass of WeakReference which includes and extra field (the key)
which can be used to help cleanup once this reference has been
enqueued.
An object to find exact subsequences within a sequence.
A Label used to mark a position in byte code.
Renderer which draws a track of sequence with a textual label.
The interface for things that can render labels for a line of information
about a sequence.
Wrapper arround MappedByteBuffers to allow long-indexed access to files
larger than 2 gigs.
LayeredRenderer handles the lane offsets for
MultiLineRenders.Wrapper implementation of FeatureHolder which calls a method
to create a contained FeatureHolder on demand.
An implementation of AnnotationDB that lazily applies a filter.
FeatureHolder which lazily applies a specified filter to another FeatureHolder.
An implementation of AnnotationDB that does a JIT search on another set.
Life Science Identifier (LSID).
Exception thrown in the event of an error in
parsing a LSID-formatted string.
A LIGHT implementation of PairDPCursor.
Deprecated.
Just use SparseVector.kernel instead...
Encapsulates the rendering info for a single line of the display.
A parser that splits a line into tag/value at a given column number.
This kernel computes the sum of the dot products between items of two lists
at corresponding indexes.
Maps one object to another.
A list that represents a series of values.
A local variable.
A set of integers, often used to represent positions on biological sequences.
Handler to the XFF location type.
Tools class containing a number of operators for working with
Location objects.The interface for something that will draw the sequence logo for a state.
StAX handler for any element which just contains a string representation of
a long.
Start/end state for HMMs.
A translation table that will handle the many-to-one mappings
that you see, for example, with genetic codes.
Builder for a data store that is backed by a java.nio.MappedByteBuffer.
A CodeGenerator that just marks a label that can be used for jumps.
A markov model.
MassCalc calculates the mass of peptides which for our
purposes are SymbolLists which contain
Symbolsfrom the protein Alphabet.This class is analogous to java.util.Matcher except that it works
on SymbolLists instead of Strings.
A BioMatcher class returned by MaxMismatchPattern.matcher() that implements
searching of a SymbolList.
This class permits searching a SymbolList with another SymbolList while
permitting a specified number of mismatches.
The results of a meme run.
Merged view onto a list of underlying Annotation objects.
FeatureHolder which exposes all the features in a set
of sub-FeatureHolders.
Produced by LocationTools as a result of union operations.
An AnnotationDB that provides a merged view of a list of underlying DBs.
A state that contains an entire sub-model.
Encapsulates the training of an entire model.
MotifTools contains utility methods for sequence
motifs.MultiLineRenderer is a SequenceRenderer
which collects a number of other SequenceRenderers
each of which render their own view of a Sequence.An implementation of RichLocation which possibly covers multiple locations,
on different strands, different circular lengths, or different sequences.
Partician multiple values for a tag into their own tag groups.
A class that mutates a
SymbolList Place Holder class that doesn't mutate its SymbolLists
Deprecated.
Use hibernate and org.biojavax.bio.db
The namespace of an entry in a database schema.
Simple implementation of SymbolTokenization which uses the `name'
field of the symbols.
Simple URL generator for Entrez at the NCBI.
Represents an NCBI Taxon entry, a combination of the taxon and taxon_name
tables in BioSQL.
Implementors are able to load taxonomy files and generate sets of NCBITaxon objects
that represent them.
Needleman and Wunsch defined the problem of global sequence alignments, from
the first till the last symbol of a sequence.
Encapsulates a kernel that wraps another kernel up.
Support class for applications which need to patch together sections
of sequence into a single SymbolList.
A Sequence which is assembled from other sequences contained
in a set of ComponentFeature objects.
Represents a Nexus block.
Builds a Nexus block from listening to events.
This abstract version knows how to build and add comments.
Listens to events from NexusBlockParser objects to create objects.
Parses Nexus blocks.
All block parsers should derive from this abstract parser.
Represents a Nexus comment, possibly nested.
Represents Nexus files.
Builds a Nexus file by listening to events.
Reads/writes Nexus files and fires events at a NexusFileListener object.
Listens to events fired by the Nexus parser.
Example abstract implementation which all others should extend.
Represents general info about nexus objects.
Class for modelling non-deterministic finite automata.
This class caches a reference to all objects that
it directs its delegate to make.
Builder for a datastore that has no practical file size limit.
Performs a normalization on the results of a nested kernel.
Note is a generic class intended to hold a term describing the note,
a value to associate with that term, and a rank.
Useful functionality for processing nucleotide sequences.
This class encapsulates all the parsing of the OBDA registry
configuration file.
Singleton class for parsers that understand OBDA URIs.
utility methods for implementing the equals() and hashCode() methods of Objects.
an interface for events that occur during parsing of .obo files
A file handler for .obo files
A class to parse the content of an OBO file.
Parses an OBO file.
OffsetRulerRenderer can render the ruler starting from an arbitrary offset from the sequence.
An ontology.
