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

Packages that use SymbolList
org.biojava.bio.alignment: Implementation of the `Alignment` interface.
org.biojava.bio.chromatogram: Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
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.das: Development client for the Distributed Annotation System.
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 into alternate coordinate systems.
org.biojava.bio.seq.ragbag: The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code.
org.biojava.bio.symbol: Representation of the Symbols that make up a sequence, and locations within them.

Uses of SymbolList in org.biojava.bio.alignment

Subinterfaces of SymbolList in org.biojava.bio.alignment
`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
`class` `AbstractULAlignment`
`class` `AbstractULAlignment.SubULAlignment`
`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.

Fields in org.biojava.bio.alignment declared as SymbolList
`protected SymbolList` `SimpleAlignmentElement.seq`

Methods in org.biojava.bio.alignment that return SymbolList
`SymbolList` `SimpleAlignmentElement.getSymbolList()`
`SymbolList` `AbstractULAlignment.SubULAlignment.symbolListForLabel(java.lang.Object label)`
`SymbolList` `AlignmentElement.getSymbolList()`
`SymbolList` `FlexibleAlignment.symbolListForLabel(java.lang.Object label)`

Methods in org.biojava.bio.alignment with parameters of type SymbolList
`protected boolean` `FlexibleAlignment.allGaps(SymbolList seq, int start, int end)` make sure that all Symbols in this range are gaps

Constructors in org.biojava.bio.alignment with parameters of type SymbolList
`SimpleAlignmentElement(java.lang.Object label, SymbolList seq, Location loc)`

Uses of SymbolList in org.biojava.bio.chromatogram

Methods in org.biojava.bio.chromatogram that return SymbolList
`protected SymbolList` `AbstractChromatogram.reverseComplementBaseCallList(java.lang.Object label)` Return a symbol list containing the reverse complement of the base call data for the given label.
`protected SymbolList` `AbstractChromatogram.createImmutableSymbolList(Alphabet alpha, java.util.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.

Methods in org.biojava.bio.chromatogram with parameters of type SymbolList
`void` `SimpleChromatogram.setSymbolLists(SymbolList dna, SymbolList offsets)` Set the DNA and OFFSETS symbol lists for the basecall alignment.
`static int` `ChromatogramTools.getIntFromSymbolList(SymbolList list, int which)` Retrieves, unwraps, and returns an `int` from a SymbolList containing `IntegerAlphabet.IntegerSymbol`s.

Uses of SymbolList in org.biojava.bio.dp

Subinterfaces of SymbolList in org.biojava.bio.dp
`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
`class` `SimpleStatePath` A no-frills implementation of StatePath.

Methods in org.biojava.bio.dp that return SymbolList
`SymbolList[]` `DPMatrix.symList()`
`SymbolList` `SimpleStatePath.symbolListForLabel(java.lang.Object label)`
`SymbolList` `SimpleStatePath.subList(int start, int end)`

Methods in org.biojava.bio.dp with parameters of type SymbolList
`protected double` `BaumWelchTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)`
`protected abstract double` `AbstractTrainer.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)`
`protected double` `BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer, SymbolList symList)`
`static double` `DP.scoreWeightMatrix(WeightMatrix matrix, SymbolList symList, int start)` Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix.
`abstract double` `DP.forward(SymbolList[] symList, ScoreType scoreType)`
`abstract double` `DP.backward(SymbolList[] symList, ScoreType scoreType)`
`abstract DPMatrix` `DP.forwardMatrix(SymbolList[] symList, ScoreType scoreType)`
`abstract DPMatrix` `DP.backwardMatrix(SymbolList[] symList, ScoreType scoreType)`
`abstract DPMatrix` `DP.forwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType)`
`abstract DPMatrix` `DP.backwardMatrix(SymbolList[] symList, DPMatrix matrix, ScoreType scoreType)`
`abstract StatePath` `DP.viterbi(SymbolList[] symList, ScoreType scoreType)`
`DPMatrix` `DP.forwardsBackwards(SymbolList[] symList, ScoreType scoreType)`

