Uses of Interface
org.biojava.bio.symbol.SymbolList

Packages that use SymbolList

Package	Description
org.biojava.bio.alignment	Classes to generate and describe sequence alignments.
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.sequence	Graphical displays of biological sequences and associated annotations.
org.biojava.bio.molbio	The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR.
org.biojava.bio.program.abi	ABI Trace Handling.
org.biojava.bio.program.fastq	FASTQ and variants sequence format I/O.
org.biojava.bio.program.phred	Parser for Phred output
org.biojava.bio.program.scf	Support for the SCF chromatogram format.
org.biojava.bio.program.ssaha	SSAHA sequence searching API.
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.homol	The classes and interfaces for defining sequence similarity and honology.
org.biojava.bio.seq.impl	Standard in-memory implementations of Sequence and Feature.
org.biojava.bio.seq.io	Classes and interfaces for processing and producing flat-file representations of sequences.
org.biojava.bio.seq.projection	Code for projecting Feature objects and systematically altering their properties.
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	The Biojava extensions packages, classes that extend the core biojava functionality The biojavax packages contain a number of extensions to the core biojava interfaces.
org.biojavax.bio.db.biosql	Interface between biojava and biosql databases
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.ga	Classes to provide a genetic algorithm framework
org.biojavax.ga.functions	GA functions A genetic algorithm requires a number of functions.
org.biojavax.ga.impl	Default implementations and abstract classes.
org.biojavax.ga.util	Utility functions and helper classes

Uses of SymbolList in org.biojava.bio.alignment

Subinterfaces of SymbolList in org.biojava.bio.alignment

Modifier and Type	Interface and Description
interface	Alignment An alignment containing multiple SymbolLists.
interface	ARAlignment ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.
interface	UnequalLengthAlignment UnequalLengthAlignment has the following behavior.

Classes in org.biojava.bio.alignment that implement SymbolList

Modifier and Type	Class and Description
class	AbstractULAlignment
class	AbstractULAlignment.SubULAlignment
class	AlignmentPair This class stores the result of an alignment procedure that creates a pairwise alignment of two sequences.
class	FlexibleAlignment FlexibleAlignment is a class which implements UnequalLengthAlignment, ARAlignment and EditableAlignment It places no restriction on where any sequence can be in the alignment so there could be gaps in the alignment.
class	SimpleAlignment A simple implementation of an Alignment.

Fields in org.biojava.bio.alignment declared as SymbolList

Modifier and Type	Field and Description
protected SymbolList	SimpleAlignmentElement.seq

Methods in org.biojava.bio.alignment that return SymbolList

Modifier and Type	Method and Description
SymbolList	SimpleAlignmentElement.getSymbolList()
SymbolList	AlignmentElement.getSymbolList()
SymbolList	Alignment.SymbolListIterator.next()
SymbolList	FlexibleAlignment.symbolListForLabel(String label)
SymbolList	AbstractULAlignment.SubULAlignment.symbolListForLabel(String label)
SymbolList	SimpleAlignment.symbolListForLabel(String label)
SymbolList	Alignment.symbolListForLabel(String label) Retrieve a single row of the alignment by label.

Methods in org.biojava.bio.alignment that return types with arguments of type SymbolList

Modifier and Type	Method and Description
Iterator<SymbolList>	AbstractULAlignment.symbolListIterator()
Iterator<SymbolList>	AbstractULAlignment.SubULAlignment.symbolListIterator()
Iterator<SymbolList>	SimpleAlignment.symbolListIterator()
Iterator<SymbolList>	Alignment.symbolListIterator() Creates an Iterator over the SymbolLists in the alignment.

Methods in org.biojava.bio.alignment with parameters of type SymbolList

Modifier and Type	Method and Description
protected boolean	FlexibleAlignment.allGaps(SymbolList seq, int start, int end) make sure that all Symbols in this range are gaps
AlignmentPair	SmithWaterman.pairwiseAlignment(SymbolList query, SymbolList subject) Overrides the method inherited from the NeedlemanWunsch and performs only a local alignment.
AlignmentPair	NeedlemanWunsch.pairwiseAlignment(SymbolList query, SymbolList subject) Global pairwise sequence alignment of two BioJava-Sequence objects according to the Needleman-Wunsch-algorithm.
abstract AlignmentPair	AlignmentAlgorithm.pairwiseAlignment(SymbolList query, SymbolList subject) Performs a pairwise sequence alignment of the two given sequences.

Constructors in org.biojava.bio.alignment with parameters of type SymbolList

Constructor and Description
SimpleAlignmentElement(String label, SymbolList seq, Location loc)

Constructor parameters in org.biojava.bio.alignment with type arguments of type SymbolList

Constructor and Description
SimpleAlignment(Map<String,SymbolList> labelToResList) Generate an alignment from a list of SymbolLists.

Uses of SymbolList in org.biojava.bio.chromatogram

Methods in org.biojava.bio.chromatogram that return SymbolList

Modifier and Type	Method and Description
protected SymbolList	AbstractChromatogram.createImmutableSymbolList(Alphabet alpha, List syms) A factory method for creating new symbol lists with a given alphabet.
static SymbolList	ChromatogramTools.getDNASequence(Chromatogram chromat) Get the called DNA sequence from a chromatogram.
static SymbolList	ChromatogramTools.getTraceOffsets(Chromatogram chromat) Get the peak offsets for the called bases of a chromatogram.
protected SymbolList	AbstractChromatogram.reverseComplementBaseCallList(Object label) Return a symbol list containing the reverse complement of the base call data for the given label.