A basic in-memory implementation of an ontology
Thrown to indicate an error in an Ontology object
A factory for Ontology instances.
This is an interface for optimizing ontology operators.
A term in an ontology which identifies another ontology.
Simple in-memory implementation of a remote ontology term.
Tools for manipulating ontologies.
The interface for filters that can potentialy optimize themselves, and
compare themselves with other filters.
Deprecated.
Use hibernate and org.biojavax.bio.db
This does a 2-point-crossover on two chromosomes keeping the Symbols in each
chromosome constant.
Provides an N'th order distribution.
Default factory for Order-N distributions.
A GA 'organism' contains one or more Chromosomes
Deprecated.
Use org.biojavax.bio.taxa framework instead
Factory which wraps SequenceBuilders in an OrganismParser.
this entry contains data about the orthologue.
Interface for classes that store and manipulate
orthologues.
An iterator for the contents of
an OrthologueSet.
Each HomologeneEntry represents a single
Homologene record that relates two
presumptive orthologues.
Interface for a Set of OrthoPairSets
Iterator for a OrthoPairCollection
represents the Homologene Group.
all OrthoPairs must meet the requirement
defined by filter.
at least one OrthoPair must meet the requirement
defined by filter.
Interface to a threadable output handler for
an external process.
Annotation implementation which allows new key-value
pairs to be layered on top of an underlying Annotation.
Overlap one map onto another.
This is a dummy interface to permit identification of renderers whose
output is to be overlaid along the lines of the Marker Interface
pattern.
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.
A SymbolList that stores symbols as bit-patterns in an array of longs.
This class makes PackedSymbolLists.
An encapsulation of the way symbols map to bit-patterns.
A factory that is used to maintain associations between alphabets and
preferred bit-packings for them.
A renderer that adds padding before and after a delegate renderer.
Class for pairing up two independant distributions.
A cursor over a DP matrix.
Storage structure for intermediate values from a pairwise
dynamic programming run.
PairwiseDiagonalRenderer renders a region of
similarity between two sequences as a straight line.Algorithms for dynamic programming (alignments) between pairs
of SymbolLists.
PairwiseFilteringRenderer wraps a
PairwiseSequenceRenderer and filters the
PairwiseRenderContexts passed to it.PairwiseOverlayRenderer allows a list of other
PairwiseSequenceRenderers to superimpose their
output.PairwiseRenderContext encapsulates information
required for the rendering of a pair of sequences.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).PairwiseSequenceRenderers render information about the
relationship between two sequences.PairwiseRendererForwarder forward events to other
renderers.A template type.
Event which signals a bad line when parsing a record.
Listener for a ParseErrorEvent.
Source for a ParseErrorEvent.
ParseException should be thrown to indicate that there was a problem with
parsing sequence information.
Low-level event based parser callback.
Encapsulate the parsing of lines from a buffered reader into tag-value
events.
Exception thrown when an error occurs in document parsing.
ParserListener is an immutable pairing of a parser and
listener.A class analogous to java.util.regex.Pattern but for SymbolLists.
A class that creates Patterns for regex matching on
SymbolLists of a specific Alphabet.
A SAX2 parser for dealing with native PDB files.
A class that converts Protein Data Bank (PDB) to
XML that will validate against the biojava:MacromolecularStructure DTD.
A concrete AbstractPeptideDigestRenderer.
Format object representing Phred Quality files.
PhredSequence is an extension of SimpleSequence that implements
Qualitative to hold Phred quality scores.
PhredTools contains static methods for working with phred
quality data.
Builds a PHYLIP file by listening to events.
Reads PHYLIP interleaved alignment files and fires events at a PHYLIPFileListener object.
Listens to events fired by the PHYLIP parser.
A painter that just draws a block (or bar).
A simple implementation of SymbolStyle that just uses a single paint for
outlines and a single paint for filling.
A location representing a single point.
This kernel computes all possible products of order features in feature
space.
A collection of GA organisms
Holds info about base positions.
Resolves a position that is fuzzy or covers a range of bases by
converting it to a single base.
The minimal resolver returns the base which provides the
average range, halfway between maximal and minimal.
The maximal resolver returns the base which provides the
largest possible range.
The minimal resolver returns the base which provides the
smallest possible range.
Implementation of XMLWriter which emits nicely formatted documents
to a PrintWriter.
Exception which is thrown if a child process managed by
ProcessTools
exceeds a specified time limit.Deprecated.
preferable to use org.biojava.utils.ExecRunner
or the org.biojava.utils.process package.
A state in a HMMer model.
Internal class used by ProjectionEngine to wrap Feature objects.
Helper class for projecting Feature objects into an alternative
coordinate system.
Interface implemented by all projected feature objects.
Interface that defines the projection between original features and
projected features.
Factory for proxy objects which project BioJava features
into alternate coordinate systems.
Internal helper class.
This is an interface for things that project feature templates.
