Uses of Interface
org.biojava.bio.symbol.SymbolList
Packages that use SymbolList
Package
Description
Classes to generate and describe sequence alignments.
Interfaces and classes for chromatogram data, as produced by DNA sequencing equipment.
Probability distributions over Alphabets.
HMM and Dynamic Programming Algorithms.
Graphical displays of biological sequences and associated annotations.
The classes and interfaces in this package cover common molecular
biological techniques such as restriction digests and PCR.
ABI Trace Handling.
FASTQ and variants sequence format I/O.
Parser for Phred output
Support for the SCF chromatogram format.
SSAHA sequence searching API.
Utilities to aid in performing various physical analysis of proteins.
Interfaces and classes for representing sequence similarity search results.
Classes and interfaces for defining biological sequences and informatics
objects.
The classes and interfaces for defining sequence similarity and
honology.
Standard in-memory implementations of
Sequence
and
Feature
.Classes and interfaces for processing and producing flat-file representations
of sequences.
Code for projecting Feature objects and systematically altering their
properties.
Representation of the Symbols that make up a sequence, and locations within
them.
This package is used to perform regular expression searches of
SymbolLists defined in arbitrary Alphabets.
The Biojava extensions packages, classes that extend the core biojava
functionality
Interface between biojava and biosql databases
Rich implementations of Sequences, Locations and Features.
Classes to provide a genetic algorithm framework
GA functions
Default implementations and abstract classes.
Utility functions and helper classes
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Uses of SymbolList in org.biojava.bio.alignment
Subinterfaces of SymbolList in org.biojava.bio.alignmentModifier and TypeInterfaceDescriptioninterface
An alignment containing multiple SymbolLists.interface
ARAlignment is an interface that defines methods for adding and removing seqeunces from an Alignment.interface
UnequalLengthAlignment has the following behavior.Classes in org.biojava.bio.alignment that implement SymbolListModifier and TypeClassDescriptionclass
class
class
This class stores the result of an alignment procedure that creates a pairwise alignment of two sequences.class
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
A simple implementation of an Alignment.Fields in org.biojava.bio.alignment declared as SymbolListMethods in org.biojava.bio.alignment that return SymbolListModifier and TypeMethodDescriptionAlignmentElement.getSymbolList()
SimpleAlignmentElement.getSymbolList()
Alignment.SymbolListIterator.next()
AbstractULAlignment.SubULAlignment.symbolListForLabel
(String label) Alignment.symbolListForLabel
(String label) Retrieve a single row of the alignment by label.FlexibleAlignment.symbolListForLabel
(String label) SimpleAlignment.symbolListForLabel
(String label) Methods in org.biojava.bio.alignment that return types with arguments of type SymbolListModifier and TypeMethodDescriptionAbstractULAlignment.SubULAlignment.symbolListIterator()
AbstractULAlignment.symbolListIterator()
Alignment.symbolListIterator()
Creates an Iterator over the SymbolLists in the alignment.SimpleAlignment.symbolListIterator()
Methods in org.biojava.bio.alignment with parameters of type SymbolListModifier and TypeMethodDescriptionprotected boolean
FlexibleAlignment.allGaps
(SymbolList seq, int start, int end) make sure that all Symbols in this range are gapsabstract AlignmentPair
AlignmentAlgorithm.pairwiseAlignment
(SymbolList query, SymbolList subject) Performs a pairwise sequence alignment of the two given sequences.NeedlemanWunsch.pairwiseAlignment
(SymbolList query, SymbolList subject) Global pairwise sequence alignment of two BioJava-Sequence objects according to the Needleman-Wunsch-algorithm.SmithWaterman.pairwiseAlignment
(SymbolList query, SymbolList subject) Overrides the method inherited from the NeedlemanWunsch and performs only a local alignment.Constructors in org.biojava.bio.alignment with parameters of type SymbolListConstructor parameters in org.biojava.bio.alignment with type arguments of type SymbolListModifierConstructorDescriptionSimpleAlignment
(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 SymbolListModifier and TypeMethodDescriptionprotected SymbolList
