## Uses of Class
org.biojava.utils.AbstractChangeable

Packages that use AbstractChangeable
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.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.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.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.symbol: Representation of the Symbols that make up a sequence, and locations within them.
org.biojava.bio.taxa: Taxonomy object for representing species information.

Uses of AbstractChangeable in org.biojava.bio

Subclasses of AbstractChangeable in org.biojava.bio
`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 AbstractChangeable in org.biojava.bio.alignment

Subclasses of AbstractChangeable in org.biojava.bio.alignment
`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 AbstractChangeable in org.biojava.bio.dist

Subclasses of AbstractChangeable in org.biojava.bio.dist
`class` `AbstractDistribution` An abstract implementation of Distribution.
`class` `AbstractOrderNDistribution` Simple base class for OrderNDistributions
`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 AbstractChangeable in org.biojava.bio.dp

Subclasses of AbstractChangeable in org.biojava.bio.dp
`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` `WMAsMM` Wraps a weight matrix up so that it appears to be a very simple HMM.

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

Subclasses of AbstractChangeable in org.biojava.bio.gui.sequence
`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` `RectangularBeadRenderer` `RectangularBeadRenderer` renders features as simple rectangles.
`class` `RoundRectangularBeadRenderer` `RoundRectangularBeadRenderer` renders features as rectangles with rounded corners.
`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` `ZiggyFeatureRenderer` A feature renderer that draws non-contiguous features as a set of boxes joined by zig-zags.

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

Subclasses of AbstractChangeable in org.biojava.bio.program.das
`class` `DAS` A collection of DAS datasources.
`class` `DASSequence` Sequence reflecting a DAS reference sequence, possibly decorated with one of more annotation sets.

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

Subclasses of AbstractChangeable in org.biojava.bio.program.hmmer
`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 AbstractChangeable in org.biojava.bio.program.phred

Subclasses of AbstractChangeable in org.biojava.bio.program.phred
`class` `PhredSequence` PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores.

Uses of AbstractChangeable in org.biojava.bio.search

Subclasses of AbstractChangeable in org.biojava.bio.search
`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 AbstractChangeable in org.biojava.bio.seq

Subclasses of AbstractChangeable in org.biojava.bio.seq
`class` `AbstractFeatureHolder` An abstract implementation of FeatureHolder.
`class` `DummySequence`
`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.

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

Subclasses of AbstractChangeable in org.biojava.bio.seq.db
`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 AbstractChangeable in org.biojava.bio.seq.distributed

Subclasses of AbstractChangeable in org.biojava.bio.seq.distributed
`class` `DistributedSequenceDB` Sequence database from the meta-DAS system.

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

Subclasses of AbstractChangeable in org.biojava.bio.seq.homol
`class` `SimpleHomology` A no-frills implementation of Homology.

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

Subclasses of AbstractChangeable in org.biojava.bio.seq.impl
`class` `AssembledSymbolList` 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` `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 AbstractChangeable in org.biojava.bio.symbol

Subclasses of AbstractChangeable in org.biojava.bio.symbol
`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` `DummySymbolList` Symbol list which just consists of non-informative symbols.
`class` `FundamentalAtomicSymbol` An atomic symbol consisting only of itself.
`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` `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.

Uses of AbstractChangeable in org.biojava.bio.taxa

Subclasses of AbstractChangeable in org.biojava.bio.taxa
`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.