Some common things you want to do while projecting features.
StAX handler for xff:prop detail elements.
Interface for objects that change tag names or properties systematically.
PropertyConstraints describes a constraint applied
to the members of an annotation bundle.A property constraint that accpepts items iff they are accepted by both
child constraints.
ByAnnotationType accepts a property value if it
belongs to type defined by AnnotationType.ByClass accepts a property value if it is an
instance of a specific Java class.Enumeration accepts a property if it is present
in the specified set of values.Matches properties if they have exactly this one value.
A property constraint that accepts items iff they are accepted by either
child constraints.
A Selection function that determines the proportion of individuals in a new
population proportionally to their fitness.
The protease class stores parameters needed by Digest to digest a protein sequence.
Registry and utility methods for Proteases.
Deprecated.
Use org.biojavax.bio.seq.io framework instead
Deprecated.
Use org.biojavax.bio.seq.io framework instead
Factory which wraps sequence builders in a ProteinRefSeqProcessor
The central port-of-call for all information and functionality specific to
SymbolLists over the protein alphabet.
ProviderNotFoundException is thrown when a sequence
database provider can not be located.Qualitative is an interface for classes wanting to hold quality
data in symbolic form such as Phred scores.
This kernel computes the radial base kernel that corresponds to a gausian
distribution.
RandomAccessReader extends Reader to
provide a means to create buffered Readers from
RandomAccessFiles.A simple implementation of Location that contains all points between
getMin and getMax inclusive.
Allows cross-references to other databases to be ranked.
Defines an object as being able to have ranked cross references associated
with it.
Represents a documentary reference.
Reader input handler
that reads the input for an external process from a
reader.
A multi threaded class
which pipes the contents of an input reader to an output
writer.
Interface for
FeatureHolder objects which know how to
instantiate new child Features.Record represents a record within an indexed flat file
databank as defined by the OBDA standard.Impl is the default implementation of Record.A Glyph that paints a rectangle shape within the bounds.
RectangularBeadRenderer renders features as simple
rectangles.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.Deprecated.
Use org.biojavax.bio.seq.io framework instead
A ValueChanger.Changer that returns a specific match value using a regex
Pattern.
An exception thrown by classes of this package.
A TagValueParser that splits a line based upon a regular expression.
A ValueChanger.Splitter that splits a line of text using a regular
expression, returning one value per match.
Registry is a factory which gets implementations of
the BioJava SequenceDBLite interface.The BioDirectory Registry is a simple system for specifying
where to find services which provide sequence databases.
A RegistryConfiguration that allows you to treat other
configurations as providing important or default configuration
information.
A simple implementation of RegistryConfiguration backed by a Map.
A
RegistryException thrown when the registry cannot
find an implementation of a requested SequenceDB.An alignment that relabels another alignment.
A feature that indicates that there is some remote feature that can't be
represented entirely on a single Sequence.
A tuple of Location and sequence ID.
The interface for objects that actually can take a RemoteFeature and
return a Sequence object with the feature resolved into a real feature.
RemotePairwiseAlignmentOutputProperties: the simplest representation of an object capable of holding
output formatting informations to be fed to a RemotePairwiseAlignmentService-implemented object.
RemotePairwiseAlignmentProperties is a interface that contains the barest of
methods for setting and getting Alignment properties.
This interface specifies minimal information needed to execute a pairwise alignment on a remote service.
This class implements RemotePairwiseAlignmentProperties by specifying several
convenient methods used to wrap the addition of Blast alignment parameters.
The RemoteQBlastOutputFormat enum acts like static fields for specifiying various
values for certain output options.
The actual implementation of the RemotePairwiseAlignmentOutputProperties
interface for the QBlast service.
RemoteQBlastService - A simple way of submitting BLAST request to the QBlast
service at NCBI.
A term in another ontology.
Simple in-memory implementation of a remote ontology term.
A good base class to implement ProjectionContext from.
SAX EntityResolve which looks up system IDs as resources
from a Java ClassLoader.
RestrictionEnzyme represents a restriction enzyme
according to the REBASE standard.RestrictionEnzymeManager manages collections of
static RestrictionEnzyme instances.RestrictionMapper is a class for annotating
Sequences with Features which represent
restriction sites.RestrictionSite represents the recognition site of a
restriction enzyme.Template for construction of
RestrictionSites.A reverse complement view onto
Sequence interface.A translation table that can also translate from the target to source
alphabet.
Annotatable objects that can have rich annotations.
An annotation collection which stores annotations as Note objects.
Represents a feature that can be given name and rank and be
moved from one sequence to another.
Added-value extension of Feature.Template including bits we're
interested in, eg. featureRelationshipSet for relationships with
other features, and rankedCrossRefs for lookups into other databases.
Some useful tools for working with features.
Represents the relation between two features.
Holds feature relationships.
Describes locations, and adds the concepts of circularity, fuzziness,
annotations, and cross-references to other databases.