AbstractChromatogram.createImmutableSymbolList
(Alphabet alpha, List syms) A factory method for creating new symbol lists with a given alphabet.static final SymbolList
ChromatogramTools.getDNASequence
(Chromatogram chromat) Get the called DNA sequence from a chromatogram.static final 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 SymbolListModifier and TypeMethodDescriptionstatic final int
ChromatogramTools.getIntFromSymbolList
(SymbolList list, int which) Retrieves, unwraps, and returns anint
from a SymbolList containingIntegerAlphabet.IntegerSymbol
s.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 SymbolListModifier and TypeMethodDescriptionstatic final SymbolList
DistributionTools.generateSymbolList
(Distribution d, int length) Produces aSymbolList
by randomly sampling a Distribution. -
Uses of SymbolList in org.biojava.bio.dp
Subinterfaces of SymbolList in org.biojava.bio.dpModifier and TypeInterfaceDescriptioninterface
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 SymbolListMethods in org.biojava.bio.dp that return SymbolListModifier and TypeMethodDescriptionSimpleStatePath.subList
(int start, int end) SimpleStatePath.symbolListForLabel
(String label) DPMatrix.symList()
Methods in org.biojava.bio.dp that return types with arguments of type SymbolListMethods in org.biojava.bio.dp with parameters of type SymbolListModifier and TypeMethodDescriptionabstract 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) 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 abstract double
AbstractTrainer.singleSequenceIteration
(ModelTrainer trainer, SymbolList symList) protected double
BaumWelchSampler.singleSequenceIteration
(ModelTrainer trainer, SymbolList symList) protected double
BaumWelchSampler.singleSequenceIteration
(ModelTrainer trainer, SymbolList symList, ScoreType scoreType) protected double
BaumWelchTrainer.singleSequenceIteration
(ModelTrainer trainer, SymbolList symList) abstract StatePath
DP.viterbi
(SymbolList[] symList, ScoreType scoreType) Constructors in org.biojava.bio.dp with parameters of type SymbolListModifierConstructorDescriptionSimpleStatePath
(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 SymbolListMethods in org.biojava.bio.dp.onehead that return SymbolListModifier and TypeMethodDescriptionDPCursor.symList()
The symbol list being looped over.SingleDPMatrix.symList()
SmallCursor.symList()
Methods in org.biojava.bio.dp.onehead with parameters of type SymbolListModifier and TypeMethodDescriptiondouble
SingleDP.backward
(SymbolList[] seq, ScoreType scoreType) SingleDP.backwardMatrix
(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType) SingleDP.backwardMatrix
(SymbolList[] seq, ScoreType scoreType) double
SingleDP.forward
(SymbolList[] seq, ScoreType scoreType) SingleDP.forwardMatrix
(SymbolList[] seq, DPMatrix matrix, ScoreType scoreType) SingleDP.forwardMatrix
(SymbolList[] seq, ScoreType scoreType) SingleDP.viterbi
(SymbolList[] symList, ScoreType scoreType) Constructors in org.biojava.bio.dp.onehead with parameters of type SymbolListModifierConstructorDescriptionSingleDPMatrix
(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 SymbolListMethods in org.biojava.bio.dp.twohead that return SymbolListMethods in org.biojava.bio.dp.twohead with parameters of type SymbolListModifier and TypeMethodDescriptiondouble
PairwiseDP.backward
(SymbolList[] seqs, ScoreType scoreType) PairwiseDP.backwardMatrix
(SymbolList[] seqs, DPMatrix d, ScoreType scoreType) PairwiseDP.backwardMatrix
(SymbolList[] seqs, ScoreType scoreType) double
PairwiseDP.forward
(SymbolList[] seqs, ScoreType scoreType) PairwiseDP.forwardMatrix
(SymbolList[] seqs, DPMatrix d, ScoreType scoreType) PairwiseDP.forwardMatrix
(SymbolList[] seqs, ScoreType scoreType) PairwiseDP.viterbi
(SymbolList[] seqs, ScoreType scoreType) Constructors in org.biojava.bio.dp.twohead with parameters of type SymbolListModifierConstructorDescriptionAbstractMatrixPairDPCursor
(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 objectMatrixPairDPCursor
(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 SymbolListModifier and TypeMethodDescriptionPairwiseRenderContext.getSecondarySymbols()
getSecondarySymbols
returns the symbols of the secondary sequence.PairwiseSequencePanel.getSecondarySymbols()
getSecondarySymbols
returns all of theSymbol
s belonging to the currently rendered secondarySequence
