Uses of Class
org.biojava.nbio.core.sequence.RNASequence
Packages that use RNASequence
Package
Description
-
Uses of RNASequence in org.biojava.nbio.core.sequence
Methods in org.biojava.nbio.core.sequence that return RNASequenceModifier and TypeMethodDescriptionDNASequence.getRNASequence()
Return the RNASequence equivalent of the DNASequence using default Transcription Engine.DNASequence.getRNASequence
(Frame frame) Allows the user to pass in the Frame shift.DNASequence.getRNASequence
(TranscriptionEngine engine) Allow a user to pass in a rules engine to do the DNA to RNA translationDNASequence.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 RNASequenceModifier and TypeMethodDescriptionstatic 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 RNASequenceModifier and TypeMethodDescriptionprotected RNASequence
DNAToRNATranslator.wrapToRna
(Sequence<NucleotideCompound> dna) Takes in the given DNA Sequence and returns an instance of RNASequence which is usingRnaSequenceView
as aProxySequenceReader
.