Uses of Interface
org.biojava.utils.Changeable
Packages that use Changeable
Package
Description
The core classes that will be used throughout the bio packages.
Classes to generate and describe sequence alignments.
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
Graphical displays of biological sequences and associated annotations.
The classes and interfaces in this package cover common molecular
biological techniques such as restriction digests and PCR.
Support for reading and writing GFF3.
Tools for working with profile Hidden Markov Models from the HMMer package.
Support classes for Homologene data.
Parser for Phred output
Objects for representing Unigene clusters.
Interfaces and classes for representing sequence similarity search results.
Classes and interfaces for defining biological sequences and informatics
objects.
Collections of biological sequence data.
Client for the OBDA BioFetch protocol.
General purpose Sequence storage in a relational database.
Support for OBDA flatfile databases.
Sequences and SequenceDBs which are composed from data taken
from a number of data sources.
The classes and interfaces for defining sequence similarity and
honology.
Standard in-memory implementations of
Sequence and
Feature.Classes and interfaces for processing and producing flat-file representations
of sequences.
Code for projecting Feature objects and systematically altering their
properties.
Representation of the Symbols that make up a sequence, and locations within
them.
Taxonomy object for representing species information.
A general-purpose API for ontologies.
Miscellaneous utility classes used by other BioJava components.
The Biojava extensions packages, classes that extend the core biojava
functionality
Classes to represent biological entities and their relationships.
Interactions between biojavax objects and a DB.
Interface between biojava and biosql databases
Interfaces to NCBI data.
Rich implementations of Sequences, Locations and Features.
Objects that model the NCBI taxonomy schema as described in the BioSQL
schema.
Classes to provide a genetic algorithm framework
GA functions
Default implementations and abstract classes.
Extensions to the biojava ontology model that represent BioSQL ontology.
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Uses of Changeable in org.biojava.bio
Subinterfaces of Changeable in org.biojava.bioModifier and TypeInterfaceDescriptioninterfaceIndicates that an object has an associated annotation.interfaceArbitrary annotation associated with one or more objects.Classes in org.biojava.bio that implement ChangeableModifier and TypeClassDescriptionclassA utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.classAnnotationChangerremaps the values of anAnnotationto new values specified by aValueChanger.classAnnotationRenamerremaps the keys of anAnnotationto new keys specified by aTagMapper.classCreate an Annotation with properties matching those of a JavaBean instance.classMerged view onto a list of underlying Annotation objects.classAnnotation implementation which allows new key-value pairs to be layered on top of an underlying Annotation.classA no-frills implementation of Annotation that is just a wrapper around aLinkedHashMap.classAnnotation that is optimized for memory usage. -
Uses of Changeable in org.biojava.bio.alignment
Subinterfaces of Changeable in org.biojava.bio.alignmentModifier and TypeInterfaceDescriptioninterfaceAn alignment containing multiple SymbolLists.interfaceARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.interfaceUnequalLengthAlignment has the following behavior.Classes in org.biojava.bio.alignment that implement ChangeableModifier and TypeClassDescriptionclassclassclassThis class stores the result of an alignment procedure that creates a pairwise alignment of two sequences.classFlexibleAlignment 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.classA simple implementation of an Alignment. -
Uses of Changeable in org.biojava.bio.dist
Subinterfaces of Changeable in org.biojava.bio.distModifier and TypeInterfaceDescriptioninterfaceAn encapsulation of a count over the Symbols within an alphabet.interfaceAn encapsulation of a probability distribution over the Symbols within an alphabet.interfaceProvides an N'th order distribution.Classes in org.biojava.bio.dist that implement ChangeableModifier and TypeClassDescriptionclassAn abstract implementation of Distribution.classSimple base class for OrderNDistributions.classThis distribution emits gap symbols.final classAn encapsulation of a count over the Symbols within a FiniteAlphabet using an AlphabetIndex object.classClass for pairing up two independant distributions.classA simple implementation of a distribution, which works with any finite alphabet.classA translated view of some underlying distribution.classAn implementation of an uniform distributionclassA distribution which does not interact with the training framework. -
Uses of Changeable in org.biojava.bio.dp
