Uses of Interface
org.biojava.utils.Changeable

Packages that use Changeable
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.molbio The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR. 
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.program.unigene Objects for representing Unigene clusters. 
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.biofetch Client for the OBDA BioFetch protocol. 
org.biojava.bio.seq.db.biosql General purpose Sequence storage in a relational database. 
org.biojava.bio.seq.db.flat Support for OBDA flatfile databases. 
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.biojava.utils Miscellaneous utility classes used by other BioJava components. 
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 Classes to provide a genetic algorithm framework 
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 Changeable in org.biojava.bio
 

Subinterfaces of Changeable in org.biojava.bio
 interface Annotatable
          Indicates that an object has an associated annotation.
 interface Annotation
           Arbitrary annotation associated with one or more objects.
 

Classes in org.biojava.bio that implement Changeable
 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 Changeable in org.biojava.bio.alignment
 

Subinterfaces of Changeable in org.biojava.bio.alignment
 interface ARAlignment
          ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.
 interface UnequalLengthAlignment
          UnequalLengthAlignment has the following behavior.
 

Classes in org.biojava.bio.alignment that implement Changeable
 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 Changeable in org.biojava.bio.dist
 

Subinterfaces of Changeable in org.biojava.bio.dist
 interface Count
           An encapsulation of a count over the Symbols within an alphabet.
 interface Distribution
           An encapsulation of a probability distribution over the Symbols within an alphabet.
 interface OrderNDistribution
          Provides an N'th order distribution.
 

Classes in org.biojava.bio.dist that implement Changeable
 class AbstractDistribution
          An abstract implementation of Distribution.
 class AbstractOrderNDistribution
          Simple base class for OrderNDistributions.
 class GapDistribution
          This distribution emits gap symbols.
 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 Changeable in org.biojava.bio.dp
 

Subinterfaces of Changeable in org.biojava.bio.dp
 interface DotState
           A Dot state.
 interface EmissionState
           A state in a markov process that has an emission spectrum.
 interface MarkovModel
          A markov model.
 interface ModelInState
          A state that contains an entire sub-model.
 interface State
          A state in a markov process.
 interface StatePath
          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 Changeable
 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 SimpleStatePath
          A no-frills implementation of StatePath.
 class WMAsMM
          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 Changeable
 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 PairwiseSequencePanel
          A PairwiseSequencePanel 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 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 SequencePanel
          A panel that displays a Sequence.
 class SequencePoster
          Deprecated. This doesn't handle loads of stuff. Use SequencePoster.
 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 TranslatedSequencePanel
          TranslatedSequencePanel is a panel that displays a Sequence.
 class ZiggyFeatureRenderer
          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.molbio
 interface RestrictionSite
          RestrictionSite represents the recognition site of a restriction enzyme.
 

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

Classes in org.biojava.bio.program.das that implement Changeable
 class DAS
          A collection of DAS datasources.
 class DASSequence
          Sequence reflecting a DAS reference sequence, possibly decorated with one of more annotation sets.
 class DASSequenceDB
           Collection of sequences retrieved from the DAS network.
 class ReferenceServer
          Reflects a reference server on the DAS network.
 

Uses of Changeable in org.biojava.bio.program.gff3
 

Subinterfaces of Changeable in org.biojava.bio.program.gff3
 interface GFF3Record
          A record in a GFF3 formatted file.
 

Classes in org.biojava.bio.program.gff3 that implement Changeable
static class GFF3Record.Impl
           
 

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

Classes in org.biojava.bio.program.hmmer that implement Changeable
 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 Changeable in org.biojava.bio.program.homologene
 

Classes in org.biojava.bio.program.homologene that implement Changeable
 class AbstractOrthologueSet
           
 class AbstractOrthoPairSet
          represents the Homologene Group.
 class SimpleOrthologueSet
           
 class SimpleOrthoPairSet
          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 Changeable
 class PhredSequence
          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.unigene
 interface UnigeneCluster
           A single unigene cluster.
 interface UnigeneDB
          A database of Unigene clusters.
 