Constructors in org.biojava.bio.dp with parameters of type SymbolList
`SimpleStatePath(double score, SymbolList sequence, SymbolList states, SymbolList scores)`
`DP.ReverseIterator(SymbolList sym)`

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

Methods in org.biojava.bio.dp.onehead that return SymbolList
`SymbolList[]` `SingleDPMatrix.symList()`

Methods in org.biojava.bio.dp.onehead with parameters of type SymbolList
`double` `SingleDP.forward(SymbolList[] seq, ScoreType scoreType)`
`double` `SingleDP.backward(SymbolList[] seq, ScoreType scoreType)`
`DPMatrix` `SingleDP.forwardMatrix(SymbolList[] seq, ScoreType scoreType)`
`DPMatrix` `SingleDP.backwardMatrix(SymbolList[] seq, ScoreType scoreType)`
`DPMatrix` `SingleDP.forwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)`
`DPMatrix` `SingleDP.backwardMatrix(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType)`
`StatePath` `SingleDP.viterbi(SymbolList[] symList, ScoreType scoreType)`

Constructors in org.biojava.bio.dp.onehead with parameters of type SymbolList
`SingleDPMatrix(DP dp, SymbolList symList)`

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

Fields in org.biojava.bio.dp.twohead declared as SymbolList
`protected SymbolList[]` `AbstractMatrixPairDPCursor.seqs`

Methods in org.biojava.bio.dp.twohead that return SymbolList
`SymbolList[]` `PairDPMatrix.symList()`

Methods in org.biojava.bio.dp.twohead with parameters of type SymbolList
`double` `PairwiseDP.backward(SymbolList[] seqs, ScoreType scoreType)`
`DPMatrix` `PairwiseDP.backwardMatrix(SymbolList[] seqs, ScoreType scoreType)`
`DPMatrix` `PairwiseDP.backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)`
`double` `PairwiseDP.forward(SymbolList[] seqs, ScoreType scoreType)`
`DPMatrix` `PairwiseDP.forwardMatrix(SymbolList[] seqs, ScoreType scoreType)`
`DPMatrix` `PairwiseDP.forwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType)`
`StatePath` `PairwiseDP.viterbi(SymbolList[] seqs, ScoreType scoreType)`

Constructors in org.biojava.bio.dp.twohead with parameters of type SymbolList
`PairDPMatrix(DP dp, SymbolList seq0, SymbolList seq1)`
`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)`
`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)`

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

Methods in org.biojava.bio.gui.sequence that return SymbolList
`SymbolList` `PairwiseRenderContext.getSecondarySymbols()` `getSecondarySymbols` returns the symbols of the secondary sequence.
`SymbolList` `SubSequenceRenderContext.getSymbols()`
`SymbolList` `SequenceRenderContext.getSymbols()` The SymbolList that is currently rendered by this SequenceRenderContext.
`SymbolList` `HeadlessRenderContext.getSymbols()`
`SymbolList` `TranslatedSequencePanel.getSymbols()` `getSymbols` returns all of the `Symbol`s belonging to the currently rendered `Sequence`.
`SymbolList` `SequencePanel.getSymbols()` Retrieve the currently rendered SymbolList
`SymbolList` `PairwiseSequencePanel.getSymbols()` `getSymbols` returns all of the `Symbol`s belonging to the currently rendered `Sequence`.
`SymbolList` `PairwiseSequencePanel.getSecondarySymbols()` `getSecondarySymbols` returns all of the `Symbol`s belonging to the currently rendered secondary `Sequence`.
`SymbolList` `SequencePoster.getSymbols()` Retrieve the currently rendered SymbolList
`SymbolList` `SubPairwiseRenderContext.getSymbols()`
`SymbolList` `SubPairwiseRenderContext.getSecondarySymbols()`

Constructors in org.biojava.bio.gui.sequence with parameters of type SymbolList
`SubSequenceRenderContext(SequenceRenderContext src, SymbolList symbols, FeatureHolder features, RangeLocation range)`
`SubPairwiseRenderContext(PairwiseRenderContext context, SymbolList symbols, SymbolList secondarySymbols, FeatureHolder features, FeatureHolder secondaryFeatures, RangeLocation range, RangeLocation secondaryRange)` Creates a new `SubPairwiseRenderContext`.

