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Packages that use IllegalSymbolException | |
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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.dp.onehead | |
org.biojava.bio.dp.twohead | |
org.biojava.bio.gui | Graphical interfaces for biojava objects. |
org.biojava.bio.program | Java wrappers for interacting with external bioinformatics tools. |
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.program.phred | Parser for Phred output |
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.seq.io | Classes and interfaces for processing and producing flat-file representations of sequences. |
org.biojava.bio.structure | Interfaces and classes for protein structure (PDB). |
org.biojava.bio.structure.io | Input and Output of Structures |
org.biojava.bio.symbol | Representation of the Symbols that make up a sequence, and locations within them. |
org.biojava.utils.automata | |
org.biojava.utils.regex | This package is used to perform regular expression searches of SymbolLists defined in arbitrary Alphabets. |
org.biojavax.bio.seq | Rich implementations of Sequences, Locations and Features. |
org.biojavax.bio.seq.io | Classes to support the I/O of RichSequence and Bioentry objects. |
org.biojavax.ga | Classes to provide a genetic algorithm framework |
org.biojavax.ga.functions | GA functions |
org.biojavax.ga.impl | Default implementations and abstract classes. |
org.biojavax.ga.util | Utility functions and helper classes |
Uses of IllegalSymbolException in org.biojava.bio.chromatogram |
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Methods in org.biojava.bio.chromatogram that throw IllegalSymbolException | |
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protected SymbolList |
AbstractChromatogram.createImmutableSymbolList(Alphabet alpha,
java.util.List syms)
A factory method for creating new symbol lists with a given alphabet. |
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 IllegalSymbolException in org.biojava.bio.dist |
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Methods in org.biojava.bio.dist that throw IllegalSymbolException | |
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void |
DistributionTrainerContext.addCount(Distribution dist,
Symbol sym,
double times)
Registers that sym was counted in this state. |
void |
SimpleDistributionTrainerContext.addCount(Distribution dist,
Symbol 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. |
void |
SimpleDistributionTrainer.addCount(DistributionTrainerContext dtc,
AtomicSymbol sym,
double count)
Deprecated. |
void |
SimpleDistribution.Trainer.addCount(DistributionTrainerContext dtc,
AtomicSymbol sym,
double times)
|
double |
IndexedCount.getCount(AtomicSymbol s)
|
double |
Count.getCount(AtomicSymbol s)
Return the counts for a given Symbol. |
double |
DistributionTrainerContext.getCount(Distribution dist,
Symbol sym)
Return the number of counts of a particular symbol which will be used to train the specified distribution. |
double |
SimpleDistributionTrainerContext.getCount(Distribution dist,
Symbol sym)
|
double |
IgnoreCountsTrainer.getCount(DistributionTrainerContext dtc,
AtomicSymbol sym)
|
double |
DistributionTrainer.getCount(DistributionTrainerContext dtc,
AtomicSymbol sym)
Get the current count for this state. |
double |
SimpleDistributionTrainer.getCount(DistributionTrainerContext dtc,
AtomicSymbol sym)
Deprecated. |
double |
SimpleDistribution.Trainer.getCount(DistributionTrainerContext dtc,
AtomicSymbol sym)
|
Distribution |
OrderNDistribution.getDistribution(Symbol sym)
|
double |
AbstractDistribution.getWeight(Symbol sym)
Retrieve the weight for this distribution. |
double |
GapDistribution.getWeight(Symbol sym)
|
double |
Distribution.getWeight(Symbol s)
Return the probability that Symbol s is emitted by this spectrum. |
double |
TranslatedDistribution.getWeight(Symbol sym)
|
double |
PairDistribution.getWeight(Symbol sym)
|
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. |
protected double |
UniformDistribution.getWeightImpl(AtomicSymbol s)
|
double |
SimpleDistribution.getWeightImpl(AtomicSymbol s)
|
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. |
void |
OrderNDistribution.setDistribution(Symbol sym,
Distribution dist)
Set the distribution assocated with a symbol. |
void |
AbstractDistribution.setWeight(Symbol sym,
double weight)
Set the weight of a given symbol in this distribution. |
void |
GapDistribution.setWeight(Symbol s,
double w)
|
void |
Distribution.setWeight(Symbol s,
double w)
Set the probability or odds that Symbol s is emitted by this state. |
void |
TranslatedDistribution.setWeight(Symbol sym,
double weight)
|
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)
|
Uses of IllegalSymbolException in org.biojava.bio.dp |
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Methods in org.biojava.bio.dp that throw IllegalSymbolException | |
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void |
TransitionTrainer.addCount(State from,
State to,
double count)
Add 'count' to the transition from->to. |
void |
WMAsMM.addState(State toAdd)
