Uses of Interface
org.biojava.nbio.core.sequence.template.Sequence

Packages that use Sequence

Package	Description
org.biojava.nbio.aaproperties.xml	Set of classes that handles the reading and writing of xml files.
org.biojava.nbio.alignment
org.biojava.nbio.alignment.routines
org.biojava.nbio.alignment.template
org.biojava.nbio.core.alignment
org.biojava.nbio.core.alignment.template
org.biojava.nbio.core.search.io
org.biojava.nbio.core.search.io.blast
org.biojava.nbio.core.sequence
org.biojava.nbio.core.sequence.compound
org.biojava.nbio.core.sequence.edits
org.biojava.nbio.core.sequence.io
org.biojava.nbio.core.sequence.io.template
org.biojava.nbio.core.sequence.io.util
org.biojava.nbio.core.sequence.loader
org.biojava.nbio.core.sequence.location.template
org.biojava.nbio.core.sequence.storage
org.biojava.nbio.core.sequence.template
org.biojava.nbio.core.sequence.transcription
org.biojava.nbio.core.sequence.views
org.biojava.nbio.core.util
org.biojava.nbio.phylo
org.biojava.nbio.structure	Interfaces and classes for protein structure (PDB).
org.biojava.nbio.structure.io	Input and Output of Structures
org.biojava.nbio.ws.alignment	This package contains the interfaces that need to be implemented by discrete alignment services.
org.biojava.nbio.ws.alignment.qblast

Uses of Sequence in org.biojava.nbio.aaproperties.xml

Methods in org.biojava.nbio.aaproperties.xml with parameters of type Sequence

Modifier and Type	Method and Description
boolean	CaseFreeAminoAcidCompoundSet.isValidSequence(Sequence<AminoAcidCompound> sequence)
boolean	ModifiedAminoAcidCompoundSet.isValidSequence(Sequence<AminoAcidCompound> sequence)

Uses of Sequence in org.biojava.nbio.alignment

Classes in org.biojava.nbio.alignment with type parameters of type Sequence

Modifier and Type	Class and Description
class	FractionalIdentityInProfileScorer<S extends Sequence<C>,C extends Compound> Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
class	FractionalIdentityScorer<S extends Sequence<C>,C extends Compound> Implements an algorithm which computes a score for a sequence alignment pair.
class	FractionalSimilarityInProfileScorer<S extends Sequence<C>,C extends Compound> Implements an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
class	FractionalSimilarityScorer<S extends Sequence<C>,C extends Compound> Implements an algorithm which computes a score for a sequence alignment pair.
class	GuideTree<S extends Sequence<C>,C extends Compound> Implements a data structure for a guide tree used during progressive multiple sequence alignment.
class	NeedlemanWunsch<S extends Sequence<C>,C extends Compound> Needleman and Wunsch defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).
class	SimpleProfileProfileAligner<S extends Sequence<C>,C extends Compound> Implements a simple (naive) Aligner for a pair of Profiles.
class	SmithWaterman<S extends Sequence<C>,C extends Compound> Smith and Waterman defined an algorithm for pairwise local sequence alignments (best match of sections from each Sequence).
class	StandardRescoreRefiner<S extends Sequence<C>,C extends Compound>
class	SubstitutionMatrixScorer<S extends Sequence<C>,C extends Compound> Scores using a substitution matrix.

Methods in org.biojava.nbio.alignment with type parameters of type Sequence

Modifier and Type	Method and Description
static <S extends Sequence<C>,C extends Compound> List<SequencePair<S,C>>	Alignments.getAllPairsAlignments(List<S> sequences, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) Factory method which computes a sequence alignment for all Sequence pairs in the given List.
static <S extends Sequence<C>,C extends Compound> List<PairwiseSequenceScorer<S,C>>	Alignments.getAllPairsScorers(List<S> sequences, Alignments.PairwiseSequenceScorerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) Factory method which sets up a sequence pair scorer for all Sequence pairs in the given List.
static <S extends Sequence<C>,C extends Compound> double[]	Alignments.getAllPairsScores(List<S> sequences, Alignments.PairwiseSequenceScorerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) Factory method which computes a sequence pair score for all Sequence pairs in the given List.
static <S extends Sequence<C>,C extends Compound> Profile<S,C>	Alignments.getMultipleSequenceAlignment(List<S> sequences, Object... settings) Factory method which computes a multiple sequence alignment for the given List of Sequences.
static <S extends Sequence<C>,C extends Compound> PairwiseSequenceAligner<S,C>	Alignments.getPairwiseAligner(S query, S target, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) Factory method which constructs a pairwise sequence aligner.
static <S extends Sequence<C>,C extends Compound> SequencePair<S,C>	Alignments.getPairwiseAlignment(S query, S target, Alignments.PairwiseSequenceAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) Factory method which computes a sequence alignment for the given Sequence pair.
static <S extends Sequence<C>,C extends Compound> Profile<S,C>	Alignments.getProgressiveAlignment(GuideTree<S,C> tree, Alignments.ProfileProfileAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix) Factory method to run the profile-profile alignments of a progressive multiple sequence alignment concurrently.
static <S extends Sequence<C>,C extends Compound> double[]	Alignments.runPairwiseScorers(List<PairwiseSequenceScorer<S,C>> scorers) Factory method to run a list of scorers concurrently.

