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

Packages that use ProxySequenceReader

org.biojava3.core.sequence
org.biojava3.core.sequence.io
org.biojava3.core.sequence.io.template
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.views

Uses of ProxySequenceReader in org.biojava3.core.sequence

Constructors in org.biojava3.core.sequence with parameters of type ProxySequenceReader

BasicSequence(ProxySequenceReader<C> reader)

ChromosomeSequence(ProxySequenceReader<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(ProxySequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet)
Allows the creation of a ChromosomeSequence using a ProxyResequenceReader for the sequence with a custom CompoundSet

DNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader)
Create a sequence where the actual storage of the sequence data is somewhere else

DNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet)
Create a sequence from a ProxySequencereader and user defined compound set

ProteinSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader)
A protein sequence where the storage of the sequence is somewhere else.

ProteinSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, CompoundSet<AminoAcidCompound> compoundSet)
A protein sequence where the storage of the sequence is somewhere else with user defined set of amino acids.

RNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader)
Create a RNA aequence from a proxy reader

RNASequence(ProxySequenceReader<NucleotideCompound> proxyLoader, CompoundSet<NucleotideCompound> compoundSet)
Create a RNA sequence from a proxy reader and user defined RNA compound set

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

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

AbstractSequence<AminoAcidCompound>	FileProxyProteinSequenceCreator.getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index) Should be able to extend the same concept to a remote URL call or database connection.
AbstractSequence<AminoAcidCompound>	ProteinSequenceCreator.getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)
AbstractSequence<NucleotideCompound>	RNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index)
AbstractSequence<NucleotideCompound>	DNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index)

Uses of ProxySequenceReader in org.biojava3.core.sequence.io.template

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

AbstractSequence<C>

SequenceCreatorInterface.getSequence(ProxySequenceReader<C> proxyLoader, long index)

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

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

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 ProxySequenceReader in org.biojava3.core.sequence.location.template

Methods in org.biojava3.core.sequence.location.template that return ProxySequenceReader

ProxySequenceReader<? extends Compound>

AccesionedLocation.getProxySequenceReader() Return the proxy reader used to get sequence for this location.

Uses of ProxySequenceReader in org.biojava3.core.sequence.storage

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

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 ProxySequenceReader in org.biojava3.core.sequence.template

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

ProxySequenceReader<C>

AbstractSequence.getProxySequenceReader()

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

void	AbstractSequence.setProxySequenceReader(ProxySequenceReader<C> proxyLoader) Very important method that allows external mappings of sequence data and features.

Constructors in org.biojava3.core.sequence.template with parameters of type ProxySequenceReader

AbstractSequence(ProxySequenceReader<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 ProxySequenceReader in org.biojava3.core.sequence.views

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

class

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