.SubPairwiseRenderContext.getSecondarySymbols()
CircularRendererPanel.getSequence()
SequencePanel.getSequence()
TranslatedSequencePanel.getSequence()
getSequence
returns the entireSequence
currently being rendered.CircularRendererContext.getSymbols()
The SymbolList that is currently rendered by this context.HeadlessRenderContext.getSymbols()
PairwiseSequencePanel.getSymbols()
getSymbols
returns all of theSymbol
s belonging to the currently renderedSequence
.SequencePanel.getSymbols()
Retrieve the currently rendered SymbolListSequencePoster.getSymbols()
Deprecated.Retrieve the currently rendered SymbolListSequenceRenderContext.getSymbols()
The SymbolList that is currently rendered by this SequenceRenderContext.SubCircularRendererContext.getSymbols()
SubPairwiseRenderContext.getSymbols()
SubSequenceRenderContext.getSymbols()
TranslatedSequencePanel.getSymbols()
getSymbols
returns all of theSymbol
s belonging to the currently renderedSequence
.Methods in org.biojava.bio.gui.sequence with parameters of type SymbolListModifier and TypeMethodDescriptionvoid
CircularRendererPanel.setSequence
(SymbolList symList) void
SequencePanel.setSequence
(SymbolList s) Set the SymboList to be rendered.void
TranslatedSequencePanel.setSequence
(SymbolList sequence) setSequence
sets theSequence
to be rendered.Constructors in org.biojava.bio.gui.sequence with parameters of type SymbolListModifierConstructorDescriptionSubCircularRendererContext
(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 newSubPairwiseRenderContext
.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 SymbolListMethods in org.biojava.bio.molbio that return SymbolListModifier and TypeMethodDescriptionRestrictionEnzyme.getRecognitionSite()
getRecognitionSite
returns the forward strand of the recognition site.Methods in org.biojava.bio.molbio with parameters of type SymbolListModifier and TypeMethodDescriptionvoid
Composition.setSymbolList
(SymbolList symbolList) Set theSymbolList
to calculation the composition of.Constructors in org.biojava.bio.molbio with parameters of type SymbolListModifierConstructorDescriptionRestrictionEnzyme
(String name, SymbolList site, int dsForward, int dsReverse) Creates a newRestrictionEnzyme
which cuts within or downstream of the recognition site.RestrictionEnzyme
(String name, SymbolList site, int usForward, int usReverse, int dsForward, int dsReverse) Creates a newRestrictionEnzyme
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 SymbolListModifier and TypeMethodDescriptionABITrace.getSequence()
Returns the original programatically determined (unedited) sequence as aSymbolList
.Methods in org.biojava.bio.program.abi with parameters of type SymbolListModifier and TypeMethodDescriptionstatic 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 SymbolListModifier and TypeMethodDescriptionstatic SymbolList
Create and return a new DNASymbolList
from the specified FASTQ formatted sequence.static SymbolList
FastqTools.createQualityScores
(Fastq fastq) Create and return a newSymbolList
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 SymbolListModifier and TypeClassDescriptionclass
PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores.Methods in org.biojava.bio.program.phred that return SymbolListModifier and TypeMethodDescriptionstatic 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.PhredSequence.getDNA()
Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolListPhredSequence.getQuality()
Extracts the quality part if the Phred Alphabet and returns it as a SymbolList over the Integer SubAlphabet from 0..99.Qualitative.getQuality()
Retreives the list of quality symbols from the underlying object.Methods in org.biojava.bio.program.phred with parameters of type SymbolListModifier and TypeMethodDescriptionstatic 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 SymbolListModifierConstructorDescriptionPhredSequence
(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 SymbolListModifier and TypeMethodDescriptionprotected SymbolList
SCF.reverseComplementBaseCallList
(String label) OverridesAbstractChromatogram.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 SymbolListModifier and TypeMethodDescriptionvoid
CompactedDataStore.search
(String seqID, SymbolList symList, SearchListener listener) void
DataStore.search
(String id, SymbolList symList, SearchListener listener) Search the DataStore with a symbol list. -