Methods in org.biojava.bio.chromatogram with parameters of type SymbolList

Modifier and Type	Method and Description
static int	ChromatogramTools.getIntFromSymbolList(SymbolList list, int which) Retrieves, unwraps, and returns an int from a SymbolList containing IntegerAlphabet.IntegerSymbols.
void	SimpleChromatogram.setSymbolLists(SymbolList dna, SymbolList offsets) Set the DNA and OFFSETS symbol lists for the basecall alignment.

Uses of SymbolList in org.biojava.bio.dist

Methods in org.biojava.bio.dist that return SymbolList

Modifier and Type	Method and Description
static SymbolList	DistributionTools.generateSymbolList(Distribution d, int length) Produces a SymbolList by randomly sampling a Distribution.

Uses of SymbolList in org.biojava.bio.dp

Subinterfaces of SymbolList in org.biojava.bio.dp

Modifier and Type	Interface and Description
interface	StatePath Extends the Alignment interface so that it is explicitly used to represent a state path through an HMM, and the associated emitted sequence and likelihoods.

Classes in org.biojava.bio.dp that implement SymbolList

Modifier and Type	Class and Description
class	SimpleStatePath A no-frills implementation of StatePath.

Methods in org.biojava.bio.dp that return SymbolList

Modifier and Type	Method and Description
SymbolList	SimpleStatePath.subList(int start, int end)
SymbolList	SimpleStatePath.symbolListForLabel(String label)
SymbolList[]	DPMatrix.symList()

Methods in org.biojava.bio.dp that return types with arguments of type SymbolList

Modifier and Type	Method and Description
Iterator<SymbolList>	SimpleStatePath.symbolListIterator()

Methods in org.biojava.bio.dp with parameters of type SymbolList

Modifier and Type	Method and Description
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)
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)
DPMatrix	DP.forwardsBackwards(SymbolList[] symList, ScoreType scoreType)
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.
protected double	BaumWelchTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
protected double	BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
protected abstract double	AbstractTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)
protected double	BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList, ScoreType scoreType)
abstract StatePath	DP.viterbi(SymbolList[] symList, ScoreType scoreType)

Constructors in org.biojava.bio.dp with parameters of type SymbolList

Constructor and Description
DP.ReverseIterator(SymbolList sym)
SimpleStatePath(double score, SymbolList sequence, SymbolList states, SymbolList scores)

Uses of SymbolList in org.biojava.bio.dp.onehead

Fields in org.biojava.bio.dp.onehead declared as SymbolList

Modifier and Type	Field and Description
protected SymbolList[]	SingleDPMatrix.symList

Methods in org.biojava.bio.dp.onehead that return SymbolList

Modifier and Type	Method and Description
SymbolList	SmallCursor.symList()
SymbolList[]	SingleDPMatrix.symList()
SymbolList	DPCursor.symList() The symbol list being looped over.

Methods in org.biojava.bio.dp.onehead with parameters of type SymbolList

Modifier and Type	Method and Description
double	SingleDP.backward(SymbolList[] seq, ScoreType scoreType)
DPMatrix	SingleDP.backwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)
DPMatrix	SingleDP.backwardMatrix(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, ScoreType scoreType)
StatePath	SingleDP.viterbi(SymbolList[] symList, ScoreType scoreType)

Constructors in org.biojava.bio.dp.onehead with parameters of type SymbolList

Constructor and Description
SingleDPMatrix(DP dp, SymbolList symList)
SmallCursor(State[] states, SymbolList symList, Iterator symIterator)

Uses of SymbolList in org.biojava.bio.dp.twohead

Fields in org.biojava.bio.dp.twohead declared as SymbolList

Modifier and Type	Field and Description
protected SymbolList[]	AbstractMatrixPairDPCursor.seqs

Methods in org.biojava.bio.dp.twohead that return SymbolList

Modifier and Type	Method and Description
SymbolList[]	PairDPMatrix.symList()

Methods in org.biojava.bio.dp.twohead with parameters of type SymbolList

Modifier and Type	Method and Description
double	PairwiseDP.backward(SymbolList[] seqs, ScoreType scoreType)
DPMatrix	PairwiseDP.backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
DPMatrix	PairwiseDP.backwardMatrix(SymbolList[] seqs, ScoreType scoreType)
double	PairwiseDP.forward(SymbolList[] seqs, ScoreType scoreType)
DPMatrix	PairwiseDP.forwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)
DPMatrix	PairwiseDP.forwardMatrix(SymbolList[] seqs, ScoreType scoreType)
StatePath	PairwiseDP.viterbi(SymbolList[] seqs, ScoreType scoreType)

Constructors in org.biojava.bio.dp.twohead with parameters of type SymbolList

Constructor and Description
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)
PairDPMatrix(DP dp, SymbolList seq0, SymbolList seq1)

