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Packages that use AbstractChangeable | |
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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.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.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.biosql | General purpose Sequence storage in a relational database. |
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.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.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 AbstractChangeable in org.biojava.bio |
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Subclasses of AbstractChangeable in org.biojava.bio | |
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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 AbstractChangeable in org.biojava.bio.alignment |
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Subclasses of AbstractChangeable in org.biojava.bio.alignment | |
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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 AbstractChangeable in org.biojava.bio.dist |
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Subclasses of AbstractChangeable in org.biojava.bio.dist | |
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class |
AbstractDistribution
An abstract implementation of Distribution. |
class |
AbstractOrderNDistribution
Simple base class for OrderNDistributions. |
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 AbstractChangeable in org.biojava.bio.dp |
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Subclasses of AbstractChangeable in org.biojava.bio.dp | |
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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 |
WMAsMM
Wraps a weight matrix up so that it appears to be a very simple HMM. |
Uses of AbstractChangeable in org.biojava.bio.gui.sequence |
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Subclasses of AbstractChangeable in org.biojava.bio.gui.sequence | |
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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 |
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 SequenceRenderer s
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
PairwiseRenderContext s passed to it. |
class |
PairwiseOverlayRenderer
PairwiseOverlayRenderer allows a list of other
PairwiseSequenceRenderer s to superimpose their
output. |
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 |
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 |
ZiggyFeatureRenderer
A feature renderer that draws non-contiguous features as a set of boxes joined by zig-zags. |
Uses of AbstractChangeable in org.biojava.bio.program.das |
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Subclasses of AbstractChangeable in org.biojava.bio.program.das | |
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class |
DAS
A collection of DAS datasources. |
class |
DASSequence
Sequence reflecting a DAS reference sequence, possibly decorated with one of more annotation sets. |
Uses of AbstractChangeable in org.biojava.bio.program.gff3 |
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Subclasses of AbstractChangeable in org.biojava.bio.program.gff3 | |
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static class |
GFF3Record.Impl
|
Uses of AbstractChangeable in org.biojava.bio.program.hmmer |
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Subclasses of AbstractChangeable in org.biojava.bio.program.hmmer | |
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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 AbstractChangeable in org.biojava.bio.program.homologene |
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Subclasses of AbstractChangeable in org.biojava.bio.program.homologene | |
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class |
AbstractOrthologueSet
|
class |
AbstractOrthoPairSet
represents the Homologene Group. |
class |
SimpleOrthologueSet
|
class |
SimpleOrthoPairSet
a no-frills implementation of a Homologene Group |
Uses of AbstractChangeable in org.biojava.bio.program.phred |
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Subclasses of AbstractChangeable in org.biojava.bio.program.phred | |
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class |
PhredSequence
PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores. |
Uses of AbstractChangeable in org.biojava.bio.search |
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Subclasses of AbstractChangeable in org.biojava.bio.search | |
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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 AbstractChangeable in org.biojava.bio.seq |
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Subclasses of AbstractChangeable in org.biojava.bio.seq | |
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class |
AbstractFeatureHolder
An abstract implementation of FeatureHolder. |
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 AbstractChangeable in org.biojava.bio.seq.db |
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Subclasses of AbstractChangeable in org.biojava.bio.seq.db | |
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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 AbstractChangeable in org.biojava.bio.seq.db.biosql |
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Subclasses of AbstractChangeable in org.biojava.bio.seq.db.biosql | |
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class |
BioSQLSequenceDB
Deprecated. Use hibernate and org.biojavax.bio.db.* |
Uses of AbstractChangeable in org.biojava.bio.seq.distributed |
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Subclasses of AbstractChangeable in org.biojava.bio.seq.distributed | |
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class |
DistributedSequenceDB
Sequence database from the meta-DAS system. |
Uses of AbstractChangeable in org.biojava.bio.seq.homol |
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Subclasses of AbstractChangeable in org.biojava.bio.seq.homol | |
