Uses of Package
org.biojava.bio.symbol
Packages that use org.biojava.bio.symbol
Package
Description
The core classes that will be used throughout the bio packages.
Classes to generate and describe sequence alignments.
Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
Tools for displaying chromatograms.
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
Graphical interfaces for biojava objects.
Graphical displays of biological sequences and associated annotations.
Classes for the handling of the layout of a WrappedSequencePanel.
The classes and interfaces in this package cover common molecular
biological techniques such as restriction digests and PCR.
Java wrappers for interacting with external bioinformatics tools.
ABI Trace Handling.
FASTQ and variants sequence format I/O.
Tools for working with profile Hidden Markov Models from the HMMer package.
Parser for Phred output
Support for the SCF chromatogram format.
SSAHA sequence searching API.
Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD.
Event-driven parsing system for the Extensible Feature Format (XFF).
Utilities to aid in performing various physical analysis of proteins.
Classes and interfaces to load Amino Acid Index database files.
Interfaces and classes for representing sequence similarity search results.
Classes and interfaces for defining biological sequences and informatics
objects.
Collections of biological sequence data.
General purpose Sequence storage in a relational database.
The classes and interfaces for defining sequence similarity and
honology.
Standard in-memory implementations of
Sequence
and
Feature
.Classes and interfaces for processing and producing flat-file representations
of sequences.
Classes for converting between AGAVE XML and BioJava objects.
Event-driven parsing system for the Gene Annotation Markup Elements (GAME).
Code for projecting Feature objects and systematically altering their
properties.
Representation of the Symbols that make up a sequence, and locations within
them.
This package is used to perform regular expression searches of
SymbolLists defined in arbitrary Alphabets.
The Biojava extensions packages, classes that extend the core biojava
functionality
Interface between biojava and biosql databases
Rich implementations of Sequences, Locations and Features.
Classes to support the I/O of RichSequence and
Bioentry objects.
Classes to provide a genetic algorithm framework
GA functions
Default implementations and abstract classes.
Utility functions and helper classes
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Classes in org.biojava.bio.symbol used by org.biojava.bioClassDescriptionA set of integers, often used to represent positions on biological sequences.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.alignmentClassDescriptionAbstract helper implementation of the SymbolList core interface.The set of AtomicSymbols which can be concatenated together to make a SymbolList.Encapsulates an edit operation on a SymbolList.An alphabet over a finite set of Symbols.This extends SymbolList with API for manipulating, inserting and deleting gaps.A set of integers, often used to represent positions on biological sequences.A single symbol.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.chromatogramClassDescriptionThe set of AtomicSymbols which can be concatenated together to make a SymbolList.A symbol that is not ambiguous.The exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.chromatogram.graphic
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Classes in org.biojava.bio.symbol used by org.biojava.bio.distClassDescriptionThe set of AtomicSymbols which can be concatenated together to make a SymbolList.Map between Symbols and index numbers.A symbol that is not ambiguous.An alphabet over a finite set of Symbols.The exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A translation table that can also translate from the target to source alphabet.A single symbol.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.dpClassDescriptionThe base-class for Symbol implementations.The set of AtomicSymbols which can be concatenated together to make a SymbolList.A symbol that is not ambiguous.A symbol that can be represented as a string of Symbols.Encapsulates an edit operation on a SymbolList.An alphabet over a finite set of Symbols.An atomic symbol consisting only of itself.The exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A set of integers, often used to represent positions on biological sequences.A single symbol.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.dp.oneheadClassDescriptionThe exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A single symbol.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.dp.twoheadClassDescriptionThe set of AtomicSymbols which can be concatenated together to make a SymbolList.The exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.guiClassDescriptionThe set of AtomicSymbols which can be concatenated together to make a SymbolList.A symbol that is not ambiguous.An alphabet over a finite set of Symbols.The exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A single symbol.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.gui.sequenceClassDescriptionA set of integers, often used to represent positions on biological sequences.A simple implementation of Location that contains all points between getMin and getMax inclusive.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.gui.sequence.tracklayoutClassDescriptionA simple implementation of Location that contains all points between getMin and getMax inclusive.