Subinterfaces of Changeable in org.biojava.bio.dpModifier and TypeInterfaceDescriptioninterfaceA Dot state.interfaceA state in a markov process that has an emission spectrum.interfaceA markov model.interfaceA state that contains an entire sub-model.interfaceA state in a markov process.interfaceExtends 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 ChangeableModifier and TypeClassDescriptionfinal classStart/end state for HMMs.classclassA Dot state that you can make and use.classclassclassclassA no-frills implementation of StatePath.classWraps 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 ChangeableModifier and TypeClassDescriptionclassRenders an ABI trace file as a chromatogram graph.classAbstractBeadRendereris a an abstract base class for the creation ofFeatureRenderers which use a 'string of beads' metaphor for displaying features.classA SequenceRenderer that renders a set of Features that match a FeatureFilter in such a way that they do not overlap in the display.classclassclassclassCrosshairRendererdraws a crosshair, optionally with coordinates.classEllipticalBeadRendererrenders features as simple ellipses.classFeatureBlockSequenceRendererforms a bridge betweenSequencerendering andFeaturerendering.classclassclassA renderer that will display a gapped sequence as a discontinuous series of regions.classA FeatureRenderer that renders a particular Glyph for Features accepted by a particular FeatureFilterclassRenderer which draws a track of sequence with a textual label.classMultiLineRendereris aSequenceRendererwhich collects a number of otherSequenceRenderers each of which render their own view of aSequence.classOffsetRulerRenderer can render the ruler starting from an arbitrary offset from the sequence.classThis 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.classA renderer that adds padding before and after a delegate renderer.classPairwiseDiagonalRendererrenders a region of similarity between two sequences as a straight line.classPairwiseFilteringRendererwraps aPairwiseSequenceRendererand filters thePairwiseRenderContexts passed to it.classPairwiseOverlayRendererallows a list of otherPairwiseSequenceRenderers to superimpose their output.classAPairwiseSequencePanelis 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).classA concrete AbstractPeptideDigestRenderer.classRectangularBeadRendererrenders features as simple rectangles.classRoundRectangularBeadRendererrenders features as rectangles with rounded corners.classA GlyphRenderer subclass that specificatlly handles Features pertaining to Secondary Structure (Helices, Turns and Strands).classA panel that displays a Sequence.classDeprecated.This doesn't handle loads of stuff.classAn implementation of SequenceRenderer that delegates rendering to another renderer.classclassClass that handles drawing in six frames for other classes.classA feature renderer that computes the data necessary to render multi-exon transcripts without CDS data.classAllows 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.classclassTranslatedSequencePanelis a panel that displays a Sequence.classA 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.molbioModifier and TypeInterfaceDescriptioninterfaceRestrictionSiterepresents the recognition site of a restriction enzyme. -
Uses of Changeable in org.biojava.bio.program.gff3
Subinterfaces of Changeable in org.biojava.bio.program.gff3Classes in org.biojava.bio.program.gff3 that implement Changeable -
Uses of Changeable in org.biojava.bio.program.hmmer
Classes in org.biojava.bio.program.hmmer that implement ChangeableModifier and TypeClassDescriptionclassThis is a class for representing the full HMMER generated Profile HMM (including loop states N and C terminal looping states).classThis is a class for representing HMMER generated Profile HMM.classA state in a HMMer model. -
Uses of Changeable in org.biojava.bio.program.homologene
Classes in org.biojava.bio.program.homologene that implement ChangeableModifier and TypeClassDescriptionclassclassrepresents the Homologene Group.classclassa 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 ChangeableModifier and TypeClassDescriptionclassPhredSequence 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.unigeneModifier and TypeInterfaceDescriptioninterfaceA single unigene cluster.interfaceA database of Unigene clusters. -
Uses of Changeable in org.biojava.bio.search
Subinterfaces of Changeable in org.biojava.bio.searchModifier and TypeInterfaceDescriptioninterfaceObjects of this type represent one particular hit (sequence and associated information) from a sequence similarity search.interfaceObjects of this type represent one particular result of a sequence similarity search.interfaceObjects 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 ChangeableModifier and TypeClassDescriptionclassDeprecated.SimpleSeqSimilaritySearchHit has been made Annotatable and is now functionally identical.classDeprecated.SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical.classDeprecated.SimpleSeqSimilaritySearchSubHit has been made Annotatable and is now functionally identical.classSimpleSeqSimilaritySearchHitobjects represent a similarity search hit of a query sequence to a sequence referenced in a SequenceDB object.classSimpleSeqSimilaritySearchResultobjects represent a result of a search of aSymbolListagainst the sequences within aSequenceDBobject.classSimpleSeqSimilaritySearchSubHitobjects represent sub-hits which make up a hit. -
Uses of Changeable in org.biojava.bio.seq