|
void |
SimpleMarkovModel.addState(State toAdd)
|
void |
MarkovModel.addState(State newState)
Adds a state to the model. |
abstract double |
DP.backward(SymbolList[] symList,
ScoreType scoreType)
|
abstract DPMatrix |
DP.backwardMatrix(SymbolList[] symList,
DPMatrix matrix,
ScoreType scoreType)
|
abstract DPMatrix |
DP.backwardMatrix(SymbolList[] symList,
ScoreType scoreType)
|
static int[][] |
DP.backwardTransitions(MarkovModel model,
State[] states)
|
double |
ScoreType.calculateScore(Distribution dist,
Symbol sym)
Calculates the score associated with a distribution and a symbol. |
double |
ScoreType.Probability.calculateScore(Distribution dist,
Symbol sym)
|
double |
ScoreType.Odds.calculateScore(Distribution dist,
Symbol sym)
|
double |
ScoreType.NullModel.calculateScore(Distribution dist,
Symbol sym)
|
protected void |
ProfileHMM.connectModel()
This is called by constructor in setting up the allowed transitions in the model |
boolean |
WMAsMM.containsTransition(State from,
State to)
|
boolean |
SimpleMarkovModel.containsTransition(State from,
State to)
|
boolean |
MarkovModel.containsTransition(State from,
State to)
Returns wether a transition exists or not. |
void |
SimpleMarkovModel.createTransition(State from,
State to)
|
void |
MarkovModel.createTransition(State from,
State to)
Makes a transition between two states legal. |
void |
SimpleMarkovModel.destroyTransition(State from,
State to)
|
void |
MarkovModel.destroyTransition(State from,
State to)
Breaks a transition between two states legal. |
static MarkovModel |
DP.flatView(MarkovModel model)
|
abstract double |
DP.forward(SymbolList[] symList,
ScoreType scoreType)
|
abstract DPMatrix |
DP.forwardMatrix(SymbolList[] symList,
DPMatrix matrix,
ScoreType scoreType)
|
abstract DPMatrix |
DP.forwardMatrix(SymbolList[] symList,
ScoreType scoreType)
|
static int[][] |
DP.forwardTransitions(MarkovModel model,
State[] states)
Returns a matrix for the specified States describing all valid Transitions between those States. |
StatePath |
DP.generate(int length)
Generates an alignment from a model. |
Distribution |
WMAsMM.getWeights(State source)
|
Distribution |
SimpleMarkovModel.getWeights(State source)
|
Distribution |
MarkovModel.getWeights(State source)
Get a probability Distribution over the transition from 'source'. |
static WeightMatrix |
XmlMarkovModel.readMatrix(org.w3c.dom.Element root)
|
static MarkovModel |
XmlMarkovModel.readModel(org.w3c.dom.Element root)
|
void |
HMMTrainer.recordEmittedSymbol(State state,
Symbol symbol,
double weight)
record that the specified symbol was emitted from the specified state. |
void |
SimpleHMMTrainer.recordEmittedSymbol(State state,
Symbol symbol,
double weight)
|
void |
WMAsMM.removeState(State toAdd)
|
void |
SimpleMarkovModel.removeState(State toGo)
|
void |
MarkovModel.removeState(State toGo)
Remove a state from the model. |
static double |
DP.scoreWeightMatrix(WeightMatrix matrix,
SymbolList symList,
int start)
Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix. |
static double |
DP.scoreWeightMatrix(WeightMatrix matrix,
SymbolList symList,
ScoreType scoreType,
int start)
Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix using a particular ScoreType. |
void |
SimpleMarkovModel.setWeights(State source,
Distribution dist)
Use this methods to customize the transition probabilities. |
void |
MarkovModel.setWeights(State source,
Distribution dist)
Set the probability distribution over the transitions from 'source'. |
protected abstract double |
AbstractTrainer.singleSequenceIteration(ModelTrainer trainer,
SymbolList symList)
|
protected double |
BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer,
SymbolList symList)
|
protected double |
BaumWelchTrainer.singleSequenceIteration(ModelTrainer trainer,
SymbolList symList)
|
protected double |
BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer,
SymbolList symList,
ScoreType scoreType)
|
State[] |
DP.stateList(MarkovModel mm)
|
void |
TransitionTrainer.train(double nullModel,
double weight)
Trains the transition, given an expected probability, and a weight for that probability. |
void |
AbstractTrainer.train(SequenceDB db,
double nullModelWeight,
StoppingCriteria stopper)
Trains the sequences in db until stopper says to finnish. |
void |
TrainingAlgorithm.train(SequenceDB db,
double nullWeight,
StoppingCriteria stopper)
Trains the sequences in db untill stopper says to finnish. |
FiniteAlphabet |
WMAsMM.transitionsFrom(State from)
|
FiniteAlphabet |
SimpleMarkovModel.transitionsFrom(State from)
|
FiniteAlphabet |
MarkovModel.transitionsFrom(State source)
Returns the FiniteAlphabet of all states that have a transition from 'source'. |
FiniteAlphabet |
WMAsMM.transitionsTo(State to)
|
FiniteAlphabet |
SimpleMarkovModel.transitionsTo(State to)
|
FiniteAlphabet |
MarkovModel.transitionsTo(State dest)
Returns the FiniteAlphabet of all states that have a transition to 'dest'. |
abstract StatePath |
DP.viterbi(SymbolList[] symList,
ScoreType scoreType)
|
Constructors in org.biojava.bio.dp that throw IllegalSymbolException | |
