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

Packages that use Accessioned

Package	Description
org.biojava.nbio.core.alignment
org.biojava.nbio.core.alignment.template
org.biojava.nbio.core.sequence
org.biojava.nbio.core.sequence.loader
org.biojava.nbio.core.sequence.location
org.biojava.nbio.core.sequence.location.template
org.biojava.nbio.core.sequence.storage
org.biojava.nbio.core.sequence.template
org.biojava.nbio.core.sequence.views

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

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

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

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

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

Modifier and Type	Interface	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.

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

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

Modifier and Type	Class	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 Accessioned in org.biojava.nbio.core.sequence.loader

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

Modifier and Type	Class	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 Accessioned in org.biojava.nbio.core.sequence.location

Classes in org.biojava.nbio.core.sequence.location that implement Accessioned

Modifier and Type	Class	Description
static class	InsdcLocations.BondLocation	Used to represent bond locations equivalent to bond(7,8) or bond(7).
static class	InsdcLocations.GroupLocation	Deprecated in INSDC yet still appears; equivalent to the order() directive except no 5' to 3' ordering is defined.
static class	InsdcLocations.OneOfLocation	Deprecated in INSDC; refers to a set of locations of which one location could be valid e.g. one-of(location, location, location).
static class	InsdcLocations.OrderLocation	Used to describe a 5' to 3' ordering but no firm assurance it is correct
class	SequenceLocation<S extends AbstractSequence<C>,C extends Compound>	A location in a sequence that keeps a reference to its parent sequence
class	SimpleLocation	Very basic implementation of the Location interface which defines a series of simple constructors.

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

Subinterfaces of Accessioned in org.biojava.nbio.core.sequence.location.template

Modifier and Type	Interface	Description
interface	AccesionedLocation	A location which is bound to an AccessionID.
interface	Location	Sets of integers used to represent the location of features on sequence.

Classes in org.biojava.nbio.core.sequence.location.template that implement Accessioned

Modifier and Type	Class	Description
class	AbstractLocation	Base abstraction of a location which encodes for the majority of important features about a location such as the start, end and strand

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

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

Modifier and Type	Class	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.

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

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

Modifier and Type	Interface	Description
interface	ProxySequenceReader<C extends Compound>
interface	Sequence<C extends Compound>	Main interface for defining a collection of Compounds and accessing them using biological indexes
interface	SequenceReader<C extends Compound>
interface	SequenceView<C extends Compound>

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

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

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

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

Modifier and Type	Class	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. 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.