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

Packages that use SequenceReader

org.biojava3.core.sequence.loader
org.biojava3.core.sequence.storage
org.biojava3.core.sequence.template
org.biojava3.core.sequence.views

Uses of SequenceReader in org.biojava3.core.sequence.loader

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

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 SequenceReader in org.biojava3.core.sequence.storage

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

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 SequenceReader in org.biojava3.core.sequence.template

Subinterfaces of SequenceReader in org.biojava3.core.sequence.template

interface

ProxySequenceReader<C extends Compound>

Uses of SequenceReader in org.biojava3.core.sequence.views

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

class

RnaSequenceView Attempts to do on the fly translation of RNA by not requesting the compounds until asked.