Uses of SymbolList in org.biojava.bio.gui.sequence

Methods in org.biojava.bio.gui.sequence that return SymbolList

Modifier and Type	Method and Description
SymbolList	SubPairwiseRenderContext.getSecondarySymbols()
SymbolList	PairwiseSequencePanel.getSecondarySymbols() getSecondarySymbols returns all of the Symbols belonging to the currently rendered secondary Sequence.
SymbolList	PairwiseRenderContext.getSecondarySymbols() getSecondarySymbols returns the symbols of the secondary sequence.
SymbolList	TranslatedSequencePanel.getSequence() getSequence returns the entire Sequence currently being rendered.
SymbolList	SequencePanel.getSequence()
SymbolList	CircularRendererPanel.getSequence()
SymbolList	TranslatedSequencePanel.getSymbols() getSymbols returns all of the Symbols belonging to the currently rendered Sequence.
SymbolList	SubSequenceRenderContext.getSymbols()
SymbolList	SubPairwiseRenderContext.getSymbols()
SymbolList	SubCircularRendererContext.getSymbols()
SymbolList	SequenceRenderContext.getSymbols() The SymbolList that is currently rendered by this SequenceRenderContext.
SymbolList	SequencePoster.getSymbols() Deprecated. Retrieve the currently rendered SymbolList
SymbolList	SequencePanel.getSymbols() Retrieve the currently rendered SymbolList
SymbolList	PairwiseSequencePanel.getSymbols() getSymbols returns all of the Symbols belonging to the currently rendered Sequence.
SymbolList	HeadlessRenderContext.getSymbols()
SymbolList	CircularRendererContext.getSymbols() The SymbolList that is currently rendered by this context.

Methods in org.biojava.bio.gui.sequence with parameters of type SymbolList

Modifier and Type	Method and Description
void	TranslatedSequencePanel.setSequence(SymbolList sequence) setSequence sets the Sequence to be rendered.
void	SequencePanel.setSequence(SymbolList s) Set the SymboList to be rendered.
void	CircularRendererPanel.setSequence(SymbolList symList)

Constructors in org.biojava.bio.gui.sequence with parameters of type SymbolList

Constructor and Description
SubCircularRendererContext(CircularRendererContext delegate, SymbolList symbols, FeatureHolder features, double radius) Create a new sub context.
SubPairwiseRenderContext(PairwiseRenderContext context, SymbolList symbols, SymbolList secondarySymbols, FeatureHolder features, FeatureHolder secondaryFeatures, RangeLocation range, RangeLocation secondaryRange) Creates a new SubPairwiseRenderContext.
SubSequenceRenderContext(SequenceRenderContext src, SymbolList symbols, FeatureHolder features, RangeLocation range)
SubSequenceRenderContext(SequenceRenderContext src, SymbolList symbols, FeatureHolder features, RangeLocation range, int symOffset)

Uses of SymbolList in org.biojava.bio.molbio

Fields in org.biojava.bio.molbio declared as SymbolList

Modifier and Type	Field and Description
protected SymbolList	RestrictionEnzyme.site

Methods in org.biojava.bio.molbio that return SymbolList

Modifier and Type	Method and Description
SymbolList	RestrictionEnzyme.getRecognitionSite() getRecognitionSite returns the forward strand of the recognition site.

Methods in org.biojava.bio.molbio with parameters of type SymbolList

Modifier and Type	Method and Description
void	Composition.setSymbolList(SymbolList symbolList) Set the SymbolList to calculation the composition of.

Constructors in org.biojava.bio.molbio with parameters of type SymbolList

Constructor and Description
RestrictionEnzyme(String name, SymbolList site, int dsForward, int dsReverse) Creates a new RestrictionEnzyme which cuts within or downstream of the recognition site.
RestrictionEnzyme(String name, SymbolList site, int usForward, int usReverse, int dsForward, int dsReverse) Creates a new RestrictionEnzyme of the unusual type which cuts both upstream and downstream of its recognition site.

Uses of SymbolList in org.biojava.bio.program.abi

Methods in org.biojava.bio.program.abi that return SymbolList

Modifier and Type	Method and Description
SymbolList	ABITrace.getSequence() Returns the original programatically determined (unedited) sequence as a SymbolList.

Methods in org.biojava.bio.program.abi with parameters of type SymbolList

Modifier and Type	Method and Description
static Alignment	ABITools.getAlignment(SymbolList abiSeq) View a symbol list over the QUALITY alphabet as an alignment.

Uses of SymbolList in org.biojava.bio.program.fastq

Methods in org.biojava.bio.program.fastq that return SymbolList

Modifier and Type	Method and Description
static SymbolList	FastqTools.createDNA(Fastq fastq) Create and return a new DNA SymbolList from the specified FASTQ formatted sequence.
static SymbolList	FastqTools.createQualityScores(Fastq fastq) Create and return a new SymbolList of quality scores from the specified FASTQ formatted sequence.

Uses of SymbolList in org.biojava.bio.program.phred

Classes in org.biojava.bio.program.phred that implement SymbolList

Modifier and Type	Class and Description
class	PhredSequence PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores.

Methods in org.biojava.bio.program.phred that return SymbolList

Modifier and Type	Method and Description
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.
SymbolList	PhredSequence.getDNA() Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolList
SymbolList	Qualitative.getQuality() Retreives the list of quality symbols from the underlying object.
SymbolList	PhredSequence.getQuality() Extracts the quality part if the Phred Alphabet and returns it as a SymbolList over the Integer SubAlphabet from 0..99.

Methods in org.biojava.bio.program.phred with parameters of type SymbolList

Modifier and Type	Method and Description
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.

Constructors in org.biojava.bio.program.phred with parameters of type SymbolList

Constructor and Description
PhredSequence(SymbolList phredSequence, String name, String urn, Annotation anno) Constructs a new PhredSequence.

Uses of SymbolList in org.biojava.bio.program.scf

Methods in org.biojava.bio.program.scf that return SymbolList

Modifier and Type	Method and Description
protected SymbolList	SCF.reverseComplementBaseCallList(String label) Overrides AbstractChromatogram.reverseComplementBaseCallList(java.lang.Object) to support the 7 quality values from the SCF.