Uses of Sequence in org.biojava.nbio.alignment.routines

Classes in org.biojava.nbio.alignment.routines with type parameters of type Sequence

Modifier and Type	Class and Description
class	AnchoredPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> This algorithm uses a divide-and-conquer approach to find optimal pairwise global sequence alignments (from the first until the last Compound of each Sequence) with the restriction that any alignment produced will connect the query sequence to the target sequence at the anchors.
class	GuanUberbacher<S extends Sequence<C>,C extends Compound> Guan and Uberbacher defined an algorithm for pairwise global sequence alignments (from the first until the last Compound of each Sequence).

Uses of Sequence in org.biojava.nbio.alignment.template

Classes in org.biojava.nbio.alignment.template with type parameters of type Sequence

Modifier and Type	Class and Description
class	AbstractMatrixAligner<S extends Sequence<C>,C extends Compound> Implements common code for an Aligner which builds a score matrix during computation.
class	AbstractPairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> Implements common code for an Aligner for a pair of Sequences.
class	AbstractProfileProfileAligner<S extends Sequence<C>,C extends Compound> Implements common code for an Aligner for a pair of Profiles.
interface	Aligner<S extends Sequence<C>,C extends Compound> Defines an algorithm which computes an alignment Profile from a list of Sequences.
class	CallablePairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> Implements a concurrency wrapper for a PairwiseSequenceAligner.
class	CallablePairwiseSequenceScorer<S extends Sequence<C>,C extends Compound> Implements a concurrency wrapper for a PairwiseSequenceScorer.
class	CallableProfileProfileAligner<S extends Sequence<C>,C extends Compound> Implements a concurrency wrapper for a ProfileProfileAligner.
interface	GuideTreeNode<S extends Sequence<C>,C extends Compound> Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment.
interface	HierarchicalClusterer<S extends Sequence<C>,C extends Compound> Defines a clustering algorithm that converts a distance matrix into a tree.
interface	MatrixAligner<S extends Sequence<C>,C extends Compound> Defines an Aligner which builds a score matrix during computation.
interface	PairInProfileScorer<S extends Sequence<C>,C extends Compound> Defines an algorithm which computes a score for a sequence alignment pair picked from an alignment Profile.
interface	PairwiseSequenceAligner<S extends Sequence<C>,C extends Compound> Defines an Aligner for a pair of Sequences.
interface	PairwiseSequenceScorer<S extends Sequence<C>,C extends Compound> Defines an algorithm which computes a score for a pair of sequences.
interface	PartitionRefiner<S extends Sequence<C>,C extends Compound> Defines an algorithm which computes a new alignment Profile by splitting a current alignment and realigning.
interface	ProfileProfileAligner<S extends Sequence<C>,C extends Compound> Defines an Aligner for a pair of Profiles.
interface	ProfileProfileScorer<S extends Sequence<C>,C extends Compound> Defines an algorithm which computes a score for a pairing of alignment profiles.
interface	RescoreRefiner<S extends Sequence<C>,C extends Compound> Defines an algorithm which computes a new alignment Profile by rescoring all pairs in an alignment and realigning.

Uses of Sequence in org.biojava.nbio.core.alignment

Classes in org.biojava.nbio.core.alignment with type parameters of type Sequence

Modifier and Type	Class and Description
class	SimpleAlignedSequence<S extends Sequence<C>,C extends Compound> Implements a data structure for a Sequence within an alignment.
class	SimpleProfile<S extends Sequence<C>,C extends Compound> Implements a data structure for the results of sequence alignment.
class	SimpleProfilePair<S extends Sequence<C>,C extends Compound> Implements a data structure for the results of the alignment of a pair of Profiles.
class	SimpleSequencePair<S extends Sequence<C>,C extends Compound> Implements a data structure for the results of pairwise sequence alignment.

Classes in org.biojava.nbio.core.alignment that implement Sequence

Modifier and Type	Class and Description
class	SimpleAlignedSequence<S extends Sequence<C>,C extends Compound> Implements a data structure for a Sequence within an alignment.

Methods in org.biojava.nbio.core.alignment with parameters of type Sequence

Modifier and Type	Method and Description
List<AlignedSequence<S,C>>	SimpleProfile.getAlignedSequences(S... sequences)

Uses of Sequence in org.biojava.nbio.core.alignment.template

Classes in org.biojava.nbio.core.alignment.template with type parameters of type Sequence

Modifier and Type	Interface and Description
interface	AlignedSequence<S extends Sequence<C>,C extends Compound> Defines a data structure for a Sequence within an alignment.
interface	MutableAlignedSequence<S extends Sequence<C>,C extends Compound> Defines a mutable (editable) data structure for an AlignedSequence.
interface	MutableProfile<S extends Sequence<C>,C extends Compound> Defines a mutable (editable) data structure for a Profile.
interface	MutableProfilePair<S extends Sequence<C>,C extends Compound> Defines a mutable (editable) data structure for a ProfilePair.
interface	MutableSequencePair<S extends Sequence<C>,C extends Compound> Defines a mutable (editable) data structure for the results of pairwise sequence alignment.
interface	Profile<S extends Sequence<C>,C extends Compound> Defines a data structure for the results of sequence alignment.
interface	ProfilePair<S extends Sequence<C>,C extends Compound> Defines a data structure for the results of the alignment of a pair of Profiles.
interface	ProfileView<S extends Sequence<C>,C extends Compound> Defines a data structure for a view of sequence alignment.
interface	SequencePair<S extends Sequence<C>,C extends Compound> Defines a data structure for the results of pairwise sequence alignment.

