Uses of Interface
org.biojava.utils.Changeable

Packages that use Changeable

Package	Description
org.biojava.bio	The core classes that will be used throughout the bio packages.
org.biojava.bio.alignment	Classes to generate and describe sequence alignments.
org.biojava.bio.dist	Probability distributions over Alphabets.
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.gui.sequence	Graphical displays of biological sequences and associated annotations.
org.biojava.bio.molbio	The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.
org.biojava.bio.program.gff3	Support for reading and writing GFF3.
org.biojava.bio.program.hmmer	Tools for working with profile Hidden Markov Models from the HMMer package.
org.biojava.bio.program.homologene	Support classes for Homologene data.
org.biojava.bio.program.phred	Parser for Phred output
org.biojava.bio.program.unigene	Objects for representing Unigene clusters.
org.biojava.bio.search	Interfaces and classes for representing sequence similarity search results.
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.db	Collections of biological sequence data.
org.biojava.bio.seq.db.biofetch	Client for the OBDA BioFetch protocol.
org.biojava.bio.seq.db.biosql	General purpose Sequence storage in a relational database.
org.biojava.bio.seq.db.flat	Support for OBDA flatfile databases.
org.biojava.bio.seq.distributed	Sequences and SequenceDBs which are composed from data taken from a number of data sources.
org.biojava.bio.seq.homol	The classes and interfaces for defining sequence similarity and honology.
org.biojava.bio.seq.impl	Standard in-memory implementations of Sequence and Feature.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.seq.projection	Code for projecting Feature objects and systematically altering their properties.
org.biojava.bio.symbol	Representation of the Symbols that make up a sequence, and locations within them.
org.biojava.bio.taxa	Taxonomy object for representing species information.
org.biojava.ontology	A general-purpose API for ontologies.
org.biojava.utils	Miscellaneous utility classes used by other BioJava components.
org.biojavax	The Biojava extensions packages, classes that extend the core biojava functionality The biojavax packages contain a number of extensions to the core biojava interfaces.
org.biojavax.bio	Classes to represent biological entities and their relationships.
org.biojavax.bio.db	Interactions between biojavax objects and a DB.
org.biojavax.bio.db.biosql	Interface between biojava and biosql databases
org.biojavax.bio.db.ncbi	Interfaces to NCBI data.
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.bio.taxa	Objects that model the NCBI taxonomy schema as described in the BioSQL schema.
org.biojavax.ga	Classes to provide a genetic algorithm framework
org.biojavax.ga.functions	GA functions A genetic algorithm requires a number of functions.
org.biojavax.ga.impl	Default implementations and abstract classes.
org.biojavax.ontology	Extensions to the biojava ontology model that represent BioSQL ontology.

Uses of Changeable in org.biojava.bio

Subinterfaces of Changeable in org.biojava.bio

Modifier and Type	Interface and Description
interface	Annotatable Indicates that an object has an associated annotation.
interface	Annotation Arbitrary annotation associated with one or more objects.

Classes in org.biojava.bio that implement Changeable

Modifier and Type	Class and Description
class	AbstractAnnotation A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.
class	AnnotationChanger AnnotationChanger remaps the values of an Annotation to new values specified by a ValueChanger.
class	AnnotationRenamer AnnotationRenamer remaps the keys of an Annotation to new keys specified by a TagMapper.
class	BeanAsAnnotation Create an Annotation with properties matching those of a JavaBean instance.
class	MergeAnnotation Merged view onto a list of underlying Annotation objects.
class	OverlayAnnotation Annotation implementation which allows new key-value pairs to be layered on top of an underlying Annotation.
class	SimpleAnnotation A no-frills implementation of Annotation that is just a wrapper around a LinkedHashMap.
class	SmallAnnotation Annotation that is optimized for memory usage.

Uses of Changeable in org.biojava.bio.alignment

Subinterfaces of Changeable in org.biojava.bio.alignment

Modifier and Type	Interface and Description
interface	Alignment An alignment containing multiple SymbolLists.
interface	ARAlignment ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.
interface	UnequalLengthAlignment UnequalLengthAlignment has the following behavior.