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DP(MarkovModel model)
|
|
ProfileHMM(Alphabet alpha,
int columns,
DistributionFactory matchFactory,
DistributionFactory insertFactory)
Deprecated. |
|
ProfileHMM(Alphabet alpha,
int columns,
DistributionFactory matchFactory,
DistributionFactory insertFactory,
java.lang.String name)
Create a new ProfileHMM. |
|
SimpleHMMTrainer(MarkovModel model)
|
|
WMAsMM(WeightMatrix wm)
|
Uses of IllegalSymbolException in org.biojava.bio.dp.onehead |
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Methods in org.biojava.bio.dp.onehead that throw IllegalSymbolException | |
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protected void |
SingleDP.backward_initialize(DPCursor dpCursor,
ScoreType scoreType)
|
protected void |
SingleDP.backward_recurse(DPCursor dpCursor,
ScoreType scoreType)
|
protected double |
SingleDP.backward_termination(DPCursor dpCursor,
ScoreType scoreType)
|
protected double |
SingleDP.backward(DPCursor dpCursor,
ScoreType scoreType)
|
double |
SingleDP.backward(SymbolList[] seq,
ScoreType scoreType)
|
double |
SingleDP.backward(SymbolList[] seq,
ScoreType scoreType)
|
DPMatrix |
SingleDP.backwardMatrix(SymbolList[] seq,
DPMatrix matrix,
ScoreType scoreType)
|
DPMatrix |
SingleDP.backwardMatrix(SymbolList[] seq,
DPMatrix matrix,
ScoreType scoreType)
|
DPMatrix |
SingleDP.backwardMatrix(SymbolList[] seq,
ScoreType scoreType)
|
DPMatrix |
SingleDP.backwardMatrix(SymbolList[] seq,
ScoreType scoreType)
|
protected void |
SingleDP.forward_initialize(DPCursor dpCursor,
ScoreType scoreType)
|
protected double |
SingleDP.forward(DPCursor dpCursor,
ScoreType scoreType)
|
double |
SingleDP.forward(SymbolList[] seq,
ScoreType scoreType)
|
double |
SingleDP.forward(SymbolList[] seq,
ScoreType scoreType)
|
DPMatrix |
SingleDP.forwardMatrix(SymbolList[] seq,
DPMatrix matrix,
ScoreType scoreType)
|
DPMatrix |
SingleDP.forwardMatrix(SymbolList[] seq,
DPMatrix matrix,
ScoreType scoreType)
|
DPMatrix |
SingleDP.forwardMatrix(SymbolList[] seq,
ScoreType scoreType)
|
DPMatrix |
SingleDP.forwardMatrix(SymbolList[] seq,
ScoreType scoreType)
|
double[] |
SingleDP.getEmission(Symbol sym,
ScoreType scoreType)
This method is public for the benefit of training algorithms, and in the future we should look at a better way of exposing the emissions cache. |
StatePath |
SingleDP.viterbi(SymbolList[] symList,
ScoreType scoreType)
|
Constructors in org.biojava.bio.dp.onehead that throw IllegalSymbolException | |
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SingleDP(MarkovModel model)
|
Uses of IllegalSymbolException in org.biojava.bio.dp.twohead |
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Methods in org.biojava.bio.dp.twohead that throw IllegalSymbolException | |
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double |
PairwiseDP.backward(SymbolList[] seqs,
ScoreType scoreType)
|
DPMatrix |
PairwiseDP.backwardMatrix(SymbolList[] seqs,
DPMatrix d,
ScoreType scoreType)
|
DPMatrix |
PairwiseDP.backwardMatrix(SymbolList[] seqs,
ScoreType scoreType)
|
CellCalculator |
DPInterpreter.backwards(ScoreType scoreType)
|
CellCalculator |
CellCalculatorFactory.backwards(ScoreType scoreType)
|
void |
CellCalculator.calcCell(Cell[][] cells)
Calculate the 'scores' array in the cell at cells[0][0]. |
double |
PairwiseDP.forward(SymbolList[] seqs,
ScoreType scoreType)
|
DPMatrix |
PairwiseDP.forwardMatrix(SymbolList[] seqs,
DPMatrix d,
ScoreType scoreType)
|
DPMatrix |
PairwiseDP.forwardMatrix(SymbolList[] seqs,
ScoreType scoreType)
|
CellCalculator |
DPInterpreter.forwards(ScoreType scoreType)
|
CellCalculator |
CellCalculatorFactory.forwards(ScoreType scoreType)
|
double[] |
EmissionCache.getEmissions(java.util.List symList)
|
double[] |
EmissionCache.getEmissions(java.util.List symList,
boolean exorcise)
Retrieve the emission scores from the cache for every EmissionState for the specified symbols. |
void |
CellCalculator.initialize(Cell[][] cells)
Initialize the cell at [0][0] to the recursion initial parameters. |
void |
PairDPCursor.next(Cell[][] cells)
retrieve the next block of cells |
void |
LightPairDPCursor.next(Cell[][] cells)
Description of the Method |
CellCalculator |
DPInterpreter.viterbi(ScoreType scoreType,
BackPointer terminal)
|
CellCalculator |
CellCalculatorFactory.viterbi(ScoreType scoreType,
BackPointer terminal)
|
StatePath |
PairwiseDP.viterbi(SymbolList[] seqs,
ScoreType scoreType)
|
Constructors in org.biojava.bio.dp.twohead that throw IllegalSymbolException | |
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AbstractMatrixPairDPCursor(SymbolList seq1,
SymbolList seq2,
int start1,
int start2,
int depth1,
int depth2,
PairDPMatrix matrix,
EmissionCache eCache)
|
|
BackMatrixPairDPCursor(SymbolList seq1,
SymbolList seq2,
int depth1,
int depth2,
PairDPMatrix matrix,
EmissionCache eCache)
|
|
LightPairDPCursor(SymbolList seq1,
SymbolList seq2,
int depth1,
int depth2,
int numStates,
EmissionCache eCache)
Constructor for the LightPairDPCursor object |
|
MatrixPairDPCursor(SymbolList seq1,
SymbolList seq2,
int depth1,
int depth2,
PairDPMatrix matrix,
EmissionCache eCache)
|
|