Uses of SymbolList in org.biojava.bio.molbio

Fields in org.biojava.bio.molbio declared as SymbolList
`protected SymbolList` `RestrictionEnzyme.site`

Methods in org.biojava.bio.molbio that return SymbolList
`SymbolList` `RestrictionEnzyme.getRecognitionSite()` `getRecognitionSite` returns the forward strand of the recognition site.

Constructors in org.biojava.bio.molbio with parameters of type SymbolList
`RestrictionEnzyme(java.lang.String name, SymbolList site, int dsForward, int dsReverse)` Creates a new `RestrictionEnzyme` which cuts within or downstream of the recognition site.
`RestrictionEnzyme(java.lang.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
`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
`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.das

Methods in org.biojava.bio.program.das that return SymbolList
`SymbolList` `DASSequence.subList(int start, int end)`
`protected SymbolList` `DASSequence.getSymbols()`

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

Classes in org.biojava.bio.program.phred that implement SymbolList
`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
`SymbolList` `Qualitative.getQuality()` Retreives the list of quality symbols from the underlying object.
`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.getQuality()` Extracts the quality part if the Phred Alphabet and returns it as a SymbolList over the Integer SubAlphabet from 0..99.
`SymbolList` `PhredSequence.getDNA()` Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolList

Methods in org.biojava.bio.program.phred with parameters of type SymbolList
`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
`PhredSequence(SymbolList phredSequence, java.lang.String name, java.lang.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
`protected SymbolList` `SCF.reverseComplementBaseCallList(java.lang.Object 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
`void` `DataStore.search(java.lang.String id, SymbolList symList, SearchListener listener)` Search the DataStore with a symbol list.
`void` `CompactedDataStore.search(java.lang.String seqID, SymbolList symList, SearchListener listener)`

Uses of SymbolList in org.biojava.bio.proteomics

Methods in org.biojava.bio.proteomics that return SymbolList
`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
`double` `IsoelectricPointCalc.getPI(SymbolList peptide, boolean hasFreeNTerm, boolean hasFreeCTerm)` Computes isoelectric point of specified peptide.
`static double` `MassCalc.getMass(SymbolList proteinSeq, java.lang.String isotopicType, boolean MH_PLUS)` `getMass` calculates the mass of this peptide.
`double` `MassCalc.getMass(SymbolList proteinSeq)` Get the Mass of this peptide.
`double[]` `MassCalc.getVariableMasses(SymbolList peptide)` Get all masses including the variable mass.
`static Protease` `ProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, java.lang.String name)` Creates and registers a new Protease.
`static Protease` `ProteaseManager.createProtease(SymbolList cleaveRes, boolean endoProtease, java.lang.String name)`

Constructors in org.biojava.bio.proteomics with parameters of type SymbolList
`Protease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes, java.lang.String name)`
`Protease(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes)` Deprecated. Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())

Uses of SymbolList in org.biojava.bio.search

Methods in org.biojava.bio.search that return SymbolList
`SymbolList` `KnuthMorrisPrattSearch.getPattern()`

Methods in org.biojava.bio.search with parameters of type SymbolList
`SeqSimilaritySearchResult` `SeqSimilaritySearcher.search(SymbolList querySeq, SequenceDB db, java.util.Map searchParameters)` Using this sequence similarity searcher, search with the given sequence against the given sequence database.
`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`).

Constructors in org.biojava.bio.search with parameters of type SymbolList
`KnuthMorrisPrattSearch(SymbolList pattern)` Constructs a KMP matcher to find exact occurances of `pattern` in `text` using the Knuth-Morris-Pratt algorithm.

