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 AbstractChromatogram.getMax(AtomicSymbol nucleotide)
           
 int Chromatogram.getMax(AtomicSymbol nucleotide)
          Gets the max intensity on the trace for the specified nucleotide.
 int[] AbstractChromatogram.getTrace(AtomicSymbol nucleotide)
           
 int[] Chromatogram.getTrace(AtomicSymbol nucleotide)
          Returns an array containing the intensities of the sampled waveform representing the chromatogram trace for base 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 DistributionTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times)
           Registers that sym was counted in this state.
 void IgnoreCountsTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times)
           
 void SimpleDistribution.Trainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times)
           
 void SimpleDistributionTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double count)
          Deprecated.  
 double Count.getCount(AtomicSymbol s)
          Return the counts for a given Symbol.
 double IndexedCount.getCount(AtomicSymbol s)
           
 double DistributionTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym)
           Get the current count for this state.
 double IgnoreCountsTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym)
           
 double SimpleDistribution.Trainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym)
           
 double SimpleDistributionTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym)
          Deprecated.  
protected abstract  double AbstractDistribution.getWeightImpl(AtomicSymbol sym)
          Override this method to implement getting the weight for an atomic symbol.
protected  double AbstractOrderNDistribution.getWeightImpl(AtomicSymbol sym)
          Get a weight from one of the sub-distributions, conditioned on the first part of the symbol.
 double SimpleDistribution.getWeightImpl(AtomicSymbol s)
           
protected  double UniformDistribution.getWeightImpl(AtomicSymbol s)
           
 void Count.increaseCount(AtomicSymbol s, double c)
          Set the probability or odds that Symbol s is emitted by this state.
 void IndexedCount.increaseCount(AtomicSymbol s, double c)
           
 void Count.setCount(AtomicSymbol s, double c)
          Set the count for the Symbol s.
 void IndexedCount.setCount(AtomicSymbol s, double c)
           
protected abstract  void AbstractDistribution.setWeightImpl(AtomicSymbol sym, double weight)
          Implement this to actually set the weight.
 void AbstractOrderNDistribution.setWeightImpl(AtomicSymbol sym, double w)
          Set a weight in one of the conditioned distributions.
protected  void SimpleDistribution.setWeightImpl(AtomicSymbol s, double w)
           
protected  void UniformDistribution.setWeightImpl(AtomicSymbol sym, double 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 BlockPainter.paintBlock(LogoContext ctxt, Rectangle2D block, AtomicSymbol sym)
           
 void PlainBlock.paintBlock(LogoContext ctxt, Rectangle2D block, AtomicSymbol sym)
           
 void TextBlock.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 DNATools.a()
           
static AtomicSymbol NucleotideTools.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 DNATools.c()
           
static AtomicSymbol NucleotideTools.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 DNATools.g()
           
static AtomicSymbol NucleotideTools.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 DNATools.t()
           
static AtomicSymbol NucleotideTools.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
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 abstract  AtomicSymbol AbstractAlphabet.getSymbolImpl(List symList)
           
protected  AtomicSymbol IntegerAlphabet.SubIntegerAlphabet.getSymbolImpl(List symL)
           
protected  AtomicSymbol SimpleAlphabet.getSymbolImpl(List symL)
           
protected  AtomicSymbol SingletonAlphabet.getSymbolImpl(List symList)
           
 

Methods in org.biojava.bio.symbol with parameters of type AtomicSymbol
protected abstract  void AbstractAlphabet.addSymbolImpl(AtomicSymbol s)
           
protected  void IntegerAlphabet.SubIntegerAlphabet.addSymbolImpl(AtomicSymbol sym)
           
protected  void SimpleAlphabet.addSymbolImpl(AtomicSymbol s)
           
 void SingletonAlphabet.addSymbolImpl(AtomicSymbol sym)
           
protected abstract  boolean AbstractAlphabet.containsImpl(AtomicSymbol s)
           
protected  boolean IntegerAlphabet.SubIntegerAlphabet.containsImpl(AtomicSymbol sym)
           
protected  boolean SimpleAlphabet.containsImpl(AtomicSymbol s)
           
protected  boolean SingletonAlphabet.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
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()