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.
-
Uses of Changeable in org.biojava.bio
Subinterfaces of Changeable in org.biojava.bioModifier and TypeInterfaceDescriptioninterface
Indicates that an object has an associated annotation.interface
Arbitrary annotation associated with one or more objects.Classes in org.biojava.bio that implement ChangeableModifier and TypeClassDescriptionclass
A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.class
AnnotationChanger
remaps the values of anAnnotation
to new values specified by aValueChanger
.class
AnnotationRenamer
remaps the keys of anAnnotation
to new keys specified by aTagMapper
.class
Create an Annotation with properties matching those of a JavaBean instance.class
Merged view onto a list of underlying Annotation objects.class
Annotation implementation which allows new key-value pairs to be layered on top of an underlying Annotation.class
A no-frills implementation of Annotation that is just a wrapper around aLinkedHashMap
.class
Annotation that is optimized for memory usage. -
Uses of Changeable in org.biojava.bio.alignment
Subinterfaces of Changeable in org.biojava.bio.alignmentModifier and TypeInterfaceDescriptioninterface
An alignment containing multiple SymbolLists.interface
ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.interface
UnequalLengthAlignment has the following behavior.Classes in org.biojava.bio.alignment that implement ChangeableModifier and TypeClassDescriptionclass
class
class
This class stores the result of an alignment procedure that creates a pairwise alignment of two sequences.class
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
A simple implementation of an Alignment. -
Uses of Changeable in org.biojava.bio.dist
Subinterfaces of Changeable in org.biojava.bio.distModifier and TypeInterfaceDescriptioninterface
An encapsulation of a count over the Symbols within an alphabet.interface
An encapsulation of a probability distribution over the Symbols within an alphabet.interface
Provides an N'th order distribution.Classes in org.biojava.bio.dist that implement ChangeableModifier and TypeClassDescriptionclass
An abstract implementation of Distribution.class
Simple base class for OrderNDistributions.class
This distribution emits gap symbols.final class
An encapsulation of a count over the Symbols within a FiniteAlphabet using an AlphabetIndex object.class
Class for pairing up two independant distributions.class
A simple implementation of a distribution, which works with any finite alphabet.class
A translated view of some underlying distribution.class
An implementation of an uniform distributionclass
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.dpModifier and TypeInterfaceDescriptioninterface
A Dot state.interface
A state in a markov process that has an emission spectrum.interface
A markov model.interface
A state that contains an entire sub-model.interface
A state in a markov process.interface
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 ChangeableModifier and TypeClassDescriptionfinal class
Start/end state for HMMs.class
class
A Dot state that you can make and use.class
class
class
class
A no-frills implementation of StatePath.class
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 ChangeableModifier and TypeClassDescriptionclass
Renders an ABI trace file as a chromatogram graph.class
AbstractBeadRenderer
is a an abstract base class for the creation ofFeatureRenderer
s which use a 'string of beads' metaphor for displaying features.class
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
class
class
class
CrosshairRenderer
draws a crosshair, optionally with coordinates.class
EllipticalBeadRenderer
renders features as simple ellipses.class
FeatureBlockSequenceRenderer
forms a bridge betweenSequence
rendering andFeature
rendering.class
class
class
A renderer that will display a gapped sequence as a discontinuous series of regions.class
A FeatureRenderer that renders a particular Glyph for Features accepted by a particular FeatureFilterclass
Renderer which draws a track of sequence with a textual label.class
MultiLineRenderer
is aSequenceRenderer
which collects a number of otherSequenceRenderer
s each of which render their own view of aSequence
.class
OffsetRulerRenderer can render the ruler starting from an arbitrary offset from the sequence.class
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
A renderer that adds padding before and after a delegate renderer.class
PairwiseDiagonalRenderer
renders a region of similarity between two sequences as a straight line.class
PairwiseFilteringRenderer
wraps aPairwiseSequenceRenderer
and filters thePairwiseRenderContext
s passed to it.class
PairwiseOverlayRenderer
allows a list of otherPairwiseSequenceRenderer
s to superimpose their output.class
APairwiseSequencePanel
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
A concrete AbstractPeptideDigestRenderer.class
RectangularBeadRenderer
renders features as simple rectangles.class
RoundRectangularBeadRenderer
renders features as rectangles with rounded corners.class
A GlyphRenderer subclass that specificatlly handles Features pertaining to Secondary Structure (Helices, Turns and Strands).class
A panel that displays a Sequence.class
Deprecated.This doesn't handle loads of stuff.class
An implementation of SequenceRenderer that delegates rendering to another renderer.class
class
Class that handles drawing in six frames for other classes.class
A feature renderer that computes the data necessary to render multi-exon transcripts without CDS data.class
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
class
TranslatedSequencePanel