Subinterfaces of Sequence in org.biojava.nbio.core.alignment.template

Modifier and Type	Interface and Description
interface	AlignedSequence<S extends Sequence<C>,C extends Compound> Defines a data structure for a Sequence within an alignment.
interface	MutableAlignedSequence<S extends Sequence<C>,C extends Compound> Defines a mutable (editable) data structure for an AlignedSequence.

Methods in org.biojava.nbio.core.alignment.template with parameters of type Sequence

Modifier and Type	Method and Description
List<AlignedSequence<S,C>>	Profile.getAlignedSequences(S... sequences) Returns a List containing some of the individual AlignedSequences of this alignment.

Uses of Sequence in org.biojava.nbio.core.search.io

Classes in org.biojava.nbio.core.search.io with type parameters of type Sequence

Modifier and Type	Class and Description
class	Hsp<S extends Sequence<C>,C extends Compound> This class models a search Hsp.

Methods in org.biojava.nbio.core.search.io that return Sequence

Modifier and Type	Method and Description
Sequence	Hit.getHitSequence() returns the reference to the original and whole sequence hit in the database.
Sequence	Result.getQuerySequence() returns the reference to the original and whole sequence used to query the database.

Method parameters in org.biojava.nbio.core.search.io with type arguments of type Sequence

Modifier and Type	Method and Description
void	ResultFactory.setDatabaseReferences(List<Sequence> sequences) Specify the collection of sequences objects used as database in the Search run.
void	ResultFactory.setQueryReferences(List<Sequence> sequences) Specify the collection of sequences objects used as queries in the Search run.

Constructors in org.biojava.nbio.core.search.io with parameters of type Sequence

Constructor and Description
Hit(int hitNum, String hitId, String hitDef, String hitAccession, int hitLen, List<Hsp> hsps, Sequence hitSequence)
Result(String program, String version, String reference, String dbFile, HashMap<String,String> programSpecificParameters, int iterationNumber, String queryID, String queryDef, int queryLength, List<Hit> hits, Sequence querySequence)

Uses of Sequence in org.biojava.nbio.core.search.io.blast

Methods in org.biojava.nbio.core.search.io.blast with parameters of type Sequence

Modifier and Type	Method and Description
BlastHitBuilder	BlastHitBuilder.setHitSequence(Sequence s)
BlastResultBuilder	BlastResultBuilder.setQuerySequence(Sequence s)

Method parameters in org.biojava.nbio.core.search.io.blast with type arguments of type Sequence

Modifier and Type	Method and Description
void	BlastTabularParser.setDatabaseReferences(List<Sequence> sequences) Intended for use with run module.
void	BlastXMLParser.setDatabaseReferences(List<Sequence> sequences)
void	BlastTabularParser.setQueryReferences(List<Sequence> sequences) Intended for use with run module.
void	BlastXMLParser.setQueryReferences(List<Sequence> sequences)

Constructors in org.biojava.nbio.core.search.io.blast with parameters of type Sequence

Constructor and Description
BlastResult(String program, String version, String reference, String dbFile, HashMap<String,String> programSpecificParameters, int iterationNumber, String queryID, String queryDef, int queryLength, List<Hit> hits, Sequence querySequence)

Uses of Sequence in org.biojava.nbio.core.sequence

Classes in org.biojava.nbio.core.sequence with type parameters of type Sequence

Modifier and Type	Class and Description
class	MultipleSequenceAlignment<S extends Sequence<C>,C extends Compound> Implements a minimal data structure for reading and writing a sequence alignment.

Classes in org.biojava.nbio.core.sequence that implement Sequence

Modifier and Type	Class and Description
class	BasicSequence<C extends Compound> Bare bones version of the Sequence object to be used sparingly.
class	CDSSequence Represents a exon or coding sequence in a gene.
class	ChromosomeSequence A ChromosomeSequence is a DNASequence but keeps track of geneSequences
class	DNASequence This is class should model the attributes associated with a DNA sequence
class	ExonSequence A gene contains a collection of Exon sequences
class	GeneSequence
class	IntronSequence
class	ProteinSequence The representation of a ProteinSequence
class	RNASequence RNASequence where RNACompoundSet are the allowed values
class	StartCodonSequence Used to map the start codon feature on a gene
class	StopCodonSequence Used to map the stop codon sequence on a gene
class	TranscriptSequence This is the sequence if you want to go from a gene sequence to a protein sequence.

Uses of Sequence in org.biojava.nbio.core.sequence.compound

Methods in org.biojava.nbio.core.sequence.compound with parameters of type Sequence

Modifier and Type	Method and Description
boolean	AminoAcidCompoundSet.isValidSequence(Sequence<AminoAcidCompound> sequence)

Uses of Sequence in org.biojava.nbio.core.sequence.edits

Methods in org.biojava.nbio.core.sequence.edits that return Sequence

Modifier and Type	Method and Description
Sequence<C>	Edit.edit(Sequence<C> sequence)
Sequence<C>	Edit.AbstractEdit.edit(Sequence<C> editingSequence)
protected Sequence<C>	Edit.AbstractEdit.getEmptySequence(Sequence<C> editingSequence) Returns an empty sequence with the given compound set of the editing sequence
protected abstract Sequence<C>	Edit.AbstractEdit.getFivePrime(Sequence<C> editingSequence) Should return the 5-prime end of the given Sequence according to the edit.
protected Sequence<C>	Edit.Delete.getFivePrime(Sequence<C> editingSequence)
protected Sequence<C>	Edit.Insert.getFivePrime(Sequence<C> editingSequence)
protected Sequence<C>	Edit.Substitute.getFivePrime(Sequence<C> editingSequence)
Sequence<C>	Edit.AbstractEdit.getTargetSequence(Sequence<C> editingSequence) Returns the Sequence which is our edit.
protected abstract Sequence<C>	Edit.AbstractEdit.getThreePrime(Sequence<C> editingSequence) Should return the 3-prime end of the given Sequence according to the edit.
protected Sequence<C>	Edit.Delete.getThreePrime(Sequence<C> editingSequence)
protected Sequence<C>	Edit.Insert.getThreePrime(Sequence<C> editingSequence)
protected Sequence<C>	Edit.Substitute.getThreePrime(Sequence<C> editingSequence)