Subinterfaces of Changeable in org.biojava.bio.seqModifier and TypeInterfaceDescriptioninterfaceFeature which represents a component in an assembly (contig).interfaceA feature within a sequence, or nested within another feature.interfaceThe interface for objects that contain features.static interfaceA named collection of Types.static interfaceA type of feature.interfaceTitle: FramedFeature.interfaceExtension of GappedSymbolList which also projects features into the gapped coordinate system.interfaceInterface forFeatureHolderobjects which know how to instantiate new child Features.interfaceA feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.interfaceA biological sequence.interfaceAdds the concept of 'strand' to features.Classes in org.biojava.bio.seq that implement ChangeableModifier and TypeClassDescriptionclassAn abstract implementation of FeatureHolder.classA circular view onto another Sequence object.static final classstatic classA simple implementation of a Repository.classWrapper implementation of FeatureHolder which calls a method to create a contained FeatureHolder on demand.classFeatureHolder which exposes all the features in a set of sub-FeatureHolders.classA Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.classA Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.classA no-frills implementation of FeatureHolder. -
Uses of Changeable in org.biojava.bio.seq.db
Subinterfaces of Changeable in org.biojava.bio.seq.dbModifier and TypeInterfaceDescriptioninterfaceA database of sequences with accessible keys and iterators over all sequences.interfaceA database of sequences.Classes in org.biojava.bio.seq.db that implement ChangeableModifier and TypeClassDescriptionclassAn abstract implementation of SequenceDB that provides the sequenceIterator method.classSequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.classSequenceDB implementation that caches the results of another SequenceDB.classDummySequenceDBis an implementation which contains only aDummySequence.classAn implementation of SequenceDB that uses an underlying HashMap to store the sequence objects.final classThis class implements SequenceDB on top of a set of sequence files and sequence offsets within these files.classclassAn abstract implementation of SequenceDB that wraps up another database.classclassSequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database.classFunctions 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 ChangeableModifier and TypeClassDescriptionclassSimple 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 ChangeableModifier and TypeClassDescriptionclassDeprecated.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 ChangeableModifier and TypeClassDescriptionclassFlatSequenceDBis an OBDA flatfile sequence databank implementation. -
Uses of Changeable in org.biojava.bio.seq.distributed
Classes in org.biojava.bio.seq.distributed that implement ChangeableModifier and TypeClassDescriptionclassSequence database from the meta-DAS system. -
Uses of Changeable in org.biojava.bio.seq.homol
Subinterfaces of Changeable in org.biojava.bio.seq.homolModifier and TypeInterfaceDescriptioninterfaceinterfaceSimilarityPairFeaturedescribes a pairwise similarity between two nucleotide sequences (as it extendsStrandedFeature).Classes in org.biojava.bio.seq.homol that implement ChangeableModifier and TypeClassDescriptionstatic final classEmptyPairwiseAlignmentempty pairwise alignment which has labels to empty symbol lists.classA no-frills implementation of Homology. -
Uses of Changeable in org.biojava.bio.seq.impl
Classes in org.biojava.bio.seq.impl that implement ChangeableModifier and TypeClassDescriptionclassSupport class for applications which need to patch together sections of sequence into a single SymbolList.final classA Sequence implementation that has a name and URI but no features, and a zero length symbol list.classFeatureHolder which lazily applies a specified filter to another FeatureHolder.classSupport class for applications which need to patch together sections of sequence into a single SymbolList.classA reverse complement view ontoSequenceinterface.classA no-frills implementation of a feature.classTitle: SimpleFramedFeature.classSimple implementation of GappedSequence.classclassA no-frills implementation of a remote feature.classSimpleRestrictionSiterepresents the recognition site of a restriction enzyme.classA basic implementation of theSequenceinterface.classSimpleSimilarityPairFeaturerepresents a similarity between a query sequence and a subject sequence as produced by a search program.classA no-frills implementation of StrandedFeature.classView a sub-section of a given sequence object, including all the features intersecting that region.classA view onto another Sequence object. -
Uses of Changeable in org.biojava.bio.seq.io