Classes in org.biojava.bio.alignment that implement Changeable

Modifier and Type	Class and Description
class	AbstractULAlignment
class	AbstractULAlignment.SubULAlignment
class	AlignmentPair This class stores the result of an alignment procedure that creates a pairwise alignment of two sequences.
class	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.
class	SimpleAlignment A simple implementation of an Alignment.

Uses of Changeable in org.biojava.bio.dist

Subinterfaces of Changeable in org.biojava.bio.dist

Modifier and Type	Interface and Description
interface	Count An encapsulation of a count over the Symbols within an alphabet.
interface	Distribution An encapsulation of a probability distribution over the Symbols within an alphabet.
interface	OrderNDistribution Provides an N'th order distribution.

Classes in org.biojava.bio.dist that implement Changeable

Modifier and Type	Class and Description
class	AbstractDistribution An abstract implementation of Distribution.
class	AbstractOrderNDistribution Simple base class for OrderNDistributions.
class	GapDistribution This distribution emits gap symbols.
class	IndexedCount An encapsulation of a count over the Symbols within a FiniteAlphabet using an AlphabetIndex object.
class	PairDistribution Class for pairing up two independant distributions.
class	SimpleDistribution A simple implementation of a distribution, which works with any finite alphabet.
class	TranslatedDistribution A translated view of some underlying distribution.
class	UniformDistribution An implementation of an uniform distribution
class	UntrainableDistribution A distribution which does not interact with the training framework.

Uses of Changeable in org.biojava.bio.dp

Subinterfaces of Changeable in org.biojava.bio.dp

Modifier and Type	Interface and Description
interface	DotState A Dot state.
interface	EmissionState A state in a markov process that has an emission spectrum.
interface	MarkovModel A markov model.
interface	ModelInState A state that contains an entire sub-model.
interface	State A state in a markov process.
interface	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.

Classes in org.biojava.bio.dp that implement Changeable

Modifier and Type	Class and Description
class	MagicalState Start/end state for HMMs.
class	ProfileHMM
class	SimpleDotState A Dot state that you can make and use.
class	SimpleEmissionState
class	SimpleMarkovModel
class	SimpleModelInState
class	SimpleStatePath A no-frills implementation of StatePath.
class	WMAsMM Wraps a weight matrix up so that it appears to be a very simple HMM.

Uses of Changeable in org.biojava.bio.gui.sequence

Classes in org.biojava.bio.gui.sequence that implement Changeable

Modifier and Type	Class and Description
class	AbiTraceRenderer Renders an ABI trace file as a chromatogram graph.
class	AbstractBeadRenderer AbstractBeadRenderer is a an abstract base class for the creation of FeatureRenderers which use a 'string of beads' metaphor for displaying features.
class	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.
class	AlignmentRenderer
class	BasicFeatureRenderer
class	BumpedRenderer
class	CrosshairRenderer CrosshairRenderer draws a crosshair, optionally with coordinates.
class	EllipticalBeadRenderer EllipticalBeadRenderer renders features as simple ellipses.
class	FeatureBlockSequenceRenderer FeatureBlockSequenceRenderer forms a bridge between Sequence rendering and Feature rendering.
class	FeatureLabelRenderer
class	FilteringRenderer
class	GappedRenderer A renderer that will display a gapped sequence as a discontinuous series of regions.
class	GlyphFeatureRenderer A FeatureRenderer that renders a particular Glyph for Features accepted by a particular FeatureFilter
class	LabelledSequenceRenderer Renderer which draws a track of sequence with a textual label.
class	MultiLineRenderer MultiLineRenderer is a SequenceRenderer which collects a number of other SequenceRenderers each of which render their own view of a Sequence.
class	OffsetRulerRenderer OffsetRulerRenderer can render the ruler starting from an arbitrary offset from the sequence.
class	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.
class	PaddingRenderer A renderer that adds padding before and after a delegate renderer.
class	PairwiseDiagonalRenderer PairwiseDiagonalRenderer renders a region of similarity between two sequences as a straight line.
class	PairwiseFilteringRenderer PairwiseFilteringRenderer wraps a PairwiseSequenceRenderer and filters the PairwiseRenderContexts passed to it.
class	PairwiseOverlayRenderer PairwiseOverlayRenderer allows a list of other PairwiseSequenceRenderers to superimpose their output.
class	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).
class	PeptideDigestRenderer A concrete AbstractPeptideDigestRenderer.
class	RectangularBeadRenderer RectangularBeadRenderer renders features as simple rectangles.
class	RoundRectangularBeadRenderer RoundRectangularBeadRenderer renders features as rectangles with rounded corners.
class	SecondaryStructureFeatureRenderer A GlyphRenderer subclass that specificatlly handles Features pertaining to Secondary Structure (Helices, Turns and Strands).
class	SequencePanel A panel that displays a Sequence.
class	SequencePoster Deprecated. This doesn't handle loads of stuff. Use SequencePoster.
class	SequenceRendererWrapper An implementation of SequenceRenderer that delegates rendering to another renderer.
class	SimpleLabelRenderer
class	SixFrameRenderer Class that handles drawing in six frames for other classes.
class	SixFrameZiggyRenderer A feature renderer that computes the data necessary to render multi-exon transcripts without CDS data.
class	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.
class	TickFeatureRenderer
class	TranslatedSequencePanel TranslatedSequencePanel is a panel that displays a Sequence.
class	ZiggyFeatureRenderer A feature renderer that draws non-contiguous features as a set of boxes joined by zig-zags.