PairwiseDP(MarkovModel mm,
CellCalculatorFactoryMaker ccfm)
|
Uses of IllegalSymbolException in org.biojava.bio.gui |
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Methods in org.biojava.bio.gui that throw IllegalSymbolException | |
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static double |
DistributionLogo.entropy(Distribution dist,
Symbol s)
Calculate the information content of a symbol in bits. |
java.awt.Paint |
SimpleSymbolStyle.fillPaint(Symbol s)
|
java.awt.Paint |
SymbolStyle.fillPaint(Symbol s)
Return the fill paint for a symbol. |
java.awt.Paint |
DNAStyle.fillPaint(Symbol s)
|
java.awt.Paint |
SimpleSymbolStyle.outlinePaint(Symbol s)
|
java.awt.Paint |
SymbolStyle.outlinePaint(Symbol s)
Return the outline paint for a symbol. |
java.awt.Paint |
DNAStyle.outlinePaint(Symbol s)
|
void |
SimpleSymbolStyle.setFillPaint(Symbol s,
java.awt.Paint paint)
|
void |
DNAStyle.setFillPaint(Symbol s,
java.awt.Paint paint)
|
void |
SimpleSymbolStyle.setOutlinePaint(Symbol s,
java.awt.Paint paint)
|
void |
DNAStyle.setOutlinePaint(Symbol s,
java.awt.Paint paint)
|
Uses of IllegalSymbolException in org.biojava.bio.program |
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Constructors in org.biojava.bio.program that throw IllegalSymbolException | |
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Meme(java.io.InputStream is,
SymbolTokenization symParser)
|
Uses of IllegalSymbolException in org.biojava.bio.program.abi |
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Methods in org.biojava.bio.program.abi that throw IllegalSymbolException | |
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static Symbol |
ABIFParser.decodeDNAToken(char token)
Decodes a character into a Symbol in the DNA alphabet. |
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 IllegalSymbolException in org.biojava.bio.program.hmmer |
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Methods in org.biojava.bio.program.hmmer that throw IllegalSymbolException | |
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protected void |
HmmerProfileHMM.connectModel()
This is called by constructor in setting up the allowed transitions in the model |
double |
ProfileEmissionState.logProb(Symbol sym)
|
double |
HmmerProfileHMM.transScore(State from,
State to,
Symbol symFrom,
Symbol symTo)
|
Constructors in org.biojava.bio.program.hmmer that throw IllegalSymbolException | |
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HmmerProfileHMM(Alphabet alpha,
int columns,
DistributionFactory matchFactory,
DistributionFactory insertFactory,
java.lang.String name)
|
Uses of IllegalSymbolException in org.biojava.bio.program.phred |
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Methods in org.biojava.bio.program.phred that throw IllegalSymbolException | |
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static SymbolList |
PhredTools.createPhred(SymbolList dna,
SymbolList quality)
Merges a Symbol List from the DNA alphabet with a SymbolList from the [0..99] subset of the IntegerAlphabet into a SymbolList from the PHRED alphabet. |
static Symbol |
PhredTools.dnaSymbolFromPhred(Symbol phredSym)
Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet. |
static Symbol |
PhredTools.getPhredSymbol(Symbol dna,
Symbol integer)
Creates a symbol from the PHRED alphabet by combining a Symbol from the DNA alphabet and a Symbol from the IntegerAlphabet (or one of its subsets). |
static IntegerAlphabet.IntegerSymbol |
PhredTools.integerSymbolFromPhred(Symbol phredSym)
Retrives the IntegerSymbol component of the Phred BasisSymbol from the PHRED alphabet. |
boolean |
PhredFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener siol)
|
Uses of IllegalSymbolException in org.biojava.bio.proteomics |
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Methods in org.biojava.bio.proteomics that throw IllegalSymbolException | |
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void |
MassCalc.addVariableModification(char residue,
double[] masses)
Add Variable modifications. |
void |
MassCalc.addVariableModification(Symbol residue,
double[] masses)
Add Variable modifications. |
static Protease |
ProteaseManager.createProtease(java.lang.String cleaveRes,
boolean endoProtease,
java.lang.String name)
|
static Protease |
ProteaseManager.createProtease(java.lang.String cleaveRes,
boolean endoProtease,
java.lang.String notCleaveRes,
java.lang.String name)
|
static Protease |
ProteaseManager.createProtease(SymbolList cleaveRes,
boolean endoProtease,
java.lang.String name)
|
static Protease |
ProteaseManager.createProtease(SymbolList cleaveRes,
boolean endoProtease,
SymbolList notCleaveRes,
java.lang.String name)
Creates and registers a new Protease. |
double |
MassCalc.getMass(SymbolList proteinSeq)
Get the Mass of this peptide. |
static double |
MassCalc.getMass(SymbolList proteinSeq,
java.lang.String isotopicType,
boolean MH_PLUS)
getMass calculates the mass of this peptide. |
double[] |
MassCalc.getVariableMasses(SymbolList peptide)
Get all masses including the variable mass. |
boolean |
MassCalc.removeVariableModifications(char residue)