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.molbioClassDescriptionThe exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.programClassDescriptionThe exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.program.abiClassDescriptionA symbol that is not ambiguous.An alphabet over a finite set of Symbols.The exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A single symbol.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.program.fastqClassDescriptionThe exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.program.hmmerClassDescriptionThe set of AtomicSymbols which can be concatenated together to make a SymbolList.A symbol that is not ambiguous.A symbol that can be represented as a string of Symbols.The exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A single symbol.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.program.phredClassDescriptionAn alphabet over a finite set of Symbols.The exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A single int value.A single symbol.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.program.scfClassDescriptionA class to represent a finite contiguous subset of the infinite IntegerAlphabetA sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.program.ssahaClassDescriptionAn alphabet over a finite set of Symbols.The exception to indicate that an invalid alphabet has been used.An encapsulation of the way symbols map to bit-patterns.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.program.ssbind
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Classes in org.biojava.bio.symbol used by org.biojava.bio.program.xffClassDescriptionAn alphabet over a finite set of Symbols.A set of integers, often used to represent positions on biological sequences.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.proteomicsClassDescriptionA symbol that is not ambiguous.An alphabet over a finite set of Symbols.The exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A single symbol.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.proteomics.aaindexClassDescriptionThe set of AtomicSymbols which can be concatenated together to make a SymbolList.Class that implements the SymbolPropertyTable interfaceclass for maintaining properties associated with a symbol
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Classes in org.biojava.bio.symbol used by org.biojava.bio.searchClassDescriptionA symbol that is not ambiguous.An alphabet over a finite set of Symbols.The exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.seqClassDescriptionThe set of AtomicSymbols which can be concatenated together to make a SymbolList.A symbol that is not ambiguous.Encapsulates an edit operation on a SymbolList.An alphabet over a finite set of Symbols.This extends SymbolList with API for manipulating, inserting and deleting gaps.The exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A set of integers, often used to represent positions on biological sequences.A translation table that will handle the many-to-one mappings that you see, for example, with genetic codes.A simple implementation of Location that contains all points between getMin and getMax inclusive.A translation table that can also translate from the target to source alphabet.A single symbol.A sequence of symbols that belong to an alphabet.class for maintaining properties associated with a symbol
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Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.dbClassDescriptionThe set of AtomicSymbols which can be concatenated together to make a SymbolList.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.db.biosqlClassDescriptionThe set of AtomicSymbols which can be concatenated together to make a SymbolList.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.homolClassDescriptionThe set of AtomicSymbols which can be concatenated together to make a SymbolList.Encapsulates an edit operation on a SymbolList.The exception to indicate that an invalid alphabet has been used.A set of integers, often used to represent positions on biological sequences.A single symbol.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.implClassDescriptionAbstract helper implementation of the SymbolList core interface.The set of AtomicSymbols which can be concatenated together to make a SymbolList.Encapsulates an edit operation on a SymbolList.This extends SymbolList with API for manipulating, inserting and deleting gaps.The exception to indicate that an invalid alphabet has been used.A set of integers, often used to represent positions on biological sequences.This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.A single symbol.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.ioClassDescriptionThe set of AtomicSymbols which can be concatenated together to make a SymbolList.An alphabet over a finite set of Symbols.The exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A class to represent a finite contiguous subset of the infinite IntegerAlphabetA set of integers, often used to represent positions on biological sequences.A single symbol.A sequence of symbols that belong to an alphabet.This interface exists to hide implementational details of SymbolLists when making chunked symbol lists.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.io.agaveClassDescriptionA set of integers, often used to represent positions on biological sequences.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.io.gameClassDescriptionA set of integers, often used to represent positions on biological sequences.A simple implementation of Location that contains all points between getMin and getMax inclusive.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.seq.projectionClassDescriptionA set of integers, often used to represent positions on biological sequences.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojava.bio.symbolClassDescriptionAn abstract implementation of