Uses of Changeable in org.biojava.bio.molbio

Subinterfaces of Changeable in org.biojava.bio.molbio

Modifier and Type	Interface and Description
interface	RestrictionSite RestrictionSite represents the recognition site of a restriction enzyme.

Uses of Changeable in org.biojava.bio.program.gff3

Subinterfaces of Changeable in org.biojava.bio.program.gff3

Modifier and Type	Interface and Description
interface	GFF3Record A record in a GFF3 formatted file.

Classes in org.biojava.bio.program.gff3 that implement Changeable

Modifier and Type	Class and Description
static class	GFF3Record.Impl

Uses of Changeable in org.biojava.bio.program.hmmer

Classes in org.biojava.bio.program.hmmer that implement Changeable

Modifier and Type	Class and Description
class	FullHmmerProfileHMM This is a class for representing the full HMMER generated Profile HMM (including loop states N and C terminal looping states).
class	HmmerProfileHMM This is a class for representing HMMER generated Profile HMM.
class	ProfileEmissionState A state in a HMMer model.

Uses of Changeable in org.biojava.bio.program.homologene

Classes in org.biojava.bio.program.homologene that implement Changeable

Modifier and Type	Class and Description
class	AbstractOrthologueSet
class	AbstractOrthoPairSet represents the Homologene Group.
class	SimpleOrthologueSet
class	SimpleOrthoPairSet a no-frills implementation of a Homologene Group

Uses of Changeable in org.biojava.bio.program.phred

Classes in org.biojava.bio.program.phred that implement Changeable

Modifier and Type	Class and Description
class	PhredSequence PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores.

Uses of Changeable in org.biojava.bio.program.unigene

Subinterfaces of Changeable in org.biojava.bio.program.unigene

Modifier and Type	Interface and Description
interface	UnigeneCluster A single unigene cluster.
interface	UnigeneDB A database of Unigene clusters.

Uses of Changeable in org.biojava.bio.search

Subinterfaces of Changeable in org.biojava.bio.search

Modifier and Type	Interface and Description
interface	SeqSimilaritySearchHit Objects of this type represent one particular hit (sequence and associated information) from a sequence similarity search.
interface	SeqSimilaritySearchResult Objects of this type represent one particular result of a sequence similarity search.
interface	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.