Uses of SymbolList in org.biojava.bio.seq

Subinterfaces of SymbolList in org.biojava.bio.seq
`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
`class` `CircularView` A circular view onto another Sequence object.
`class` `DummySequence`
`class` `SimpleAssembly` A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
`class` `SimpleGappedSequence` Simple implementation of GappedSequence.
`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 that return SymbolList
`static SymbolList` `RNATools.createRNA(java.lang.String rna)` Return a new RNA SymbolList for rna.
`static SymbolList` `RNATools.complement(SymbolList list)` Retrieve a complement view of list.
`static SymbolList` `RNATools.reverseComplement(SymbolList list)` Retrieve a reverse-complement view of list.
`static SymbolList` `RNATools.transcribe(SymbolList list)` Transcribe DNA into RNA.
`static SymbolList` `RNATools.translate(SymbolList syms)` Translate RNA into protein (with termination symbols).
`static SymbolList` `NucleotideTools.createNucleotide(java.lang.String nucleotide)` Return a new Nucleotide SymbolList for nucleotide.
`static SymbolList` `NucleotideTools.complement(SymbolList list)` Retrieve a complement view of list.
`static SymbolList` `NucleotideTools.reverseComplement(SymbolList list)` Retrieve a reverse-complement view of list.
`static SymbolList` `DNATools.createDNA(java.lang.String dna)` Return a new DNA SymbolList for dna.
`static SymbolList` `DNATools.complement(SymbolList list)` Retrieve a complement view of list.
`static SymbolList` `DNATools.reverseComplement(SymbolList list)` Retrieve a reverse-complement view of list.
`SymbolList` `Feature.getSymbols()` Return a list of symbols that are contained in this feature.
`SymbolList` `ViewSequence.subList(int start, int end)`
`SymbolList` `CircularView.subList(int start, int end)` Over rides ViewSequence.
`SymbolList` `StrandedFeature.getSymbols()` Return a list of symbols that are contained in this feature.
`SymbolList` `SimpleAssembly.subList(int start, int end)`
`static SymbolList` `GeneticCodes.transcribe(SymbolList theList)` Transcribe DNA into RNA.
`static SymbolList` `GeneticCodes.translate(SymbolList theList)` Translate RNA into protein (with termination symbols).
`SymbolList` `SubSequence.subList(int start, int end)`
`SymbolList` `DummySequence.subList(int start, int end)`
`static SymbolList` `ProteinTools.createProtein(java.lang.String theProtein)` Return a new Protein SymbolList for protein.

Methods in org.biojava.bio.seq with parameters of type SymbolList
`static SymbolList` `RNATools.complement(SymbolList list)` Retrieve a complement view of list.
`static SymbolList` `RNATools.reverseComplement(SymbolList list)` Retrieve a reverse-complement view of list.
`static SymbolList` `RNATools.transcribe(SymbolList list)` Transcribe DNA into RNA.
`static SymbolList` `RNATools.translate(SymbolList syms)` Translate RNA into protein (with termination symbols).
`static SymbolList` `NucleotideTools.complement(SymbolList list)` Retrieve a complement view of list.
`static SymbolList` `NucleotideTools.reverseComplement(SymbolList list)` Retrieve a reverse-complement view of list.
`static SymbolList` `DNATools.complement(SymbolList list)` Retrieve a complement view of list.
`static SymbolList` `DNATools.reverseComplement(SymbolList list)` Retrieve a reverse-complement view of list.
`Sequence` `SequenceFactory.createSequence(SymbolList symList, java.lang.String uri, java.lang.String name, Annotation annotation)` Creates a sequence using these parameters.
`static SymbolList` `GeneticCodes.transcribe(SymbolList theList)` Transcribe DNA into RNA.
`static SymbolList` `GeneticCodes.translate(SymbolList theList)` Translate RNA into protein (with termination symbols).
`static Sequence` `SequenceTools.createSequence(SymbolList syms, java.lang.String uri, java.lang.String name, Annotation ann)`

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

Classes in org.biojava.bio.seq.homol that implement SymbolList
`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
`SymbolList` `SimilarityPairFeature.EmptyPairwiseAlignment.symbolListForLabel(java.lang.Object label)`
`SymbolList` `SimilarityPairFeature.EmptyPairwiseAlignment.subList(int index1, int index2)`

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

Classes in org.biojava.bio.seq.impl that implement SymbolList
`class` `AssembledSymbolList` 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` `SimpleSequence` A basic implementation of the `Sequence` interface.