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class |
SimpleHomology
A no-frills implementation of Homology. |
Uses of AbstractChangeable in org.biojava.bio.seq.impl |
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Subclasses of AbstractChangeable in org.biojava.bio.seq.impl | |
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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 |
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. |
Uses of AbstractChangeable in org.biojava.bio.seq.io |
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Subclasses of AbstractChangeable in org.biojava.bio.seq.io | |
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class |
ReferenceAnnotation
Deprecated. Use org.biojavax.bio.seq.io framework instead |
Uses of AbstractChangeable in org.biojava.bio.seq.projection |
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Subclasses of AbstractChangeable in org.biojava.bio.seq.projection | |
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class |
ProjectedFeatureHolder
Helper class for projecting Feature objects into an alternative coordinate system. |
Uses of AbstractChangeable in org.biojava.bio.symbol |
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Subclasses of AbstractChangeable in org.biojava.bio.symbol | |
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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 |
DummySymbolList
Symbol list which just consists of non-informative symbols. |
class |
FundamentalAtomicSymbol
An atomic symbol consisting only of itself. |
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 |
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. |
Uses of AbstractChangeable in org.biojava.bio.taxa |
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Subclasses of AbstractChangeable in org.biojava.bio.taxa | |
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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 AbstractChangeable in org.biojava.ontology |
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Subclasses of AbstractChangeable in org.biojava.ontology | |
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class |
AbstractTerm
Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties. |
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 |
Variable.Impl
|
Uses of AbstractChangeable in org.biojavax |
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Subclasses of AbstractChangeable in org.biojavax | |
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class |
SimpleComment
An implementaion of Comment. |
class |
SimpleDocRef
A basic DocRef implementation. |
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 AbstractChangeable in org.biojavax.bio |
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Subclasses of AbstractChangeable in org.biojavax.bio | |
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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 AbstractChangeable in org.biojavax.bio.db |
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Subclasses of AbstractChangeable in org.biojavax.bio.db | |
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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 AbstractChangeable in org.biojavax.bio.db.biosql |
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Subclasses of AbstractChangeable in org.biojavax.bio.db.biosql | |
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class |
BioSQLBioEntryDB
|
class |
BioSQLRichSequenceDB
|
Uses of AbstractChangeable in org.biojavax.bio.db.ncbi |
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Subclasses of AbstractChangeable in org.biojavax.bio.db.ncbi | |
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class |
GenbankRichSequenceDB
This class contains functions accessing DNA sequences in Genbank format. |
class |
GenpeptRichSequenceDB
This class contains functions accessing Peptide sequences in Genpept format. |
Uses of AbstractChangeable in org.biojavax.bio.seq |
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Subclasses of AbstractChangeable in org.biojavax.bio.seq | |
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class |
CompoundRichLocation
An implementation of RichLocation which covers multiple locations, but on the same strand of the same (optionally circular) sequence. |
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 AbstractChangeable in org.biojavax.bio.taxa |
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Subclasses of AbstractChangeable in org.biojavax.bio.taxa | |
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class |
SimpleNCBITaxon
Reference implementation of NCBITaxon. |
Uses of AbstractChangeable in org.biojavax.ga.functions |
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Subclasses of AbstractChangeable in org.biojavax.ga.functions | |
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class |
AbstractCrossOverFunction
Abstract implementation of CrossOverFunction . |
class |
AbstractMutationFunction
Abstract implementation of MutationFunction all custom
implementations should inherit from here. |
class |
OrderCrossover
This does a 2-point-crossover on two chromosomes keeping the Symbols in each chromosome constant. |
class |
SimpleCrossOverFunction
Simple Implementation of the CrossOverFunction interface |
class |
SimpleMutationFunction
Simple no frills Implementation of the MutationFunction interface |
class |
SwapMutationFunction
This class does a sort of mutation by exchanging two positions on the chromosome. |
Uses of AbstractChangeable in org.biojavax.ga.impl |
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Subclasses of AbstractChangeable in org.biojavax.ga.impl | |
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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 AbstractChangeable in org.biojavax.ontology |
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Subclasses of AbstractChangeable in org.biojavax.ontology | |
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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. |
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