Methods in org.biojava.nbio.core.sequence.edits with parameters of type Sequence

Modifier and Type	Method and Description
Sequence<C>	Edit.edit(Sequence<C> sequence)
Sequence<C>	Edit.AbstractEdit.edit(Sequence<C> editingSequence)
protected Sequence<C>	Edit.AbstractEdit.getEmptySequence(Sequence<C> editingSequence) Returns an empty sequence with the given compound set of the editing sequence
int	Edit.Substitute.getEnd(Sequence<C> sequence) Must use this rather than the no-args getEnd as this can return -1 and the length of a sub is dependent on the length of the Sequence; we cannot assume 1:1 mapping between characters in a String and the number of compounds we will have to insert.
protected abstract Sequence<C>	Edit.AbstractEdit.getFivePrime(Sequence<C> editingSequence) Should return the 5-prime end of the given Sequence according to the edit.
protected Sequence<C>	Edit.Delete.getFivePrime(Sequence<C> editingSequence)
protected Sequence<C>	Edit.Insert.getFivePrime(Sequence<C> editingSequence)
protected Sequence<C>	Edit.Substitute.getFivePrime(Sequence<C> editingSequence)
Sequence<C>	Edit.AbstractEdit.getTargetSequence(Sequence<C> editingSequence) Returns the Sequence which is our edit.
protected abstract Sequence<C>	Edit.AbstractEdit.getThreePrime(Sequence<C> editingSequence) Should return the 3-prime end of the given Sequence according to the edit.
protected Sequence<C>	Edit.Delete.getThreePrime(Sequence<C> editingSequence)
protected Sequence<C>	Edit.Insert.getThreePrime(Sequence<C> editingSequence)
protected Sequence<C>	Edit.Substitute.getThreePrime(Sequence<C> editingSequence)
protected void	Edit.AbstractEdit.setSequence(Sequence<C> sequence)

Constructors in org.biojava.nbio.core.sequence.edits with parameters of type Sequence

Constructor and Description
Insert(Sequence<C> sequence, int position)
Insert(Sequence<C> sequence, int start, int stop)
Substitute(Sequence<C> sequence, int position)

Uses of Sequence in org.biojava.nbio.core.sequence.io

Classes in org.biojava.nbio.core.sequence.io with type parameters of type Sequence

Modifier and Type	Class and Description
class	FastaReader<S extends Sequence<?>,C extends Compound> Use FastaReaderHelper as an example of how to use this class where FastaReaderHelper should be the primary class used to read Fasta files
class	FastaWriter<S extends Sequence<?>,C extends Compound> The FastaWriter writes a collection of sequences to an outputStream.
class	GenbankWriter<S extends Sequence<?>,C extends Compound>

Methods in org.biojava.nbio.core.sequence.io with parameters of type Sequence

Modifier and Type	Method and Description
static void	GenbankWriterHelper.writeSequence(File file, Sequence<?> sequence) Write a sequence to a file
static void	FastaWriterHelper.writeSequence(File file, Sequence<?> sequence) Write a sequence to a file
static void	GenbankWriterHelper.writeSequence(OutputStream outputStream, Sequence<?> sequence) Write a sequence to OutputStream
static void	FastaWriterHelper.writeSequence(OutputStream outputStream, Sequence<?> sequence) Write a sequence to OutputStream

Method parameters in org.biojava.nbio.core.sequence.io with type arguments of type Sequence

Modifier and Type	Method and Description
static void	GenbankWriterHelper.writeSequences(OutputStream outputStream, Collection<Sequence<?>> sequences) Method which will write your given Sequences to the specified OutputStream.
static void	FastaWriterHelper.writeSequences(OutputStream outputStream, Collection<Sequence<?>> sequences) Method which will write your given Sequences to the specified OutputStream.

Uses of Sequence in org.biojava.nbio.core.sequence.io.template

Classes in org.biojava.nbio.core.sequence.io.template with type parameters of type Sequence

Modifier and Type	Interface and Description
interface	FastaHeaderFormatInterface<S extends Sequence<?>,C extends Compound>
interface	GenbankHeaderFormatInterface<S extends Sequence<?>,C extends Compound>
interface	SequenceHeaderParserInterface<S extends Sequence<?>,C extends Compound>

Uses of Sequence in org.biojava.nbio.core.sequence.io.util

Methods in org.biojava.nbio.core.sequence.io.util with type parameters of type Sequence

Modifier and Type	Method and Description
static <S extends Sequence<C>,C extends Compound> int	IOUtils.getGCGChecksum(List<S> sequences) Calculates GCG checksum for entire list of sequences
static <S extends Sequence<C>,C extends Compound> int	IOUtils.getGCGChecksum(S sequence) Calculates GCG checksum for a given sequence
static <S extends Sequence<C>,C extends Compound> String	IOUtils.getGCGHeader(List<S> sequences) Assembles a GCG file header
static <S extends Sequence<C>,C extends Compound> String	IOUtils.getIDFormat(List<S> sequences) Creates format String for accession IDs

