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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. |
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