Uses of SymbolList in org.biojava.bio.program.ssaha

Methods in org.biojava.bio.program.ssaha with parameters of type SymbolList

Modifier and Type	Method and Description
void	DataStore.search(String id, SymbolList symList, SearchListener listener) Search the DataStore with a symbol list.
void	CompactedDataStore.search(String seqID, SymbolList symList, SearchListener listener)

Uses of SymbolList in org.biojava.bio.proteomics

Methods in org.biojava.bio.proteomics that return SymbolList

Modifier and Type	Method and Description
SymbolList	Protease.getCleaveageResidues() The list of residues that the protease will cleave at.
SymbolList	Protease.getNotCleaveResidues() The list of residues that will prevent cleavage if they follow the cleavage residue.

Methods in org.biojava.bio.proteomics with parameters of type SymbolList

Modifier and Type	Method and Description
static Protease	ProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, String name)
static Protease	ProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, String name) Creates and registers a new Protease.
static double	IsoelectricPointCalc.getIsoelectricPoint(SymbolList peptide) Static public method to compute the pI for a polypeptide in denaturating and reduced conditions with both free ends.
double	MassCalc.getMass(SymbolList proteinSeq) Get the Mass of this peptide.
static double	MassCalc.getMass(SymbolList proteinSeq, String isotopicType, boolean MH_PLUS) getMass calculates the mass of this peptide.
static double	MassCalc.getMolecularWeight(SymbolList proteinSeq) Calculate the molecular weight of a protein, making estimates whenever it is possible like averaging mass values for ambiguity symbols or counting zero when gaps are encountered.
double	IsoelectricPointCalc.getPI(SymbolList peptide, boolean hasFreeNTerm, boolean hasFreeCTerm) Computes isoelectric point of specified peptide.
double[]	MassCalc.getVariableMasses(SymbolList peptide) Get all masses including the variable mass.

Constructors in org.biojava.bio.proteomics with parameters of type SymbolList

Constructor and Description
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, String name)

Uses of SymbolList in org.biojava.bio.search

Methods in org.biojava.bio.search that return SymbolList

Modifier and Type	Method and Description
SymbolList	MaxMismatchPattern.getPattern()
SymbolList	KnuthMorrisPrattSearch.getPattern()
SymbolList	MaxMismatchMatcher.group()
SymbolList	BioMatcher.group() Get the matching region as a SymbolList.

Methods in org.biojava.bio.search with parameters of type SymbolList

Modifier and Type	Method and Description
int[]	KnuthMorrisPrattSearch.findMatches(SymbolList text) This will return an int[] giving the offsets of the matches in text (ie the location of the first symbol of each match in the text).
BioMatcher	SeqContentPattern.matcher(SymbolList symList)
BioMatcher	MaxMismatchPattern.matcher(SymbolList symList)
BioMatcher	BioPattern.matcher(SymbolList symList) Get a matcher that will use these parameters to search a SymbolList.
SeqSimilaritySearchResult	SeqSimilaritySearcher.search(SymbolList querySeq, SequenceDB db, Map searchParameters) Using this sequence similarity searcher, search with the given sequence against the given sequence database.
void	MaxMismatchPattern.setPattern(SymbolList pattern)

Constructors in org.biojava.bio.search with parameters of type SymbolList

Constructor and Description
KnuthMorrisPrattSearch(SymbolList pattern) Constructs a KMP matcher to find exact occurances of pattern in text using the Knuth-Morris-Pratt algorithm.
MaxMismatchPattern(SymbolList pattern, int mismatches)

Uses of SymbolList in org.biojava.bio.seq

Subinterfaces of SymbolList in org.biojava.bio.seq

Modifier and Type	Interface and Description
interface	GappedSequence Extension of GappedSymbolList which also projects features into the gapped coordinate system.
interface	Sequence A biological sequence.

Classes in org.biojava.bio.seq that implement SymbolList

Modifier and Type	Class and Description
class	CircularView A circular view onto another Sequence object.
class	NewSimpleAssembly A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
class	SimpleAssembly A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.

Methods in org.biojava.bio.seq that return SymbolList

Modifier and Type	Method and Description
static SymbolList	RNATools.complement(SymbolList list) Retrieve a complement view of list.
static SymbolList	NucleotideTools.complement(SymbolList list) Retrieve a complement view of list.
static SymbolList	DNATools.complement(SymbolList list) Retrieve a complement view of list.
static SymbolList	DNATools.createDNA(String dna) Return a new DNA SymbolList for dna.
static SymbolList	NucleotideTools.createNucleotide(String nucleotide) Return a new Nucleotide SymbolList for nucleotide.
static SymbolList	ProteinTools.createProtein(String theProtein) Return a new Protein SymbolList for protein.
static SymbolList	RNATools.createRNA(String rna) Return a new RNA SymbolList for rna.
static SymbolList	DNATools.flip(SymbolList list, StrandedFeature.Strand strand) Returns a SymbolList that is reverse complemented if the strand is negative, and the origninal one if it is not.
SymbolList	StrandedFeature.getSymbols() Return a list of symbols that are contained in this feature.
SymbolList	Feature.getSymbols() Return a list of symbols that are contained in this feature.
static SymbolList	RNATools.reverseComplement(SymbolList list) Retrieve a reverse-complement view of list.
static SymbolList	NucleotideTools.reverseComplement(SymbolList list) Retrieve a reverse-complement view of list.
static SymbolList	DNATools.reverseComplement(SymbolList list) Retrieve a reverse-complement view of list.
SymbolList	SimpleAssembly.subList(int start, int end)
SymbolList	NewSimpleAssembly.subList(int start, int end)
SymbolList	CircularView.subList(int start, int end) Over rides ViewSequence.
static SymbolList	DNATools.toProtein(SymbolList syms) Convenience method that directly converts a DNA sequence to RNA then to protein.
static SymbolList	DNATools.toProtein(SymbolList syms, int start, int end) Convenience method to translate a region of a DNA sequence directly into protein.
static SymbolList	DNATools.toRNA(SymbolList syms) Converts a SymbolList from the DNA Alphabet to the RNA Alphabet.
static SymbolList	RNATools.transcribe(SymbolList list) Deprecated. The naming of this method is confusing and inconsistent use either DNATools.toRNA(SymbolList list) or DNATools.transcribeToRNA(SymbolList list) depending on the desired behaivour.
static SymbolList	GeneticCodes.transcribe(SymbolList theList) Transcribe DNA into RNA.
static SymbolList	DNATools.transcribeToRNA(SymbolList syms) Transcribes DNA to RNA.
static SymbolList	RNATools.translate(SymbolList syms) Translate RNA into protein (with termination symbols).
static SymbolList	GeneticCodes.translate(SymbolList theList) Translate RNA into protein (with termination symbols).