Classes in org.biojava.bio.search that implement Changeable

Modifier and Type	Class and Description
class	SequenceDBSearchHit Deprecated. SimpleSeqSimilaritySearchHit has been made Annotatable and is now functionally identical.
class	SequenceDBSearchResult Deprecated. SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical.
class	SequenceDBSearchSubHit Deprecated. SimpleSeqSimilaritySearchSubHit has been made Annotatable and is now functionally identical.
class	SimpleSeqSimilaritySearchHit SimpleSeqSimilaritySearchHit objects represent a similarity search hit of a query sequence to a sequence referenced in a SequenceDB object.
class	SimpleSeqSimilaritySearchResult SimpleSeqSimilaritySearchResult objects represent a result of a search of a SymbolList against the sequences within a SequenceDB object.
class	SimpleSeqSimilaritySearchSubHit SimpleSeqSimilaritySearchSubHit objects represent sub-hits which make up a hit.

Uses of Changeable in org.biojava.bio.seq

Subinterfaces of Changeable in org.biojava.bio.seq

Modifier and Type	Interface and Description
interface	ComponentFeature Feature which represents a component in an assembly (contig).
interface	Feature A feature within a sequence, or nested within another feature.
interface	FeatureHolder The interface for objects that contain features.
static interface	FeatureTypes.Repository A named collection of Types.
static interface	FeatureTypes.Type A type of feature.
interface	FramedFeature Title: FramedFeature.
interface	GappedSequence Extension of GappedSymbolList which also projects features into the gapped coordinate system.
interface	RealizingFeatureHolder Interface for FeatureHolder objects which know how to instantiate new child Features.
interface	RemoteFeature A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.
interface	Sequence A biological sequence.
interface	StrandedFeature Adds the concept of 'strand' to features.

Classes in org.biojava.bio.seq that implement Changeable

Modifier and Type	Class and Description
class	AbstractFeatureHolder An abstract implementation of FeatureHolder.
class	CircularView A circular view onto another Sequence object.
static class	FeatureHolder.EmptyFeatureHolder
static class	FeatureTypes.RepositoryImpl A simple implementation of a Repository.
class	LazyFeatureHolder Wrapper implementation of FeatureHolder which calls a method to create a contained FeatureHolder on demand.
class	MergeFeatureHolder FeatureHolder which exposes all the features in a set of sub-FeatureHolders.
class	NewSimpleAssembly A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
class	SimpleAssembly A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
class	SimpleFeatureHolder A no-frills implementation of FeatureHolder.

Uses of Changeable in org.biojava.bio.seq.db

Subinterfaces of Changeable in org.biojava.bio.seq.db

Modifier and Type	Interface and Description
interface	SequenceDB A database of sequences with accessible keys and iterators over all sequences.
interface	SequenceDBLite A database of sequences.

Classes in org.biojava.bio.seq.db that implement Changeable

Modifier and Type	Class and Description
class	AbstractSequenceDB An abstract implementation of SequenceDB that provides the sequenceIterator method.
class	AnnotatedSequenceDB SequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.
class	CachingSequenceDB SequenceDB implementation that caches the results of another SequenceDB.
class	DummySequenceDB DummySequenceDB is an implementation which contains only a DummySequence.
class	HashSequenceDB An implementation of SequenceDB that uses an underlying HashMap to store the sequence objects.
class	IndexedSequenceDB This class implements SequenceDB on top of a set of sequence files and sequence offsets within these files.
class	NCBISequenceDB
class	SequenceDBWrapper An abstract implementation of SequenceDB that wraps up another database.
class	SubSequenceDB
class	ViewingSequenceDB SequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database.
class	WebSequenceDB Functions for access to a web based database that returns sequences in a variety of formats.

Uses of Changeable in org.biojava.bio.seq.db.biofetch

Classes in org.biojava.bio.seq.db.biofetch that implement Changeable

Modifier and Type	Class and Description
class	BioFetchSequenceDB Simple SequenceDB implementation backed by a BioFetch (HTTP) server.

Uses of Changeable in org.biojava.bio.seq.db.biosql

Classes in org.biojava.bio.seq.db.biosql that implement Changeable

Modifier and Type	Class and Description
class	BioSQLSequenceDB Deprecated. Use hibernate and org.biojavax.bio.db.*

Uses of Changeable in org.biojava.bio.seq.db.flat

Classes in org.biojava.bio.seq.db.flat that implement Changeable

Modifier and Type	Class and Description
class	FlatSequenceDB FlatSequenceDB is an OBDA flatfile sequence databank implementation.