This class represents a strand on which a location may lie.
Some useful tools for working with Locations.
This interface allows a class to generate Rich objects based on a class
name and some parameters.
Runs a service that builds rich objects, and provides some default values
for things like default ontology, default namespace, etc.
This class implements all methods of RichSeqIOListener and takes no action.
An interface for classes that listen to BioEntry or
RichSequence I/O streams.
A rich sequence is a combination of a org.biojavax.bio.Bioentry and a
Sequence.
A set of convenience methods for handling common file formats.
Used to iterate over a single rich sequence
Stores a number of useful terms used across many sequence formats for
consistency's sake.
Some useful tools for working with RichSequence objects.
An interface for objects that can build RichSequences.
Simple factory for constructing new RichSequenceBuilder objects.
A database of RichSequences with accessible keys and iterators over all
sequences.
A database of RichSequences.
Allows a file format to be read/written as RichSequences.
Provides a basic format with simple things like line-widths precoded.
Provides the basic implementation required for simple header/footer-less files such as Genbank.
An interface for classes that know how to handle subsequence operations.
Essentially the same as SequenceIterator.
Parses a stream into sequences.
Writes all of the sequences from a SequenceIterator to a stream with a
particular format.
Useful functionality for processing DNA and RNA sequences.
RoundRectangularBeadRenderer renders features
as rectangles with rounded corners.RulerRenderer renders numerical scales in sequence
coordinates.Reader for
FastqVariant.FASTQ_SANGER formatted sequences.Writer for
FastqVariant.FASTQ_SANGER formatted sequences.Lightweight adaptor which translates SAX content events into
StAX form, and provides delegation services.
Lightweight adaptor which translates SAX content events into
StAX form, and provides delegation services.
A
Chromatogram as loaded from an
SCF v2 or v3 file.This class computes the score that is used to be used
in a DP optimisation.
In this class, calculateScore returns the probability of
a Symbol being emitted by the null model.
In this class, calculateScore returns the odds ratio
of a symbol being emitted.
In this class, calculateScore returns the probability
of a Symbol being emitted.
A utility class to make searching a Sequence with many regex patterns
easier.
Interface for a class that will recieve match information
from this class.
The
SearchBuilder interface is to be used by objects
which accumulate state via a SearchContentHandler and
then construct a SeqSimilaritySearchResult object.
An adapter for SearchContentHandler.
Filtering implementation of SearchContentHandler that by default passes
all messages on to the next delegate in the chain.
SearchContentHandler is a notification interface for
objects which listen to search stream parsers.This class prints to a PrintStream
calls to the SearchContentHandler interface
in human readable form.
There has been some failure that prevents a search from completing.
The interface used to inform interested parties that some sequence has
been searched and something found.
A SearchListener that prints events out to a PrintStream.
A simple listener that filters out all hits that are too short.
A SearchListener that passes events on to two delegate listeners.
A simple wrapper implementation.
A GlyphRenderer subclass that specificatlly handles Features pertaining to Secondary Structure
(Helices, Turns and Strands).
This interface provides a collective name for IO classes that implement a
seek function (e.g.,
RandomAccessFile).Selects Organisms for Replication and returns the offspring.
Selects individuals who's fitness exceeds a threshold value.
A pattern that can be used to find regions with given sequence content.
Deprecated.
Use org.biojavax.bio.seq.io framework instead
Adapter class for SeqIOListener that has empty methods.
SeqIOConstants contains constants used to identify
sequence formats, alphabets etc, in the context of reading and
writing sequences.Deprecated.
Use org.biojavax.bio.seq.io framework instead
Base-class for listeners that pass filtered events onto another listener.
Notification interface for objects which listen to a sequence stream
parser.
Deprecated.
use org.biojavax.bio.seq.RichSequence.IOTools
A
SeqSimilarityAdapter converts SAX events into method
calls on a SearchContentHandler implementation.Objects of this type represent one particular installation (not
just implementation) of a sequence similarity searcher such as
BLASTP.
Objects of this type represent one particular hit (sequence and
associated information) from a sequence similarity search.
ByScoreComparator compares
SeqSimilaritySearchHits by their score.BySubHitCountComparator compares
SeqSimilaritySearchHits by their number of
sub-hits.Objects of this type represent one particular result of a sequence
similarity search.
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.
ByScoreComparator compares
SeqSimilaritySearchSubHits by their score.BySubjectStartComparator compares
SeqSimilaritySearchSubHits by their start position
on the subject sequence.SeqSimilarityStAXAdapter is a handler for XML
conforming to the BioJava BlastLike DTD.SeqSimilarityStAXHandler is a base class for creating
modular StAX handlers which send callbacks to a
SeqSimilarityStAXAdapter.
A biological sequence.
A SAX2 parser for dealing with a sequence alignments.
An object which adds some additional information to a Sequence.
Interface for objects which accumulate state via SeqIOListener,
then construct a Sequence object.