Uses of SymbolList in org.biojava.bio.proteomics
Methods in org.biojava.bio.proteomics that return SymbolListModifier and TypeMethodDescriptionProtease.getCleaveageResidues()
The list of residues that the protease will cleave at.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 SymbolListModifier and TypeMethodDescriptionstatic 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 final double
MassCalc.getMass
(SymbolList proteinSeq, String isotopicType, boolean MH_PLUS) getMass
calculates the mass of this peptide.static final 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 SymbolListModifierConstructorDescriptionProtease
(SymbolList cleaveRes, boolean endoProtease, SymbolList notCleaveRes) Deprecated.Creating a Protease with this constructor will not register it with the ProteaseManager (use ProteaseManager.createProtease())protected
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 SymbolListModifier and TypeMethodDescriptionKnuthMorrisPrattSearch.getPattern()
MaxMismatchPattern.getPattern()
BioMatcher.group()
Get the matching region as a SymbolList.MaxMismatchMatcher.group()
Methods in org.biojava.bio.search with parameters of type SymbolListModifier and TypeMethodDescriptionint[]
KnuthMorrisPrattSearch.findMatches
(SymbolList text) This will return an int[] giving the offsets of the matches intext
(ie the location of the first symbol of each match in thetext
).BioPattern.matcher
(SymbolList symList) Get a matcher that will use these parameters to search a SymbolList.MaxMismatchPattern.matcher
(SymbolList symList) SeqContentPattern.matcher
(SymbolList symList) 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 SymbolListModifierConstructorDescriptionKnuthMorrisPrattSearch
(SymbolList pattern) Constructs a KMP matcher to find exact occurances ofpattern
intext
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.seqModifier and TypeInterfaceDescriptioninterface
Extension of GappedSymbolList which also projects features into the gapped coordinate system.interface
A biological sequence.Classes in org.biojava.bio.seq that implement SymbolListModifier and TypeClassDescriptionclass
A circular view onto another Sequence object.class
A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.class
A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.Methods in org.biojava.bio.seq that return SymbolListModifier and TypeMethodDescriptionstatic SymbolList
DNATools.complement
(SymbolList list) Retrieve a complement view of list.static SymbolList
NucleotideTools.complement
(SymbolList list) Retrieve a complement view of list.static SymbolList
RNATools.complement
(SymbolList list) Retrieve a complement view of list.static SymbolList
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
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.Feature.getSymbols()
Return a list of symbols that are contained in this feature.StrandedFeature.getSymbols()
Return a list of symbols that are contained in this feature.static SymbolList
DNATools.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
RNATools.reverseComplement
(SymbolList list) Retrieve a reverse-complement view of list.CircularView.subList
(int start, int end) Over rides ViewSequence.NewSimpleAssembly.subList
(int start, int end) SimpleAssembly.subList
(int start, int end) 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 aSymbolList
from the DNAAlphabet
to the RNAAlphabet
.static SymbolList
GeneticCodes.transcribe
(SymbolList theList) Transcribe DNA into RNA.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
DNATools.transcribeToRNA
(SymbolList syms) Transcribes DNA to RNA.static SymbolList
GeneticCodes.translate
(SymbolList theList) Translate RNA into protein (with termination symbols).static SymbolList
RNATools.translate
(SymbolList syms) Translate RNA into protein (with termination symbols).Methods in org.biojava.bio.seq with parameters of type SymbolListModifier and TypeMethodDescriptionstatic SymbolList
DNATools.complement
(SymbolList list) Retrieve a complement view of list.static SymbolList
NucleotideTools.complement
(SymbolList list) Retrieve a complement view of list.static SymbolList
RNATools.complement
(SymbolList list) Retrieve a complement view of list.SequenceFactory.createSequence
(SymbolList symList, String uri, String name, Annotation annotation) Deprecated.Creates a sequence using these parameters.static Sequence