Remove all variable modifications assocaited with this residue. |
void |
MassCalc.setSymbolModification(char symbolToken,
double mass)
Use this to set a post translational modification for the Symbol represented by this character. |
Constructors in org.biojava.bio.proteomics that throw IllegalSymbolException | |
---|---|
Protease(java.lang.String cleavageRes,
boolean endoProtease)
Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease()) |
|
Protease(java.lang.String cleaveRes,
boolean endoProtease,
java.lang.String notCleaveRes)
Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease()) |
|
Protease(SymbolList cleaveRes,
boolean endoProtease,
SymbolList notCleaveRes)
Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease()) |
|
Protease(SymbolList cleaveRes,
boolean endoProtease,
SymbolList notCleaveRes,
java.lang.String name)
|
Uses of IllegalSymbolException in org.biojava.bio.search |
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Methods in org.biojava.bio.search that throw IllegalSymbolException | |
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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 IllegalSymbolException in org.biojava.bio.seq |
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Methods in org.biojava.bio.seq that throw IllegalSymbolException | |
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static Symbol |
DNATools.complement(Symbol sym)
Complement the symbol. |
static Symbol |
NucleotideTools.complement(Symbol sym)
Complement the symbol. |
static Symbol |
RNATools.complement(Symbol sym)
Complement the symbol. |
static SymbolList |
DNATools.createDNA(java.lang.String dna)
Return a new DNA SymbolList for dna. |
static Sequence |
DNATools.createDNASequence(java.lang.String dna,
java.lang.String name)
Return a new DNA Sequence for dna. |
static Sequence |
SequenceTools.createDummy(Alphabet alpha,
int length,
Symbol sym,
java.lang.String uri,
java.lang.String name)
Create a new Sequence that contains a single symbol repeated over and over. |
static GappedSequence |
DNATools.createGappedDNASequence(java.lang.String dna,
java.lang.String name)
Get a new dna as a GappedSequence |
static GappedSequence |
ProteinTools.createGappedProteinSequence(java.lang.String theProtein,
java.lang.String name)
Get a new protein as a GappedSequence |
static SymbolList |
NucleotideTools.createNucleotide(java.lang.String nucleotide)
Return a new Nucleotide SymbolList for nucleotide. |
static Sequence |
NucleotideTools.createNucleotideSequence(java.lang.String nucleotide,
java.lang.String name)
Return a new Nucleotide Sequence for nucleotide. |
static SymbolList |
ProteinTools.createProtein(java.lang.String theProtein)
Return a new Protein SymbolList for protein. |
static Sequence |
ProteinTools.createProteinSequence(java.lang.String protein,
java.lang.String name)
Return a new PROTEIN Sequence for protein. |
static SymbolList |
RNATools.createRNA(java.lang.String rna)
Return a new RNA SymbolList for rna. |
static Sequence |
RNATools.createRNASequence(java.lang.String rna,
java.lang.String name)
Return a new RNA Sequence for rna. |
static char |
DNATools.dnaToken(Symbol sym)
Get a single-character token for a DNA symbol |
static Symbol |
DNATools.forSymbol(char token)
Retrieve the symbol for a symbol. |
static Symbol |
NucleotideTools.forSymbol(char token)
Retrieve the symbol for a symbol. |
static Symbol |
RNATools.forSymbol(char token)
Retrieve the symbol for a symbol. |
static int |
DNATools.index(Symbol sym)
Return an integer index for a symbol - compatible with forIndex . |
static int |
NucleotideTools.index(Symbol sym)
Return an integer index for a symbol - compatible with forIndex . |
static int |
RNATools.index(Symbol sym)
Return an integer index for a symbol - compatible with forIndex. |
static char |
NucleotideTools.nucleotideToken(Symbol sym)
Get a single-character token for a Nucleotide symbol |
Uses of IllegalSymbolException in org.biojava.bio.seq.io |
---|
Methods in org.biojava.bio.seq.io that throw IllegalSymbolException | |
---|---|
static void |
SeqIOTools.biojavaToFile(int fileType,
java.io.OutputStream os,
java.lang.Object biojava)
Deprecated. Converts a Biojava object to the given filetype. |
static void |
SeqIOTools.biojavaToFile(java.lang.String formatName,
java.lang.String alphabetName,
java.io.OutputStream os,
java.lang.Object biojava)
Deprecated. Writes a Biojava SequenceIterator ,
SequenceDB , Sequence or Aligment
to an OutputStream |
void |
StreamParser.characters(char[] data,
int start,
int len)
|
void |
StreamParser.close()
|
SymbolList |
ChunkedSymbolListFactory.make(SymbolReader sr)
Method to create a Sequence with a SymbolReader. |
protected Symbol[] |
WordTokenization.parseString(java.lang.String s)
|
Symbol |
SymbolTokenization.parseToken(java.lang.String token)
Returns the symbol for a single token. |
Symbol |
SubIntegerTokenization.parseToken(java.lang.String seq)
|
Symbol |
DoubleTokenization.parseToken(java.lang.String seq)
|
Symbol |
CrossProductTokenization.parseToken(java.lang.String token)
|
Symbol |
CharacterTokenization.parseToken(java.lang.String token)
