Uses of Interface
org.biojava3.core.sequence.template.Sequence

Packages that use Sequence

org.biojava3.core.sequence
org.biojava3.core.sequence.compound
org.biojava3.core.sequence.edits
org.biojava3.core.sequence.io
org.biojava3.core.sequence.io.template
org.biojava3.core.sequence.io.util
org.biojava3.core.sequence.loader
org.biojava3.core.sequence.location.template
org.biojava3.core.sequence.storage
org.biojava3.core.sequence.template
org.biojava3.core.sequence.transcription
org.biojava3.core.sequence.views
org.biojava3.core.util

Uses of Sequence in org.biojava3.core.sequence

Classes in org.biojava3.core.sequence with type parameters of type Sequence

class

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

Classes in org.biojava3.core.sequence that implement Sequence

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.biojava3.core.sequence.compound

Methods in org.biojava3.core.sequence.compound with parameters of type Sequence

void	AminoAcidCompoundSet.verifySequence(Sequence<AminoAcidCompound> sequence)

Uses of Sequence in org.biojava3.core.sequence.edits

Methods in org.biojava3.core.sequence.edits that return Sequence

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.biojava3.core.sequence.edits with parameters of type Sequence

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.biojava3.core.sequence.edits with parameters of type Sequence

Edit.Insert(Sequence<C> sequence, int position)

Edit.Insert(Sequence<C> sequence, int start, int stop)

Edit.Substitute(Sequence<C> sequence, int position)

Uses of Sequence in org.biojava3.core.sequence.io

Classes in org.biojava3.core.sequence.io with type parameters of type Sequence

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.

Methods in org.biojava3.core.sequence.io with parameters of type Sequence

static void	FastaWriterHelper.writeSequence(File file, Sequence<?> sequence) Write a sequence to a file
static void	FastaWriterHelper.writeSequence(OutputStream outputStream, Sequence<?> sequence) Write a sequence to OutputStream

Method parameters in org.biojava3.core.sequence.io with type arguments of type Sequence

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.biojava3.core.sequence.io.template

Classes in org.biojava3.core.sequence.io.template with type parameters of type Sequence

interface	FastaHeaderFormatInterface<S extends Sequence<?>,C extends Compound>
interface	FastaHeaderParserInterface<S extends Sequence<?>,C extends Compound>

Uses of Sequence in org.biojava3.core.sequence.io.util

Methods in org.biojava3.core.sequence.io.util with type parameters of type Sequence

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.biojava3.core.sequence.loader

Classes in org.biojava3.core.sequence.loader that implement Sequence

class	ArrayListProxySequenceReader<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.biojava3.core.sequence.location.template

Methods in org.biojava3.core.sequence.location.template that return 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. those locations which are not complex and define the true Sequence represented
<C extends Compound> Sequence<C>	AbstractLocation.getRelevantSubSequence(Sequence<C> sequence)
<C extends Compound> Sequence<C>	Location.getSubSequence(Sequence<C> sequence) Will return a SequenceReader object which represents the outer bounds of this Location
<C extends Compound> Sequence<C>	AbstractLocation.getSubSequence(Sequence<C> sequence) If circular this will return the sequence represented by the sub locations joined.
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.biojava3.core.sequence.location.template with parameters of type Sequence

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>	Location.getRelevantSubSequence(Sequence<C> sequence) Will return a SequenceReader object which offers a view of all resolved locations i.e. those locations which are not complex and define the true Sequence represented
<C extends Compound> Sequence<C>	AbstractLocation.getRelevantSubSequence(Sequence<C> sequence)
<C extends Compound> Sequence<C>	Location.getSubSequence(Sequence<C> sequence) Will return a SequenceReader object which represents the outer bounds of this Location
<C extends Compound> Sequence<C>	AbstractLocation.getSubSequence(Sequence<C> sequence) If circular this will return the sequence represented by the sub locations joined.
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.biojava3.core.sequence.storage

Classes in org.biojava3.core.sequence.storage that implement Sequence

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.biojava3.core.sequence.storage with parameters of type Sequence

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.biojava3.core.sequence.storage with parameters of type Sequence

BitSequenceReader.BitArrayWorker(Sequence<C> sequence)

FourBitSequenceReader.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.

