Uses of Class
org.biojava.utils.AbstractChangeable

Packages that use AbstractChangeable

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.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 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.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 AbstractChangeable in org.biojava.bio

Subclasses of AbstractChangeable in org.biojava.bio

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 AbstractChangeable in org.biojava.bio.alignment

Subclasses of AbstractChangeable in org.biojava.bio.alignment

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 AbstractChangeable in org.biojava.bio.dist

Subclasses of AbstractChangeable in org.biojava.bio.dist

Modifier and Type	Class and Description
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

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	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

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	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.gff3

Subclasses of AbstractChangeable in org.biojava.bio.program.gff3

Modifier and Type	Class and Description
static class	GFF3Record.Impl

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

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

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 AbstractChangeable in org.biojava.bio.program.homologene

Subclasses of AbstractChangeable in org.biojava.bio.program.homologene

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 AbstractChangeable in org.biojava.bio.program.phred

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

Modifier and Type	Class and Description
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

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 AbstractChangeable in org.biojava.bio.seq

Subclasses of AbstractChangeable in org.biojava.bio.seq

Modifier and Type	Class and Description
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

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 AbstractChangeable in org.biojava.bio.seq.db.biosql

Subclasses of AbstractChangeable in org.biojava.bio.seq.db.biosql

Modifier and Type	Class and Description
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

Modifier and Type	Class and Description
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

Modifier and Type	Class and Description
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

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	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

Modifier and Type	Class and Description
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

Modifier and Type	Class and Description
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

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	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	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

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 AbstractChangeable in org.biojava.ontology

Subclasses of AbstractChangeable in org.biojava.ontology

Modifier and Type	Class and Description
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

Modifier and Type	Class and Description
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

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 AbstractChangeable in org.biojavax.bio.db

Subclasses of AbstractChangeable in org.biojavax.bio.db

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 AbstractChangeable in org.biojavax.bio.db.biosql

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

Modifier and Type	Class and Description
class	BioSQLBioEntryDB
class	BioSQLRichSequenceDB

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

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

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 AbstractChangeable in org.biojavax.bio.seq

Subclasses of AbstractChangeable in org.biojavax.bio.seq

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	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

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

Uses of AbstractChangeable in org.biojavax.ga.functions

Subclasses of AbstractChangeable in org.biojavax.ga.functions

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.
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 AbstractChangeable in org.biojavax.ga.impl

Subclasses of AbstractChangeable in org.biojavax.ga.impl

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 AbstractChangeable in org.biojavax.ontology

Subclasses of AbstractChangeable in org.biojavax.ontology

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.