SequenceTools.createSequence
(SymbolList syms, String uri, String name, Annotation ann) 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
DNATools.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
RNATools.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 aSymbolList
from the DNAAlphabet
to the RNAAlphabet
.static SymbolList
GeneticCodes.transcribe
(SymbolList theList) Transcribe DNA into RNA.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
DNATools.transcribeToRNA
(SymbolList syms) Transcribes DNA to RNA.static SymbolList
GeneticCodes.translate
(SymbolList theList) Translate RNA into protein (with termination symbols).static SymbolList
RNATools.translate
(SymbolList syms) 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 SymbolListModifier and TypeClassDescriptionstatic final class
EmptyPairwiseAlignment
empty pairwise alignment which has labels to empty symbol lists.Methods in org.biojava.bio.seq.homol that return SymbolListModifier and TypeMethodDescriptionSimilarityPairFeature.EmptyPairwiseAlignment.subList
(int index1, int index2) SimilarityPairFeature.EmptyPairwiseAlignment.symbolListForLabel
(String label) Methods in org.biojava.bio.seq.homol that return types with arguments of type SymbolListModifier and TypeMethodDescriptionSimilarityPairFeature.EmptyPairwiseAlignment.symbolListIterator()
-
Uses of SymbolList in org.biojava.bio.seq.impl
Classes in org.biojava.bio.seq.impl that implement SymbolListModifier and TypeClassDescriptionclass
Support class for applications which need to patch together sections of sequence into a single SymbolList.final class
A Sequence implementation that has a name and URI but no features, and a zero length symbol list.class
Support class for applications which need to patch together sections of sequence into a single SymbolList.class
A reverse complement view ontoSequence
interface.class
Simple implementation of GappedSequence.class
A basic implementation of theSequence
interface.class
View a sub-section of a given sequence object, including all the features intersecting that region.class
A view onto another Sequence object.Methods in org.biojava.bio.seq.impl that return SymbolListModifier and TypeMethodDescriptionSimpleFeature.getSymbols()
SimpleStrandedFeature.getSymbols()
AssembledSymbolList.subList
(int start, int end) DummySequence.subList
(int start, int end) NewAssembledSymbolList.subList
(int start, int end) SimpleSequence.subList
(int start, int end) SubSequence.subList
(int start, int end) ViewSequence.subList
(int start, int end) Methods in org.biojava.bio.seq.impl with parameters of type SymbolListModifier and TypeMethodDescriptionSimpleSequenceFactory.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 SymbolListModifierConstructorDescriptionSimpleSequence
(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 SymbolListModifier and TypeMethodDescriptionChunkedSymbolListFactory.make
(SymbolReader sr) Method to create a Sequence with a SymbolReader.ChunkedSymbolListFactory.makeSymbolList()
Converts accumulated Symbols to a SymbolListMethods in org.biojava.bio.seq.io with parameters of type SymbolListModifier and TypeMethodDescriptionAlternateTokenization.tokenizeSymbolList
(SymbolList sl) CharacterTokenization.tokenizeSymbolList
(SymbolList sl) SymbolTokenization.tokenizeSymbolList
(SymbolList symList) Return a string representation of a list of symbols.WordTokenization.tokenizeSymbolList
(SymbolList sl) Constructors in org.biojava.bio.seq.io with parameters of type SymbolListModifierConstructorDescriptionCreates a newSymbolListCharSequence
wrapping aSymbolList
. -
Uses of SymbolList in org.biojava.bio.seq.projection
Methods in org.biojava.bio.seq.projection that return SymbolList -
Uses of SymbolList in org.biojava.bio.symbol
Subinterfaces of SymbolList in org.biojava.bio.symbolModifier and TypeInterfaceDescriptioninterface
This extends SymbolList with API for manipulating, inserting and deleting gaps.Classes in org.biojava.bio.symbol that implement SymbolListModifier and TypeClassDescriptionclass
Abstract helper implementation of the SymbolList core interface.class
SymbolList implementation using constant-size chunks.class
Symbol list which just consists of non-informative symbols.class
A SymbolList that stores symbols as bit-patterns in an array of longs.class
An alignment that relabels another alignment.class
