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Packages that use AtomicSymbol | |
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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 |
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Methods in org.biojava.bio.chromatogram with parameters of type AtomicSymbol | |
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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 |
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Methods in org.biojava.bio.dist with parameters of type AtomicSymbol | |
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void |
SimpleDistribution.Trainer.addCount(DistributionTrainerContext dtc,
AtomicSymbol sym,
double times)
|
void |
IgnoreCountsTrainer.addCount(DistributionTrainerContext dtc,
AtomicSymbol sym,
double times)
|
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. |
double |
Count.getCount(AtomicSymbol s)
Return the counts for a given Symbol. |
double |
IndexedCount.getCount(AtomicSymbol s)
|
double |
SimpleDistribution.Trainer.getCount(DistributionTrainerContext dtc,
AtomicSymbol sym)
|
double |
IgnoreCountsTrainer.getCount(DistributionTrainerContext dtc,
AtomicSymbol sym)
|
double |
SimpleDistributionTrainer.getCount(DistributionTrainerContext dtc,
AtomicSymbol sym)
Deprecated. |
double |
DistributionTrainer.getCount(DistributionTrainerContext dtc,
AtomicSymbol sym)
Get the current count for this state. |
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 double |
UniformDistribution.getWeightImpl(AtomicSymbol s)
|
protected abstract double |
AbstractDistribution.getWeightImpl(AtomicSymbol sym)
Override this method to implement getting the weight for an atomic symbol. |
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 void |
SimpleDistribution.setWeightImpl(AtomicSymbol s,
double w)
|
void |
AbstractOrderNDistribution.setWeightImpl(AtomicSymbol sym,
double w)
Set a weight in one of the conditioned distributions. |
protected void |
UniformDistribution.setWeightImpl(AtomicSymbol sym,
double weight)
|
protected abstract void |
AbstractDistribution.setWeightImpl(AtomicSymbol sym,
double weight)
Implement this to actually set the weight. |
Uses of AtomicSymbol in org.biojava.bio.dp |
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Subinterfaces of AtomicSymbol in org.biojava.bio.dp | |
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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 | |
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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 |
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Methods in org.biojava.bio.gui with parameters of type AtomicSymbol | |
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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 |
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Fields in org.biojava.bio.program.abi declared as AtomicSymbol | |
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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 | |
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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 |
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Classes in org.biojava.bio.program.hmmer that implement AtomicSymbol | |
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class |
ProfileEmissionState
A state in a HMMer model. |
Uses of AtomicSymbol in org.biojava.bio.proteomics |
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Methods in org.biojava.bio.proteomics that return AtomicSymbol | |
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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 |
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Methods in org.biojava.bio.search with parameters of type AtomicSymbol | |
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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 |
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Methods in org.biojava.bio.seq that return AtomicSymbol | |
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static AtomicSymbol |
NucleotideTools.a()
|
static AtomicSymbol |
RNATools.a()
|
static AtomicSymbol |
DNATools.a()
|
static AtomicSymbol |
ProteinTools.a()
Returns the AtomicSymbol for the amino acid
Alanine |
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 |
RNATools.c()
|
static AtomicSymbol |
DNATools.c()
|
static AtomicSymbol |
ProteinTools.c()
Returns the AtomicSymbol for the amino acid
Cysteine |
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 |
RNATools.g()
|
static AtomicSymbol |
DNATools.g()
|
static AtomicSymbol |
ProteinTools.g()
Returns the AtomicSymbol for the amino acid
Glycine |
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 |
RNATools.u()
|
static AtomicSymbol |
ProteinTools.u()
Returns the AtomicSymbol for the amino acid
Selenocysteine |
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 |
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Classes in org.biojava.bio.symbol that implement AtomicSymbol | |
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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 | |
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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 |
SimpleAlphabet.getSymbolImpl(List symL)
|
protected AtomicSymbol |
IntegerAlphabet.SubIntegerAlphabet.getSymbolImpl(List symL)
|
protected AtomicSymbol |
SingletonAlphabet.getSymbolImpl(List symList)
|
protected abstract AtomicSymbol |
AbstractAlphabet.getSymbolImpl(List symList)
|
Methods in org.biojava.bio.symbol with parameters of type AtomicSymbol | |
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protected void |
SimpleAlphabet.addSymbolImpl(AtomicSymbol s)
|
protected void |
IntegerAlphabet.SubIntegerAlphabet.addSymbolImpl(AtomicSymbol sym)
|
void |
SingletonAlphabet.addSymbolImpl(AtomicSymbol sym)
|
protected abstract void |
AbstractAlphabet.addSymbolImpl(AtomicSymbol s)
|
protected boolean |
SimpleAlphabet.containsImpl(AtomicSymbol s)
|
protected boolean |
IntegerAlphabet.SubIntegerAlphabet.containsImpl(AtomicSymbol sym)
|
protected boolean |
SingletonAlphabet.containsImpl(AtomicSymbol s)
|
protected abstract boolean |
AbstractAlphabet.containsImpl(AtomicSymbol s)
|
void |
SimpleReversibleTranslationTable.setTranslation(AtomicSymbol from,
AtomicSymbol to)
Alter the translation mapping. |
void |
SimpleManyToOneTranslationTable.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 | |
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SingletonAlphabet(AtomicSymbol sym)
|
Uses of AtomicSymbol in org.biojavax.ga.util |
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Methods in org.biojavax.ga.util that return AtomicSymbol | |
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static AtomicSymbol |
GATools.one()
|
static AtomicSymbol |
GATools.zero()
|
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