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Packages that use org.biojava.bio.symbol | |
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.chromatogram | Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment. |
org.biojava.bio.chromatogram.graphic | Tools for displaying chromatograms. |
org.biojava.bio.dist | Probability distributions over Alphabets. |
org.biojava.bio.dp | HMM and Dynamic Programming Algorithms. |
org.biojava.bio.dp.onehead | |
org.biojava.bio.dp.twohead | |
org.biojava.bio.gui | Graphical interfaces for biojava objects. |
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 | Java wrappers for interacting with external bioinformatics tools. |
org.biojava.bio.program.abi | ABI Trace Handling. |
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.scf | Support for the SCF chromatogram format. |
org.biojava.bio.program.ssaha | SSAHA sequence searching API. |
org.biojava.bio.program.ssbind | Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD. |
org.biojava.bio.program.xff | Event-driven parsing system for the Extensible Feature Format (XFF). |
org.biojava.bio.proteomics | Utilities to aid in performing various physical analysis of proteins. |
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.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.io.agave | Classes for converting between AGAVE XML and BioJava objects. |
org.biojava.bio.seq.io.game | Event-driven parsing system for the Gene Annotation Markup Elements (GAME). |
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. |
Classes in org.biojava.bio.symbol used by org.biojava.bio | |
Location
A set of integers, often used to represent positions on biological sequences. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.alignment | |
AbstractSymbolList
Abstract helper implementation of the SymbolList core interface. |
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Alignment
An alignment containing multiple SymbolLists. |
|
Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList. |
|
Edit
Encapsulates an edit operation on a SymbolList. |
|
GappedSymbolList
This extends SymbolList with API for manipulating, inserting and deleting gaps. |
|
Location
A set of integers, often used to represent positions on biological sequences. |
|
Symbol
A single symbol. |
|
SymbolList
A sequence of symbols that belong to an alphabet. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.chromatogram | |
Alignment
An alignment containing multiple SymbolLists. |
|
Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList. |
|
AtomicSymbol
A symbol that is not ambiguous. |
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IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
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IllegalSymbolException
The exception to indicate that a symbol is not valid within a context. |
|
SymbolList
A sequence of symbols that belong to an alphabet. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.chromatogram.graphic | |
Symbol
A single symbol. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.dist | |
Alignment
An alignment containing multiple SymbolLists. |
|
Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList. |
|
AlphabetIndex
Map between Symbols and index numbers. |
|
AtomicSymbol
A symbol that is not ambiguous. |
|
FiniteAlphabet
An alphabet over a finite set of Symbols. |
|
IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
|
IllegalSymbolException
The exception to indicate that a symbol is not valid within a context. |
|
ReversibleTranslationTable
A translation table that can also translate from the target to source alphabet. |
|
Symbol
A single symbol. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.dp | |
AbstractSymbol
The base-class for Symbol implementations. |
|
Alignment
An alignment containing multiple SymbolLists. |
|
Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList. |
|
AtomicSymbol
A symbol that is not ambiguous. |
|
BasisSymbol
A symbol that can be represented as a string of Symbols. |
|
Edit
Encapsulates an edit operation on a SymbolList. |
|
FiniteAlphabet
An alphabet over a finite set of Symbols. |
|
FundamentalAtomicSymbol
An atomic symbol consisting only of itself. |
|
IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
|
IllegalSymbolException
The exception to indicate that a symbol is not valid within a context. |
|
Location
A set of integers, often used to represent positions on biological sequences. |
|
Symbol
A single symbol. |
|
SymbolList
A sequence of symbols that belong to an alphabet. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.dp.onehead | |
IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
|
IllegalSymbolException
The exception to indicate that a symbol is not valid within a context. |
|
Symbol
A single symbol. |
|
SymbolList
A sequence of symbols that belong to an alphabet. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.dp.twohead | |
Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList. |
|
IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
|
IllegalSymbolException
The exception to indicate that a symbol is not valid within a context. |
|
SymbolList
A sequence of symbols that belong to an alphabet. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.gui | |
Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList. |
|
AtomicSymbol
A symbol that is not ambiguous. |
|
FiniteAlphabet
An alphabet over a finite set of Symbols. |
|
IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
|
IllegalSymbolException
The exception to indicate that a symbol is not valid within a context. |
|
Symbol
A single symbol. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.gui.sequence | |
Location
A set of integers, often used to represent positions on biological sequences. |
|
RangeLocation
A simple implementation of Location that contains all points between getMin and getMax inclusive. |
|
SymbolList
A sequence of symbols that belong to an alphabet. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.molbio | |
IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
|
SymbolList
A sequence of symbols that belong to an alphabet. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.program | |
IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
|
IllegalSymbolException
The exception to indicate that a symbol is not valid within a context. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.program.abi | |
Alignment
An alignment containing multiple SymbolLists. |
|
AtomicSymbol