This implementation of GappedSymbolList wraps a SymbolList, allowing you to insert gaps.class
Basic implementation of SymbolList.Fields in org.biojava.bio.symbol declared as SymbolListModifier and TypeFieldDescriptionstatic final SymbolList
SymbolList.EMPTY_LIST
A useful object that represents an empty symbol list, to avoid returning null.final SymbolList
Edit.replacement
Methods in org.biojava.bio.symbol that return SymbolListModifier and TypeMethodDescriptionstatic SymbolList
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.GappedSymbolList.getSourceSymbolList()
Return the underlying (ungapped) SymbolList.SimpleGappedSymbolList.getSourceSymbolList()
PackedSymbolListFactory.makeSymbolList
(Symbol[] symbolArray, int size, Alphabet alfa) Makes a packed SymbolList out of a list of Symbols.SimpleSymbolListFactory.makeSymbolList
(Symbol[] symbolArray, int size, Alphabet alfa) Create a factory for SimpleSymbolLists.SymbolListFactory.makeSymbolList
(Symbol[] symbolArray, int size, Alphabet alfa) makes a SymbolList containing size Symbols from a Symbol array.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.AbstractSymbolList.subList
(int start, int end) ChunkedSymbolList.subList
(int start, int end) RelabeledAlignment.subList
(int min, int max) 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 editedSymbolList.subList
(int start, int end) Return a new SymbolList for the symbols start to end inclusive.static SymbolList
SymbolListViews.subList
(SymbolList parent, int start, int end) View a portion of a SymbolList.RelabeledAlignment.symbolListForLabel
(String label) AbstractLocationDecorator.symbols
(SymbolList seq) AbstractRangeLocation.symbols
(SymbolList seq) CircularLocation.symbols
(SymbolList seq) FuzzyPointLocation.symbols
(SymbolList slist) Location.symbols
(SymbolList seq) Return the symbols in a sequence that fall within this range.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 SymbolListModifier and TypeMethodDescriptionvoid
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 towindow
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 theSymbolList
.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.AbstractLocationDecorator.symbols
(SymbolList seq) AbstractRangeLocation.symbols
(SymbolList seq) CircularLocation.symbols
(SymbolList seq) FuzzyPointLocation.symbols
(SymbolList slist) Location.symbols
(SymbolList seq) Return the symbols in a sequence that fall within this range.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 SymbolListModifierConstructorDescriptionChunkedSymbolList
(SymbolList[] chunks, int chunkSize, int length, Alphabet alpha) Edit
(int pos, int length, SymbolList replacement) Create a new Edit.Edit
(int pos, int length, SymbolList replacement, Map<String, Object> props) Create a new Edit with some properties.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.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 -
Uses of SymbolList in org.biojava.utils.regex
Methods in org.biojava.utils.regex that return SymbolListModifier and TypeMethodDescriptionMatcher.group()
Returns the input subsequence matched by the previous match.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 SymbolListModifier and TypeMethodDescriptionPattern.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.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 SymbolListModifier and TypeMethodDescriptionCrossReferenceResolver.getRemoteSymbolList
(CrossRef cr, Alphabet a) Given a cross reference, return the corresponding symbol list.DummyCrossReferenceResolver.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 SymbolListModifier and TypeMethodDescriptionBioSQLCrossReferenceResolver.getRemoteSymbolList
(CrossRef cr, Alphabet a) Given a cross reference, return the corresponding symbol list.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.seqModifier and TypeInterfaceDescriptioninterface
A rich sequence is a combination of a org.biojavax.bio.Bioentry and a Sequence.Classes in org.biojavax.bio.seq that implement SymbolListModifier and TypeClassDescriptionclass
A symbol list that isInteger.MAX_VALUE
long, never gives index out of bounds and always returns ambiguity symbols for everything.class
A simple implementation of RichSequence.class
A simple implementation of RichSequence.Methods in org.biojavax.bio.seq that return SymbolListModifier and TypeMethodDescriptionRichSequence.getInternalSymbolList()