Uses of Changeable in org.biojava.bio.seq.distributed

Classes in org.biojava.bio.seq.distributed that implement Changeable

Modifier and Type	Class and Description
class	DistributedSequenceDB Sequence database from the meta-DAS system.

Uses of Changeable in org.biojava.bio.seq.homol

Subinterfaces of Changeable in org.biojava.bio.seq.homol

Modifier and Type	Interface and Description
interface	HomologyFeature
interface	SimilarityPairFeature SimilarityPairFeature describes a pairwise similarity between two nucleotide sequences (as it extends StrandedFeature).

Classes in org.biojava.bio.seq.homol that implement Changeable

Modifier and Type	Class and Description
static class	SimilarityPairFeature.EmptyPairwiseAlignment EmptyPairwiseAlignment empty pairwise alignment which has labels to empty symbol lists.
class	SimpleHomology A no-frills implementation of Homology.

Uses of Changeable in org.biojava.bio.seq.impl

Classes in org.biojava.bio.seq.impl that implement Changeable

Modifier and Type	Class and Description
class	AssembledSymbolList Support class for applications which need to patch together sections of sequence into a single SymbolList.
class	DummySequence A Sequence implementation that has a name and URI but no features, and a zero length symbol list.
class	LazyFilterFeatureHolder FeatureHolder which lazily applies a specified filter to another FeatureHolder.
class	NewAssembledSymbolList Support class for applications which need to patch together sections of sequence into a single SymbolList.
class	RevCompSequence A reverse complement view onto Sequence interface.
class	SimpleFeature A no-frills implementation of a feature.
class	SimpleFramedFeature Title: SimpleFramedFeature.
class	SimpleGappedSequence Simple implementation of GappedSequence.
class	SimpleHomologyFeature
class	SimpleRemoteFeature A no-frills implementation of a remote feature.
class	SimpleRestrictionSite SimpleRestrictionSite represents the recognition site of a restriction enzyme.
class	SimpleSequence A basic implementation of the Sequence interface.
class	SimpleSimilarityPairFeature SimpleSimilarityPairFeature represents a similarity between a query sequence and a subject sequence as produced by a search program.
class	SimpleStrandedFeature A no-frills implementation of StrandedFeature.
class	SubSequence View a sub-section of a given sequence object, including all the features intersecting that region.
class	ViewSequence A view onto another Sequence object.

Uses of Changeable in org.biojava.bio.seq.io

Subinterfaces of Changeable in org.biojava.bio.seq.io

Modifier and Type	Interface and Description
interface	SymbolTokenization Encapsulate a mapping between BioJava Symbol objects and some string representation.

Classes in org.biojava.bio.seq.io that implement Changeable

Modifier and Type	Class and Description
class	AlternateTokenization Implementation of SymbolTokenization which binds symbols to strings of characters.
class	CharacterTokenization Implementation of SymbolTokenization which binds symbols to single unicode characters.
class	CrossProductTokenization Tokenization for cross-product alphabets.
class	DoubleTokenization
class	IntegerTokenization
class	NameTokenization Simple implementation of SymbolTokenization which uses the `name' field of the symbols.
class	ReferenceAnnotation Deprecated. Use org.biojavax.bio.seq.io framework instead
class	SubIntegerTokenization
class	WordTokenization Base class for tokenizations which accept whitespace-separated `words'.

Uses of Changeable in org.biojava.bio.seq.projection

Classes in org.biojava.bio.seq.projection that implement Changeable

Modifier and Type	Class and Description
class	ProjectedFeature Internal class used by ProjectionEngine to wrap Feature objects.
class	ProjectedFeatureHolder Helper class for projecting Feature objects into an alternative coordinate system.