Uses of Changeable in org.biojava.bio.search
 

Subinterfaces of Changeable in org.biojava.bio.search
 interface SeqSimilaritySearchHit
          Objects of this type represent one particular hit (sequence and associated information) from a sequence similarity search.
 interface SeqSimilaritySearchResult
          Objects of this type represent one particular result of a sequence similarity search.
 interface SeqSimilaritySearchSubHit
          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 Changeable
 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 Changeable in org.biojava.bio.seq
 

Subinterfaces of Changeable in org.biojava.bio.seq
 interface ComponentFeature
          Feature which represents a component in an assembly (contig).
 interface Feature
          A feature within a sequence, or nested within another feature.
 interface FeatureHolder
          The interface for objects that contain features.
static interface FeatureTypes.Repository
          A named collection of Types.
static interface FeatureTypes.Type
          A type of feature.
 interface FramedFeature
          Title: FramedFeature.
 interface GappedSequence
          Extension of GappedSymbolList which also projects features into the gapped coordinate system.
 interface RealizingFeatureHolder
          Interface for FeatureHolder objects which know how to instantiate new child Features.
 interface RemoteFeature
          A feature that indicates that there is some remote feature that can't be represented entirely on a single Sequence.
 interface Sequence
           A biological sequence.
 interface StrandedFeature
          Adds the concept of 'strand' to features.
 

Classes in org.biojava.bio.seq that implement Changeable
 class AbstractFeatureHolder
          An abstract implementation of FeatureHolder.
 class CircularView
           A circular view onto another Sequence object.
static class FeatureHolder.EmptyFeatureHolder
           
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 Changeable in org.biojava.bio.seq.db
 

Subinterfaces of Changeable in org.biojava.bio.seq.db
 interface SequenceDB
          A database of sequences with accessible keys and iterators over all sequences.
 interface SequenceDBLite
          A database of sequences.
 

Classes in org.biojava.bio.seq.db that implement Changeable
 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 Changeable in org.biojava.bio.seq.db.biofetch
 

Classes in org.biojava.bio.seq.db.biofetch that implement Changeable
 class BioFetchSequenceDB
          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 Changeable
 class BioSQLSequenceDB
          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 Changeable
 class FlatSequenceDB
          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 Changeable
 class DistributedSequenceDB
          Sequence database from the meta-DAS system.
 

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

Subinterfaces of Changeable in org.biojava.bio.seq.homol
 interface HomologyFeature
           
 interface SimilarityPairFeature
          SimilarityPairFeature describes a pairwise similarity between two nucleotide sequences (as it extends StrandedFeature).
 

Classes in org.biojava.bio.seq.homol that implement Changeable
static class SimilarityPairFeature.EmptyPairwiseAlignment
          EmptyPairwiseAlignment empty pairwise alignment which has labels to empty symbol lists.
 class SimpleHomology
          A no-frills implementation of Homology.
 

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

Classes in org.biojava.bio.seq.impl that implement Changeable
 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 LazyFilterFeatureHolder
          FeatureHolder which lazily applies a specified filter to another FeatureHolder.
 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.
 class SubSequence
          View a sub-section of a given sequence object, including all the features intersecting that region.
 class ViewSequence
          A view onto another Sequence object.
 

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

Subinterfaces of Changeable in org.biojava.bio.seq.io
 interface SymbolTokenization
          Encapsulate a mapping between BioJava Symbol objects and some string representation.
 

Classes in org.biojava.bio.seq.io that implement Changeable
 class CharacterTokenization
          Implementation of SymbolTokenization which binds symbols to single unicode characters.
 class CrossProductTokenization
          Tokenization for cross-product alphabets.
 class DoubleTokenization
           
 class IntegerTokenization
           
 class NameTokenization
          Simple implementation of SymbolTokenization which uses the `name' field of the symbols.
 class ReferenceAnnotation
          Deprecated. Use org.biojavax.bio.seq.io framework instead
 class SubIntegerTokenization
           