A special function that returns the SymbolList that this RichSequence is based around.SimpleRichSequence.getInternalSymbolList()
A special function that returns the SymbolList that this RichSequence is based around.ThinRichSequence.getInternalSymbolList()
A special function that returns the SymbolList that this RichSequence is based around.SimpleRichFeature.getSymbols()
Return a list of symbols that are contained in this feature.DummyRichSequenceHandler.subList
(RichSequence seq, int start, int end) Return a new SymbolList for the symbols start to end inclusive.InfinitelyAmbiguousSymbolList.subList
(int start, int end) Return a new SymbolList for the symbols start to end inclusive.RichSequenceHandler.subList
(RichSequence seq, int start, int end) Return a new SymbolList for the symbols start to end inclusive.ThinRichSequence.subList
(int start, int end) Return a new SymbolList for the symbols start to end inclusive.CompoundRichLocation.symbols
(SymbolList seq) Return the symbols in a sequence that fall within this range.EmptyRichLocation.symbols
(SymbolList seq) Return the symbols in a sequence that fall within this range.SimpleRichLocation.symbols
(SymbolList seq) Return the symbols in a sequence that fall within this range.Methods in org.biojavax.bio.seq with parameters of type SymbolListModifier and TypeMethodDescriptionstatic RichSequence
RichSequence.Tools.createRichSequence
(String name, SymbolList syms) Create a new RichSequence in the default namespace.static RichSequence
RichSequence.Tools.createRichSequence
(Namespace ns, String name, SymbolList syms) Create a new RichSequence in the specified namespace.CompoundRichLocation.symbols
(SymbolList seq) Return the symbols in a sequence that fall within this range.EmptyRichLocation.symbols
(SymbolList seq) Return the symbols in a sequence that fall within this range.SimpleRichLocation.symbols
(SymbolList seq) Return the symbols in a sequence that fall within this range.Constructors in org.biojavax.bio.seq with parameters of type SymbolListModifierConstructorDescriptionSimpleRichSequence
(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 SymbolListModifier and TypeMethodDescriptionOrganism.getChromosomes()
Gets the organisms 'chromosome' sequencesMethods in org.biojavax.ga with parameters of type SymbolListModifier and TypeMethodDescriptionvoid
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 SymbolListModifier and TypeMethodDescriptionGACross.getChromosomes()
Gets the chromosomes after the crossGACrossResult.getChromosomes()
Gets the chromosomes after the crossSimpleGACrossResult.getChromosomes()
MutationFunction.mutate
(SymbolList seq) Produces a new SymbolList by mutation.MutationFunction.NoMutation.mutate
(SymbolList syml) SimpleMutationFunction.mutate
(SymbolList seq) SwapMutationFunction.mutate
(SymbolList seq) Methods in org.biojavax.ga.functions with parameters of type SymbolListModifier and TypeMethodDescriptionMutationFunction.mutate
(SymbolList seq) Produces a new SymbolList by mutation.MutationFunction.NoMutation.mutate
(SymbolList syml) SimpleMutationFunction.mutate
(SymbolList seq) SwapMutationFunction.mutate
(SymbolList seq) CrossOverFunction.NoCross.performCrossOver
(SymbolList chromA, SymbolList chromB) CrossOverFunction.performCrossOver
(SymbolList chromA, SymbolList chromB) Performs a cross between the pair of chromosomesOrderCrossover.performCrossOver
(SymbolList chromA, SymbolList chromB) SimpleCrossOverFunction.performCrossOver
(SymbolList chromA, SymbolList chromB) Constructors in org.biojavax.ga.functions with parameters of type SymbolListModifierConstructorDescriptionSimpleGACrossResult
(PointLocation[] crossOverPositions, SymbolList[] chromosomes) -
Uses of SymbolList in org.biojavax.ga.impl
Fields in org.biojavax.ga.impl declared as SymbolListMethods in org.biojavax.ga.impl that return SymbolListMethods in org.biojavax.ga.impl with parameters of type SymbolListModifier and TypeMethodDescriptionprotected abstract void
AbstractOrganism.setChromImpl
(SymbolList[] chromosomes) protected void
SimpleOrganism.setChromImpl
(SymbolList[] chromosomes) final void
AbstractOrganism.setChromosomes
(SymbolList[] chromosomes) -
Uses of SymbolList in org.biojavax.ga.util
Methods in org.biojavax.ga.util that return SymbolListModifier and TypeMethodDescriptionstatic SymbolList
GATools.createBinary
(String binarySequence) Creates aSymbolList
in the GABinaryAlphabet