Uses of Changeable in org.biojava.bio.symbol

Subinterfaces of Changeable in org.biojava.bio.symbol

Modifier and Type	Interface and Description
interface	Alphabet The set of AtomicSymbols which can be concatenated together to make a SymbolList.
interface	AlphabetIndex Map between Symbols and index numbers.
interface	AtomicSymbol A symbol that is not ambiguous.
interface	BasisSymbol A symbol that can be represented as a string of Symbols.
interface	FiniteAlphabet An alphabet over a finite set of Symbols.
interface	GappedSymbolList This extends SymbolList with API for manipulating, inserting and deleting gaps.
interface	Symbol A single symbol.
interface	SymbolList A sequence of symbols that belong to an alphabet.

Classes in org.biojava.bio.symbol that implement Changeable

Modifier and Type	Class and Description
class	AbstractAlphabet An abstract implementation of Alphabet.
class	AbstractSymbol The base-class for Symbol implementations.
class	AbstractSymbolList Abstract helper implementation of the SymbolList core interface.
class	ChunkedSymbolList SymbolList implementation using constant-size chunks.
class	DoubleAlphabet An efficient implementation of an Alphabet over the infinite set of double values.
static class	DoubleAlphabet.DoubleRange A range of double values.
static class	DoubleAlphabet.DoubleSymbol A single double value.
static class	DoubleAlphabet.SubDoubleAlphabet A class to represent a contiguous range of double symbols.
class	DummySymbolList Symbol list which just consists of non-informative symbols.
class	FundamentalAtomicSymbol An atomic symbol consisting only of itself.
class	IntegerAlphabet An efficient implementation of an Alphabet over the infinite set of integer values.
static class	IntegerAlphabet.IntegerSymbol A single int value.
static class	IntegerAlphabet.SubIntegerAlphabet A class to represent a finite contiguous subset of the infinite IntegerAlphabet
class	PackedSymbolList A SymbolList that stores symbols as bit-patterns in an array of longs.
class	RelabeledAlignment An alignment that relabels another alignment.
class	SimpleAlphabet A simple no-frills implementation of the FiniteAlphabet interface.
class	SimpleAtomicSymbol A basic implementation of AtomicSymbol.
class	SimpleCodonPref a simple no-frills implementation of the CodonPref object that encapsulates codon preference data.
class	SimpleGappedSymbolList This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.
class	SimpleSymbolList Basic implementation of SymbolList.
class	SingletonAlphabet An alphabet that contains a single atomic symbol.
class	SoftMaskedAlphabet Soft masking is usually displayed by making the masked regions somehow different from the non masked regions.
class	SoftMaskedAlphabet.CaseSensitiveTokenization This SymbolTokenizer works with a delegate to softmask symbol tokenization as appropriate.

Uses of Changeable in org.biojava.bio.taxa

Subinterfaces of Changeable in org.biojava.bio.taxa

Modifier and Type	Interface and Description
interface	Taxon Deprecated. replaced by classes in org.biojavax.bio.taxa

Classes in org.biojava.bio.taxa that implement Changeable

Modifier and Type	Class and Description
class	AbstractTaxon Deprecated. replaced by classes in org.biojavax.bio.taxa
class	SimpleTaxon Deprecated. replaced by classes in org.biojavax.bio.taxa
class	WeakTaxon Deprecated. replaced by classes in org.biojavax.bio.taxa

Uses of Changeable in org.biojava.ontology

Subinterfaces of Changeable in org.biojava.ontology

Modifier and Type	Interface and Description
interface	Ontology An ontology.
interface	OntologyTerm A term in an ontology which identifies another ontology.
interface	RemoteTerm A term in another ontology.
interface	Term A term in an ontology.
interface	Triple A triple in an ontology.
interface	Variable

Classes in org.biojava.ontology that implement Changeable

Modifier and Type	Class and Description
class	AbstractTerm Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.
class	IntegerOntology
class	IntegerOntology.IntTerm
static class	Ontology.Impl A basic in-memory implementation of an ontology
static class	OntologyTerm.Impl Simple in-memory implementation of a remote ontology term.
static class	RemoteTerm.Impl Simple in-memory implementation of a remote ontology term.
static class	Term.Impl Simple in-memory implementation of an ontology term.
static class	Triple.Impl Basic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriple
static class	Variable.Impl

Uses of Changeable in org.biojava.utils

Classes in org.biojava.utils that implement Changeable

Modifier and Type	Class and Description
class	AbstractChangeable Useful base-class for objects implementing Changeable
class	Unchangeable This is a utility implementation of Changeable that doesn't fire any events or keep references to any listeners.