A symbol that is not ambiguous. |
|
FiniteAlphabet
An alphabet over a finite set of Symbols. |
|
IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
|
IllegalSymbolException
The exception to indicate that a symbol is not valid within a context. |
|
Symbol
A single symbol. |
|
SymbolList
A sequence of symbols that belong to an alphabet. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.program.das | |
Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList. |
|
Edit
Encapsulates an edit operation on a SymbolList. |
|
Symbol
A single symbol. |
|
SymbolList
A sequence of symbols that belong to an alphabet. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.program.hmmer | |
Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList. |
|
AtomicSymbol
A symbol that is not ambiguous. |
|
BasisSymbol
A symbol that can be represented as a string of Symbols. |
|
IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
|
IllegalSymbolException
The exception to indicate that a symbol is not valid within a context. |
|
Symbol
A single symbol. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.program.phred | |
Alignment
An alignment containing multiple SymbolLists. |
|
FiniteAlphabet
An alphabet over a finite set of Symbols. |
|
IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
|
IllegalSymbolException
The exception to indicate that a symbol is not valid within a context. |
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IntegerAlphabet.IntegerSymbol
A single int value. |
|
Symbol
A single symbol. |
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SymbolList
A sequence of symbols that belong to an alphabet. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.program.scf | |
IntegerAlphabet.SubIntegerAlphabet
A class to represent a finite contiguous subset of the infinite IntegerAlphabet |
|
SymbolList
A sequence of symbols that belong to an alphabet. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.program.ssaha | |
FiniteAlphabet
An alphabet over a finite set of Symbols. |
|
IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
|
Packing
An encapsulation of the way symbols map to bit-patterns. |
|
SymbolList
A sequence of symbols that belong to an alphabet. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.program.ssbind | |
FiniteAlphabet
An alphabet over a finite set of Symbols. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.program.xff | |
FiniteAlphabet
An alphabet over a finite set of Symbols. |
|
Location
A set of integers, often used to represent positions on biological sequences. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.proteomics | |
AtomicSymbol
A symbol that is not ambiguous. |
|
FiniteAlphabet
An alphabet over a finite set of Symbols. |
|
IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
|
IllegalSymbolException
The exception to indicate that a symbol is not valid within a context. |
|
Symbol
A single symbol. |
|
SymbolList
A sequence of symbols that belong to an alphabet. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.search | |
Alignment
An alignment containing multiple SymbolLists. |
|
SymbolList
A sequence of symbols that belong to an alphabet. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.seq | |
AbstractSymbolList
Abstract helper implementation of the SymbolList core interface. |
|
Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList. |
|
AtomicSymbol
A symbol that is not ambiguous. |
|
Edit
Encapsulates an edit operation on a SymbolList. |
|
FiniteAlphabet
An alphabet over a finite set of Symbols. |
|
GappedSymbolList
This extends SymbolList with API for manipulating, inserting and deleting gaps. |
|
IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
|
IllegalSymbolException
The exception to indicate that a symbol is not valid within a context. |
|
Location
A set of integers, often used to represent positions on biological sequences. |
|
ReversibleTranslationTable
A translation table that can also translate from the target to source alphabet. |
|
SimpleGappedSymbolList
This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps. |
|
Symbol
A single symbol. |
|
SymbolList
A sequence of symbols that belong to an alphabet. |
|
SymbolPropertyTable
class for maintaining properties associated with a symbol |
|
TranslationTable
Encapsulates the mapping from a source to a destination alphabet. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.db | |
Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.db.biosql | |
Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.homol | |
Alignment
An alignment containing multiple SymbolLists. |
|
Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList. |
|
Edit
Encapsulates an edit operation on a SymbolList. |
|
IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
|
Location
A set of integers, often used to represent positions on biological sequences. |
|
Symbol
A single symbol. |
|
SymbolList
A sequence of symbols that belong to an alphabet. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.impl | |
AbstractSymbolList
Abstract helper implementation of the SymbolList core interface. |
|
Alignment
An alignment containing multiple SymbolLists. |
|
Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList. |
|
Edit
Encapsulates an edit operation on a SymbolList. |
|
IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
|
Location
A set of integers, often used to represent positions on biological sequences. |
|
Symbol
A single symbol. |
|
SymbolList
A sequence of symbols that belong to an alphabet. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.io | |
Alignment
An alignment containing multiple SymbolLists. |
|
Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList. |
|
FiniteAlphabet
An alphabet over a finite set of Symbols. |
|
IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
|
IllegalSymbolException
The exception to indicate that a symbol is not valid within a context. |
|
Location
A set of integers, often used to represent positions on biological sequences. |
|
Symbol
A single symbol. |
|
SymbolList
A sequence of symbols that belong to an alphabet. |
|
SymbolListFactory
This interface exists to hide implementational details of SymbolLists when making chunked symbol lists. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.io.agave | |
Location
A set of integers, often used to represent positions on biological sequences. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.io.game | |
Location
A set of integers, often used to represent positions on biological sequences. |
