Uses of Class
org.biojava.nbio.core.sequence.RNASequence

Packages that use RNASequence

Package	Description
org.biojava.nbio.core.sequence
org.biojava.nbio.core.sequence.io
org.biojava.nbio.core.sequence.transcription

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

Methods in org.biojava.nbio.core.sequence that return RNASequence

Modifier and Type	Method and Description
RNASequence	DNASequence.getRNASequence() Return the RNASequence equivalent of the DNASequence using default Transcription Engine.
RNASequence	DNASequence.getRNASequence(Frame frame) Allows the user to pass in the Frame shift.
RNASequence	DNASequence.getRNASequence(TranscriptionEngine engine) Allow a user to pass in a rules engine to do the DNA to RNA translation
RNASequence	DNASequence.getRNASequence(TranscriptionEngine engine, Frame frame)

Uses of RNASequence in org.biojava.nbio.core.sequence.io

Methods in org.biojava.nbio.core.sequence.io that return types with arguments of type RNASequence

Modifier and Type	Method and Description
static LinkedHashMap<String,RNASequence>	FastaReaderHelper.readFastaRNASequence(File file)
static LinkedHashMap<String,RNASequence>	FastaReaderHelper.readFastaRNASequence(File file, boolean lazySequenceLoad) Selecting lazySequenceLoad=true will parse the FASTA file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.
static LinkedHashMap<String,RNASequence>	FastaReaderHelper.readFastaRNASequence(InputStream inStream) Read a fasta RNA sequence
static LinkedHashMap<String,RNASequence>	GenbankReaderHelper.readGenbankRNASequence(File file)
static LinkedHashMap<String,RNASequence>	GenbankReaderHelper.readGenbankRNASequence(File file, boolean lazySequenceLoad) Selecting lazySequenceLoad=true will parse the Genbank file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.
static LinkedHashMap<String,RNASequence>	GenbankReaderHelper.readGenbankRNASequence(InputStream inStream) Read a Genbank RNA sequence

Uses of RNASequence in org.biojava.nbio.core.sequence.transcription

Methods in org.biojava.nbio.core.sequence.transcription that return RNASequence

Modifier and Type	Method and Description
protected RNASequence	DNAToRNATranslator.wrapToRna(Sequence<NucleotideCompound> dna) Takes in the given DNA Sequence and returns an instance of RNASequence which is using RnaSequenceView as a ProxySequenceReader.