Uses of Interface
org.biojava.bio.symbol.AtomicSymbol
Packages that use AtomicSymbol
Package
Description
Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
Graphical interfaces for biojava objects.
ABI Trace Handling.
Tools for working with profile Hidden Markov Models from the HMMer package.
Utilities to aid in performing various physical analysis of proteins.
Interfaces and classes for representing sequence similarity search results.
Classes and interfaces for defining biological sequences and informatics
objects.
Representation of the Symbols that make up a sequence, and locations within
them.
Utility functions and helper classes
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Uses of AtomicSymbol in org.biojava.bio.chromatogram
Methods in org.biojava.bio.chromatogram with parameters of type AtomicSymbolModifier and TypeMethodDescriptionintAbstractChromatogram.getMax(AtomicSymbol nucleotide) intChromatogram.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 basenucleotide.protected final voidAbstractChromatogram.setTrace(AtomicSymbol nuc, int[] trace, int maxVal) Provides the trace samples for a particular nucleotide.voidSimpleChromatogram.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 AtomicSymbolModifier and TypeMethodDescriptionvoidDistributionTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times) Registers that sym was counted in this state.voidIgnoreCountsTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times) voidSimpleDistribution.Trainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double times) voidSimpleDistributionTrainer.addCount(DistributionTrainerContext dtc, AtomicSymbol sym, double count) Deprecated.doubleCount.getCount(AtomicSymbol s) Return the counts for a given Symbol.doubleDistributionTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym) Get the current count for this state.doubleIgnoreCountsTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym) doubleIndexedCount.getCount(AtomicSymbol s) doubleSimpleDistribution.Trainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym) doubleSimpleDistributionTrainer.getCount(DistributionTrainerContext dtc, AtomicSymbol sym) Deprecated.protected abstract doubleAbstractDistribution.getWeightImpl(AtomicSymbol sym) Override this method to implement getting the weight for an atomic symbol.protected doubleAbstractOrderNDistribution.getWeightImpl(AtomicSymbol sym) Get a weight from one of the sub-distributions, conditioned on the first part of the symbol.doubleSimpleDistribution.getWeightImpl(AtomicSymbol s) protected doubleUniformDistribution.getWeightImpl(AtomicSymbol s) voidCount.increaseCount(AtomicSymbol s, double c) Set the probability or odds that Symbol s is emitted by this state.voidIndexedCount.increaseCount(AtomicSymbol s, double c) voidCount.setCount(AtomicSymbol s, double c) Set the count for the Symbol s.voidIndexedCount.setCount(AtomicSymbol s, double c) protected abstract voidAbstractDistribution.setWeightImpl(AtomicSymbol sym, double weight) Implement this to actually set the weight.voidAbstractOrderNDistribution.setWeightImpl(AtomicSymbol sym, double w) Set a weight in one of the conditioned distributions.protected voidSimpleDistribution.setWeightImpl(AtomicSymbol s, double w) protected voidUniformDistribution.setWeightImpl(AtomicSymbol sym, double weight) -
Uses of AtomicSymbol in org.biojava.bio.dp
Subinterfaces of AtomicSymbol in org.biojava.bio.dpModifier and TypeInterfaceDescriptioninterfaceA Dot state.interfaceA state in a markov process that has an emission spectrum.interfaceA state that contains an entire sub-model.interfaceA state in a markov process.Classes in org.biojava.bio.dp that implement AtomicSymbolModifier and TypeClassDescriptionfinal classStart/end state for HMMs.classA Dot state that you can make and use.classclass -
Uses of AtomicSymbol in org.biojava.bio.gui