 class WordTokenization
          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 Changeable
 class ProjectedFeature
          Internal class used by ProjectionEngine to wrap Feature objects.
 class ProjectedFeatureHolder
          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.symbol
 interface Alignment
          An alignment containing multiple SymbolLists.
 interface Alphabet
           The set of AtomicSymbols which can be concatenated together to make a SymbolList.
 interface AlphabetIndex
           Map between Symbols and index numbers.
 interface AtomicSymbol
           A symbol that is not ambiguous.
 interface BasisSymbol
           A symbol that can be represented as a string of Symbols.
 interface FiniteAlphabet
          An alphabet over a finite set of Symbols.
 interface GappedSymbolList
          This extends SymbolList with API for manipulating, inserting and deleting gaps.
 interface Symbol
          A single symbol.
 interface SymbolList
          A sequence of symbols that belong to an alphabet.
 

Classes in org.biojava.bio.symbol that implement Changeable
 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 DoubleAlphabet
           An efficient implementation of an Alphabet over the infinite set of double values.
static class DoubleAlphabet.DoubleRange
          A range of double values.
static class DoubleAlphabet.DoubleSymbol
          A single double value.
static class DoubleAlphabet.SubDoubleAlphabet
          A class to represent a contiguous range of double symbols.
 class DummySymbolList
          Symbol list which just consists of non-informative symbols.
 class FundamentalAtomicSymbol
          An atomic symbol consisting only of itself.
 class IntegerAlphabet
           An efficient implementation of an Alphabet over the infinite set of integer values.
static class IntegerAlphabet.IntegerSymbol
          A single int value.
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 RelabeledAlignment
          An alignment that relabels another alignment.
 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.
 class SoftMaskedAlphabet
          Soft masking is usually displayed by making the masked regions somehow different from the non masked regions.
 class SoftMaskedAlphabet.CaseSensitiveTokenization
          This SymbolTokenizer 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.taxa
 interface Taxon
          Deprecated. replaced by classes in org.biojavax.bio.taxa
 

Classes in org.biojava.bio.taxa that implement Changeable
 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 Changeable in org.biojava.ontology
 

Subinterfaces of Changeable in org.biojava.ontology
 interface Ontology
          An ontology.
 interface OntologyTerm
          A term in an ontology which identifies another ontology.
 interface RemoteTerm
          A term in another ontology.
 interface Term
          A term in an ontology.
 interface Triple
          A triple in an ontology.
 interface Variable
           
 

Classes in org.biojava.ontology that implement Changeable
 class AbstractTerm
          Abstract implementation of term
 class IntegerOntology
           
 class IntegerOntology.IntTerm
           
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 Triple.Impl
          Basic in-memory implementation of a Triple in an ontology
static class Variable.Impl
           
 

Uses of Changeable in org.biojava.utils
 

Classes in org.biojava.utils that implement Changeable
 class AbstractChangeable
          Useful base-class for objects implementing Changeable
 class Unchangeable
          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.biojavax
 interface Comment
          A simple ranked comment designed to be used for BioEntry comments in BioSQL.
 interface CrossRef
          Represents a cross reference to another database.
 interface DocRef
          Represents a documentary reference.
 interface DocRefAuthor
          Represents an author of a documentary reference.
 interface Namespace
          The namespace of an entry in a database schema.
 interface Note
          Note is a generic class intended to hold a term describing the note, a value to associate with that term, and a rank.
 interface RankedCrossRef
          Allows cross-references to other databases to be ranked.
 interface RankedCrossRefable
          Defines an object as being able to have ranked cross references associated with it.
 interface RankedDocRef
          Represents a documentary reference.
 interface RichAnnotatable
          Annotatable objects that can have rich annotations.
 interface RichAnnotation
          An annotation collection which stores annotations as Note objects.
 

Classes in org.biojavax that implement Changeable
 class EmptyRichAnnotation
          A place holder for a RichAnnotation that prevents null having to be used
 class SimpleComment
          An implementaion of Comment.
 class SimpleCrossRef
          A basic CrossRef implementation.
 class SimpleDocRef
          A basic DocRef implementation.
 class SimpleDocRefAuthor
          Represents an author of a documentary reference.
 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 Changeable in org.biojavax.bio
 

Subinterfaces of Changeable in org.biojavax.bio
 interface BioEntry
          This class relates to the bioentry table in BioSQL.
 interface BioEntryRelationship
          Represents the relation between two bioentries.
 