Methods in org.biojava.bio.seq with parameters of type SymbolList

Modifier and Type	Method and Description
static SymbolList	RNATools.complement(SymbolList list) Retrieve a complement view of list.
static SymbolList	NucleotideTools.complement(SymbolList list) Retrieve a complement view of list.
static SymbolList	DNATools.complement(SymbolList list) Retrieve a complement view of list.
static Sequence	SequenceTools.createSequence(SymbolList syms, String uri, String name, Annotation ann)
Sequence	SequenceFactory.createSequence(SymbolList symList, String uri, String name, Annotation annotation) Deprecated. Creates a sequence using these parameters.
static SymbolList	DNATools.flip(SymbolList list, StrandedFeature.Strand strand) Returns a SymbolList that is reverse complemented if the strand is negative, and the origninal one if it is not.
static SymbolList	RNATools.reverseComplement(SymbolList list) Retrieve a reverse-complement view of list.
static SymbolList	NucleotideTools.reverseComplement(SymbolList list) Retrieve a reverse-complement view of list.
static SymbolList	DNATools.reverseComplement(SymbolList list) Retrieve a reverse-complement view of list.
static SymbolList	DNATools.toProtein(SymbolList syms) Convenience method that directly converts a DNA sequence to RNA then to protein.
static SymbolList	DNATools.toProtein(SymbolList syms, int start, int end) Convenience method to translate a region of a DNA sequence directly into protein.
static SymbolList	DNATools.toRNA(SymbolList syms) Converts a SymbolList from the DNA Alphabet to the RNA Alphabet.
static SymbolList	RNATools.transcribe(SymbolList list) Deprecated. The naming of this method is confusing and inconsistent use either DNATools.toRNA(SymbolList list) or DNATools.transcribeToRNA(SymbolList list) depending on the desired behaivour.
static SymbolList	GeneticCodes.transcribe(SymbolList theList) Transcribe DNA into RNA.
static SymbolList	DNATools.transcribeToRNA(SymbolList syms) Transcribes DNA to RNA.
static SymbolList	RNATools.translate(SymbolList syms) Translate RNA into protein (with termination symbols).
static SymbolList	GeneticCodes.translate(SymbolList theList) Translate RNA into protein (with termination symbols).

Uses of SymbolList in org.biojava.bio.seq.homol

Classes in org.biojava.bio.seq.homol that implement SymbolList

Modifier and Type	Class and Description
static class	SimilarityPairFeature.EmptyPairwiseAlignment EmptyPairwiseAlignment empty pairwise alignment which has labels to empty symbol lists.

Methods in org.biojava.bio.seq.homol that return SymbolList

Modifier and Type	Method and Description
SymbolList	SimilarityPairFeature.EmptyPairwiseAlignment.subList(int index1, int index2)
SymbolList	SimilarityPairFeature.EmptyPairwiseAlignment.symbolListForLabel(String label)

Methods in org.biojava.bio.seq.homol that return types with arguments of type SymbolList

Modifier and Type	Method and Description
Iterator<SymbolList>	SimilarityPairFeature.EmptyPairwiseAlignment.symbolListIterator()

Uses of SymbolList in org.biojava.bio.seq.impl

Classes in org.biojava.bio.seq.impl that implement SymbolList

Modifier and Type	Class and Description
class	AssembledSymbolList Support class for applications which need to patch together sections of sequence into a single SymbolList.
class	DummySequence A Sequence implementation that has a name and URI but no features, and a zero length symbol list.
class	NewAssembledSymbolList Support class for applications which need to patch together sections of sequence into a single SymbolList.
class	RevCompSequence A reverse complement view onto Sequence interface.
class	SimpleGappedSequence Simple implementation of GappedSequence.
class	SimpleSequence A basic implementation of the Sequence interface.
class	SubSequence View a sub-section of a given sequence object, including all the features intersecting that region.
class	ViewSequence A view onto another Sequence object.