Methods in org.biojava.bio.gui with parameters of type AtomicSymbolModifier and TypeMethodDescriptionvoidBlockPainter.paintBlock(LogoContext ctxt, Rectangle2D block, AtomicSymbol sym) voidPlainBlock.paintBlock(LogoContext ctxt, Rectangle2D block, AtomicSymbol sym) voidTextBlock.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 AtomicSymbolModifier and TypeFieldDescriptionstatic final AtomicSymbolABITools._0The poorly supported symbol.static final AtomicSymbolABITools._1The well supported symbol.Methods in org.biojava.bio.program.abi with parameters of type AtomicSymbolModifier and TypeMethodDescriptionint[]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 -
Uses of AtomicSymbol in org.biojava.bio.proteomics
Methods in org.biojava.bio.proteomics that return AtomicSymbol -
Uses of AtomicSymbol in org.biojava.bio.search
Methods in org.biojava.bio.search with parameters of type AtomicSymbolModifier and TypeMethodDescriptionintSeqContentPattern.getMaxCounts(AtomicSymbol as) Get the maximum counts required for a symbol.intSeqContentPattern.getMinCounts(AtomicSymbol as) Get the minimum counts required for a symbol.voidSeqContentPattern.setMaxCounts(AtomicSymbol as, int count) Set the maximum counts required for a symbol.voidSeqContentPattern.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 AtomicSymbolModifier and TypeMethodDescriptionstatic AtomicSymbolDNATools.a()static AtomicSymbolNucleotideTools.a()static AtomicSymbolProteinTools.a()Returns theAtomicSymbolfor the amino acid Alaninestatic AtomicSymbolRNATools.a()static AtomicSymbolProteinTools.ala()Returns theAtomicSymbolfor the amino acid Alanine (A)static AtomicSymbolProteinTools.arg()Returns theAtomicSymbolfor the amino acid Arginine (R)static AtomicSymbolProteinTools.asn()Returns theAtomicSymbolfor the amino acid Asparagine (N)static AtomicSymbolProteinTools.asp()Returns theAtomicSymbolfor the amino acid Aspartic Acid (D)static AtomicSymbolDNATools.c()static AtomicSymbolNucleotideTools.c()static AtomicSymbolProteinTools.c()Returns theAtomicSymbolfor the amino acid Cysteinestatic AtomicSymbolRNATools.c()static AtomicSymbolProteinTools.cys()Returns theAtomicSymbolfor the amino acid Cysteine (C)static AtomicSymbolProteinTools.d()Returns theAtomicSymbolfor the amino acid Aspartic Acidstatic AtomicSymbolProteinTools.e()Returns theAtomicSymbolfor the amino acid Glutamic Acidstatic AtomicSymbolProteinTools.f()Returns theAtomicSymbolfor the amino acid Phenylalaninestatic AtomicSymbolDNATools.g()static AtomicSymbolNucleotideTools.g()static AtomicSymbolProteinTools.g()Returns theAtomicSymbolfor the amino acid Glycinestatic AtomicSymbolRNATools.g()static AtomicSymbolProteinTools.gln()Returns theAtomicSymbolfor the amino acid Glutamine (Q)static AtomicSymbolProteinTools.glu()Returns theAtomicSymbolfor the amino acid Glutamic Acid (E)static AtomicSymbolProteinTools.gly()Returns theAtomicSymbolfor the amino acid Glycine (G)static AtomicSymbolProteinTools.h()Returns theAtomicSymbolfor the amino acid Histidinestatic AtomicSymbolProteinTools.his()Returns theAtomicSymbolfor the amino acid Histidine (H)static AtomicSymbolProteinTools.i()Returns theAtomicSymbolfor the amino acid Isoleucinestatic AtomicSymbolProteinTools.ile()Returns theAtomicSymbolfor the amino acid Isoleucine (I)static AtomicSymbolProteinTools.k()Returns theAtomicSymbolfor the amino acid Lysinestatic AtomicSymbolProteinTools.l()Returns theAtomicSymbolfor the amino acid Leucinestatic AtomicSymbolProteinTools.leu()Returns theAtomicSymbolfor the amino acid Leucine (L)static AtomicSymbolProteinTools.lys()Returns theAtomicSymbolfor the amino acid Lysine (K)static AtomicSymbolProteinTools.m()Returns theAtomicSymbolfor the amino acid Methioninestatic AtomicSymbolProteinTools.met()Returns theAtomicSymbolfor the amino acid Methionine (M)static AtomicSymbolProteinTools.n()Returns theAtomicSymbolfor the amino acid Asparaginestatic AtomicSymbolProteinTools.o()Returns theAtomicSymbolfor the amino acid Pyrrolysinestatic AtomicSymbolProteinTools.p()Returns theAtomicSymbolfor the amino acid Prolinestatic AtomicSymbolProteinTools.phe()Returns theAtomicSymbolfor the amino acid Phenylalanine (F)static