is a panel that displays a Sequence.class
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.molbioModifier and TypeInterfaceDescriptioninterface
RestrictionSite
represents 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 TypeClassDescriptionclass
This is a class for representing the full HMMER generated Profile HMM (including loop states N and C terminal looping states).class
This is a class for representing HMMER generated Profile HMM.class
A 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 TypeClassDescriptionclass
class
represents the Homologene Group.class
class
a 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 TypeClassDescriptionclass
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.unigeneModifier and TypeInterfaceDescriptioninterface
A single unigene cluster.interface
A database of Unigene clusters. -
Uses of Changeable in org.biojava.bio.search
Subinterfaces of Changeable in org.biojava.bio.searchModifier and TypeInterfaceDescriptioninterface
Objects of this type represent one particular hit (sequence and associated information) from a sequence similarity search.interface
Objects of this type represent one particular result of a sequence similarity search.interface
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 ChangeableModifier and TypeClassDescriptionclass
Deprecated.SimpleSeqSimilaritySearchHit has been made Annotatable and is now functionally identical.class
Deprecated.SimpleSeqSimilaritySearchResult has been made Annotatable and is now functionally identical.class
Deprecated.SimpleSeqSimilaritySearchSubHit has been made Annotatable and is now functionally identical.class
SimpleSeqSimilaritySearchHit
objects represent a similarity search hit of a query sequence to a sequence referenced in a SequenceDB object.class
SimpleSeqSimilaritySearchResult
objects represent a result of a search of aSymbolList
against the sequences within aSequenceDB
object.class
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.seqModifier and TypeInterfaceDescriptioninterface
Feature which represents a component in an assembly (contig).interface
A feature within a sequence, or nested within another feature.interface
The interface for objects that contain features.static interface
A named collection of Types.static interface
A type of feature.interface
Title: FramedFeature.interface
Extension of GappedSymbolList which also projects features into the gapped coordinate system.interface
Interface forFeatureHolder
objects which know how to instantiate new child Features.interface
A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.interface
A biological sequence.interface
Adds the concept of 'strand' to features.Classes in org.biojava.bio.seq that implement ChangeableModifier and TypeClassDescriptionclass
An abstract implementation of FeatureHolder.class
A circular view onto another Sequence object.static final class
static class
A simple implementation of a Repository.class
Wrapper implementation of FeatureHolder which calls a method to create a contained FeatureHolder on demand.class
FeatureHolder which exposes all the features in a set of sub-FeatureHolders.class
A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.class
A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.class
A no-frills implementation of FeatureHolder. -
Uses of Changeable in org.biojava.bio.seq.db
Subinterfaces of Changeable in org.biojava.bio.seq.dbModifier and TypeInterfaceDescriptioninterface
A database of sequences with accessible keys and iterators over all sequences.interface
A database of sequences.Classes in org.biojava.bio.seq.db that implement ChangeableModifier and TypeClassDescriptionclass
An abstract implementation of SequenceDB that provides the sequenceIterator method.class
SequenceDB implementation which lazily applies a SequenceAnnotator to sequences retrieved from a SequenceDB.class
SequenceDB implementation that caches the results of another SequenceDB.class
DummySequenceDB
is an implementation which contains only aDummySequence
.class
An implementation of SequenceDB that uses an underlying HashMap to store the sequence objects.final class
This class implements SequenceDB on top of a set of sequence files and sequence offsets within these files.class
class
An abstract implementation of SequenceDB that wraps up another database.class
class
SequenceDB implementation that returns new SequenceView instances wrapping the sequences in an underlying database.class
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 ChangeableModifier and TypeClassDescriptionclass
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 ChangeableModifier and TypeClassDescriptionclass
Deprecated.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 TypeClassDescriptionclass
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 ChangeableModifier and TypeClassDescriptionclass
Sequence 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 TypeInterfaceDescriptioninterface
interface
SimilarityPairFeature
describes a pairwise similarity between two nucleotide sequences (as it extendsStrandedFeature
).Classes in org.biojava.bio.seq.homol that implement ChangeableModifier and TypeClassDescriptionstatic final class
EmptyPairwiseAlignment
empty pairwise alignment which has labels to empty symbol lists.class
A 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 TypeClassDescriptionclass
Support class for applications which need to patch together sections of sequence into a single SymbolList.final class
A Sequence implementation that has a name and URI but no features, and a zero length symbol list.class
FeatureHolder which lazily applies a specified filter to another FeatureHolder.class