Methods in org.biojava.bio.seq.impl that return SymbolList

Modifier and Type	Method and Description
SymbolList	SimpleStrandedFeature.getSymbols()
SymbolList	SimpleFeature.getSymbols()
SymbolList	ViewSequence.subList(int start, int end)
SymbolList	SubSequence.subList(int start, int end)
SymbolList	SimpleSequence.subList(int start, int end)
SymbolList	NewAssembledSymbolList.subList(int start, int end)
SymbolList	DummySequence.subList(int start, int end)
SymbolList	AssembledSymbolList.subList(int start, int end)

Methods in org.biojava.bio.seq.impl with parameters of type SymbolList

Modifier and Type	Method and Description
Sequence	SimpleSequenceFactory.createSequence(SymbolList symList, String uri, String name, Annotation annotation)
void	AssembledSymbolList.putComponent(Location l, SymbolList sl)

Constructors in org.biojava.bio.seq.impl with parameters of type SymbolList

Constructor and Description
SimpleSequence(SymbolList sym, String urn, String name, Annotation annotation) Create a SimpleSequence with the symbols and alphabet of sym, and the sequence properties listed.
SimpleSequence(SymbolList sym, String urn, String name, Annotation annotation, FeatureRealizer realizer) Create a SimpleSequence using a specified FeatureRealizer.

Uses of SymbolList in org.biojava.bio.seq.io

Methods in org.biojava.bio.seq.io that return SymbolList

Modifier and Type	Method and Description
SymbolList	ChunkedSymbolListFactory.make(SymbolReader sr) Method to create a Sequence with a SymbolReader.
SymbolList	ChunkedSymbolListFactory.makeSymbolList() Converts accumulated Symbols to a SymbolList

Methods in org.biojava.bio.seq.io with parameters of type SymbolList

Modifier and Type	Method and Description
String	WordTokenization.tokenizeSymbolList(SymbolList sl)
String	SymbolTokenization.tokenizeSymbolList(SymbolList symList) Return a string representation of a list of symbols.
String	CharacterTokenization.tokenizeSymbolList(SymbolList sl)
String	AlternateTokenization.tokenizeSymbolList(SymbolList sl)

Constructors in org.biojava.bio.seq.io with parameters of type SymbolList

Constructor and Description
SymbolListCharSequence(SymbolList syms) Creates a new SymbolListCharSequence wrapping a SymbolList.

Uses of SymbolList in org.biojava.bio.seq.projection

Methods in org.biojava.bio.seq.projection that return SymbolList

Modifier and Type	Method and Description
SymbolList	ProjectedFeature.getSymbols()

Uses of SymbolList in org.biojava.bio.symbol

Subinterfaces of SymbolList in org.biojava.bio.symbol

Modifier and Type	Interface and Description
interface	GappedSymbolList This extends SymbolList with API for manipulating, inserting and deleting gaps.

Classes in org.biojava.bio.symbol that implement SymbolList

Modifier and Type	Class and Description
class	AbstractSymbolList Abstract helper implementation of the SymbolList core interface.
class	ChunkedSymbolList SymbolList implementation using constant-size chunks.
class	DummySymbolList Symbol list which just consists of non-informative symbols.
class	PackedSymbolList A SymbolList that stores symbols as bit-patterns in an array of longs.
class	RelabeledAlignment An alignment that relabels another alignment.
class	SimpleGappedSymbolList This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.
class	SimpleSymbolList Basic implementation of SymbolList.

Fields in org.biojava.bio.symbol declared as SymbolList

Modifier and Type	Field and Description
static SymbolList	SymbolList.EMPTY_LIST A useful object that represents an empty symbol list, to avoid returning null.
SymbolList	Edit.replacement

Methods in org.biojava.bio.symbol that return SymbolList

Modifier and Type	Method and Description
static SymbolList	SymbolListViews.emptyList(Alphabet alpha) Get a new immutable, empty symbol list with the given alphabet.
static SymbolList	DoubleAlphabet.fromArray(double[] dArray) Retrieve a SymbolList view of an array of doubles.
static SymbolList	IntegerAlphabet.fromArray(int[] iArray) Retrieve a SymbolList view of an array of integers.
SymbolList	SimpleGappedSymbolList.getSourceSymbolList()
SymbolList	GappedSymbolList.getSourceSymbolList() Return the underlying (ungapped) SymbolList.
SymbolList	SymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa) makes a SymbolList containing size Symbols from a Symbol array.
SymbolList	SimpleSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa) Create a factory for SimpleSymbolLists.
SymbolList	PackedSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa) Makes a packed SymbolList out of a list of Symbols.
static SymbolList	SymbolListViews.orderNSymbolList(SymbolList source, int order) An n-th order view of another SymbolList.
static SymbolList	SymbolListViews.reverse(SymbolList symbols) A reversed view onto a SymbolList.
SymbolList	SymbolList.subList(int start, int end) Return a new SymbolList for the symbols start to end inclusive.
SymbolList	SimpleSymbolList.subList(int start, int end) create a subList of the original, this will be a view until either the original symbolList or the sublist is edited
SymbolList	RelabeledAlignment.subList(int min, int max)
SymbolList	ChunkedSymbolList.subList(int start, int end)
SymbolList	AbstractSymbolList.subList(int start, int end)
static SymbolList	SymbolListViews.subList(SymbolList parent, int start, int end) View a portion of a SymbolList.
SymbolList	RelabeledAlignment.symbolListForLabel(String label)
SymbolList	Location.symbols(SymbolList seq) Return the symbols in a sequence that fall within this range.
SymbolList	FuzzyPointLocation.symbols(SymbolList slist)
SymbolList	CircularLocation.symbols(SymbolList seq)
SymbolList	AbstractRangeLocation.symbols(SymbolList seq)
SymbolList	AbstractLocationDecorator.symbols(SymbolList seq)
static SymbolList	SymbolListViews.translate(SymbolList symbols, TranslationTable table) Provides a 'translated' view of an underlying SymbolList.
static SymbolList	SymbolListViews.windowedSymbolList(SymbolList source, int wsize) A view of windows onto another SymbolList.