Classes in org.biojavax.bio that implement Changeable
 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 Changeable in org.biojavax.bio.db
 

Subinterfaces of Changeable in org.biojavax.bio.db
 interface RichSequenceDB
          A database of RichSequences with accessible keys and iterators over all sequences.
 interface RichSequenceDBLite
          A database of RichSequences.
 

Classes in org.biojavax.bio.db that implement Changeable
 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 Changeable in org.biojavax.bio.db.biosql
 

Classes in org.biojavax.bio.db.biosql that implement Changeable
 class BioSQLBioEntryDB
           
 class BioSQLRichSequenceDB
           
 

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

Classes in org.biojavax.bio.db.ncbi that implement Changeable
 class GenbankRichSequenceDB
          This class contains functions accessing DNA sequences in Genbank format.
 

Uses of Changeable in org.biojavax.bio.seq
 

Subinterfaces of Changeable in org.biojavax.bio.seq
 interface RichFeature
          Represents a feature that can be given name and rank and be moved from one sequence to another.
 interface RichFeatureHolder
          Holds feature relationships.
 interface RichFeatureRelationship
          Represents the relation between two features.
 interface RichLocation
          Describes locations, and adds the concepts of circularity, fuzziness, annotations, and cross-references to other databases.
 interface RichSequence
          A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.
 

Classes in org.biojavax.bio.seq that implement Changeable
 class CompoundRichLocation
          An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence.
 class EmptyRichLocation
          An Empty implementation of RichLocation.
 class InfinitelyAmbiguousSymbolList
          A symbol list that is Integer.MAX_VALUElong, never gives index out of bounds and always returns ambiguity symbols for everything.
 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 Changeable in org.biojavax.bio.taxa
 

Subinterfaces of Changeable in org.biojavax.bio.taxa
 interface NCBITaxon
          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
 class SimpleNCBITaxon
          Reference implementation of NCBITaxon.
 

Uses of Changeable in org.biojavax.ga
 

Subinterfaces of Changeable in org.biojavax.ga
 interface GeneticAlgorithm
          The class that runs the cycles of reproduction, evolution and selection, potentially on multiple Populations
 interface Organism
          A GA 'organism' contains one or more Chromosomes
 interface Population
          A collection of GA organisms
 

Uses of Changeable in org.biojavax.ga.functions
 

Subinterfaces of Changeable in org.biojavax.ga.functions
 interface CrossOverFunction
          Crosses two chromosomes.
 interface MutationFunction
          A class that mutates a SymbolList
 

Classes in org.biojavax.ga.functions that implement Changeable
 class AbstractCrossOverFunction
          Abstract implementation of CrossOverFunction.
 class AbstractMutationFunction
          Abstract implementation of MutationFunction all custom implementations should inherit from here.
 class AbstractSelectionFunction
           Abstract implementation of FitnessFunction.
static class CrossOverFunction.NoCross
          A place holder CrossOverFunction that doesn't perform cross overs
static class MutationFunction.NoMutation
           Place Holder class that doesn't mutate its SymbolLists
 class ProportionalSelection
          A Selection function that determines the proportion of individuals in a new population proportionally to their fitness.
static class SelectionFunction.Threshold
          Selects individuals who's fitness exceeds a threshold value.
 class SimpleCrossOverFunction
          Simple Implementation of the CrossOverFunction interface
 class SimpleMutationFunction
           Simple no frills Implementation of the MutationFunction interface
 

Uses of Changeable in org.biojavax.ga.impl
 

Classes in org.biojavax.ga.impl that implement Changeable
 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 Changeable in org.biojavax.ontology
 

Subinterfaces of Changeable in org.biojavax.ontology
 interface ComparableOntology
          An Ontology that can be compared to another.
 interface ComparableTerm
          Makes Term objects comparable properly and adds some extra features to them.
 interface ComparableTriple
          Comparable triples, obviously.
 

Classes in org.biojavax.ontology that implement Changeable
 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.