Methods in org.biojava.bio.seq.impl that return SymbolList
`SymbolList` `SimpleStrandedFeature.getSymbols()`
`SymbolList` `AssembledSymbolList.subList(int start, int end)`
`SymbolList` `SimpleSequence.subList(int start, int end)`
`SymbolList` `SimpleFeature.getSymbols()`

Methods in org.biojava.bio.seq.impl with parameters of type SymbolList
`Sequence` `SimpleSequenceFactory.createSequence(SymbolList symList, java.lang.String uri, java.lang.String name, Annotation annotation)`
`void` `AssembledSymbolList.putComponent(Location l, SymbolList sl)`

Constructors in org.biojava.bio.seq.impl with parameters of type SymbolList
`SimpleSequence(SymbolList sym, java.lang.String urn, java.lang.String name, Annotation annotation)` Create a SimpleSequence with the symbols and alphabet of sym, and the sequence properties listed.
`SimpleSequence(SymbolList sym, java.lang.String urn, java.lang.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
`SymbolList` `ChunkedSymbolListFactory.makeSymbolList()` Converts accumulated Symbols to a SymbolList
`SymbolList` `ChunkedSymbolListFactory.make(SymbolReader sr)` Method to create a Sequence with a SymbolReader.
`SymbolList` `ChunkedSymbolListBuilder.makeSymbolList()`

Methods in org.biojava.bio.seq.io with parameters of type SymbolList
`java.lang.String` `CharacterTokenization.tokenizeSymbolList(SymbolList sl)`
`java.lang.String` `SymbolTokenization.tokenizeSymbolList(SymbolList sl)` Return a string representation of a list of symbols.
`java.lang.String` `WordTokenization.tokenizeSymbolList(SymbolList sl)`

Constructors in org.biojava.bio.seq.io with parameters of type SymbolList
`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
`SymbolList` `ProjectedFeature.getSymbols()`
`SymbolList` `ProjectedStrandedFeature.getSymbols()`

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

Classes in org.biojava.bio.seq.ragbag that implement SymbolList
`(package private) class` `org.biojava.bio.seq.ragbag.RagbagAbstractSequence` object that instantiates a sequence in Ragbag.
`class` `RagbagAssembly` object that instantiates a sequence when given a Ragbag directory.

Uses of SymbolList in org.biojava.bio.symbol

Subinterfaces of SymbolList in org.biojava.bio.symbol
`interface` `Alignment` An alignment containing multiple SymbolLists.
`interface` `GappedSymbolList` This extends SymbolList with API for manipulating, inserting and deleting gaps.

Classes in org.biojava.bio.symbol that implement SymbolList
`class` `AbstractSymbolList` Abstract helper implementation of the SymbolList core interface.
`class` `DummySymbolList` Symbol list which just consists of non-informative symbols.
`class` `PackedDnaSymbolList` a class that implements storage of symbols in packed form (2 symbols per byte).
`class` `PackedSymbolList` A SymbolList that stores symbols as bit-patterns in an array of longs.
`class` `RelabeledAlignment` An alignment that relabels another alignment.
`class` `SimpleAlignment` A simple implementation of an Alignment.
`class` `SimpleGappedSymbolList` This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.
`class` `SimpleSymbolList` Basic implementation of SymbolList.
`static class` `SymbolList.EmptySymbolList` The empty immutable implementation.