|
Symbol |
NameTokenization.parseToken(java.lang.String token)
|
Symbol |
IntegerTokenization.parseToken(java.lang.String seq)
|
protected Symbol |
CharacterTokenization.parseTokenChar(char c)
|
protected void |
EmblLikeFormat.processSequenceLine(java.lang.String line,
StreamParser parser)
Deprecated. Dispatch symbol data from SQ-block line of an EMBL-like file. |
boolean |
GenbankFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Deprecated. Reads a sequence from the specified reader using the Symbol parser and Sequence Factory provided. |
boolean |
SequenceFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener. |
boolean |
EmblLikeFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Deprecated. |
boolean |
GenbankXmlFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Deprecated. |
boolean |
FastaFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener siol)
Deprecated. Reads information from a flatfile to a SeqIOListener
using a SymbolTokenizer to convert sequence strings
to Symbol objects. |
Symbol |
SymbolReader.readSymbol()
Return a single symbol from the stream. |
int |
SymbolReader.readSymbols(Symbol[] buffer,
int start,
int length)
Read one or more symbols from the stream. |
protected java.util.List |
WordTokenization.splitString(java.lang.String str)
|
java.lang.String |
SymbolTokenization.tokenizeSymbol(Symbol sym)
Return a token representing a single symbol. |
java.lang.String |
SubIntegerTokenization.tokenizeSymbol(Symbol sym)
|
java.lang.String |
DoubleTokenization.tokenizeSymbol(Symbol sym)
|
java.lang.String |
CrossProductTokenization.tokenizeSymbol(Symbol s)
|
java.lang.String |
CharacterTokenization.tokenizeSymbol(Symbol s)
|
java.lang.String |
NameTokenization.tokenizeSymbol(Symbol s)
|
java.lang.String |
IntegerTokenization.tokenizeSymbol(Symbol sym)
|
java.lang.String |
SymbolTokenization.tokenizeSymbolList(SymbolList symList)
Return a string representation of a list of symbols. |
java.lang.String |
WordTokenization.tokenizeSymbolList(SymbolList sl)
|
void |
FastaAlignmentFormat.write(java.io.OutputStream os,
Alignment align,
int fileType)
Writes out the alignment to an FASTA file. |
void |
MSFAlignmentFormat.write(java.io.OutputStream os,
Alignment align,
int fileType)
|
void |
FastaAlignmentFormat.writeDna(java.io.OutputStream os,
Alignment align)
|
void |
MSFAlignmentFormat.writeDna(java.io.OutputStream os,
Alignment align)
|
void |
FastaAlignmentFormat.writeProtein(java.io.OutputStream os,
Alignment align)
|
void |
MSFAlignmentFormat.writeProtein(java.io.OutputStream os,
Alignment align)
|
Uses of IllegalSymbolException in org.biojava.bio.structure |
---|
Methods in org.biojava.bio.structure that throw IllegalSymbolException | |
---|---|
static double |
AlphaCTools.getPhiAngle(Symbol phiPsiSym)
extracts the Phi angle from a Symbol . |
static Symbol |
AlphaCTools.getPhiPsiSymbol(double phiAngle,
double psiAngle)
Makes a Phi - Psi Symbol from the ALPHA CARBON ANGLES alphabet. |
static double |
AlphaCTools.getPsiAngle(Symbol phiPsiSym)
extracts the Psi angle from a Symbol . |
Uses of IllegalSymbolException in org.biojava.bio.structure.io |
---|
Methods in org.biojava.bio.structure.io that throw IllegalSymbolException | |
---|---|
java.lang.Character |
PDBFileParser.convert_3code_1code(java.lang.String code3)
convert three character amino acid codes into single character e.g. |
Uses of IllegalSymbolException in org.biojava.bio.symbol |
---|
Methods in org.biojava.bio.symbol that throw IllegalSymbolException | |
---|---|
void |
AbstractAlphabet.addSymbol(Symbol s)
|
void |
SimpleSymbolList.addSymbol(Symbol sym)
Add a new Symbol to the end of this list. |
void |
FiniteAlphabet.addSymbol(Symbol s)
Adds a symbol to this alphabet. |
void |
SingletonAlphabet.addSymbolImpl(AtomicSymbol sym)
|
protected abstract void |
AbstractAlphabet.addSymbolImpl(AtomicSymbol s)
|
protected void |
SimpleAlphabet.addSymbolImpl(AtomicSymbol s)
|
void |
UkkonenSuffixTree.addSymbolList(SymbolList list,
java.lang.String name,
boolean doNotTerminate)
|
void |
SuffixTree.addSymbols(SymbolList sList,
int window)
Add a count for all motifs with length of up to window
to this tree. |
static Symbol |
AlphabetManager.createSymbol(Annotation annotation,
java.util.List symList,
Alphabet alpha)
Generates a new Symbol instance that represents the tuple of Symbols in symList. |
static Symbol |
AlphabetManager.createSymbol(Annotation annotation,
java.util.Set symSet,
Alphabet alpha)
Generates a new Symbol instance that represents the tuple of Symbols in symList. |
static Symbol |
AlphabetManager.createSymbol(char token,
Annotation annotation,
java.util.List symList,
Alphabet alpha)
Deprecated. use the new version, without the token argument |
static Symbol |
AlphabetManager.createSymbol(char token,
Annotation annotation,
java.util.Set symSet,
Alphabet alpha)
Deprecated. use the three-arg version of this method instead. |
protected abstract java.util.Set |
AbstractManyToOneTranslationTable.doUntranslate(Symbol sym)
this method is expected to reverse-translate any symbol in the source alphabet. |
protected abstract Symbol |
