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 Implementation of the Alignment interface. 
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.hmmer Tools for working with profile Hidden Markov Models from the HMMer package. 
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 into alternate coordinate systems. 
org.biojava.bio.seq.ragbag The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code. 
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.utils Miscellaneous utility classes used by other BioJava components. 
 

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 Map.
 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
          Creates a distribution that is a translated view of an 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 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 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 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 RectangularBeadRenderer
          RectangularBeadRenderer renders features as simple rectangles.
 class RoundRectangularBeadRenderer
          RoundRectangularBeadRenderer renders features as rectangles with rounded corners.
 class SequencePanel
          A panel that displays a Sequence.
 class SequencePoster
          A panel that displays a Sequence.
 class SequenceRendererWrapper
           
 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.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.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.
 class DummySequence
           
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 ProjectedFeatureHolder
          Helper class for projecting Feature objects into an alternative coordinate system.
 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.
 class SimpleGappedSequence
          Simple implementation of GappedSequence.
 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.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
          SequenceDB keyed off a BioSQL database.
 

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 LazyFilterFeatureHolder
          FeatureHolder which lazily applies a specified filter to another FeatureHolder.
 class RevCompSequence
          A reverse complement view onto Sequence interface.
 class SimpleFeature
          A no-frills implementation of a feature.
 class SimpleFramedFeature
          Title: SimpleFramedFeature.
 class SimpleHomologyFeature
           
 class SimpleRemoteFeature
          A no-frills implementation of a remote feature.
 class SimpleRestrictionSite
          SimpleRestrictionSite represents the recognition site of a restriction enzyme.
 class SimpleSequence
          A basic implementation of the Sequence interface.
 class SimpleSimilarityPairFeature
          SimpleSimilarityPairFeature represents a similarity between a query sequence and a subject sequence as produced by a search program.
 class SimpleStrandedFeature
          A no-frills implementation of StrandedFeature.
 

Uses of 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 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 ProjectedStrandedFeature
          Internal class used by ProjectedFeatureHolder to wrap StrandedFeatures.
 

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

Classes in org.biojava.bio.seq.ragbag that implement Changeable
(package private)  class org.biojava.bio.seq.ragbag.RagbagAbstractSequence
          object that instantiates a sequence in Ragbag.
 class RagbagAssembly
          object that instantiates a sequence when given a Ragbag directory.
 

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 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 PackedDnaSymbolList
          a class that implements storage of symbols in packed form (2 symbols per byte).
 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.
(package private)  class org.biojava.bio.symbol.SimpleBasisSymbol
          A basic implementation of BasisSymbol.
 class SimpleGappedSymbolList
          This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.
(package private)  class org.biojava.bio.symbol.SimpleSymbol
          A basic implementation of Symbol.
 class SimpleSymbolList
          Basic implementation of SymbolList.
 class SingletonAlphabet
          An alphabet that contains a single atomic symbol.
static class SymbolList.EmptySymbolList
          The empty immutable implementation.
 

Uses of Changeable in org.biojava.bio.taxa
 

Subinterfaces of Changeable in org.biojava.bio.taxa
 interface Taxon
          A taxon within a classification.
 

Classes in org.biojava.bio.taxa that implement Changeable
 class AbstractTaxon
          An abstract implementation of Taxon.
 class SimpleTaxon
          A no-frills implementatation of Taxon.
 class WeakTaxon
          An implementation of Taxon that keeps only weak references to children, but full references to parents.
 

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.