Basic SequenceBuilder implementation which accumulates all
notified information.
Simple factory for constructing new SequenceBuilder objects.
Base-class for builders that pass filtered events onto another builder.
StAX handler for elements containing sequence
A database of sequences with accessible keys and iterators over all
sequences.
Turn an entire SequenceDB instance into a DistDataSource.
A SequenceDBInstallation has the functionality of a factory for
SequenceDB objects and additionally manages the SequenceDB objects
created by itself such that the minimum number of SequenceDB
objects is created by a particular SequenceDBInstallation
object.
A database of sequences.
Interfaces for named resources that can provide sequences via a
database given some configuration information as defined by the
OBDA standard.
Deprecated.
SimpleSeqSimilaritySearchHit has been made Annotatable
and is now functionally identical.
Deprecated.
SimpleSeqSimilaritySearchResult has been made
Annotatable and is now functionally identical.
Deprecated.
SimpleSeqSimilaritySearchSubHit has been made
Annotatable and is now functionally identical.
This SequenceBuilder has a variety of modes of operation.
An abstract implementation of SequenceDB that wraps up another database.
Deprecated.
use org.biojavax.bio.seq.io.RichSequenceBuilder or
use org.biojavax.bio.seq.io.SequenceBuilder
Defines what a sequence format does.
mark interface
An iterator over a bag of sequences.
A panel that displays a Sequence.
Handles multiple SequencePanels and Ranges so that a Sequence can be wrapped
over more than one line on screen.
Deprecated.
This doesn't handle loads of stuff.
A context within which sequence information may be rendered.
The metric object for the 'border' area - the area between the extent of
the rendered area and the beginning or end of the sequence.
The interface for things that can render a line of information about a
sequence.
An implementation of SequenceRenderer that delegates rendering to another
renderer.
Turns a sequence database into a GFF event stream.
Methods for manipulating sequences.
An event indicating that a mouse gesture was recognised within a widget that
renders sequences.
Utility methods for handling META-INF/services files
This kernel implements a three layer neural net.
SimilarityPairBuilder annotates query and subject
Sequence with SimilarityPairFeatures
created from SAX events supplied via a
SeqSimilarityAdapter.SimilarityPairFeature describes a pairwise
similarity between two nucleotide sequences (as it extends
StrandedFeature).EmptyPairwiseAlignment empty pairwise alignment
which has labels to empty symbol lists.Template for construction of
SimilarityPairFeatures.Each HomologeneEntry represents a single
Homologene record that relates two
presumptive orthologues.
A simple implementation of an Alignment.
SimpleSimpleAlignment is a simple implementation of
AlignmentElement.
Simple implementation for specifying markup styles.
A simple no-frills implementation of the FiniteAlphabet interface.
A no-frills implementation of Annotation that is just a wrapper
around a
LinkedHashMap.A no-frills implementation of AnnotationDB.
Basic implementation of AGAVEAnnotFilter
A Sequence which is assembled from other sequences contained
in a set of ComponentFeature objects.
Basic SequenceBuilder implementation which accumulates all
notified information and creates a SimpleAssembly.
A basic implementation of AtomicSymbol.
Reference implementation of a BioEntry object which has no features or sequence.
Represents a relationship between two bioentries that is described by a term
and given a rank.
A basic chromatogram implementation which provides public mutators
for setting the various attributes of the chromatogram.
a simple no-frills implementation of the
CodonPref object that encapsulates
codon preference data.
An implementaion of Comment.
Represents an ontology that can be compared to other ontologies.
A Term object that can be compared and thus sorted.
Basic comparable triple, BioSQL style.
Simple Implementation of the
CrossOverFunction interfaceA basic CrossRef implementation.
A simple implementation of a distribution, which works with any finite alphabet.
Deprecated.
Distribution impls should be providing custom trainers.
A no-frills implementation of DistributionTrainerContext.
A basic DocRef implementation.
Represents an author of a documentary reference.
A Dot state that you can make and use.
A no-frills implementation of a feature.
A no-frills implementation of FeatureHolder.
FeatureRealizer which uses a lookup table to map template classes
to implementations.
Title: SimpleFramedFeature.
Simple implementation of the
GACross interface.Simple implementation of GappedSequence.
This implementation of GappedSymbolList wraps a SymbolList, allowing you to
insert gaps.
An aligned block.
A simple implementation of the
GeneticAlgorithm interface it
is not intended that this class be overidden, hence it is final.A genetic code translation table representing a translation table in the
DDBJ/EMBL/GenBank Feature Table (appendix V).
A no-frills implementation of a GFFRecord.
A simple no-frills implementation of the HomologeneBuilder interface.
A no-frills implementation of Homology.
This is a no-frills implementation of the Index interface.
Simple input handler
that reads the input for an external process from an
input stream.
A no-frills implementation of ItemValue.
