Uses of Interface
org.biojava.bio.symbol.AtomicSymbol

Packages that use AtomicSymbol

Package	Description
org.biojava.bio.chromatogram	Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
org.biojava.bio.dist	Probability distributions over Alphabets.
org.biojava.bio.dp	HMM and Dynamic Programming Algorithms.
org.biojava.bio.gui	Graphical interfaces for biojava objects.
org.biojava.bio.program.abi	ABI Trace Handling.
org.biojava.bio.program.hmmer	Tools for working with profile Hidden Markov Models from the HMMer package.
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.symbol	Representation of the Symbols that make up a sequence, and locations within them.
org.biojavax.ga.util	Utility functions and helper classes

Uses of AtomicSymbol in org.biojava.bio.chromatogram

Methods in org.biojava.bio.chromatogram with parameters of type AtomicSymbol

Modifier and Type	Method and Description
int	Chromatogram.getMax(AtomicSymbol nucleotide) Gets the max intensity on the trace for the specified nucleotide.
int	AbstractChromatogram.getMax(AtomicSymbol nucleotide)
int[]	Chromatogram.getTrace(AtomicSymbol nucleotide) Returns an array containing the intensities of the sampled waveform representing the chromatogram trace for base nucleotide.
int[]	AbstractChromatogram.getTrace(AtomicSymbol nucleotide)
protected void	AbstractChromatogram.setTrace(AtomicSymbol nuc, int[] trace, int maxVal) Provides the trace samples for a particular nucleotide.
void	SimpleChromatogram.setTraceValues(AtomicSymbol nuc, int[] trace, int maxVal) Sets the trace array for one of the DNA nucleotides.

Uses of AtomicSymbol in org.biojava.bio.dist

Methods in org.biojava.bio.dist with parameters of type AtomicSymbol

Modifier and Type	Method and Description
void	SimpleDistributionTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double count) Deprecated.
void	DistributionTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times) Registers that sym was counted in this state.
void	SimpleDistribution.Trainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times)
void	IgnoreCountsTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times)
double	IndexedCount.getCount(AtomicSymbol s)
double	Count.getCount(AtomicSymbol s) Return the counts for a given Symbol.
double	SimpleDistributionTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym) Deprecated.
double	DistributionTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym) Get the current count for this state.
double	SimpleDistribution.Trainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym)
double	IgnoreCountsTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym)
protected double	UniformDistribution.getWeightImpl(AtomicSymbol s)
double	SimpleDistribution.getWeightImpl(AtomicSymbol s)
protected double	AbstractOrderNDistribution.getWeightImpl(AtomicSymbol sym) Get a weight from one of the sub-distributions, conditioned on the first part of the symbol.
protected abstract double	AbstractDistribution.getWeightImpl(AtomicSymbol sym) Override this method to implement getting the weight for an atomic symbol.
void	IndexedCount.increaseCount(AtomicSymbol s, double c)
void	Count.increaseCount(AtomicSymbol s, double c) Set the probability or odds that Symbol s is emitted by this state.
void	IndexedCount.setCount(AtomicSymbol s, double c)
void	Count.setCount(AtomicSymbol s, double c) Set the count for the Symbol s.
protected void	UniformDistribution.setWeightImpl(AtomicSymbol sym, double weight)
protected void	SimpleDistribution.setWeightImpl(AtomicSymbol s, double w)
void	AbstractOrderNDistribution.setWeightImpl(AtomicSymbol sym, double w) Set a weight in one of the conditioned distributions.
protected abstract void	AbstractDistribution.setWeightImpl(AtomicSymbol sym, double weight) Implement this to actually set the weight.

Uses of AtomicSymbol in org.biojava.bio.dp

Subinterfaces of AtomicSymbol in org.biojava.bio.dp

Modifier and Type	Interface and Description
interface	DotState A Dot state.
interface	EmissionState A state in a markov process that has an emission spectrum.
interface	ModelInState A state that contains an entire sub-model.
interface	State A state in a markov process.