Fields in org.biojava.bio.symbol declared as SymbolList
`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
`SymbolList` `CircularLocation.symbols(SymbolList seq)`
`SymbolList` `SimpleAlignment.symbolListForLabel(java.lang.Object label)`
`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` `SymbolList.subList(int start, int end)` Return a new SymbolList for the symbols start to end inclusive.
`SymbolList` `SymbolList.EmptySymbolList.subList(int start, int end)`
`SymbolList` `GappedSymbolList.getSourceSymbolList()` Return the underlying (ungapped) SymbolList.
`SymbolList` `AbstractRangeLocation.symbols(SymbolList seq)`
`SymbolList` `SymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)` makes a SymbolList containing size Symbols from a Symbol array.
`SymbolList` `RelabeledAlignment.symbolListForLabel(java.lang.Object label)`
`SymbolList` `RelabeledAlignment.subList(int min, int max)`
`SymbolList` `Location.symbols(SymbolList seq)` Return the symbols in a sequence that fall within this range.
`static SymbolList` `SymbolListViews.orderNSymbolList(SymbolList source, int order)` An n-th order view of another SymbolList.
`static SymbolList` `SymbolListViews.windowedSymbolList(SymbolList source, int wsize)` A view of windows onto another SymbolList.
`static SymbolList` `SymbolListViews.reverse(SymbolList symbols)` A reversed view onto a SymbolList.
`static SymbolList` `SymbolListViews.translate(SymbolList symbols, TranslationTable table)` Provides a 'translated' view of an underlying SymbolList.
`SymbolList` `AbstractLocationDecorator.symbols(SymbolList seq)`
`SymbolList` `PackedSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)`
`SymbolList` `FuzzyPointLocation.symbols(SymbolList slist)`
`static SymbolList` `DoubleAlphabet.fromArray(double[] dArray)` Retrieve a SymbolList view of an array of doubles.
`SymbolList` `SimpleGappedSymbolList.getSourceSymbolList()` Return the underlying (ungapped) SymbolList.
`SymbolList` `AbstractSymbolList.subList(int start, int end)`
`SymbolList` `Alignment.symbolListForLabel(java.lang.Object label)` Retrieve a single row of the alignment by label.
`SymbolList` `SimpleSymbolListFactory.makeSymbolList(Symbol[] symbolArray, int size, Alphabet alfa)` Create a factory for SimpleSymbolLists.
`SymbolList` `UkkonenSuffixTree.stringToSymbolList(java.lang.String string)` Converts a string that came from symbolListToString back to a SymbolList.
`static SymbolList` `IntegerAlphabet.fromArray(int[] iArray)` Retrieve a SymbolList view of an array of integers.

Methods in org.biojava.bio.symbol with parameters of type SymbolList
`SymbolList` `CircularLocation.symbols(SymbolList seq)`
`SymbolList` `AbstractRangeLocation.symbols(SymbolList seq)`
`SymbolList` `Location.symbols(SymbolList seq)` Return the symbols in a sequence that fall within this range.
`static int` `PackingFactory.primeWord(SymbolList symList, int wordLength, Packing packing)`
`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 SymbolList` `SymbolListViews.windowedSymbolList(SymbolList source, int wsize)` A view of windows onto another SymbolList.
`static SymbolList` `SymbolListViews.reverse(SymbolList symbols)` A reversed view onto a SymbolList.
`static SymbolList` `SymbolListViews.translate(SymbolList symbols, TranslationTable table)` Provides a 'translated' view of an underlying SymbolList.
`static Alignment` `SymbolListViews.alignment(java.util.List labels, SymbolList symList)` View a SymbolList over a cross-product Alphabet as an Alignment.
`SymbolList` `AbstractLocationDecorator.symbols(SymbolList seq)`
`SymbolList` `FuzzyPointLocation.symbols(SymbolList slist)`
`java.lang.String` `UkkonenSuffixTree.symbolListToString(SymbolList list)` Makes a string out of a SymbolList, this string should only be used for internal or testing purposes, as it will necessarily consist of visible characters.
`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 java.lang.String` `MotifTools.createRegex(SymbolList motif)` `createRegex` creates a regular expression which matches the `SymbolList`.

Constructors in org.biojava.bio.symbol with parameters of type SymbolList
`SimpleSymbolList(SymbolList sl)` Construct a copy of an existing SymbolList.
`Edit(int pos, int length, SymbolList replacement)` Create a new Edit.
`SimpleGappedSymbolList(SymbolList source)` Create a new SimpleGappedSymbolList that will view source.
`PackedSymbolList(Packing packing, SymbolList symList)` Create a new PackedSymbolList as a packed copy of another symbol list.
`PackedDnaSymbolList(SymbolList symList)` constructor taking another symbol list.