A no-frills implementation of a translation table that
maps between two alphabets.
Simple no frills Implementation of the MutationFunction interface
A basic Namespace implemenation.
Reference implementation of NCBITaxon.
Represents a name class plus name combination for an NCBITaxon object.
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/ .
Simple implementation of Note.
A Simple Haploid Organism implementation
this entry contains data about the orthologue.
A no-frills implementation of the OrthoPair interface
a no-frills implementation of a Homologene Group
Simple output handler
that pipes the output of an external process to an
output stream.
Simple concrete implementation of the
Population interfaceA simple implementation of the Position interface.
Simple implementation of RankedCrossRef.
Represents a documentary reference.
A no-frills implementation of a remote feature.
SimpleRestrictionSite represents the recognition site
of a restriction enzyme.A no-frills implementation of TranslationTable that uses a Map to map from
symbols in a finite source alphabet into a target alphabet.
Simple annotation wrapper.
A simple implementation of RichFeature.
Represents a relationship between two features that is described by a term.
A simple implementation of RichLocation.
Creates objects and returns them, and stores them in an internal
map of singletons for reference.
A simple implementation of RichSequence.
Constructs BioEntry objects by listening to events.
Generates RichSequenceBuilder objects.
SimpleSeqSimilaritySearchHit objects represent a
similarity search hit of a query sequence to a sequence referenced
in a SequenceDB object.SimpleSeqSimilaritySearchResult objects represent a
result of a search of a SymbolList against the
sequences within a SequenceDB object.SimpleSeqSimilaritySearchSubHit objects represent
sub-hits which make up a hit.A basic implementation of the
Sequence interface.Basic SequenceBuilder implementation which accumulates all
notified information and creates a SimpleSequence.
This class is an implementation of interface SequenceDBInstallation
that manages a set of SequenceDB objects.
A no-frills implementation of SequenceFactory that produces SimpleSequence
objects.
SimpleSimilarityPairFeature represents a similarity
between a query sequence and a subject sequence as produced by a
search program.A no-frills implementation of StatePath.
A no-frills implementation of StrandedFeature.
A no-frills implementation of an SVM classifier model.
No-frills implementation of SVMTarget.
Basic implementation of SymbolList.
This class makes SimpleSymbolLists.
Class that implements the SymbolPropertyTable interface
A simple implementation of a symbol property table database.
A no-frills implementation of SymbolStyle.
Helper class to wrap one TagValueListener inside another one.
Deprecated.
replaced by classes in
org.biojavax.bio.taxaDeprecated.
replaced by classes in
org.biojavax.bio.taxaSimpleThreadPool is a basic implementation of
ThreadPool for use where we don't wish to introduce a
dependency on a 3rd-party pool.A TrackLayout implenentation that wraps the sequence smoothly after a set number of residues
A no-frills implementation of TranslationTable that uses a Map to map from
symbols in a finite source alphabet into a target alphabet.
A simple XML DocumentHandler that processes SAX2 events
to create a sensibly formatted XML as it parsed
without populating objects with data.
An implementation of DP that aligns a single sequence against a single model.
The dynamic programming matrix for a single sequence.
An alphabet that contains a single atomic symbol.
Class that handles drawing in six frames for other
classes.
A feature renderer that computes the data necessary to render
multi-exon transcripts without CDS data.
Annotation that is optimized for memory usage.
Constant-memory implementation of single-head DP cursor.
Lightweight implementation of Map which uses little memory to store a
small number of mappings, at the expense of scalability.
Lightweight implementation of Set which uses little memory to store a small
number of items, at the expense of scalability.
Basic SequenceBuilder implementation which accumulates all
notified information and chooses a sequence implementation
suited to the size of the sequence.
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).
Train a regression support vector machine using the Sequential Minimal
Optimization algorithm.
Train a support vector machine using the Sequential Minimal
Optimization algorithm.
A in memory cache using soft references.
Soft masking is usually displayed by making the masked regions somehow
different from the non masked regions.
Implementations will define how soft masking looks.
Cache which is cleared according to memory pressure.
Reader for
FastqVariant.FASTQ_SOLEXA formatted sequences.Writer for
FastqVariant.FASTQ_SOLEXA formatted sequences.An implementation of a sparse vector.
A version of the standard dot-product kernel that scales each column
independently.
An implementatoin of UnigeneFactory that manages it's data in an SQL
database.
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.
A logo painter that paints in stacked areas.
A state in a markov process.
This class implements a state machine for parsing events from
the Parser class.
Interface implemented by State listeners that
want notification when a transition leaves the State.
Interface for a State within this StateMachine
Class that produces StateMachineInstance objects.
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.
Interface for StAX content handlers.
Interface for StAX content handlers.
Simple implementation of the
StAXContentHandler
interface, with empty implementations for all the methods.Simple implementation of the
StAXContentHandler
interface, with empty implementations for all the methods.StAX handler shamelessly ripped off from Thomas Down's
XFFFeatureSetHandler.
