Uses of Class
org.biojava.nbio.core.sequence.RNASequence
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Packages that use RNASequence Package Description org.biojava.nbio.core.sequence org.biojava.nbio.core.sequence.io org.biojava.nbio.core.sequence.transcription -
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Uses of RNASequence in org.biojava.nbio.core.sequence
Methods in org.biojava.nbio.core.sequence that return RNASequence Modifier and Type Method 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 translationRNASequence
DNASequence. getRNASequence(TranscriptionEngine engine, Frame frame)
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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 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 sequencestatic 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 Description protected RNASequence
DNAToRNATranslator. wrapToRna(Sequence<NucleotideCompound> dna)
Takes in the given DNA Sequence and returns an instance of RNASequence which is usingRnaSequenceView
as aProxySequenceReader
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