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

Packages that use SequenceReader

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

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

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

Constructor and Description
ChromosomeSequence(SequenceReader<NucleotideCompound> proxyLoader) Fairly important constructor given the size of a ChromsomeSequence where the ProxySequenceReader could load from disk via RandomAccessFile so that the sequence doesn't need to be kept in memory.
ChromosomeSequence(SequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet) Allows the creation of a ChromosomeSequence using a ProxyResequenceReader for the sequence with a custom CompoundSet
DNASequence(SequenceReader<NucleotideCompound> proxyLoader) Create a sequence where the actual storage of the sequence data is somewhere else
DNASequence(SequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet) Create a sequence from a ProxySequencereader and user defined compound set

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

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

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 SequenceReader in org.biojava.nbio.core.sequence.storage

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

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.

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

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

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

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

Modifier and Type	Method and Description
SequenceReader<C>	AbstractSequence.getProxySequenceReader()

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

Modifier and Type	Method and Description
void	AbstractSequence.setProxySequenceReader(SequenceReader<C> proxyLoader) Very important method that allows external mappings of sequence data and features.

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

Constructor and Description
AbstractSequence(SequenceReader<C> proxyLoader, CompoundSet<C> compoundSet) A ProxySequenceReader allows abstraction of both the storage of the sequence data and the location of the sequence data.

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

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

Modifier and Type	Class and Description
class	RnaSequenceView Attempts to do on the fly translation of RNA by not requesting the compounds until asked.