Methods in org.biojava.bio.symbol with parameters of type SymbolList

Modifier and Type	Method and Description
void	UkkonenSuffixTree.addSymbolList(SymbolList list, 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 Alignment	SymbolListViews.alignment(List labels, SymbolList symList) View a SymbolList over a cross-product Alphabet as an Alignment.
static String	MotifTools.createRegex(SymbolList motif) createRegex creates a regular expression which matches the SymbolList.
static int	PackingFactory.nextWord(SymbolList symList, int word, int offset, int wordLength, Packing packing)
static SymbolList	SymbolListViews.orderNSymbolList(SymbolList source, int order) An n-th order view of another SymbolList.
static int	PackingFactory.primeWord(SymbolList symList, int wordLength, Packing packing)
static SymbolList	SymbolListViews.reverse(SymbolList symbols) A reversed view onto a SymbolList.
static SymbolList	SymbolListViews.subList(SymbolList parent, int start, int end) View a portion of a SymbolList.
SymbolList	Location.symbols(SymbolList seq) Return the symbols in a sequence that fall within this range.
SymbolList	FuzzyPointLocation.symbols(SymbolList slist)
SymbolList	CircularLocation.symbols(SymbolList seq)
SymbolList	AbstractRangeLocation.symbols(SymbolList seq)
SymbolList	AbstractLocationDecorator.symbols(SymbolList seq)
String	SoftMaskedAlphabet.CaseSensitiveTokenization.tokenizeSymbolList(SymbolList sl)
static SymbolList	SymbolListViews.translate(SymbolList symbols, TranslationTable table) Provides a 'translated' view of an underlying SymbolList.
static SymbolList	SymbolListViews.windowedSymbolList(SymbolList source, int wsize) A view of windows onto another SymbolList.

Constructors in org.biojava.bio.symbol with parameters of type SymbolList

Constructor and Description
ChunkedSymbolList(SymbolList[] chunks, int chunkSize, int length, Alphabet alpha)
Edit(int pos, int length, SymbolList replacement) Create a new Edit.
PackedSymbolList(Packing packing, SymbolList symList) Create a new PackedSymbolList as a packed copy of another symbol list.
SimpleGappedSymbolList(SymbolList source) Create a new SimpleGappedSymbolList that will view source.
SimpleSymbolList(SymbolList sl) Construct a copy of an existing SymbolList.

Uses of SymbolList in org.biojava.utils.automata

Methods in org.biojava.utils.automata with parameters of type SymbolList

Modifier and Type	Method and Description
void	PatternBlitz.search(SymbolList sl)

Uses of SymbolList in org.biojava.utils.regex

Methods in org.biojava.utils.regex that return SymbolList

Modifier and Type	Method and Description
SymbolList	Matcher.group() Returns the input subsequence matched by the previous match.
SymbolList	Matcher.group(int group) Returns the input subsequence captured by the given group during the previous match operation.

Methods in org.biojava.utils.regex with parameters of type SymbolList

Modifier and Type	Method and Description
Matcher	Pattern.matcher(SymbolList sl) Creates a matcher that will match the given input against this pattern.
boolean	Search.Listener.reportMatch(SymbolList seq, Pattern pattern, int start, int end)
Matcher	Matcher.reset(SymbolList sl) Resets this matcher with a new input SymbolList.
void	Search.search(SymbolList seq) search the Sequence with the patterns already registered with this object.
void	Search.search(SymbolList seq, int loLimit, int hiLimit) search part of the SymbolList with the patterns already registered with this object.

Uses of SymbolList in org.biojavax

Methods in org.biojavax that return SymbolList

Modifier and Type	Method and Description
SymbolList	DummyCrossReferenceResolver.getRemoteSymbolList(CrossRef cr, Alphabet a) Given a cross reference, return the corresponding symbol list.
SymbolList	CrossReferenceResolver.getRemoteSymbolList(CrossRef cr, Alphabet a) Given a cross reference, return the corresponding symbol list.

Uses of SymbolList in org.biojavax.bio.db.biosql

Methods in org.biojavax.bio.db.biosql that return SymbolList

Modifier and Type	Method and Description
SymbolList	BioSQLCrossReferenceResolver.getRemoteSymbolList(CrossRef cr, Alphabet a) Given a cross reference, return the corresponding symbol list.
SymbolList	BioSQLRichSequenceHandler.subList(RichSequence seq, int start, int end) Return a new SymbolList for the symbols start to end inclusive.

Uses of SymbolList in org.biojavax.bio.seq

Subinterfaces of SymbolList in org.biojavax.bio.seq

Modifier and Type	Interface and Description
interface	RichSequence A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.

Classes in org.biojavax.bio.seq that implement SymbolList

Modifier and Type	Class and Description
class	InfinitelyAmbiguousSymbolList A symbol list that is Integer.MAX_VALUElong, never gives index out of bounds and always returns ambiguity symbols for everything.
class	SimpleRichSequence A simple implementation of RichSequence.
class	ThinRichSequence A simple implementation of RichSequence.