AtomicSymbolProteinTools.pro()Returns theAtomicSymbolfor the amino acid Proline (P)static AtomicSymbolProteinTools.pyl()Returns theAtomicSymbolfor the amino acid Pyrrolysine (O)static AtomicSymbolProteinTools.q()Returns theAtomicSymbolfor the amino acid Glutaminestatic AtomicSymbolProteinTools.r()Returns theAtomicSymbolfor the amino acid Argininestatic AtomicSymbolProteinTools.s()Returns theAtomicSymbolfor the amino acid Serinestatic AtomicSymbolProteinTools.sec()Returns theAtomicSymbolfor the amino acid Selenocysteine (U)static AtomicSymbolProteinTools.ser()Returns theAtomicSymbolfor the amino acid Serine (S)static AtomicSymbolDNATools.t()static AtomicSymbolNucleotideTools.t()static AtomicSymbolProteinTools.t()Returns theAtomicSymbolfor the amino acid Threoninestatic AtomicSymbolProteinTools.ter()Returns theAtomicSymbolfor the termination (*) placeholderstatic AtomicSymbolProteinTools.thr()Returns theAtomicSymbolfor the amino acid Threonine (T)static AtomicSymbolProteinTools.trp()Returns theAtomicSymbolfor the amino acid Tryptophan (W)static AtomicSymbolProteinTools.tyr()Returns theAtomicSymbolfor the amino acid Tyrosine (Y)static AtomicSymbolNucleotideTools.u()static AtomicSymbolProteinTools.u()Returns theAtomicSymbolfor the amino acid Selenocysteinestatic AtomicSymbolRNATools.u()static AtomicSymbolProteinTools.v()Returns theAtomicSymbolfor the amino acid Valinestatic AtomicSymbolProteinTools.val()Returns theAtomicSymbolfor the amino acid Valine (V)static AtomicSymbolProteinTools.w()Returns theAtomicSymbolfor the amino acid Tryptophanstatic AtomicSymbolProteinTools.y()Returns theAtomicSymbolfor the amino acid Tyrosine -
Uses of AtomicSymbol in org.biojava.bio.symbol
Classes in org.biojava.bio.symbol that implement AtomicSymbolModifier and TypeClassDescriptionstatic classA single double value.classAn atomic symbol consisting only of itself.static classA single int value.classA basic implementation of AtomicSymbol.Methods in org.biojava.bio.symbol that return AtomicSymbolModifier and TypeMethodDescriptionstatic AtomicSymbolAlphabetManager.createSymbol(char token, String name, Annotation annotation) Deprecated.Use the two-arg version of this method instead.static AtomicSymbolAlphabetManager.createSymbol(String name) Generate a new AtomicSymbol instance with a name and an Empty Annotation.static AtomicSymbolAlphabetManager.createSymbol(String name, Annotation annotation) Generate a new AtomicSymbol instance with a name and Annotation.protected abstract AtomicSymbolAbstractAlphabet.getSymbolImpl(List symList) protected AtomicSymbolIntegerAlphabet.SubIntegerAlphabet.getSymbolImpl(List symL) protected AtomicSymbolSimpleAlphabet.getSymbolImpl(List symL) protected AtomicSymbolSingletonAlphabet.getSymbolImpl(List symList) Methods in org.biojava.bio.symbol with parameters of type AtomicSymbolModifier and TypeMethodDescriptionprotected abstract voidAbstractAlphabet.addSymbolImpl(AtomicSymbol s) protected voidIntegerAlphabet.SubIntegerAlphabet.addSymbolImpl(AtomicSymbol sym) protected voidSimpleAlphabet.addSymbolImpl(AtomicSymbol s) voidSingletonAlphabet.addSymbolImpl(AtomicSymbol sym) protected abstract booleanAbstractAlphabet.containsImpl(AtomicSymbol s) protected booleanIntegerAlphabet.SubIntegerAlphabet.containsImpl(AtomicSymbol sym) protected booleanSimpleAlphabet.containsImpl(AtomicSymbol s) protected booleanSingletonAlphabet.containsImpl(AtomicSymbol s) voidSimpleManyToOneTranslationTable.setTranslation(AtomicSymbol from, AtomicSymbol to) Alter the translation mapping.voidSimpleReversibleTranslationTable.setTranslation(AtomicSymbol from, AtomicSymbol to) Alter the translation mapping.voidSimpleTranslationTable.setTranslation(AtomicSymbol from, AtomicSymbol to) Alter the translation mapping.Constructors in org.biojava.bio.symbol with parameters of type AtomicSymbol -
Uses of AtomicSymbol in org.biojavax.ga.util
Methods in org.biojavax.ga.util that return AtomicSymbolModifier and TypeMethodDescriptionstatic AtomicSymbolGATools.one()static AtomicSymbolGATools.zero()