Uses of Sequence in org.biojava.nbio.core.sequence.loader

Classes in org.biojava.nbio.core.sequence.loader that implement Sequence

Modifier and Type	Class and Description
class	ArrayListProxySequenceReader<C extends Compound>
class	GenbankProxySequenceReader<C extends Compound>
class	SequenceFileProxyLoader<C extends Compound> This class represents the storage container of a sequence stored in a fasta file where the initial parsing of the file we store the offset and length of the sequence.
class	StringProxySequenceReader<C extends Compound> An example of a ProxySequenceReader that is created from a String.
class	UniprotProxySequenceReader<C extends Compound> Pass in a Uniprot ID and this ProxySequenceReader when passed to a ProteinSequence will get the sequence data and other data elements associated with the ProteinSequence by Uniprot.

Uses of Sequence in org.biojava.nbio.core.sequence.location.template

Methods in org.biojava.nbio.core.sequence.location.template that return Sequence

Modifier and Type	Method and Description
<C extends Compound> Sequence<C>	AbstractLocation.getRelevantSubSequence(Sequence<C> sequence)
<C extends Compound> Sequence<C>	Location.getRelevantSubSequence(Sequence<C> sequence) Will return a SequenceReader object which offers a view of all resolved locations i.e.
<C extends Compound> Sequence<C>	AbstractLocation.getSubSequence(Sequence<C> sequence) If circular this will return the sequence represented by the sub locations joined.
<C extends Compound> Sequence<C>	Location.getSubSequence(Sequence<C> sequence) Will return a SequenceReader object which represents the outer bounds of this Location
protected <C extends Compound> Sequence<C>	AbstractLocation.reverseSequence(Sequence<C> sequence) Reverses and (if possible) complements the Sequence so as to represent the reverse strand (if one exists).

Methods in org.biojava.nbio.core.sequence.location.template with parameters of type Sequence

Modifier and Type	Method and Description
protected <C extends Compound> boolean	AbstractLocation.canComplement(Sequence<C> sequence) Uses the Sequence's CompoundSet to decide if a compound can be assgined to ComplementCompound meaning it can complement
<C extends Compound> Sequence<C>	AbstractLocation.getRelevantSubSequence(Sequence<C> sequence)
<C extends Compound> Sequence<C>	Location.getRelevantSubSequence(Sequence<C> sequence) Will return a SequenceReader object which offers a view of all resolved locations i.e.
<C extends Compound> Sequence<C>	AbstractLocation.getSubSequence(Sequence<C> sequence) If circular this will return the sequence represented by the sub locations joined.
<C extends Compound> Sequence<C>	Location.getSubSequence(Sequence<C> sequence) Will return a SequenceReader object which represents the outer bounds of this Location
protected <C extends Compound> Sequence<C>	AbstractLocation.reverseSequence(Sequence<C> sequence) Reverses and (if possible) complements the Sequence so as to represent the reverse strand (if one exists).

Uses of Sequence in org.biojava.nbio.core.sequence.storage

Classes in org.biojava.nbio.core.sequence.storage that implement Sequence

Modifier and Type	Class and Description
class	ArrayListSequenceReader<C extends Compound> Stores a Sequence as a collection of compounds in an ArrayList
class	BitSequenceReader<C extends Compound> An implementation of the popular bit encodings.
class	FourBitSequenceReader<C extends Compound> Four bit encoding of the bit formats.
class	JoiningSequenceReader<C extends Compound> This reader actually proxies onto multiple types of sequence in order to allow a number of sequence objects to act as if they are one sequence.
class	SingleCompoundSequenceReader<C extends Compound> An implementation of the SequenceReader interface which for every call will return only 1 compound (given to it during construction; a String is also valid but will require a CompoundSet).
class	TwoBitSequenceReader<C extends NucleotideCompound> Implementation of the 2bit encoding.

Methods in org.biojava.nbio.core.sequence.storage with parameters of type Sequence

Modifier and Type	Method and Description
void	BitSequenceReader.BitArrayWorker.populate(Sequence<C> sequence) Loops through the Compounds in a Sequence and passes them onto BitSequenceReader.BitArrayWorker.setCompoundAt(Compound, int)

Constructors in org.biojava.nbio.core.sequence.storage with parameters of type Sequence

Constructor and Description
BitArrayWorker(Sequence<C> sequence)
FourBitArrayWorker(Sequence<C> sequence)
FourBitSequenceReader(Sequence<C> sequence)
JoiningSequenceReader(CompoundSet<C> compoundSet, Sequence<C>... sequences)
JoiningSequenceReader(Sequence<C>... sequences) Allows creation of the store from Vargs Sequence objects.
TwoBitArrayWorker(Sequence<C> sequence)
TwoBitSequenceReader(Sequence<C> sequence)

Constructor parameters in org.biojava.nbio.core.sequence.storage with type arguments of type Sequence

Constructor and Description
JoiningSequenceReader(CompoundSet<C> compoundSet, List<Sequence<C>> sequences)
JoiningSequenceReader(List<Sequence<C>> sequences) Allows creation of the store from List>.

Uses of Sequence in org.biojava.nbio.core.sequence.template

Classes in org.biojava.nbio.core.sequence.template with type parameters of type Sequence

Modifier and Type	Interface and Description
interface	LightweightProfile<S extends Sequence<C>,C extends Compound> Defines a minimal data structure for reading and writing a sequence alignment.