Uses of Changeable in org.biojavax

Subinterfaces of Changeable in org.biojavax

Modifier and Type	Interface and Description
interface	Comment A simple ranked comment designed to be used for BioEntry comments in BioSQL.
interface	CrossRef Represents a cross reference to another database.
interface	DocRef Represents a documentary reference.
interface	DocRefAuthor Represents an author of a documentary reference.
interface	Namespace The namespace of an entry in a database schema.
interface	Note Note is a generic class intended to hold a term describing the note, a value to associate with that term, and a rank.
interface	RankedCrossRef Allows cross-references to other databases to be ranked.
interface	RankedCrossRefable Defines an object as being able to have ranked cross references associated with it.
interface	RankedDocRef Represents a documentary reference.
interface	RichAnnotatable Annotatable objects that can have rich annotations.
interface	RichAnnotation An annotation collection which stores annotations as Note objects.

Classes in org.biojavax that implement Changeable

Modifier and Type	Class and Description
class	EmptyRichAnnotation A place holder for a RichAnnotation that prevents null having to be used
class	SimpleComment An implementaion of Comment.
class	SimpleCrossRef A basic CrossRef implementation.
class	SimpleDocRef A basic DocRef implementation.
class	SimpleDocRefAuthor Represents an author of a documentary reference.
class	SimpleNamespace A basic Namespace implemenation.
class	SimpleNote Simple implementation of Note.
class	SimpleRankedCrossRef Simple implementation of RankedCrossRef.
class	SimpleRankedDocRef Represents a documentary reference.
class	SimpleRichAnnotation Simple annotation wrapper.

Uses of Changeable in org.biojavax.bio

Subinterfaces of Changeable in org.biojavax.bio

Modifier and Type	Interface and Description
interface	BioEntry This class relates to the bioentry table in BioSQL.
interface	BioEntryRelationship Represents the relation between two bioentries.

Classes in org.biojavax.bio that implement Changeable

Modifier and Type	Class and Description
class	SimpleBioEntry Reference implementation of a BioEntry object which has no features or sequence.
class	SimpleBioEntryRelationship Represents a relationship between two bioentries that is described by a term and given a rank.

Uses of Changeable in org.biojavax.bio.db

Subinterfaces of Changeable in org.biojavax.bio.db

Modifier and Type	Interface and Description
interface	RichSequenceDB A database of RichSequences with accessible keys and iterators over all sequences.
interface	RichSequenceDBLite A database of RichSequences.

Classes in org.biojavax.bio.db that implement Changeable

Modifier and Type	Class and Description
class	AbstractBioEntryDB An abstract implementation of BioEntryDB that provides the getBioEntryIterator method.
class	AbstractRichSequenceDB An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method.
class	HashBioEntryDB An implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects.
class	HashRichSequenceDB An implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects.

Uses of Changeable in org.biojavax.bio.db.biosql

Classes in org.biojavax.bio.db.biosql that implement Changeable

Modifier and Type	Class and Description
class	BioSQLBioEntryDB
class	BioSQLRichSequenceDB

Uses of Changeable in org.biojavax.bio.db.ncbi

Classes in org.biojavax.bio.db.ncbi that implement Changeable

Modifier and Type	Class and Description
class	GenbankRichSequenceDB This class contains functions accessing DNA sequences in Genbank format.
class	GenpeptRichSequenceDB This class contains functions accessing Peptide sequences in Genpept format.

Uses of Changeable in org.biojavax.bio.seq

Subinterfaces of Changeable in org.biojavax.bio.seq

Modifier and Type	Interface and Description
interface	RichFeature Represents a feature that can be given name and rank and be moved from one sequence to another.
interface	RichFeatureRelationship Represents the relation between two features.
interface	RichLocation Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.
interface	RichSequence A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.