Methods in org.biojavax.bio.seq that return SymbolList

Modifier and Type	Method and Description
SymbolList	ThinRichSequence.getInternalSymbolList() A special function that returns the SymbolList that this RichSequence is based around.
SymbolList	SimpleRichSequence.getInternalSymbolList() A special function that returns the SymbolList that this RichSequence is based around.
SymbolList	RichSequence.getInternalSymbolList() A special function that returns the SymbolList that this RichSequence is based around.
SymbolList	SimpleRichFeature.getSymbols() Return a list of symbols that are contained in this feature.
SymbolList	ThinRichSequence.subList(int start, int end) Return a new SymbolList for the symbols start to end inclusive.
SymbolList	InfinitelyAmbiguousSymbolList.subList(int start, int end) Return a new SymbolList for the symbols start to end inclusive.
SymbolList	RichSequenceHandler.subList(RichSequence seq, int start, int end) Return a new SymbolList for the symbols start to end inclusive.
SymbolList	DummyRichSequenceHandler.subList(RichSequence seq, int start, int end) Return a new SymbolList for the symbols start to end inclusive.
SymbolList	SimpleRichLocation.symbols(SymbolList seq) Return the symbols in a sequence that fall within this range.
SymbolList	EmptyRichLocation.symbols(SymbolList seq) Return the symbols in a sequence that fall within this range.
SymbolList	CompoundRichLocation.symbols(SymbolList seq) Return the symbols in a sequence that fall within this range.

Methods in org.biojavax.bio.seq with parameters of type SymbolList

Modifier and Type	Method and Description
static RichSequence	RichSequence.Tools.createRichSequence(Namespace ns, String name, SymbolList syms) Create a new RichSequence in the specified namespace.
static RichSequence	RichSequence.Tools.createRichSequence(String name, SymbolList syms) Create a new RichSequence in the default namespace.
SymbolList	SimpleRichLocation.symbols(SymbolList seq) Return the symbols in a sequence that fall within this range.
SymbolList	EmptyRichLocation.symbols(SymbolList seq) Return the symbols in a sequence that fall within this range.
SymbolList	CompoundRichLocation.symbols(SymbolList seq) Return the symbols in a sequence that fall within this range.

Constructors in org.biojavax.bio.seq with parameters of type SymbolList

Constructor and Description
SimpleRichSequence(Namespace ns, String name, String accession, int version, SymbolList symList, Double seqversion) Creates a new instance of SimpleRichSequence.

Uses of SymbolList in org.biojavax.ga

Methods in org.biojavax.ga that return SymbolList

Modifier and Type	Method and Description
SymbolList[]	Organism.getChromosomes() Gets the organisms 'chromosome' sequences

Methods in org.biojavax.ga with parameters of type SymbolList

Modifier and Type	Method and Description
void	Organism.setChromosomes(SymbolList[] chromosomes) Sets the organisms 'chromosome' sequences.

Uses of SymbolList in org.biojavax.ga.functions

Methods in org.biojavax.ga.functions that return SymbolList

Modifier and Type	Method and Description
SymbolList[]	SimpleGACrossResult.getChromosomes()
SymbolList[]	GACrossResult.getChromosomes() Gets the chromosomes after the cross
SymbolList[]	GACross.getChromosomes() Gets the chromosomes after the cross
SymbolList	SwapMutationFunction.mutate(SymbolList seq)
SymbolList	SimpleMutationFunction.mutate(SymbolList seq)
SymbolList	MutationFunction.mutate(SymbolList seq) Produces a new SymbolList by mutation.
SymbolList	MutationFunction.NoMutation.mutate(SymbolList syml)

Methods in org.biojavax.ga.functions with parameters of type SymbolList

Modifier and Type	Method and Description
SymbolList	SwapMutationFunction.mutate(SymbolList seq)
SymbolList	SimpleMutationFunction.mutate(SymbolList seq)
SymbolList	MutationFunction.mutate(SymbolList seq) Produces a new SymbolList by mutation.
SymbolList	MutationFunction.NoMutation.mutate(SymbolList syml)
GACrossResult	SimpleCrossOverFunction.performCrossOver(SymbolList chromA, SymbolList chromB)
GACrossResult	OrderCrossover.performCrossOver(SymbolList chromA, SymbolList chromB)
GACrossResult	CrossOverFunction.performCrossOver(SymbolList chromA, SymbolList chromB) Performs a cross between the pair of chromosomes
GACrossResult	CrossOverFunction.NoCross.performCrossOver(SymbolList chromA, SymbolList chromB)

Constructors in org.biojavax.ga.functions with parameters of type SymbolList

Constructor and Description
SimpleGACrossResult(PointLocation[] crossOverPositions, SymbolList[] chromosomes)

Uses of SymbolList in org.biojavax.ga.impl

Fields in org.biojavax.ga.impl declared as SymbolList

Modifier and Type	Field and Description
protected SymbolList[]	AbstractOrganism.chromosomes

Methods in org.biojavax.ga.impl that return SymbolList

Modifier and Type	Method and Description
SymbolList[]	AbstractOrganism.getChromosomes()

Methods in org.biojavax.ga.impl with parameters of type SymbolList

Modifier and Type	Method and Description
protected void	SimpleOrganism.setChromImpl(SymbolList[] chromosomes)
protected abstract void	AbstractOrganism.setChromImpl(SymbolList[] chromosomes)
void	AbstractOrganism.setChromosomes(SymbolList[] chromosomes)

Uses of SymbolList in org.biojavax.ga.util

Methods in org.biojavax.ga.util that return SymbolList

Modifier and Type	Method and Description
static SymbolList	GATools.createBinary(String binarySequence) Creates a SymbolList in the GABinary Alphabet