Subinterfaces of Sequence in org.biojava.nbio.core.sequence.template

Modifier and Type	Interface and Description
interface	ProxySequenceReader<C extends Compound>
interface	SequenceReader<C extends Compound>
interface	SequenceView<C extends Compound>

Classes in org.biojava.nbio.core.sequence.template that implement Sequence

Modifier and Type	Class and Description
class	AbstractSequence<C extends Compound> The base class for DNA, RNA and Protein sequences.
class	SequenceProxyView<C extends Compound>

Methods in org.biojava.nbio.core.sequence.template that return Sequence

Modifier and Type	Method and Description
Sequence<T>	AbstractCompoundTranslator.createSequence(Sequence<F> originalSequence)
Sequence<T>	CompoundTranslator.createSequence(Sequence<F> originalSequence)
Sequence<C>	SequenceView.getViewedSequence()
Sequence<C>	SequenceProxyView.getViewedSequence()
static <C extends Compound> Sequence<C>	SequenceMixin.shuffle(Sequence<C> sequence) Implements sequence shuffling by first materializing the given Sequence into a List, applying Collections.shuffle(List) and then returning the shuffled elements in a new instance of SequenceBackingStore which behaves as a Sequence.

Methods in org.biojava.nbio.core.sequence.template that return types with arguments of type Sequence

Modifier and Type	Method and Description
List<Sequence<T>>	AbstractCompoundTranslator.createSequences(Sequence<F> originalSequence)
List<Sequence<T>>	CompoundTranslator.createSequences(Sequence<F> originalSequence)
protected List<Sequence<T>>	AbstractCompoundTranslator.workingListToSequences(List<List<T>> workingList)

Methods in org.biojava.nbio.core.sequence.template with parameters of type Sequence

Modifier and Type	Method and Description
static <C extends Compound> String	SequenceMixin.checksum(Sequence<C> sequence) Performs a simple CRC64 checksum on any given sequence.
static int	SequenceMixin.countAT(Sequence<NucleotideCompound> sequence) Returns the count of AT in the given sequence
static <C extends Compound> int	SequenceMixin.countCompounds(Sequence<C> sequence, C... compounds) For the given vargs of compounds this method counts the number of times those compounds appear in the given sequence
static int	SequenceMixin.countGC(Sequence<NucleotideCompound> sequence) Returns the count of GC in the given sequence
static <C extends Compound> Iterator<C>	SequenceMixin.createIterator(Sequence<C> sequence) Creates a simple sequence iterator which moves through a sequence going from 1 to the length of the Sequence.
Sequence<T>	AbstractCompoundTranslator.createSequence(Sequence<F> originalSequence)
Sequence<T>	CompoundTranslator.createSequence(Sequence<F> originalSequence)
List<Sequence<T>>	AbstractCompoundTranslator.createSequences(Sequence<F> originalSequence)
List<Sequence<T>>	CompoundTranslator.createSequences(Sequence<F> originalSequence)
static <C extends Compound> SequenceView<C>	SequenceMixin.createSubSequence(Sequence<C> sequence, int start, int end) Creates a simple sub sequence view delimited by the given start and end.
static <C extends Compound> Map<C,Integer>	SequenceMixin.getComposition(Sequence<C> sequence) Does a linear scan over the given Sequence and records the number of times each base appears.
static <C extends Compound> Map<C,Double>	SequenceMixin.getDistribution(Sequence<C> sequence) Analogous to SequenceMixin.getComposition(Sequence) but returns the distribution of that Compound over the given sequence.
static <C extends Compound> int	SequenceMixin.indexOf(Sequence<C> sequence, C compound) Performs a linear search of the given Sequence for the given compound.
static <C extends Compound> SequenceView<C>	SequenceMixin.inverse(Sequence<C> sequence) A method which attempts to do the right thing when is comes to a reverse/reverse complement
boolean	CompoundSet.isValidSequence(Sequence<C> sequence)
boolean	AbstractCompoundSet.isValidSequence(Sequence<C> sequence)
static <C extends Compound> int	SequenceMixin.lastIndexOf(Sequence<C> sequence, C compound) Performs a reversed linear search of the given Sequence by wrapping it in a ReversedSequenceView and passing it into SequenceMixin.indexOf(Sequence, Compound).
static <C extends Compound> List<SequenceView<C>>	SequenceMixin.nonOverlappingKmers(Sequence<C> sequence, int kmer) Produces kmers of the specified size e.g.
static <C extends Compound> List<SequenceView<C>>	SequenceMixin.overlappingKmers(Sequence<C> sequence, int kmer) Used to generate overlapping k-mers such i.e.
static <C extends Compound> boolean	SequenceMixin.sequenceEquality(Sequence<C> source, Sequence<C> target) A case-sensitive manner of comparing two sequence objects together.
static <C extends Compound> boolean	SequenceMixin.sequenceEquality(Sequence<C> source, Sequence<C> target) A case-sensitive manner of comparing two sequence objects together.
static <C extends Compound> boolean	SequenceMixin.sequenceEqualityIgnoreCase(Sequence<C> source, Sequence<C> target) A case-insensitive manner of comparing two sequence objects together.
static <C extends Compound> boolean	SequenceMixin.sequenceEqualityIgnoreCase(Sequence<C> source, Sequence<C> target) A case-insensitive manner of comparing two sequence objects together.
static <C extends Compound> Sequence<C>	SequenceMixin.shuffle(Sequence<C> sequence) Implements sequence shuffling by first materializing the given Sequence into a List, applying Collections.shuffle(List) and then returning the shuffled elements in a new instance of SequenceBackingStore which behaves as a Sequence.
static <C extends Compound> List<C>	SequenceMixin.toList(Sequence<C> sequence) For the given Sequence this will return a List filled with the Compounds of that Sequence.
static <C extends Compound> String	SequenceMixin.toString(Sequence<C> sequence) Shortcut to SequenceMixin.toStringBuilder(org.biojava.nbio.core.sequence.template.Sequence) which calls toString() on the resulting object.
static <C extends Compound> StringBuilder	SequenceMixin.toStringBuilder(Sequence<C> sequence) For the given Sequence this will return a StringBuilder object filled with the results of Compound#toString().
static <C extends Compound> void	SequenceMixin.write(Appendable appendable, Sequence<C> sequence) Used as a way of sending a Sequence to a writer without the cost of converting to a full length String and then writing the data out

