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Packages that use Unchangeable | |
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org.biojava.bio.dist | Probability distributions over Alphabets. |
org.biojava.bio.dp | HMM and Dynamic Programming Algorithms. |
org.biojava.bio.program.das | Development client for the Distributed Annotation System. |
org.biojava.bio.seq | Classes and interfaces for defining biological sequences and informatics objects. |
org.biojava.bio.seq.db.biofetch | Client for the OBDA BioFetch protocol. |
org.biojava.bio.seq.db.flat | Support for OBDA flatfile databases. |
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.symbol | Representation of the Symbols that make up a sequence, and locations within them. |
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.seq | Rich implementations of Sequences, Locations and Features. |
Uses of Unchangeable in org.biojava.bio.dist |
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Subclasses of Unchangeable in org.biojava.bio.dist | |
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class |
GapDistribution
This distribution emits gap symbols. |
Uses of Unchangeable in org.biojava.bio.dp |
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Subclasses of Unchangeable in org.biojava.bio.dp | |
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class |
SimpleStatePath
A no-frills implementation of StatePath. |
Uses of Unchangeable in org.biojava.bio.program.das |
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Subclasses of Unchangeable in org.biojava.bio.program.das | |
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class |
DASSequenceDB
Collection of sequences retrieved from the DAS network. |
Uses of Unchangeable in org.biojava.bio.seq |
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Subclasses of Unchangeable in org.biojava.bio.seq | |
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class |
CircularView
A circular view onto another Sequence object. |
static class |
FeatureHolder.EmptyFeatureHolder
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Uses of Unchangeable in org.biojava.bio.seq.db.biofetch |
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Subclasses of Unchangeable in org.biojava.bio.seq.db.biofetch | |
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class |
BioFetchSequenceDB
Simple SequenceDB implementation backed by a BioFetch (HTTP) server. |
Uses of Unchangeable in org.biojava.bio.seq.db.flat |
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Subclasses of Unchangeable in org.biojava.bio.seq.db.flat | |
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class |
FlatSequenceDB
FlatSequenceDB is an OBDA flatfile sequence databank
implementation. |
Uses of Unchangeable in org.biojava.bio.seq.homol |
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Subclasses of Unchangeable in org.biojava.bio.seq.homol | |
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static class |
SimilarityPairFeature.EmptyPairwiseAlignment
EmptyPairwiseAlignment empty pairwise alignment
which has labels to empty symbol lists. |
Uses of Unchangeable in org.biojava.bio.seq.impl |
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Subclasses of Unchangeable in org.biojava.bio.seq.impl | |
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class |
ViewSequence
A view onto another Sequence object. |
Uses of Unchangeable in org.biojava.bio.seq.io |
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Subclasses of Unchangeable in org.biojava.bio.seq.io | |
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class |
CharacterTokenization
Implementation of SymbolTokenization which binds symbols to single unicode characters. |
class |
CrossProductTokenization
Tokenization for cross-product alphabets. |
class |
DoubleTokenization
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class |
IntegerTokenization
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class |
NameTokenization
Simple implementation of SymbolTokenization which uses the `name' field of the symbols. |
class |
SubIntegerTokenization
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class |
WordTokenization
Base class for tokenizations which accept whitespace-separated `words'. |
Uses of Unchangeable in org.biojava.bio.symbol |
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Subclasses of Unchangeable in org.biojava.bio.symbol | |
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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 |
IntegerAlphabet
An efficient implementation of an Alphabet over the infinite set of integer values. |
static class |
IntegerAlphabet.IntegerSymbol
A single int value. |
class |
RelabeledAlignment
An alignment that relabels another alignment. |
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 Unchangeable in org.biojava.ontology |
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Subclasses of Unchangeable in org.biojava.ontology | |
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class |
IntegerOntology
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class |
IntegerOntology.IntTerm
|
static class |
Triple.Impl
Basic in-memory implementation of a Triple in an ontology |
Uses of Unchangeable in org.biojavax |
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Subclasses of Unchangeable in org.biojavax | |
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class |
EmptyRichAnnotation
A place holder for a RichAnnotation that prevents null having to be used |
class |
SimpleCrossRef
A basic CrossRef implementation. |
class |
SimpleDocRefAuthor
Represents an author of a documentary reference. |
Uses of Unchangeable in org.biojavax.bio.seq |
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Subclasses of Unchangeable in org.biojavax.bio.seq | |
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class |
EmptyRichLocation
An Empty implementation of RichLocation. |
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