StAX handler shamelessly ripped off from Thomas Down's
XFFFeatureSetHandler.
StAX handler shamelessly ripped off from Thomas Down's XFFFeatureSetHandler.
StAXHandlerBindings associates an
ElementRecognizer with a factory which creates
StAXContentHandlers for elements which it the
ElementRecognizer accepts.StAXHandlerFactory is an interface for factories
producing StAXContentHandlers which are used by the
SeqSimilarityStAXAdapter.Factory for StAX content handlers.
Factory for StAX content handlers.
Factory for StAX content handlers.
StAX handler shamelessly ripped off from Thomas Down's
XFFFeatureSetHandler.
StAX handler shamelessly ripped off from Thomas Down's
XFFFeatureSetHandler.
A callback that is invoked during the training of an HMM.
Compute sites of stop codons.
Adds the concept of 'strand' to features.
Class to represent the 'strandedness' of a feature.
Template class for parameterizing the creation of a new
StrandedFeature.StAX handler for XFF strandedFeature type.
Process strings and return strand objects.
Event based parser callback.
Parse a stream of characters into BioJava symbols.
A multi threaded class
which pipes the contents of an input stream to an output stream.
Parses a stream into sequences.
Writes all of the sequences from a SequenceIterator to a stream with a
particular format.
StAX handler for any element which just contains a string.
Utility class for formatting strings into regular-sized blocks.
Simple access to protein seccondary structure assignments.
A renderer context that allows some or all properties of another context to
be over-ridden.
SubPairwiseRenderContext is a rendering context
which wraps a delegate context and effectively hides some of the
delegate's properties with its own.View a sub-section of a given sequence object, including all the
features intersecting that region.
TargetContext that implements the mapping between the parent sequence and this
sub-sequence.
Allows a new renderer to "wrap" another one, replacing one or more values.
This object is able to read a substitution matrix file and constructs a short
matrix in memory.
Suffix tree implementation.
A node in the suffix tree.
Computes the dot-product of two suffix-trees as the sum of the products
of the counts of all nodes they have in common.
Encapsulates the scale factor to apply at a given depth.
Scale using a multiple of two DepthScalers.
Scales by 4^depth - equivalent to dividing by a probablistic flatt prior
null model
Scale using a BitSet to allow/disallow depths.
Scale all depths by 1.0
An SVM classifier model.
Kernel for support vector machines and related methods.
An SVM classifier model.
This class does a sort of mutation by exchanging two positions on the
chromosome.
Deprecated.
Use org.biojavax.bio.seq.io framework instead
Deprecated.
Use org.biojavax.bio.seq.io framework instead
Factory which wraps SequenceBuilders in a SwissprotProcessor
This class contains functions accessing sequences in swiss-prot.
A single symbol.
A sequence of symbols that belong to an alphabet.
SymbolListCharSequence is a CharSequence
implementation which wraps a SymbolList.This interface exists to hide implementational details
of SymbolLists when making chunked symbol lists.
Tools class for constructing views of
SymbolList objects.class for maintaining properties associated with a symbol
Database of
SymbolPropertyTable objects.Iterator over
SymbolPropertyTable objects.Encapsulate a stream of Symbols being parsed from some input
stream.
SymbolSequenceRenderer renders symbols of a
SymbolList.The interface for things that say how to paint a symbol.
Encapsulate a mapping between BioJava Symbol objects and
some string representation.
A registry that loads up the standard biodirectory files.
Parse tab-delimited ontology files into Ontology objects.
Implements IndexStore as a serialized file for the java data and a
tab-delimited file of offsets.
Pushes a new parser and listener, or delegate to a listener depending on the
tag.
Silently drop all tags except those specified, and pass the rest onto a
delegate.
TagMapper maps arbitrary object keys to new keys.
Rename tags using a TagMapper.
Utility class for representing tag-value pairs for TagValueParser
implementors.
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.
An object that wishes to be informed of events during the parsing of a file.
Tokenize single records (lines of text, objects) into a tag and a value.
Interface for TagValueListeners that wrap other TagValueListeners
Represents Nexus taxa blocks.
Builds Nexus taxa blocks.
Listens to events that represent Nexus taxa blocks.
Parses Nexus taxa blocks.
Deprecated.
replaced by classes in
org.biojavax.bio.taxaDeprecated.
replaced by classes in
org.biojavax.bio.taxaDeprecated.
replaced by classes in
org.biojavax.bio.taxaDeprecated.
Use hibernate and org.biojavax.bio.db
Common things you may want to do with feature templates.
A term in an ontology.
Simple in-memory implementation of an ontology term.
A BlockPainter that renders letters in proportion to the size of the signal.
A logo painter that paints in stacked letters.
A simple implementation of RichSequence.
ThreadPool specifies basic thread-pooling
operations such that third-party implementations may be used
without requiring changes to BioJava.Tournament Selection chooses the best organisms from n random subsets of a
given population.