|
RangeLocation
A simple implementation of Location that contains all points between getMin and getMax inclusive. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.projection | |
Location
A set of integers, often used to represent positions on biological sequences. |
|
SymbolList
A sequence of symbols that belong to an alphabet. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.ragbag | |
Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList. |
|
IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
|
RangeLocation
A simple implementation of Location that contains all points between getMin and getMax inclusive. |
|
Symbol
A single symbol. |
|
SymbolList
A sequence of symbols that belong to an alphabet. |
Classes in org.biojava.bio.symbol used by org.biojava.bio.symbol | |
AbstractAlphabet
An abstract implementation of Alphabet . |
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AbstractLocation
An abstract implementation of Location . |
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AbstractLocationDecorator
Abstract Location decorator (wrapper). |
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AbstractRangeLocation
Base class for simple contiguous Location implementations. |
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AbstractSymbol
The base-class for Symbol implementations. |
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AbstractSymbolList
Abstract helper implementation of the SymbolList core interface. |
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AbstractSymbolList.EditScreener
This adapter screens all edit events to see if they overlap with a window of interest. |
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Alignment
An alignment containing multiple SymbolLists. |
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Alphabet
The set of AtomicSymbols which can be concatenated together to make a SymbolList. |
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AlphabetIndex
Map between Symbols and index numbers. |
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AlphabetManager
Utility methods for working with Alphabets. |
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AtomicSymbol
A symbol that is not ambiguous. |
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BasisSymbol
A symbol that can be represented as a string of Symbols. |
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CircularLocation
Circular view onto an underlying Location instance. |
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DoubleAlphabet
An efficient implementation of an Alphabet over the infinite set of double values. |
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DoubleAlphabet.DoubleRange
A range of double values. |
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DoubleAlphabet.DoubleSymbol
A single double value. |
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DoubleAlphabet.SubDoubleAlphabet
A class to represent a contiguous range of double symbols. |
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Edit
Encapsulates an edit operation on a SymbolList. |
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FiniteAlphabet
An alphabet over a finite set of Symbols. |
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FuzzyLocation
A 'fuzzy' location a-la Embl fuzzy locations. |
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FuzzyLocation.RangeResolver
Determines how a FuzzyLocation should be treated when used
as a normal Location . |
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FuzzyPointLocation
FuzzyPointLocation represents two types of EMBL-style
partially-defined locations. |
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FuzzyPointLocation.PointResolver
Determines how a FuzzyPointLocation should be treated when used
as a normal Location . |
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GappedSymbolList
This extends SymbolList with API for manipulating, inserting and deleting gaps. |
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IllegalAlphabetException
The exception to indicate that an invalid alphabet has been used. |
|
IllegalSymbolException
The exception to indicate that a symbol is not valid within a context. |
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IntegerAlphabet
An efficient implementation of an Alphabet over the infinite set of integer values. |
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IntegerAlphabet.IntegerSymbol
A single int value. |
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IntegerAlphabet.SubIntegerAlphabet
A class to represent a finite contiguous subset of the infinite IntegerAlphabet |
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Location
A set of integers, often used to represent positions on biological sequences. |
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MergeLocation
Produced by LocationTools as a result of union operations. |
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Packing
An encapsulation of the way symbols map to bit-patterns. |
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RangeLocation
A simple implementation of Location that contains all points between getMin and getMax inclusive. |
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ReversibleTranslationTable
A translation table that can also translate from the target to source alphabet. |
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SimpleGappedSymbolList.Block
An aligned block. |
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SimpleTranslationTable
A no-frills implementation of TranslationTable that uses a Map to map from symbols in a finite source alphabet into a target alphabet. |
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SuffixTree.SuffixNode
A node in the suffix tree. |
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Symbol
A single symbol. |
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SymbolList
A sequence of symbols that belong to an alphabet. |
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SymbolListFactory
This interface exists to hide implementational details of SymbolLists when making chunked symbol lists. |
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SymbolPropertyTable
class for maintaining properties associated with a symbol |
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TranslationTable
Encapsulates the mapping from a source to a destination alphabet. |
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