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

Packages that use AtomicSymbol
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
`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
`void` `SimpleDistributionTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double count)` Deprecated.
`void` `SimpleDistribution.Trainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times)`
`void` `IgnoreCountsTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times)`
`void` `DistributionTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times)` Registers that sym was counted in this state.
`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` `SimpleDistribution.Trainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym)`
`double` `IgnoreCountsTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym)`
`double` `DistributionTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym)` Get the current count for this state.
`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
`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
`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
`void` `TextBlock.paintBlock(LogoContext ctxt, Rectangle2D block, AtomicSymbol sym)`
`void` `PlainBlock.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
`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
`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
`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
`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
`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
`static AtomicSymbol` `RNATools.a()`
`static AtomicSymbol` `ProteinTools.a()` Returns the `AtomicSymbol` for the amino acid Alanine
`static AtomicSymbol` `NucleotideTools.a()`
`static AtomicSymbol` `DNATools.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` `RNATools.c()`
`static AtomicSymbol` `ProteinTools.c()` Returns the `AtomicSymbol` for the amino acid Cysteine
`static AtomicSymbol` `NucleotideTools.c()`
`static AtomicSymbol` `DNATools.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` `RNATools.g()`
`static AtomicSymbol` `ProteinTools.g()` Returns the `AtomicSymbol` for the amino acid Glycine
`static AtomicSymbol` `NucleotideTools.g()`
`static AtomicSymbol` `DNATools.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` `ProteinTools.t()` Returns the `AtomicSymbol` for the amino acid Threonine
`static AtomicSymbol` `NucleotideTools.t()`
`static AtomicSymbol` `DNATools.t()`
`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` `RNATools.u()`
`static AtomicSymbol` `ProteinTools.u()` Returns the `AtomicSymbol` for the amino acid Selenocysteine
`static AtomicSymbol` `NucleotideTools.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
`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
`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` `SingletonAlphabet.getSymbolImpl(List symList)`
`protected AtomicSymbol` `SimpleAlphabet.getSymbolImpl(List symL)`
`protected AtomicSymbol` `IntegerAlphabet.SubIntegerAlphabet.getSymbolImpl(List symL)`
`protected abstract AtomicSymbol` `AbstractAlphabet.getSymbolImpl(List symList)`

Methods in org.biojava.bio.symbol with parameters of type AtomicSymbol
`void` `SingletonAlphabet.addSymbolImpl(AtomicSymbol sym)`
`protected void` `SimpleAlphabet.addSymbolImpl(AtomicSymbol s)`
`protected void` `IntegerAlphabet.SubIntegerAlphabet.addSymbolImpl(AtomicSymbol sym)`
`protected abstract void` `AbstractAlphabet.addSymbolImpl(AtomicSymbol s)`
`protected boolean` `SingletonAlphabet.containsImpl(AtomicSymbol s)`
`protected boolean` `SimpleAlphabet.containsImpl(AtomicSymbol s)`
`protected boolean` `IntegerAlphabet.SubIntegerAlphabet.containsImpl(AtomicSymbol sym)`
`protected abstract boolean` `AbstractAlphabet.containsImpl(AtomicSymbol s)`
`void` `SimpleTranslationTable.setTranslation(AtomicSymbol from, AtomicSymbol to)` Alter the translation mapping.
`void` `SimpleReversibleTranslationTable.setTranslation(AtomicSymbol from, AtomicSymbol to)` Alter the translation mapping.
`void` `SimpleManyToOneTranslationTable.setTranslation(AtomicSymbol from, AtomicSymbol to)` Alter the translation mapping.

Constructors in org.biojava.bio.symbol with parameters of type AtomicSymbol
`SingletonAlphabet(AtomicSymbol sym)`

Uses of AtomicSymbol in org.biojavax.ga.util

Methods in org.biojavax.ga.util that return AtomicSymbol
`static AtomicSymbol` `GATools.one()`
`static AtomicSymbol` `GATools.zero()`