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.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. 
 

Uses of AtomicSymbol in org.biojava.bio.chromatogram
 

Methods in org.biojava.bio.chromatogram with parameters of type AtomicSymbol
 int[] AbstractChromatogram.getTrace(AtomicSymbol nucleotide)
           
 int AbstractChromatogram.getMax(AtomicSymbol nucleotide)
           
protected  void AbstractChromatogram.setTrace(AtomicSymbol nuc, int[] trace, int maxVal)
          Provides the trace samples for a particular nucleotide.
 int Chromatogram.getMax(AtomicSymbol nucleotide)
          Gets the max intensity on the trace for the specified nucleotide.
 int[] Chromatogram.getTrace(AtomicSymbol nucleotide)
          Returns an array containing the intensities of the sampled waveform representing the chromatogram trace for base 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 DistributionTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times)
           Registers that sym was counted in this state.
 double DistributionTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym)
           Get the current count for this state.
 void SimpleDistributionTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double count)
           
 double SimpleDistributionTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym)
           
 double Count.getCount(AtomicSymbol s)
          Return the counts for a given Symbol.
 void Count.setCount(AtomicSymbol s, double c)
          Set the count for the Symbol s.
 void Count.increaseCount(AtomicSymbol s, double c)
          Set the probability or odds that Symbol s is emited by this state.
protected  double AbstractOrderNDistribution.getWeightImpl(AtomicSymbol sym)
          Get a weight from one of the sub-distributions, conditioned on the first part of the symbol.
 void AbstractOrderNDistribution.setWeightImpl(AtomicSymbol sym, double w)
          Set a weight in one of the conditioned distributions.
 double SimpleDistribution.getWeightImpl(AtomicSymbol s)
           
protected  void SimpleDistribution.setWeightImpl(AtomicSymbol s, double w)
           
 void SimpleDistribution.Trainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times)
           
 double SimpleDistribution.Trainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym)
           
protected  double UniformDistribution.getWeightImpl(AtomicSymbol s)
           
protected  void UniformDistribution.setWeightImpl(AtomicSymbol sym, double weight)
           
 double IndexedCount.getCount(AtomicSymbol s)
           
 void IndexedCount.setCount(AtomicSymbol s, double c)
           
 void IndexedCount.increaseCount(AtomicSymbol s, double c)
           
protected abstract  void AbstractDistribution.setWeightImpl(AtomicSymbol sym, double weight)
           
protected abstract  double AbstractDistribution.getWeightImpl(AtomicSymbol sym)
           
 void IgnoreCountsTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times)
           
 double IgnoreCountsTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym)
           
 

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 BlockPainter.paintBlock(LogoContext ctxt, java.awt.geom.Rectangle2D block, AtomicSymbol sym)
           
 void TextBlock.paintBlock(LogoContext ctxt, java.awt.geom.Rectangle2D block, AtomicSymbol sym)
           
 void PlainBlock.paintBlock(LogoContext ctxt, java.awt.geom.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.getC()
           
 AtomicSymbol StructureTools.getH()
           
 AtomicSymbol StructureTools.getG()
           
 AtomicSymbol StructureTools.getI()
           
 AtomicSymbol StructureTools.getE()
           
 AtomicSymbol StructureTools.getB()
           
 AtomicSymbol StructureTools.getT()
           
 AtomicSymbol StructureTools.getS()
           
 

Uses of AtomicSymbol in org.biojava.bio.seq
 

Methods in org.biojava.bio.seq that return AtomicSymbol
static AtomicSymbol RNATools.a()
           
static AtomicSymbol RNATools.g()
           
static AtomicSymbol RNATools.c()
           
static AtomicSymbol RNATools.u()
           
static AtomicSymbol NucleotideTools.a()
           
static AtomicSymbol NucleotideTools.g()
           
static AtomicSymbol NucleotideTools.c()
           
static AtomicSymbol NucleotideTools.t()
           
static AtomicSymbol NucleotideTools.u()
           
static AtomicSymbol DNATools.a()
           
static AtomicSymbol DNATools.g()
           
static AtomicSymbol DNATools.c()
           
static AtomicSymbol DNATools.t()
           
 

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

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

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