Support class for applications which need to patch together sections of sequence into a single SymbolList.class
A reverse complement view ontoSequence
interface.class
A no-frills implementation of a feature.class
Title: SimpleFramedFeature.class
Simple implementation of GappedSequence.class
class
A no-frills implementation of a remote feature.class
SimpleRestrictionSite
represents the recognition site of a restriction enzyme.class
A basic implementation of theSequence
interface.class
SimpleSimilarityPairFeature
represents a similarity between a query sequence and a subject sequence as produced by a search program.class
A no-frills implementation of StrandedFeature.class
View a sub-section of a given sequence object, including all the features intersecting that region.class
A view onto another Sequence object. -
Uses of Changeable in org.biojava.bio.seq.io
Subinterfaces of Changeable in org.biojava.bio.seq.ioModifier and TypeInterfaceDescriptioninterface
Encapsulate a mapping between BioJava Symbol objects and some string representation.Classes in org.biojava.bio.seq.io that implement ChangeableModifier and TypeClassDescriptionclass
Implementation of SymbolTokenization which binds symbols to strings of characters.class
Implementation of SymbolTokenization which binds symbols to single unicode characters.class
Tokenization for cross-product alphabets.class
class
class
Simple implementation of SymbolTokenization which uses the `name' field of the symbols.class
Deprecated.Use org.biojavax.bio.seq.io framework insteadclass
class
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 ChangeableModifier and TypeClassDescriptionclass
Internal class used by ProjectionEngine to wrap Feature objects.final class
Helper 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 TypeInterfaceDescriptioninterface
The set of AtomicSymbols which can be concatenated together to make a SymbolList.interface
Map between Symbols and index numbers.interface
A symbol that is not ambiguous.interface
A symbol that can be represented as a string of Symbols.interface
An alphabet over a finite set of Symbols.interface
This extends SymbolList with API for manipulating, inserting and deleting gaps.interface
A single symbol.interface
A sequence of symbols that belong to an alphabet.Classes in org.biojava.bio.symbol that implement ChangeableModifier and TypeClassDescriptionclass
An abstract implementation ofAlphabet
.class
The base-class for Symbol implementations.class
Abstract helper implementation of the SymbolList core interface.class
SymbolList implementation using constant-size chunks.final class
An efficient implementation of an Alphabet over the infinite set of double values.static class
A range of double values.static class
A single double value.static class
A class to represent a contiguous range of double symbols.class
Symbol list which just consists of non-informative symbols.class
An atomic symbol consisting only of itself.final class
An efficient implementation of an Alphabet over the infinite set of integer values.static class
A single int value.static class
A class to represent a finite contiguous subset of the infinite IntegerAlphabetclass
A SymbolList that stores symbols as bit-patterns in an array of longs.class
An alignment that relabels another alignment.class
A simple no-frills implementation of the FiniteAlphabet interface.class
A basic implementation of AtomicSymbol.class
a simple no-frills implementation of the CodonPref object that encapsulates codon preference data.class
This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.class
Basic implementation of SymbolList.class
An alphabet that contains a single atomic symbol.final class
Soft masking is usually displayed by making the masked regions somehow different from the non masked regions.class
ThisSymbolTokenizer
works 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 TypeInterfaceDescriptioninterface
Deprecated.replaced by classes inorg.biojavax.bio.taxa
Classes in org.biojava.bio.taxa that implement ChangeableModifier and TypeClassDescriptionclass
Deprecated.replaced by classes inorg.biojavax.bio.taxa
class
Deprecated.replaced by classes inorg.biojavax.bio.taxa
class
Deprecated.replaced by classes inorg.biojavax.bio.taxa
-
Uses of Changeable in org.biojava.ontology
Subinterfaces of Changeable in org.biojava.ontologyModifier and TypeInterfaceDescriptioninterface
An ontology.interface
A term in an ontology which identifies another ontology.interface
A term in another ontology.interface
A term in an ontology.interface
A triple in an ontology.interface
Classes in org.biojava.ontology that implement ChangeableModifier and TypeClassDescriptionclass
Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.class
final class
static final class
A basic in-memory implementation of an ontologystatic final class
Simple in-memory implementation of a remote ontology term.static final class
Simple in-memory implementation of a remote ontology term.static class
Simple in-memory implementation of an ontology term.static final class
Basic 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 TypeClassDescriptionclass
Useful base-class for objects implementing Changeableclass
This 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 TypeInterfaceDescriptioninterface
A simple ranked comment designed to be used for BioEntry comments in BioSQL.interface
Represents a cross reference to another database.interface
Represents a documentary reference.interface
Represents an author of a documentary reference.interface
The namespace of an entry in a database schema.interface
