## Uses of Interface
org.biojava.utils.Changeable

Packages that use Changeable
org.biojava.bio: The core classes that will be used throughout the bio packages.
org.biojava.bio.alignment: Implementation of the `Alignment` interface.
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.das: Development client for the Distributed Annotation System.
org.biojava.bio.program.hmmer: Tools for working with profile Hidden Markov Models from the HMMer package.
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 into alternate coordinate systems.
org.biojava.bio.seq.ragbag: The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code.
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.utils: Miscellaneous utility classes used by other BioJava components.

Uses of Changeable in org.biojava.bio

Subinterfaces of Changeable in org.biojava.bio
`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
`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 Map.
`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
`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
`class` `AbstractULAlignment`
`class` `AbstractULAlignment.SubULAlignment`
`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.

Uses of Changeable in org.biojava.bio.dist

Subinterfaces of Changeable in org.biojava.bio.dist
`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
`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` Creates a distribution that is a translated view of an 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
`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
`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
`class` `AbiTraceRenderer` Renders an ABI trace file as a chromatogram graph.
`class` `AbstractBeadRenderer` `AbstractBeadRenderer` is a an abstract base class for the creation of `FeatureRenderer`s which use a 'string of beads' metaphor for displaying features.
`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` `LabelledSequenceRenderer` Renderer which draws a track of sequence with a textual label.
`class` `MultiLineRenderer` `MultiLineRenderer` is a `SequenceRenderer` which collects a number of other `SequenceRenderer`s each of which render their own view of a `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 `PairwiseRenderContext`s passed to it.
`class` `PairwiseOverlayRenderer` `PairwiseOverlayRenderer` allows a list of other `PairwiseSequenceRenderer`s 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` `RectangularBeadRenderer` `RectangularBeadRenderer` renders features as simple rectangles.
`class` `RoundRectangularBeadRenderer` `RoundRectangularBeadRenderer` renders features as rectangles with rounded corners.
`class` `SequencePanel` A panel that displays a Sequence.
`class` `SequencePoster` A panel that displays a Sequence.
`class` `SequenceRendererWrapper`
`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
`interface` `RestrictionSite` `RestrictionSite` represents the recognition site of a restriction enzyme.

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

Classes in org.biojava.bio.program.das that implement Changeable
`class` `DAS` A collection of DAS datasources.
`class` `DASSequence` Sequence reflecting a DAS reference sequence, possibly decorated with one of more annotation sets.
`class` `DASSequenceDB` Collection of sequences retrieved from the DAS network.
`class` `ReferenceServer` Reflects a reference server on the DAS network.

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

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

Classes in org.biojava.bio.program.phred that implement Changeable
`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
`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
`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
`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
`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
`class` `AbstractFeatureHolder` An abstract implementation of FeatureHolder.
`class` `CircularView` A circular view onto another Sequence object.
`class` `DummySequence`
`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` `ProjectedFeatureHolder` Helper class for projecting Feature objects into an alternative coordinate system.
`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.
`class` `SimpleGappedSequence` Simple implementation of GappedSequence.
`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.db

Subinterfaces of Changeable in org.biojava.bio.seq.db
`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
`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
`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
`class` `BioSQLSequenceDB` SequenceDB keyed off a BioSQL database.

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

Classes in org.biojava.bio.seq.db.flat that implement Changeable
`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
`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
`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
`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
`class` `AssembledSymbolList` Support class for applications which need to patch together sections of sequence into a single SymbolList.
`class` `LazyFilterFeatureHolder` FeatureHolder which lazily applies a specified filter to another FeatureHolder.
`class` `RevCompSequence` A reverse complement view onto `Sequence` interface.
`class` `SimpleFeature` A no-frills implementation of a feature.
`class` `SimpleFramedFeature` Title: SimpleFramedFeature.
`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.

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

Subinterfaces of Changeable in org.biojava.bio.seq.io
`interface` `SymbolTokenization` Encapsulate a mapping between BioJava Symbol objects and some string representation.

Classes in org.biojava.bio.seq.io that implement Changeable
`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` `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
`class` `ProjectedFeature` Internal class used by ProjectionEngine to wrap Feature objects.
`class` `ProjectedStrandedFeature` Internal class used by ProjectedFeatureHolder to wrap StrandedFeatures.

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

Classes in org.biojava.bio.seq.ragbag that implement Changeable
`(package private) class` `org.biojava.bio.seq.ragbag.RagbagAbstractSequence` object that instantiates a sequence in Ragbag.
`class` `RagbagAssembly` object that instantiates a sequence when given a Ragbag directory.

Uses of Changeable in org.biojava.bio.symbol

Subinterfaces of Changeable in org.biojava.bio.symbol
`interface` `Alignment` An alignment containing multiple SymbolLists.
`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
`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` `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` `PackedDnaSymbolList` a class that implements storage of symbols in packed form (2 symbols per byte).
`class` `PackedSymbolList` A SymbolList that stores symbols as bit-patterns in an array of longs.
`class` `RelabeledAlignment` An alignment that relabels another alignment.
`class` `SimpleAlignment` A simple implementation of an Alignment.
`class` `SimpleAlphabet` A simple no-frills implementation of the FiniteAlphabet interface.
`class` `SimpleAtomicSymbol` A basic implementation of AtomicSymbol.
`(package private) class` `org.biojava.bio.symbol.SimpleBasisSymbol` A basic implementation of BasisSymbol.
`class` `SimpleGappedSymbolList` This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.
`(package private) class` `org.biojava.bio.symbol.SimpleSymbol` A basic implementation of Symbol.
`class` `SimpleSymbolList` Basic implementation of SymbolList.
`class` `SingletonAlphabet` An alphabet that contains a single atomic symbol.
`static class` `SymbolList.EmptySymbolList` The empty immutable implementation.

Uses of Changeable in org.biojava.bio.taxa

Subinterfaces of Changeable in org.biojava.bio.taxa
`interface` `Taxon` A taxon within a classification.

Classes in org.biojava.bio.taxa that implement Changeable
`class` `AbstractTaxon` An abstract implementation of Taxon.
`class` `SimpleTaxon` A no-frills implementatation of Taxon.
`class` `WeakTaxon` An implementation of Taxon that keeps only weak references to children, but full references to parents.

Uses of Changeable in org.biojava.utils

Classes in org.biojava.utils that implement Changeable
`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.