## 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: 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.program.das: Development client for the Distributed Annotation System.
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.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.biosql: General purpose Sequence storage in a relational database.
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.biojavax: The Biojava extensions packages, classes that extend the core biojava functionality
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.functions: GA 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 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 `LinkedHashMap`.
`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` 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 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` `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 `SequenceRenderer`s 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 `PairwiseRenderContext`s passed to it.
`class` `PairwiseOverlayRenderer` `PairwiseOverlayRenderer` allows a list of other `PairwiseSequenceRenderer`s to superimpose their output.
`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` `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` `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.gff3

Subclasses of AbstractChangeable in org.biojava.bio.program.gff3
`static class` `GFF3Record.Impl`

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.homologene

Subclasses of AbstractChangeable in org.biojava.bio.program.homologene
`class` `AbstractOrthologueSet`
`class` `AbstractOrthoPairSet` represents the Homologene Group.
`class` `SimpleOrthologueSet`
`class` `SimpleOrthoPairSet` a no-frills implementation of a Homologene Group

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.
`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 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.db.biosql

Subclasses of AbstractChangeable in org.biojava.bio.seq.db.biosql
`class` `BioSQLSequenceDB` Deprecated. Use hibernate and org.biojavax.bio.db.*

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` `DummySequence` A Sequence implementation that has a name and URI but no features, and a zero length symbol list.
`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.

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

Subclasses of AbstractChangeable in org.biojava.bio.seq.io
`class` `ReferenceAnnotation` Deprecated. Use org.biojavax.bio.seq.io framework instead

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

Subclasses of AbstractChangeable in org.biojava.bio.seq.projection
`class` `ProjectedFeatureHolder` Helper class for projecting Feature objects into an alternative coordinate system.

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` `ChunkedSymbolList` SymbolList implementation using constant-size chunks.
`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` `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.
`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.

Uses of AbstractChangeable in org.biojava.bio.taxa

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

Subclasses of AbstractChangeable in org.biojava.ontology
`class` `AbstractTerm` Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.
`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` `Variable.Impl`

Uses of AbstractChangeable in org.biojavax

Subclasses of AbstractChangeable in org.biojavax
`class` `SimpleComment` An implementaion of Comment.
`class` `SimpleDocRef` A basic DocRef implementation.
`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 AbstractChangeable in org.biojavax.bio

Subclasses of AbstractChangeable in org.biojavax.bio
`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 AbstractChangeable in org.biojavax.bio.db

Subclasses of AbstractChangeable in org.biojavax.bio.db
`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 AbstractChangeable in org.biojavax.bio.db.biosql

Subclasses of AbstractChangeable in org.biojavax.bio.db.biosql
`class` `BioSQLBioEntryDB`
`class` `BioSQLRichSequenceDB`

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

Subclasses of AbstractChangeable in org.biojavax.bio.db.ncbi
`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 AbstractChangeable in org.biojavax.bio.seq

Subclasses of AbstractChangeable in org.biojavax.bio.seq
`class` `CompoundRichLocation` An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.
`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 AbstractChangeable in org.biojavax.bio.taxa

Subclasses of AbstractChangeable in org.biojavax.bio.taxa
`class` `SimpleNCBITaxon` Reference implementation of NCBITaxon.

Uses of AbstractChangeable in org.biojavax.ga.functions

Subclasses of AbstractChangeable in org.biojavax.ga.functions
`class` `AbstractCrossOverFunction` Abstract implementation of `CrossOverFunction`.
`class` `AbstractMutationFunction` Abstract implementation of `MutationFunction` all custom implementations should inherit from here.
`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
`class` `SwapMutationFunction` This class does a sort of mutation by exchanging two positions on the chromosome.

Uses of AbstractChangeable in org.biojavax.ga.impl

Subclasses of AbstractChangeable in org.biojavax.ga.impl
`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

Uses of AbstractChangeable in org.biojavax.ontology

Subclasses of AbstractChangeable in org.biojavax.ontology
`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.