Note is a generic class intended to hold a term describing the note, a value to associate with that term, and a rank.interface
Allows cross-references to other databases to be ranked.interface
Defines an object as being able to have ranked cross references associated with it.interface
Represents a documentary reference.interface
Annotatable objects that can have rich annotations.interface
An annotation collection which stores annotations as Note objects.Classes in org.biojavax that implement ChangeableModifier and TypeClassDescriptionclass
A place holder for a RichAnnotation that prevents null having to be usedclass
An implementaion of Comment.class
A basic CrossRef implementation.class
A basic DocRef implementation.class
Represents an author of a documentary reference.class
A basic Namespace implemenation.class
Simple implementation of Note.class
Simple implementation of RankedCrossRef.class
Represents a documentary reference.class
Simple annotation wrapper. -
Uses of Changeable in org.biojavax.bio
Subinterfaces of Changeable in org.biojavax.bioModifier and TypeInterfaceDescriptioninterface
This class relates to the bioentry table in BioSQL.interface
Represents the relation between two bioentries.Classes in org.biojavax.bio that implement ChangeableModifier and TypeClassDescriptionclass
Reference implementation of a BioEntry object which has no features or sequence.class
Represents 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 TypeInterfaceDescriptioninterface
A database of RichSequences with accessible keys and iterators over all sequences.interface
A database of RichSequences.Classes in org.biojavax.bio.db that implement ChangeableModifier and TypeClassDescriptionclass
An abstract implementation of BioEntryDB that provides the getBioEntryIterator method.class
An abstract implementation of RichSequenceDB that provides the getRichSequenceIterator method.class
An implementation of RichSequenceDB that uses an underlying HashMap to store the RichSequence objects.class
An 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 TypeClassDescriptionclass
This class contains functions accessing DNA sequences in Genbank format.class
This 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 TypeInterfaceDescriptioninterface
Represents a feature that can be given name and rank and be moved from one sequence to another.interface
Represents the relation between two features.interface
Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.interface
A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.Classes in org.biojavax.bio.seq that implement ChangeableModifier and TypeClassDescriptionclass
An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.class
An Empty implementation of RichLocation.class
A symbol list that isInteger.MAX_VALUE
long, never gives index out of bounds and always returns ambiguity symbols for everything.class
An implementation of RichLocation which possibly covers multiple locations, on different strands, different circular lengths, or different sequences.class
A simple implementation of RichFeature.class
Represents a relationship between two features that is described by a term.class
A simple implementation of RichLocation.class
A simple implementation of RichSequence.class
A simple implementation of RichSequence. -
Uses of Changeable in org.biojavax.bio.taxa
Subinterfaces of Changeable in org.biojavax.bio.taxaModifier and TypeInterfaceDescriptioninterface
Represents 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 TypeInterfaceDescriptioninterface
The class that runs the cycles of reproduction, evolution and selection, potentially on multiplePopulation
sinterface
A GA 'organism' contains one or more Chromosomesinterface
A collection of GA organisms -
Uses of Changeable in org.biojavax.ga.functions
Subinterfaces of Changeable in org.biojavax.ga.functionsModifier and TypeInterfaceDescriptioninterface
Crosses two chromosomes.interface
A class that mutates aSymbolList
Classes in org.biojavax.ga.functions that implement ChangeableModifier and TypeClassDescriptionclass
Abstract implementation ofCrossOverFunction
.class
Abstract implementation ofMutationFunction
all custom implementations should inherit from here.static final class
A place holder CrossOverFunction that doesn't perform cross oversstatic final class
Place Holder class that doesn't mutate its SymbolListsclass
This does a 2-point-crossover on two chromosomes keeping the Symbols in each chromosome constant.class
Simple Implementation of theCrossOverFunction
interfacefinal class
Simple no frills Implementation of the MutationFunction interfaceclass
This 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 TypeClassDescriptionclass
Base class from which most implementations of GeneticAlgorithm will inherit.class
Abstract implementation of Organism.class
Most Population implementations will want to inherit from here.final class
A simple implementation of theGeneticAlgorithm
interface it is not intended that this class be overidden, hence it is final.class
A Simple Haploid Organism implementationfinal class
Simple concrete implementation of thePopulation
interface -
Uses of Changeable in org.biojavax.ontology
Subinterfaces of Changeable in org.biojavax.ontologyModifier and TypeInterfaceDescriptioninterface
An Ontology that can be compared to another.interface
Makes Term objects comparable properly and adds some extra features to them.interface
Comparable triples, obviously.Classes in org.biojavax.ontology that implement ChangeableModifier and TypeClassDescriptionclass
Represents an ontology that can be compared to other ontologies.class
A Term object that can be compared and thus sorted.class
Basic comparable triple, BioSQL style.