Classes in org.biojava.bio.dp that implement AtomicSymbol

Modifier and Type	Class and Description
class	MagicalState Start/end state for HMMs.
class	SimpleDotState A Dot state that you can make and use.
class	SimpleEmissionState
class	SimpleModelInState

Uses of AtomicSymbol in org.biojava.bio.gui

Methods in org.biojava.bio.gui with parameters of type AtomicSymbol

Modifier and Type	Method and Description
void	PlainBlock.paintBlock(LogoContext ctxt, Rectangle2D block, AtomicSymbol sym)
void	TextBlock.paintBlock(LogoContext ctxt, Rectangle2D block, AtomicSymbol sym)
void	BlockPainter.paintBlock(LogoContext ctxt, Rectangle2D block, AtomicSymbol sym)

Uses of AtomicSymbol in org.biojava.bio.program.abi

Fields in org.biojava.bio.program.abi declared as AtomicSymbol

Modifier and Type	Field and Description
static AtomicSymbol	ABITools._0 The poorly supported symbol.
static AtomicSymbol	ABITools._1 The well supported symbol.

Methods in org.biojava.bio.program.abi with parameters of type AtomicSymbol

Modifier and Type	Method and Description
int[]	ABITrace.getTrace(AtomicSymbol base) Returns one of the four traces - all of the y-coordinate values, each of which correspond to a single x-coordinate relative to the position in the array, so that if element 4 in the array is 972, then x is 4 and y is 972 for that point.

Uses of AtomicSymbol in org.biojava.bio.program.hmmer

Classes in org.biojava.bio.program.hmmer that implement AtomicSymbol

Modifier and Type	Class and Description
class	ProfileEmissionState A state in a HMMer model.

Uses of AtomicSymbol in org.biojava.bio.proteomics

Methods in org.biojava.bio.proteomics that return AtomicSymbol

Modifier and Type	Method and Description
AtomicSymbol	StructureTools.get_()
AtomicSymbol	StructureTools.getB()
AtomicSymbol	StructureTools.getC()
AtomicSymbol	StructureTools.getE()
AtomicSymbol	StructureTools.getG()
AtomicSymbol	StructureTools.getH()
AtomicSymbol	StructureTools.getI()
AtomicSymbol	StructureTools.getS()
AtomicSymbol	StructureTools.getT()

Uses of AtomicSymbol in org.biojava.bio.search

Methods in org.biojava.bio.search with parameters of type AtomicSymbol

Modifier and Type	Method and Description
int	SeqContentPattern.getMaxCounts(AtomicSymbol as) Get the maximum counts required for a symbol.
int	SeqContentPattern.getMinCounts(AtomicSymbol as) Get the minimum counts required for a symbol.
void	SeqContentPattern.setMaxCounts(AtomicSymbol as, int count) Set the maximum counts required for a symbol.
void	SeqContentPattern.setMinCounts(AtomicSymbol as, int count) Set the minimum counts required for a symbol.