AbstractReversibleTranslationTable.doUntranslate(Symbol sym)
this method is expected to reverse-translate any symbol in the source alphabet. |
static java.util.List |
AlphabetManager.factorize(Alphabet alpha,
java.util.Set symSet)
Return a list of BasisSymbol instances that uniquely sum up all AtomicSymbol instances in symSet. |
static AlphabetIndex |
AlphabetManager.getAlphabetIndex(Symbol[] syms)
Get an indexer for an array of symbols. |
Symbol |
Alphabet.getAmbiguity(java.util.Set syms)
Get a symbol that represents the set of symbols in syms. |
Symbol |
AbstractAlphabet.getAmbiguity(java.util.Set syms)
|
Symbol |
IntegerAlphabet.getAmbiguity(java.util.Set symSet)
|
Symbol |
DoubleAlphabet.getAmbiguity(java.util.Set syms)
|
protected Symbol |
AbstractAlphabet.getAmbiguityImpl(java.util.Set syms)
Backend for getAmbiguity, called when it is actually necessarly to create a new symbol. |
SuffixTree.SuffixNode |
SuffixTree.getChild(SuffixTree.SuffixNode node,
Symbol s)
Get a child of a SuffixTree.SuffixNode, constructing a new one if need be. |
double |
SymbolPropertyTable.getDoubleValue(Symbol s)
|
double |
SimpleSymbolPropertyTable.getDoubleValue(Symbol s)
|
Distribution |
CodonPref.getFrequencyForSynonyms(Symbol residue)
returns a Distribution giving the frequency of synonymous codons. |
Distribution |
SimpleCodonPref.getFrequencyForSynonyms(Symbol residue)
|
DoubleAlphabet.DoubleSymbol |
DoubleAlphabet.SubDoubleAlphabet.getSymbol(double val)
|
IntegerAlphabet.IntegerSymbol |
IntegerAlphabet.SubIntegerAlphabet.getSymbol(int val)
|
Symbol |
SoftMaskedAlphabet.getSymbol(java.util.List l)
Gets the compound symbol composed of the Symbols in the List. |
Symbol |
Alphabet.getSymbol(java.util.List rl)
Get a symbol from the Alphabet which corresponds to the specified ordered list of symbols. |
Symbol |
AbstractAlphabet.getSymbol(java.util.List syms)
|
Symbol |
IntegerAlphabet.getSymbol(java.util.List symList)
|
Symbol |
DoubleAlphabet.getSymbol(java.util.List symList)
|
Symbol |
DoubleAlphabet.SubDoubleAlphabet.getSymbol(java.util.List rl)
|
protected AtomicSymbol |
SingletonAlphabet.getSymbolImpl(java.util.List symList)
|
protected abstract AtomicSymbol |
AbstractAlphabet.getSymbolImpl(java.util.List symList)
|
protected AtomicSymbol |
IntegerAlphabet.SubIntegerAlphabet.getSymbolImpl(java.util.List symL)
|
protected AtomicSymbol |
SimpleAlphabet.getSymbolImpl(java.util.List symL)
|
WobbleDistribution |
CodonPref.getWobbleDistributionForSynonyms(Symbol residue)
returns a WobbleDistribution for a specified residue. |
WobbleDistribution |
SimpleCodonPref.getWobbleDistributionForSynonyms(Symbol residue)
|
int |
AlphabetIndex.indexForSymbol(Symbol s)
Return the unique index for a symbol. |
boolean |
SoftMaskedAlphabet.isMasked(BasisSymbol s)
Determines if a Symbol is masked. |
static int |
PackingFactory.nextWord(SymbolList symList,
int word,
int offset,
int wordLength,
Packing packing)
|
byte |
Packing.pack(Symbol sym)
Return a byte representing the packing of a symbol. |
Symbol |
SoftMaskedAlphabet.CaseSensitiveTokenization.parseToken(java.lang.String token)
|
static int |
PackingFactory.primeWord(SymbolList symList,
int wordLength,
Packing packing)
|
void |
SimpleGappedSymbolList.removeGap(int pos)
|
void |
GappedSymbolList.removeGap(int pos)
Remove a single gap at position pos in this GappedSymbolList. |
void |
SimpleGappedSymbolList.removeGaps(int pos,
int length)
|
void |
GappedSymbolList.removeGaps(int pos,
int length)
Remove some gaps at position pos in this GappedSymbolList. |
void |
SingletonAlphabet.removeSymbol(Symbol sym)
|
void |
SimpleAlphabet.removeSymbol(Symbol s)
|
void |
FiniteAlphabet.removeSymbol(Symbol s)
Remove a symbol from this alphabet. |
void |
SimpleSymbolPropertyTable.setDoubleProperty(Symbol s,
java.lang.String value)
|
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. |
java.lang.String |
SoftMaskedAlphabet.CaseSensitiveTokenization.tokenizeSymbol(Symbol s)
|
java.lang.String |
SoftMaskedAlphabet.CaseSensitiveTokenization.tokenizeSymbolList(SymbolList sl)
|
Symbol |
TranslationTable.translate(Symbol sym)
Translate a single symbol from source alphabet to the target alphabet. |
Symbol |
DNANoAmbPack.unpack(byte b)
|
Symbol |
Packing.unpack(byte packed)
Return the symbol for a packing. |
java.util.Set |
AbstractManyToOneTranslationTable.untranslate(Symbol sym)
returns a Set of Atomic Symbols that are the reverse translation of the specified Symbol in the target alphabet. |
java.util.Set |
ManyToOneTranslationTable.untranslate(Symbol sym)
Translate a single symbol from target alphabet to the source alphabet. |
Symbol |
AbstractReversibleTranslationTable.untranslate(Symbol sym)
|
Symbol |
ReversibleTranslationTable.untranslate(Symbol sym)
Translate a single symbol from target alphabet to the source alphabet. |
void |
SoftMaskedAlphabet.validate(Symbol s)
|
void |
Alphabet.validate(Symbol s)
Throws a precanned IllegalSymbolException if the symbol is not contained within this Alphabet. |
void |
AbstractAlphabet.validate(Symbol sym)
|
void |
IntegerAlphabet.validate(Symbol s)
|
void |
DoubleAlphabet.validate(Symbol s)
