Uses of Interface
org.biojava.nbio.core.sequence.template.ProxySequenceReader
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Uses of ProxySequenceReader in org.biojava.nbio.core.sequence
Constructors in org.biojava.nbio.core.sequence with parameters of type ProxySequenceReader Constructor Description BasicSequence(ProxySequenceReader<C> reader)
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 readerRNASequence(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.biojava.nbio.core.sequence.io
Methods in org.biojava.nbio.core.sequence.io with parameters of type ProxySequenceReader Modifier and Type Method Description AbstractSequence<AminoAcidCompound>
CasePreservingProteinSequenceCreator. getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)
AbstractSequence<NucleotideCompound>
DNASequenceCreator. getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index)
AbstractSequence<NucleotideCompound>
FileProxyDNASequenceCreator. getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index)
Should be able to extend the same concept to a remote URL call or database connection.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<NucleotideCompound>
FileProxyRNASequenceCreator. getSequence(ProxySequenceReader<NucleotideCompound> 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)
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Uses of ProxySequenceReader in org.biojava.nbio.core.sequence.io.template
Methods in org.biojava.nbio.core.sequence.io.template with parameters of type ProxySequenceReader Modifier and Type Method Description AbstractSequence<C>
SequenceCreatorInterface. getSequence(ProxySequenceReader<C> proxyLoader, long index)
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Uses of ProxySequenceReader in org.biojava.nbio.core.sequence.loader
Classes in org.biojava.nbio.core.sequence.loader that implement ProxySequenceReader 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 ProxySequenceReader in org.biojava.nbio.core.sequence.location.template
Methods in org.biojava.nbio.core.sequence.location.template that return ProxySequenceReader Modifier and Type Method Description ProxySequenceReader<? extends Compound>
AccesionedLocation. getProxySequenceReader()
Return the proxy reader used to get sequence for this location. -
Uses of ProxySequenceReader in org.biojava.nbio.core.sequence.storage
Classes in org.biojava.nbio.core.sequence.storage that implement ProxySequenceReader Modifier and Type Class Description 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.biojava.nbio.core.sequence.views
Classes in org.biojava.nbio.core.sequence.views that implement ProxySequenceReader Modifier and Type Class Description class
RnaSequenceView
Attempts to do on the fly translation of RNA by not requesting the compounds until asked.
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