Subinterfaces of Changeable in org.biojava.bio.seq.ioModifier and TypeInterfaceDescriptioninterfaceEncapsulate a mapping between BioJava Symbol objects and some string representation.Classes in org.biojava.bio.seq.io that implement ChangeableModifier and TypeClassDescriptionclassImplementation of SymbolTokenization which binds symbols to strings of characters.classImplementation of SymbolTokenization which binds symbols to single unicode characters.classTokenization for cross-product alphabets.classclassclassSimple implementation of SymbolTokenization which uses the `name' field of the symbols.classDeprecated.Use org.biojavax.bio.seq.io framework insteadclassclassBase 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 ChangeableModifier and TypeClassDescriptionclassInternal class used by ProjectionEngine to wrap Feature objects.final classHelper 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.symbolModifier and TypeInterfaceDescriptioninterfaceThe set of AtomicSymbols which can be concatenated together to make a SymbolList.interfaceMap between Symbols and index numbers.interfaceA symbol that is not ambiguous.interfaceA symbol that can be represented as a string of Symbols.interfaceAn alphabet over a finite set of Symbols.interfaceThis extends SymbolList with API for manipulating, inserting and deleting gaps.interfaceA single symbol.interfaceA sequence of symbols that belong to an alphabet.Classes in org.biojava.bio.symbol that implement ChangeableModifier and TypeClassDescriptionclassAn abstract implementation ofAlphabet.classThe base-class for Symbol implementations.classAbstract helper implementation of the SymbolList core interface.classSymbolList implementation using constant-size chunks.final classAn efficient implementation of an Alphabet over the infinite set of double values.static classA range of double values.static classA single double value.static classA class to represent a contiguous range of double symbols.classSymbol list which just consists of non-informative symbols.classAn atomic symbol consisting only of itself.final classAn efficient implementation of an Alphabet over the infinite set of integer values.static classA single int value.static classA class to represent a finite contiguous subset of the infinite IntegerAlphabetclassA SymbolList that stores symbols as bit-patterns in an array of longs.classAn alignment that relabels another alignment.classA simple no-frills implementation of the FiniteAlphabet interface.classA basic implementation of AtomicSymbol.classa simple no-frills implementation of the CodonPref object that encapsulates codon preference data.classThis implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.classBasic implementation of SymbolList.classAn alphabet that contains a single atomic symbol.final classSoft masking is usually displayed by making the masked regions somehow different from the non masked regions.classThisSymbolTokenizerworks with a delegate to softmask symbol tokenization as appropriate. -
Uses of Changeable in org.biojava.bio.taxa
Subinterfaces of Changeable in org.biojava.bio.taxaModifier and TypeInterfaceDescriptioninterfaceDeprecated.replaced by classes inorg.biojavax.bio.taxaClasses in org.biojava.bio.taxa that implement ChangeableModifier and TypeClassDescriptionclassDeprecated.replaced by classes inorg.biojavax.bio.taxaclassDeprecated.replaced by classes inorg.biojavax.bio.taxaclassDeprecated.replaced by classes inorg.biojavax.bio.taxa -
Uses of Changeable in org.biojava.ontology
Subinterfaces of Changeable in org.biojava.ontologyModifier and TypeInterfaceDescriptioninterfaceAn ontology.interfaceA term in an ontology which identifies another ontology.interfaceA term in another ontology.interfaceA term in an ontology.interfaceA triple in an ontology.interfaceClasses in org.biojava.ontology that implement ChangeableModifier and TypeClassDescriptionclassAbstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.classfinal classstatic final classA basic in-memory implementation of an ontologystatic final classSimple in-memory implementation of a remote ontology term.static final classSimple in-memory implementation of a remote ontology term.static classSimple in-memory implementation of an ontology term.static final classBasic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriplestatic class -
Uses of Changeable in org.biojava.utils
Classes in org.biojava.utils that implement ChangeableModifier and TypeClassDescriptionclassUseful base-class for objects implementing ChangeableclassThis 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.biojavaxModifier and TypeInterfaceDescriptioninterfaceA simple ranked comment designed to be used for BioEntry comments in BioSQL.interfaceRepresents a cross reference to another database.interfaceRepresents a documentary reference.interfaceRepresents an author of a documentary reference.interfaceThe namespace of an entry in a database schema.interfaceNote is a generic class intended to hold a term describing the note, a value to associate with that term, and a rank.interfaceAllows cross-references to other databases to be ranked.interfaceDefines an object as being able to have ranked cross references associated with it.interfaceRepresents a documentary reference.interfaceAnnotatable objects that can have rich annotations.interfaceAn annotation collection which stores annotations as Note objects.Classes in org.biojavax that implement ChangeableModifier and TypeClassDescriptionclassA place holder for a RichAnnotation that prevents null having to be usedclassAn implementaion of Comment.classA basic CrossRef implementation.classA basic DocRef implementation.classRepresents an author of a documentary reference.classA basic Namespace implemenation.classSimple implementation of Note.classSimple implementation of RankedCrossRef.classRepresents a documentary reference.classSimple annotation wrapper. -