Alphabet
.An abstract implementation ofLocation
.AbstractLocation
decorator (wrapper).an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.Base class for simple contiguous Location implementations.an abstract class implementing basic functionality of a translation table that translates Symbols from one Alphabet to another.The base-class for Symbol implementations.Abstract helper implementation of the SymbolList core interface.This adapter screens all edit events to see if they overlap with a window of interest.The set of AtomicSymbols which can be concatenated together to make a SymbolList.Map between Symbols and index numbers.Utility methods for working with Alphabets.A symbol that is not ambiguous.A symbol that can be represented as a string of Symbols.Circular view onto an underlying Location instance.An efficient implementation of an Alphabet over the infinite set of double values.A range of double values.A single double value.A class to represent a contiguous range of double symbols.Encapsulates an edit operation on a SymbolList.An alphabet over a finite set of Symbols.A 'fuzzy' location a-la Embl fuzzy locations.Determines how aFuzzyLocation
should be treated when used as a normalLocation
.FuzzyPointLocation
represents two types of EMBL-style partially-defined locations.Determines how aFuzzyPointLocation
should be treated when used as a normalLocation
.This extends SymbolList with API for manipulating, inserting and deleting gaps.The exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.An efficient implementation of an Alphabet over the infinite set of integer values.A single int value.A class to represent a finite contiguous subset of the infinite IntegerAlphabetA set of integers, often used to represent positions on biological sequences.A translation table that will handle the many-to-one mappings that you see, for example, with genetic codes.Produced by LocationTools as a result of union operations.An encapsulation of the way symbols map to bit-patterns.A simple implementation of Location that contains all points between getMin and getMax inclusive.A translation table that can also translate from the target to source alphabet.An aligned block.A no-frills implementation of a translation table that maps between two alphabets.Soft masking is usually displayed by making the masked regions somehow different from the non masked regions.Implementations will define how soft masking looks.A node in the suffix tree.A single symbol.A sequence of symbols that belong to an alphabet.This interface exists to hide implementational details of SymbolLists when making chunked symbol lists.class for maintaining properties associated with a symbolEncapsulates the mapping from a source to a destination alphabet.end Tree modification methodsan object to return statistics about the frequency of the wobble base in a set of synonymous codons. -
Classes in org.biojava.bio.symbol used by org.biojava.utils.automataClassDescriptionAn alphabet over a finite set of Symbols.The exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A single symbol.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojava.utils.regexClassDescriptionAn alphabet over a finite set of Symbols.The exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A single symbol.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojavaxClassDescriptionThe set of AtomicSymbols which can be concatenated together to make a SymbolList.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojavax.bio.db.biosqlClassDescriptionThe set of AtomicSymbols which can be concatenated together to make a SymbolList.Encapsulates an edit operation on a SymbolList.The exception to indicate that an invalid alphabet has been used.A single symbol.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojavax.bio.seqClassDescriptionThe set of AtomicSymbols which can be concatenated together to make a SymbolList.Encapsulates an edit operation on a SymbolList.An alphabet over a finite set of Symbols.The exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A set of integers, often used to represent positions on biological sequences.A single symbol.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojavax.bio.seq.ioClassDescriptionThe set of AtomicSymbols which can be concatenated together to make a SymbolList.The exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A single symbol.This interface exists to hide implementational details of SymbolLists when making chunked symbol lists.
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Classes in org.biojava.bio.symbol used by org.biojavax.gaClassDescriptionThe exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojavax.ga.functionsClassDescriptionThe exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A location representing a single point.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojavax.ga.implClassDescriptionThe exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A sequence of symbols that belong to an alphabet.
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Classes in org.biojava.bio.symbol used by org.biojavax.ga.utilClassDescriptionA symbol that is not ambiguous.An alphabet over a finite set of Symbols.The exception to indicate that an invalid alphabet has been used.The exception to indicate that a symbol is not valid within a context.A sequence of symbols that belong to an alphabet.