Constructors in org.biojava.nbio.core.sequence.template with parameters of type Sequence

Constructor and Description
SequenceIterator(Sequence<C> sequence)
SequenceProxyView(Sequence<C> sequence)
SequenceProxyView(Sequence<C> sequence, Integer bioStart, Integer bioEnd) Main constructor for working with SequenceProxyViews

Uses of Sequence in org.biojava.nbio.core.sequence.transcription

Methods in org.biojava.nbio.core.sequence.transcription that return Sequence

Modifier and Type	Method and Description
Sequence<NucleotideCompound>	DNAToRNATranslator.createSequence(Sequence<NucleotideCompound> originalSequence)
Sequence<NucleotideCompound>	DNAToRNATranslator.createSequence(Sequence<NucleotideCompound> originalSequence, Frame frame)
Sequence<AminoAcidCompound>	TranscriptionEngine.translate(Sequence<NucleotideCompound> dna) Quick method to let you go from a CDS to a Peptide quickly.
<C extends NucleotideCompound> Sequence<C>	Frame.wrap(Sequence<C> incoming) Optionally wraps a Sequence in a reverse complementing view (if the frame is on the reverse strand) and creates a sub sequence view if it is required.

Methods in org.biojava.nbio.core.sequence.transcription that return types with arguments of type Sequence

Modifier and Type	Method and Description
List<Sequence<NucleotideCompound>>	DNAToRNATranslator.createSequences(Sequence<NucleotideCompound> originalSequence) Overloaded local version which delegates to an optional translator when told to (specified during construction).
List<Sequence<AminoAcidCompound>>	RNAToAminoAcidTranslator.createSequences(Sequence<NucleotideCompound> originalSequence) Performs the core conversion of RNA to Peptide.
Map<Frame,Sequence<AminoAcidCompound>>	TranscriptionEngine.multipleFrameTranslation(Sequence<NucleotideCompound> dna, Frame... frames) A way of translating DNA in a number of frames

Methods in org.biojava.nbio.core.sequence.transcription with parameters of type Sequence

Modifier and Type	Method and Description
Sequence<NucleotideCompound>	DNAToRNATranslator.createSequence(Sequence<NucleotideCompound> originalSequence)
Sequence<NucleotideCompound>	DNAToRNATranslator.createSequence(Sequence<NucleotideCompound> originalSequence, Frame frame)
List<Sequence<NucleotideCompound>>	DNAToRNATranslator.createSequences(Sequence<NucleotideCompound> originalSequence) Overloaded local version which delegates to an optional translator when told to (specified during construction).
List<Sequence<AminoAcidCompound>>	RNAToAminoAcidTranslator.createSequences(Sequence<NucleotideCompound> originalSequence) Performs the core conversion of RNA to Peptide.
Map<Frame,Sequence<AminoAcidCompound>>	TranscriptionEngine.multipleFrameTranslation(Sequence<NucleotideCompound> dna, Frame... frames) A way of translating DNA in a number of frames
Sequence<AminoAcidCompound>	TranscriptionEngine.translate(Sequence<NucleotideCompound> dna) Quick method to let you go from a CDS to a Peptide quickly.
<C extends NucleotideCompound> Sequence<C>	Frame.wrap(Sequence<C> incoming) Optionally wraps a Sequence in a reverse complementing view (if the frame is on the reverse strand) and creates a sub sequence view if it is required.
protected RNASequence	DNAToRNATranslator.wrapToRna(Sequence<NucleotideCompound> dna) Takes in the given DNA Sequence and returns an instance of RNASequence which is using RnaSequenceView as a ProxySequenceReader.

Uses of Sequence in org.biojava.nbio.core.sequence.views

Classes in org.biojava.nbio.core.sequence.views that implement Sequence

Modifier and Type	Class and Description
class	ComplementSequenceView<C extends ComplementCompound> For a given sequence this class will create a view over the top of it and for every request the code will return the complement of the underlying base e.g.
class	ReversedSequenceView<C extends Compound> For a given sequence this class will return the base at the reversed position i.e.
class	RnaSequenceView Attempts to do on the fly translation of RNA by not requesting the compounds until asked.