Uses of AtomicSymbol in org.biojava.bio.seq

Methods in org.biojava.bio.seq that return AtomicSymbol

Modifier and Type	Method and Description
static AtomicSymbol	NucleotideTools.a()
static AtomicSymbol	DNATools.a()
static AtomicSymbol	ProteinTools.a() Returns the AtomicSymbol for the amino acid Alanine
static AtomicSymbol	RNATools.a()
static AtomicSymbol	ProteinTools.ala() Returns the AtomicSymbol for the amino acid Alanine (A)
static AtomicSymbol	ProteinTools.arg() Returns the AtomicSymbol for the amino acid Arginine (R)
static AtomicSymbol	ProteinTools.asn() Returns the AtomicSymbol for the amino acid Asparagine (N)
static AtomicSymbol	ProteinTools.asp() Returns the AtomicSymbol for the amino acid Aspartic Acid (D)
static AtomicSymbol	NucleotideTools.c()
static AtomicSymbol	DNATools.c()
static AtomicSymbol	ProteinTools.c() Returns the AtomicSymbol for the amino acid Cysteine
static AtomicSymbol	RNATools.c()
static AtomicSymbol	ProteinTools.cys() Returns the AtomicSymbol for the amino acid Cysteine (C)
static AtomicSymbol	ProteinTools.d() Returns the AtomicSymbol for the amino acid Aspartic Acid
static AtomicSymbol	ProteinTools.e() Returns the AtomicSymbol for the amino acid Glutamic Acid
static AtomicSymbol	ProteinTools.f() Returns the AtomicSymbol for the amino acid Phenylalanine
static AtomicSymbol	NucleotideTools.g()
static AtomicSymbol	DNATools.g()
static AtomicSymbol	ProteinTools.g() Returns the AtomicSymbol for the amino acid Glycine
static AtomicSymbol	RNATools.g()
static AtomicSymbol	ProteinTools.gln() Returns the AtomicSymbol for the amino acid Glutamine (Q)
static AtomicSymbol	ProteinTools.glu() Returns the AtomicSymbol for the amino acid Glutamic Acid (E)
static AtomicSymbol	ProteinTools.gly() Returns the AtomicSymbol for the amino acid Glycine (G)
static AtomicSymbol	ProteinTools.h() Returns the AtomicSymbol for the amino acid Histidine
static AtomicSymbol	ProteinTools.his() Returns the AtomicSymbol for the amino acid Histidine (H)
static AtomicSymbol	ProteinTools.i() Returns the AtomicSymbol for the amino acid Isoleucine
static AtomicSymbol	ProteinTools.ile() Returns the AtomicSymbol for the amino acid Isoleucine (I)
static AtomicSymbol	ProteinTools.k() Returns the AtomicSymbol for the amino acid Lysine
static AtomicSymbol	ProteinTools.l() Returns the AtomicSymbol for the amino acid Leucine
static AtomicSymbol	ProteinTools.leu() Returns the AtomicSymbol for the amino acid Leucine (L)
static AtomicSymbol	ProteinTools.lys() Returns the AtomicSymbol for the amino acid Lysine (K)
static AtomicSymbol	ProteinTools.m() Returns the AtomicSymbol for the amino acid Methionine
static AtomicSymbol	ProteinTools.met() Returns the AtomicSymbol for the amino acid Methionine (M)
static AtomicSymbol	ProteinTools.n() Returns the AtomicSymbol for the amino acid Asparagine
static AtomicSymbol	ProteinTools.o() Returns the AtomicSymbol for the amino acid Pyrrolysine
static AtomicSymbol	ProteinTools.p() Returns the AtomicSymbol for the amino acid Proline
static AtomicSymbol	ProteinTools.phe() Returns the AtomicSymbol for the amino acid Phenylalanine (F)
static AtomicSymbol	ProteinTools.pro() Returns the AtomicSymbol for the amino acid Proline (P)
static AtomicSymbol	ProteinTools.pyl() Returns the AtomicSymbol for the amino acid Pyrrolysine (O)
static AtomicSymbol	ProteinTools.q() Returns the AtomicSymbol for the amino acid Glutamine
static AtomicSymbol	ProteinTools.r() Returns the AtomicSymbol for the amino acid Arginine
static AtomicSymbol	ProteinTools.s() Returns the AtomicSymbol for the amino acid Serine
static AtomicSymbol	ProteinTools.sec() Returns the AtomicSymbol for the amino acid Selenocysteine (U)
static AtomicSymbol	ProteinTools.ser() Returns the AtomicSymbol for the amino acid Serine (S)
static AtomicSymbol	NucleotideTools.t()
static AtomicSymbol	DNATools.t()
static AtomicSymbol	ProteinTools.t() Returns the AtomicSymbol for the amino acid Threonine
static AtomicSymbol	ProteinTools.ter() Returns the AtomicSymbol for the termination (*) placeholder
static AtomicSymbol	ProteinTools.thr() Returns the AtomicSymbol for the amino acid Threonine (T)
static AtomicSymbol	ProteinTools.trp() Returns the AtomicSymbol for the amino acid Tryptophan (W)
static AtomicSymbol	ProteinTools.tyr() Returns the AtomicSymbol for the amino acid Tyrosine (Y)
static AtomicSymbol	NucleotideTools.u()
static AtomicSymbol	ProteinTools.u() Returns the AtomicSymbol for the amino acid Selenocysteine
static AtomicSymbol	RNATools.u()
static AtomicSymbol	ProteinTools.v() Returns the AtomicSymbol for the amino acid Valine
static AtomicSymbol	ProteinTools.val() Returns the AtomicSymbol for the amino acid Valine (V)
static AtomicSymbol	ProteinTools.w() Returns the AtomicSymbol for the amino acid Tryptophan
static AtomicSymbol	ProteinTools.y() Returns the AtomicSymbol for the amino acid Tyrosine

