Uses of Interface
org.biojava.nbio.core.sequence.template.SequenceReader
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Uses of SequenceReader in org.biojava.nbio.core.sequence
Constructors in org.biojava.nbio.core.sequence with parameters of type SequenceReader Constructor 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 CompoundSetDNASequence(SequenceReader<NucleotideCompound> proxyLoader)
Create a sequence where the actual storage of the sequence data is somewhere elseDNASequence(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 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 Description class
ArrayListSequenceReader<C extends Compound>
Stores a Sequence as a collection of compounds in an ArrayListclass
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 Description interface
ProxySequenceReader<C extends Compound>
Methods in org.biojava.nbio.core.sequence.template that return SequenceReader Modifier and Type Method Description SequenceReader<C>
AbstractSequence. getProxySequenceReader()
Methods in org.biojava.nbio.core.sequence.template with parameters of type SequenceReader Modifier and Type Method 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 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 Description class
RnaSequenceView
Attempts to do on the fly translation of RNA by not requesting the compounds until asked.
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