Methods in org.biojava.nbio.core.sequence.views that return Sequence

Modifier and Type	Method and Description
Sequence<C>	WindowedSequence.getBackingSequence() Access the sequence which backs this window

Constructors in org.biojava.nbio.core.sequence.views with parameters of type Sequence

Constructor and Description
ComplementSequenceView(Sequence<C> sequence)
ReversedSequenceView(Sequence<C> sequence)
RnaSequenceView(Sequence<NucleotideCompound> sourceDna)
RnaSequenceView(Sequence<NucleotideCompound> sourceDna, CompoundSet<NucleotideCompound> rnaCompounds)
WindowedSequence(Sequence<C> sequence, int windowSize)

Uses of Sequence in org.biojava.nbio.core.util

Methods in org.biojava.nbio.core.util that return Sequence

Modifier and Type	Method and Description
Sequence<?>	SequenceTools.getSequenceFromString(String sequence)

Uses of Sequence in org.biojava.nbio.phylo

Methods in org.biojava.nbio.phylo with type parameters of type Sequence

Modifier and Type	Method and Description
static <C extends Sequence<D>,D extends Compound> org.forester.msa.Msa	ForesterWrapper.convert(MultipleSequenceAlignment<C,D> msa) Convert a BioJava MultipleSequenceAlignment to a forester Msa.
static <C extends Sequence<D>,D extends Compound> org.forester.evoinference.matrix.distance.DistanceMatrix	DistanceMatrixCalculator.dissimilarityScore(MultipleSequenceAlignment<C,D> msa, SubstitutionMatrix<D> M) The dissimilarity score is the additive inverse of the similarity score (sum of scores) between two aligned sequences using a substitution model (Substitution Matrix).
static <C extends Sequence<D>,D extends Compound> org.forester.evoinference.matrix.distance.DistanceMatrix	DistanceMatrixCalculator.fractionalDissimilarity(MultipleSequenceAlignment<C,D> msa) The fractional dissimilarity (D) is defined as the percentage of sites that differ between two aligned sequences.
static <C extends Sequence<D>,D extends Compound> org.forester.evoinference.matrix.distance.DistanceMatrix	DistanceMatrixCalculator.fractionalDissimilarityScore(MultipleSequenceAlignment<C,D> msa, SubstitutionMatrix<D> M) The fractional dissimilarity score (Ds) is a relative measure of the dissimilarity between two aligned sequences.
static <C extends Sequence<D>,D extends Compound> org.forester.evoinference.matrix.distance.DistanceMatrix	DistanceMatrixCalculator.jointSeqStrucDistance(double[][] rmsdMat) The joint sequence-structure distance (dSS) is a combination of the sequence-based and the structure-based distances.
static <C extends Sequence<D>,D extends Compound> org.forester.evoinference.matrix.distance.DistanceMatrix	DistanceMatrixCalculator.kimuraDistance(MultipleSequenceAlignment<C,D> msa) The Kimura evolutionary distance (d) is a correction of the fractional dissimilarity (D) specially needed for large evolutionary distances.
static <C extends Sequence<D>,D extends Compound> org.forester.evoinference.matrix.distance.DistanceMatrix	DistanceMatrixCalculator.pamMLdistance(MultipleSequenceAlignment<C,D> msa) The PAM (Point Accepted Mutations) distance is a measure of evolutionary distance in protein sequences.
static <C extends Sequence<D>,D extends Compound> org.forester.evoinference.matrix.distance.DistanceMatrix	DistanceMatrixCalculator.percentageIdentity(MultipleSequenceAlignment<C,D> msa) BioJava implementation for percentage of identity (PID).
static <C extends Sequence<D>,D extends Compound> org.forester.evoinference.matrix.distance.DistanceMatrix	DistanceMatrixCalculator.poissonDistance(MultipleSequenceAlignment<C,D> msa) The Poisson (correction) evolutionary distance (d) is a function of the fractional dissimilarity (D), given by:
static <C extends Sequence<D>,D extends Compound> org.forester.evoinference.matrix.distance.DistanceMatrix	DistanceMatrixCalculator.structuralDistance(double[][] rmsdMat, double alpha, double rmsdMax, double rmsd0) The structural distance (dS) uses the structural similarity (or dissimilarity) from a the structural alignment of two protein strutures.

Uses of Sequence in org.biojava.nbio.structure

Methods in org.biojava.nbio.structure that return Sequence

Modifier and Type	Method and Description
Sequence<?>	Chain.getBJSequence() Converts the SEQRES groups of a Chain to a Biojava Sequence object.
Sequence<?>	ChainImpl.getBJSequence() Converts the SEQRES groups of a Chain to a Biojava Sequence object.

Uses of Sequence in org.biojava.nbio.structure.io

Method parameters in org.biojava.nbio.structure.io with type arguments of type Sequence

Modifier and Type	Method and Description
static AFPChain	FastaAFPChainConverter.fastaToAfpChain(SequencePair<Sequence<AminoAcidCompound>,AminoAcidCompound> alignment, Structure structure1, Structure structure2) Provided only for convenience.

Uses of Sequence in org.biojava.nbio.ws.alignment

Methods in org.biojava.nbio.ws.alignment with parameters of type Sequence

Modifier and Type	Method and Description
String	RemotePairwiseAlignmentService.sendAlignmentRequest(Sequence<Compound> seq, RemotePairwiseAlignmentProperties rpa) Doing the actual analysis on the instantiated service using specified parameters and the RichSequence object

Uses of Sequence in org.biojava.nbio.ws.alignment.qblast

Methods in org.biojava.nbio.ws.alignment.qblast with parameters of type Sequence

Modifier and Type	Method and Description
String	NCBIQBlastService.sendAlignmentRequest(Sequence<Compound> seq, RemotePairwiseAlignmentProperties rpa) Converts given sequence to String and calls NCBIQBlastService.sendAlignmentRequest(String, RemotePairwiseAlignmentProperties)