Classes in org.biojavax.bio.seq that implement Changeable

Modifier and Type	Class and Description
class	CompoundRichLocation An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.
class	EmptyRichLocation An Empty implementation of RichLocation.
class	InfinitelyAmbiguousSymbolList A symbol list that is Integer.MAX_VALUElong, never gives index out of bounds and always returns ambiguity symbols for everything.
class	MultiSourceCompoundRichLocation An implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences.
class	SimpleRichFeature A simple implementation of RichFeature.
class	SimpleRichFeatureRelationship Represents a relationship between two features that is described by a term.
class	SimpleRichLocation A simple implementation of RichLocation.
class	SimpleRichSequence A simple implementation of RichSequence.
class	ThinRichSequence A simple implementation of RichSequence.

Uses of Changeable in org.biojavax.bio.taxa

Subinterfaces of Changeable in org.biojavax.bio.taxa

Modifier and Type	Interface and Description
interface	NCBITaxon Represents an NCBI Taxon entry, a combination of the taxon and taxon_name tables in BioSQL.

Classes in org.biojavax.bio.taxa that implement Changeable

Modifier and Type	Class and Description
class	SimpleNCBITaxon Reference implementation of NCBITaxon.

Uses of Changeable in org.biojavax.ga

Subinterfaces of Changeable in org.biojavax.ga

Modifier and Type	Interface and Description
interface	GeneticAlgorithm The class that runs the cycles of reproduction, evolution and selection, potentially on multiple Populations
interface	Organism A GA 'organism' contains one or more Chromosomes
interface	Population A collection of GA organisms

Uses of Changeable in org.biojavax.ga.functions

Subinterfaces of Changeable in org.biojavax.ga.functions

Modifier and Type	Interface and Description
interface	CrossOverFunction Crosses two chromosomes.
interface	MutationFunction A class that mutates a SymbolList

Classes in org.biojavax.ga.functions that implement Changeable

Modifier and Type	Class and Description
class	AbstractCrossOverFunction Abstract implementation of CrossOverFunction.
class	AbstractMutationFunction Abstract implementation of MutationFunction all custom implementations should inherit from here.
static class	CrossOverFunction.NoCross A place holder CrossOverFunction that doesn't perform cross overs
static class	MutationFunction.NoMutation Place Holder class that doesn't mutate its SymbolLists
class	OrderCrossover This does a 2-point-crossover on two chromosomes keeping the Symbols in each chromosome constant.
class	SimpleCrossOverFunction Simple Implementation of the CrossOverFunction interface
class	SimpleMutationFunction Simple no frills Implementation of the MutationFunction interface This class is final, custom implementations should extend AbstractMutationFunction
class	SwapMutationFunction This class does a sort of mutation by exchanging two positions on the chromosome.

Uses of Changeable in org.biojavax.ga.impl

Classes in org.biojavax.ga.impl that implement Changeable

Modifier and Type	Class and Description
class	AbstractGeneticAlgorithm Base class from which most implementations of GeneticAlgorithm will inherit.
class	AbstractOrganism Abstract implementation of Organism.
class	AbstractPopulation Most Population implementations will want to inherit from here.
class	SimpleGeneticAlgorithm A simple implementation of the GeneticAlgorithm interface it is not intended that this class be overidden, hence it is final.
class	SimpleOrganism A Simple Haploid Organism implementation
class	SimplePopulation Simple concrete implementation of the Population interface Internally the SimplePopulation store Organisms in a HashMap

Uses of Changeable in org.biojavax.ontology

Subinterfaces of Changeable in org.biojavax.ontology

Modifier and Type	Interface and Description
interface	ComparableOntology An Ontology that can be compared to another.
interface	ComparableTerm Makes Term objects comparable properly and adds some extra features to them.
interface	ComparableTriple Comparable triples, obviously.

Classes in org.biojavax.ontology that implement Changeable

Modifier and Type	Class and Description
class	SimpleComparableOntology Represents an ontology that can be compared to other ontologies.
class	SimpleComparableTerm A Term object that can be compared and thus sorted.
class	SimpleComparableTriple Basic comparable triple, BioSQL style.