Uses of Changeable in org.biojavax.bio
Subinterfaces of Changeable in org.biojavax.bioModifier and TypeInterfaceDescriptioninterfaceThis class relates to the bioentry table in BioSQL.interfaceRepresents the relation between two bioentries.Classes in org.biojavax.bio that implement ChangeableModifier and TypeClassDescriptionclassReference implementation of a BioEntry object which has no features or sequence.classRepresents 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.dbModifier and TypeInterfaceDescriptioninterfaceA database of RichSequences with accessible keys and iterators over all sequences.interfaceA database of RichSequences.Classes in org.biojavax.bio.db that implement ChangeableModifier and TypeClassDescriptionclassAn abstract implementation of BioEntryDB that provides the getBioEntryIterator method.classAn abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method.classAn implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects.classAn 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 -
Uses of Changeable in org.biojavax.bio.db.ncbi
Classes in org.biojavax.bio.db.ncbi that implement ChangeableModifier and TypeClassDescriptionclassThis class contains functions accessing DNA sequences in Genbank format.classThis class contains functions accessing Peptide sequences in Genpept format. -
Uses of Changeable in org.biojavax.bio.seq
Subinterfaces of Changeable in org.biojavax.bio.seqModifier and TypeInterfaceDescriptioninterfaceRepresents a feature that can be given name and rank and be moved from one sequence to another.interfaceRepresents the relation between two features.interfaceDescribes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.interfaceA rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.Classes in org.biojavax.bio.seq that implement ChangeableModifier and TypeClassDescriptionclassAn implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.classAn Empty implementation of RichLocation.classA symbol list that isInteger.MAX_VALUElong, never gives index out of bounds and always returns ambiguity symbols for everything.classAn implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences.classA simple implementation of RichFeature.classRepresents a relationship between two features that is described by a term.classA simple implementation of RichLocation.classA simple implementation of RichSequence.classA simple implementation of RichSequence. -
Uses of Changeable in org.biojavax.bio.taxa
Subinterfaces of Changeable in org.biojavax.bio.taxaModifier and TypeInterfaceDescriptioninterfaceRepresents an NCBI Taxon entry, a combination of the taxon and taxon_name tables in BioSQL.Classes in org.biojavax.bio.taxa that implement Changeable -
Uses of Changeable in org.biojavax.ga
Subinterfaces of Changeable in org.biojavax.gaModifier and TypeInterfaceDescriptioninterfaceThe class that runs the cycles of reproduction, evolution and selection, potentially on multiplePopulationsinterfaceA GA 'organism' contains one or more ChromosomesinterfaceA collection of GA organisms -
Uses of Changeable in org.biojavax.ga.functions
Subinterfaces of Changeable in org.biojavax.ga.functionsModifier and TypeInterfaceDescriptioninterfaceCrosses two chromosomes.interfaceA class that mutates aSymbolListClasses in org.biojavax.ga.functions that implement ChangeableModifier and TypeClassDescriptionclassAbstract implementation ofCrossOverFunction.classAbstract implementation ofMutationFunctionall custom implementations should inherit from here.static final classA place holder CrossOverFunction that doesn't perform cross oversstatic final classPlace Holder class that doesn't mutate its SymbolListsclassThis does a 2-point-crossover on two chromosomes keeping the Symbols in each chromosome constant.classSimple Implementation of theCrossOverFunctioninterfacefinal classSimple no frills Implementation of the MutationFunction interfaceclassThis 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 ChangeableModifier and TypeClassDescriptionclassBase class from which most implementations of GeneticAlgorithm will inherit.classAbstract implementation of Organism.classMost Population implementations will want to inherit from here.final classA simple implementation of theGeneticAlgorithminterface it is not intended that this class be overidden, hence it is final.classA Simple Haploid Organism implementationfinal classSimple concrete implementation of thePopulationinterface -
Uses of Changeable in org.biojavax.ontology
Subinterfaces of Changeable in org.biojavax.ontologyModifier and TypeInterfaceDescriptioninterfaceAn Ontology that can be compared to another.interfaceMakes Term objects comparable properly and adds some extra features to them.interfaceComparable triples, obviously.Classes in org.biojavax.ontology that implement ChangeableModifier and TypeClassDescriptionclassRepresents an ontology that can be compared to other ontologies.classA Term object that can be compared and thus sorted.classBasic comparable triple, BioSQL style.