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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 FeatureRenderer s 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 SequenceRenderer s
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
PairwiseRenderContext s passed to it. |
class |
PairwiseOverlayRenderer
PairwiseOverlayRenderer allows a list of other
PairwiseSequenceRenderer s 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. |
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