TwoBitSequenceReader.TwoBitArrayWorker(Sequence<C> sequence)

TwoBitSequenceReader(Sequence<C> sequence)

Constructor parameters in org.biojava3.core.sequence.storage with type arguments of type Sequence

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.biojava3.core.sequence.template

Classes in org.biojava3.core.sequence.template with type parameters of type Sequence

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.biojava3.core.sequence.template

interface	ProxySequenceReader<C extends Compound>
interface	SequenceReader<C extends Compound>
interface	SequenceView<C extends Compound>

Classes in org.biojava3.core.sequence.template that implement Sequence

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

Methods in org.biojava3.core.sequence.template that return Sequence

Sequence<T>	CompoundTranslator.createSequence(Sequence<F> originalSequence)
Sequence<T>	AbstractCompoundTranslator.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.biojava3.core.sequence.template that return types with arguments of type Sequence

List<Sequence<T>>	CompoundTranslator.createSequences(Sequence<F> originalSequence)
List<Sequence<T>>	AbstractCompoundTranslator.createSequences(Sequence<F> originalSequence)
protected List<Sequence<T>>	AbstractCompoundTranslator.workingListToSequences(List<List<T>> workingList)

Methods in org.biojava3.core.sequence.template with parameters of type Sequence

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>	CompoundTranslator.createSequence(Sequence<F> originalSequence)
Sequence<T>	AbstractCompoundTranslator.createSequence(Sequence<F> originalSequence)
List<Sequence<T>>	CompoundTranslator.createSequences(Sequence<F> originalSequence)
List<Sequence<T>>	AbstractCompoundTranslator.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
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> 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.biojava3.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().
void	CompoundSet.verifySequence(Sequence<C> sequence)
void	AbstractCompoundSet.verifySequence(Sequence<C> sequence)
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.biojava3.core.sequence.template with parameters of type Sequence

SequenceMixin.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.biojava3.core.sequence.transcription

Methods in org.biojava3.core.sequence.transcription that return Sequence

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.biojava3.core.sequence.transcription that return types with arguments of type Sequence

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

Methods in org.biojava3.core.sequence.transcription with parameters of type Sequence

Sequence<NucleotideCompound>	DNAToRNATranslator.createSequence(Sequence<NucleotideCompound> originalSequence)
Sequence<NucleotideCompound>	DNAToRNATranslator.createSequence(Sequence<NucleotideCompound> originalSequence, Frame frame)
List<Sequence<AminoAcidCompound>>	RNAToAminoAcidTranslator.createSequences(Sequence<NucleotideCompound> originalSequence) Performs the core conversion of RNA to Peptide.
List<Sequence<NucleotideCompound>>	DNAToRNATranslator.createSequences(Sequence<NucleotideCompound> originalSequence) Overloaded local version which delegates to an optional translator when told to (specified during construction).
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.biojava3.core.sequence.views

Classes in org.biojava3.core.sequence.views that implement Sequence

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. base A will become base T
class	ReversedSequenceView<C extends Compound> For a given sequence this class will return the base at the reversed position i.e. in a sequence of size 10, if you request base 2 you will get back the base at position 9.
class	RnaSequenceView Attempts to do on the fly translation of RNA by not requesting the compounds until asked.

Methods in org.biojava3.core.sequence.views that return Sequence

Sequence<C>

WindowedSequence.getBackingSequence() Access the sequence which backs this window

Constructors in org.biojava3.core.sequence.views with parameters of type Sequence

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.biojava3.core.util

Methods in org.biojava3.core.util that return Sequence

Sequence<?>

SequenceTools.getSeqeunceFromString(String sequence)