Uses of AtomicSymbol in org.biojava.bio.symbol

Classes in org.biojava.bio.symbol that implement AtomicSymbol

Modifier and Type	Class and Description
static class	DoubleAlphabet.DoubleSymbol A single double value.
class	FundamentalAtomicSymbol An atomic symbol consisting only of itself.
static class	IntegerAlphabet.IntegerSymbol A single int value.
class	SimpleAtomicSymbol A basic implementation of AtomicSymbol.

Methods in org.biojava.bio.symbol that return AtomicSymbol

Modifier and Type	Method and Description
static AtomicSymbol	AlphabetManager.createSymbol(char token, String name, Annotation annotation) Deprecated. Use the two-arg version of this method instead.
static AtomicSymbol	AlphabetManager.createSymbol(String name) Generate a new AtomicSymbol instance with a name and an Empty Annotation.
static AtomicSymbol	AlphabetManager.createSymbol(String name, Annotation annotation) Generate a new AtomicSymbol instance with a name and Annotation.
protected AtomicSymbol	IntegerAlphabet.SubIntegerAlphabet.getSymbolImpl(List symL)
protected AtomicSymbol	SingletonAlphabet.getSymbolImpl(List symList)
protected abstract AtomicSymbol	AbstractAlphabet.getSymbolImpl(List symList)
protected AtomicSymbol	SimpleAlphabet.getSymbolImpl(List symL)

Methods in org.biojava.bio.symbol with parameters of type AtomicSymbol

Modifier and Type	Method and Description
protected void	IntegerAlphabet.SubIntegerAlphabet.addSymbolImpl(AtomicSymbol sym)
void	SingletonAlphabet.addSymbolImpl(AtomicSymbol sym)
protected abstract void	AbstractAlphabet.addSymbolImpl(AtomicSymbol s)
protected void	SimpleAlphabet.addSymbolImpl(AtomicSymbol s)
protected boolean	IntegerAlphabet.SubIntegerAlphabet.containsImpl(AtomicSymbol sym)
protected boolean	SingletonAlphabet.containsImpl(AtomicSymbol s)
protected abstract boolean	AbstractAlphabet.containsImpl(AtomicSymbol s)
protected boolean	SimpleAlphabet.containsImpl(AtomicSymbol s)
void	SimpleManyToOneTranslationTable.setTranslation(AtomicSymbol from, AtomicSymbol to) Alter the translation mapping.
void	SimpleReversibleTranslationTable.setTranslation(AtomicSymbol from, AtomicSymbol to) Alter the translation mapping.
void	SimpleTranslationTable.setTranslation(AtomicSymbol from, AtomicSymbol to) Alter the translation mapping.

Constructors in org.biojava.bio.symbol with parameters of type AtomicSymbol

Constructor and Description
SingletonAlphabet(AtomicSymbol sym)

Uses of AtomicSymbol in org.biojavax.ga.util

Methods in org.biojavax.ga.util that return AtomicSymbol

Modifier and Type	Method and Description
static AtomicSymbol	GATools.one()
static AtomicSymbol	GATools.zero()