An interface for the handling of the layout of a WrappedSequencePanel.
Flags an object as being able to register itself with a model trainer.
This is a small and ugly class for storing a trainer and a transition.
This is a small and ugly class for storing a transition.
An object that can be used to train the transitions within a MarkovModel.
A translated view of some underlying distribution.
TranslatedSequencePanel is a panel that displays a
Sequence.A ProjectionContext that translates and optionaly flips features.
Encapsulates the mapping from a source to a destination
alphabet.
Represents Nexus trees blocks.
A simple representation of a Newick tree as a single string.
Builds Nexus taxa blocks.
Listens to events that represent Nexus trees blocks.
Parses Nexus taxa blocks.
A triple in an ontology.
Basic in-memory implementation of a Triple in an ontology
This can be used to implement Ontology.createTriple
Class that represents the tristate values possible in
a logical operation: true, false and indeterminate.
A Glyph that paints a wide 'H' line within the bounds
A Glyph that paints a two headed arrow within the bounds
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.
A suffix tree is an efficient method for encoding the frequencies
of motifs in a sequence.
end Tree modification methods
This is a utility implementation of Changeable that doesn't fire any events
or keep references to any listeners.
This class decompresses an input stream containing data compressed with
the unix "compress" utility (LZC, a LZW variant).
UnequalLengthAlignment has the following behavior.
An implementation of an uniform distribution
A single unigene cluster.
A database of Unigene clusters.
Objects that can be used to produce a
UnigeneDB instance
given a URL.Usefull tools for working with Unigene.
A class to describe events for alternative product comments.
A class to describe protein-protein interactions.
A class to describe isoforms for alternative product comments.
A class to describe seq caution entries.
Format reader for UniProt files.
Implements some UniProt-specific terms.
Parses UniProt location strings into RichLocation objects.
Format reader for UniProtXML files.
Implements some UniProtXML-specific terms.
Deprecated.
Use hibernate and org.biojavax.bio.db
Exception indicating that some provided data does not represent
a supported chromatogram format.
A distribution which does not interact with the training framework.
URLFactory defines a means of obtaining a URL
associated with an object.Interface for a factory method to return a list of
0, 1 or more
DatabaseURLGenerator instances.An implementation of TrackLayout that that wraps a sequence over an arbitrary set of ranges
Just make the property follow the common case
Intercept the values associated with some tags and change them
systematically.
SequenceDB implementation that returns new SequenceView instances
wrapping the sequences in an underlying database.
A view onto another Sequence object.
ViewSequenceFactory is a base class for creating
search handlers which create and cache views on the query and
subject sequences.Things that will be shown filters.
Objects that can walk over a filter expression, showing each element to a
visitor.
A cache which retains weak references to objects
Deprecated.
replaced by classes in
org.biojavax.bio.taxaDeprecated.
replaced by classes in
org.biojavax.bio.taxaMap implementation which keeps weak references to values.
Functions for access to a web based database that returns sequences
in a variety of formats.
Inspred by the BioJava Distribution objects the WeightedSet is a map from
a Key to a Weight.
A log odds weight matrix.
Annotates a sequence with hits to a weight-matrix.
Wraps a weight matrix up so that it appears to be a very simple HMM.
an object to return statistics about
the frequency of the wobble base
in a set of synonymous codons.
Base class for tokenizations which accept whitespace-separated
`words'.
Simple output handler
that writes the output of an external process to an
writer.
StAX handler which converts and stream of parse events for an XFF
featureSet element into BioJava SeqIO events.
Factory for StAX content handlers.
Common functionality for manipulating XFF.
Simple XFF writing code, ripped off from Dazzle 0.08.
StAX handler for parsing AnnotationTypes in FilterXML documents.
Handler for an individual
CollectionConstraint in an AnnotationType.Handler Factory for a
CollectionConstraint in an AnnotationType.Handler for an individual
PropertyConstraint in an AnnotationType.Handler Factory for a
PropertyConstraint in an AnnotationType.Main class for writing AnnotationTypes as XML.
Writer for types of CollectionConstraint.
Writer for types of PropertyConstraint.
Construct java beans from XML elements
A SAX parser that reads an XML representation of a
Distribution from a file and recreates it as a Distribution Object.
Writes an OrderNDistribution or simple Distribution to an XML file.
Factory producing content handlers for parsing FilterXML elements.
StAXContentHandler for a particular type of FeatureFilter.
Factory of StAXContentHandlers for a particular type of FeatureFilter.
Write FeatureFilters in XML format.
Interface for an object which can write a FeatureFilter as XML.
Utility class for reading chunks of XML files and feeding them to SAX.
Object which knows how to represent itself as an XML element.
Simple interface for building XML documents.
A feature renderer that draws non-contiguous features as a set of boxes
joined by zig-zags.
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.
org.biojavax.bio.taxa