|
void |
DoubleAlphabet.SubDoubleAlphabet.validate(Symbol sym)
|
static void |
CodonPrefTools.writeToXML(CodonPref codonPref,
java.io.PrintWriter writer)
write out a specified CodonPref object in XML format. |
Constructors in org.biojava.bio.symbol that throw IllegalSymbolException | |
---|---|
DummySymbolList(Alphabet alpha,
int length,
Symbol sym)
|
|
Edit(int pos,
Alphabet alpha,
Symbol replacement)
Convenience construtor for making single residue changes |
|
SimpleAtomicSymbol(Annotation annotation,
java.util.List syms)
|
|
SimpleSymbolList(Alphabet alpha,
java.util.List rList)
Construct a SymbolList containing the symbols in the specified list. |
|
SimpleSymbolList(SymbolTokenization parser,
java.lang.String seqString)
Construct a SymbolList from a string. |
Uses of IllegalSymbolException in org.biojava.utils.automata |
---|
Methods in org.biojava.utils.automata that throw IllegalSymbolException | |
---|---|
protected int |
FiniteAutomaton.alphaIndex(Symbol sym)
|
protected int |
Nfa.alphaIndex(Symbol sym)
|
Uses of IllegalSymbolException in org.biojava.utils.regex |
---|
Methods in org.biojava.utils.regex that throw IllegalSymbolException | |
---|---|
char |
Search.charValue(Symbol sym)
|
char |
PatternFactory.charValue(Symbol sym)
Returns the character that represents the specified Symbol in the Alphabet that this PatternFactory was defined for. |
Uses of IllegalSymbolException in org.biojavax.bio.seq |
---|
Methods in org.biojavax.bio.seq that throw IllegalSymbolException | |
---|---|
protected void |
SimpleRichSequence.setAlphabetName(java.lang.String alphaname)
|
protected void |
ThinRichSequence.setAlphabetName(java.lang.String alphaname)
|
protected void |
SimpleRichSequence.setStringSequence(java.lang.String seq)
|
Uses of IllegalSymbolException in org.biojavax.bio.seq.io |
---|
Methods in org.biojavax.bio.seq.io that throw IllegalSymbolException | |
---|---|
boolean |
EMBLFormat.readRichSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener rlistener,
Namespace ns)
Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. |
boolean |
GenbankFormat.readRichSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener rlistener,
Namespace ns)
Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. |
boolean |
INSDseqFormat.readRichSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener rlistener,
Namespace ns)
Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. |
boolean |
UniProtFormat.readRichSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener rlistener,
Namespace ns)
Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. |
boolean |
EMBLxmlFormat.readRichSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener rlistener,
Namespace ns)
Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. |
boolean |
UniProtXMLFormat.readRichSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener rlistener,
Namespace ns)
Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. If namespace is null, then the namespace of the sequence in the fasta is used. |
boolean |
RichSequenceFormat.readRichSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener listener,
Namespace ns)
Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. |
boolean |
FastaFormat.readRichSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener rsiol,
Namespace ns)
Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. If namespace is null, then the namespace of the sequence in the fasta is used. |
boolean |
EMBLFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener. |
boolean |
GenbankFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener. |
boolean |
INSDseqFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener. |
boolean |
UniProtFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener. |
boolean |
EMBLxmlFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener. |
boolean |
UniProtXMLFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener. |
boolean |
FastaFormat.readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener. |
Uses of IllegalSymbolException in org.biojavax.ga |
---|
Methods in org.biojavax.ga that throw IllegalSymbolException | |
---|---|
void |
GeneticAlgorithm.run(GAStoppingCriteria stoppingCriteria)
Iterates the Algorithm until the stopping criteria are met. |
Uses of IllegalSymbolException in org.biojavax.ga.functions |
---|
Methods in org.biojavax.ga.functions that throw IllegalSymbolException | |
---|---|
SymbolList |
MutationFunction.mutate(SymbolList seq)
Produces a new SymbolList by mutation. |
SymbolList |
SimpleMutationFunction.mutate(SymbolList seq)
|
Uses of IllegalSymbolException in org.biojavax.ga.impl |
---|
Methods in org.biojavax.ga.impl that throw IllegalSymbolException | |
---|---|
void |
SimpleGeneticAlgorithm.run(GAStoppingCriteria stoppingCriteria)
|
Uses of IllegalSymbolException in org.biojavax.ga.util |
---|
Methods in org.biojavax.ga.util that throw IllegalSymbolException | |
---|---|
static SymbolList |
GATools.createBinary(java.lang.String binarySequence)
Creates a SymbolList in the GABinary Alphabet |
|
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